Microbiology: A Human Perspective, 6th Edition

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A HUMAN PERSPECTIVE

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sixth edition

A HUMAN PERSPECTIVE

Eugene W. Nester University of Washington

Denise G. Anderson University of Washington

C. Evans Roberts, Jr. University of Washington

Martha T. Nester

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MICROBIOLOGY: A HUMAN PERSPECTIVE, SIXTH EDITION

Published by McGraw-Hill, a business unit of The McGraw-Hill Companies, Inc., 1221 Avenue of the Americas, New York, NY 10020. Copyright © 2009 by The McGraw-Hill Companies, Inc. All rights reserved. Previous editions © 2007, 2004, 2001, 1998, and 1995. No part of this publication may be reproduced or distributed in any form or by any means, or stored in a database or retrieval system, without the prior written consent of The McGraw-Hill Companies, Inc., including, but not limited to, in any network or other electronic storage or transmission, or broadcast for distance learning. Some ancillaries, including electronic and print components, may not be available to customers outside the United States. This book is printed on recycled, acid-free paper containing 10% postconsumer waste. 1 2 3 4 5 6 7 8 9 0 QPD/QPD 0 9 8 ISBN 978–0–07–299543–5 MHID 0–07–299543–2

Publisher: Michelle Watnick Senior Sponsoring Editor: James F. Connely Director of Development: Kristine Tibbetts Senior Developmental Editor: Lisa A. Bruflodt Project Coordinator: Mary Jane Lampe Senior Production Supervisor: Laura Fuller Senior Media Project Manager: Tammy Juran Senior Designer: David W. Hash Cover/Interior Designer: Jamie E. O’Neal (USE) Cover Image: color enhanced photomicrograph of Salmonella Enteritidis, ©Dennis Kunkel Microscopy, Inc. Senior Photo Research Coordinator: John C. Leland Photo Research: David Tietz/Editorial Image, LLC Compositor: Electronic Publishing Services Inc., NY Typeface: 10/12 Times Printer: Quebecor World Dubuque, IA The credits section for this book begins on page C-1 and is considered an extension of the copyright page.

Library of Congress Cataloging-in-Publication Data Microbiology : a human perspective / Eugene W. Nester ... [et al.]. — 6th ed. p. cm. Includes index. ISBN 978–0–07–299543–5 — ISBN 0–07–299543–2 (hard copy : alk. paper) 1. Microbiology. I. Nester, Eugene W. [DNLM: 1. Microbiological Techniques. 2. Communicable Diseases—microbiology. QW 4 M62555 2009] QR41.2.M485 2009 616.9’041—dc22 2008019596

www.mhhe.com

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We dedicate this book to our students; we hope it helps to enrich their lives and to make them better informed citizens,

to our families whose patience and endurance made completion of this project a reality,

to Anne Nongthanat Panarak Roberts in recognition of her invaluable help, patience, and understanding,

to our colleagues for continuing encouragement and advice.

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PART I LIFE AND DEATH OF MICROORGANISMS 1 2 3 4 5 6 7 8 9

Humans and the Microbial World 1 The Molecules of Life 18 Microscopy and Cell Structure 40 Dynamics of Prokaryotic Growth 83 Control of Microbial Growth 107 Metabolism: Fueling Cell Growth 126 The Blueprint of Life, from DNA to Protein 161 Bacterial Genetics 185 Biotechnology and Recombinant DNA 212

PART IV INFECTIOUS DISEASES 22 23 24 25 26 27 28 29

Respiratory System Infections 495 Skin Infections 531 Wound Infections 559 Digestive System Infections 581 Genitourinary Infections 618 Nervous System Infections 647 Blood and Lymphatic Infections 674 HIV Disease and Complications of Immunodeficiency 697

PART II THE MICROBIAL WORLD 10 Identification and Classification of Prokaryotic Organisms 232 11 The Diversity of Prokaryotic Organisms 251 12 The Eukaryotic Members of the Microbial World 280 13 Viruses of Bacteria 302 14 Viruses, Prions, and Viroids: Infectious Agents of Animals and Plants 320

PART V APPLIED MICROBIOLOGY 30 Microbial Ecology 721 31 Environmental Microbiology: Treatment of Water, Wastes, and Polluted Habitats 738 32 Food Microbiology 753

APPENDICES A-1 GLOSSARY G-1

PART III MICROORGANISMS AND HUMANS 15 16 17 18 19 20 21

CREDITS C-1 INDEX I-1

The Innate Immune Response 346 The Adaptive Immune Response 366 Host-Microbe Interactions 391 Immunologic Disorders 414 Applications of Immune Responses 431 Epidemiology 450 Antimicrobial Medications 469

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CHAPTER TWO

About the Authors xxii Preface xxiv Guided Tour xxx

The Molecules of Life 18 A Glimpse of History 18 Key Terms 19

2.1

Atoms and Elements 18

2.2

Chemical Bonds and the Formation of Molecules 20 Ionic Bonds 20 Covalent Bonds 21 Hydrogen Bonds 22

2.3

Chemical Components of the Cell 23 Water 23 pH 24 Small Molecules in the Cell 25 Macromolecules and Their Component Parts 25

2.4

Proteins and Their Functions 25 Amino Acid Subunits 26 Peptide Bonds and Their Synthesis 28 Protein Structure 28 Substituted Proteins 30

2.5

Carbohydrates 30 Monosaccharides 30 Disaccharides 32 Polysaccharides 32

2.6

Nucleic Acids 32 DNA 32 RNA 34

2.7

Lipids 35 Simple Lipids 35 Compound Lipids 36

PART I LIFE AND DEATH OF MICROORGANISMS CHAPTER ONE

Humans and the Microbial World 1 A Glimpse of History 1 Key Terms 2

1.1

The Origin of Microorganisms 1 Theory of Spontaneous Generation Revisited 2

1.2

Microbiology: A Human Perspective 6 Features of the Microbial World 6 Vital Activities of Microorganisms 6 Applications of Microbiology 6 Medical Microbiology 7 Microorganisms As Model Organisms 9

1.3

Members of The Microbial World 9 Bacteria 10 Archaea 10 Eucarya 10 Nomenclature 12

1.4

Viruses, Viroids, and Prions 12

1.5

Size in the Microbial World 14 PERSPECTIVE 2.1: Isotopes: Valuable Tools for the Study of Biological

PERSPECTIVE 1.1: The Long and the Short of It 15 FUTURE CHALLENGES: Entering a New Golden Age 16 SUMMARY 16 REVIEW QUESTIONS 17

Systems 26

FUTURE CHALLENGES: Fold Properly: Do Not Bend or Mutilate 37 SUMMARY 37 REVIEW QUESTIONS 38

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CONTENTS

CHAPTER THREE

Ribosomes 68 Cytoskeleton 68 Storage Granules 68 Gas Vesicles 68 Endospores 69

Microscopy and Cell Structure 40 A Glimpse of History 40 Key Terms 41

THE EUKARYOTIC CELL

MICROSCOPY AND CELL MORPHOLOGY 3.1

Microscopic Techniques: The Instruments 41 Principles of Light Microscopy: The Bright-Field Microscope 41 Light Microscopes That Increase Contrast 43 Electron Microscopes 46 Atomic Force Microscopy 48

3.10

The Plasma Membrane 72

3.11

Transfer of Molecules Across the Plasma Membrane 73 Transport Proteins 73 Endocytosis and Exocytosis 73 Secretion 74

3.2

Microscopic Techniques: Dyes and Staining 48 Differential Stains 49 Special Stains to Observe Cell Structures 50 Fluorescent Dyes and Tags 51

3.12

Protein Structures Within the Cell 74 Ribosomes 74 Cytoskeleton 74 Flagella and Cilia 74

3.3

Morphology of Prokaryotic Cells 52 Shapes 52 Groupings 53 Multicellular Associations 53

3.13

Membrane-Bound Organelles 75 The Nucleus 75 Mitochondria 76 Chloroplasts 77 Endoplasmic Reticulum (ER) 77 The Golgi Apparatus 78 Lysosomes and Peroxisomes 79

THE STRUCTURE OF THE PROKARYOTIC CELL 3.4

3.5

3.6

The Cytoplasmic Membrane 55 Structure and Chemistry of the Cytoplasmic Membrane 56 Permeability of the Cytoplasmic Membrane 56 The Role of the Cytoplasmic Membrane in Energy Transformation 57

PERSPECTIVE 3.1: The Origins of Mitochondria and Chloroplasts 77 FUTURE CHALLENGES: A Case of Breaking and Entering 79 SUMMARY 79 REVIEW QUESTIONS 81

Directed Movement of Molecules Across the Cytoplasmic Membrane 57 Transport Systems 58 Secretion 59 Cell Wall 59 Peptidoglycan 60 The Gram-Positive Cell Wall 61 The Gram-Negative Cell Wall 62 Antibacterial Substances that Target Peptidoglycan 63 Differences in Cell Wall Composition and the Gram Stain 63 Characteristics of Bacteria that Lack a Cell Wall 63 Cell Walls of the Domain Archaea 64

3.7

Capsules and Slime Layers 64

3.8

Filamentous Protein Appendages 65 Flagella 65 Pili 66

3.9

Internal Structures 67 The Chromosome 67 Plasmids 68

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CHAPTER FOUR

Dynamics of Prokaryotic Growth 83 A Glimpse of History 83 Key Terms 84

4.1

Principles of Prokaryotic Growth 84

4.2

Bacterial Growth in Nature 85 Biofilms 85 Interactions of Mixed Microbial Communities 86

4.3

Obtaining a Pure Culture 86 Cultivating Bacteria on a Solid Culture Medium 86 The Streak-Plate Method 87 Maintaining Stock Cultures 88

4.4

Bacterial Growth in Laboratory Conditions 88 The Growth Curve 88 Colony Growth 89 Continuous Culture 90

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CONTENTS

4.5

4.6

4.7

4.8

Environmental Factors That Influence Microbial Growth 90 Temperature Requirements 90 Oxygen (O2) Requirements 91 pH 92 Water Availability 93 Nutritional Factors That Influence Microbial Growth 93 Required Elements 93 Growth Factors 94 Energy Sources 94 Nutritional Diversity 95 Cultivating Prokaryotes in the Laboratory 95 General Categories of Culture Media 95 Special Types of Culture Media 96 Providing Appropriate Atmospheric Conditions 97 Enrichment Cultures 98

5.4

Using Other Physical Methods to Remove or Destroy Microbes 115 Filtration 115 Radiation 115 High Pressure 116

5.5

Using Chemicals to Destroy Microorganisms and Viruses 116 Potency of Germicidal Chemical Formulations 117 Selecting the Appropriate Germicidal Chemical 117 Classes of Germicidal Chemicals 118

5.6

Preservation of Perishable Products 121 Chemical Preservatives 122 Low-Temperature Storage 122 Reducing the Available Water 122

PERSPECTIVE 5.1: Contamination of an Operating Room by a Bacterial Pathogen 121

FUTURE CHALLENGES: Too Much of a Good Thing? 123 SUMMARY 123 REVIEW QUESTIONS 124

Methods to Detect and Measure Bacterial Growth 99 Direct Cell Counts 99 Viable Cell Counts 100 Measuring Biomass 102 Detecting Cell Products 103

CHAPTER SIX

Metabolism: Fueling Cell Growth 126 A Glimpse of History 126

PERSPECTIVE 4.1: Can Prokaryotes Live on Only Rocks and Water? 94

Key Terms 127

FUTURE CHALLENGES: Seeing How the Other 99% Lives 104

6.1

Principles of Metabolism 127 Harvesting Energy 128 Components of Metabolic Pathways 129 Precursor Metabolites 131 Overview of Metabolism 132

6.2

Enzymes 134 Mechanisms and Consequences of Enzyme Action 134 Cofactors and Coenzymes 135 Environmental Factors That Influence Enzyme Activity 136 Allosteric Regulation 137 Enzyme Inhibition 137

6.3

The Central Metabolic Pathways 138 Glycolysis 139 Pentose Phosphate Pathway 139 Transition Step 141 Tricarboxylic Acid (TCA) Cycle 142

6.4

Respiration 142 The Electron Transport Chain—Generating Proton Motive Force 143 ATP Synthase—Harvesting the Proton Motive Force to Synthesize ATP 145 ATP Yield of Aerobic Respiration in Prokaryotes 146

SUMMARY 104 REVIEW QUESTIONS 105

CHAPTER FIVE

Control of Microbial Growth 107 A Glimpse of History 107 Key Terms 108

5.1

Approaches to Control 107 Principles of Control 108 Situational Considerations 108

5.2

Selection of an Antimicrobial Procedure 110 Type of Microorganism 110 Numbers of Microorganisms Initially Present 110 Environmental Conditions 111 Potential Risk of Infection 111 Composition of the Item 111

5.3

Using Heat to Destroy Microorganisms and Viruses 111 Moist Heat 112 Dry Heat 114

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6.5

Fermentation 147

7.6

Regulation of Eukaryotic Gene Expression 179

6.6

Catabolism of Organic Compounds Other Than Glucose 148 Polysaccharides and Disaccharides 149 Lipids 150 Proteins 150

7.7

Sensing and Responding to Environmental Fluctuations 180 Signal Transduction 180 Natural Selection 181

7.8

6.7

Chemolithotrophs 150

Genomics 181 Analyzing a Prokaryotic DNA Sequence 181

6.8

Photosynthesis 151 Capturing Radiant Energy 152 Converting Radiant Energy into Chemical Energy 153

6.9

Carbon Fixation 154 Calvin Cycle 154

6.10

Anabolic Pathways—Synthesizing Subunits from Precursor Molecules 155 Lipid Synthesis 155 Amino Acid Synthesis 156 Nucleotide Synthesis 157

PERSPECTIVE 6.1: Mining with Microbes 151

PERSPECTIVE 7.1: RNA: The First Macromolecule? 175 FUTURE CHALLENGES: Gems in the Genomes? 182 SUMMARY 182 REVIEW QUESTIONS 183

CHAPTER EIGHT

Bacterial Genetics 185 A Glimpse of History 185 Key Terms 186

8.1

FUTURE CHALLENGES: Going to Extremes 158 SUMMARY 158 REVIEW QUESTIONS 160

GENE MUTATION AS A MECHANISM OF GENETIC CHANGE 8.2

Spontaneous Mutation 187 Base Substitution 188 Removal or Addition of Nucleotides 189 Transposable Elements (Jumping Genes) 189

8.3

Induced Mutations 190 Chemical Mutagens 190 Transposition 191 Radiation 192

8.4

Repair of Damaged DNA 192 Repair of Errors in Base Incorporation 192 Repair of Thymine Dimers 193 Repair of Modified Bases in DNA 193 SOS Repair 193

8.5

Mutant Selection 195 Direct Selection 195 Indirect Selection 195 Testing of Chemicals for Their Cancer-Causing Ability 196

CHAPTER SEVEN

The Blueprint of Life, from DNA to Protein 161 A Glimpse of History 161 Key Terms 162

7.1

Overview 162 Characteristics of DNA 162 Characteristics of RNA 164 Regulating the Expression of Genes 164

7.2

DNA Replication 164 Initiation of DNA Replication 166 The Replication Fork 166

7.3

Gene Expression in Bacteria 168 Transcription 168 Translation 170

7.4

Differences Between Eukaryotic and Prokaryotic Gene Expression 175

7.5

Regulation of Bacterial Gene Expression 176 Principles of Regulation 176 Mechanisms to Control Transcription 176 The lac Operon As a Model for Control of Metabolic Pathways 177

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Genetic Change in Bacteria 186

GENE TRANSFER AS A MECHANISM OF GENETIC CHANGE 8.6

DNA-Mediated Transformation 199 Natural Competence 200 Artificial Competence 201

8.7

Transduction 201

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CONTENTS

8.8

Conjugation 202 Plasmid Transfer 202 Chromosome Transfer 203 F’ Donors 204

8.9

The Mobile Gene Pool 205 Plasmids 205 Transposons 207 Genomic Islands 208

PART II THE MICROBIAL WORLD

PERSPECTIVE 8.1: The Biological Function of DNA: A Discovery

CHAPTER TEN

Ahead of Its Time 199

PERSPECTIVE 8.2: Bacteria Can Conjugate with Plants: A Natural Case

Identification and Classification of Prokaryotic Organisms 232

of Genetic Engineering 206

FUTURE CHALLENGES: Hunting for Magic Bullets 208

A Glimpse of History 232

SUMMARY 209 REVIEW QUESTIONS 210

CHAPTER NINE

Key Terms 233

10.1

Principles of Taxonomy 233 Strategies Used to Identify Prokaryotes 233 Strategies Used to Classify Prokaryotes 233 Nomenclature 235

10.2

Using Phenotypic Characteristics to Identify Prokaryotes 237 Microscopic Morphology 237 Metabolic Capabilities 238 Serology 240 Fatty Acid Analysis (FAME) 240

10.3

Using Genotypic Characteristics to Identify Prokaryotes 241 Detecting Specific Nucleotide Sequences Using Nucleic Acid Probes 242 Amplifying Specific DNA Sequences Using the Polymerase Chain Reaction 242 Sequencing Ribosomal RNA Genes 242

10.4

Characterizing Strain Differences 243 Biochemical Typing 243 Serological Typing 243 Genomic Typing 243 Phage Typing 244 Antibiograms 245

10.5

Classifying Prokaryotes 246 16S rDNA Sequence Analysis 246 DNA Hybridization 247 DNA Base Ratio (G+C Content) 248 Phenotypic Methods 248

Biotechnology and Recombinant DNA 212 A Glimpse of History 212 Key Terms 213

9.1

Fundamental Tools Used in Biotechnology 213 Restriction Enzymes 213 Gel Electrophoresis 214

9.2

Applications of Genetic Engineering 215 Genetically Engineered Bacteria 215 Genetically Engineered Eukaryotes 217

9.3

Techniques Used in Genetic Engineering 218 Obtaining DNA 218 Generating a Recombinant DNA Molecule 218 Introducing the Recombinant DNA into a New Host 220

9.4

Concerns Regarding Genetic Engineering and Other DNA Technologies 221

9.5

DNA Sequencing 221 Techniques Used in DNA Sequencing 221

9.6

Polymerase Chain Reaction (PCR) 223 Techniques Used in PCR 224 The Three-Step Amplification Cycle 224

9.7

Probe Technologies 227 Colony Blotting 228 Fluorescence in situ Hybridization (FISH) 228 DNA Microarrays 228

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PERSPECTIVE 10.1: Tracing the Source of an Outbreak of Foodborne Disease 244

PERSPECTIVE 9.1: Science Takes the Witness Stand 225 SUMMARY 230 REVIEW QUESTIONS 230

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FUTURE CHALLENGES: Tangled Branches in the Phylogenetic Tree 249 SUMMARY 249 REVIEW QUESTIONS 250

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CHAPTER ELEVEN

SUMMARY 277 REVIEW QUESTIONS 278

The Diversity of Prokaryotic Organisms 251 A Glimpse of History 251 Key Terms 252

CHAPTER TWELVE

The Eukaryotic Members of the Microbial World 280 A Glimpse of History 280

METABOLIC DIVERSITY 11.1

11.2

Anaerobic Chemotrophs 253 Anaerobic Chemolithotrophs 253 Anaerobic Chemoorganotrophs—Anaerobic Respiration 254 Anaerobic Chemoorganotrophs— Fermentation 254 Anoxygenic Phototrophs 256 The Purple Bacteria 256 The Green Bacteria 257 Other Anoxygenic Phototrophs 257

11.3

Oxygenic Phototrophs 257 The Cyanobacteria 258

11.4

Aerobic Chemolithotrophs 259 The Sulfur-Oxidizing Bacteria 259 The Nitrifiers 260 The Hydrogen-Oxidizing Bacteria 260

11.5

Aerobic Chemoorganotrophs 261 Obligate Aerobes 261 Facultative Anaerobes 262 ECOPHYSIOLOGICAL DIVERSITY

11.6

11.7

11.8

11.9

Thriving in Terrestrial Environments 263 Bacteria That Form a Resting Stage 264 Bacteria That Associate with Plants 267 Thriving in Aquatic Environments 266 Sheathed Bacteria 266 Prosthecate Bacteria 266 Bacteria That Derive Nutrients from Other Organisms 267 Bacteria That Move by Unusual Mechanisms 269 Bacteria That Form Storage Granules 270

Key Terms 281

12.1

Algae 281 Classification of Algae 282 Algal Habitats 282 Structure of Algae 282 Algal Reproduction 283 Paralytic Shellfish Poisoning 284

12.2

Protozoa 285 Classification of Protozoa 285 Protozoan Habitats 286 Structure of Protozoa 287 Protozoan Reproduction 287 Protozoa and Human Disease 288

12.3

Fungi 288 Classification of Fungi 288 Fungal Habitats 290 Fungal Disease in Humans 292 Symbiotic Relationships Between Fungi and Other Organisms 292 Economic Importance of Fungi 293

12.4

Slime Molds and Water Molds 294 Plasmodial and Cellular Slime Molds 294 Oomycetes (Water Molds) 294

12.5

Multicellular Parasites: Arthropods and Helminths 295 Arthropods 295 Helminths 297

PERSPECTIVE 12.1: How Marine Phytoplankton Help Combat Global Warming 285

FUTURE CHALLENGES: The Continued Fight to Eradicate Malaria 299

SUMMARY 300 REVIEW QUESTIONS 301

Animals As Habitats 270 Bacteria That Inhabit the Skin 270 Bacteria That Inhabit Mucous Membranes 272 Obligate Intracellular Parasites 273

CHAPTER THIRTEEN

Viruses of Bacteria 302

Archaea That Thrive in Extreme Conditions 275 Extreme Halophiles 275 Extreme Thermophiles 275

FUTURE CHALLENGES: Astrobiology: The Search for Life on Other Planets 276

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A Glimpse of History 302 Key Terms 303

13.1

General Characteristics of Viruses 302 Virus Architecture 303

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CONTENTS

The Viral Genome 304 Replication Cycle—Overall Features 304 13.2

13.3

13.4

Phage Interactions with Host Cells 306 Lytic Phage Replication by Double-Stranded DNA Phages 306 Lytic Single-Stranded RNA Phages 308 Phage Replication in a Latent State—Phage Lambda 308 Extrusion Following Phage Replication—Filamentous Phages 311 Lytic Infection by Single-Stranded DNA Phages 311

14.7

PART III MICROORGANISMS AND HUMANS CHAPTER FIFTEEN

Microbe Mimicker 305

The Innate Immune Response 346

PERSPECTIVE 13.2: Viral Soup 309 FUTURE CHALLENGES: Take Two Phage and Call Me in the

A Glimpse of History 346

Morning 316

Key Terms 347

15.1

Overview of the Innate Defenses 347

15.2

First-Line Defenses 348 Physical Barriers 348 Antimicrobial Substances 348 Normal Microbiota (Flora) 349

15.3

The Cells of the Immune System 350 Granulocytes 350 Mononuclear Phagocytes 350 Dendritic Cells 352 Lymphocytes 352

15.4

Cell Communication 353 Surface Receptors 353 Cytokines 353 Adhesion Molecules 354

15.5

Sensor Systems 354 Toll-Like Receptors and NOD Proteins 355 The Complement System 355 Sensors That Detect Long Double-Stranded RNA (dsRNA) 357

15.6

Phagocytosis 358 The Process of Phagocytosis 358 Specialized Attributes of Macrophages 358 Specialized Attributes of Neutrophils 359

15.7

Inflammation—A Coordinated Response to Invasion or Damage 360 Factors That Initiate the Inflammatory Response 360

CHAPTER FOURTEEN

Viruses, Prions, and Viroids: Infectious Agents of Animals and Plants 320 A Glimpse of History 320 Key Terms 321

14.1

14.2

Structure and Classification of Animal Viruses 321 Classification of Animal Viruses 321 Groupings Based on Routes of Transmission 322 Interactions of Animal Viruses with their Hosts 325 Acute Infections 325 Persistent Infections 329

14.3

Viruses and Human Tumors 333 Retroviruses and Human Tumors 333

14.4

Viral Genetic Alterations 335 Genome Exchange in Segmented Viruses 335

14.5

Methods Used to Study Viruses 336 Cultivation of Host Cells 336 Quantitation 337

14.6

Plant Viruses 339 Spread of Plant Viruses 339 Insect Transmission of Plant Viruses 340

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343

SUMMARY 343 REVIEW QUESTIONS 344

Host Range of Phages 314 Receptors on the Bacterial Surface 314 Restriction-Modification System 314

SUMMARY 316 REVIEW QUESTIONS 318

Other Infectious Agents 340 Prions 341 Viroids 342

PERSPECTIVE 14.1: A Whodunit in Molecular Virology 336 FUTURE CHALLENGES: Great Promise, Greater Challenges

Transduction 313 Generalized Transduction 313 Specialized Transduction 313

PERSPECTIVE 13.1:

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CONTENTS

The Inflammatory Process 360 Outcomes of Inflammation 361 Apoptosis—Controlled Cell Death That Circumvents the Inflammatory Process 362 15.8

Positive and Negative Selection of Self-Reactive T Cells 387 PERSPECTIVE 16.1: What Flavor Are Your Major Histocompatibility Complex Molecules? 385

Fever 362

SUMMARY 388 REVIEW QUESTIONS 389

PERSPECTIVE 15.1: For Schistosoma, the Inflammatory Response Delivers 362

CHAPTER SEVENTEEN

SUMMARY 363 REVIEW QUESTIONS 364

Host-Microbe Interactions 391

CHAPTER SIXTEEN

A Glimpse of History 391 Key Terms 392

The Adaptive Immune Response 366

MICROBES, HEALTH, AND DISEASE

A Glimpse of History 366

16.1

Key Terms 367

17.1

Strategy of the Adaptive Immune Response 367 Overview of Humoral Immunity 367 Overview of Cellular Immunity 368

The Anatomical Barriers As Ecosystems 392 Symbiotic Relationships Between Microorganisms and Hosts 392

17.2

The Normal Microbiota 393 The Protective Role of the Normal Microbiota 393 The Dynamic Nature of the Normal Microbiota 393

17.3

Principles of Infectious Diseases 394 Pathogenicity 394 Characteristics of Infectious Disease 394

17.4

Establishing the Cause of Infectious Disease 395 Koch’s Postulates 396 Molecular Koch’s Postulates 396

16.2

Anatomy of the Lymphoid System 369 Lymphatic Vessels 370 Secondary Lymphoid Organs 370 Primary Lymphoid Organs 370

16.3

The Nature of Antigens 370

16.4

The Nature of Antibodies 371 Structure and Properties of Antibodies 371 Protective Outcomes of Antibody-Antigen Binding 372 Immunoglobulin Classes 373

16.5

Clonal Selection and Expansion of Lymphocytes 375

16.6

B Lymphocytes and the Antibody Response 376 B-Cell Activation 377 Characteristics of the Primary Response 377 Characteristics of the Secondary Response 379 The Response to T-Independent Antigens 379

16.7

T Lymphocytes: Antigen Recognition and Response 379 General Characteristics of T Cells 380 Activation of T Cells 381 Functions of TC (CD8) Cells 382 Functions of TH (CD4) Cells 383 Subsets of Dendritic Cells and T Cells 383

16.8

Natural Killer (NK) Cells 384

16.9

Lymphocyte Development 385 Generation of Diversity 387 Negative Selection of Self-Reactive B Cells 387

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MECHANISMS OF PATHOGENESIS 17.5

Establishment of Infection 397 Adherence 397 Colonization 398 Delivery of Effector Molecules to Host Cells 398

17.6

Invasion—Breaching the Anatomical Barriers 399 Penetration of Skin 399 Penetration of Mucous Membranes 399

17.7

Avoiding the Host Defenses 400 Hiding Within a Host Cell 400 Avoiding Killing by Complement System Proteins 400 Avoiding Destruction by Phagocytes 401 Avoiding Antibodies 403

17.8

Damage to the Host 403 Exotoxins 403

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CONTENTS

CHAPTER NINETEEN

Endotoxin and Other Bacterial Cell Wall Components 407 Damaging Effects of the Immune Response 408 17.9

Applications of Immune Responses 431

Mechanisms of Viral Pathogenesis 408 Binding to Host Cells and Invasion 408 Avoiding Immune Responses 409

17.10 Mechanisms of Eukaryotic Pathogenesis 410 Fungi 410 Protozoa and Helminths 410 FUTURE CHALLENGES:

A Glimpse of History 431 Key Terms 432

IMMUNIZATION 19.1

Principles of Immunization 432 Active Immunity 432 Passive Immunity 432

19.2

Vaccines and Immunization Procedures 433 Attenuated Vaccines 433 Inactivated Vaccines 435 An Example of Vaccination Strategy—The Campaign to Eliminate Poliomyelitis 436 The Importance of Routine Immunizations for Children 436 Current Progress in Immunization 437

The Potential of Probiotics 411

SUMMARY 411 REVIEW QUESTIONS 412

CHAPTER EIGHTEEN

Immunologic Disorders 414 A Glimpse of History 414 Key Terms 415

18.1

Type I Hypersensitivities: Immediate IgE-Mediated 415 Localized Anaphylaxis 416 Generalized Anaphylaxis 417 Treatments to Prevent Allergic Reactions 417

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IMMUNOLOGICAL TESTING 19.3

Principles of Immunological Testing 439 Obtaining Antibodies 439 Quantifying Antigen-Antibody Reactions 439

18.2

Type II Hypersensitivities: Cytotoxic 418 Transfusion Reactions 418 Hemolytic Disease of the Newborn 418

19.4

Observing Antigen-Antibody Aggregations 441 Precipitation Reactions 441 Agglutination Reactions 443

18.3

Type III Hypersensitivities: Immune Complex—Mediated 420

19.5

18.4

Type IV Hypersensitivities: Delayed Cell–Mediated 421 Tuberculin Skin Test 421 Delayed Hypersensitivity in Infectious Diseases 422 Contact Hypersensitivities 422

Using Labeled Antibodies to Detect Antigen-Antibody Interactions 444 Fluorescent Antibody (FA) Tests 444 Enzyme-Linked Immunosorbent Assay (ELISA) 445 Western Blotting 446 Fluorescence-Activated Cell Sorter (FACS) 447

18.5

Rejection of Transplanted Tissues 423

18.6

Autoimmune Diseases 424 The Spectrum of Autoimmune Reactions 425 Treatment of Autoimmune Diseases 425

18.7

Immunodeficiency Disorders 426 Primary Immunodeficiencies 426 Secondary Immunodeficiencies 427

PERSPECTIVE 18.1:

FUTURE CHALLENGES: Global Immunization 447 SUMMARY 447 REVIEW QUESTIONS 448

CHAPTER TWENTY

Epidemiology 450 A Glimpse of History 450 Key Terms 451

The Fetus As an Allograft 423

FUTURE CHALLENGES:

New Approaches to Correcting Immunologic

Disorders 428

SUMMARY 428 REVIEW QUESTIONS 429

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PERSPECTIVE 19.1: Monoclonal Antibodies 440

20.1

Principles of Epidemiology 451 Rate of Disease in a Population 451 Reservoirs of Infection 453 Portals of Exit 454

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CONTENTS

Transmission 454 Portals of Entry 455 Factors That Influence the Epidemiology of Disease 455 20.2

Epidemiological Studies 457 Descriptive Studies 457 Analytical Studies 458 Experimental Studies 458

20.3

Infectious Disease Surveillance 459 National Disease Surveillance Network 459 Worldwide Disease Surveillance 460

20.4

Trends in Disease 460 Reduction and Eradication of Disease 460 Emerging Diseases 461

20.5

Healthcare-Associated Infections 462 Reservoirs of Infectious Agents in Healthcare Settings 462 Transmission of Infectious Agents in Healthcare Settings 464 Preventing Healthcare-Associated Infections 464

21.3

Mechanisms of Action of Antibacterial Drugs 473 Antibacterial Medications That Inhibit Cell Wall Synthesis 475 Antibacterial Medications That Inhibit Protein Synthesis 477 Antibacterial Medications That Inhibit Nucleic Acid Synthesis 478 Antibacterial Medications That Inhibit Metabolic Pathways 478 Antibacterial Medications That Interfere with Cell Membrane Integrity 479 Antibacterial Medications That Interfere with Processes Essential to Mycobacterium tuberculosis 479

21.4

Determining the Susceptibility of a Bacterial Strain to an Antimicrobial Drug 480 Determining the Minimum Inhibitory and Bactericidal Concentrations 480 Conventional Disc Diffusion Method 481 Commercial Modifications of Antimicrobial Susceptibility Testing 482

21.5

Resistance to Antimicrobial Drugs 483 Mechanisms of Acquired Resistance 483 Acquisition of Resistance 484 Examples of Emerging Antimicrobial Resistance 484 Slowing the Emergence and Spread of Antimicrobial Resistance 485

21.6

Mechanisms of Action of Antiviral Drugs 486 Entry Inhibitors 486 Viral Uncoating 486 Nucleic Acid Synthesis 487 Integrase Inhibitors 488 Assembly and Release of Viral Particles 488

21.7

Mechanisms of Action of Antifungal Drugs 488 Plasma Membrane Synthesis and Function 488 Cell Wall Synthesis 489 Cell Division 489 Nucleic Acid Synthesis 489

21.8

Mechanisms of Action of Antiprotozoan and Antihelminthic Drugs 490

PERSPECTIVE 20.1: Standard Precautions—Protecting Patients and Healthcare Personnel 465

FUTURE CHALLENGES: Maintaining Vigilance Against Bioterrorism 466

SUMMARY 466 REVIEW QUESTIONS 467

CHAPTER TWENTY ONE

Antimicrobial Medications 469 A Glimpse of History 469 Key Terms 470

21.1

History and Development of Antimicrobial Drugs 469 Discovery of Antimicrobial Drugs 469 Discovery of Antibiotics 470 Development of New Generations of Drugs 470

21.2

Features of Antimicrobial Drugs 471 Selective Toxicity 471 Antimicrobial Action 471 Spectrum of Activity 471 Effects of Combinations of Antimicrobial Drugs 472 Tissue Distribution, Metabolism, and Excretion of the Drug 472 Adverse Effects 472 Resistance to Antimicrobials 472

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PERSPECTIVE 21.1: Measuring the Concentration of an Antimicrobial Drug in Blood or Other Body Fluids 481

FUTURE CHALLENGES: War with the Superbugs 491 SUMMARY 491 REVIEW QUESTIONS 493

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CONTENTS

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FUTURE CHALLENGES: Global Preparedness vs. Emerging Respiratory Viruses 528

SUMMARY 528 REVIEW QUESTIONS 529

PART IV INFECTIOUS DISEASES

CHAPTER TWENTY THREE

Skin Infections 531 A Glimpse of History 531 Key Terms 532

CHAPTER TWENTY TWO

Respiratory System Infections 495 A Glimpse of History 495

23.1

Anatomy and Physiology 531

23.2

Normal Microbiota of the Skin 533 Diphtheroids 533 Staphylococci 534 Fungi 534

23.3

Bacterial Skin Diseases 535 Hair Follicle Infections 535 Scalded Skin Syndrome 537 Streptococcal Impetigo 538 Rocky Mountain Spotted Fever 540 Lyme Disease 542

23.4

Skin Diseases Caused by Viruses 545 Chickenpox (Varicella) 545 Measles (Rubeola) 547 German Measles (Rubella) 549 Other Viral Rashes of Childhood 552 Warts 552

23.5

Skin Diseases Caused by Fungi 554 Superficial Cutaneous Mycoses 554

Key Terms 496

22.1 22.2

Anatomy and Physiology 495 The Mucociliary Escalator 498 Normal Microbiota 498

INFECTIONS OF THE UPPER RESPIRATORY SYSTEM 22.3

22.4

Bacterial Infections of the Upper Respiratory System 499 Strep Throat (Streptococcal Pharyngitis) 499 Diphtheria 502 Pinkeye, Earache, and Sinus Infections 504 Viral Infections of the Upper Respiratory System 507 The Common Cold 507 Adenoviral Pharyngitis 508

INFECTIONS OF THE LOWER RESPIRATORY SYSTEM 22.5

22.6

22.7

Bacterial Infections of the Lower Respiratory System 509 Pneumococcal Pneumonia 509 Klebsiella Pneumonia 511 Mycoplasmal Pneumonia 511 Whooping Cough (Pertussis) 513 Tuberculosis 514 Legionnaires’ Disease 517

CASE PRESENTATION 551 PERSPECTIVE 23.1: The Ghost of Smallpox, An Evil Shade 554 FUTURE CHALLENGES: The Ecology of Lyme Disease 556 SUMMARY 556 REVIEW QUESTIONS 557

CHAPTER TWENTY FOUR

Wound Infections 559

Viral Infections of the Lower Respiratory System 519 Influenza 519 Respiratory Syncytial Virus Infections 521 Hantavirus Pulmonary Syndrome 522

24.1

Fungal Infections of the Lung 525 Valley Fever (Coccidioidomycosis) 525 Spelunkers’ Disease (Histoplasmosis) 526

Anatomy and Physiology 560 Wound Abscesses 560 Anaerobic Wounds 561

24.2

Common Bacterial Wound Infections 562 Staphylococcal Wound Infections 562 Group A Streptococcal “Flesh Eaters” 563 Pseudomonas aeruginosa Infections 564

PERSPECTIVE 22.1: Terror by Mail: Inhalation Anthrax 512 PERSPECTIVE 22.2: What to Do About Bird Flu 524

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A Glimpse of History 559 Key Terms 560

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24.3

24.4

24.5

CONTENTS

Diseases Due to Anaerobic Bacterial Wound Infections 566 “Lockjaw“ (Tetanus) 566 Gas Gangrene (Clostridial Myonecrosis) 568 “Lumpy Jaw“ (Actinomycosis) 570 Bacterial Bite Wound Infections 572 Pasteurella multocida Bite Wound Infections 572 Cat Scratch Disease 572 Streptobacillary Rat Bite Fever 574 Human Bites 574

LOWER DIGESTIVE SYSTEM INFECTIONS 25.5

Bacterial Diseases of the Lower Digestive System 595 Cholera 596 Shigellosis 598 Escherichia coli Gastroenteritis 599 Salmonellosis 601 Campylobacteriosis 602

25.6

Viral Diseases of the Lower Digestive System 604 Rotaviral Gastroenteritis 604 Norovirus Gastroenteritis 604 Hepatitis A 605 Hepatitis B 606 Hepatitis C 608

25.7

Protozoan Diseases of the Lower Digestive System 609 Giardiasis 609 Cryptosporidiosis 610 Cyclosporiasis 612 Amebiasis 612

Fungal Wound Infections 576 “Rose Gardener’s Disease“ (Sporotrichosis) 576

CASE PRESENTATION 573 PERSPECTIVE 24.1: Infection Caused by a Human “Bite“ 575 FUTURE CHALLENGES: Staying Ahead in the Race with Staphylococcus aureus 578

SUMMARY 578 REVIEW QUESTIONS 579

CHAPTER TWENTY FIVE

Digestive System Infections 581 A Glimpse of History 581

CASE PRESENTATION 591 PERSPECTIVE 25.1: Ecology of Cholera 597 FUTURE CHALLENGES: Defeating Diarrhea SUMMARY 614 REVIEW QUESTIONS 616

Key Terms 582

25.1

25.2

Anatomy and Physiology 582 The Mouth 582 Salivary Glands 582 The Esophagus 583 The Stomach 584 The Small Intestine 584 The Pancreas 584 The Liver 584 The Large Intestine 585 Normal Microbiota 585 The Mouth 585 The Intestines 585

CHAPTER TWENTY SIX

Genitourinary Infections 618 A Glimpse of History 618 Key Terms 619

26.1

Anatomy and Physiology 619 The Urinary System 619 The Genital System 620

26.2

Normal Microbiota of the Genitourinary System 620

26.3

Urinary System Infections 621 Bacterial Cystitis 621 Leptospirosis 622

26.4

Genital System Diseases 625 Bacterial Vaginosis 625 Vulvovaginal Candidiasis 625 Staphylococcal Toxic Shock Syndrome 626

26.5

Sexually Transmitted Diseases: Scope of the Problem 628

26.6

Bacterial STDs 629 Gonorrhea 629

UPPER DIGESTIVE SYSTEM INFECTIONS 25.3

Bacterial Diseases of the Upper Digestive System 586 Tooth Decay (Dental Caries) 586 Periodontal Disease 588 Trench Mouth 588 Helicobacter pylori Gastritis 589

25.4

Viral Diseases of the Upper Digestive System 592 Herpes Simplex (Cold Sores or Fever Blisters) 592 Mumps 593

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CONTENTS

Chlamydial Genital System Infections 631 Syphilis 633 Chancroid 636 26.7

26.8

Viral STDs 638 Genital Herpes Simplex 638 Papillomavirus STDs: Genital Warts and Cervical Cancer 639 AIDS 640

CHAPTER TWENTY EIGHT

Blood and Lymphatic Infections 674 A Glimpse of History 674 Key Terms 675

28.1

Anatomy and Physiology 675 The Heart 675 Arteries 676 Veins 676 Lymphatics (Lymphatic Vessels) 676 Spleen 677

28.2

Bacterial Diseases of the Blood Vascular System 677 Subacute Bacterial Endocarditis 677 Gram-Negative Septicemia 678

28.3

Bacterial Diseases of the Lymph Nodes and Spleen 680 “Rabbit Fever” (Tularemia) 680 “Undulant Fever” (Brucellosis, “Bang’s Disease”) 681 “Black Death” (Plague) 682

28.4

Viral Diseases of the Lymphoid and Blood Vascular Systems 686 “Kissing Disease” (Infectious Mononucleosis, “Mono”) 686 Yellow Fever 688

28.5

Protozoan Diseases 690 Malaria 691

Protozoal STDs 642 “Trich” (Trichomoniasis) 642

CASE PRESENTATION 623 PERSPECTIVE 26.1: The Demise of Syphilis? 634 FUTURE CHALLENGES: Getting Control of Sexually Transmitted Diseases 643

SUMMARY 644 REVIEW QUESTIONS 645

CHAPTER TWENTY SEVEN

Nervous System Infections 647 A Glimpse of History 647 Key Terms 648

27.1 27.2

27.3

Anatomy and Physiology 648 Pathways to the Central Nervous System 649 Bacterial Nervous System Infections 650 Meningococcal Meningitis 650 Listeriosis 653 Hansen’s Disease (Leprosy) 655 Botulism 657

Fungal Diseases of the Nervous System 666 Cryptococcal Meningoencephalitis 666

27.5

Protozoan Diseases of the Nervous System 667 African Sleeping Sickness 667

27.6

CASE PRESENTATION 688 PERSPECTIVE 28.1: Arteriosclerosis: The Infection Hypothesis 676 PERSPECTIVE 28.2: Walter Reed and Yellow Fever 690 FUTURE CHALLENGES: Rethinking Malaria Control 694

Viral Diseases of the Nervous System 658 Viral Meningitis 659 Viral Encephalitis 659 Infantile Paralysis, Polio (Poliomyelitis) 661 Rabies 663

27.4

Transmissible Spongiform Encephalopathies 669 Transmissible Spongiform Encephalopathy in Humans 669

CASE PRESENTATION 651 PERSPECTIVE 27.1: A Rabies Survivor! 665 FUTURE CHALLENGES: Eradicate Polio: Then What? 670 SUMMARY 671 REVIEW QUESTIONS 672

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SUMMARY 694 REVIEW QUESTIONS 695

CHAPTER TWENTY NINE

HIV Disease and Complications of Immunodeficiency 697 A Glimpse of History 697 Key Terms 698

29.1

Human Immunodeficiency Virus (HIV) Infection and AIDS 698 HIV Disease 699 HIV Vaccine Prospects 709

29.2

Malignant Tumors That Complicate Acquired Immunodeficiencies 710 Kaposi’s Sarcoma 710 B-Lymphocytic Tumors of the Brain 711 Cervical and Anal Carcinoma 711

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29.3

CONTENTS

Infectious Complications of Acquired Immunodeficiency 712 Pneumocystosis 712 Toxoplasmosis 713 Cytomegalovirus Disease 715 Mycobacterial Diseases 717

CASE PRESENTATION 707 PERSPECTIVE 29.1: Origin of AIDS-Causing Viruses FUTURE CHALLENGES: AIDS and Poverty 718

30.5

Mutualistic Relationships between Microorganisms and Eukaryotes 733 Mycorrhizae 733 Symbiotic Nitrogen-Fixers and Plants 734 Microorganisms and Herbivores 735 SUMMARY 735 REVIEW QUESTIONS 736

705

SUMMARY 719 REVIEW QUESTIONS 720

CHAPTER THIRTY ONE

Environmental Microbiology: Treatment of Water, Wastes, and Polluted Habitats 738 A Glimpse of History 738 Key Terms 739

31.1

Microbiology of Wastewater Treatment 739 Biochemical Oxygen Demand (BOD) 739 Municipal Wastewater Treatment Methods 739 Individual Wastewater Treatment Systems 744

PART V APPLIED MICROBIOLOGY

31.2

Drinking Water Treatment and Testing 744 Water Treatment Processes 745 Water Testing 746

CHAPTER THIRTY

31.3

Microbiology of Solid Waste Treatment 747 Sanitary Landfills for Solid Waste Disposal 747 Municipal and Backyard Composting—Alternative to Landfills 747

31.4

Microbiology of Bioremediation 749 Pollutants 749 Means of Bioremediation 749

Microbial Ecology 721 A Glimpse of History 721 Key Terms 722

30.1

30.2

30.3

30.4

Principles of Microbial Ecology 722 Nutrient Acquisition 722 Bacteria in Low-Nutrient Environments 723 Microbial Competition and Antagonism 723 Microorganisms and Environmental Changes 723 Microbial Communities 724 Studying Microbial Ecology 724

PERSPECTIVE 31.1: Now They’re Cooking with Gas 743 FUTURE CHALLENGES: Better Identification of Pathogens in Water and Wastes 750

SUMMARY 751 REVIEW QUESTIONS 751

Aquatic Habitats 725 Marine Environments 726 Freshwater Environments 726 Specialized Aquatic Environments 726 Terrestrial Habitats 727 Characteristics of Soil 727 Microorganisms in Soil 727 The Rhizosphere 728 Biogeochemical Cycling and Energy Flow 728 Carbon Cycle 728 Nitrogen Cycle 730 Sulfur Cycle 731 Phosphorus Cycle and Other Cycles 732 Energy Sources for Ecosystems 732

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CHAPTER THIRTY TWO

Food Microbiology 753 A Glimpse of History 753 Key Terms 754

32.1

Factors Influencing the Growth of Microorganisms in Foods 754 Intrinsic Factors 755 Extrinsic Factors 755

32.2

Microorganisms in Food and Beverage Production 756 Lactic Acid Fermentations by the Lactic Acid Bacteria 756

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CONTENTS

32.3

32.4

32.5

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Alcoholic Fermentations by Yeast 758 Changes Due to Mold Growth 761

APPENDIX I Microbial Mathematics A-1

Food Spoilage 762 Common Spoilage Bacteria 762 Common Spoilage Fungi 762

APPENDIX III Pronunciation Key for Bacterial, Fungal, Protozoan, and Viral Names A-4

Foodborne Illness 762 Foodborne Intoxication 763 Foodborne Infection 764

APPENDIX V Answers to Multiple Choice Questions A-11

Food Preservation 765

APPENDIX II Microbial Terminology A-2

APPENDIX IV Metabolic Pathways A-7

GLOSSARY G-1 CREDITS C-1 INDEX I-1

PERSPECTIVE 32.1: Botox for Beauty and Pain Relief 764 FUTURE CHALLENGES: Using Microorganisms to Nourish the World 766

SUMMARY 766 REVIEW QUESTIONS 767

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Eugene Nester Eugene (Gene) Nester performed his undergraduate work at Cornell University and received his Ph.D. in Microbiology from Case Western University. He then pursued postdoctoral work in the Department of Genetics at Stanford University with Joshua Lederberg. Since 1962, Gene has been a faculty member in the Department of Microbiology at the University of Washington. Gene’s research has focused on gene transfer systems in bacteria. His laboratory demonstrated that Agrobacterium transfers DNA into plant cells, the basis for the disease crown gall. He continues to study this unique system of gene transfer which has become a cornerstone of plant biotechnology. In 1990, Gene Nester was awarded the inaugural Australia Prize along with an Australian and a German scientist for their work on Agrobacterium transformation of plants. In 1991, he was awarded the Cetus Prize in Biotechnology by the American Society of Microbiology. He has been elected to Fellowship in the National Academy of Sciences, the American Academy for the Advancement of Science, the American Academy of Microbiology, and the National Academy of Sciences in India. Throughout his career, Gene has been actively involved with the American Society for Microbiology in several leadership positions. In addition to his research activities, Gene has taught an introductory microbiology course for students in the allied health sciences for many years. He wrote the original version of the present text, Microbiology: Molecules, Microbes and Man, with C. Evans Roberts, Brian McCarthy, and Nancy Pearsall more than 30 years ago because they felt no suitable text was available for this group of students. The original text pioneered the organ system approach to the study of infectious disease. Gene enjoys traveling, museum hopping, and the study and collecting of Northwest Coast Indian Art. He and his wife, Martha, live on Lake Washington with their labradoodle, Twana, and a well-used kayak. Their two children and four grandchildren live in the Seattle area.

Denise Anderson Denise Anderson is a Senior Lecturer in the Department of Microbiology at the University of Washington, where she teaches a variety of courses including general microbiology, recombinant DNA techniques, medical bacteriology laboratory, and medical mycology/parasitology laboratory. Equipped with a diverse educational background, including undergraduate work in nutrition and graduate work in food science and in microbiology, she first discovered a passion for teaching when she taught microbiology laboratory courses as part of her graduate training. Her enthusiastic teaching style, fueled by regular doses of Seattle’s famous caffeine, receives high reviews by her students. Outside of academic life, Denise relaxes in the Phinney Ridge neighborhood of Seattle, where she lives with her husband, Richard Moore, and dog, Dudley (neither of whom are well trained). When not planning lectures, grading papers, or writing textbook chapters, she can usually be found chatting with the neighbors, fighting the weeds in her garden, or enjoying a fermented beverage at the local pub.

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ABOUT THE AUTHORS

C. Evans Roberts, Jr. Evans Roberts was a mathematics student at Haverford College when a chance encounter landed him a summer job at the Marine Biological Laboratory in Woods Hole, Massachusetts. There, interactions with leading scientists awakened an interest in biology and medicine. After finishing his degree at Haverford, he went on to get a M.D. degree at Columbia University College of Physicians and Surgeons, complete an intership at University of Rochester School of Medicine and Dentistry, and a residency in medicine at University of Washington School of Medicine where he also completed a fellowship in Infectious Diseases under Dr. William M. M. Kirby, and a traineeship in Diagnostic Microbiology under Dr. John Sherris. Subsequently, Dr. Roberts taught microbiology at University of Washington, University of Oregon, and Chiang Mai University, in Chiagmai, Thailand, returning to University of Washington thereafter. He has directed diagnostic medical microbiology laboratories, served on hospital infection control committees, and taught infectious diseases to nurse practitioners in a camp for Karen refugees in Northern Thailand. He has had extensive experience in the practice of medicine as it relates to infectious diseases. He is certified both by the American Board of Microbiology and the American Board of Internal Medicine. Evans Roberts worked with Gene Nester in the early development of Microbiology: A Human Perspective. His professional publications concern susceptibility testing as a guide to treatment of infectious diseases, etiology of Whipple’s disease, group A streptococcal epidemiology, use of fluorescent antibody in diagnosis, bacteriocin typing, antimicrobial resistance in gonorrhea and tuberculosis, Japanese B encephalitis, and rabies. For relaxation, he enjoys hiking, bird watching and traveling worldwide.

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Martha Nester Martha Nester received an undergraduate degree in biology from Oberlin College and a Master’s degree in education from Stanford University. She has worked in university research laboratories and has taught elementary school. She currently works in an environmental education program at the Seattle Audubon Society. Martha has worked with her husband, Gene, for more than 40 years on microbiology textbook projects, at first informally as an editor and sounding board, and then as one of the authors of Microbiology: A Human Perspective. Martha’s favorite activities include spending time with their four grandchildren, all of whom live in the Seattle area. She also enjoys playing the cello with a number of musical groups in the Seattle area.

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T

his is an exciting yet challenging time to be teaching and learning about microbiology. The need to provide accurate and current information about the good and bad microbes seems greater than ever. Almost every day a newspaper article describes illness arising from a contaminated food, the discovery of microbes in an environment once considered impossible to sustain life, the sequencing of another microbial genome, or the death of an individual from a rare infectious disease. Anyone glancing at the front page cannot help but realize the impact that microorganisms have in our daily lives. The announcements of the many scientific advances being made about the microbial world often bring with them vehement arguments related to the science. Are plants that contain genes of microorganisms safe to eat? Is it wise to put antimicrobial agents in soaps and animal feed? What agents of biological warfare might endanger the citizens of the world? Are we facing another flu pandemic? This book presents what we believe are the most important facts and concepts about the microbial world and the important role its members play in our daily lives. With the information presented, students should be able to form reasoned opinions and discuss intelligently their views on these questions. An important consideration in revising this textbook is the diverse interests among students who take an introductory microbiology course. As always, many students take microbiology as a prerequisite for nursing, pharmacy, and dental programs. A suitable textbook must provide a solid foundation in health-related aspects of microbiology, including coverage of medically important bacteria, antimicrobial medications, and immunization. An increasing number of students take microbiology as a step in the pursuit of other fields, including biotechnology, food science, and ecology. For these students, topics such as recombinant DNA technologies, fermentation processes, and microbial diversity are essential. With the recent outbreaks of foodborne illnesses traced to products that had been distributed widely, the subject of microbial identification becomes more relevant. Microbiology is also popular as an elective for biology students, who are particularly interested in topics that highlight the relevance of microorganisms in the biological world. Because of the wide range of career goals and interests of students, we have made a particular effort to maintain a broad scope, providing a balanced approach, yet retaining our strength in medical microbiology. Diversity in the student population is manifested not only in the range of career goals, but also in educational backgrounds. For some, microbiology may be their first college-level science course; for others, microbiology builds on an already strong background in biology and chemistry. To address this broad range of student backgrounds, we have incorporated numerous learning

aids that will facilitate review for some advanced students, and will be a tremendous support to those who are seeing this material for the first time. Preparing a textbook that satisfies such a broad range of needs and interests is a daunting task, but also extremely rewarding. We hope you will find that the approach and structure of this edition presents a modern and balanced view of microbiology in our world, acknowledging the profound and essential impact that microbes have on our lives today and their possible roles in our lives tomorrow.

Features of the Sixth Edition Completely updated and including the most current topics in microbiology today, Microbiology: A Human Perspective, sixth edition, continues to be a classic. It has always been our goal to present sound scientific content that students can understand and rely upon for accuracy and currency, and thereby succeed in their preparation for meaningful careers. We have used constructive comments from numerous microbiology instructors and their students to continue to enhance the robust features of this proven text.

Expert Approach to Writing We, as a strong and diverse team of scientists and teachers, solidly present the connection between microorganisms and humans. Because of our individual specializations and our research and educational backgrounds, we remain in the hub of the scientific community and can provide accurate and modern coverage spanning the breadth of microbiology. More importantly, as teachers, we constantly strive to present material that easily speaks to the students reading it. We recognize that a textbook, no matter how exciting the subject matter, is not a novel. Few students will read the text from cover to cover and few instructors will include all of the topics covered in their course. We have used judicious redundancy to help present each major topic as a complete unit. We have avoided the chatty, superficial style of writing in favor of clarity and conciseness. The text is not “watered down” but rather provides students the depth of coverage needed to fully understand and appreciate the role of microorganisms in the biological sciences and human affairs. “Without a doubt Microbiology: A Human Perspective is one of the most readable science texts I have ever had the pleasure of reading. The text is not scary or overly weighty in its approach to microbiology.” (Robyn Senter, Lamar State College–Orange)

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PREFACE

“I like the simple, straight-forward wording. An introductory student with no or little background in biology should have no problems understanding these concepts.” (Karen Nakaoka, Weber State University) “Students can relate to the examples/analogies and apply them to their daily lives. The text clearly demonstrates the connection between microbes and humans!” (Michelle Fisher, Three Rivers Community College)

Instructive Art Program that Speaks a Thousand Words Microorganisms, by definition, are invisible to the naked eye. It becomes ever more important to allow students to visualize organisms as well as processes to reinforce learning. The art program continues as a key element of the learning process. Each figure in Microbiology: A Human Perspective was developed as the narrative was written and is referenced in bold in the supporting text. Colors and symbols are used consistently throughout the text. Legends are short, clear, and descriptive. Various types of art styles are used as needed to bring concepts to life. Overview Figures simplify complex interactions and provide a sound study tool. Image Pathways help students follow the progression of a discussion over several pages by highlighting and visualizing in detail each step of an overview figure. Process Figures include step-by-step descriptions and supporting text so that the figure walks through a compact summary of important concepts. Combination Figures tie together the features that can be illustrated by an artist with the appearance of organisms in the real world. Stunning Micrographs used generously throughout the text bring the microbial world to life. In the chapters presenting infectious diseases (chapters 22 to 29), micrographs are often combined with photographs showing the symptoms that the organisms cause.

Unmatched Clinical Coverage Evans Roberts, Jr.—a member of the author team who is licensed and board certified in internal medicine by the American Board of Internal Medicine, and in public health and medical laboratory microbiology by the American Board of Microbiology—ensures that clinical coverage is accurate, modern, and instructive to those planning to enter health careers. The incomparable treatment of infectious diseases, which are organized by human body systems, is supported with generous photographs, summary tables, case histories, and critical thinking questions. Elements of the unparalleled clinical coverage include: Consistent coverage of all diseases, including individual sections that describe the symptoms, pathogenesis, causative agent, epidemiology, prevention, and treatment. Disease summaries that feature a drawing of a human showing symptoms, portals of entry and exit, location of pathology,

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and a step-by-step description of the infection process for each major disease. Case presentations of realistic clinical situations. Modern coverage of topics such as emerging diseases, new vaccines, and nosocomial infections. Dedicated chapters covering wound infections and HIV.

Learning System that Actively Involves Students In today’s classroom, it is important to pursue active learning by students. This edition of Microbiology challenges students to think critically by providing several avenues of practice in analyzing data, drawing conclusions, synthesizing information, interpreting graphs, and applying concepts to practical situations. These learning tools, developed by critical thinking expert Robert Allen, will benefit students pursuing any discipline.

What’s New In This Edition? We moved the chapter on host-microbe interactions so that it now immediately follows the chapters on innate and adaptive immunity. This makes it easier for instructors to present a trilogy of topics: Part I, “The Immune Wars” (innate and adaptive immunity); Part II, “The Microbes Fight Back” (pathogenesis); and Part III, “The Return of the Humans” (vaccination, epidemiology, and antimicrobial medications). We also moved the chapter on respiratory infections forward. This puts the major discussion of Streptococcus pyogenes early in the infectious disease section, providing students with a solid framework to help them understand the additional coverage in subsequent chapters. The following are new features in each chapter. Other changes and updates include:

Chapter Highlights Chapter 1 Humans and the Microbial World

New figure showing advances in microbiology in the context of other historical events

Chapter 2 The Molecules of Life

New section on molarity New table summarizing the characteristics of various sugars and their importance

Chapter 3 Microscopy and Cell Structure

Description of the bacterial cytoskeleton has been added Lipid rafts in eukaryotic membranes are described New figure of a model bacterium emphasizing the layers that envelop the cell

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PREFACE

Chapter 4 Dynamics of Prokaryotic Growth

New table highlighting the impact of exponential growth The concept of limiting nutrients is described Updated figure and description of an anaerobe container

Chapter 5 Control of Microbial Growth

New figure on membrane filtration

New description of Wolbachia New equations that emphasize the energy sources and terminal electron acceptors used by the microbes covered in the section on metabolic diversity

Chapter 12 The Eukaryotic Members of the Microbial World

Revised figure on the anatomy of the mosquito New Future Challenge

Chapter 6

Chapter 13

Metabolism: Fueling Cell Growth

Viruses of Bacteria

The importance of microbial metabolism in the production of biofuels is discussed The description of the steps of glycolysis has been simplified by grouping them into two phases: investment and payoff

Expanded discussion on the importance of phage New figure on restriction-modification New Perspective on mimiviruses Revised figure on restriction-modification

Chapter 7

Chapter 15

The Blueprint of Life, from DNA to Protein

The Innate Immune Response

New section describing the role of RNA interference in eukaryotic gene expression Alternative sigma factors are now discussed in the section on mechanisms to control transpiration Figures showing quorum sensing and two component regulatory systems have been added

Chapter 8 Bacterial Genetics

Reorganized to create a new section on mobile genetic elements, highlighting the importance of horizontal gene transfer New table that lists mobile genetic elements

Chapter 9 Biotechnology and Recombinant DNA

Reorganized so that methods immediately follow applications In recognition of the fact that many of the applications of Southern Blotting have been replaced by PCR, information on the technique has been moved to the web Updated information and explanatory figure on DNA sequencing The Human Microbiome Project is described Discussion of metagenomics has been added

Chapter 10 Identification and Classification of Prokaryotic Organisms

Updated boxed story on tracing an E. coli O157:H7 outbreak Updated example of the importance of distinguishing different strains of a species

Chapter 11 The Diversity of the Prokaryotic Organisms

New description of Epulopiscium

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New figure that illustrates how lymph is formed Neutrophil extracellular traps (NETs) are described

Chapter 16 The Adaptive Immune Response

The importance of regulatory T cells in preventing autoimmune disease is included Information on the recently discovered TH17 cells is included in the subsets of effector helper T cells

Chapter 17 Host-Microbe Interactions

Moved chapter forward so that it directly follows the information about innate and adaptive immunity, emphasizing the importance of evading the immune response in pathogenesis Added description of the hygiene hypothesis New Future Challenge on probiotics

Chapter 18 Immunologic Disorders

Added information on childhood allergies and bone marrow transplantation Revised sections on immunotherapy, transfusion reactions, and erythroblastosis fetalis

Chapter 19 Applications of the Immune Response

New information about the HPV vaccine Mention of a lipid A derivative as a new adjuvant has been added New application question that directs student to the vaccine schedule on the CDC website

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PREFACE

Chapter 20

Chapter 28

Epidemiology

Blood and Lymphatic Infections

Expanded Future Challenge on bioterrorism to include category A, B, and C agents Expanded and renamed section on nosocomial infections so that it now reflects the general concerns regarding healthcareassociated infections Updated coverage of Universal Precautions (Perspective 20.1)

Chapter 21 Antimicrobial Medications

Information about entry inhibitors and integrase inhibitors in the section on antiviral medications has been added Added new information about glycylcyclines

Chapter 22

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Updated illustrations on tularemia, yellow fever, and malaria incidence

Chapter 29 HIV Disease and Complications of Immunodeficiency

Updated information on HIV/AIDS distribution, deaths, impact on women Updated nomenclature for the causative agent of pneumocystosis Added normal comparison figure for CMV eye involvement

Chapter 30 Microbial Ecology

Figure illustrating how dead zones develop has been added

Respiratory Infections

Moved this chapter topic to the beginning of the coverage of infectious diseases so that the complete description of Streptococcus pyogenes is now consolidated in the section on strep throat Consolidated material on Streptococcus pyogenes from other chapters Information on avian influenza has been added

Chapter 23 Skin Infections

Consolidated material on Staphylococcus aureus from other chapters Added information on MRSA Added a photograph of individual with erythema infectiosum

Chapter 24 Wound Infections

Added a new case presentation on gangrene

Chapter 25 Digestive System Infections

Revised figure on Helicobacter pylori infection Photograph of individual with herpes simplex labialis has been added Revised figure on cholera mode of action Updated figures on mumps and hepatitis A

Chapter 26 Genitourinary Infections

Updated information on herpes simplex latency, prevention of papilloma virus infection, and changes in the HIV/AIDS pandemic

Chapter 27 Nervous System Infections

Added a new table on the causes of meningitis; updated illustrations on West Nile and invasive Haemophilus influenzae

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Chapter 32 Food Microbiology

Updated example of an E. coli O157:H7 outbreak

Teaching and Learning Supplements ARIS The ARIS (Assessment, Review, and Instruction System) website that accompanies this textbook includes self-quizzing with immediate feedback, animations of key processes with self-quizzing, electronic flashcards to review key vocabulary, additional clinical case presentations and more—a whole semester’s worth of study help for students. Instructors will find an instructor’s manual, PowerPoint lecture outlines, and test questions that are directly tied to Microbiology, 6/e as well as a complete electronic homework management system where they can create and share course materials and assignments with colleagues in just a few clicks of the mouse. Instructors can also edit questions, import their own content, and create announcements and/or due dates for assignments. ARIS offers automatic grading and reporting of easy-to-assign homework, quizzing, and testing. Check out www.aris.mhhe.com, select your subject and textbook, and start benefiting today!

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Photos—The photos collection contains digital files of photographs from the text that can be reproduced for multiple classroom uses. Tables—Every table that appears in the text has been saved in electronic form for use in classroom presentation and/or quizzes. Animations—More than 50 full-color animations are available to harness the visual impact of processes in motion. Import these dynamic files into classroom presentations or online course materials. Lecture Outlines—Specially prepared custom outlines for each chapter are offered in easy-to-use PowerPoint slides.

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Laboratory Manual The sixth edition of Microbiology Experiments: A Health Science Perspective, by the late John Kleyn and by Mary Bicknell, has been prepared to directly support the text (although it may also be used with other microbiology textbooks). The laboratory manual features health-oriented experiments and endeavors that also reflect the goals and safety regulation guidelines of the American Society for Microbiology. Engaging student projects introduce some more intriguing members of the microbial world and expand the breadth of the manual beyond health-related topics. New experiments introduce modern techniques in biotechnology such as the use of restriction enzymes and use of a computer database to identify sequence information. McGraw-Hill publishes additional microbiology laboratory manuals. Please contact your McGraw-Hill sales representative for more information.

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Reviewers of the Sixth Edition Gene Nester, Evans Roberts, Brian McCarthy, and Nancy Pearsall shared a vision many years ago to write a new breed of microbiology textbook especially for students planning to enter nursing and other health-related careers. Today there are other books of this type, but we were extremely gratified to learn that a majority of the students we surveyed intend to keep their copies of Microbiology: A Human Perspective because they feel it will benefit them greatly as they pursue their studies in these fields. Special thanks to the many students who used Microbiology: A Human Perspective over the years and who shared their thoughts with us about how to improve the presentation for the students who will use this edition of the text. We offer our sincere appreciation to the many gracious and expert professionals who helped us with this revision by offering helpful suggestions. In addition to thanking those individuals listed here who carefully reviewed chapters, we also thank those who responded to our information surveys, those who participated

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PREFACE

in regional focus groups, and those participants who chose not to be identified. All of you have contributed significantly to this work and we thank you. Cynthia Anderson, Mt. San Antonio College James Barbaree, Auburn University Morris Blaylock, Darton College Alfred Brown, Auburn University George Bullerjahn, Bowling Green State University Thomas Danford, West Virginia Northern Community College Charlie Dick, Pasco Hernando Community College James Dickson, Iowa State University Matthew Dodge, Simmons College Fahd Z. Eissa, Voorhees College Melissa Elliott, Butler Community College Noel Espina, Schenectady County Community College Michelle Fisher, Three Rivers Community College Joe Gauthier, University of AL–Birmingham Virginia Gutierrez-Osborne, Fresno City College Katina Harris, Tidewater Community College Daniel Herman, University of WI–Eau Claire Chike Igboechi, Medgar Evers College of CUNY Judith Krey, Waubonsee Community College Ruhul Kuddus, Utah Valley State University William Lorowitz, Weber State University Shannon Meadows, Roane State Community College Catherine Murphy, Ocean County College Karen Nakaoka, Weber State University Joseph Newhouse, Lock Haven University Marcia Pierce, Eastern Kentucky University Madhura Pradhan, Ohio State University Carmen Rexach, Mt. San Antonio College Susan Roman, Georgia State University Barbara Rundell, College of DuPage Pushpa Samkutty, Southern University–Baton Rouge Robyn Senter, Lamar State College–Orange Sasha Showsh, Univ. of WI–Eau Claire Christina Strickland, Clackamas Community College Renato Tameta, Schenectady Community College Steve Thurlow, Jackson Community College Michael Troyan, Penn State University Richard Van Enk, Western Michigan University Roger Wainwright, University of Central Arkansas Winfred Watkins, McLennan Community College Alan Wilson, Darton College Carola Wright, Mt. San Antonio College

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Acknowledgments We thank our colleagues in the Department of Microbiology at the University of Washington who have lent their support of this project over many years. Our special thanks go to John Leigh, Mary Bicknell, Mark Chandler, Kendall Gray, Jimmie Lara, Sharon Schultz, Michael Lagunoff, and James Staley for their general suggestions and encouragement. We would also like to thank Denise’s husband, Richard Moore, who was “forced” to proofread and critique many of the chapters. Although he has no formal scientific education, or perhaps because of that fact, his suggestions have been instrumental in making the text more “reader-friendly.” Much to his own surprise, Richard has learned enough about the fundamentals of microbiology to actually become intrigued with the subject. Special thanks to the reviewers and other instructors who helped guide us in this revision. Deciding what to eliminate, what to add, and what to rearrange is always difficult, so we appreciate your input. Thanks also to Deborah Allen and David Hurley, who helped shape the book through their work on earlier editions. Deborah taught us the true meaning of excellence, both by example and through gentle guidance. David was instrumental in helping us navigate the murky waters during a substantial revision that updated the coverage of innate and adaptive immunity. A list of acknowledgments is not complete without thanking the people from McGraw-Hill—Jim Connely, Lisa Bruflodt, Tami Petsche, and Peggy Lucas—who gave inspiration and sound advice throughout this revision. Jayne Klein, Mary Jane Lampe, and our copyeditor, Sue Dillon, were instrumental in making sure the correct words actually made it onto paper. Additionally, we would like to thank Joseph Gauthier, Elizabeth McPherson, and Donald Rubbelke for producing new media resources to support us and other instructors who lecture from our text. We hope very much that this text will be interesting, educational for students, a help to their instructors, and will convey the excitement that we all feel for the subject. We would appreciate any comments and suggestions from our readers. Eugene Nester Denise Anderson C. Evans Roberts, Jr. Martha Nester

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Instructive Artwork Makes the Difference A picture is worth a thousand words, especially in microbiology. Microbiology: A Human Perspective employs a combination of art styles to bring concepts to life and to provide concrete, visual reinforcement of the topics discussed throughout the text.

Overview Figures Overview figures simplify complex interactions and provide a sound study tool. Humoral Immunity (adaptive) Extracellular antigen

Antibodies bind antigen Antibody production

Proliferation and differentiation of activated B cell B cell

Plasma cell

Cellular Immunity (adaptive)

Activates B cells that bind antigen recognized by the TH cell

Proliferation and differentiation of activated helper T cell Helper T cell

TH cell

Activated macrophage

Stimulates TC cells that bind antigen

Activates T cells that bind antigen representing danger

Dendritic cell (Innate immunity)

Activates macrophages that have engulfed antigen recognized by the TH cell

Virus

Proliferation and differentiation of activated cytotoxic T cell Cytotoxic T cell

TC cell

Induces apoptosis in infected host cells (host cells routinely present samples of cytoplasmic proteins for inspection). Host cell undergoes apoptosis.

FIGURE 16.1 Overview of Humoral and Cellular Immunity Memory cells are not shown in this diagram. Cellular immunity is also called cellmediated immunity (CMI).

xxx

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GLUCOSE

(b) Pentose phosphate pathway (less commonly used than glycolysis) Initiates the oxidation of glucose

Yields

Reducing power

Precursor metabolites

(a) Glycolysis Oxidizes glucose to pyruvate

~ ~

Yields

+

Reducing power

Image Pathways

+

ATP substrate-level phosphorylation

Image pathways help students follow the progression of a discussion over several pages by highlighting and illustrating each step of an overview figure.

Precursor metabolites + (f) Fermentation Reduces pyruvate or a derivative

Biosynthesis

Pyruvate

Pyruvate

CO2

Acids, alcohols, and gases

CO2

(c) Transition step Reducing power

Acetyl-CoA

Reducing power

Acetyl-CoA

GLUCOSE Precursor metabolites

(a) Glycolysis Oxidizes glucose to pyruvate

(b) Pentose phosphate pathway (less commonly used than glycolysis) Initiates the oxidation of glucose

~ ~

Yields

+

Reducing power

+

ATP substrate-level phosphorylation

Glucose

FIGURE 6.8 Overview of Metabolism (a) Glycolysis, (b) the pentose phosphate pathway, (c) the transition step, and (d) the tricarboxylic acid cycle (TCA cycle) are used to gradually oxidize glucose completely to CO2. Together, these pathways produce ATP, reducing power, and intermediates that function as precursor metabolites (depicted as gray bars). (e) Respiration uses the reducing power to generate ATP by oxidative phosphorylation, ultimately passing the electrons to a terminal electron acceptor. (f) Fermentation stops short of oxidizing glucose completely, and instead uses pyruvate or a derivative as an electron acceptor.

Yields

Reducing power

Precursor metabolites

CO2

~ ~

ATP

+ (f) Fermentation Reduces pyruvate or a derivative

Biosynthesis

Pyruvate

Pyruvate

CO2

CO2

(e) Respiration Uses the electron transport chain to convert reducing power to proton motive force

Acids, alcohols, and gases

CO2

(c) Transition step Reducing power

Acetyl-CoA

(d) TCA cycle Incorporates an acetyl group and releases CO2

Reducing power

Acetyl-CoA

~ ~

Yields

CO2 (e) Respiration Uses the electron transport chain to convert reducing power to proton motive force

CO2

ATP oxidative phosphorylation Yields

~ ~

(d) TCA cycle Incorporates an acetyl group and releases CO2

Glucose 6-phosphate

Precursor metabolites Yields

~ ~ +

Reducing power

Step 2: A chemical rearrangement occurs.

+

ATP substrate-level phosphorylation

Precursor metabolites Yields

~ ~ +

Step 1: ATP is expended to add a phosphate group.

ATP ~ oxidative phosphorylation

ADP

Reducing power

+

ATP substrate-level phosphorylation

Fructose 6-phosphate

~ ~

Step 3: ATP is expended to add a phosphate group.

~ Fructose 1,6-bisphosphate Step 4: The 6-carbon molecule is split into two 3-carbon molecules. Dihydroxyacetone phosphate Step 5: A chemical rearrangement of one of the molecules occurs. Glyceraldehyde 3-phosphate Step 6: The addition of a phosphate group is coupled to a redox reaction, generating NADH and NADH + H+ a high-energy phosphate bond.

NAD+ NADH 1,3-bisphosphoglycerate

+H

NAD+

+

~

~

~

The overview figure is shown in the image pathways to help students follow a process through each step.

~

~ ~

~ ~

Step 7: ATP is produced by substrate-level phosphorylation.

3-phosphoglycerate Step 8: A chemical rearrangement occurs. 2-phosphoglycerate

Phosphoenolpyruvate

~

FIGURE 6.14 Glycolysis The glycolytic pathway oxidizes glucose to pyruvate, generating ATP by substratelevel phosphorylation, reducing power in the form of NADH, and six different precursor metabolites.

H2O

~ ~ ~

Step 9: Water is removed, causing the phosphate bond to become high-energy.

~

H2O

~ ~ ~

Step 10: ATP is produced by substrate-level phosphorylation.

Pyruvate

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Process Figures Process figures include step-by-step descriptions to walk the student through a compact summary of important concepts.

Immature B cells: As these develop, a functionally limitless assortment of B cell receptors is randomly generated.

Naive B cells: Each cell is programmed to recognize a specific epitope on an antigen; B-cell receptors guide that recognition.

Stem cell

Antigen X

B cell "W"

B cell "X" recognizing antigen "X"

B cell "Y"

Activated B cells: These cells are able to proliferate because their B-cell receptors are bound to antigen X and the cells have received required accessory signals from TH cells.

B cell "Z"

Selected B cell receives "second opinion" from TH cell (not shown here; process is illustrated in figure 16.9).

Plasma cells (effector B cells): These descendants of activated B cells secrete large quantities of antibody molecules that bind to antigen X.

Memory B cells: These long-lived descendants of activated B cells recognize antigen X.

FIGURE 16.8 Clonal Selection and Expansion During the Antibody Response

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Combination Figures Combination figures tie together the appearance of organisms in the real world with features that can be illustrated by an artist.

Root cells of plants (cross-section)

Ectomycorrhizae

(b) Endomycorrhiza

Endomycorrhizae (a) Diagram of Mycorrhizae

(c) Ectomycorrhiza

Micrographs Stunning micrographs used generously throughout the text bring the microbial world to life.

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Unmatched Clinical Coverage Organized by human body systems, the infectious disease chapters (chapters 22 to 29) are highlighted with yellow shading in the top corner of the page for easy reference. Additional case presentations and clinical reference material are available through ARIS (aris.mhhe.com).

22.3

gens. Farther inside the nasal passages, the microbial population increasingly resembles that of the nasopharynx (the part of pharynx behind the nose). The nasopharynx contains mostly a-hemolytic viridans streptococci, non-hemolytic streptococci, Moraxella catarrhalis, and diphtheroids. Anaerobic Gram-negative bacteria, including species of Bacteroides, are also present in large numbers in the nasopharynx. In addition, commonly pathogenic bacteria such as Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis are often found, especially during the cooler seasons of the year. viridans streptococci, p. 97

Bacterial Infections of the Upper Respiratory System

499

MICROCHECK 22.2 Except in parts of the upper respiratory tract, the respiratory system is free of a normal microbiota. The upper respiratory tract microbiota is highly diverse, including aerobes, anaerobes, facultative anaerobes, and aerotolerant bacteria. Although most of them are of low virulence, these organisms can sometimes cause disease. What are some possible advantages to the body of providing a niche for normal flora in the upper respiratory tract? How can strict anaerobes exist in the upper respiratory tract?

INFECTIONS OF THE UPPER RESPIRATORY SYSTEM

22.3 Bacterial Infections of the Upper Respiratory System Focus Points Compare the distinctive characteristics of strep throat and diphtheria. List the parts of upper respiratory system commonly infected by Streptococcus pneumoniae and Haemophilus influenzae.

A number of different species of bacteria can infect the upper respiratory system. Some, such as Haemophilus influenzae and b-hemolytic streptococci of Lancefield group C, can cause sore throats but generally do not require treatment because the bacteria are quickly eliminated by the immune system. Other infections require treatment because they are not so easily eliminated and can cause serious complications.

Causative Agent Streptococcus pyogenes, the cause of strep throat, is a Gram-positive coccus that grows in chains of varying lengths (figure 22.2). It can be differentiated from other streptococci that normally inhabit the throat by its characteristic colonial morphology when grown on blood agar. Streptococcus pyogenes produces hemolysins, enzymes that lyse red blood cells, which result in the colonies being surrounded by a zone of b-hemolysis (figure 22.3). Because of their characteristic hemolysis, S. pyogenes and other streptococci that show a similar phenotype are called b-hemolytic streptococci. In contrast, species of Streptococcus that are typically part of the normal throat microbiota are either non-hemolytic, or they produce a-hemolysis, characterized by a zone of incomplete, often greenish clearing around colonies grown on blood agar. streptococcal hemolysis, p. 97 Streptococcus pyogenes is commonly referred to as the group A streptococcus. The group A carbohydrate in the cell wall of S. pyogenes differs antigenically from that of most other streptococci and serves as a convenient basis for identification (see figure 19.9). Lancefield grouping uses antibodies to differentiate the various

Strep Throat (Streptococcal Pharyngitis) Sore throat is one of the most common reasons that people in the United States seek medical care, resulting in about 27 million doctor visits per year. Many of these visits are due to a justifiable fear of streptococcal pharyngitis, commonly known as strep throat.

Symptoms Streptococcal pharyngitis typically is characterized by pain, difficulty swallowing, and fever. The throat is red, with patches of adhering pus and scattered tiny hemorrhages. The lymph nodes in the neck are enlarged and tender. Abdominal pain or headache may be prominent in older children and young adults. Not usually present are red, weepy eyes, cough, or runny nose, common symptoms with viral pharyngitis. Most patients with streptococcal sore throat recover spontaneously after about a week. In fact, many infected people have only mild symptoms or no symptoms at all.

10 mm

FIGURE 22.2 Streptococcus pyogenes Chain formation in fluid culture Product as revealed by fluorescence microscopy.

Incomparable Treatment of Diseases Each disease is presented systematically and predictably. Individual sections describe the disease’s symptoms, causative agents, pathogenesis, epidemiology, and prevention and treatment.

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TABLE 22.2 Virulence Factors of Streptococcus pyogenes Effect

C5a peptidase

Inhibits attraction of phagocytes by destroying C5a

Hyaluronic acid capsule

Inhibits phagocytosis; aids penetration of epithelium

M protein

Interferes with phagocytosis by causing breakdown of C3b opsonin

Protein F

Responsible for attachment to host cells

Protein G

Interferes with phagocytosis by binding Fc segment of IgG

Streptococcal pyrogenic exotoxins (SPEs)

Superantigens responsible for scarlet fever, toxic shock, “flesh-eating” fasciitis

Streptolysins O and S

Lyse leukocytes and erythrocytes

Tissue degrading enzymes

Enhance spread of bacteria by breaking down DNA, proteins, blood clots, tissue hyaluronic acid

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Disease Summaries Major diseases are represented with a summary table that includes an outline of pathogenesis keyed to a human figure showing the entry and exit of the pathogen.

TABLE 22.3 Strep Throat (Streptococcal Pharyngitis) Streptococcus pyogenes enters by inhalation (nose), or by ingestion (mouth). Pharyngitis, fever, enlarged lymph nodes; sometimes tonsillitis, abcess; scarlet fever with strains that produce erythrogenic toxin.

6

Symptoms

Sore, red throat, with pus and tiny hemorrhages, enlargement and tenderness of lymph nodes in the neck; less frequently, abscess formation involving tonsils; occasionally, rheumatic fever and glomerulonephritis as sequels

Incubation period

2 to 5 days

Causative agent

Streptococcus pyogenes, Lancefield group A b-hemolytic streptococci

Pathogenesis

Virulence associated with hyaluronic acid capsule and M protein, both of which inhibit phagocytosis; protein G binds Fc segment of IgG; protein F for mucosal attachment; multiple enzymes.

Epidemiology

Direct contact and droplet infection; ingestion of contaminated food.

Prevention and treatment

Avoidance of crowding; adequate ventilation; daily penicillin to prevent recurrent infection in those with a history of rheumatic heart disease. Treatment: 10 days of penicillin or erythromycin.

1 3

2

2

Symptoms go away.

5

S. pyogenes exits by nose and mouth.

7

Late complications appear:

5

glomerulonephritis

4

rheumatic fever neurological abnormalities Complications subside. Damaged heart valves leak, heart failure develops.

5

CASE PRESENTATION A 63-year-old woman, healthy except for mild diabetes, underwent surgery for a diseased gallbladder. The surgery went well, but within 72 hours the repaired surgical incision became swollen and pale. Within hours the swollen area widened and developed a bluish discoloration. The woman’s surgeon suspected gangrene. Antibiotic therapy was started and she was rushed back to the operating room where the entire swollen area, including the repaired operative incision, was surgically removed. After that, the wound healed normally, although she required a skin graft to close the large skin deficit. Large numbers of Clostridium perfringens grew from the wound culture. Six days later, a 58-year-old woman underwent surgery in the same operating room for a malignant tumor of the colon. The surgery was performed without difficulty, but 48 hours later she developed rapidly advancing swelling and bluish discoloration of her surgical wound. As with the first case, gangrene was suspected and she was treated with antibiotics and surgical removal of the affected tissue. She also required skin grafting. Her wound culture also showed a heavy growth of Clostridium perfringens. Because the surgery department had never had any of its patients develop surgical wound infections with Clostridium perfringens, much less two cases so close together, the hospital epidemiologist was asked to do an investigation. Among the findings of the investigation:

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1. Cultures of horizontal surfaces in the operating room grew large numbers of Clostridium perfringens: 2. Unknown to the medical staff, a workman had recently serviced a fan in the ventilation system of the operating room, and for a time air was allowed to flow into the operating room, rather than out of it. 3. Heavy machinery was doing grading outside the hospital, creating clouds of dust. As a result of these findings, the operating room and its ventilating system were cleaned and upgraded. No further cases of surgical wound gangrene developed. 1. Was the surgeon’s diagnosis correct? 2. Many other patients had surgery in the same operation room. Why did only these two patients develop wound gangrene? 3. What could be done to help identify the source of the patients’ infections? Discussion 1. Clostridium perfringens is commonly cultivated from wounds without any evidence of infection. However, in these cases, there was not only a heavy growth of the organism but a clinical picture compatible with gangrene. The surgeon’s diagnosis was undoubtedly correct.

2. In both cases there was an underlying condition that increased the two patients’ susceptibility to infection—cancer in one, and diabetes in the other. Moreover, both had a recognized source for the organism. Cultures of as many as 20% of diseased gallbladders are positive for Clostridium perfringens, while the organism is commonly found in large numbers in the human intestine— a potential source in the case involving removal of the bowel malignancy. 3. The surgeon favored the idea that the infecting organism came from the patients themselves because such strains tend to be much more virulent than strains that live and sporulate in the soil. One the other hand, the gross contamination of the operating room as revealed by the cultures of its surfaces could indicate a very large infecting dose at the operative site, possibly compensating for lesser virulence. Moreover, no further cases occurred after cleaning the operating room and fixing the ventilation system. Unfortunately, in this case, no cultures of the excised gallbladder or bowel tumor were done, nor were the strains isolated from the wounds and the environment compared. Comparing the antibiotic susceptibility, toxin production, and other characteristics of the different isolates could have helped identify the source of the infections.

Case Presentations Each infectious disease chapter includes a case presentation of a realistic clinical situation.

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Applications Promote Further Interest Applications throughout Microbiology: A Human Perspective not only help students understand microbiology’s history but also how microbiology influences their daily lives and their futures.

Glimpse of History

6

Each chapter opens with an engaging story about the men and women who pioneered the field of microbiology.

Wine—a beverage produced using microbial metabolism.

Metabolism: Fueling Cell Growth

Perspective Boxes

A Glimpse of History In the 1850s, Louis Pasteur, a chemist, accepted the challenge Nobel Prize in 1907. He was the first of many investigators who of studying how alcohol arises from grape juice. Biologists had received Nobel Prizes for studies on the processes by which cells already observed that when grape juice is held in large vats, alcohol degrade sugars. and carbon dioxide are produced and the number of yeast cells increases. They argued that the multiplying yeast cells convert the o grow, all cells must accomplish two fundamental tasks. sugar in the juice to alcohol and carbon dioxide. Pasteur agreed, They must continually synthesize new components includbut could not convince two very powerful and influential German ing cell walls, membranes, ribosomes, nucleic acids, and chemists, Justus von Liebig and Friedrich Wöhler, who refused to believe that microorganisms caused the breakdown of sugar. Both surface structures such as flagella. These allow the cell to enlarge men lampooned the hypothesis and tried to discredit it by publishand eventually divide. In addition, cells need to harvest energy and ing pictures of yeast cells looking like miniature animals taking in convert it to a form that is usable to power biosynthetic reactions, grape juice through one orifice and releasing carbon dioxide and transport nutrients and other molecules, and in some cases, move. alcohol through the other. The sum total of chemical reactions used for biosynthetic and Pasteur studied the relationship between yeast and alcohol energy-harvesting processes is called metabolism. production using a strategy commonly employed by scientists Bacterial metabolism is important to humans for a numtoday—that is, simplifying the experimental system so that relationber of reasons. Many bacterial products are commercially or floor off the coast of Namibia in Africa. It is a We might prokaryotes have ships can be more easily identified. First, he prepared a clearassume solution that because medically important. For example, as scientists look for new spherical organism 70 times larger in volume than been He so then intensively of sugar, ammonia, mineral salts, and trace elements. added studied over the past hundred supplies of energy, some are investigating biofuels, which are Epulopisicium. Since it grows on sulfur compounds a few yeast cells. As the yeast grew, the sugar years, level decreased no major and surprisesfuels are left to be discovered. made from a renewable biological source such as plants the alcohol level increased, indicating that the sugar being conand contains glistening globules of sulfur, it was This,was however is far from truth.waste In theproducts. mid- Microorganisms andthe organic or their enzymes verted to alcohol as the cells multiplied. This strongly suggested namedbreaking Thiomargarita namibiensis, which means 1990s, a large, that peculiar-looking organism was seen are currently producing these fuels, down solid mateliving cells caused the chemical transformation. Liebig, however, still pearl of Namibia” (figure when the intestinal tractsrials of certain fish from both sugar“sulfur such as corn stalks, cane, and wood to a fuel such 2). Although sciwould not believe the process was actually occurring inside microorentists were initially skeptical that prokaryotes the Red Sea in the MiddleasEast and theAs Great Barrierexample, cheese-makers intentionally ethanol. another ganisms. To convince him, Pasteur tried to extract something from could species be so to large, is the no question in their Reef in Australia were examined. This organism, add Lactococcus and Lactobacillus milk there because inside the yeast cells that would convert the sugar. He failed, like mindscontribute now. In contrast to these named Epulopisicium cannot be cultured in the labo- bacteria metabolic wastes of these to the flavor and large bacteria, a many others before him. cellsome was of isolated the products Mediterranean Sea that is of various cheeses. these in same ratory (figure Its largetexture size, 600 mm long and Yet In 1897, Eduard Buchner, a German chemist, showed1). that contribute to tooth decay bacteria growing on m m in width. It isare a eukaryote because it contains 80 mmand wide, visible without anywhen1 related We it clearly crushed yeast cells could convert sugar to ethanol CO2.makes teeth. Microbial important the laboratory, nucleus eveninthough it is about the size of a now know that enzymes of the crushed cells carried out this transmagnification, and suggested that this metabolism organism isaalso because products are characteristic of a specific group of formation. For these pioneering studies, Buchner was awarded the typical bacterium. was a eukaryote. It did not, however have athat mem-

T

Perspective boxes introduce a “human” perspective by showing how microorganisms and their products influence our lives in a myriad of different ways.

PERSPECTIVE 1.1

The Long and the Short of It

126

Future Challenges

brane bound nucleus. A chemical analysis of the cell confirmed that it was a prokaryote and a member of the domain Bacteria. This very long, slender organism is an exception to the rule that prokaryotes are always smaller than eukaryotes. In 1999, an even larger prokaryote in volume was isolated from the sulfurous muck of the ocean

Today, an unfortunate challenge in epidemiology is to maintain vigilance against bioterrorism—the deliberate release of infectious agents or their toxins as a means to cause harm. Even as we work to control, and seek to eradicate, some diseases, we must be aware that microbes pose a threat as agents of bioterrorism. Hopefully, future attacks will never occur, but it is crucial to be prepared for the possibility. Prompt recognition of such an event, followed by rapid and appropriate Epulopiscium isolation and treatment procedures, can help to mini(prokaryote) mize the consequences. The CDC, in cooperation with the Association for Professionals in Infection Control and Epidemiology (APIC), has prepared a bioterrorism Paramecium (eukaryote) readiness plan to be used as a template by healthcare facilities. Many of the recommendations are based on the Standard Precautions already employed by0.2 hospimm 0.1 mm tals to prevent the spread of infectious agents (see Perspective 20.1). FIGURE 1 Longest Known Bacterium, FIGURE 2 Thiomargarita namibiensis The CDC separates bioterrorism agents into three The average Thiomargarita namibiensis is twoEpulopisicium Mixed With Paramecategories based on the ease of spread and severity of tenths of a millimeter, but some reach three cia Note how large this prokaryote is comdisease. Category A agents pose the highest risk times that size. ■ Thiomargarita, p. 263 pared with the four eukaryotic paramecia. because they are easily spread or transmitted from person to person and result in high mortality. These agents include: Bacillus anthracis. Endospores of this bacterium were used in the bioterrorism events of 2001. The most severe outcome, inhalational anthrax, results when an individual breathes in the airborne spores. It can lead to a rapidly fatal systemic illness. Cutaneous anthrax, which occurs when the organism enters the skin, manifests as a blister that develops into a skin ulcer with a black center. Although this usually heals without treatment, it can also progress to a

Many chapters end with a pending challenge facing microbiologists and future microbiologists.

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member of the Archaea (figure 3). These tiny organisms, also members of the Archaea, have been named Nanoarchaeum equitans, which means “riding the fire sphere.” The organism to which N. equitans is attached is Ignicoccus, which means “fire ball.” Ignicoccus grows very well without its rider. N. equitans is spherical and only about 400 nanometers in diameter, about a quarter the diameter of Ignicoccus. Also, the amount of genetic information (DNA) contained in N. equitans is less than in any known organism, and only about one-tenth the amount found in the common gut organism, Escherichia coli. This sets the record for the smallest amount of DNA in any organism. How small can an organism be? An answer to Thus, this organism may contain only the essential this question may be at hand as a result of a new DNA required for life. Further analysis of these cells microorganism discovered off the coast of Iceland. suggests that they may resemble the earliest cells FUTURE The organism, found in an ocean vent where the and therefore theCHALLENGES ancestor of all life. The scientists temperature was close to the boiling point of water, who discovered N. equitans suggest that many more cannot be grown in the laboratory by itself,Maintaining but only unusualVigilance organisms related to N. equitans will be disAgainst Bioterrorism grows when it is attached to another much larger covered. They are probably right! fatal bloodstream infection. Gastrointestinal anthrax results from consuming contaminated food, leading to vomiting of blood and severe diarrhea; it is not common but has a high mortality rate. Anthrax can be prevented by vaccination, but that option is not widely available. Prophylaxis with antimicrobial medications is possible for those who might have been exposed, but this requires prompt recognition of exposure. Fortunately, person-to-person transmission of the agent is not likely. Botulism. Botulism is caused naturally by the ingestion of botulinum toxin, produced by Clostridium botulinum. Any mucous membrane can absorb the toxin, so aerosolized toxin could be1used mm as a weapon. Botulism can be prevented by vaccination, but that option is not widely available. antitoxin also“N. available in limited FIGURE 3AnFive Cellsis of equitans,” supplies. on Botulism is not contagious. Attached the Surface of the (Central) Yersinia pestis. plague, caused by Ignicoccus Cell Pneumonic Platinum shadowed.

inhalation of Yersinia pestis, is the most likely form of plague to result from a biological weapon. Although no effective vaccine is available, postexposure prophylaxis with antimicrobial medications is possible. Special isolation precautions must be used for patients who have pneumonic plague because the disease is easily transmitted by respiratory droplets. Smallpox. Although a vaccine is available to prevent infection with this virus, routine immunization was stopped over 30 years ago because the natural disease has been eradicated. As is the case with nearly all infections caused by viruses, effective drug therapy is not available.

Special isolation precautions must be used for smallpox patients because the virus can be acquired through droplet, airborne, or contact transmission. Francisella tularensis. This bacterium, naturally found in animals such as rodents and rabbits, causes the disease tularemia. Inhalation of the bacterium results in severe pneumonia, which is incapacitating but would probably have a lower mortality rate than inhalational anthrax or plague. A vaccine is not available, but post-exposure prophylaxis with antimicrobial medications is possible. Fortunately, person-to-person transmission of the agent is not likely. Viruses that cause hemorrhagic fevers. These include various viruses such as Ebola and Marburg. Symptoms vary depending on the virus, but severe cases show signs of bleeding from many sites. There are no vaccines against these viruses, and generally no treatment. Some, but not all, of these viruses can be transmitted from person to person, so patient isolation in these cases is important. Category B agents pose moderate risk because they are relatively easy to spread and cause moderate morbidity. These agents include organisms that cause food- and waterborne illness, various biological toxins, Brucella species, Burkholderia mallei and pseudomallei, Coxiella burnetii, and Chlamydophila (Chlamydia) psittaci. Category C agents are emerging pathogens that could be engineered for easy dissemination. These include Nipah virus, which was first recognized in 1999, and hantavirus, first recognized in 1993.

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GUIDED TOUR

xxxvii

An Active Learning System In today’s classroom, it is important to pursue active learning by students. Carefully devised question and problem sets have been provided throughout the text and at the end of each chapter, allowing students to build their working knowledge of microbiology while also developing reasoning and analytical skills.

MICROCHECK 3.4

Microchecks Major sections end with a short “Microcheck” that summarizes the major concepts in that section and offers both review questions and critical thinking questions (in blue) to assess understanding of the preceding section.

160

CHAPTER SIX

6.9

Metabolism: Fueling Cell Growth

Carbon Fixation

Calvin Cycle (figure 6.26) The most common pathway used to incorporate CO2 into an organic form is the Calvin cycle.

6.10

The cytoplasmic membrane is a phospholipid bilayer embedded with a variety of different proteins. It serves as a barrier between the cell and the surrounding environment, allowing relatively few types of molecules to pass through freely. The electron transport chain within the membrane expels protons, generating a proton motive force. ✓ Explain the fluid mosaic model. ✓ Name three molecules that can pass freely through the lipid bilayer. ✓ Why is the word “fluid” in fluid mosaic model an appropriate term?

Anabolic Pathways—Synthesizing Subunits from Precursor Molecules (figure 6.27)

Lipid Synthesis The fatty acid components of fat are synthesized by progressively adding 2-carbon units to an acetyl group. The glycerol component is synthesized from dihydroxyacetone phosphate.

Amino Acid Synthesis Synthesis of glutamate from a-ketoglutarate and ammonia provides a mechanism for cells to incorporate nitrogen into organic molecules (figure 6.28). Synthesis of aromatic amino acids requires a multistep branching pathway. Allosteric enzymes regulate key steps of the pathway (figure 6.29). Nucleotide Synthesis Purine nucleotides are synthesized on the sugar-phosphate component; the pyrimidine ring is made first and then attached to the sugar-phosphate (figure 6.30).

REVIEW QUESTIONS Short Answer 1. 2. 3. 4. 5. 6. 7. 8. 9. 10.

Explain the difference between catabolism and anabolism. How does ATP serve as a carrier of free energy? How do enzymes catalyze chemical reactions? Explain how precursor molecules serve as junctions between catabolic and anabolic pathways. How do cells regulate enzyme activity? Why do the electrons carried by FADH2 result in less ATP production than those carried by NADH? Name three food products produced with the aid of microorganisms. In photosynthesis, what is encompassed by the term “lightindependent reactions?” Unlike the cyanobacteria, the anoxygenic photosynthetic bacteria do not evolve oxygen (O2). Why not? What is the role of transamination in amino acid biosynthesis?

Multiple Choice 1. Which of these factors does not affect enzyme activity? a) temperature b) inhibitors c) coenzymes d) humidity e) pH 2. Which of the following statements is false? Enzymes a) bind to substrates. b) lower the energy of activation. c) convert coenzymes to products. d) speed up biochemical reactions. e) can be named after the kinds of reaction they catalyze. 3. Which of these is not a coenzyme? a) FAD b) coenzyme A c) NAD+ d) ATP e) NADP+ 4. What is the end product of glycolysis? a) glucose b) citrate c) oxaloacetate d) a-ketoglutarate e) pyruvate 5. The major pathway(s) of central metabolism are a) glycolysis and the TCA cycle only. b) glycolysis, the TCA cycle, and the pentose phosphate pathway. c) glycolysis only. d) glycolysis and the pentose phosphate pathway only. e) the TCA cycle only.

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6. Which of these pathways gives a cell the potential to produce the most ATP? a) TCA cycle b) pentose phosphate pathway c) lactic acid fermentation d) glycolysis 7. In fermentation, the terminal electron acceptor is a) oxygen (O2). b) hydrogen (H2). c) carbon dioxide (CO2). d) an organic compound. 8. In the process of oxidative phosphorylation, the energy of proton motive force is used to generate a) NADH. b) ADP. c) ethanol. d) ATP. e) glucose. 9. In the TCA cycle, the carbon atoms contained in acetate are converted into a) lactic acid. b) glucose. c) glycerol. d) CO2. e) all of these. 10. Degradation of fats as an energy source involves all of the following, except a) b-oxidation. b) acetyl-CoA. c) glycerol. d) lipase. e) transamination.

End-of-Chapter Review Short Answer questions review major chapter concepts. Multiple Choice questions allow self-testing; answers are provided in Appendix V. Applications provide an opportunity to use knowledge of microbiology to solve realworld problems. Critical Thinking questions, written by leading critical thinking expert, Robert Allen, encourage practice in analysis and problem solving that can be used in the study of any subject.

Applications 1. A worker in a cheese-making facility argues that whey, a nutrientrich by-product of cheese, should be dumped in a nearby pond where it could serve as fish food. Explain why this proposed action could actually kill the fish by depleting the oxygen in the pond. 2. Scientists working with DNA in vitro often store it in solutions that contain EDTA, a chelating agent that binds magnesium (Mg2+). This is done to prevent enzymes called DNases from degrading the DNA. Explain why EDTA would interfere with enzyme activity.

Critical Thinking 1. A student argued that aerobic and anaerobic respiration should produce the same amount of ATP. He reasoned that they both use basically the same process; only the terminal electron acceptor is different. What is the primary error in this student’s argument? 2. Chemolithotrophs near hydrothermal vents support a variety of other life forms there. Explain how their role there is analogous to that of photosynthetic organisms in terrestrial environments.

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1 Van Leeuwenhoek’s engravings (1.5μ), 1695. Drawings that van Leeuwenhoek made in 1695 of the shapes of microorganisms he saw through his single lens microscope. He also observed the movement of organism B moving from C to D.

Humans and the Microbial World A Glimpse of History Microbiology as a science was born in 1674 when Antony van Leeuwenhoek (1632–1723), an inquisitive Dutch drapery merchant, peered at a drop of lake water through a glass lens he had carefully ground. For several centuries it was known that curved glass would magnify objects, but it took the skillful hands of a craftsman and his questioning mind to revolutionize the understanding of the world in which we live. What he observed through this simple magnifying glass was undoubtedly one of the most startling and amazing sights that humans have ever beheld—the first glimpse of the world of microbes. As van Leeuwenhoek wrote in a letter to the Royal Society of London, he saw “Very many little animalcules, whereof some were roundish, while others a bit bigger consisted of an oval. On these last, I saw two little legs near the head, and two little fins at the hind most end of the body. Others were somewhat longer than an oval, and these were very slow amoving, and few in number. These animalcules had diverse colours, some being whitish and transparent; others with green and very glittering little scales, others again were green in the middle, and before and behind white; others yet were ashed grey. And the motion of most of these animalcules in the water was so swift, and so various, upwards, downwards, and round about, that ‘twas wonderful to see.” Although van Leeuwenhoek was the first to observe bacteria, Robert Hooke, an English microscopist was the first to observe a microorganism. In 1665, he published a description of a microfungus, which he called a “microscopical mushroom.” His drawing was so accurate that his specimen could later be identified as the common bread mold. Hooke also described how to make the kind of microscope that van Leeuwenhoek made almost 10 years later. In light of their almost simultaneous discovery of the microbial world, both men should be given equal credit for first describing the organisms you are about to study.

M

icroorganisms are the foundation for all life on earth. It has been said that the twentieth century was the age of physics. Now we can say that the twenty-first century will be the age of biology and biotechnology, with microbiology as the most important branch.

1.1 The Origin of Microorganisms Focus Points Describe the key experiments that disproved spontaneous generation. Name the scientists who carried them out. Explain why endospores confused the studies on spontaneous generation.

Microorganisms have existed on earth for about 3.5 billion years, and over this time, plants and animals have evolved from these microscopic forms. The discovery of microorganisms raised an intriguing question: “Where did these microscopic forms originate?” The theory of spontaneous generation suggested that organisms, such as tiny worms, can arise spontaneously from non-living material. It was completely debunked by Francesco Redi, an Italian biologist and physician, at the end of the seventeenth century. By a simple experiment, he demonstrated conclusively that worms found on rotting meat originated from the eggs of flies, not directly from the decaying meat as proponents of spontaneous generation believed. To prove this, he simply covered the meat with gauze fine enough to prevent flies from depositing their eggs. No worms appeared. 1

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2

CHAPTER ONE Humans and the Microbial World

KEY TERMS Biodiversity The variety of species inhabiting a particular environment. Bioremediation The degradation of environmental pollutants by living organisms. Domain The highest level in classification above the level of kingdom. All organisms can be assigned to one of three domains: Bacteria, Archaea, and Eucarya. Emerging Diseases Diseases that have increased in incidence in the past 20 years.

Eukaryote Organism composed of one or more eukaryotic cells; members of the domain Eucarya are eukaryotes. Eukaryotic Cell Cell type characterized by a membrane-bound nucleus. Normal Microbiota The population of microorganisms that normally grow on the healthy human body or other specified environment. Obligate Intracellular Parasite An organism or other agent that can only multiply inside living cells.

Theory of Spontaneous Generation Revisited Despite Redi’s work that explained the origin of worms on decaying meat, the theory of spontaneous generation of microorganisms was difficult to disprove. In fact, it took 200 more years to conclusively refute this idea. One reason for the delay was that various experiments carried out in different laboratories yielded conflicting results. For example, in 1749, John Needham, a scientist and Catholic priest, showed that various infusions (solutions obtained by soaking hay, chicken, or other nutrient source in water) gave rise to microorganisms even when the solutions had been boiled and sealed with a cork. Because even brief boiling was thought to kill all organisms, this suggested that microbes did indeed arise spontaneously. In 1776, however, the animal physiologist and priest, Father Spallanzani, observed quite the opposite; no bacteria appeared in his infusions after boiling. His experiments differed from Needham’s in two significant ways: Spallanzani boiled the infusions for longer periods and he sealed the flasks by melting their glass necks. Using these techniques, he repeatedly demonstrated that infusions remained sterile (free of microorganisms). However, if the neck of the flask cracked, the infusion rapidly became cloudy. Spallanzani concluded that the microbes must have entered the broth with the air, and that the corks used by many investigators did not keep out air. However, others argued that heating the contents of the flask destroyed a “vital force” necessary for spontaneous generation. The controversy continued to rage and further experiments, with proper controls, were needed to settle the matter.

Experiments of Pasteur One giant in science who did much to disprove the theory of spontaneous generation was the French chemist Louis Pasteur, considered by many to be the father of modern microbiology. In 1861, Pasteur refuted spontaneous generation by a series of clever experiments. First, he demonstrated that air is filled with microorganisms. He did this by filtering air through a cotton plug, trapping organisms that he then examined with a microscope. Many of these trapped organisms looked identical microscopically to those that had previously been observed by others in many infusions. Pasteur further showed that if the cotton plug was then dropped into a sterilized infusion, it became cloudy because the organisms quickly multiplied.

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Pathogen An organism or virus able to cause disease. Prokaryote Single-celled organism consisting of a prokaryotic cell; members of the domains Bacteria and Archaea are prokaryotes. Prokaryotic Cell Cell type characterized by the lack of a membrane-bound nucleus. Spontaneous Generation Living organisms arising from non-living material.

Most importantly, Pasteur’s experiment demonstrated that sterile infusions would remain sterile in specially constructed flasks even when they were left open to the air. Organisms from the air settled in the bends and sides of these swannecked flasks, never reaching the fluid in the bottom of the flask (figure 1.1). Only when the flasks were tipped would bacteria be able to enter the broth and grow. These simple and elegant experiments ended the arguments that unheated air or the infusions themselves contained a “vital force” necessary for spontaneous generation.

Experiments of Tyndall Although most scientists were convinced by Pasteur’s experiments, others were not. This skepticism in part stemmed from the fact that some reputable scientists could not reproduce Pasteur’s results. One of these was an English physicist, John Tyndall. It was Tyndall who finally explained differences in experimental results obtained in different laboratories and, in turn, proved Pasteur correct. Tyndall concluded that different infusions required different boiling times to be sterilized. Thus, boiling for 5 minutes would sterilize some materials, whereas others, most notably hay infusions, could be boiled for 5 hours and they still contained living organisms! Furthermore, if hay was in the laboratory, it became almost impossible to sterilize the infusions that had previously been sterilized by boiling for 5 minutes. What did hay contain that caused this effect? Tyndall finally realized that heat-resistant forms of life were being brought into his laboratory on the hay. These heat-resistant life forms must then have been transferred to all other infusions on dust particles, thereby making everything difficult to sterilize. Tyndall concluded that some microorganisms could exist in two forms: a cell that is readily killed by boiling, and one that is heat resistant. In the same year (1876), a German botanist, Ferdinand Cohn, also discovered the heat-resistant forms of bacteria, now termed endospores. The following year, Robert Koch demonstrated that anthrax was caused by Bacillus anthracis and that the usual means of transmission in animals involved resistant spores. In 2001, the deliberate transmission of anthrax spores to humans was instigated by bioterrorists in the United States. ■ endospores, p. 69

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1.1 The Origin of Microorganisms Trapped air escapes from open end of flask.

Bacteria and dust from air settle in bend.

Years

1. Broth sterilized

2. Broth allowed to cool slowly

3

Hours/ days

3. Broth stays sterile indefinitely.

4. Flask tilted so that the sterile broth comes in contact with bacteria and dust from air

5. Bacteria multiply in broth.

FIGURE 1.1 Pasteur’s Experiment with the Swan-Necked Flask If the flask remains upright, no microbial growth occurs. (1–3) If the flask is tipped, the microorganisms trapped in the neck reach the sterile liquid and grow. (4, 5) Why did bacteria grow in the flask only after the flask was tipped?

The extreme heat resistance of endospores explains the differences between Pasteur’s results and those of other investigators. Organisms that produce endospores are commonly found in the soil and most likely were present in hay infusions. Because Pasteur used only infusions prepared from sugar or yeast extract, his broth most likely did not contain endospores. At the time of these experiments on spontaneous generation, scientists did not appreciate the importance of the source of the infusion. In hindsight, the source was critical to the results observed and conclusions drawn. These experiments on spontaneous generation point out an important lesson for all scientists. In repeating an experiment and comparing results with previous experiments, it is absolutely essential to reproduce all conditions of an experiment as closely as possible. It may seem surprising that the concept of spontaneous generation was disproved less than a century and a half ago in light of the remarkable progress that has been made since that time. Figure 1.2

lists some of the more important advances made over the centuries in the context of other historical events. Rather than cover more history of microbiology at this time, we will return to many of these milestones in more detail in subsequent chapters in vignettes which open each chapter. How far the science of microbiology and all biological sciences have advanced over the last 150 years!

MICROCHECK 1.1 Antony van Leeuwenhoek first observed bacteria about 300 years ago. Pasteur and Tyndall finally refuted the theory of spontaneous generation less than 150 years ago. ✓ Give two reasons why it took so long to disprove the theory of spontaneous generation. ✓ What experiment disproved the notion that a “vital force” in air was responsible for spontaneous generation? ✓ If Pasteur’s swan-necked flasks had contained endospores, what results would have been observed?

FRANK & ERNEST: © Thaves/Dist. By Newspaper Enterprise Association, Inc.

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4

CHAPTER ONE Humans and the Microbial World

• Pilgrims establish

• Egyptians ferment

• Robert Hooke publishes his

Plymouth Colony: 1620

cereal grains to make beer: 1500 B.C.

discovery of cells and sees the first microorganism: 1665

• Harvard College, • Tutankhamen in

• Edward Jenner introduces

first college in the U.S., founded: 1636

Egypt: 1300 B.C.

vaccination for smallpox: 1796

Historical Events

• Lewis and Clark explore the west: 1804–1806

• War of 1812 with England: 1812–1814

Milestones in Microbiology

• Ferdinand Magellan’s

• First permanent English

ships circle the globe: 1519–1522

• American Revolution:

settlement in America, Jamestown: 1607

1775–1783

• Girolamo Fracastoro suggests

• Antony van Leeuwenhoek

that invisible organisms may cause disease: 1546

observes bacteria: 1676

• Napoleon defeated at Waterloo: 1815

• Battle of the

• Louis Pasteur demonstrates

Alamo: 1836

• J. Henle proposes

that yeast can degrade sugar to ethanol and carbon dioxide: 1857

• California Gold Rush: 1848

the germ theory of disease: 1840

• Louis Pasteur refutes spontaneous generation: 1861

• Mathias Schleiden and Theodor Schwann propose that all organisms are composed of cells:1838–1839

• Darwin publishes Origin of Species: 1859

• American Civil War: 1861–1865

• John Snow demonstrates

• Mexican War: the epidemic spread of cholera 1846–1848 through a contaminated water supply: 1853–1854 • Ignaz Semmelwels demonstrates that childbed fever is a contagious disease transmitted by doctors during childbirth: 1847–1850

• Louis Pasteur develops pasteurization to destroy organisms in wine: 1864

• Christian Gram describes the Gram stain: 1884

• Blacks given the right to vote: 1870

• U.S. acquires Alaska from Russia: 1867

• Robert Koch introduces pure culture techniques in the laboratory: 1881

• Robert Koch demonstrates that a bacterium causes anthrax: 1876

• Elie Metchnikoff discovers phagocytic cells which engulf bacteria: 1884 • Koch states Koch’s Postulates: 1884

• Joseph Lister publishes the first work on antiseptic surgery: 1867

• Custer’s Last Stand: 1876

• Koch discovers the cause

• Statue of Liberty

of tuberculosis: 1882 • Walter and Fanny Hesse introduce agar-agar as a solidifying gel for culture media: 1882

dedicated: 1886

• Dmitri Iwanowski discovers that a filterable agent, a virus, causes tobacco-mosaic disease: 1892

(a)

FIGURE 1.2 Some major milestones in microbiology—and their timeline in relation to other historical events.

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1.1 The Origin of Microorganisms • Women given the

• F. Peyton Rous discovers that a virus

• Frederick Griffith discovers

right to vote: 1919

can cause cancer in chickens: 1911

genetic transformation in bacteria: 1928

• Charles Lindbergh

• Wright Brothers make controlled sustained flight: 1903

5

makes first non-stop transatlantic flight: 1927

• World wide influenza epidemic: 1918

• Alexander Fleming discovers

Historical Events

first antibiotic, penicillin: 1929

• Prohibition of alcoholic beverages repealed: 1933

• World War II:

Milestones in Microbiology

1939–1945

• Paul Ehrlich develops

• World War I: the drug salvarsan, 1914–1918 the first chemotherapeutic • First woman elected agent to treat syphilis: 1908 to Congress: 1916

• Alcoholic beverages

• First talking motion

prohibited in US: 1920

picture made: 1928

• Avery, MacLeod, and McCarty demonstrate that Griffith’s transforming principle is DNA: 1944

• D. Carlton Gajdusek • Herbert Boyer and Stanley Cohen, clone DNA: 1973

• Equal Rights Amendment

demonstrates the slow infectious nature of the • Joshua Lederberg and Edward Tatum disease kuru, later shown demonstrate the transfer of DNA to be caused by a prion: 1957 between bacteria: 1944

gives women equal rights: 1971

• Jackie Robinson baseball

• Theodor Diener demonstrates

• Michael Bishop and Harold

fundamental differences between viroids and viruses: 1971

Varmus discover that cancercausing genes, are found in normal tissues: 1976

• US enters Vietnam War: 1959

playing days: 1947–1956

• Korean War: 1950 –1953

• Barbara McClintock discovers transposable elements in maize: 1948

• Carl Woese classifies all organisms into three domains: 1977

• Watson, Crick, Franklin, • Voting age lowered

• Willie Mays baseball

from 21 to 18: 1971

• Milstein,Kohler, and Jeme

and Wilkins determine the structure of DNA: 1953

playing days: 1951–1973

• Abortion is

develop monoclonal antibodies: 1975

legalized: 1970

• Hamilton Smith discovers the first restriction enzyme: 1970

• A retrovirus causing rare cancer in humans is discovered: 1980 • World Health Organization declares smallpox is eradicated: 1980

• Sony introduces the Walkman: 1981 • Cellphone becomes commercially available: 1983

• Attack on World • The first complete nucleotide sequence of a bacterial chromosome is reported: 1995

• Persian Gulf War drives Iraq out of Kuwait: 1991

Trade Center: 2001

• The first new antibiotic in 35 years, Zyvox or linezolid, is approved by the Food and Drug Administration: 2000

• The outbreak of SARS in Southeast Asia occurs: 2003

• Iraq War: 2003–

• First product of genetic engineering introduced–human insulin: 1982

• Avian influenza • Bioterrorism by anthrax • Personal computer considered a major spores is waged against Robert Gallo isolate produced: 1989 threat: 2005 the United States: 2001 and characterize the human immunodeficiency • Ford Doolittle proposes that virus (HIV): 1983 • The Food and Drug Administration evolution proceeded through approves a genetically engineered horizontal gene transfer between • Kary Mullis invents food for human consumption: 1994 the three domains: 1999 the polymerase

• Barry Marshall demonstrates that a bacterium causes ulcers: 1982 • Stanley Prusiner isolates a protein; a prion from a slow disease infection: 1982

• Luc Montagnier and

chain reaction: 1983

(b)

FIGURE 1.2 (Continued)

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6

CHAPTER ONE Humans and the Microbial World

1.2 Microbiology: A Human Perspective Focus Points List the reasons why life could not exist without microorganisms. Describe five applications of microbiology. Discuss why emerging diseases are appearing in industrialized countries.

Microoganisms have had, and continue to have, an enormous impact on all living things. On one hand, microorganisms and other infectious agents, the viruses, have killed far more people than have ever been killed in war. Yet, without microorganisms, life as we know it could not exist. They are responsible for continually recycling the carbon, oxygen, and nitrogen that all living beings require.

Features of the Microbial World Members of the microbial world are incredibly diverse. They include bacteria, archaea, protozoa, algae, fungi, some multicellular parasites, and non-living agents such as viruses, viroids, and prions. Because they include both living and non-living forms, as a group, they are called microbes. The most common feature of most members of the microbial world is that they can be seen only with the aid of a microscope. Other than their small size, microorganisms share few other properties. They are extremely diverse in their appearance, metabolism, physiology, and genetics. In fact, plants are more closely related to animals than certain bacteria are to one another. There is tremendous biodiversity in the microbial world, biodiversity being the variety of species present in a particular environment. The visible forms, the plants and animals, by which biodiversity is usually measured, represent only a tiny fraction of the organisms that contribute to biodiversity. Microorganisms not only represent the most abundant forms of life on earth in terms of weight, or biomass, but they are also the oldest and therefore have had the longest time to evolve. The most important and underappreciated forms of life are those that cannot be seen. It has been estimated that 500 to 1,000 species of bacteria live on the healthy human body and for every human cell, there are 10 bacterial cells. Yet, the true contribution and biological role of microorganisms is vastly underestimated because less than 1% of the total number of microorganisms in any environment can be cultivated in the laboratory. Let us now consider some of the roles that microorganisms play in our lives, both beneficial and harmful. In large part this section and the remainder of this chapter will introduce you to what will be covered in more detail in later chapters.

Vital Activities of Microorganisms The activities of microorganisms are responsible for the survival of all other organisms, including humans on this planet. A few examples readily prove this point. Nitrogen is an essential part of most of the important molecules in our bodies, such as nucleic acids and proteins. Nitrogen is also the most common gas in the atmosphere. Neither plants nor animals, however, can use nitrogen gas. Without certain bacteria that are able to convert the nitrogen in air into a form that plants can use, life as we know it would not exist.

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All animals including humans require oxygen (O2) to breathe. The supply of O2 in the atmosphere, however, would be depleted in about 20 years, were it not replenished. On land, plants are important producers of O2, but when all land and aquatic environments are considered, microorganisms are primarily responsible for continually replenishing the supply of O2. Microorganisms can also break down a wide variety of materials that no other forms of life can degrade. For example, the bulk of the carbohydrate in terrestrial (land) plants is in the form of cellulose, which humans and most animals cannot digest. Certain microorganisms can, however. As a result, leaves and downed trees do not pile up in the environment. Cellulose is also degraded by billions of microorganisms in the digestive tracts of cattle, sheep, deer, and other ruminants. The digestion products are used by the cattle for energy. Without these bacteria, ruminants would not survive. Microorganisms also play an indispensable role in degrading a wide variety of materials in sewage and wastewater.

Applications of Microbiology In addition to the crucial roles that microorganisms play in maintaining all life, they also have made life more comfortable for humans over the centuries.

Food Production By taking advantage of what microorganisms do naturally, Egyptian bakers as early as 2100 b.c. used yeast to make bread. Today, bakeries use essentially the same technology. ■ breadmaking, p. 761 The excavation of early tombs in Egypt revealed that by 1500 b.c., Egyptians employed a highly complex procedure for fermenting cereal grains to produce beer. Today, brewers use the same fundamental techniques to make beer and other fermented drinks. ■ beer, p. 759 Virtually every human population that has domesticated milkproducing animals such as cows and goats also has developed the technology to ferment milk to produce foods such as yogurt, cheeses, and buttermilk. Today, the bacteria added to some fermented milk products are being touted as protecting against intestinal infections and bowel cancer, the field of probiotics. ■ milk products, p. 756 ■ probiotics, p. 411

Bioremediation The use of living organisms to degrade environmental pollutants is termed bioremediation. Bacteria are being used to destroy such dangerous chemical pollutants as polychlorinated biphenyls (PCBs), dichlorodiphenyltrichloroethane (DDT), and trichloroethylene, a highly toxic solvent used in dry cleaning. All three organic compounds and many more have been detected in contaminated soil and water. Bacteria are also being used to degrade oil, assist in the cleanup of oil spills, and treat radioactive wastes. A bacterium was discovered that can live on trinitrotoluene (TNT). ■ bioremediation, p. 86

Useful Products from Bacteria Bacteria can synthesize a wide variety of different products in the course of their metabolism, some of which have great commercial value. Although these same products can be synthesized in fac-

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1.2 Microbiology: A Human Perspective

tories, bacteria often can do it faster and cheaper. For example, different bacteria produce: Cellulose used in stereo headsets Hydroxybutyric acid used in the manufacture of disposable diapers and plastics Ethanol, as a substitute for gasoline—a “biofuel” Chemicals poisonous to insects Antibiotics used in the treatment of disease Amino acids, used as dietary supplements

Medical Microbiology In addition to the useful roles that many microbes play in our daily lives, some also play a sinister role. For example, more Americans died of influenza in 1918–1919 than were killed in World War I, World War II, the Korean War, and the Vietnam and Iraq wars combined (figure 1.3). Modern sanitation, vaccination, and effective antibiotic treatments have reduced the incidence of some of the worst diseases, such as smallpox, bubonic plague, and influenza, to a small fraction of their former numbers. To maintain this decrease, however, we must educate future generations to continue their vigilance. Meanwhile, another disease, acquired immunodeficiency syndrome (AIDS), has risen as a modern-day plague for which no vaccine is effective.

Past Triumphs About the time that spontaneous generation was finally disproved to everyone’s satisfaction, the Golden Age of medical microbiology was born. Between the years 1875 and 1918, most diseasecausing bacteria were identified, and early work on viruses had begun. Once people realized that some of these invisible agents could cause disease, they tried to prevent their spread from sick to healthy people. The great successes in the area of human health in the last 100 years have resulted from the prevention of infectious diseases with vaccines and treatment of these diseases with antibiotics. The results have been astounding!

7

The viral disease smallpox was one of the greatest killers the world has ever known. Approximately 10 million people have died from this disease over the past 4,000 years. It was brought to the New World by the Spaniards and made it possible for Hernando Cortez, with fewer than 600 soldiers, to conquer the Aztec Empire, whose subjects numbered in the millions. During a crucial battle in Mexico City, an epidemic of smallpox raged, killing mainly the Aztecs who had never been exposed to the disease before. In recent times, an active worldwide vaccination program has resulted in no cases being reported since 1977. Although the disease will probably never reappear on its own, its potential use as an agent in bioterrorist attacks is raising great concern. Plague has been another great killer. One-third of the entire population of Europe, approximately 25 million people, died of this bacterial disease between 1346 and 1350. Now, generally less than 100 people in the entire world die each year from this disease. In large part, this dramatic decrease is a result of controlling the population of rodents that harbor the bacterium. Further, the discovery of antibiotics in the early twentieth century made the isolated outbreaks treatable and the disease is no longer the scourge it once was. Epidemics are not limited to human populations. In 2001, a catastrophic outbreak of foot-and-mouth disease of animals ran out of control in England. To contain this disease, one of the most contagious diseases known, almost 4 million pigs, sheep, and cattle were destroyed. Epidemic spread of diseases of food plants has led to starvation in human populations.

Present and Future Challenges Although progress has been very impressive against bacterial diseases, a great deal still remains to be done, especially in the treatment of viral diseases and diseases that are prevalent in developing countries. Even in wealthy developed countries with their sophisticated health care systems, infectious diseases remain a serious threat. For example, about 750 million cases of infectious diseases occur in the United States each year, leading to 200,000 deaths and costing tens of billions of health care dollars. Respiratory infections and diarrheal diseases cause most illness and deaths in the world today. Emerging Diseases In addition to the well-recognized diseases, seemingly “new” emerging diseases continue to arise. In the last several decades, they have included: Legionnaires’ disease, p. 517 Toxic shock syndrome, p. 626 Lyme disease, p. 542 Acquired immunodeficiency syndrome (AIDS), p. 698 Hantavirus pulmonary syndrome, p. 522 Hemolytic uremic syndrome, p. 598 Mad cow disease (Bovine spongiform encephalopathy), p. 320 West Nile virus disease, p. 660 Severe acute respiratory syndrome (SARS), p. 528

FIGURE 1.3 Students wearing gauze masks to protect themselves against infection with the influenza virus in 1918.

nes95432_Ch01_001-017.indd 7

Few of these diseases are really new, but an increased occurrence and wider distribution have brought them to the attention of health workers. Using the latest techniques, biomedical

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8

CHAPTER ONE Humans and the Microbial World

scientists have isolated, characterized, and identified the agents causing the diseases. Now, better methods need to be developed to prevent them. A number of factors account for these emerging diseases arising even in industrially advanced countries. One reason is that changing lifestyles bring new opportunities for infectious agents to cause disease. For example, the vaginal tampons used by women provide an environment in which the organism causing toxic shock syndrome can grow and produce a toxin. In another example, the suburbs of cities are expanding into rural areas, bringing people into closer contact with animals previously isolated from humans. Consequently, people become exposed to viruses and infectious organisms that had been far removed from their environment. A good example is the hantavirus. This virus infects rodents, usually without causing disease. The infected animals, however, shed virus in urine, feces, and saliva; from there, it can be inhaled by humans as an aerosol. This disease, as well as Lyme disease, are only two of many emerging human diseases associated with small-animal reservoirs. Some emerging diseases arise because the infectious agents change abruptly and gain the ability to infect new hosts. It appears that HIV (Human Immunodeficiency Virus), the cause of AIDS, arose from a virus that once could infect only chimpanzees. The virus causing SARS is related to viruses found in animals and may have been transmitted from animals to humans. Some bacterial pathogens, organisms capable of causing disease, differ from their non-pathogenic relatives in that the pathogens contain large pieces of DNA that confer on the organism the ability to cause disease. These pieces of DNA may have originated in unrelated organisms.

Figure 1.4 shows the countries in the world where, since 1976, new infectious diseases of humans and animals have first appeared. Are there other agents out there that may cause “new” diseases in the future? The answer is undoubtedly yes! Resurgence of Old Diseases Not only are “new” diseases emerg-

ing, but many infectious diseases once on the wane in the United States have begun to increase again. One reason for this resurgence is that thousands of foreign visitors and U.S. citizens returning from travel abroad enter this country daily. About one in five comes from a country where such diseases as malaria, cholera, plague, and yellow fever still exist. In developed countries these diseases have been eliminated largely through sanitation, vaccination, and quarantine. An international traveler incubating a disease in his or her body, however, could theoretically circle the globe, touch down in several countries, and expose many people before he or she became ill. As a result these diseases are recurring in countries where they had been virtually eliminated. Further, many of these diseases are more serious today because the causative agents resist the antibiotics once used to treat them. A second reason that certain diseases are on the rise is that in both developed and developing countries many childhood diseases have been so effectively controlled by childhood vaccinations that some parents have become lax about having their children vaccinated. The unvaccinated children are highly susceptible, and the number of those infected has increased dramatically. These diseases include measles, polio, mumps, whooping cough, and diphtheria. A third reason for the rise in infectious diseases is that the population contains an increasing proportion of elderly 2002 Severe acute respiratory syndrome (SARS) China

1988 Salmonella enteritidis PT4 United Kingdom

1982 E. coli O157:H7 United States 1981 AIDS United States 1976 Legionnaires' Disease United States 1976 Cryptosporidiosis United States

1986 Bovine spongiform encephalopathy United Kingdom

1977 Hantaan virus Republic of Korea 1980 Human T-cell lymphotropic virus 1 Japan

1980 Hepatitis D (Delta) 1989 Italy Hepatitis C United States 1991 Venezuelan hemorrhagic fever Venezuela

1994 Brazilian hemorrhagic fever Brazil

1992 Vibrio cholerae 0139 India

1997 Avian flu (H5N1) Hong Kong

1999 Malaysian encephalitis Malaysia

1976 Ebola 1994 hemorrhagic fever Human and equine Zaire morbilivirus Australia

FIGURE 1.4 “New” Infectious Diseases in Humans and Animals Since 1976 Countries where cases first appeared or were identified appear in a darker shade. Why are the United States and Western European countries so prominent?

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1.3 Members of the Microbial World

people, who have weakened immune systems and are susceptible to diseases that younger people readily resist. In addition, individuals infected with HIV are especially susceptible to a wide variety of diseases, such as tuberculosis and Kaposi’s sarcoma. Chronic Diseases Caused by Bacteria In addition to the diseases long recognized as being caused by microorganisms or viruses, some illnesses once attributed to other causes may in fact be caused by bacteria. The best-known example is peptic ulcers. This common affliction has been shown to be caused by a bacterium, Helicobacter pylori, and is treatable with antibiotics. Chronic indigestion, which affects 25% to 40% of the people in the Western world, may also be caused by the same bacterium. Some scientists have also implicated a bacterium in Crohn’s Disease, an inflammation of the gastrointestinal tract. In 2002, it was shown that the worm responsible for the tropical disease river blindness must contain a specific bacterium that apparently causes the disease. Infectious agents likely play roles in other diseases of unknown origin.

Host-Bacterial Interactions All surfaces of the human body are populated with bacteria, most of which protect against disease. These bacteria are termed normal microbiota or normal flora. These bacteria play a number of indispensable roles in the life of the body. They successfully compete with occasional disease-causing bacteria and keep them from breaching host defenses that prevent disease. Further, they play important roles in the development of the intestine. Bacteria also degrade foodstuffs in the intestine that the body cannot digest. Pathogenic microbes, including bacteria, fungi, protozoa, and viruses, can damage tissues of the body, leading to symptoms of disease. They use the human body as a habitat for multiplication, persistence, and transmission to other hosts. The disease symptoms are often offshoots of the body’s defense mechanisms, which may damage the host as well as the pathogen.

9

MICROCHECK 1.2 Microorganisms are essential to all life and affect the life of humans in both beneficial and harmful ways. Microorganisms have been used for food production for thousands of years using essentially the same techniques that are used today. They are now being used to degrade toxic pollutants and produce a variety of compounds more cheaply than can be done in the chemical laboratory. Enormous progress has been made in preventing and curing most infectious diseases, but new ones continue to emerge around the world. Microbes represent wonderful model organisms, and many principles of biochemistry and genetics have been discovered from studying them. ✓ Discuss activities that microbes carry out that are essential to life on earth. ✓ Discuss several reasons for the reemergence of old diseases. ✓ Why would it seem logical, even inevitable, that at least some bacteria would attack the human body and cause disease?

1.3 Members of The Microbial World Focus Points Name the three domains of life and their distinguishing properties. Compare and contrast the three eukaryotic groups of the microbial world.

The microbial world includes the kinds of cells that van Leeuwenhoek observed looking through his simple microscope (figure 1.5). Although he could not realize it at the time, members

Lens Specimen holder

Microorganisms As Model Organisms Microorganisms are wonderful model organisms to study because they display the same fundamental metabolic and genetic properties found in higher forms of life. For example, all cells are composed of the same elements and synthesize their cell structures by the same basic mechanisms. They all duplicate their DNA by similar processes, and they degrade food materials to harvest energy via the same metabolic pathways. To paraphrase a Nobel Prize-winning microbiologist, Dr. Jacques Monod, what is true of elephants is also true of bacteria. The study of bacteria has many advantages. They are easy to study and results can be obtained very quickly because they grow rapidly and form billions of cells per milliliter on simple inexpensive media. Thus, most of the major advances made in the last century toward understanding life have come through the study of microorganisms. The number of Nobel Prizes that have been awarded to microbiologists, and especially the ones awarded in 2001, proves this point (see inside cover). Such studies constitute basic research, and they continue today.

nes95432_Ch01_001-017.indd 9

Focus screw

Handle

FIGURE 1.5 Model of van Leeuwenhoek’s Microscope The original made in 1673 could magnify the object being viewed almost 300 times. The object being viewed is brought into focus with the adjusting screws. Note the small size.

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10

CHAPTER ONE Humans and the Microbial World

of the microbial world, in fact all living organisms, can be separated into three distinct groups called domains. Organisms in each domain consist of cells with the same properties that distinguish them from members of the other domains. Many characteristics, however, are common among members of different domains. The three domains are the Bacteria (formerly called Eubacteria), Archaea (formerly called Archaebacteria, meaning ancient bacteria), and Eucarya. Microscopically, members of the Bacteria and Archaea look indentical. Both are prokaryotes, meaning they are single-celled organisms consisting of a prokaryotic cell (meaning “prenucleus”). This type of cell does not contain a membrane-bound nucleus nor any other intracellular lipid-bound organelles. Their genetic information is stored in deoxyribonucleic acid (DNA) in a region called the nucleoid. Although all members of Bacteria and Archaea are prokaryotes, they are genetically quite different. In fact, the Archaea are as closely related to humans as they are to the Bacteria. Members of the Eucarya are eukaryotes, meaning they are composed of one or more eukaryotic cells (meaning “true nucleus”). These cells always contain a membrane-bound nucleus and other organelles, making them far more complex than the simple prokaryotes. All algae, fungi, protozoa, and multicellular parasites are eukaryotes.

Bacteria Most of the prokaryotes covered in this text are members of the domain Bacteria. Even within this group, much diversity is seen in the shape and properties of the organisms. Their most prominent features are: They are all single-celled prokaryotes. Most have specific shapes, most commonly cylindrical (rodshaped), spherical (round), or spiral. ■ bacterial shapes, p. 52 Most have rigid cell walls, which are responsible for the shape of the organism. The walls contain an unusual chemical compound called peptidoglycan, which is not found in organisms in the other domains (see figure 3.32). They multiply by binary fission in which one cell divides into two cells, each generally identical to the original cell. ■ binary fission, p. 53

Many can move using appendages extending from the cell, called flagella (sing: flagellum). ■ flagella, p. 65

Archaea Archaea have the same shape, size, and appearance as the Bacteria. Like the Bacteria, the Archaea multiply by binary fission and move primarily by means of flagella. They also have rigid cell walls. The chemical composition of their cell wall, however, differs from that in the Bacteria. The Archaea do not have peptidoglycan as part of their cell walls. Other chemical differences also exist between these two groups. An interesting feature of many members of the Archaea is their ability to grow in extreme environments in which most organisms cannot survive. For example, some archaea can grow in salt concentrations 10 times higher than that found in seawater. These organisms grow in such habitats as the Great Salt Lake and the Dead Sea. Other archaea grow best at extremely high temperatures. One member can grow at a temperature of 121°C. (100°C is the temperature at which water boils at sea level). Some archaea can be found in the boiling hot springs at Yellowstone National Park. Members of the Archaea, however, are spread far beyond extreme environments. They are widely distributed in the oceans, and they are found in the cold surface waters of Antarctica and Alaska.

Eucarya The microbial members of the domain Eucarya comprise single-celled and multicellular organisms that have a eukaryotic cell structure. These members include algae (sing: alga), fungi (sing: fungus), and protozoa (sing: protozoan). Algae and protozoa are also referred to as protists. In addition, some multicellular organisms are considered in this text because they kill millions of people around the world, especially in developing nations. They are given the general name of helminths and include organisms such as roundworms and tapeworms. Since they derive nutrients from the host organism they are termed parasites. The Bacteria, Archaea, and Eucarya are compared in table 1.1.

Algae The algae are a diverse group of eukaryotes; some are single-celled and others, multicellular. Many different shapes and sizes are represented, but they all share some fundamental characteristics (figure 1.6). They all contain chloroplasts, some of which have a green pigment, chlorophyll. Some also contain other pigments that give them characteristic colors. The pigments absorb the energy of light, which is used in photosynthesis. Algae are usually found

TABLE 1.1 Comparison of Bacteria, Archaea, and Eucarya Bacteria

Archaea

Typical Size

0.3–2 m m

0.3–2 m m

5–50 m m

Nuclear Membrane

No

No

Yes

Cell Wall

Peptidoglycan present

No peptidoglycan

No peptidoglycan

Membrane-bound Organelles

No

No

Yes

Where Found

In all environments

In all environments

In environments that are not extreme

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Eucarya

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1.3 Members of the Microbial World

11

(a)

FIGURE 1.6 Alga Micrasterias, a green alga composed of two symmetri-

Reproductive structures (spores)

cal halves (100μ).

near the surface of either salt or fresh water. Their cell walls are rigid, but their chemical composition is quite distinct from that of the Bacteria and the Archaea. Many algae move by means of flagella, which are structurally more complex and unrelated to flagella in prokaryotes.

Mycelium

(b)

Fungi

FIGURE 1.7 Two Forms of Fungi (a) Living cells of yeast form,

Fungi are also a diverse group of eukaryotes. Some are singlecelled yeasts, but many are large multicellular organisms such as molds and mushrooms (figure 1.7). In contrast to algae, fungi gain their energy from degrading organic materials and are found wherever organic materials are present. Unlike algae, which live primarily in water, fungi live mostly on land.

Cryptococcus neoformans. (b) Aspergillus, a typical mold form whose reproductive structures rise above the mycelium.

Protozoa Protozoa are a diverse group of microscopic, single-celled organisms that live in both aquatic and terrestrial environments. Although microscopic, they are very complex organisms and much larger than prokaryotes (figure 1.8). Unlike algae and fungi, protozoa do not have a rigid cell wall. However, many do have a specific shape based on a gelatinous region just beneath the plasma membrane of the cell. Most protozoa require organic compounds as sources of food, which they ingest as particles. Most groups of protozoa are motile, and a major feature of their classification is their means of locomotion. The eukaryotic members of the microbial world are compared in table 1.2.

FIGURE 1.8 Protozoan A paramecium moves with the aid of cilia on the cell surface.

20 μm

TABLE 1.2 Comparison of Eukaryotic Members of the Microbial World Algae

Fungi

Protozoa

Cell Organization

Single- or multicellular

Single- or multicellular

Single-celled

Source of Energy

Sunlight

Organic compounds

Organic compounds

Size

Microscopic or macroscopic

Microscopic or macroscopic

Microscopic

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CHAPTER ONE Humans and the Microbial World

Nomenclature In biology, the Binomial System of Nomenclature devised by Carl Linnaeus refers to a two word naming system. The first word in the name indicates the genus, with the first letter always capitalized; the second indicates the species and is not capitalized. Both words are always italicized or underlined, for example, Escherichia coli. The genus name is commonly abbreviated, with the first letter capitalized: that is, E. coli. A number of different species are included in the same genus. Members of the same species may vary from one another in minor ways, but not enough to give the organisms different species names. These differences, however, may result in the organism being given different strain designations, for example, E. coli strain B or E. coli strain K12. Bacteria are often referred to informally by names resembling genus names but are not italicized. For example, species of Staphylococcus are often called staphylococci.

MICROCHECK 1.3 All organisms fall into one of three large groups based on their cell structure and chemical composition: the Bacteria, the Archaea, or the Eucarya. The Bacteria and the Archaea are prokaryotes. Both are identical in appearance but distinctly different in many aspects of their chemical composition. The Eucarya are eukaryotes. The algae, fungi, protozoa, and multicellular parasites belong to this group. Bacteria, like all organisms, are classified according to the Binomial System of Nomenclature. ✓ Name one feature that distinguishes the domain Bacteria from the domain Archaea. ✓ List two features that distinguish prokaryotes from eukaryotes. ✓ The binomial system of classification uses both a genus and a species name. Why bother with two names? Wouldn’t it be easier to use a single, unique name for each different kind of microorganism?

1.4 Viruses, Viroids, and Prions Focus Points Distinguish among viruses, viroids, and prions. Discuss the reasons why viruses, viroids, and prions are not organisms.

The organisms discussed so far are living members of the microbial world. In order to be alive, an organism must be composed of one or more cells. Viruses, viroids, and prions are not living, are acellular and are termed agents. ■ viroids, p. 342 ■ prions, p. 341 Viruses consist of a piece of nucleic acid surrounded by a protein coat. They come in a variety of shapes (figure 1.9). Viruses need to produce copies of themselves, otherwise they would not exist in nature. Viruses can only multiply inside living host cells, whose multiplication machinery and nutrients they use for reproduction. Outside the hosts, they are inactive. Thus, viruses are obligate intracellular parasites. All forms of life including members of the Bacteria, Archaea, and Eucarya can be infected by viruses but of different types. Although viruses frequently kill the cells in which they multiply, some types exist harmoniously within the host cell without causing obvious ill effects. Viroids are simpler than viruses, consisting of a single, short piece of ribonucleic acid (RNA), without a protective coat. They are much smaller than viruses (figure 1.10), and, like viruses, can reproduce only inside cells. Viroids cause a number of plant diseases, and some scientists speculate that they may cause diseases in humans. Prions consist of only protein, without any nucleic acid (figure 1.11). They are very unusual agents consisting of an abnormal form of a cellular protein and are responsible for at least seven neurodegenerative diseases in humans and animals; these are always fatal.

Nucleic acid Protein coat

Head (a)

50 nm

(b)

Nucleic acid

Sheath

Nucleic acid

50 nm

50 nm

(c)

FIGURE 1.9 Viruses That Infect Three Kinds of Organisms (a) Tobacco mosaic virus that infects tobacco plants. A long hollow protein coat surrounds a molecule of RNA. (b) A bacterial virus (bacteriophage), which infects bacteria. Nucleic acid is surrounded by a protein coat (head). (c) Influenza virus, thin section. This virus infects humans and causes flu.

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1.4 Viruses, Viroids, and Prions

13

50 nm

FIGURE 1.10 The Size of a Viroid Compared with a Molecule of DNA from a Virus That Infects Bacteria (T7) The red arrows point to the potato spindle tuber viroids (PSTV); the other arrow points to the bacterial virus T7 DNA.

FIGURE 1.11 Prion Prions isolated from the brain of a scrapie-infected hamster. This neurodegenerative disease is caused by a prion.

The distinguishing features of the non-living members of the microbial world are given in table 1.3. The relationships of the major groups of the microbial world to one another are presented in figure 1.12.

MICROCHECK 1.4 The acellular agents are viruses, viroids, and prions. ✓ Compare the chemical composition of viruses, viroids, and prions. ✓ What groups of organisms are infected by each of the following: viruses, viroids, prions? ✓ How might one argue that viruses are actually living organisms?

TABLE 1.3 Distinguishing Characteristics of Viruses, Viroids, and Prions Viruses

Viroids

Prions

Obligate intracellular agents

Obligate intracellular agents

Abnormal form of a cellular protein

Consist of either DNA or RNA, surrounded by a protein coat

Consist only of RNA; no protein coat

Consist only of protein; no DNA or RNA

MICROBIAL WORLD

Infectious agents (non-living)

Organisms (living)

Domain

Bacteria

Archaea

Eucarya

Prokaryotes (unicellular)

Viroids

Prions

Eukaryotes

Algae (unicellular or multicellular)

Protozoa (unicellular)

Protists

nes95432_Ch01_001-017.indd 13

Viruses

Fungi (unicellular or multicellular)

Helminths (multicellular parasites)

FIGURE 1.12 The Microbial World Although adult helminths are generally not microscopic, some stages in the life cycle of many disease-causing helminths are.

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CHAPTER ONE Humans and the Microbial World

1.5 Size in the Microbial World Focus Point Compare the differences in sizes among members of the microbial world.

Members of the microbial world cover a tremendous range of sizes, as seen in figure 1.13. The smallest viruses are about 1 million times smaller than the largest eukaryotic cells. Even within a single group, wide variations exist. For example, Bacillus megaterium and Mycoplasma pneumoniae are both bacteria, but they differ enormously in size (see figure 1.13). The variation in size of bacteria was recently expanded when a bacterium longer than 0.5 mm was discovered (see Perspective 1.1). In fact, it is so big that it is visible to the naked eye. More recently, an even larger bacterium, round in shape, was discovered. Its volume is 70 times larger than the previous record holder. Likewise, a eukaryotic cell was recently

discovered that is not much larger than a typical bacterium. These, however, are rare exceptions to the rule that eukaryotes are larger than prokaryotes, which in turn are larger than viruses. As you might expect, the small size and broad size range of some members of the microbial world have required the use of measurements not commonly used in everyday life. The use of logarithms has proved to be enormously helpful, especially in designating the sizes of prokaryotes and viruses. A brief discussion of measurements and logarithms is given in Appendix I.

MICROCHECK 1.5 The range in size of the members of the microbial world is tremendous. As a general rule, the obligate intracellular parasites are the smallest and the eukaryotes the largest. ✓ Place in order with respect to typical size (arrange from smallest to largest) bacteria, eukaryotic cells, and viruses. ✓ What factor limits the size of free-living cells?

Limit of visibility

Meters

Relative sizes of organisms and viruses

The basic unit of length is the meter (m), and all other units are fractions of a meter. nanometer (nm) = 10 –9 meter = .000000001 meter micrometer (µm) = 10 –6 meter = .000001 meter millimeter (mm) = 10 –3 meter = .001 meter 1 meter = 39.4 inches

These units of measurement correspond to units in an older but still widely used convention. 1 angstrom (Å) = 10 –10 meter 1 micron (µ) = 10 –6 meter

10 –2

10 mm

10 –3

1,000 µm or 1 mm

10 –4

100 µm

10 –5

10 µm

10 –6

1,000 nm or 1 µm

10 –7

100 nm

10 –8

10 nm

10 –9

1 nm

Adult roundworm Helminth

Eye

Eukaryotic cell Yeast

Bacillus megaterium Prokaryotic cells Escherichia coli Light microscope

Electron microscope

Mycoplasma

Virus

FIGURE 1.13 Sizes of Organisms and Viruses

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1.5 Size in the Microbial World

15

PERSPECTIVE 1.1 The Long and the Short of It We might assume that because prokaryotes have been so intensively studied over the past hundred years, no major surprises are left to be discovered. This, however is far from the truth. In the mid1990s, a large, peculiar-looking organism was seen when the intestinal tracts of certain fish from both the Red Sea in the Middle East and the Great Barrier Reef in Australia were examined. This organism, named Epulopisicium cannot be cultured in the laboratory (figure 1). Its large size, 600 mm long and 80 mm wide, makes it clearly visible without any magnification, and suggested that this organism was a eukaryote. It did not, however have a membrane bound nucleus. A chemical analysis of the cell confirmed that it was a prokaryote and a member of the domain Bacteria. This very long, slender organism is an exception to the rule that prokaryotes are always smaller than eukaryotes. In 1999, an even larger prokaryote in volume was isolated from the sulfurous muck of the ocean

floor off the coast of Namibia in Africa. It is a spherical organism 70 times larger in volume than Epulopisicium. Since it grows on sulfur compounds and contains glistening globules of sulfur, it was named Thiomargarita namibiensis, which means “sulfur pearl of Namibia” (figure 2). Although scientists were initially skeptical that prokaryotes could be so large, there is no question in their minds now. In contrast to these large bacteria, a cell was isolated in the Mediterranean Sea that is 1 m m in width. It is a eukaryote because it contains a nucleus even though it is about the size of a typical bacterium. How small can an organism be? An answer to this question may be at hand as a result of a new microorganism discovered off the coast of Iceland. The organism, found in an ocean vent where the temperature was close to the boiling point of water, cannot be grown in the laboratory by itself, but only grows when it is attached to another much larger

member of the Archaea (figure 3). These tiny organisms, also members of the Archaea, have been named Nanoarchaeum equitans, which means “riding the fire sphere.” The organism to which N. equitans is attached is Ignicoccus, which means “fire ball.” Ignicoccus grows very well without its rider. N. equitans is spherical and only about 400 nanometers in diameter, about a quarter the diameter of Ignicoccus. Also, the amount of genetic information (DNA) contained in N. equitans is less than in any known organism, and only about one-tenth the amount found in the common gut organism, Escherichia coli. This sets the record for the smallest amount of DNA in any organism. Thus, this organism may contain only the essential DNA required for life. Further analysis of these cells suggests that they may resemble the earliest cells and therefore the ancestor of all life. The scientists who discovered N. equitans suggest that many more unusual organisms related to N. equitans will be discovered. They are probably right!

Epulopiscium (prokaryote)

Paramecium (eukaryote)

0.1 mm

FIGURE 1 Longest Known Bacterium, Epulopisicium Mixed With Paramecia Note how large this prokaryote is compared with the four eukaryotic paramecia.

nes95432_Ch01_001-017.indd 15

0.2 mm

FIGURE 2 Thiomargarita namibiensis The average Thiomargarita namibiensis is twotenths of a millimeter, but some reach three times that size. ■ Thiomargarita, p. 263

1 mm

FIGURE 3 Five Cells of “N. equitans,” Attached on the Surface of the (Central) Ignicoccus Cell Platinum shadowed.

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16

CHAPTER ONE Humans and the Microbial World

FUTURE CHALLENGES Entering a New Golden Age For all the information that has been gathered about the microbial world, it is remarkable how little we know about its prokaryotic members. This is not surprising in view of the fact that less than 1% of the prokaryotes have ever been studied. In large part, this is because only one in a hundred of the prokaryotes in the environment can be cultured in the laboratory. Part of the current revolution in microbiology, however, will allow us to inventory the millions of species that are out there waiting to be discovered. This is now being done. Using techniques that helped decipher the human genome, scientists have begun to analyze the biological content of the oceans. In a small volume of water from the Sargasso Sea, an area of the ocean that contains few

nutrients and therefore presumably few organisms, scientists found 1,800 species of bacteria that were previously unknown. The biodiversity of the microbial world is astounding! Exploring the unknowns in the microbial world is a major challenge and should answer many intriguing questions fundamental to understanding the biological world. What are the extremes of temperature, salt, pH, radioactivity, and pressure in which prokaryotes can live? Are there organisms growing in even more extreme environments? If life can exist on this planet under such extreme conditions, what does this mean about the possibility of finding living organisms on other planets? Although considered highly unlikely, is it

possible that living organisms exist whose chemical structure is not based on the carbon atom? Will living organisms be found whose genetic information is coded in a chemical other than deoxyribonucleic acid? What new metabolic pathways remain to be discovered? As extreme environments are mined for their living biological diversity, there seems little doubt that many surprises will be found. In many cases these surprises will be translated into new biotechnology products on this planet, and they will help shape the way we look for life on other planets. One hundred years ago we were in the Golden Age of medical microbiology. We are now entering the Golden Age of microbial biodiversity.

SUMMARY 1.1

The Origin of Microorganisms

Theory of Spontaneous Generation Revisited The experiments of Pasteur refuted the theory of spontaneous generation (figure 1.1). Tyndall and Cohn demonstrated the existence of heat-resistant forms of bacteria that could account for the growth of bacteria in heated infusions.

1.2

Microbiology: A Human Perspective

Features of the Microbial World Microorganisms represent the most diverse forms of life on earth. Vital Activities of Microorganisms The activities of microorganisms are vital for the survival of all other organisms, including humans. Bacteria are necessary to convert the nitrogen gas in air into a form that plants and other organisms can use. Microorganisms replenish the oxygen on earth and degrade waste materials. Applications of Microbiology For thousands of years, bread, wine, beer, and cheeses have been made by using technology still applied today. Bacteria are being used to degrade dangerous toxic pollutants. Bacteria are used to synthesize a variety of different products, such as cellulose, hydroxybutyric acid, ethanol, antibiotics, and amino acids. Medical Microbiology Many devastating diseases such as smallpox, plague, and influenza have determined the course of history (figure 1.3). “New” emerging diseases are arising, partly, because people are engaging in different lifestyles and living in regions where formerly only animals lived (figure 1.4). “Old” diseases once on the wane have begun to reemerge. Many are brought to this country by people visiting foreign lands. Several chronic diseases such as ulcers are caused by bacteria. Microorganisms As Model Organisms Microorganisms are excellent model organisms to study because they grow rapidly on simple, inexpensive media, but follow the same genetic, metabolic, and biochemical principles as higher organisms.

nes95432_Ch01_001-017.indd 16

1.3

Members of the Microbial World (figure 1.12)

Members of the microbial world consist of two major cell types: the simple prokaryotic and the complex eukaryotic. All organisms fall into one of three domains, based on their chemical composition and cell structure. These are the Bacteria, the Archaea, and the Eucarya (table 1.1).

Bacteria Bacteria are single-celled prokaryotes that have peptidoglycan in their cell wall. Archaea Archaea are single-celled prokaryotes that are identical in appearance to the Bacteria. They do not have peptidoglycan in their cell walls and are unrelated to the Bacteria. Many of the Archaea grow in extreme environments such as hot springs and salt flats. Eucarya Eucarya have eukaryotic cell structures and may be single-celled or multicellular. Microbial members of the Eucarya are the algae, fungi, and protozoa. Algae can be single-celled or multicellular, and use sunlight as a source of energy (figure 1.6, table 1.2). Fungi are either single-celled yeasts or multicellular molds and mushrooms and use organic compounds as food (figure 1.7, table 1.2). Protozoa are motile single-celled organisms and use organic compounds as food (figure 1.8, table 1.2).

Nomenclature Organisms are named according to a binomial system. Each organism has a genus and a species name, written in italics or underlined.

1.4

Viruses, Viroids, and Prions

The non-living members of the microbial world are not composed of cells but are obligate intracellular parasites and include viruses and viroids. Viruses are a piece of nucleic acid surrounded by a pro-

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Review Questions tein coat (figure 1.9, table 1.3). Viroids are composed of a single, short RNA molecule (figure 1.10, table 1.3). Prions consist only of protein, without any nucleic acid and are an abnormal cellular protein (figure

1.5

17

Size in the Microbial World

Sizes of members of the microbial world vary enormously (figure 1.13).

1.11, table 1.3).

REVIEW QUESTIONS Short Answer 1. Name the prokaryotic groups in the microbial world. 2. List five beneficial applications of bacteria. 3. Name three non-living groups in the microbial world and describe their major properties. 4. In the designation Escherichia coli B, what is the genus? What is the species? What is the strain? 5. Where would you go to isolate members of the Archaea? 6. How might you distinguish a prokaryotic cell from a eukaryotic cell? 7. Give three reasons why life could not exist without the activities of microorganisms. 8. Why are viruses not microorganisms? 9. Name two diseases that have been especially destructive in the past. What is the status of those diseases today? 10. State three reasons why there is a resurgence of infectious diseases today.

Multiple Choice 1. The prokaryotic members of the microbial world include 1. algae. 2. fungi. 3. prions. 4. bacteria. 5. archaea. a) 1, 2 b) 2, 3 c) 3, 4 d) 4, 5 e) 1, 5 2. The Archaea 1. are microscopic. 2. are commonly found in extreme environments. 3. contain peptidoglycan. 4. contain mitochondria. 5. are most commonly found in the soil. a) 1, 2 b) 2, 3 c) 3, 4 d) 4, 5 e) 1, 5 3. The most fundamental division of cell types is between the a) algae, fungi, and protozoa. b) eukaryotes and prokaryotes. c) viruses and viroids. d) bacteria and archaea. e) Eucarya, Bacteria, and Archaea. 4. The number of bacteria in the human body compared to the number of non-bacterial cells is estimated to be a) about 10 times more non-bacterial cells than bacteria. b) about equal numbers of bacteria and non-bacterial cells. c) about 10 times more bacteria than non-bacteria. 5. An organism isolated from a hot spring in an acidic environment is most likely a member of the a) Bacteria. b) Archaea. c) Eucarya. d) virus family. e) Fungi.

nes95432_Ch01_001-017.indd 17

6. The agent that contains no nucleic acid is a a) virus. b) prion. c) viroid. d) bacterium. e) fungus. 7. Prokaryotes do not have a) cell walls. b) flagella. c) a nuclear membrane. d) specific shapes. e) genetic information. 8. Nucleoids are associated with 1. genetic information. 2. prokaryotes. 3. eukaryotes. 4. viruses. 5. prions. a) 1, 2 b) 2, 3 c) 3, 4 d) 4, 5 e) 1, 5 9. Which of the following are eukaryotes? 1. Algae 2. Viruses 3. Bacteria 4. Prions 5. Protozoa a) 1, 2 b) 2, 3 c) 3, 4 d) 4, 5 e) 1, 5 10. The person best known for his microscopy of microorganisms is a) Antony van Leeuwenhoek. b) Louis Pasteur. c) John Tyndall. d) Ferdinand Cohn.

Applications 1. The American Society of Microbiology is preparing a “MicrobeFree” banquet to emphasize the importance of microorganisms in the diet. What foods would not be on the menu if microorganisms were not available for our use? 2. If you were asked to nominate one of the individuals mentioned in this chapter for the Nobel Prize, who would it be? Make a statement supporting your choice.

Critical Thinking 1. A microbiologist obtained two pure isolated biological samples: one of a virus, and the other of a viroid. Unfortunately, the labels had been lost from the two samples. The microbiologist felt she could distinguish the two by analyzing for the presence or absence of a single chemical element. What element would she search for and why? 2. Why are the spores of Bacillus anthracis such an effective agent of bioterrorism?

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2 Ball-and-stick model of water molecules.

The Molecules of Life A Glimpse of History Louis Pasteur (1822–1895) is often considered the father of bacteriology. His contributions to this science, especially in its early formative years, were enormous and are discussed in many of the succeeding chapters. Pasteur started his scientific career as a chemist, initially working in the science of crystallography. He first studied two compounds, tartaric and paratartaric acids, which form thick crusts within wine barrels. These two substances form crystals that have the same number and arrangement of atoms, yet they rotate (twist) polarized light differently when that light passes through the crystal. Tartaric acid rotates the light; paratartaric acid does not. Therefore, the two molecules must differ in some way, even though they are chemically identical. Pasteur was determined to find out how the crystals differed. Under a microscope, he saw that the crystals of tartaric acid all looked identical but paratartaric acid consisted of two different kinds of crystals. Using tweezers, he carefully separated the two kinds into separate piles and dissolved each in a separate flask of water. When he shone polarized light through each solution, one rotated the light to the left and the other rotated it to the right. When he mixed equal numbers of each kind of crystal into water and shone polarized light through the solution, the light was not rotated. Apparently, the two components counteracted each other, and as a result, the mixture did not rotate the light. Pasteur concluded that paratartaric acid is a mixture of two compounds, each being the mirror image, or stereoisomer, of the other. This mixture of two stereoisomers can be viewed as a mixture of right- and left-handed molecules, represented as a right and left hand facing each other (see figure 2.14). They cannot be superimposed on each other, much as a right-handed glove cannot fit the left hand. Stereoisomers of the same molecule have greatly different properties. For example, the amino acid phenylalanine, one of the key ingredients in the artificial sweetener aspartame, makes aspartame

sweet when it is in one form but bitter when in the other form. Thus, what Pasteur studied as a straightforward problem in chemistry has implications far beyond what he ever imagined. It is often difficult to predict where research will lead or the significance of interesting but seemingly unimportant observations.

T

o understand how cells live and interact with one another and with their environment, we must be familiar with the molecules that comprise all living matter. For some, this information may serve as a review of material already studied in other courses. For others, it may be a first encounter with the chemistry of biological molecules. In this case, you likely will return to this chapter frequently. The discussion proceeds from the lowest level of chemical organization, the atoms and elements, to the highly complex associations between small molecules that often form large molecules, the macromolecules.

2.1 Atoms and Elements Focus Point Name the three major components of atoms and describe their properties.

Atoms, the basic units of all matter, are made up of three major components: the negatively charged electrons; positively charged protons; and uncharged neutrons (figure 2.1). The protons and neutrons, the heaviest components, are found in the heaviest part of

18

nes95432_Ch02_018-039.indd 18

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2.1

KEY TERMS ATP An abbreviation for adenosine triphosphate, the form in which chemical energy is stored in the cell. Carbohydrate A compound characterized by a large number of —OH groups and containing principally carbon, hydrogen, and oxygen in a ratio of 1:2:1.

Hydrogen Bond A weak bond resulting from the attraction between a positively charged hydrogen atom in one compound and a negatively charged atom in another compound.

Peptide Bond A covalent bond formed between the —COOH group of one amino acid and the —NH2 group of another amino acid; their formation is an important reaction in the synthesis of a protein.

Lipid A heterogenous group of organic molecules characterized by being insoluble in water, but soluble in organic solvents.

Covalent Bond A strong chemical bond formed by the sharing of electrons between atoms.

Macromolecule A very large molecule usually consisting of repeating subunits.

Dehydration Synthesis A chemical reaction that joins two molecules to form a larger molecule by removing water.

Nucleic Acid A macromolecule consisting of chains of nucleotide subunits to form either DNA or RNA, the two types of nucleic acid.

Shells

Proton Neutron

Nucleus

Electrons travel primarily in this volume of space around the nucleus.

FIGURE 2.1 Atom The proton has a positive charge, the neutron has a neutral charge, and the electron has a negative charge. The electrons that orbit the nucleus are arranged in shells of different energy levels.

19

Organic Compound A chemical in which a carbon atom is covalently bonded to a hydrogen atom.

Inorganic Compound A chemical that has no carbon-hydrogen bonds.

Electron

Atoms and Elements

pH The abbreviation for potential hydrogen, a measure on a scale of 0 to 14 of the acidity of a solution. Protein A macromolecule consisting of one or more chains of amino acids.

the atom, the nucleus. The very light electrons orbit the nucleus. The number of protons normally equals the number of electrons, and so the atom as a whole has no charge. The relative sizes and motion of the parts of an atom can be illustrated by the following analogy. If a single atom were enlarged to the size of a football stadium, the nucleus would be the size of a marble and it would be positioned somewhere above the 50-yard line. The electrons would resemble fruit flies zipping around the stands. Their orbits would be mostly inside the stadium, but on occasion they would travel outside it. An element is a substance that consists of a single type of atom. Although 92 naturally occurring elements exist, four elements make up over 99% of all living material by weight. These are carbon (abbreviated C), hydrogen (H), oxygen (O), and nitrogen (N). Two other elements, phosphorus (P), and sulfur (S), together make up an additional 0.5% of the elements in living systems (table 2.1). All of the remaining elements together account for less than 0.5% of living material. In general, the basic chemical composition of all living cells is remarkably similar. Each element is identified by two numbers: its atomic number and its atomic weight or mass. The atomic number is the number of protons, which equals the number of electrons. For example, hydrogen has 1 proton, and thus its atomic number is 1; oxygen

TABLE 2.1 Atomic Structure of Elements Commonly Found in the Living World Element

Symbol

Atomic Number (Total Number of Protons)

Atomic Weight (Protons + Neutrons)

Number of Possible Covalent Bonds*

Approximate % of Atoms in Cells

Hydrogen

H

1

1

1

49

Carbon

C

6

12

4

25

Nitrogen

N

7

14

3

Oxygen

O

8

16

2

Phosphorus

P

15

31

3

0.1

Sulfur

S

16

32

2

0.4

0.5 25

*The number of electrons required to fill the outer shell equals the number of possible covalent bonds—its valence. The number of electrons in a completed outer shell varies depending on the distance of the shell from the nucleus.

nes95432_Ch02_018-039.indd 19

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20

CHAPTER TWO The Molecules of Life

has 8 protons, and its atomic number is 8. The atomic weight is the sum of the number of protons and neutrons (electrons are too light to contribute to the weight). The atomic weight of hydrogen is 1, which is abbreviated 1H, reflecting 1 proton and no neutrons. It is the lightest element known. The atomic weight of oxygen is 16, consisting of 8 protons and 8 neutrons, and is abbreviated 16O. Electrons are arranged in shells of differing energy levels. The electrons farthest from the nucleus with its positive charge travel the fastest and have the highest energy level. Electrons can move from one shell to another as they gain or lose energy (see figure 2.1). Each shell can contain only a certain number of electrons with the first shell (closest to the nucleus) containing a maximum of 2 electrons, the next 8, and the next also 8. Other atoms, which have little biological importance, have additional electrons. Each shell must be filled, starting with the one closest to the nucleus, before electrons can occupy the next outer shell.

MICROCHECK 2.1 All living organisms contain the same elements. The four most important are carbon, hydrogen, oxygen, and nitrogen. The basic unit of all matter, the atom, is composed of protons, electrons, and neutrons. ✓ Of all the elements found in cells, which element is found most frequently? ✓ Why is the energy level of an electron higher the farther it is from the nucleus?

2.2 Chemical Bonds and the Formation of Molecules

covalent bonds, and hydrogen bonds are weaker still. Even relatively weak bonds are important in biological systems, however, because they allow molecules to recognize one another. This recognition depends on large numbers of atoms on the surfaces of molecules matching each other precisely. In addition, large numbers of bonds can hold molecules tightly together. An analogy would be the hook and loop fasteners of VelcroTM. A single hook and loop attachment does not provide much strength, but many such attachments result in a strong connection. Like hook and loop attachments, weak bonds can be formed and broken quickly and easily, allowing the molecules to separate.

Ionic Bonds Ionic bonds join charged atoms termed ions (figure 2.2). As already mentioned, an atom can fill its outer shell by gaining, losing, or sharing electrons. If electrons from one atom are attracted very strongly by another nearby atom, the electrons completely leave the first atom and become a part of the outer electron shell of the second, without any sharing. The loss or gain of electrons leads to an electrically charged atom. An atom that gains electrons becomes negatively charged, whereas an atom that gives up electrons becomes positively charged. The type and amount of charge, which is the difference between the

A

Focus Points

Loss of electron

B

from A

Name the strongest bond and two weak bonds. Explain the difference between polar and non-polar covalent bonds and explain why polar bonds are important in biology. Describe the properties of the carbon atom that make it the most important atom in all organisms.

For an atom to be stable, its outer shell must contain the maximum number of electrons. Most atoms do not have that number, however, and therefore to achieve it they tend to gain, lose, or share electrons with other atoms. This is the basis for chemical bonds. When two or more atoms are joined by chemical bonds, the substance is called a molecule. The atoms that make up a molecule may be of the same or different elements. For example, H2 is a molecule of hydrogen gas formed from two atoms of hydrogen; water (H2O) is an association of two hydrogen atoms with one oxygen atom. Water is a compound, a molecule that consists of two or more different elements. Three general types of chemical bonds join atoms—ionic, covalent, and hydrogen. Covalent bonds are generally the strongest of the three. Ionic bonds are typically weaker than

nes95432_Ch02_018-039.indd 20

Gain of electron by B

Ionic bond A

B

Positively charged ion—A+

Negatively charged ion—B-

FIGURE 2.2 Ionic Bond Atom A gives up an electron to atom B; hence, atom A acquires a positive charge and atom B a negative charge. Both atoms then have their outer shells filled with the maximum number of electrons leading to maximum stability. The attraction of the positively charged A; ion to the negatively charged B: ion forms the bond.

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2.2 Chemical Bonds and the Formation of Molecules

number of protons and electrons in the ion, is indicated by a superscript number. If only a ⫹ or ⫺ is indicated, then the charge is 1. For example, Na⫹ indicates a Na ion with one positive charge. Positively charged ions are called cations; negatively charged ones are anions. The attraction of a cation to an anion forms the ionic bond. In water (aqueous solutions), ionic bonds are about 100 times weaker than strong covalent bonds because water molecules tend to move between the ions, thereby greatly reducing their attraction to one another. Thus, in aqueous solution, which is common in all biological systems, weak ionic bonds are readily broken at room temperature.

Carbon needs four more electrons to fill its outer shell. H

H

Outer shell

C

Nucleus

Each hydrogen atom requires another electron to fill its outer shell.

H

H

Four hydrogen atoms bond with one carbon atom to form one methane molecule.

21

Covalent Bonds Atoms often achieve stability by sharing electrons with other atoms, thereby filling their outer shells. This sharing creates strong covalent bonds. The number of covalent bonds an atom can form—its valence—is the number of electrons the atom must gain or lose to fill its outer shell (see table 2.1). Carbon (C), the most important single atom in biology, is frequently involved in covalent bonding. This element has four electrons but requires a total of eight to fill its outer shell. Thus, its valence is 4. A hydrogen (H) atom has one electron and requires an additional one to fill its outer shell. Accordingly, the C atom can fill its outer shell by sharing electrons with four H atoms, creating methane (CH4) (figure 2.3; see also table 2.1). Because a C atom can bond with four other atoms, it can build up a large number of different molecules, which explains why it is the key atom in all cells. When C forms covalent bonds with H atoms, an organic compound is formed. Inorganic compounds do not contain C to H bonds. A single covalent bond is designated by a dash between the two atoms sharing the electrons and is written as C—H. Sometimes two pairs of electrons are shared between atoms in order to fill their outer shells. This forms a double covalent bond indicated by two lines between the atoms—for example OKCKO (CO2). Covalent bonds are strong. The stronger the bond, the more difficult it is to break. Consequently, covalent bonds do not break unless exposed to strong chemicals or large amounts of energy, generally as heat. Molecules formed by covalent bonds do not break apart spontaneously at temperatures compatible with life. Because most biological systems cannot tolerate the high temperatures required to break these bonds, cells utilize protein catalysts called enzymes, which can break covalent bonds at the temperatures found in living systems. Enzymes and their functions are covered in chapter 6. ■ enzymes, pp. 129, 134

Non-Polar and Polar Covalent Bonds Two atoms connected by a covalent bond may have the same or different attractions for the electrons. In covalent bonds between identical atoms, such as H—H, the electrons are shared equally. Equal sharing also occurs between different atoms, such as C—H, if both have a similar attraction for electrons (table 2.2).

H

H

C

H

H

TABLE 2.2 Non-Polar and Polar Covalent Bonds Type of Covalent Bond

Atoms Involved and Charge Distribution

Non-polar

CJC CJH

Methane

C and H have equal attractions for electrons, so there is an equivalent charge on each atom.

HJH Polar

FIGURE 2.3 Covalent Bonds The carbon atom fills its outer electron shell by sharing a total of 8 electrons. Four belong to the four H atoms and four belong to the one carbon atom. The outer shells of each of these atoms are then filled—2 in the case of the H atom and 8 in the case of the C atom.

nes95432_Ch02_018-039.indd 21

OJH NJH OJC NJC

The O and N atoms have a stronger attraction for electrons than do C and H, so the O and N have a slight negative charge; the C and H have a slight positive charge.

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22

CHAPTER TWO The Molecules of Life

do the hydrogen atoms (figure 2.4). Consequently, the oxygen atom has a slight negative charge and the two hydrogen atoms, a slight positive charge. Polar covalent bonds play a key role in biological systems because they result in the formation of hydrogen bonds.

H

Hydrogen Bonds O

H

+

Hydrogen part of the water molecule has a slightly positive charge.

H

H

O

+

– Oxygen part of the water molecule has a slightly negative charge.

FIGURE 2.4 Formation of Polar Covalent Bonds in a Water Molecule In a water molecule the oxygen atom has a greater attraction for the shared electrons than do the hydrogen atoms. Hence, the electron is closer to the oxygen and confers a slight negative charge on a portion of this atom. Each of the hydrogen atoms has a slight positive charge on a portion of the atom. Because of these charges, water is a polar molecule.

This results in a non-polar covalent bond. If, however, one atom has a much greater attraction for electrons than the other, the electrons are shared unequally, and polar covalent bonds result. One part of the molecule has a slight positive charge and another, a slight negative charge. An example is water, in which the oxygen atom attracts the shared electrons more strongly than

Hydrogen bonds are weak bonds formed when a positively charged hydrogen atom in a polar molecule is attracted to a negatively charged atom, frequently oxygen (O) or nitrogen (N) in another polar molecule (figure 2.5; see also table 2.2). Such bonds can form between atoms in the same molecule or between two different molecules. Molecules that contain nitrogen or oxygen atoms bonded to hydrogen atoms are common in biological systems, thereby creating the possibility for many hydrogen bonds. Like other weak bonds, these are important in recognizing matching surfaces and holding molecules on these surfaces together (figure 2.6). For example, in order for an enzyme to break covalent bonds of a compound (the substrate), the enzyme binds to the substrate through many weak non-covalent bonds. Hydrogen bonds between water molecules are constantly being formed and broken at room temperature because the energy produced by the movement of water is enough to break these bonds. The average lifetime of a single hydrogen bond is only a fraction of a second at room temperature, so enzymes are not needed to form or break these bonds. Although a single hydrogen bond is too weak to keep molecules together, a large number can hold them together firmly. A good example is the double-stranded DNA molecule. The two strands are held together by many hydrogen bonds up and down the length of the molecule. The two strands will come apart only if energy is supplied, usually in the form of heat approaching temperatures of 100∞C.

Molarity A chemical reaction can be likened to a recipe you follow in the kitchen—it uses relative quantities of different substances. But while chefs work with measures such as a dozen, chemists work with moles; one mole is 6.022  1023 molecules. That number is not important from a practical standpoint, but the concept is essential in chemistry—a mole of one compound has the same number of molecules as a mole of any other. A more practical definition of a mole is that it is the amount (in grams) equal to the sum of the atomic weights of the atoms that make up the molecule. That sum is the molecular weight of the Hydrogen bond

FIGURE 2.5 Hydrogen Bond Formation The N atom has a greater attraction for electrons than the H atom, thereby conferring a slight positive charge on the H atom. The O atom has a greater attraction for electrons than the H atom to which it is covalently bonded, thereby gaining a slight negative charge. The bonds between NJH and OJH are polar covalent bonds. The positively charged H atom weakly bonds to the negatively charged O atom, thereby forming a hydrogen bond.

nes95432_Ch02_018-039.indd 22

N

H

O

H

–

+

–

+

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2.3 Chemical Components of the Cell

Water

Substrate

–

– –

+ –

+

–

+ +

– + –

+ –

–

23

+

+ +

– +

Enzyme

–

+

FIGURE 2.6 Weak Ionic Bonds and Molecular Recognition Weak bonds, such as ionic and hydrogen bonds, are important for molecules to recognize each other. Many weak bonds are required to hold the two molecules together, in this case, the substrate binding to an enzyme.

Unquestionably, water is the most important molecule in the world. It makes up over 70% of all living organisms by weight. The importance of water in large part depends on its unusual properties.

Bonding Properties of Water Hydrogen bonding plays a very important role in giving water the properties required for life (figure 2.7a). Since water is a polar molecule, the positive H portion of the molecule is attracted to the negative O portion of other water molecules, thereby creating hydrogen bonds. The extent of hydrogen bonding between water molecules depends on the temperature. At room temperature, the weak bonds continually form and break. As the temperature is lowered, the breakage and formation decreases, and in ice, a crystalline structure forms. Each water molecule bonds to four other molecules to create a rigid lattice structure (figure 2.7b). When ice melts, the water molecules move closer together. Consequently, liquid water is denser than ice, which explains

compound. Sodium chloride (NaCl), for example, has a molecular weight of 58.4, meaning that 58.4 grams of NaCl has approximately 6.022  1023 molecules. The molarity of a solution is defined as the number of moles of a compound dissolved in water to make 1 liter of solution. Therefore, a 1-molar solution of NaCl has 58.4 grams of that chemical dissolved in 1 liter of solution. Note that a 1-molar solution of two different compounds will contain different numbers of grams but the same number of molecules.

(a) Liquid water Hydrogen

Oxygen

+

+ –

MICROCHECK 2.2

–

+ –

+

+ –

+ +

–

+

+

Hydrogen bond

Molecules are formed by bonding between atoms. Bonds are formed when electrons from one atom interact with another atom. The bonds between the atoms that make up a molecule are strong covalent bonds; bonds between molecules are generally weak bonds such as ionic and hydrogen bonds. ✓ Compare the relative strengths of covalent, hydrogen, and ionic bonds. ✓ Which type of bond requires an enzyme to break it? ✓ Why does an atom that gives up electrons become positively charged? What causes the positive charge?

+

+

– +

–

+

+

– +

+

+

(b) Ice –

+

–

–

+

2.3 Chemical Components of the Cell

–

+

+

–

+

–

+

+

+

+

+

–

+

–

+

– +

+

+

+ –

–

+

–

+

–

+

+

+

Focus Points

+

–

+

+

Describe the bonding properties of a water molecule and explain why they are important in biology.

+

+

–

+

–

–

+

+

+

+

Define pH, and state what the pH numbers tell you about the acidity of a solution.

–

+

+

+

+

+

– +

Name the four macromolecules found in all cells.

The most important molecule in the cell is water and the life of all organisms depends on its special properties.

nes95432_Ch02_018-039.indd 23

FIGURE 2.7 Water (a) In liquid water, each H2O molecule hydrogen bonds to one or more H2O molecules. These bonds continuously break and re-form. (b) In ice, each H2O molecule hydrogen bonds to four other H2O molecules, forming a rigid crystalline structure. The bonds do not break continuously.

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CHAPTER TWO The Molecules of Life

pH An important property of every aqueous solution is how acidic it is. This property is measured as the pH of the solution (an abbreviation for potential Hydrogen), defined as the concentration of H; in moles per liter. pH is measured on a logarithmic scale of 0 to 14 in which the lower the number, the more acidic the solution. Water has a slight tendency to split (ionize) into hydrogen ions H; (protons), which are acidic, and OH: ions (hydroxyl), which are basic or alkaline. In pure water, the number of H; and OH: ions is equal, and the concentration of each is 10:7 molar

+ + + + –+ + + + – – + – –+ + – – + + + – – – + + + + – +– + + + + – + + – –+ + + + –+ + + – + + + – + + – + + –+ + – – + – + –+ + + –+ + – + – + – + + – + + + + + – + + – + – + + + – – + + – + + + + + – –+ – + + + + –+ – + – + + + –+ + – – + – + + + –+ + + + – –+ – + – + – – – + – + – + + + + + + + + – – +– + + + –+ – + + + + –+ + +– + – – + + + – + – + + – + + + – – + + +–+ + + – – – + +– + + –+ + – + + + – + + + + + – + + + + – + – + –+ – + + –+ + – + + –+ – + +– + + – – + + – + +– + + + – + + + +– + + +– +– + –+ + –+ – + – + – – – + + + + + + + + –+ + – + – + + + – + + + + – –+ –+ + + – + –+ – + + + + –++ – + + + – + + +– –+ + + – – + – + + – + + + – – + + + + –+ –+ + + +–

(10:7 M). The product of the concentration of H; and OH: must always be 10:14 M (10:7!10:7). (Exponents are added when numbers are multiplied.) Thus, if H; ions are added to an aqueous solution such that the concentration of H; increases tenfold to 10:6 M, then the concentration of OH: must decrease by a factor of 10 (to 10:8 M). The pH scale ranges from 0 to 14 because the concentrations of H; and OH: ions vary within these limits (figure 2.9). When the concentrations of H; and OH: are equal, the pH of the solution is 7 and is neutral. However, for every unit on the log scale, the concentration of H; ions changes by a factor of 10. Most bacteria can live within only a narrow pH range, near neutrality (neutrophiles). Some, however, can live under very acidic conditions (acidophiles) and a few under alkaline conditions (alkalophiles). ■ acidophiles, p. 93 ■ alkalophiles, p. 93

Compounds called buffers stabilize the pH of solutions. These are sometimes added to bacterial growth media because bacteria often produce acids and, less commonly, bases when they degrade compounds to harvest energy. Buffers prevent drastic shifts in pH, which would be deleterious to growth. A common buffer is a mixture of two salts of phosphoric acid, Na2HPO4 and NaH2PO4. These salts can combine chemically with the H; ions of acids and the OH: of bases to produce neutral compounds, thereby maintaining the pH of the solution near neutrality. pH 100 [OH:] & 10:14 [H+]

14

1 M NaOH Drain cleaner

13 MORE BASIC (higher pH)

why ice floats. This explains how fish can live in apparently frozen bodies of water. They actually live in the water, which remains liquid below the ice. The polar nature of water also accounts for its ability to dissolve a large number of compounds. Water has been referred to as the universal solvent of life because it dissolves so many compounds. To dissolve in water, compounds must consist of atoms with positive or negative charges. In water, they ionize or split into their component charged atoms. For example, NaCl dissolves in water to form Na; and Cl: ions. In solution, these ions tend to be surrounded by water molecules. The OH: of HOH forms weak bonds with Na;, whereas the H; forms weak bonds with Cl: (figure 2.8). The Na; and the Cl: cannot associate, and this accounts for the solubility of NaCl in water. Water containing dissolved substances freezes at a lower temperature than pure water and so in nature, most water does not freeze unless the temperature drops below 0°C. Consequently, microorganisms can usually multiply in liquids below 0°C, because the water remains liquid.

+

10:7 [OH:] & 10:7 [H+]

10:10 [OH:] & 10:4 [H+]

MORE ACIDIC (lower pH)

24

12

Lye

Household ammonia

11 Milk of magnesia 10 Detergent solution 9

8

Seawater

7

Blood NEUTRAL

6

Milk Urine Unpolluted rainwater

5

Black coffee Beer

4 Vinegar 3

Cola Lemon juice

–

— Cl-

+

2

— Na+

Stomach acid 1

FIGURE 2.8 Salt (NaCl) Dissolving in Water In water, the Na; and Cl: are separated by H2O molecules. The Na; hydrogen bonds to the slightly negatively charged O: and the Cl: hydrogen bonds to the slightly positively charged H; portion of the water molecules. In the absence of water, the salt is highly structured because of ionic bond formation between Na; and Cl: ions.

nes95432_Ch02_018-039.indd 24

10:14 [OH:] & 100 [H+]

0

Battery acid

FIGURE 2.9 pH Scale The concentration of H+ ions varies by a factor of 10 between each pH number since the scale is logarithmic.

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2.4 Proteins and Their Functions

Small Molecules in the Cell

25

(a) Dehydration Synthesis

All cells contain a variety of small organic and inorganic molecules, many of which occur in the form of ions. About 1% of the weight of a bacterial cell, once the water is removed (dry weight), is composed of inorganic ions, principally Na; (sodium), K; (potassium), Mg2; (magnesium), Ca2; (calcium), Fe2; (iron), Cl: (chloride), PO43: (phosphate), and SO42: (sulfate). Certain enzymes require positively charged ions in minute amounts to function. The organic small molecules include the building blocks of large molecules, the macromolecules, which will be considered in the next section. The building blocks include amino acids, purines and pyrimidines, and various sugars. An especially important small organic molecule is adenosine triphosphate (ATP), the storage form of energy in the cell. The molecule is composed of the sugar ribose, the purine adenine, and three phosphate groups, arranged in tandem (figure 2.10). This is an energy-rich molecule because two of the bonds which join the three phosphate molecules are readily broken with the release of energy. The breakage of the terminal high-energy bond of ATP results in the formation of adenosine diphosphate (ADP), inorganic phosphate, and the release of energy. The role of ATP in energy metabolism is covered more fully in chapter 6.

Macromolecules and Their Component Parts Macromolecules are very large molecules (macro means “large”). The four major classes of biologically important macromolecules are proteins, polysaccharides, nucleic acids, and lipids. These four groups differ from each other in their chemical structure. However, other aspects of their structure, as well as how they are synthesized, have features in common. Most macromolecules are polymers (poly means “many”), large molecules formed by joining together small molecules, the subunits. Each different class of macromolecules is composed of different subunits, each with a different structure. The synthesis of macromolecules involves subunits being joined, one by one, generally forming a chain. This involves chemical reactions in which H2O is removed, termed dehydration synthesis (figure 2.11a). The reverse reactions, breaking a macromolecule down to its subunits, use H2O and are called hydrolytic reactions or hydrolysis (figure 2.11b). Both reactions require specific enzymes.

H OH Short polymer

H Subunit (monomer) H2O

HO

H Longer polymer H2O

(b) Hydrolysis (hydrolytic reaction)

HO

H OH Short polymer

H Subunit (monomer)

FIGURE 2.11 The Synthesis and Breakdown of Polymers (a) Subunits are joined (polymerized) by removal of water, a dehydration reaction. (b) In the reverse reaction, hydrolysis, the addition of water breaks bonds between the subunits. These reactions take place in the formation of many different polymers (macromolecules).

MICROCHECK 2.3 The weak polar bonds of water molecules are responsible for the many properties of water required for life. The degree of acidity of an aqueous solution is expressed as pH. Macromolecules consist of many repeating subunits, each subunit being similar or identical to the other subunits. ✓ Why is water a polar molecule? Give three examples of why this property is important in microbiology. ✓ Name the four important classes of large molecules in cells. ✓ In pure water, what must be done to decrease the OHconcentration? To decrease the H+ concentration?

2.4 Proteins and Their Functions Focus Points Name the subunits of proteins and the bonds that join them.

Adenosine

Name the four levels of protein structure and what distinguishes each level.

NH2 Phosphate groups

HO

N N

O O-

P O-

O

~

O

P

O

~

O

O-

High-energy bonds

P O-

O

N

CH2

N Adenine

O

OH OH Ribose

FIGURE 2.10 ATP Adenosine triphosphate (ATP) serves as the energy currency of a cell. The bonds are high energy because of the tandem arrangement of the negatively charged phosphate groups.

nes95432_Ch02_018-039.indd 25

Proteins constitute more than 50% of the dry weight of cells and a typical bacterial cell contains 600 to 800 different kinds of proteins at any one time. Of all the cellular macromolecules, they are the most versatile. In the microbial world, proteins are responsible for: Catalyzing all enzymatic reactions of the cell.

■ enzymes,

pp. 129, 134

The structure and shape of certain structures such as ribosomes, the protein-building machinery. ■ ribosomes, p. 68 Cell movement by flagella. ■ flagella, p. 65

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26

CHAPTER TWO The Molecules of Life

PERSPECTIVE 2.1 Isotopes: Valuable Tools for the Study of Biological Systems One important tool in the analysis of living cells is the use of isotopes, variant forms of the same element that have different atomic weights. The nuclei of certain elements can have greater or fewer neutrons than usual and thereby be heavier or lighter than is typical. For example, the most common form of the hydrogen atom contains one proton and zero neutrons and has an atomic weight of 1 (1H). Another form, however, also exists in nature in very low amounts. This isotope, 2H (deuterium), contains one neutron. A third, even heavier isotope, 3H (tritium), is not found in nature but can be made by a nuclear reaction in which stable atoms are bombarded with high-energy particles. This latter isotope is unstable and gives off radiation (decays) in the form of rays or electrons, which can be very sensitively measured by a radioactivity counter. Once the atom has finished disintegrating, it no longer gives off radiation and is stable. The other properties of isotopes are very similar to their non-radioactive counterparts. For example, tritium combines with oxygen to form water and with carbon to form hydrocarbons, and both molecules have biological properties similar to those of their non-radioactive counterparts. The only difference is that the molecules containing tritium can be detected by the radiation they emit.

Isotopes are used in numerous ways in biological research. They are frequently added to growing cells in order to label particular molecules, thereby making them detectable. For example, tritiated thymidine (a component of DNA) added to growing bacteria will specifically label DNA and no other molecules. Tritiated uridine, a component of RNA, will label RNA. Isotopes

(a)

(b)

FIGURE 1 Radioactive Isotopes (a) Physicians use scintillation counters such as this to detect radioactive isotopes. (b) A scan of the thyroid gland 24 hours after the patient received radioactive iodine.

Taking nutrients into the cell. ■ transport proteins, p. 58 Turning genes on and off. ■ gene regulation, p. 176 Determining certain properties of various membranes in the cell. ■ cytoplasmic membrane, p. 55 ■ outer membrane, p. 61

Amino Acid Subunits Proteins are unbranched macromolecules composed of numerous combinations of 20 major amino acids. The properties of a protein depend mainly on its shape, which in turn depends on the arrangement of the amino acids that make up the protein. All amino acids have at one end a carbon atom to which a carboxyl group and an amino group are bonded (figure 2.12). This carbon atom also is bonded to a side chain or backbone (labeled R), which gives each amino acid its characteristic properties. In solution at pH 7, both the amino and carboxyl groups are ionized. The JNH2 group becomes JNH3; and the JCOOH

FIGURE 2.12 Generalized Amino Acid This figure illustrates the three groups that all amino acids possess. The R side chain differs with each amino acid and determines the properties of the amino acid.

nes95432_Ch02_018-039.indd 26

H

H

H

O

N

C

C

Amino group

are also used in medical diagnosis. For example, to evaluate proper functioning of the human thyroid gland, which produces the iodine-containing hormone thyroxin, doctors often administer radioactive iodine and then scan the gland later to locate the gland and determine if the amount and distribution of the iodine in the gland is normal (figure 1).

R Side chain

OH

Carboxyl group

group becomes JCOO:, with the overall charge being zero. The amino acids are subdivided into several different groups based on properties of their side chains (figure 2.13). The types and positions of the various side chains in the amino acids that make up a protein govern the solubility of that protein, its shape, and how it interacts with other proteins inside the cell. Amino acids that contain many methyl (CH3) groups are non-polar and therefore do not interact with water molecules. Thus, they are poorly soluble in water and are termed hydrophobic (“water-fearing”). These amino acids tend to be on the inside of protein molecules away from water molecules. Other amino acids contain polar side chains, which make them more soluble in water. They are termed hydrophilic (“water-loving”) and usually occur on the surface of protein molecules. All amino acids except glycine can exist in two stereoisomeric forms, a D (right-handed) or L (left-handed) form. Each is a mirror image or stereoisomer of the other (figure 2.14; see A Glimpse of History). Only l-amino acids occur in proteins, and accordingly, they are designated the natural amino acids. d-amino acids are rare in nature but are found in a few compounds mostly associated with bacteria. They are found primarily in the cell walls and in certain antibiotics, antimicrobial medications that many bacteria produce. The bacterium Bacillus anthracis, which causes the disease anthrax and has been used as an agent of bioterrorism in the United States, has an outer coat of d-glutamic acid.

7/17/08 1:43:14 PM

2.4 Proteins and Their Functions

Glycine (gly)

H

H

H

O

N

C

C

L-Alanine (ala)

OH

H

H

H

O

N

C

C

L-Valine (val)

OH

H

H

H

O

N

C

C

CH 3

H

L-Leucine (leu)

OH

H

H

H

O

N

C

C

CH

27

L-Isoleucine (ile)

OH

H

H

H

O

N

C

C

CH 2

H 3C

CH 3

CH CH 2

CH H 3C

OH

CH 3

H 3C

CH 3

Hydrophobic amino acids

L-Serine (ser)

H

H

H

O

N

C

C

L-Threonine (thr)

OH

H

CH 2

H

H

O

N

C

C

H

C

CH 3

OH

L-Tyrosine (tyr)

OH

H

H

H

O

N

C

C

L-Phenylalanine (phe)

OH

H

H

H

O

N

C

C

CH 2

L-Tryptophan (trp)

OH

H

H

H

O

N

C

C

CH 2

OH

CH 2 C

OH

CH NH

Alcoholic amino acids (hydrophilic)

L-Aspartic acid (asp)

H

H

H

O

N

C

C

OH

L-Glutamic acid (glu)

H

H

H

O

N

C

C

OH

(hydrophobic)

(hydrophilic)

Aromatic amino acids

L-Lysine (lys)

OH

H

H

H

O

N

C

C

L-Arginine (arg)

OH

H

O

N

C

C

CH 2

CH 2

CH 2

C

CH 2

CH 2

CH 2

C

CH 2

NH CH 2

O -O

O

H 3N +

H 3N +

CH 2

Acidic amino acids (hydrophilic)

L- Asparagine (asn)

H

H

H

CH 2

-O

H

H

O

N

C

C

H

H

H

O

N

C

C

CH 2 C

NH 2

O

L- Cysteine (cys)

H

H

O

N

C

C

OH

CH 2 C HC

N +H N

CH H

OH

H

H

H

O

N

C

C

L- Methionine (met)

OH

H

H

H

O

N

C

C

CH 2

CH 2

CH 2

SH

CH 2

O

OH

H

NH

CH 2

C

Amides (hydrophilic)

C

L-Histidine (his)

Basic amino acids (hydrophilic)

L- Glutamine (gln)

OH

(hydrophobic)

NH 2

S

Sulfur containing amino acids

L- Proline (pro)

OH

H

H

O

N

C

C

CH 2

OH

CH 2 CH 2

CH 3

Imino amino acid

FIGURE 2.13 Common Amino Acids All amino acids have one feature in common—a carboxyl group and an amino group bonded to the same carbon atom. This carbon atom is also bonded to a side chain (shaded). In solution, the JCOOH group is ionized to JCOO$ and the JNH2 group to JNH3 giving a net charge of zero to the amino acid. The basic and acidic amino acids have a net positive or negative charge, respectively. The three-letter code name for each amino acid is given.

nes95432_Ch02_018-039.indd 27

7/17/08 1:43:15 PM

28

CHAPTER TWO The Molecules of Life

other has a free carboxyl (JCOOH) group, the C terminal, or carboxyl terminal, end. Some proteins consist of a single polypeptide chain, whereas others consist of one or more chains joined together by weak bonds. Sometimes, the chains are identical; in other cases, they are different. In proteins that consist of several chains, the individual polypeptide chains generally do not have biological activity by themselves. Proteins vary greatly in size, but an average-size protein consists of a single polypeptide chain of about 400 amino acids.

Mirror

Mirror image of left hand Left hand

■ protein synthesis, p. 170

Protein Structure

L-Amino acid

D-Amino acid

FIGURE 2.14 Mirror Images (Stereoisomers) of an Amino Acid The joining of a carbon atom to four different groups leads to asymmetry in the molecule. The molecule can exist in either the L - or D - form, each being the mirror image of the other. There is no way that the two molecules can be rotated in space to give two identical molecules.

Peptide Bonds and Their Synthesis Proteins are made up of amino acids held together by peptide bonds, a unique type of covalent linkage formed when the carboxyl group of one amino acid reacts with the amino group of another, with the release of water (dehydration synthesis) (figure 2.15). A chain of amino acids joined by peptide bonds is called a polypeptide chain. A protein molecule is a long polypeptide chain. One end of the chain has a free amino (JNH 2) group, termed the N terminal, or amino terminal, end; the

H 2N

H

O

C

C

OH + H

R1

H

O

N

C

C

OH

R2

H 2O

H 2N

H

H 2O

H

O

H

H

O

C

C

N

C

C

R1

Peptide bond

OH

R2

FIGURE 2.15 Peptide Bond Formation by Dehydration Synthesis

nes95432_Ch02_018-039.indd 28

Proteins have four levels of structure: primary, secondary, tertiary, and quaternary. The number and arrangement or sequence of amino acids in the polypeptide chain determines its primary structure (figure 2.16a). The primary structure in large part determines the other features of the protein. Parts of the polypeptide chain can form helixes, or folds. This is the protein’s secondary structure (figure 2.16b). A helical structure is termed an alpha (a) helix and a pleated structure is called a beta (b) sheet (figure 2.16b). These structures result from the amino acids forming weak bonds, such as hydrogen bonds, with other amino acids. This explains why certain sequences of amino acids lead to distinctive secondary structures in various parts of the molecule. The entire protein next folds into its distinctive three-dimensional shape, its tertiary structure (figure 2.16c). Two major shapes exist: globular, which tends to be spherical; and fibrous, which has an elongated structure (figure 2.16c). The shape is determined in large part by the sequence of amino acids and whether or not they interact with water. Hydrophilic amino acids are located on the outside of the protein molecule, where they can interact with charged polar water molecules. Hydrophobic amino acids are pushed together and cluster inside the molecule to avoid water molecules. The non-polar amino acids form weak interactions with each other, termed hydrophobic interactions. In addition to these weak bonds, some amino acids can form strong covalent bonds with other amino acids. One example is the formation of bonds between sulfur atoms (SJS bonds) in different cysteine molecules. The combination of strong and weak bonds between the various amino acids results in the proteins’ tertiary structure. Proteins often consist of more than one polypeptide chain, either identical or different, held together by many weak bonds. The specific shape is termed the quaternary structure of the protein (figure 2.16d). Of course, only proteins that consist of more than one polypeptide chain have a quaternary structure. Sometimes different proteins, each having different functions, associate with one another to make even larger structures termed multiprotein complexes. For example, sometimes enzymes involved in the pathway of synthesis of the same amino acid are joined in a multi-enzyme complex. On occasion, enzymes involved in the degradation of a particular compound form a multi-enzyme complex.

7/17/08 1:43:15 PM

2.4 Proteins and Their Functions

29

(a) Primary structure Peptide (covalent) bonds

Amino acids

Amino terminal end

O

Carboxyl terminal end

H2N

C

OH

Direction of chain growth (b) Secondary structure Hydrogen bond

Amino acids

Amino acids

Hydrogen bond

a chains

Helical structure (a-helix)

Pleated structure (b-sheet)

(c) Tertiary structure Pleated sheet Helix

b chains Globular protein

Fibrous protein

(d) Quaternary structure

FIGURE 2.16 Protein Structures (a) The primary structure is determined by the amino acid composition. (b) The secondary structure results from folding of the various parts of the protein into two major patterns—helices and sheets. (c) The tertiary structure is the overall shape of the molecule, globular and fibrous. (d) Quaternary structure results from several polypeptide chains interacting to form the protein. This protein is hemoglobin and consists of two pairs of identical chains, a and b.

Proteins form extremely rapidly. Within seconds, cellular processes join amino acids together to yield a polypeptide chain. How this occurs will be discussed in chapter 7. The polypeptide chain then folds into its correct shape. Although many shapes are possible, only one is functional. Most proteins fold spontaneously into their most stable state correctly. To help certain proteins assume their proper shape, however, cells have proteins called chaperones that aid proteins to fold correctly. Incorrectly folded proteins are degraded into their amino acid subunits, which are then used to make more proteins.

Heated to 100°C

Protein Denaturation A protein must have its proper shape to function. When a protein encounters different conditions such as high temperature, high or low pH, or certain solvents, bonds within the protein are broken and its shape changes (figure 2.17). The protein becomes denatured and no longer functions. This explains why most bacteria cannot grow at very high temperatures. Denaturation may be

nes95432_Ch02_018-039.indd 29

Active protein properly folded

Inactive denatured protein

FIGURE 2.17 Denaturation of a Protein

7/17/08 1:43:16 PM

30

CHAPTER TWO The Molecules of Life

subunits. Oligosaccharides are short chains. The term sugar is often applied to both monosaccharides (mono means “one”), a single subunit, and disaccharides (di means “two”), which are two monosaccharides joined together by covalent bonds. Carbohydrates also usually contain an aldehyde group O

K

reversible in some cases; in other cases, it is irreversible. For example, boiling an egg denatures the egg white protein, an irreversible process since cooling the egg does not restore the protein to its original appearance. If the denaturating agent is a chemical and is removed, the protein may refold spontaneously into its original shape.

JCJH

Substituted Proteins

MICROCHECK 2.4 The side chains of amino acids determine their properties. The sequence of amino acids in a protein determines how the protein folds into its three-dimensional shape. ✓ What type of bond joins amino acids to form proteins? ✓ Name two groups of amino acids that are hydrophilic. ✓ What elements must all amino acids contain? What elements will only some amino acids contain?

2.5 Carbohydrates Focus Points Distinguish among the various carbohydrates based on the number of their subunits. Name the most characteristic feature of carbohydrates in terms of their chemical composition.

and less commonly, a keto group O

K

The proteins that play important roles in certain structures of the cell often have other molecules covalently bonded to the side chains of amino acids and are called substituted proteins. The proteins are named after the molecules that are covalently joined to the amino acids. If sugar molecules are bonded, the protein is termed a glycoprotein; if lipids, the protein is termed a lipoprotein. Sugars and lipids are covered later in this chapter.

JCJ The JOH groups on sugars can be replaced by carboxyl, amino, acetyl, or other groups to form molecules important in the structures of the cell. For example, acetyl glucosamine is an important component of the cell wall of bacteria. ■ bacterial cell wall, p. 60

Monosaccharides Monosaccharides are classified by the number of carbon atoms they contain. The most common monosaccharides have 5- or 6-carbon atoms (table 2.3). The 5-carbon sugars, ribose and deoxyribose, are the sugars in nucleic acids (figure 2.18). Note that these monosaccharides are identical except that deoxyribose has one less molecule of oxygen than does ribose (de means “away from”). Thus, deoxyribose is ribose “away from” oxygen. Common 6-carbon sugars include glucose, galactose, and fructose. The carbon atoms are numbered, with carbon atom 1 being closest to the aldehyde or keto group. Sugars occur in two interconvertible forms: a linear and a ring form (figure 2.18). Both naturally occur in the cell, but most molecules are in the ring form. In diagrams, the lower portion of the ring form is thickened to suggest a three-dimensional structure. Sugars can exist in two different forms termed alpha (a) and beta (b) based on whether the —OH group on the carbon atom that carries the aldehyde or ketone is above or below the plane of the ring (figure 2.19). The a and b forms are interchangeable but once the carbon atom is joined to another sugar molecule, the a or b form is frozen.

Carbohydrates comprise a heterogeneous group of compounds of various sizes that play important roles in the life of all organisms: Carbohydrates are a common food source from which organisms can harvest energy and make cellular material. ■ metabolism, p. 126 Two sugars form a part of the nucleic acids, DNA and RNA.

H 1C

O

H

2

3

C

OH

C

OH

HOH 2C 5

■ nucleic acids, p. 32

Certain carbohydrates can be stored as a reserve source of nutrients in bacteria. ■ storage granules, p. 68 Sugars form a part of the bacterial cell wall. ■ cell wall structure, p. 59 All carbohydrates (which means a “hydrate of carbon”) contain carbon, hydrogen, and oxygen atoms in an approximate ratio of 1:2:1 respectively. This is because they contain a large number of alcohol groups (JOH) in which the C is also bonded to an H atom to form HJCJOH. Polysaccharides are high molecular weight compounds that are linear or branched polymers of their

nes95432_Ch02_018-039.indd 30

Deoxyribose

Ribose H

H H

4

5

C C

4C

OH

H

OH

O

OH

HOH 2C 5

OH

C3

H C1 C H 2

C3

H C1 C H

OH

OH

OH

H

H

4C

O

H

H

2

H (a)

(b)

FIGURE 2.18 Ribose and Deoxyribose with the Carbon Atoms Numbered (a) Ribose in linear and ring form. (b) Deoxyribose in ring form. Although both structures occur in the cell, the ring form predominates. The plane of the ring is perpendicular to the plane of the paper with the shaded line on the ring closest to the reader.

7/17/08 1:43:16 PM

2.5

Carbohydrates

31

TABLE 2.3 Common Monosaccharides, Disaccharides, and Polysaccharides Name of Sugar

Components

Comments

Monosaccharides (5-carbon) Ribose

Component of RNA

Deoxyribose

Component of DNA

(6-carbon) Glucose

Common subunit of disaccharides

Galactose

Component of milk sugar (see below)

Fructose

Fruit sugar

Mannose

Found on the surface of some microbes

Disaccharides Lactose

Glucose  galactose

Milk sugar

Maltose

Glucose  glucose

Breakdown product of starch

Sucrose

Glucose  fructose

Table sugar from sugar canes and beets

Agar

Polymer of galactose

Hardening agent in bacteriological media; extracted from the cell walls of some algae

Cellulose

Polymer of glucose, in a b 1, 4 linkage; no branching

Main structural polysaccharide in plant cell walls

Chitin

Polymer of N-acetyl-glucosamine

Major organic component in exoskeleton of insects and crustaceans

Dextran

Polymer of glucose in an a 1, 6 linkage; branching

Storage product in some bacterial cells

Glycogen

Polymer of glucose in an a 1, 4 linkage; branching

Main storage polysaccharide in animal and bacterial cells

Starch

Polymer of glucose

Main storage product in plants

Polysaccharides

Sugars also form structural isomers, molecules that contain the same number of the same elements but in different arrangements that are not mirror images. They are different sugars with different names. For example, common hexoses of biological importance include glucose, galactose, and mannose. They all contain the same atoms but differ in the arrangements of the JH and JOH groups relative to the carbon atoms. Glucose and galactose are identical except for the arrangement of the JH and JOH groups attached to carbon 4. Mannose and glucose differ in the arrangement of the JH and JOH groups joined to carbon 2 (figure 2.20). Structural isomers result in three distinct sugars with different properties and different names. For example, glucose has a sweet taste as does mannose, but mannose has a bitter aftertaste.

Glucose

Galactose

Mannose

Fructose

O

O

O

H

1C

H

2

HO

3

H

4

H

5

H

6

1C

H

C

OH

C

H

HO

C

OH

HO

C

OH

H

C

OH

H

H

2

3

4

5

6

H b form

HOH 2C 5 Ribose

O

4C H H C3

OH

6CH2OH 5

a form

OH H C1 C H 2

OH

HOH 2C 5

O

4C H H C3

OH

H H C1 C OH

H H 4 OH HO 3

H

H

C

OH

HO

C

H

HO

C

H

H

C

OH

H

C

OH

H

6CH2OH 5

O H 1

H 2

OH

OH

HO H 4 OH H 3

H

H

C

H

C

H

C

OH

H

C

OH

H

C

OH

H

2

3

4

5

6

H

H

1C

1C

2

HO

3

4

5

6

6CH2OH 5

H 1

H 2

OH

OH

H H 4 OH HO

C

O

C

H

C

OH

C

OH

C

OH

H

H

O

OH

6

O H OH

3

2

H

H

1

OH

HOCH2 5

H

O

H 4

OH

OH OH

2

CH2OH 3 1 H

2

OH

FIGURE 2.19 a and b Links The a and b forms of ribose are interconvert-

FIGURE 2.20 Formulas of Some Common Sugars Represented in Their Linear and Ring Forms Note that glucose, galactose, and mannose

ible and only differ in whether the OH group on carbon 1 is above or below the plane of the ring.

all have an aldehyde group, involving C atom 1 (shaded), whereas fructose has a keto group, involving C atom 2 (shaded).

nes95432_Ch02_018-039.indd 31

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32

CHAPTER TWO The Molecules of Life

Disaccharides The two most common disaccharides in nature are the milk sugar, lactose, and the common table sugar, sucrose (table 2.3). Lactose consists of glucose and galactose, whereas sucrose, which comes from sugar cane or sugar beets, is composed of glucose and fructose. The monosaccharides are joined together by a dehydration reaction between hydroxyl groups of two monosaccharides, with the loss of water. Note that this reaction is similar to that used to join two amino acids. The reaction is reversible, so that the addition of a water molecule, the process of hydrolysis, yields the two original molecules. Great diversity is possible in molecules formed by joining monosaccharides. The carbon atoms involved in the joining together of monosaccharides may differ and the position of the JOH groups, a and b, involved in the bonding may also differ.

Polysaccharides Polysaccharides, which are found in many different places in nature, serve different functions (see table 2.3). Cellulose, the most abundant Cellulose Weak bonds

organic molecule on earth, is a polymer of glucose subunits and is the principal constituent of plant cell walls. Some bacteria synthesize cellulose in the form of fibrils that attach bacteria to various surfaces. Glycogen, a carbohydrate storage product of animals and some bacteria, and dextran, which is also synthesized by bacteria as a storage product for carbon and energy, resemble cellulose in some ways. Cellulose, glycogen, and dextran are composed of glucose subunits, but they differ from one another in many important ways. These include (1) the size of the polymer; (2) the degree of chain branching (the side chains of monosaccharides can branch from the main chain); (3) the particular carbon atoms of the two sugar molecules involved in covalent bond formation, such as a 1, 4 linkage when carbon atom number 1 of one sugar is joined to number 4 carbon atom of the adjacent sugar; and (4) the orientation of the covalent bond between the sugar molecules. Thus, the same subunits can yield a large variety of polysaccharides that have different properties. How these various features of the structure of a polysaccharide fit into the structures of cellulose, glycogen, and dextran are shown in figure 2.21. Polysaccharides and oligosaccharides can also contain different monosaccharide subunits in the same molecule. For example, the cell walls of the domain Bacteria contain a polysaccharide consisting of alternating subunit molecules of two different amino sugars.

MICROCHECK 2.5 CH2OH

Non-branching

O

C1

2.6 Nucleic Acids

6

O

5C

4C

O

C4

C1 O 3C

C1 O

CH2OH

6

5C

Carbohydrates perform a variety of functions in cells, including serving as a source of energy and forming part of the cells’ structures. Carbohydrates with the same subunit composition can have distinct properties because of different arrangements of the atoms in the molecules. ✓ Distinguish between structural isomers and stereoisomers. ✓ What is the general name given to a single sugar? ✓ How could you distinguish sucrose and lactose from a protein molecule by analyzing the elements in the molecules?

3C

C2

C2

Glucose Glycogen CH2OH

CH2OH

6

6

O

5C 4C

O

5C

C2

3C

O

C4

C1 O

O

C2

3C

Focus Points Compare and contrast the chemical compositions of RNA and DNA. Describe the major functions of RNA and DNA.

Branching

Nucleic acids carry the genetic information that is then decoded into the sequence of amino acids in protein molecules. There are two types of nucleic acids: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), and their subunits are nucleotides.

Dextran CH2

6

5C

O

4C

C1 3C

C2

6

O

CH2 5C

DNA

O

C4

C1 3C

C2

O

Branching

FIGURE 2.21 Structures of Three Important Polysaccharides The three molecules shown consist of the same subunit, glucose, yet they are distinctly different molecules because of differences in linkage that join the molecules ( and ; 1,4 or 1,6), the degree of branching, and the bonds involved in branching (not shown). Weak hydrogen bonds are also involved.

nes95432_Ch02_018-039.indd 32

DNA is the master molecule of the cell—all of the cell’s properties are determined by its DNA. This information is coded in the sequence of nucleotides. The code is then converted into a specific sequence of amino acids that make up protein molecules. The details of this process are covered in chapter 7. In addition to their role in the structure of DNA, nucleotides play other roles in the cell. They carry chemical energy in their bonds. ■ adenosine triphosphate, p. 130

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2.6

N 6

5

H

9

N

5

N

H

3

N

N

H

P

O

H

H

2 3

H

H

N

N

H

H

3´

OH

1´

Guanine

Deoxyribose (5-carbon sugar)

H

H

2´

H

H

H

H 3C

4

N

5

3

FIGURE 2.22 A Nucleotide This is one subunit of DNA. This subunit is called adenylic acid or deoxyadenosine-5¢-phosphate because the base is adenine. If the base is thymine, the nucleotide is thymidylic acid; if guanine, guanylic acid; and if cytosine, cytidylic acid. If the nucleotide lacks the phosphate molecule, it is called a nucleoside, in this case, deoxyadenosine.

They are part of certain enzymes. ■ CoA, p. 136 They serve as specific signaling molecules. ■ cyclic AMP, p. 179 The nucleotides of DNA are composed of three different parts: a nitrogen-containing ring compound, called a base; which is covalently bonded to a 5-carbon sugar molecule, deoxyribose; which in turn is bonded to a phosphate molecule (figure 2.22). The four different bases in nucleic acids can be divided into two groups according to their

O

N

N

1

H

N

Cytosine

HO

2´

Sugar (deoxyribose)

1´

H 2O

Backbone of alternating phosphate and sugar molecules

O

G

P T

P 4´

5' end has a phosphate attached to the number 5 carbon of the sugar.

Sugar

O

5´ CH 2

3´

Uracil

ring structures: two purines (adenine and guanine), which consist of two fused rings; and two pyrimidines (cytosine and thymine), which consist of a single ring (figure 2.23). To form nucleic acid chains, the nucleotide subunits are joined by a covalent bond between the phosphate of one nucleotide and the sugar of the adjacent nucleotide (figure 2.24a). Thus, the phosphate is a bridge that joins the number 3 carbon atom (termed

O

4´

3´

2´

O

atoms are numbered consecutively.

5´ CH2

O

N H

5' P

P

H

FIGURE 2.23 Formulas of Purines and Pyrimidines Both N and C

O Base

O

Thymine

OH O

N

H

H

Phosphate group

P

H

H

2

6

H

Deoxyadenosine-5´-phosphate

O

O

N

Deoxyadenosine

HO

N

Pyrimidines

H

OH

N H

Adenine

OH 4´

N

H

CH 2 O

Phosphate group

N

1

4 9

5´

HO

6

8

2

4

H

N

7

1

8

O

N

Base

7

O

N

N

33

H

H

Purines

H

H Adenine

Nucleic Acids

1´

C

OH Covalent bond

O

OH

P HO

HO

O

P

O

P

G

O

O

P 5´

CH2

5´

CH 2 O

O 4´

3´

OH

2´

1´

4´

3´

2´

P

1´

OH

(a)

FIGURE 2.24 Joining Nucleotide Subunits (a) Formation of covalent bond between nucleotides by dehydration synthesis. The nucleotide that is added comes from a nucleoside triphosphate and not a nucleotide as illustrated. The two terminal phosphate groups of the nucleoside triphosphate are released as the covalent bond is formed between the nucleotides by dehydration synthesis. This release provides the energy for the joining together of the nucleotides by dehydration synthesis. (b) Chain of nucleotides showing the differences between 5¢ end and 3¢ end. The chain always is extended at the 3¢ end, which has the unbonded JOH hydroxyl group.

nes95432_Ch02_018-039.indd 33

T

3' end has —OH attached to the number 3 carbon of the sugar The DNA molecule grows by adding more nucleotides to this end of the chain.

C

P A OH

(b)

3'

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CHAPTER TWO The Molecules of Life

P T

5′

P

C

C G G C T A C G AT T A

C

T

G C T A 5′

C G

A

T A G C C G

P

P

G C T A

G

G

P

5′

3′

3′

A

P

3′

Sugarphosphate backbone

G

Sugar

P C G

AT AT P

P A

OH 3′

T

Hydrogen bonds between bases

G C C G T A

P

RNA is involved in decoding the information in the DNA into a sequence of amino acids in proteins. This complex multi-step process will be examined in chapter 7. Although the structure of RNA resembles that of DNA, it differs in several ways. First, RNA contains the pyrimidine uracil in place of thymine and the sugar ribose in place of deoxyribose (see figures 2.23 and 2.18). Also, whereas DNA is a long, doublestranded helix, RNA is considerably shorter and exists as a single chain of nucleotides. Although single-stranded, it may form short, double-stranded stretches as a result of hydrogen bonding between complementary bases in the single strand.

C

P

RNA

3′ OH

5′ P

P

3 prime and written 3„) of one sugar to the number 5 carbon atom (termed 5„) of the other. This results in a molecule with a backbone of alternating sugar and phosphate molecules, with two different ends. The 5„ end has a phosphate molecule attached to the sugar; the 3„ end has a hydroxyl group (figure 2.24b). During DNA synthesis, the chain is elongated by adding more nucleotides to the 3„ end. This topic is covered in chapter 7. The DNA of a typical bacterium is a single molecule composed of nucleotides joined together and arranged in a double-stranded helix, with about 4 million nucleotides in each strand (figure 2.25). This molecule can be pictured as a spiral staircase with two railings. The railings represent the sugar-phosphate backbone of the molecule, and the stairs are a pair of bases attached to the railings. Each pair of stairs (bases) is held together by weak hydrogen bonds. A specificity exists in the bonding between bases, however, in that adenine (A) can only hydrogen bond to thymine (T), and guanine (G) to cytosine (C). The pair of bases that bond are complementary to each other. Thus, G is complementary to C, and A to T. As a result, one entire strand of DNA is complementary to the other strand. This explains why in all DNA molecules, the number of adenine molecules equals the number of thymine molecules and the number of guanines equals the number of cytosines. Three hydrogen bonds join each G to C, but only two join A to T. Each of the hydrogen bonds is weak, but their large number in a DNA molecule holds the two strands together. In addition to the differences in their sequence of bases, the two complementary strands differ from each other in orientation. The two strands are arranged in opposite directions. One goes in the 3„ to the 5„ direction; the other in the 5„ to 3„. Consequently, the two ends of the strands opposite each other differ; one is a 5„ end, the other, a 3„ end (see figure 2.25).

P

34

5′

(a)

3′

5′

(b)

FIGURE 2.25 DNA Double-Stranded Helix (a) The sugar-phosphate backbone and the hydrogen bonding between bases. There are two hydrogen bonds between adenine and thymine and three between guanine and cytosine. (b) The spiral staircase of the sugar-phosphate backbone with the bases on the inside. The railings go in opposite directions.

MICROCHECK 2.6 DNA carries the genetic code in the sequence of purine and pyrimidine bases in its double-helical structure. The information is transferred to RNA and then into a sequence of amino acids in proteins. ✓ What are the two types of nucleic acids? ✓ If the DNA molecule were placed in boiling water, how would the molecule change?

FRANK & ERNEST: © Thaves/Dist. By Newspaper Enterprise Association, Inc.

nes95432_Ch02_018-039.indd 34

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2.7

2.7 Lipids

Saturated fatty acid

Lipids

Unsaturated fatty acid H

H

Focus Points

H

C

H

H

Name the one property common to all lipids.

H

C

H

Explain how the chemical structure of a phospholipid prevents the entry and exit of substances into and out of the cell.

H

C

H

H

C

H

Lipids play an indispensable role in all living cells. They are critically important in the structure of all membranes, which act as gatekeepers of cells. They keep a cell’s internal contents inside the cell and keep many molecules from entering the cell. ■ cytoplasmic membrane, p. 55 Lipids are a very heterogeneous group of molecules. Their defining feature is their slight solubility in water contrasted with their great solubility in most organic solvents such as ether, benzene, and chloroform. These solubility properties result from their non-polar, hydrophobic nature. Lipids have molecular weights of no more than a few thousand and so are the smallest of the macromolecules we have discussed. Further, unlike the other macromolecules, they are not composed of similar subunits; rather, they consist of a wide variety of substances that differ in their chemical structure. Lipids can be divided into two general classes: the simple and the compound, which differ in important aspects of their chemical composition.

H

C

H

Simple Lipids

H

C

H

H

C

H

H

C

H

H

C

H

H

C

H

C C

H

C

H

H

C

H

O

C

C H

C H C H

H

C H C

Double bond C

H

H

C

H

H

C

H

C

H

H

H C

H H

H

C

H

C

H

Three fatty acids + Glycerol

Triglyceride

H

C

H

H

C

H O

C HO

HO

Simple lipids contain only carbon, hydrogen, and oxygen. The most common are fats, a combination of fatty acids and glycerol that are solid at room temperature (figure 2.26). Fatty acids are molecules with long chains of C atoms bonded to H atoms with an acidic group (JCOOH) on one end (figure 2.27). Since glycerol has three hydroxyl groups, a maximum of three fatty acid molecules, either the same or different, can be linked through covalent bonds between the JOH group of glycerol and the JCOOH group of the fatty acid. If only one fatty acid is bound to glycerol, the fat is called a monoglyceride; when two are joined, it is a diglyceride; when three are bound, a triglyceride is formed. Fatty acids are stored in the body as an energy reserve in the form of triglycerides. Although hundreds of different fatty acids exist, they can be divided into two groups based on whether or not any double bonds are present in the portion of the molecule containing only carbon and hydrogen atoms. If there are no double bonds, the fatty acid is termed saturated with H atoms. If it contains one or more double bonds, it is unsaturated. Unsaturated fats tend to be liquid and are then called oils. Oils are liquid because these unsaturated fatty acids develop kinks in their long tails that

H C H

H

H

H

H C

H H

H

H

C

H

H

H

35

(a) Palmitic acid

(b) Oleic acid

FIGURE 2.27 Fatty Acids The saturated fatty acids (a) are solids, and the unsaturated fatty acids (b) are liquids.

prevent tight packing. The saturated fats can pack their straight, long tails tightly together and therefore are solid (figure 2.27a). Oleic acid, with its one double bond, is a common monounsaturated fatty acid (figure 2.27b). Other fatty acids containing numerous double bonds are polyunsaturated. Different lipids are called highly saturated or highly unsaturated when they contain mostly saturated or unsaturated fatty acids. Another very important group of simple lipids is the steroids. All members of this group have the four-membered ring structure shown in (figure 2.28a). These compounds differ from the fats in (a) Steroid ring

(b) Sterol (cholesterol)

CH3 CH3

O R

C

H O H

HO

C

O 3H2O

O R

C

R

H

O H

HO

C

H

C

CH3

O

C

H

O

C

H

O

C

H

O R

O R

C

C

H

C O

O H

HO

C H

H

R

C

H

FIGURE 2.26 Formation of a Fat The R group of the fatty acids commonly contains 16 or 18 carbon atoms bonded to hydrogen atoms.

nes95432_Ch02_018-039.indd 35

HO Hydroxyl group attached to a ring

FIGURE 2.28 Steroid (a) General formula showing the four-membered ring and (b) the JOH group that make the molecule a sterol. The sterol shown here is cholesterol. The carbon atoms in the ring structures and the attached hydrogen atoms are not shown.

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36

CHAPTER TWO The Molecules of Life

chemical structure, but both are classified as lipids because they are insoluble in water. If a hydroxyl group is attached to one of the rings, the steroid is called a sterol, an example being cholesterol (figure 2.28b). Other important compounds in this group of lipids are certain hormones such as cortisone, progesterone, and testosterone.

Watery exterior of cell

Phospholipid bilayer

Compound lipids contain fatty acids and glycerol as well as elements other than carbon, hydrogen, and oxygen, Biologically, some of the most important members of this group are the phospholipids, which contain a phosphate molecule in addition to the fatty acids and glycerol (figure 2.29). The phosphate is further linked to a variety of other polar molecules, such as an alcohol, a sugar, or one of certain amino acids. This entire group is referred to as a polar head and is soluble in water (hydrophilic). In contrast, the fatty acid portion is insoluble in water (hydrophobic). Phospholipids are an integral part of cytoplasmic membranes, the structure that separates the internal contents of a cell from the outside environment (see figure 2.29). The phospholipid molecules orient themselves in the membrane as opposing layers, forming a bilayer. In other words, the hydrophilic polar heads face outward, toward either the external, in the case of one of the bilayers, or internal (cytoplasmic) environment, in the case of the other. The fatty acids orient themselves inward, interacting hydrophobically with the fatty acids of the phospholipid molecules in the opposing bilayer. Water-soluble substances, which are the most common and most important in the cell’s environment, cannot pass through the hydrophobic portion. Therefore, the cell has special mechanisms to bring these molecules into the cell. These will be discussed in chapter 3. Other compound lipids are found in the outer covering of bacterial cells and will also be discussed in chapter 3. These include the lipoproteins, covalent associations of proteins and lipids, and the lipopolysaccharides, molecules of lipid linked with polysaccharides through covalent bonds. Some of the most important properties of macromolecules of biological importance are summarized in table 2.4.

Watery interior of cell Phospholipid Polar head group

R O O

P

O

Phosphate group

O

Hydrophilic head Hydrophobic tail

CH2

CH

O

O O

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH

CH2

CH2

Glycerol

O C

C

CH

CH2

CH2

CH2 CH2 CH2 CH2 CH2 CH2 CH3

Saturated fatty acid

Compound Lipids

CH2 CH2 CH2 CH2 CH2 CH2

MICROCHECK 2.7

CH3

Unsaturated fatty acid

FIGURE 2.29 Phospholipid and the Bilayer That Phospholipids Form in the Membrane of Cells In phospholipids, two of the JOH groups of glycerol are linked to fatty acids and the third JOH group is linked to a hydrophilic head group, which contains a phosphate ion and a polar molecule, labeled R.

Phospholipids, with one end hydrophilic and the other, hydrophobic, form a major part of cell membranes where they exist as a bilayer. They limit the entry and exit of molecules into and out of cells. ✓ What are the two main types of lipids and how do they differ from one another? ✓ What are the main functions of lipids in cells? ✓ Some molecules such as many alcohols are soluble in both water and hydrophobic liquids such as oils. How easily do you think these molecules would cross the cell membrane?

TABLE 2.4 Structure and Function of Macromolecules Name

Subunit

Some Functions of Macromolecules

Protein

Amino acid

Catalysts; structural portion of many cell components

Nucleic acids

Nucleotide

RNA—Various roles in protein synthesis; DNA—Carrier of genetic information

Polysaccharide

Monosaccharide

Structural component of plant cell wall; storage products

Lipids

Varies—Subunits are not similar

Important in structure of cell membranes

nes95432_Ch02_018-039.indd 36

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Summary

37

FUTURE CHALLENGES Fold Properly: Do Not Bend or Mutilate The properties of all organisms depend on the proteins they contain. These include the structural proteins as well as enzymes. Even though a cell may be able to synthesize a protein, unless that protein is folded correctly and achieves its correct shape, it will not function properly. A major challenge is to understand how proteins fold correctly—the protein-folding problem. Not only is this an important problem from a purely scientific point of view, but a number of serious neurodegenerative diseases result from protein misfolding. These include Alzheimers disease and the neurodegenerative diseases caused by prions. If we could understand why

proteins fold incorrectly, we might be able to prevent such diseases. The information that determines how a protein folds into its three-dimensional shape is contained in the sequence of its amino acids. It is not yet possible, however, to predict accurately how a protein will fold from its amino acid sequence. The folding occurs in a matter of seconds after the protein is synthesized. The protein folds rapidly into its secondary structure and then more slowly into its tertiary structure. These slower reactions are still poorly understood, but various attractive and repulsive interactions between the

amino acid side chains allow the flexible molecule to “find its way” to the correct tertiary structure. Proteins called chaperones can assist the process by preventing detrimental interactions. Mistakes still occur, but improperly folded proteins can be recognized and degraded by enzymes called proteases. The proteinfolding problem has such important implications for medicine and is so challenging a scientific question, that a super-computer with a huge memory is now being used to help predict the three-dimensional structure of a protein from its amino acid sequence. ■ prions, pp. 12, 341

SUMMARY 2.1

Atoms and Elements

Atoms are composed of electrons, protons, and neutrons element consists of a single type of atom.

2.2

(figure 2.1).

An

Chemical Bonds and the Formation of Molecules

For maximum stability, the outer shell of electrons of an atom must be filled. The electrons in different shells have different energy levels. Bonds form between atoms to fill their outer shells with electrons. Ionic Bonds When electrons leave the shells of one atom and enter the shells of another atom, an ionic bond forms between the atoms (figure 2.2). Covalent Bonds Covalent bonds are strong bonds formed by atoms sharing electrons (figure 2.3). When atoms have an equal attraction for electrons, a non-polar covalent bond is formed between them (table 2.2). When one atom has a greater attraction for electrons than another atom, polar covalent bonds are formed between them (figure 2.4). Hydrogen Bonds Hydrogen bonds are weak bonds that result from the attraction of a positively charged hydrogen atom in a polar molecule to a negatively charged atom in another polar molecule (figure 2.5). Hydrogen bonds are important in the weak association of enzymes with their substrate (figure 2.6).

cules. ATP, the energy currency of the cell, stores energy in two high-energy phosphate bonds which, when broken, release energy (figure 2.10).

Macromolecules and Their Component Parts Macromolecules are large molecules usually composed of subunits with similar properties. Synthesis of macromolecules occurs by dehydration synthesis, the removal of water, and their degradation occurs by hydrolysis, the addition of water.

2.4

Proteins and Their Functions

Proteins are the most versatile of the macromolecules in what they do. Activities of proteins include catalyzing reactions, being a component of cell structures, moving cells, taking nutrients into the cell, turning genes on and off, and being a part of cell membranes. Amino Acid Subunits Proteins are composed of 20 major amino acids (figure 2.13). All amino acids consists of a carboxyl group at one end and an amino group bonded to the same carbon atom as the carboxyl group and a side chain which confers unique properties on the amino acid (figure 2.12). Peptide Bonds and Their Synthesis Amino acids are joined through peptide bonds, joining an amino with a carboxyl group and splitting out water (figure 2.15).

pH pH is the degree of acidity of a solution; it is measured on a scale of 0 to 14. Buffers prevent the rise or fall of pH (figure 2.9).

Protein Structure (figure 2.16) The primary structure of a protein is its amino acid sequence. The secondary structure of a protein is determined by intramolecular bonding between amino acids to form helices and sheets. The tertiary structure of a protein describes the three-dimensional shape of the protein, either globular or fibrous. The quaternary structure describes the structure resulting from the interaction of several polypeptide chains. When the intramolecular bonds within the protein are broken, the protein changes shape and no longer functions; the proteins are denatured (figure 2.17).

Small Molecules in the Cell All cells contain a variety of small organic and inorganic molecules. A key element in all cells is carbon; it occurs in all organic mole-

Substituted Proteins Substituted proteins contain other molecules such as sugars and lipids, bonded to the side chains of amino acids in the protein.

2.3

Chemical Components of the Cell

Water Water is the most important molecule in the cell. Water makes up over 70% of all living organisms by weight. Hydrogen bonding plays a very important role in the properties of water (figures 2.7, 2.8).

nes95432_Ch02_018-039.indd 37

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38

2.5

CHAPTER TWO The Molecules of Life

Carbohydrates

Carbohydrates comprise a heterogeneous group of compounds that perform a variety of functions in the cell. Carbohydrates have carbon, hydrogen, and oxygen atoms in a ratio of approximately 1:2:1. Monosaccharides Monosaccharides are classified by the number of carbon atoms they contain, most commonly 5 or 6 (table 2.3, figure 2.20). Sugars can exist in two interchangeable forms: a and b, depending on whether the —OH group on carbon atom 1 is above or below the plane of the ring (figure 2.19). Sugars can exist as structural isomers—molecules that have the same number of the same elements but are arranged differently (figure 2.20, table 2.3). Disaccharides Disaccharides consist of two monosaccharides joined by a covalent bond between their hydroxyl groups (table 2.3). Polysaccharides Polysaccharides are macromolecules consisting of monosaccharide subunits, sometimes identical, other times not (figure 2.21, table 2.3).

2.6

Nucleic Acids

Nucleic acids are macromolecules whose subunits are nucleotides (figure 2.22). There are two types of nucleic acids: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA DNA is the master molecule of the cell and carries all of the cell’s genetic information in its sequence of nucleotides.

DNA is a double-stranded helical molecule with a backbone composed of covalently bonded sugar and phosphate groups. The purine and pyrimidine bases extend into the center of the helix (figure 2.23, figure 2.25a). The two strands of DNA are complementary and are held together by hydrogen bonds between the bases (figure 2.25b). RNA RNA is involved in decoding the genetic information contained in DNA. RNA is a single-stranded molecule and contains uracil in place of thymine in DNA (figure 2.23).

2.7

Lipids

Lipids are a heterogeneous group of molecules that are slightly soluble in water and very soluble in most organic solvents. They comprise two groups: simple and compound lipids. Simple Lipids Simple lipids contain carbon, hydrogen, and oxygen and may be liquid or solid at room temperature. Fats are common simple lipids and consist of glycerol bound to fatty acids (figure 2.26). Fatty acids may be saturated, in which the fatty acid contains no double-bonds between carbon atoms, or unsaturated, in which one or more double bonds exist (figure 2.27). Some simple lipids consist of a four-membered ring, and include steroids and sterols (figure 2.28). Compound Lipids Compound lipids contain elements other than carbon, hydrogen, and oxygen. Phospholipids are common and important examples of compound lipids. They are essential components of bilayer membranes in cells (figure 2.29).

REVIEW QUESTIONS Short Answer 1. Differentiate between an atom, an element, an ion, and a molecule. 2. Which solution is more acidic, one with a pH of 4 or a pH of 5? What is the concentration of H+ ions in each? The concentration of OH- ions? 3. How do the two types of nucleic acids differ from one another in (a) composition, (b) size, and (c) function? 4. Name the subunits of proteins, polysaccharides, and nucleic acids. 5. What are the two major groups of lipids? Give an example of each group. What feature is common to all lipids? 6. How does the primary structure of a protein determine its overall structure? 7. Why is water a good solvent? 8. Give an example of a dehydration synthesis reaction. Give an example of a hydrolysis reaction. How are these types of reactions related? 9. List four functions of proteins. 10. What is a steroid?

Multiple Choice 1. Choose the list that goes from the lightest to the heaviest: a) Proton, atom, molecule, compound, electron b) Atom, proton, compound, molecule, electron c) Electron, proton, atom, molecule, compound d) Atom, electron, proton, molecule, compound e) Proton, atom, electron, molecule, compound

nes95432_Ch02_018-039.indd 38

2. The strongest chemical bonds between two atoms in solution are a) covalent. b) ionic. c) hydrogen bonds. d) hydrophobic interactions. 3. Dehydration synthesis is involved in the synthesis of all of the following, except a) DNA b) proteins c) polysaccharides d) lipids e) monosaccharides 4. The primary structure of a protein relates to its a) sequence of amino acids b) length c) shape d) solubility e) bonds between amino acids 5. Pure water has all of the following properties, except a) polarity. b) ability to dissolve lipids. c) pH of 7. d) covalent joining of its atoms. e) ability to form hydrogen bonds. 6. The macromolecules that are composed of carbon, hydrogen, and oxygen in an approximate ratio of 1 : 2 : 1 are a) proteins. b) lipids. c) polysaccharides. d) DNA. e) RNA. 7. In proteins, a helices and b pleated structures are associated with the a) primary structure. b) secondary structure. c) tertiary structure. d) quaternary structure. e) multiprotein complexes. 8. Complementarity plays a major role in the structure of a) proteins. b) lipids. c) polysaccharides. d) DNA. e) RNA.

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Review Questions 9. A bilayer is associated with a) proteins. b) DNA. c) RNA. d) complex polysaccharides. e) phospholipids. 10. Isomers are associated with 1. carbohydates. 2. amino acids. 3. nucleotides. 4. RNA. 5. fatty acids. a) 1, 2 b) 2, 3 c) 3, 4 d) 4, 5 e) 1, 5

Applications 1. A group of bacteria known as thermophiles thrive at high temperatures that would normally destroy other bacteria. Yet these thermophiles cannot survive well at the lower temperatures normally found on the earth. Propose a plausible explanation for this observation. 2. Microorganisms use hydrogen bonds to attach themselves to the surfaces that they live upon. Many of them lose hold of the surface because of the weak nature of these bonds and end up dying. Contrast the benefits and disadvantages of using covalent bonds as a means of attaching to surfaces.

Critical Thinking 1. What properties of the carbon atom make it ideal as the key atom for all molecules in organisms?

nes95432_Ch02_018-039.indd 39

39

2. A biologist determined the amounts of several amino acids in two separate samples of pure protein. His data are shown here: Amino Acid Protein A Protein B

Leucine Alanine 7% 7%

12% 12%

Histidine

Cysteine

Glycine

4% 4%

2% 2%

5% 5%

He concluded that protein A and protein B were the same protein. Do you agree with this conclusion? Justify your answer. 3. This table indicates the freezing and boiling points of several molecules: Molecule

Freezing Point (°C)

Water 0 Carbon tetrachloride (CCl4) -23 Methane (CH4) -182

Boiling Point (°C) 100 77 -164

Carbon tetrachloride and methane are non-polar molecules. How does the polarity and non-polarity of these molecules explain why the freezing and boiling points for methane and carbon tetrachloride are so much lower than those for water?

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3 Color-enhanced TEM of bacterial cells.

Microscopy and Cell Structure A Glimpse of History Hans Christian Joachim Gram (1853–1938) was a Danish physician working in a laboratory at the morgue of the City Hospital in Berlin, microscopically examining the lungs of patients who had died of pneumonia. He was working under the direction of Dr. Carl Friedlander, who was trying to identify the cause of pneumonia by studying patients who had died of it. Gram’s task was to stain the infected lung tissue to make the bacteria easier to see under the microscope. Strangely, one of the methods he developed did not stain all bacteria equally; some types retained the first dye applied in this multistep procedure, whereas others did not. Gram’s staining method revealed that two different kinds of bacteria were causing pneumonia, and that these types retained the dye differently. We now recognize that this important staining method, called the Gram stain, efficiently identifies two large, distinct groups of bacteria: Gram-positive and Gram-negative. The variation in the staining outcome of these two groups reflects a fundamental difference in the structure and chemistry of their cell walls. For a long time, historians thought that Gram did not appreciate the significance of his discovery. In more recent years, however, several letters show that Gram did not want to offend the famous Dr. Friedlander under whom he worked; therefore, he played down the importance of his staining method. In fact, the Gram stain has been used as a key test in the initial identification of bacterial species ever since the late 1880s.

I

magine the astonishment Antony van Leeuwenhoek must have felt in the 1600s when he first observed microorganisms with his handcrafted microscopes, instruments that could magnify images approximately 300-fold (300μ). Even today, observing diverse microbes interacting in a sample of stagnant pond water can provide enormous education and entertainment.

Microscopic study of cells has revealed two fundamental types: prokaryotic and eukaryotic. The cells of all members of the Domains Bacteria and Archaea are prokaryotic. In contrast, cells of all animals, plants, protozoa, fungi, and algae are eukaryotic. The similarities and differences between these two basic cell types are important from a scientific standpoint and also have significant consequences to human health. For example, chemicals that interfere with processes unique to prokaryotic cells can be used to selectively destroy bacteria without harming humans. ■ prokaryotic cells, p. 10 Prokaryotic cells are generally much smaller than most eukaryotic cells—a trait that carries with it certain advantages as well as disadvantages. On one hand, their high surface area relative to their low volume makes it easier for these cells to take in nutrients and excrete waste products. Because of this, they can multiply much more rapidly than can their eukaryotic counterparts. On the other hand, their small size makes them vulnerable to an array of threats. Predators, parasites, and competitors constantly surround them. Prokaryotic cells, although simple in structure, have developed many unique attributes that enhance their evolutionary success. Eukaryotic cells are considerably more complex than prokaryotic cells. Not only are they larger, but many of their cellular processes take place within membrane-bound compartments. Eukaryotic cells are defined by the presence of a membrane-bound nucleus, which contains the chromosomes. Although eukaryotic cells share many of the same characteristics as prokaryotic cells, many of their structures and cellular processes are fundamentally different. ■ eukaryotic cells, p. 10

40

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3.1 Microscopic Techniques: The Instruments

KEY TERMS Capsule A distinct, thick gelatinous material that surrounds some microorganisms. Chemotaxis Directed movement of an organism toward or away from a certain chemical in the environment. Cytoplasmic Membrane A phospholipid bilayer embedded with proteins that surrounds the cytoplasm and defines the boundary of the cell. Endospore A type of dormant cell that is extraordinarily resistant to damaging conditions including heat, desiccation, ultraviolet light, and toxic chemicals.

Flagellum A structure that provides a mechanism for motility. Gram-Negative Bacteria Bacteria that have a cell wall composed of a thin layer of peptidoglycan surrounded by an outer membrane; when Gram stained, these cells are pink. Gram-Positive Bacteria Bacteria that have a cell wall composed of a thick layer of peptidoglycan; when Gram stained, these cells are purple. Lipopolysaccharide (LPS) Molecule that makes up the outer layer of the outer membrane of Gram-negative bacteria. Peptidoglycan A macromolecule that provides rigidity to the cell wall; it is found only in bacteria.

41

Periplasm The gel-like material that fills the region between the cytoplasmic membrane and the outer membrane of Gram-negative bacteria. Pili Cell surface structures that generally enable cells to adhere to certain surfaces; some types are involved in a mechanism of DNA transfer. Plasmid Extrachromosomal DNA molecule that replicates independently of the chromosome. Ribosome Structure intimately involved in protein synthesis. Transport Systems Mechanisms used to transport nutrients and other small molecules across the cytoplasmic membrane.

MICROSCOPY AND CELL MORPHOLOGY

3.1 Microscopic Techniques: The Instruments Focus Points Describe the importance of magnification, resolution, and contrast in microscopy. Compare and contrast light microscopes, electron microscopes, and atomic force microscopes.

One of the most important tools for studying microorganisms is the light microscope, which uses visible light for observing objects. These instruments can magnify images approximately 1,000μ, making it relatively easy to observe the size, shape, and motility of prokaryotic cells. The electron microscope, introduced in 1931, can magnify images in excess of 100,000μ, revealing many fine details of cell structure. A major advancement came in the 1980s with the development of the atomic force microscope, which allows scientists to produce images of individual atoms on a surface.

Principles of Light Microscopy: The Bright-Field Microscope In light microscopy, light typically passes through a specimen and then through a series of magnifying lenses. The most common type of light microscope, and the easiest to use, is the bright-field microscope, which evenly illuminates the field of view.

nes95432_Ch03_040-082.indd 41

Magnification The modern light microscope has two magnifying lenses—an objective lens and an ocular lens—and is called a compound microscope (figure 3.1). These lenses in combination visually enlarge an object by a factor equal to the product of each lens’ magnification. For example, an object is magnified 1,000-fold when it is viewed through a 10μ ocular lens in conjunction with a 100μ objective lens. Most compound microscopes have a selection of objective lenses that are of different powers—typically 4μ, 10μ, 40μ, and 100μ. This makes a choice of different magnifications possible with the same instrument.

Ocular lens (eyepiece). Magnifies the image, usually 10-fold (10x).

Specimen stage.

Objective lens. A selection of lens options provide different magnifications. The total magnification is the product of the magnifying power of the ocular lens and the objective lens.

Condenser. Focuses the light. Iris diaphragm. Controls the amount of light that enters the objective lens.

Light source with means to control amount of light. Knob to control intensity of light.

FIGURE 3.1 A Modern Light Microscope The compound microscope employs a series of magnifying lenses.

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CHAPTER THREE Microscopy and Cell Structure

FIGURE 3.2 Resolving Power These images of an onion root tip magnified 450μ illustrate the difference in resolving power between a light microscope and an electron microscope. Note the difference in the degree of detail that can be seen at the same magnification.

Light microscope (450x)

The condenser lens does not affect the magnification but, positioned between the light source and the specimen, is used to focus the light on the specimen.

Resolution The usefulness of a microscope depends both on its degree of magnification, and its ability to clearly separate, or resolve, two objects that are very close together. The resolving power is defined as the minimum distance existing between two objects when those objects can still be observed as separate entities. The resolving power therefore determines how much detail actually can be seen (figure 3.2). The resolving power of a microscope depends on the quality and type of lens, wavelength of the light, magnification, and how the specimen under observation has been prepared. The maximum resolving power of the best light microscope is 0.2 mm. This is sufficient to observe the general morphology of a prokaryotic cell but too low to distinguish a particle the size of most viruses.

Electron microscope (450x)

To obtain maximum resolution when using certain highpower objectives such as the 100μ lens, oil must be used to displace the air between the lens and the specimen. This avoids the bending of light rays, or refraction, that occurs when light passes from glass to air (figure 3.3). Refraction can prevent those rays from entering the relatively small openings of higher-power objective lenses. The oil has nearly the same refractive index as glass. Refractive index is a measure of the relative velocity of light as it passes through a medium. As light travels from a medium of one refractive index to another, those rays are bent. When oil displaces air at the interface of the glass slide and glass lens, light rays pass with little refraction occurring.

Contrast Contrast reflects the number of visible shades in a specimen—high contrast being just two shades, black and white. Different specimens require various degrees of contrast to reveal the most information. One example is bacteria, which are essentially transparent against

FIGURE 3.3 Refraction As light passes from one medium to another, the light rays may bend, depending on the refractive index of the two media. (a) The pencil in water appears bent because the refractive index of water is different from that of air. (b) Light rays bend as they pass from air to glass because of the different refractive indexes of these media; some rays are lost to the objective. Oil and glass have the same refractive index, and therefore the light rays are not bent.

Objective lens

Air

Oil

Slide Light source (a)

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(b)

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3.1 Microscopic Techniques: The Instruments

43

a bright colorless background. The lack of contrast presents a problem when viewing objects (see figure 11.18). One way to overcome this problem is to stain the bacteria with any one of a number of dyes. The types and characteristics of these stains will be discussed shortly.

Light Microscopes That Increase Contrast Special light microscopes that increase the contrast between microorganisms and their surroundings overcome some of the difficulties of observing unstained bacteria. Staining kills microbes; therefore, some of these microscopes are invaluable when the goal is to examine characteristics of living organisms such as motility. Characteristics of these and other microscopes are summarized in table 3.1.

The Phase-Contrast Microscope The phase-contrast microscope amplifies the slight difference between the refractive index of cells and the surrounding medium, resulting in a darker appearance of the denser material (figure 3.4). As light passes through cells, it is refracted slightly differently than when it passes through its surroundings. Special optical devices boost those differences, thereby increasing the contrast.

The Interference Microscope The interference microscope causes the specimen to appear as a three-dimensional image (figure 3.5). This microscope, like the phase-contrast microscope, depends on differences in refractive index as light passes through different materials. The most frequently used microscope of this type is the Nomarski differential interference contrast (DIC) microscope, which has a device for separating light into two beams that pass through the specimen and then recombine. The light waves are out of phase when they recombine, thereby yielding the three-dimensional appearance of the specimen.

The Dark-Field Microscope Organisms viewed through a dark-field microscope stand out as bright objects against a dark background (figure 3.6). The microscope operates on the same principle that makes dust visible

30 μm

FIGURE 3.5 Nomarski Differential Interference Contrast (DIC) Microscopy Protozoan (Paracineta) attached to a green alga (Spongomorpha).

when a beam of bright light shines into a dark room. A special mechanism directs light toward the specimen at an angle, so that only light scattered by the specimen enters the objective lens. Dark-field microscopy can detect Treponema pallidum, the causative agent of syphilis. These thin, spiral-shaped organisms stain poorly and are difficult to see via bright-field microscopy (see figure 11.26).

The Fluorescence Microscope The fluorescence microscope is used to observe cells or other materials that are either naturally fluorescent or have been stained or tagged with fluorescent dyes. A fluorescent molecule absorbs light at one wavelength (usually ultraviolet light) and then emits light of a longer wavelength. The fluorescence microscope projects ultraviolet light through a specimen, but then captures only the light emitted by the fluorescent molecules to form the image. This allows

Filamentous alga (Spirogyra)

Colonial alga (Volvox)

25 mm

25 μm

FIGURE 3.4 Phase-Contrast Photomicrograph Paramecium bursaria

FIGURE 3.6 Dark-Field Photomicrograph Volvox (sphere) and Spiro-

containing endosymbiotic Chlorella (a green alga).

gyra (filaments), both of which are eukaryotes.

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CHAPTER THREE Microscopy and Cell Structure

TABLE 3.1 A Summary of Microscopic Instruments and Their Characteristics Instrument

Mechanism

Uses/Comment

Light Microscopes

Visible light passes through a series of lenses to produce a magnified image.

Relatively easy to use; considerably less expensive than confocal and electron microscopes.

Illuminates the field of view evenly.

Most common type of microscope.

Amplifies differences in refractive index to create contrast.

Makes unstained cells more readily visible.

Two light beams pass through the specimen and then recombine.

Causes the specimen to appear as a three-dimensional image.

Light is directed toward the specimen at an angle.

Makes unstained cells more readily visible; organisms stand out as bright objects against a dark background.

Bright-field

Phase-contrast

Interference

Dark-field

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3.1 Microscopic Techniques: The Instruments

45

TABLE 3.1 A Summary of Microscopic Instruments and Their Characteristics (continued) Instrument

Mechanism

Uses/Comment

Projects ultraviolet light, causing fluorescent molecules in the specimen to emit longer wavelength light.

Used to observe cells that have been stained or tagged with a fluorescent dye.

Mirrors scan a laser beam across successive regions and planes of a specimen. From that data, a computer constructs an image.

Used to construct a three-dimensional image of a structure; provides detailed sectional views of intact cells.

Electron beams are used in place of visible light to produce the magnified image.

Can clearly magnify images 100,000μ.

Transmits a beam of electrons through a specimen.

Elaborate specimen preparation is required.

A beam of electrons scans back and forth over the surface of a specimen.

Used for observing surface details; produces a three-dimensional effect.

A probe moves in response to even the slightest force between it and the sample.

Produces a map showing the bumps and valleys of the atoms on the surface of the sample.

Fluorescence

Confocal

Electron Microscopes Transmission

Scanning

Atomic Force Microscope

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CHAPTER THREE Microscopy and Cell Structure

and planes until the entire specimen has been scanned. Each plane corresponds to an image of one fine slice of the specimen. A computer then assembles the data and constructs a three-dimensional image, which is displayed on a screen. In effect, this microscope is a miniature CAT scan for cells. Frequently, the specimens are first stained or tagged with a fluorescent dye. By using certain fluorescent tags that bind specifically to a given protein or other compound, the precise cellular location of that compound can be determined. In some cases, multiple different tags that bind to specific molecules are used, each having a distinct color.

Electron Microscopes 10 μm

FIGURE 3.7 Fluorescence Photomicrograph A rod-shaped bacterium tagged with fluorescent marker.

fluorescent cells to stand out as illuminated objects against a dark background (figure 3.7). The types and characteristics of fluorescent dyes and tags will be discussed shortly. ■ fluorescent dyes and tags, p. 51

A common variation of the standard fluorescence microscope is the epifluorescence microscope, which projects the ultraviolet light through the objective lens and onto the specimen. Because the light is not transmitted through the specimen, cells attached to soil particles or other opaque materials can be observed.

The Confocal Scanning Laser Microscope The confocal scanning laser microscope is used to construct a three-dimensional image of a thick structure such as a community of microorganisms (figure 3.8). The instrument can also provide detailed sectional views of the interior of an intact cell. In confocal microscopy, lenses focus a laser beam to illuminate a given point on one vertical plane of a specimen. Mirrors then scan the laser beam across the specimen, illuminating successive regions

Electron microscopy is in some ways comparable to light microscopy. Rather than using glass lenses, visible light, and the eye to observe the specimen, the electron microscope uses electromagnetic lenses, electrons, and a fluorescent screen to produce the magnified image (figure 3.9). That image can be captured on photographic film to create an electron photomicrograph. Sometimes, the black and white images are artificially enhanced with color to add visual clarity. ■ electrons, p. 18 Since the electrons have a wavelength about 1,000 times shorter than visible light, the resolving power increases about 1,000-fold, to about 0.3 nanometers (nm) or 0.3!10⫺3 mm (see figure 1.13). Consequently, considerably more detail can be observed due to the much higher resolution. These instruments can clearly magnify an image 100,000μ. One of the biggest drawbacks of the microscope is that the lenses and specimen must all be in a vacuum. Otherwise, the molecules composing air would interfere with the path of the electrons. This results in an expensive, bulky unit and requires substantial and complex specimen preparation.

The Transmission Electron Microscope The transmission electron microscope (TEM) is used to observe fine details of cell structure, such as the number of layers that envelop a cell. The instrument directs a beam of electrons at a

FIGURE 3.8 Confocal Microscopy This can be used to produce a clear image of a single plane in a thick structure. (a) Confocal photomicrography of fava bean mitosis. (b) Regular photomicrograph.

(a)

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(b)

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3.1 Microscopic Techniques: The Instruments Light Microscope

Lamp

47

Transmission Electron Microscope Tungsten filament (cathode)

Electron gun

Anode Condenser lens

Specimen

Condenser lens magnet

Objective lens

Objective lens magnet

Eyepiece

Projector lens magnet

Final image seen by eye

(a)

Specimen

1 μm

Final image on fluorescent screen or Final image on photographic film when screen is lifted aside

FIGURE 3.9 Comparison of the Principles of Light and the Electron Microscopy For the sake of comparison, the light source for the light micro-

(b)

1 μm

FIGURE 3.10 Transmission Electron Photomicrograph A rod-shaped bacterium prepared by (a) thin section; (b) freeze etching.

scope has been inverted (the light is shown at the top and the eyepiece, or ocular lens, at the bottom).

specimen. Depending on the density of a particular region in the specimen, electrons will either pass through or be scattered to varying degrees. The darker areas of the resulting image correspond to the denser portions of the specimen (figure 3.10). Transmission electron microscopy requires elaborate and painstaking specimen preparation. To view details of internal structure, a process called thin sectioning is used. Cells are carefully treated with a preservative and dehydrated in an organic solvent before being embedded in a plastic resin. Once embedded, they can be cut into exceptionally thin slices with a diamond or glass knife and then stained with heavy metals. Even a single bacterial cell must be cut into slices this way to be viewed via TEM. Unfortunately, the procedure can severely distort the cells. Consequently, a major concern in using TEM is distinguishing actual cell components from artifacts occurring as a result of specimen preparation. A process called freeze fracturing is used to observe the shape of structures within the cell. The specimen is rapidly frozen and then fractured by striking it with a knife blade. The cells break open, usually along the middle of internal membranes. Next, the surface of the section is coated with a thin layer of carbon to create a replica of the surface. This replica is then examined in the electron microscope. A variation of freeze fracturing is freeze etching. In this process, the frozen surface exposed by fracturing is dried slightly under vacuum, which allows underlying regions to be exposed.

nes95432_Ch03_040-082.indd 47

The Scanning Electron Microscope The scanning electron microscope (SEM) is used for observing surface details of cells. A beam of electrons scans back and forth over the surface of a specimen coated with a thin film of metal. As those beams move, electrons are released from the specimen and reflected back into the viewing chamber. This reflected radiation is observed with the microscope. Relatively large specimens can be viewed, and a dramatic three-dimensional effect is observed with the SEM (figure 3.11).

2 μm

FIGURE 3.11 Scanning Electron Photomicrograph A rod-shaped bacterium.

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CHAPTER THREE Microscopy and Cell Structure

3.2 Microscopic Techniques: Dyes and Staining Focus Points Describe the principles of the Gram stain and the acid-fast stain. Describe the techniques used to observe capsules, endospores, and flagella. Describe the benefits of using fluorescent dyes and tags.

It can be difficult to observe living microorganisms with the bright-field microscope. Most microorganisms are nearly transparent and often move rapidly about the slide. To remedy this problem, cells are frequently immobilized and stained with dyes. Many different dyes and staining procedures can be used; each has specific applications (table 3.2). 0.3 mm

FIGURE 3.12 Atomic Force Microscopy Micrograph of a fragment of DNA. The bright peaks are enzymes attached to the DNA.

TABLE 3.2 A Summary of Stains and Their Characteristics Stain

Characteristics

Simple Stains

Employ a basic dye to impart a color to a cell. Easy way to increase the contrast between otherwise colorless cells and a transparent background.

Differential Stains

Distinguish one group of microorganisms from another.

Atomic Force Microscopy The atomic force microscope (AFM) produces detailed images of surfaces (figure 3.12). The resolving power is much greater than that of an electron microscope, and the samples do not need the special preparation required for electron microscopy. In fact, the instrument can inspect samples either in air or submerged in liquid. The mechanics of AFM can be compared to that of a stylus mounted on the arm of a record player. A very sharp probe (stylus) moves across the surface of the sample, “feeling” the bumps and valleys of the atoms on that surface. As the probe scans the sample, a laser measures its motion, and a computer produces a surface map of the sample. ■ atom, p. 18

Gram stain

Used to separate bacteria into two major groups, Gram-positive and Gram-negative. The staining characteristics of these groups reflect a fundamental difference in the chemical structure of their cell walls. This is by far the most widely used staining procedure.

Acid-fast stain

Used to detect organisms that do not readily take up stains, such as members of the genus Mycobacterium.

Special Stains

Stain specific structures inside or outside of a cell.

Capsule stain

Capsule stains exploit the fact that viscous capsules do not readily take up certain stains; the capsules stand out against a stained background. This is an example of a negative stain.

Endospore stain

Stains endospores, a type of dormant cell that does not readily take up stains. These are produced by Bacillus and Clostridium species.

Flagella stain

The staining agent adheres to and coats the otherwise thin flagella, making them visible with the light microscope.

MICROCHECK 3.1 The usefulness of a microscope depends on its resolving power. The most common type of microscope is the bright-field microscope. Variations of light microscopes are designed to increase contrast between a microorganism and its surroundings. The fluorescence microscope is used to observe microbes stained with special dyes. The confocal scanning laser microscope is used to construct a threedimensional image of a thick structure. Electron microscopes can magnify images 100,000μ. The atomic force microscope produces detailed images of surfaces. ✓ Why must oil be employed when using the 100μ lens? ✓ Why are microscopes that enhance contrast used to view live rather than stained specimens? ✓ If an object being viewed under the phase-contrast microscope has the same refractive index as the background material, how would it appear?

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Fluorescent Dyes and Tags

Fluorescent dyes and tags absorb ultraviolet light and then emit light of a longer wavelength. They are used in conjunction with a fluorescence microscope.

Fluorescent dyes

Some fluorescent dyes bind to compounds found in all cells; others bind to compounds specific to only certain types of cells.

Fluorescent tags

Antibodies to which a fluorescent molecule has been attached are used to tag specific molecules.

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3.2 Microscopic Techniques: Dyes and Staining

Spread thin film of specimen over slide.

Allow to air dry.

Pass slide through flame to fix specimen.

Flood with stain, rinse and dry.

49

Examine with microscope.

FIGURE 3.13 Staining Bacteria for Microscopic Observation

Basic dyes, which carry a positive charge, are more commonly used for staining than are negatively charged acidic dyes. Because opposite charges attract, basic dyes stain the negatively charged components of cells, including nucleic acid and many proteins, whereas acidic dyes are repelled. Common basic dyes include methylene blue, crystal violet, safranin, and malachite green. Simple staining employs one of these basic dyes to stain the cells. Acidic dyes are sometimes used to stain backgrounds against which colorless cells can be seen, a technique called negative staining. To stain microorganisms, a drop of liquid containing the microbe is placed on a microscope slide and allowed to dry. The resulting specimen forms a film, or smear. The organisms are then attached, or fixed, to the slide, usually by passing the slide over a flame (figure 3.13). Dye is then applied and the excess washed off with water. Heat fixing and subsequent staining steps kill the microorganisms and may distort their shape.

Differential Stains Differential staining procedures are used to distinguish one group of bacteria from another. The two most frequently used

(a)

Steps in Staining

State of Bacteria

Step 1: Crystal violet (primary stain)

Cells stain purple.

Step 2: Iodine (mordant)

Cells remain purple.

Step 3: Alcohol (decolorizer)

Gram-positive cells remain purple; Gram-negative cells become colorless.

Step 4: Safranin (counterstain)

Gram-positive cells remain purple; Gram-negative cells appear red.

differential staining techniques are the Gram stain and the acidfast stain.

Gram Stain The Gram stain is by far the most widely used procedure for staining bacteria. The basis for it was developed over a century ago by Dr. Hans Christian Gram (see A Glimpse of History). He showed that bacteria can be separated into two major groups: Gram-positive and Gram-negative. We now know that the difference in the staining properties of these two groups reflects a fundamental difference in the structure of their cell walls. Gram staining involves four basic steps (figure 3.14). 1. The smear is first flooded with the primary stain, crystal violet in this case. The primary stain is the first dye applied in any multistep staining procedure and generally stains all cells. 2. The smear is rinsed to remove excess crystal violet and then flooded with a dilute solution of iodine, called Gram’s iodine. Iodine is a mordant, a substance that increases the affinity of cellular components for a dye. The iodine combines with the crystal violet to form a dye-iodine complex, thereby decreasing the solubility of the dye within the cell.

(b)

10 μm

FIGURE 3.14 Gram Stain (a) Steps in the Gram stain procedure. (b) Results of a Gram stain. The Gram-positive cells (purple) are Staphylococcus aureus; the Gram-negative cells (reddish-pink) are Escherichia coli.

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CHAPTER THREE Microscopy and Cell Structure

3. The stained smear is rinsed again, and then 95% alcohol or a mixture of alcohol and acetone is briefly added. These solvents act as decolorizing agents and readily remove the dye-iodine complex from Gram-negative, but not Grampositive, bacteria. 4. A counterstain is then applied to impart a contrasting color to the now colorless Gram-negative bacteria. For this purpose, the red dye safranin is used. This dye stains Gramnegative as well as Gram-positive bacteria, but because the latter are already stained purple, it imparts little difference to those cells. To obtain reliable results, the Gram stain must be done properly. One of the most common mistakes is to decolorize a smear for too long a time period. Even Gram-positive cells can lose the crystal violet-iodine complex during prolonged decolorization. An over-decolorized Gram-positive cell will appear pink after counterstaining. Another important consideration is the age of the culture. As bacterial cells age, they lose their ability to retain the crystal violet–iodine dye complex, presumably because of changes in their cell wall. As a result, cells from old cultures may appear pink. Thus, the Gram stain results of fresh cultures (less than 24 hours old) are more reliable.

Acid-Fast Stain The acid-fast stain is a procedure used to stain a small group of organisms that do not readily take up stains. Among these are members of the genus Mycobacterium, including a species that causes tuberculosis and one that causes Hansen’s disease (leprosy). The cell wall of these bacteria contains high concentrations of lipid, preventing the uptake of dyes, including those used in the Gram stain. Therefore, harsh methods are needed to stain these organisms. Once stained, however, these same cells are very resistant to decolorization. Because mycobacteria are among the few organisms that retain the dye in this procedure, the acid-fast stain can be used to presumptively identify them in clinical specimens that might contain a variety of different bacteria. ■ tuberculosis, p. 514 ■ Hansen’s disease, p. 655

FIGURE 3.15 Acid-Fast Stain Mycobacterium species retain the red primary stain, carbol fuchsin. Counterstaining with methylene blue imparts a blue color to cells that are not acid-fast.

of that structure. The function of each of these structures will be discussed in more depth later in the chapter.

Capsule Stain A capsule is a viscous layer that envelops a cell and is sometimes correlated with an organism’s ability to cause disease. Capsules stain poorly, a characteristic exploited with a capsule stain, an example of a negative stain. It colors the background, allowing the capsule to stand out as a halo around an organism (figure 3.16). ■ capsule, p. 64 In one method to observe capsules, a liquid specimen is placed on a slide next to a drop of India ink. A thin glass coverslip is then placed over the two drops, causing them to flow together. This creates a gradient of India ink concentration across the specimen. Unlike the stains discussed previously, this capsule stain is done as a wet mount—a drop of liquid on which a coverslip has been placed—rather than as a smear. At the optimum concentration of

The acid-fast stain, like the Gram stain, requires multiple steps. The primary stain in this procedure is carbol fuchsin, a red dye. In the classic procedure, the stain-flooded slide is heated, which facilitates the staining. A current variation does not employ heat, instead it uses a prolonged application of a more concentrated solution of dye. The slide is then rinsed briefly to remove the residual stain before being flooded with acid-alcohol, a potent decolorizing agent. This step removes the carbol fuchsin from tissue cells and most bacteria. Those few species that retain the dye are called acid-fast. Methylene blue is then used as a counter-stain, imparting a blue color to non-acid-fast cells. Acid-fast organisms, which do not take up the methylene blue, appear a bright reddish-pink (figure 3.15).

Special Stains to Observe Cell Structures Dyes can also be used to stain specific structures inside or outside the cell. The staining procedure for each component of the cell is different, being geared to the chemical composition and properties

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10 mm

FIGURE 3.16 Capsule Stain Capsules stain poorly, and so they stand out against the India ink-stained background as a halo around the organism. This photomicrograph shows Cryptococcus neoformans, an encapsulated yeast.

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3.2 Microscopic Techniques: Dyes and Staining

51

1 μm

10 μm

FIGURE 3.17 Endospore Stain Endospores retain the green primary stain,

FIGURE 3.18 Flagella Stain The staining agent adheres to and coats the fla-

malachite green. Counterstaining with safranin imparts a red color to other cells.

gella. This increases their diameter so they can be seen with the light microscope.

India ink, the fine particles of the stain darken the background enough to allow the capsule to be visible.

Flagella Stain

Endospore Stain Members of certain Gram-positive genera, including Bacillus and Clostridium, form a special type of dormant cell, an endospore, that is resistant to destruction and to staining. Although these structures do not stain with the Gram stain, they can often be seen as clear, smooth objects within otherwise purple-stained cells. To make endospores more readily noticeable, a spore stain is used. ■ endospore, p. 69 The endospore stain is a multistep procedure that employs a primary stain as well as a counterstain. Generally, malachite green is used as a primary stain. Its uptake by endospores is facilitated by gentle heat. When water is then used to rinse the smear, only endospores retain the malachite green. The smear is then counterstained, most often with the red dye safranin. The endospores appear green amid a background of pink cells (figure 3.17).

(a)

Flagella are appendages that provide the most common mechanism of motility for prokaryotic cells, but they are ordinarily too thin to be seen with the light microscope. The flagella stain employs a mordant that allows the staining agent to adhere to and coat the thin flagella, effectively increasing their diameter—which makes them visible using light microscopy. Not all bacteria have flagella, but those that do can have them in different arrangements around a cell, so that the presence and distribution of these appendages can be used to identify bacteria (figure 3.18). Unfortunately, this staining procedure is difficult and requires patience and expertise. ■ flagella, p. 65

Fluorescent Dyes and Tags Depending on the procedure employed, fluorescence can be used to observe total cells, a subset of cells, or cells with certain proteins on their surface (figure 3.19).

(b) 10 μm

(c) 10 μm

10 μm

FIGURE 3.19 Fluorescent Dyes and Tags (a) Dyes that cause live cells to fluoresce green and dead ones red. (b) Auramine is used to stain Mycobacterium species in a modification of the acid-fast technique. (c) Fluorescent antibodies tag specific molecules—in this case, the antibody binds to a molecule unique to Streptococcus pyogenes.

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CHAPTER THREE Microscopy and Cell Structure

Fluorescent Dyes

MICROCHECK 3.2

Some fluorescent dyes bind to compounds found in all cells. For example, acridine orange binds DNA, making it useful for determining the total number of microorganisms in a sample. Other fluorescent dyes are changed by cellular processes of living cells, enabling microbiologists to distinguish between cells that are alive and those that are dead. For example, the dye CTC is made fluorescent by cellular proteins involved in respiration. Consequently, CTC only fluoresces when bound to live cells. There are also fluorescent dyes that bind to compounds primarily found in certain types of cells. Calcofluor white binds to a component of the cell walls of fungi and certain bacteria, causing those cells to fluoresce bright blue. The fluorescent dyes auramine and rhodamine bind to a compound found in the cell walls of members of the genus Mycobacterium. These two dyes can be used in a staining procedure analogous to the acid-fast stain; cells of Mycobacterium will emit a bright yellow or orange fluorescence. ■ respiration, p. 132

Dyes can be used to stain cells so they stand out against the unstained background. The Gram stain is by far the most widely used differential stain. The acid-fast stain detects species of Mycobacterium. Specific dyes and techniques can be used to observe cell structures such as capsules, endospores, and flagella. Fluorescent dyes and tags can be used to observe total cells, a subset of cells, or cells that have certain proteins on their surface. ✓ What are the functions of a primary stain and a counterstain? ✓ Describe one error in the staining procedure that would result in a Gram-positive bacterium appearing pink. ✓ What color would a Gram-negative bacterium be in an acidfast stain?

3.3 Morphology of Prokaryotic Cells Focus Points

Immunofluorescence

Describe the common shapes and groupings of bacteria.

Immunofluorescence is a technique used to tag specific proteins with a fluorescent compound. By tagging a protein unique to a given microbe, immunofluorescence can be used to detect that specific organism in a sample containing a mixture of cells. Immunofluorescence uses an antibody to deliver the fluorescent tag (see figure 19.10). An antibody is produced by the immune system in response to a foreign compound, usually a protein; it binds specifically to that compound. ■ antibody, pp. 367, 371

Describe two multicellular associations of bacteria.

(b)

Most common bacteria are one of two shapes: spherical, called a coccus (plural: cocci); and cylindrical, called a rod (figure 3.20).

Coccobacillus

(c)

Spirillum

Vibrio

(d)

Shapes

Rod (bacillus)

Coccus

(a)

Prokaryotic cells come in a variety of simple shapes and often form characteristic groupings. Some aggregate, living as multicellular associations.

(e)

Spirochete

(f)

FIGURE 3.20 Typical Shapes of Common Bacteria (a) Coccus; (b) rod; (c) coccobacillus; (d) vibrio; (e) spirillum; (f) spirochete. Electron micrographs.

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3.3 Morphology of Prokaryotic Cells

A rod-shaped bacterium is sometimes called a bacillus (plural: bacilli). The descriptive term “bacillus” should not be confused with Bacillus, the name of a genus. While members of the genus Bacillus are rod-shaped, so are many other bacteria, including Escherichia coli. Cells have a variety of other shapes. A rod-shaped bacterium so short that it can easily be mistaken for a coccus is often called a coccobacillus. A short, curved rod is called a vibrio (plural: vibrios), whereas a curved rod long enough to form spirals is called a spirillum (plural: spirilla). A long, helical cell with a flexible cell wall and a unique mechanism of motility is a spirochete. Bacteria that characteristically vary in their shape are called pleomorphic (pleo meaning “many” and morphic referring to shape). Perhaps the greatest diversity in cell shapes is found in aquatic environments, where maximizing their surface area helps microbes absorb dilute nutrients (figure 3.21). Some aquatic bacteria have cytoplasmic extensions, giving them a starlike appearance. Square, tilelike archaeal cells have been found in the salty pools of the Sinai Peninsula in Egypt.

Groupings Most prokaryotes divide by binary fission, a process in which one cell divides into two. Cells adhering to one another following division form a characteristic arrangement that depends on the planes in which the organisms divide. This is seen especially in the cocci because they may divide in more than one plane (figure 3.22). Cells that divide in one plane may

53

Diplococcus Cell divides in one plane.

Chain of cocci

(a) Chains

Cell divides in two or more planes perpendicular to one another.

Packet

(b) Packets

Cell divides in several planes at random. Cluster (c) Clusters

FIGURE 3.22 Typical Cell Groupings The planes in which cells divide determine the arrangement of the cells. These characteristic arrangements can provide important clues in the identification of certain bacteria: (a) chains; (b) packets; (c) clusters.

form chains of varying length. Cocci that typically occur in pairs are routinely called diplococci. An important clue in the identification of Neisseria gonorrhoeae is its characteristic diplococcus arrangement. Some cocci form long chains; this characteristic is typical of some, but not all, members of the genus Streptococcus. Cocci that divide in two or three planes perpendicular to one another form cubical packets. Members of the genus Sarcina form such packets. Cocci that divide in several planes at random may form clusters. Species of Staphylococcus typically form characteristic grapelike clusters.

(a) 1 μm

(b) 1 μm

FIGURE 3.21 Diverse Shapes of Aquatic Prokaryotes (a) Square, tilelike archaeal cell. (b) Ancalomicrobium adetum, a bacterium that has a starlike appearance.

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Multicellular Associations Some types of bacteria typically live as multicellular associations. For example, members of a group of bacteria called myxobacteria glide over moist surfaces together, forming

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CHAPTER THREE Microscopy and Cell Structure

a swarm of cells that move as a pack. These cells release enzymes, which enables the pack to degrade organic material, including other bacterial cells. When water or nutrients are depleted, cells aggregate to form a structure called a fruiting body, which is visible to the naked eye (see figure 11.17). ■ myxobacteria, p. 264

In their natural habitat, most types of bacteria live on surfaces in associations called biofilms. These will be described in chapter 4. ■ biofilms, p. 85

MICROCHECK 3.3 Most common prokaryotes are cocci or rods, but as a group, they come in a variety of shapes and sizes. Cells may form characteristic arrangements such as chains or clusters. Some form multicellular associations. ✓ Which environmental habitat has the greatest diversity of bacterial shapes? ✓ What causes some bacteria to form characteristic cell arrangements?

THE STRUCTURE OF THE PROKARYOTIC CELL

The overall structure of the prokaryotic cell is deceptively simple (figure 3.23). The cytoplasmic membrane surrounds the cell, acting as a barrier between the external environment and the interior of the cell. This membrane permits the passage of only certain molecules into and out of the cell. Enclosing the cytoplasmic membrane is the cell wall, a rigid barrier that functions as a tight corset to keep the cell contents from bursting out. Cloaking the wall may be additional layers, some of which serve to protect the cell from predators and environmental assaults. The cell may also

have appendages, giving it useful traits, including motility and the ability to adhere to certain surfaces. The capsule (if present), cell wall, and cytoplasmic membrane together make up the cell envelope. Enclosed within this envelope are the contents of the cell—the cytoplasm and nucleoid. The cytoplasm is a viscous fluid composed of a variety of substances including water, enzymes and other proteins, carbohydrates, lipids, and various inorganic molecules. Structures within the cytoplasm include ribosomes and various storage granules. The nucleoid is the gel-

Pilus

Chromosome (DNA) Ribosomes Cytoplasm Nucleoid Cytoplasmic membrane Cell wall Capsule

(a)

Pili

(b)

0.5 μm

Flagellum

FIGURE 3.23 Typical Prokaryotic Cell A representation of typical structures within and outside a bacterial cell. (a) Diagrammatic representation. (b) Electron micrograph.

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3.4

like region where the chromosome resides. Unlike the nucleus that characterizes eukaryotic cells, the nucleoid is not enclosed within a membrane. The components of a prokaryote, together, enable the cell to survive and multiply in a given environment. Some structures are essential for survival and, as such, are common among all prokaryotic cells; others might be considered optional. Without these “optional” components, the cell may grow in the protected confines of a laboratory, but might not survive in the competitive surroundings of the outside world. The characteristics of typical structures of prokaryotic cells are summarized in table 3.3. Understanding the components of prokaryotic cells is essential for recognizing how these microbes function, but the information is relevant for other reasons as well. For example, certain features are characteristic of select groups of microbes and can be used as identifying markers, allowing scientists to distinguish different groups of bacteria. In addition, structures and processes unique to bacteria are potential targets for selective toxicity. By interfering with these, we can kill bacteria or inhibit their growth without harming the human host.

The Cytoplasmic Membrane

55

3.4 The Cytoplasmic Membrane Focus Points Describe the structure and chemistry of the cytoplasmic membrane, focusing on how it relates to membrane permeability. Briefly describe how the electron transport chain generates a proton motive force, focusing on how it relates to membrane permeability.

The cytoplasmic membrane is a delicate, thin, fluid structure that surrounds the cytoplasm and defines the boundary of the cell. It serves as an important semipermeable barrier between the cell and its external environment. Although the membrane primarily allows only water, gases, and some small hydrophobic molecules to pass through freely, specific proteins embedded within it act as selective gates. These permit nutrients to enter the cell, and waste products to exit. Other proteins within the membrane serve as sensors of environmental conditions. Thus, while the cytoplasmic

TABLE 3.3 A Summary of Prokaryotic Cell Structures Structure

Characteristics

Extracellular Filamentous appendages

Composed of protein subunits that form a helical chain.

Flagella

Provide the most common mechanism of motility.

Pili

Different types of pili have different functions. The common types, often called fimbriae, enable cells to adhere to surfaces. A few types mediate twitching or gliding motility. Sex pili join cells as a prelude to DNA transfer.

Capsules and slime layers

Layers outside the cell wall, usually made of polysaccharide.

Capsule

Distinct and gelatinous. Enables bacteria to adhere to specific surfaces; allows some organisms to thwart innate defense systems and thus cause disease.

Slime layer

Diffuse and irregular. Enables bacteria to adhere to specific surfaces.

Cell wall

Peptidoglycan provides rigidity to bacterial cell walls, preventing the cells from lysing.

Gram-positive

Thick layer of peptidoglycan that contains teichoic adds and lipoteichoic acids.

Gram-negative

Thin layer of peptidoglycan surrounded by an outer membrane. The outer layer of the outer membrane is lipopolysaccharide.

Cell Boundary Cytoplasmic membrane

Phospholipid bilayer embedded with proteins. Surrounds the cytoplasm, separating it from the outside environment. Also functions as a discriminating conduit between the cell and its surroundings.

Intracellular DNA

Contains the genetic information of the cell.

Chromosomal

Carries the genetic information essential to a cell, Typically a single, circular, double-stranded DNA molecule.

Plasmid

Extrachromosomal DNA molecule. Generally carries only genetic information that may be advantageous to a cell in certain situations.

Endospore

A type of dormant cell. Generally extraordinarily resistant to heat, desiccation, ultraviolet light, and toxic chemicals.

Cytoskeleton

Involved in cell division and controls cell shape.

Gas vesicles

Small, rigid structures that provides buoyancy to a cell.

Granules

Accumulations of high molecular weight polymers, synthesized from a nutrient available in relative excess.

Ribosomes

Intimately involved in protein synthesis. Two subunits, 30S and 50S, join to form the 70S ribosome.

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CHAPTER THREE Microscopy and Cell Structure

membrane acts as a barrier, it also functions as an effective and highly discriminating conduit between the cell and its surroundings. ■ hydrophobic, p. 26

move through by a process called simple diffusion. Other molecules must be transported across the membrane by specific transport mechanisms that will be discussed later.

Structure and Chemistry of the Cytoplasmic Membrane

Simple Diffusion

The structure of the bacterial cytoplasmic membrane is typical of other biological membranes—a lipid bilayer embedded with proteins (figure 3.24). The bilayer consists of two opposing layers composed of phospholipids. At one end of each phospholipid molecule are two fatty acid chains, which act as hydrophobic tails. The other end, containing glycerol, a phosphate group, and other polar molecules, functions as a hydrophilic head. The phospholipid molecules are arranged in each layer of the bilayer so that their hydrophobic tails face in, toward the other layer. Their hydrophilic heads face outward. As a consequence, the inside of the bilayer is water insoluble whereas the two surfaces interact freely with aqueous solutions. ■ phospholipids, p. 36 ■ hydrophilic, p. 26 More than 200 different membrane proteins have been found in E. coli. Many function as receptors, binding to specific molecules in the environment. This provides a mechanism for the cell to sense and adjust to its surroundings. Proteins are not stationary within the fluid bilayer; rather, they constantly change position. Such movement is necessary for the functions the membrane performs. This structure, with its resulting dynamic nature, is called the fluid mosaic model. Members of the Bacteria and Archaea have the same general structure of their cytoplasmic membranes, but the lipid compositions are distinctly different. The side chains of the membrane lipids of Archaea are connected to glycerol by a different type of chemical linkage. In addition, the side chains are hydrocarbons rather than fatty acids. These differences represent important distinguishing characteristics between these two domains of prokaryotes. ■ fatty acid, p. 35

Simple diffusion is the process by which some molecules move freely into and out of the cell. Water, small hydrophobic molecules, and gases such as oxygen and carbon dioxide are among the few substances that move through the cytoplasmic membrane by simple diffusion. The speed and direction of diffusion depend on the relative concentration of molecules on each side of the membrane. The greater the difference in concentration, the higher the rate of diffusion (from the higher to the lower concentration). The molecules continue to pass through at a diminishing rate until their concentration is the same on both sides of the membrane. The ability of water to move freely through the membrane has important biological consequences. The cytoplasm of a cell is a concentrated solution of inorganic salts, sugars, amino acids, and various other molecules. However, the environments in which prokaryotes normally grow contain only small amounts of some salts and other small molecules. Since the concentration of dissolved molecules, or solute, tends to equalize inside and outside the cell, water flows from the surrounding medium into the cell, thereby reducing the concentration of solute inside the cell (figure 3.25). This is the process of osmosis. This Membrane

Permeability of the Cytoplasmic Membrane The cytoplasmic membrane is selectively permeable; relatively few types of molecules can pass through freely. Those that do,

Solute molecules

Solute molecules

(a)

Water flow

Solute molecules Cell wall Higher solute concentration inside cell

Cytoplasmic membrane

Cytoplasmic membrane

Transport protein

Phospholipid bilayer

Opposing layers

H2O flows into cell.

Cytoplasmic membrane is forced against cell wall.

Higher solute concentration outside cell

Hydrophilic head Receptor

Hydrophobic tail

H2O flows out of cell.

Cytoplasmic membrane pulls away from cell wall.

(b)

FIGURE 3.24 The Structure of the Cytoplasmic Membrane Two opposing leaflets make up the phospholipid bilayer. Embedded within the bilayer are a variety of different proteins, some of which span the membrane.

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FIGURE 3.25 Osmosis (a) Water flows across a membrane toward the side that has the highest concentration of molecules and ions, thereby equalizing the concentrations on both sides. (b) The effect of osmosis on cells.

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3.5 Directed Movement of Molecules Across the Cytoplasmic Membrane

inflow of water exerts tremendous osmotic pressure on the cytoplasmic membrane, much more than it generally can resist. However, the rigid cell wall surrounding the membrane generally withstands such high pressure. The cytoplasmic membrane is forced up against the wall but cannot balloon further. Damage to the cell wall weakens the structure, and consequently, cells may burst or lyse.

The Role of the Cytoplasmic Membrane in Energy Transformation The cytoplasmic membrane of prokaryotic cells plays an indispensable role in converting energy to a usable form. This is an important distinction between prokaryotic and eukaryotic cells; in eukaryotic cells energy is transformed in membrane-bound organelles, which will be discussed later in this chapter. As part of their energy-harvesting processes, most prokaryotes have a series of protein complexes, the electron transport chain, embedded in their membrane. These sequentially transfer electrons and, in the process, eject protons from the cell. The details of these processes will be explained in chapter 6. The expulsion of protons by the electron transport chain results in the formation of a proton gradient across the cell membrane. Positively charged protons are concentrated immediately outside the membrane, whereas negatively charged hydroxyl ions accumulate directly inside the membrane (figure 3.26). This separation of charged ions creates an electrochemical gradient across the membrane; inherent in it is a form of energy, called proton motive force. This is analogous to the energy stored in a battery. ■ electron transport chain, p. 142 Energy of the proton motive force can be harvested when protons are allowed to move back into the cell. This is used directly to drive certain cellular processes, including some transport mechanisms that carry small molecules across the membrane and some forms of motility. It is also used to synthesize ATP. ■ ATP, p. 25

H+ H+

H+ H+ H+ H+

H+

H+

MICROCHECK 3.4 The cytoplasmic membrane is a phospholipid bilayer embedded with a variety of different proteins. It serves as a barrier between the cell and the surrounding environment, allowing relatively few types of molecules to pass through freely. The electron transport chain within the membrane expels protons, generating a proton motive force. ✓ Explain the fluid mosaic model. ✓ Name three molecules that can pass freely through the lipid bilayer. ✓ Why is the word “fluid” in fluid mosaic model an appropriate term?

3.5 Directed Movement of Molecules Across the Cytoplasmic Membrane Focus Points Compare and contrast facilitated diffusion and active transport. Describe the role of signal sequences in secretion.

Nearly all molecules that enter or exit a cell must cross the otherwise impermeable cytoplasmic membrane through proteins that function as selective gates. Mechanisms allowing nutrients and other small molecules to enter the cell are called transport systems. These systems are also used to expel wastes and compounds such as antibiotics and disinfectants that are otherwise deleterious to the cell. Cells actively move certain proteins they synthesize out of the cell—a process called secretion. Some of these secreted proteins make up structures such as flagella, which are appendages used for motility. Others are enzymes secreted to break down substances that would otherwise be too large to transport into the cell.

H+

H+

H+

57

H+

+

H

H+

Outside

Electron transport chain

Bilayer membrane

OH– OH–

OH–

–

OH OH– OH– OH– OH–

OH–

OH–

Inside

FIGURE 3.26 Proton Motive Force The electron transport chain, a series of protein complexes within the membrane, ejects protons from the cell. This creates an electrochemical gradient, a form of energy called proton motive force.

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By permission of John Deering and Creators Syndicate, Inc.

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CHAPTER THREE Microscopy and Cell Structure

Transport Systems Mechanisms used to transport molecules across the membrane employ highly specific proteins called transport proteins, permeases, or carriers. These proteins span the membrane, so that one end projects into the surrounding environment and the other into the cell. The interaction between the transport protein and the molecule it carries is highly specific. Consequently, a single carrier generally transports only a specific type of molecule. As a carrier transports a molecule, its shape changes, facilitating the passage of the molecule (figure 3.27). The mechanisms of transport are summarized in table 3.4.

Facilitated Diffusion Facilitated diffusion, or passive transport, moves substances from one side of the membrane to the other by exploiting a concentration gradient. Molecules are transported across until their concentration is the same on both sides of the membrane. This mechanism can only eliminate a difference in concentration, it cannot create one. As prokaryotes typically grow in relatively nutrient-poor environments, they generally cannot rely on facilitated diffusion to take in nutrients.

Active Transport Active transport moves compounds against a concentration gradient. This requires an expenditure of energy. There are two primary mechanisms of active transport, each utilizing a different form of energy. Nutrient molecules Outside of cell

Inside of cell Transport protein

Change of shape of transport protein

TABLE 3.4 A Summary of Transport Mechanisms Used by Prokaryotic Cells Transport Mechanism

Characteristics

Facilitated Diffusion

Rarely used by prokaryotes. Exploits a concentration gradient to move molecules; can only eliminate a gradient, not create one. No energy is expended.

Active Transport

Energy is expended to accumulate molecules against a concentration gradient.

Major facilitator superfamily

In bacteria, the proton motive force drives these transporters. As a proton is allowed into the cell another substance is either brought along or expelled.

ABC transporters

ATP is used as an energy source. Extracellular binding proteins deliver a molecule to the transporter.

Group Translocation

The transported molecule is chemically altered as it passes into the cell.

Transport Systems That Use Proton Motive Force Many bacterial transport systems can accumulate or extrude small molecules and ions using the energy of a proton motive force. Transporters of this type allow a proton into the cell and simultaneously either bring along or expel another substance (figure 3.28). For example, the permease that transports lactose brings the sugar into the cell along with a proton. Expulsion of waste products, on the other hand, relies on transporters that eject the compound as a proton passes in. Efflux pumps, which are used by some bacteria to oust antimicrobial drugs, use this latter mechanism. These systems are part of a large group of transporters, collectively known as the major facilitator superfamily (MFS), found in prokaryotes as well as eukaryotes. Transport Systems That Use ATP Transport mechanisms called

ABC transport systems require ATP as an energy source (ABC stands for ATP Binding-Cassette). These systems are relatively elaborate, involving multiple protein components (figure 3.29). ABC transport systems use binding proteins that reside immediately outside of the cytoplasmic membrane. These proteins each scavenge and deliver a given molecule to a specific transport complex within the membrane.

Outside of cell

Inside of cell

(a)

FIGURE 3.27 Transport Protein A transport protein changes its shape to facilitate passage of a compound across the cytoplasmic membrane.

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(b)

FIGURE 3.28 Active Transport Systems That Use Proton Motive Force Transporters of this type allow a proton into cell and simultaneously either (a) bring along another substance or (b) expel a substance.

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3.6 Binding protein

Transport protein

Outside

Inside

ATP

59

The general secretory pathway requires at least 11 different proteins and uses ATP to drive the process. However, the precise mechanism by which the proteins move across the membrane is still poorly understood.

MICROCHECK 3.5 Facilitated transport does not require energy but is rarely used by bacteria. Active transport via the major facilitator superfamily uses proton motive force. Active transport via an ABC transporter uses ATP as an energy source. Group translocation chemically modifies a molecule as it enters the cell. Proteins that have a signal sequence are secreted from a cell by the general secretory pathway. ✓ Transport proteins may be referred to as what two other terms? ✓ Describe the role of binding proteins in an ABC transport system. ✓ Can you argue that group translocation is a form of active transport?

ADP

3.6 Cell Wall

FIGURE 3.29 Active Transport Systems That Use ATP ABC transport systems require energy in the form of ATP. A binding protein that resides outside of the cytoplasmic membrane delivers a given molecule to a specific transport protein.

Cell Wall

Focus Points

Group Translocation

Describe the chemistry and structure of peptidoglycan.

Group translocation is a transport process that chemically alters a molecule during its passage through the cytoplasmic membrane (figure 3.30). Glucose and several other sugars are phosphorylated during their transport into the cell by the phosphotransferase system. The energy expended to phosphorylate the sugar can be regained when that sugar is later broken down to provide energy.

Compare and contrast the structure and chemistry of the Grampositive and Gram-negative cell walls, and describe how the differences account for the Gram staining characteristics. Explain why Gram-negative bacteria are typically less susceptible than Gram-positive bacteria to penicillin and lysozyme, and why Mycoplasma species are not affected by these agents. Describe the cell walls of members of the Archaea.

Secretion The general secretory pathway is the primary mechanism used to secrete proteins synthesized by the cell. It recognizes proteins destined for secretion by their signal sequence, a characteristic sequence of amino acids that make up one end.

The cell wall of most common prokaryotes is a rigid structure that determines the shape of the organism. A primary function of the wall is to hold the cell together and prevent it from bursting. If the cell wall is somehow breached, undamaged parts maintain their original shape (figure 3.31).

Transport protein

Outside

Inside

R

P R

1 μm P

FIGURE 3.30 Group Translocation This process chemically alters a molecule during its passage through the cytoplasmic membrane.

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FIGURE 3.31 The Rigid Cell Wall Determines the Shape of the Bacterium Even though the cell has split apart, the cell wall maintains its original shape.

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CHAPTER THREE Microscopy and Cell Structure

The type of cell wall distinguishes two main groups of bacteria—Gram-positive and Gram-negative. A comparison of the features of these groups is presented in table 3.5.

TABLE 3.5

Comparison of Features of GramPositive and Gram-Negative Bacteria Peptidoglycan and teichoic acids

Peptidoglycan Although the structure varies in Gram-positive and Gram-negative cells, the rigidity of bacterial cell walls is due to a layer of peptidoglycan, a macromolecule found only in bacteria. The basic structure of peptidoglycan is an alternating series of two major subunits, N-acetylmuramic acid (NAM) and N-acetylglucosamine (NAG). These subunits, which are related to glucose, are covalently joined to one another to form a glycan chain (figure 3.32).

Outer membrane

Cytoplasmic membrane

Peptidoglycan

Periplasm Cytoplasmic membrane

Gram-Positive

Gram-Negative

Color of Gram Stained Cell

Purple

Reddish-pink

Representative Genera

Bacillus, Staphylococcus, Streptococcus

Escherichia, Neisseria, Pseudomonas

Distinguishing Structures/Components N-acetylmuramic acid (NAM)

N-acetylglucosamine (NAG)

CH2OH

CH2OH O

H

O H

O

O H H

H

NH

OH

H

H

NH

O HC C

C

CH3

O

C

CH3

O

O H

Thin layer Absent

Outer membrane

Absent

Present

Lipopolysaccharide Absent (endotoxin)

Present

Porin proteins

Absent (unnecessary because there is no outer membrane)

Present; allow passage of molecules through outer membrane

Periplasm

Absent

Present

General Characteristics

NAM

NAG

NAM

Glycan chain

Peptidoglycan

Tetrapeptide chain (amino acids)

Sensitivity to penicillin

Generally more susceptible (with notable exceptions)

Generally less susceptible (with notable exceptions)

Sensitivity to lysozyme

Yes

No

Sugar backbone

NAM

NAG

Peptide interbridge (Gram-positive cells)

Tetrapeptide chain (amino acids)

Tetrapeptide chains

Glycan chain

Thick layer Present

O

CH3

OH

NAG

Peptidoglycan Teichoic acids

NAM

NAG

NAM

NAG Tetrapeptide chain (amino acids)

(a)

Peptide interbridge

(b)

FIGURE 3.32 Components and Structure of Peptidoglycan (a) Chemical structure of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM); the ring structures of the two molecules are glucose. Glycan chains are composed of alternating subunits of NAG and NAM joined by covalent bonds. Adjacent glycan chains are cross-linked via their tetrapeptide chains to create peptidoglycan. (b) Interconnected glycan chains form a very large three-dimensional molecule of peptidoglycan.

nes95432_Ch03_040-082.indd 60

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3.6

This high molecular weight linear polymer serves as the backbone of the peptidoglycan molecule. Attached to each of the NAM molecules is a string of four amino acids, a tetrapeptide chain, that plays an important role in the structure of the peptidoglycan molecule. Cross-linkages can form between tetrapeptide chains, thus joining adjacent glycan chains to form a single, very large three-dimensional molecule. In Gram-negative bacteria, tetrapeptides are joined directly. In Gram-positive bacteria, they are usually joined indirectly by a series of amino acids, a peptide interbridge, the composition of which may vary among species. An assortment of only a few different amino acids make up the tetrapeptide chain. One of these, diaminopimelic acid, which is related to the amino acid lysine, is not found in any other place in nature. Some of the others are d-isomers, a form not found in proteins. ■ D-Isomer, p. 26 ■ lysine, p. 27

The Gram-Positive Cell Wall A relatively thick layer of peptidoglycan characterizes the cell wall of Gram-positive bacteria (figure 3.33). As many as 30 layers, or sheets, of interconnected glycan chains make up the polymer. Regardless of its thickness, peptidoglycan is fully permeable to many substances including sugars and amino acids. A prominent component of the Gram-positive cell wall is a group of molecules called teichoic acids (from the Greek word teichos, meaning wall). These are chains of a common subunit, either ribitol-phosphate or glycerol-phosphate, to which various sugars and d-alanine are usually attached. Teichoic acids are joined to the peptidoglycan molecule through covalent bonds to N-acetylmuramic acid. Some, which are called lipoteichoic acids, are linked to the cytoplasmic membrane. Teichoic acids and lipoteichoic acids both stick out above the peptidoglycan layer and, because they are negatively charged, give the cell its negative polarity.

The Gram-Negative Cell Wall The cell wall of Gram-negative bacteria is far more complex than that of Gram-positive organisms (figure 3.34). It contains only a thin layer of peptidoglycan. Outside of that layer is the outer membrane, a unique lipid bilayer embedded with proteins. The peptidoglycan layer is sandwiched between the cytoplasmic membrane and the outer membrane.

The Outer Membrane Like the cytoplasmic membrane, which in Gram-negative bacteria is sometimes called the inner membrane, the outer membrane serves as a barrier to the passage of most molecules. Thus, it serves as a protective barrier, excluding many compounds that are deleterious to the cell, including certain antimicrobial medications. This is one reason why Gram-negative bacteria are generally less sensitive to many such medications. Small molecules and ions can cross the membrane through porins, specialized channel-forming proteins that span the outer membrane. Some porins are specific for certain molecules; others allow many different molecules to pass. Proteins produced by the cell that are destined for secretion are moved across the outer membrane by mechanisms known as secretion systems.

nes95432_Ch03_040-082.indd 61

Cell Wall

61

The outer membrane is unlike any other membrane in nature. Its lipid bilayer structure is typical of other membranes, but the outside layer is made up of lipopolysaccharides rather than phospholipids. For this reason, the outer membrane is also called the lipopolysaccharide layer, or LPS. The outer membrane is joined to peptidoglycan by means of lipoprotein molecules. ■ lipoproteins, p. 30 The Lipopolysaccharide Molecule The lipopolysaccharide molecule is extremely important from a medical standpoint. When purified lipopolysaccharide is injected into an animal, it elicits symptoms characteristic of infections caused by live bacteria. The same symptoms occur regardless of the bacterial species. To reflect the fact that the molecule that elicits the symptoms is an inherent part of the cell wall, it is called endotoxin. ■ endotoxin, p. 407 Two parts of the LPS molecule are notable for their medical significance (see figure 3.34c):

Lipid A is the portion that anchors the LPS molecule in the lipid bilayer. Its chemical make-up plays a significant role in the body’s ability to recognize the presence of invading bacteria. When lipid A is introduced into the body in small amounts, such as when microbes contaminate a small lesion, the defense system responds and effectively eliminates the invader. If, however, large amounts of lipid A are present, such as when Gram-negative bacteria are actively growing in the bloodstream, the magnitude of the defense system’s response damages even our own cells. This response to lipid A causes the symptoms associated with endotoxin. The O-specific polysaccharide side chain is the portion of LPS directed away from the membrane, at the end opposite that of lipid A. It is made up of a chain of sugar molecules, the number and composition of which varies among different species of bacteria. The differences can be exploited to identify certain species or strains. For example, the “O157” in E. coli O157:H7 refers to the characteristic O-side chain of the strains.

Periplasm The region between the cytoplasmic membrane and the outer membrane of Gram-negative bacteria is filled with a gel-like fluid called periplasm. All secreted proteins in these bacteria are contained within the periplasm unless they are specifically moved across the outer membrane as well. Thus, the periplasm is filled with proteins involved in a variety of cellular activities, including nutrient degradation and transport. For example, the enzymes that cells secrete to break down peptides and other molecules are found in the periplasm. Similarly, the binding proteins of the ABC transport systems are found there.

Antibacterial Substances that Target Peptidoglycan Compounds that interfere with the synthesis of peptidoglycan or alter its structural integrity weaken the rigid molecule to a point where it cannot prevent the cell from bursting. These substances have no effect on eukaryotic cells because peptidoglycan is unique to bacteria. Examples of compounds that target peptidoglycan include the antibiotic penicillin and the enzyme lysozyme.

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CHAPTER THREE Microscopy and Cell Structure

Peptidoglycan and teichoic acids

N-acetylglucosamine

Cytoplasmic membrane

N-acetylmuramic acid

Teichoic acid

Peptidoglycan (cell wall)

Gram-positive (a)

Cytoplasmic membrane

Peptidoglycan

Cytoplasmic membrane

Transport protein (b)

0.15 μm (c)

FIGURE 3.33 Gram-Positive Cell Wall (a) The Gram-positive cell wall is characterized by a relatively thick layer of peptidoglycan. (b) It is made up of many sheets of interconnected glycan chains. (c) Transmission electron photomicrograph of a typical Gram-positive cell (Bacillus subtilis).

Penicillin Penicillin is the most thoroughly studied of a group of antibiotics that interfere with peptidoglycan synthesis. Penicillin binds proteins involved in cell wall synthesis and, subsequently, prevents the cross-linking of adjacent glycan chains. ■ penicillin, p. 475 Generally, but with notable exceptions, penicillin is far more effective against Gram-positive cells than Gram-negative cells. This is because the outer membrane of Gram-negative cells prevents the medication from reaching its site of action, the peptidoglycan layer.

Lysozyme Lysozyme, an enzyme found in many body fluids including tears and saliva, breaks the bond that links the alternating N-acetylglucosamine and N-acetylmuramic acid molecules of peptidoglycan. This destroys the structural integrity of the glycan chain, the back-

nes95432_Ch03_040-082.indd 62

bone of the peptidoglycan molecule. Lysozyme is sometimes used in the laboratory to remove the peptidoglycan layer from bacteria for experimental purposes.

Differences in Cell Wall Composition and the Gram Stain Differences in the cell wall composition of Gram-positive and Gram-negative bacteria account for their staining characteristics. It is not the cell wall, however, but the inside of the cell that is stained by the crystal violet-iodine complex. The Gram-positive cell wall somehow retains the crystal violet-iodine complex within the cell even when subjected to acetone-alcohol treatment, whereas the Gram-negative cell wall cannot. The precise mechanism that accounts for the differential aspect of the Gram stain is not entirely understood.

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3.6 Outer membrane

Cell Wall

63

Peptidoglycan

O-specific polysaccharide (varies in length and composition) Porin protein

Core polysaccharide

Periplasm Cytoplasmic membrane Lipid A (embedded in lipid bilayer)

(a) (c) Lipopolysaccharide (LPS)

Outer membrane (lipid bilayer)

Periplasm

Lipoprotein

Cytoplasmic membrane (inner membrane; lipid bilayer)

Peptidoglycan

(b)

Transport protein

Peptidoglycan

Outer membrane

Periplasm

Cytoplasmic membrane

FIGURE 3.34 Gram-Negative Cell Wall (a) The Gram-negative cell wall is characterized by a very thin layer of peptidoglycan surrounded by an outer membrane. (b) The peptidoglycan layer is made up of only one or two sheets of interconnected glycan chains. The outer membrane is a typical phospholipid bilayer, except the outer leaflet contains lipolysaccharide. Porins span the membrane to allow specific molecules to pass. Periplasm fills the region between the cytoplasmic and outer membranes. (c) Structure of lipopolysaccharide. The Lipid A portion, which anchors the LPS molecule in the lipid bilayer, is responsible for the symptoms associated with endotoxin. The composition and length of the O-specific polysaccharide side chain varies among different species of bacteria. (d) A transmission electron micrograph of a typical Gramnegative cell wall (Pseudomonas aeruginosa).

(d)

0.15 μm

Presumably, the decolorizing agent dehydrates the thick layer of peptidoglycan; in this dehydrated state the wall acts as a permeability barrier, holding the dye within the cell. In contrast, the solvent action of acetone-alcohol easily damages the outer membrane of Gram-negative bacteria, and the relatively thin layer of peptidoglycan cannot retain the dye complex. These bacteria lose the dye complex more readily than their Gram-positive counterparts.

Characteristics of Bacteria that Lack a Cell Wall Some bacteria naturally lack a cell wall. Species of Mycoplasma, one of which causes a mild form of pneumonia, have an extremely variable shape because they lack a rigid cell wall (figure 3.35). As expected, neither penicillin nor lysozyme

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2 μm

FIGURE 3.35 Mycoplasma pneumoniae These cells vary in shape because they lack a cell wall.

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CHAPTER THREE Microscopy and Cell Structure Cell in intestine

affects these organisms. Mycoplasma and related bacteria can survive without a cell wall because their cytoplasmic membrane is stronger than that of most other bacteria. They have sterols in their membrane; these rigid, planar molecules stabilize membranes, making them stronger.

Cell Walls of the Domain Archaea As a group, members of the Archaea inhabit a wide range of extreme environments, and so it is not surprising they contain a greater variety of cell wall types than do members of the Bacteria. However, because most of these organisms have not been studied as extensively as the Bacteria, less is known about the structure of their walls. None contain peptidoglycan, but some do have a similar molecule, pseudopeptidoglycan.

MICROCHECK 3.6

Capsule (glycocalyx)

(a)

2 μm

Peptidoglycan is a molecule unique to bacteria that provides rigidity to the cell wall. The Gram-positive cell wall is composed of a relatively thick layer of peptidoglycan as well as teichoic acids. The Gram-negative cell wall has a thin layer of peptidoglycan and an outer membrane, which contains lipopolysaccharide. The outer membrane excludes molecules with the exception of those that pass through porins; proteins are secreted via special mechanisms. Penicillin and lysozyme interfere with the structural integrity of peptidoglycan. Mycoplasma species lack a cell wall. Members of the Archaea have a variety of cell wall types. ✓ What is the significance of lipid A? ✓ How does the action of penicillin differ from that of lysozyme? ✓ Explain why penicillin will kill only actively multiplying cells, whereas lysozyme will kill cells in any stage of growth. (b)

1 μm

FIGURE 3.36 Capsules and Slime Layers These layers enable bacteria

3.7 Capsules and Slime Layers Focus Point Compare and contrast the structure and function of capsules and slime layers.

Many bacteria envelop themselves with a gel-like layer that generally functions as a mechanism of either protection or attachment (figure 3.36). If the layer is distinct and gelatinous, it is called a capsule. If, instead, the layer is diffuse and irregular, it is called a slime layer. Colonies that form either of these often appear moist and glistening. Capsules and slime layers vary in their chemical composition depending on the species of bacteria. Most are composed of polysaccharides, and are commonly referred to as a glycocalyx (glyco means “sugar” and calyx means “shell”). A few capsules consist of polypeptides made up of repeating subunits of only one or two amino acids. Interestingly, the amino acids are generally of the d-stereoisomeric form, one of the few places d-amino acids are found in nature. ■ polysaccharide, pp. 30, 32 ■ D-amino acid, p. 26 Some types of capsules and slime layers enable bacteria to adhere to specific surfaces, including teeth, rocks, and other bacteria. These often enable microorganisms to grow as a biofilm,

nes95432_Ch03_040-082.indd 64

to attach to specific surfaces. (a) Capsules facilitating the attachment of bacteria to cells in the intestine (EM). (b) Masses of cells of Eikenella corrodens adhering in a layer of slime (SEM).

a polysaccharide-encased mass of bacteria coating a surface. One example is dental plaque, a biofilm on teeth. Streptococcus mutans uses sucrose to synthesize a capsule, which enables it to adhere to and grow in the crevices of the tooth. Other bacteria can then adhere to the layer created by S. mutans. Acid production by bacteria in the biofilm damages the tooth surface. ■ Streptococcus mutans, p. 587 ■ sucrose, p. 32 ■ dental caries, p. 586

Some capsules enable bacteria to thwart innate defense systems that otherwise protect against infection. Streptococcus pneumoniae, an organism that causes bacterial pneumonia, can only cause disease if it has a capsule. Unencapsulated cells are quickly engulfed and killed by phagocytes, an important cell of the body’s defense system. ■ Streptococcus pneumoniae, p. 509 ■ phagocytes, p. 358

MICROCHECK 3.7 Capsules and slime layers enable organisms to adhere to surfaces and sometimes protect bacteria from our innate defense system. ✓ How do capsules differ from slime layers? ✓ What is dental plaque? ✓ Explain why a sugary diet can lead to tooth decay.

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3.8

Filamentous Protein Appendages

65

3.8 Filamentous Protein Appendages Focus Points Describe the structure and function of flagella, and explain how the direction of their rotation is involved in chemotaxis. Compare and contrast the structure and function of fimbriae and sex pili.

Many bacteria have protein appendages that are anchored in the cytoplasmic membrane and protrude out from the surface. These structures are not essential to the life of the cell, but they do allow some bacteria to exist in certain environments in which they otherwise might not survive.

(a)

1 μm

Flagella The flagellum is a long protein structure responsible for most types of bacterial motility (figure 3.37). By spinning like a propeller, using proton motive force as energy, the flagellum pushes the bacterium through liquid much as a ship is driven through water. Flagella must work very hard to move a cell, since water has the same relative viscosity to bacteria as molasses has to humans. Nevertheless, their speed is quite phenomenal; flagella can rotate more than 100,000 revolutions per minute (rpm), propelling the cell at a rate of 20 body lengths per second. This is the equivalent of a 6-foot man running 82 miles per hour! In some cases, flagella are important in the ability of an organism to cause disease. For example, Helicobacter pylori, the bacterium that causes gastric ulcers, has powerful multiple flagella at one end of its spiral-shaped cell. These flagella allow H. pylori to penetrate the viscous mucous gel that coats the stomach epithelium. ■ Helicobacter pylori, p. 589

(b)

1 μm

FIGURE 3.37 Flagella (a) Peritrichous flagella (SEM); (b) polar flagellum (SEM). Filament

Structure and Arrangement of Flagella Flagella are composed of three basic parts (figure 3.38). The filament is the portion extending into the exterior environment. It is composed of identical subunits of a protein called flagellin. These Hook

Flagellin (protein subunits that make up the filament)

FIGURE 3.38 The Structure of a Flagellum in a Gram-Negative Bacterium The flagellum is composed of three basic parts—a filament, a hook, and a basal body.

Flagellum Outer membrane of cell wall

Basal body

Peptidoglycan layer of cell wall Periplasm

Rod E. coli

Cytoplasmic membrane

nes95432_Ch03_040-082.indd 65

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CHAPTER THREE Microscopy and Cell Structure

subunits form a chain that twists into a helical structure with a hollow core. Connecting the filament to the cell surface is a curved structure, the hook. The basal body anchors the flagellum to the cell wall and cytoplasmic membrane. The numbers and arrangement of flagella can be used to characterize flagellated bacteria. For example, E. coli have flagella distributed over the entire surface, an arrangement called peritrichous (peri means “around”). Other common bacteria have a polar flagellum, a single flagellum at one end of the cell. Other arrangements include a tuft of flagella at one or both ends of a cell (see figures 3.18 and 3.20e).

Flagellum

Magnetite particles 0.4 mm

FIGURE 3.40 Magnetic Particles Within a Magnetotactic Bacterium The chain of particles of magnetite (Fe3O4) within the spirillum Magnetospirillum magnetotacticum serve to align the cell along geomagnetic lines (TEM).

Chemotaxis Motile bacteria sense the presence of chemicals and respond by moving in a certain direction—a phenomenon called chemotaxis. If a compound is a nutrient, it may serve as an attractant, enticing cells to move toward it. On the other hand, if the compound is toxic, it may act as a repellent, causing cells to move away. The movement of a bacterium toward an attractant is anything but direct (figure 3.39). When E. coli travels, it progresses in a given direction for a short time, then stops and tumbles for a fraction of a second, and then moves again in a relatively straight line. But after rolling around, the cell is often oriented in a completely different direction. The seemingly odd pattern of movement is due to the rotation of the flagella. When the flagella rotate counterclockwise, the bacterium is propelled in a forward movement called a run. The flagella of E. coli and other peritrichously flagellated bacteria rotate in a coordinated fashion, forming a tight propelling bundle. After a brief period, the direction of rotation of the flagella is reversed. This abrupt change causes the cell to stop and roll, called a tumble. Movement toward an attractant is due to runs of longer duration that occur when cells are going in the right direction; this occurs because cells tumble less frequently when Key

Tumble (T)

Run (R)

Tumble (T)

T T T T R R

(a) No attractant or repellent

(b) Gradient of attractant concentration

FIGURE 3.39 Chemotaxis (a) A cell moves via a random series of short runs and tumbles when the attractant or repellent is uniformly distributed. (b) The cell tumbles less frequently resulting in longer runs when it senses that it is moving closer to the attractant.

nes95432_Ch03_040-082.indd 66

they sense they are moving closer to an attractant. In contrast, they tumble more frequently when they sense they are moving closer to a repellent. In addition to reacting to chemicals, some bacteria can respond to variations in light (phototaxis). Other bacteria can respond to the concentration of oxygen (aerotaxis). Organisms that require oxygen for growth will move toward it, whereas bacteria that grow only in its absence tend to be repelled by it. Certain motile bacteria can react to the earth’s magnetic field by the process of magnetotaxis. They actually contain a row of magnetic particles that cause the cells to line up in a north-to-south direction much as a compass does (figure 3.40). The magnetic forces of the earth attract the organisms so that they move downward and into sediments where the concentration of oxygen is low, which is the environment best suited for their growth. Some bacteria can also move toward certain temperatures (thermotaxis).

Pili Pili are considerably shorter and thinner than flagella, but they have a similar structural theme to the filament of flagella— a string of protein subunits arranged helically to form a long cylindrical molecule with a hollow core (figure 3.41). The functions of pili, however, are distinctly different from those of flagella. Many types of pili enable attachment of cells to specific surfaces; these pili are also called fimbriae. At the tip or along the length of the molecule is located another protein, an adhesin, that adheres by binding to a very specific molecule. For example, certain strains of E. coli that cause a severe watery diarrhea can attach to the cells that line the small intestine. They do this through specific interactions between adhesins on their pili and the intestinal cell surface. Without the ability to attach, these cells would simply be propelled through the small intestine along with the other intestinal contents. ■ enterotoxigenic E. coli, p. 600 Pili also appear to play a role in the movement of populations of cells on solid media. Twitching motility, characterized by short, jerking movements, and some types of gliding motility, characterized by smooth sliding motion, involve pili. Another type of pilus, called a sex pilus, is used to join one bacterium to another as a prelude to a specific type of DNA transfer. This and other mechanisms of DNA transfer will be described in chapter 8. ■ DNA transfer, p. 199

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3.9

Internal Structures

67

Epithelial cell Sex pilus Bacterium

Bacterium with pili Flagellum

Other pili

(b)

(a) 1 μm

5 μm

FIGURE 3.41 Pili (a) Pili on an Escherichia coli cell. The short pili (fimbriae) mediate adherence; the sex pilus is involved in DNA transfer. (b) Escherichia coli attaching to epithelial cells in the small intestine of a pig.

MICROCHECK 3.8 Flagella are the most common mechanism for bacterial motility. Chemotaxis is the directed movement of cells toward an attractant or away from a repellent. Pili provide a mechanism for attachment to specific surfaces and, in some cases, a type of motility. Sex pili join cells as a prelude to DNA transfer. ✓ What role does a series of runs and tumbles play in chemotaxis? ✓ E. coli cells have peritrichous flagella. What does this mean?

3.9 Internal Structures

(a) 0.5 μm

Focus Points Describe the structure and function of the chromosomes, plasmids, ribosomes, storage granules, gas vesicles, and endospores. Describe the processes of sporulation and germination.

DNA fibers

Prokaryotic cells have a variety of structures within the cell. Some, such as the chromosome and ribosomes, are essential for the life of all cells, whereas others confer certain selective advantages.

Membrane Ruptured cell

The Chromosome The chromosome of prokaryotes resides as an irregular mass within the cytoplasm, forming a gel-like region called the nucleoid. Typically, it is a single, circular double-stranded DNA molecule that contains all the genetic information required by a cell. Chromosomal DNA is tightly packed into about 10% of the total volume of the cell (figure 3.42). Rather than being a loose circle it is typically in a twisted form called supercoiled, which

nes95432_Ch03_040-082.indd 67

(b)

FIGURE 3.42 The Chromosome (a) Color-enhanced transmission electron micrograph of a thin section of Escherichia coli, with the DNA shown in red. (b) Chromosome released from a gently lysed cell of E. coli. Note how tightly packed the DNA must be inside the bacterium.

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CHAPTER THREE Microscopy and Cell Structure

appears to be stabilized by the binding of positively charged proteins. Supercoiling can be visualized by cutting a rubber band and twisting one end several times before rejoining the ends. The resulting circle will twist and coil in response.

Plasmids Most plasmids are circular, supercoiled, double-stranded DNA molecules. They are generally 0.1% to 10% of the size of the chromosome and carry from a few to several hundred genes. A single cell can harbor multiple types of plasmids. A cell generally does not require the genetic information carried by a plasmid. However, the encoded characteristics may be advantageous in certain situations. For example, many plasmids code for the production of one or more enzymes that destroy certain antibiotics, enabling the organism to resist the otherwise lethal effect of these medications. Because a bacterium can sometimes transfer a copy of a plasmid to another bacterial cell, this accessory genetic information can spread, which accounts in large part for the increasing frequency of antibiotic-resistant organisms worldwide. ■ mobile gene pool, p. 205

Ribosomes Ribosomes are intimately involved in protein synthesis, where they serve as the structures that facilitate the joining of amino acids. Each ribosome is composed of a large and a small subunit, which are made up of ribosomal proteins and ribosomal RNAs. ■ function of ribosomes, p. 171

The relative size and density of ribosomes and their subunits are expressed as a distinct unit, S (for Svedberg), that reflects how fast they settle when spun at very high speeds in an ultracentrifuge. The faster they move toward the bottom, the higher the S value and the greater the density. Prokaryotic ribosomes are 70S ribosomes. Note that S units are not strictly arithmetic; the 70S ribosome is composed of a 30S and a 50S subunit (figure 3.43). Prokaryotic ribosomes differ from eukaryotic ribosomes, which are 80S. Differences in the structures serve as targets for certain antibiotics.

Cytoskeleton It was once thought that bacteria lacked a cytoskeleton, an interior protein framework. Several bacterial proteins that have similarities to those of the eukaryotic cytoskeleton have now been characterized, and these appear to be intimately involved in cell division and controlling cell shape.

Storage Granules Storage granules are accumulations of high molecular weight polymers synthesized from a nutrient that a cell has in relative excess. For example, if nitrogen and/or phosphorus are lacking, E. coli cannot multiply even if a carbon and energy source such as glucose is plentiful. Rather than waste the carbon/energy source, cells use it to produce glycogen, a glucose polymer. Later, when conditions are appropriate, cells degrade and use the glycogen. Other bacterial species store carbon and energy as poly-bhydroxybutyrate (figure 3.44). This microbial compound is now being employed to produce a biodegradable polymer, which can be used in place of petroleum-based plastics. Some types of granules can be readily detected by light microscopy. Volutin granules, a storage form of phosphate, stain red with blue dyes such as methylene blue, whereas the surrounding cellular material stains blue. Because of this, they are often called metachromatic granules (meta means “change” and chromatic means “color”). Recent evidence suggests that the role of these granules is more complex than originally thought. The volutin granules of some bacteria are membrane-bound and appear to resemble eukaryotic organelles that are thought to be involved with energy storage and pH balance. Regardless of the precise function of the granules, bacteria that produce them are beneficial in wastewater treatment because they scavenge phosphate, an environmental pollutant.

Gas Vesicles Some aquatic bacteria produce gas vesicles—small, rigid, proteinbound compartments that provide buoyancy to the cell. Gases, but not water, flow freely into the vesicles, thereby decreasing the

70S ribosome

30S subunit

30S + 50S combined

0.5 μm 50S subunit

FIGURE 3.43 The Ribosome The 70S ribosome is composed of 50S and 30S subunits.

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Storage granules

FIGURE 3.44 Storage Granules The large unstained areas in the photosynthetic bacterium Rhodospirillum rubrum are granules of polyb-hydroxybutyrate.

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3.9

density of the cell. By regulating the number of gas vesicles within the cell, an organism can float or sink to its ideal position in the water column. For example, bacteria that use sunlight as a source of energy float closer to the surface, where light is available.

Endospores An endospore is a unique type of dormant cell produced by a process called sporulation within cells of certain bacterial species, such as members of the genera Bacillus and Clostridium (figure 3.45). The structures may remain dormant for perhaps 100 years, or even longer, and are extraordinarily resistant to damaging conditions including heat, desiccation, toxic chemicals, and ultraviolet irradiation. Immersion in boiling water for hours may not kill them. Endospores that survive these treatments can germinate, or exit the dormant stage, to become a typical multiplying cell, called a vegetative cell. The consequences of these resistant dormant forms are farreaching. Because endospores can survive so long in a variety of conditions, they can be found virtually anywhere. They are common in soil, which can make its way into environments such as laboratories and hospitals and onto products such as food, media used to cultivate microbes, and medical devices. Because the exclusion of microbes in these environments and on these products is of paramount importance, special precautions must be taken to destroy these resistant structures. Endospores are sometimes called spores. However, this latter term is also used to refer to the structures produced by unrelated microorganisms such as fungi. Bacterial endospores are much more resistant to environmental conditions than are other types of spores. Several species of endospore-formers can cause disease. For example, botulism results from the ingestion of a deadly toxin produced by vegetative cells of Clostridium botulinum. Other disease-causing species of endospore-formers include Clostridium tetani, which causes tetanus; Clostridium perfringens, which causes gas gangrene; and Bacillus anthracis, which causes anthrax. ■ botulism, p. 657 ■ tetanus, p. 566 ■ gas gangrene, p. 568

Internal Structures

69

Sporulation Endospore formation is a complex, highly ordered sequence of changes that initiates when sporeforming bacteria are grown in low amounts of carbon or nitrogen (figure 3.46). Apparently the cells sense starvation conditions and therefore begin the 8-hour process that prepares them for rough times ahead. After vegetative growth stops, DNA is duplicated and then a septum forms between the two chromosomes, dividing the cell asymmetrically. The larger compartment then engulfs the smaller compartment, forming a forespore within a mother cell. These two portions take on different roles in synthesizing the components that will make up the endospore. The forespore, which is enclosed by two membranes, will ultimately become the core of the endospore. Peptidoglycan-containing material is laid down between these two membranes, forming the core wall and the cortex. Meanwhile, the mother cell makes proteins that will form the spore coat. Ultimately, the mother cell is degraded and the endospore released.

Vegetative growth stops; DNA is duplicated.

A septum forms, dividing the cell asymmetrically.

The larger compartment then engulfs the smaller compartment, forming a forespore within a mother cell.

■ anthrax, p. 512

Forespore

Mother cell

Peptidoglycan-containing material is laid down between the two membranes that now surround the forespore. Peptidoglycan-containing material Core wall

The mother cell is degraded and the endospore released. Endospore

1 μm Cortex

Spore coat

FIGURE 3.45 Endospores Endospore inside a vegetative cell of a Clostridium species (TEM).

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FIGURE 3.46 The Process of Sporulation

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CHAPTER THREE Microscopy and Cell Structure

The layers of the endospore shield it from damage. The spore coat is thought to function as a sieve, excluding molecules such as lysozyme. The cortex helps maintain the core in a dehydrated state, protecting it from the effects of heat. In addition, the core has small, acid-soluble proteins that bind the DNA, thereby protecting it from damage. The core is rich in an unusual compound called dipicolinic acid, which combines with calcium ions. This complex appears to also play an important role in spore resistance.

Germination Germination can be triggered by a brief exposure to heat or certain chemicals. Following such exposure, the endospore takes on water and swells. The spore coat and cortex then crack open, and a vegetative cell grows out. Since one vegetative cell gives rise to one endospore, sporulation is not a means of cell reproduction.

MICROCHECK 3.9 The prokaryotic chromosome is usually a circular, double-stranded DNA molecule that contains all of the genetic information required by a cell. Plasmids generally only encode information that is advantageous to a cell in certain conditions. Ribosomes are the structures that facilitate the joining of amino acids to form a protein. The cytoskeleton is an interior framework involved in cell division and controlling cell shape.Storage granules are polymers synthesized from a nutrient a cell has in relative excess. Gas vesicles provide buoyancy to a cell. An endospore is a highly resistant dormant stage produced by certain bacterial species. ✓ Explain how glycogen granules benefit a cell. ✓ Explain why endospores are an important consideration for the canning industry. ✓ Why are the processes of sporulation and germination not considered a mechanism of multiplication?

THE EUKARYOTIC CELL

Eukaryotic cells are generally much larger than prokaryotic cells, and their internal structures are far more complex (figure 3.47). One of their distinguishing characteristics is the abundance Nuclear Smooth envelope endoplasmic reticulum Centriole

Nucleus Nucleolus Cytoplasm Rough endoplasmic reticulum

Mitochondrion Peroxisome

Ribosomes

Actin filament

of membrane-enclosed compartments or organelles. The most important of these is the nucleus, which contains the DNA. The organelles, which can take up half the total cell volume, enable the cell to perform complex functions in separated regions. For example, degradative enzymes contained within an organelle digest food and other material without posing a threat to the integrity of the cell itself. Each organelle contains a variety of proteins and other molecules, many of which are synthesized at other locations. To deliver these to the lumen, or interior, of another organelle, an elaborate transportation system is required. To transfer material,

Microtubule Lysosome

Intermediate filament Cytoskeleton

Plasma membrane

Golgi complex

(a)

Cytoskeleton Actin filament

Smooth endoplasmic reticulum

Nucleus

Nucleolus Nucleus Rough endoplasmic reticulum

Microtubule Intermediate filament

Nuclear membrane

Ribosomes

Plasma membrane Golgi complex

Cell membrane

Nuclear envelope

Mitochondrion

Central vacuole

Cell wall Lysosome

Mitochondrion Cytoplasm

Adjacent cell wall

(b)

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(c) 1 mm

Peroxisome

FIGURE 3.47 Eukaryotic Cells (a) Diagrammatic representation of an

Chloroplast (opened to show thylakoids)

animal cell. (b) Diagrammatic representation of a plant cell. (c) Micrograph of an animal cell shows several membrane-bound structures including mitochondria and a nucleus.

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The Eukaryotic Cell

TABLE 3.6

Protein

71

A Summary of Eukaryotic Cell Structures Characteristics

Plasma Membrane Budding vesicle

Migrating transport vesicle

Fusion of vesicle with Golgi apparatus

FIGURE 3.48 Vesicle Formation and Fusion A vesicle forms when a section of an organelle buds off. The mobile vesicle can then move to other parts of the cell, ultimately fusing with the membrane of another organelle.

a section of an organelle will bud or pinch off, forming a small membrane-enclosed vesicle (figure 3.48). This mobile vesicle, containing a sampling of the contents of the organelle, can move to other parts of the cell. When that vesicle encounters the lipid membrane of another organelle, the two membranes fuse to become one contiguous unit. By doing so, the vesicle introduces its contents to the lumen of the organelle. A similar process is used to export molecules synthesized within an organelle to the external environment. As a group, eukaryotic cells are highly variable. For example, protozoa, which are single-celled organisms, must function exclusively as self-contained units that seek and ingest food. These cells must be mobile and flexible to take in food particles. Consequently, they lack cell walls that would otherwise provide rigidity. Animal cells also lack a cell wall, because they too must be flexible to accommodate movement. Fungi, on the other hand, are stationary and benefit from the protection provided by a rigid cell wall. Compounds that make up fungal cell walls include glucan and mannan, which are polysaccharides, and chitin, a polymer of N-acetylglucosamine that is also found in crustaceans and insects. Plant cells, which are also stationary, have cell walls composed of cellulose, a polymer of glucose. ■ polysaccharides, pp. 30, 32 The individual cells of a multicellular organism can be distinctly different from one another. Mammals, for example, are composed of several hundred different types of cells, and it is obvious that a liver cell is quite different from a bone cell. Cells of plants and animals function in cooperative associations called tissues. The tissues in your body include muscle, connective, nerve, epithelial, blood, and lymphoid. Each of these provides a unique function. Combinations of various tissues function together to make up larger units, organs. These include skin, heart, and liver. Organs and the tissues that constitute them will be covered in more detail in chapters 22 through 29 on infectious diseases. A comprehensive coverage of all aspects of eukaryotic cells is beyond the scope of this textbook. Instead, this section will focus on key characteristics, particularly those that directly affect the interaction of a microbe with a human host. These characteristics are summarized in table 3.6. A comparison of

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Asymmetric lipid bilayer embedded with proteins. Selective permeability, conduit to external environment.

Internal Protein Structures Cilia

Appear to project out of a cell. Beat in synchrony to provide movement. Composed of microtubules in a 9+2 arrangement.

Cytoskeleton

Dynamic filamentous network that provides structure to the cell.

Flagella

Appear to project out of a cell. Propel or push the cell with a whiplike or thrashing motion. Composed of microtubules in a 9+2 arrangement.

Ribosomes

Two subunits, 60S and 40S, join to form the 80S ribosome.

Membrane-Bound Organelles Chloroplasts

Site of photosynthesis; the organelle harvests the energy of sunlight to generate ATP, which is then used to convert CO2 to carbohydrates. Within the stroma are chlorophyll-containing, disclike thylakoids. The membranes of these contain the components of the electron transport chain and the proteins that use proton motive force to synthesize ATP.

Endoplasmic reticulum

Site of synthesis of macromolecules destined for other organelles or the external environment.

Rough

Attached ribosomes thread proteins they are synthesizing into the lumen of the organelle.

Smooth

Site of lipid synthesis and degradation, and Ca2+ storage.

Golgi apparatus

Site where macromolecules synthesized in the endoplasmic reticulum are modified before they are transported in vesicles to other destinations.

Lysosome

Digestion of macromolecules.

Mitochondria

Harvest the energy released during the degradation of organic compounds to generate ATP. Within the highly folded inner membrane are the components of the electron transport chain and the proteins that use proton motive force to synthesize ATP.

Nucleus

Contains the DNA.

Peroxisome

Oxidation of lipids and toxic chemicals occurs.

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CHAPTER THREE Microscopy and Cell Structure

TABLE 3.7

Comparison of Prokaryotic and Eukaryotic Cell Structures/Functions Prokaryotic

Eukaryotic

General Characteristics Size

Generally 0.3– 2 mm in diameter.

Generally 5– 50 mm in diameter.

Cell Division

Chromosome replication followed by binary fission.

Mitosis followed by division.

Chromosome location

Located in the nucleoid, which is not membranebound.

Contained within the membrane-bound nucleus.

Cell membrane

Relatively symmetric with respect to the lipid content of the bilayers.

Highly asymmetric; lipid composition of outer layer differs significantly from that of inner layer.

Cell wall

Composed of peptidoglycan (Bacteria); Gramnegative bacteria have an outer membrane as well.

Absent in animal cells; composition in other cell types may include: chitin, glucans and mannans (fungi), and cellulose (plants).

Chromosome

Single, circular DNA molecule is typical.

Multiple, linear DNA molecules. DNA is wrapped around histones.

Flagella

Composed of protein subunits.

Made up of a 9+2 arrangement of microtubules.

Membrane-bound organelles

Absent.

Present; includes the nucleus, mitochondria, chloroplasts (only in plant cells), endoplasmic reticulum, Golgi apparatus, lysosomes, and peroxisomes.

Nucleus

Absent; DNA resides as an irregular mass forming the Present. nucleoid region.

Ribosomes

70S ribosomes, which are made up of 50S and 30S subunits.

80S ribosomes, which are made up of 60S and 40S subunits. Mitochondria and chloroplasts have 70S ribosomes.

Degradation of extracellular substances

Enzymes are secreted that degrade macromolecules outside of the cell. The resulting small molecules are transported into the cell.

Macromolecules are brought into the cell by endocytosis. Lysosomes carry digestive enzymes.

Motility

Generally involves flagella, which are composed of protein subunits. Flagella rotate like propellers, using proton motive force for energy.

Involves cilia and flagella, which are made up of a 9+2 arrangement of microtubules, Cilia move in synchrony; flagella propel a cell with a whiplike motion or thrash back and forth to pull a cell forward. Both use ATP for energy.

Protein secretion

A characteristic signal sequence marks proteins for secretion by the general secretory pathway.

Secreted proteins are moved to the lumen of the rough endoplasmic reticulum as they are being synthesized. From there, they are transported to the Golgi apparatus for processing and packaging.

Strength and rigidity

Peptidoglycan-containing cell wall (Bacteria).

Cytoskeleton composed of microtubules, intermediate filaments, and microfilaments. Some have a cell wall; some have sterols in the membrane.

Transport

Primarily active transport. Group translocation.

Facilitated diffusion and active transport. Ion channels.

Structures

Functions

functional aspects of prokaryotic and eukaryotic cells is presented in table 3.7.

3.10 The Plasma Membrane Focus Point Describe the structure of the eukaryotic plasma membrane, comparing and contrasting it with the bacterial cytoplasmic membrane.

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All eukaryotic cells have a cytoplasmic membrane, or plasma membrane, which is similar in chemical structure and function to that of prokaryotic cells. It is a typical phospholipid bilayer embedded with proteins. The lipid and protein composition of the layer that faces the cytoplasm, however, differs significantly from that facing the outside of the cell. The same is true for membranes that surround the organelles. The layer facing the lumen of the organelle is similar to its counterpart facing the cell exterior. This lack of symmetry reflects the important role these membranes play in the complex processes occuring within the eukaryotic cell. The proteins in the lipid bilayer perform a variety of functions. Some are involved in transport and others are attached to internal structures, helping to maintain cell integrity. Those in the outer layer often

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3.11 Transfer of Molecules Across the Plasma Membrane

function as receptors. Typically, these receptors are glycoproteins, proteins that have various sugars attached. A given receptor binds a specific molecule, which is referred to as its ligand. These receptorligand interactions are extremely important in multicellular organisms because they allow cells to communicate with each other—a process called signaling. For example, in our bodies, some cells secrete a specific protein when they encounter certain compounds perceived as dangerous. Other cells of the immune system have receptors for that protein on their surface. When the protein binds its receptor, those cells recognize the signal as a call for help and respond accordingly. This cell-to-cell communication enables a multicellular organism to function as a cohesive unit. ■ glycoproteins, p. 30 The membranes of many eukaryotic cells contain sterols, which provide strength to the otherwise fluid structure. Recall that Mycoplasma, a group of bacteria lacking a cell wall, also have sterols in their membrances. The sterol found in animal cell membranes is cholesterol, whereas fungal membranes contain ergosterol. This difference is exploited by antifungal medications that act by interfering with ergosterol synthesis or function. ■ antifungal medications, p. 488 ■ oligosaccharides, p. 30

Within the fluid lipid layer of the plasma membrane are cholesterol-rich regions called lipid rafts. The role of these regions is still being elucidated, but they appear to be important in allowing the cell to detect and respond to signals in the external environment. From a microbiologist’s perspective, they are also important because many viruses appear to use these regions when they exit a cell. The plasma membrane plays no role in ATP synthesis; instead, that task is performed by mitochondria (discussed later). Although proton motive force is not generated across the membrane, an electrochemical gradient is maintained by energy-consuming mechanisms that expel either sodium ions or protons. ■ electrochemical gradient, p. 57

MICROCHECK 3.10 The plasma membrane is an asymmetric lipid bilayer embedded with proteins. Specific receptors on the outer layer mediate cell-to-cell signaling. Sterols provide strength to the fluid membrane. ✓ What is the medical significance of ergosterol in the fungal membranes? ✓ Describe why signaling is important in animal cells. ✓ How could one argue that the lumen of an organelle is “outside” of a cell?

73

transport proteins; others are taken in through a process called endocytosis. Exocytosis, the reverse of endocytosis, can be used to expel material.

Transport Proteins The transport proteins of eukaryotic cells function as either carriers or channels. Carriers are analogous to proteins in prokaryotic cells that mediate facilitated diffusion and active transport. Channels are pores in the membrane. These pores are so small that only specific ions can diffuse through. They allow ions to move with the concentration gradient; they do not create such a gradient. To control ion passage, the channel has a gate, which can be either opened or closed, depending on environmental conditions. Cells of multicellular organisms can often take up nutrients by facilitated diffusion, because the nutrient concentration of surrounding environments can be controlled. For example, glucose levels in the blood are maintained at a concentration higher than in most tissues. Consequently, animal cells generally do not need to expend energy transporting glucose. The active transport mechanisms of eukaryotic cells are structurally analogous to those of prokaryotic cells. Some are of medical interest because they can eject drugs from the cell. For example, some human cancer cells use an ABC transporter that ejects therapeutic drugs intended to kill those cells.

Endocytosis and Exocytosis Endocytosis is the process by which eukaryotic cells take up material from the surrounding environment (figure 3.49). The type of endocytosis common to most animal cells is pinocytosis. In this process a cell internalizes and pinches off small pieces of its own membrane, bringing along a small volume of liquid and any material attached to the membrane. This endocytic vesicle becomes a

Pinocytosis

Fusion with lysosomes

Endocytic vesicle Endosome

Digestive enzymes Lysosome

3.11 Transfer of Molecules Across the Plasma Membrane

Vesicle

Fusion with lysosomes

Phagosome

Focus Points

Phagolysosome (digestion occurs)

Compare and contrast the roles of channels and carriers in transport. Exocytosis

Describe the processes of endocytosis and exocytosis. Describe the role of the endoplasmic reticulum in secretion.

Pseudopod Phagocytosis

Nutrients, signaling molecules, and waste products pass through the plasma membrane. Some of these enter and exit the cell via

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FIGURE 3.49 Endocytosis and Exocytosis Endocytosis includes pinocytosis and phagocytosis.

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CHAPTER THREE Microscopy and Cell Structure

membrane-enclosed, low-pH compartment called an endosome. This then fuses with digestive organelles called lysosomes. The characteristics of lysosomes will be discussed shortly. ■ lysosome, p. 79 Animal cells often take up material by receptor-mediated endocytosis, which can be viewed as a variation of pinocytosis that allows cells to internalize extracellular ligands that bind to receptors on the cell’s surface. When the receptors bind their ligand, the region is internalized to form an endocytic vesicle that contains the receptors along with their bound ligands. The low pH of the endosome frees the ligands from the receptors, which are often recycled. The endosome then fuses with lysosomes. Many viruses, including those that cause influenza and rabies, exploit receptor-mediated endocytosis to enter animal cells. By binding to a specific receptor, they too are taken up. ■ influenza, p. 519 ■ rabies, p. 663 Protozoa and phagocytes, both of which ingest bacteria and large debris, use a specific type of endocytosis called phagocytosis. Phagocytes are important cells of the body’s defense system. The cells send out armlike extensions, pseudopods, which surround and enclose extracellular material, including bacteria. This action envelops the material, bringing it into the cell in an enclosed compartment called a phagosome. These ultimately fuse with lysosomes to form a phagolysosome. Phagocytes have a greater abundance of lysosomes than do other animal cells, which reflects their specialized function. In addition, their lysosomes contain a wider array of powerful digestive enzymes. Thus, most microbes are readily dispatched within the phagolysosome. Those that resist the killing effects are able to cause disease. ■ phagocytes, p. 358 ■ survival within a phagocyte, p. 403 The process of exocytosis is the reverse of endocytosis. Membrane-bound vesicles inside the cell fuse with the plasma membrane and release their contents into the external medium. The processes of endocytosis and exocytosis result in the exchange of material between the inside and outside of the cell.

Secretion Proteins destined for a non-cytoplasmic region, either outside of the cell or the lumen of an organelle, must be moved across a membrane. Ribosomes synthesizing a protein that will be secreted attach to the membrane of the endoplasmic reticulum (ER). The characteristics of this organelle will be described shortly. As the protein is being made, it is threaded through the membrane and into the lumen of the ER. The lumen of any organelle can be viewed as equivalent to an extracellular space. Once a protein or any substance is there, it can readily be transported by vesicles to the lumen of another organelle, or to the exterior of the cell. ■ endoplasmic reticulum, p. 77

MICROCHECK 3.11 Gated channels allow specific ions to pass across the membrane. Carriers facilitate the passage of molecules across the membrane and often use energy. Pinocytosis allows cells to internalize small molecules. Protozoa and phagocytes internalize bacteria and debris by phagocytosis. Exocytosis is used to expel material. Secreted proteins are moved across the membrane of the endoplasmic reticulum as they are being made. ✓ How does a cell bring in ligands? ✓ How is the formation of an endocytic vesicle different from that of a phagosome? ✓ How might a bacterium resist the killing effects of a phagolysosome?

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3.12 Protein Structures Within the Cell Focus Point Describe the structure and function of the eukaryotic cytoskeleton, flagella, and cilia.

Eukaryotic cells have a variety of important protein structures within the cell. These include ribosomes, the cytoskeleton, flagella, and cilia.

Ribosomes The eukaryotic ribosome is 80S, which is made up of a 60S and a 40S subunit. Recall that the prokaryotic ribosomes are 70S. Like prokaryotic ribosomes, eukaryotic ribosomes are composed of ribosomal RNA and protein.

Cytoskeleton The threadlike proteins that make up the cytoskeleton continually reconstruct to adapt to the cell’s constantly changing needs. The network is composed of three elements: microtubules, actin filaments, and intermediate filaments (figure 3.50). Microtubules, the thickest of the cytoskeleton structures, are long hollow cylinders composed of protein subunits called tubulin. Microtubules form the mitotic spindles, the machinery that partitions chromosomes between two cells in the process of cell division. Without mitotic spindles, cells could not reproduce. Microtubules also are the main structures that make up the cilia and flagella, the mechanisms of locomotion in certain eukaryotic cells. In addition, microtubules also function as the framework along which organelles and vesicles move within a cell. Organelles called centrioles are involved in the assembly of microtubules. The antifungal drug griseofulvin is thought to interfere with the structural integrity of the microtubules of some fungi. ■ mitosis, p. 284 Actin filaments enable the cell cytoplasm to move. They are composed of a polymer of actin, which can rapidly assemble and subsequently disassemble, causing motion. For example, pseudopod formation relies on actin polymerization in one part of the cell and depolymerization in another. Some intracellular pathogens exploit the process and trigger a rapid polymerization of actin, propelling them within that cell. This can move the pathogens with enough force to be ejected into an adjacent cell. Intermediate filaments function like ropes, strengthening the cell mechanically. They enable cells to resist physical stresses.

Flagella and Cilia Flagella and cilia are flexible structures that appear to project out of a cell yet are covered by an extension of the plasma membrane (figure 3.51). Both are composed of long microtubules grouped in what is called a 9+2 arrangement: nine pairs of microtubules surrounding two individual ones. They originate from a basal body within the cell; the basal body has a slightly different arrangement of microtubules.

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3.13

Membrane-Bound Organelles

75

Intermediate filament

Microtubule

Cell membrane Actin filament

FIGURE 3.50 Cytoskeleton Diagrammatic representation of the dynamic filamentous network that provides structure to the cell; the cytoskeleton is composed of three elements—microtubules, actin filaments, and intermediate filaments.

Although eukaryotic flagella provide cells with motility, they are structurally very different from their prokaryotic counterparts. Using ATP as a source of energy, they either propel the cell with a whiplike motion or thrash back and forth to pull the cell forward. Cilia are shorter than flagella, often covering a cell and moving in synchrony (see figure 1.8). This motion can move a cell forward in an aqueous solution, or propel surrounding material along a stationary cell. For example, epithelial cells that line the respiratory tract have cilia that beat together in a directed fashion. This moves

Microtubules

the mucus film that covers those cells, directing it upward toward the mouth, where it can be swallowed. This action removes microorganisms that have been inhaled before they can enter the lungs.

MICROCHECK 3.12 The 80S eukaryotic ribosome is composed of 60S and 40S subunits. The cytoskeleton is a dynamic filamentous network that provides structure to the cell; it is composed of microtubules, actin filaments, and intermediate filaments. Flagella function in motility. Cilia either propel a cell or move material along a stationary cell. ✓ Explain how actin filaments are related to phagocytosis. ✓ Explain what is meant by the 9+2 structure of cilia and flagella.

Plasma membrane

3.13 Membrane-Bound Organelles Flagellum

Basal body

Focus Point Describe the function of the nucleus, mitochondria, chloroplasts, endoplasmic reticulum, Golgi apparatus, lysosomes, and peroxisomes.

The presence of membrane-bound organelles is an important feature that sets eukaryotic cells apart from their prokaryotic counterparts.

The Nucleus Microtubules

FIGURE 3.51 Flagella Flexible structures involved in movement.

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The predominant distinguishing feature of the eukaryotic cell is the nucleus, which contains the DNA. The boundary of this structure is the nuclear envelope, which is composed of two lipid bilayer

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CHAPTER THREE Microscopy and Cell Structure

Nucleolus

Nuclear envelope

Nucleus

Nuclear pore

Nuclear pores

Nuclear pores

Vacuole

Inner membrane Nucleoplasm

Outer membrane

(b)

0.3 μm

(a)

FIGURE 3.52 Nucleus Organelle that contains the DNA. (a) Diagrammatic representation. (b) Electron micrograph of a yeast cell (Geotrichum candidium) by freeze-fracture technique.

membranes: the inner membrane and the outer membrane. Spanning the envelope are complex protein structures that form nuclear pores, allowing large molecules such as ribosomal subunits and proteins to be transported into and out of the nucleus (figure 3.52). The nucleolus is a region within the nucleus where ribosomal RNAs are synthesized. The nucleus contains multiple chromosomes, each one encoding different genetic information. Unlike the situation in most prokaryotic cells, double-stranded chromosomal DNA is linear. To add structure and order to the long DNA molecule, it is packed by winding it around positively charged proteins called histones. These bind tightly to the negatively charged DNA molecule. One packing unit, called a nucleosome, consists of a complex of histones around which the linear DNA wraps twice. The complex of DNA and proteins that together form the chromosomes is called chromatin. Events that take place in the nucleus during cell division distinguish eukaryotes from prokaryotes. In eukaryotic cells, after DNA is replicated, chromosomes go through a nuclear division process called

mitosis, which ensures the daughter cells receive the same number of chromosomes as the original parent. Through mitosis, a cell that is diploid, or has two copies of each chromosome, will generate two diploid daughter cells. A different process, meiosis, generates haploid daughter cells, which each have a single copy of each chromosome.

Mitochondria Mitochondria function as ATP-generating powerhouses, and are found in nearly all eukaryotic cells. They are highly complex structures about the size of a bacterial cell, and are bounded by two lipid bilayer membranes (figure 3.53). These are referred to as the outer and inner membranes. The outer membrane is smooth, but the inner membrane is highly folded, forming invaginations called cristae. These folds increase the surface area of the membrane, maximizing the ATP-generating capabilities of the organelle (the processes will be discussed in chapter 6).

Outer membrane Intermembrane space Crista

(a)

Inner membrane Matrix

(b)

0.1 μm

FIGURE 3.53 Mitochondria These harvest the energy released during the degradation of organic compounds to synthesize ATP. (a) Diagrammatic representation. (b) Electron micrograph.

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Membrane-Bound Organelles

77

PERSPECTIVE 3.1 The Origins of Mitochondria and Chloroplasts Mitochondria and chloroplasts bear such a striking similarity to prokaryotic cells that it is no wonder scientists speculated for many decades that these organelles evolved from bacteria. The endosymbiont theory states that the ancestors of mitochondria and chloroplasts were bacteria residing within other cells in a mutually beneficial partnership. The intracellular bacterium in such a partnership is called an endosymbiont. As time went on each partner became indispensable to the other, and the endosymbiont eventually lost key features such as a cell wall and the ability to replicate independently. Several early observations have supported the endosymbiont theory. Mitochondria and chloroplasts, unlike other eukaryotic organelles, both carry some of the genetic information necessary for their function.

These include genes for some of the ribosomal proteins and ribosomal RNAs that make up their 70S ribosomes. These ribosomes contrast with the typical 80S ribosomes that characterize eukaryotic cells and, in fact, are equivalent to the prokaryotic 70S ribosomes. Interestingly, nuclear DNA encodes some of the components that make up these ribosomes. Another characteristic that supports the theory that mitochondria and chloroplasts were once intracellular bacteria is the double membrane that surrounds these organelles. Present-day endosymbionts retain their cytoplasmic membranes and live within membrane-bound compartments in their eukaryotic host cell. Evidence in favor of the endosymbiont theory continues to accumulate. Recent technology enables scientists to readily determine the precise order or

Enclosed by the inner membrane is the matrix, which contains DNA, ribosomes, and other molecules necessary for protein synthesis. Notably, the ribosomes are 70S rather than the 80S ribosome found in the cytoplasm of eukaryotic cells. These observations, along with the fact that mitochondria elongate and divide in a fashion similar to that of bacteria, were among the first pieces of evidence that led scientists to conclude that mitochondria evolved from bacterial cells (see Perspective 3.1).

sequence, of nucleotides that make up DNA. This allows comparison of the nucleotide sequences of organelle DNA with genomes of different bacteria. It has become apparent that some mitochondrial DNA sequences bear a striking resemblance to DNA sequences of members of a group of obligate intracellular parasites, the rickettsias. These are probably relatives of modern-day mitochondria. A tremendous effort is now under way to determine the nucleotide sequence of mitochondria from a wide variety of eukaryotes, including plants, animals, and protists. While the size of mitochondrial DNA varies a great deal among these different eukaryotic organisms, common sequence themes are emerging. Today, researchers are no longer discussing “if” but “when” these organelles evolved from intracellular prokaryotes.

mitochondria, chloroplasts are bounded by two membranes (figure 3.54). Within the chloroplast’s stroma, the region analogous to the mitochondrial matrix, are membrane-bound, disclike structures called thylakoids. Chlorophyll and other pigments that capture radiant energy are embedded in the thylakoid membranes. Like mitochondria, chloroplasts appear to have evolved from bacterial cells (see Perspective 3.1). They contain DNA and 70S ribosomes, elongate and divide, and have photosynthetic mechanisms similar to a group of bacteria called cyanobacteria.

Chloroplasts Chloroplasts, found exclusively in plants and algae, are the site of photosynthesis in eukaryotic cells. They harvest the energy of sunlight to generate ATP, which is then used to convert CO2 to organic compounds like sugar and starch. Like

Endoplasmic Reticulum (ER) The endoplasmic reticulum (ER) is a complex, three-dimensional internal membrane system of flattened sheets, sacs, and tubes

Outer membrane Inner membrane

Thylakoid

Stroma

FIGURE 3.54 Chloroplasts These harvest the energy of sunlight to generate ATP. The ATP is then used to convert CO2 to an organic form.

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CHAPTER THREE Microscopy and Cell Structure

Ribosomes Rough endoplasmic reticulum

Smooth endoplasmic reticulum

0.08 µm

FIGURE 3.55 Endoplasmic Reticulum Site of synthesis of macromolecules destined for other organelles or the external environment.

(figure 3.55). The rough endoplasmic reticulum has a characteristic bumpy appearance due to the multitude of ribosomes coating it. It is the site where proteins not destined for the cytoplasm are synthesized. These include proteins targeted for the lumen of an organelle or for secretion outside the cell. Membrane proteins such as receptors are also synthesized on the rough ER. The ribosomes making these proteins attach to the ER surface. As the ribosomes synthesize the proteins, they thread them through gated pores in the membrane, delivering the proteins to the lumen of the ER. There, the proteins fold to assume their three-dimensional shapes. Vesicles that bud off from the ER transfer the newly synthesized molecules to the Golgi apparatus for further modification and sorting.

Some regions of the ER are smooth. This smooth endoplasmic reticulum functions in lipid synthesis and degradation, and calcium ion storage. As with material made in the rough ER, vesicles transfer compounds from the smooth ER to the Golgi apparatus.

The Golgi Apparatus The Golgi apparatus consists of a series of membrane-bound flattened sacs (figure 3.56). It is the site where macromolecules synthesized in the endoplasmic reticulum are modified before they are transported to other destinations. These modifications, such as the addition of carbohydrate and phosphate groups, take place in

Transport vesicles

Secretory vesicles

Vesicle

0.57 mm

FIGURE 3.56 Golgi Apparatus Site where macromolecules synthesized in the endoplasmic reticulum are modified before being transported to other destinations in vesicles.

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3.13

a sequential order in different Golgi sacs. Much like an assembly line, the molecules are transferred in vesicles from one Golgi sac to another. These various molecules are then sorted and delivered in vesicles destined either for specific cellular compartments or to the outside of the cell.

Lysosomes and Peroxisomes Lysosomes are organelles that contain a number of powerful degradative enzymes that could destroy the cell if not contained within the organelle. Endosomes and phagosomes fuse with lysosomes, allowing digestion of material taken up by the cell. In a similar manner, exhausted organelles can fuse with lysosomes so that their contents are digested. Peroxisomes are the organelles in which oxygen is used to oxidize substances, breaking down lipids and detoxifying certain chemicals. As a consequence, their enzymes generate highly reactive molecules such as hydrogen peroxide and superoxide. The peroxisome contains these molecules and ultimately degrades them, protecting the cell from their toxic effects. ■ hydrogen peroxide, p. 92 ■ superoxide, p. 92

Membrane-Bound Organelles

79

MICROCHECK 3.13 The nucleus, which contains DNA, is the predominant distinguishing feature of eukaryotes. Mitochondria are ATP-generating powerhouses. Chloroplasts are the site of photosynthesis. The rough endoplasmic reticulum is the site where proteins not destined for the cytoplasm are synthesized. The smooth endoplasmic reticulum functions in lipid synthesis and degradation, and calcium ion storage. The Golgi apparatus modifies and sorts molecules synthesized in the rough ER. Lysosomes are the structures within which digestion takes place; peroxisomes are the organelles in which oxygen is used to oxidize substances. ✓ Describe the structure of the nucleus. ✓ How does the function of the rough endoplasmic reticulum differ from that of the smooth endoplasmic reticulum? ✓ If enzymes contained in a peroxisome are to act on a substrate, what must first occur?

FUTURE CHALLENGES A Case of Breaking and Entering Unraveling the complex mechanisms that prokaryotic and eukaryotic cells use to transport materials across their membranes can potentially aid in the development of new antimicrobial medications. Armed with a precise model of the structure and function of bacterial transporter proteins, scientists might be able to design new drugs that exploit these systems. One strategy would be to design compounds that irreversibly bind to transporter molecules and jam the mechanism. If the

microbes can be prevented from bringing in nutrients and removing wastes, their growth would cease. Another strategy would be to enhance the uptake or decrease the efflux of a specific compound that interferes with intracellular processes. This is already being done to some extent as new derivatives of current antibiotics are being produced, but more precise understanding of the processes by which bacteria take up or remove compounds could expedite drug development.

A more thorough understanding of eukaryotic uptake systems could be used to develop better antiviral drugs. Viruses exploit the process of receptor-mediated endocytosis to gain entry into the cell. Once they are enclosed within the endosome, their protective protein coat is removed, releasing their genetic material. New drugs can potentially be developed that block these steps, preventing the entry or uncoating of infectious viral particles.

SUMMARY Microscopy and Cell Morphology 3.1

Microscopic Techniques: The Instruments (table 3.1)

Principles of Light Microscopy: The Bright-Field Microscope The most commonly used type of microscope is the bright-field microscope (figure 3.1). The objective lens and the ocular lens in combination magnify an object by a factor equal to the product of the magnification of each of the individual lenses. The usefulness of a microscope depends largely on its resolving power (figure 3.2). Light Microscopes That Increase Contrast The phase-contrast microscope amplifies differences in refraction (figure 3.4). The interference microscope causes the specimen to appear as a three-dimensional image (figure 3.5). The dark-field microscope makes organisms stand out as bright objects against a dark background (figure 3.6). The fluorescence microscope is used to observe cells that have been stained with fluorescent dyes (figure 3.7). The confocal scanning laser microscope is used to construct a three-dimensional image of a thick structure and to provide detailed sectional views of the interior of an intact cell (figure 3.8).

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Electron Microscopes Transmission electron microscopes (TEMs) transmit electrons through a specimen that has been prepared by thin sectioning, freeze fracturing, or freeze etching (figure 3.10). Scanning electron microscopes (SEM) scan a beam of electrons back and forth over the surface of a specimen, producing a three-dimensional effect (figure 3.11). Atomic Force Microscopes Atomic force microscopes map the bumps and valleys of a surface on an atomic scale (figure 3.12).

3.2

Microscopic Techniques: Dyes and Staining (table 3.2)

Differential Stains The Gram stain is widely used for staining bacteria; Gram-positive bacteria stain purple and Gram-negative bacteria stain pink (figure 3.14). The acid-fast stain is used to stain organisms such as Mycobacterium species; acid-fast organisms stain pink and all other organisms stain blue (figure 3.15). Special Stains to Observe Cell Structures The capsule stain allows the capsule to stand out as a halo around an organism (figure 3.16). The spore stain uses heat to facilitate the staining of

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CHAPTER THREE Microscopy and Cell Structure

endospores (figure 3.17). The flagella stain employs a mordant that enables the stain to adhere to and coat the otherwise thin flagella (figure 3.18). Fluorescent Dyes and Tags Some fluorescent dyes bind compounds that characterize all cells; others bind compounds specific to certain cell types (figure 3.19). Immunofluorescence is used to tag a specific protein of interest with a fluorescent compound.

The Gram-Positive Cell Wall (figure 3.33) The Gram-positive cell wall contains a relatively thick layer of peptidoglycan. Teichoic acids project out of the peptidoglycan layer.

Shapes Most prokaryotes are cocci or rods; other shapes include coccobacilli, vibrios, spirilla, and spirochetes. Pleomorphic bacteria have variable shapes (figure 3.20).

The Gram-Negative Cell Wall (figure 3.34) The Gram-negative cell wall has a relatively thin layer of peptidoglycan sandwiched between the cytoplasmic membrane and an outer membrane. The outer membrane contains lipopolysaccharides. The lipid A portion of the lipopolysaccharide molecule is responsible for the toxic effects, which is why LPS is called endotoxin. Porins form small channels that permit small molecules to pass through the outer membrane. Periplasm contains a variety of proteins, including those involved in nutrient degradation and transport.

Groupings Cells adhering to one another following division form characteristic arrangements such as chains, packets, and clusters (figure 3.22).

Antibacterial Substances That Target Peptidoglycan Penicillin prevents peptidoglycan synthesis. Lysozyme destroys the structural integrity of peptidoglycan.

Multicellular Associations Cells within biofilms often alter their activities when a critical number of cells are present.

Differences in Cell Wall Composition and the Gram Stain The Gram-positive, but not the Gram-negative, cell wall retains the crystal violet-iodine dye complex within the cell even when subjected to acetone-alcohol treatment.

The Structure of the Prokaryotic Cell

Characteristics of Bacteria That Lack a Cell Wall Mycoplasma species are extremely variable in shape and are not affected by lysozyme or penicillin (figure 3.35).

3.3

Morphology of Prokaryotic Cells

(figure 3.23,

table 3.3)

3.4

The Cytoplasmic Membrane

Structure and Chemistry of the Cytoplasmic Membrane (figure 3.24) The cytoplasmic membrane is a phospholipid bilayer embedded with a variety of different proteins including transport proteins and receptors. Permeability of the Cytoplasmic Membrane The cytoplasmic membrane is selectively permeable; water, gases, and small hydrophobic molecules are among the few compounds that can pass through by simple diffusion. The Role of the Cytoplasmic Membrane in Energy Transformation The electron transport chain expels protons, generating an electrochemical gradient, a source of energy called proton motive force (figure 3.26).

3.5

Directed Movement of Molecules Across the Cytoplasmic Membrane

Transport Systems (table 3.4) Facilitated diffusion, or passive transport, moves compounds by exploiting a concentration gradient (figure 3.27). Active transport uses energy, either proton motive force or ATP, to accumulate compounds against a concentration gradient. Group translocation chemically modifies a molecule during its transport (figure 3.30). Secretion The presence of a characteristic signal sequence targets proteins for secretion.

3.6

Cell Wall

Peptidoglycan (figure 3.32) Peptidoglycan is found only in the domain Bacteria and provides rigidity to the cell wall. Peptidoglycan is composed of glycan strands, which are alternating subunits of N-acetylmuramic acid (NAM) and N-acetylglucosamine (NAG), interconnected via the tetrapeptide chains on NAM.

nes95432_Ch03_040-082.indd 80

Cell Walls of the Domain Archaea Archaea have a greater variety of cell wall types than do the Bacteria and they all lack peptidoglycan.

3.7

Capsules and Slime Layers

Capsules and slime layers enable bacteria to adhere to surfaces. Some capsules allow disease-causing microorganisms to thwart the innate defense system (figure 3.36).

3.8

Filamentous Protein Appendages

Flagella (figure 3.37) The flagellum is a long protein structure commonly responsible for bacterial motility (figure 3.38). Chemotaxis is the directed movement toward an attractant or away from a repellent (figure 3.39). Phototaxis, aerotaxis, magnetotaxis, and thermotaxis are directed movements toward light, oxygen, a magnetic field, and temperature, respectively. Pili (figure 3.41) Many types of pili (fimbriae) enable specific attachment of cells to surfaces. Sex pili are involved in a form of DNA transfer.

3.9

Internal Structure

The Chromosome (figure 3.42) The chromosome of prokaryotes resides in the nucleoid rather than within a membrane bound nucleus; it contains all the genetic information required by a cell. Plasmids Plasmids only encode genetic information that may be advantageous, but not required by the cell.

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Review Questions

81

Ribosomes (figure 3.43) Ribosomes facilitate the joining of amino acids. The 70S bacterial ribosome is composed of a 50S and a 30S subunit.

Secretion Proteins destined for a non-cytoplasmic region are made by ribosomes bound to the endoplasmic reticulum.

Cytoskeleton The cytoskeleton is an interior framework involved in cell division and regulation of cell shape.

3.12

Storage Granules (figure 3.44) Storage granules are synthesized from a nutrient that a cell has in relative excess.

Cytoskeleton (figure 3.50) The cytoskeleton is composed of microtubules, actin filaments, and intermediate filaments.

Gas Vesicles Gas vesicles provide buoyancy to aquatic cells.

Flagella and Cilia (figure 3.51) Flagella propel a cell or pull the cell forward. Cilia move in synchrony to either propel a cell or move material along a stationary cell.

Endospores Endospores are extraordinarily resistant to heat, desiccation, toxic chemicals, and ultraviolet irradiation; they can germinate to become vegetative cells (figures 3.45, 3.46).

The Eukaryotic Cell 3.10

(figure 3.47, table 3.6)

The Plasma Membrane

The plasma membrane is a phospholipid bilayer embedded with proteins. Proteins in the membrane are involved in transport, structural integrity, and signaling.

3.11

Transfer of Molecules Across the Plasma Membrane

Transport Proteins Carriers mediate facilitated diffusion and active transport. Channels are pores in the membrane that are so small that only specific ions can pass through. These channels are gated. Endocytosis and Exocytosis (figure 3.49) Pinocytosis is the most common form of endocytosis in animal cells. The endocytic vesicle fuses with an endosome, which then fuses with a lysosome. Protozoa and phagocytes take up bacteria and debris through the process of phagocytosis. The phagosome fuses with the lysosome, where the material is digested. Exocytosis expels material.

Protein Structures Within the Cell

Ribosomes The 80S ribosome is composed of 60S and 40S subunits.

3.13

Membrane-Bound Organelles

The Nucleus (figure 3.52) The nucleus is the predominant distinguishing feature of eukaryotic cells. Mitochondria Mitochondria use the energy released during the degradation of organic compounds to generate ATP (figure 3.53). Chloroplasts Chloroplasts capture the energy of sunlight; this is then used to synthesize ATP that is expended to convert CO2 to an organic form (figure 3.54). Endoplasmic Reticulum (ER) (figure 3.55) The rough endoplasmic reticulum is the site where proteins not located in the cytoplasm are synthesized. Within the smooth endoplasmic reticulum, lipids are synthesized and degraded, and calcium is stored. The Golgi Apparatus (figure 3.56) The Golgi apparatus modifies and sorts molecules synthesized in the endoplasmic reticulum. Lysosomes and Peroxisomes Lysosomes carry digestive enzymes. Peroxisomes are the organelles in which oxygen is used to oxidize certain substances.

REVIEW QUESTIONS Short Answer 1. Explain why resolving power is important in microscopy. 2. Explain why basic dyes are used more frequently than acidic dyes in staining. 3. Describe what happens at each step in the Gram stain. 4. Compare and contrast ABC transport systems with group translocation. 5. Give two reasons that the outer membrane of Gram-negative bacteria is significant medically. 6. Compare and contrast penicillin and lysozyme. 7. Describe how a plasmid can help a cell. 8. How is an organ different from tissue?

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9. How is receptor-mediated endocytosis different from phagocytosis? 10. Explain how the Golgi apparatus cooperatively functions with the endoplasmic reticulum.

Multiple Choice 1. Which of the following is most likely to be used in a typical microbiology laboratory? a) Bright-field microscope b) Confocal scanning microscope c) Phase-contrast microscope d) Scanning electron microscope e) Transmission electron microscope

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CHAPTER THREE Microscopy and Cell Structure

2. Which of the following stains is used to detect Mycobacterium species? a) Acid-fast stain b) Capsule stain c) Endospore stain d) Gram stain e) Simple stain 3. Penicillin 1. is generally effective against Gram-positive bacteria. 2. is generally effective against Gram-negative bacteria. 3. functions in the cytoplasm of the cell. 4. is effective against mycoplasma. 5. kills only growing cells. a) 1,2 b) 2,3 c) 3,4 d) 4,5 e) 1,5 4. Endotoxin is associated with a) Gram-positive bacteria. b) Gram-negative bacteria. c) the cytoplasmic membrane. d) the endospore. 5. In prokaryotes, lipid bilayers are associated with the 1. Gram-positive cell wall. 2. Gram-negative cell wall. 3. cytoplasmic membrane. 4. capsule. 5. nuclear membrane. a) 1,2 b) 2,3 c) 3,4 d) 4,5 e) 1,5 6. In bacteria, the cytoplasmic membrane functions in 1. protein synthesis. 2. ribosome synthesis. 3. generation of ATP. 4. transport of molecules. 5. attachment. a) 1,2 b) 2,3 c) 3,4 d) 4,5 e) 1,5 7. Attachment is mediated by the 1. capsule. 2. cell wall. 3. cytoplasmic membrane. 4. periplasm. 5. pilus. a) 1,2 b) 2,3 c) 3,4 d) 4,5 e) 1,5 8. Endocytosis is associated with a) mitochondria. b) prokaryotic cells. c) eukaryotic cells. d) chloroplasts. e) ribosomes. 9. Protein synthesis is associated with 1. lysosomes. 2. the cytoplasmic membrane. 3. the Golgi apparatus. 4. rough endoplasmic reticulum. 5. ribosomes. a) 1,2 b) 2,3 c) 3,4 d) 4,5 e) 1,5 10. All of the following are composed of tubulin, except: a) actin b) cilia c) eukaryotic flagella d) microtubules e) more than one of these

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Applications 1. You are working in a laboratory producing new antibiotics for human and veterinary use. One compound with potential value inhibits the action of prokaryotic ribosomes. The compound, however, was shown to inhibit the growth of animal cells in culture. What is one possible explanation for its effect on animal cells? 2. A research laboratory is investigating environmental factors that would inhibit the growth of Archaea. One question they have is if adding the antibiotic penicillin would be effective in controlling their growth. Explain the probable results of an experiment in which penicillin is added to a culture of Archaea.

Critical Thinking 1. This graph shows facilitated diffusion of a compound across a cytoplasmic membrane and into a cell. As the external concentration of the compound is increased, the rate of uptake increases until it reaches a point where it slows and then begins to plateau. This is not the case with passive diffusion, where the rate of uptake continually increases. Why does the rate of uptake slow and then eventually plateau with facilitated diffusion?

Solute transport rate

82

.3

.2

.1

0 0

5 Solute concentration

10

2. Most medically useful antibiotics interfere with either peptidoglycan synthesis or ribosome function. Why would the cytoplasmic membrane be a poor target for antibacterial medications?

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4 Bacteria on an agar plate.

Dynamics of Prokaryotic Growth A Glimpse of History The greatest contributor to methods of cultivating bacteria was Robert Koch (1843–1910), a German physician who combined a medical practice with a productive research career for which he received a Nobel Prize in 1905. Koch was primarily interested in identifying disease-causing bacteria. To do this, however, he soon realized it was necessary to have simple methods to isolate and grow these particular species. He recognized that a single bacterial cell could multiply on a solid medium in a limited area and form a distinct visible mass of descendants. Koch initially experimented with growing bacteria on the cut surfaces of potatoes, but he found that a lack of nutrients in the potatoes prevented growth of some species. To overcome this difficulty, Koch realized it would be advantageous to be able to solidify any liquid nutrient medium. Gelatin was used initially, but there were two major drawbacks—it melts at the temperature preferred by many medically important organisms and some bacteria can digest it. In 1882, Fannie Hess, the wife of an associate of Koch, suggested using agar. This solidifying agent was used to harden jelly at the time and proved to be the perfect answer. Today, we take pure culture techniques for granted because of their relative ease and simplicity. Their development in the late 1800s, however, had a major impact on microbiology. Within 20 years, the

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agents causing most of the major bacterial diseases of humans were isolated and characterized.

P

rokaryotes can be found growing even in the harshest climates and the most severe conditions. Environments that no unprotected human could survive, such as the ocean depths, volcanic vents, and the polar regions, have thriving species of prokaryotes. Indeed many scientists believe that if life exists on other planets, it may resemble these microorganisms. Each species, however, has a limited set of environmental conditions in which it can grow; even then, it will grow only if specific nutrients are available. Some prokaryotes can grow at temperatures above the boiling point of water but not at room temperature. Many species can only grow within an animal host, and then only in specific areas of that host. Because of the medical significance of some bacteria, as well as the nutritional and industrial use of microbial by-products, microbiologists must be able to identify, isolate, and cultivate many species. To do this, one needs to understand the basic principles involved in prokaryotic growth while recognizing that a vast sea of information is yet to be discovered.

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KEY TERMS Biofilm Polysaccharide-encased community of microorganisms. Chemically Defined Medium Bacteriological growth medium composed of precise mixtures of known pure chemicals; generally used for specific experiments when nutrients must be precisely controlled. Complex Medium Bacteriological medium that contains protein digests, extracts, or other ingredients that vary in their chemical composition. Differential Medium Bacteriological medium that contains an ingredient that can be changed

Obligate Anaerobe Organism that cannot multiply, and is often killed, in the presence of O2.

by certain bacteria in a recognizable way; used to differentiate organisms based on their metabolic traits.

Plate Count Method to measure the concentration of viable cells by determining the number of colonies that arise from a sample added to an agar plate.

Exponential (Log) Phase Stage of growth in which cells divide at a constant rate; generation time is measured during this period of active multiplication.

Pure Culture A population of organisms descended from a single cell and therefore separated from all other species.

Facultative Anaerobe Organism that grows best if O2 is available, but can also grow without it. Generation Time The time it takes for a population to double in number.

Selective Medium Bacteriological medium to which additional ingredients have been added that inhibit the growth of many organisms other than the one being sought.

Obligate Aerobe Organism that requires molecular oxygen (O2).

4.1 Principles of Prokaryotic Growth

DNA attached to cytoplasmic membrane.

Focus Point Describe binary fission and explain how it relates to generation time.

Prokaryotes generally multiply by the process of binary fission (figure 4.1). After a cell has increased in size and doubled its components, it divides. One cell divides into two, those two divide to become four, those four become eight, and so on. In other words, the increase in cell numbers is exponential. Because it is neither practical, nor particularly meaningful, to determine the relative size of the cells in a given population, microbial growth is defined as an increase in the number of cells in a population. The time it takes for a population to double in number is the generation, or doubling, time. This varies greatly depending on the species of the organism and the conditions in which it is grown. Some common organisms, such as Escherichia coli, can double in approximately 20 minutes; others, such as the causative agent of tuberculosis, Mycobacterium tuberculosis, require at least 12 hours to double even under the most favorable conditions. The environmental and nutritional factors that affect the rate of growth will be discussed shortly. The exponential multiplication of bacteria has important health consequences. For example, a mere 10 cells of a food-borne pathogen in a potato salad, sitting for 4 hours in the warm sun at a picnic, may multiply to more than 40,000 cells. A simple equation expresses the relationship between the number of cells in a population at a given time (Nt), the original number of cells in the population (N0), and the number of divisions those cells have undergone during that time (n). If any two values are known, the third can be easily calculated from the equation:

Cell enlarges and DNA duplicates.

DNA is partitioned into each future daughter cell and cross wall forms.

Cell divides into two cells.

Cells separate.

Daughter cells

FIGURE 4.1 Binary Fission The chromosomal DNA is attached to the cytoplasmic membrane. As the cell increases in length, the DNA is replicated and then partitioned into each of the two daughter cells.

Nt = N0 ! 2n In this example, let us assume that we know that 10 cells of a disease-causing organism were initially added to the potato salad and we also know that the organism has a generation time of 20 minutes. The first step is to determine the number of cell divisions that will occur in a given time. Because the organism divides

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every 20 minutes, 3 times every hour, we know that in 4 hours it will divide 12 times. Now that we know the original number of cells and the number of divisions, we can solve for Nt: 10 ! 212 = Nt = 40,960

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4.2 Bacterial Growth in Nature

85

TABLE 4.1 Example of Exponential Growth Time in Minutes (t) 0

Initial Population (N 0)

Number of Generations (n) 2n

10

Population N0¥2n

0

10 1

20

10

1

2 (⫽2)

20

40

10

2

22(⫽2 ⫻ 2)

40

60 (1 hour)

10

3

23(⫽2 ⫻ 2 ⫻ 2)

80

4

2 (⫽2 ⫻ 2 ⫻ 2 ⫻ 2)

160

5

80

10

4

100

10

5

2 (⫽2 ⫻ 2 ⫻ 2 ⫻ 2 ⫻ 2)

320

120 (2 hours)

10

6

26

640

140

10

7

27

1,280

160

10

8

28

2,560

9

2

9

5,120

2

10

10,240

2

11

20,480

2

12

40,960

180 (3 hours) 200

10 10

220

10

240 (4 hours)

10

Thus, after 4 hours the potato salad in the example will have 40,960 cells of our pathogen (table 4.1). Keep this in mind, and your potato salad in a cooler, the next time you go to a picnic!

MICROCHECK 4.1 Most prokaryotes multiply by binary fission. Microbial growth is an increase in the number of cells in a population. The time required for a population to double in number is the generation time. ✓ Explain why microbial growth refers to a population rather than a cell size. ✓ If a bacterium has a generation time of 30 minutes, and you start with 100 cells at time 0, how many cells will you have in 30, 60, 90, and 120 minutes?

10 11 12

They may not produce these adherent structures when growing in the laboratory. In fact, microbial cells actually sense various surrounding chemicals and then respond by synthesizing compounds useful for growth in that particular environment. Cells often grow in multicellular associations that function cooperatively to increase the chance of survival of the population as a whole. ■ slime layer, p. 64

Biofilms In nature, prokaryotes can live suspended in an aqueous environment, but many attach to surfaces and live in polysaccharideencased communities called biofilms (figure 4.2). Biofilms cause the slipperiness of rocks in a stream bed, the slimy “gunk” that

4.2 Bacterial Growth in Nature Focus Points Describe a biofilm and give one positive and one negative impact that biofilms have on humans. Explain why bacteria that grow naturally in mixed communities sometimes cannot be grown in pure culture.

Historically, microorganisms have been studied by growing them in the laboratory, but scientists now recognize that the dynamic and complex conditions of the natural environment, which differ greatly from the conditions in the laboratory, have profound effects on microbial growth and behavior. When growing in a running stream, for example, prokaryotes frequently synthesize slime layers or other structures that allow them to attach to rocks or other solid surfaces.

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FIGURE 4.2 Biofilm on a Stainless Steel Surface A biofilm is a polysaccharide-encased community of microorganisms.

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CHAPTER FOUR Dynamics of Prokaryotic Growth

wastes of one species may serve as a nutrient for another. Often, however, cells in these communities compete for nutrients, and some even resort to a type of biological warfare, synthesizing toxic compounds that inhibit competitors. Understandably, the conditions in these close associations are exceedingly difficult to reproduce in the laboratory. ■ microbial competition and antagonism, p. 723

MICROCHECK 4.2

FIGURE 4.3 Architecture of a Biofilm Superimposed time sequence image shows a single latex bead moving through a biofilm water channel. The large light gray shapes are clusters of bacteria (scale bar=50mm).

coats kitchen drains, the scum that gradually accumulates in toilet bowls, and the dental plaque that forms on teeth. Biofilm formation begins when planktonic, or free-floating, bacteria adhere to a surface where they multiply and synthesize slime layers to which unrelated cells can attach and grow. Surprisingly, biofilms are not generally haphazard mixtures of microbes in a layer of slime, but instead have characteristic architectures with open channels through which nutrients and waste materials can pass (figure 4.3). Cells communicate with one another by synthesizing and responding to chemical signals, an exchange that appears to be important in establishing structure. Biofilms are more than just an unsightly annoyance. Dental plaque leads to tooth decay and gum disease. Even troublesome, persistent ear infections and the complications of cystic fibrosis are thought to be due to bacteria that grow as a biofilm. In fact, it is estimated that 65% of human bacterial infections involve biofilms. Treatment of these infections is difficult because microorganisms growing within the protective slime are often able to resist the effects of antibiotics, as well as the body’s defenses. Biofilms are also important in industry, where their growth in pipes, drains, and cooling water towers can interfere with processes and damage equipment. Again, the structure of the biofilm shields the microbes growing within it, and bacteria in a biofilm may be hundreds of times more resistant to disinfectants than are their planktonic counterparts. ■ disinfectants, p. 108 While biofilms can be damaging, they also can be beneficial. Many bioremediation efforts, which use bacteria to degrade harmful chemicals, are enhanced by biofilms. Thus, as some industries are exploring ways to destroy biofilms, others, such as wastewater treatment facilities, are looking for ways to foster their development. ■ bioremediation, p. 749 ■ wastewater treatment, p. 739

Interactions of Mixed Microbial Communities Prokaryotes in the environment regularly grow in close associations with many different species. Sometimes the interactions are cooperative, even fostering the growth of members that otherwise could not survive. For example, organisms that cannot multiply in the presence of O2 can grow in the mouth. This is because other microbes found there consume O2 during their metabolism, creating microenvironments that lack O2. In addition, the metabolic

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Biofilms have a characteristic architecture with open channels through which nutrients and waste products can pass. In nature, prokaryotes often grow in close associations with many different species. ✓ Give three examples of biofilms. ✓ Describe a situation in which the activities of one species benefit another. ✓ Why would bacteria in a biofilm be more resistant to harmful chemicals?

4.3 Obtaining a Pure Culture Focus Point Describe how the streak-plate method is used to obtain a pure culture, and how the resulting culture can be stored.

In the laboratory, prokaryotes are generally isolated and grown in pure culture in order to identify them and study the activities of a particular species. A pure culture is defined as a population of organisms descended from a single cell and therefore separated from all other species. Results obtained using pure cultures are much easier to interpret, but as discussed earlier, the organisms sometimes behave differently than they do in their natural environment. Another complicating issue is that only an estimated 1% of all prokaryotes can currently be cultivated successfully. This makes it exceedingly difficult to study the vast majority of environmental microorganisms. Fortunately for humanity, most known medically significant bacteria can be grown in pure culture. Pure cultures are obtained using a variety of special techniques. All glassware, media, and instruments must be sterile, or free of microbes, prior to use. These are then handled using aseptic techniques, procedures that minimize the chance of other organisms being accidentally introduced. The medium that the cells are grown in, or on, is a mixture of nutrients dissolved in water and may be in a liquid broth or a solidified gel-like form. The medium is called a culture medium. ■ aseptic techniques, p. 109 ■ sterilization, p. 108

Cultivating Bacteria on a Solid Culture Medium The basic requirements for obtaining a pure culture are a solid culture medium, a media container that can be maintained in an aseptic condition, and a method to separate individual bacterial cells. A single bacterium, supplied with the right nutrients and conditions, will multiply on the solid medium in a limited area to form a colony, a mass of cells descended from the original one (figure 4.4). About 1 million cells are required for a colony to be easily visible to the naked eye.

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4.3 Obtaining a Pure Culture

87

stay liquid until cooled to a temperature below 45°C. Therefore, nutrients that would be destroyed at high temperatures can be added at lower temperatures before the agar hardens. Once solidified, an agar medium will remain so until it is heated above 95°C. Thus, unlike gelatin, which is liquid at 37°C, agar remains solid over the entire temperature range at which the majority of bacteria grow. ■ polysaccharide, pp. 30, 32 The culture medium is contained in a Petri dish—a two-part, covered container made of glass or plastic. While not airtight, the Petri dish does exclude airborne microbial contaminants. A Petri dish containing a medium is commonly referred to as a plate of that medium type—for example, a nutrient agar plate or, more simply, an agar plate. FIGURE 4.4 Colonies Growing on Agar Medium

The Streak-Plate Method

Agar, a polysaccharide extracted from marine algae, is used to solidify a liquid culture medium. Unlike other gelling agents such as gelatin, very few bacteria can degrade agar. It is not destroyed at high temperatures and can therefore be sterilized by heating, a process that also liquefies it. Melted agar will

The streak-plate method is the simplest and most commonly used technique for isolating bacteria (figure 4.5). A sterilized inoculating loop is dipped into a solution containing the organism of interest and then lightly drawn several times across an agar plate, creating a set of parallel streaks covering approximately one-third of the plate. The loop is then sterilized and

(1) Loop is sterilized. (6) Loop is sterilized.

(4) Loop is sterilized. (2) Loop is inoculated.

(3) First set of streaks made.

(5) Second set of streaks made.

Starting point Agar containing nutrients

(7) Final set of streaks made.

(8) Isolated colonies develop after incubation.

FIGURE 4.5 The Streak-Plate Method A sterilized inoculating loop (1) is dipped into a culture (2) and is then lightly drawn several times across an agar plate (3). The loop is sterilized again (4), and a new series of streaks is made at an angle to the first set (5). The loop is sterilized again (6), and another set of parallel streaks is made (7). The successive streaks dilute the concentration of cells. By the third set of streaks, cells should be separated enough so that isolated colonies develop after incubation (8).

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CHAPTER FOUR Dynamics of Prokaryotic Growth

a new series of parallel streaks is made across and at an angle to the previous ones, covering another third of the plate. This drags some of those cells streaked onto the first portion of the plate over to a previously uninoculated portion, creating a region containing a more dilute inoculum. The loop is sterilized again, and another set of parallel streaks is made, dragging into a third area some of the organisms that had been moved into the second section. The object is to reduce the number of cells being spread with each successive series of streaks, effectively diluting the sample. By the third set of streaks, cells should be separated enough so that distinct, well-isolated colonies will form.

Maintaining Stock Cultures Once a pure culture has been obtained, it can be maintained as a stock culture, a culture stored for use as an inoculum in later procedures. Often, a stock culture is stored in the refrigerator as growth on an agar slant. This is agar medium in a tube that was held at a shallow angle as the medium solidified, creating a larger surface area. For longterm storage, stock cultures can be frozen at :70°C in a solution that prevents ice crystals from forming and damaging cells. Alternatively, cells can be lyophilized, or freeze-dried. ■ lyophilization, p. 122

MICROCHECK 4.3 Only an estimated 1% of prokaryotes can be cultivated in the laboratory. Agar is used to solidify nutrient-containing broth. The streakplate method is used to obtain a pure culture. ✓ What properties of agar make it ideal for use in bacteriological media? ✓ How does the streak-plate method separate individual cells? ✓ What might be a reason that medically significant bacteria can be grown in pure culture more often than environmental organisms?

4.4 Bacterial Growth in Laboratory Conditions Focus Point Describe the five distinct stages of a growth curve, and compare this closed system to colony growth and continuous culture.

In the laboratory, bacteria are typically grown in broth contained in a tube or flask, or on an agar plate. These are considered closed or batch systems because nutrients are not renewed, nor are waste products removed. Under these conditions, the cell population increases in number in a predictable fashion and then eventually declines. As the population in a closed system grows, it follows a pattern of stages, called a growth curve. This growth pattern is most distinct in a shaken broth culture, because all cells are exposed to the same environment. In a colony, cells on the outer edge of a colony experience very different conditions from those at the center.

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Stationary phase

10 Cell number (logarithmic scale)

88

Phase of prolonged decline

8 Log or exponential phase

6

Death phase

4 2

Lag phase

0 Time (hr)

(days/months/years)

FIGURE 4.6 Growth Curve The growth curve is characterized by five distinct stages: lag phase, exponential or log phase, stationary phase, death phase, and phase of prolonged decline.

To maintain cells in a state of continuous growth, nutrients must be continuously added and waste products removed. This is called an open system, or continuous culture.

The Growth Curve A growth curve is characterized by five distinct stages—the lag phase, the exponential or log phase, the stationary phase, the death phase, and the phase of prolonged decline (figure 4.6).

Lag Phase When a bacterial culture is diluted and then transferred into a different medium, the number of viable cells does not immediately increase. They go through a “tooling up” or lag phase prior to active multiplication. During this time they synthesize macromolecules required for multiplication, including enzymes, ribosomes, and nucleic acids, and they generate energy in the form of ATP. The length of the lag phase depends on conditions in the original culture and the medium into which the bacteria are transferred. If cells are transferred from a nutrient-rich medium to one containing fewer nutrients, the lag time tends to be longer. This is because cells must begin making enzymes to synthesize components missing in the new medium. A similar situation occurs when a stock culture stored in the refrigerator for several weeks is inoculated into fresh medium. In contrast, if young cells are transferred to a medium similar in composition, the lag time is quite short.

Exponential Phase (Log Phase) During the exponential or log phase, cells divide at a constant rate and their numbers increase by the same percentage during each time interval. The generation time is measured during this period of active multiplication. Because bacteria are most susceptible to antibiotics and other chemicals during this time, the log phase is important medically.

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4.4 Bacterial Growth in Laboratory Conditions

During the initial phase of exponential growth, the cells’ activities are directed toward increasing cell mass. Cells produce compounds such as amino acids and nucleotides, the respective building blocks of proteins and nucleic acids. Cells are remarkably precise in their ability to regulate the synthesis of these compounds, ensuring that each is made in the appropriate relative amount for efficient assembly into macromolecules. Compounds synthesized during this period of active multiplication are called primary metabolites. A metabolite is any product of a chemical reaction in a cell and includes compounds required for growth, as well as waste materials. Some primary metabolites are commercially valuable as flavoring agents and food supplements. Understandably, industries that harvest these compounds are working to develop methods to manipulate bacteria to overproduce certain primary metabolites. ■ regulation of gene expression, p. 176 Cells’ activities shift as they enter a stage called late log phase, which marks the transition to stationary phase. This change occurs in response to multiple factors inevitable in a closed system, such as depletion of nutrients and buildup of waste products. If the cells are able to form endospores, they initiate the process of sporulation. If they cannot, they still “hunker down” in preparation for the starvation conditions ahead. The cells become rounder in shape and more resistant to harmful chemicals and radiation. Changes in the composition of their cell walls and cytoplasmic membranes also occur. As their surrounding environment changes, cells begin synthesizing a new group of metabolites, termed secondary metabolites (figure 4.7). Commercially, the most important of these are antibiotics, which inhibit the growth of or kill other organisms.

89

During the stationary phase, the viable cells continue to synthesize secondary metabolites and maintain the altered properties they demonstrated in late log phase. The length of time cells remain in the stationary phase varies depending on the species and on environmental conditions. Some populations remain in the stationary phase for only a few hours, whereas others remain for days.

Death Phase The death phase is the period when the total number of viable cells in the population decreases as cells die off at a constant rate. Like bacterial growth, death is exponential. However, the cell population usually dies off much more slowly than it multiplies during the log phase. Once about 99% of the cells have died off, the remaining members of the population enter a different phase.

Phase of Prolonged Decline The phase of prolonged decline is marked by a very gradual decrease in the number of viable cells in the population, lasting for days to years. Superficially, it might seem like a gradual march towards death of the population, but dynamic changes are actually occurring. Many members of the population are dying and releasing their nutrients, while a few “fitter” cells more able to cope with the deteriorating environmental conditions are multiplying. This dynamic process generates successive waves of slightly modified populations, each more fit to survive than the previous ones (figure 4.8). Thus, the statement “survival of the fittest” even holds true for closed cultures of bacteria.

Colony Growth

Stationary Phase Cells enter the stationary phase when they no longer have supplies of energy and nutrients adequate for sustained growth. The total number of viable cells in the overall population remains relatively constant, but some cells are dying while others are multiplying. How can cells multiply when they have exhausted their supply of nutrients? Cells that die release their contents, providing a source of nutrients and energy to fuel the growth of other cells.

Growth of a bacterial colony on a solid medium involves many of the same features as bacteria growing in liquid, but it is marked by some important differences. After a lag phase, cells multiply exponentially and eventually compete with one another for available nutrients and become very crowded. Unlike a liquid culture, the position of a single cell within a colony markedly determines its environment. Cells multiplying on the edge of the colony face relatively little competition and can use O2 in the air and obtain nutrients from the agar medium. In contrast, in the center of the colony the high density of cells rapidly depletes available O2 and

Primary metabolite Lag

Secondary metabolite

Cell number (logarithmic scale)

Log

Synthesis of metabolites

Number of viable cells

Stationary

Time (hr)

FIGURE 4.7 Primary and Secondary Metabolite Production Primary metabolites are synthesized during the period of active multiplication. Late in the log phase, cells begin synthesizing secondary metabolites. These compounds, which continue to be synthesized in stationary phase, appear to make the cells more resistant to environmental conditions.

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Time

FIGURE 4.8 Dynamic Population Changes in the Phase of Prolonged Decline Many members of the population are dying and releasing their nutrients, while a few “fitter” cells are actively multiplying.

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CHAPTER FOUR Dynamics of Prokaryotic Growth

nutrients. Toxic metabolic wastes such as acids accumulate. As a consequence, cells at the edge of the colony may be growing exponentially, whereas those in the center may be in the death phase. Cells in locations between these two extremes may be in stationary phase.

Continuous Culture Bacteria can be maintained in a state of continuous exponential growth by using a chemostat. This device continually drips fresh medium into a liquid culture contained in a growth chamber. With each drop that enters, an equivalent volume—containing cells, wastes, and spent medium—leaves through an outlet. By manipulating the concentration of nutrients in the medium and the rate at which it enters the growth chamber, a constant cell density and generation time of log phase cells can be maintained. This makes it possible to study a uniform population of log phase cells over a long period of time. The effect of adding various supplements to the medium or altering the cellular environment on long-term cell growth can be determined.

TABLE 4.2

Environmental Factors that Influence Microbial Growth

Environmental Factor/ Descriptive Terms Temperature

Optimum temperature between :5°C and 15°C.

Psychrotroph

Optimum temperature between 20°C and 30°C, but grows well at refrigeration temperatures.

Mesophile

Optimum temperature between 25°C and 45°C.

Thermophile

Optimum temperature between 45°C and 70°C.

Hyperthermophile

Optimum temperature of 70°C or greater.

Oxygen (O2) Availability

Focus Point

Requires O2.

Obligate anaerobe

Cannot multiply in the presence of O2.

Facultative anaerobe

Grows best if O2 is present, but can also grow without it.

Microaerophile

Requires small amounts of O2, but higher concentrations are inhibitory.

Aerotolerant anaerobe (obligate fermenter)

Indifferent to O2.

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Prokaryotes that live in pH extremes appear to maintain a near neutral internal pH by pumping protons out of or into the cell.

Neutrophile

Multiplies in the range of pH 5 to 8.

Acidophile

Grows optimally at a pH below 5.5.

Alkalophile

Grows optimally at a pH above 8.5.

Water Availability

List the descriptive terms that express a prokaryote’s requirements for temperature, oxygen, pH, and water availability.

As a group, prokaryotes inhabit nearly every environment on earth. Those we associate with disease and rapid food spoilage live in habitats that humans consider quite comfortable. Some prokaryotes, however, live in harsh environments that would kill most other organisms. Most of these, called extremophiles (phile means “loving”), are members of the Domain Archaea. Recognizing the environmental factors that influence microbial growth—such as temperature, amount of oxygen, pH, and water availability—helps scientists study microorganisms in the laboratory and aids in understanding their role in the complex ecology of the planet. The major environmental conditions that influence the growth of microorganisms are summarized in table 4.2.

Oxygen (O2) requirement/tolerance reflects the organism’s energyconverting mechanisms (aerobic respiration, anaerobic respiration, and fermentation) and its ability to detoxify O2 derivatives.

Obligate aerobe

pH

4.5 Environmental Factors That Influence Microbial Growth

Thermostability appears to be due to protein structure.

Psychrophile

MICROCHECK 4.4 When grown in a closed system, a bacterial population goes through five distinct phases: lag, log, stationary, death, and prolonged decline. Cells within a colony may be in any one of the growth phases, depending on their relative location. ✓ Explain the difference between the lag phase and the log phase. ✓ Describe how a chemostat keeps a culture in a continuous stage of growth. ✓ Why would bacteria be more susceptible to antibiotics during the log phase?

Characteristics

Prokaryotes that can grow in high solute solutions maintain the availability of water in the cell by increasing their internal solute concentration.

Halotolerant

Can grow in relatively high salt solutions, up to approximately 10% NaCl.

Halophile

Requires high levels of sodium chloride.

Temperature Requirements Each species of prokaryote has a well-defined upper and lower temperature limit within which it grows. Within this range lies the optimum growth temperature, the temperature at which the organism multiplies most rapidly. As a general rule, this optimum temperature is close to the upper limit of the organism’s range. This is because the speed of enzymatic reactions in the

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Growth rate

4.5 Environmental Factors That Influence Microbial Growth

Thermophile

Mesophile

Hyperthermophile

Psychrotroph Psychrophile

91

Why can some prokaryotes withstand very high temperatures but most cannot? As a general rule, proteins from thermophiles are not denatured at high temperatures. This thermostability is due to the sequence of the amino acids in the protein. This controls the number and position of the bonds that form within the protein, which in turn determines its threedimensional structure. For example, the formation of many covalent bonds, as well as many hydrogen and other weak bonds, prevents denaturation of proteins. Heat-stable enzymes that degrade fats and other proteins are being used in hightemperature detergents. ■ protein denaturation, p. 29

Temperature and Food Preservation -10

0

10

20

30

40

50

60

70

80

90

100 110 120

Temperature (°C)

FIGURE 4.9 Temperature Requirements for Growth Prokaryotes are commonly divided into five groups based on their optimum growth temperatures. This graph depicts a typical example of each group. Note that the optimum temperature, the point at which the growth rate is highest, is near the upper limit of the range.

cell approximately doubles for each 10°C rise in temperature. At a critical point, however, the temperature becomes too high and enzymes required for growth are denatured and can no longer function. As a result, the cells die. Prokaryotes are commonly divided into five groups based on their optimum growth temperatures (figure 4.9). Note, however, that this merely represents a convenient organization scheme. In reality, no sharp dividing line exists between each group. Furthermore, not every organism in a group can grow in the entire temperature range typical for its group. Psychrophiles have their optimum between :5°C and 15°C. These organisms are usually found in such environments as the Arctic and Antarctic regions and in lakes fed by glaciers. Psychrotrophs have a temperature optimum between 20°C and 30°C, but grow well at lower temperatures. They are an important cause of food spoilage. ■ food spoilage, p. 762 Mesophiles which include E. coli and most other common bacteria, have their optimum temperature between 25°C and about 45°C. Disease-causing bacteria, which are adapted to growth in the human body, typically have an optimum between 35°C and 40°C. Mesophiles that inhabit soil, a colder environment, generally have a lower optimum, close to 30°C. Thermophiles have an optimum temperature between 45°C and 70°C. These organisms commonly occur in hot springs and compost heaps. They also are found in artificially created thermal environments such as water heaters. ■ composting, p. 747

Hyperthermophiles have an optimum growth temperature of 70°C or greater. These are usually members of the Archaea. One member, isolated from the wall of a hydrothermal vent deep in the ocean, has a maximum growth temperature of 121°C, the highest yet recorded.

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Storage of fruits, vegetables, and cheeses at refrigeration temperatures (approximately 4°C) retards food spoilage because it limits the growth of otherwise fast-growing mesophiles. Psychrophiles and psychrotrophs, however, can still multiply and consequently spoilage will still occur, albeit more slowly. Because of this, foods and other perishable products that can withstand belowfreezing temperatures should be frozen for long-term storage. Microorganisms, which require liquid water to grow, cannot multiply under these conditions. It is important to recognize, however, that freezing is not an effective means of destroying microbes. Recall that freezing is routinely used to preserve stock cultures. ■ low-temperature storage, p. 122 ■ food spoilage, p. 762

Temperature and Disease Significant variations exist in the temperature of various parts of the human body. Although the heart, brain, and gastrointestinal tract are near 37°C, the temperature of the extremities may be much lower. For these reasons, some microorganisms can cause disease more readily in certain body parts but not in others. For example, Hansen’s disease (leprosy) typically involves the coolest regions of the body (ears, hands, feet, and fingers) because the causative organism, Mycobacterium leprae, grows best at these lower temperatures. The same situation applies to syphilis, in which lesions appear on the genitalia and then on the lips, tongue, and throat. Indeed, for more than 30 years the major treatment of syphilis was to induce fever by deliberately introducing the agent that causes malaria, which results in very high fevers. ■ Hansen’s disease, p. 655 ■ syphilis, p. 633

Oxygen (O2) Requirements The oxygen (O2) level in different environments varies greatly, providing many different habitats with respect to its availability. Gaseous oxygen accounts for about 20% of the earth’s atmosphere. Beneath the surface of soil and in swamps, however, very limited amounts, if any, may be available. The human body alone provides many different habitats. While the surface of the skin is exposed to the atmosphere, the stomach and intestines are relatively anaerobic, meaning they contain little or no O2. Like humans, some bacteria have an absolute requirement for O2. Others thrive in anaerobic environments, and many of these are killed if O2 is present. The O2 requirements of some organisms can be determined by growing them in shake tubes. To prepare a shake tube, a tube of nutrient agar is boiled, which both melts the agar and drives off the O2. The agar is then allowed to cool

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CHAPTER FOUR Dynamics of Prokaryotic Growth

TABLE 4.3

Oxygen (O2) Requirements of Prokaryotes

Obligate aerobe

Facultative anaerobe

Obligate anaerobe

Microaerophile

Aerotolerant

Bacteria Bacteria

Enzymes in Cells for O2 Detoxification Catalase: 2H2O2

2H2O + O2

Superoxide dismutase: O +H O 2O - + 2H+ 2

2

Catalase, superoxide dismutase

Small amounts of catalase and superoxide dismutase

Superoxide dismutase

2 2

to 50°C. Next, the test organism is added and dispersed by gentle shaking or swirling. The agar is allowed to harden and the tube is incubated at an appropriate temperature. Because the solidified agar impedes the diffusion of O2, the level of O2 in the tube is high at the top, whereas the bottom portion is anaerobic. The bacteria grow in the region that has the level of O2 that suits their requirements (table 4.3). Based on their O2 requirements, prokaryotes can be separated into these groups: Obligate aerobes have an absolute requirement for oxygen (O2). They use it to transform energy in the process of aerobic respiration. This and other ATP-generating pathways will be discussed in detail in chapter 6. Obligate aerobes include Micrococcus species, which are common in the environment. ■ aerobic respiration, pp. 133, 144 ■ ATP, p. 25

Obligate anaerobes cannot multiply if any O2 is present; in fact, they are often killed in environments that have even traces of O2 because of its toxic derivatives, which will be discussed shortly. Obligate anaerobes transform energy by fermentation or anaerobic respiration; the details of these processes will be discussed in chapter 6. Obligate anaerobes include members of the genus Bacteroides (the major inhabitants of the large intestine), Clostridium botulinum (the causative agent of botulism), and many others. In fact, it is estimated that one-half of all the cytoplasm on earth is in anaerobic bacteria! ■ fermentation, pp. 133, 147 ■ anaerobic respiration, pp. 133, 145

Facultative anaerobes grow better if O2 is present, but can also grow without it. The term “facultative” means that the organism is flexible, in this case in its requirements for O2. Facultative anaerobes use aerobic respiration if oxygen is available, but use fermentation or anaerobic respiration in its absence. Growth is more rapid when oxygen is present because aerobic respiration yields the most ATP of all these processes. An example is E. coli, a common inhabitant of the large intestine. Microaerophiles require small amounts of O2 (2% to 10%) for aerobic respiration; higher concentrations are inhibitory.

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Neither catalase nor superoxide dismutase in most

An example is Helicobacter pylori, which causes gastric and duodenal ulcers. Aerotolerant anaerobes are indifferent to O2. They can grow in its presence, but they do not use it to transform energy. Because they do not use aerobic or anaerobic respiration, they are also called obligate fermenters. An example is Streptococcus pyogenes, which causes strep throat.

Toxic Derivatives of Oxygen (O2) Although not toxic itself, O2 can be converted into a number of compounds that are highly toxic. Some of these, such as superoxide (O2:), are produced both as a part of normal metabolic processes and as chemical reactions involving oxygen and light. Others, such as hydrogen peroxide (H2O2), result from metabolic processes involving oxygen. To survive in an environment containing O2, cells must have enzymes that can convert these toxic derivatives to non-toxic forms. The enzyme superoxide dismutase degrades superoxide to produce hydrogen peroxide. Catalase breaks down hydrogen peroxide to H2O and O2. Together, these two enzymes detoxify these reactive products of O2. Although most strict anaerobes do not have superoxide dismutase, some do, while a few aerobes lack it. Therefore, other unknown factors must also be playing a role in protecting organisms from the toxic forms of oxygen.

pH Each bacterial species can survive within a range of pH values; within this range is its pH optimum. Despite the pH of the external environment, cells maintain a constant internal pH, typically near neutral. ■ pH, p. 24 Most bacteria can live and multiply within the range of pH 5 (acidic) to pH 8 (basic) and have a pH optimum near neutral (pH 7). These bacteria are called neutrophiles. Preservation methods that acidify foods, such as pickling, are intended to inhibit the growth of these organisms. Surprisingly, some neutrophiles have adapted special mechanisms that enable them to grow at a very low pH. For example, Helicobacter pylori grows in the stomach, where it can cause ulcers. To maintain the pH close to neutral in its imme-

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4.6 Nutritional Factors That Influence Microbial Growth

diate surroundings, H. pylori produces the enzyme urease, which splits urea in the stomach into carbon dioxide and ammonia. The ammonia neutralizes the stomach acid in the bacterium’s immediate surroundings. ■ pickling, p. 758 Acidophiles grow optimally at a pH below 5.5. For example, Acidothiobacillus ferroxidans, grows best at a pH of approximately 2. This bacterium obtains its energy by oxidizing sulfur compounds, producing sulfuric acid in the process. It maintains its internal pH near neutral by pumping out protons (H;) as quickly as they enter the cell. Picrophilus oshimae, a member of the Archaea, has an optimum pH of less than 1! This prokaryote, which was isolated from the dry, acid soils of a gas-emitting volcanic fissure in Japan, has an unusual cytoplasmic membrane that is unstable at a pH above 4.0. Alkalophiles grow optimally at a pH above 8.5. For instance, the bacterium Bacillus alcalophilus grows best at pH 10.5. It appears that alkalophiles maintain a relatively neutral internal pH by exchanging internal sodium ions for external protons. Alkalophiles often live in alkaline lakes and soils.

Water Availability All microorganisms require water for growth. Even if water is present, however, it may not be available in certain environments. For example, dissolved substances such as salt (NaCl) and sugars interact with water molecules and make the water unavailable to the cell. In many environments, particularly in certain natural habitats such as salt marshes, prokaryotes are faced with this situation. If the solute concentration is higher in the medium than in the cell, water diffuses out of the cell due to osmosis. This causes the cytoplasm to dehydrate and shrink from the cell wall, a phenomenon called plasmolysis (figure 4.10). ■ solute p. 56 ■ osmosis, p. 56 Prokaryotes able to live in high-salt environments maintain the availability of water in the cell by increasing their internal solute concentration. Some bacteria do this by synthesizing certain small organic compounds, such as the amino acid proline, that have no detrimental effect on normal cellular activity. ■ proline, p. 27

Bacteria that can tolerate high concentrations of salt, up to approximately 10% NaCl, are called halotolerant. Staphylococcus species, which reside on the dry salty environment of the skin,

Dissolved substances (solute)

Cytoplasmic membrane shrinks from the cell wall (plasmolysis).

Cytoplasmic membrane

Cell wall

93

are an example. Some organisms actually require high levels of sodium chloride to grow and are called halophiles (halo means “salt”). Many marine bacteria are mildly halophilic, requiring concentrations of approximately 3% sodium chloride. Certain members of the Archaea are extreme halophiles, requiring 9% sodium chloride or more. Extreme halophiles are found in environments such as the salt flats of Utah and the Dead Sea. The growth-inhibiting effect of high concentrations of salt and sugars is used in food preservation. High levels of salt are added to preserve such foods as bacon, salt pork, and anchovies. High concentrations of sugars can also inhibit the growth of bacteria. Many foods with a high sugar content, such as jams, jellies, and honey, are naturally preserved. ■ food preservation, p. 765

MICROCHECK 4.5 A prokaryotic species can be categorized according to its optimum growth temperature. A species can also be grouped according to its oxygen requirements. Most species grow best near neutral pH, although some prefer acidic conditions and others grow best in alkaline conditions. Halophiles require high-salt conditions. ✓ List four environmental factors that influence bacterial growth. ✓ List the categories into which bacteria can be classified according to their requirements for oxygen. ✓ Why would small organic compounds affect the water content of cells?

4.6 Nutritional Factors That Influence Microbial Growth Focus Points Give an example of a bacterium that is fastidious. Define the terms photoautotroph, chemolithoautotroph, photoheterotroph, and chemoorganoheterotroph.

Growth of any prokaryote depends not only on a suitable physical environment, but also on the availability of nutrients. From these, the cell must synthesize all of the cell components discussed in chapter 3, including lipid membranes, cell walls, proteins, and nucleic acids. These components are made from building blocks such as fatty acids, sugars, amino acids, and nucleotides. In turn, each of these building blocks is composed of a variety of elements, including carbon and nitrogen. What sets the prokaryotic world apart from all other forms of life is their remarkable ability to use diverse sources of these elements. For example, prokaryotes are the only organisms able to use atmospheric nitrogen (N2) as a nitrogen source.

H2O flows out of cell

Required Elements FIGURE 4.10 Effects of Solute Concentration on Cells The cytoplasmic membrane allows water molecules to pass through freely. If the solute concentration is higher outside of the cell, water moves out. The dehydrated cytoplasm shrinks from the cell wall, a process called plasmolysis.

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Elements that make up cell constituents are called major elements. These include carbon, oxygen, hydrogen, nitrogen, sulfur, phosphorus, potassium, magnesium, calcium, and iron. They are

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CHAPTER FOUR Dynamics of Prokaryotic Growth

PERSPECTIVE 4.1 Can Prokaryotes Live on Only Rocks and Water? Prokaryotes have been isolated from diverse environments that previously were thought to be incapable of sustaining life. For example, members of the Archaea have been isolated from environments 10 times more acidic than that of lemon juice. Other Archaea have been isolated from oil wells a mile below the surface of the earth at temperatures of 70°C and pressures of

160 atmospheres (at sea level, the pressure is 1 atmosphere). The isolation of these organisms suggests that thermophiles may be widespread in the earth’s crust. Perhaps the most unusual environment from which prokaryotes have been isolated are the volcanic rocks 1 mile below the earth’s surface near the Columbia River in Washington State. What do these organ-

isms use for food? They apparently get their energy from hydrogen gas that is produced chemically in a reaction between the iron-rich minerals in the rock and the groundwater. The groundwater also contains dissolved CO2, which the bacteria use as a source of carbon. Thus, these bacteria apparently exist on nothing more than rocks and water.

the essential components of proteins, carbohydrates, lipids, and nucleic acids (table 4.4). ■ elements, p. 19 The source of carbon distinguishes different groups of prokaryotes. Those that use organic carbon are called heterotrophs (hetero means “different” and troph means “nourishment”). Medically important bacteria are typically heterotrophs, using organic carbon sources such as glucose. Autotrophs (auto means “self”) use inorganic carbon in the form of carbon dioxide. They play a critical role in the cycling of carbon in the environment because they can convert inorganic carbon (CO2) to an organic form, the process of carbon fixation. Without carbon fixation, the earth would quickly run out of organic carbon, which is essential to humans and other animals. ■ carbon cycle, p. 728 Some prokaryotes are able to use nitrogen gas (N2), converting it to ammonia, which can be incorporated into cellular material.This process, called nitrogen fixation, is unique to prokaryotes. Like carbon fixation, it is essential to life on this planet.

hand), a limiting nutrient dictates the maximum level of microbial growth. Algal blooms in a small Seattle lake were curtailed by chemical treatment that removed excess phosphate in the lake. Some elements, termed trace elements, are required in very minute amounts by all cells. They include cobalt, zinc, copper, molybdenum, and manganese, which are required for enzyme function. Very small amounts of these trace elements are found in most natural environments, including water.

■ nitrogen cycle, p. 730

Microorganisms display a wide spectrum in their growth factor requirements, reflecting differences in their biosynthetic capabilities. For example, E. coli is quite versatile and does not require any growth factors. It grows in a medium containing only glucose and six different inorganic salts. In contrast, species of Neisseria require at least 40 additional ingredients, including 7 vitamins and all of the 20 amino acids. Bacteria such as Neisseria that require many growth factors are called fastidious. Fastidious bacteria are exploited to determine the quantity of specific vitamins in food products. To do this, a well-characterized species that requires a specific vitamin to grow is inoculated into a medium that lacks the vitamin but is supplemented with a measured amount of the food product. The amount of growth of the bacterium is related to the amount of test vitamin in the product.

Phosphorus and iron are important because they are often limiting nutrients, meaning they are present at the lowest concentration relative to need. Just as the quantity of chocolate chips in your kitchen would limit the number of chocolate chip cookie batches you can make (assuming the other ingredients are on

TABLE 4.4

Representative Functions of the Major Elements

Chemical

Function

Carbon, oxygen, and hydrogen

Component of cellular constituents including amino acids, lipids, nucleic acids, and sugars.

Nitrogen

Component of amino acids and nucleic acids.

Sulfur

Component of some amino acids.

Phosphorus

Component of nucleic acids, membrane lipids, and ATP.

Potassium, magnesium, and calcium

Required for the functioning of certain enzymes; additional functions as well.

Iron

Part of certain enzymes.

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Growth Factors Some bacteria cannot synthesize some of their cell constitutents, such as amino acids, vitamins, purines, and pyrimidines. Consequently, these organisms can only grow in environments that contain these compounds. Low molecular weight compounds required by a particular bacterium are called growth factors. ■ purines, p. 33 ■ pyrimidines, p. 33

Energy Sources Organisms derive energy either from sunlight or by oxidizing chemical compounds. These processes will be discussed in chapter 6. Organisms that harvest the energy of sunlight are called phototrophs (photo means “light”). These include plants, algae, and photosynthetic bacteria. Organisms that obtain energy by oxidizing chemical compounds are called chemotrophs (chemo means “chemical”). Mammalian cells, fungi, and many types of bacteria oxidize organic compounds such as sugars, amino acids,

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4.7 Cultivating Prokaryotes in the Laboratory

TABLE 4.5

Energy and Carbon Sources Used by Different Groups of Prokaryotes

Type

Energy Source

Carbon Source

Photoautotroph

Sunlight

CO2

Photoheterotroph

Sunlight

Organic compounds :

2;

Chemolithoautotroph

Inorganic chemicals (H2, NH3, NO2 , Fe , H2S)

CO2

Chemoorganoheterotroph

Organic compounds (sugars, amino acids, etc.)

Organic compounds

and fatty acids. Some prokaryotes can extract energy from seemingly unlikely sources such as hydrogen sulfide, hydrogen gas, and other inorganic compounds, an ability that distinguishes them from eukaryotes.

Nutritional Diversity Microbiologists often group prokaryotes according to the energy and carbon sources they utilize (table 4.5): Photoautotrophs use the energy of sunlight and the CO2 in the atmosphere to make organic compounds. These are eventually consumed by other organisms, including humans. Because of this, photoautotrophs are called primary producers. Cyanobacteria are important examples that inhabit soil and both freshwater and saltwater environments. Many can fix nitrogen, providing another indispensable role in the biosphere; they are the only organisms that can fix both N2 and CO2. Chemolithoautotrophs (lith means “stone”), commonly referred to simply as chemoautotrophs or chemolithotrophs, use inorganic compounds for energy and derive their carbon from CO2. These prokaryotes live in seemingly inhospitable environments such as sulfur hot springs, which are rich in reduced inorganic compounds such as hydrogen sulfide. In some regions of the ocean depths, near hydrothermal vents, chemoautotrophs serve as the primary producers, supporting rich communities of life in these habitats utterly devoid of sunlight (see figure 30.11). ■ hydrothermal vents, p. 732 Photoheterotrophs use the energy of sunlight and derive their carbon from organic compounds. Some are facultative in their nutritional capabilities. For example, some members of a group of bacteria called the purple nonsulfur bacteria can grow anaerobically using light as an energy source and organic compounds as a carbon source (photoheterotrophs). They can also grow aerobically in the dark using organic sources of carbon and energy (chemoheterotrophs). ■ purple nonsulfur bacteria, p. 257

Chemoorganoheterotrophs, also referred to as chemoheterotrophs or chemoorganotrophs use organic compounds for energy and as a carbon source. They are by far the most common group associated with humans and other animals. Individual species of chemoheterotrophs differ in the number of organic compounds they can use. For example, certain members of the genus Pseudomonas can derive carbon and/or energy from more than 80 different organic com-

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95

pounds, including such unusual compounds as naphthalene (the ingredient associated with the smell of mothballs). At the other extreme, some organisms can degrade only a few compounds. For example, Bacillus fastidiosus can use only urea and certain of its derivatives as a source of both carbon and energy.

MICROCHECK 4.6 Organisms require a source of major and trace elements. Heterotrophs use an organic carbon source, and autotrophs use CO2. Phototrophs harvest the energy of sunlight, and chemotrophs obtain energy by oxidizing chemicals. ✓ List the major elements required for growth of bacteria. ✓ What is the carbon source of a photoautotroph? Of a chemoautotroph? ✓ Why would human-made materials (such as many plastics) be degraded only slowly or not at all?

4.7 Cultivating Prokaryotes in the Laboratory Focus Points Compare and contrast complex, chemically defined, selective, and differential media. Explain how the correct atmospheric conditions are provided to cultivate obligate aerobes, capnophiles, microaerophiles, and obligate anaerobes. Describe the purpose of an enrichment culture.

By knowing the environmental and nutritional factors that influence growth of specific prokaryotes, it is often possible to provide appropriate conditions for their cultivation. These include a medium on which to grow the organisms and a suitable atmosphere.

General Categories of Culture Media Considering the diversity of bacteria, it is not surprising that a wide variety of media is used to cultivate them. For routine purposes, one of the many types of complex media is used; chemically defined media are generally used only for specific research

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TABLE 4.6

Characteristics of Representative Media Used to Cultivate Bacteria

Medium

Characteristic

Blood agar

Complex medium used routinely in clinical labs. Differential because colonies of hemolytic organisms are surrounded by a zone of clearing of the red blood cells. Not selective.

Chocolate agar

Complex medium used to culture fastidious bacteria, particularly those found in clinical specimens. Not selective or differential.

Glucose-salts

Chemically defined medium. Used in laboratory experiments to study nutritional requirements of bacteria. Not selective or differential.

MacConkey agar

Complex medium used to isolate Gram-negative rods that typically reside in the intestine. Selective because bile salts and dyes inhibit Gram-positive organisms and Gram-negative cocci. Differential because the pH indicator turns pink-red when the sugar in the medium, lactose, is fermented.

Nutrient agar

Complex medium used for routine laboratory work. Supports the growth of a variety of nonfastidious bacteria. Not selective or differential.

Thayer-Martin

Complex medium used to isolate Neisseria species, which are fastidious. Selective because it contains antibiotics that inhibit most organisms except Neisseria species. Not differential.

experiments when the type and quantity of nutrients must be precisely controlled. Table 4.6 summarizes the characteristics of various types of media.

Complex Media A complex medium contains a variety of ingredients such as meat juices and digested proteins, making what might be viewed as a tasty soup for microbes. Although a specific amount of each ingredient is in the medium, the exact chemical composition of these can be highly variable. One common ingredient is peptone. This is a mixture of amino acids and short peptides produced by digesting protein from any of a variety of different sources with enzymes, acids or alkali. Extracts, which are the water-soluble components of a substance, are also common ingredients. For example, beef extract is a water extract of lean meat and provides vitamins, minerals, and other nutrients. A commonly used complex medium, nutrient broth, consists of peptone and beef extract in distilled water. If agar is added, then nutrient agar results. Many medically important bacteria are fastidious, requiring a medium even richer than nutrient agar. One rich medium commonly used in clinical laboratories is blood agar. This contains red blood cells, which supply a variety of nutrients including hemin, in addition to other ingredients. A medium used to cultivate even more fastidious bacteria is chocolate agar, named for its brownish appearance rather than its ingredients. Chocolate agar contains lysed red blood cells and additional nutrients. Additional ingredients are often incorporated into complex media to counteract compounds that may be toxic to some exquisitely sensi-

nes95432_Ch04_083-106.indd 96

tive bacteria. For example, cornstarch sometimes included because it binds fatty acids, which can be toxic to Neisseria species. Hundreds of different types of media are manufactured. Even with the availability of all of these, however, some medically important organisms and most environmental ones have not yet been grown on culture media.

Chemically Defined Media Chemically defined media are composed of precise amounts of pure chemicals. This type of medium is invaluable when studying nutritional requirements of bacteria. Glucose-salts, which supports the growth of E. coli, contains only those chemicals listed in table 4.7. More elaborate recipes containing as many as 46 different ingredients can be used to make chemically defined media that support the growth of fastidious bacteria such as Neisseria gonorrhoeae, the organism that causes gonorrhea. ■ gonorrhea, p. 629 To maintain the pH near neutrality, buffers are often added to the medium. They are especially important in a defined medium because some bacteria produce so much acid as a by-product of metabolism that they inhibit their own growth. This typically is not as much of a problem in complex media because the amino acids and other natural components provide at least some buffering function. ■ buffer, p. 24

Special Types of Culture Media To detect or isolate a bacterium that is part of a mixed population, it is often necessary to make it more prevalent or more obvious. For these purposes selective and differential media are used. These can be either complex or chemically defined, depending on the needs of the microbiologist.

Selective Media Selective media inhibit the growth of organisms other than the one being sought. For example, Thayer-Martin agar is used to isolate Neisseria gonorrhoeae, the cause of gonorrhea, from clinical specimens. This is chocolate agar to which three or more antimicrobial drugs have been added. The antimicrobials inhibit fungi, Grampositive bacteria, and Gram-negative rods. Because these drugs do not inhibit most strains of N. gonorrhoeae, they allow those strains to grow with little competition from other organisms.

TABLE 4.7

Ingredients in Two Representative Types of Media that Support the Growth of E. coli

Nutrient Broth (complex medium)

Glucose-Salts (defined medium)

Peptone

Glucose

Meat extract

Dipotassium phosphate

Water

Monopotassium phosphate Magnesium sulfate Ammonium sulfate Calcium chloride Iron sulfate Water

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4.7 Cultivating Prokaryotes in the Laboratory Colony

97

Zone of clearing

(a)

(b)

FIGURE 4.11 Blood Agar This complex medium is differential for hemolysis. (a) A zone of complete clearing around a colony growing on blood agar is called beta hemolysis. (b) A zone of greenish clearing is called alpha hemolysis.

MacConkey agar is used to isolate Gram-negative rods from various clinical specimens such as urine. This complex medium contains, in addition to peptones and other nutrients, two inhibitory compounds: crystal violet, a dye, inhibits Gram-positive bacteria, and bile salts inhibit most non-intestinal bacteria.

Differential Media Differential media contain a substance that certain bacteria change in a recognizable way. For example, blood agar, in addition to being nutritious, is differential; it is used to detect bacteria that produce a hemolysin, which lyses red blood cells (figure 4.11). The lysis appears as a zone of clearing around the colony growing on the blood agar plate. The type of hemolysis is used as an identifying characteristic. For example, species of Streptococcus that reside harmlessly in the throat often cause a type of hemolysis called alpha hemolysis, characterized by a zone of greenish partial clearing around the colonies. In contrast, Streptococcus pyogenes, which causes strep throat, causes beta hemolysis, characterized by a clear zone of hemolysis. Still other bacteria have no effect on red blood cells. ■ Streptococcus pyogenes, p. 499 MacConkey agar, which is selective, is also differential (figure 4.12). In addition to containing peptones and other nutrients, it has lactose and a pH indicator. Bacteria that ferment the sugar produce acid, which turns the pH indicator pink. Thus, E. coli and other lactose-fermenting bacteria growing on MacConkey agar form pink colonies. Lactose-negative bacteria form tan or colorless colonies. ■ lactose, p. 32

Increased CO2 Providing an environment with increased levels of CO2 enhances the growth of many medically important bacteria, including species of Neisseria and Haemophilus. Organisms requiring increased CO2, along with approximately 15% oxygen, are called capnophiles. One of the simplest ways to provide this atmosphere is to incubate the bacteria in a closed candle jar. A lit candle in the jar consumes some of the O2 in the air, generating CO2 and H2O; the flame soon extinguishes because of insufficient oxygen. Although a candle jar atmosphere contains about 3.5% CO2, enough O2 remains to support the growth of obligate aerobes and prevent the growth of obligate anaerobes. Special incubators are also available that maintain CO2 at prescribed levels.

Providing Appropriate Atmospheric Conditions To cultivate bacteria in the laboratory, appropriate atmospheric conditions must be provided. For instance, broth cultures of obligate aerobes grow best when tubes or flasks containing the media are shaken, providing maximum aeration. Special methods create atmospheric environments such as increased CO2, microaerophilic, and anaerobic conditions.

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FIGURE 4.12 MacConkey Agar This complex medium is differential for lactose fermentation and selective for Gram-negative rods. Bacteria that ferment the sugar produce acid, which turns the pH indicator pink, resulting in pink colonies. Lactose-negative colonies are tan or colorless. The bile salts and dyes in the media inhibit all but certain Gram-negative rods.

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Microaerophilic Microaerophilic bacteria typically require O2 concentrations less than what is achieved in a candle jar. Therefore, these bacteria are often incubated in a gastight container with a special disposable packet; the packet holds chemicals that react with O2, reducing its concentration to approximately 5–15%.

Anaerobic Cultivation of obligate anaerobes presents a great challenge to the microbiologist, because the cells may be killed if they are exposed to O2 for even a short time. Obviously, special techniques to exclude O2 are required. Anaerobes that can tolerate a brief exposure to O2 are cultivated in an anaerobe container (figure 4.13). This is the same type of container used to incubate microaerophiles, but the chemical composition of the disposable packet produces an anaerobic environment. Another method to cultivate anaerobes incorporates reducing agents into the culture medium. These react with O2 and thus eliminate dissolved O2; they include sodium thioglycollate, cysteine, and ascorbic acid. In some cases, immediately before the bacteria are inoculated, the medium is boiled to drive out dissolved O2. Media that employ reducing agents frequently contain an O2-indicating dye such as methylene blue. A more stringent method for working with anaerobes is to use an anaerobic chamber, an enclosed compartment that can be maintained as an anaerobic environment (figure 4.14). A special port, which can be filled with an inert gas, is used to add or remove items. Airtight gloves enable researchers to handle items within the chamber.

FIGURE 4.14 Anaerobic Chamber The enclosed compartment can be maintained as an anaerobic environment. A special port (visible on the right side of this device), which can be filled with inert gas, is used to add or remove items. The airtight gloves enable the researcher to handle items within the chamber.

Enrichment Cultures An enrichment culture provides conditions in a broth that preferentially enhance the growth of one particular species in a mixed population (figure 4.15). This is helpful in isolating an organism from natural sources when the bacterium of interest is present in relatively small numbers. For example, if an organism is present at a concentration of only 1 cell/ml and it is outnumbered 10,000fold by other organisms, isolating it using the streak-plate method would be difficult, even if a selective medium were used. To enrich for a species, a sample such as pond water is placed into a liquid medium that favors the growth of the desired organism over others. For example, if the target organism can grow using atmospheric nitrogen as a source of nitrogen, then nitrogen is left out of the medium. If it can use an unusual carbon source such as phenol, then that is added as the only carbon source. In some cases selective agents such as bile are added: the procedure is then referred to as a selective enrichment. The culture is incubated under temperature and atmospheric conditions that preferentially promote the growth of the desired organism. During this time, the relative concentration of a microorganism that initially made up only a minor fraction of the population can increase dramatically. A pure culture can then be obtained by streaking the enrichment onto an appropriate agar medium and selecting a single colony.

MICROCHECK 4.7 Culture media can be either complex or chemically defined. Some media contain additional ingredients that make them selective or differential. Appropriate atmospheric conditions must be provided to isolate microaerophiles and anaerobes. An enrichment culture increases the relative concentration of an organism growing in a broth.

FIGURE 4.13 Anaerobe Container A disposable packet contains chemicals that react with O2, thereby producing an anaerobic environment.

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✓ Distinguish between a complex and a chemically defined medium. ✓ Describe two methods to create anaerobic conditions. ✓ Would bacteria that cannot utilize lactose be able to grow on MacConkey agar?

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4.8 Methods to Detect and Measure Bacterial Growth

99

FIGURE 4.15 Enrichment Culture Medium and incubation conditions favor the growth of the desired species over other bacteria in the same sample.

Plate out

Medium contains select nutrient sources chosen because few bacteria, other than the organism of interest, can use them.

Sample that contains a wide variety of organisms, including the organism of interest, is added to the medium.

Organism of interest can multiply, whereas most others cannot.

4.8 Methods to Detect and Measure Bacterial Growth

A variety of techniques are available to monitor bacterial growth. The choice depends on various characteristics of the sample and the goals of the measurements. Characteristics of the common methods for measuring bacterial growth are summarized in table 4.8.

Direct Cell Counts

Focus Point Compare and contrast direct cell counts, viable cell counts, measuring biomass, and detecting cell products to measure bacterial growth.

TABLE 4.8

Enriched sample is plated onto appropriate agar medium. A pure culture is obtained by selecting a single colony of the organism of interest.

Direct cell counts are particularly useful for determining the total numbers of bacteria in a specimen, including those that

Methods Used to Measure Bacterial Growth

Method Direct Cell Counts

Characteristics and Limitations Used to determine total number of cells; counts include living and dead cells.

Direct microscopic count

Rapid, but at least 107 cells/ml must be present to be effectively counted.

Cell-counting instruments

Coulter counters and flow cytometers count total cells in dilute solutions. Flow cytometers can also be used to count organisms to which fluorescent dyes or tags have been attached.

Viable Cell Counts

Plate count

Used to determine the number of viable bacteria in a sample, but that number only includes those that can grow in given conditions. Requires an incubation period of approximately 24 hours or longer. Selective and differential media can be used to enumerate specific species of bacteria. Time-consuming but technically simple method that does not require sophisticated equipment. Generally used only if the sample has at least 102 cells/ml.

Membrane filtration

Concentrates bacteria by filtration before they are plated; thus can be used to count cells in dilute environments.

Most probable number

Statistical estimation of likely cell number; it is not a precise measurement. Can be used to estimate numbers of bacteria in relatively dilute solutions.

Measuring Biomass

Biomass can be correlated to cell number.

Turbidity

Very rapid method; used routinely. A one-time correlation with plate counts is required in order to use turbidity for determining cell number.

Total weight

Tedious and time-consuming; however, it is one of the best methods for measuring the growth of filamentous microorganisms.

Measuring Cell Products

Methods are rapid but results must be correlated to cell number. Frequently used to detect growth, but not routinely used for quantitation.

Acid

Titration can be used to quantify acid production. A pH indicator is often used to detect growth.

Gases

Carbon dioxide can be detected by using a molecule that fluoresces when the medium becomes slightly more acidic. Gases can be trapped in an inverted Durham tube in a tube of broth.

ATP

Firefly luciferase catalyzes light-emitting reaction when ATP is present.

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CHAPTER FOUR Dynamics of Prokaryotic Growth

cannot be grown in culture. Unfortunately, they generally do not distinguish between living and dead cells.

Direct Microscopic Count 0 0 0 0 2 5 8 9

One of the most rapid methods of determining the number of cells in a suspension is the direct microscopic count. The number of cells in a measured volume of liquid is counted using special glass slides—counting chambers—that hold a known volume of liquid (figure 4.16). These can be viewed under the light microscope, and the number of cells can be counted precisely. At least 10 million bacteria (107) per milliliter are required to gain an accurate estimate. Otherwise, few, if any, cells will be seen in the microscope field.

Automatic counter Sample in liquid

Bacterial cell

Cell-Counting Instruments

Tube

A Coulter counter is an electronic instrument that counts cells in a suspension as they pass single file through a minute aperture (figure 4.17). The suspending liquid must be an electrically conducting fluid, because the machine counts the brief changes in resistance that occur when non-conducting particles such as bacteria pass by. A flow cytometer is similar in principle to a Coulter counter except it measures the scattering of light by cells as they pass by a laser. The instrument can be used to count either total cells or, by using special techniques, a specific population. This is done by first staining cells with a fluorescent dye or tag that binds only to the cells of interest; the flow cytometer then counts those cells that carry the fluorescent marker. ■ fluorescent dyes and tags, p. 51

Viable Cell Counts Viable cell counts are used to quantify the number of cells capable of multiplying. These methods require knowledge of appropriate growth conditions for a particular microorganism as well as the time to allow growth to occur. By using selective and differential media, a particular species of bacteria can often be enumerated.

Coverslip

Grid

Slide Bacterial suspension placed on slide; fills shallow space of known volume over grid.

Microscopic observation; all cells in large square counted.

Coverslip

Pipet Slide with ridges that support coverslip; has shallow wells and inscribed grid.

Sample added here. Whole grid has 24 large squares, a total area of 1 sq mm and a total volume of 0.02 mm3.

FIGURE 4.16 A Counting Chamber This special glass slide holds a known volume of liquid. The number of bacteria in that volume can be counted precisely.

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Counting orifice

Electronic detector

FIGURE 4.17 A Coulter Counter This instrument counts cells as they pass through a minute aperture. The bacteria, which are suspended in an electrically conducting liquid, cause a brief change in resistance as they pass by the counter.

Viable cell counts are invaluable for monitoring bacterial growth in samples such as food and water that often contain numbers too low to be seen using a direct microscopic count.

Plate Counts Plate counts measure the number of viable cells in a sample by exploiting the fact that an isolated cell on a nutrient agar plate will give rise to one colony. A simple count of the colonies determines how many cells were in the initial sample (figure 4.18). As the ideal number of colonies to count is between 30 and 300, and samples frequently contain many more bacteria than this, it is usually necessary to dilute the samples before plating the cells. Samples are normally diluted in 10-fold increments, making the resulting math relatively simple. The diluent, or sterile solution used to make the dilutions, is generally physiological saline (0.85% NaCl in water). In the pour-plate method, 0.1 to 1.0 ml of the final dilution is transferred into a sterile Petri dish and then overlaid with melted nutrient agar that has been cooled to 50°C. At this temperature, agar is still liquid. The dish is then gently swirled to mix the bacteria with the liquid agar. When the agar hardens, the individual cells are fixed in place and, after incubation, form distinguishable colonies. In the spread-plate method, 0.1 to 0.2 ml of the final dilution is transferred directly onto a plate of solidified nutrient agar. This solution is then spread over the surface of the agar with a sterilized bent glass rod, which resembles a miniature hockey stick. In both methods the plates are then incubated for a specific time period to allow the colonies to form, which can then be counted. By knowing how much the sample was diluted prior to being plated, along with the amount of the dilution used in

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4.8 Methods to Detect and Measure Bacterial Growth

0.1 – 1.0 ml Transfer 1 ml

Transfer 1 ml

Transfer 1 ml

10-fold dilution

10-fold dilution

10-fold dilution

0.1 – 0.2 ml

Glass rod Melted, cooled nutrient agar

Solidified nutrient agar

Sterile Petri dish 9 ml diluent

9 ml diluent

9 ml diluent

Total dilution 1:10

Total dilution 1:100

Total dilution 1:1000

10 ml culture

101

(a) Serial dilutions

Dish is swirled to mix solution; dish is incubated.

(b) Pour plate

Rod spreads solution evenly; dish is incubated.

(c) Spread plate

FIGURE 4.18 Plate Counts (a) A sample is first diluted in 10-fold increments. (b) In the pour-plate method, 0.1–1.0 ml of a dilution is transferred to a sterile Petri dish and mixed with melted, cooled nutrient agar. When the agar hardens, the plate is incubated and colonies form on the surface and within the agar. (c) In the spread-plate method, 0.1–0.2 ml of a dilution is spread on a hardened agar plate with a sterile glass rod. After incubation, colonies form only on the surface of the agar.

plating, the concentration of viable cells in the original sample can then be calculated. Because bacterial cells often attach to one another and then grow to form a single colony, counts are expressed as colony-forming units. Pour plates and spread plates are generally only used if a sample contains more than 100 organisms/ml. Otherwise, few if any cells will be transferred to the plates. In these situations, alternative methods give more reliable results.

Membrane Filtration Membrane filtration is used when the numbers of organisms in a sample are relatively low, as might occur in dilute environments such

(a)

as natural waters. This method concentrates the bacteria by filtration before they are plated. A known volume of liquid is passed through a sterile membrane filter, which has a pore size that retains bacteria (figure 4.19). The filter is subsequently placed on an appropriate agar medium and then incubated. The number of colonies that grow on the filter indicates the number of bacteria in the volume filtered.

Most Probable Number (MPN) The most probable number (MPN) method is a statistical assay of cell numbers based on the theory of probability. The goal is to successively dilute a sample and determine the point at which subsequent dilutions receive no cells.

2 μm

FIGURE 4.19 Membrane Filtration This technique concentrates bacteria before they are plated. (a) A known volume of liquid is passed through a sterile membrane filter, which has a pore size that retains bacteria. (b) The filter is then placed on an appropriate agar medium and incubated. The number of colonies that grow on the filter indicates the number of bacteria that were in the volume filtered.

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(b)

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102

CHAPTER FOUR Dynamics of Prokaryotic Growth Volume of inoculum

Number of positive tubes in set of five

Observation after incubation (gas production noted)

4

10 ml

+

–

+

+

3

+

+

–

1

–

–

+

4-0-0

13

4-0-1

17

4-1-0

17

4-1-1

21

4-1-2

26

4-2-0

22

4-2-1

26

4-3-0

27

4-3-1

33

4-4-0

34

5-0-0

23

5-0-1

30

5-0-2

40

5-1-0

30

5-1-1

50

5-1-2

60

+

0.1 ml

–

MPN Index/100 ml

+

1 ml

–

Combination of positives

–

FIGURE 4.20 The Most Probable Number (MPN) Method In this example, three sets of five tubes containing the same growth medium were prepared. Each set received the indicated amount of inoculum. After incubation the presence or absence of gas in each tube was noted. The results were then compared to an MPN table to get a statistical estimate of the concentration of gas-producing bacteria.

To determine the MPN, three sets of three or five tubes containing the same growth medium are prepared (figure 4.20). Each set receives a measured amount of a sample such as water, soil, or food. The amount added is determined, in part, by the expected bacterial concentration in that sample. What is important is that the second set receives 10-fold less than the first, and the third set 100-fold less. In other words, each set is inoculated with an amount 10-fold less than the previous set. After incubation, the presence or absence of turbidity or other indication of growth is noted; the results are then compared against an MPN table, which gives a statistical estimate of the cell concentration. The MPN method is most commonly used to determine the approximate number of coliforms in a water sample. Coliforms are lactosefermenting, Gram-negative rods that typically reside in the intestine and thus serve as a bacterial indicator of fecal contamination. ■ coliforms, p. 746

Measuring Biomass Instead of measuring the number of cells, the cell mass can be determined. This can be done by measuring the turbidity or the total weight.

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Turbidity Cloudiness or turbidity of a bacterial suspension such as a broth culture is due to the scattering of light passing through the liquid by cells (figure 4.21). The amount scattered is proportional to the concentration of cells. To measure turbidity, a spectrophotometer is used. This instrument transmits light through a specimen and measures the percentage that reaches a light detector. That number is inversely proportional to the optical density. To use turbidity to estimate cell numbers, a one-time correlation between optical density and cell concentration for the specific organism and conditions under study must be made. Once this correlation has been determined, the turbidity measurement becomes a rapid and relatively accurate assay. One limitation of assaying turbidity is that a medium must contain relatively high numbers of bacteria in order to be cloudy. A solution containing 1 million bacteria (106) per ml is still perfectly clear, and if it contains 10 million cells (107) per ml, it is barely turbid. Thus, although a turbid culture indicates that bacteria are present, a clear solution does not guarantee their absence. Not recognizing these facts can have serious consequences in the laboratory as well as outside. Experienced hikers, for example,

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4.8 Methods to Detect and Measure Bacterial Growth

0

Light cell Light source suspension

103

100

Light detector

0

100

Heavy cell suspension (a)

(b)

FIGURE 4.21 Measuring Turbidity with a Spectrophotometer (a) The cloudiness, or turbidity, of the liquid in the tube on the left is proportional to the concentration of cells. (b) The percentage of light that reaches the detector is inversely proportional to the optical density. To use turbidity to estimate cell number, a one-time experiment must be done to determine the correlation between cell concentration and optical density of a culture.

know that the clarity of mountain streams does not necessarily mean that the water is free of Giardia or other harmful organisms. ■ giardiasis, p. 609

Total Weight Determining the total weight of a culture is a tedious and timeconsuming method that can be used to measure growth of filamentous organisms. These do not readily separate into the individual cells necessary for a valid plate count. To measure the wet weight, cells growing in liquid culture are centrifuged and the liquid supernate removed. The weight of the resulting packed cell mass is proportional to the number of cells in the culture. The dry weight can be determined by drying the centrifuged cells at approximately 100°C for 8 to 12 hours before weighing them. About 70% of the weight of a cell is water.

Detecting Cell Products Products of microbial growth can be used to estimate the number of microorganisms or, more commonly, to confirm their presence. These products include acids, gases, and ATP.

Acid Production As a consequence of the metabolic breakdown of sugars, which are used as an energy source, microorganisms produce a variety of acids. The precise amount of acid can be measured using chemical means. Most commonly, however, acid production is used to detect growth by incorporating a pH indicator into a medium. A pH indicator changes from one color to another as the pH of a medium changes. Several pH indicators are available, and they differ in the pH value at which their color changes.

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Gases Production of gases such as CO2 can be monitored in several ways. A method used in clinical labs employs a fluorescent molecule to detect bacteria growing in blood taken from patients who are suspected of having a bloodstream infection. The slight decrease in pH that accompanies the production of CO2 increases the fluorescence.

ATP The presence of ATP can be detected by adding the firefly enzyme luciferase. The enzyme catalyzes a chemical reaction that uses ATP as an energy source to produce light. This method is sometimes used to assess the effectiveness of chemical agents formulated to kill bacteria. Light is produced only if viable organisms remain.

MICROCHECK 4.8 Direct microscopic counts and cell-counting instruments generally do not distinguish between living and dead cells. Plate counts determine the number of cells capable of multiplying; membrane filtration can be used to concentrate the sample. The most probable number is a statistical assay based on probability. Turbidity of a culture is a rapid measurement that can be correlated to cell number. The total weight of a culture can be correlated to the number of cells present. Microbial growth can be detected by the presence of cell products such as acid, gas, and ATP. ✓ Why is an MPN an estimate rather than an accurate number? ✓ Why would a direct microscopic count yield a higher number than a pour plate if a sample of seawater was examined by both methods?

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FUTURE CHALLENGES Seeing How the Other 99% Lives One of the biggest challenges for the future is the development of methodologies to cultivate and study a wider array of environmental prokaryotes. Without these microbes, humans and other animals would not be able to exist. Yet, considering their importance, we still know very little about most species, including the relative contributions of each to such fundamental processes as O2 generation and N2 and CO2 fixation.

Studying environmental microorganisms can be difficult. Much of our understanding of prokaryotic processes comes from work with pure cultures. Yet, over 99% of prokaryotes have never been successfully grown in the laboratory. At the same time, when organisms are removed from their natural habital, and especially when they are separated from other organisms, their environment changes drastically. Consequently, the study of pure cultures may not be the ideal for studying natural situations.

Technological advances such as flow cytometry and fluorescent labeling, along with the recombinant DNA techniques discussed in chapter 9, may make it easier to study environmental bacteria. This may well lead to a better understanding of the diversity and the roles of microorganisms in our ecosystem. Scientists have learned a great deal about microorganisms since the days of Pasteur, but most of the microbial world is still a mystery.

SUMMARY 4.1

Principles of Prokaryotic Growth

Most prokaryotes multiply by binary fission (figure 4.1). Microbial growth is an increase in the number of cells in a population. The time required for a population to double in number is the generation time (table 4.1).

4.2

Bacterial Growth in Nature

Biofilms (figure 4.2) Prokaryotes often live in a biofilm, a polysaccharide-encased community. Interactions of Mixed Microbial Communities Prokaryotes often grow in close associations containing multiple different species: the metabolic activities of one organism often affects the growth of another.

4.3

Obtaining a Pure Culture

Only an estimated 1% of prokaryotes have been cultivated in the laboratory. Cultivating Bacteria on a Solid Culture Medium A single bacterial cell deposited on a solid medium will multiply to form a visible colony (figure 4.4). The Streak-Plate Method (figure 4.5) The streak-plate method is used to isolate bacteria in order to obtain a pure culture. Maintaining Stock Cultures Stock cultures can be stored on an agar slant in the refrigerator, frozen, or lyophilized.

4.4

Bacterial Growth in Laboratory Conditions

4.5

Environmental Factors That Influence Microbial Growth (table 4.2)

Temperature Requirements (figure 4.9) Organisms can be grouped as psychrophiles, psychrotrophs, mesophiles, thermophiles, or hyperthermophiles based on their optimum growth temperatures. Oxygen (O2) Requirements (table 4.3) Organisms can be grouped as obligate aerobes, obligate anaerobes, facultative anaerobes, microaerophiles or aerotolerant anaerobes based on their oxygen (O2) requirements. Although O2 itself is not toxic, it can be converted to superoxide and hydrogen peroxide, both of which are toxic. Superoxide dismutase and catalase can break these down. pH Organisms can be grouped as neutrophiles, acidophiles, or alkalophiles based on their optimum pH. Water Availability Halophiles are adapted to live in high salt environments.

4.6

Nutritional Factors That Influence Microbial Growth

Required Elements (table 4.4) The major elements make up cell constituents and include carbon, nitrogen, sulfur, and phosphorus. Trace elements are required in very minute amounts. Growth Factors Bacteria that cannot synthesize cell constituents such as amino acids and vitamins require these as growth factors.

The Growth Curve (figure 4.6) When grown in a closed system, a population of bacterial cells goes through five phases: lag, log, stationary, death, and prolonged decline.

Energy Sources Organisms derive energy either from sunlight or from the oxidation of chemical compounds.

Colony Growth The position of a single cell within a colony markedly determines its environment.

Nutritional Diversity (table 4.5) Photoautotrophs use the energy of sunlight and the carbon in the atmosphere to make organic compounds. Chemolithoautotrophs use inorganic compounds for energy and derive their carbon from CO2. Photoheterotrophs use the energy of sunlight and derive their carbon from organic compounds. Chemoorganoheterotrophs use organic compounds for energy and as a carbon source.

Continuous Culture Bacteria can be maintained in a state of continuous exponential growth by using a chemostat.

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Summary

4.7

Cultivating Prokaryotes in the Laboratory

General Categories of Culture Media (table 4.6) A complex medium contains a variety of ingredients such as peptones and extracts. A chemically defined medium is composed of precise mixtures of pure chemicals. Special Types of Culture Media A selective medium inhibits organisms other than the one being sought. A differential medium contains a substance that certain bacteria change in a recognizable way. Providing Appropriate Atmospheric Conditions A candle jar provides increased CO2, which enhances the growth of many medically important bacteria. Microaerophilic bacteria are incubated in a gastight container along with a packet that generates low O2 conditions. Anaerobes may be incubated in an anaerobe container or an anaerobic chamber (figures 4.13, 4.14). Enrichment Cultures (figure 4.15) An enrichment culture provides conditions in a broth that enhance the growth of one particular organism in a mixed population.

4.8

105

Methods to Detect and Measure Bacterial Growth (table 4.8)

Direct Cell Counts Direct cell counts do not distinguish between living and dead cells. One of the most rapid methods of determining the number of cells is the direct microscopic count (figure 4.16). Both a Coulter counter and a flow cytometer count cells as they pass through a minute aperture (figure 4.17). Viable Cell Counts Plate counts measure the number of viable cells by exploiting the fact that an isolated cell will form a single colony (figure 4.18). Membrane filtration concentrates bacteria by filtration; the filter is then incubated on an agar plate (figure 4.19). The most probable number (MPN) method is a statistical assay used to estimate cell numbers (figure 4.20). Measuring Biomass Turbidity of a culture can be correlated with the number of cells; a spectrophotometer is used to measure turbidity (figure 4.21). Wet weight and dry weight are proportional to the number of cells in a culture. Detecting Cell Products Products including acid, gas, and ATP can indicate growth.

REVIEW QUESTIONS Short Answer 1. Define a pure culture. 2. If the number of bacteria in lake water were determined using both a direct microscopic count and a plate count, which method would most likely give a higher number? Why? 3. List the five categories of optimum temperature, and describe a corresponding environment in which a representative might thrive. 4. Explain why obligate anaerobes are significant to the canning industry. 5. Explain why O2-containing atmospheres kill some bacteria. 6. Explain why photoautotrophs are the primary producers. 7. Distinguish between a selective medium and a differential medium. 8. Explain what occurs during each of the five phases of growth. 9. Explain how the environment of a colony differs from that of cells growing in a liquid broth. 10. Describe a detrimental and a beneficial effect of biofilms.

Multiple Choice 1. E. coli is present in a liquid sample at a concentration of between 104 and 106 bacteria per ml. To determine the precise number of living bacteria in the sample, it would be best to a) use a counting chamber. b) plate out an appropriate dilution of the sample on nutrient agar. c) determine cell number by using a spectrophotometer. d) Any of these three methods would be satisfactory. e) None of these three methods would be satisfactory. 2. E. coli, a facultative anaerobe, is grown for 24 hours on the same solid medium, but under two different conditions: one aerobic, the other anaerobic. The size of the colonies would be a) the same under both conditions. b) larger when grown under aerobic conditions. c) larger when grown under anaerobic conditions.

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3. A soil sample is placed in liquid and the number of bacteria in the sample determined in two ways: (1) by colony count and (2) by counting the cells in a counting chamber (slide). How would the results compare? a) Methods 1 and 2 would give approximately the same number of bacteria. b) Many more bacteria would be estimated by method 1. c) Many more bacteria would be estimated by method 2. d) Depending on the soil sample, sometimes method 1 would be higher and sometimes method 2 would be higher. 4. Nutrient broth is an example of a a) synthetic medium. b) complex medium. c) selective medium. d) indicator medium. e) defined medium. 5. E. coli does not use vitamins in the medium in which it grows. This is because E. coli a) does not use vitamins for growth. b) gets vitamins from its host. c) is a chemoheterotroph. d) can synthesize vitamins from the simple compounds provided in the medium. 6. Cells are most sensitive to penicillin during which phase of the growth curve? a) lag b) log c) stationary d) death e) more than one of these. 7. Streptomyces cells would most likely synthesize antibiotics during which phase of the growth curve? a) lag b) log c) stationary d) death e) more than one of these. 8. Compared with their growth in the laboratory, bacteria in nature generally grow a) more slowly. b) faster. c) at the same rate.

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CHAPTER FOUR Dynamics of Prokaryotic Growth

9. If there are 103 cells per ml at the middle of log phase, and the generation time of the cells is 30 minutes, how many cells will there be 2 hours later? a) 2 ! 103 b) 4! 103 c) 8 ! 103 4 7 d) 1.6 ! 10 e) 1 ! 10 10. The major effect of a temperature of 60°C on a mesophile is to a) destroy the cell wall. b) denature proteins. c) destroy nucleic acids. d) destroy the cytoplasmic membrane. e) cause the formation of endospores.

Critical Thinking 1. This figure shows a growth curve plotted on a non-logarithmic, or linear, scale. Compare this with figure 4.6. In both figures, the number of cells increases dramatically during the log or exponential phase. In this phase, the cell number increases more and more rapidly (this effect is more apparent in the accompanying figure). Why should the increase be speeding up?

Log phase

1. You are a microbiologist working for a pharmaceutical company and discover a new metabolite that can serve as a medication. Your company asked you to oversee the production of the metabolite. What are some factors you must consider if you need to grow 5,000-liter cultures of bacteria? 2. High-performance boat manufacturers know that bacteria can collect on a boat, ruining the boat’s hydrodynamic properties. Periodic cleaning of the boat’s surface and repainting eventually ruin that surface and do not solve the problem. A boat-manufacturing facility recently hired you to help with this problem because of your microbiology background. What strategies can you use to come up with a long-term remedy for the problem?

Number of cells

Applications

Lag phase Time

2. In question 1, how would the curve appear if the availability of nutrients were increased?

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5 Medical settings warrant a high level of microbial control.

Control of Microbial Growth A Glimpse of History The British Medical Journal stated that the British physician Joseph Lister (1827–1912) “saved more lives by the introduction of his system than all the wars of the 19th century together had sacrificed.” He revolutionized surgery by developing effective methods that prevent surgical wounds from becoming infected. Impressed with Pasteur’s work on fermentation (said to be caused by “minute organisms suspended in the air”), Lister wondered if “minute organisms” might be responsible also for the pus that formed in surgical wounds. He then experimented with a phenolic compound, carbolic acid, introducing it at full strength into wounds by means of a saturated rag. Lister was particularly proud of the fact that, after carbolic acid wound dressings became standard in his practice, his patients no longer developed gangrene. Lister’s work provided impressive evidence for the germ theory of disease, even though microorganisms specific for various diseases were not identified for another decade. Later, Lister improved his methods by introducing surgical procedures that excluded bacteria from wounds by maintaining a clean environment in the operating room and by sterilizing instruments. These procedures were preferable to killing the bacteria after they had entered wounds because they avoided the toxic effects of the disinfectant on the wound. Lister was knighted in 1883 and subsequently became a baron and a member of the House of Lords.

U

ntil the late nineteenth century, patients undergoing even minor surgery were at great risk of developing fatal infections due to unsanitary medical practices and hospital conditions. Physicians did not know that their hands could pass diseases from one patient to the next. Nor did they understand that airborne microscopic organisms could infect open wounds. Fortunately, today’s modern hospitals use rigorous procedures to avoid microbial contamination, allowing surgical operations to be performed with relative safety.

The growth of microorganisms affects more than our health. Producers of a wide variety of goods recognize that unless microbial growth is controlled, the quality of their products can be compromised. This ranges from undesirable changes in the safety, appearance, taste, or odor of food products to the decay of untreated lumber. This chapter covers methods to destroy, remove, and inhibit the growth of microorganisms on inanimate objects and some body surfaces. Most of these approaches are non-selective in that they can adversely impact all forms of life. Antibiotics and other antimicrobial medications will be discussed in chapter 21. These medications are particularly valuable in combating infectious diseases because their toxicity is specifically targeted to microbes.

5.1 Approaches to Control Focus Points Define the terms sterile, disinfection, disinfectant, biocide, germicide, antiseptic, degerming, pasteurization, decontamination, sanitize, and preservation. Compare and contrast the rigor of the methods used to control microbial growth in daily life, and in hospitals, microbiology laboratories, food and food production facilities, water treatment facilities, and other industries.

The processes used to control microorganisms are either physical or chemical, though a combination of both can be used. Physical methods include heat treatment, irradiation, filtration, and mechanical removal (washing). Chemical 107

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CHAPTER FIVE Control of Microbial Growth

KEY TERMS Antiseptic A disinfectant that is non-toxic enough to be used on skin.

Degerm Treatment used to decrease the number of microbes in an area, usually skin. Disinfectant A chemical used to destroy many microorganisms and viruses.

Sterilant A chemical used to destroy all microorganisms and viruses in a product, rendering it sterile.

Germicide Kills microorganisms and viruses.

Sterile Completely free of all viable microbes; an absolute term.

Bactericidal Kills bacteria.

Pasteurization A treatment, usually brief heating, used to reduce the number of spoilage organisms and to kill disease-causing microbes.

Sterilization The process of destroying or removing all microorganisms and viruses, through physical or chemical means.

Bacteriostatic Prevents the growth of, but does not kill, bacteria.

Preservation The process of inhibiting the growth of microorganisms in products to delay spoilage.

Aseptic Technique Procedures that minimize the chance of unwanted microbes being accidentally introduced.

methods use any of a variety of antimicrobial chemicals. The method chosen depends on the circumstances and degree of control required.

Principles of Control The process of removing or destroying all microorganisms and viruses on or in a product is called sterilization. These procedures include removing microbes by filtration, or destroying them using heat, certain chemicals, or irradiation. Destruction of microorganisms means they cannot be “revived” to multiply even when transferred from the sterilized product to an ideal growth medium. A sterile item is one that is absolutely free of microbes, including endospores and viruses. It is important to note, however, that the term sterile does not consider prions. These infectious protein particles are not destroyed by standard sterilization procedures. ■ endospores, p. 69 ■ prions, p. 341

Disinfection is the process that eliminates most or all pathogens on or in a material. Unlike sterilization, disinfection suggests that some viable microbes may persist. In practice, the term disinfection generally implies the use of antimicrobial chemicals. Those used for disinfecting inanimate objects are called disinfectants. Disinfectants are biocides (bio means “life,” and cida means “to kill”). Although they are at least somewhat toxic to many forms of life, they are typically used in a manner that targets microscopic organisms, including bacteria and their endospores, fungi, and viruses. Thus, they are often called germicides. They are also described as bactericidal, meaning they kill bacteria. When disinfectants are formulated for use on skin they are called antiseptics. Antiseptics are routinely used to decrease the number of bacteria on skin to prepare for invasive procedures such as surgery. ■ pathogen, p. 394 Pasteurization uses a brief heat treatment to reduce the number of spoilage organisms and kill pathogens. Foods and inanimate objects can be pasteurized. Decontamination is a treatment used to reduce the number of pathogens to a level considered safe to handle. The treatment can be as simple as thorough washing, or it may involve the use of heat or disinfectants. Degerming is a treatment used to decrease the number of microbes in an area, particularly the skin. In other words, antiseptics are degerming agents. Sanitized generally implies a substantially reduced microbial population that meets accepted health standards. Most people also expect a sanitized object to be clean in appearance. Note that this term does not denote any specific level of control.

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Preservation is the process of delaying spoilage of foods or other perishable products. This is done by adding growthinhibiting ingredients or adjusting storage conditions to impede growth of microorganisms.

Situational Considerations Methods used to control microbial growth vary greatly depending on the situation and degree of control required (figure 5.1). Control measures adequate for routine circumstances of daily life might not be sufficient for situations such as hospitals, microbiology laboratories, foods and food production facilities, water treatment facilities, and other industries.

Daily Life Washing and scrubbing with soaps and detergents achieves routine control of undesirable microorganisms and viruses. In fact, simple handwashing with plain soap and water is considered the single most important step in preventing the spread of many infectious diseases. Plain soap itself generally does not destroy many organisms; it simply aids in the mechanical removal of transient microbes, including most pathogens, as well as dirt, organic material, and cells of the outermost layer of skin. Regular handwashing and bathing does not adversely impact the beneficial normal skin microbiota, which reside more deeply on underlying layers of skin cells and in hair follicles. ■ normal microbiota of the skin, p. 533 Other methods used to control microorganisms in daily life include cooking foods, cleaning surfaces, and refrigeration.

Hospitals Minimizing the numbers of microorganisms in a hospital is particularly important because of the danger of hospital-acquired, or nosocomial, infections. Hospitalized patients are often more susceptible to infectious agents because of their weakened condition. In addition, patients may be subject to invasive procedures such as surgery, which breaches the intact skin that would otherwise help prevent infection. Finally, pathogens are more likely to be found in hospitals because of the high concentration of patients with infectious disease. These patients may shed pathogens in their feces, urine, respiratory droplets, or other body secretions. Thus, hospitals must be scrupulous in their control of microorganisms. Nowhere is this more important than in the operating rooms, where instruments used in invasive procedures must be sterile to avoid introducing even normally benign microbes into deep body tissue where they could easily establish infection. ■ nosocomial infections, p. 462

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5.1 Approaches to Control

109

(c)

(b)

(a)

(e)

(d)

FIGURE 5.1 Situations that Warrant Different Levels of Microbial Control (a) Daily home life; (b) foods and food production facilities; (c) hospitals; (d) water treatment facilities; (e) other industries.

Prions are a relatively new concern for hospitals. Fortunately, disease caused by prions is thought to be exceedingly rare, less than 1 case per 1 million persons per year. Hospitals, however, must take special precautions when handling tissue that may be contaminated with prions, because these infectious particles are very difficult to destroy.

Microbiology Laboratories Microbiology laboratories routinely work with microbial cultures and consequently must use rigorous methods of controlling microorganisms. To work with pure cultures, all media and instruments that contact the culture must first be rendered sterile to avoid contaminating the culture with environmental microbes. All materials

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used to grow microorganisms must again be treated before disposal to avoid contamination of workers and the environment. The use of specific methods to exclude contaminating microorganisms from an environment is called aseptic technique. Although all microbiology laboratory personnel must use these prudent measures, those who work with known disease-causing microbes must be even more diligent.

Foods and Food Production Facilities Foods and other perishable products retain their quality longer when the growth of contaminating microorganisms is prevented. This can be accomplished by physically removing or destroying microorganisms or by adding chemicals that impede their growth.

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Heat treatment is the most common and reliable method used to kill microbes, but heating can alter the flavor and appearance of food. Irradiation can destroy microbes without causing perceptible changes in food, but the Food and Drug Administration (FDA) has approved this technology to treat only certain foods. Chemicals can prevent the growth of microorganisms, but the risk of toxicity must always be a concern. Because of this, the FDA regulates chemical additives used in food and must deem them safe for consumption. Food-processing facilities need to keep surfaces relatively free of microorganisms to avoid contamination. If machinery used to grind meat, for example, is not cleaned properly, it can create an environment in which bacteria multiply, eventually contaminating large quantities of product.

Water Treatment Facilities Water treatment facilities need to ensure that drinking water is free of pathogenic bacteria, protozoa, and viruses. Chlorine has traditionally been used to disinfect water, saving hundreds of thousands of lives by preventing transmission of waterborne illnesses such as cholera. Disinfectants including chlorine, however, can react with naturally occurring chemicals in the water to form compounds called disinfection by-products (DBPs). Some of these have been linked to long-term health risks. In addition, certain pathogens, particularly the oocysts of Cryptosporidium parvum, are resistant to traditional chemical disinfection procedures. To address these problems, water treatment regulations have been amended to require that facilities minimize the level of both DBPs and C. parvum oocysts in treated water. ■ Cryptosporidium parvum, p. 611

Other Industries Many diverse industries have specialized concerns regarding microbial growth. Manufacturers of cosmetics, deodorants, or any other product that will be applied to the skin must avoid microbial contamination that could affect the product’s quality or safety.

MICROCHECK 5.1 The methods used to control microbial growth depend on the situation and the degree of control required. ✓ How is sterilization different from disinfection? ✓ What is an antiseptic? ✓ Why would the term sterilization not necessarily encompass prions?

5.2 Selection of an Antimicrobial Procedure Focus Point Explain why the type of microbe, number of microbes initially present, environmental conditions, potential risk of infection, and composition of the item influence the selection of an antimicrobial procedure.

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Selection of an effective antimicrobial procedure is complicated by the fact that every procedure has drawbacks that limit its use. An ideal, multipurpose, non-toxic method simply does not exist. The ultimate choice depends on many factors including the type of microbes present, extent of contamination, environmental conditions, potential risk of infection associated with use of the item, and the composition of the item.

Type of Microorganism One of the most critical considerations in selecting an antimicrobial procedure is the type of microbial population present on or in the product. Products contaminated with microorganisms highly resistant to killing require a more rigorous heat or chemical treatment. Some of the highly resistant microbes include: Bacterial endospores. The endospores of Bacillus and Clostridium (and related genera) are the most resistant form of life typically encountered. Only extreme heat or chemical treatment ensures their complete destruction. Chemical treatments that kill vegetative bacteria in 30 minutes may require 10 hours to destroy their endospores. ■ endospores, p. 69 Protozoan cysts and oocysts. Cysts and oocysts are stages in the life cycle of certain intestinal protozoan pathogens such as Giardia lamblia and Cryptosporidium parvum. These disinfectant-resistant forms are excreted in the feces of infected animals, including humans, and can cause diarrheal disease if ingested. They are of particular concern in water treatment. Unlike endospores, they are readily destroyed by boiling. ■ Cryptosporidium parvum, p. 611 ■ Giardia lamblia, p. 609 Mycobacterium species. The waxy cell walls of mycobacteria make them resistant to many chemical treatments. Thus, stronger, more toxic disinfectants must be used to disinfect environments that may contain Mycobacterium tuberculosis, the causative agent of tuberculosis. ■ tuberculosis, p. 514 Pseudomonas species. These common environmental organisms are not only resistant to some chemical disinfectants, but in some cases can actually grow in them. Pseudomonas species are of particular importance in hospitals, where they are a common cause of infections. ■ Pseudomonas infections, p. 564 Naked viruses. Viruses such as poliovirus that lack a lipid envelope are more resistant to disinfectants. Conversely, enveloped viruses, such as HIV, tend to be very sensitive to heat and chemical disinfectants. ■ naked viruses, p. 303 ■ enveloped viruses, p. 303

Numbers of Microorganisms Initially Present The time it takes for heat or chemicals to kill a population of microorganisms is dictated in part by the number of cells initially present. It takes more time to kill a large population than it does to kill a small population, because only a fraction of organisms die during a given time interval. For example, if 90% of a bacterial population is killed during the first 3 minutes, then approximately 90% of those remaining will be killed during the next 3 minutes, and so on.

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5.3 Using Heat to Destroy Microorganisms and Viruses

potential risk of transmitting infectious agents. Those that pose the greatest threat of transmitting disease must be subject to more rigorous germicidal procedures.

108 Log decrease of 1 107

Log10 (number of survivors)

106 Logarithmic killing

105 104 103

Log decrease of 1

102 101

"D"

"D"

1 0

30

60

111

90

120

150

Time (min)

FIGURE 5.2 D Value The D value is the time it takes to reduce the population by 90%.

In the commercial canning industry, the decimal reduction time, or D value, is the time required for killing 90% of a population of bacteria under specific conditions (figure 5.2). The temperature of the process may be indicated by a subscript, for example, D121. A one D process reduces the number of cells by one exponent. Thus, if the D value for an organism is 2 minutes, then it would take 4 minutes (2 D values) to reduce a population of 100 (102) cells to only one (100) survivor. It would take 20 minutes (10 D values) to reduce a population of 1010 cells to only one survivor. Removing organisms by washing or scrubbing can minimize the time necessary to sterilize or disinfect a product.

Environmental Conditions Factors such as pH, temperature, and presence of fats and other organic materials strongly influence microbial death rates. A solution of sodium hypochlorite (household bleach) can kill a suspension of M. tuberculosis in 150 seconds at a temperature of 50°C; whereas it takes only 60 seconds to kill the same suspension with bleach if the temperature is increased to 55°C. The hypochlorite solution is even more effective at a low pH. The presence of dirt, grease, and organic compounds such as blood and other body fluids can interfere with heat penetration and the action of chemical disinfectants. This is another reason why it is important to thoroughly clean items before disinfection or sterilization.

Critical instruments come into direct contact with body tissues. These items, including needles, scalpels, and biopsy forceps, must be sterilized to avoid transmission of all infectious agents. Semicritical instruments come into contact with mucous membranes, but do not penetrate body tissue. These items, including gastrointestinal endoscopes and endotracheal tubes, must be free of all viruses and vegetative bacteria including mycobacteria. Low numbers of endospores that may remain on semicritical instruments pose little risk of infection because mucous membranes are effective barriers against their entry into deeper tissue. Non-critical instruments and surfaces pose little risk of infection because they only come into contact with unbroken skin. Countertops, stethoscopes, and blood pressure cuffs are examples of non-critical items.

Composition of the Item Some sterilization and disinfection procedures are inappropriate for certain types of material. For example, although heat treatment is generally the method of choice because it is so dependable and relatively inexpensive, many plastics and other materials are heat-sensitive. In addition, moist heat corrodes metals, dulling some instruments. Heat-sensitive material can be irradiated, but the process damages some types of plastics. Moisture-sensitive material cannot be treated with liquid chemical disinfectants, which can also damage metals and rubber.

MICROCHECK 5.2 The types and numbers of microorganisms initially present, environmental conditions, the potential risks associated with use of the item, and the composition of the item must all be considered when determining which sterilization or disinfection procedure to employ. ✓ Describe three groups of microorganisms that are resistant to certain chemical treatments. ✓ Define the term D value. ✓ Would it be safe to say that if all bacterial endospores had been killed, then all other medically important microorganisms had also been killed?

5.3 Using Heat to Destroy Microorganisms and Viruses Focus Points

Potential Risk of Infection To guide medical biosafety personnel in their selection of germicidal procedures, medical items such as surgical instruments, endoscopes, and stethoscopes are categorized according to their

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Compare and contrast pasteurization, sterilization using pressurized steam, and the commercial canning process. Explain the drawbacks and benefits of using dry heat rather than moist heat to kill microorganisms.

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CHAPTER FIVE Control of Microbial Growth

TABLE 5.1

Physical Methods Used to Destroy Microorganisms and Viruses Characteristics

Uses

Moist Heat

Denatures proteins. Relatively fast, reliable, safe, and inexpensive.

Widely used.

Boiling

Boiling for 5 minutes destroys most microorganisms and viruses; a notable exception is endospores.

Boiling for at least 5 minutes can be used to treat drinking water.

Pasteurization

Significantly decreases the numbers of heat-sensitive microorganisms, including spoilage microbes and pathogens (except sporeformers).

Milk is pasteurized by heating it to 72°C for 15 seconds. Juices are also routinely pasteurized.

Pressurized steam (autoclaving)

Typical treatment is 121°C/15 psi for 15 minutes or longer, a process that destroys endospores.

Widely used to sterilize microbiological media, laboratory glassware, surgical instruments, and other items that can be penetrated by steam. The canning process renders foods commercially sterile.

Incineration

Oxidizes cell components to ashes.

Flaming of wire inoculating loops. Also used to destroy medical wastes and contaminated animal carcasses.

Dry heat ovens

Oxidizes cell components and denatures proteins. Less efficient than moist heat, requiring longer times and higher temperatures.

Laboratory glassware is sterilized by heating it to 160°C to 170°C for 2 to 3 hours. Powders, oils, and other anhydrous materials are also sterilized in ovens.

Filtration

Filter retains microbes while letting the suspending fluid or air pass through small holes.

Filtration of fluids

Various pore sizes are available; 0.2 mm is commonly used to remove bacteria.

Used to produce beer and wine, and to sterilize some heatsensitive medications.

Filtration of air

HEPA filters are used to remove microbes that have a diameter greater than 0.3 mm.

Used in biological safety cabinets, specialized hospital rooms, and airplanes. Also used in some vacuum cleaners and home air purification units.

Radiation

Type of cell damage depends on the wavelength of the radiation.

Ionizing radiation

Destroys DNA and possibly damages cytoplasmic membranes. Produces reactive molecules that damage other cell components. Items can be sterilized even after packaging.

Used to sterilize heat-sensitive materials including medical equipment, disposable surgical supplies, and drugs such as penicillin. Also used to destroy microbes in spices, herbs, and approved types of produce and meats.

Ultraviolet radiation

Damages DNA. Penetrates poorly.

Used to destroy microbes in the air and drinking water, and to disinfect surfaces.

High Pressure

Treatments of 130,000 psi are thought to denature proteins and alter the permeability of the cell. Products retain color and flavor.

Used to extend the shelf life of certain commercial food products such as guacamole.

Dry Heat

Heat treatment is one of the most useful methods of microbial control because it is reliable, safe, relatively fast and inexpensive, and it does not introduce potentially toxic substances into the material being treated. Some heat-based methods sterilize the product, whereas others decrease the numbers of microorganisms and viruses. Table 5.1 summarizes the characteristics of heat treatment and other physical methods of control.

Moist Heat Moist heat destroys microorganisms by irreversibly coagulating their proteins. Examples of moist heat treatment include boiling, pasteurization, and pressurized steam.

Boiling Boiling (100°C at sea level) easily destroys most microorganisms and viruses. Because of this, drinking water that has potentially been contaminated because of floods or other emergency situ-

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ations should be boiled for at least 5 minutes. Boiling is not an effective means of sterilization, however, because endospores can survive many hours of the treatment.

Pasteurization Louis Pasteur developed the brief heat treatment we now call pasteurization as a way of avoiding spoilage of wine. The process does not sterilize substances but significantly reduces the numbers of heat-sensitive organisms, including pathogens. Today, pasteurization is still used to destroy spoilage organisms in wine, vinegar, and a few other foods, but it is most widely used for killing pathogens in milk and juices. It increases the shelf life of foods and protects consumers by killing organisms that cause diseases such as tuberculosis, brucellosis, salmonellosis, and typhoid fever, without significantly altering the quality of the food. ■ food spoilage, p. 762 Today, most pasteurization protocols employ the hightemperature-short-time (HTST) method. Using this method, milk is heated to 72°C and held for 15 seconds. The parameters

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5.3 Using Heat to Destroy Microorganisms and Viruses Exhaust valve to remove steam after sterilization

113

15 minutes. The temperatures and times used vary according to the organisms present and the heat stability of the material.

Valve to control steam to chamber

Pressure gauge Safety valve

Sterilization Using Pressurized Steam Pressure cookers and their commercial counterpart, the autoclave, heat water in an enclosed vessel that achieves temperatures above 100°C (figure 5.3). As heated water in the vessel forms steam, the steam causes the pressure in the vessel to increase beyond atmospheric pressure. The higher pressure, in turn, increases the temperature at which steam forms. Whereas steam produced at atmospheric pressure never exceeds 100°C, steam produced at an additional 15 psi (pounds/square inch) is 121°C, a temperature that kills endospores. Note that the pressure itself plays no direct role in the killing. Autoclaving is generally the preferred method to sterilize heatand moisture-tolerant items that steam can penetrate. Examples include surgical instruments, most microbiological media, reusable glassware and other supplies. Autoclaving is also used to sterilize microbial cultures and other biohazards before disposal. Typical conditions used for sterilization are 15 psi and 121°C for 15 minutes. Longer time periods are necessary when sterilizing large volumes because it takes longer for heat to completely penetrate the liquid. For example, it takes longer to sterilize 4 liters of liquid in a flask than it would if the same volume were distributed into small tubes. When rapid sterilization is important, such as in operating rooms when sterile instruments must always be available, flash autoclaving at higher temperature can be used. By increasing the temperature to 135°C, sterilization is achieved in only 3 minutes. Autoclaving at a temperature of 132°C for 4.5 hours is thought to destroy prions. Autoclaving is a consistently effective means of sterilizing most objects, provided the process is done correctly. The temperature and pressure gauge should both be monitored to ensure proper operating conditions. It is also critical that steam enter items and displace the air. Long, thin containers should be placed on their sides. Likewise, containers and bags should never be closed tightly. To provide a visual signal that an item has been heated, tape that contains a heat-sensitive indicator can be attached to the item before it is autoclaved. The indicator turns black during autoclaving (figure 5.4a). A changed indicator, however, does not always mean that the object is sterile, because heating may not have been uniform.

Door Steam

Air Jacket

Trap Thermometer

Pressure regulator Steam supply

FIGURE 5.3 Autoclave Steam first travels in an enclosed layer, or jacket, surrounding the chamber. It then enters the autoclave, displacing the air downward and out through a port in the bottom of the chamber.

must be adjusted to the individual food product. For example, ice cream, which is richer in fats than is milk, requires a pasteurization process of 82°C for about 20 seconds. The single-serving containers of cream served in restaurants are processed using the ultra-high-temperature (UHT) method. Because this process is designed to render the product free of all microorganisms that can grow under normal storage conditions, it is technically not a type of pasteurization. The milk is rapidly heated to a temperature of 140°C to 150°C, held for several seconds, then rapidly cooled. The product is then aseptically packaged in containers that have been treated with the chemical germicide hydrogen peroxide. Shelf-stable boxed juices and milk are processed and packaged in a similar manner. Items such as cloth and rubber can be pasteurized by regulating the temperature of the water in a washing machine. For example, hospital anesthesia masks can be pasteurized at 80°C for

FIGURE 5.4 Indicator Used in Autoclaving (a) Chemical indicators. The pack on the left has been autoclaved. Diagonal marks on the tape have turned black, indicating that the object was exposed to heat. (b) Biological indicators. Following incubation, a change of color to yellow indicates growth of endospore-forming organisms. Why would a biological indicator be better than other indicators to determine if sterilization had been completely effective?

(a)

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(b)

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Biological indicators are used to ensure that the autoclave is working properly (figure 5.4b). A tube containing the heatresistant endospores of Geobacillus (Bacillus) stearothermophilus is placed near the center of an item or package being autoclaved. After autoclaving, the endospores are mixed with a growth medium by crushing a container within the tube. Following incubation, a change of color of the medium indicates growth of the organisms and thus faulty autoclaving.

1. Foods are sorted to remove any that are damaged, and then are washed. Washing reduces the number of microorganisms on the food.

The Commercial Canning Process

2. Treatment with hot water or steam destroys enzymes that alter the flavor of the food as well as lowers the number of microorganisms.

The commercial canning process uses pressurized steam in an industrial-sized autoclave called a retort. Conditions of the process are designed to ensure that endospores of Clostridium botulinum are destroyed. This is critical because surviving spores can germinate and the resulting vegetative cells can grow in the anaerobic conditions of low-acid canned foods, such as vegetables and meats, and produce botulinum toxin, one of the most potent toxins known. In killing all endospores of C. botulinum, the process also kills all other organisms capable of growing under normal storage conditions. Endospores of some thermophilic bacteria may survive the canning process, but these are usually of no concern because they only can grow at temperatures well above those of normal storage. Because of this, canned foods are called commercially sterile to reflect the fact that the endospores of some thermophiles may survive. Figure 5.5 shows the steps involved in the commercial canning of foods. ■ botulism, p. 657 Several factors dictate the time and temperature of the canning process. First, as discussed earlier, the higher the temperature, the shorter the time needed to kill all organisms. Second, the higher the concentration of bacteria, the longer the heat treatment required to kill all organisms. To provide a wide margin of safety, the commercial canning process is designed to reduce a population of 1012 C. botulinum endospores to only one. In other words, it is a 12 D process. It is virtually impossible for a food to have this high a level of initial concentration of endospores, and so the process has a wide safety margin.

Dry Heat Dry heat is not as efficient as wet heat in killing microbes, requiring longer times and higher temperatures. For example, 200°C for 90 minutes of dry heat is the killing equivalent of 121°C for 15 minutes of moist heat. Incineration oxidizes the cell components to ashes. In microbiology laboratories, for example, the wire loops continually reused to transfer bacterial cultures are sterilized by flaming—heating them in a flame until they are red hot. Alternatively, they can be heated to the same point in a benchtop incinerator designed for this purpose. Incineration is also used to destroy medical wastes and contaminated animal carcasses. Temperatures achieved in hot air ovens oxidize cell components and irreversibly denature proteins. Glass Petri dishes and glass pipets are sterilized in ovens with non-circulating air at temperatures of 160°C to 170°C for 2 to 3 hours. Ovens with a fan that circulates the hot air can sterilize in a shorter time because of the more efficient transfer of heat. Powders, oils, and other anhydrous material are also sterilized in hot ovens.

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3. The cans are filled.

4. The cans are heated and the air exhausted from (driven out of) the can.

5. The cans are sealed.

6. The cans are heated by steam under pressure. They are cooled by spraying with water or submerging in cold water. Sterilization

Cooling

7. Cans are labeled, packaged, and shipped.

FIGURE 5.5 Steps in the Commercial Canning of Foods

MICROCHECK 5.3 Moist heat such as boiling water destroys most microorganisms and viruses. Pasteurization significantly reduces the numbers of heat-sensitive organisms. Autoclaves use pressurized steam to achieve high temperatures that kill microbes, including endospores. The commercial canning process is designed to destroy the endospores of Clostridium botulinum. Dry heat takes longer than moist heat to kill microbes. ✓ Why is it important that the commercial canning process destroys the endospores of Clostridium botulinum? ✓ What are two purposes of pasteurization? ✓ Would endospores be destroyed in the pasteurization process?

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5.4 Using Other Physical Methods to Remove or Destroy Microbes

5.4 Using Other Physical Methods to Remove or Destroy Microbes Focus Points Describe how depth filters, membrane filters, and HEPA filters are used to remove microorganisms. Describe how gamma irradiation, ultraviolet irradiation, and microwaves destroy microorganisms.

Some materials are either heat-sensitive or impractical to treat using heat. For these items, other physical methods including filtration, irradiation, and high-pressure treatment can be used to either destroy or remove microorganisms.

Filtration Recall that membrane filtration, which is used to determine the number of bacteria in a liquid medium, retains bacteria while allowing the fluid to pass through. That same principle can be employed to physically remove microbes from liquids or air. ■ membrane filtration, p. 101

Filtration of Fluids Filtration is used extensively to remove organisms from heat-sensitive fluids. Examples include production of unpasteurized beer, sterilization of sugar solutions, and clarification of wine. Specially designed filtration units are also used by backpackers and campers to remove Giardia cysts and bacteria from water. Paper-thin membrane filters have microscopic pores that allow liquid to flow through while trapping particles that are too large to pass through the pores (figure 5.6). A vacuum is commonly used to help pull the liquid through the filter; alternatively, pressure may be applied to push the liquid through. Membrane filters are available in a variety of different pore sizes, extending below the dimensions of

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the smallest known viruses. Pore sizes smaller than necessary should be avoided, however, because they slow the flow. Filters with a pore size of 0.2 micrometers (mm) are commonly used to remove bacteria. The filters are made of compounds such as polycarbonate or cellulose nitrate that are relatively inert chemically and absorb very little of the fluid or its biologically important constituents such as enzymes. Depth filters trap material within thick filtration material such as cellulose fibers or diatomaceous earth. They have complex, torturous passages that retain microorganisms while letting the suspending fluid pass through the small holes. The diameter of the passages is often considerably larger than that of the microorganisms they retain, and trapping of microbes partly results from electrical charges on the walls of the filter passages.

Filtration of Air Special filters called high-efficiency particulate air (HEPA) filters remove nearly all microorganisms that have a diameter greater than 0.3 mm from air. These filters are employed for keeping microorganisms out of specialized hospital rooms designed for patients who are extremely susceptible to infection. The filters are also used in biological safety cabinets, laminar flow hoods, in which laboratory personnel work with dangerous airborne pathogens such as Mycobacterium tuberculosis. A continuous flow of incoming and outgoing air is filtered through the HEPA filters to contain microorganisms within the cabinet. Biological safety cabinets are used not only to protect the worker from contamination by the sample, but also to protect the sample from environmental contamination.

Radiation Radio waves, microwaves, visible and ultraviolet light rays, X rays, and gamma rays are all examples of a form of energy called electromagnetic radiation. This energy travels at the speed of light in waves and has no mass. The amount of energy in electromagnetic radiation is related to its wavelength, which is the distance from crest to crest (or trough to trough) of a wave, and frequency, which is the number of waves per second. Radiation that has short waves, and therefore high frequency, has more energy than that which has long waves and low frequency. The full range of wavelengths is called the electromagnetic spectrum (figure 5.7).

Ultraviolet (UV) light

Visible light

Bactericidal

Filter 200

300

400

500 Wavelength (nm)

600

700

Ionizing radiation Gamma rays

Flask

10 -5

Vacuum pump

10 -3

X rays

UV

1

Infrared

10 3

Microwaves

10 6

Radio waves

10 9

10 12

Wavelength (nm) Increasing energy Crest

Sterilized fluid

One wavelength

Trough

FIGURE 5.6 Filtration of Fluids Using a Membrane Filter The liquid

Increasing wavelength

to be sterilized flows through the filter on top of the flask in response to a vacuum produced in the flask by means of a pump. Scanning electron micrograph (5,000μ) shows a membrane filter retaining cells of Pseudomonas.

FIGURE 5.7 The Electromagnetic Spectrum Visible wavelengths

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include the colors of the rainbow.

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Electromagnetic radiation can be either ionizing, meaning it can strip electrons off of atoms, or non-ionizing. Both types can be used to destroy microbes, but the mechanisms of destruction differ.

Ionizing Radiation There are three sources of ionizing radiation: gamma rays, which are emitted from decaying radioisotopes (such as cobalt-60), X rays, and electron accelerators. The radiation causes biological harm both directly, by destroying DNA and possibly damaging cytoplasmic membranes, and indirectly, by producing reactive molecules such as superoxide and hydroxyl free radicals. The latter is a highly unstable molecule because it has one unpaired electron. Bacterial endospores are among the most radiationresistant microbial forms, whereas Gram-negative bacteria such as Salmonella and Pseudomonas species are among the most susceptible. ■ superoxide, p. 92 Radiation is used extensively to sterilize heat-sensitive materials including medical equipment, disposable surgical supplies, and drugs such as penicillin. Radiation can generally be carried out after packaging. Foods can be either sterilized or pasteurized using radiation, depending on the doses employed. Treatments designed to sterilize food can cause undesirable flavor changes, however, which limits their usefulness. More commonly, food is irradiated as a method of pasteurization, eliminating pathogens and decreasing the numbers of spoilage organisms. For example, it can be used to kill pathogens such as Salmonella species in poultry with little or no change in taste of the product. In the United States, irradiation has been used for many years to control microorganisms on spices and herbs. The Food and Drug Administration (FDA) has also approved irradiation of fruits, vegetables, and grains to control insects; pork to control the trichina parasite; and most recently, meats including poultry, beef, lamb, and pork to control pathogens such as Salmonella species and E. coli O157:H7. Many consumers refuse to accept irradiated products, even though the FDA and officials of the World Health and the United Nations Food and Agriculture Organizations have endorsed the technique. Some people erroneously believe that irradiated products are radioactive. Others think that irradiation-induced toxins or carcinogens are present in food, even though available scientific evidence indicates that consumption of irradiated food is safe. Another argument raised against irradiation is that it will cause a relaxation of other prudent food-handling practices. Irradiation, however, is intended to complement, not replace, proper food-handling procedures by producers, processors, and consumers.

Ultraviolet Radiation Ultraviolet light in wavelengths of approximately 220 to 300 nm destroys microorganisms by damaging their DNA. Actively multiplying organisms are the most easily killed, whereas bacterial endospores are the most UV-resistant. Ultraviolet light is used extensively to destroy microbes in the air and drinking water and to disinfect surfaces. It penetrates poorly, however, so even a thin film of grease on the UV bulb or extraneous material covering microorganisms can

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markedly reduce its effective microbial killing. It is not useful for destroying microbes in solid substances or turbid liquids. Since most types of glass and plastic screen out ultraviolet radiation, UV light is most effective when used at close range against exposed microorganisms. It must be used carefully because UV rays can also damage the skin and eyes and promote the development of skin cancers.

Microwaves Microwaves do not affect microorganisms directly, but they can kill microbes by the heat they generate in an item. Organisms often survive microwave cooking, however, because the food heats unevenly.

High Pressure High-pressure processing is used to pasteurize commercial food products such as guacamole without the use of high temperatures. The process, which employs pressures of up to 130,000 psi (pounds per square inch), is thought to destroy microorganisms by denaturing proteins and altering the permeability of the cell. Products treated with high-pressure processes retain the color and flavor associated with fresh foods.

MICROCHECK 5.4 Filters can be used to remove microorganisms and viruses from liquids and air. Gamma irradiation can be used to sterilize products and to decrease the number of microorganisms in foods. Ultraviolet light can be used to disinfect surfaces and air. Microwaves do not kill microbes directly, but by the heat they generate. Extreme pressure can kill microorganisms. ✓ What is the difference between the mechanism of a depth filter and that of a membrane filter? ✓ How does ultraviolet light kill microorganisms? ✓ Why could sterilization by gamma irradiation be carried out even after packaging?

5.5 Using Chemicals to Destroy Microorganisms and Viruses Focus Points Describe the difference between sterilants, high-level disinfectants, intermediate-level disinfectants, and low-level disinfectants. Describe five important factors to consider when selecting an appropriate germicidal chemical. Compare and contrast the characteristics and use of alcohols, aldehydes, biguanides, ethylene oxide gas, halogens, metals, ozone, peroxygens, phenolic compounds, and quaternary ammonium compounds as germicidal chemicals.

Germicidal chemicals can be used to disinfect and, in some cases, sterilize. Most chemical germicides react irreversibly with vital proteins, DNA, cytoplasmic membranes or viral envelopes

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5.5 Using Chemicals to Destroy Microorganisms and Viruses Cytoplasmic Membrane • Biguanides • Phenolics • Quats

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Intermediate-level and low-level disinfectants are also called general-purpose disinfectants. They are used in hospitals for disinfecting furniture, floors, and walls.

Proteins • Alcohols • Aldehydes • Halogens • Metals • Ozone • Peroxygens • Phenolics

To perform properly, germicides must be used strictly according to the manufacturer’s directions, especially as they relate to dilution, temperature, and the amount of time they must be in contact with the object being treated. It is extremely important that the object be thoroughly cleaned and free of organic material before the germicidal procedure is begun.

DNA • Ethylene oxide • Aldehydes

Selecting the Appropriate Germicidal Chemical 3 μm

FIGURE 5.8 Sites of Action Germicidal Chemicals

(figure 5.8). Their precise mechanisms of action, however, are often not completely understood. Although generally less reliable than heat, these chemicals are suitable for treating large surfaces and many heat-sensitive items. Some are sufficiently non-toxic to be used as antiseptics. Those that have a bacteriostatic action, meaning they prevent the growth of (but do not kill) bacteria, can be used as preservatives.

Potency of Germicidal Chemical Formulations Numerous different germicidal chemicals are marketed for medical and industrial use under a variety of trade names. Frequently, they contain more than one antimicrobial chemical as well as other chemicals such as buffers that can influence their antimicrobial activity. In the United States, the Food and Drug Administration (FDA) is responsible for regulating chemicals that can be used to process medical devices in order to ensure they perform as claimed. Most chemical disinfectants are considered pesticides and, as such, are regulated by the Environmental Protection Agency (EPA). To be registered with either the FDA or EPA, manufacturers of germicidal chemicals must document the potency of their products using testing procedures originally defined by the EPA. Germicides are grouped according to their potency: Sterilants can destroy all microorganisms, including endospores and viruses. Destruction of endospores usually requires a 6- to 10-hour treatment. Sterilants are used to treat heatsensitive critical instruments such as scalpels. High-level disinfectants destroy all viruses and vegetative microorganisms, but they do not reliably kill endospores. Most are simply sterilants used for time periods as short as 30 minutes, not long enough to ensure endospore destruction. They can be used to treat semicritical instruments such as gastrointestinal endoscopes. Intermediate-level disinfectants destroy all vegetative bacteria including mycobacteria, fungi, and most, but not all, viruses. They do not kill endospores even with prolonged exposure. They are used to disinfect non-critical instruments such as stethoscopes. Low-level disinfectants destroy fungi, vegetative bacteria except mycobacteria, and enveloped viruses. They do not kill endospores, nor do they reliably destroy naked viruses.

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Selecting the appropriate germicide is a complex decision. Some points to consider include: Toxicity. Germicides are at least somewhat toxic to humans and the environment. Therefore, the benefit of disinfecting or sterilizing an item or surface must be weighed against the risks associated with using the germicidal procedure. For example, the risk of being exposed to a pathogenic microorganism in a hospital environment warrants using the most effective chemical germicides, even considering the potential risks of their use. The microbiological risks associated with typical household and office situations, however, may not justify the use of many of those same germicides. Activity in the presence of organic matter. Many germicidal chemicals, such as hypochlorite, are readily inactivated by organic matter and are not appropriate to use in situations where organic material is present. Chemicals such as phenolics, however, tolerate the presence of some organic matter. Compatibility with the material being treated. Items such as electrical equipment often cannot tolerate liquid chemical germicides, and so gaseous alternatives must be employed. Likewise, corrosive germicides such as hypochlorite often damage some metals and rubber. Residue. Many chemical germicides leave a residue that is toxic or corrosive. If a germicide that leaves a residue is used to sterilize or disinfect an item, the item must be thoroughly rinsed with sterile water to entirely remove the residue. Cost and availability. Some germicides are less expensive and more readily available than others. For example, hypochlorite can easily be purchased in the form of household bleach. On the other hand, ethylene oxide gas is not only more expensive, but it must be used in a special chamber, which influences the cost and practicality of the procedure. Storage and stability. Some germicides are available in concentrated stock solutions, decreasing the required storage space. The stock solutions are simply diluted according to the manufacturer’s instructions before use. Others, such as chlorine dioxide, come in two-component systems that have a limited shelf life once mixed. Environmental risk. Germicides that retain their antimicrobial activity after use can interfere with sewage treatment systems that utilize microorganisms to degrade sewage. The activity of those germicides must be neutralized before disposal.

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TABLE 5.2

Chemicals Used in Sterilization, and Disinfection, and Preservation of Non-Food Substances

Chemical (examples)

Characteristics

Uses

Alcohols (ethanol and isopropanol)

Easy to obtain and inexpensive. Rapid evaporation limits their contact time.

Aqueous solutions of alcohol are used as antiseptics to degerm skin in preparation for procedures that break intact skin, and as disinfectants for treating instruments.

Aldehydes (glutaraldehyde,

Capable of destroying all forms of microbial life. Irritating to the respiratory tract, skin, and eyes.

Glutaraldehyde and orthophthalaldehyde are used to sterilize medical instruments. Formalin is used in vaccine production and to preserve biological specimens.

Biguanides (chlorhexidine)

Relatively low toxicity, destroys a wide range of microbes, adheres to and persists on skin and mucous membranes.

Chlorhexidine is widely used as an antiseptic in soaps and lotions, and impregnated into catheters and surgical mesh.

Ethylene Oxide Gas

Easily penetrates hard-to-reach places and fabrics and does not damage moisture-sensitive material. It is toxic, explosive, and potentially carcinogenic.

Commonly used to sterilize medical devices.

Halogens (chlorine and iodine)

Chlorine solutions are inexpensive and readily available; however, organic compounds and other impurities neutralize the activity. Some forms of chlorine may react with organic compounds to form toxic chlorinated products. Iodine is more expensive than chlorine and does not reliably kill endospores.

Solutions of chlorine are widely used to disinfect inanimate objects, surfaces, drinking water, and wastewater. Tincture of iodine and iodophores can be used as disinfectants or antiseptics.

Metals (silver)

Most metal compounds are too toxic to be used medically.

Silver sulfadiazine is used in topical dressings to prevent infection of burns. Silver nitrate drops can be used to prevent eye infections caused by Neisseria gonorrhoeae in newborns. Some metal compounds are used to prevent microbial growth in industrial processes.

Ozone

This unstable form of molecular oxygen readily breaks down.

Used to disinfect drinking water and wastewater.

Peroxygens (hydrogen peroxide and

Readily biodegradable and less toxic than traditional alternatives. The effectiveness of hydrogen peroxide as an antiseptic is limited because the enzyme catalase breaks it down. Peracetic acid is a more potent germicide than is hydrogen peroxide.

Hydrogen peroxide is used to sterilize containers for aseptically packaged juices and milk. Peracetic acid is widely used to disinfect and sterilize medical devices.

Wide range of activity, reasonable cost, remains effective in the presence of detergents and organic contaminants, leaves an active antimicrobial residue.

Triclosan is used in a variety of personal care products, including toothpastes, lotions, and deodorant soaps. Hexachlorophene is highly effective against Staphylococcus aureus, but its use is limited because it can cause neurological damage.

orthophthalaldehyde, and formaldehyde)

peracetic acid)

Phenolic Compounds (triclosan and hexachlorophene)

Quaternary Ammonium Compounds Non-toxic enough to be used on food preparation Widely used to disinfect inanimate objects and to (benzalkonium chloride and cetylpyridinium chloride)

surfaces. Inactivated by anionic soaps and detergents.

Classes of Germicidal Chemicals Germicides are represented in a number of chemical families. Each type has characteristics that make it more or less appropriate for specific uses (table 5.2).

Alcohols Aqueous solutions of 60% to 80% ethyl or isopropyl alcohol rapidly kill vegetative bacteria and fungi. They do not, however, reliably destroy bacterial endospores and some naked viruses. Alcohol probably acts by coagulating enzymes and other essential proteins

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preserve non-food substances.

and by damaging lipid membranes. Proteins are more soluble and denature more easily in alcohol mixed with water, which is why the aqueous solutions are more effective than pure alcohol. Alcohol solutions are commonly used as antiseptics to degerm skin before procedures such as injections that break intact skin. In addition, the Centers for Disease Control recently recommended that alcohol-based hand sanitizers be used routinely by healthcare personnel as a means to protect patients. Alcohol solutions are also used as disinfectants for treating instruments and surfaces. They are relatively non-toxic and inexpensive, and do not leave a residue, but they evaporate quickly,

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5.5 Using Chemicals to Destroy Microorganisms and Viruses

which limits their effective contact time and, consequently, their germicidal effectiveness. In addition, they may damage some materials, such as rubber and some plastics. Other antimicrobial chemicals are sometimes dissolved in alcohol. These alcohol-based solutions, called tinctures, can be more effective than the corresponding aqueous solutions.

Aldehydes The aldehydes glutaraldehyde, orthophthalaldehyde (OPA), and formaldehyde destroy microorganisms and viruses by inactivating proteins and nucleic acids. A 2% solution of alkaline glutaraldehyde is one of the most widely used liquid chemical sterilants for treating heat-sensitive medical items. Immersion in this solution for 10 to 12 hours destroys all forms of microbial life, including endospores, and viruses. Soaking times as short as 10 minutes can be used to destroy vegetative bacteria. Glutaraldehyde is toxic, however, so treated items must be thoroughly rinsed with sterile water before use. Orthophthalaldehyde is a relatively new type of disinfectant that provides an alternative to glutaraldehyde. It requires shorter processing times and is less irritating to eyes and nasal passages, but it stains proteins grey, including those of the skin. Formaldehyde is used as a gas or an aqueous 37% solution called formalin. It is an extremely effective germicide that kills most forms of microbial life within minutes. Formalin is used to kill bacteria and to inactivate viruses for use as vaccines. It has also been used to preserve biological specimens. Formaldehyde’s irritating vapors and suspected carcinogenicity, however, now limit its use.

Biguanides Chlorhexidine, the most effective of a group of chemicals called biguanides, is extensively used in antiseptic products. It adheres to and persists on skin and mucous membranes, is of relatively low toxicity, and destroys a wide range of microbes, including vegetative bacteria, fungi, and some enveloped viruses. Chlorhexidine is an ingredient in many products including antiseptic skin creams, disinfectants, and mouthwashes. Chlorhexidine-impregnated catheters and implanted surgical mesh are used in medical procedures. Even tiny chips have been developed that can be inserted into periodontal pockets, where they slowly release chlorhexidine to treat periodontal gum disease. Adverse side effects of chlorhexidine are rare, but severe allergic reactions have been reported.

Ethylene Oxide Ethylene oxide is an extremely useful gaseous sterilizing agent that destroys all microbes, including endospores and viruses, by reacting with proteins. As a gas, it penetrates well into fabrics, equipment, and implantable devices such as pacemakers and artificial hips. It is particularly useful for sterilizing heat- or moisture-sensitive items such as electrical equipment, pillows, and mattresses. Many disposable laboratory items, including plastic Petri dishes and pipets, are also sterilized with ethylene oxide. A special chamber that resembles an autoclave is used to sterilize items with ethylene oxide. This allows careful control of factors such as temperature, relative humidity, and ethylene oxide

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concentration, all of which influence the effectiveness of the gas. Because ethylene oxide is explosive, it is generally mixed with a non-flammable gas such as carbon dioxide. Under these carefully controlled conditions, objects can be sterilized in 3 to 12 hours. The toxic ethylene oxide must then be eliminated from the treated material using heated forced air for 8 to 12 hours. Absorbed ethylene oxide must be allowed to dissipate because of its irritating effects on tissues and persistent antimicrobial effect, which, in the case of Petri dishes and other items used for culturing bacteria, is unacceptable. Ethylene oxide is mutagenic and therefore potentially carcinogenic. Indeed, studies have shown a slightly increased risk of malignancies in long-term users of the gas.

Halogens Chlorine and iodine are common disinfectants that are thought to act by oxidizing proteins and other essential cell components. Chlorine Chlorine destroys all types of microorganisms and viruses but is too irritating to skin and mucous membranes to be used as an antiseptic. Chlorine-releasing compounds such as sodium hypochlorite can be used to disinfect waste liquids, swimming pool water, instruments, and surfaces, and at much lower concentrations, to disinfect drinking water. Chlorine solutions are inexpensive, readily available disinfectants. An effective disinfection solution can easily be made by diluting liquid household bleach (5.25% sodium hypochlorite) 1:100 in water, resulting in a solution of 500 ppm (parts per million) chlorine. This concentration is several hundred times the amount required to kill most pathogenic microorganisms and viruses, but it is usually necessary for fast, reliable killing. In situations when excessive organic material is present, a 1:10 dilution of bleach may be required. This is because chlorine readily reacts with organic compounds and other impurities in water, disrupting its germicidal activity. The use of high concentrations, however, should be avoided when possible, because chlorine is both corrosive and toxic. Diluted solutions of liquid bleach deteriorate over time; thus, fresh solutions need to be prepared regularly. More stable forms of chlorine, including sodium dichloroisocyanurate and chloramines, are often used in hospitals. Properly chlorinated drinking water contains approximately 0.5 ppm chlorine, much less than that used for disinfectant solutions. The exact amount of chlorine that must be added depends on the amount of organic material in the water. The presence of organic compounds is also a problem because chlorine can react with some organic compounds to form trihalomethanes, which are potential carcinogens. Note also that the concentrations of chlorine typically used to disinfect drinking water are not effective against Cryptosporidium parvum oocysts and Giardia lamblia cysts. Chlorine dioxide (ClO2) is a strong oxidizing agent that is increasingly being used as a disinfectant and sterilant. It has an advantage over chlorine-releasing compounds in that it does not react with organic compounds to form trihalomethanes or other toxic chlorinated products. Compressed chlorine dioxide gas, however, is explosive and liquid solutions decompose readily, so that it must be generated on-site. It is used to treat drinking water, wastewater, and swimming pools.

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Iodine, unlike chlorine, does not reliably kill endospores, but it can be used as a disinfectant. It is used as a tincture in which the iodine is dissolved in alcohol, or more commonly as an iodophore, in which the iodine is linked to a carrier molecule that releases free (unbound) iodine slowly. Iodophores are not as irritating to the skin as tincture of iodine nor are they as likely to stain. Iodophores used as disinfectants contain more free iodine (30 to 50 ppm) than do those used as antiseptics (1 to 2 ppm). Stock solutions must be strictly diluted according to the manufacturer’s instructions because dilution affects the amount of free iodine available. Surprisingly, some Pseudomonas species survive in the concentrated stock solutions of iodophores. The reasons are unclear, but it could be due to inadequate levels of free iodine in concentrated solutions, because iodine may be released from the carrier only with dilution. Pseudomonas species also can form biofilms, which are less permeable to chemicals. Nosocomial infections can result if a Pseudomonas-contaminated iodophore is unknowingly used to disinfect instruments. ■ biofilm, p. 85

Iodine

Metal Compounds Metal compounds kill microorganisms by combining with sulfhydryl groups (—SH) of enzymes and other proteins, thereby interfering with their function. Unfortunately, most metals at high concentrations are too toxic to human tissue to be used medically. Silver is one of the few metals still used as a disinfectant. Creams containing silver sulfadiazine, a combination of silver and a sulfa drug, are applied topically to prevent infection of second- and third-degree burns. Commercially available bandages with silver-containing pads can be used on minor scalds, cuts, and scrapes. For many years, doctors were required by law to instill drops of another silver compound, 1% silver nitrate, into the eyes of newborns to prevent ophthalmia neonatorum, an eye infection caused by Neisseria gonorrhoeae, which is acquired from infected mothers during the birth process. Drops of antibiotics have now largely replaced use of silver nitrate because they are less irritating to the eye and more effective against another genitally acquired pathogen, Chlamydia trachomatis. ■ Neisseria gonorrhoeae, p. 629 ■ Chlamydia trachomatis, p. 631

Compounds of mercury, tin, arsenic, copper, and other metals were once widely used as preservatives in industrial products and to prevent microbial growth in recirculating cooling water. Their extensive use resulted in serious pollution of natural waters, which has prompted strict controls.

Ozone Ozone (O3) is an unstable form of oxygen that is a powerful oxidizing agent. It decomposes quickly, however, so it must be generated on-site, usually by passing air or oxygen between two electrodes. Ozone is used as an alternative to chlorine for disinfecting drinking water and wastewater.

Peroxygens Hydrogen peroxide and peracetic acid are powerful oxidizing agents that under controlled conditions can be used as sterilants.

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They are readily biodegradable and, in normal concentrations of use, appear to be less toxic than the traditional alternatives, ethylene oxide and glutaraldehyde. Hydrogen Peroxide The effectiveness of hydrogen peroxide (H2O2) as a germicide depends in part on whether it is used on living tissue, such as a wound, or on an inanimate object. This is because all cells that use aerobic metabolism, including the body’s cells, produce the enzyme catalase, which inactivates hydrogen peroxide by breaking it down to water and oxygen gas. Thus, when a solution of 3% hydrogen peroxide is applied to a wound, our cellular enzymes quickly break it down. When the same solution is used on an inanimate surface, however, it overwhelms the relatively low concentration of catalase produced by microscopic organisms. ■ catalase, p. 92 Hydrogen peroxide is particularly useful as a disinfectant because it leaves no residue and does not damage stainless steel, rubber, plastic, or glass. Hot solutions are commonly used in the food industry to yield commercially sterile containers for aseptically packaged juices and milk. Vapor-phase hydrogen peroxide is more effective than liquid solutions and can be used as a sterilant. Peracetic Acid Peracetic acid is an even more potent germicide than hydrogen peroxide. A 0.2% solution of peracetic acid, or a combination of peracetic acid and hydrogen peroxide, can be used to sterilize items in less than 1 hour. It is effective in the presence of organic compounds, leaves no residue, and can be used on a wide range of materials. It has a sharp, pungent odor, however, and like other oxidizing agents, it is irritating to the skin and eyes.

Phenolic Compounds (Phenolics) Phenol (carbolic acid) is important historically because it was one of the earliest disinfectants, but its use is now limited because it has an unpleasant odor and irritates the skin. Derivatives of phenol, called phenolics, have greater germicidal activity, which enables effective use of more dilute and therefore less irritating solutions. Phenolic compounds are the active ingredients in LysolTM. Phenolics destroy cytoplasmic membranes of microorganisms and denature proteins. They kill most vegetative bacteria and, in high concentrations (from 5% to 19%), many can kill Mycobacterium tuberculosis. They do not, however, reliably inactivate all groups of viruses. The major advantages of phenolic compounds include their wide range of activity, reasonable cost, and ability to remain effective in the presence of detergents and organic contaminants. They also leave an active antimicrobial residue, which in some cases is desirable. Some phenolics, such as triclosan and hexachlorophene, are sufficiently non-toxic to be used in soaps and lotions. Triclosan is widely used as an ingredient in a variety of personal care products such as deodorant soaps, lotions, and toothpaste. Hexachlorophene has substantial activity against Staphylococcus aureus, the leading cause of wound infections, but high levels have been associated with symptoms of neurotoxicity. Although once widely used in over-the-counter products, antiseptic skin cleansers containing hexachlorophene are now available only with a prescription.

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5.6

Preservation of Perishable Products

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PERSPECTIVE 5.1 Contamination of an Operating Room by a Bacterial Pathogen A patient with burns infected with Pseudomonas aeruginosa was taken to the operating room for cleaning of the wounds and removal of dead tissue. After the procedure was completed, samples of various surfaces in the room were cultured to determine the extent of contamination. P. aeruginosa was recovered from all parts of the room. Figure 1 shows how readily and extensively an operating room can become contaminated by an infected patient. Operating rooms and other patient care rooms must be thoroughly cleaned after use, in a process known as terminal cleaning.

FIGURE 1 Diagram of an operating room in which dead tissue infected with Pseudomonas aeruginosa was removed from a patient with burns. Reddish areas indicate places where P. aeruginosa was recovered following the surgical procedure.

Quaternary Ammonium Compounds (Quats) Quaternary ammonium compounds, also commonly called quats, are cationic (positively charged) detergents that are nontoxic enough to be used to disinfect food preparation surfaces. Like all detergents, quats have both a charged hydrophilic region and an uncharged hydrophobic region. This enables them to reduce the surface tension of liquids and help wash away dirt and organic material, facilitating the mechanical removal of microorganisms from surfaces. Unlike most common household soaps and detergents, however, which are anionic (negatively charged) and repelled by the negatively charged microbial cell surface, quats are attracted to the cell surface. They react with membranes, destroying many vegetative bacteria and enveloped viruses. They are not effective, however, against endospores, mycobacteria, or naked viruses. Quaternary ammonium compounds are economical and effective agents that are widely used to disinfect clean inanimate objects and to preserve non-food substances. The ingredients of many personal care products include quats such as benzalkonium chloride or cetylpyridinium chloride. They also enhance the effectiveness of some other disinfectants. Cationic soaps and organic material such as gauze, however, can neutralize their effectiveness. In addition, Pseudomonas, a troublesome cause of nosocomial infections, resists the effects of quats and can even grow in solutions preserved with them.

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MICROCHECK 5.5 Germicidal chemicals can be used to disinfect and, in some cases, sterilize, but they are less reliable than heat. They are especially useful for destroying microorganisms and viruses on heat-sensitive items and large surfaces. ✓ Describe four factors that must be considered when selecting a germicidal chemical. ✓ Explain why it is essential to dilute iodophores properly. ✓ Why would a heavy metal be a more serious pollutant than most organic compounds?

5.6 Preservation of Perishable Products Focus Point Explain how chemical preservatives, low-temperature storage, adding salt or sugar, and drying food can all be used to preserve perishable products.

Preventing or slowing the growth of microorganisms extends the shelf life of products such as food, soaps, medicines,

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CHAPTER FIVE Control of Microbial Growth

deodorants, cosmetics, and contact lens solutions. Preservative chemicals are often added to these products to prevent or slow the growth of microbes that are inevitably introduced from the environment. Other common methods of decreasing the growth rate of microbes include low-temperature storage such as refrigeration or freezing, and reducing available water. These methods are particularly important in preserving foods. ■ food spoilage, p. 762 ■ factors influencing the growth of microorganisms

in foods, p. 754

Chemical Preservatives Some of the germicidal chemicals previously described can be used to preserve non-food items. For example, mouthwash may contain a quaternary ammonium compound, nasal sprays may contain thimerosal, and leather belts may be treated with one or more phenol derivatives. Food preservatives, however, must be non-toxic for repeated safe ingestion. Benzoic, sorbic, and propionic acids are weak organic acids that are sometimes added to foods such as bread, cheese, and juice to prevent microbial growth. At a low pH, these weak acids alter cell membrane functions and interfere with energy transformation. The low pH at which they are most effective is itself sufficient to prevent the growth of most bacteria, so these preservatives are primarily added to acidic foods to prevent the growth of fungi, which otherwise grow well at acidic pH. These organic acids also occur naturally in some foods such as cranberries and Swiss cheese. Another preservative, nitrate, and its reduced form, nitrite, serve a dual purpose in processed meats. From a microbiological viewpoint, their most important function is to inhibit the germination of endospores and subsequent growth of Clostridium botulinum. Without the addition of low levels of nitrate or nitrite to cured meats such as bologna, ham, bacon, and smoked fish, C. botulinum may grow and produce deadly botulinum toxin. At higher concentrations than are required for preservation, nitrate and nitrite react with myoglobin in the meat to form a stable pigment that gives a desirable pink color associated with fresh meat. Nitrates and nitrites also pose a potential hazard, however, because they can be converted to nitrosamines during the frying of meats in hot oil or by the metabolic activities of intestinal bacteria. Nitrosamines are potent carcinogens, which has caused concern regarding the use of nitrate and nitrite as preservatives.

Freezing is also an important means of preserving foods and other products. Freezing essentially stops all microbial growth. While the formation of ice crystals can kill some of the microbial cells, the remaining organisms can grow and spoil foods once they are thawed.

Reducing the Available Water For many years, salting and drying have been used to preserve food. Both processes decrease the availability of water in food below the limits required for growth of most microorganisms. The high-solute environment causes plasmolysis, which damages microbial cells (see figure 4.10). ■ plasmolysis, p. 93 ■ water availability, p. 93

Adding Salt or Sugar Sugar and salt draw water out of cells, dehydrating them. High concentrations of sugars or salts are added to many foods as preservatives. For example, fruit is made into jams and jellies by adding sugar, and fish and meats are cured by soaking them in salty water, or brine. Some caution should be exercised when using salt as a preservative, however, because the food-poisoning bacterium Staphylococcus aureus can grow under quite high salt conditions. ■ Staphylococcus aureus, p. 763

Drying Food Removing water, or desiccating, food is often supplemented by salting or adding high concentrations of sugar or small amounts of chemical preservatives. For example, meat jerkies usually have added salt and sometimes sugar. Lyophilization (freeze-drying) is widely used for preserving foods such as coffee, milk, meats, and vegetables. In the process of freeze-drying, the food is first frozen and then dried in a vacuum. When water is added to the lyophilized material, it reconstitutes. The quality of the reconstituted product is often much better than that of products treated with ordinary drying methods. The light weight and stability without refrigeration of freeze-dried foods make them popular with hikers. Although drying stops microbial growth, it does not reliably kill bacteria and fungi in or on foods. For example, numerous cases of salmonellosis have been traced to dried eggs. Eggshells and even egg yolks may be heavily contaminated with Salmonella species from the gastrointestinal tract of the hen. To prevent the transmission of such pathogens, some states have laws requiring dried eggs to be pasteurized before they are sold.

MICROCHECK 5.6

Low-Temperature Storage The growth of many pathogens and spoilage microorganisms is inhibited by refrigeration because their critical enzyme reactions are slowed or stopped. Thus, low temperature storage is extremely useful in preservation. Psychrotrophic and some psychrophilic organisms, however, can grow at normal refrigeration temperatures. ■ psychrophiles, p. 91

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Preservation techniques slow or halt the growth of microorganisms to delay spoilage. ✓ What organism that causes food poisoning is able to grow under high-salt conditions? ✓ What is the risk of consuming nitrate- or nitrite-free cured meats? ✓ Preservation by freezing is sometimes compared to drying. Why would this be so?

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Summary

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FUTURE CHALLENGES Too Much of a Good Thing? In our complex world, the solution to one challenge may inadvertently lead to the creation of another. Scientists have long been pursuing less toxic alternatives to many traditional biocidal chemicals. For example, glutaraldehyde has now largely replaced the more toxic formaldehyde, chlorhexidine is generally used in place of hexachlorophene, and gaseous alternatives to ethylene oxide are now being sought. Meanwhile, ozone and hydrogen peroxide, which are both readily biodegradable, may eventually replace glutaraldehyde. While these less toxic alternatives are better for human health and the environment, their widespread acceptance and use may be unwittingly contributing to an additional problem—the overuse and misuse of germicidal chemicals. Many products, including soaps, toothbrushes, and even clothing and toys are marketed with the claim of containing antimicrobial ingredients. Already there are reports of bacterial resistance to some of the chemicals included in these products.

The issues surrounding the excessive use of antimicrobial chemicals are complicated. On the one hand, there is no question that some microorganisms cause disease. Even those that are not harmful to human health can be troublesome because they produce metabolic end products that ruin the quality of perishable products. Based on that information, it seems prudent to destroy or inhibit the growth of microorganisms whenever possible. The role of microorganisms in our life, however, is not that simple. Our bodies actually harbor a greater number of microbial cells than human cells, and this normal microbiota plays an important role in maintaining our health. Excessive use of antiseptics or other antimicrobials may actually predispose a person to infection by damaging the normal microbiota. An even more worrisome concern is that overuse of disinfectants and other germicidal chemicals will select for microorganisms that are more resistant to those chemicals, a situation analogous to our current

problems with antibiotic resistance. By using antimicrobial chemicals indiscriminately, we may eventually make these useful tools obsolete. Excessive use of disinfectants may even be contributing to the problems of antibiotic resistance. Disinfectant-resistant bacteria sometimes over-produce efflux pumps that expel otherwise damaging chemicals, including antibiotics, from the cell. Thus, by overusing disinfectants, we may be inadvertently increasing antibiotic resistance. Another concern is over the misguided belief that “non-toxic” or “biodegradable” chemicals cause no harm, and the common notion that “if a little is good, more is even better.” For example, concentrated solutions of hydrogen peroxide, though biodegradable, can cause serious damage, even death, when used improperly. Other chemicals, such as chlorhexidine, can elicit severe allergic reactions in some people. As less toxic germicidal chemicals are developed, people must be educated on the appropriate use of these alternatives.

SUMMARY 5.1

Approaches to Control

The methods used to destroy or remove microorganisms and viruses can be physical, such as heat treatment, irradiation, and filtration, or chemical.

Environmental Conditions Factors such as pH and presence of organic materials influence microbial death rates.

Principles of Control A variety of terms are used to describe antimicrobial agents and processes.

Potential Risk of Infection To guide medical biosafety personnel in their selection of germicidal procedures, instruments are categorized as critical, semicritical, and non-critical according to their potential risk of transmitting infectious agents.

Situational Considerations (figure 5.1) Situations encountered in daily life, hospitals, microbiology laboratories, food production facilities, water treatment facilities, and other industries warrant different degrees of microbial control.

Composition of the Item Some sterilization and disinfection procedures are inappropriate for certain types of material.

5.2

Selection of an Antimicrobial Procedure

Type of Microorganism One of the most critical considerations in selecting a method of destroying microorganisms and viruses is the type of microbial population thought to be present on or in the product. Numbers of Microorganisms Initially Present The amount of time it takes for heat or chemicals to kill a population of microorganisms is dictated in part by the number of cells initially present. Microbial death generally occurs at a constant rate. The D value, or decimal reduction time, is the time it takes to kill 90% of a population of bacteria under specific conditions (figure 5.2).

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5.3

Using Heat to Destroy Microorganisms and Viruses (figure 5.1)

Moist Heat Moist heat destroys microorganisms by causing irreversible coagulation of their proteins. Pasteurization utilizes a brief heat treatment to destroy spoilage and disease-causing organisms. Pressure cookers and autoclaves heat water in an enclosed vessel that causes the pressure in the vessel to increase beyond atmospheric pressure, increasing the temperature of steam, which kills endospores (figure 5.3). The most important aspect of the commercial canning process is to ensure that endospores of Clostridium botulinum are destroyed (figure 5.5).

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CHAPTER FIVE Control of Microbial Growth

Dry Heat Incineration oxidizes cell components to ashes. Temperatures achieved in hot air ovens oxidize cell components and irreversibly denature proteins.

5.4

Using Other Physical Methods to Remove or Destroy Microbes

Filtration (figure 5.6) Membrane filters and depth filters retain microorganisms while letting the suspending fluid pass through. High-efficiency particulate air (HEPA) filters remove nearly all microorganisms. Radiation (figure 5.7) Gamma rays cause biological damage by producing superoxide and hydroxyl free radicals. Ultraviolet light damages the structure and function of nucleic acids. Microwaves do not affect microorganisms directly, but kill microorganisms by the heat they generate in a product. High Pressure High pressure is thought to destroy microorganisms by denaturing proteins and altering the permeability of the cell.

5.5

Using Chemicals to Destroy Microorganisms and Viruses

Potency of Germicidal Chemical Formulations Germicides are grouped according to their potency as sterilants, high-level disinfectants, intermediate-level disinfectants, or low- level disinfectants. Selecting the Appropriate Germicidal Chemical Factors that must be included in the selection of an appropriate germicidal chemical include toxicity, residue, activity in the presence of organic matter, compatibility with the material being treated, cost and availability, storage and stability, and ease of disposal.

Classes of Germicidal Chemicals (table 5.2) Solutions of 60% to 80% ethyl or isopropyl alcohol in water rapidly kill vegetative bacteria and fungi by coagulating enzymes and other essential proteins, and by damaging lipid membranes. Glutaraldehyde, orthophthalaldehyde and formaldehyde destroy microorganisms and viruses by inactivating proteins and nucleic acids. Chlorhexidine is a biguanide extensively used in antiseptic products. Ethylene oxide is a gaseous sterilizing agent that penetrates well and destroys microorganisms and viruses by reacting with proteins. Sodium hypochlorite (liquid bleach) is one of the least expensive and most readily available forms of chlorine. Chlorine dioxide is used as a sterilant and disinfectant. Iodophores are iodine-releasing compounds used as antiseptics. Metals interfere with protein function. Silver-containing compounds are used to prevent wound infections. Ozone is used as an alternative to chlorine in the disinfection of drinking water and wastewater. Peroxide and peracetic acid are both strong oxidizing agents that can be used alone or in combination as sterilants. Phenolic compounds destroy cytoplasmic membranes and denature proteins. Triclosan is used in lotions and deodorant soaps. Quaternary ammonium compounds are cationic detergents; they are nontoxic enough to be used to disinfect food preparation surfaces.

5.6

Preservation of Perishable Products

Chemical Preservatives Benzoic, sorbic, and propionic acids are sometimes added to foods to prevent microbial growth. Nitrate and nitrite are added to some foods to inhibit the germination and subsequent growth of Clostridium botulinum endospores. Low-Temperature Storage Low temperatures above freezing inhibit microbial growth. Freezing essentially stops all microbial growth. Reducing the Available Water Sugar and salt draw water out of cells, preventing the growth of microorganisms. Lyophilization is used for preserving food. The food is first frozen and then dried in a vacuum.

REVIEW QUESTIONS Short Answer 1. What is the primary reason that milk is pasteurized? 2. What is the primary reason that wine is pasteurized? 3. What is the most chemically resistant non-spore-forming bacterial pathogen? 4. Why are low acid foods processed at higher temperatures than high acid foods? 5. Explain why it takes longer to kill a population of 109 cells than it does to kill a population of 103 cells. 6. How is an iodophore different from a tincture of iodine? 7. How does microwaving a food product kill bacteria? 8. How is preservation different from pasteurization? 9. How are heat-sensitive liquids sterilized? 10. Name two products commonly sterilized using ethylene oxide gas.

Multiple Choice 1. Unlike a disinfectant, an antiseptic a) sanitizes objects rather than sterilizes them. b) destroys all microorganisms. c) is nontoxic enough to be used on human skin.

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d) requires heat to be effective. e) can be used in food products. 2. The D value is defined as the time it takes to kill a) all bacteria in a population. b) all pathogens in a population. c) 99.9% of bacteria in a population. d) 90% of bacteria in a population. e) 10% of bacteria in a population. 3. Which of the following is the most resistant to destruction by chemicals and heat? a) Bacterial endospores b) Fungal spores c) Mycobacterium tuberculosis d) E. coli e) HIV 4. Ultraviolet light kills bacteria by a) generating heat. b) damaging DNA. c) inhibiting protein synthesis. d) damaging cell walls. e) damaging cytoplasmic membranes.

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Review Questions

Critical Thinking 1. This graph shows the time it takes to kill populations of the same microorganism under different conditions. What conditions would explain the differences in lines a, b, and c?

Number of survivors

5. Which concentration of ethyl alcohol is the most effective germicide? a) 100% b) 75% c) 50% d) 25% e) 5% 6. Which of the following chemical agents can most reliably be used to sterilize objects? a) Alcohol b) Phenolic compounds c) Ethylene oxide gas d) Iodine 7. All of the following are routinely used to preserve foods, except a) high concentrations of sugar. b) high concentrations of salt. c) benzoic acid. d) freezing. e) ethylene oxide. 8. Aseptically boxed juices and cream containers are processed using which of the following heating methods? a) Canning b) High-temperature-short-time (HTST) method c) Low-temperature-long-time (LTLT) method d) Ultra-high-temperature (UHT) method 9. Commercial canning processes are designed to ensure destruction of which of the following? a) All vegetative bacteria b) All vegetative bacteria and their endospores c) Endospores of Clostridium botulinum d) E. coli e) Mycobacterium tuberculosis 10. Which of the following is false? a) A chemical that is a high-level disinfectant cannot be used as a sterilant. b) Critical items must be sterilized before use. c) Low numbers of endospores may remain on semicritical items. d) Standard sterilization procedures do not destroy prions. e) Quaternary ammonium compounds can be used to disinfect food preparation surfaces.

a b

c

Time

2. This diagram shows the filter paper method used to evaluate the inhibitory effect of chemical agents, heavy metals, and antibiotics on bacterial growth. A culture of test bacteria is spread uniformly over the surface of an agar plate. Small filter paper discs containing the material to be tested are then placed on the surface of the medium. A disc that has been soaked in sterile distilled water is sometimes added as a control. After incubation, a film of growth will cover the plate, but a clear zone will surround those discs that contain an inhibitory compound. The size of the zone reflects several factors, one of which is the effectiveness of the inhibitory agent. What are two other factors that might affect the size of the zone of inhibition? What is the purpose of the control disc? If a clear area were apparent around the control disc, how would you interpret the observation?

Applications 1. An agriculture extension agent is preparing pamphlets on preventing the spread of disease. In the pamphlet, he must explain the appropriate situations for using disinfectants around the house. What situations should the agent discuss? 2. As a microbiologist representing a food corporation, you have been asked to serve on a health food panel to debate the need for chemical preservatives in foods. Your role is to prepare a statement that compares the benefits of chemical preservatives and the risks. What points must you bring up that indicate the benefits of chemical preservatives?

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125

Control disc

A

E

Filter paper discs soaked in material to be tested (A–E) Clear area around disc

B

D

C

Bacterial growth on agar surface

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6 Wine—a beverage produced using microbial metabolism.

Metabolism: Fueling Cell Growth A Glimpse of History In the 1850s, Louis Pasteur, a chemist, accepted the challenge of studying how alcohol arises from grape juice. Biologists had already observed that when grape juice is held in large vats, alcohol and carbon dioxide are produced and the number of yeast cells increases. They argued that the multiplying yeast cells convert the sugar in the juice to alcohol and carbon dioxide. Pasteur agreed, but could not convince two very powerful and influential German chemists, Justus von Liebig and Friedrich Wöhler, who refused to believe that microorganisms caused the breakdown of sugar. Both men lampooned the hypothesis and tried to discredit it by publishing pictures of yeast cells looking like miniature animals taking in grape juice through one orifice and releasing carbon dioxide and alcohol through the other. Pasteur studied the relationship between yeast and alcohol production using a strategy commonly employed by scientists today—that is, simplifying the experimental system so that relationships can be more easily identified. First, he prepared a clear solution of sugar, ammonia, mineral salts, and trace elements. He then added a few yeast cells. As the yeast grew, the sugar level decreased and the alcohol level increased, indicating that the sugar was being converted to alcohol as the cells multiplied. This strongly suggested that living cells caused the chemical transformation. Liebig, however, still would not believe the process was actually occurring inside microorganisms. To convince him, Pasteur tried to extract something from inside the yeast cells that would convert the sugar. He failed, like many others before him. In 1897, Eduard Buchner, a German chemist, showed that crushed yeast cells could convert sugar to ethanol and CO2. We now know that enzymes of the crushed cells carried out this transformation. For these pioneering studies, Buchner was awarded the

Nobel Prize in 1907. He was the first of many investigators who received Nobel Prizes for studies on the processes by which cells degrade sugars.

T

o grow, all cells must accomplish two fundamental tasks. They must continually synthesize new components including cell walls, membranes, ribosomes, nucleic acids, and surface structures such as flagella. These allow the cell to enlarge and eventually divide. In addition, cells need to harvest energy and convert it to a form that is usable to power biosynthetic reactions, transport nutrients and other molecules, and in some cases, move. The sum total of chemical reactions used for biosynthetic and energy-harvesting processes is called metabolism. Bacterial metabolism is important to humans for a number of reasons. Many bacterial products are commercially or medically important. For example, as scientists look for new supplies of energy, some are investigating biofuels, which are fuels made from a renewable biological source such as plants and organic waste products. Microorganisms or their enzymes are currently producing these fuels, breaking down solid materials such as corn stalks, sugar cane, and wood to a fuel such as ethanol. As another example, cheese-makers intentionally add Lactococcus and Lactobacillus species to milk because the metabolic wastes of these bacteria contribute to the flavor and texture of various cheeses. Yet some of these same products contribute to tooth decay when related bacteria are growing on teeth. Microbial metabolism is also important in the laboratory, because products that are characteristic of a specific group of

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6.1

KEY TERMS Adenosine Triphosphate (ATP) The energy currency of cells. Hydrolysis of its unstable phosphate bonds can be used to power endergonic (energy-consuming) reactions. Anabolism Processes that utilize energy stored in ATP to synthesize and assemble the subunits (building blocks) of macromolecules that make up the cell; biosynthesis. Catabolism Processes that harvest energy released during the breakdown of compounds such as glucose, using it to synthesize ATP. Electron Transport Chain Group of membrane-embedded electron carriers that pass electrons from one to another, and, in the process, move protons across the membrane to create a proton motive force.

Enzyme A protein that functions as a catalyst, speeding up a biological reaction. Fermentation Metabolic process that stops short of oxidizing glucose or other organic compounds completely, using an organic intermediate such as pyruvate or a derivative as a terminal electron acceptor. Oxidative Phosphorylation Synthesis of ATP using the energy of a proton motive force created by harvesting chemical energy. Photophosphorylation Synthesis of ATP using the energy of a proton motive force created by harvesting radiant energy. Precursor Metabolites Metabolic intermediates that can either be used to make the subunits of macromolecules, or be oxidized to generate ATP.

microorganisms can be used as identifying markers. In addition, the metabolic pathways of organisms such as E. coli have served as an invaluable model for studying analogous processes in eukaryotic cells, including those of humans. Metabolic processes unique to prokaryotes are potential targets for antimicrobial drugs.

Principles of Metabolism Proton Motive Force Form of energy generated as an electron transport chain moves protons across a membrane, creating a chemiosmotic gradient. Respiration Process that involves transfer of electrons stripped from a chemical energy source to an electron transport chain, generating a proton motive force that is then used to synthesize ATP.

Substrate-Level Phosphorylation Synthesis of ATP using the energy released in an exergonic (energy-releasing) chemical reaction. Terminal Electron Acceptor Chemical such as O2 that is ultimately reduced as a consequence of fermentation or respiration.

during catabolism is used in anabolism. In addition, some of the compounds produced in steps of the catabolic processes can be diverted by the cell and used as precursors of subunits employed in anabolic processes.

CATABOLISM

6.1 Principles of Metabolism

127

ANABOLISM

Energy source (glucose)

Cell structures (cell wall, membrane, ribosomes, surface structures)

Focus Points Compare and contrast catabolism and anabolism.

Energy

Describe the energy sources used by photosynthetic organisms and chemoorganoheterotrophs.

Macromolecules (proteins, nucleic acids)

Describe the components of metabolic pathways (enzymes, ATP, chemical energy source, redox reactions, electron carriers, and precursor metabolites).

Energy Subunits (amino acids, nucleotides)

List the three central metabolic pathways. Distinguish between respiration and fermentation. Energy

Metabolism can be viewed as having two components— catabolism and anabolism (figure 6.1). Catabolism encompasses processes that harvest energy released during the disassembly or breakdown of compounds such as glucose, using that energy to synthesize ATP, the energy currency of all cells. In contrast, anabolism, or biosynthesis, includes processes that utilize energy stored in ATP to synthesize and assemble subunits (building blocks) of macromolecules that make up the cell. These subunits include amino acids, nucleotides, and lipids. ■ ATP, p. 25 Although catabolism and anabolism are often discussed separately, they are intimately linked. As mentioned, ATP generated

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Precursors

Waste products (acids, carbon dioxide)

Nutrients (source of nitrogen, sulfur, etc.)

FIGURE 6.1 The Relationship Between Catabolism and Anabolism Catabolism encompasses processes that harvest energy released during disassembly of compounds, using it to synthesize ATP; it also provides precursor metabolites used in biosynthesis. Anabolism, or biosynthesis, includes processes that utilize ATP and precursor metabolites to synthesize and assemble subunits of macromolecules that make up the cell.

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CHAPTER SIX Metabolism: Fueling Cell Growth

Radiant energy

Photosynthetic organisms (harvest energy of sunlight and use it to synthesize organic compounds from CO2)

FIGURE 6.2 Forms of Energy Potential energy is stored energy, such as water held behind a dam. Kinetic energy is the energy of motion, such as movement of water from behind the dam.

Harvesting Energy Energy is defined as the capacity to do work. It can exist as potential energy, which is stored energy, and kinetic energy, which is energy of motion (figure 6.2). Potential energy can be stored in various forms including chemical bonds, a rock on a hill, or water behind a dam. Energy in the universe can never be created or destroyed; however, it can be changed from one form to another. In other words, while energy cannot be created, potential energy can be converted to kinetic energy and vice versa, and one form of potential energy can be converted to another. For example, hydroelectric dams unleash the potential energy of water stored behind a dam, creating the kinetic energy of moving water; this can then be used to generate an electrical current, which can then be used to charge a battery. Photosynthetic organisms harvest the energy of sunlight, using it to power the synthesis of organic compounds such as glucose (figure 6.3). In other words, they convert the kinetic energy of photons to the potential energy of chemical bonds. Chemoorganotrophs obtain energy by degrading organic compounds such as glucose, releasing the energy of their chemical bonds. Thus, most chemoorganotrophs ultimately depend on solar energy harvested by photosynthetic organisms, because this is what is used to power the synthesis of glucose. The amount of energy available for harvest by breaking down a compound can be explained by the concept of free energy. This is the energy available to do work; from a biological perspective, it is the energy that can be released when a chemical bond is broken. In a chemical reaction, some bonds are broken and others are formed. If the reactants, or starting compounds, have more free energy than the products, or final compounds, energy is released in the reaction. The reaction is said to be exergonic. In contrast, if

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Radiant energy converted by photosynthetic organisms

CO2 H2O

Organic compounds (including glucose) Organic compounds degraded by chemoorganotrophs Chemoorganotrophs (generate ATP by degrading organic compounds)

FIGURE 6.3 Most Chemoorganotrophs Depend on the Radiant Energy Harvested by Photosynthetic Organisms Photosynthetic organisms use the energy of sunlight to power the synthesis of organic compounds; chemoorganotrophs can then use those organic compounds as an energy source.

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6.1

the products have more free energy than the reactants, the reaction requires an input of energy and is termed endergonic. The change in free energy for a given reaction is the same regardless of the number of steps involved. For example, converting glucose to carbon dioxide and water in a single step by combustion releases the same amount of energy as degrading it in a series of steps. Cells exploit this fact to slowly release free energy from compounds, harvesting the energy released at each step. A specific energy-releasing reaction is used to power an energyutilizing reaction.

Components of Metabolic Pathways Metabolic processes often occur as a series of sequential chemical reactions, which constitute a metabolic pathway (figure 6.4). A series of intermediates are produced as the starting compound is gradually converted into the final product, or end product. A metabolic pathway can be linear, branched, or cyclical, and, like the flow of a river controlled by dams, its activity can be modulated at certain points. In this way, a cell can regulate certain processes, ensuring that specific molecules are produced in precise quantities

Principles of Metabolism

129

when needed. If a metabolic step is blocked, all products “downstream” of that blockage will be affected. The intermediates and end products of metabolic pathways are sometimes organic acids, which are weak acids. Depending on the pH, these may exist primarily as either the undissociated form or the dissociated (ionized) form. Biologists often use the names of the two forms interchangeably—for example, pyruvic acid and pyruvate. Note, however, that at the near-neutral pH inside the cell, the ionized form predominates, whereas outside of the cell, the acid may predominate. ■ pH, p. 24 To recognize what metabolic pathways accomplish, it is helpful to first understand the critical components—enzymes, ATP, the chemical energy source, electron carriers, and precursor metabolites.

The Role of Enzymes A specific enzyme facilitates each step of a metabolic pathway. Enzymes are proteins that function as biological catalysts, accelerating the conversion of one substance, the substrate, into another, the product. Without enzymes, energy-yielding reactions would still occur, but at rates so slow they would be imperceptible.

(a) Linear metabolic pathway

Starting compound

Intermediatea

Intermediateb

End product

Intermediateb1

End product1

Intermediateb2

End product2

(b) Branched metabolic pathway

Starting compound

Intermediatea

(c) Cyclical metabolic pathway Starting compound

Intermediated

End product

Intermediatea

FIGURE 6.4 Metabolic Pathways Intermediatec Intermediateb

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Metabolic processes often occur as a series of sequential chemical reactions that convert starting compounds into intermediates and then, ultimately, into end products. A metabolic pathway can be (a) linear, (b) branched, or (c) cyclical.

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An enzyme catalyzes a chemical reaction by lowering the activation energy of that reaction (figure 6.5). This is the energy it takes to initiate a chemical reaction; even exergonic chemical reactions have an activation energy. By lowering the activation energy barrier, enzymes allow chemicals to undergo rearrangements. Enzymes will be described in more detail later in the chapter. ■ enzymes, p. 134

High-energy bonds

P~ P~ P ATP Pi

Pi

The Role of ATP Adenosine triphosphate (ATP) is the energy currency of a cell, serving as the ready and immediate donor of free energy. It is composed of the sugar ribose, the nitrogenous base adenine, and three phosphate groups (see figure 2.10). Its counterpart, adenosine diphosphate (ADP), can be viewed as an acceptor of free energy. An input of energy is required to add an inorganic phosphate group (Pi) to ADP, forming ATP; energy is released when that group is removed from ATP, yielding ADP (figure 6.6). ■ ATP, p. 25

The phosphate groups of ATP are arranged in tandem (see figure 2.10). Their negative charges repel each other, making the bonds that join them unstable. The bonds are readily hydrolyzed, releasing the phosphate group and a sufficient amount of energy to power an endergonic reaction. Because of the relatively high amount of free energy released when the bonds between the phosphate groups are hydrolyzed, they are called high-energy phosphate bonds, denoted by the symbol ~. ■ hydrolysis, p. 25 Cells constantly turn over ATP, powering biosynthetic reactions by hydrolyzing the high-energy phosphate bond, and then exploiting energy-releasing reactions to form it again. Two different processes are used by chemoorganotrophs to provide the energy necessary to form the high-energy phosphate

Energy released in catabolic pathways

Energy used in anabolic pathways

P~ P ADP

FIGURE 6.6 ATP Energy is released when unstable (“high-energy”) phosphate bonds are broken; an input of energy is required to convert ADP back to ATP.

bond. Substrate-level phosphorylation uses the chemical energy released in an exergonic reaction to add Pi to ADP; oxidative phosphorylation harvests the energy of proton motive force to do the same thing. Recall from chapter 3 that proton motive force is the form of energy that results from the electrochemical gradient established as protons are expelled from the cell (see figure 3.26). The electron transport chain that generates this type of energy will be discussed later in this chapter. Photosynthetic organisms can generate ATP using the process of photophosphorylation, utilizing radiant energy of the sun to drive the formation of a proton motive force. The mechanisms they use to do this will be discussed later. ■ proton motive force, p. 57

The Role of the Chemical Energy Source

Relative energy

The compound broken down by a cell to release energy is called the energy source. As a group, prokaryotes show remarkable diversity in the variety of energy sources they can use. Many use organic compounds such as glucose. Others use inorganic compounds including hydrogen sulfide and ammonia. Harvesting energy from a compound involves a series of coupled oxidationreduction reactions. Energy of activation with an enzyme

Energy of reactant

Energy of activation without an enzyme

Oxidation-Reduction Reactions In oxidation-reduction reactions, or redox reactions, one or more electrons are transferred from one substance to another (figure 6.7). The molecule that loses electrons becomes oxidized; the one that gains those electrons becomes reduced. ■ electrons, p. 18 When electrons are removed from a molecule in a biochemical reaction, protons (H+) often follow. In other words, an electron-proton pair, or hydrogen atom, is often removed. Thus, the removal of a hydrogen atom is an oxidation; correspondingly, the addition of a hydrogen atom is a reduction. An oxidation reaction

Energy of product

Progress of reaction (a) Enzyme b

Enzyme a Starting compound

Intermediatea

Enzyme c Intermediateb

End product

(b)

FIGURE 6.5 The Role of Enzymes Enzymes function as biological catalysts. (a) An enzyme catalyzes a chemical reaction by lowering the activation energy of the reaction. (b) A specific enzyme facilitates each step of a metabolic pathway.

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131

Loss of electron (oxidation)

Compound A

+

Compound A (oxidized)

Compound B

+

Compound B (reduced)

Gain of electron (reduction)

FIGURE 6.7 Oxidation-Reduction Reactions The compound that loses one or more electrons becomes oxidized; the compound that gains those electrons become reduced.

in which an electron and an accompanying proton are removed is called a dehydrogenation. A reduction reaction in which an electron and an accompanying proton are added is called a hydrogenation. When electrons are removed from the energy source, or electron donor, they are temporarily transferred to a specific molecule that serves as an electron carrier. That carrier can also be viewed as a hydrogen carrier if a proton accompanies the electron. Protons, however, unlike electrons, do not require carriers when in an aqueous solution. Because of this, the whereabouts of protons in biological reactions are often ignored.

The Role of Electron Carriers Just as cells use ATP as a carrier of free energy, they use designated molecules as carriers of electrons. Cells have several different types of electron carriers, and each serves a different function. Three types of electron carriers directly participate in reactions that oxidize the energy source (table 6.1). They are NAD+ (nicotinamide adenine dinucleotide), FAD (flavin adenine dinucleotide), and NADP+ (NAD phosphate). The reduced forms of these carriers are NADH, FADH2, and NADPH, respectively. These electron carriers can also be considered hydrogen carriers because along with electrons, they carry protons. NAD+ and NADP+ can each carry a hydride ion, which consists of two electrons and one proton; FADH2 carries two electrons and two protons.

TABLE 6.1

Reduced electron carriers represent reducing power because their bonds contain a form of usable energy. The reducing power of NADH and FADH2 is used to generate the proton motive force, which drives the synthesis of ATP in the process of oxidative phosphorylation. Ultimately the electrons are transferred to a molecule such as O2 that functions as a terminal electron acceptor. The reducing power of NADPH has an entirely different fate; it is used in biosynthetic reactions when a reduction is required. Note, however, that many microbial cells have a membrane-associated enzyme that is able to use proton motive force to reduce NADP+. This allows them to convert reducing power in the form of NADH to NADPH.

Precursor Metabolites Precursor metabolites are metabolic intermediates produced at specific steps in catabolic pathways that can be used in anabolic pathways. In anabolism, they serve as raw material used to make the subunits of macromolecules (see figure 6.1). For example, the precursor metabolite pyruvate can be converted to the amino acid alanine. Many organisms, including Escherichia coli, can make all of their cell components, including proteins, lipids, carbohydrates, and nucleic acids, using only a dozen or so precursor metabolites. Recall from chapter 4 that E. coli can grow in glucose-salts medium, which contains only glucose and a few inorganic salts. The glucose in the medium not only serves as the energy source,

Electron Carriers

Carrier

Oxidized Form

Reduced Form

electron +

–

+

electron carrier

G NADH+H+

Nicotinamide adenine dinucleotide (carries 2 electrons and 1 proton)

NAD +2e +2H

Flavin adenine dinucleotide (carries 2 electrons and 2 protons; i.e., 2 hydrogen atoms)

FAD++2e–+2H+ G FADH2

Nicotinamide adenine dinucleotide phosphate (carries 2 electrons and 1 proton)

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Typical Fate of Electrons Carried

NADP++2e–+2H+ G NADPH+H+

Used to generate a proton motive force that can drive ATP synthesis Used to generate a proton motive force that can drive ATP synthesis Biosynthesis

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TABLE 6.2

Precursor Metabolites

Precursor Metabolite

Pathway Generated

Biosynthetic Role

Glucose 6-phosphate

Glycolysis

Lipopolysaccharide

Fructose 6-phosphate

Glycolysis

Peptidoglycan

Dihydroxyacetone phosphate

Glycolysis

Lipids (glycerol component)

3-phosphoglycerate

Glycolysis

Protein (the amino acids cysteine, glycine, and serine)

Phosphoenolpyruvate

Glycolysis

Protein (the amino acids phenylalanine, tryptophan, and tyrosine)

Pyruvate

Glycolysis

Proteins (the amino acids alanine, leucine, and valine)

Ribose 5-phosphate

Pentose phosphate cycle

Nucleic acids and proteins (the amino acid histidine)

Erythrose 4-phosphate

Pentose phosphate cycle

Protein (the amino acids phenylalanine, tryptophan, and tyrosine)

Acetyl-CoA

Transition step

Lipids (fatty acids)

a-ketoglutarate

TCA cycle

Protein (the amino acids arginine, glutamate, glutamine, and proline)

Oxaloacetate

TCA cycle

Protein (the amino acids aspartate, asparagine, isoleucine, lysine, methionine, and threonine)

Some organisms use succinyl-coA as a precursor in heme biosynthesis; E. coli uses glutamate.

but also the source of precursor metabolites from which all other cell components are made (table 6.2). Some organisms, however, are not as versatile as E. coli with respect to their biosynthetic capabilities. Any essential compounds that a cell cannot synthesize from the appropriate precursor metabolite must be provided from an external source. ■ glucose-salts medium, p. 96

Overview of Metabolism Three key metabolic pathways, called the central metabolic pathways, are used to gradually oxidize glucose, the preferred energy source of many cells, completely to carbon dioxide (figure 6.8). The central metabolic pathways include: Glycolysis Pentose phosphate pathway Tricarboxylic acid cycle (TCA cycle) In a step-wise process, the central metabolic pathways provide cells with energy in the form of ATP, reducing power, and the precursor metabolites needed to synthesize the cells’ building blocks. The pathways are catabolic, but the precursor metabolites and reducing power they generate can also be diverted for use in biosynthesis. To reflect the dual role of these pathways, they are sometimes called amphibolic pathways (amphi meaning “both kinds”). The most common pathway that initiates the breakdown of sugars is glycolysis (glycos means “sugar” and lysis means “dissolution”) (figure 6.8a). This pathway is also called the Embden-MeyerhofParnas pathway (to honor the scientists who described it). This multistep pathway gradually oxidizes the 6-carbon sugar glucose to form two molecules of pyruvate, a 3-carbon compound. At about midpoint in the pathway, a 6-carbon derivative of glucose is split into two 3-carbon molecules. Both of these latter molecules then undergo the same series of transformations to produce pyruvate molecules. Glycolysis provides the cell with a small amount of energy in the form of ATP, some reducing power in the form of NADH, and a

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number of different precursor metabolites. Some bacteria have a different pathway called the Entner-Doudoroff pathway (named after the scientists who described it) instead of or in addition to the glycolytic pathway; some archaea have a slightly modified version of the Entner-Doudoroff pathway. Like glycolysis, the Entner-Doudoroff pathway generates pyruvate, but it uses different enzymes, generates reducing power in the form of NADPH, and yields less ATP. The pentose phosphate pathway also breaks down glucose, but its primary role in metabolism is the production of compounds used in biosynthesis, including reducing power in the form of NADPH and precursor metabolites. It operates in conjunction with other glucose-degrading pathways (glycolysis and the EntnerDoudoroff pathway) (figure 6.8b). Most intermediates it generates are drawn off for use in biosynthesis, but one compound is directed to a mid-point step of glycolysis for further breakdown. Pyruvate generated in any of the preceding pathways must then be converted into a specific 2-carbon fragment. This is accomplished in a complex reaction called the transition step, which removes CO2, generates reducing power, and joins the resulting acetyl group to a compound called coenzyme A, forming acetyl-CoA (figure 6.8c). Note that the transition step is repeated twice for each molecule of glucose broken down. The 2-carbon acetyl group of acetyl-CoA enters the tricarboxylic acid cycle (TCA cycle), also called the Krebs cycle (in honor of the scientist who first described it), or the citric acid cycle (figure 6.8d). This initiates a series of oxidations that result in the release of two molecules of CO2. For every acetyl-CoA that enters the TCA cycle, the cyclic pathway “turns” once. Therefore, it must “turn” twice to complete the oxidation of one molecule of glucose. The TCA cycle generates precursor metabolites, a great deal of reducing power, and ATP. Respiration uses the reducing power accumulated in glycolysis, the transition step, and the TCA cycle to generate ATP by oxidative phosphorylation (figure 6.8e). The electron carriers NADH and FADH2 transfer their electrons to the electron transport chain, which ejects protons from the cell (or the matrix of a

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Principles of Metabolism

133

GLUCOSE

(b) Pentose phosphate pathway (less commonly used than glycolysis) Initiates the oxidation of glucose

Yields

Reducing power

Precursor metabolites

(a) Glycolysis Oxidizes glucose to pyruvate

~ ~

Yields

+

Reducing power

+

ATP substrate-level phosphorylation

Precursor metabolites + (f) Fermentation Reduces pyruvate or a derivative

Biosynthesis

Pyruvate

Pyruvate

CO2

Acids, alcohols, and gases

CO2

(c) Transition step Reducing power

Acetyl-CoA

Reducing power

Acetyl-CoA

CO2

FIGURE 6.8 Overview of Metabolism (a) Glycolysis, (b) the pentose phosphate pathway, (c) the transition step, and (d) the tricarboxylic acid cycle (TCA cycle) are used to gradually oxidize glucose completely to CO2. Together, these pathways produce ATP, reducing power, and intermediates that function as precursor metabolites (depicted as gray bars). (e) Respiration uses the reducing power to generate ATP by oxidative phosphorylation, ultimately passing the electrons to a terminal electron acceptor. (f) Fermentation stops short of oxidizing glucose completely, and instead uses pyruvate or a derivative as an electron acceptor.

CO2

ATP oxidative phosphorylation Yields

~ ~

(d) TCA cycle Incorporates an acetyl group and releases CO2 Precursor metabolites Yields

mitochondrion) to generate a proton motive force. This transfer of electrons also serves to recycle the carriers so they can once again accept electrons during catabolic reactions. In aerobic respiration, electrons are ultimately passed to molecular oxygen (O2), the terminal electron acceptor, producing water. Anaerobic respiration is similar to aerobic respiration, but uses a molecule other than O2 as a terminal electron acceptor. In addition, modified versions of the TCA cycle that generate less reducing power are used during anaerobic respiration. Organisms that use respiration, either aerobic or anaerobic, are said to respire.

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(e) Respiration Uses the electron transport chain to convert reducing power to proton motive force

~ ~ +

Reducing power

+

ATP substrate-level phosphorylation

Cells that cannot respire are limited by their relative inability to recycle reduced electron carriers. A cell only has a limited number of carrier molecules; if electrons are not removed from the reduced carriers, none will be available to accept electrons. As a consequence, subsequent catabolic processes cannot occur. Fermentation provides a solution to this problem, but it results in only the partial oxidation of glucose (figure 6.8f). Thus, compared with respiration, fermentation produces relatively little ATP. It is used by facultative anaerobes when a suitable inorganic terminal electron acceptor is not available and by organisms that

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TABLE 6.3

ATP-Generating Processes of Prokaryotic Chemoorganoheterotrophs ATP Generated by Substrate-Level Phosphorylation (Theoretical Maximum)

Uses an Electron Transport Chain

Terminal Electron Acceptor

Aerobic respiration

Yes

O2

2 in glycolysis (net) 2 in the TCA cycle 4 total

Anaerobic respiration

Yes

Molecule other than O2 such as nitrate (NO3–), nitrite (NO2–), sulfate (SO42–)

Number varies; however, the ATP yield of anaerobic respiration is less than that of aerobic respiration but more than that of fermentation.

Fermentation

No

Organic molecule (pyruvate or a derivative)

2 in glycolysis (net) 2 total

Metabolic Process

lack an electron transport chain. These cells stop short of oxidizing glucose completely, thereby limiting the amount of reducing power generated. Instead of oxidizing pyruvate in the TCA cycle, they use pyruvate or a derivative as a terminal electron acceptor. By transferring the electrons carried by NADH to pyruvate or a derivative, NAD+ is regenerated so it can once again accept electrons in the steps of glycolysis. Note that fermentation always uses an organic molecule as the terminal electron acceptor. Although fermentation does not use the TCA cycle, organisms that ferment still employ certain key steps of it to generate the precursor molecules required for biosynthesis. ■ facultative anaerobes, p. 92 A comparison of aerobic respiration, anaerobic respiration, and fermentation is summarized in table 6.3.

MICROCHECK 6.1 Catabolic pathways gradually oxidize an energy source to harvest energy. A specific enzyme catalyzes each step. Substrate-level phosphorylation uses chemical energy to synthesize ATP; oxidative phosphorylation employs a proton motive force to do the same. Reducing power in the form of NADH and FADH2 is used to generate the proton motive force; the reducing power of NADPH is utilized in biosynthesis. Precursor metabolites are metabolic intermediates that can be used in biosynthesis. The central metabolic pathways generate ATP, reducing power, and precursor metabolites. ✓ How does the fate of electrons carried by NADPH differ from those carried by NADH? ✓ Why are the central metabolic pathways called amphibolic pathways? ✓ Why does fermentation release less energy than respiration?

6.2 Enzymes Focus Points Describe the active site of an enzyme and explain how it relates to the enzyme-substrate complex.

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ATP Generated by Oxidative Phosphorylation Total ATP Generated (Theoretical Maximum) (Theoretical Maximum) 34

0

38

2

Compare and contrast cofactors and coenzymes. List two environmental factors that influence enzyme activity. Describe allosteric regulation. Compare and contrast non-competitive enzyme inhibition and competitive enzyme inhibition.

Recall that enzymes are proteins that act as biological catalysts, facilitating the conversion of a substrate into a product (see figure 6.5). They do this with extraordinary specificity and speed, usually acting on only one, or a very limited number of, substrates. They are neither consumed nor permanently changed during a reaction, allowing a single enzyme molecule to be rapidly used over and over again. In only one second, the fastest enzymes can transform more than 104 substrate molecules to products. More than a thousand different enzymes exist in a cell; most are given a common name that reflects their function and ends with the suffix -ase. For example, those that degrade proteins are collectively called proteases. ■ enzymes, p. 129

Mechanisms and Consequences of Enzyme Action An enzyme has on its surface an active, or catalytic, site, typically a relatively small crevice (figure 6.9). This is the critical site to which a substrate binds by weak forces. The binding of the substrate to the active site causes the shape of the flexible enzyme to change slightly. This mutual interaction, or induced fit, results in a temporary intermediate called an enzyme-substrate complex. The substrate is held within this complex in a specific orientation so that the activation energy for a given reaction is lowered, allowing the products to be formed. The products are then released, leaving the enzyme unchanged and free to combine with new substrate molecules. Note that enzymes may also catalyze reactions that join two substrates to create one product. Theoretically, all enzyme-catalyzed reactions are reversible. The free energy

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6.2

Enzymes

135

Substrate Products are released. Enzyme-substrate complex formed

Enzyme Active site Enzyme unchanged (a)

Enzyme

Enzyme

Substrate

(b)

Substrate

(c)

FIGURE 6.9 Mechanism of Enzyme Action (a) The substrate binds to the active site, forming an enzyme-substrate complex. The products are then released, leaving the enzyme unchanged and free to combine with new substrate molecules. (b) A model showing an enzyme and its substrate. (c) The binding of the substrate to the active site causes the shape of the flexible enzyme to change slightly.

change of certain reactions, however, makes them effectively non-reversible. The interaction of an enzyme with its substrate is very specific. The substrate fits into the active site like a hand into a glove. Not only must it fit spatially, but appropriate chemical interactions such as hydrogen and ionic bonding need to occur to induce the fit. This requirement for a precise fit and interaction explains why, with minor exceptions, a different enzyme is required to catalyze every reaction in a cell. Very few molecules of any particular enzyme are needed, however, as each is swiftly reused again and again. ■ hydrogen bonds, p. 22 ■ ionic bonds, p. 20

Cofactors and Coenzymes Some enzymes act with the assistance of a non-protein component called a cofactor (figure 6.10). Coenzymes are organic cofactors that act as loosely bound carriers of molecules or

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FIGURE 6.10 Some Enzymes Act in Conjunction with a Cofactor Cofactors are non-protein components, either coenzymes or trace elements.

Enzyme

Cofactor

Substrate

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TABLE 6.4

Some Coenzymes and Their Function

Coenzyme

Vitamin from Which It Is Derived

Substance Transferred

Example of Use

Nicotinamide adenine dinucleotide (NAD+)

Niacin

Hydride ions (2 electrons and 1 proton)

Carrier of reducing power

Flavin adenine dinucleotide (FAD)

Riboflavin

Hydrogen atoms (2 electrons and 2 protons)

Carrier of reducing power

Coenzyme A

Pantothenic acid

Acyl groups

Carries the acetyl group that enters the TCA cycle

Thiamin pyrophosphate

Thiamine

Aldehydes

Facilitates the removal of CO2 from pyruvate in the transition step

Pyridoxal phosphate

Pyridoxine

Amino groups

Transfers amino groups in amino acid synthesis

Tetrahydrofolate

Folic acid

1-carbon molecules

Used in nucleotide synthesis

electrons (table 6.4). They include the electron carriers FAD, NAD+, and NADP+. Other cofactors attach tightly to enzymes. For example, magnesium, zinc, copper, and other trace elements required for growth often function as cofactors. ■ trace

different enzymes whose activity requires the corresponding coenzyme are impaired. Thus, a single vitamin deficiency has serious consequences.

elements, p. 94

Environmental Factors That Influence Enzyme Activity

All coenzymes transfer substances from one compound to another, but they function in different ways. Some remain bound to the enzyme during the transfer process, whereas others separate from the enzyme, carrying the substance being transferred along with them. The same coenzyme can assist different enzymes. Because of this, far fewer different coenzymes are required than enzymes. Like enzymes, coenzymes are recycled as they function and, consequently, are needed only in minute quantities. Most coenzymes are derived from vitamins (see table 6.4). Some bacteria, such as E. coli, can synthesize vitamins and convert them to the necessary coenzymes. In contrast, humans and other animals must be provided with vitamins from external sources. Most often they must be supplied in the diet, but in some cases vitamins synthesized by bacteria residing in the intestine can be absorbed. If an animal lacks a vitamin, the functions of all the

Several environmental factors influence how well enzymes function and in this way determine how rapidly microorganisms multiply (figure 6.11). Each enzyme has a narrow range of factors—including temperature, pH, and salt concentration—at which it operates optimally. A 10°C rise in temperature approximately doubles the speed of enzymatic reactions, until optimal activity is reached; this explains why bacteria tend to grow more rapidly at higher temperatures. If the temperature gets too high, however, proteins will denature and no longer function. Most enzymes operate best at low salt concentrations and at pH values slightly above 7. Not surprisingly then, most microbes grow fastest under these same conditions. Some prokaryotes, however, particularly certain members of the Archaea, are found in environ-

FIGURE 6.11 Environmental Factors That Influence Enzyme Activity

Enzyme activity

Denatured enzyme

Enzyme activity

(a) A rise in temperature increases the speed of enzymatic activity until the optimum temperature is reached. If the temperature gets too high, the enzyme denatures and no longer functions. (b) Most enzymes function best at pH values slightly above 7.

1

Optimum temp.

(a)

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2

3

High acidity (low pH)

Temperature

4

5

6

7

9 10 11 12 13

Optimum pH

Low acidity (high pH)

(b)

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6.2

Enzyme Allosteric inhibitor

Allosteric site

(a)

Substrate

Substrate

(b)

Active site

137

FIGURE 6.12 Regulation of Allosteric Enzymes (a) Allosteric enzymes

Allosteric site

Enzyme

Enzymes

have, in addition to the active site, an allosteric site. (b) The binding of regulatory molecule to the allosteric site causes the shape of the enzyme to change, altering the relative affinity of the enzyme for its substrate. (c) The end product of a given biosynthetic pathway generally acts as an allosteric inhibitor of the first enzyme of that pathway.

Active site

Allosteric inhibitor

Enzyme b

Enzyme a Intermediatea

Starting compound

Enzyme c Intermediateb

End product

(c)

ments where conditions are extreme. They may require high salt concentrations, grow under very acidic conditions, or be found where temperatures are near boiling. ■ pH, p. 24 ■ temperature and growth requirements, p. 90

Allosteric Regulation Cells can rapidly fine-tune or regulate the activity of certain key enzymes using other molecules that reversibly bind to and distort them (figure 6.12). This has the effect of regulating the activity of metabolic pathways. These enzymes can be controlled because they are allosteric enzymes (allo means “other”), which have a binding site called an allosteric site that is separate from their active site. When a regulatory molecule binds to the allosteric site, the shape of the enzyme changes. This distortion alters the relative affinity, or chemical attraction, of the enzyme for its substrate. In some cases the binding of the regulatory molecule enhances the affinity for the substrate, but in other cases it decreases it. Allosteric enzymes generally catalyze the step that either initiates or commits to a given pathway. Because their activity can be controlled, they provide the cell with a means to modulate the pace of metabolic processes, turning off some pathways and activating others. Cells can also control the amount of enzyme they synthesize; this control mechanism, which will be discussed in chapter 7, also involves allosteric proteins. ■ regulation, p. 176

TABLE 6.5

The end product of a given biosynthetic pathway generally acts as an allosteric inhibitor of the first enzyme of that pathway—a mechanism called feedback inhibition (figure 6.12c). This mechanism allows the product of the pathway to modulate its own synthesis. For example, the first enzyme of the multistep pathway used to convert the amino acid threonine to isoleucine is an allosteric enzyme that is inhibited by the binding of isoleucine. This amino acid must be present at a relatively high concentration, however, to bind and inhibit the enzyme. Thus, the pathway will only be shut down when a cell accumulates sufficient isoleucine to fill its immediate needs. Because the binding of the inhibitor is reversible, the enzyme can again become active when isoleucine levels decrease. Compounds that reflect a cell’s relative energy stores often regulate allosteric enzymes of catabolic pathways, enabling cells to modulate the flow of these pathways in response to changing energy needs. High levels of ATP inhibit certain enzymes and, as a consequence, slow down catabolic processes. In contrast, high levels of ADP warn that a cell’s energy stores are low, and they function to stimulate the activity of some enzymes.

Enzyme Inhibition Enzymes can be inhibited by a variety of compounds other than the regulatory molecules normally used by the cell (table 6.5).

Characteristics of Enzyme Inhibitors

Type

Characteristics

Non-competitive inhibition (by regulatory molecules)

Inhibitor temporarily changes the enzyme, altering the enzyme’s relative affinity for the substrate. This mechanism provides cells with a means to control the activity of allosteric enzymes.

Non-competitive inhibition (by enzyme poisons)

Inhibitor permanently changes the enzyme, rendering the enzyme non-functional. Enzyme poisons such as mercury are used in certain antimicrobial compounds.

Competitive inhibition

Inhibitor binds to the active site of the enzyme, obstructing the access of the substrate. Competitive inhibitors such as sulfa drugs are used as antibacterial medications.

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Structural differences PABA (substrate) H

H N O Sulfa (inhibitor)

Sulfa (inhibitor)

S

HO O

C

Sulfa molecules more likely to bind to enzyme

N Enzyme

Enzyme

O

H

Enzyme

N H

Sulfanilamide (a)

H

H PABA

(b)

FIGURE 6.13 Competitive Inhibition of Enzymes (a) The inhibitor competes with the normal substrate for binding to the active site. The greater the proportion of inhibitor relative to substrate, the more likely the active site of the enzyme will be occupied by an inhibitor. (b) A competitive inhibitor generally has a chemical structure similar to the normal substrate.

These inhibitory compounds can be exploited to prevent microbial growth. The site on the enzyme to which the molecules bind determines whether they function as competitive or non-competitive inhibitors.

Non-Competitive Inhibition Non-competitive inhibition occurs when the inhibitor and the substrate act at different sites on the enzyme. Allosteric inhibition, discussed previously, is an example of non-competitive reversible inhibition and is used by the cell to modulate its processes (see figure 6.12). Non-competitive, non-reversible inhibitors damage the enzyme permanently so that it can no longer function; the inhibitor acts as an enzyme poison. For example, mercury in the antibacterial compound mercurochrome inhibits growth because it oxidizes the S—H groups of the amino acid cysteine in proteins. This converts cysteine to cystine, which cannot form the important covalent disulfide bond (S—S). As a result, the protein cannot achieve its proper shape.

Competitive Inhibition In competitive inhibition, the inhibitor binds to the active site of the enzyme, obstructing access of the substrate to that site (figure 6.13). Generally this occurs because the inhibitor has a chemical structure similar to the normal substrate. A good example of competitive inhibition is the action of sulfanilamide, one of the sulfa drugs used as an antimicrobial medication. Sulfa drugs inhibit an enzyme in the pathway that bacteria use to synthesize the vitamin folic acid by binding to the active site of the enzyme. The drug does not affect human metabolism because humans cannot synthesize folic acid; it must be provided in the diet. Sulfa drugs have a structure similar to para-aminobenzoic acid (PABA), an intermediate in the bacterial pathway for folic acid synthesis. Because of this, they fit into the active site of the enzyme that normally uses

nes95432_Ch06_126-160.indd 138

PABA as a substrate, preventing the attachment of PABA. The greater the proportion of sulfa molecules relative to PABA molecules, the more likely the active site of the enzyme will be occupied by a sulfa molecule. Once the sulfa is removed, the enzyme functions normally with PABA as the substrate. ■ sulfa drugs, p. 479

MICROCHECK 6.2 Enzymes facilitate the conversion of a substrate into a product with extraordinary speed and specificity. They are neither consumed nor permanently changed in the reaction. Some enzymes act with the assistance of a cofactor. Environmental factors influence enzyme activity and, by doing so, determine how rapidly microorganisms multiply. The activity of allosteric enzymes can be regulated. A variety of different compounds adversely affect enzyme activity. ✓ Explain why sulfa drugs inhibit the growth of bacteria without harming the human host. ✓ Explain the function of a coenzyme. ✓ Why is it important for a cell that allosteric inhibition be reversible?

6.3 The Central Metabolic Pathways Focus Point List the amount of ATP and reducing power and the number of different precursor molecules generated by each of the central metabolic pathways.

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6.3 The Central Metabolic Pathways

139

The three central metabolic pathways—glycolysis, the pentose phosphate pathway, and the tricarboxylic acid cycle—modify organic molecules in a step-wise fashion to form:

one molecule of glucose is converted into two molecules of pyruvate. This generates a net gain of two molecules of ATP and two molecules of NADH. The overall process can be summarized as:

Intermediates with high-energy bonds that can be used to synthesize ATP by substrate-level phosphorylation Intermediates that can be oxidized to generate reducing power Intermediates and end products that function as precursor metabolites

glucose (6 C)+2 NAD++2 ADP+2 Pi D2 pyruvate (3 C)+2 NADH+2 H++2 ATP

This section describes how a molecule of glucose is broken down in the central metabolic pathways, but bear in mind that a cell has many millions of molecules of glucose, and different molecules can have different fates. For example, a cell might oxidize one glucose molecule completely to CO2, thereby producing the maximum amount of ATP. Another glucose molecule might enter glycolysis, or perhaps the pentose phosphate pathway, only to be siphoned off as a precursor metabolite for use in biosynthesis. The step and rate at which the various intermediates are removed for biosynthesis will dramatically affect the overall energy gain of catabolism. This is generally overlooked in descriptions of the ATP-generating functions of these pathways for the sake of simplicity. However, because these pathways serve more than one function, the energy yields are only theoretical. The pathways of central metabolism are compared in table 6.6. The entire pathways with chemical formulas and enzyme names are illustrated in Appendix IV.

In addition to generating ATP and reducing power (NADH), the pathway produces six different precursor molecules needed by E. coli (see table 6.2). The 10-step pathway can be viewed as having two phases: Investment or preparatory phase (figure 6.14, steps 1 through 5)—This consumes energy because two different steps transfer a high-energy phosphate group to the 6-carbon sugar. In eukaryotic cells, both of the high-energy phosphates come from ATP, as shown in figure 6.14. In bacteria, the first high-energy phosphate is added as glucose is transported into the cell via group translocation and the other comes from ATP. The 6-carbon sugar is then split to yield two 3-carbon molecules. Pay-off phase (figure 6.14, steps 6 through 10)—This oxidizes and rearranges the 3-carbon molecules to form pyruvate, generating 1 NADH and 2 ATP. Note that the steps of this phase occur twice for each molecule of glucose that entered glycolysis because the 6-carbon sugar was split into two 3-carbon molecules in the previous phase.

Glycolysis

Yield of Glycolysis

Glycolysis is the primary pathway used by many organisms to convert glucose to pyruvate (figure 6.14). In the 10-step pathway,

For every glucose molecule degraded, the steps of glycolysis produce:

TABLE 6.6 Pathway Glycolysis

Comparison of the Central Metabolic Pathways Characteristics Glycolysis generates: • 2 ATP (net) by substrate-level phosphorylation • 2 NADH+2 H+ • six different precursor metabolites

Pentose phosphate cycle

The pentose phosphate cycle generates: • NADPH+H+ (amount varies) • two different precursor metabolites

Transition step

The transition step, repeated twice to oxidize two molecules of pyruvate to acetyl-CoA, generates: +

• 2 NADH+2 H

• one precursor metabolite TCA cycle

The TCA cycle, repeated twice to incorporate two acetyl groups, generates: • 2 ATP by substrate-level phosphorylation (may involve conversion of GTP) • 6 NADH+6 H+ • 2 FADH2 • two different precursor metabolites

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ATP—The maximum possible energy gain as ATP in glycolysis is: Energy expended 2 ATP molecules (investment phase) Energy harvested 4 ATP molecules (pay-off phase) Net gain 2 ATP molecules Reducing power—The payoff phase converts 2 NAD+ to 2 NADH+2 H+. Precursor metabolites—Five intermediates of glycolysis as well as the end product, pyruvate, are precursor metabolites used by E. coli.

Pentose Phosphate Pathway The other central metabolic pathway used by cells to break down glucose is the pentose phosphate pathway. This complex pathway generates 5- and 7-carbon sugars. In addition, glyceraldehyde 3-phosphate (G3P) is produced, and can be directed to a step in glycolysis for further breakdown. The greatest importance of the pentose phosphate pathway is its contribution to biosynthesis. The reducing power it generates is in the form of NADPH, which is used in biosynthetic reactions when a reduction is required. In addition, two of its intermediates, ribose 5-phosphate and erythrose 4-phosphate, are important precursor metabolites.

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140

CHAPTER SIX Metabolism: Fueling Cell Growth GLUCOSE

(b) Pentose phosphate pathway (less commonly used than glycolysis) Initiates the oxidation of glucose

Yields

Reducing power

Precursor metabolites

(a) Glycolysis Oxidizes glucose to pyruvate

~ ~

Yields

+

Reducing power

+

ATP substrate-level phosphorylation

Glucose

~ ~

ATP

Precursor metabolites + (f) Fermentation Reduces pyruvate or a derivative

Biosynthesis

~

ADP Pyruvate

Pyruvate

CO2

Step 1: ATP is expended to add a phosphate group.

Acids, alcohols, and gases

CO2

(c) Transition step Reducing power

Acetyl-CoA

Reducing power

Acetyl-CoA

CO2 (e) Respiration Uses the electron transport chain to convert reducing power to proton motive force

CO2 (d) TCA cycle Incorporates an acetyl group and releases CO2

ATP oxidative phosphorylation Yields

~ ~

Glucose 6-phosphate

Precursor metabolites Yields

~ ~ +

Reducing power

Step 2: A chemical rearrangement occurs.

+

ATP substrate-level phosphorylation

Fructose 6-phosphate

~ ~

ATP

Step 3: ATP is expended to add a phosphate group.

~

ADP Fructose 1,6-bisphosphate

Step 4: The 6-carbon molecule is split into two 3-carbon molecules. Dihydroxyacetone phosphate

Step 5: A chemical rearrangement of one of the molecules occurs.

Glyceraldehyde 3-phosphate Step 6: The addition of a phosphate group is coupled to a redox reaction, generating NADH and + NADH + H a high-energy phosphate bond.

NAD+ NADH 1,3-bisphosphoglycerate

ADP ATP

NAD+

+ H+

~

~

~

~

~ ~

~ ~

Step 7: ATP is produced by substrate-level phosphorylation.

3-phosphoglycerate Step 8: A chemical rearrangement occurs. 2-phosphoglycerate

H2O

ADP ATP

~

Phosphoenolpyruvate

~ ~ ~

Step 9: Water is removed, causing the phosphate bond to become high-energy.

~

H2O

~ ~ ~

Step 10: ATP is produced by substrate-level phosphorylation.

Pyruvate

FIGURE 6.14 Glycolysis The glycolytic pathway oxidizes glucose to pyruvate, generating ATP by substrate-level phosphorylation, reducing power in the form of NADH, and six different precursor metabolites.

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6.3 The Central Metabolic Pathways

Yield of the Pentose Phosphate Pathway The yield of the pentose phosphate pathway varies, depending on which of several possible alternatives are taken. It can produce: Reducing power—A variable amount of reducing power in the form of NADPH is produced. Precursor metabolites—Two intermediates of the pentose phosphate pathway are precursor metabolites.

141

Transition Step The transition step links glycolysis to the TCA cycle (figure 6.15). In prokaryotic cells, the entire oxidation process takes place in the cytoplasm. In eukaryotic cells, however, pyruvate must first enter the mitochondria since the enzymes of the glycolytic pathway are located in the cytoplasm of the cell, whereas those of the TCA cycle are found only within the matrix of the mitochondria. ■ mitochondria, p. 76

GLUCOSE Precursor metabolites

(a) Glycolysis Oxidizes glucose to pyruvate

(b) Pentose phosphate pathway (less commonly used than glycolysis) Initiates the oxidation of glucose

~ ~

Yields

+

Reducing power

+

ATP substrate-level phosphorylation

Pyruvate Yields

Reducing power

NAD+

Precursor metabolites + (f) Fermentation Reduces pyruvate or a derivative

Biosynthesis

Pyruvate

Pyruvate

CO2

Acids, alcohols, and gases

CO2

Reducing power

Acetyl-CoA

NADH

CoA

(c) Transition step Reducing power

+ H+

Acetyl-CoA

CO2

CO2 (e) Respiration Uses the electron transport chain to convert reducing power to proton motive force

CO2

ATP oxidative phosphorylation Yields

Transition step: A redox reaction generates NADH, CO2 is removed, and coenzyme A is added.

~ ~

(d) TCA cycle Incorporates an acetyl group and releases CO2 Precursor metabolites

~ ~ +

Yields

Reducing power

+

Acetyl-CoA

ATP substrate-level phosphorylation

CoA

NADH + H+

Step 1: The acetyl group is transferred to initiate a round of the cycle.

Oxaloacetate Step 2: A chemical rearrangement occurs.

Citrate

Step 8: A redox reaction generates NADH. NAD+ Isocitrate

NAD+ Step 3: CO2 is removed and a redox reaction generates NADH.

Malate Step 7: A molecule of water is added.

NADH + H+

H2O CO2 Fumarate a-ketoglutarate NAD+

FADH2

Step 4: A redox reaction generates NADH, CO2 is removed, and coenzyme A is added.

CoA

NADH + H+

Step 6: A redox reaction generates FADH2. CO2

FAD Succinyl-CoA

Succinate

Step 5: The energy released when CoA is removed is harvested to produce ATP.

CoA

~

~ ~ ATP

+ Pi

ADP

FIGURE 6.15 The Transition Step and the Tricarboxylic Acid Cycle The transition step links glycolysis and the TCA cycle, converting pyruvate to acetyl-CoA; it generates reducing power and one precursor metabolite. The TCA cycle incorporates the acetyl group of acetyl-CoA and, using a series of steps, releases CO2; it generates ATP, reducing power in the form of both NADH and FADH2, and two different precursor metabolites.

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CHAPTER SIX Metabolism: Fueling Cell Growth

The transition step involves several integrated reactions catalyzed by a large multi-enzyme complex. In the concerted series of reactions, carbon dioxide is first removed from the pyruvate, a process called decarboxylation. Then, an oxidation occurs, reducing NAD+ to form NADH+ H+. Finally, the remaining 2-carbon acetyl group is joined to the coenzyme A to form acetyl-CoA.

Yield of the Transition Step Reducing power—The transition step, which occurs twice for every molecule of glucose that enters glycolysis, oxidizes pyruvate. This reduces 2 NAD+ to form 2 NADH+2 H+. Precursor metabolites—The end product of the transition step, acetyl-CoA, is a precursor metabolite.

Yield of the TCA Cycle The tricarboxylic acid cycle “turns” once for each acetyl-CoA that enters. Because two molecules of acetyl-CoA are generated for each glucose molecule that enters glycolysis, the breakdown of one molecule of glucose causes the cycle to “turn” twice. These two “turns” generate: ATP—2 ATP produced in step 5. Reducing power—Redox reactions at steps 3, 4, 6 and 8 produce a total of 6 NADH+6 H+ and 2 FADH2. Precursor metabolites—Two precursor metabolites used by E. coli are formed as a result of steps 3 and 8.

MICROCHECK 6.3

Tricarboxylic Acid (TCA) Cycle The eight steps of the tricarboxylic acid (TCA) cycle complete the oxidation of glucose (see figure 6.15). The cycle incorporates the acetyl groups from the transition step, releasing CO2 in this net reaction: 2 acetyl groups (2 C)+6 NAD++2 FAD+2 ADP+2 Pi D4 CO2+6 NADH+6 H++2 FADH2+2 ATP In addition to generating ATP and reducing power, the steps of the TCA cycle form two more precursor metabolites used by E. coli (see table 6.2). Step 1 The cycle begins when CoA transfers its acetyl group to the 4-carbon compound oxaloacetate, thereby forming the 6-carbon compound citrate. Step 2 Citrate is chemically rearranged to form a structural isomer, isocitrate. ■ structural isomer, p. 31 Step 3 Isocitrate is oxidized and a molecule of CO2 is removed, forming the 5-carbon compound a-ketoglutarate. During the oxidation, NAD+ is reduced to form NADH+H+. Step 4 Like the transition step that converts pyruvate to acetylCoA, this involves a group of reactions catalyzed by a complex of enzymes. In this step, a-ketoglutarate is oxidized, CO2 is removed, and CoA is added, producing the 4-carbon compound succinyl-CoA. During the oxidation, NAD+ is reduced to form NADH+H+. Step 5 This removes CoA from succinyl-CoA, harvesting the energy to make ATP. The reaction forms succinate. Note that some types of cells make guanosine triphosphate (GTP) rather than ATP at this step. This compound, however, can be converted to ATP. Step 6 Succinate is oxidized to form fumarate. During the oxidation, FAD is reduced to form FADH2. Step 7 A molecule of water is added to fumarate, forming malate. Step 8 Malate is oxidized to form oxaloacetate; note that oxaloacetate is the starting compound to which acetyl-CoA is added to initiate the cycle. During the oxidation, NAD+ is reduced to form NADH+H+.

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Glycolysis oxidizes glucose to pyruvate, yielding some ATP and NADH and six different precursor metabolites. The pentose phosphate pathway initiates the breakdown of glucose; its greatest significance is its contribution of two different precursor metabolites and NADPH for biosynthesis. The transition step and the TCA cycle, repeated twice, complete the oxidation of glucose, yielding some ATP, a great deal of reducing power, and three different precursor metabolites. ✓ What is the product of the transition step? ✓ Explain why the TCA cycle ultimately results in a greater ATP gain than glycolysis. ✓ Which compound contains more free energy—pyruvate or oxaloacetate? Why?

6.4 Respiration Focus Points Describe how the electron transport chain generates a proton motive force. Compare and contrast the electron transport chains of eukaryotes and prokaryotes. Describe how proton motive force is used to synthesize ATP.

As mentioned earlier, respiration uses the NADH and FADH2 generated in gycolysis, the transition step, and the TCA cycle to synthesize ATP. The process, called oxidative phosphorylation, occurs through the combined action of two mechanisms—the electron transport chain, which generates proton motive force, and an enzyme called ATP synthase, which harvests the energy of the proton motive force to drive the synthesis of ATP. In 1961, the British scientist Peter Mitchell originally proposed the chemiosmotic theory, which describes the remarkable mechanism by which ATP synthesis is linked to electron transport, but his hypothesis was widely dismissed. Only through years of self-funded research was he finally able to convince others of its validity, and he was awarded the Nobel Prize in 1978. ■ proton motive force, p. 57

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6.4

The Electron Transport Chain—Generating Proton Motive Force The electron transport chain is a group of membrane-embedded electron carriers that pass electrons sequentially from one to another. In prokaryotes, it is located in the cytoplasmic membrane, whereas in eukaryotic cells it is in the inner membrane of mitochondria (see figure 3.53). Because of the asymmetrical arrangement of the electron carriers, the sequential oxidation/reduction reactions result in the ejection of protons to the outside of the cell or, in the case of mitochondria, to the space between the inner and outer membranes. This expulsion of protons creates a proton gradient, or electrochemical gradient, across the membrane. Energy of this gradient, proton motive force, can be harvested by cells and used to fuel the synthesis of ATP. Recall from chapter 3 that prokaryotes can also use proton motive force as a source of energy to transport substances into or out of the cell, and to power the rotation of flagella. Four types of electron carriers participate in the electron transport chain: flavoproteins, iron-sulfur proteins, quinones, and cytochromes. Flavoproteins are proteins to which an organic molecule called a flavin is attached. FAD is an example of a flavin. Iron-sulfur proteins are proteins that contain iron and sulfur molecules arranged in a cluster. Quinones are lipidsoluble molecules that move freely in the membrane and can therefore transfer electrons between different enzyme structures in the membrane. Several types of quinones exist, one of the most common being ubiquinone (meaning ubiquitous quinone). Cytochromes are proteins that contain heme, a chemical structure that holds an iron atom in the center. Several different cytochromes exist, each distinguished with a letter after the term, for example, cytochrome c. Because of the order of the carriers in the electron transport chain, energy is gradually released as the electrons are passed from one carrier to another, much like a ball falling down a flight of stairs (figure 6.16). Energy release is coupled to the ejection of protons to establish a proton gradient.

General Mechanisms of Proton Ejection An important characteristic of the electron carriers is that some accept only hydrogen atoms (proton-electron pairs), whereas others accept only electrons. The spatial arrangement of these two types of carriers in the membrane causes protons to be shuttled from the inside of the membrane to the outside. This occurs because a hydrogen carrier that receives electrons from an electron carrier must pick up protons; because of the hydrogen carrier’s relative location in the membrane, those protons come from inside the cell (or matrix of the mitochondrion). Conversely, when a hydrogen carrier passes electrons to a carrier that accepts electrons but not protons, the protons are released to the outside of the cell (or intermembrane space of the mitochondrion). The net effect of these processes is that protons are pumped from one side of the membrane to the other, establishing the concentration gradient across the membrane. Most carriers of the electron transport chain are grouped into several large protein complexes that function as proton pumps; other carriers shuttle electrons from one complex to the next.

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Respiration

143

Electrons from energy source

e-

High energy

Energy to generate a proton motive force

Electron transport chain

Low energy

e-

1/2 O2 + 2H+

water

FIGURE 6.16 Electron Transport Energy released as electrons are passed along carriers of the electron transport chain is used to establish a proton gradient.

The Electron Transport Chain of Mitochondria Mitochondria have four different protein complexes, three of which function as proton pumps (complexes I, III, and IV). In addition, two electron carriers (coenzyme Q and cytochrome c) shuttle electrons between the complexes. The electron transport chain of mitochondria consists of these components (figure 6.17): Complex I (also called NADH dehydrogenase complex). This accepts electrons from NADH, ultimately transferring them to coenzyme Q; in the process, four protons are pumped across the membrane. Complex II (also called succinate dehydrogenase complex). This accepts electrons from the TCA cycle, when FADH2 is formed during the oxidation of succinate (see figure 6.15, step 6). Electrons are then transferred to coenzyme Q. Coenzyme Q (also called ubiquinone). This lipid soluble carrier accepts electrons from either complex I or complex II and then shuttles them to complex III. Note that the electrons carried by FADH2 have entered the electron transport chain “downstream” of those carried by NADH. Because of this, a pair of electrons carried by NADH result in more protons being expelled than does a pair carried by FADH2. Complex III (also called cytochrome bc1 complex). This accepts electrons from coenzyme Q, ultimately transferring them to cytochrome c; in the process, four protons are pumped across the membrane. Cytochrome c. This accepts electrons from complex III and then shuttles them to complex IV.

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144

CHAPTER SIX Metabolism: Fueling Cell Growth GLUCOSE

(b) Pentose phosphate pathway (less commonly used than glycolysis) Initiates the oxidation of glucose

Yields

Reducing power

Precursor metabolites

(a) Glycolysis Oxidizes glucose to pyruvate

~ ~

Yields

+

Reducing power

Eukaryotic cell

+

ATP substrate-level phosphorylation

Precursor metabolites + (f) Fermentation Reduces pyruvate or a derivative

Biosynthesis

Pyruvate

Pyruvate

CO2

Acids, alcohols, and gases

CO2

(c) Transition step Reducing power

Acetyl-CoA

Reducing power

Acetyl-CoA

CO2 (e) Respiration Uses the electron transport chain to convert reducing power to proton motive force

CO2

ATP oxidative phosphorylation Yields

Inner mitochondrial membrane

~ ~

(d) TCA cycle Incorporates an acetyl group and releases CO2 Precursor metabolites

~ ~ +

Yields

Reducing power

+

ATP substrate-level phosphorylation

Complex III 4 H+

Complex I 4 H+

Coenzyme Q

Complex IV 2 H+

ATP synthase Proton motive force is used to drive:

(ATP synthesis)

10 H+

Cytochrome c

H2O NADH + H+

Complex II

Intermembrane space

Mitochondrial matrix

1/2 O2

NAD

3 ADP + 3 Pi

3 ATP

FIGURE 6.17 The Electron Transport Chain of Mitochondria The electrons carried by NADH are passed to complex I. They are then passed to coenzyme Q, which transfers them to complex III. Cytochrome c then transfers electrons to complex IV. From there, they are passed to O2. Unlike the electrons carried by NADH, those carried by FADH2 are passed to complex II, which then passes them to coenzyme Q; from there, the electrons follow the same path as the ones donated by NADH. Protons are shuttled from the mitochondrial matrix to the intermembrane space by complex I, III and IV, creating the proton motive force. ATP synthase allows protons to reenter the mitochondrial matrix, using the energy released to drive ATP synthesis.

Complex IV (also called cytochrome c oxidase complex). This accepts electrons from cytochrome c, ultimately transferring them to oxygen (O2), forming H2O. In the process, two protons are pumped across the membrane. Complex IV is a terminal oxidoreductase, meaning that it transfers the electrons to the terminal electron acceptor, which, in this case, is O2.

The Electron Transport Chains of Prokaryotes Considering the flexibility and diversity of prokaryotes, it is not surprising that they vary with respect to the types and arrangement of their electron transport components. In fact, a single species may have several alternative carriers so that the system as a whole can function optimally under changeable growth conditions. In the laboratory, the different electron transport components provide a mechanism to distinguish between certain types of bacteria. For example, the activity of cytochrome c oxidase, which is found in species of Neisseria, Pseudomonas, Campylobacter, and certain other genera, is detected using the rapid biochemical test called

nes95432_Ch06_126-160.indd 144

the oxidase test and is important in the identification scheme of these organisms (see table 10.5). The electron transport chain of E. coli provides an excellent example of the diversity found even in a single organism. This organism preferentially uses aerobic respiration, but when molecular oxygen is not available, it can switch to anaerobic respiration provided that a suitable terminal electron acceptor such as nitrate is available. The E. coli electron transport chain serves as a model for both aerobic and anaerobic respiration. Aerobic Respiration When growing aerobically in a glucosecontaining medium, E. coli can use two different NADH dehydrogenases (figure 6.18). One is a proton pump functionally equivalent to complex I of the mitochondrion. E. coli also has a succinate dehydrogenase that is functionally equivalent to complex II of the mitochondrion. In addition to these enzyme complexes, E. coli can produce several alternatives, enabling the organism to optimally use a variety of different energy sources, including hydrogen gas. E. coli does not have the equivalent of complex III or cytochrome c; instead quinones, including ubiquinone, shuttle the electrons

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6.4

Respiration

145

Prokaryotic cell

Cytoplasmic membrane

NADH dehydrogenase H+ (0 or 4)

Ubiquinol oxidase H+ (2 or 4)

Proton motive force is used to drive:

ATP synthase (ATP synthesis) 10 H+

Rotation of flagella

Active transport (one mechanism) H+

substance

1,200 H+

Outside of cytoplasmic membrane

Ubiquinone

NADH + H+ NAD

Succinate dehydrogenase

1/2 O2

H2O Inside of cytoplasmic membrane 3 ADP + 3 Pi

3 ATP

FIGURE 6.18 The Electron Transport Chain of E. coli Growing Aerobically in a Glucose-Containing Medium The electrons carried by NADH are passed to one of two different NADH dehydrogenases. They are then passed to ubiquinone, which transfers them to one of two ubiquinol oxidases. From there they are passed to O2. Unlike the electrons carried by NADH, those carried by FADH2 are passed to succinate dehydrogenase, which then transfers them to ubiquinone; from there, the electrons follow the same path as the ones donated by NADH. Protons are ejected by one of the two NADH dehydrogenases and both ubiquinol oxidases, creating the proton motive force. ATP synthase allows protons to reenter the cell, using the energy released to drive ATP synthesis. The proton motive force is also used to drive one form of active transport and to power the rotation of flagella. E. coli has other components of the electron transport chain that function under different growth conditions.

directly to a terminal oxidoreductase. When O2 is available to serve as a terminal electron acceptor, one of two variations of a terminal oxidoreductase called ubiquinol oxidase is used. One form functions optimally only in high O2 conditions and results in the expulsion of 4 protons. The other results in the ejection of only 2 protons, but it can more effectively scavenge O2 and thus is particularly useful when the supply of O2 is limited. Anaerobic Respiration Anaerobic respiration is a less efficient form of energy transformation than is aerobic respiration. This is partly due to the lesser amount of energy released in reactions that involve the reduction of chemicals other than molecular oxygen. Alternative electron carriers are used in the electron transport chain during anaerobic respiration. When oxygen is absent and nitrate is available, E. coli responds by synthesizing a terminal oxidoreductase that uses nitrate as a terminal electron acceptor, producing nitrite. The organism then converts nitrite to ammonia, avoiding the toxic effects of nitrite. Other bacteria can reduce nitrate further than E. coli can, forming compounds such as nitrous oxide (N2O), and nitrogen gas (N2).

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The quinone that bacteria use during anaerobic respiration, menaquinone, provides humans and other mammals with a source of the nutrient called vitamin K. This vitamin is required for the proper coagulation of blood, and mammals are able to obtain at least part of their requirement by absorbing menaquinone produced by bacteria growing in the intestinal tract. A group of obligate anaerobes called the sulfate-reducers use sulfate (SO42–) as a terminal electron acceptor, producing hydrogen sulfide as an end product. The diversity and ecology of sulfate-reducing bacteria will be discussed in chapter 11. ■ sulfate-reducing bacteria, p. 254

ATP Synthase—Harvesting the Proton Motive Force to Synthesize ATP Just as energy is required to establish a concentration gradient, energy is released when a gradient is eased. The enzyme ATP synthase uses that energy to synthesize ATP. It permits protons to flow back into the bacterial cell (or matrix of the mitochondrion) in a controlled manner, harvesting the energy released to fuel the addition of a phosphate

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CHAPTER SIX Metabolism: Fueling Cell Growth

group to ADP. One molecule of ATP is formed from the entry of approximately three protons. The precise mechanism of how this occurs is not well understood.

GLUCOSE

Glycolysis

~ ~

Theoretical ATP Yield of Oxidative Phosphorylation

2 ATP

net gain = 0

~ ~ 2 ATP

The complexity of oxidative phosphorylation makes it exceedingly difficult to determine the actual maximum yield of ATP. Unlike the yield of substrate-level phosphorylation, which can be calculated based on the stoichiometry of relatively 2 NADH ~ ~ simple chemical reactions, oxidative phosphorylaOxidative 6 ATP tion involves processes that have many variables. phosphorylation This is particularly true for prokaryotic cells because ~ ~ they use proton motive force to drive activities other Substrate-level 2 ATP phosphorylation than ATP synthesis, including flagella rotation and membrane transport. In addition, as a group, they use different carriers in their electron transport chain, and these may vary in the number of protons ejected per pair of electrons passed. For each pair of electrons transferred to the Pyruvate Pyruvate electron transport chain by NADH, between 2 and 3 ATP may be generated; for each pair trans2 NADH ~ ~ ferred by FADH2, the yield is between 1 and 2 Oxidative 6 ATP ATP. Although experimental studies using rat phosphorylation mitochondria indicate that the yield is approxiAcetyl-CoA Acetyl-CoA mately 2.5 ATP/NADH and 1.5 ATP/FADH2, for simplicity we will use whole numbers (3 ATP/NADH and 2 ATP/FADH2) to calculate the maximum ATP gain of oxidative phosphorylation in a prokaryotic cell. Note, however, that 6 NADH ~ ~ these numbers are only theoretical and serve Oxidative 18 ATP phosphorylation primarily as a means of comparing the relative ~ ~ energy gains of respiration and fermentation. 2 FADH2 Oxidative 4 ATP The ATP gain as a result of oxidative phosphosphorylation phorylation will be at least slightly different in eukaryotic cells than in prokaryotic cells because TCA cycle ~ ~ of the fate of the reducing power (NADH) generSubstrate-level 2 ATP phosphorylation ated during glycolysis. Recall that in eukaryotic cells, glycolysis takes place in the cytoplasm, FIGURE 6.19 Maximum Theoretical Energy Yield from Aerobic Respiration in a Prowhereas the electron transport chain is located karyotic Cell This maximum energy yield calculation assumes that for every pair of electrons in the mitochondria. Consequently, the electrons transferred to the electron transport chain, 3 ATP are synthesized; and for every pair of electrons carried by cytoplasmic NADH must be translo- donated by FADH2, 2 ATP are synthesized. Note that these values are theoretical; a variety of faccated across the mitochondrial membrane before tors, including the electron carriers employed and use of the proton motive force to drive other they can enter the electron transport chain. This processes, affects the yield. requires an expenditure of approximately 2 ATP. The maximum theoretical energy yield for oxidative phosTotal maximum ATP yield from oxidative, phosphorylaphorylation in a prokaryotic cell that uses an electron transport tion = 34 chain similar to that of mitochondria is: From glycolysis: 2 NADHD6 ATP (assuming 3 for each NADH) From the transition step: 2 NADHD6 ATP (assuming 3 for each NADH) From the TCA cycle: 6 NADHD18 ATP (assuming 3 for each NADH) 2 FADH2D4 ATP (assuming 2 for each FADH2)

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ATP Yield of Aerobic Respiration in Prokaryotes Now that the ATP-yielding components of the central metabolic pathways have been considered, we can calculate the theoretical maximum ATP yield of aerobic respiration in prokaryotes. This yield is illustrated in figure 6.19.

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6.5

Substrate-level phosphorylation: 2 ATP (from glycolysis; net gain) 2 ATP (from the TCA cycle) 4 ATP (total; substrate-level phosphorylation) Oxidative phosphorylation: 6 ATP (from the reducing power gained in glycolysis) 6 ATP (from the reducing power gained in the transition step) 22 ATP (from the reducing power gained in the TCA cycle) 34 (total; oxidative phosphorylation) Total ATP gain (theoretical maximum) = 38

147

GLUCOSE

Yields

Reducing power

Precursor metabolites

(a) Glycolysis Oxidizes glucose to pyruvate

(b) Pentose phosphate pathway (less commonly used than glycolysis) Initiates the oxidation of glucose

~ ~

Yields

+

Reducing power

+

ATP substrate-level phosphorylation

Precursor metabolites + (f) Fermentation Reduces pyruvate or a derivative

Biosynthesis

Pyruvate

Pyruvate

CO2

Acids, alcohols, and gases

CO2

(c) Transition step Reducing power

Acetyl-CoA

Reducing power

Acetyl-CoA

CO2 (e) Respiration Uses the electron transport chain to convert reducing power to proton motive force

CO2

ATP oxidative phosphorylation Yields

~ ~

(d) TCA cycle Incorporates an acetyl group and releases CO2 Precursor metabolites

~ ~ +

Yields

Reducing power

+

ATP substrate-level phosphorylation

MICROCHECK 6.4 Respiration uses the NADH and FADH2 generated in glycolysis, the transition step, and the TCA cycle to synthesize ATP. The electron transport chain is used to convert reducing power into a proton motive force. ATP synthase then harvests that energy to synthesize ATP. The overall process is called oxidative phosphorylation. In aerobic respiration, O2 serves as the terminal electron acceptor; anaerobic respiration employs a molecule other than O2. ✓ Why is the overall ATP yield in aerobic respiration only a theoretical number? ✓ In bacteria, what is the role of the molecule that serves as a source of vitamin K for humans? ✓ Why could an oxidase also be called a reductase?

Fermentation

NADH

O H 3C

C

+ H+

NAD+

O C

O–

H 3C

OH

O

C

C

O–

H Pyruvate

Lactate

(a)

CO2

H 3C

O

O

C

C

NADH

+ H+

NAD+

O O–

H 3C

C

OH H

H 3C

C

H

H Pyruvate

6.5 Fermentation Focus Point Describe six common end products of fermentation, and explain the importance of each.

Fermentation is used by organisms that cannot respire, either because a suitable inorganic terminal electron acceptor is not available or because they lack an electron transport chain. Escherichia coli is a facultative anaerobe that has the ability to use any of three ATP-generating options—aerobic respiration, anaerobic respiration, and fermentation; the choice depends in part on the availability of terminal electron acceptors. In contrast, members of a group of aerotolerant anaerobes called the lactic acid bacteria lack the ability to respire; they only ferment, regardless of the presence of oxygen (O2). Because they can grow in the presence of oxygen but never use it as a terminal electron acceptor, they are sometimes called obligate fermenters. The situation is different for obligate anaerobes that use fermentation pathways; they cannot even grow in the presence of O2, and many are rapidly killed in its presence. In general, the only ATP-yielding reactions of fermentation are those of glycolysis, and involve substrate-level phosphorylation. The other steps function primarily to consume excess reducing power, thereby providing a mechanism for recycling NADH (figure 6.20). If this reduced carrier were not recycled, no NAD+ would be available to accept elec-

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Acetaldehyde

Ethanol

(b)

FIGURE 6.20 Fermentation Pathways Use Pyruvate or a Derivative As a Terminal Electron Acceptor (a) In lactic acid fermentation, pyruvate serves directly as a terminal electron acceptor, producing lactate. (b) In ethanol fermentation, pyruvate is first converted to acetaldehyde, which then serves as the terminal electron acceptor, producing ethanol.

trons in subsequent rounds of glycolysis, blocking that ATPgenerating pathway. To consume reducing power, fermentation pathways use an organic intermediate such as pyruvate or a derivative as a terminal electron acceptor. The end products of fermentation are significant for a number of reasons (figure 6.21). Because a given type of organism uses a characteristic fermentation pathway, end products can sometimes be used as a marker to aid in identification. In addition, some end products are commercially valuable. In fact, much of chapter 32 is devoted to the fermentations used to produce certain beverages and food products. Important end products of fermentation pathways include the following (note that organic acids produced during fermentation are traditionally referred to by the name of their undissociated form): Lactic acid. Lactic acid (the ionized form is lactate) is produced when pyruvate itself serves as the terminal electron acceptor. The end products of a group of Gram-positive organisms called the lactic acid bacteria are instrumental in creating the flavor and texture of cheese, yogurt, pickles, cured sausages, and other foods. On the other hand, lactic acid causes tooth decay and spoilage of some foods. Some animal

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CHAPTER SIX Metabolism: Fueling Cell Growth

Butyric acid Butyl alcohol Acetone Isopropyl alcohol CO2 H2

Ethyl alcohol CO2

Saccharomyces

Acetic acid Lactic acid Succinic acid Ethyl alcohol CO2 H2

Clostridium

Pyruvate

Propionibacterium

Propionic acid Acetic acid CO2

Enterobacter

Streptococcus Lactobacillus

Lactic acid

Formic acid Ethyl alcohol Lactic acid 2,3-Butanediol CO2 H2

it is further modified to form propionate. Members of the genus Propionibacterium use this pathway; their growth is encouraged in the production of Swiss cheese. The CO2 they form makes the holes, and propionic acid gives the cheese its characteristic flavor. ■ cheese, p. 757 2, 3-Butanediol. This is produced in a multistep pathway that uses two molecules of pyruvate to generate acetoin and two molecules of CO2. Acetoin is then used as the terminal electron acceptor. The primary significance of this pathway is that it serves to differentiate certain members of the family Enterobacteriaceae; the Voges-Proskauer test detects acetoin, distinguishing members that use this pathway, such as Klebsiella and Enterobacter, from those that do not, such as E. coli (see table 10.4). ■ Voges-Proskauer test, p. 240 Mixed acids. These are produced in a multistep branching pathway, generating a variety of different fermentation end products including lactic acid, succinic acid (the ionized form is succinate), ethanol, acetic acid (the ionized form is acetate), CO2, and gases. This is another pathway used to differentiate certain members of the family Enterobacteriaceae; the methyl-red test detects its end products, distinguishing members that use this pathway, such as E. coli, from those that do not, such as Klebsiella and Enterobacter (see table 10.4). ■ methyl-red test, p. 240

MICROCHECK 6.5 FIGURE 6.21 End Products of Fermentation Pathways Because a given type of organism uses a characteristic fermentation pathway, the end products can be used as an identifying marker. Some end products are commercially valuable.

cells use this fermentation pathway on a temporary basis when molecular oxygen is in short supply; the accumulation of lactic acid in muscle tissue causes the pain and fatigue sometimes associated with strenuous exercise. ■ lactic acid bacteria, p. 255 ■ cheese, yogurt and other fermented milk products, p. 756 ■ pickled vegetables, p. 758 ■ fermented meat products, p. 758

Ethanol. Ethanol is produced in a pathway that first removes CO2 from pyruvate, generating acetaldehyde, which then serves as the terminal electron acceptor. The end products of these sequential reactions are ethanol and CO2, which are used to make wine, beer, spirits, and bread (see figures 32.4, 32.5, and 32.6). Ethanol is also an important biofuel. Members of Saccharomyces (yeast) and Zymomonas (bacteria) use this pathway. ■ wine, p. 758 ■ beer, p. 759 ■ distilled spirits, p. 760 ■ bread, p. 761 Butyric acid. Butyric acid (the ionized form is butyrate) and a variety of other end products are produced in a complex multistep pathway used by species of Clostridium, which are obligate anaerobes. Under certain conditions, some species use a variation of this pathway to produce the organic solvents butanol and acetone. Propionic acid. Propionic acid (the ionized form is propionate) is generated in a multistep pathway that first removes CO2 from pyruvate, generating a compound that then serves as a terminal electron acceptor. After NADH reduces this,

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Fermentation stops short of the TCA cycle, using pyruvate or a derivative of it as a terminal electron acceptor. Many end products of fermentation are commercially valuable. ✓ How do the Voges-Proskauer and methyl-red tests differentiate between certain members of the Enterobacteriaceae? ✓ Why do cells use fermentation rather than having pyruvate as the end product? ✓ Fermentation is used as a means of preserving foods. Why would it slow spoilage?

6.6 Catabolism of Organic Compounds Other Than Glucose Focus Point Briefly describe how polysaccharides and disaccharides, lipids, and proteins are degraded and utilized by a cell.

Microbes can use a variety of organic compounds other than glucose as energy sources, including macromolecules such as polysaccharides, lipids, and proteins. To break these down into their respective sugar, amino acid, and lipid subunits, cells synthesize hydrolytic enzymes, which break bonds by adding water. To use a macromolecule in the surrounding medium, a cell must secrete the appropriate hydrolytic enzyme and then transport the resulting subunits into the cell. Inside the cell, the subunits are further degraded to form appropriate precursor metabolites (figure 6.22). Recall that precursor metabolites can be either

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6.6 Catabolism of Organic Compounds Other Than Glucose POLYSACCHARIDES Starch Cellulose

DISACCHARIDES Lactose Maltose Sucrose

LIPIDS (fats) lipases

149

PROTEINS proteases

GLUCOSE amylases

cellulases disaccharidases simple sugars

glycerol

+ Glycolysis

amino acids deamination

fatty acids NH3

Applies to both branches in glycolysis

Pentose phosphate pathway

Beta-oxidation removes 2-carbon units. Pyruvate

Pyruvate

Acetyl-CoA

Acetyl-CoA

TCA cycle

FIGURE 6.22 Catabolism of Organic Compounds Other Than Glucose The subunits of macromolecules are degraded to form the appropriate precursor metabolites. These metabolites can then either be oxidized in one of the central metabolic pathways or be used in anabolism.

oxidized in one of the central metabolic pathways or used in biosynthesis. ■ hydrolysis, p. 25

Polysaccharides and Disaccharides Starch and cellulose are both polymers of glucose, but different types of chemical bonds join their subunits. The nature of this difference profoundly affects the mechanisms by which they are degraded. Enzymes called amylases are produced by a wide variety of organisms to digest starches. In contrast, cellulose is digested by enzymes called cellulases, which are produced by relatively few organisms. Among the organisms that can degrade

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cellulose are bacteria that reside in the rumen of animals, and many types of fungi. Considering that cellulose is the most abundant organic compound on earth, it is not surprising that fungi are important decomposers in terrestrial habitats. The glucose subunits released when polysaccharides are hydrolyzed can then enter glycolysis to be oxidized to pyruvate. ■ polysaccharides, p. 32 ■ cellulose, p. 32 ■ rumen, p. 735

Disaccharides including lactose, maltose, and sucrose are hydrolyzed by specific disaccharidases. For example, the enzyme b-galactosidase breaks down lactose, forming glucose and galactose. Glucose can enter glycolysis directly, but the other monosaccharides must first be modified. ■ disaccharides, p. 32

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Lipids The most common simple lipids are fats, which are a combination of fatty acids joined to glycerol. Fats are hydrolyzed by enzymes called lipases. The glycerol component is then converted to the precursor metabolite dihydroxyacetone phosphate, which then enters the glycolytic pathway. The fatty acids are degraded using a series of reactions collectively called b-oxidation. Each sequential reaction transfers a 2-carbon unit from the end of the fatty acid to coenzyme A, forming acetyl-CoA; this can enter the TCA cycle. Each reaction is a redox reaction, generating one NADH + H+ and one FADH2. ■ simple lipids, p. 35

Prokaryotes as a group are unique in their ability to use reduced inorganic chemicals such as hydrogen sulfide (H2S) and ammonia (NH3) as a source of energy. Note that these are the very compounds produced as a result of anaerobic respiration, when inorganic molecules such as sulfate and nitrate serve as terminal electron acceptors. This is one important example of how nutrients are cycled; the waste products of one organism serve as an energy source for another. ■ biogeochemical cycling and energy flow, p. 728 Chemolithotrophs fall into four general groups (table 6.7): Hydrogen bacteria oxidize hydrogen gas. Sulfur bacteria oxidize hydrogen sulfide. Iron bacteria oxidize reduced forms of iron. Nitrifying bacteria include two groups of bacteria—one oxidizes ammonia, forming nitrite, and the other oxidizes nitrite, forming nitrate.

Proteins Proteins are hydrolyzed by enzymes called proteases, which break peptide bonds that join amino acid subunits. The amino group of the resulting amino acids is removed by a reaction called a deamination. The remaining carbon skeletons are then converted into the appropriate precursor molecules. ■ protein, p. 25

MICROCHECK 6.6 In order for polysaccharides, lipids, and proteins to be used as energy sources, they are first hydrolyzed to release their respective subunits. These are then converted to the appropriate precursor metabolites so they can enter a central metabolic pathway. ✓ Why do cells secrete hydrolytic enzymes? ✓ Explain the process used to degrade fatty acids. ✓ How would cellulose-degrading bacteria in the rumen of a cow benefit the animal?

6.7 Chemolithotrophs Focus Point Explain how chemolithotrophs obtain energy.

TABLE 6.7

The chemolithotrophs extract electrons from inorganic energy sources and then use the electrons to generate ATP by oxidative phosphorylation. The electrons are passed along an electron transport chain to generate a proton motive force, analogous to the processes described earlier. The amount of energy gained in metabolism depends on the energy source and the terminal electron acceptor; figure 6.23 illustrates this relationship. Chemolithotrophs generally thrive in very specific environments where reduced inorganic compounds are found. For example, Acidithiobacillus ferrooxidans is found in certain acidic environments that are rich in sulfides. Because these organisms oxidize metal sulfides, they can be used to enhance the recovery of metals (see Perspective 6.1). Thermophilic chemolithotrophs thrive near hydrothermal vents of the deep ocean, harvesting the energy of reduced inorganic compounds that spew from the vents. The diversity and ecology of some of these organisms will be discussed in chapter 11. Unlike organisms that use organic molecules to fill both their energy and carbon needs, chemolithotrophs incorporate inorganic carbon, CO2, into an organic form. This process, called carbon fixation, will be described later.

Metabolism of Chemolithotrophs

Common Name of Organism

Source of Energy

Oxidation Reaction (Energy Yielding)

Important Features of Group

Common Genera In Group

Hydrogen bacteria

H2 gas

H2+1⁄2 O2DH2O

Can also use simple organic compounds for energy

Hydrogenomonas

Sulfur bacteria (non-photosynthetic)

H 2S

H2S+1⁄2 O2DH2O+S

Some members of this group can live at a pH of less than 1.

Acidithiobacillus Thiobacillus Beggiatoa Thiothrix

Iron bacteria

Reduced Iron (Fe2+)

2 Fe2++1⁄2 O2+H2OD 2 Fe3++2 OH–

Iron oxide present in the sheaths of these bacteria

Sphaerotilus Gallionella

Nitrifying bacteria

NH3

NH3+11⁄2 O2DHNO2+H2O

Important in nitrogen cycle

Nitrosomonas

HNO2

HNO2+1⁄2 O2DHNO3

Important in nitrogen cycle

Nitrobacter

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S+11⁄2 O2+H2ODH2SO4

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6.8

Photosynthesis

151

PERSPECTIVE 6.1 Mining with Microbes Microorganisms have been used for thousands of years in the production of bread and wine. It is only in the past several decades, however, that they are being used with increasing frequency in another area—the mining industry. The mining process traditionally consists of digging crude ores from the earth, crushing them, and then extracting the desired minerals from the contaminants. The extraction process of such minerals as copper and gold frequently involves harsh conditions, such as smelting, and burning off the contaminants before extracting the metal with cyanide. Such activities are expensive and deleterious to the

environment. With the development of biomining, some of these problems are being solved. In the process of biomining copper, the low grade ore is dumped outside the mine and then treated with sulfuric acid. The acidic conditions encourage the growth of Acidithiobacillus species present naturally in the ore. These acidophilic bacteria use CO2 as a source of carbon and gain energy by oxidizing sulfides of iron first to sulfur and then to sulfuric acid. The sulfuric acid dissolves the insoluble copper and gold from the ore. Currently about 25% of all copper produced in the world comes from the

process of biomining. Similar processes are being applied to gold mining. The current process of biomining employs microbes indigenous to the ore. Many improvements should be possible. For example, the oxidation of the minerals generates heat to the point that the bacteria may be killed. The use of thermophiles should overcome this problem. Further, many ores contain heavy metals, such as mercury, cadmium, and arsenic, which are toxic to the bacteria. It should be possible to isolate bacteria that are resistant to these metals. Biomining is still in its infancy.

MICROCHECK 6.7 Chemolithotrophs use reduced inorganic compounds as an energy source. They use carbon dioxide as a carbon source. ✓ Describe the roles of hydrogen sulfide and carbon dioxide in chemolithoautotrophic metabolism. ✓ Which energy source, Fe2+ or H2S, would result in the greatest energy yield when O2 is used as a terminal electron acceptor (hint: refer to figure 6.23)?

Energy sources

Energy released

CO2 SO4

O c rg a r a bn o i nc

FeOOH Fe

2+

NH4+

NO2– (to form NH4+)

Terminal electron acceptors

HCOOH CH2O Glucose H2 O c rg a a r n b i o c H2S n 0 CH4 S

NO3– (to form NH4+)

6.8 Photosynthesis Focus Points Describe the role of chlorophylls, bacteriochlorophylls, accessory pigments, reaction-center pigments, and antennae pigments in capturing radiant energy. Compare and contrast the tandem photosystems of cyanobacteria and photosynthetic eukaryotes with the single photosystems of purple and green bacteria.

2+

Mn

MnO2

NO3– (to form N2) O2

Plants, algae, and several groups of bacteria harvest the radiant energy of sunlight, and then use it to power the synthesis of organic compounds from CO2. This capture and subsequent conversion of light energy into chemical energy is called photosynthesis. The general reaction of photosynthesis can be summarized as: Light Energy

FIGURE 6.23 Relative Energy Gain of Different Types of Metabolism The left axis shows potential energy sources, ordered according to their relative tendency to give up electrons; those at the top lose electrons most easily. The right axis shows potential terminal electron acceptors, ordered according to their relative tendency to gain electrons; those at the bottom accept electrons most readily. Energy is released only when electrons are transferred from an energy source to a terminal electron acceptor that is lower on the chart; the greater the downward slope, the more energy that can be harvested to make ATP.

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6 CO2+12 H2X

D C6H12O6+12 X+6 H2O

Photosynthetic processes are generally considered in two distinct stages. The light-dependent reactions, often simply called the light reactions, are used to capture the energy from light and convert it to chemical energy in the form of ATP. The light-independent reactions, also termed the dark reactions, use that energy to synthesize organic compounds. The process that converts carbon

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TABLE 6.8

Comparison of the Photosynthetic Mechanisms Used by Different Organisms Oxygenic Photosynthesis

Anoxygenic Photosynthesis

Plants, Algae

Cyanobacteria

Purple Bacteria

Green Bacteria

Location of the photosystem

In membranes of thylakoids, which are within the stroma of chloroplasts

In membranes of thylakoids, located within the cell

Within the cytoplasmic membrane; extensive invaginations in that membrane effectively increase the surface area.

Primarily within the cytoplasmic membrane; chlorosomes attached to the inner surface of the membrane contain the accessory pigments.

Type of photosystem

Photosystem I and photosystem II

Similar to photosystem II

Similar to photosystem I

Primary light harvesting pigment

Chlorophyll a

Bacteriochlorophylls

Mechanism for generating Non-cyclic photophosphorylation using both photosystems reducing power Source of electrons for reducing power

H 2O

CO2 fixation

Calvin cycle

Accessory pigments

Carotenoids

Non-cyclic use of the photosystem

Varies among the organisms in the group; may include H2S, H2, or organic compounds. Carotenoids, phycobilins

dioxide into organic compounds is called carbon fixation. We will describe the steps of carbon fixation in a separate section (see section 6.9) because, as mentioned earlier, a variety of prokaryotes other than photosynthetic ones use the process. Characteristics of various photosynthetic mechanisms are summarized in table 6.8.

Capturing Radiant Energy Photosynthetic organisms are highly visible in their natural habitats because they possess various colored pigments that capture light energy. The color we observe is due to the wavelengths reflected by the pigment; for example, pigments that absorb only blue and red light will appear green (see figure 5.7). Multiple pigments are involved in photosynthesis, increasing the range of wavelengths of light that can be absorbed by a cell. The pigments are located together in protein complexes called photosystems, which specialize in capturing and using light (figure 6.24). Electron transport chain

Light Reaction-center chlorophyll

Chlorophyll molecules Photosystem

FIGURE 6.24 Photosystem Chlorophyll and other pigments capture the energy of light and then transfer it to reaction-center chlorophyll, which emits an electron that is then passed to an electron transport chain.

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Reversed electron transport

Calvin cycle

Reversed TCA cycle

Carotenoids

Carotenoids

Photosynthetic pigments include chlorophylls, bacteriochlorophylls, and accessory pigments. Chlorophylls are found in plants, algae, and a large group of bacteria called cyanobacteria. The various types of chlorophylls are designated with a letter following the term; for example, chlorophyll a. Bacteriochlorophylls are found in anoxygenic photosynthetic bacteria (“anoxygenic” means they do not generate O2). These pigments absorb wavelengths not absorbed by chlorophylls, enabling the bacteria to grow in habitats where other photosynthetic organisms cannot. Accessory pigments increase the efficiency of light capture by absorbing wavelengths not absorbed by the other pigments. Accessory pigments include carotenoids, which are found in a wide variety of photosynthetic organisms, including both prokaryotes and eukaryotes, and phycobillins, which are unique to cyanobacteria and red algae. Within the photosystems, certain pigments function as reaction-center pigments and others function as antennae pigments (see figure 6.24). Reaction-center pigments are electron donors in the photosynthetic process. In response to excitation by radiant energy, the pigment emits an electron, which is then passed to an electron transport chain similar to that used in respiration. The oxygenic photosynthetic organisms (plants, algae, and cyanobacteria) use chlorophyll a as the reaction-center pigment, whereas the anoxygenic photosynthetic organisms (purple and green bacteria) use one of the bacteriochlorophylls. Antennae pigments make up what is called the antenna complex, which acts as a funnel, capturing the energy of light and then transferring it to the reaction-center pigment. The photosystems of cyanobacteria are embedded in the membranes of stacked structures called thylakoids located within the cells. Plants and algae also have thylakoids, in the stroma of the chloroplast (see figure 3.54). The similarity between the structure of chloroplasts and cyanobacteria is not surprising considering that genetic evidence indicates that the organelle descended from an ancestor of a cyanobacterium (see Perspective 3.1).

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6.8

The photosystems of the purple and green bacteria are embedded in the cytoplasmic membrane. Purple bacteria have extensive invaginations in the membrane that maximize the surface area. Green bacteria have specialized structures called chlorosomes attached to the inner surface of the cytoplasmic membrane. These structures contain the accessory pigments.

Converting Radiant Energy into Chemical Energy Photosynthetic organisms use the light-dependent reactions to accomplish two tasks. First, they must use radiant energy to fuel the synthesis of ATP, the process of photophosphorylation. They also need to generate reducing power so they can fix CO2. Depending on the method used to fix CO2, the type of reducing power required may be either NADPH or NADH.

Light-Dependent Reactions in Cyanobacteria and Photosynthetic Eukaryotic Cells Cyanobacteria and chloroplasts have two distinct photosystems that work in tandem (figure 6.25). The sequential absorption of energy by the two photosystems allows the process to raise the energy level of electrons stripped from water high enough to be used to generate a proton motive force as well as produce reducing power. The process is oxygenic—that is, it generates O2. First we will consider the simplest situation, which occurs when the cell needs to synthesize ATP but not reducing power (NADPH). To accomplish this, only photosystem I is used. Radiant energy is absorbed by this photosystem, exciting the reaction-center chloro-

Photosynthesis

153

phylls, which causes them to emit high-energy electrons. The electrons are then passed to an electron carrier, which transports them to a proton pump; this pump is analogous to complex III in the respiratory chain of mitochondria. After being used to pump protons across the membrane, thus generating a proton motive force, the electrons are returned to photosystem I. As occurs in oxidative phosphorylation, ATP synthase harvests the energy of the proton motive force to synthesize ATP. This overall process is called cyclic photophosphorylation because the molecule that serves as the electron donor, reaction-center chlorophyll, is also the terminal electron acceptor; the electrons have followed a cyclical path. When cells must produce both ATP and reducing power, noncyclic photophosphorylation is used. In this process, the electrons emitted by photosystem I are not passed to the proton pump, but instead are donated to NADP+ to produce NADPH. While this action provides reducing power, the cell must now replenish the electrons emitted by reaction center chlorophyll from another source. In addition, the cell must still generate a proton motive force in order to synthesize ATP. Photosystem II plays a pivotal role in this process. When photosystem II absorbs radiant energy, the reaction-center chlorophylls emit high-energy electrons that can be donated to photosystem I. First, however, the electrons are passed to the proton pump, which uses some of their energy to establish the proton motive force. In order to replenish the electrons emitted from photosystem II, an enzyme within that complex extracts the electrons from water, donating them to the reaction-center chlorophyll. Removal of electrons from two molecules of water generates O2. In essence, photosystem II captures the energy of light and then uses it to raise the energy level of electrons stripped

Proton gradient formed for ATP synthesis

H+ Electron carrier

Energy of electrons

Excited chlorophyll

eProton pump

Electron carrier

Excited chlorophyll

e-

e-

Electron carrier

NADP reductase Reactioncenter chlorophyll

NADP+ NADPH Radiant energy

Reaction-center chlorophyll Radiant energy

Water-splitting enzyme Z

e-

2H2O 4H+ + O2

Photosystem II

Proton pump

Photosystem I

NADP reductase

FIGURE 6.25 The Tandem Photosystems of Cyanobacteria and Chloroplasts Radiant energy captured by photosynthetic pigments excites the reaction-center chlorophyll, causing it to emit a high-energy electron, which is then passed to an electron transport chain. In cyclic photophosphorylation, electrons emitted by photosystem I are returned to that photosystem; the path of the electrons is shown in green arrows. In non-cyclic photophosphorylation, the electrons used to replenish photosystem I are donated by radiant energy-excited photosystem II; the path of these electrons is shown in orange arrows. In turn, photosystem II replenishes its own electrons by stripping them from water, producing O2.

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from water molecules to a high enough level that they can be used to power photophosphorylation. Photosystem I then accepts those electrons, which still retain some residual energy, and again captures the energy of light to boost the energy of the electrons to an even higher level so they can be used to reduce NADPH.

Light-Dependent Reactions in Anoxygenic Photosynthetic Bacteria Anoxygenic photosynthetic bacteria employ only a single photosystem and are unable to use water as an electron donor for reducing power. This is why they are anoxygenic, or do not evolve O2. Molecules used as electron donors by these bacteria include hydrogen gas (H2), hydrogen sulfide (H2S), and organic compounds. There are two general groups of anoxygenic photosynthetic bacteria—the purple bacteria and the green bacteria. Purple bacteria use a photosystem similar to the photosystem II of cyanobacteria and eukaryotes to synthesize ATP. However, the photosystem does not raise the electrons to a high enough energy level to reduce NAD+ (or NADP+), so the purple bacteria must use an alternative mechanism to generate reducing power. To do this they employ a process called reversed electron transport, which uses ATP to run the electron transport chain in the reverse direction, or “uphill.” Green bacteria employ a photosystem similar to photosystem I. The electrons emitted from this photosystem can be used to either generate a proton motive force or reduce NAD+.

MICROCHECK 6.8 Photosynthetic organisms harvest the energy of sunlight and use it to power the synthesis of organic compounds from CO2. Various pigments are used to capture radiant energy. These pigments are arranged in complexes called photosystems. When reaction-center chlorophyll absorbs the energy of light, a high-energy electron is emitted. This is then passed along an electron transport chain to generate a proton motive force, which is used to synthesize ATP. Plants and cyanobacteria use water as a source of electrons for reducing power, generating oxygen. Anoxygenic photosynthetic bacteria obtain electrons from a reduced compound other than water, and therefore do not evolve oxygen. ✓ b-carotene is a carotenoid that mammals can use as a source of vitamin A. What is the function of carotenoids in photosynthetic organisms? ✓ What is the advantage of having tandem photosystems? ✓ It requires energy to reverse the flow of the electron transport chain. Why would this be so?

6.9 Carbon Fixation Focus Point Describe the three stages of the Calvin cycle.

Chemolithoautotrophs and photoautotrophs use carbon dioxide to synthesize organic compounds, the process of carbon fixation. In photosynthetic organisms, the process occurs in the light-

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independent reactions. Carbon fixation consumes a great deal of ATP and reducing power, which should not be surprising considering that the reverse process—oxidizing those same compounds to CO2—liberates a great deal of energy. The Calvin cycle is the most common pathway used to fix carbon, but some prokaryotes incorporate CO2 using other mechanisms. For example, the green bacteria and some members of the Archaea use a pathway that effectively reverses the steps of the TCA cycle.

Calvin Cycle The Calvin cycle, or Calvin-Benson cycle, named in honor of the scientists who described much of it, is a complex cycle that can be viewed as having three essential stages—incorporation of CO2 into an organic compound, reduction of the resulting molecule, and regeneration of the starting compound (figure 6.26). Because of the complexities of the cycle, it is easiest to consider the process as consisting of six “turns” of the cycle. Together, these six “turns” generate a net gain of two molecules of glyceraldehyde 3-phosphate, which can be converted into one molecule of fructose 6-phosphate. The Calvin cycle consists of three stages: Stage 1 Carbon dioxide enters the cycle when the enzyme ribulose bisphosphate carboxylase, commonly called rubisco, joins it to a 5-carbon compound, ribulose 1, 5-bisphosphate. The resulting compound spontaneously hydrolyzes to produce two molecules of a 3-carbon compound, 3-phosphoglycerate (3PG). Interestingly, although rubisco is unique to autotrophs, it is thought to be the most abundant enzyme on earth! Stage 2 A sequential input of energy (ATP) and reducing power (NADPH) is used in steps that, together, convert 3PG to glyceraldehyde 3-phosphate (G3P). This compound is identical to the precursor metabolite formed as an intermediate in glycolysis. It can be converted to a number of different compounds used in biosynthesis, oxidized to make other precursor compounds, or converted to a 6-carbon sugar. A critical aspect of the pathway of CO2 fixation, however, stems from the fact that it operates as a cycle—ribulose 1, 5-bisphosphate must be regenerated from G3P for the process to continue. Consequently, in six cycles, a maximum of 2 G3P can be converted to a 6-carbon sugar, the rest is used to regenerate ribulose 1, 5-bisphosphate. Stage 3 Many of the steps used to regenerate ribulose 1, 5bisphosphate involve reactions of the pentose phosphate cycle.

Yield of the Calvin Cycle One molecule of the 6-carbon sugar fructose can be generated for every six “turns” of the cycle. These six “turns” consume 18 ATP and 12 NADPH+H+.

MICROCHECK 6.9 The process of carbon dioxide fixation consumes a great deal of ATP and reducing power. The Calvin cycle is the most common pathway used to incorporate inorganic carbon into an organic form. ✓ What is the role of rubisco? ✓ What would happen if ribulose 1, 5-bisphosphate were depleted in a cell?

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6.10 Anabolic Pathways—Synthesizing Subunits from Precursor Molecules

6

155

CO2

12 molecules 3-phosphoglycerate

~ ~ 12 ATP

6 molecules ribulose 1,5-bisphosphate STAGE 1

~ 12 ADP

12 molecules 1, 3-bisphosphoglycerate

~ 6 ADP

~

STAGE 3

STAGE 2

~ ~

12

NADPH

+ H+

6 ATP

6 molecules ribulose 5-phosphate

12 12 molecules glyceraldehyde 3-phosphate

NADP+

12 Pi

Series of complex reactions

1 molecule fructose 6-phosphate

FIGURE 6.26 The Calvin Cycle The Calvin cycle has three essential stages: (1) incorporation of CO2 into an organic compound; (2) reduction of the resulting molecule; and (3) regeneration of the starting compound.

6.10 Anabolic Pathways—Synthesizing Subunits from Precursor Molecules

Cell constituents

pathway must have the end product provided from an external source. This is why fastidious bacteria, such as lactic acid bacteria, require many different growth factors. Once the subunits are synthesized or taken up, they can be assembled to make macromolecules. Various different macromolecules can then be joined to form the structures that make up the cell. ■ fastidious, p. 94

Focus Point Describe the synthesis of lipids, amino acids, and nucleotides.

Prokaryotes, as a group, are highly diverse with respect to the compounds they use for energy, but they are remarkably similar in their biosynthetic processes. They synthesize the necessary subunits, employing specific anabolic pathways that use ATP, reducing power in the form of NADPH, and the precursor metabolites formed in the central metabolic pathways (figure 6.27). Organisms lacking one or more enzymes in a given biosynthetic

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Lipid Synthesis Synthesis of most lipids in microorganisms can be viewed as having two essential components—fatty acid synthesis and glycerol synthesis. Synthesis starts with transfer of the acetyl group of the precursor metabolite produced in the transition step, acetyl-CoA, to a carrier protein called acyl carrier protein (ACP). This carrier holds the fatty acid chain as 2-carbon units are progressively added. When the newly synthesized fatty acid reaches its required length, usually 14, 16, or 18 carbons long, it is released from ACP.

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CHAPTER SIX Metabolism: Fueling Cell Growth

Glycolysis

Pentose phosphate pathway

Ribose 5-phosphate Erythrose 5-phosphate

Nucleotides amino acids (histidine) Amino acids (phenylalanine, tryptophan, tyrosine) Lipids (glycerol component)

Amino acids (cysteine, glycine, serine) Amino acids (phenylalanine, tryptophan, tyrosine)

Glucose 6-phosphate

Lipopolysaccharide (polysaccharide)

Fructose 6-phosphate

Peptidoglycan

Dihydroxyacetone phosphate

3-phosphoglycerate Phosphoenolpyruvate

Pyruvate

Pyruvate

Acetyl-CoA

Amino acids (aspartate, asparagine, isoleucine, lysine, methionine, threonine)

Acetyl-CoA

Amino acids (alanine, leucine,valine)

Lipids (fatty acids)

Oxaloacetate TCA cycle a-ketoglutarate

FIGURE 6.27 The Use of Precursor Metabolites in Biosynthesis

Amino acids (arginine, glutamate, glutamine, proline)

The size of the arrows indicates the relative quantity of each precursor metabolite needed to produce a given weight of E. coli cells.

The glycerol component of the fat is synthesized from the precursor metabolite dihydroxyacetone phosphate, which is generated in glycolysis.

Proteins are composed of various combinations of 20 different amino acids. Amino acids can be grouped into structurally related families that share common pathways of biosynthesis. Some are synthesized from precursor metabolites formed during glycolysis, while others are derived from compounds of the TCA cycle (see table 6.2).

nism for bacteria to incorporate nitrogen into an organic material. Recall from chapter 4 that many bacteria utilize ammonium (NH4+) provided in the medium as their source of nitrogen; it is primarily through the synthesis of glutamate that they do this. Glutamate is synthesized in a single-step reaction that adds ammonia to the precursor metabolite a-ketoglutarate, produced in the TCA cycle (figure 6.28a). Once glutamate has been formed, its amino group can be transferred to other carbon compounds to produce amino acids such as aspartate (figure 6.28b). This transfer of the amino group, a transamination, regenerates a-ketoglutarate from glutamate. The a-ketoglutarate can then be used again to incorporate more ammonia. ■ amino group, p. 26

Glutamate

Aromatic Amino Acids

Amino acids are necessary for protein synthesis, but glutamate is especially important because its synthesis provides a mecha-

Synthesis of aromatic amino acids such as tyrosine, phenylalanine, and tryptophan requires a multistep, branching pathway (figure 6.29).

Amino Acid Synthesis

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157

NH2 + NH4+ a-ketoglutarate

Glutamate

(a) NH2

NH2 + Glutamate

+ a-ketoglutarate

Oxaloacetate

Aspartate

(b)

FIGURE 6.28 Glutamate (a) Glutamate is synthesized in a single-step reaction that adds ammonia to the precursor metabolite a-ketoglutarate. (b) The amino group of glutamate can be transferred to other carbon compounds in order to produce other amino acids. For example, transferring it to oxaloacetate produces aspartate.

This serves as an excellent illustration of many important features of the regulation of amino acid synthesis. The pathway begins with the formation of a 7-carbon compound, resulting from the joining of two precursor metabolites, erythrose 4-phosphate (4-carbon) and phosphoenolpyruvate (3-carbon). These precursors originate in the pentose phosphate pathway and glycolysis, respectively. The 7-carbon compound is modified through a series of steps until a branch point is reached. At this juncture, two options are possible. If synthesis proceeds in one direction, tryptophan is produced. In the other direction, another branch point is reached; from there, either tyrosine or phenylalanine can be made. When a given amino acid is provided to a cell, it would be a waste of carbon, energy, and reducing power for that cell to continue synthesizing it. But when only one product of a branched pathway is present, how does the cell control synthesis? In the pathway for aromatic acid biosynthesis, this partly occurs by regulating the enzymes at the branch points. Tryptophan acts as a feedback inhibitor of the enzyme that directs the branch to its synthesis; this sends the pathway to the steps leading to the synthesis of the other amino acids—tyrosine and phenylalanine. Likewise, these two amino acids each inhibit the first enzyme of the branch leading to their synthesis.

In addition, the three amino acids each control the first step of the full pathway, the formation of the 7-carbon compound. Three different enzymes can catalyze this step; each has the same active site, but they have different allosteric sites. Each aromatic amino acid acts as a feedback inhibitor for one of the enzymes. If all three amino acids are present in the environment, then very little of the 7-carbon compound will be synthesized. If only one or two of those amino acids are present, then proportionally more of the compound will be synthesized. ■ allosteric enzymes, p. 137

Nucleotide Synthesis Nucleotide subunits of DNA and RNA are composed of three units: a 5-carbon sugar, a phosphate group, and a nitrogenous base, either a purine or a pyrimidine. They are synthesized as ribonucleotides, but these can then be converted to deoxyribonucleotides by replacing the hydroxyl group on the 2„ carbon of the sugar with a hydrogen atom. ■ nucleotides, p. 32 ■ purine, p. 33 ■ pyrimidine, p. 33

The purine nucleotides are synthesized in a distinctly different manner from the pyrimidine nucleotides. Purine nucleotides are synthesized on the sugar phosphate component in a very complex process. In fact, nearly every carbon and nitrogen of

Phenylalanine

From glycolytic pathway Compound a

3-C + 4-C

7-C Compound

Branch point II

Branch point I

Tyrosine

Compound b

Tryptophan

From pentose phosphate pathway

FIGURE 6.29 Synthesis of Aromatic Amino Acids A multistep branching pathway is used to synthesize aromatic amino acids. The end product of a branch inhibits the first enzyme of that branch; in addition, the end product inhibits one of the three enzymes that catalyze the first step of the pathway.

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158

CHAPTER SIX Metabolism: Fueling Cell Growth Amino group of aspartic acid

H C

N

H

N C H

C N

Formic acid

N

acid, which are components of the nucleic acids. To synthesize pyrimidine nucleotides, the pyrimidine ring is made first, and then attached to ribose 5-phosphate. After one pyrimidine nucleotide is formed, the base component can be converted into one of the other pyrimidines. ■ adenylic acid, p. 33 ■ guanylic acid, p. 33

Glycine

CO2

Formic acid

H

MICROCHECK 6.10 Amide nitrogen of glutamine Purine Ring

FIGURE 6.30 Source of the Carbons and Nitrogen Atoms in Purine Rings Nearly every carbon and nitrogen of the purine ring comes from a different source.

the purine ring comes from a different source (figure 6.30). The starting compound is ribose 5-phosphate, a precursor metabolite generated in the pentose phosphate pathway. Then, in a highly ordered sequence, atoms from the other sources are added. Once this purine is formed, it is converted to adenylic or guanylic

Biosynthetic processes of different organisms are remarkably similar, using precursor metabolites, NADPH, and ATP to form subunits. Synthesis of the amino acid glutamate provides a mechanism for bacteria to incorporate nitrogen in the form of ammonia into organic material. Allosteric enzymes are used to regulate certain biosynthetic pathways. The purine nucleotides are synthesized in a very different manner from the pyrimidine nucleotides. ✓ Explain why the synthesis of glutamate is particularly important for a cell. ✓ What are three general products of the central metabolic pathways that a cell requires in order to carry out biosynthesis? ✓ With a branched biochemical pathway, why would it be important for a cell to shut down the first step as well as branching steps?

FUTURE CHALLENGES Going to Extremes The remarkable speed and precision of enzyme activity are already exploited in a number of different processes. For example, the enzyme glucose isomerase is used to modify corn syrup, converting some of the glucose into fructose, which is much sweeter than glucose. The resulting highfructose corn syrup is used in the commercial production of a variety of beverages and food products. Other enzymes, including proteases, amylases, and lipases, are used in certain laundry detergents to facilitate stain removal. These enzymes break down proteins, starches, and fats, respectively, which otherwise adhere strongly to fabrics. Similar enzymes are being added to some dishwashing detergents, decreasing the reliance on chlorine

bleaching agents and phosphates that can otherwise pollute the environment. Enzymes are also used by the pulp and paper industry to facilitate the bleaching process. Even with the current successes of enzyme technology, however, only a small fraction of enzymes in nature have been characterized. Recognizing that the field is still in its infancy, some companies are actively searching diverse environments for microorganisms that produce novel enzymes, hoping that some may be commercially valuable. Among the most promising are those produced by the extremophiles, microbes that preferentially live in conditions inhospitable to other forms of

life. Because these organisms live in severe environments, their enzymes likely withstand the harsh conditions that characterize certain processes. For example, the enzymes of the extreme thermophiles should withstand temperatures that would quickly inactivate enzymes of mesophiles. With the aid of enzymes, many of which are still to be discovered, scientists may eventually be able to precisely control a greater variety of commercially important chemical processes. This will hopefully result in fewer unwanted by-products and a decreased reliance on chemicals that damage the environment.

SUMMARY 6.1

Principles of Metabolism

Catabolism encompasses processes that capture and store energy by breaking down complex molecules. Anabolism includes processes that use energy to synthesize and assemble the building blocks of a cell (figure 6.1). Harvesting Energy Photosynthetic organisms harvest the energy of sunlight, using it to power the synthesis of organic compounds. Chemoorganotrophs harvest energy contained in organic compounds (figure 6.3). Exergonic reactions release energy; endergonic reactions utilize energy. Components of Metabolic Pathways A specific enzyme facilitates each step of a metabolic pathway (figure 6.5). ATP is the energy currency of the cell. The energy source is oxidized to

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release its energy; the redox reactions reduce an electron carrier 6.7). NAD+, NADP+, and FAD are electron carriers (table 6.1).

(figure

Precursor Metabolites Precursor metabolites are used to make the subunits of macromolecules, and they can also be oxidized to generate energy in the form of ATP (table 6.2). Overview of Metabolism (figure 6.8) The central metabolic pathways are glycolysis, the pentose phosphate pathway, and the tricarboxylic acid cycle (TCA cycle). Respiration uses the reducing power accumulated in the central metabolic pathways to generate ATP by oxidative phosphorylation. Aerobic respiration uses O 2 as a terminal electron acceptor; anaerobic respiration uses a molecule other than O2 as a terminal

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Summary

159

electron acceptor (table 6.3). Fermentation uses pyruvate or a derivative as a terminal electron acceptor; this recycles the reduced electron carrier NADH.

ATP Yield of Aerobic Respiration in Prokaryotes (figure 6.19) The theoretical maximum yield of ATP of aerobic respiration is 38 ATP.

6.2

6.5

Enzymes

Enzymes function as biological catalysts; they are neither consumed nor permanently changed during a reaction. Mechanisms and Consequences of Enzyme Action (figure 6.9) The substrate binds to the active site or catalytic site to form a temporary intermediate called an enzyme-substrate complex. Cofactors and Coenzymes (figure 6.10, table 6.4) Enzymes sometimes act in conjunction with cofactors such as coenzymes and trace elements. Environmental Factors That Influence Enzyme Activity (figure 6.11) The factors most important in influencing enzyme activities are temperature, pH, and salt concentration.

Fermentation

In general, the only ATP-yielding reactions of fermentations are those of the glycolytic pathway; the other steps provide a mechanism for recycling NADH (figure 6.20). Some end products of fermentation are commercially valuable (figure 6.21). Because a given type of organism uses a specific fermentation pathway, the end products can be used as markers that aid in identification.

6.6

Catabolism of Organic Compounds Other Than Glucose (figure 6.22)

Hydrolytic enzymes break down macromolecules into their respective subunits.

Allosteric Regulation (figure 6.12) Cells can fine-tune the activity of an allosteric enzyme by using a regulatory molecule that binds to the allosteric site of the enzyme.

Polysaccharides and Disaccharides Amylases digest starch, releasing glucose subunits, and are produced by many organisms. Cellulases degrade cellulose. Sugar subunits released when polysaccharides are broken down can then enter glycolysis to be oxidized to pyruvate.

Enzyme Inhibition Non-competitive inhibition occurs when the inhibitor and the substrate act at different sites on the enzyme. Competitive inhibition occurs when the inhibitor competes with the normal substrate for the active binding site (figure 6.13).

Lipids Fats are hydrolyzed by lipase, releasing glycerol and fatty acids. Glycerol is converted to dihydroxyacetone phosphate; fatty acids are degraded by b-oxidation, generating reducing power and the precursor metabolite acetyl-CoA.

6.3

Proteins Proteins are hydrolyzed by proteases. Deamination removes the amino group; the remaining carbon skeleton is then converted into the appropriate precursor molecule.

The Central Metabolic Pathways (table 6.6)

Glycolysis (figure 6.14) Glycolysis converts one molecule of glucose into two molecules of pyruvate; the theoretical net yield is 2 ATP, 2 NADH + H+, and six different precursor metabolites.

6.7

Chemolithotrophs

Pentose Phosphate Pathway The pentose phosphate pathway forms NADPH+ and two different precursor metabolites.

Prokaryotes, as a group, are unique in their ability to use reduced inorganic compounds such as hydrogen sulfide (H2S) and ammonia (NH3) as a source of energy (figure 6.23). Chemolithotrophs are autotrophs.

Transition Step (figure 6.15) The transition step converts pyruvate to acetyl-CoA. Repeated twice, this produces 2 NADH+2 H+ and 1 precursor metabolite.

6.8

Tricarboxylic Acid (TCA) Cycle (figure 6.15) The TCA cycle completes the oxidation of glucose; the theoretical yield of two “turns” is 6 NADH+6 H+, 2 FADH2, 2 ATP, and two different precursor metabolites.

6.4

Respiration

The Electron Transport Chain—Generating Proton Motive Force The electron transport chain sequentially passes electrons, and, as a result, ejects protons. The mitochondrial electron transport chain has three different complexes (complexes I, III and IV) that function as proton pumps (figure 6.17). Prokaryotes vary with respect to the types and arrangements of their electron transport components (figure 6.18). Some prokaryotes can use molecules other than O2 as terminal electron acceptors. This process of anaerobic respiration harvests less energy than aerobic respiration. ATP Synthase—Harvesting the Proton Motive Force to Synthesize ATP ATP synthase permits protons to flow back across the membrane, harvesting the energy released to fuel the synthesis of ATP.

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Photosynthesis

The light-dependent reactions capture energy from light and convert it to chemical energy in the form of ATP. The light-independent reactions use that energy to synthesize organic carbon compounds. Capturing Radiant Energy Various pigments such as chlorophylls, bacteriochlorophylls, carotenoids, and phycobilins are used to capture radiant energy. Reaction center pigments function as the electron donor in the photosynthetic process; antennae pigments funnel radiant energy to the reaction center pigment. Converting Radiant Energy into Chemical Energy The high-energy electrons emitted by reaction center chlorophylls are passed to an electron transport chain, which uses them to generate a proton motive force. The energy of proton motive force is harvested by ATP synthase to fuel the synthesis of ATP (figure 6.24). Photosystems I and II of cyanobacteria and chloroplasts raise the energy level of electrons stripped from water to a high enough level to be used to generate a proton motive force and produce reducing power; this process evolves oxygen (figure 6.25). Purple and green bacteria employ only a single photosystem; they must obtain electrons from a reduced compound other than water and therefore do not evolve oxygen.

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CHAPTER SIX Metabolism: Fueling Cell Growth

6.9

Carbon Fixation

Calvin Cycle (figure 6.26) The most common pathway used to incorporate CO2 into an organic form is the Calvin cycle.

6.10

Anabolic Pathways—Synthesizing Subunits from Precursor Molecules (figure 6.27)

Lipid Synthesis The fatty acid components of fat are synthesized by progressively adding 2-carbon units to an acetyl group. The glycerol component is synthesized from dihydroxyacetone phosphate.

Amino Acid Synthesis Synthesis of glutamate from a-ketoglutarate and ammonia provides a mechanism for cells to incorporate nitrogen into organic molecules (figure 6.28). Synthesis of aromatic amino acids requires a multistep branching pathway. Allosteric enzymes regulate key steps of the pathway (figure 6.29). Nucleotide Synthesis Purine nucleotides are synthesized on the sugar-phosphate component; the pyrimidine ring is made first and then attached to the sugar-phosphate (figure 6.30).

REVIEW QUESTIONS Short Answer 1. 2. 3. 4. 5. 6. 7. 8. 9. 10.

Explain the difference between catabolism and anabolism. How does ATP serve as a carrier of free energy? How do enzymes catalyze chemical reactions? Explain how precursor molecules serve as junctions between catabolic and anabolic pathways. How do cells regulate enzyme activity? Why do the electrons carried by FADH2 result in less ATP production than those carried by NADH? Name three food products produced with the aid of microorganisms. In photosynthesis, what is encompassed by the term “lightindependent reactions?” Unlike the cyanobacteria, the anoxygenic photosynthetic bacteria do not evolve oxygen (O2). Why not? What is the role of transamination in amino acid biosynthesis?

Multiple Choice 1. Which of these factors does not affect enzyme activity? a) temperature b) inhibitors c) coenzymes d) humidity e) pH 2. Which of the following statements is false? Enzymes a) bind to substrates. b) lower the energy of activation. c) convert coenzymes to products. d) speed up biochemical reactions. e) can be named after the kinds of reaction they catalyze. 3. Which of these is not a coenzyme? a) FAD b) coenzyme A c) NAD+ d) ATP e) NADP+ 4. What is the end product of glycolysis? a) glucose b) citrate c) oxaloacetate d) a-ketoglutarate e) pyruvate 5. The major pathway(s) of central metabolism are a) glycolysis and the TCA cycle only. b) glycolysis, the TCA cycle, and the pentose phosphate pathway. c) glycolysis only. d) glycolysis and the pentose phosphate pathway only. e) the TCA cycle only.

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6. Which of these pathways gives a cell the potential to produce the most ATP? a) TCA cycle b) pentose phosphate pathway c) lactic acid fermentation d) glycolysis 7. In fermentation, the terminal electron acceptor is a) oxygen (O2). b) hydrogen (H2). c) carbon dioxide (CO2). d) an organic compound. 8. In the process of oxidative phosphorylation, the energy of proton motive force is used to generate a) NADH. b) ADP. c) ethanol. d) ATP. e) glucose. 9. In the TCA cycle, the carbon atoms contained in acetate are converted into a) lactic acid. b) glucose. c) glycerol. d) CO2. e) all of these. 10. Degradation of fats as an energy source involves all of the following, except a) b-oxidation. b) acetyl-CoA. c) glycerol. d) lipase. e) transamination.

Applications 1. A worker in a cheese-making facility argues that whey, a nutrientrich by-product of cheese, should be dumped in a nearby pond where it could serve as fish food. Explain why this proposed action could actually kill the fish by depleting the oxygen in the pond. 2. Scientists working with DNA in vitro often store it in solutions that contain EDTA, a chelating agent that binds magnesium (Mg2+). This is done to prevent enzymes called DNases from degrading the DNA. Explain why EDTA would interfere with enzyme activity.

Critical Thinking 1. A student argued that aerobic and anaerobic respiration should produce the same amount of ATP. He reasoned that they both use basically the same process; only the terminal electron acceptor is different. What is the primary error in this student’s argument? 2. Chemolithotrophs near hydrothermal vents support a variety of other life forms there. Explain how their role there is analogous to that of photosynthetic organisms in terrestrial environments.

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7 DNA double helix.

The Blueprint of Life, from DNA to Protein A Glimpse of History In 1866, the Czech monk Gregor Mendel showed that traits are inherited by means of physical units, which we now call genes. It was not until 1941, however, that the precise function of genes was revealed when George Beadle, a geneticist, and Edward Tatum, a chemist, published a scientific paper reporting that genes determine the structure of enzymes. Biochemists had already shown that enzymes catalyze the conversion of one compound into another in a biochemical pathway. Beadle and Tatum studied Neurospora crassa, a common bread mold that grows on a very simple medium containing sugar and simple inorganic salts. Beadle and Tatum created N. crassa strains with altered properties, mutants, by treating cells with X rays, which were known to alter genes. Some of these mutants could no longer grow on the glucose-salts medium unless growth factors such as vitamins were added to the medium. To isolate these, Beadle and Tatum had to laboriously screen thousands of progeny to find the relatively few that required the growth factors. Each mutant presumably contained a defective gene. The next task for Beadle and Tatum was to identify the specific biochemical defect of each mutant. To do this, they added different growth factors, one at a time, to each mutant culture. The one that allowed a particular mutant to grow had presumably bypassed the function of a defective enzyme. In this manner, they were able to pinpoint in each mutant the specific step in the biochemical pathway that was defective. Then, using these same mutants, Beadle and Tatum showed that the requirement for each growth factor was inherited as a single gene, ultimately leading to their conclusion that a single gene determines the production of one enzyme. Their conclusion has been modified somewhat, because we now know that some enzymes are made up of more than one protein. A single gene usually determines the production of one protein. In 1958, Beadle and Tatum shared the Nobel Prize in Medicine, largely for these pioneering studies that ushered in the era of modern biology.

C

onsider for a moment the vast diversity of cellular life forms that exist. Our world contains a remarkable variety of microorganisms and specialized cells that make up plants and animals. Every characteristic of each of these cells, from its shape to its function, is dictated by information contained in its deoxyribonucleic acid (DNA). DNA encodes the master plan, the blueprint, for all cell structures and processes. Yet for all the complexity this would seem to require, DNA is a string composed of only four different nucleotides, each containing a particular nitrogenous base: adenine (A), thymine (T), cytosine (C), or guanine (G). ■ nucleotides, p. 32 While it might seem improbable that the vast array of life forms can be encoded by a molecule consisting of only four different units, think about how much information can be transmitted by binary code, the language of all computers, which has a base of only two. A simple series of ones and zeros can code for each letter of the alphabet. String enough of these together in the right sequence and the letters become words, and the words can become complete sentences, chapters, books, or even whole libraries. The four nucleotides of a DNA molecule convey information in a similar fashion. A set of three nucleotides encodes a specific amino acid. In turn, a string of amino acids makes up a protein, the function of which is dictated by the order of the amino acid subunits. Some proteins serve as structural components of a cell. Others, such as enzymes, mediate cellular activities including biosynthesis and energy conversion. Together, proteins synthesized by a cell are responsible for every aspect of that cell. Thus, the sequential order of nucleotide bases in a cell’s DNA ultimately dictates the characteristics of that cell. ■ amino acids, p. 26 ■ protein structure, p. 28 ■ enzymes, pp. 129, 134

This chapter will focus on the processes used to replicate DNA and convert the information encoded within it into proteins, concentrating primarily on the mechanisms used by bacterial cells. The eukaryotic processes have many similarities, but are considerably 161

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162

CHAPTER SEVEN The Blueprint of Life, from DNA to Protein

KEY TERMS Codon A series of three nucleotides that code for a specific amino acid. DNA Polymerase Enzyme that synthesizes DNA, using an existing strand as a template to synthesize the complementary strand. DNA Replication Duplication of a DNA molecule. Gene The functional unit of the genome; it encodes a product, most often a protein. Genome Complete set of genetic information in a cell or a virus.

Messenger RNA (mRNA) Type of RNA molecule that is translated during protein synthesis.

RNA Polymerase Enzyme that synthesizes RNA using one strand of DNA as a template.

Primer Fragment of nucleic acid to which DNA polymerase can add nucleotides.

Transcription The process that copies the information encoded by DNA into RNA.

Promoter Nucleotide sequence to which RNA polymerase binds to initiate transcription. Ribosomal RNA (rRNA) Type of RNA molecule present in ribosomes. Ribosome Structure that facilitates the joining of amino acids during the process of translation; it is composed of ribosomal RNA (rRNA) and protein.

Transfer RNA (tRNA) Type of RNA molecule that acts as a key, interpreting the genetic code; each tRNA molecule carries a specific amino acid. Translation The process that interprets the information carried by mRNA to synthesize the encoded protein.

more complicated and will only be discussed briefly. The processes in archaea are often similar to those of bacteria, but sometimes resemble those of eukaryotic cells.

7.1 Overview

Replication

DNA

DNA

Duplicate of original molecule

Transcription

Focus Points Compare and contrast the characteristics of DNA and RNA.

RNA

Explain why it is important that a cell be able to regulate the expression of certain genes.

The complete set of genetic information for a cell is referred to as its genome. Technically, this includes plasmids as well as the chromosome; however, the term “genome” is often used interchangeably with chromosome. The genome of all cells is composed of DNA, but some viruses have an RNA genome. The functional unit of the genome is a gene. A gene encodes a product, the gene product, most commonly a protein. The study of the function and transfer of genes is called genetics, whereas the study and analysis of the nucleotide sequence of DNA is called genomics. ■ chromosome, p. 67 ■ plasmid, p. 68 All living cells must accomplish two general tasks in order to multiply. The double-stranded DNA must be duplicated before cell division so that its encoded information can be passed on to the next generation. This is the process of DNA replication. In addition, the information encoded by the DNA must be deciphered, or expressed, so that the cell can synthesize the necessary gene products at the appropriate time. Gene expression involves two interrelated processes—transcription and translation. Transcription copies the information encoded in DNA into a slightly different molecule, RNA. The RNA serves as a transitional, temporary form of the genetic information and is the one actually deciphered. Translation interprets information carried by RNA to synthesize the encoded protein. The flow of information from DNA to RNA to protein is often referred to as the central dogma of molecular biology (figure 7.1). It was once believed that information flow proceeded only in this direction. Although this direction is by far the most

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Translation

Protein

FIGURE 7.1 Overview of Replication, Transcription, and Translation DNA replication is the process that duplicates DNA so that its encoded information can be passed on to future generations. Transcription is the process that copies the genetic information into a transitional form, RNA. Translation is the process that deciphers the encoded information to synthesize a specific protein.

common, certain viruses, retroviruses, have an RNA genome but copy that information into the form of DNA. HIV is a retrovirus.

Characteristics of DNA A single strand of DNA is composed of a series of deoxyribonucleotide subunits, more commonly called nucleotides. These are joined in a chain by a covalent bond between the 5„PO4 (5 prime phosphate) of one nucleotide and the 3„OH (3 prime hydroxyl) of the next. Note that the designations 5„ and 3„ refer to the numbered carbon atoms of the pentose sugar of the nucleotide (see figure 2.22). Joining of the nucleotides in this manner creates a series of alternating sugar and phosphate units, called the sugar-phosphate backbone. Connected to each sugar is one of the nitrogenous bases—an adenine (A), thymine (T), guanine (G), or cytosine (C). Because of the chemical structure of the nucleotides and how

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7.1

A highly coiled line is used to depict genomic DNA.

Red and blue lines placed in a helical arrangement depict the two complementary strands and highlight the three-dimensional structure of DNA.

A circular arrangement of the red and blue lines is used as the simplified form of prokaryotic DNA.

Overview

163

Red and blue lines separated by a thin black line are used as a simple representation of the double-stranded DNA molecule.

Base-pairing

Two parallel lines are used to emphasize the base-pairing interactions and nucleotide sequence characteristics of the two complementary strands. The "tracks" between the lines are not intended to depict a specific number of base pairs, only the general interaction between complementary strands.

Either a red or a blue line can be depicted as the "top" strand, since DNA is a three-dimensional structure.

Denatured DNA is depicted as separate red and blue lines to emphasize its single-stranded nature.

FIGURE 7.2 Diagrammatic Representations of the Structure of DNA Although DNA is a double-stranded helical structure, explanatory diagrams may depict it in a number of different ways. In chapter 7 we will use these representations.

individual hydrogen bonds are readily broken, the duplex structure of double-stranded DNA is generally quite stable because of the sheer number of bonds that occurs along its length. Short fragments of DNA have correspondingly fewer hydrogen bonds, so they are readily separated into single-stranded pieces. Separating the two strands is called melting, or denaturing. ■ hydrogen bonds, p. 22 The two strands of double-stranded DNA are complementary (figure 7.3). Wherever an adenine is in one strand, a

they are joined, a single strand of DNA will always have a 5„PO4 at one end and a 3„OH at the other. These ends, often referred to as the 5„ end and the 3„ end, have important implications in DNA and RNA synthesis that will be discussed later. ■ deoxyribonucleic acid (DNA), p. 32, ■ nucleotides, p. 32

DNA in a cell usually occurs as a double-stranded, helical structure (figure 7.2). The two strands are held together by weak hydrogen bonds between the nitrogenous bases of the opposing strands. While

OH

P

O

Base pairs A

T

G

C

C

G

O

P

Sugar–phosphate backbone

FIGURE 7.3 The Double Helix of DNA The two strands of DNA are antiparallel; one strand is oriented in the 5„ to 3„ direction, and its complement is oriented in the 3„ to 5„ direction. Hydrogen bonding occurs between the complementary base pairs; three bonds form between a GJC base pair, and two bonds form between an AJT base pair.

Sugar

5'

3'

Sugar Sugar O

O

P

P

Sugar

Sugar O Sugar

O

P

P

Nucleotide

Sugar O

T

A

C

G

O

P

P

Sugar Sugar O

O

P

P

Sugar Hydrogen bonds

Sugar–phosphate backbone

5'

HO 3'

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CHAPTER SEVEN The Blueprint of Life, from DNA to Protein

thymine is in the other; these opposing bases are held together by two hydrogen bonds between them. Similarly, wherever a cytosine is in one strand, a guanine is in the other. These are held together by three hydrogen bonds, a slightly stronger attraction than that of an A-T pair. The characteristic bonding of A to T and G to C is called base-pairing and is fundamental to the remarkable functionality of DNA. Because of the rules of base-pairing, one strand can always be used as a template for the synthesis of the complementary opposing strand. ■ complementary, p. 34

While the two strands of DNA in the double helix are complementary, they are also antiparallel. That is, they are oriented in opposite directions. One strand is oriented in the 5„ to 3„ direction and its complement is oriented in the 3„ to 5„ direction. This also has important implications in the function and synthesis of nucleic acids.

sequence of proteins, but because not all proteins are required by a cell in the same quantity and at all times, mechanisms that determine the extent and duration of their synthesis are needed. In other words, DNA must also code for mechanisms to regulate expression of genes. One of the key mechanisms a cell uses to control protein synthesis is to regulate the synthesis of mRNA molecules. Unless a gene is transcribed into mRNA, the encoded protein cannot be synthesized. The number of mRNA copies of the gene also influences the level of expression. If transcription of a gene ceases, the level of gene expression rapidly declines. This is because mRNA is generally short-lived, often lasting only a few minutes, due to the activity of enzymes called RNases that rapidly degrade it. Eukaryotic cells have mechanisms to modulate the stability of RNA, providing an additional level of control.

MICROCHECK 7.1

Characteristics of RNA RNA is in many ways comparable to DNA, but with some important exceptions. One difference is that RNA is made up of ribonucleotides rather than deoxynucleotides, although in both cases these are usually referred to simply as nucleotides. Another distinction is that RNA contains the nitrogenous base uracil in place of the thymine found in DNA. Like DNA, RNA consists of a sequence of nucleotides, but RNA usually exists as a singlestranded linear molecule that is much shorter than DNA. ■ ribo-

Replication is the process of duplicating double-stranded DNA. Transcription is the process of copying the information encoded in DNA into RNA. Translation is the process of interpreting the information carried by messenger RNA in order to synthesize the encoded protein. ✓ How does the 5„ end of DNA differ from the 3„ end? ✓ If the nucleotide sequence of one strand of DNA is 5„ ACGTTGCA 3„, what is the sequence of the complementary strand? ✓ Why is a short-lived RNA important in cell control mechanisms?

nucleic acid (RNA), p. 34 ■ nucleotide, p. 32

A fragment of RNA, a transcript, is synthesized using a region of one of the two strands of DNA as a template. In making the RNA transcript, the same base-pairing rules of DNA apply except that uracil, rather than thymine, base-pairs with adenine. This base-pairing is only transient, however, and the molecule quickly leaves the DNA template. Numerous different RNA transcripts can be generated from a single chromosome using specific regions as templates. Either strand may serve as the template. In a region the size of a single gene, however, only one of the two strands is generally transcribed. As a result, two complementary strands of RNA are not normally generated. There are three different functional groups of RNA molecules, each transcribed from different genes. Most genes encode proteins and are transcribed into messenger RNA (mRNA). These molecules are translated during protein synthesis. Encrypted information in mRNA is deciphered according to the genetic code, which correlates each set of three nucleotides, called a codon, to a particular amino acid. Some genes are never translated into proteins; instead the RNAs themselves are the ultimate products. These genes encode either ribosomal RNA (rRNA) or transfer RNA (tRNA), each of which plays a different but critical role in protein synthesis.

Regulating the Expression of Genes Although the basic structure of DNA and RNA is relatively simple, the information encoded is extensive and complex. The nucleotide sequence of the genes codes for the amino acid

nes95432_Ch07_161-184.indd 164

7.2 DNA Replication Focus Point Describe the process of replication, focusing on initiation of replication and the events that occur at the replication fork.

DNA is replicated in order to create a second DNA molecule, identical to the original. Each of the two cells generated during binary fission then receives one complete copy. ■ binary fission, p. 84 DNA replication is generally bidirectional. From a distinct starting point in circular DNA, replication proceeds in opposite directions, creating an ever-expanding “bubble” of two identical replicated portions of the chromosome (figure 7.4). Bidirectional replication allows an entire chromosome to be replicated in half the time it would take if replication were unidirectional. Replication of double-stranded DNA is semiconservative. Each of the two molecules generated contains one of the original strands (the template strand) and one newly synthesized strand. Thus, the two cells produced as a result of division each have one of the original strands of DNA paired with a new complementary strand. The process of DNA replication requires the coordinated action of many different enzymes and other proteins (table 7.1). The most critical of these exist together as a complex that appears

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7.2

DNA Replication

165

Origin of replication Replication

DNA

DNA

Duplicate of original molecule Original double-stranded DNA

Transcription

RNA

Replication of chromosomal DNA is bidirectional; as replication proceeds in both directions, an ever-expanding "bubble" of two identical, replicated portions is created.

Translation

Protein

Original double-stranded molecule

Original strands

Original strand

New strands Replication is semiconservative; each of the two molecules ultimately generated contains one of the original strands (the template strand) and one newly synthesized strand. Original strand

New strand

New strand

Replication forks

FIGURE 7.4 Replication of Chromosomal DNA of Prokaryotes

TABLE 7.1

Components of DNA Replication in Bacteria

Component

Comments

DNA gyrase

Enzyme that temporarily breaks the strands of DNA, relieving the tension caused by unwinding the two strands of the DNA helix.

DNA ligase

Enzyme that joins two DNA fragments by forming a covalent bond between the sugar-phosphate residues of adjacent nucleotides.

DNA polymerases

Enzymes that synthesize DNA; they use one strand of DNA as a template to generate the complementary strand. Nucleotides can only be added to the 3„ end of an existing fragment, therefore synthesis always occurs in the 5„ to 3„ direction.

Helicases

Enzymes that unwind the DNA helix ahead of the replication fork.

Okazaki fragment

Nucleic acid fragment generated during discontinuous replication of the lagging strand of DNA.

Origin of replication

Distinct region of a DNA molecule at which replication is initiated.

Primase

Enzyme that synthesizes small fragments of RNA to serve as primers for DNA synthesis.

Primer

Fragment of nucleic acid to which DNA polymerase can add nucleotides (the enzyme can only add nucleotides to an existing fragment).

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CHAPTER SEVEN The Blueprint of Life, from DNA to Protein

two progeny resulting from cell division will get one complete chromosome that has already started another round of replication.

to act as a fixed DNA-synthesizing factory, reeling in the DNA to be replicated. DNA polymerases are enzymes that synthesize DNA, using one strand as a template to generate the complementary strand. These enzymes can only add nucleotides onto a preexisting fragment of nucleic acid, either DNA or RNA. Thus, the fragment serves as a primer from which synthesis can continue. DNA is synthesized one nucleotide at a time as a subunit (dATP, dGTP, dCTP, or dTTP) is covalently joined to the nucleotide at the 3„ end of the growing strand. Hydrolysis of a phosphate bond in the incoming molecule provides energy for the reaction. DNA polymerase always adds the nucleotide to the 3„ end of the chain, elongating the strand in the 5„ to 3„ direction (figure 7.5). The base-pairing rules determine the specific nucleotides added. The replication process is very accurate, resulting in only one mistake approximately every billion nucleotides. Part of the reason for this remarkable precision is the proofreading ability of some DNA polymerases. If an incorrect nucleotide is incorporated into the growing chain, the enzyme can edit the mistake by replacing that nucleotide before moving on. It takes approximately 40 minutes for the chromosome of E. coli to be replicated. How, then, can E. coli sometimes multiply with a generation time of only 20 minutes? Under favorable growing conditions, a cell initiates replication before the preceding round of replication is completed. In this way, each of the

P

P

CH2

To begin the process of DNA replication, specific proteins must recognize and bind to a distinct region of the DNA, an origin of replication. All molecules of DNA, including chromosomes and plasmids, must have this region of approximately 250 nucleotides for replication to be initiated. The binding of the proteins causes localized melting of a specific region within the origin. Using the exposed single strands as templates, a primase synthesizes small fragments of RNA to serve as primers for DNA synthesis. The enzymes that synthesize RNA do not require a primer.

The Replication Fork The bidirectional progression of replication around a circular DNA molecule creates two advancing Y-shaped regions where active replication is occurring. Each of these is called a replication fork. The template strands continue to “unzip” at each fork due to the activity of enzymes called helicases. Synthesis of one new strand proceeds continuously in the 5„ to

A

P

CH2

O

T

O

A

G

T

C

O

O

CH2

OH

Initiation of DNA Replication

P

CH2

O

■ generation time, p. 84

P

O

CH2

OH

CH2

P

P

P P

Template strand 3'

5'

T

T

A

C

G

G

T

A

C

T

Direction

A

G

T

A

G

T

A

G

T

C

G

A

T

T

C

G

A

A

T

T

C

A

T

C

A

T

C

A G

C

T

A

A

G

C

T

T

A

of synthesis 5'

3' A

New strand DNA polymerase

FIGURE 7.5 The Process of DNA Synthesis DNA polymerase synthesizes a new strand by adding one nucleotide at a time to the 3„ end of the elongating strand. The base-pairing rules determine the specific nucleotides that are added.

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7.2

DNA Replication

167

3' 5'

Synthesis of the leading strand proceeds continuously. Helicase separates the double-stranded molecule. 5' 3' Synthesis of the lagging strand is discontinuous; synthesis is reinitiated periodically, generating a series of fragments that are later joined.

RNA primer 1. Primase synthesizes an RNA primer.

2. DNA polymerase adds nucleotides onto the 3' end of the fragment. 3. DNA polymerase replaces the RNA primer with deoxynucleotides.

3' 4. DNA ligase seals the gaps between adjacent fragments.

5'

FIGURE 7.6 The Replication Fork This simplified diagram of the replication fork highlights the key steps in the synthesis of the lagging strand.

3„ direction, as fresh single-stranded template DNA is exposed (figure 7.6). This strand is called the leading strand. Synthesis of the opposing strand, the lagging strand, is considerably more complicated because the DNA polymerase cannot add nucleotides to the 5„ end of DNA. Instead, synthesis must be reinitiated periodically as advancement of the replication fork exposes more of the template DNA. Each initiation event must be preceded by the synthesis of an RNA primer by a primase. The result is the synthesis of a series of fragments, called Okazaki fragments, each of which begins with a short stretch of RNA. As DNA polymerase adds nucleotides to the 3„ end of an Okazaki fragment, it eventually reaches the initiating point of the previous fragment. A different type of DNA polymerase then removes those RNA primer nucleotides and simultaneously replaces them with deoxynucleotides. The enzyme DNA ligase seals the gaps between fragments by catalyzing the formation of a covalent bond between the adjacent nucleotides. Several other proteins are also involved in DNA replication. Among them is DNA gyrase, an enzyme that temporarily breaks the strands of DNA, relieving the tension caused by the

nes95432_Ch07_161-184.indd 167

unwinding of the two strands of the DNA helix. This enzyme is a target of ciprofloxacin and other members of a class of antibacterial drugs called fluoroquinolones. By inhibiting the function of gyrase, the fluoroquinolones interfere with bacterial DNA replication and prevent the growth of bacteria. ■ fluoroquinolones, p. 478

MICROCHECK 7.2 DNA polymerases synthesize DNA in the 5„ to 3„ direction, using one strand as a template to generate the complementary strand. Replication of DNA begins at a specific sequence called the origin of replication, and then proceeds bidirectionally, creating two replication forks. ✓ Why is a primer required for DNA synthesis? ✓ How does synthesis of the lagging strand differ from that of the leading strand? ✓ If DNA replication were shown to be “conservative,” what would this mean?

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CHAPTER SEVEN The Blueprint of Life, from DNA to Protein

7.3 Gene Expression in Bacteria

TABLE 7.2

Components of Transcription in Bacteria

Component

Comments

(–) strand

Strand of DNA that serves as the template for RNA synthesis; the resulting RNA molecule is complementary to this strand.

Describe the process of translation, focusing on the role of mRNA, ribosomes, ribosome-binding sites, rRNAs, tRNAs, and codons.

(+) strand

Strand of DNA complementary to the one that serves as the template for RNA synthesis; the sequence of the resulting RNA molecule is analogous to this strand.

Gene expression involves two separate but interrelated processes, transcription and translation. Transcription is the process of synthesizing RNA from a DNA template. During translation, information encoded on an mRNA transcript is deciphered to synthesize a protein.

Promoter

Nucleotide sequence to which RNA polymerase binds to initiate transcription.

RNA polymerase

Enzyme that synthesizes RNA using singlestranded DNA as a template; synthesis always occurs in the 5„ to 3„ direction.

Sigma (s) factor

Component of RNA polymerase that recognizes the promoter regions. A cell may have different types of s factors that recognize different promoters. These may be expressed at different stages of cell growth, enabling the cell to transcribe specialized sets of genes as needed.

Terminator

Sequence at which RNA synthesis stops; the RNA polymerase falls off the DNA template and releases the newly synthesized RNA.

Focus Points Describe the process of transcription, focusing on the role of RNA polymerase, sigma (s) factor, promoters, and terminators.

Transcription The enzyme RNA polymerase catalyzes the process of transcription, producing a single-stranded RNA molecule complementary and antiparallel to the DNA template (figure 7.7). To describe the two strands of DNA in a region that is transcribed into RNA, the terms minus (–) strand and plus (+) strand are sometimes used (table 7.2). The strand that serves as the template for RNA synthesis is called the minus (–) strand, whereas its complement is called the plus (+) strand. Recall that the base-pairing rules of DNA and RNA are the same, except that RNA contains uracil in place of thymine. Therefore, because the RNA is complementary to the (–) strand, its nucleotide sequence is the same as the (+) strand, except it has uracil rather than thymine. Likewise, the RNA transcript has the same 5„ to 3„ direction, or polarity, as the (+) strand. In prokaryotes, an mRNA molecule can carry the information for one or multiple genes. A transcript that carries one gene is called monocistronic (a cistron is synonymous with a gene). Those that carry multiple genes are called polycistronic. Generally, the proteins encoded on a polycistronic message are all involved in a single biochemical pathway. This enables the cell to express related genes in a coordinated manner. Transcription begins when RNA polymerase recognizes a nucleotide sequence on DNA called a promoter. The promoter

identifies the region of the DNA molecule that will be transcribed into RNA. In addition, the promoter orients the RNA polymerase in one of the two possible directions. This dictates which of the two DNA strands is used as a template (figure 7.8). Like DNA polymerase, RNA polymerase can only add nucleotides to the 3„ end of a chain, and therefore synthesizes nucleic acid in the 5„ to 3„ direction. Unlike DNA polymerase, however, RNA polymerase can initiate synthesis without a primer. The RNA molecule can be used as a reference point to describe direction on the analogous DNA. Upstream implies the direction toward the 5„ end of the (+) strand of DNA, whereas downstream implies the direction toward the 3„ end. Thus, a promoter is upstream of a gene.

5' Replication

DNA

DNA

Duplicate of original molecule

A

T G C T G A

T T

A

T C C G C G T

A G G T G C T

T

A C G A C T

A A

T

A G G C G C A

T C C A

3' Plus (+) strand A G of DNA

C G A T C

3'

5' Minus (–) strand of DNA

5'

3' RNA

Transcription

RNA Translation

Protein

nes95432_Ch07_161-184.indd 168

A U G C U G

A U U A

U C C G C G U A G G U G C U A G

FIGURE 7.7 RNA Is Transcribed from a DNA Template The DNA strand that serves as a template for RNA synthesis is called the (:) strand of DNA. The nucleotide sequence of the transcript is analogous to that of the (;) strand, with uracil (U) occurring in place of thymine (T) in the RNA.

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7.3 Gene Expression in Bacteria

169

Replication

DNA

Duplicate of original molecule

DNA

A sequence of nucleotides, called a promoter, identifies the region of DNA that will be transcribed into RNA.

Transcription

5'

3'

3'

5'

RNA

DNA Translation

Promoter 1

Promoter 2

The promoter orients RNA polymerase, determining the direction of transcription.

Protein

RNA polymerase

Template strand 5'

3'

3'

5'

DNA

The direction of transcription dictates which strand of DNA is used as the template. RNA 3'

5'

5'

Template strand

3' RNA

FIGURE 7.8 Promoters Direct Transcription A promoter not only identifies the region of DNA that will be transcribed into RNA, its orientation determines which strand will be used as the template. Note that the color depiction of each RNA molecule indicates which strand of DNA was used as a template. The light blue RNA was transcribed from the red DNA strand (and is therefore analogous in sequence to the blue DNA strand), whereas the pink RNA was transcribed from the blue DNA strand (and is therefore analogous in sequence to the red DNA strand).

Initiation of RNA Synthesis

Elongation

Transcription begins after RNA polymerase recognizes and binds to a promoter on the double-stranded DNA molecule. The binding melts a short stretch of DNA, creating a region of exposed nucleotides that serves as a template for RNA synthesis. In bacteria, a particular subunit of RNA polymerase recognizes the promoter region prior to the initiation of transcription. This subunit, sigma (s) factor, can dissociate from the enzyme shortly after transcription is initiated. This leaves the remaining portion of RNA polymerase, called the core enzyme, to complete transcription. A cell can have different types of s factors that recognize different promoters. These may be expressed at different stages of cell growth, enabling the cell to transcribe specialized sets of genes as needed. The RNA polymerases of eukaryotic cells and archaea use transcription factors to recognize promoters.

In the elongation phase, the RNA polymerase moves along the template strand of DNA, synthesizing the complementary single-stranded RNA molecule. The RNA molecule is synthesized in the 5„ to 3„ direction as the enzyme adds nucleotides to the 3„ end of the growing chain. The core RNA polymerase advances along the DNA, melting a new stretch and allowing the previous stretch to close (figure 7.9). This exposes a new region of the template, permitting the elongation process to continue. Once elongation has proceeded far enough for RNA polymerase to clear the promoter, another molecule of RNA polymerase can bind, initiating a new round of transcription. Thus, a single gene can be transcribed multiple times in a very short time interval.

FRANK & ERNEST: © Thaves/Dist. By Newspaper Enterprise Association, Inc.

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CHAPTER SEVEN The Blueprint of Life, from DNA to Protein

5'

3'

3'

5' Promoter Transcription terminator

RNA polymerase binds to the promoter and melts a short stretch of DNA. RNA polymerase 5'

3'

INITIATION 3'

5' Sigma

Template strand

Sigma factor then dissociates from RNA polymerase, leaving the core enzyme to complete transcription. The RNA transcript is synthesized in the 5' to 3' direction as the enzyme adds nucleotides to the 3'OH of the growing chain.

5' ELONGATION

3'

3'

5' Promoter 5'

mRNA When RNA polymerase encounters a terminator, it falls off the template and releases the newly synthesized RNA.

GA C U G C T GA C

5'

3'

TERMINATION 3'

5' Promoter 5' Hairpin loop RNA polymerase dissociates from template.

FIGURE 7.9 The Process of RNA Synthesis Bacterial RNA polymerases include a sigma subunit (as illustrated); the RNA polymerases of eukaryotic cells and archaea use transcription factors to recognize promoters.

Termination Just as an initiation of transcription occurs at a distinct site on the DNA, so does termination. When RNA polymerase encounters a terminator, it falls off the DNA template and releases the newly synthesized RNA. The terminator is a sequence of nucleotides in the DNA that, when transcribed, permits two complementary regions of the resulting RNA to base-pair, forming a hairpin loop structure. For reasons that are not yet understood, this causes the RNA polymerase to stall, resulting in its dissociation from the DNA template and release of the RNA.

Translation Translation is the process of decoding the information carried on the mRNA to synthesize the specified protein. The process requires three major components—mRNA, ribosomes, and tRNAs—in addition to various accessory proteins (table 7.3).

The Role of mRNA The mRNA is a temporary copy of genetic information; it carries encoded instructions for synthesis of a specific polypeptide,

nes95432_Ch07_161-184.indd 170

or in the case of a polycistronic message, a specific group of polypeptides. That information is deciphered using the genetic code, which correlates each series of three nucleotides, a codon, with one amino acid (figure 7.10). The genetic code is practically universal, meaning that it is used in nearly its entirety by all living things. Because a codon is a sequence of any combination of the four nucleotides, there are 64 different codons (43). Three are stop codons, which will be discussed later. The remaining 61 translate to the 20 different amino acids. This means that more than one codon can code for a specific amino acid. For example, both ACA and ACG encode the amino acid threonine. Because of this redundancy, the genetic code is said to be degenerate. Note, however, that different amino acids are never coded for by the same codon. An equally important aspect of mRNA is that it carries the information that indicates where the coding region actually begins. This is critical because the genetic code is read as groups of three nucleotides. Thus, any given sequence has three possible reading frames, or ways in which triplets can be grouped (figure 7.11). If translation occurs in the wrong reading frame, a

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7.3 Gene Expression in Bacteria

TABLE 7.3

171

Components of Translation in Bacteria

Component

Comments

Anticodon

Sequence of three nucleotides in a tRNA molecule that is complementary to a particular codon in mRNA. The anticodon allows the tRNA to recognize and bind to the appropriate codon.

mRNA

Type of RNA molecule that contains the genetic information deciphered during translation.

Polyribosome (polysome)

Multiple ribosomes attached to a single mRNA molecule.

Reading frame

Grouping of a stretch of nucleotides into sequential triplets; an mRNA molecule has three reading frames, but only one is typically used in translation.

Ribosome

Structure that facilitates the joining of amino acids during the process of translation; composed of protein and ribosomal RNA. The prokaryotic ribosome (70S) consists of a 30S and 50S subunit.

Ribosome-binding site

Sequence of nucleotides in mRNA to which a ribosome binds; the first time the codon for methionine (AUG) appears after that site, translation generally begins.

rRNA

Type of RNA molecule present in ribosomes.

Start codon

Codon at which translation is initiated; it is typically the first AUG after a ribosome-binding site.

Stop codon

Codon that terminates translation, signaling the end of the protein; there are three stop codons.

tRNA

Type of RNA molecule that act as keys that interpret the genetic code; each tRNA molecule carries a specific amino acid.

very different, and generally non-functional, polypeptide would be synthesized.

sequences on the mRNA molecule, such as the point at which protein synthesis should be initiated. The ribosome moves along the mRNA in the 5„ to 3„ direction, “presenting” each codon in a sequential order for deciphering, while maintaining the correct reading frame. A prokaryotic ribosome is composed of a 30S subunit and a 50S subunit, each made up of protein and rRNA (figure 7.12); the “S” stands for Svedberg unit, which is a measure of size. Some of the ribosomal components are important in other

The Role of Ribosomes Ribosomes serve as the sites of translation; their structure facilitates the joining of one amino acid to another. A ribosome brings each amino acid into a favorable position so that an enzyme can catalyze the formation of a peptide bond between them. It also helps to identify key punctuation

Middle Letter

First Letter

Reading frame

Reading frame

Reading frame 5' 3'

5' 3'

5' 3'

A

C

U

G Reading frame 5' 3'

Last Letter

UUU UUC

Phenylalanine Phenylalanine

UCU UCC

Serine Serine

UAU UAC

Tyrosine Tyrosine

UGU UGC

Cysteine Cysteine

U C

UUA UUG

Leucine Leucine

UCA UCG

Serine Serine

UAA UAG

(Stop) (Stop)

UGA UGG

(Stop) Tryptophan

A G

CUU CUC

Leucine Leucine

CCU CCC

Proline Proline

CAU CAC

Histidine Histidine

CGU CGC

Arginine Arginine

U C

CUA CUG

Leucine Leucine

CCA CCG

Proline Proline

CAA CAG

Glutamine Glutamine

CGA CGG

Arginine Arginine

A G

AUU AUC

Isoleucine Isoleucine

ACU ACC

Threonine Threonine

AAU AAC

Asparagine Asparagine

AGU AGC

Serine Serine

U C

AUA AUG

Isoleucine Methionine

ACA ACG

Threonine Threonine

AAA AAG

Lysine Lysine

AGA AGG

Arginine Arginine

A G

U

C

A

(Start)

GUU GUC

Valine Valine

GCU GCC

Alanine Alanine

GAU GAC

Aspartate Aspartate

GGU GGC

Glycine Glycine

U C

GUA GUG

Valine Valine

GCA GCG

Alanine Alanine

GAA GAG

Glutamate Glutamate

GGA GGG

Glycine Glycine

A G

G

nes95432_Ch07_161-184.indd 171

FIGURE 7.10 The Genetic Code The genetic code correlates each series of three nucleotides, a codon, with one amino acid. Three of the codons do not code for an amino acid and instead serve as a stop codon, terminating translation. AUG functions as a start codon.

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CHAPTER SEVEN The Blueprint of Life, from DNA to Protein

mRNA sequence

A

U

G

G

C

A

U

U

G

C

C

U

U

A

U

Reading frame #1

A

U

G

G

C

A

U

U

G

C

C

U

U

A

U

Methionine

Reading frame #2

A

U

G

Alanine

G

C

Tryptophan

A

Reading frame #3

U

G

G

A

Leucine

U

Histidine

C

Glycine

A

U

U

Proline

G

C

C

Cysteine

U

G

Isoleucine

C

U

Tyrosine

Initiation of Translation

U

In prokaryotes, translation begins as the mRNA is still being synthesized (figure 7.14). The 30S subunit of the ribosome binds to a sequence in mRNA called the ribosome-binding site. The first time the codon for methionine (AUG) appears after that site, translation generally starts. Note that AUG functions as a start

A

U

A

U

Leucine

C

Alanine

U

is made possible because each tRNA has an anticodon—three nucleotides complementary to a particular codon in the mRNA. The amino acid each tRNA carries is dictated by its anticodon and the genetic code (figure 7.13).

U

Amino acid Aspartate

Leucine

Covalent bond

FIGURE 7.11 Reading Frames A nucleotide sequence has three potential reading frames. Because each reading frame encodes a very different order of amino acids, translation of the correct reading frame is important. tRNA

aspects of microbiology as well. For example, comparison of the nucleotide sequences of rRNA molecules is playing an increasingly prominent role in the establishment of the genetic relatedness of various organisms. Medically, ribosomal proteins and rRNA are significant because they are the targets of several groups of antimicrobial drugs. ■ ribosomal subunits, p. 68

Hydrogen bonds

■ sequencing ribosomal RNA genes, p. 242

C

The Role of Transfer RNA The tRNAs are segments of RNA able to carry specific amino acids, and act as keys that interpret the genetic code. Each recognizes and base-pairs with a specific codon and in the process delivers the appropriate amino acid to that site. This recognition 30S

UG

Anticodon

G AC

3' mRNA

5' Codon (a)

Amino acid

50S

Anticodon (b)

70S

FIGURE 7.12 The Structure of the 70S Ribosome The 70S ribosome is composed of a 30S subunit and a 50S subunit.

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FIGURE 7.13 The Structure of Transfer RNA (tRNA) (a) Two dimensional illustration of tRNA. The anticodon of the tRNA base-pairs with a specific codon in the mRNA; by doing so, the appropriate amino acid is delivered to the site. The amino acid that the tRNA carries is dictated by the genetic code. The tRNA that recognizes the codon GAC carries the amino acid aspartate. (b) Three-dimensional illustration of tRNA.

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7.3 Gene Expression in Bacteria 5' Replication

DNA

DNA

173 3'

3'

5' mRNA strand Ribosome

Duplicate of original molecule

Transcription

Start codon

DNA

AUG

5'

Polypeptide

RNA Translation

Protein

FIGURE 7.14 In Prokaryotes, Translation Begins as the mRNA Molecule Is Still Being Synthesized Ribosomes begin translating the 5„ end of the transcript even as the 3„ end is still being synthesized. More than one ribosome can be translating the same mRNA molecule.

codon only when preceded by a ribosome-binding site; at other sites, it simply encodes methionine. The position of the first AUG is critical, as it determines the reading frame used for translation of the remainder of that protein. At that first AUG, the ribosome begins to assemble. First, an initiation complex forms. This consists of the 30S ribosomal subunit, a tRNA that carries a chemically altered form of the amino acid methionine, N-formylmethionine or f-Met, and proteins called initiation factors. Shortly thereafter, the 50S subunit of the ribosome joins that complex and the initiation factors leave, forming the 70S ribosome. The elongation phase then begins.

The assembly of multiple ribosomes attached to a single mRNA molecule is called a polyribosome or a polysome.

Elongation

Polypeptides must often be modified after they are synthesized in order to attain their functional properties. For example, some must be folded into their final functional shape, a process that requires the assistance of a protein called a chaperone. Polypeptides destined for transport outside of the cytoplasmic membrane also must be modified. These have a characteristic series of hydrophobic amino acids, a signal sequence, at their amino terminal end, which “tags” them for transport through the membrane. The signal sequence is removed during transport. ■ chaperones, p. 29 ■ hydrophobic

The 70S ribosome has two sites to which tRNA-carrying amino acids can bind (figure 7.15). One is called the P-site (peptidyl site), and the other is called the A-site (aminoacyl site, commonly referred to as the acceptor site). The initiating tRNA, carrying the f-Met, binds to the P-site. A tRNA that recognizes the next codon on the mRNA then fills the unoccupied A-site. An enzyme then creates a peptide bond between the carboxyl group of the f-Met carried by the tRNA in the P-site and the amino group of the amino acid carried by the tRNA that just entered the A-site. This transfers the amino acid from the initiating tRNA to the amino acid carried by the incoming tRNA. ■ peptide bond, p. 28 The ribosome then advances, or translocates, a distance of one codon, and the tRNA that carried the f-Met is released through an adjacent site called the E-site (exit site). Translocation requires several different proteins, called elongation factors. As a result of translocation, the remaining tRNA, which now carries the two-amino-acid chain, occupies the P-site; the A-site is transiently vacant. A tRNA that recognizes the next codon then quickly fills the empty A-site, and the process repeats. Once translation has progressed far enough for the ribosome to clear the ribosome-binding site and the first AUG, another ribosome can bind, beginning another round of synthesis of the encoded polypeptide. Thus, at any one time, multiple ribosomes can be translating a single mRNA molecule. This allows the maximal expression of protein from a single mRNA template.

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Termination Elongation of the polypeptide terminates when the ribosome reaches a stop codon, a codon that does not code for an amino acid and is not recognized by a tRNA. At this point, enzymes called release factors free the polypeptide by breaking the covalent bond that joins it to the tRNA. The ribosome falls off the mRNA and dissociates into its two component subunits, 30S and 50S. These can then be reused to initiate translation at other sites.

Post-Translational Modification

amino acids, p. 26

MICROCHECK 7.3 RNA polymerase initiates RNA synthesis after it binds to a promoter on DNA. Using one strand of DNA as a template, RNA is synthesized in the 5„ to 3„ direction. Synthesis stops when RNA polymerase encounters a terminator. Translation occurs as ribosomes move along mRNA in the 5„ to 3„ direction, with the ribosomes serving as the structure that facilitates the joining of one amino acid to another. tRNAs carry specific amino acids, thus acting to decode the genetic code. ✓ How does the orientation of the promoter dictate which strand is used as a template for RNA synthesis? ✓ Explain why it is important for the translation machinery to recognize the correct reading frame. ✓ Could two mRNAs have different nucleotide sequences and yet code for the same protein?

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CHAPTER SEVEN The Blueprint of Life, from DNA to Protein f-Met

P-site

A-site

E-site

mRNA U A C A U G C C G U A C G A A G A U U A A U A C G A U

5'

3'

Initiation The initiating tRNA, carrying the amino acid f-Met, base-pairs with the start codon and occupies the P-site.

3'

A tRNA that recognizes the next codon then fills the unoccupied A-site.

3'

The amino acid carried by the tRNA in the P-site is covalently joined to the amino acid carried by the tRNA in the A-site.

Pro

f-Met

E-site

U A C G G C A U G C C G U A C G A A G A U U A A U A C G A U

5'

f-Met

Pro

E-site

U A C G G C A U G C C G U A C G A A G A U U A A U A C G A U

5'

Ty r

f-Met Pro

C U A

A

U

G

G G C A U G C C G U A C G A A G A U U A A U A C G A U

5'

Elongation Translocation results in the advancement of the ribosome a distance of one codon. The tRNA that occupied the P-site exits through the E-site and the tRNA that was in the A-site, which now carries the two-amino-acid chain, occupies the P-site. A tRNA that recognizes the next codon quickly fills the empty A-site. 3'

Ribosome moves along mRNA. f-Met

Pro

Tyr Glu Asp

C

U

U

Stop codon

C U A A U G C C G U A C G A A G A U U A A U A C G A U

5'

3'

Termination The process continues until a stop codon terminates the process. No tRNA molecules recognize a stop codon.

f-Met Pro Tyr Glu

Asp

C

U

The components dissemble, releasing the newly formed polypeptide. A

FIGURE 7.15 The Process of Translation For simplicity, this diagram shows a polypeptide only five amino acids long being synthesized. Note, however, that most polypeptides are over 100 amino acids long.

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PERSPECTIVE 7.1 RNA: The First Macromolecule? The 1989 Nobel Prize in Chemistry was awarded to two Americans. Sidney Altman of Yale University and Thomas Cech of the University of Colorado, who independently made the surprising and completely unexpected observation that RNA molecules can act as enzymes. Before their studies, it was believed that only proteins had enzymatic activity. Cech made the key observation in 1982 when he was trying to understand how introns were removed from precursor ribosomal RNA in the eukaryotic protozoan Tetrahymena. Since he was convinced that proteins were responsible for cutting out these introns, he added all of the protein in the cells’ nuclei to the RNA that still contained the introns. As expected, the introns were cut out. As a control, Cech looked at the ribosomal RNA to which no nuclear proteins had been added, fully expecting that

nothing would happen. Much to his surprise, the introns were also removed. It did not make any difference whether the protein was present—the introns were removed regardless. Thus, Cech could only conclude that the RNA acted on itself to cut out pieces of RNA. The question remained of how widespread this phenomenon was. Did RNA have catalytic properties other than that of cutting out introns from rRNA? The studies of Altman and his colleagues, carried out simultaneously to and independently of Cech’s, provided answers to these further questions. Altman’s group found that RNA could convert a tRNA molecule from a precursor form to its final functional state. Additional studies have shown that enzymatic reactions in which catalytic RNAs, termed ribozymes,

7.4 Differences Between Eukaryotic and Prokaryotic Gene Expression

Major Differences Between Prokaryotic and Eukaryotic Transcription and Translation

TABLE 7.4

Focus Point Describe four differences between prokaryotic and eukaryotic gene expression.

Eukaryotes differ significantly from prokaryotes in several aspects of transcription and translation (table 7.4). In eukaryotic cells for example, most mRNA molecules are extensively modified, or processed, in the nucleus during and after transcription. Shortly after transcription begins, the 5„ end of the transcript is modified, or capped, by the addition of a methylated guanine derivative, creating what is called a cap. The cap binds specific proteins that stabilize the transcript and enhance translation. The 3„ end of the molecule is also modified, even before transcription has been terminated. This process, called polyadenylation, involves cleaving the transcript at a specific sequence of nucleotides and then adding approximately 200 adenine derivatives to the newly exposed 3„ end. This creates what is called a poly A tail, which is thought to stabilize the transcript as well as enhance translation. Another important modification is splicing, a process that removes specific segments of the transcript (figure 7.16). Splicing is necessary because eukaryotic genes are not always contiguous; they are often interrupted by non-coding nucleotide sequences. These intervening sequences, or introns, are transcribed along with the expressed regions, or exons, generating what is called precursor mRNA. The introns must be removed from precursor mRNA to form the mature mRNA that is then translated. The mRNA in eukaryotic cells must be transported out of the nucleus before it can be translated in the cytoplasm. Thus, the same mRNA molecule cannot be transcribed and translated at the same time or even in the same cellular location. Unlike in prokaryotes, the mRNA of eukaryotes is generally monocistronic. Translation of the message generally begins at the first occurrence of AUG in the molecule. The ribosomes of eukaryotes are different from those of prokaryotes. Whereas the prokaryotic ribosome is 70S, made up of

play a role are very widespread. Ribozymes have been found in the mitochondria of eukaryotic cells and shown to catalyze other reactions that resemble the polymerization of RNA. These observations have profound implications for evolution: which came first, proteins or nucleic acids? The answer seems to be that nucleic acids came first, specifically RNA, which acted both as a carrier of genetic information as well as an enzyme. Billions of years ago, before the present universe in which DNA, RNA, and protein are found, probably the only macromolecule that existed was RNA. Once tRNA became available, these adapters could carry amino acids present in the environment to specific nucleotide sequences on a strand of RNA. In this scenario, the RNA functions as the genes as well as the mRNA.

Prokaryotes

Eukaryotes

mRNA is not processed.

A cap is added to the 5„ end of mRNA, and a poly A tail is added to the 3„ end.

mRNA does not contain introns. mRNA contains introns, which are removed by splicing. Translation of mRNA begins as it is being transcribed.

The mRNA transcript is transported out of the nucleus so that it can be translated in the cytoplasm.

mRNA is often polycistronic; translation usually begins at the first AUG that follows a ribosome-binding site.

mRNA is monocistronic; translation begins at the first AUG.

Eukaryotic DNA contains introns, which interrupt coding regions. Eukaryotic DNA

Intron

Intron

Transcription generates precursor mRNA that contains introns.

Precursor mRNA

Splicing removes introns to form mRNA. mRNA

FIGURE 7.16 Splicing of Eukaryotic RNA

175

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CHAPTER SEVEN The Blueprint of Life, from DNA to Protein

30S and 50S subunits, the eukaryotic ribosome is 80S, made up of 40S and 60S subunits. The differences in ribosome structure account for the ability of certain types of antibiotics to kill bacteria without causing significant harm to mammalian cells. Some of the proteins that play essential roles in translation differ between eukaryotic and prokaryotic cells. Diphtheria toxin, which selectively kills eukaryotic but not prokaryotic cells, illustrates this difference. This toxin is produced by Corynebacterium diphtheriae; it binds to and inactivates one of the elongation factors of eukaryotes. Since this protein is required for translocation of the ribosome, translation ceases and the eukaryotic cell dies, resulting in the typical symptoms of diphtheria. ■ diphtheria toxin, p. 503

ways must be activated, using energy and markedly slowing cell division. Cells dividing several times an hour in a nutrient-rich environment might divide only once every 24 hours in a famished mammalian gut. A cell controls its metabolic pathways by two general mechanisms. The most immediate of these is the allosteric inhibition of enzymes. The most energy-efficient strategy, however, is to control the actual synthesis of the enzymes, making only what is required. To do this, cells control expression of certain genes.

MICROCHECK 7.4

Not all genes are subjected to the same type of regulation. Many are routinely expressed, whereas others are either turned on or off by certain conditions. Enzymes are often described according to characteristics of the regulation that governs their synthesis:

Eukaryotic mRNA must be processed, which involves capping, polyadenylation, and splicing. In eukaryotic cells, the mRNA must be transported out of the nucleus before it can be translated in the cytoplasm. Eukaryotic mRNA is monocistronic. ✓ What is an intron? ✓ Explain the mechanism of action of diphtheria toxin. ✓ Would a deletion of two base pairs have a greater consequence if it occurred in an intron or in an exon?

7.5 Regulation of Bacterial Gene Expression Focus Points Give a functional example of a constitutive enzyme, an inducible enzyme, and a repressible enzyme. Using the lac operon as a model, explain the role of inducers and repressors.

To cope with changing conditions in their environment, microorganisms have evolved elaborate control mechanisms to synthesize the maximum amount of cell material from a limited supply of energy. This is critical, because generally a microorganism must reproduce more rapidly than its competitors to be successful. Consider the situation of Escherichia coli. For over 100 million years, it has successfully inhabited the gut of mammals, where it reaches concentrations of 106 cells per milliliter. In this habitat, it must cope with alternating periods of feast and famine. For a limited time after a mammal eats, E. coli in the large intestine prosper, wallowing in the milieu of amino acids, vitamins, and other nutrients. The cells actively take up these compounds they would otherwise synthesize, expending minimal energy. Simultaneously, the cells shut down their biosynthetic pathways, channeling the conserved energy into the rapid synthesis of macromolecules, including DNA, RNA, and protein. Under these conditions, the cells divide at their most rapid rate. Famine, however, follows the feast. Between meals—a period of time that might be many days in the case of some mammals—the rich source of nutrients is depleted. Now the cells’ biosynthetic path-

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■ allosteric regulation, p. 137

Principles of Regulation

Constitutive enzymes are synthesized constantly; the genes that encode these enzymes are always active. Constitutive enzymes usually play indispensable roles in the central metabolic pathways. For example, the enzymes of glycolysis are constitutive. ■ central metabolic pathways, pp. 132, 138 Inducible enzymes are not produced regularly; instead, their synthesis is turned on by certain conditions. Inducible enzymes are often involved in the utilization of specific energy sources. A cell would waste precious resources if it synthesized the enzyme when the energy source is not present. An example of an inducible enzyme is b-galactosidase, whose sole function is to break down the disaccharide lactose into its two component monosaccharides, glucose and galactose. The mechanisms by which the cell controls b-galactosidase synthesis serve as an important model for regulation and will be described shortly. Repressible enzymes are synthesized routinely, but they can be turned off by certain conditions. Repressible enzymes are generally involved in biosynthetic (anabolic) pathways, such as those that produce amino acids. Cells require a sufficient amount of a given amino acid to multiply; thus, the amino acid must be either synthesized or available as a component of the growth medium. If a certain amino acid is not present in the medium, then the cell must synthesize the enzymes involved in its manufacture. When the amino acid is supplied, however, synthesis of the enzymes would waste energy.

Mechanisms to Control Transcription The mechanisms a cell uses to prevent or facilitate transcription must be readily reversible, allowing cells to effectively control the relative number of transcripts made. In some cases, the control mechanisms affect the transcription of only a limited number of genes; in other cases, a wide array of genes is controlled coordinately. For example, in E. coli, the expression of more than 300 different genes is affected by the availability of glucose as an energy source. The simultaneous regulation of numerous genes is called global control. Two of the most common methods of regulation in bacterial cells are alternative sigma factors and DNA-binding proteins.

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7.5 Regulation of Bacterial Gene Expression

Alternative Sigma Factors Recall that sigma factor is a loose component of RNA polymerase and functions in recognizing specific promoters. E. coli, for example, has a standard sigma factor (sigma 70) that recognizes promoters for genes that need to be expressed during routine growth conditions. A cell can also produce other types of sigma factors, called alternative sigma factors. Each of these recognizes a different set of promoters, thereby controlling the expression of specific groups of genes. One alternative sigma factor (sigma S) is produced when the cell experiences a general stress such as starvation. This sigma factor directs RNA polymerase to transcribe the multitude of genes required to enter stationary phase. Another (sigma F) directs the expression of genes required for flagella synthesis. The cell can also express anti-sigma factors, which inhibit the function of specific sigma factors.

Transcription off (blocked). Repressor binds to operator, blocking transcription.

Mechanism 1 (inducible) Repressor

Gene B Transcription on. Inducer binds to the repressor and alters its shape, preventing the repressor from binding to the operator.

+ Inducer

Repressor

Operator

Gene B

Transcription

Mechanism 2 (repressible)

Transcription on. Repressor alone cannot bind to the operator.

Repressor

Operator

DNA-Binding Proteins

177

Promoter (with RNA polymerase)

Gene A

Transcription

Transcription of genes is often controlled by Transcription off (blocked). means of a regulatory region near the pro- Corepressor Corepressor binds to the repressor moter to which a specific protein can bind, and alters its shape, enabling the + repressor to bind to the operator. acting as a sophisticated on/off switch. When Repressor a regulatory protein binds DNA, it can either act as a repressor, which blocks transcription, or an activator, which facilitates transcription. Gene A A set of genes coordinately controlled by a regulatory protein and transcribed as a single FIGURE 7.17 Transcriptional Regulation by Repressors polycistronic message is called an operon. Repressors A repressor is a regulatory protein that blocks transcription. It does this by binding to a sequence of DNA Activators An activator is a regulatory protein that facilitates called an operator, located immediately downstream of a protranscription. Genes controlled by an activator have an ineffecmoter. When a repressor is bound to an operator, RNA polytive promoter preceded by an activator-binding site. The bindmerase cannot progress past that region. Regulation involving ing of the activator to the DNA enhances the ability of RNA a repressor is called negative control. Specific molecules can polymerase to initiate transcription at that promoter. Regulation bind to the repressor and thereby alter the ability of the represinvolving an activator is sometimes called positive control. sor to bind DNA. This can occur because a repressor is an alLike repressors, activators are allosteric proteins whose funclosteric protein, meaning that the binding of a specific tion can be modulated by the binding of other molecules. When a molecule causes the protein’s shape to change. The altered molecule called an inducer binds to an activator, the shape of the the shape of the repressor affects its ability to bind DNA. As activator is altered so that it can effectively bind to the activatorshown in figure 7.17, there are two general mechanisms by binding site (figure 7.18). Thus, the term “inducer” applies to a which different repressors can function: molecule that turns on transcription, either by stimulating the 1. The repressor is synthesized as a form that effectively binds function of an activator or interfering with the function of to the operator, blocking transcription. When a molecule a repressor. called an inducer binds to the repressor, however, the shape of the repressor is altered so that it no longer binds to the The lac Operon As a Model for Control operator. Consequently, the gene can then be transcribed. of Metabolic Pathways 2. The repressor is synthesized as a form that alone cannot Originally elucidated in the early 1960s by Francois Jacob and bind to the operator. When a molecule termed a corepresJacques Monod, the lac operon has served as an important model sor binds to the repressor, however, the shape of the for understanding the control of gene expression in bacteria. repressor is altered so that it can bind to the operator, The operon, which consists of three genes involved with lactose blocking transcription.

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CHAPTER SEVEN The Blueprint of Life, from DNA to Protein

Activator

Transcription off (not activated). Activator cannot bind to the activator-binding site, thus RNA polymerase cannot bind to the promoter and initiate transcription.

RNA polymerase

The Effect of Lactose on the Control of the Lactose Operon

Gene C Activatorbinding site Promoter

Transcription on (activated). Inducer binds to the activator and changes its shape, enabling the activator to bind to the site. RNA polymerase can then bind to the promoter and initiate transcription.

Activator Inducer

+

degradation, along with regulatory components, is subject to dual control by both a repressor and an activator (figure 7.19). The net effect is that the genes are expressed only when lactose is present but glucose is absent.

Gene C

Transcription

The lac operon employs a repressor that prevents transcription of the genes when lactose is unavailable. When lactose is not present, the repressor binds to the operator, effectively blocking transcription. When lactose is present in the cell, however, some of the molecules are converted into a compound called allolactose. This compound binds to the repressor, altering its shape so that it no longer binds to the operator. Thus, when lactose is present, the repressor no longer prevents RNA polymerase from transcribing the operon. Note, however, that the activator described in the next section is needed for successful transcription.

FIGURE 7.18 Transcriptional Regulation by Activators

Gene 1

Activator(CAP) binding site

Promoter

Gene 2

Operator

Gene 3

lac operon. The lactose operon contains three genes. Transcription is controlled by regulatory proteins that bind to an activator-binding site and an operator.

RNA polymerase

CAP

Transcription not activated AND blocked. Low cAMP; CAP cannot bind. In addition, repressor is bound to the operator, blocking polymerase.

Glucose present No lactose Repressor

Transcription not activated. Low cAMP; CAP cannot bind. At the same time, inducer (allolactose) prevents repressor from binding to the operator.

Glucose present Lactose present

Inducer (allolactose) Transcription activated but blocked. High cAMP; CAP/cAMP complex binds to activatorbinding site. Repressor is bound to operator, however, blocking polymerase.

No glucose No lactose cAMP

Transcription

No glucose Lactose present

Transcription activated. High cAMP; CAP/cAMP complex binds to activatorbinding site. In addition, inducer (allolactose) prevents repressor from binding to the operator.

FIGURE 7.19 Regulation of the lac Operon

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7.6 Regulation of Eukaryotic Gene Expression

179

MICROCHECK 7.5

Log number of viable cells

Lactose exhausted

Glucose exhausted

Glucose and lactose added

Growth on lactose

Growth on glucose

Time of incubation (hr)

FIGURE 7.20 Diauxic Growth Curve of E. coli Growing in a Medium Containing Glucose and Lactose Cells preferentially use glucose. Only when the supply of glucose is exhausted do cells start metabolizing lactose. Note that the growth on lactose is slower than it is on glucose.

The Effect of Glucose on the Control of the Lactose Operon Escherichia coli preferentially uses glucose over other sugars such as lactose. This can be demonstrated by observing growth and sugar utilization of E. coli in a medium containing glucose and lactose. Cells grow, metabolizing only glucose until its supply is exhausted (figure 7.20). Growth then ceases for a short period until the cells begin utilizing lactose. At this point, the cells start multiplying again. This two-step growth response, called diauxic growth, represents the ability of glucose to repress the enzymes of lactose degradation—a phenomenon called catabolite repression. The regulatory mechanism of catabolite repression does not directly sense glucose in a cell. Instead, it recognizes the concentration of a nucleotide derivative, cyclic AMP (cAMP), which is low when glucose is being transported into the cell and high when it is not. cAMP is an inducer of the operon; it binds to an activator that facilitates transcription of the lac operon. This activator, called CAP (catabolite activator protein), is only able to bind to the lac promoter when cAMP is bound to it. The higher the concentration of cAMP, the more likely it is to bind to CAP. Thus, when glucose concentrations in the medium are low (and therefore cAMP levels are high), the lac operon can be transcribed. Note, however, that even in the presence of a functional activator, the repressor prevents transcription unless lactose is present. Catabolite repression is significant biologically because it forces cells to first use the carbon source that is most easily metabolized. Only when the supply of glucose is exhausted do cells begin degrading lactose, a carbon source that requires additional enzymatic steps to metabolize.

nes95432_Ch07_161-184.indd 179

Enzymes can be constitutive, inducible, or repressible. A repressor blocks transcription when it binds to an operator. An activator enhances transcription when it binds to an activator-binding site. The functioning of specific activators and repressors may require or be blocked by other molecules. ✓ Explain the difference between a constitutive enzyme and an inducible enzyme. ✓ Explain how glucose represses the lactose operon. ✓ Why would it be advantageous for a cell to control the activity of an enzyme as well as its synthesis?

7.6 Regulation of Eukaryotic Gene Expression Focus Point Describe how RNA interference silences genes.

Considering the complexity of eukaryotic cells and the diversity of cell types found in multicellular organisms, it is not surprising that gene regulation in eukaryotic cells is much more complicated than that in prokaryotic cells. Eukaryotic cells use a variety of control methods, including modifying the structure of the chromosome, regulating the initiation of transcription, and altering transcript processing and modification. We will focus only on a recently discovered mechanism called RNA interference (RNAi) that now makes it possible for scientists to silence select genes. Andrew Fire and Craig Mello received a Noble Prize in 2006 for their discovery of this process. RNA interference (RNAi) uses short pieces of single-stranded RNA to direct the degradation of specific RNA transcripts. After a short RNA molecule (approximately 20 to 26 nucleotides in length) is produced by the cell, it is loaded into a multi-protein complex called an RNA-induced silencing complex (RISC). The single-stranded RNA molecule within the complex binds to complementary sequences on mRNA, effectively tagging that transcript for destruction by enzymes that make up the RISC (figure 7.21). Because the components of the RISC are not destroyed in the process, the complex is catalytic, providing a rapid and effective means of silencing genes that have already been transcribed. Two different types of RNA molecules are used in RNAi—microRNA

RNA-induced silencing complex (RISC) Binding of short-stranded RNA in the RNA-induced silencing complex (RISC) to mRNA tags the mRNA for destruction. Enzymes cut mRNA; RISC can then bind to another mRNA molecule.

FIGURE 7.21 RNA Interference (RNAi)

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CHAPTER SEVEN The Blueprint of Life, from DNA to Protein

(miRNA) and short interfering RNA (siRNA). These are functionally equivalent, but differ in how they are produced. The discovery of RNAi has revolutionized current views on gene regulation. In addition, it provides a new mechanism to alter gene expression. By using RNAi to turn off selected genes in vitro, scientists are able to more precisely identify the function of those genes. An ultimate hope is that RNA interference could be used as a form of gene therapy to silence abnormal genes.

Environmental stimulus

Outside cell

Sensor protein

Cytoplasmic membrane Inside cell

MICROCHECK 7.6 RNA interference uses short, single strands of RNA to direct the destruction of specific RNA transcripts. ✓ What is the role of miRNA and siRNA in regulation of gene expression?

Response regulator

The sensor protein spans the cytoplasmic membrane. The response regulator is a protein inside the cell.

7.7 Sensing and Responding to Environmental Fluctuations

Outside

Cytoplasmic membrane

Focus Points Describe how two-component regulatory systems and quorum sensing allow cells to adapt to fluctuating environmental conditions.

Inside P P

Compare and contrast antigenic variation and phase variation.

Microorganisms adapt to fluctuating conditions by altering the level of expression of certain genes. For example, certain pathogenic bacteria have mechanisms to sense when they are within the tissues of an animal; in response they can activate certain genes that facilitate their survival against the impending onslaught of host defenses.

Signal Transduction Signal transduction is a process that transmits information from outside a cell to the inside, allowing that cell to respond to changing environmental conditions. For example, cells turn on or off certain genes in response to variations in such factors as osmotic pressure, cell concentration, and nitrogen availability.

Two-Component Regulatory Systems An important mechanism that cells use to relay information about the external environment is a two-component regulatory system (figure 7.22). This relies on the coordinated activities of two different proteins, a sensor and a response regulator. The sensor spans the cytoplasmic membrane so that the part recognizing changes in the environment is positioned outside the cell. In response to specific external variations, the sensor chemically modifies a region on its internal portion, usually by phosphorylating a specific amino acid. The phosphoryl group is then transferred to a response regulator. The modified response regulator can act as either an activator or a repressor, turning on or off genes, depending on the system.

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In response to a specific change in the environment, the sensor phosphorylates a region on its internal portion. The phosphoryl group is transferred to the response regulator, which can then act as an activator or a repressor, depending on the system.

FIGURE 7.22 Two-Component Regulatory System

Bacteria use different two-component regulatory systems to detect and respond to a wide variety of environmental cues. E. coli, for example, uses such systems to control the expression of genes for its alternative types of metabolism. When nitrate is present in anaerobic conditions, cells activate genes required to use nitrate as a terminal electron acceptor. Some pathogens use two-component regulatory systems to sense environmental magnesium concentrations, and then activate specific genes in response. Because the magnesium concentration within certain tissue cells is generally lower than that of extracellular sites, these pathogens are able to recognize whether or not they are within a cell. In turn, they can activate appropriate genes that help them evade the host defenses intended to protect that relative site.

Quorum Sensing Some organisms can “sense” the density of cells within their own population—a phenomenon called quorum sensing. This enables them to activate genes that are only beneficial when expressed by a critical mass of cells. The cooperative activities leading to biofilm formation are controlled by quorum sensing. ■ biofilms, p. 85

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7.8

Bacterial cell

When many cells are present, the concentration of the AHL is high. High concentrations of AHL induce expression of specific genes.

FIGURE 7.23 Quorum Sensing

In the most thoroughly studied quorum sensing systems, the bacteria synthesize one or more varieties of an acylated homoserine lactone (AHL) (or HSL for homoserine lactone). When few cells are present, the concentration of a given AHL is very low. As the cells multiply in a confined area, however, the concentration of that AHL increases proportionally. Only when it reaches a critical level does it induce the expression of specific genes (figure 7.23).

Natural Selection Natural selection can also play a role in gene expression. The expression of some genes changes randomly, presumably enhancing the chances of survival of at least a part of a population under certain environmental conditions. The role of natural selection is readily apparent in bacteria that undergo antigenic variation, an alteration in the characteristics of certain surface proteins such as flagella, pili, and outer membrane proteins. Pathogens able to change these proteins can stay one step ahead of the body’s defenses by altering the very molecules our immune systems must learn to recognize. One of the most well characterized examples is Neisseria gonorrhoeae, a bacterium that successfully disguises itself from the immune system by changing several of its surface proteins. N. gonorrhoeae has many different genes for pilin, the protein subunit that makes up pili, yet most are silent. The only one that is expressed resides in a particular chromosomal location called an expression locus. N. gonorrhoeae cells have a mechanism to shuffle the pilin genes, randomly moving different ones in and out of the expression locus. In a population of 104 cells, at least one is expressing a different type of pilin. It appears that expression of different pilin genes is not regulated in any controlled manner but occurs randomly. Only some of the changes, however, are advantageous to a cell’s survival. When the body’s immune system eventually begins to respond to a specific pilin type, those cells that have already “switched” to produce a different type will survive and then multiply. Eventually, the immune system learns to recognize those, but by that time, another subpopulation will have “switched” its pilin type. ■ pili, p. 66 ■ Neisseria gonorrhoeae, p. 630

Another mechanism of randomly altering gene expression is phase variation, the routine switching on and off of certain genes.

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181

Presumably, phase variation helps an organism adapt to selective pressures. By altering the expression of certain critical genes, at least a part of the population is poised for change and thus able to survive and multiply. For example, phase variation of genes that encode fimbriae may allow some members of a population to attach to a surface, while permitting others to detach and colonize surfaces elsewhere. ■ fimbriae, p. 66

Signaling molecule

When few cells are present, the concentration of the signaling molecule acylated homoserine lactone (AHL) is low.

Genomics

MICROCHECK 7.7 Signal transduction allows a cell to respond to changing conditions outside of that cell. The expression of some genes changes randomly, presumably enhancing the chances of survival of at least a subset of a population of cells under varying environmental conditions. ✓ Explain the mechanism by which certain bacteria can “sense” the density of cells. ✓ Why would it be advantageous for a bacterium to synthesize more than one type of homoserine lactone?

7.8 Genomics Focus Point Explain how protein-encoding regions are found when analyzing a DNA sequence.

Increasingly rapid methods of determining the nucleotide sequence of DNA have led to exciting advancements in genomics. In 1995, the sequence of the chromosome of Haemophilus influenzae was published, marking the first complete genomic sequence ever determined. Since then, microbial genome sequencing has become almost commonplace. A table describing some of the representative prokaryotes that have been sequenced is available at the Online Learning Center (www.mhhe.com/nester6). Although sequencing methodologies are becoming more rapid, analyzing the resulting data and extracting the pertinent information is far more complex than it might initially seem. One of the most difficult steps is to locate and characterize the potential protein-encoding regions. Imagine trying to determine the amino acid sequence of a protein encoded by a 1,000-base-pair (bp) stretch of DNA, without knowing anything about the orientation of the promoter or the reading frame of the transcribed mRNA. Since either strand of the double-stranded DNA molecule could be the template strand, two entirely different mRNA molecules could potentially code for the protein. In turn, each of those two molecules has three reading frames, for a total of six reading frames. Yet only one of these actually codes for the protein. Understandably, computers are an invaluable aid and are used extensively in deciphering the meaning of the raw sequence data. In turn, this has resulted in the emergence of a new field, bioinformatics, which creates the computer technology to store, retrieve, and analyze nucleotide sequence data.

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Analyzing a Prokaryotic DNA Sequence When analyzing a DNA sequence, the nucleotide sequence of the (+) strand is used to infer information contained in the corresponding RNA transcript. Because of this, terms like start codon, which actually refers to a sequence in mRNA, are used to describe sequences in DNA. In other words, to locate the start codon AUG, which would be found in mRNA, one would look for the analogous sequence, ATG, in the (+) strand of DNA. In most cases it is not initially known which of the two strands is actually used as a template for RNA synthesis. Only after a promoter is located can this be determined. To locate protein-encoding regions, computers are used to search for open reading frames (ORFs), stretches of DNA, generally longer than 300 bp, that begin with a start codon and end with a stop codon. An ORF potentially encodes a protein. Other characteristics, such as the presence of an upstream sequence that can serve as a ribosome-binding site, also indicate that an ORF encodes a protein. The nucleotide sequence of the ORF or deduced amino acid sequence of the encoded protein can be compared with other known sequences by searching computerized databases

of published sequences. Not surprisingly, as genomes of more organisms are being sequenced, information contained in these databases is growing at a remarkable rate. If the encoded protein shows certain amino acid similarities, or homology, to characterized proteins, a putative function can sometimes be assigned. For example, proteins that bind DNA have similar amino acid sequences in certain regions. Likewise, regulatory regions in DNA such as promoters can sometimes be identified based on similarities to known sequences.

MICROCHECK 7.8 Sequencing methodologies are quickly becoming more rapid, but analyzing the data and extracting the pertinent information is difficult. ✓ What is an open reading frame? ✓ Describe two things that you can learn by searching a computerized database for sequences that have homologies to a newly sequenced gene. ✓ There are characteristic differences in the nucleotide sequences of the leading and lagging strands. Why might this be so?

FUTURE CHALLENGES Gems in the Genomes? From a medical standpoint, one of the most exciting challenges will be to capitalize on the rapidly accruing genomic information and use that knowledge to develop new drugs and therapies. The potential gains are tremendous, particularly in the face of increasing resistance to current antimicrobial drugs. For example, by studying the genomes of pathogenic microorganisms, scientists can learn more about specific genes that enable an organism to cause disease. By learning more

about the signals and mechanisms that turn these genes on and off, scientists may be able to one day design a drug that prevents the synthesis of critical bacterial proteins. Such a drug could interfere with that pathogen’s ability to survive within our body and thereby render it harmless. ■ resistance to antimicrobial drugs, p. 483

Learning more about the human genome provides another means of developing drug therapies. Already,

companies are searching genomic databases, a process called genome mining, to locate ORFs that may encode proteins of medical value. What they generally look for are previously uncharacterized proteins that have certain sequence similarities to proteins of proven therapeutic value. Some of their discoveries are now in clinical trials to test their efficacy. Genes encoding many other medically useful proteins are probably still hidden, waiting to be discovered.

SUMMARY 7.1

Overview (figure 7.1)

Characteristics of DNA (figure 7.3) A single strand of DNA has a 5„ end and a 3„ end; the two strands of DNA in the double helix are antiparallel. Characteristics of RNA A single-stranded RNA fragment is transcribed from one of the two strands of DNA. There are three different functional groups of RNA molecules: messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA). Regulating the Expression of Genes Protein synthesis is generally controlled by regulating the synthesis of mRNA.

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7.2

DNA Replication

DNA replication is generally bidirectional and semiconservative (figure 7.4). The DNA chain always elongates in the 5„ to 3„ direction (figure 7.5). Initiation of DNA Replication DNA replication begins at the origin of replication. DNA polymerase synthesizes DNA in the 5„ to 3„ direction, using one strand as a template to generate the complementary strand. The Replication Fork (figure 7.6) The bidirectional progression of replication around a circular DNA molecule creates two replication forks; numerous enzymes and other proteins are involved.

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Review Questions

7.3

Gene Expression in Bacteria

Transcription RNA polymerase catalyzes the process of transcription, producing a singlestranded RNA molecule that is complementary and antiparallel to the DNA template (figure 7.7). Transcription begins after RNA polymerase recognizes and binds to a promoter (figure 7.8). RNA is synthesized in the 5„ to 3„ direction (figure 7.9). When RNA polymerase encounters a terminator, it falls off the DNA template and releases the newly synthesized RNA. Translation The information encoded by mRNA is deciphered using the genetic code (figure 7.10). A nucleotide sequence has three potential reading frames (figure 7.11). Ribosomes function as the site of translation (figure 7.12). tRNAs carry specific amino acids and act as keys that interpret the genetic code (figure 7.13). In prokaryotes, initiation of translation begins when the ribosome binds to the ribosome-binding site of the mRNA molecule. Translation starts at the first AUG downstream of that site (figure 7.14). The ribosome moves along mRNA in the 5„ to 3„ direction; translation terminates when the ribosome reaches a stop codon (figure 7.15). Polypeptides are often modified after they are synthesized.

7.4

Differences Between Eukaryotic and Prokaryotic Gene Expression (table 7.4)

Eukaryotic mRNA is processed; a cap and a poly A tail are added. Eukaryotic genes often contain introns which are removed from precursor mRNA by a process called splicing (figure 7.16). In eukaryotic cells, the mRNA must be transported out of the nucleus before it can be translated in the cytoplasm.

7.5

Regulation of Bacterial Gene Expression

Principles of Regulation Constitutive enzymes are constantly synthesized. The synthesis of inducible enzymes can be turned on by certain conditions. The synthesis of repressible enzymes can be turned off by certain conditions.

183

The lac Operon As a Model for Control of Metabolic Pathways (figure 7.19) The lac operon employs a repressor that prevents transcription of the genes when lactose is not available. Catabolite repression prevents transcription of the lac operon when glucose is available.

7.6

Regulation of Eukaryotic Gene Expression

Regulation in eukaryotic cells is much more complicated than that in prokaryotic cells. RNA interference (RNAi) is a recently discovered mechanism that uses either microRNA (miRNA) or short interfering RNA (siRNA) to direct the degradation of RNA transcripts.

7.7

Sensing and Responding to Environmental Fluctuations

Signal Transduction Two-component regulatory systems utilize a sensor that recognizes changes outside the cell and then transmits that information to a response regulator. Bacteria that utilize quorum sensing synthesize a compound that activates specific genes when it reaches a critical concentration. Natural Selection The expression of some genes changes randomly, enhancing the chances of survival of at least a subset of a population under varying environmental conditions. Antigenic variation is a routine change in the expression of surface proteins. Phase variation is the routine switching on and off of certain genes.

7.8

Genomics

Analyzing a Prokaryotic DNA Sequence When analyzing a DNA sequence, the nucleotide sequence of the (+) strand is used to infer information carried by the corresponding RNA transcript; computers are used to search for open reading frames (ORFs).

Mechanisms to Control Transcription Repressors block transcription (figure 7.17). Activators enhance transcription (figure 7.18).

REVIEW QUESTIONS Short Answer 1. Explain what the term semiconservative means with respect to DNA replication. 2. How can E. coli have a generation time of only 20 minutes when it takes 40 minutes to replicate its chromosome? 3. What is the function of primase in DNA replication? Why is this enzyme necessary? 4. What is polycistronic mRNA? 5. Explain why knowing the orientation of a promoter is critical when determining the amino acid sequence of an encoded protein. 6. What is the function of a sigma factor? 7. What is the fate of a protein that has a signal sequence? 8. Compare and contrast regulation by a repressor and an activator.

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9. Explain how some bacteria sense the density of cells in their own population. 10. Explain why it is sometimes difficult to locate genomic regions that encode a protein.

Multiple Choice 1. All of the following are involved in transcription, except a) polymerase. b) primer. c) promoter. d) sigma factor. e) uracil. 2. All of the following are involved in DNA replication, except a) elongation factors. b) gyrase. c) polymerase. d) primase. e) primer.

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3. All of the following are directly involved in translation, except a) promoter. b) ribosome. c) start codon. d) stop codon. e) tRNA. 4. Using the DNA strand depicted here as a template, what will be the sequence of the RNA transcript? 5„ GCGTTAACGTAGGC 3„ D J J J promoter 3„ CGCAATTGCATCCG 5„ a) 5„ GCGUUAACGUAGGC 3„ b) 5„ CGGAUGCAAUUGCG 3„ c) 5„ CGCAAUUGCAUCCG 3„ d) 5„ GCCUACGUUAACGC 3„ 5. A ribosome binds to the following mRNA at the site indicated by the dark box. At which codon will translation likely begin? 5„ ■ GCCGGAAUGCUGCUGGC a) GCC b) GGC c) AUG d) AAU 6. Allolactose induces the lac regulon by binding to a(n) a) operator. b) repressor. c) activator. d) CAP protein. 7. Under which of the following conditions will transcription of the lac operon occur? a) Lactose present/glucose present b) Lactose present/glucose absent c) Lactose absent/glucose present d) Lactose absent/glucose absent e) A and B 8. Which of the following statements about gene expression is false? a) More than one RNA polymerase can be transcribing a specific gene at a given time. b) More than one ribosome can be translating a specific transcript at a given time. c) Translation begins at a site called a promoter. d) Transcription stops at a site called a terminator. e) Some amino acids are coded for by more than one codon. 9. Which of the following is not characteristic of eukaryotic gene expression? a) 5„ cap is added to the mRNA. b) A poly A tail is added to the 3„ end of mRNA. c) Introns must be removed to create the mRNA that is translated. d) The mRNA is often polycistronic. e) Translation begins at the first AUG. 10. Which of the following statements is false? a) A derivative of lactose serves as an inducer of the lac operon. b) Signal transduction provides a mechanism for a cell to sense the conditions of its external environment.

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c) The function of an acylated homoserine lactone is to enable a cell to sense the density of like cells. d) An example of a two-component regulatory system is the lactose operon, which is controlled by a repressor and an activator. e) An ORF is a stretch of DNA that may encode a protein.

Applications 1. A graduate student is trying to identity the gene coding for an enzyme found in a bacterial species that degrades trinitrotoluene (TNT). The student is frustrated to find that the organism does not produce the enzyme when grown in nutrient broth, making it is difficult to collect the mRNA needed to help identify the gene. What could the student do to potentially increase the amount of the desired enzyme? 2. A student wants to remove the introns from a segment of DNA coding for protein X. Devise a strategy to do this.

Critical Thinking 1. The study of protein synthesis often uses a cell-free system where cells are ground with an abrasive to release the cell contents and then filtered to remove the abrasive. These materials are added to the system, generating the indicated results: Materials Added

Results

Radioactive amino acids Radioactive protein produced Radioactive amino acids No radioactive protein produced and RNase (an RNA-digesting enzyme) What is the best interpretation of these observations? 2. In a variation of the experiment in the previous question, the following materials were added to three separate cell-free systems, generating the indicated results: Materials Added

Results

Radioactive amino acids Radioactive protein produced Radioactive amino acids Radioactive protein produced and DNase (a DNA-digesting enzyme) Several hours after grinding: Radioactive amino acids No radioactive protein produced and DNase What is the best interpretation of these observations?

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8 DNA bursts from this treated bacterial cell.

Bacterial Genetics A Glimpse of History Barbara McClintock (1902–1992) was a remarkable scientist who made several very important discoveries in genetics. She carried out her studies before the age of large interdisciplinary research teams and before the sophisticated tools of molecular genetics were available. Her tools consisted of a clear mind and a consuming curiosity that could make sense of confusing and revolutionary observations. She worked 12-hour days, 6 days a week in a small laboratory at Cold Spring Harbor on Long Island, New York. In 1983, at age 81, McClintock received the Nobel Prize in Medicine or Physiology largely for her discovery 40 years earlier of transposable elements, or transposons, popularly called “jumping genes.” Her experimental system consisted of kernels of corn. She observed kernels of various colors produced by different enzymes (see figure 8.6). If the gene coding for an enzyme responsible for a particular color was inactivated, the kernel was not pigmented. If the enzyme was only partially inactivated, the kernel was partially pigmented. Thus, by looking at kernel colors, McClintock could detect changes in gene function. From her genetic analysis, she concluded that something, most likely pieces of DNA, must be moving into and out of genes to account for the differences in kernel color. When a piece of DNA, called a transposable element, moved into a gene, the gene could no longer function. When the transposable element left the gene, it was restored to its original state, and would function normally again. When McClintock published her results, most scientists believed that chromosomal DNA was very stable and unchanging. Consequently, most geneticists were very skeptical of McClintock’s heretical ideas. As a result, she stopped publishing many of her observations and it was not until the late 1970s that her ideas began to be accepted. By that time, transposable elements had been discovered in many organisms, including bacteria. Although

transposons were first discovered in plants, once they were found in bacteria, the field moved ahead very quickly. The techniques of molecular biology, biochemistry, and genetics made the understanding of “jumping genes” possible.

S

taphylococcus aureus, the Gram-positive coccus commonly called Staph, is a frequent cause of skin infections, such as boils and pimples. Since the 1970s the usual treatment for these infections has been penicillin-like antibiotics, such as methicillin. Today, however, this treatment is likely to fail. In 2003, well over 60% of the S. aureus strains isolated in hospitals were resistant to this antibiotic. Unfortunately, methicillin-resistant Staph is also resistant to a variety of other antibiotics. These resistant organisms now are commonly treated with a less effective antimicrobial, vancomycin, often considered the drug of last resort. However, in 2002 the situation became more worrisome—Staph isolated from foot ulcers on a diabetes patient in Detroit was vancomycin-resistant. This organism was also resistant to most common antibiotics, including penicillin, methicillin, and ciprofloxacin. How do multiple resistant strains arise and evolve? How are these resistance traits transferred so readily to other bacteria? The answer to these and many other questions important to human health requires a basic understanding of bacterial genetics. This subject encompasses the study of heredity—how genes function (chapter 7), how they can change, and how they are transferred to other cells in the population. With this knowledge you will understand why antibiotics are no longer miracle drugs against infectious diseases.

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KEY TERMS Auxotroph A microorganism that requires an organic growth factor. Conjugation Mechanism of horizontal gene transfer in which the donor cell must physically contact the recipient cell. DNA-Mediated Transformation Mechanism of horizontal gene transfer between bacteria in which the bacterial DNA is transferred as “naked” DNA. Extrachromosomal DNA that is not part of a chromosome. Genomic Island Large segment of DNA that has been acquired from another species through horizontal gene transfer. Examples include pathogenicity islands and antibiotic resistant islands. Genotype The sequence of nucleotides in the DNA of an organism. Haploid Containing only a single set of genes.

Homologous Recombination Genetic exchange between stretches of similar or identical nucleotide sequences. Involves a type of breakage and rejoining of DNA into new combinations and replacement of DNA.

Prototroph A microorganism that has no requirements for organic growth factors because it can synthesize them.

Horizontal Gene Transfer Transmission of DNA from one bacterium to another by conjugation, DNA-mediated transformation, or transduction. Also called lateral gene transfer.

Reactive Oxygen Toxic forms of oxygen that modify and damage DNA.

Mutation A change in the nucleotide sequence of a cell’s DNA, which is then passed on to daughter cells. A mutation can alter the protein which it encodes.

Replicon A piece of DNA that has an origin of replication and is therefore capable of replicating.

Non-Homologous Recombination Genetic recombination that does not require the two DNAs to have similar sequences in the region of recombination. Frequently the process involves addition and not replacement of genes. Phenotype The observed characteristics of a cell resulting from expression of the genotype.

8.1 Genetic Change in Bacteria Focus Points Name the two genetic changes that can alter the properties of bacteria. Distinguish between the genotype and the phenotype of a cell.

In the ever-changing conditions that characterize most environments, all organisms need to adapt in order to succeed. If they fail, competing organisms more “fit” to multiply in the new setting will soon predominate. This is the process of natural selection. Bacteria have two general means by which they routinely adjust to new circumstances: regulating gene expression (discussed in the previous chapter), and genetic change, which is the focus of this chapter. ■ regulation of gene expression, p. 176 A genetic change alters an organism’s genotype, the sequence of nucleotides in its DNA. This can have a profound impact on bacteria because they are haploid, meaning they contain only a single set of genes. There is no “backup copy” of a gene in a haploid organism. Because of this, a change in genotype can easily alter the observable characteristics of an organism, its phenotype. Note, however, that the phenotype involves more than just the genetic makeup of an organism; it is also influenced by environmental conditions. For example, Serratia marcescens colonies are

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Plasmid A small extrachromosomal DNA molecule that replicates independently of the chromosome and generally encodes information not essential to the life of the cell.

Transduction Mechanism of horizontal gene transfer between bacteria in which bacterial DNA is transferred inside a phage coat. Transposable Element (Transposon) Genes that move from one replicon to another site on the same replicon, or to another replicon in the same cell. Involves non-homologous recombination.

typically red when incubated at 22°C, but white when incubated at 37°C. This reversible change in the phenotype is governed by the organism’s environment—temperature in this case. Altering the genotype of S. marcescens by removing the genes that direct production of the red pigment will also change the phenotype of the organism. Genetic change in an organism can occur by two mechanisms—mutation and gene transfer. Mutation is a change in the existing nucleotide sequence of a cell’s DNA, which is then passed on to daughter cells. The modified organism is referred to as a mutant, and the progeny (offspring) will be mutants as well. Because a mutation arises in a single cell and is then passed to the progeny, this adaptation is referred to as vertical gene transfer (figure 8.1a). The other mechanism of genetic change, gene transfer, is the acquisition of genes from another organism. It is commonly referred to as either horizontal gene transfer or lateral gene transfer, to emphasize that the cell acquires DNA from a different source (figure 8.1b). Like mutations, the changes are then passed to the progeny of the altered organism.

MICROCHECK 8.1 The properties of bacteria can change either through mutations, or by acquiring genetic information from other sources. ✓ Contrast genotype and phenotype. ✓ Which has a longer-lived effect on a cell—a change in the genotype or a change in the phenotype?

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8.2

Spontaneous Mutation

187

FIGURE 8.1 The Acquisition and Transfer of Genetic Information to Progeny (a) Spontaneous mutation. All progeny of mutant cells will be

(a) Vertical gene transfer Spontaneous mutation in genome

mutant. (b) Gene transfer or horizontal acquisition of genetic information. All progeny of the cell acquiring the plasmid will also carry the plasmid by vertical gene transfer. A copy of the plasmid remains in the cell that transfers the plasmid. Genes can be transferred by several different mechanisms.

(b) Horizontal gene transfer Plasmid

Vertical gene transfer

Plasmid transferred

GENE MUTATION AS A MECHANISM OF GENETIC CHANGE

Mutation changes the DNA base sequence so that it differs from that of the wild-type organism, a strain whose properties are similar to the organism first isolated from nature. The change in a nucleotide sequence may lead to an altered phenotype. A change in phenotype results when the protein coded by the gene does not function properly. The substitution of even one amino acid for another in a critical location in the protein such as in the catalytic site may cause the protein to be dysfunctional, thereby changing the properties of the cell. For example, if any gene of the tryptophan operon is altered so that the encoded enzyme no longer functions properly, the cells will grow well only if this amino acid is in its environment. A mutant that requires a growth factor is called an auxotroph (auxo means “increase,” as an increase in requirements). Cells that grow in the absence of any added growth factors are termed prototrophs. ■ enzymes, pp. 129, 134 ■ protein structure, p. 28

sensitive, StrS, and this is not indicated when the phenotype of the cell is described.

■ operon, p. 177 ■ growth factor, p. 94

Spontaneous mutations are those that occur in the cell’s natural environment. Mutations occur randomly, and each gene mutates spontaneously and infrequently at a characteristic rate. The rate of mutation is defined as the probability that a mutation will occur in a given gene each time a cell divides; this rate is generally expressed as a negative exponent. The mutation rate of different genes usually varies between 10⫺4 and 10⫺12 per cell division. In other words, the chances that any single gene will undergo a mutation when one cell divides into two are between

By convention, the auxotrophic requirements of a cell are designated by three-letter abbreviations. For example, a cell that cannot make tryptophan is designated Trp⫺. The first letter is in caps. Each growth factor has its own three-letter designation. If a cell grows without the addition of tryptophan, it is Trp⫹. However, for convenience, only growth factors required are indicated. Likewise, only if a cell is resistant to an antimicrobial agent such as streptomycin is this indicated, such as StrR. Otherwise, the cells are assumed to be

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8.2 Spontaneous Mutations Focus Points Name three types of mutations that can occur spontaneously. Name three types of mutations that can result from base substitutions. Explain how mutations relate to natural selection.

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one in 10,000 (10⫺4) and one in a trillion (10⫺12).

■ exponents,

Appendix 1, p. A-1

Genes mutate independently of one another. Consequently, the chance that two given mutations will occur within the same cell is very low. Indeed, the actual occurrence is the product of the individual rates of mutation of the two genes (calculated by taking the sum of the exponents). For example, if the mutation rate to streptomycin resistance is 10⫺6 per cell division and the mutation rate to penicillin resistance is 10⫺8 per cell division, the probability that both mutations will occur within the same cell is 10⫺6 ⫻ 10⫺8, or 10⫺14. For this reason, two or more drugs may be administered simultaneously in the treatment of some diseases such as tuberculosis and AIDS. Any mutant cell or virus resistant to one antimicrobial medication is likely to still be sensitive to the other and therefore will be killed by the combination of the two antimicrobials. Mutations are stable so that the progeny of a mutant will retain the genotype. On rare occasions, however, the mutation will change back to its original, non-mutant state. This change in a mutated gene is termed reversion and, like the original mutation, it occurs spontaneously at low frequencies. Because of mutations, the concept that all cells arising from a single cell are identical is not strictly true, since every large population contains mutants. Even in a single colony that contains about 1 million cells, all cells are not completely identical because of spontaneous random mutations. These mutations provide a mechanism by which organisms, with their altered characteristics, can respond to a changing environment. This is the process of natural selection. The environment does not cause the mutation but rather selects those cells that can grow under its conditions. Thus, a spontaneous mutation to antimicrobial resistance, though rare, will result in the mutant becoming the dominant organism in a hospital environment where the antimicrobial medication is present. The antimicrobial kills the sensitive cells and thereby allows the resistant cells to take over the population.

—

DNA undergoing replication; a cytosine is incorporated opposite adenine by mistake.

—

—

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A

G C

G

T—

—A

—A T— G C

Codon A A G transcribed Amino acid translated

A

—A

T—

—A

C— G

G

Base Substitution The most common type of mutation occurs during DNA synthesis, when an incorrect base is incorporated into DNA, an event called base substitution (figure 8.2). If only one base pair is changed, the mutation is called a point mutation. Three outcomes are possible from base substitutions: a silent mutation, missense mutation, or nonsense mutation (figure 8.3). A silent mutation results from a nucleotide change that generates a codon that still specifies the wild type amino acid. This is possible because the genetic code is degenerate, meaning that different codons can encode the same amino acid. A missense mutation results when the new codon specifies a different amino acid. The effect of this type of mutation depends on the position of the change and the difference between the original and new amino acid. In many cases, cells with a missense mutation in a gene of tryptophan synthesis can grow slowly in the absence of tryptophan because the encoded protein is partially functional. Such a mutation is termed leaky. A nonsense mutation occurs when the new codon is a stop codon, resulting in a shortened, or truncated, protein. The site of the nonsense mutation dictates the length of the protein; in most cases, the truncated protein is non-functional. Any mutation that totally inactivates the gene is

—

T—

A

—A

T—

A

C

T—

—A G

—

C

C

T—

T—

C

—A

T—

A —

—A

T—

A

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G

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T—

—A

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C

—A T—

G

C

G

T—

C

—A

T—

T—

C

T—

—A T— G C

A G G

A A G

A A G

Lysine

Arginine

Lysine

Lysine

Wild type

Mutant

Wild type

Wild type

FIGURE 8.2 Base Substitution Shown here is the generation of a mutant organism as a result of the incorporation of a pyrimidine base (cytosine) in place of thymine in DNA replication. The mutation is a missense mutation.

termed a null or knockout mutation.

■ genetic code, p. 170 ■ codon,

p. 170 ■ stop codon, p. 173

Note that geneticists sometimes use the term “silent mutation” to indicate a mutation that does not alter the function of the protein. With this broad definition, any base substitution that does not affect protein function would be a silent mutation.

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8.2 5' 3'

. . . . . . . . . .

T A T . . . . . A T A . . . . .

Mutation

3' 5'

T A A T

G C

T A T A T A

Mutation

U

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U

Transcribed codon

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U

DNA – Minus (–) strand

G C C A T G C A A T T T

Transcribed codon

C G G U A C G U U A A A

Amino acid translated

Arginine

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T G T A C A

C

189

Wild Type

DNA

T A C A T G

A

Spontaneous Mutations

A

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Tyrosine

Valine

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Mutant Base addition

Tyrosine (silent mutation)

Cysteine Stop codon Tyrosine (missense (nonsense (wild type) mutation) mutation)

Amino acid translated

DNA

G C C T A T G C A A T T T

Transcribed codon

C G G A U A C G U U A A

Amino acid translated

Arginine

Type of Mutation

FIGURE 8.3 Three Types of Mutations Resulting from Base Substitutions The cells remain wild type if there is no misincorporation.

Isoleucine

Arginine

STOP

FIGURE 8.4 Frameshift Mutation As a Result of Base Addition

Oxygen in the environment can increase the frequency of base substitutions. As discussed in chapter 4, O2 can be readily converted through cellular metabolism or by environmental factors into forms highly toxic to cells, such as superoxide (O2⫺) and hydrogen peroxide (H2O2). In part, this toxicity results from these reactive forms of oxygen damaging cellular DNA and causing mutations. These reactive forms of oxygen can oxidize guanine before or after it has been incorporated into DNA, and DNA polymerase often mispairs oxidized guanine with adenine rather than cytosine, thereby resulting in a base substitution and a point mutation.

Removal or Addition of Nucleotides The deletion or addition of nucleotides, which may occur in the course of DNA replication, is another type of spontaneous mutation. The consequence of this depends on how many nucleotides are deleted or added. If three nucleotides are deleted (or added), this effectively removes (or adds) one codon from the DNA. When the gene is expressed, one additional (or one fewer) amino acid will be in the resulting protein. How serious this change is depends on the location of the change in the encoded protein. Adding or subtracting one or two nucleotides is more significant than adding or subtracting three because it causes a frameshift mutation. This results because translation of a gene begins at a specific codon and proceeds one codon at a time. Thus, the deletion or addition of a nucleotide shifts the codons of the DNA when it is transcribed into mRNA (figure 8.4). Consequently, a frameshift mutation changes the reading frame, so that an entirely different set of codons is used. Frequently, one of the resulting downstream codons will be a stop codon. As a result, a frameshift mutation is likely to result in a protein that is truncated and probably non-functional—a knockout mutation. ■ reading frame, p. 171 ■ downstream, p. 170

nes95432_Ch08_185-211.indd 189

The addition of a nucleotide (T) to the DNA results in a frameshift when the DNA is transcribed into mRNA and a new triplet code word is translated as a new amino acid. The deletion of a nucleotide would have essentially the same effect. The protein chain terminates when a stop codon appears in the DNA.

Transposable Elements (Jumping Genes) Transposable elements, also called transposons or jumping genes, are distinct segments of DNA that can direct their own movement in a process called transposition. Inside a single cell, a transposon can “jump” to a different location within the chromosome, or to a plasmid, or vice versa (figure 8.5). The gene into which a transposon inserts no longer encodes a functional protein because the insertion disrupts the gene; this is an example of insertional inactivation. Because most transposons contain transcriptional terminators that stop mRNA synthesis, the expression of genes downstream of the insertion in the same operon will also be affected. The structure and biology of transposons will be described later in this chapter. ■ transcriptional terminators, p. 170 ■ operon, p. 177

1'

1

2 3 3'

+

“Jumping” genes A

Gene B disrupted B C

B A 1 2

3 B C

1'

3'

+

FIGURE 8.5 Transposition The transposon consisting of (genes 1, 2, 3), has the ability to “jump” from one piece of DNA to another, where it becomes integrated. In this case, the transposon has jumped into gene B, thereby mutating it.

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Consequently, geneticists spend much time isolating mutants. One reason why bacteria represent an excellent experimental system for genetic studies and why more is known about E. coli than any other organism in the world is because bacterial mutants with a broad range of properties are easier to isolate than mutants in any other system. Bacteria grow rapidly to enormous numbers in very small volumes of inexpensive media. Thus, rare mutations will be represented in a small volume of medium. Further, since bacteria are haploid, with only one copy of each gene generally, the mutation will not be obscured by a wild-type gene. Because the frequency of spontaneous mutations is so low, investigators trying to isolate certain mutants must resort to using mutagens—chemicals or radiation that can increase the frequency of mutations at least 1,000-fold. Such mutations are said to be induced by the mutagen. FIGURE 8.6 Transposition Detected by Color Changes Variegation

Chemical Mutagens

in color observed in the kernels of corn is caused by the insertion of transposable elements into genes involved in the synthesis of different pigments, thereby altering the synthesis of the pigments.

Any chemical treatment that alters the hydrogen-bonding properties of a purine or pyrimidine base in the DNA will increase the frequency of mutations as the DNA replicates.

The classic studies of transposition were carried out by Dr. Barbara McClintock (see A Glimpse of History). She observed variation in the colors of corn kernels as a result of transposons moving into and out of genes concerned with pigment synthesis (figure 8.6).

Chemical Modification of Purines and Pyrimidines

MICROCHECK 8.2 Mutations, changes in the nucleotide sequences of DNA, may result in proteins that are dysfunctional, thereby altering the properties of the cell. A leaky mutation results in a partially functional protein; a knockout mutation results in a non-functional protein. Mutations most commonly occur spontaneously as a result of mistakes in DNA replication, in some cases because of reactive oxygen molecules that have modified the guanine in DNA. ✓ How would the growth requirements change in a cell that has a silent mutation in a gene for histidine synthesis? How would it change if the mutation were a knockout? ✓ If the rate of mutation to streptomycin resistance is 10⫺6 and that of penicillin resistance is 10⫺4, what is the rate of mutation to simultaneous resistance to both antibiotics? ✓ Is it as effective to take two antibiotics sequentially as it is to take them simultaneously, as long as the total length of time that they are both taken is the same? Explain.

8.3 Induced Mutations Focus Points

A large number of chemicals can alter the structure of purines and pyrimidines. The biggest group of chemical mutagens consists of alkylating agents, highly reactive chemicals that add alkyl groups (short chains of carbon atoms) onto purines and pyrimidines, thereby altering their hydrogen-bonding properties. A common alkylating agent used in research laboratories is nitrosoguanidine. Many compounds formerly used in cancer therapy are in this group. These compounds kill rapidly dividing cancer cells, but they also damage DNA in normal cells. As a result, these agents have caused cancers that appear more than 10 years after they were used to treat the original cancer. ■ purines and pyrimidines, p. 33 Another example of a powerful mutagen is nitrous acid (HNO2). This chemical converts amino (⫺NH2) to keto (⫺CKO) groups— for example, converting cytosine to uracil, which pairs with adenine rather than guanine when the DNA is replicated. Nitrous acid also removes amino groups from adenine and guanine.

Base Analogs Base analogs are compounds that structurally resemble purine or pyrimidine bases closely enough that they can be mistakenly incorporated in place of the natural bases as nucleotides are synthesized. These can then be incorporated into DNA in place of the natural nucleotides. Base analogs such as 5-bromouracil and 2-amino purine, however, do not have the same hydrogen-bonding properties as the natural bases, thymine and adenine respectively. This difference increases the probability that, once incorporated into DNA, the base analog will pair with the wrong base as the complementary strand is being synthesized (figure 8.7). ■ DNA replication, p. 164

Name four mechanisms by which mutagens act on DNA.

Intercalating Agents

Describe the effect of UV light on DNA.

A number of chemical mutagens, termed intercalating agents, increase the frequency of frameshift mutations. They are planar (flat) molecules of about the same size as a pair of nucleotides in DNA. These molecules do not alter hydrogen-bonding properties of the bases; rather, they insert, or intercalate, between adjacent base pairs

Mutants in nature are important because they are the raw material on which natural selection operates. They are also essential for studying and understanding most aspects of genetics.

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8.3

TABLE 8.1

Common Mutagens

Agent

Action

Result

Converts amino group to keto group in adenine and cytosine

Base substitution

Adds alkyl groups (CH3 and others) to nitrogenous bases such as guanine

Base substitution

Base analogs Example: 5-bromouracil

Incorporates in place of normal nucleotide in DNA

Base substitution

Intercalating agents Example: ethidium bromide

Inserts between base pairs in either the template or new strand

Addition or subtraction of base pairs

Transposons

Random insertion of transposon into any gene

Insertional inactivation

Chemical Agent Chemical modification of bases Examples: nitrous acid

alkylating agents

Transposition A common procedure to generate mutants in research laboratories is to introduce a transposon into a cell. The transposon, which cannot replicate on its own because it lacks an origin of replication,

3'

5' —

C—

G —

A

Intrastrand thymine dimer formation

Base substitution

Single- and doublestrand breaks in DNA

Deletion of bases

3' —G

T—

—A

T

A

X rays

A

Intercalating agent —

C

G—

—

C

Normal nitrogenous base

Analog

O

O

6 5

1

4

2

N

Br

3

O

N

2

—

3

5 8

—

O

6

Replaced by

9

N

2 3

N

5

1

4

2

8

1N

H Adenine (6-amino purine)

G—

Base addition

3'

C—

A

—G

T— A

—A

T A

A

T C

G—

—

C

C—

T—

T

G—

H

N

3

N

H 2-amino purine

H N H

FIGURE 8.7 Common Base Analogs and the Normal Bases They Replace in DNA The important differences between the normal bases and the analogs are in boxes. Like the natural bases, they are incorporated as nucleotides into replicating DNA.

nes95432_Ch08_185-211.indd 191

T—

N 7

6

G

—

N

N

4

H

N

H 5-bromouracil

N 4

1

H

H

7

5

N

H Thymine

9

6

Replaced by

C—

DNA continues replication.

5'

H

5'

T

in one of the strands of DNA. This pushes the nucleotides apart, producing enough space between bases that errors are made during replication. If the intercalating agent inserts into the old strand of DNA, a base pair will be added as the new strand is synthesized. If it inter-

H 3C

191

calates into the strand being synthesized, a deletion of a base pair will occur. In either case, the result is a frameshift mutation (figure 8.8). As in spontaneous frameshift mutants, the addition or subtraction of a nucleotide often results in a stop codon being generated prematurely in the mRNA transcribed from the altered DNA, and a shortened protein being synthesized. An intercalating agent commonly used in the laboratory to stain DNA is ethidium bromide. The manufacturer now warns users that ethidium bromide should be handled with great care because it likely is a carcinogen—a cancer-causing agent. Another intercalating agent is chloroquine, which has been used for many years to treat malaria. ■ DNA replication, p. 164

Radiation Ultraviolet (UV)

Induced Mutations

FIGURE 8.8 Base Addition in Newly Synthesized Strand of DNA Caused by An Intercalating Agent The intercalating agent pushes nucleotides apart when it intercalates in the old strand. This allows for an additional base being incorporated into the newly synthesized strand.

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must integrate into the cell’s genome in order to be replicated. The gene into which the transposon has inserted will usually be inactivated as a result of the insertion and usually results in a knockout mutation.

8.4 Repair of Damaged DNA Focus Points

Radiation Two kinds of radiation are mutagens: ultraviolet (UV) light and X rays. ■ wavelengths of radiation, p. 115

Ultraviolet Irradiation

Explain how DNA polymerase can correct base substitutions and prevent misincorporation of nucleotides. Explain three mechanisms by which UV light damage can be repaired. Explain how a mutation caused by reactive oxygen is repaired.

Irradiation of cells with ultraviolet light causes covalent bond formation between adjacent thymine molecules on the same strand of DNA (intrastrand bonding), resulting in the formation of thymine dimers (figure 8.9). The covalent bonding distorts the DNA strand so much that the dimer cannot fit properly into the double helix, resulting in badly damaged DNA. The DNA molecule cannot be replicated, nor genes transcribed, beyond this site of damage and, as a result, the cells should die. How then can UV light be mutagenic? The major mutagenic action of UV light results from the cells repairing the damage by a mechanism termed SOS repair (see the next section). ■ gene transcription, p. 168

X Rays X rays cause several types of damage: single- and double-strand breaks in DNA, and alterations to the bases. Double-strand breaks often result in deletions that are lethal. Table 8.1 summarizes information on the common mutagens.

MICROCHECK 8.3 The frequency of spontaneous mutations can be increased significantly by treating cells with chemicals and radiation. These treatments induce mutations, which most frequently result from the alteration of hydrogen-bonding properties of the nitrogenous bases, or the addition or deletion of bases in DNA. ✓ How does UV light affect cells? ✓ Do you think that mutations caused by reactive oxygen should be considered spontaneous or induced? Justify your answer.

Thymine

Thymine dimer

Probably no function is more important to a cell than being able to repair damaged DNA because no molecule is more critical to the proper functioning of the cell. The amount of spontaneous and mutagen-induced damage to DNA in cells is enormous. Every 24 hours, the DNA in every cell in the human body is damaged spontaneously more than 10,000 times. This damage, if not repaired, can lead to cell death and, in animals, cancer. In humans, two breast cancer susceptibility genes code for enzymes that repair damaged DNA. Mutations in either one result in a high (80%) probability of breast cancer. A major reason why observed mutations are so rare is that alterations in DNA are repaired shortly after they occur and before they can be passed on to progeny and change their properties. It is not surprising that, in the course of many million of years of evolution, all cells, both prokaryotic and eukaryotic, have developed several different mechanisms for repairing any damage that their DNA might suffer either spontaneously or by mutagens in the environment.

Repair of Errors in Base Incorporation A common cause of spontaneous mutations is the incorporation of the wrong base by DNA polymerase as it replicates DNA. The resulting mispairing of bases results in a slight distortion in the DNA helix, which is recognized by enzymes within the cell that repair such mistakes. By quickly repairing the error before the DNA is replicated, the cell prevents the mutation. Two mechanisms exist for repairing errors in base incorporation: proofreading by DNA polymerase and mismatch repair. ■ DNA polymerase, p. 166

Thymine Covalent bonds

Ultraviolet light Sugar-phosphate backbone

FIGURE 8.9 Thymine Dimer Formation Convalent bonds form between adjacent thymine molecules on the same strand of DNA when DNA is exposed to UV light. This distorts the shape of the DNA and prevents replication past the dimer.

nes95432_Ch08_185-211.indd 192

Proofreading by DNA Polymerase DNA polymerases are complex enzymes that not only synthesize DNA, but also verify the accuracy of their actions—a characteristic called proofreading or editing. The enzymes can back up and excise (remove) any nucleotides that are not correctly hydrogen bonded to the base in the template strand. Following excision, the DNA polymerase then incorporates the correct nucleotide. Although the proofreading function of DNA polymerases is very efficient, it is not infallible.

Mismatch Repair Mismatch repair fixes errors missed by the proofreading of DNA polymerase. A specific protein binds to the site of

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8.4 Repair of Damaged DNA

Repair of Thymine Dimers

Template strand

CH3 CH3

CH3

5'

3' A mistake is made in the incorporation of a base during the original DNA synthesis.

C T A A G C T G A G

1

G A T T T G A C T C 3'

5'

Newly synthesized strand

CH3 CH3

CH3

C T A A G C T G A G 2 G A T T T G A C T C

An endonuclease recognizes the mistake in the strand that is not methylated and makes a cut in the DNA near the mismatch.

Cut CH3 CH3

CH3

C T A A G C T G A G

3

G A

C T C

A gap forms after an enzyme degrades up the single stranded DNA.

CH3 CH3

CH3

C T A A G C T G A G G A T T C G A C T C

CH3

DNA polymerase closes the gap by synthesizing a new strand complementary to the template strand, incorporating the correct base.

CH3

C T A A G C T G A G

5

G A T T C G A C T C

DNA ligase joins the newly synthesized fragment to the original strand.

DNA ligase

FIGURE 8.10 Mismatch Repair The endonuclease cuts the DNA near the misincorporated base and another enzyme chews up the single-stranded DNA, creating a gap in the backbone. A new complementary strand is then synthesized and joined to the original strand by DNA ligase.

the mismatched base, directing an enzyme to cut the DNA backbone of one strand (figure 8.10). Another enzyme then degrades a short region of DNA of that strand, thereby removing the misincorporated nucleotide. How does the cell know which strand to excise? If the enzyme cuts the original strand and not the one being synthesized, the wrong base would remain. The key lies in methylation of DNA bases. Soon after a strand of DNA is synthesized, an enzyme adds methyl groups to certain nucleotide bases. However, immediately after the new strand is synthesized, it is still unmethylated. This difference in methylation distinguishes old and recently synthesized strands of DNA and ensures that the repair enzyme cleaves the correct strand. The combined actions of DNA polymerase and DNA ligase then fill in and seal the gap left by the removal of the DNA segment. ■ DNA ligase, p. 167 Mismatch repair also occurs in humans. Defects in this repair system lead to an increased incidence of colorectal cancers.

nes95432_Ch08_185-211.indd 193

Because UV light is a part of sunlight, cells are frequently exposed to this mutagenic agent. Bacteria have developed several mechanisms to combat the harmful effects of these rays. In one mechanism, an enzyme uses the energy of visible light to break the covalent bond of the thymine dimer, restoring the DNA to its original state (figure 8.11a). Because light is required for this mechanism, it is called photoreactivation, or light repair. This enzyme is found only in prokaryotes. Some bacteria have an enzyme that recognizes the major distortions in DNA that result from thymine dimer formation. In this process, excision repair, or dark repair, the enzyme makes single-stranded cuts that flank both sides of the damaged region, resulting in excision of the region (figure 8.11b). The actions of DNA polymerase and DNA ligase then fill in and seal the gap left by the removal of the segment.

Repair of Modified Bases in DNA

A gap in the DNA

4

193

Modified bases such as oxidized guanine can result in base substitutions if they are not repaired before the DNA is replicated. An important mechanism for repairing this defect uses an enzyme called a glycosylase, which removes the oxidized base from the sugarphosphate backbone (figure 8.12). Another enzyme recognizes that a base is missing and cuts the DNA at this site. DNA polymerase degrades a short section of this strand to remove the damage. This same enzyme then synthesizes another strand with the proper bases. DNA ligase seals the gap in the single-stranded DNA. Humans have repair enzymes analogous to glycosylases in bacteria. Mutations in the genes coding for these repair enzymes result in an increased rate of colon cancer.

SOS Repair If DNA is heavily damaged by UV light such that it contains many thymine dimers, photoreactivation and excision repair may not be able to correct all of the dimers and the cells will die. Therefore, bacteria have a mechanism, termed SOS repair, that bypasses the damaged DNA and allows replication to continue. The damaged DNA activates the expression of over 30 genes which encode the SOS system. One of the most important of these genes codes for a DNA polymerase that is able to synthesize DNA at the site of the damaged DNA. However, unlike the standard DNA polymerase, which is relatively error-free because of its proofreading ability but cannot copy at the site of the lesion, this newly synthesized polymerase makes many mistakes and incorporates the wrong bases in the DNA strand it is synthesizing. Further, it cannot correct these mistakes because it has no proofreading ability. As a result, mutations arise. This process is called SOS mutagenesis. Table 8.2 summarizes the key features of the major DNA repair systems in bacteria. Note that the cell cannot repair all types of mutations, such as insertional inactivation caused by transposition. However, if the transposon jumps to a new location, the gene that it leaves may regain normal function.

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CHAPTER EIGHT

Bacterial Genetics Thymine dimer results in a distortion of the sugar-phosphate backbone.

Covalent bonds CH3

CH3 CH3

CH3

5'

3' G

C

G

A

T

C

G

C

T

A

T A

G

A

C

G

C

T

G

C

3'

3'

5' C

T

A

A

G

C

T

G

A

T

T

C

G

A

3'

Unmodified guanine 5'

CH3

CH3

Oxidized guanine formed 5'

CH3

Visible light and photoreactivating enzyme; light repair

CH3

An enzyme requiring visible light for activity breaks the two bonds joining the two thymine molecules together. The two strands of DNA assume their original shape.

CH3

CH3 CH3

3'

5' C

T

A

A

G–O C

T

G

A

T

T

C

A

CH3

5'

5' CH3

3' G

C

G

A

T

T

G

A

C

G

C

G

C

T

A

A

C

T

G

C

3' CH3

CH3

Glycosylase removes G–O from the backbone. CH3 CH3

5'

(a)

G

3'

3'

5'

CH3

C

T

A

A

G

A

T

T

C

C

T

G

A

3' Thymine dimer results in a distortion of the sugar-phosphate backbone.

Covalent bonds CH3

3' C

G

A

C

G

C

T

T A

T

G

A

C

G

A

C

T

G

C

3'

Gap in the backbone 3' C T

5' C

T

A

A

G

A

T

T

C

G

Another enzyme cleaves the backbone near the missing purine and DNA polymerase degrades the DNA, resulting in a short gap.

A

3'

5' CH3

5' CH3

CH3

CH3 CH3

CH3

5' G

5' CH3

CH3

Repair by DNA polymerase

CH3 CH3 CH3

3'

5' Excision (repair) enzyme acts CH

Excision enzyme acts CH3

3

T

5'

A

G

C

C

G

T

3'

G

A

G

C

T

A

A portion of the DNA which contains the thymine dimer is cut out by a repair enzyme.

A

C

T

C

G

G

C

3'

C

T

A

A

G

C

T

G

A

T

T

C

G

A

3'

5' CH3

CH3

FIGURE 8.12 Repair of Oxidized Guanine in DNA In this diagram the correct base cytosine is based-paired with oxidized guanine, G–O.

5' CH3

Repair by DNA polymerase Direction of DNA synthesis

CH3 A new single strand of DNA complementary to the undamaged strand is synthesized by DNA polymerase. DNA ligase joins the newly synthesized DNA fragment to the original strand.

DNA ligase acts

MICROCHECK 8.4

5'

3' G

C

G

A

T

T

G

A

C

G

C

G

C

T

A

A

C

T

G

C

CH3

CH3

3'

(b)

5'

FIGURE 8.11 Repair of Thymine Dimers (a) In photoreactivation, a light-requiring enzyme breaks the two covalent bonds (light repair). (b) In excision, or dark repair, the single strand of DNA containing the thymine dimer is removed and destroyed. The newly synthesized strand is joined to the end of the original strand by the enzyme DNA ligase. Light is not required.

nes95432_Ch08_185-211.indd 194

Bacteria use a variety of mechanisms to repair damaged DNA that contains errors resulting from the incorporation of wrong nucleotides. These include proofreading by DNA polymerase, and excising the nucleotide errors by mismatch repair. Specific glycosylases can remove modified bases. Thymine dimers can be repaired through light and dark repair mechanisms; severe damage can be overcome by the SOS repair system. ✓ How does UV light cause mutations? ✓ Distinguish between light and dark repair of thymine dimers. ✓ If you wish to maximize the number of mutations following UV irradiation, should you incubate the irradiated cells in the light or in the dark, or does it make any difference? Explain your answer.

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8.5

TABLE 8.2 Spontaneous

Mutant Selection

195

Repair of Damaged DNA Type of Defect

Repair Mechanism

Biochemical Mechanism

Result

Wrong base incorporated during DNA replication

Proofreading by DNA polymerase

Removal of mispaired base by DNA polymerase

Potential mutation eliminated

Mismatch repair

Cleavage and degradation of short stretch of single-stranded DNA and synthesis of new strand by DNA polymerase

Potential mutation in nonmethylated DNA strand eliminated

Action of glycosylase

Glycosylase removes the oxidized guanine. Short piece of DNA degraded and guanine incorporated.

Potential mutation eliminated

Reactive oxygen forms oxidized guanine in DNA.

Mutagen—Induced Chemical

Wrong base incorporated during DNA replication

Same as for spontaneous mutations

Same as for spontaneous mutations

Same as for spontaneous mutations

UV light

Thymine dimer formation

Photoreactivation (light repair)

Breaking of covalent bond forming thymine molecules

Original DNA molecule restored

Excision repair (dark repair)

Excision of a short stretch of singlestranded DNA containing thymine dimer and synthesis of a new strand by DNA polymerase

Mutation eliminated; original DNA molecule restored

SOS repair

DNA synthesis by a new DNA polymerase bypasses damaged DNA

Cell survives but numerous mutations are generated

8.5 Mutant Selection Focus Point Distinguish between direct and indirect selection, and describe how mutants of each type are selected.

Even when mutagens are used, mutations rarely appear in the population. This presents a major challenge to the investigator who wants to isolate a desired mutant. As discussed in chapter 4, bacteria can multiply on simple media and produce several billion cells per milliliter of medium in less than 24 hours. In such a large population, every gene should have a mutation in at least one cell in the population. The major problem becomes how to find and identify the rare cells containing the desired mutation. Depending on the type of mutant being sought, one of two simple techniques can be used—direct or indirect selection. A major reason why the field of microbial genetics has advanced so rapidly is because the process of detection and isolation of mutants is so simple and fast.

Indirect Selection Indirect selection is required to isolate an auxotroph, such as a Trp⫺ mutant, from a prototrophic parent strain. This process is more cumbersome and takes a longer time than direct selection because there is no medium on which the desired mutant will grow and the prototroph will not. Trp⫺ cells can grow only on an enriched complex medium because this supplies the tryptophan they require, but Trp⫹ cells readily grow on this same medium. To overcome this problem, replica plating is used, sometimes preceded by penicillin enrichment of mutants. Bacteria are treated routinely with a mutagen prior to the selection process.

Streptomycinresistant cell Streptomycinsensitive cells

Direct Selection Direct selection involves inoculating cells onto a medium on which the mutant, but not the parent, can grow. For example, mutants resistant to the antibiotic streptomycin can be easily selected directly by inoculating cells onto a medium containing streptomycin. Only the rare resistant cells in the population will form a colony (figure 8.13). Mutants that can grow under conditions in which the parent cells cannot are usually easy to isolate by direct selection.

nes95432_Ch08_185-211.indd 195

Medium containing streptomycin

Medium without streptomycin

FIGURE 8.13 Direct Selection of Mutants Only the streptomycinresistant cells will grow on the streptomycin-containing medium. All cells will grow on media without streptomycin and have the same appearance.

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Replica Plating An ingenious technique for indirect selection of auxotrophic mutants, replica plating, was devised by the husband-andwife team of Joshua and Esther Lederberg in the early 1950s (figure 8.14). In this technique, the mutagenized bacterial culture is plated on an enriched medium on which both mutant and non-mutant cells grow as individual colonies. This serves as a master plate. The master plate is pressed onto sterile velvet, a fabric with tiny threads that stand on end like tiny bristles (figure 8.14, step 1). This operation transfers some cells of every bacterial colony onto the velvet. Next, two sterile plates—one containing a glucose-salts (minimal) medium and the second an enriched, complex medium—are pressed in succession and in the same orientation onto the same velvet (step 2). This procedure transfers cells imprinted on the velvet from the master plate to both the glucose-salts medium and the enriched medium. Following incubation, all prototrophs will form colonies on both the enriched and the glucose-

Master plate with bacteria (enriched complex medium)

Pressed onto sterile velvet

salts medium, but auxotrophs will only form colonies on the enriched medium (step 3). ■ glucose-salts medium, p. 96 By keeping the orientation of the two plates the same as they touch the velvet, any colony on the master plate that can grow on the enriched medium but not on the glucose-salts medium can be identified. The particular growth factor required can then be determined by adding the various factors individually to the glucose-salts medium and determining which one promotes cell growth.

Penicillin Enrichment of Mutants Even using mutagenic agents, the frequency of mutation in a particular gene is low, ranging perhaps from less than one in 1,000 to one in 100 million cells. In cases where the parent cell is sensitive to penicillin, the proportion of auxotrophic mutants in the population can be increased significantly by a technique called penicillin enrichment. Following treatment with a mutagen, the cells are grown in a glucose-salts medium containing penicillin. Since penicillin kills only growing cells, the prototrophs will grow and be killed, while the non-multiplying auxotrophs will survive (figure 8.15). The enzyme penicillinase is then added to destroy the penicillin, and the cells are plated on an enriched medium. This plate can then be replica plated onto a glucosesalts medium. Any colonies that grow on the enriched medium but not on the glucose-salts medium must be auxotrophs. ■ action of penicillin, p. 62

Step 1

Sterile velvet

Testing of Chemicals for Their Cancer-Causing Ability Strong evidence exists that a substantial proportion of all cancers are caused by chemicals in the environment called carcinogens. How can the thousands of chemicals released into the environment, such as pesticides, herbicides, hair dyes, cosmetics, food additives, and the by-products of manufacturing processes, be

Colonies imprinted on velvet

Step 2

Sterile plate pressed to velvet

Enriched complex medium

Glucose-salts medium

Sterile plate pressed to velvet

Synthetic medium (glucose-salts)

Prototroph

Plates incubated about 24 hours

Step 3 Auxotroph

Auxotrophs

+ Penicillin incubate Penicillin kills actively multiplying cells

Position of auxotroph

Most prototrophs are killed; auxotrophs survive because they cannot multiply in the medium.

+ Penicillinase (destroys penicillin) Auxotroph Prototroph

Enriched complex medium; all colonies grow.

Glucose-salts medium; auxotrophs do not grow.

Enriched complex medium

FIGURE 8.14 Indirect Selection of Mutants by Replica Plating The procedure shown is the one first used by the Lederbergs and continues to be used today in many laboratories.

nes95432_Ch08_185-211.indd 196

FIGURE 8.15 Penicillin Enrichment of Mutants Since auxotrophs require a growth factor to multiply, they are not killed.

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8.5

Bacteria requiring histidine for growth (His – )

Mutant Selection

197

Bacteria requiring histidine for growth (His – )

Glucose-salts medium

Glucose-salts medium

Liquid containing suspected mutagen

Liquid without suspected mutagen

Incubation Many His + revertant colonies

If chemical is a mutagen, many colonies form.

Most remain His –

If chemical is not a mutagen, far fewer colonies form. (a) Test plates

Few colonies form.

(b) Control plate

FIGURE 8.16 Ames Test to Screen for Mutagens (a) The chemical will increase the frequency of reversion of His: to His; cells if it is a mutagen and, therefore, a potential carcinogen. (b) The control plate contains only the liquid in which the suspected mutagen is dissolved.

tested for their carcinogenic activity? Testing in animals for tumor formation takes 2 to 3 years and may cost $100,000 or more to test a single compound. Today, a number of much less expensive, more rapid, and simpler tests have been devised. All are based on assaying the effect of the potential carcinogen on DNA in a microbiological system. The first one was devised by Bruce Ames and his colleagues in the 1960s and illustrates the concept of such tests. The Ames test, takes only a few days to get results and is based on three observations: (1) the reversion frequency of a mutant gene in a biosynthetic pathway, such as histidine biosynthesis, can be readily measured; (2) the low frequency of spontaneous reversions is increased by mutagens; and (3) most carcinogens affect DNA and therefore are mutagens. Specifically, the Ames test compares the effect of a test chemical on the rate of reversion of a histidine-requiring auxotroph of Salmonella, to the reversion frequency when no chemical is added (figure 8.16). If the chemical is mutagenic, it will increase the reversion rate of the strain relative to that observed when no chemical is added (the control). The test also gives some idea about how powerful the mutagen is, and therefore how potentially hazardous the chemical is, by the number of revertants that arise. The Ames test fails to detect many carcinogens because some substances are not carcinogenic themselves but can be converted to active carcinogens by enzymatic reactions that occur in animals but not in bacteria. Therefore, an extract of ground-up rat liver,

nes95432_Ch08_185-211.indd 197

which has the enzymes to carry out these conversions, is added to the Petri plates containing the suspected mutagen (carcinogen) being analyzed by the Ames test. To increase the sensitivity of the test, a mutant strain that lacks repair enzymes is often used. As a result, more revertants will be observed because the damaged DNA cannot be repaired. Additional testing must be done on any mutagenic agent identified in the Ames test to confirm that it is actually carcinogenic in animals. Although data are not available on the percentage of mutagens that are carcinogens, it is clear that the Ames test is useful as a rapid screening test to identify those compounds that have a high probability of being carcinogenic. Thus far, no compound with a negative Ames test has been shown to be carcinogenic in animals.

MICROCHECK 8.5 Mutants can be selected using either direct techniques or indirect techniques such as replica plating. Penicillin enrichment can often help in the isolation of auxotrophic mutants by killing multiplying cells. ✓ Distinguish between the kinds of mutants that can be isolated by direct and indirect selection. ✓ When does penicillin enrichment not work? ✓ How could you demonstrate by replica plating that the environment selects but does not mutate genes in bacteria?

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Bacterial Genetics

GENE TRANSFER AS A MECHANISM OF GENETIC CHANGE

In addition to mutation, the genetic information in a cell can be altered if the cell gains genes from other cells, a common occurrence in the microbial world. The movement of DNA from one cell, the donor, to another, the recipient, is called horizontal, or lateral, gene transfer. This mechanism of genetic change is largely responsible for the rapid spread of antibiotic resistance, such as described for S. aureus earlier in this chapter. Gene transfer can only be studied if genetic differences exist between the donor and recipient cells, and this is one reason why bacterial geneticists frequently isolate mutants. These differences make it possible to determine whether genetic recombination, the combining of DNA or genes from two different cells, has occurred. Genetic recombination can be readily recognized because the resulting cells, termed recombinants, have a combination of properties of each of the original strains. Figure 8.17 shows how this can be demonstrated. Two bacterial strains, neither of which can grow on a glucose-salts medium because of multiple growth factor requirements, are mixed. Strain A requires histidine (His⫺) and tryptophan (Trp⫺), and is resistant to streptomycin (StrR). Strain B does not require histidine or

tryptophan, but does require leucine (Leu⫺) and threonine (Thr⫺), and is killed by streptomycin (StrS). Neither population is likely to give rise to a spontaneous mutant that can grow on the glucose-salts medium because multiple simultaneous mutations in the same cell would be required. After the strains are mixed, they are plated on a glucose-salts medium that contains streptomycin. In order for cells to grow and form colonies on this medium, they must be prototrophic and resistant to streptomycin. Therefore they must acquire genes from the other strain. Following its transfer, the transferred DNA must replicate in order to be passed on to daughter cells and confer on them new genetic information. Therefore, the transferred DNA must have an origin of replication. If it does not, it must become part of a DNA molecule such as a chromosome or a plasmid that can replicate and be passed on to all daughter cells. Such a molecule is termed a replicon (figure 8.18). ■ origin of replication, p. 166

Bacterial chromosome

DNA fragment (no origin of replication) DNA molecules without an origin of replication cannot replicate in a cell.

Only one daughter cell will have a copy of the DNA fragment. Str R His – Trp –

Mixture

Str S Leu – Thr – (a) Non-integrated DNA fragment

DNA fragment A DNA fragment inserted into a bacterial chromosome can be replicated and passed on to daughter cells. No colonies Glucose-salts medium + streptomycin

No colonies Glucose-salts medium + streptomycin All daughter cells will have a copy of the fragment.

Mixture plated

(b) Integrated DNA fragment Recombinants Glucose-salts medium + streptomycin

FIGURE 8.18 DNA Without an Origin of Replication Must Become Part of a Replicon in Order to Be Maintained in a Population of Cells (a) Without an origin of replication, the DNA will not be passed on to

FIGURE 8.17 General Experimental Approach for Detecting Gene Transfer in Bacteria Recombinants will only arise if the genes transferred

daughter cells and thus will not confer new properties on the population. (b) Transferred DNA becomes integrated into a replicon in the recipient cell and is passed on to all daughter cells.

are part of a replicon or integrate into a replicon.

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8.6

Genes in nature are transferred between bacteria by three different mechanisms: 1. DNA-mediated transformation, in which DNA is transferred as “naked” DNA. 2. Transduction, in which bacterial DNA is transferred by a virus that infects bacterial cells. 3. Conjugation, in which DNA is transferred directly from one bacterium to another when the cells are in contact with one another. To detect gene transfer, it is most convenient to select directly for recombinants by inoculating the mixture of cells on a medium on which only the recombinants will form colonies. Since several billion bacteria can be plated on agar in a single Petri dish, a few colony-forming recombinants can be detected readily and very rare events observed.

DNA-Mediated Transformation

199

8.6 DNA-Mediated Transformation Focus Point Describe the process of DNA-mediated transformation.

DNA-mediated transformation, commonly referred to as transformation, involves the uptake of “naked” DNA by recipient cells (Perspective 8.1). Naked DNA is simply DNA that is free in the surroundings; it is not contained within a cell or a virus. The fact that the DNA is naked can be demonstrated by adding DNAse, an enzyme that degrades DNA outside the cell. Since DNAse prevents DNA-mediated transformation, this process must involve naked DNA transfer.

PERSPECTIVE 8.1 The Biological Function of DNA: A Discovery Ahead of Its Time In the 1930s, it was well known that DNA occurred in all cells, including bacteria. Its function, however, was a mystery. Since DNA consists of only four repeating subunits, most scientists believed that it could not be a very important molecule. Its important biological role was discovered through a series of experiments conducted during a 20-year period by scientists in England and the United States. In the 1920s, Frederick Griffith, an English bacteriologist, was studying pneumococci, the bacteria that cause pneumonia. It was known that pneumococci could cause this disease only if they made a polysaccharide capsule. In trying to understand the role of this capsule in causing disease, Griffith killed encapsulated pneumococci and mixed them with living mutant pneumococci that could not synthesize a capsule. When he inoculated this mixture of organisms into mice, much to his surprise, they developed pneumonia and died (figure 1). Griffith isolated living encapsulated pneumococci from the dead mice. When he injected the dead encapsulated cells and living non-encapsulated cells into separate mice, they did not develop pneumonia. Two years after Griffith reported these findings, another investigator, M. H. Dawson, lysed heat-killed encapsulated pneumococci and passed the suspension of ruptured cells through a very fine filter, through which only the cytoplasmic contents of the bacteria could pass. When he mixed the filtrate (the material passing through the filter) with living bacteria unable to make a capsule, some bacteria were able to make a capsule. Moreover, the progeny of these bacteria could also make a capsule. Something in the filtrate was “transforming” the harmless unencapsulated bacteria into ones that could make a capsule. What was this transforming principle? In 1944, after years of painstaking chemical analysis of lysates capable of transforming pneumococci, three investigators from the Rockefeller Institute, Oswald T. Avery, Colin MacLeod, and Maclyn McCarty, purified the active compound and then wrote one of the most important papers ever published in biology.

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Organisms injected

Results

Mouse dies.

Living encapsulated cells

No effect Living non-encapsulated cells

No effect Heat-killed encapsulated cells

Heat-killed encapsulated cells Mouse dies.

+ Living non-encapsulated cells

Living encapsulated cells isolated

FIGURE 1 Demonstration of the Transforming Principle In it, they reported that the transforming molecule was DNA. The significance of their discovery was not appreciated at the time. Perhaps the discovery was premature, and scientists were slow to recognize its significance. None of the three investigators received a Nobel Prize, although many scientists believe that they

deserved it. Their studies pointed out that DNA is a key molecule in the scheme of life and led to James Watson and Francis Crick’s determination of its structure, which they published in 1953. The understanding of the structure and function of DNA revolutionized the study of biology and ushered in the era of molecular biology. Microbial genetics serves as its foundation.

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Bacterial Genetics

One source of naked DNA in some genera is lysed cells in a population of bacteria. As cells burst open, the long chromosomal DNA molecules that are tightly jammed into the cells typically break up into hundreds of pieces as they explode through the broken cell walls. Other genera of bacteria secrete small segments of DNA, presumably as a means of promoting transformation. In order to take up naked DNA, the recipient cell must be competent—a specific physiological state that allows DNA to enter a cell. Once inside the cell, the DNA can integrate into the recipient’s genome. Over 40 species are naturally competent, but cells can also take up DNA if they are treated with certain chemicals or electric currents that alter the permeability of their cell walls.

Gene conferring StrR Gene conferring StrS

Recipient DNA (a) Degradation of one donor strand by nucleases

Single strand of donor DNA enters

(b) Pairing of donor DNA with homologous region of recipient chromosome

Natural Competence Among the species that can become naturally competent, the ability to take up DNA is a tightly controlled physiological state, and the mechanism of control varies. Some species are always competent, whereas others become so only under specific conditions, as when the population reaches a critical density or under certain nutritional conditions. In the case of Bacillus subtilis, a two-component regulatory system recognizes a limiting supply of nitrogen or carbon in the environment and activates a set of genes required for the competent state. Competence also requires that the bacterial concentration be high, which is a function of a quorum sensing system. Presumably, the high concentration of cells ensures that the DNA in the medium will contact the competent bacteria. However, even under optimal conditions, only 10% of the population ever becomes competent. Perhaps non-competent cells are releasing DNA that can be taken up by the competent cells. This means that presumably identical cells in a population can differ in their physiological properties. The fact that some species of bacteria become competent only under precise environmental conditions highlights the remarkable ability of these seemingly simple cells to sense their surroundings and adjust their behavior accordingly. ■ two-component regulatory system, p. 180 ■ quorum sensing, p. 180

Transforming DNA (double-stranded) attaches to recipient cell surface.

Gene conferring StrR

(c) Integration of single-stranded donor DNA by homologous recombination

(d)

(e) Bacteria placed on streptomycin medium

Transformed cells multiply.

Non-transformed cell dies.

Entry of DNA Double-stranded DNA molecules bind to specific receptors on the surface of competent cells (figure 8.19). However, only one strand enters the cell; nucleases at the cell surface degrade the other. Most competent bacteria take up DNA regardless of its origin, but some only accept DNA from closely related species. The cells recognize closely related DNA by characteristic nucleotide sequences found throughout the genome.

Integration of Donor DNA Once the donor DNA is inside the recipient cell, it integrates into the genome by the process of homologous recombination, which can only occur if the donor DNA is similar in sequence, or is homologous, to a region in the recipient cell’s genome. Thus, transformation occurs only between closely related species. The single-stranded donor DNA becomes positioned next to the complementary region of the recipient DNA. A nuclease then cleaves one strand of the recipient cell’s DNA on either side of where the donor DNA is aligned. This fragment of DNA is released and will

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(f)

FIGURE 8.19 DNA-Mediated Transformation The donor DNA comes from a cell that is streptomycin resistant (StrR). The recipient cell is streptomycin sensitive (StrS). The genes for resistance and sensitivity to streptomycin may differ by only a single nucleotide.

be degraded by nucleases. The donor DNA then replaces precisely a single strand of the recipient DNA.

Multiplication of Transformed Cells In the laboratory, DNA transformation is most easily detected if the transformed cells can multiply under selective conditions in which the non-transformed cells cannot grow and form colonies. For example, if the donor cells are StrR and the recipient cells are StrS, then cells transformed to StrR will grow on medium that contains streptomycin. Since only one strand of the recipient cell’s DNA is transformed initially to streptomycin resistance, only half

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8.7

Cell wall

Doublestranded DNA

Cytoplasmic membrane

Treat with electric current

Transduction

201

Integrated DNA

+

Recipient cell

Fragments of donor DNA

Transformed cell

FIGURE 8.20 Electroporation The electric current makes holes in both the cell wall and the cytoplasmic membrane through which the DNA can pass. These holes are then repaired by the cell, and the DNA becomes incorporated into the chromosome of the cell.

of the daughter cells will be streptomycin resistant. The other half will be streptomycin sensitive and will die on streptomycincontaining medium (see figure 8.19d and 8.19e). Although many other donor genes besides StrR will be transferred and integrated into the chromosome of the recipient cells, these transformants will go undetected because the donor and recipient cells are identical in these other genes.

Artificial Competence Although not all bacteria become naturally competent, double- and single-stranded DNA can be introduced into most cells, including those of bacteria, animals, and plants, through a special treatment of the recipient cells. In one technique called electroporation, bacteria and DNA are mixed together and the mixture is subjected to an electric current (figure 8.20). The current apparently makes holes in the bacterial cell wall and cytoplasmic membrane through which the DNA enters.

MICROCHECK 8.6 Gene transfer can occur in many Gram-positive and Gram-negative bacteria by DNA-mediated transformation in which DNA is released from some cells and is taken up by other competent cells. Competent cells have undergone a number of changes that allow them to bind DNA, take DNA into the cell in a single-stranded form, and integrate the DNA. Artificial means such as electroporation can be used to get DNA into cells that do not become competent naturally. ✓ What effect would adding deoxyribonuclease to the culture have on transformation? ✓ If cells do not become competent naturally, can they still be made to take up DNA? Explain. ✓ Can you devise a test using DNA-mediated transformation that could test chemicals for their mutagenic activity?

Bacterial viruses, called bacteriophages or simply phages, can transfer bacterial genes from a donor to a recipient by a process called transduction. To understand this process, you need to know something about phages and how they infect bacterial cells. Phages consist of genetic material, either DNA or RNA, surrounded by a protein coat. They infect bacteria by attaching to a cell and then injecting their nucleic acid into that cell. Enzymes encoded by the phage genome then degrade the bacterial DNA. Next, the cell’s enzymes replicate the phage nucleic acid and synthesize proteins that make up the empty phage coat. The phage nucleic acid then enters the phage coat and the various components of the phage assemble to produce complete phage particles, which are released, usually as a result of host cell lysis. The phage particles then attach to other bacterial cells, beginning new cycles of infection. Transduction results from rare errors that occur during the infection cycle, giving rise to phage progeny that carry bacterial genes in place of phage genes inside the coat. When these progeny then infect other bacteria, they inadvertently transfer bacterial genes to another bacterium. There are two types of transduction: generalized and specialized. In generalized transduction, any genes of the donor cell can be transferred. It results from of an error during construction of the phage inside the infected cell; a fragment of bacterial DNA is mistakenly substituted for phage DNA within the protein coat (figure 8.21). The product is referred to as a transducing particle. Like a phage, however, the transducing particle will attach to a bacterium and inject the nucleic acid into that cell. Inside the cell, the injected DNA must integrate into the chromosome by homologous recombination if it is to be maintained by the cell. In specialized transduction, only a few specific genes can be transferred. This process will be described in chapter 13, after more details of the infection cycles of bacteriophages are discussed.

MICROCHECK 8.7

8.7 Transduction Focus Points Describe the process of bacterial gene transfer by transduction. Distinguish between generalized and specialized transduction.

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Transduction results from an error that occurs during the infection cycle of bacteriophages, leading to the transfer of bacterial genes from one bacterial cell to another. ✓ How is generalized transduction different from specialized transduction? ✓ Two genes are transduced simultaneously. What does this suggest about the location of the two genes relative to each other? Explain.

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202

CHAPTER EIGHT Phage

Bacterial Genetics

Empty phage coat remains on outside of bacterium.

8.8 Conjugation

Phage DNA enters the cell.

Bacterial host #1

When a phage infects a host cell, the entering nucleic acid codes for deoxyribonuclease which degrades the host DNA.

Phage coat proteins are synthesized and phage DNA is replicated.

During construction (maturation) of the virus particles, a few phage heads may envelop fragments of bacterial DNA instead of phage DNA. Only bacterial DNA is present in the transducing particles.

Focus Points Compare an F⫹ to an F⫺ cell in terms of morphology and gene content. Compare and contrast the state of the F plasmid in a cell (1) that transfers only the plasmid, with a cell that (2) can transfer chromosomal DNA, and a cell that (3) transfers both plasmid and chromosomal DNA.

An important and common mechanism of gene transfer in both Gram-positive and Gram-negative bacteria is conjugation. The process is quite different in the two groups but we will only consider conjugation in Gram-negative bacteria. Conjugation requires contact between donor and recipient cells. This can be shown through the following experiment. If two different auxotrophic mutants are placed on either side of a filter through which fluids, but not bacteria, can pass, genetic recombination does not occur. If the filter is removed, however, allowing cellto-cell contact, genetic recombination takes place. Both plasmids and chromosomal DNA can be transferred by conjugation. The process is complex and many aspects are not understood even though it was first observed in E. coli more than 50 years ago. ■ plasmid, p. 68

The phage carrying the bacterial DNA infects another cell, transferring the bacterial DNA into the new cell.

Bacterial DNA Bacterial host #2

Replaced host DNA

When this bacterial DNA is introduced into a new host cell, it integrates into the bacterial chromosome by homologous recombination. Only genes that are located close together will be transduced together.

Bacteria multiply with new genetic material. Replaced host DNA is degraded.

FIGURE 8.21 Transduction (Generalized) Any piece of the chromosomal DNA of the donor cell can be transferred in this process. All of the DNA molecules of the bacterial virus and the bacteria are double-stranded.

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Plasmid Transfer Transfer of plasmids to other cells is most frequently mediated by conjugation. Conjugative plasmids direct their own transfer from donor to recipient cells. Since plasmids are replicons with an origin of replication, they can replicate inside cells independent of the chromosome. The most thoroughly studied example is the F (fertility) plasmid of E. coli. Although this plasmid does not encode any notable characteristics other than those required for transfer, other conjugative plasmids encode resistance to certain antibiotics, which explains how such resistance can easily spread among a population of cells. E. coli cells that harbor the F plasmid are designated Fⴙ, whereas those that do not are Fⴚ. The F plasmid encodes several proteins required for conjugation, including the F pilus, also referred to as the sex pilus. This pilus attaches to the recipient cell (figure 8.22). ■ F pilus, p. 66 Plasmid transfer can be divided into four steps (figure 8.23): Step 1 Contact between donor and recipient cells. The F pilus of the donor cell recognizes and binds to a specific receptor on the cell wall of the recipient cell. After attachment, the F pilus acts as a grappling hook, pulling the two cells together. Step 2 Mobilization or activation of DNA transfer. The plasmid becomes mobilized for transfer when a plasmidencoded enzyme, an endonuclease, cleaves one strand of the plasmid at a specific nucleotide sequence, the origin of transfer. This results in the formation of a single-stranded DNA molecule with the endonuclease attached to the end.

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8.8

Conjugation

203

F pilus

Step 3 Plasmid transfer. Within minutes of the F⫹ cell contacting the F⫺ cell, a single strand of the F plasmid with the attached endonuclease enters the F⫺ cell. This transfer takes about 2 minutes. Recent research indicates that the DNA passes through the F pilus. Step 4 Synthesis of a functional plasmid inside the recipient and donor cells. Once inside the recipient cell, a strand of DNA complementary to the single-stranded transferred DNA is synthesized. Likewise, a strand complementary to the single-stranded plasmid DNA remaining in the donor is synthesized. Thus, both the donor and recipient cells are now F⫹ and can act as donors of the F plasmid.

Chromosome Transfer 2 mm

FIGURE 8.22 F or Sex Pilus Holding Together Donor and Recipient Cells of E. coli During DNA Transfer During the actual transfer of DNA, the pilus becomes much shorter as it pulls the cells together. The DNA passes through the pilus from donor to recipient cells.

F plasmid Chromosome Origin of transfer

The F + donor cell containing an F plasmid synthesizes an F pilus.

+ Donor cell F +

F pilus

Recipient cell F –

STEP 1 Contact

The F pilus contacts the recipient F – cell.

STEP 2 Activation of DNA for transfer

The plasmid is activated for transfer when an endonuclease cleaves one strand of DNA within the origin of transfer. The F pilus retracts and pulls the donor and recipient cells together.

Chromosomal DNA transfer is less common than plasmid transfer and involves Hfr strains (meaning high frequency of recombination). These are strains in which the F plasmid has integrated into the chromosome at specific sites, which happens occasionally (figure 8.24). Like F⫹ cells, Hfr cells produce an F pilus, and the F plasmid DNA directs its transfer to the recipient cell. However, because the F plasmid DNA is integrated into the chromosome, chromosomal DNA is also transferred as a single stranded DNA molecule (figure 8.25). The entire chromosome is generally not transferred because it would take approximately 100 minutes for this to occur, an unlikely event because the connection between the two cells is likely to break before this time. Unlike the F plasmid, the transferred chromosomal DNA is not a replicon, and so it must integrate into the chromosome of the recipient cell through homologous recombination if it is to be maintained.

Conjugation

Origin of transfer STEP 3 Plasmid transfer

The F plasmid is transferred as a single-stranded DNA molecule. The other strand remains inside the donor cell.

E.coli chromosome

+ F+ Cell

F plasmid

Integration of F plasmid

F plasmid origin of transfer STEP 4 Synthesis of a functional plasmid

The complementary strands to both F plasmid strands are synthesized in the donor and recipient cells. Both cells are F + and synthesize the F pilus. Hfr Cell

F + cell

F + cell

FIGURE 8.23 Conjugation—Transfer of the F Plasmid

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FIGURE 8.24 Hfr Formation Integration of the F plasmid into the bacterial chromosome to form Hfr. Homologous sites, termed insertion sequences, on the F plasmid and the chromosome allow the integration to occur. There is no replacement of DNA in the chromosome; the integration of the F plasmid increases the size of the chromosome. ■ insertion sequence, p. 207

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Bacterial Genetics

The donor cell synthesizes a sex pilus.

F plasmid

Integrated F plasmid

Chromosome

Chromosomal DNA

F' plasmid Chromosome

+ F pilus

Donor cell F +

Recipient cell F – Hfr Cell

Integration of F plasmid

The F pilus contacts the recipient F – cell and pulls the cells together. Genes are indicated as 1, 2, 3, and 4.

Integrated F plasmid

F' Cell

FIGURE 8.26 Formation of F„ Plasmid This F„ plasmid has the transfer properties of the F plasmid but carries chromosomal DNA. This process is reversible.

Genes

1

2

4

3 Hfr cell

Breakage donor DNA strand

The donor chromosome is transferred as singlestranded DNA starting at the origin of transfer. Gene A, closest to the origin, is transferred first. The integrated F plasmid is both at the beginning and at the end of the DNA being transferred. Origin of transfer

2 4

MICROCHECK 8.8

1

3

The donor and recipient cells separate, usually before the entire chromosome is transferred. The single strand in both the recipient cell and donor cell are made double-stranded.

1

4

2

2 1 1'

3

2' Transferred (donor) chromosomal DNA The donor DNA transferred is integrated into the recipient cell’s chromosome. The recipient cell remains F –. The donor cell synthesizes a strand complementary to the untransferred strand of DNA and remains Hfr.

Hfr Cell

Recipient cell DNA

1'

1

2'

2

Integration of donor chromosomal DNA

Conjugation requires contact between donor and recipient cells. Transfer is from a donor cell that synthesizes a F pilus to one that does not. Both plasmid and chromosomal DNA can be transferred. Following transfer, plasmids replicate but chromosomal DNA must be integrated into a replicon. ✓ For which two characteristics essential for conjugation does the F plasmid encode? ✓ Describe the outcomes of the three types of matings ( F⫹ ⫻ F⫺, Hfr ⫻ F⫺, and F„ ⫻ F⫺). ✓ Would you expect transfer of chromosomal DNA by conjugation to be more efficient if cells were plated together on solid medium (agar) or mixed together in a liquid in a shaking flask? Explain.

TABLE 8.3

Comparison of Mechanisms of DNA Transfer

F – Cell

FIGURE 8.25 Conjugation-Transfer of Chromosomal DNA The DNA is transferred as a single-stranded DNA molecule. The recipient genes are designated with a prime („). The corresponding DNA in the donor lacks the prime („).

F„ Donors The F plasmid in Hfr strains can be excised from the chromosome because the process of F plasmid integration into the chromosome is reversible. In some instances, an error occurs in the process of excision, and a small piece of the bacterial chromosome becomes incorporated into the F plasmid (figure 8.26). This F plasmid with its incorporated chromosome is called F„ (F prime), and like the F plasmid it is rapidly and efficiently transferred to F⫺ cells in the

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population. Consequently, any chromosomal genes incorporated into the F plasmid are also transferred. The F„ plasmid usually remains extrachromosomal—that is, it remains independent of the recipient cell’s chromosome. On rare occasions, however, it can integrate into the chromosome of recipient cells, which then become Hfr because they contain the F plasmid integrated into the chromosome. The three mechanisms of DNA transfer are compared in table 8.3.

Mechanism

Main Features

Size of Sensitivity DNA to DNase Transferred addition*

Transformation

Naked DNA transferred

About 20 genes

Yes

Transduction

DNA enclosed in a bacteriophage coat

Small fraction of the chromosome

No

Plasmid transfer

Cell-to-cell contact required

Entire plasmid No

Chromosome transfer

Cell-to-cell contact required; only certain cells can be donors (Hfr)

Variable fraction of chromosome

Conjugation

No

*DNase is an abbreviation of deoxyribonuclease, an enzyme that degrades DNA.

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8.9 The Mobile Gene Pool

8.9 The Mobile Gene Pool Focus Points

TABLE 8.4

Some Plasmid-Coded Traits

Trait

Advances in genomics have uncovered surprising variation in the gene pool (the sum of all genes) of even a single species. For example, nucleotide sequence analysis of many E. coli strains indicates that only about 75% of a strain’s genes are found in all strains of that species. These make up the conserved, or core genome of the species. The remaining genes, which are not conserved, vary considerably among different strains, and are associated with various plasmids, transposons, and regions of DNA called genomic islands. Phage DNA, which we will discuss in chapter 13, is also in this group. Surprisingly, when all the non-conserved genome components of E. coli strains are considered, these sequences vastly outnumber sequences in the core genome. Many of the components of the non-conserved genome are mobile genetic elements, meaning they encode their own transfer, either within the genome of a cell or between cells.

Plasmids Plasmids are common in the microbial world and are found in most members of the Bacteria and Archaea, as well as Eucarya. Like chromosomes, most plasmids are double-stranded DNA molecules that have an origin of replication and therefore can be replicated by the cell before it divides. The machinery required for replication is provided by the cell in which the plasmid resides. Plasmids, however, generally do not encode any information essential to the growth of cells. ■ plasmid, p. 68 ■ origin of replication, p. 166

Plasmids vary in many of their properties; some carry only a few genes, others carry a thousand. Plasmids also vary in the number of copies present in a cell. Low-copy-number plasmids occur in only one or a few copies per cell, whereas high-copynumber plasmids are present in numerous copies, perhaps 500. Most plasmids, termed narrow host range, can replicate in only one species. A few, however, called broad host range, can replicate in many different species. Plasmids are divided into different compatibility groups and only members of a different compatibility group can co-exist in the same cell. Many bacterial plasmids are readily transferred by conjugation. Conjugative, or self-transmissible, plasmids carry all of the genetic information needed for transfer, including an origin of transfer. In contrast, mobilizable plasmids encode an origin of transfer but lack other genetic information required for their own transfer. A conjugative plasmid can help transfer a mobilizable plasmid present in the same cell. Some plasmids, termed promiscuous, can transfer between unrelated species and even between Gram-positive and Gram-negative bacteria. Certain plasmids can even be transferred into plant cells. Some of the traits encoded by plasmids are listed in table 8.4.

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Organisms in Which Trait is Found

Antibiotic resistance

Escherichia coli, Salmonella sp., Neisseria sp., Staphylococcus sp., Shigella sp., and many other organisms

Pilus synthesis

E. coli, Pseudomonas sp.

Tumor formation in plants

Agrobacterium sp. (see Perspective 8.2)

Nitrogen fixation

Rhizobium sp.

Oil degradation

Pseudomonas sp.

Gas vacuole production

Halobacterium sp.

Insect toxin synthesis

Bacillus thuringiensis

Plant hormone synthesis

Pseudomonas sp.

Antibiotic synthesis

Streptomyces sp.

Increased virulence

Yersinia enterocolitica

Toxin production

Bacillus anthracis

Describe how plasmids differ from bacterial chromosomes. Compare and contrast transposons and genomic islands.

205

Not only can plasmids be acquired by a cell, but they can also be lost from a cell. Occasionally, a cell will divide without distributing its plasmids to a daughter cell. If a cell can multiply faster as a consequence of losing the plasmid, the progeny of the cell will eventually predominate. In the laboratory, cells can be grown under conditions that increase the likelihood that a plasmid will be lost. The resulting population has been cured of the plasmid.

Resistance Plasmids Resistance, or R, plasmids confer resistance to many different widely used antimicrobial medications and heavy metals, such as mercury and arsenic. Many of these plasmids are conjugative and are composed of two parts: the resistance, or R, genes, which encode the resistance traits, and a resistance transfer factor, or RTF, which encodes the properties required for conjugation (figure 8.27). Perhaps the most important feature of conjugative R Plasmid Carbenicillin-resistance gene

Chloramphenicolresistance gene

Tetracyclineresistance gene

Origin of replication R genes RTF genes

Pilus-synthesis genes

Origin of transfer

FIGURE 8.27 Two Regions of an R Plasmid The R (resistance) genes code for resistance to various antimicrobials; the RTF (resistance transfer factor) region codes for plasmid replication and the transfer of the plasmid to other bacteria.

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PERSPECTIVE 8.2 Bacteria Can Conjugate with Plants: A Natural Case of Genetic Engineering For more than 50 years, scientists have known that DNA can be transferred between bacteria. Thirty years ago, it was shown that a bacterium can even transfer its genes into plant cells, such as tobacco, carrots, and cedar trees, through a process analogous to conjugation. What led to this discovery started about 100 years ago in the laboratory of a plant pathologist, Dr. Erwin Smith. He showed that the causative agent of a common plant disease, termed crown gall, is a bacterium, Agrobacterium tumefaciens. This disease is characterized by large galls or swellings that occur on the plant at the site of infection, usually near the soil line, the crown of the plant. When other investigators cultured the diseased plant tissue, it had properties that differed from normal plant tissue. Whereas normal tissue requires several plant hormones for growth, crown gall tissue grows in the absence of these added hormones. In addition, crown gall tissue synthesizes large amounts of a compound, an opine, which neither normal plant tissue nor Agrobacterium synthesizes. The most surprising observation was that the plant cells maintained their altered nutritional requirements and the ability to synthesize opine even after the bacteria were killed by penicillin. Investigators concluded that the crown gall plant cells are permanently transformed. Although Agrobacterium is required to start the infection, they are not necessary to maintain the altered nutritional requirements and biosynthetic capabilities of the plant cells.

Chromosome

The explanation of the process by which Agrobacterium causes crown gall tumors and transforms plant cells was established in 1977 following a report that all strains of Agrobacterium capable of causing crown gall tumors contained a large plasmid termed the tumor-inducing, or Ti, plasmid. A group of microbiologists then showed that a specific piece of the Ti plasmid, termed the transferred DNA, or T-DNA, is transferred from the bacterial cell to the plant cell, where it becomes incorporated into the plant chromosome (figure 1). Since no regions of DNA in the plant are similar to those of bacteria, integration occurs through non-homologous recombination. Like conjugation between bacteria, a pilus is required for DNA transfer. The transferred DNA acts like plant DNA because its promoters resemble those of plants rather than those of bacteria. Therefore, the genetic information in the T-DNA is expressed in plants but not in Agrobacterium. This DNA encodes enzymes for the synthesis of the plant hormones as well as for the opine. The expression of these genes supplies the plant cells with the plant hormones, explaining why the transformed plant cells can grow in the absence of added hormones and are able to synthesize the opine. Thus, once incorporated into the plant chromosome, the DNA provides the transformed cell with additional genetic information that confers new properties on the plant cell. ■ promoter, p. 168

Why does Agrobacterium transform plants? This bacterium has the ability to use the opine as a source of carbon and energy, whereas most other bacteria in the soil, as well as plants, cannot. Therefore, Agrobacterium subverts the metabolism of the plant to produce food that only Agrobacterium can use. Thus, Agrobacterium is a natural genetic engineer of plants. The Agrobacterium-crown gall system is of great interest for several reasons. First, it shows that DNA can be transferred from prokaryotes to eukaryotes. Many people believed that such transfer would be impossible in nature and could only occur in the laboratory. Second, this system has spawned an industry of plant biotechnology dedicated to improving the quality of higher plants. Thus, it is possible to replace the genes of hormone and opine synthesis in the Ti plasmid with any other genes, which will then be transferred and incorporated into the plant. With this technology, genes conferring resistance to bacteria, viruses, insects, and different herbicides have been incorporated into a wide variety of plants. Rice has been transformed to synthesize high levels of b-carotene, the precursor of vitamin A. Genetic engineering of plants became a reality once scientists learned how a common soil bacterium caused a well-recognized and serious plant disease. This system serves as a beautiful example of how solving a riddle in basic science can lead to major industrial applications.

T-DNA

T-DNA Chloroplast Plant DNA

Plant cell nucleus

Ti plasmid Agar medium Agrobacterium tumefaciens cell

Agrobacterium cells inoculated into stem of plant

Crown gall tumor develops at site of inoculation.

Bacteria-free tumor tissue is hormone independent and synthesizes an opine.

Plant tumor cell contains T-DNA integrated into the plant chromosome.

FIGURE 1 Agrobacterium sp. Causes Crown Gall and Transforms Plant Cells

R plasmids is that their transfer confers simultaneous resistance to numerous antimicrobials encoded by the R genes. Further, many R plasmids have a broad host range and can multiply in a wide variety of different Gram-negative genera, including Shigella, Salmonella, Escherichia, Yersinia, Klebsiella, Vibrio,

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and Pseudomonas. Transfer of promiscous plasmids can give rise to a wide array of organisms resistant to many different antimicrobials. Members of the normal microbiota, such as E. coli, can serve as a reservoir for R plasmids, which then can be transferred to disease-causing organisms. This is one reason why so many

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8.9 The Mobile Gene Pool Gene coding for the enzyme required for transposition (transposase)

FIGURE 8.28 Transposable Elements (a) Insertion sequence. Note that the sequence of bases at the end of the IS element in one strand is the same as the sequence in the opposite strand reading in the same direction (5„ to 3„). This is the inverted repeat sequence. Only 6 of the 15 to 25 base pairs are shown. (b) Composite transposon. Antibiotic-resistance locus flanked by two insertion elements. The sizes of the various parts are not drawn to scale.

Inverted repeat 5'

3'

3' TCGATG

CATCGA

AGCTAC

GTAGCT

Insertion sequence (IS)

207

5' Inverted repeat

(a) Insertion sequence

Antibiotic-resistance gene 5'

3'

TCGATG

CATCGA

TCGATG

CATCGA

AGCTAC

GTAGCT

AGCTAC

GTAGCT

(IS)

3'

5'

(IS)

(b) Composite transposon

different organisms in a hospital environment are resistant to a variety of antimicrobials. ■ microbiota, p. 348

Transposons In addition to causing mutations, transposons can provide a mechanism for mobilizing genes for transfer. Transposons can move into other replicons in the same cell without any specificity. Several types of transposons exist, varying in the complexity of their structure. The simplest, an insertion sequence (IS), encodes only the enzyme transposase, which is responsible for transposition (figure 8.28a). Flanking the gene are short sequences, usually 15 to 25 base pairs in length, that are identical and usually oriented in opposite directions. These are called inverted repeats. Two regions of DNA are said to be inverted repeats when the sequence of nucleotides in one strand in one region, when read in the 5„ to 3„ direction, is the same as the sequence in the other strand, also read in the 5„ to 3„ direction. Composite transposons (named Tn1, Tn2, and so on) consist of at least one gene whose product often is easily recognized, such as a gene coding for antimicrobial resistance, flanked by ISs (figure 8.28b). Composite transposons, like insertion sequences, can move in the same replicon or from one to another in the cell. Their movement is readily followed by the easily recognized gene product they encode. They integrate into their new location through non-homologous recombination, a process that does not require a similar sequence in the region of recombination. If a composite transposon inserts into a conjugative plasmid, it can be transferred to other cells. In theory, any gene or group of genes can move to another site if they are bounded by ISs, but those that carry genes for antibiotic resistance are particularly important medically. The introduction in this chapter presented a real-life example of how a transposon enabled a strain of Staphylococcus aureus to become resistant to vancomycin. The patient initially was infected with a strain of S. aureus that was susceptible to vancomycin, but resistant to many common antibiotics. After treatment with vancomycin, a strain of S. aureus resistant to that drug was isolated from the patient. The only obvious difference between the two isolates was that the latter had a gene that encoded resistance to vancomycin inserted into a plasmid harbored by both strains. But where did the

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gene come from? Further analysis suggested that it was acquired from a vancomycin-resistant strain of Enterococcus faecalis isolated from the same patient. The resistance gene of that bacterium was identical to the one of the S. aureus isolate, and was also part of a transposon integrated into a plasmid. It appears that E. faecalis transferred this plasmid containing the transposon to the sensitive S. aureus by conjugation (figure 8.29). This entering plasmid was apparently destroyed by enzymes in S. aureus, but before it was Vancomycin resistance gene

E. faecalis resistant to vancomycin

Plasmid from E. faecalis destroyed

Plasmid

S. aureus sensitive to vancomycin E. faecalis plasmid transferred by conjugation

Transposon jumps from one plasmid to another Vancomycin resistant S. aureus

FIGURE 8.29 Transfer of Vancomycin Resistance to S. aureus Both E.

Vancomycin resistant S. aureus

faecalis and S. aureus are Gram ; cocci but are unrelated to one another. It is quite possible that the vancomycin resistance gene was originally in the chromosome of E. faecalis and jumped to a plasmid.

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destroyed, the transposon jumped to the plasmid that was already in the S. aureus cell, thereby creating the vancomycin-resistant S. aureus. Considering the ease at which DNA can move among a bacterial population, is it any wonder that antibiotic resistance is such a serious problem in treating infectious diseases today?

Genomic Islands Genomic Islands are other members of the mobile gene pool. They are large DNA segments in a cell’s genome that are thought to have originated in other species. This assumption is based on the fact that their base composition is quite different from the rest of the cell’s genomic sequences. In general, each bacterial species has a characteristic proportion of G:C base pairs, so a large segment of DNA that has a very different G:C ratio suggests that the segment originated from a foreign source and was transferred to the cell through horizontal gene transfer. ■ base composition, p. 248 The characteristics encoded by genomic islands include utilization of specific energy sources, acid tolerance, development of symbiosis, and ability to cause disease. Genomic islands that encode the latter are called pathogenicity islands.

TABLE 8.5

Some members of the mobile gene pool are summarized in table 8.5.

MICROCHECK 8.9 Plasmids vary in size, copy number, host range, genetic composition, compatibility to co-exist with other plasmids, and their ability to be transferred to other cells. One of the most important plasmids is the R plasmid, which codes for resistance to various antimicrobial medications and heavy metals. Transposons can move from one location to another in the same replicon or to other replicons. Transposition requires that the gene being transposed has inverted repeat sequences on its ends and the enzyme transposase as part of the insertion sequence. Genomic islands are large DNA segments that are thought to have originated in other species. ✓ What functions must a plasmid code for in order to be selftransmissible? ✓ How does transposition promote gene transfer between bacteria? ✓ What does the phrase, “reservoir for R plasmids” mean when referring to plasmids carried by non-disease-causing bacteria?

Mobile Genetic Elements

Name

Composition

Properties

Transposon

Moves to different locations in DNA in same cell

Insertion Sequence (IS)

Transposase gene flanked by short repeat sequences

Composite Transposon

Recognizable gene flanked by ISs

Same as insertion sequence

Plasmid

Circular double-stranded DNA replicon; smaller than chromosomes

Generally codes only for non-essential genetic information

Genomic Island

A large fragment of DNA in a chromosome or plasmid

Codes for genes which allow cell to occupy specific environmental locations

FUTURE CHALLENGES Hunting for Magic Bullets Because of the increasing resistance of microorganisms to current antimicrobial medications, the demand for new antimicrobials that will kill these resistant organisms is rapidly increasing. It is surprising and sobering to realize that only two new classes of antimicrobials have been introduced into clinics in the past 40 years. The great challenge is to develop new antimicrobial agents that strike at targets different from those attacked by current antimicrobials. With the revolution that has been occurring in biology over the past 15 years, the development of new antimicrobial agents may become a reality. Promising new strategies are based on knowing the genomic sequence of microbial pathogens. Many of the microbial genomes which have now been sequenced

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are human pathogens. The study and analysis of the nucleotide sequence of DNA is called genomics. The next step is to identify genes necessary for the survival of the microorganism or required to cause disease. To gain some understanding of the function of any gene, one must compare its DNA sequence with the sequence of all other genes that have been put into a database, called GenBank. If the gene that has been sequenced is similar in sequence to any other gene, then it is assumed that the two genes have similar functions. Thus, if the function of a gene that has been sequenced in any organism is known, the function of all genes with a similar sequence is likely to be similar. This is the science of bioinformatics, which involves the analysis of the nucleotide sequence of DNA in order to understand what it codes for. Genes that are

required for virulence in the pathogen but are not found in the host are potential targets. It should be possible to design a protein that inhibits the virulence protein and thereby prevents disease. To develop an antimicrobial that inhibits an enzyme required for virulence requires a great deal of information about the enzyme, how it folds, what its three-dimensional structure is, and whether or not it interacts with other proteins. In the past, the search for antimicrobial medications has relied on random screening. Scientists looked for growth inhibition of a pathogen by a large number of organisms isolated from soil samples collected from around the world. Today, new technologies based on microbial genomics should identify new targets and provide a rational approach to developing new antimicrobials.

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Summary

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SUMMARY 8.1 Genetic Change in Bacteria

8.4 Repair of Damaged DNA (table 8.2)

The genotype of bacteria can change either through mutations, permanent changes in the existing nucleotide sequence of a cell’s DNA, or through the acquisition of DNA from other organisms. Bacteria contain only a single set of genes (haploid) so any changes in DNA are expressed rapidly. Genes can be transferred from one organism to another, horizontal gene transfer (figure 8.1b), and from parent to offspring, vertical gene transfer (figure 8.1a).

Repair of Errors in Base Incorporation DNA polymerase has a proofreading function. In mismatch repair, an endonuclease makes a cut in one strand of DNA, and another enzyme degrades a portion of the strand, removing the misincorporated nucleotide. A new DNA strand is then synthesized (figure 8.10).

Gene Mutation As a Source of Genetic Change 8.2 Spontaneous Mutations Spontaneous mutations are changes in the nucleotide sequences in DNA that occur without the addition of agents known to cause mutations. These mutations are rare and occur at a characteristic frequency for each gene. They are stable but on rare occasion can undergo a change back to the non-mutant form—a reversion. Genes mutate independently of one another, and the chance that two mutations will occur within the same cell is the product of the individual mutation rates. Base Substitution (figure 8.3) Base substitutions usually occur during DNA replication; point mutations occur when only one base pair is changed (figure 8.2). Reactive oxygen molecules can modify guanine in DNA, leading to an increased frequency of base substitutions during DNA replication. Removal or Addition of Nucleotides (figure 8.4) Frameshift mutations involve the addition or deletion of nucleotides, often resulting in the formation of a stop codon and the synthesis of a shortened protein. Transposable Elements (Jumping Genes) (figure 8.29) Certain genes, called transposons, have the ability to move to any other location in the genome. Introduction of a transposon into another gene insertionally inactivates that gene (figure 8.5).

8.3 Induced Mutations (table 8.1) Chemical Mutagens Chemical mutagens frequently alter hydrogen-bonding properties of purines and pyrimidines, increasing the frequency of mutations. Base analogs with different hydrogen-bonding properties can be incorporated into DNA in place of the usual purines and pyrimidines (figure 8.7). Intercalating agents are flat molecules that insert into the double helix and push nucleotides apart, resulting in a frameshift mutation (figure 8.8). Transposition Insertional inactivation results when a transposon integrates into a new site in the cell’s genome and inactivates the gene (figure 8.5). Radiation Ultraviolet irradiation results in thymine dimers due to the formation of covalent bonds between adjacent thymine molecules on the same strand of DNA (figure 8.9). X rays cause single-strand breaks, double-strand breaks, and alterations to the DNA bases.

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Repair of Thymine Dimers In light repair, a photoreactivating enzyme breaks the bonds of the thymine dimer, thereby restoring the original molecule (figure 8.11a). In excision, or dark repair, the damaged single-stranded segment is excised by an endonuclease. A new strand is synthesized by DNA polymerase (figure 8.11b).

Repair of Modified Bases in DNA Specific glycosylases can remove modified bases, such as oxidized guanine and alkylated bases in DNA (figure 8.12). SOS Repair SOS repair is a last-ditch repair mechanism in which about 20 enzymes are induced by damaged DNA, including a new DNA polymerase that can bypass the damaged DNA but does not proofread the DNA it synthesizes. Consequently, the synthesized DNA contains many mutations. SOS repair accounts for the mutagenic activity of UV irradiation.

8.5 Mutant Selection Direct Selection Direct selection involves inoculating cells onto a medium on which the mutant, but not the parent, can grow; these are easy mutants to isolate (figure 8.13).

Indirect Selection Indirect selection is required when no medium supports the growth of only the desired mutant. Replica plating involves the simultaneous transfer of all the colonies on one plate to two other plates and the comparison of the growth of individual colonies on both plates (figure 8.14). Penicillin enrichment increases the proportion of mutants in a population by killing growing bacteria in a medium on which only non-mutants will grow (figure 8.15). Testing of Chemicals for Their Cancer-Causing Ability The Ames test measures whether a chemical, a suspected carcinogen, increases the frequency of reversion; a positive test indicates the subject chemical is a mutagen and is therefore a possible carcinogen (figure 8.16).

Gene Transfer As a Mechanism of Genetic Change (table 8.3) 8.6 DNA-Mediated Transformation DNA-mediated transformation involves the transfer of “naked” DNA. DNA must be integrated into the recipient’s genome to be maintained (figure 8.18). Deoxyribonuclease addition prevents the transfer (figure 8.19). Natural Competence Natural competence is the ability of a cell to take up and integrate DNA. DNA enters the cell as a single-stranded molecule and is integrated by replacing recipient cell genes via homologous recombination.

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Artificial Competence Cells can be made artificially competent by electroporation; in this process, the cells are treated with an electric current, which makes holes in the cell envelope through which DNA can pass (figure 8.20).

8.9 The Mobile Gene Pool (table 8.5)

8.7 Transduction

Plasmids (table 8.4) Plasmids are extrachromosomal replicons that code for non-essential information; many are readily transferred by conjugation. Self-transmissible or conjugative plasmids carry all the genetic information needed for their transfer. R plasmids code for antibiotic resistance (figure 8.27).

Transduction involves the transfer of bacterial DNA by a bacteriophage (figure 8.21). DNA must be integrated to be maintained (figure 8.18).

8.8 Conjugation Conjugation requires cell-to-cell contact (figure 8.22). Plasmid Transfer The donor cells synthesize an F pilus encoded on an F plasmid, which recipient cells do not have; the F plasmid is transferred from an F⫹ to an F⫺ cell through the pilus (figure 8.23). Chromosome Transfer Chromosome transfer occurs when the F plasmid integrates into a chromosome and the resulting cell can transfer a portion of the chromosome into a recipient cell (figures 8.24, 8.25). DNA must be integrated into a replicon of the recipient in order to be maintained (figure 8.18).

Many members of the gene pool can be transferred to other locations within a cell or to other cells. These members include plasmids, transposons, and genomic islands.

Transposons (figure 8.28) Transposons provide a mechanism for mobilizing genes because they can move into other replicons in the same cell. The simplest transposon is an insertion sequence (IS), which only contains a gene that codes for the enzyme transposase (figure 8.28a). A composite transposon consists of one or more genes flanked by insertion sequences (figure 8.28b). Genomic Islands Genomic islands are large DNA segments in a cell that are thought to have originated in other species.

F„ Donors In an F„ donor, the F plasmid is excised from the chromosome and carries a piece of chromosome with it. This piece is transferred together with the F plasmid (figure 8.26).

REVIEW QUESTIONS Short Answer 1. What one activity must all plasmids carry out? 2. What is the term that describes a plasmid that can transfer itself from E. coli into Pseudomonas, where it can replicate? 3. What type of mutation in an operon is most likely to affect the synthesis of more than one protein? 4. What are the two necessary features of an insertion sequence? 5. What enzyme has proofreading ability? How does it function in proofreading? 6. Give an example of gene transfer that involves homologous recombination. Give one that involves non-homologous recombination. 7. Single-strand integration of DNA has been shown to be a feature of which mechanism of DNA transfer? 8. What feature of an F„ particle is similar to chromosomal DNA? To a plasmid? 9. Name three mobile genetic elements. 10. Name three ways in which plasmids differ from bacterial chromosomes.

Multiple Choice 1. A culture of E. coli is irradiated with ultraviolet (UV) light. Answer questions 1 and 2 based on this statement. The effect of the UV light is to specifically a) join the two strands of DNA together by covalent bonds. b) join the two strands of DNA together by hydrogen bonds. c) form covalent bonds between thymine molecules on the same strand of DNA. d) form covalent bonds between guanine and cytosine. e) delete bases.

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2. The highest frequency of mutations would be obtained if, after irradiation, the cells were immediately a) placed in the dark. b) exposed to visible light. c) shaken vigorously. d) incubated at a temperature below their optimum for growth. e) The frequency would be the same no matter what the environmental conditions are after irradiation. 3. Penicillin enrichment of mutants works on the principle that a) only Gram-positive cells are killed. b) cells are most sensitive to antimicrobial medications during the lag phase of growth. c) most Gram-negative cells are resistant to penicillin. d) penicillin only kills growing cells. e) penicillin inhibits formation of the lipopolysaccharide layer. 4. Repair mechanisms that occur during DNA synthesis are 1. mismatch repair. 2. proofreading by DNA polymerase. 3. light repair. 4. SOS repair. 5. excision repair. a) 1, 2 b) 2, 3 c) 3, 4 d) 4, 5 e) 1, 5 5. You are trying to isolate a mutant of wild-type E. coli that requires histidine for growth. This can best be done using 1. direct selection. 2. replica plating. 3. penicillin enrichment. 4. a procedure for isolating conditional mutants. 5. reversion. a) 1, 2 b) 2, 3 c) 3, 4 d) 4, 5 e) 1, 5

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Review Questions 6. The properties that all plasmids share are that they 1. all carry genes for antimicrobial resistance. 2. are self-transmissible to other bacteria. 3. always occur in multiple copies in the cells. 4. code for non-essential functions. 5. replicate in the cells in which they are found. a) 1, 2 b) 2, 3 c) 3, 4 d) 4, 5 e) 1, 5 7. The addition of deoxyribonuclease to a mixture of donor and recipient cells will prevent gene transfer via a) DNA transformation. b) chromosome transfer by conjugation. c) plasmid transfer by conjugation. d) generalized transduction. 8. An F pilus is essential for 1. DNA transformation. 2. chromosome transfer by conjugation. 3. plasmid transfer by conjugation. 4. generalized transduction. 5. cell movement. a) 1, 2 b) 2, 3 c) 3, 4 d) 4, 5 e) 1, 5 9. A plasmid that can replicate in E. coli and Pseudomonas is most likely a/an a) broad host range plasmid. b) self-transmissible plasmid. c) high-copy-number plasmid. d) essential plasmid. e) low-copy-number plasmid. 10. The frequency of transfer of an F„ DNA molecule by conjugation is closest to the frequency of transfer of a) chromosomal genes by conjugation. b) an F plasmid by conjugation.

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211

c) an F plasmid by transformation. d) an F plasmid by transduction. e) an R plasmid by DNA transformation.

Applications 1. Some bacteria are more resistant to UV light than others. Discuss two reasons why this might be the case. What experiments could you do to determine whether each of the two possibilities could be correct? 2. A pharmaceutical researcher is disturbed to discover that the major ingredient of a new drug formulation causes frameshift mutations in bacteria. What other information would the researcher want before looking for a substitute chemical?

Critical Thinking 1. You have the choice of different kinds of mutants for use in the Ames test to determine the frequency of reversion by suspected carcinogens. You can choose a deletion, a point mutation, or a frameshift mutation. Would it make any difference which one you chose? Explain. 2. You have isolated a strain of E. coli that is resistant to penicillin, streptomycin, chloramphenicol, and tetracycline. You also observe that when you mix this strain with cells of E. coli that are sensitive to the four antibiotics, they become resistant to streptomycin, penicillin, and chloramphenicol but remain sensitive to tetracycline. Explain what is going on.

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9 Researcher in a molecular biology laboratory.

Biotechnology and Recombinant DNA A Glimpse of History In 1976, Argentinean newspapers reported a violent shootout between soldiers and the occupants of a house in suburban Buenos Aires, leaving the five extremists inside dead. Conspicuously absent from those reports was the identity of the “extremists”—a young couple and their three children, ages 6 years, 5 years, and 6 months. Over the next seven years, similar scenarios recurred as the military junta that ruled Argentina eliminated thousands of citizens it perceived as threats. This “Dirty War,” as it came to be known, finally ended in 1983 with the collapse of the military junta and the election of a democratic government. The new leaders opened previously sealed records, which confirmed what many had already suspected—that more than 200 children survived the carnage and had in fact been kidnapped and placed with families in favor with the junta. Dr. Mary-Claire King was at the University of California at Berkeley when her help was enlisted in the effort to return the children to the surviving members of their biological families. Dr. King and others recognized that DNA technology could be used for this important humanitarian cause. By analyzing certain DNA sequences, blood and tissue samples from one individual can be distinguished from those of another. These same principles can also be used to show that a particular child is the progeny of a given set of parents. Because a person has two copies of each chromosome—one inherited from each parent—one half of a child’s DNA will represent maternal sequences and the other half will represent paternal traits. The case of the Argentinean children presented a great challenge, however, as most of the parents were dead or missing. Often, the only surviving relatives were aunts and grandmothers, and it is difficult to use chromosomal DNA to show genetic relatedness between a child and such relatives. Dr. King decided to investigate mitochondrial DNA (mtDNA). This organelle DNA, unlike chromosomal DNA, is inherited only from the mother. A child will have the same nucleotide

sequence of mtDNA as his or her siblings, the mother and her siblings, as well as the maternal grandmother. By comparing the nucleotide sequences of mtDNA in different individuals, Dr. King was able to locate key positions that varied extensively among unrelated people, but were similar in maternal relatives. Dr. King’s technique, born out of a desire to help reunite families victimized by war, has now found many uses. Today her lab, which is now at the University of Washington, remains very active using molecular biology techniques for humanitarian efforts, identifying the remains of victims of atrocities around the world.

A

revolution has occurred in molecular biology over the past several decades—the science has been transformed from a descriptive study of what cells are, to an intricate study of how they function. A driving force in that revolution was the development of simple methods to extract and manipulate DNA, the blueprint of life. Biotechnology is the use of microbiological and biochemical techniques to solve practical problems and produce useful products. In the past, this usually meant laboriously searching for naturally occurring mutants that produced maximal product or expressed other desirable characteristics. Today, the rapid developments in recombinant DNA techniques, the methods scientists use to study and manipulate DNA, have made it possible to genetically alter organisms to give them more useful traits. Researchers can isolate genes from one organism, manipulate the purified DNA in vitro, and then transfer the genes into another organism, a process called gene cloning. In fact, biotechnology is now nearly synonymous with genetic engineering, the process of

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9.1 Fundamental Tools Used in Biotechnology

KEY TERMS Colony Blotting Technique used to determine which colonies on an agar plate contain a given nucleotide sequence. DNA Microarray Technique used to study gene expression patterns in an organism. DNA Probe Single-stranded piece of DNA tagged with a detectable marker and used to detect its complement.

DNA Sequencing Technique used to determine the sequence of nucleotides in a DNA molecule. Fluorescence in situ Hybridization (FISH) Technique used to detect a given nucleotide sequence within intact cells affixed to a microscope slide.

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Polymerase Chain Reaction (PCR) Technique used to exponentially amplify specific regions of a DNA molecule. Recombinant DNA Molecule DNA molecule created by joining DNA fragments from two different sources.

Gel Electrophoresis A procedure used to separate DNA fragments (or other macromolecules) according to their size.

Restriction Enzyme Type of enzyme that recognizes and cleaves a specific sequence of DNA.

Genetic Engineering Deliberately altering an organism’s genetic information using in vitro techniques.

Vector DNA molecule, often a plasmid, that acts as a carrier of cloned DNA.

deliberately altering an organism’s genetic information using in vitro techniques. Since the advent of gene cloning, a virtual toolbox of DNA technologies has been developed. These have generated information and innovations that are impacting society in innumerable ways—from agricultural practices and medical diagnoses to evidence used in the courtroom.

EcoRI recognition sequence (a)

G G C T G A A T T C G C T T C C G A C T T A A G C G A A

9.1 Fundamental Tools Used in Biotechnology

Chromosomal DNA is digested with EcoRI, generating restriction fragments.

Cohesive ("sticky") ends

Focus Point A A T T C G C T T

G G C T G

Describe the role of restriction enzymes and gel electrophoresis in biotechnology.

Before exploring the application of biotechnology, it is helpful to understand some of the basic components of a molecular biologist’s “tool kit.” These include restriction enzymes, which cut DNA into fragments, and gel electrophoresis, which separates DNA fragments according to size. As we describe these, it is important to remember that diagrams focus on only one or a few DNA molecules in a solution to illustrate what is happening at a molecular level. In reality, scientists are generally working with DNA isolated from cultures containing well over a million cells.

Restriction Enzymes Restriction enzymes are naturally occurring enzymes that allow scientists to easily cut DNA into fragments in a predictable and controllable manner (figure 9.1a). Each enzyme recognizes a specific 4 to 6 base-pair nucleotide sequence (table 9.1). The sequences are characteristically palindromes, meaning that the sequence is the same on both strands when each is read in the 5„ to 3„ direction. Wherever the palindrome recognized by a particular restriction enzyme is found, that enzyme cuts each strand within

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C C G A C T T A A

G C G A A

(b)

N N N N G

+

N N N N C T T A A

A A T T C N N N N G N N N N

Complementary cohesive ends can anneal. N N N N G

A A T T C N N N N

N N N N C T T A A

G N N N N DNA ligase forms a covalent bond between adjacent nucleotides.

N N N N G A A T T C N N N N N N N N C T T A A G N N N N

FIGURE 9.1 Action of Restriction Enzymes (a) Digesting DNA with a restriction enzyme generates restriction fragments. (b) Fragments that have complementary cohesive ends can anneal, regardless of their original source (N=nucleotide, meaning that it could be any of the 4 bases as long as base-pairing rules are followed).

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TABLE 9.1

Examples of Common Restriction Enzymes D

Recognition Sequence (arrows Enzyme Microbial Source indicate cleavage sites) Arthrobacter luteus

5„ A G C T 3„ 3„ T C G A 5„

BamHI

Bacillus amyloliquefaciens H

5„ G G A T C C 3„ 3„ C C T A G G 5„

EcoRI

Escherichia coli RY13

5„ G A A T T C 3„ 3„ C T T A A G 5„ D

D

D

D

D

AluI

or near that sequence, thereby cleaving the double-stranded DNA molecules. This action digests the DNA, generating a series of pieces called restriction fragments. ■ restriction enzymes, p. 314 Each restriction enzyme has been given a name that represents the bacterium from which the enzyme was first isolated. The (a)

first letter represents the first letter of the genus name, and the next two letters are derived from the species name. Any other numbers or letters designate the strain and order of discovery. For example, a restriction enzyme from E. coli strain RY13 is called EcoRI. Researchers use restriction enzymes not only to cut DNA, but also to generate fragments that can easily be joined to fragments from an entirely different source. This is possible because many restriction enzymes produce a staggered cut in the recognition sequence, generating ends with a short overhang of usually 4 bases (see figure 9.1b). The overhangs are called sticky ends or cohesive ends because they will form base pairs, or anneal, with one another. Any two complementary cohesive ends can anneal, even those from two different organisms. The relatively weak hydrogen bonds that hold the strands together are only temporary, however. The enzyme DNA ligase forms a covalent bond between the sugar-phosphate residues of adjacent nucleotides, joining the two molecules. Thus, if restriction enzymes are viewed as scissors that cut DNA into fragments, then DNA ligase is the glue that pastes the fragments together. The combined actions of restriction enzymes and DNA ligase enable researchers to join fragments of DNA from diverse sources, creating recombinant DNA molecules. ■ DNA ligase, p. 167

Gel Electrophoresis Gel electrophoresis is used to separate DNA fragments according to size (figure 9.2). The technique uses a slab of gel that has the consistency of a very firm gelatin and is made of either agarose, a highly purified form of agar, or polyacrylamide. A DNA sample is put into a well in the gel; there are generally numerous wells

Sample Sample Sample Size 1 2 3 standard

– 23 kb* 9.4 kb 6.6 kb 4.4 kb

Longer fragments

2.3 kb 2.0 kb

Shorter fragments

Samples are loaded into wells.

+

DNA migrates to the positivelycharged electrode. The sievelike effect of the gel impedes long fragments while allowing short ones to pass through more quickly.

Fragments in the samples are separated according to size.

* Fragment sizes in size standard kb = 1,000 base pairs

(b)

FIGURE 9.2 Gel Electrophoresis (a) Gel electrophoresis separates DNA fragments according to size. (b) DNA on the gel is visible when stained with ethidium bromide and viewed with UV light; each fluorescent band represents millions of molecules of a specific-sized fragment.

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9.2 Applications of Genetic Engineering

in a gel so that multiple samples can be analyzed simultaneously. As a means to eventually determine the size of the various DNA fragments in the samples, a size standard is routinely put into a well of the same gel. This is simply a mixture of DNA fragments of known sizes that can be used as a basis for later comparison. The gel is then subjected to an electrical current. DNA is negatively charged, so the fragments migrate toward the positively charged electrode. As the DNA moves through the gel, however, not all fragments progress at the same rate. This is because the gel acts as a sieve, impeding the long fragments while allowing the shorter ones to pass through more quickly. Because of the sieve-like effect of the gel, the restriction fragments are separated according to their size. The DNA is not visible in the gel unless it is stained. To do this, the gel containing the separated DNA fragments is immersed in a solution containing ethidium bromide. This dye binds DNA and fluoresces when viewed with UV light (see figure 9.2b). Each fluorescent band represents millions of molecules of a specificsized fragment of DNA. Gel electrophoresis can also be used to separate other macromolecules, specifically RNA and proteins, according to their size. The basic principles are similar to that illustrated for separating DNA, but the gel compositions differ.

MICROCHECK 9.1 Restriction enzymes recognize specific nucleotide sequences, and then cut the DNA, generating restriction fragments. Gel electrophoresis is used to separate DNA fragments according to their size. ✓ How does gel electrophoresis separate different-sized DNA fragments? ✓ What is the significance of cohesive ends? ✓ Based on the protocol for naming restriction enzymes, what is the name of one isolated from Staphylococcus aureus strain 3A?

TABLE 9.2

215

Some Applications of Genetic Engineering

Example

Use

PROTEIN PRODUCTION Pharmaceutical proteins Alpha interferon

Treating cancer and viral infections

Erythropoietin

Treating some types of anemia

Beta interferon

Treating multiple sclerosis

Deoxyribonuclease

Treating cystic fibrosis

Factor VIII

Treating hemophilia

Gamma interferon

Treating cancer

Glucocerebrosidase

Treating Gaucher disease

Growth hormone

Treating dwarfism

Insulin

Treating diabetes

Platelet derived growth factor

Treating foot ulcers in diabetics

Streptokinase

Dissolving blood clots

Tissue plasminogen activator

Dissolving blood clots

Vaccines Hepatitis B

Preventing hepatitis

HPV

Preventing cervical cancer

Foot-and-mouth disease

Preventing foot-and-mouth disease in animals

Other proteins Bovine somatotropin

Increasing milk production in cows

Chymosin

Cheese-making

Restriction enzymes

Cutting DNA into fragments

DNA PRODUCTION DNA for study

9.2 Applications of Genetic Engineering

Determining nucleotide sequences; obtaining DNA probes

RESEARCHING GENE FUNCTION AND REGULATION Creating gene fusions

Studying the conditions that affect gene activity

TRANSGENIC PLANTS

Focus Point Describe three general applications of genetically engineered bacteria, and one application of genetically engineered plants.

Genetic engineering brought biotechnology into a new era by providing a powerful tool for manipulating microorganisms for medical, industrial, and research uses (table 9.2). More recently, techniques that permit the genetic engineering of plants and animals have been developed.

Pest-resistant plants

Insect-resistant corn, cotton, and potatoes

Herbicide-resistant plants

Biodegradable herbicide can be used to kill weeds without killing engineered plants (soybean, cotton, corn)

Plants with improved nutritional value

Rice that produces vitamin A and iron

Plants that function as edible vaccines

Enables researchers to study foods as vehicles for edible vaccines

Genetically Engineered Bacteria Genetic engineering relies on DNA cloning, a process that involves isolating DNA from one organism, using restriction enzymes to cut the DNA into fragments, and then introducing those fragments into cells of another organism, most commonly E. coli. As part of the process, the cloned DNA must replicate in

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the recipient in order for it to be passed to daughter cells, generating a population of cells, each harboring a copy of the DNA fragment (see figure 8.18). Most DNA fragments, however, are unlikely to contain an origin of replication and therefore will not replicate independently in a cell, nor will they integrate into the

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chromosome. To overcome this problem, each fragment being cloned must be inserted into a plasmid or other independently replicating DNA molecule to from a recombinant molecule. The DNA molecule used as a carrier of the cloned DNA is called a vector, and is commonly a plasmid that has been genetically modified. The DNA that has been incorporated into the vector is called an insert. If a gene coding for a valuable protein is inserted into a high-copy-number vector and then introduced into a bacterium, that organism will then make increased amounts of the protein, because each gene copy can be transcribed and translated (figure 9.3). ■ origin of replication, p. 166 ■ high-copy-number

Bacterium X

Isolate the total DNA from the organism

Use restriction enzymes to generate genomic fragments B

A

plasmid, p. 205

E

An approach frequently used to clone a specific gene is to clone a set of restriction fragments that together make up the entire genome of the organism being studied into a population of E. coli cells (figure 9.4). While each cell in the resulting population contains only one fragment of the genome, the entire genome is represented in the population as a whole. Because each cloned molecule can be viewed as one “book” of the total genetic information, the collection of clones is called a DNA library. Once a DNA library has been prepared, colony blots (which will be described later) can be used to determine which cells contain the gene of interest. Genetically engineered bacteria have a variety of uses, including protein production, DNA production, and research. In fact, a great deal of the information described in this textbook has been revealed through research involving genetically engineered bacteria.

D

C F

G

H Join genomic fragments to vectors

Vector molecules

A Recombinant molecules

B

F

E

D

C G

H

Introduce the recombinant molecules into E. coli cells

D

B

Protein Production

A

A number of different pharmaceutical proteins are now produced by genetically engineered microorganisms. In the past, these proteins were extracted from live animal or cadaver tissues, which made them expensive and limited in supply. Human insulin, used in treating diabetes, was one of the first important pharmaceutical proteins to be produced through genetic engineering. The original commercial product, extracted from pancreatic glands of cattle and pigs, sometimes caused allergic reactions. Once the gene for human insulin was cloned into bacteria, microorganisms became

E

FIGURE 9.3 Cloning into a HighCopy-Number Vector When a gene is inserted into a high-copy-number vector, multiple copies of that gene will be present in a single cell, resulting in the synthesis of many more molecules of the encoded protein.

High-copynumber vector

Gene

+

Gene inserted into vector

Multiple copies of the gene produced

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C

A population of E. coli cells that, together, contain all of the fragments of the genome of Bacterium X

F G H

FIGURE 9.4 A DNA Library Each cell contains one fragment of a given organism’s genome.

the major source of insulin sold in the United States. A 2,000-liter culture of E. coli that contains the insulin gene yields 100 grams of purified insulin—an amount that would require 1,600 pounds of pancreatic glands! Using microbes to produce insulin is safer and more economical than extracting it from animal tissues. Another medically important use of genetically engineered microorganisms is vaccine production. Vaccines protect against disease by harmlessly exposing a person’s immune system to killed or weakened forms of the pathogen, or to a part of the pathogen. Although vaccines are generally composed of whole bacterial cells or viral particles, only specific proteins, or parts of the proteins, are actually necessary to induce protection, or immunize, against the disease. The genes coding for these proteins can be cloned into yeast or bacteria so that these cells produce large amount of immunizing the proteins, which can then be purified. This type of vaccine is currently used to prevent hepatitis B and cervical cancer in humans and foot-and-mouth disease of domestic animals. ■ vaccines, p. 433

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One of the most widely used proteins made by genetically engineered organisms is chymosin, a proteolytic enzyme used in cheese production. It is a natural component of rennin, a preparation from the stomach of calves. Chymosin causes milk to coagulate and produces desirable changes in the characteristics of cheeses as they ripen. Using genetically engineered bacteria to produce chymosin is preferable to isolating rennin from calves because the microbial product is less expensive and more reliably available. Other proteins produced by genetically engineered microbes include various restriction enzymes and bovine somatotropin, a growth hormone used to increase milk production in dairy cows.

DNA Production In many cases, a researcher is interested in obtaining readily available supplies of certain DNA fragments. By cloning a segment of DNA into a well-characterized bacterium such as E. coli, a readily available source of that sequence is available for study and further manipulation. Human genes are often cloned into bacteria to make them easier to study. A human cell contains an estimated 25,000 genes, whereas E. coli contains only 4,500 genes; thus, a human gene cloned into the bacterium on a high-copy-number vector represents a much higher percentage of the total DNA in the recipient cell than in the original cell. This makes it easier to isolate the DNA as well as the gene product. Random samples of DNA from any environment can be cloned into E. coli and then the nucleotide sequence determined. By doing this, the genomic characteristics of some of the 99% of bacteria that have not been growth in culture can be studied. This “shotgun cloning” is the first step in metagenomics, the study of the total genomes in a sample. Metagenomics will be discussed when we describe the applications of DNA sequencing.

organism. Transgenic plants are of particular interest to microbiologists because their development was spawned as a result of basic research studying Agrobacterium tumefaciens; this bacterium harbors a plasmid, the Ti plasmid, that has been genetically manipulated so it can be used as a vector to deliver desirable genes to plant cells (see Perspective 8.2). Corn, cotton, and potatoes have been engineered to produce a biological insecticide called Bt-toxin, which is naturally produced by the bacterium Bacillus thuringiensis as it forms endospores. Unlike many chemically synthesized toxins, Bt-toxin is toxic only to insects, including their larvae. Soybeans, cotton, and corn have been engineered to resist the effects of the herbicide glyphosate (RoundupTM). This enables growers to apply this biodegradable herbicide, which kills weeds and other non-engineered plants, in place of more persistent alternatives. Also, because the herbicide can be applied throughout the growing season, the soil can be tilled less frequently, preventing erosion. Plants with improved nutritional value are also being developed. For example, genes that code for the synthesis of b-carotene, a precursor of vitamin A, have been introduced into rice. The rice was also engineered to provide more dietary iron. The diet of a significant proportion of the world’s population is deficient in these essential nutrients, so advances such as this could have a profound impact on world health. Plants that function as edible vaccines are also being developed. Researchers have successfully genetically engineered potatoes and rice to produce certain proteins from pathogens and have shown that the immune system responds to these, raising hopes for an edible vaccine. Whether the immune response is strong enough to protect against disease remains to be determined. ■ endospore, p. 69

Green fluorescent protein (GFP) gene (reporter gene) GFP GFP inserted into gene A

Researching Gene Function and Regulation Gene function and regulation can more easily be studied in E. coli because systems for manipulating its DNA have been developed. For example, regulation of gene expression can be studied by creating a gene fusion—joining the gene being studied and a reporter gene (figure 9.5). The reporter gene encodes a readily observable phenotype such as fluorescence, making it possible to directly observe the expression of the gene. This, in turn, makes it possible to determine the conditions that affect gene activity. One widely used reporter gene encodes a protein called green fluorescent protein (GFP).

Genetically Engineered Eukaryotes Yeasts can be genetically engineered to perform many of the functions described for bacteria. They serve as an important model for gene function and regulation in eukaryotic cells. Multicellular organisms can also be genetically engineered. A plant or animal into which a cloned gene has been introduced is called a transgenic

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217

Promoter

Operator

Gene A

Expression of gene A observed through GFP expression

GFP Cells fluoresce when the GFP gene is expressed, indicating that the regulatory elements of gene A are turned on. Gene On Green fluorescent protein produced

Gene Off No fluorescence

FIGURE 9.5 The Function of a Reporter Gene Expression of a reporter gene can be readily detected, making it useful in the study of gene regulation.

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MICROCHECK 9.2 Genetically engineered bacteria can be used to produce a variety of products including medically important proteins, vaccines, commercially important proteins, and DNA for study. They are also used as research tools. Genetic engineering can be used to develop pestresistant plants, herbicide-resistant plants, and plants with improved nutritional value. ✓ Name a disease that is treated by using a protein produced by genetically engineered microorganisms. ✓ Describe the attributes of two different types of transgenic plants.

1. Isolate DNA.

2. Use a restriction enzyme to generate fragments of DNA.

9.3 Techniques Used in Genetic Engineering

Vector

Linear vector

3. Generate a recombinant molecule.

4. Introduce recombinant molecule into new host.

Focus Points Explain how introns are removed from eukaryotic genes.

New host

Describe the characteristics of a typical vector. Explain how cells that harbor recombinant molecules are obtained.

This section will describe methods used to clone DNA in bacterial cells (figure 9.6). For information regarding the engineering of eukaryotic organisms, see Perspective 8.2 and visit the Online Learning Center (www.mhhe.com/nester6).

Obtaining DNA The first step of a cloning experiment is to obtain the DNA that will be cloned. To do this, cells in a broth culture are lysed by adding a detergent. As the cells burst open, the relatively fragile DNA is inevitably sheared into many pieces of varying lengths. When cloning eukaryotic genes into bacteria, the introns must first be removed if the goal is protein production. To do this, mRNA from which the eukaryotic cell has already removed the introns is first isolated from the appropriate eukaryotic tissue. Then, a strand of DNA complementary to the mRNA is synthesized in vitro using reverse transcriptase, an enzyme encoded by retroviruses. That strand of DNA is then used as a template for

FIGURE 9.6 The Steps of a Cloning Experiment

synthesis of its complement, creating double-stranded DNA. The resulting copy of DNA, or cDNA, encodes the same protein as the original DNA, but lacks the introns (figure 9.7). ■ introns, p. 175 ■ retrovirus, p. 333

Generating a Recombinant DNA Molecule As described earlier, restriction enzymes and DNA ligase are used to create recombinant molecules consisting of a vector and insert. The vector, usually a modified plasmid or bacteriophage, has an origin of replication and functions as a carrier of the cloned DNA (figure 9.8). Vectors also must have at least one restriction enzyme recognition site. This allows the circular vector to be cut, forming a linear molecule to which the insert can

FRANK & ERNEST: © Thaves/Dist. By Newspaper Enterprise Association, Inc.

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9.3 Techniques Used in Genetic Engineering Intron

219

Intron

Eukaryotic DNA

Eukaryotic DNA

Transcription of eukaryotic DNA generates precursor mRNA. mRNA Precursor mRNA

Splicing removes the introns from the precursor mRNA, generating mRNA. mRNA (within eukaryotic cells) mRNA extracted from cells

Isolated mRNA

DNA (cDNA)

mRNA (isolated) Reverse transcriptase synthesizes DNA from mRNA. Single strand of cDNA

DNA polymerase completes the cDNA, free from introns. Double-stranded cDNA

FIGURE 9.7 Making cDNA from Eukaryotic mRNA In order for eukaryotic genes to be expressed by a prokaryotic cell, a copy of DNA without introns must be cloned. The cDNA encodes the same protein as the original DNA but lacks introns. Origin of replication

be joined. Many vectors have been engineered to contain a short sequence called a multiple-cloning site that has the recognition sequences of several different restriction enzymes. The value of a multiple-cloning site is its versatility; a fragment obtained by digesting with any of a number of different restriction enzymes can be inserted into the site. Vectors typically encode some type of selectable marker, a gene whose product allows cells to grow in conditions that would otherwise be inhibitory or lethal. A common selectable marker is a gene that codes for resistance to ampicillin or another antibiotic; cells that harbor a vector or recombinant molecule are able to grow on the antibiotic-containing medium. This is important because when DNA is added to a host, most cells do not take up that DNA. The selectable marker is used to eliminate cells that have not taken up vector sequences. ■ antibiotic, p. 470

Selectable Marker A gene encoding resistance to an antibiotic such as ampicillin

Second Genetic Marker A gene such as lacZ´ that encodes an observable phenotype

■ ampicillin, p. 476

Most vectors have a second genetic marker, in addition to the selectable marker, used to distinguish cells that contain recombinant plasmids from those containing intact vector. This is significant because when the vector and insert DNA are both cut with the same restriction enzyme and the fragments mixed together, not all will form the desired recombinant molecules. For example, the two ends of the vector can anneal to each other, regenerating the circular vector, which can replicate when introduced into a cell. The second genetic marker is situated so that it is insertionally inactivated when the DNA to be cloned is successfully ligated into the multiplecloning site of the vector. A good illustration of the utility of the second genetic marker is provided by the common vector,

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TAC GAATTC CCC GGATCC GTCGAC C ATG CTTAAG GGG CCTAGG CAGCTG G EcoRI BamHI Sal I Multiple-Cloning Site Contains the recognition sequence of several different restriction enzymes

FIGURE 9.8 Typical Properties of an Ideal Vector Most vectors have an origin of replication, a selectable marker, and a multiple-cloning site. A second genetic marker, used to differentiate cells containing recombinant plasmids from those that contain intact vector, spans the multiplecloning site.

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FIGURE 9.9 The Function of the lacZ„ Gene in a Vector The lacZ„ gene is used to differentiate cells that contain recombinant plasmid from those that contain vector alone. A functional lacZ„ gene results in blue colonies when bacteria harboring intact vector are plated on a medium containing x-gal. Because disruption of the gene by an insert generates a non-functional product, cells harboring recombinant plasmids form white colonies.

Vector

Portion of lacZ´ gene

Portion of lacZ´ gene

lacZ´gene Insert

mRNA

mRNA

Functional lacZ´ gene product

Non-functional protein

Bacterial cells plated on medium containing x-gal Blue colonies

pUC18 (figure 9.9). The second genetic marker of pUC18 is a gene called lacZ„. The product of lacZ„ enables cells to cleave a colorless chemical, x-gal, to form a blue compound. Because the multiple-cloning site of pUC18 is within the gene, creation of a vector-insert hybrid results in a non-functional gene product. Thus, colonies of cells that harbor intact vector have a functional lacZ„ gene and are blue, whereas those that contain a recombinant molecule are white. ■ insertional inactivation, p. 189 ■ phenotype, p. 186

The type of vector used to clone eukaryotic DNA into a bacterial cell depends largely on the ultimate purpose of the procedure. If the goal of cloning is to produce the protein encoded by the DNA, then a vector designed to optimize transcription and translation of the insert DNA is used. To create a DNA library of a human or other eukaryotic genome, however, a vector that can carry a large insert is generally used. For more information about these vectors, visit the Online Learning Center (www. mhhe.com/nester6).

White colonies

treated to induce them to take up DNA. An alternative technique is to introduce the DNA by electroporation, a procedure that subjects the cells to an electric current. ■ DNA-mediated transformation, p. 199 ■ electroporation, p. 201

After the DNA is introduced into the new host, the transformed bacteria are cultivated on a medium that both selects for cells containing vector sequences and differentiates those carrying recombinant plasmids. The medium exploits the selective marker encoded on the vector to permit growth of only those cells that have taken up either a recombinant molecule or an intact vector. If, for example, the vector encodes resistance to the antibiotic ampicillin, then the transformed cells are grown on ampicillin-containing medium. The medium exploits the second genetic marker to differentiate the cells that took up a recombinant plasmid from those that took up intact vector. If that marker is the lacZ„ gene, the chemical x-gal is added to the medium. Colonies that are white (rather than blue) likely harbor a vector carrying an insert; these colonies are then further characterized to determine if they harbor the gene of interest (see figure 9.9).

Introducing the Recombinant DNA into a New Host

■ ampicillin, p. 476

Once recombinant plasmids are generated, they must be transferred into a suitable host where the molecules can replicate. For routine cloning experiments, one of the many wellcharacterized laboratory strains of E. coli is generally used. These strains are easy to grow and much is known about their genetics and biochemistry. They also have known phenotypic characteristics such as sensitivity to specific antibiotics. ■

Introns must first be removed if eukaryotic DNA is to be expressed in a prokaryotic cell. Vectors typically have an origin of replication, a selectable marker, a multiple-cloning site, and a second genetic marker. ✓ Explain the role of reverse transcriptase in the procedure to clone eukaryotic DNA. ✓ Explain how the lacZ„ gene is used to distinguish colonies that harbor a recombinant plasmid. ✓ What would happen if a cell took up a molecule of circular insert DNA?

antibiotics, p. 470

A common method of introducing DNA into a bacterial host is DNA-mediated transformation. E. coli cells must be specially

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9.5

9.4 Concerns Regarding Genetic Engineering and Other DNA Technologies Focus Point

DNA Sequencing

221

MICROCHECK 9.4 Concerns about genetic engineering are varied, including ethical and moral issues associated with genomics, and potentially adverse impacts of genetically modified organisms on human health and the environment. ✓ Describe two concerns regarding information that can be gained by analyzing a person’s DNA. ✓ Describe two concerns regarding the use of genetically modified organisms.

Describe some of the concerns regarding DNA technologies.

The advent of any new technology should also bring scrutiny about the safety and efficacy of the outcome. When recombinant DNA technologies first allowed gene cloning over two decades ago, controversies swirled about their use and possible abuse. Even the scientists who developed the technologies were concerned about potential dangers. In response, the National Institutes of Health (NIH) formed the Recombinant DNA Advisory Committee (RAC) to develop guidelines for conducting research involving recombinant DNA techniques and gene cloning. Today, we are enjoying the fruits of many of those technologies, as evidenced by the list of commercially available products in table 9.2. Despite the fact that the technologies can be used to produce life-saving products, however, there can never be a guarantee that they will not be used for malicious purposes. Today, the idea that “superbugs” are being created for the purpose of bioterrorism is a disturbing possibility. Recent advances in genomics have generated new cause for concern, primarily involving ethical issues regarding the appropriateness and confidentiality of information gained by analyzing a person’s DNA. For example, will it be in an individual’s best interest to be told of a genetic life-terminating disease? Could such information be used to deny an individual certain rights and privileges? It is important that ongoing discussions about these complex issues continue as the technologies advance. Genetically modified (GM) organisms hold many promises, but the debate over their use has raised concerns, some logical and others not. For example, some people have expressed fear over the fact that GM foods “contain DNA.” Considering that DNA is consumed routinely as we eat plants and animals, this is obviously an irrational concern. Other fears include the worry that unanticipated allergens could be introduced into a food product, posing a threat to the health of some people. To address this issue, the FDA has implemented strict guidelines, including the requirement for producers to demonstrate that GM products intended for human consumption do not unduly elicit allergic reactions. Incidents such as the inadvertent use of GM corn that had not been approved for human consumption as an ingredient in tortilla chips continue to fuel apprehension about the strictness of regulatory control over GM products. Another concern about GM products is their possible unintended effects on the environment. For example, some laboratory studies have shown that pollen from plants genetically modified to produce Bt toxin can inadvertently kill monarch butterflies; other studies, however, have refuted the evidence. In addition, there are indications that herbicide-resistance genes can be transferred to weeds, decreasing the usefulness of the herbicide. As with any new technology, the impact of GM organisms will need to be carefully scrutinized to avoid any negative consequences.

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9.5 DNA Sequencing Focus Points Describe two applications of DNA sequencing. Describe the automated dideoxy chain termination method of DNA sequencing.

The Human Genome Project, the completed undertaking to determine the nucleotide sequence of the human genome, resulted in highly automated and efficient DNA sequencing techniques. These enabled scientists to more readily determine the genomic sequence of other organisms, including both prokaryotes and eukaryotes, fueling the rapidly growing field of genomics. The resulting explosion of data spawned a new field, bioinformatics, to analyze the information. ■ genomics, p. 181 ■ bioinformatics, p. 181 By determining the DNA sequence of a genome, the amino acid sequence of encoded proteins can be determined, thereby making it possible to compare the characteristics of various proteins in different organisms. Non-coding sequences and mobile genetic elements can be compared as well. DNA sequencing also provides a mechanism for determining the evolutionary relatedness of organisms, a topic that will be discussed in the next chapter. ■ mobile genetic elements, p. 205 Sequencing technologies have become so efficient that a new project has been intiated—the Human Microbiome Project—which uses genomics to determine the biological diversity in the normal microbiota of the human body. This project will not only use traditional approaches by sequencing the genome of individual strains, it will also employ metagenomics, the study of total genomes in a sample. With a metagenomics approach, all microbes, not just cultivable entities, can be studied. Goals of the Human Microbiome Project include determining the extent of variation in the microbiota among different individuals and comparing the composition of the normal microbiota in health and disease. ■ normal microbiota, p. 9 Metagenomics is also being used to study the extent of biodiversity in the open oceans and in soils. Analyzing these sequences will probably lead to the discovery of new antibiotics and other medically useful compounds.

Techniques Used in DNA Sequencing DNA sequencing technologies have advanced markedly in the last decades. While the Human Genome Project initiated in 1990

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took 13 years to complete and cost about 440 million dollars to sequence one human genome, a company recently announced that it had sequenced an individual’s genome in only a matter of months, for a cost of one million dollars. A race is now on to develop the technology to sequence 100 human genomes within 10 days for a cost of no more than $ 10,000 each! The most widely used technique for determining the sequence of DNA is the dideoxy chain termination method. The procedure is now typically done using automated sequencing instruments, making it a rapid and efficient process. Several newer sequencing methods have been developed, and these are speeding the process even more.

PO4 5'

5'

PO4 5'

A single-stranded piece of DNA, the template, from which a complementary copy is synthesized. ■ template, p. 164 DNA polymerase, the enzyme that catalyzes DNA synthesis. ■ DNA polymerase, p. 166

A primer that anneals to the single-stranded template. This allows the technician to dictate the site at which synthesis will initiate; recall that DNA polymerase can only add nucleotides to an existing fragment of DNA, thereby extending the fragment (figure 9.10). The DNA being sequenced usually has been cloned into a vector; because the nucleotide sequences of vectors are known, a primer that anneals to a portion of the

Primer

3'

5' T G G C C G

A T T G C C G T A C C G G C C C T T A A A T T G A A T 3' Primer is added to single-stranded DNA.

Polymerase Nucleotide

3'

5'

G

T

A T G G C C G A T T G C C G T A C C G G C C C T T A A A T T G A A T

C

3' Primer anneals to complementary sequence, serving as the nucleic acid fragment to which DNA polymerase can add nucleotides.

5' T G G C C G G G A A T T T A A C A T T G C C G T A C C G G C C C T T A A A T T G A A T

T T

3' Final product

FIGURE 9.10 Primer Through appropriate primer selection, a researcher can choose the site where in vitro DNA synthesis will initiate.

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Incorporation of a deoxynucleotide(dNTP) elongates the chain. A subsequent nucleotide can be added to the 3'OH.

H Incorporation of a dideoxynucleotide (ddNTP); the ddNTP lacks a 3'OH.

3'OH

3'OH

5'

H 3'OH

The fundamental aspect of the dideoxy chain termination method is an in vitro DNA synthesis reaction. This requires:

3'OH

3'OH

5'

Dideoxy Chain Termination Method

OH

X

PO4

OH

5'

Chain elongation is terminated. No additional nucleotides can be added due to the lack of a 3'OH.

FIGURE 9.11 Chain Termination by a Dideoxynucleotide Once a dideoxynucleotide is incorporated into a growing strand, subsequent nucleotides cannot be added due to the lack of a 3„OH.

vector adjacent to the DNA to be sequenced can be readily obtained. ■ primer, p. 166 Each of the four deoxynucleotides that are used in DNA synthesis—dATP, dGTP, dCTP, and dTTP. ■ nucleotide, p. 32 If these were the only ingredients in the reaction, full-length molecules complementary to the template DNA would be synthesized. A key additional ingredient is added, however—dideoxynucleotides (ddNTPs). These are identical to their deoxynucleotide (dNTP) counterparts except they lack the 3„ OH group, the portion of a nucleotide required for the addition of subsequent nucleotides during DNA synthesis (figure 9.11). Because they lack the 3„OH group, dideoxynucleotides are chain terminators. When one of these is incorporated into a growing strand of DNA, no additional nucleotides can be added, and elongation of the strand ceases. In automated sequencing reaction, each of the different dideoxynucleotides (ddATP, ddGTP, ddCTP and ddTTP) carries a distinct fluorescent marker. 5' In an automated sequencing reaction, DNA polymerase, template DNA, primer, the four deoxynucleotides, and a very small amount of the four labeled dideoxynucleotides are mixed together (figure 9.12). When the reaction is incubated at an appropriate temperature, each primer anneals to a template molecule and DNA synthesis begins. In every case, the nucleotide chain is elongated until a dideoxynucleotide is incorporated, terminating synthesis at that point. 5' Termination, however, is an infrequent event because of the numerous template molecules and the small amount of the ddNTPs relative to the dNTPs. This generates fragments of various lengths, but in each case, the fluorescent 3' marker of the chain terminator indicates which nucleotide was incorporated at the terminating position. The sample A is then heated to denature the DNA, and electrophoresis is used to separate the DNA fragments and determine their 5' relative size. The conditions (pH, temperature, and gel concentration) maintain the DNA in a single-stranded state and enable separation of fragments that differ by only one nucleotide in length. A laser is used to detect the colors of

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9.6 Polymerase Chain Reaction (PCR)

Key ingredients in the reaction: • Primer and template (both single-stranded)

223

ATAGCTACCTAG • DNA polymerase • Deoxynucleotides (dATP, dTTP, dGTP, dCTP) • Fluorescently labeled dideoxynucleotides (ddATP, ddTTP, ddGTP, ddCTP; a very small amount of each) (a) Chain elongation is terminated randomly when DNA polymerase incorporates a dideoxynucleotide. Products of the reaction:

The fragments are denatured, and the single strands then separated by gel electrophoresis. The color of the flourescent marker indicates the terminating dideoxynucleotide. Results:

T A T C G A T G G A T C* ATAGCTACCTAG

T A T C G A T G G A T* ATAGCTACCTAG

T A T C G A T G G A* ATAGCTACCTAG

FIGURE 9.13 Results of Automated DNA Sequencing The order of the colored peaks reflects the nucleotide sequence of the DNA.

T A T C G A T G G* ATAGCTACCTAG

T A T C G A T G* ATAGCTACCTAG Decreasing fragment size

T A T C G A T* ATAGCTACCTAG

T A T C G A* ATAGCTACCTAG

T A T C G* ATAGCTACCTAG

fluorescent bands as they run past, recording their intensity as a peak. The order of the colored peaks reflects the nucleotide sequence of the DNA (figure 9.13).

MICROCHECK 9.5 Efficient DNA sequencing methods have fueled the rapidly growing field of genomics. The automated dideoxy chain termination method is a widely used sequencing technique. ✓ What is the Human Microbiome Project? ✓ How does a ddNTP terminate DNA synthesis? ✓ What would happen in the sequencing reaction if the relative concentration of a dideoxynucleotide were increased?

T A T C* ATAGCTACCTAG

9.6 Polymerase Chain Reaction (PCR)

T A T* ATAGCTACCTAG

Focus Points T A*

Describe one application of PCR.

ATAGCTACCTAG

Explain how PCR can be used to exponentially amplify a select region of DNA.

T* ATAGCTACCTAG (b)

(c)

FIGURE 9.12 Dideoxy Chain Termination Method of DNA Sequencing This figure illustrates the principles of the automated method, which employs dideoxynucleotides that carry a fluorescent label.

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Development of the polymerase chain reaction (PCR) revolutionized research by making it possible to create millions of copies of a given region of DNA in a matter of hours. The technique exploits the specificity of primers to selectively replicate only chosen regions, referred to as target DNA. As a result, starting with just a few DNA molecules, millions of molecules of target

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CHAPTER NINE Biotechnology and Recombinant DNA DNA from Patient A

5'

3'

5'

3'

5'

3'

DNA from Patient B

as primers. The selection of these primers will be discussed shortly.

3' 5'

PCR amplifies specific sequence of interest.

The Three-Step Amplification Cycle PCR requires a repeating cycle consisting of three steps (figure 9.15). In the first step, the double-stranded DNA is denatured by heating the sample to a near-boiling temperature, approximately 95°C. In the second step, the temperature is lowered to approximately 50°C; within seconds, the primers anneal to their complementary sequences on the denatured target DNA. In the third step, DNA synthesis occurs when the temperature is raised to the optimal temperature for Taq DNA polymerase, approximately 70°C. The DNA polymerase adds nucleotides to the 3„ end of the DNA primer using the opposing strand as a template. The net result is the synthesis of two new strands of DNA, each complementary to the other. In other words, the three-step cycle results in the duplication of the original target DNA. Since each of the newly synthesized strands can then serve as a template strand for the next cycle, the DNA is amplified exponentially. After a single cycle of the three-step reaction, there will be two double-stranded DNA molecules for every original double-stranded target; after the next cycle, there will be four; after the next cycle there will be eight, and so on.

No DNA amplified Gel electrophoresis of PCR amplified samples Patient A

Patient B

Conclusion: Patient A is positive (infected); Patient B is negative.

FIGURE 9.14 PCR Amplifies Selected Sequences By amplifying a chosen sequence unique to a given organism, that organism can be detected in a sample.

DNA are synthesized. In fact, target DNA can be generated in sufficient concentration to be visible to the unaided eye when fragments in the sample are separated by gel electrophoresis, stained with ethidium bromide, and illuminated with 5' UV light (figure 9.14). 3' By choosing primers that anneal to sequences unique to a given organism, PCR can be used to detect that organism, even in sample that contains a 5' wide assortment of different microbes. For example, if a nucleotide sequence found only in Neisseria gonorrhoeae can be amplified from a vaginal secre3' tion, then N. gonorrhoeae must be present in that specimen, indicating that the patient has the sexually transmitted disease gonorrhea. Likewise, PCR can be 5' used to detect HIV nucleotide sequences in a sample of blood cells, diagnosing HIV infection.

The polymerase chain reaction starts with a doublestranded DNA molecule, from which millions of identical copies of a select region can be produced. The process involves a series of DNA synthesis reaction and the following key ingredients: Double-stranded DNA containing the region to be amplified, the target DNA. Taq polymerase, a heat-stable DNA polymerase from the thermophile Thermus aquaticus. Each of the four nucleotides (dATP, dGTP, dCTP, dTTP). Short, single-stranded segments of DNA, generally about 20 nucleotides in length, to serve

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5'

(1) Heating to 95°C denatures DNA. 3' Primer

Primer

5' (2) Cooling to 50°C allows the added primers to anneal to the single-stranded templates. 3' 3' 5'

Techniques Used in PCR

3'

Region of DNA to be amplified

5'

3'

3'

5' (3) DNA synthesis occurs when the temperature is raised to 72°C.

5'

3' 5'

3' 5'

3'

3'

5'

5' 3'

3' 5' 5'

3' 5'

3' The products of one 3-step cycle of PCR

FIGURE 9.15 Steps of a Single Cycle of PCR

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9.6 Polymerase Chain Reaction (PCR)

225

PERSPECTIVE 9.1 Science Takes the Witness Stand After serving more than 10 years on a rape charge, a wrongfully convicted young man was released from prison when a new DNA typing technique exonerated him. The new technique, which used polymerase chain reaction (PCR) to amplify specific sequences, showed that the semen sample taken from the rape victim did not contain the man’s DNA. Indeed, a database indicated a DNA match with a man currently in prison for an unrelated rape charge. Stories abound about the growing power of DNA evidence for obtaining convictions and also clearing the wrongly accused, but how is DNA used in forensics? It is not practical to compare the entire nucleotide sequence of two people; instead, specific regions that vary significantly between individuals are analyzed. In the past, forensics labs have used a method that employs the probe-based technique called Southern blot hybridization to detect differences. This method provides valuable information but cannot be used on small or degraded samples and is quite time-consuming. Most forensics labs have now switched to using a PCRbased method because results can be obtained in less than 5 hours from a sample as small as a drop of blood the size of a pinhead. In fact, the FBI now catalogs PCRbased DNA profiles from unsolved crimes and convicted violent offenders, making it easier to track or link the crimes of serial offenders. The national database is called CODIS (Combined DNA Index System). PCR-based DNA typing amplifies certain chromosomal regions that contain short tandem repeats (STRs). These consist of a core sequence of 2 to 6 base pairs that repeat a variable number of times in different people. On chromosome 2, for example, in an intron within the thyroid peroxidase gene, the sequence AATG is repeated sequentially between 5 to 14 times. In one individual, there may be 9 of these STRs in one copy of that chromosome and 7 in the other, whereas another individual may have 11 and 5 (figure 1). This variation, or polymorphism, makes tandem repeats a useful genetic

marker for distinguishing individuals. With PCR, using primers that bind regions flanking the repeating sequences, the number of repeats can be determined. A fragment that contains 9 repeats, for example, will be longer than one that contains only 7. The PCR-amplified fragments can be quickly separated using a rapid type of gel electrophoresis called capillary electrophoresis. Their size can then be determined by comparing their positions as they move out of the gel to those of known standards.

Individual A

Chromosomal copy 1 (9 copies of the STR)

Individual B

Chromosomal copy 1 (11 copies of the STR)

AATG TTAC

AATG TTAC

Tandem repeats Sequences used as PCR primers

Chromosomal copy 2 (7 copies of the STR)

Chromosomal copy 2 (5 copies of the STR)

Amplified regions

FIGURE 1 Using PCR to Type (“Fingerprint”) DNA PCR is used to amplify chromosomal regions containing short tandem repeats (STRs). The number of copies of a given STR vary among people, resulting in corresponding differences in the length of the amplified fragments. Typically, at least 13 different STR locations are analyzed.

A critical factor in PCR is the heat-stable DNA polymerase of a thermophilic bacterium, Thermus aquaticus. Taq polymerase, unlike the DNA polymerase of E. coli, is not destroyed at the high temperature used to denature the DNA in the first step of each amplification cycle. If a heat-stable polymerase were not used, fresh polymerase would need to be added for every cycle of the reaction. Thus, the discovery and characterization of T. aquaticus through basic research was key to developing this widely used and commercially valuable method. ■ thermophile, p. 91

Generating a Discrete-Sized Fragment While the preceding description explains how PCR amplifies the target DNA exponentially, it does not clarify how a discrete-

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The FBI’s CODIS database catalogs the amplification pattern of 13 different STR loci (chromosomal locations). Commercially available kits contain fluorescently labeled primers that allow simultaneous amplification and subsequent recognition of each of the 13 loci. A laser detects the color of each amplified fragment as it moves out of the capillary gel, and computer analysis generates a pattern of peaks that reflect the STR profile of the DNA sample.

length fragment, referred to as the PCR product, becomes the predominant product. The generation of fragments of a particular size is important, because it enables the technician to use PCR coupled with gel electrophoresis to readily detect the presence of target DNA in a sample. After PCR, the amplified target (PCR product) can be viewed as a single band on the ethidium bromidetreated gel. To understand how discrete-sized fragments of target DNA are generated, you must consider the exact sites to which the primers anneal, and visualize at least three cycles of replication (figure 9.16). In the first cycle, two new fragments are generated. Note, however, that these fragments are shorter than the original full-length template molecules but longer than the target DNA. Their 5„ end is primer DNA. These mid-length

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CHAPTER NINE Biotechnology and Recombinant DNA Target DNA Template 5'

3'

3' Mid-length fragment

Cycle 1

Primer

Mid-length strands are synthesized from the full-length templates. The sites to which the primers annealed dictate the 5' end of these strands.

5' Primer Mid-length fragment

5'

3'

3'

5' Template

Short fragment 5'

3' 5'

3' Cycle 1 mid-length fragment (template)

Cycle 2

When the mid-length strands are used as templates, short strands are generated.

Cycle 1 mid-length fragment (template) 3'

5' 5'

3' Short fragment

Short fragment 5'

3'

3'

5' Cycle 2 short fragment (template)

Cycle 3 5'

Cycle 2 short fragment (template)

When the short strands are used as templates, like-sized strands are generated. 3' 5'

3' Short fragment

FIGURE 9.16 The PCR Product Is a Fragment of Discrete Size The positions to which the primers anneal to the template dictate the size and sequence of the fragment amplified exponentially.

products will be generated whenever the original full-length molecule is used as a template, which is one time each replication cycle. In the next cycle, the full-length molecules will again be used as templates, repeating the process just described. More importantly, the mid-length fragments created during the first cycle will be used as templates for DNA synthesis. As before, the primers will anneal to these fragments and then nucleotides will be added to the 3„ end. Elongation, however, will stop at the 5„ end of the template molecule, because DNA synthesis requires a template. Recall that the 5„ end of the template is primer DNA. Thus, whenever a mid-length fragment is used as a template, a short fragment is generated. The 5„ and 3„ ends of this fragment are determined by the sites to which the primers initially annealed. In the third round of replication, the full-length and the midlength fragments again will be used as templates, repeating the processes just described. The short fragments generated in the preceding round will also be used as templates, however, generating short double-stranded molecules. Continuing to follow the events in further rounds of replication will reveal that it is this fragment that is exponentially amplified (figure 9.17). Ultimately, enough of these short fragments are generated to be detectable using gel electrophoresis followed by ethidium bromide staining.

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Selecting Primer Pairs The nucleotide sequences of the two primers are critical because the primers dictate which portion of the DNA is amplified. Each must be complementary to a sequence on the appropriate strand, flanking the region to be synthesized. The synthesis reaction will then add nucleotides onto the primers, elongating the DNA chain so that the DNA between those primers is copied. Thus, if a technician wants to amplify a DNA sequence that encodes a specific protein, then he or she must first determine the nucleotide sequences flanking the gene that encodes the protein and then synthesize the appropriate pair of oligonucleotides to serve as primers.

MICROCHECK 9.6 The polymerase chain reaction (PCR) is used to rapidly increase the amount of either a specific segment or total DNA in a sample. ✓ What happens during each of the three temperature steps of PCR (95°C, 50°C, and 70°C)? ✓ Explain why it is important to use a polymerase from a thermophile in the PCR reaction. ✓ Sequencing reactions can be done using PCR. In this case would two primers be necessary?

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Time 0

End of cycle 1

End of cycle 2

End of cycle 3

End of cycle 4

End of cycle 5

FIGURE 9.17 Exponential Amplification of Target DNA During PCR, mid-length fragments are amplified linearly (arithmetically), whereas the discrete-sized target DNA, referred to as PCR product, is amplified exponentially. After 30 cycles of PCR, over a billion molecules of PCR product will have been synthesized.

9.7 Probe Technologies Focus Point Compare and contrast the applications of colony blotting, FISH, and DNA microarray technologies. (2)

DNA probes are used to locate specific nucleotide sequences in DNA or RNA samples that have been affixed to a solid surface (figure 9.18). The probe is a single-stranded piece of DNA that has been tagged, or labeled, with a detectable marker such as a radioactive isotope or a fluorescent dye. Because of the label the probe carries, its presence can easily be determined. Double-stranded DNA, when exposed to a high temperature or a high pH solution, will denature, or separate into two single strands. When the temperature is lowered and the pH is adjusted to neutral, the two strands will come together, or anneal, because of the base-pairing interactions of the complementary strands. Two complementary strands from different sources will also anneal, and this process is called hybridization because each strand originated from a different source to create a hybrid molecule. Thus, a probe will hybridize to its complement, essentially “finding” the sequence of interest in a sample and making it detectable. Label

(8)

Probe

3'

5' T G G C C G

A T T G C C G T A C C G G C C C T T A A A T T G A A T 3'

5' Probe is added to single-stranded DNA that has been affixed to a solid surface. (22) 5'

3'

T G G C C G A T T G C C G T A C C G G C C C T T A A A T T G A A T 3'

A variety of technologies employ DNA probes to locate specific nucleotide sequences. They include colony blotting, fluorescence in situ hybridization (FISH), and DNA microarrays. The technique called Southern blotting also uses probes, but its applications have been largely replaced by PCR. For a description of Southern blotting, visit the Online Learning Center (www.mhhe.com/nester6).

5' Probe anneals to complementary sequence. Because of the label it carries, its location can easily be determined.

FIGURE 9.18 DNA Probes These single-stranded pieces of DNA tagged (labeled) with a detectable marker are used to detect specific nucleotide sequences in DNA or RNA samples that have been affixed to a solid surface.

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CHAPTER NINE Biotechnology and Recombinant DNA

Colony Blotting

Fluorescence in situ Hybridization (FISH)

Colony blotting uses probes to detect specific DNA sequences in colonies grown on agar plates (figure 9.19). This method is commonly used to determine which of a collection of clones contain the DNA of interest. The term “blot” in the name reflects the fact that the colonies are transferred in place (“blotted”) onto a nylon membrane, creating a pattern of colonies identical to that of the original plate. The membrane serves as a durable, permanent support for the cells of the colonies and their DNA. After the transfer, the membrane is soaked in an alkaline solution to simultaneously lyse the cells and denature their DNA, generating singlestranded DNA molecules. A solution containing the probe is then added to the membrane and incubated under conditions that allow the probe to hybridize to complementary sequences on the filter. Any probe that has not bound is then washed off. If the probe was labeled with a radioactive isotope, a process called autoradiography is used to locate the position of the hybridized probe. In this procedure, X-ray film is placed on the filter containing the probe-bound DNA and incubated. After the film is developed, visible black grains can be seen at the sites where probe was located. Different methods are used to detect probes that have been labeled with other markers.

Fluorescence in situ hybridization (FISH) uses a fluorescently labeled probe to detect specific nucleotide sequences within intact cells affixed to a microscope slide. Cells containing the hybridized probe can then be viewed using a fluorescence microscope. To study prokaryotes, a probe that binds to ribosomal RNA (rRNA) is generally used. Because actively growing cells can have thousands of copies of rRNA, this increases the sensitivity of the technique. Other characteristics of rRNA that make it useful for identifying prokaryotes are discussed in chapter 10. ■ fluorescence microscope, p. 43 ■ using genotypic characteristics to identify prokaryotes, p. 241

FISH is revolutionizing the study of microbial ecology and holds great promise in clinical laboratories. It provides a means to rapidly identify microorganisms directly in a specimen, bypassing the need to grow them in culture. FISH can be used to observe either a specific species or a group of related organisms, depending on the nucleotide sequence of the probe employed. For example, FISH can determine the relative proportion of two different groups of prokaryotes in the same specimen by using two separate probes, one specific for each group, labeled with different colored fluorescent markers (figure 9.20). Another use is to identify and enumerate cells of Mycobacterium tuberculosis, the cause of tuberculosis, in a sputum specimen. ■ microbial ecology, p. 722 ■ tuberculosis, p. 514

Colonies transferred

Nylon membrane

Membrane soaked in an alkaline solution

Colonies on agar plate

Cells in colonies lyse and DNA is denatured.

Sample preparation is a critical aspect of fluorescence in situ hybridization. The sample must first be treated with chemicals to preserve the shape of the cells, inactivate enzymes that might otherwise degrade the nucleic acid, and make the cells more permeable so that the labeled probe molecules can readily enter. Once the specimen has been prepared, it is put on a glass slide, bathed with a solution containing the fluorescently labeled probe, and incubated under conditions that allow hybridization to occur. Unbound probe is then washed off. Finally, the specimen is viewed using a fluorescence microscope.

DNA Microarrays Probe is added. Single-stranded probe

Probe hybridizes to complementary sequences on membrane.

Membrane is washed; autoradiograph detects hybridized probe. Autoradiograph Match dark spots with original plate

FIGURE 9.19 Colony Blotting This technique is used to determine which colonies on an agar plate contain a given DNA sequence. In this example, the probe is labeled with a radioactive isotope, which can be detected using autoradiography.

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DNA microarrays are used to study gene expression in organisms whose genome has been sequenced. They can also be used to detect a specific sequence in a DNA sample of interest. A DNA microarray consists of a glass slide or other small, solid support that carries an arrangement of tens or hundreds of thousands of short DNA fragments. Each DNA fragment functions in a manner analogous to a probe, enabling a researcher to screen a single sample for a vast range of different sequences simultaneously. Unlike typical probes, however, the arrays do not carry a detectable label. Instead, the label must be attached to the nucleic acid of interest. For example, to study gene expression, mRNA can be isolated from an organism, and converted to labeled, single-stranded cDNA using reverse transcriptase (see figure 9.7) and fluorescently labeled nucleotides. That cDNA is then added to a microarray constructed to include a sequence specific for each gene of a particular organism. The locations of the labeled cDNA molecules are detected using a computerized scanner, allowing the researcher to discover which genes were expressed by

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FIGURE 9.20 Fluorescence in situ Hybridization (FISH) Two different probes have been used to stain the cells. The probe that hybridizes to Ignicoccus rRNA fluoresces green; the one that hybridizes to Nanoarchaeum rRNA fluoresces red. Size bar=1 mm.

the organism. By doing the experiment using cultures grown under different sets of conditions, and labeling their cDNAs with different fluorescent markers, variations in gene expression can be revealed (figure 9.21). This is how researchers determined that pathogens express some genes only when they are in certain locations within the human body. To use microarrays to detect specific sequences, the DNA is digested into small fragments, labeled with a fluorescent marker, denatured, and then added to an appropriate microarray. Because the sequence of each of the fragments that make up the array is known, the location of the label can be used to determine the presence of specific sequences in the DNA of interest. The applications and principles of probe technologies, as well as other DNA-based technologies described in this chapter, are summarized in table 9.3.

TABLE 9.3

FIGURE 9.21 A DNA Microarray Two different nucleic acid samples (one labeled with a red fluorescent marker and the other with a green fluorescent marker) were simultaneously hybridized to the microarray. Red dots indicate the positions to which one sample hybridized, and green dots indicate the positions of the other. Yellow dots indicate that both samples hybridized. The arrays, read with the aid of computerized scanners, are often used to study gene expression.

MICROCHECK 9.7 Colony blotting uses probes to identify colonies that contain a given sequence of DNA. Fluorescence in situ hybridization is used to observe individual cells that contain a given sequence. DNA microarrays enable researchers to study gene expression and to screen a sample for a vast range of different sequences simultaneously. ✓ What role does colony blotting play in cloning? ✓ What is a probe that binds to rRNA used in FISH? ✓ Why would a pathogen express different genes when inside the body?

Summary of DNA-Based Biotechnologies

Technology

Applications

Principles of the Technique

Genetic engineering

Genetically engineered microorganisms are used to produce medically and commercially valuable proteins, to produce specific DNA sequences, and as a tool for researching gene function and regulation.

Restriction enzymes and DNA ligase are used to insert specific segments of DNA into vector molecules, which are then introduced into a new host.

DNA sequencing

Once a DNA sequence has been determined, it can be used to decipher the amino acid sequence of the encoded proteins, compare properties of the organism’s genome to others that have been sequenced, and establish genetic relatedness of the organism to different isolates.

In the dideoxy chain termination method, DNA synthesis reactions generate a set of DNA fragments, each terminated when a specific dideoxynucleotide is incorporated. By separating these fragments using gel electrophoresis, the specific dideoxynucleotide that terminated each fragment can be determined, thereby revealing the position of the nucleotides in the DNA sequence.

Polymerase chain reaction (PCR)

The presence of a specific segment of DNA can be detected, and the size determined, in only a matter of hours. By amplifying DNA specific to a pathogen, PCR can be used in diagnosis. It is also used to “fingerprint” DNA for forensic evidence.

Multiple cycles of a DNA synthesis reaction using specific primers amplify a given stretch of DNA. The locations to which the primers anneal dictate which portion is amplified.

Probe technologies

Colony blots are used to detect colonies that contain a specific sequence; fluorescence in situ hybridization (FISH) is used to identify cells directly in a specimen; DNA microarrays are used to study gene expression.

A DNA probe is used to locate a nucleotide sequence of interest in a colony, individual cells, or mRNA extracted from a sample.

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CHAPTER NINE Biotechnology and Recombinant DNA

SUMMARY 9.1

Fundamental Tools Used in Biotechnology

Restriction Enzymes (figure 9.1) Restriction enzymes cut DNA into fragments. Cohesive ends will anneal with one another, making it possible to join DNA from two different organisms. Gel Electrophoresis (figure 9.2) Gel electrophoresis separates DNA fragments according to their size.

9.2

Applications of Genetic Engineering (table 9.2)

Genetically Engineered Bacteria (figures 9.3, 9.4) Bacteria can be engineered to produce pharmaceutical proteins, vaccines, and other proteins more efficiently. By cloning a segment of DNA into E. coli, an easy source of that sequence is available for study and further manipulation. Genetically Engineered Eukaryotes Transgenic plants have been engineered to resist pests and herbicides, have improved nutritional value, and function as edible vaccines.

9.3

Techniques Used in Genetic Engineering (figure 9.6)

Obtaining DNA To isolate DNA, cells are lysed by adding a detergent. To obtain eukaryotic DNA without introns, reverse transcriptase is used to make a copy of DNA from an mRNA template (figure 9.7). Generating a Recombinant DNA Molecule DNA ligase is used to join the vector and the insert (figures 9.8, 9.9). Introducing the Recombinant DNA into a New Host The recombinant molecule is introduced into the new host, usually E. coli, using transformation or electroporation. The transformed cells are cultivated on medium that both selects for cells containing vector sequences and differentiates those that carry recombinant molecules.

9.4

Concerns Regarding Genetic Engineering and Other DNA Technologies

Advances in genomics raise ethical issues and concerns about confidentiality. Genetically modified organisms hold many promises, but concerns exist about the inadvertent introduction of allergens into a food product and adverse effects on the environment.

9.5

DNA Sequencing

By determining the DNA sequence of a genome, the encoded information can be compared to that of other organisms. Techniques Used in DNA Sequencing A key ingredient in a sequencing reaction is a dideoxynucleotide, a nucleotide that lacks the 3„OH and therefore functions as a chain terminator (figure 9.11). The sizes of fragments in a sequencing reaction indicate the positions of the terminating nucleotide base in the synthesized DNA strands (figures 9.12, 9.13).

9.6

The Polymerase Chain Reaction (PCR)

PCR is used to rapidly increase the amount of a specific DNA segment in a sample (figure 9.14). Techniques Used in PCR Double-stranded DNA is denatured, primers anneal to their complementary sequences, and then DNA is synthesized, amplifying the target sequence (figure 9.15). The discrete-sized fragment ultimately amplified exponentially is obtained after three cycles of replication (figures 9.16, 9.17). The primers dictate which portion of the DNA is amplified.

9.7

Probe Technologies

DNA probes are used to locate specific nucleotide sequences (figure 9.18).

Colony Blotting Colony blotting uses a probe to identify colonies that contain a given sequence of DNA (figure 9.19). Fluorescence in situ Hybridization (FISH) Fluorescence in situ hybridization (FISH) uses a fluorescently labeled probe to detect specific nucleotide sequences within intact cells affixed to a microscope slide (figure 9.20). DNA Microarrays DNA microarrays contain tens or hundreds of thousands of oligonucleotides that each function in a manner analogous to a probe (figure 9.21).

REVIEW QUESTIONS Short Answer 1. 2. 3. 4. 5. 6.

Why are restriction enzymes useful in biotechnology? Describe three general uses of genetically engineered bacteria. Describe the function of a reporter gene. Describe four uses of genetically engineered plants. Describe the function of a probe. Explain how DNA microarray technology can be used to study gene expression. 7. What is cDNA? Why is it used when cloning eukaryotic genes? 8. Explain how gel electrophoresis separates DNA fragments.

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9. How many different temperatures are used in each cycle of the polymerase chain reaction? 10. Explain how PCR eventually generates a discrete-sized fragment from a much longer piece of DNA.

Multiple Choice 1. What is the function of a vector? a) Destroys cells that do not contain cloned DNA b) Allows cells to take up foreign DNA c) Carries cloned DNA, enabling it to replicate in cells

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Review Questions

2.

3.

4.

5.

6.

7.

8.

d) Encodes herbicide resistance e) Encodes Bt-toxin The Ti plasmid of Agrobacterium tumefaciens is used to genetically engineer which of the following cell types? a) Animals b) Bacteria c) Plants d) Yeast e) All of these Which of the following can be used to generate a DNA library? a) PCR b) Sequencing c) Colony blotting d) Microarrays e) Cloning An ideal vector has all of the following, except a) an origin of replication. b) a gene encoding a restriction enzyme. c) a gene encoding resistance to an antibiotic. d) a multiple-cloning site. e) the lacZ„ gene. Which of the following describes the function of the lacZ„ gene in a cloning vector? a) Means of selecting for cells that contain vector sequences b) Means of distinguishing cells that have taken up recombinant molecules c) Site required for the vector to replicate d) Mechanism by which cells take up the DNA e) Gene for a critical nutrient required by transformed cells Which is used for cloning eukaryotic genes but not prokaryotic genes? a) Restriction enzymes b) DNA ligase c) Reverse transcriptase d) Vector e) Selectable marker Which of the following does a dideoxynucleotide lack? a) 5„PO4 b) 3„OH c) 5„OH d) 3„PO4 e) C and D In a sequencing reaction, the dATP was left out of the tube. What would be the result of this error? a) No synthesis would occur. b) Synthesis would never continue past the first A. c) Synthesis would not stop until the end of the template.

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231

d) Synthesis would terminate randomly, regardless of the nucleotide incorporated. e) The error would have no effect. 9. The polymerase chain reaction uses Taq polymerase rather than a DNA polymerase from E. coli, because Taq polymerase a) introduces fewer errors during DNA synthesis. b) is heat-stable. c) can initiate DNA synthesis at a wider variety of sequences. d) can denature a double-stranded DNA template. e) is easier to obtain. 10. The polymerase chain reaction generates a fragment of a distinct size even when an intact chromosome is used as a template. What determines the boundaries of the amplified fragment? a) The concentration of one particular deoxynucleotide in the reaction. b) The duration of the elongation step in each cycle. c) The position of a termination sequence, which causes the Taq polymerase to fall off the template. d) The sites to which the primers anneal. e) The temperature of the elongation step in each cycle.

Applications 1. Two students in a microbiology class are arguing about the origins of biotechnology. One student argued that biotechnology started with the advent of genetic engineering. The other student disagreed, saying that biotechnology was as old as ancient civilization. What was the rationale for the argument by the second student? 2. A student wants to clone Gene X. On both sides of the gene are the recognition sequences for AluI and BamHI (look at table 9.1). Which enzyme would be easier to use for the cloning experiment and why?

Critical Thinking 1. Discuss some potential issues regarding gene therapy, the use of genetic engineering to correct genetic defects. 2. An effective DNA probe can sometimes be developed by knowing the amino acid sequence of the protein encoded by the gene. A student argued that this is too time-consuming since the complete amino acid sequence must be determined in order to create the probe. Does the student have a valid argument? Why or why not?

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10 Bacterial cells.

Identification and Classification of Prokaryotic Organisms A Glimpse of History In the early 1870s, the German botanist Ferdinand Cohn published several papers on bacterial classification, grouping microorganisms according to shape: spherical, short rods, elongated rods, and spirals. However, that classification, based solely on shapes, was not adequate for categorizing all of the different bacteria. There were too many kinds and too few shapes. The second major attempt at bacterial classification was initiated by Sigurd Orla-Jensen. His early training in Copenhagen was in chemical engineering, but he soon became interested in microbiology. In 1908, he proposed that bacteria be classified according to their physiological properties rather than morphology. A quarter of a century later, two Dutch microbiologists, Albert Kluyver and C. B. van Niel, proposed classification systems based on presumed evolutionary relationships. They recognized a very serious problem, however: There was no way to distinguish between “resemblance” and “relatedness.” The fact that two prokaryotes look alike does not mean they are genetically related. In 1970, Roger Stanier, a microbiologist at the University of California, Berkeley, pointed out that relationships could be determined by comparing either gene products, such as proteins and cell walls, or nucleotide sequences. At that time, most microbiologists, including Stanier, assumed that all prokaryotes are basically similar. When the chemical compositions of a wide variety of prokaryotes were examined in detail, however, it was found that many had features that differed from those of Escherichia coli, considered a “typical” bacterium. These “unusual” features pertained to the chemical nature of the cell wall, cytoplasmic membrane, and ribosomal RNA.

In the late 1970s, Carl Woese and his colleagues at the University of Illinois determined the nucleotide sequence of ribosomal RNA in a wide variety of organisms. Based on the data, they recognized that prokaryotes could be divided into two major groups that differ from one another as much as they differ from eukaryotic cells. This led to a revolutionary system of classification that separates prokaryotes into two domains—the Archaea and the Bacteria. Each of these is on the same level as the Eucarya, which includes the animals, plants, and fungi (all eukaryotes).

I

nformation that is logically organized is easier to both retrieve and understand. Newspapers, for instance, do not scatter various subjects throughout the paper; rather they are divided into sections such as local news, sports, and entertainment. A large library would be extremely difficult to use if the multitude of books were not split into sections by subject matter. Likewise, scientists have divided living organisms into different groups, the better to understand the relationships among the species. Take a moment and think about how you would group bacteria if you were to arrange a classification system. Would you group them according to shape? Or would it make more sense to group them according to their motility? Perhaps you would group them according to their medical significance. But then, how would you classify two apparently identical bacteria that differed in their disease-causing potential?

232

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10.1

KEY TERMS Classification The process of arranging organisms into similar or related groups (taxa), primarily to provide easy identification and study. Dichotomous Key Flowchart of tests used for identifying organisms. Domain A collection of similar kingdoms; there are three domains—Bacteria, Archaea, and Eucarya. Genus A collection of related species.

Identification The process of characterizing an isolate in order to determine the group (taxon) to which it belongs. Lateral (Horizontal) Gene Transfer Transfer of DNA from one organism to another through conjugation, DNA-mediated transformation, or transduction. Nomenclature The system of assigning names to organisms. Phylogeny Evolutionary relatedness of organisms.

10.1 Principles of Taxonomy Focus Point Describe how prokaryotes are identified, classified, and assigned names.

Taxonomy is the science that studies organisms in order to arrange them into groups (taxa). Those organisms with similar properties are grouped together and separated from ones that are different. Taxonomy can be viewed as three separate but interrelated areas: Identification—the process of characterizing an isolate to determine the group (taxon) to which it belongs. Classification—the process of arranging organisms into similar or related groups, primarily to provide easy identification and study. Nomenclature—the system of assigning names to organisms.

Strategies Used to Identify Prokaryotes In practical terms, identifying the genus and species of a prokaryote may be more important than understanding its genetic relationship to other microbes. For example, a food manufacturer is most interested in detecting the presence of microbial contaminants that can spoil a food product. In a clinical laboratory, it is critical to quickly identify a pathogen isolated from a patient so the best possible treatment can be given. To characterize and identify microorganisms, a wide assortment of technologies may be used including microscopic examination, culture characteristics, biochemical tests, and nucleic acid analysis. In a clinical laboratory, the patient’s disease symptoms play an important role in identifying the infectious agent. For example, pneumonia in an otherwise healthy adult is typically caused by Streptococcus pneumoniae, an organism that is easily differentiated from others using a few specific tests. In contrast, diagnosing the cause of a wound infection is often more difficult,

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Principles of Taxonomy

233

Signature Sequence Characteristic sequences in the ribosomal RNA genes, or their products, that can be used to classify or identify certain organisms. Species A group of closely related isolates or strains; the basic unit of taxonomy. Strain An isolate; subgroup within a species. Taxonomy The science that studies organisms in order to arrange them into groups (taxa); involves three interrelated areas—identification, classification, and nomenclature.

because many different microorganisms could be involved. Often, however, it is only necessary to rule out the presence of organisms known to cause a particular disease, rather than to conclusively identify each and every organism in the specimen. For instance, a fecal specimen from a patient complaining of a diarrhea and fever would generally only be tested for the presence of specific organisms that cause those symptoms. ■ Streptococcus pneumoniae, p. 509 The various methods used to identify prokaryotes will be discussed in detail later in the chapter.

Strategies Used to Classify Prokaryotes Understanding the evolutionary relatedness, or phylogeny, of prokaryotes is important in constructing a classification scheme that reflects the actual evolution and biology of these organisms. Such a scheme is more useful than one that simply groups organisms by arbitrary characteristics, because it is less prone to the bias of human perceptions. It also makes it easier to classify newly recognized organisms and allows scientists to make predictions, such as which genes are likely to be transferred between organisms. Unfortunately, determining genetic relatedness among prokaryotes is more difficult than it is for plants and animals. Not only do prokaryotes have few differences in size and shape, they do not undergo sexual reproduction. In higher organisms such as plants and animals, the basic taxonomic unit, a species, is generally considered to be a group of morphologically similar organisms that are capable of interbreeding to produce fertile offspring. Obviously, it is not possible to apply these same criteria to prokaryotes, thus making classification problematic. Historically, taxonomists have relied heavily on phenotypic attributes to classify prokaryotes. The development and application of molecular techniques such as nucleotide sequencing, however, is finally making it possible to determine the genetic relatedness of microorganisms. ■ phenotype, p. 186

Taxonomic Hierarchies Taxonomic classification categories are arranged in a hierarchical order, with the species being the basic unit. The species designation gives a formal taxonomic status to a group of related isolates or strains, which, in turn, permits their identification. Without

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CHAPTER TEN Identification and Classification of Prokaryotic Organisms

classification, scientists and others would not be able to communicate about organisms with any degree of accuracy. Taxonomic categories include:

taxonomic category of kingdom. This is because the use of kingdoms within the Bacteria is still in a state of flux.

Species—a group of closely related isolates or strains. Note that members of a species are not all identical; individual strains may vary in minor properties. The difficulty for the taxonomist is to decide how different two isolates must be in order to be classified as separate species rather than strains of the same species.

Taxonomy is still an evolving discipline, with systems of classification that change over the years as new information is discovered. There is no such thing as an “official” classification system, and, as new ones are introduced, others fall into disfavor. The classification scheme currently favored by most microbiologists is the three-domain system. This designates all organisms as belonging to one of the three domains—Bacteria, Archaea, and Eucarya (figure 10.1). The system is based on the work of Carl Woese and colleagues who compared the sequences of nucleotide bases in ribosomal RNA from a wide variety of organisms. They showed that prokaryotes could be divided into two major groups that differ from one another as much as they do from the eukaryotic cell. The ribosomal RNA data are consistent with other observed differences between the Archaea and Bacteria, including the chemical compositions of their cell wall and cytoplasmic membrane (table 10.2). ■ Bacteria, p. 10 ■ Archaea, p. 10 ■ Eucarya, p. 10 Before the three-domain classification system was introduced, the most widely accepted scheme was the five-kingdom system, proposed by R. H. Whittaker in 1969. The five kingdoms in this system are Plantae, Animalia, Fungi, Protista (mostly single-celled eukaryotes), and Prokaryotae. While the five-kingdom system recognizes the obvious morphological differences between plants and animals, it does not reflect the recent genetic insights of the ribosomal RNA data, which indicates that plants and animals are more closely related to each other than Archaea are to Bacteria. Bergey’s Manual of Systematic Bacteriology While there is no “official” classification of prokaryotes, microbiologists generally rely on the reference text Bergey’s Manual of Systematic Bacteriology as a guide. All known species are described there, including those that have not yet been cultivated. If the properties of a newly isolated organism do not agree with any description in Bergey’s Manual, then presumably a new organism has been isolated. The newest edition of this comprehensive manual is being published in five volumes and classifies prokaryotes according to the most recent information on their genetic relatedness (table 10.3). In some cases, this classification differs substantially from that of the previous edition, which grouped organisms according to their phenotypic characteristics. In addition to containing descriptions of organisms, all volumes contain information on the ecology, methods of enrichment, culture, and isolation of the organisms as well as methods for their maintenance and preservation. However, the heart of the work is a description of all characterized prokaryotes and their groupings.

Genus—a collection of similar species. Family—a collection of similar genera. In prokaryotic nomenclature, the name of the family ends in the suffix -aceae. Order—a collection of similar families. In prokaryotic nomenclature, the name of the order ends in the suffix -ales. Class—a collection of similar orders. Phylum or Division—a collection of similar classes. Kingdom—a collection of similar phyla or divisions. Domain—a collection of similar kingdoms. The domain is a relatively new taxonomic category that reflects the characteristics of the cells that make up the organism. Note, however, that microbiologists often group prokaryotes into informal categories based on one or more distinctive characteristic, rather than utilizing the higher taxonomic ranks such as order, class, and phylum. Examples of such informal groupings include the lactic acid bacteria, the anoxygenic phototrophs, the endosporeformers and the sulfate reducers. Organisms within these groupings share similar phenotypic and physiological characteristics, but may not be genetically related. ■ lactic acid bacteria, p. 255 ■ anoxygenic phototrophs, p. 256 ■ sulfate reducers, p. 254

An example of how a particular bacterial species is classified is shown in table 10.1. Note that the table intentionally omits the

TABLE 10.1 Taxonomic Ranks of the Bacterium Escherichia coli Formal Rank

Example

Domain

Bacteria

Phylum

Proteobacteria

Class

Gammaproteobacteria

Order

Enterobacteriales

Family

Enterobacteriaceae

Genus

Escherichia

Species

coli

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Classification Systems

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10.1 Bacteria

Principles of Taxonomy

235

Eucarya

Archaea

Animals Entamoebae

Filamentous Anoxygenic Phototrophic bacteria

Slime molds Fungi

Spirochetes

Grampositive bacteria

Proteobacteria

Cyanobacteria

Methanosarcina Halobacteria

Methanobacterium Thermococcus MethanoThermoproteus coccus

Plants Ciliates

Thermoplasma

Pyrodictium Flagellates

Flavobacteria

Trichomonads Thermotoga

Aquifex

Microsporidia Diplomonads

FIGURE 10.1 The Three-Domain System of Classification This classification system separates prokaryotic organisms into two domains—Bacteria and Archaea. The third domain, Eucarya, contains all organisms composed of eukaryotic cells. This system of classification is based on ribosomal RNA sequence data.

Nomenclature Bacteria are given names according to an official set of internationally recognized rules, the International Code for the Nomenclature of Bacteria. Bacterial names may originate from any language, but they must be given a Latin suffix. In some cases the name reflects a characteristic of an organism such as its habitat, but often bacteria are named in honor of a prominent researcher. Just as classification is always in a state of flux, so is the assignment of names. While revision of names is desirable from a scientific perspective, it is often a great source of confusion from a practical standpoint, particularly when the names of medically important bacteria are changed. To ease the transition of nomenclature changes, the former name is sometimes included

in parentheses. For example, Lactococcus lactis, a bacterium that was included in the genus Streptococcus, is sometimes indicated as Lactococcus (Streptococcus) lactis.

MICROCHECK 10.1 Taxonomy consists of three interrelated areas: identification, classification, and nomenclature. In clinical laboratories, identifying the genus and species of an organism is more important than understanding its evolutionary relationship to other organisms. ✓ Why might it be easier to determine the cause of pneumonia than the cause of a wound infection? ✓ Why do microbiologists prefer the three-domain system of classification? ✓ Some biologists have been reluctant to accept the threedomain system. Why might this be?

TABLE 10.2 A Comparison of Some Properties of the Three Domains—Archaea, Bacteria, and Eucarya Cell Feature

Archaea

Bacteria

Eucarya

Peptidoglycan cell wall

No

Yes

No

Cytoplasmic membrane lipids

Hydrocarbons (not fatty acids) linked to glycerol by ether linkage

Fatty acids linked to glycerol by ester linkage

Fatty acids linked to glycerol by ester linkage

Ribosomes

70S

70S

80S

Presence of introns

Sometimes

No

Yes

Membrane-bound nucleus

No

No

Yes

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TABLE 10.3 Taxonomic Outline of Bergey’s Manual of Systematic Bacteriology, 2nd edition Representative Genera Volume 1: The Archaea and the Deeply Branching Phototrophic Bacteria Domain Archaea Phylum Crenarchaeota

Pyrodictium, Ignicoccus

Phylum Euryarchaeota

Halobacterium, Methanococcus, Natronococcus, Picrophilus

Domain Bacteria Phylum Aquificae

Aquifex

Phylum Thermotogae

Thermotoga

Phylum Thermodesulfobacteria

Thermodesulfobacterium

Phylum Deinococcus–Thermus

Deinococcus, Thermus

Phylum Chrysiogenetes

Chrysiogenes

Phylum Chloroflexi

Chloroflexus

Phylum Thermomicrobia

Thermomicrobium

Phylum Nitrospira

Nitrospira

Phylum Deferribacteres

Deferribacter

Phylum Cyanobacteria

Anabaena, Spirulina, Synechococcus

Phylum Chlorobi

Chlorobium, Pelodictyon

Volume 2: The Proteobacteria Phylum Proteobacteria Class Alphaproteobacteria

Agrobacterium, Caulobacter, Ehrlichia, Nitrobacter, Rhodospirillum, Rickettsia, Rhizobium

Class Betaproteobacteria

Neisseria, Nitrosomonas, Thiobacillus

Class Gammaproteobacteria

Azotobacter, Chromatium, Escherichia, Legionella, Nitrosococcus, Pseudomonas, Vibrio

Class Deltaproteobacteria

Bdellovibrio, Myxococcus

Class Epsilonproteobacteria

Campylobacter, Helicobacter

Volume 3: The Low G+C Gram-Positive Bacteria Phylum Firmicutes Class I. Clostridia

Clostridium, Heliobacterium

Class II. Mollicutes

Mycoplasma

Class III. Bacilli

Bacillus, Streptococcus, Listeria, Staphylococcus

Volume 4: The High G+C Gram-Positive Bacteria Phylum Actinobacteria

Corynebacterium, Bifidobacterium, Micrococcus, Mycobacterium, Streptomyces

Volume 5: The Planctomycetes, Spirochaetes, Fibrobacteres, Bacteroides, Fusobacteria Phylum Planctomycetes

Planctomyces

Phylum Chlamydiae

Chlamydia

Phylum Spirochaetes

Borrelia, Treponema

Phylum Fibrobacteres

Fibrobacter

Phylum Acidobacteria

Acidobacterium

Phylum Bacteroidetes

Bacteroides

Phylum Fusobacteria

Fusobacterium

Phylum Verrucomicrobia

Verrucomicrobium

Phylum Dictyoglyomi

Dictyoglomus

Phylum Gemmatimonadetes

Gemmatinonas

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10.2 Using Phenotypic Characteristics to Identify Prokaryotes

10.2 Using Phenotypic Characteristics to Identify Prokaryotes

237

Candida albicans

Focus Point Describe how phenotypic characteristics including microscopic morphology, metabolic capabilities, serology, and fatty acid analysis can be used to identify prokaryotes.

Phenotypic characteristics such as cell morphology, colony morphology, biochemical traits, and the presence of specific proteins can all be used in the process of identifying microorganisms. Most of these methods do not require sophisticated equipment and can easily be done anywhere in the world. Methods used to identify prokaryotes are summarized in table 10.4.

(a)

Roundworm egg

Microscopic Morphology An important initial step in identifying a microorganism is to determine its size, shape, and staining characteristics. Microscopic examination gives information very quickly and is sometimes enough to make a presumptive identification.

(b)

Size and Shape The size and shape of a microorganism can readily be determined by microscopically examining a wet mount. Based only on the size and shape, one can readily decide whether the organism in question is a prokaryote, fungus, or protozoan. In a clinical lab, this can sometimes provide all the information needed for diagnosis of certain eukaryotic infections. For example, a wet mount of vaginal secretions is routinely used

FIGURE 10.2 Wet Mounts of Clinical Specimens (a) Vaginal secretions containing yeast (Candida albicans, 410μ); (b) roundworm (Ascaris) eggs in a stool (400μ).

to diagnose infections caused by yeast and one of stool is examined for the eggs of parasites when certain roundworms are suspected (figure 10.2). ■ wet mount, p. 50

TABLE 10.4 Methods Used to Identify Prokaryotes Method Phenotypic Characteristics

Comments Most of these methods do not require sophisticated equipment and can easily be done anywhere in the world.

Microscopic morphology

Size, shape, and staining characteristics such as Gram stain can give suggestive information as to the identity of the organism. Further testing, however, is needed to confirm the identification.

Metabolic capabilities

Culture characteristics can give suggestive information. A battery of biochemical tests can be used to confirm the identification.

Serology

Proteins and polysaccharides that make up a prokaryote are sometimes characteristic enough to be considered identifying markers. These can be detected using specific antibodies.

Fatty acid analysis

Cellular fatty acid composition can be used as an identifying marker and is analyzed by gas chromatography.

Genotypic Characteristics

These methods are increasingly being used to identify microorganisms.

Nucleic acid probes to detect specific nucleotide sequences

Probes can be used to identify prokaryotes grown in culture. In some cases, the method is sensitive enough to detect the organism directly in a specimen.

Amplifying specific DNA sequences using PCR

Even an organism that occurs in very low numbers in a mixed culture can be identified.

Sequencing rRNA genes

This requires amplifying and then sequencing rRNA genes, but it can be used to identify organisms that have not yet been grown in culture.

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Gram Stain The Gram stain distinguishes between Gram-positive and Gramnegative bacteria (see figure 3.14). This relatively rapid test narrows the list of possible identities of an organism and provides suggestive information that can be helpful in the identification process. ■ Gram stain, p. 49 In a clinical lab, the Gram stain of a specimen by itself is generally not sensitive or specific enough to diagnose the cause of most infections, but it is still an extremely useful tool. The clinician can see the Gram reaction, the shape and arrangement of the bacteria, and whether the organisms appear to be growing as a pure culture or with other bacteria and/or cells of the host. However, most medically important bacteria cannot be identified by Gram stain alone. For example, Streptococcus pyogenes, which causes strep throat, cannot be distinguished microscopically from the other streptococci that are part of the normal flora of the throat. A Gram stain of a stool specimen cannot distinguish Salmonella species from E. coli. These organisms generally must be isolated in pure culture and tested for their biochemical attributes to provide precise identification. ■ strep throat, p. 499 In certain cases, the Gram stain gives enough information to start appropriate antimicrobial therapy while awaiting more accurate identification. For example, a Gram stain of sputum showing numerous white blood cells and Gram-positive encapsulated diplococci is highly suggestive of Streptococcus pneumoniae, an organism that causes pneumonia (figure 10.3a). In certain other cases, the result of a Gram stain is enough for accurate diagnosis. For instance, the presence of Gram-negative diplococci clustered in white blood cells in a

Streptococcus pneumoniae

(a)

Neisseria gonorrhoeae (Gram-negative diplococci)

sample of a urethral secretion from a man is considered diagnostic for gonorrhea, the sexually transmitted disease caused by Neisseria gonorrhoeae (figure 10.3b). This diagnosis can be made because N. gonorrhoeae is the only Gram-negative diplococcus found inhabiting the male urethra. ■ pneumonia, p. 509 ■ gonorrhea, p. 629

Special Stains Certain microorganisms have unique characteristics that can be detected with special staining procedures. As an example, members of the genus Mycobacterium are some of the few microorganisms that are acid-fast (see figure 3.15). If a patient has symptoms of tuberculosis, then an acid-fast stain will be done on a sample of his or her sputum to determine whether Mycobacterium tuberculosis can be detected. ■ acid-fast stain, p. 50

Metabolic Capabilities The identification of most prokaryotes relies on analyzing their metabolic capabilities such as the types of sugars utilized or the end products produced. In some cases these characteristics are revealed by the growth and colony morphology on cultivation media, but most often they are demonstrated using biochemical tests. ■ growth of colonies, p. 86

Culture Characteristics Microorganisms that can be grown in pure culture are the easiest to identify, because it is possible to obtain high numbers of a single type. Even the colony morphology can give initial clues to the identity of the organism. For example, colonies of streptococci are generally fairly small relative to many other bacteria such as staphylococci. Colonies of Serratia marcescens are often red when incubated at 22°C due to the production of a pigment. Pseudomonas aeruginosa often produces a soluble greenish pigment, which discolors the growth medium (see figure 11.12). In addition, cultures of P. aeruginosa have a distinct fruity odor. In a clinical lab, where rapid but accurate diagnosis is essential, specimens are inoculated onto media specially designed to provide important clues as to the identity of the disease-causing organism. For instance, a specimen taken by swabbing the throat of a patient complaining of a sore throat is inoculated onto blood agar. This allows detection of the characteristic b-hemolytic colonies typical of Streptococcus pyogenes (see figure 4.11). Urine collected from a patient suspected of having a urinary tract infection is plated onto MacConkey agar. E. coli, the most common cause of urinary tract infections, forms characteristic pink colonies on MacConkey agar due to its ability to ferment lactose (see figure 4.12). ■ blood agar, p. 97 ■ MacConkey agar, p. 97

Biochemical Tests

White blood cell

(b)

FIGURE 10.3 Gram Stains of Clinical Specimens (a) Sputum showing Gram-positive Streptococcus pneumoniae and (b) male urethra secretions showing Gram-negative Neisseria gonorrhoeae inside white blood cells.

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Growth characteristics on culture media can give clues as to the identity of an organism, but biochemical tests are generally necessary for a more conclusive identification. One of the simplest is an assay for the enzyme catalase (figure 10.4a). Most bacteria that grow in the presence of oxygen are catalase positive. Important exceptions are the lactic acid bacteria, which include members of the genus Streptococcus. Thus, if a throat culture yields b-hemolytic colonies but further testing reveals they are all catalase positive, then Streptococcus pyogenes has been ruled out. ■ catalase, p. 92 ■ Streptococcus pyogenes, p. 499

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10.2 Using Phenotypic Characteristics to Identify Prokaryotes

(a)

(b)

239

Most biochemical tests rely on a pH indicator or chemical reaction that results in a color change when a compound is degraded. To test for the ability of an organism to ferment a given sugar, a broth medium containing that sugar and a certain pH indicator is employed. Fermentation of the sugar results in acid production, which lowers the pH, resulting in a color change; an inverted tube traps any gas produced (figure 10.4b). A medium designed to detect urease, an enzyme that degrades urea to produce carbon dioxide and ammonia, contains urea and a pH indicator (figure 10.4c). The characteristics of these and other important biochemical tests are summarized in table 10.5. The basic strategy for identifying bacteria based on biochemical tests relies on the use of a dichotomous key, a flowchart of tests that give either a positive or negative result (figure 10.5). Because each test often requires an incubation period, however, it would be too time-consuming to proceed one step at a time. In addition, relying on a single biochemical test at each step could lead to misidentification. For example, if a strain that normally gives a positive result for a certain test lost the ability to produce a key enzyme, it would instead produce a negative result. Therefore, simultaneously inoculating multiple tests identifies the organism faster and more conclusively. In certain cases, biochemical testing can be done without culturing the organism. Helicobacter pylori, the cause of most stomach ulcers, can be detected using the breath test, which assays for the presence of urease. The patient drinks a solution containing urea that has been labeled with an isotope of carbon. If H. pylori is present, its urease breaks down the urea, releasing labeled carbon dioxide, which escapes through the airway. Several hours after drinking the solution, the patient exhales into a balloon. The expired air is then tested for labeled carbon dioxide. This test is less invasive and, consequently, much cheaper and faster than the stomach biopsy that would otherwise need to be performed to culture the organism. ■ Helicobacter pylori, p. 589 ■ isotope, p. 26

Commercial Modifications of Traditional Biochemical Tests

(c)

FIGURE 10.4 Biochemical Tests (a) Catalase production. Bacteria that produce catalase break down hydrogen peroxide to release oxygen gas (2 H2O2D2 H2O+O2), which causes the bubbling shown on the left. A negative catalase test is shown on the right. (b) Sugar fermentation. The tube on the left shows acid (yellow color) and gas, indicating that the sugar was fermented and gas was produced during the process. The center tube shows no color change, indicating that the sugar was not utilized. The tube on the right is an uninoculated control. (c) Urease production. Breakdown of urea releases ammonia, which turns the pH indicator pink, as shown in the left tube. The tube in the center shows no color change, indicating that urease was not produced. The tube on the right is an uninoculated control.

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Several less labor-intensive commercial modifications of traditional biochemical tests are available (figure 10.6). The APITM system utilizes a strip holding a series of tiny cups that contain dehydrated media. A liquid suspension of the test bacterium is inoculated into each compartment, thus rehydrating the media. Because the formulations of the media are similar in composition to those used in traditional tests, the positive results give rise to similar color changes. After a 16-hour incubation of the inoculated test strip, the results are determined by inspection. The pattern of results is converted to a numerical score, which can then be entered into a computer to identify the organism. A similar system is the EnterotubeTM, a tube with small compartments, each containing a different type of medium. One end of a metal rod that runs through the tube is used to touch a bacterial colony. When the rod is withdrawn, it inoculates each of the compartments. A system by Biolog uses a microtiter plate, a small tray containing 96 wells, to assay simultaneously an organism’s ability to use a wide variety of carbon sources. Modifications of these plates enable researchers to characterize the metabolic capabilities of microbial communities, such as those in soil, water, or wastewater.

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TABLE 10.5 Characteristics of Some Important Biochemical Tests Biochemical Test

Principle of the Test

Positive Reaction

Catalase

Detects the activity of the enzyme catalase, which causes the breakdown of hydrogen peroxide to produce O2 and water.

The reagent bubbles.

Citrate

Determines whether or not citrate can be used as a sole carbon source.

Growth, which is usually accompanied by the color change of a pH indicator.

Gelatinase

Detects enzymatic breakdown of gelatin to polypeptides.

The solid gelatin is converted to liquid.

Hydrogen sulfide production

Detects H2S liberated as a result of the degradation of sulfur-containing amino acids.

A black precipitate forms due to the reaction of H2S with iron salts in the medium.

Indole

Detects the enzymatic removal of the amino group from tryptophan.

The product, indole, reacts with a chemical reagent that is added, turning the reagent a deep red color.

Lysine decarboxylase

Detects the enzymatic removal of the carboxyl group from lysine.

The medium becomes more alkaline, causing a pH indicator to change color.

Methyl red

Detects mixed acids, the characteristic end products of a particular fermentation pathway. ■ mixed acids, p. 148

The medium becomes acidic (pH65

Age

FIGURE 20.4 Typical Incidence of Tetanus by Age Group

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20.2

the relative importance of genetic, cultural, and environmental factors. In a few instances, however, the genetic basis for resistance to infectious disease is known. For example, many people of black African ancestry are not susceptible to malaria caused by Plasmodium vivax because they lack a specific red blood cell receptor used by the organism. Some populations of Northern European ancestry are less susceptible to HIV infection because they lack a certain receptor on their white blood cells.

MICROCHECK 20.1 The reservoir of a disease agent can be infected people, other animals, or the environment. In order to spread, infectious microbes must exit a host. Handwashing and vector control can prevent many diseases; airborne transmission of pathogens is difficult to control. The portal of entry can affect the outcome of disease. The outcome of transmission is affected by the dose of the infecting agent, the incubation period, and characteristics of the host population. ✓ Explain why smallpox was successfully eradicated but rabies probably never will be. ✓ Explain how the incubation period can influence the spread of an infectious agent. ✓ Considering that circulating blood is not normally released from the body, describe how blood-borne microbes might exit.

20.2 Epidemiological Studies

Epidemiological Studies

457

place, and the time. That information is used to compile a list of possible risk factors involved in the spread of disease.

The Person Determining the profile of those who become ill is critical to defining the population at risk. Variables such as age, sex, race/ ethnicity, occupation, personal habits, previous illnesses, socioeconomic class, and marital status may all yield clues about risk factors for developing the disease. For example, in the Swiss ski resort epidemic of typhoid fever mentioned earlier, cases occurred only in tourists because the local people rarely drank water, preferring wine instead.

The Place The geographic location of disease acquisition identifies the general site of contact between the person and the infectious agent. This helps pinpoint the exact source. The location may also give clues about potential reservoirs, vectors, or geographical boundaries that might affect disease transmission. For example, malaria can only be transmitted in regions that have the appropriate mosquito vector.

The Time The timing of the outbreak may also yield helpful clues. A rapid rise in the numbers of people who became ill suggests that they were all exposed to a single, common source of the infectious agent, such as contaminated chicken at a picnic. This is called a common-source epidemic. In contrast, if the numbers of ill people rise gradually, then the disease is likely contagious, with one person transmitting it to several others, who each then transmit it to several more, and so on. This is called a propagated epidemic (figure 20.5). The first case in such an outbreak is called the index

Focus Point Compare and contrast descriptive studies, analytical studies, and experimental studies.

Propagated epidemic

Number of new cases

Epidemiologists investigate a disease outbreak to determine the causative agent as well as its reservoir and route of transmission so as to recommend ways to minimize the spread. The British physician John Snow illustrated the power of a well-designed epidemiological study over a century ago. Years before the relationship between microbes and disease was accepted, he documented that the cholera epidemics plaguing England from 1849 to 1854 were due to contaminated water supplies. He did this by carefully comparing the conditions of households that were affected by cholera to those that were not, eventually determining that the primary difference was their water supply. At one point, he ordered the removal of the handle of a public water pump in the neighborhood of an outbreak; this simple act helped halt an epidemic that in 10 days had killed more than 500 people. ■ cholera, p. 596

Common-source outbreak

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Descriptive Studies When a disease outbreak occurs, epidemiologists conduct a descriptive study to define characteristics such as the person, the

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FIGURE 20.5 Comparison of Propagated Versus Common-Source Epidemics The graph depicts the number of new cases that develop over a period of days.

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Cross-Sectional Studies

Percentage of positive specimens

50

Antigen detection in specimen

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Virus isolated from specimen

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20

A cross-sectional study surveys a range of people to determine the prevalence of any of a number of characteristics including disease, risk factors associated with disease, or previous exposure to a disease-causing agent. This survey provides a rapid assessment of the features of a population at a given point in time and may suggest associations between risk factors and disease. The crosssectional survey does not attempt to follow a certain group, nor does it establish cause of disease.

Retrospective Studies 10

0 Jan.

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FIGURE 20.6 Typical Seasonal Occurrence of Respiratory Infections Caused by Respiratory Syncytial Virus

case. In a propagated epidemic, if a direct chain of contacts can be established, the time between the onset of symptoms in one case and the next reflects the incubation period of the disease. The season in which the epidemic occurs may also be significant. Respiratory diseases including influenza, respiratory syncytial virus infections, and the common cold are more easily transmitted in crowded indoor conditions during the winter (figure 20.6). Conversely, vector and foodborne diseases are more often transmitted in warm weather when people are more likely to be exposed to mosquitoes and ticks, or eat picnic food that has not been stored properly (figure 20.7).

Analytical Studies Analytical studies are designed to determine which of the potential risk factors identified by the descriptive studies are actually relevant in the spread of the disease.

A retrospective study is done following a disease outbreak. It compares the actions and events surrounding clinical cases (individuals who developed the disease) against appropriate controls (those who remained healthy). Thus, a case-control study starts by looking at the effect, which is the disease, and attempts to identify the causative chain of events. The activity or event that was common among the cases but not the controls is likely to have been a factor in the development of the disease. It is important to select controls that match the cases with respect to variables not thought to be associated with disease. Matching these variables, which might include factors such as age, sex, and socioeconomic status, ensures that all controls had equal probability of coming in contact with the disease agent.

Prospective Studies A prospective study looks ahead to see if the risk factors identified by the retrospective study predict a tendency to develop the disease. Cohort groups, which are study groups that have a known exposure to the risk factor, are selected and then followed over time. The incidence of disease in those who were exposed to the risk factor and those who were not is then compared. By following cohort groups, the study attempts to determine if the hypothesized cause does indeed correlate with the expected effect. This type of study is less prone to the bias of inaccurate recall than a retrospective study. It is generally more time-consuming and expensive, however, particularly when examining a disease that has a long incubation period. Also, an error in the initial identification of the risk factor renders the entire study useless.

Rate per 100,000 population

Experimental Studies 30

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FIGURE 20.7 Seasonal Occurrence of Gastrointestinal Diseases

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An experimental study is used to judge the cause-and-effect relationship of the risk factors or, more commonly, the preventative factors and the development of disease. Experimental studies are done most frequently to assess the value of a particular intervention or treatment, such as antimicrobial drug therapy. The effectiveness of the treatment is compared with one of known value or with a placebo. A placebo is a mock drug—it looks and tastes like the experimental drug but has no medicinal value. To assess the value of the experimental drug, a group of patients is divided into two subgroups, one of which will be given the treatment and the other an alternative or a placebo. To avoid bias, the study should ideally be double-blind, where neither the physicians nor the patients know who is receiving the actual treatment. Ethical issues sometimes necessitate the use of experimental animals rather than patients in experimental studies.

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MICROCHECK 20.2

Infectious Disease Surveillance

459

National Disease Surveillance Network

Descriptive epidemiological studies attempt to identify the potential risk factors that lead to disease. Analytical studies try to determine which factors are actually relevant to disease development. Experimental studies are generally used to evaluate the effectiveness of a treatment or an intervention in preventing disease. ✓ On what three factors does a descriptive study focus? ✓ What is the value of a double-blind experimental study? ✓ Why is it important to include a placebo in a scientific study to assess the effectiveness of a drug?

20.3 Infectious Disease Surveillance Focus Point Compare and contrast the roles of the Centers for Disease Control and Prevention, state public health departments, and the World Health Organization.

Infectious disease surveillance, nationally and worldwide, is one of the most important aspects of disease prevention.

Infectious disease control nationwide depends heavily on a network of agencies across the country that monitors disease development. It is partly because of this network that infectious diseases do not claim more lives in the United States.

Centers for Disease Control and Prevention The Centers for Disease Control and Prevention (CDC) is part of the U.S. Department of Health and Human Services and is located in Atlanta, Georgia. It provides support for infectious disease laboratories in the United States and abroad and collects data on diseases of public health importance. Each week, the CDC publishes the Morbidity and Mortality Weekly Report (MMWR), which summarizes the status of a number of diseases. The MMWR is available online (http://www.cdc.gov/mmwr/), making it readily accessible to anyone in the world. The number of new cases of over 50 notifiable diseases is reported to the CDC by individual states (table 20.1). The list of diseases considered notifiable is determined through collaborative efforts of the CDC and state health departments. Typically the diseases are of relatively high incidence or otherwise a potential danger to public health. The data collected by the CDC are published in the MMWR along with historical numbers to reflect any trends. Potentially significant case reports, such as the 1981 report

TABLE 20.1 Notifiable Infectious Diseases Individual states and territories require physicians to report cases of these notifiable diseases. In turn, the number of cases is reported to the CDC, where they are collated and published in the MMWR.

• AIDS • Anthrax • Arboviral neuroinvasive and non-neuroinvasive diseases • Botulism • Brucellosis • Chancroid • Chlamydia trachomatis, genital infections • Cholera • Coccidioidomycosis • Cryptosporidiosis • Cyclosporiasis • Diphtheria • Ehrlichiosis/Anaplasmosis • Giardiasis • Gonorrhea • Haemophilus influenzae, invasive disease • Hansen’s disease (leprosy) • Hantavirus pulmonary syndrome • Hemolytic uremic syndrome, post-diarrheal • Hepatitis, viral, acute and chronic • HIV infection • Influenza-associated pediatric mortality

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• Legionellosis (Legionnaires’ disease) • Listeriosis • Lyme disease • Malaria • Measles • Meningococcal disease • Mumps • Novel influenza A infections • Pertussis • Plague • Poliomyelitis, paralytic • Poliovirus infection, nonparalytic • Psittacosis • Q fever • Rabies, animal and human • Rocky Mountain spotted fever • Rubella • Rubella, congenital syndrome • Salmonellosis • Severe acute respiratory syndromeassociated coronavirus (SARS-CoV) disease • Shiga toxin producing Escherichia coli (STEC)

• Shigellosis • Smallpox • Streptococcal disease, invasive, group A • Streptococcal toxic shock syndrome • Streptococcus pneumoniae, drug-resistant, invasive disease • Streptococcus pneumoniae, invasive in children3 feet if possible. Patient placement. Prioritize for single-patient room if patient is at increased risk of transmission, is likely to contaminate the environment, does not maintain appropriate hygiene, or is at increased risk of acquiring infection or developing adverse outcome following infection. Patient-care equipment and instruments/devices. If the equipment is soiled, handle in a manner that prevents transfer of microorganisms to others and to the environment; wear gloves if visibly contaminated; perform hand hygiene. Care of the environment. Develop procedures for routine care, cleaning, and disinfection of environmental surfaces, especially frequently touched surfaces in patient-care areas. Textiles and laundry. Handle in a manner that prevents transfer of microorganisms to others and to the environment. Safe injection practices. Use aseptic technique to avoid contamination of sterile injection equipment. Specific precautions describe how medications and IV solutions are stored and administered. Infection control practices for special lumbar puncture procedures. Wear a surgical mask when placing a catheter or injection material into the spinal canal or subdural space. Worker safety. Adhere to federal and state requirements for protection of healthcare personnel from exposure to bloodborne pathogens. From Siegel, J.D., Rhinehart, E., Jackson, M., Chiarello, L., and the Healthcare Infection Control Practices Advisory Committee, 2007 Guidelines for Isolation Precautions: Preventing Transmission of Infectious Agents in Healthcare Settings, June 2007. http://www.cdc.gov/ncidod/ dhqp/pdf/isolation2007.pdf

MICROCHECK 20.5 Healthcare-associated infections may originate from other patients, the healthcare environment, medical personnel, or the patient’s own normal flora. Diagnostic and therapeutic procedures can potentially transmit infectious agents. The most important steps in preventing healthcare-associated infections are to first detect their occurrence and then establish policies to prevent their development. ✓ Explain why an IV catheter poses a risk to a patient. ✓ Describe two ways in which infectious agents can be transmitted to a patient. ✓ The rate of nosocomial infections is often relatively high in emergency room settings. Explain why this might be so.

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FUTURE CHALLENGES Maintaining Vigilance Against Bioterrorism Today, an unfortunate challenge in epidemiology is to maintain vigilance against bioterrorism—the deliberate release of infectious agents or their toxins as a means to cause harm. Even as we work to control, and seek to eradicate, some diseases, we must be aware that microbes pose a threat as agents of bioterrorism. Hopefully, future attacks will never occur, but it is crucial to be prepared for the possibility. Prompt recognition of such an event, followed by rapid and appropriate isolation and treatment procedures, can help to minimize the consequences. The CDC, in cooperation with the Association for Professionals in Infection Control and Epidemiology (APIC), has prepared a bioterrorism readiness plan to be used as a template by healthcare facilities. Many of the recommendations are based on the Standard Precautions already employed by hospitals to prevent the spread of infectious agents (see Perspective 20.1). The CDC separates bioterrorism agents into three categories based on the ease of spread and severity of disease. Category A agents pose the highest risk because they are easily spread or transmitted from person to person and result in high mortality. These agents include: Bacillus anthracis. Endospores of this bacterium were used in the bioterrorism events of 2001. The most severe outcome, inhalational anthrax, results when an individual breathes in the airborne spores. It can lead to a rapidly fatal systemic illness. Cutaneous anthrax, which occurs when the organism enters the skin, manifests as a blister that develops into a skin ulcer with a black center. Although this usually heals without treatment, it can also progress to a

fatal bloodstream infection. Gastrointestinal anthrax results from consuming contaminated food, leading to vomiting of blood and severe diarrhea; it is not common but has a high mortality rate. Anthrax can be prevented by vaccination, but that option is not widely available. Prophylaxis with antimicrobial medications is possible for those who might have been exposed, but this requires prompt recognition of exposure. Fortunately, person-to-person transmission of the agent is not likely. Botulism. Botulism is caused naturally by the ingestion of botulinum toxin, produced by Clostridium botulinum. Any mucous membrane can absorb the toxin, so aerosolized toxin could be used as a weapon. Botulism can be prevented by vaccination, but that option is not widely available. An antitoxin is also available in limited supplies. Botulism is not contagious. Yersinia pestis. Pneumonic plague, caused by inhalation of Yersinia pestis, is the most likely form of plague to result from a biological weapon. Although no effective vaccine is available, postexposure prophylaxis with antimicrobial medications is possible. Special isolation precautions must be used for patients who have pneumonic plague because the disease is easily transmitted by respiratory droplets. Smallpox. Although a vaccine is available to prevent infection with this virus, routine immunization was stopped over 30 years ago because the natural disease has been eradicated. As is the case with nearly all infections caused by viruses, effective drug therapy is not available.

Special isolation precautions must be used for smallpox patients because the virus can be acquired through droplet, airborne, or contact transmission. Francisella tularensis. This bacterium, naturally found in animals such as rodents and rabbits, causes the disease tularemia. Inhalation of the bacterium results in severe pneumonia, which is incapacitating but would probably have a lower mortality rate than inhalational anthrax or plague. A vaccine is not available, but post-exposure prophylaxis with antimicrobial medications is possible. Fortunately, person-to-person transmission of the agent is not likely. Viruses that cause hemorrhagic fevers. These include various viruses such as Ebola and Marburg. Symptoms vary depending on the virus, but severe cases show signs of bleeding from many sites. There are no vaccines against these viruses, and generally no treatment. Some, but not all, of these viruses can be transmitted from person to person, so patient isolation in these cases is important. Category B agents pose moderate risk because they are relatively easy to spread and cause moderate morbidity. These agents include organisms that cause food- and waterborne illness, various biological toxins, Brucella species, Burkholderia mallei and pseudomallei, Coxiella burnetii, and Chlamydophila (Chlamydia) psittaci. Category C agents are emerging pathogens that could be engineered for easy dissemination. These include Nipah virus, which was first recognized in 1999, and hantavirus, first recognized in 1993.

SUMMARY 20.1 Principles of Epidemiology Epidemiologists study the frequency and distribution of disease in order to identify its cause, source, and route of transmission. Rate of Disease in a Population Epidemiologists focus on the rate of disease. Diseases that are constantly present in a population are endemic; an unusually large number of cases in a population constitutes an epidemic (figure 20.2). Reservoirs of Infection Preventing susceptible people from coming in contact with a reservoir of infection can prevent infectious disease. People who have asymptomatic infections or are colonized with a pathogen are carriers of the infectious agent. Zoonotic diseases are those such as plague and rabies that can be transmitted to humans but exist primarily in other animals. Pathogens that have environmental reservoirs are probably impossible to eliminate. Portals of Exit Pathogens may be shed in feces, in respiratory droplets, on skin cells, in genital secretions, and in urine.

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Transmission Handwashing is a key control measure in preventing diseases that are spread through direct or indirect contact, as well as those that spread via contaminated food. Direct contact occurs when one person physically touches another. Indirect contact involves transfer of pathogens via fomites. Droplet transmission of respiratory pathogens is considered contact because of the close proximity involved. Foodborne pathogens can originate from the animal reservoir or from contamination during food preparation. Waterborne pathogens often originate from sewage contamination. Airborne transmission of pathogens is the most difficult to control. Prevention of vector-borne disease relies on mosquito, tick, and insect control. Portals of Entry The portal of entry of a pathogen can affect the outcome of disease. Factors That Influence the Epidemiology of Disease The probability of infection and disease is generally lower if an individual is exposed to small numbers of pathogens. Diseases with a long incubation period can spread extensively before the first cases appear. A disease is unlikely to spread very widely in a population in which 90% of the people are immune to the disease agent. Malnutrition, overcrowding, and fatigue increase the

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susceptibility of people to infectious diseases. The very young and the elderly are generally more susceptible to infectious agents (figure 20.4). Natural immunity can vary with genetic background, but it is difficult to determine the relative importance of genetic, cultural, and environmental factors.

20.4 Trends in Disease

20.2 Epidemiological Studies

Emerging Diseases Emerging diseases include those that are new or newly recognized and familiar ones that are reemerging after years of decline. Factors that contribute to the emergence and reemergence of diseases include microbial evolution, the breakdown of public health infrastructure, changes in human behavior, advances in technology, population expansion, economic development, mass distribution and importation of food, war, and climate changes.

Descriptive Studies Descriptive studies attempt to identify potential risk factors that correlate with the development of disease. Determining the time that the illness occurred helps distinguish a common-source epidemic from a propagated epidemic (figure 20.5). Analytical Studies Analytical studies try to determine which risk factors are actually relevant to disease development. A retrospective study compares the activities of cases with controls to determine the cause of the epidemic. A prospective study compares cohort groups, to determine if the identified risk factors predict a tendency to develop disease. Experimental Studies Experimental studies are generally used to evaluate the effectiveness of a treatment or intervention in preventing disease.

20.3 Infectious Disease Surveillance National Disease Surveillance Network The Centers for Disease Control and Prevention (CDC) collects data on diseases of public health importance and summarizes their status in the Morbidity and Mortality Weekly Report (MMWR); other activities of the CDC include research, assistance in controlling epidemics, and support for infectious disease laboratories. State public health departments are involved in infection surveillance and control.

Reduction and Eradication of Disease Smallpox has been eradicated. The WHO hopes to soon eliminate polio, measles, and dracunculiasis.

20.5 Healthcare-Associated Infections Reservoirs of Infectious Agents in Healthcare Settings The organisms that cause healthcare-associated infections may originate from other patients, the healthcare environment, healthcare personnel, or the patient’s own flora. Transmission of Infectious Agents in Healthcare Settings Healthcare-associated infections can result from medical devices that breach the first-line barriers of the normal host defense. Health care personnel should routinely wash or disinfect their hands after touching one patient before going on to the next in order to prevent transmission of disease-causing organisms. Preventing Healthcare-Associated Infections The most important steps in preventing healthcare-associated infections are to first recognize their occurrence and then establish policies to prevent both their development and spread.

Worldwide Disease Surveillance The World Health Organization (WHO) is devoted to achieving the highest possible level of health for all peoples.

REVIEW QUESTIONS Short Answer 1. Explain the difference between incidence and prevalence. 2. What is the epidemiological significance of people who have asymptomatic infections? 3. Explain why zoonotic diseases are often severe in humans. 4. Name the most important control measure for preventing person-toperson transmission of a disease. 5. Explain why Shigella and Giardia species are readily transmitted in day care centers. 6. Explain how smallpox was eradicated. 7. Describe three factors that contribute to the emergence of disease. 8. Draw a representative graph (time versus number of people ill) depicting both a propagated and common-source epidemic. 9. What are three important factors that a descriptive epidemiological study attempts to determine? 10. Describe the difference between a retrospective (case-control) study and a prospective (cohort) study.

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Multiple Choice 1. Which of the following is an example of a fomite? a) Table b) Flea c) Staphylococcus aureus carrier d) Water e) Air 2. Which of the following would be the easiest to eradicate? a) A pathogen that is common in wild animals but sometimes infects humans b) A disease that occurs exclusively in humans, always resulting in obvious symptoms c) A mild disease of humans that often results in no obvious symptoms d) A pathogen found in marine sediments e) A pathogen that readily infects both wild animals and humans 3. Which of the following methods of disease transmission is the most difficult to control? a) Airborne b) Foodborne c) Waterborne d) Vector-borne e) Direct person to person

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4. Which of the following statements is false? a) A botulism epidemic that results from improperly canned green beans is an example of a common-source outbreak. b) Droplet nuclei fall quickly to the gound. c) Congenital syphilis is an example of a disease acquired through vertical transmission. d) Plague is endemic in the prairie dog population in parts of the United States. e) The first case in an outbreak is called the index case. 5. Which of the following statements is false? a) A disease with a long incubation period might spread extensively before an epidemic is recognized. b) A person exposed to a low dose of a pathogen might not develop disease. c) The young and the aged are more likely to develop certain disease. d) Malnourished populations are more likely to develop certain diseases. e) Herd immunity occurs when a population does not engage in a given behavior, such as eating raw fish, that would otherwise increase their risk of disease. 6. The purpose of an analytical study is to a) identify the person, place, and time of an outbreak. b) identify risk factors that result in high frequencies of disease. c) assess the effectiveness of preventative measures. d) determine the effectiveness of a placebo. e) None of the above 7. Which of the following causes of emerging diseases is thought to be a new pathogen? a) Giardia b) Vibrio cholerae O139 c) Mycobacterium tuberculosis d) Shigella dysenteriae e) Schistosoma 8. All of the following are thought to contribute to the emergence of disease, except a) advances in technology. b) breakdown of public health infrastructure.

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c) construction of dams. d) mass distribution and importation of food. e) widespread vaccination programs. 9. Which of the following common causes of healthcare-associated infections is an environmental organism that grows readily in nutrient-poor solutions? a) Enterococcus b) Escherichia coli c) Pseudomonas aeruginosa d) Staphylococcus aureus 10. What is the most common type of nosocomial infection? a) Bloodstream infection b) Gastrointestinal infection c) Pneumonia d) Surgical wound infection e) Urinary tract infection

Applications 1. A news station reported about a potentially fatal epidemic disease occurring in a small Laotian village. An epidemiologist from the CDC was interviewed to discuss the disease and was very distressed that it was not being contained. Why did the epidemiologist feel the disease was a concern for people in North America? 2. An international team was gathered to discuss how funding should be spent to eliminate human infectious disease. There is only enough funding to eliminate one disease. How would the scientists go about choosing the next disease to be eliminated from the planet?

Critical Thinking 1. Yersinia pestis and hantavirus are both found in wild rodents in the southwestern United States. What is the risk of trying to stop a hantavirus epidemic by destroying rodents in that region? 2. A student disagreed with the presentation of the examples in figure 20.5. She claimed that the number of cases from a common-source outbreak could remain high over a much longer period of time in some cases and not decrease to zero. Is the student’s claim reasonable? Why or why not?

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21 A few of the many important antimicrobial medications.

Antimicrobial Medications A Glimpse of History Paul Ehrlich (1854–1915), a German physician and bacteriologist, was born into a wealthy family. As the only son after many daughters, family and servants indulged his interests, even though his large collection of frogs and snakes occasionally entered the laundry room. As an adult, he was rarely without a good cigar and habitually scribbled notes on his shirt cuffs. After receiving a degree in medicine in 1878, he became intrigued with the way various types of body cells differ in their ability to take up dyes and other substances. When he observed that certain dyes stain bacterial cells but not animal cells, indicating that the two cell types are somehow fundamentally different, it occurred to him that it might be possible to find a chemical that selectively harms bacteria without affecting human cells. Ehrlich began a systematic search attempting to find a “magic bullet,” a term he used to describe a drug that would kill a microbial pathogen without harming the human host. He began by looking for a chemical that would cure the sexually transmitted disease syphilis, which is caused by the bacterium Treponema pallidum. Much of the mental illness during this time resulted from tertiary syphilis, a late stage of the disease. Ehrlich knew that an arsenic compound had shown some success in treating a protozoan disease of animals, and so he and his colleagues began tediously synthesizing hundreds of different arsenic compounds in search for a cure for syphilis. In 1910, the 606th compound tested, arsphenamine, proved to be highly effective in treating the disease in laboratory animals. Although the drug itself was potentially lethal for patients, it did cure infections that were previously considered hopeless. The drug was given the name Salvarsan, a term derived from the words salvation and arsenic. The use of Salvarsan to cure syphilis proved that chemicals could selectively kill pathogens without permanently harming the human host.

lococcal infection was grim before the discovery and widespread availability of penicillin in the 1940s. Physicians were able to identify the cause of the disease, but were generally unable to recommend treatments other than bed rest. Today, however, antimicrobials are routinely prescribed, and the simple cure they provide for so many infectious diseases is often taken for granted. Unfortunately, the misuse of these life-saving medications, coupled with bacteria’s amazing ability to adapt, has led to an increase in the number of drug-resistant organisms. Some people even speculate that we are in danger of seeing an end to the era of antimicrobial medications. In response, scientists are scrambling to develop new drugs.

21.1 History and Development of Antimicrobial Drugs Focus Points Describe the discovery of antimicrobial drugs and antibiotics. Explain how new generations of antimicrobial drugs are developed.

To appreciate the unique antibiotic era in which we now live, it is important to understand the history and development of these life-saving remedies.

Discovery of Antimicrobial Drugs

T

hink back to the last time you were prescribed an antimicrobial medication. Could you have recovered from the infection without the drug? The prognosis for people with common diseases such as bacterial pneumonia and severe staphy-

The development of Salvarsan by Paul Ehrlich was the first documented example of a chemical used successfully as an antimicrobial medication. The next breakthrough in the developing science of antimicrobial chemotherapy came almost 25 years later. 469

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KEY TERMS Acquired Resistance Resistance that develops through mutation or acquisition of new genes. Antibiotic A compound naturally produced by molds or bacteria that inhibits the growth of or kills other microorganisms. Antimicrobial Drug A chemical that inhibits the growth of or kills microorganisms; the term encompasses antibiotics and chemically synthesized drugs.

Antimicrobial Medications Antiviral Drug A drug that interferes with the replication of viruses.

Chemotherapeutic Agent A chemical used to treat disease.

Bactericidal Drug An antimicrobial drug that kills bacteria.

Innate (Intrinsic) Resistance Resistance due to inherent characteristics of the organism.

Bacteriostatic Drug An antimicrobial drug that inhibits the growth of bacteria.

Narrow-Spectrum Antimicrobial An antimicrobial drug that is effective against a limited range of microorganisms.

Broad-Spectrum Antimicrobial An antimicrobial drug that is effective against a wide range of microorganisms, often including both Gram-positive and Gram-negative bacteria.

R Plasmid A plasmid that encodes resistance to one or more antimicrobial drugs.

In 1932, the German chemist Gerhard Domagk, using the same dogged persistence demonstrated by Ehrlich, discovered that a red dye called Prontosil was dramatically effective in treating streptococcal infections in animals. Surprisingly, Prontosil had no effect on streptococci growing in test tubes. It was later discovered that enzymes in the blood of the animal split the Prontosil molecule, producing a smaller molecule called sulfanilamide; this breakdown product acted against the infecting streptococci. Thus, the discovery of sulfanilamide, the first sulfa drug, was based on luck as well as scientific effort. If Prontosil had only been screened against bacteria in test tubes and not given to infected animals, its effectiveness might never have been discovered. Salvarsan and Prontosil were the first documented examples of chemicals used successfully as antimicrobial medications. Any chemical that is used to treat a disease is called a chemotherapeutic agent. One used to treat microbial infections can also be called an antimicrobial drug or, more simply, an antimicrobial.

scientists to determine the chemical structure of penicillin and to develop the means for its large-scale production so that it could be used to treat infected soldiers and workers. Several different penicillins were found in the Penicillium cultures, and were designated alphabetically. Penicillin G (or benzyl penicillin) was found to be the most suitable for treating infections. This was the first of what we now call antibiotics—antimicrobial drugs naturally produced by microorganisms. Soon after the discovery of penicillin, Selman Waksman isolated a bacterium from soil, Streptomyces griseus, that produced an antibiotic he called streptomycin. The realization that bacteria as well as molds could produce medically useful antimicrobial drugs prompted researchers to begin laboriously screening hundreds of thousands of different strains of microorganisms for antibiotic production. Even today, pharmaceutical companies examine soil samples from around the world for organisms that produce novel antibiotics.

Discovery of Antibiotics

Development of New Generations of Drugs

In 1928, Alexander Fleming, a British scientist, was working with cultures of Staphylococcus when he noticed that colonies growing near a contaminating mold looked as if they were dissolving. Recognizing that the mold might be secreting a substance that killed the bacteria, he proceeded to study it more carefully. He identified the mold as a species of Penicillium and found it was indeed producing a bacteria-killing substance; he called this penicillin. Even though Fleming was unable to purify penicillin, he showed it was remarkably effective in killing many different kinds of bacteria and could be injected into rabbits and mice without adverse effects. Fleming recognized the potential medical significance of his discovery, but became discouraged with his inability to purify the compound and eventually abandoned his study of it. Approximately ten years after Fleming’s discovery, two other scientists in Britain, Ernst Chain and Howard Florey, were successful in their attempts to purify penicillin. In 1941, the drug was tested for the first time on a police officer with a life-threatening Staphylococcus aureus infection. He improved so dramatically that within 24 hours his illness seemed under control. Unfortunately, the supply of purified penicillin ran out, and the man eventually died of the infection. Later, with greater supplies of the drug, two deathly ill patients were successfully cured. World War II spurred cooperation of British and American

In the 1960s scientists discovered they could alter the chemical structure of drugs such as penicillin G, giving them new properties. For example, penicillin G, which is active mainly against Gram-positive bacteria, can be altered to produce ampicillin, a drug that kills a variety of Gram-negative species as well. Other changes to penicillin created the drug methicillin, which is less susceptible to enzymes used by some bacteria to inactivate penicillin. Thus, methicillin can be used to treat infections caused by certain penicillin-resistant organisms. Today a variety of penicillin-like medications exist, making up what is referred to as the family of penicillins (figure 21.1). Other unrelated antimicrobial drugs have also been altered to give them new characteristics.

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MICROCHECK 21.1 Antimicrobials are chemotherapeutic agents that are effective in treating microbial infections. Antibiotics are antimicrobial chemicals naturally produced by particular microorganisms. ✓ How is the microbe that makes penicillin different from the one that makes streptomycin? ✓ Define and contrast the terms chemotherapeutic agent, antimicrobial, and antibiotic. ✓ How might Streptomyces griseus cells protect themselves from the effects of streptomycin?

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21.2 Features of Antimicrobial Drugs Temocillin

1980

Mezlocillin Piperacillin Talampicillin

Apalcillin

Carfecillin

Bacampicillin

Epicillin Cyclacillin Amoxicillin

Ticarcillin

Pivmecillinam

Selective Toxicity

Mecillinam 1970 Flucloxacillin

Pivampicillin

Azidocillin Carbenicillin

1965 Dicloxacillin Cloxacillin Oxacillin Nafcillin

Ampicillin Propicillin Phenethicillin

1960

Methicillin

6-APA 1955 Penicillin V

1950 Penicillin G

Penicillium chrysogenum

FIGURE 21.1 Family Tree of Penicillins All of the derivatives contain 6-aminopenicillanic acid (6-APA), the core portion of penicillin G.

21.2 Features of Antimicrobial Drugs Focus Point Describe the important features of antimicrobial drugs that physicians must consider when prescribing an appropriate medication, including selective toxicity; antimicrobial action; spectrum of activity; tissue distribution, metabolism, and excretion; effects of combinations of antimicrobial drugs; adverse effects; and resistance to antimicrobials.

Most modern antibiotics come from microorganisms that normally reside in the soil; these include species of Streptomyces and Bacillus (bacteria), and Penicillium and Cephalosporium (fungi). To commercially produce an antibiotic, a carefully selected strain of the appropriate species is inoculated into a broth medium and incubated in a huge vat. As soon as the maximum antibiotic concentration is reached, the drug is extracted from the medium and extensively purified. In many cases, the antibiotic is chemically altered after purification to impart new characteristics such as increased stability. These chemically modified compounds are called semisynthetic.

nes95432_Ch21_469-494.indd 471

In some cases, the entire drug can be synthesized in the laboratory. By convention, these partially or totally synthetic chemicals are still called antibiotics because microorganisms produce them naturally. Numerous different antimicrobial drugs are now available, each with characteristics that make it more or less suitable for a given clinical situation. Hundreds of tons and many millions of dollars’ worth of antibiotics are now produced each year.

1975

Azlocillin

Carindacillin Sulbenicillin

471

Medically useful antimicrobial drugs exhibit selective toxicity, causing greater harm to microorganisms than to the human host. They do this by interfering with essential biological structures or biochemical processes that are common in microorganisms but not human cells. While the ideal antimicrobial drug is non-toxic to humans, most can be harmful at high concentrations. In other words, selective toxicity is a relative term. The toxicity of a given drug is expressed as the therapeutic index, which is the lowest dose toxic to the patient divided by the dose typically used for therapy. Antimicrobials that have a high therapeutic index are less toxic to the patient, often because the drug acts against a vital biochemical process of bacteria that does not exist in human cells. For example, penicillin G, which interferes with bacterial cell wall synthesis, has a very high therapeutic index. When an antimicrobial that has a low therapeutic index is administered, the concentration in the patient’s blood must be carefully monitored to ensure it does not reach a toxic level. Drugs that are too toxic for systemic use can sometimes be used for topical applications, such as first-aid antibiotic skin ointments.

Antimicrobial Action Antimicrobial drugs either kill microorganisms or inhibit their growth. Those that inhibit bacterial growth are called bacteriostatic. These drugs depend on the normal host defenses to kill or eliminate the pathogen after its growth has been inhibited. For example, sulfa drugs, which are frequently prescribed for urinary tract infections, inhibit the growth of bacteria in the bladder until they are eliminated by the body’s defenses. Drugs that kill bacteria are bactericidal. These are particularly useful in situations in which the normal host defenses cannot be relied on to remove or destroy pathogens. A given drug can be bactericidal in one situation yet bacteriostatic in another, depending on the concentration of the drug and the growth stage of the microorganism.

Spectrum of Activity Antimicrobial drugs vary with respect to the range of microorganisms they kill or inhibit. Some kill or inhibit a narrow range of microorganisms, such as only Gram-positive bacteria, whereas others affect a wide range, generally including both Gram-positive and Gram-negative organisms. Antimicrobials that affect a wide range of bacteria are called broad-spectrum antimicrobials. These are very important in the treatment of acute life-threatening diseases when immediate antimicrobial therapy is essential and there is no time to culture and identify the disease-causing agent. The disadvantage of broad-spectrum antimicrobials is that, by affecting a wide range of organisms, they disrupt the normal microbiota that

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play an important role in excluding pathogens. This in turn can leave the patient predisposed to other infections. Antimicrobials that affect a limited range of bacteria are narrow-spectrum antimicrobials. Their use requires identification of the pathogen and testing of its susceptibility to antimicrobials, but they cause less disruption to the normal microbiota. ■ normal microbiota, pp. 349, 393

Effects of Combinations of Antimicrobial Drugs Combinations of antimicrobials are sometimes used to treat infections, but care must be taken when selecting the combinations because some drugs will counteract the effects of others. For example, bacteriostatic drugs typically interfere with the effects of other drugs that kill only actively dividing cells. Counteracting combinations such as this are called antagonistic. In contrast, combinations in which the activity of one drug enhances the activity of the other are called synergistic. Combinations that are neither synergistic nor antagonistic are called additive.

Tissue Distribution, Metabolism, and Excretion of the Drug Antimicrobials differ not only in their action and activity, but also in how they are distributed, metabolized, and excreted by the body. For example, only some drugs are able to cross from the blood into the cerebrospinal fluid, an important factor for a physician to consider when prescribing a drug to treat meningitis. Drugs that are unstable at low pH are destroyed by stomach acid when taken orally, and so these drugs must instead be administered through intravenous or intramuscular injection. ■ meningitis, p. 650 Another important characteristic of an antimicrobial is its rate of elimination, which is expressed as the half-life. The half-life of a drug is the time it takes for the body to eliminate one-half of the original concentration in the serum. The half-life of a drug dictates the size and frequency of doses required to maintain an effective level in the body. Penicillin V, which has a very short half-life, needs to be taken four times a day, whereas azithromycin, with a half-life of over 24 hours, is taken only once a day or less. Patients who have kidney or liver dysfunction often excrete or metabolize drugs more slowly, and so their drug dosages must be adjusted accordingly to avoid toxic levels.

Adverse Effects As with any medication, several concerns and dangers are associated with antimicrobial drugs. It is important to remember, however, that antimicrobials are extremely valuable drugs that save countless lives when properly prescribed and used.

Allergic Reactions Some people develop hypersensitivities or allergies to antimicrobials. An allergic reaction to penicillin or other related drugs usually results in a fever or rash but can abruptly cause life-threatening anaphylactic shock. For this reason, people who have allergic reactions to a given antimicrobial must alert their physicians and pharmacists so that an alternative drug can be prescribed. They should also wear a bracelet or necklace that records that information in case of emergency. ■ anaphylactic shock, p. 417

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Toxic Effects Several antimicrobials are toxic at high concentrations or occasionally cause adverse reactions. Aminoglycosides such as streptomycin can damage kidneys, impair the sense of balance, and even cause irreversible deafness. Patients taking these drugs must be closely monitored because of the low therapeutic index. Some antimicrobials have such severe potential side effects that they are reserved for only life-threatening conditions. For example, in rare cases, chloramphenicol causes the potentially lethal condition aplastic anemia, in which the body is unable to make white and red blood cells. For this reason, chloramphenicol is usually used only when no other alternatives are available.

Suppression of the Normal Microbiota The normal microbiota plays an important role in host defense by excluding pathogens. When the composition of the normal microbiota is altered, which happens when a person takes an antimicrobial, pathogens normally unable to compete may multiply to high numbers. Patients who take broad-spectrum antibiotics orally sometimes develop the life-threatening disease called antibioticassociated colitis, caused by the growth of toxin-producing strains of Clostridium difficile. This organism generally is not able to establish itself in the intestine due to competition from other bacteria. When members of the normal intestinal microbiota are inhibited or killed, however, C. difficile can sometimes flourish and cause serious intestinal damage. ■ normal microbiota, pp. 349, 393 ■ Clostridium difficile, p. 586

Resistance to Antimicrobials Just as humans are assembling a vast array of antimicrobial drugs, microorganisms have their own genetic toolbox of mechanisms to avoid their effects. In some cases, certain types of bacteria are inherently resistant to the effects of a particular drug; this is called innate, or intrinsic, resistance. Members of the genus Mycoplasma lack a cell wall, so, not surprisingly, they are resistant to any drug such as penicillin that exerts its action by interfering with cell wall synthesis. Many Gram-negative organisms are intrinsically resistant to certain drugs because the lipid bilayer of their outer membrane excludes entry of the drug. In other instances, previously sensitive organisms develop resistance through spontaneous mutation or the acquisition of new genetic information; this is called acquired resistance. The mechanisms and acquisition of resistance will be discussed later. ■ characteristics of bacteria that lack a cell wall, p. 63 ■ Gram-negative cell wall, p. 61

MICROCHECK 21.2 When choosing an antimicrobial to prescribe, a physician must consider a variety of factors including the therapeutic index, antimicrobial action, spectrum of activity, effects of combinations of antimicrobials, tissue distribution, half-life, adverse effects, and resistance of the microbe. ✓ Which would you rather take: an antimicrobial that has a low therapeutic index or one that has a high therapeutic index? Why? ✓ In what clinical situation is it most appropriate to use a broadspectrum antimicrobial? ✓ Why would antimicrobials that have toxic side effects be used at all?

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21.3 Mechanisms of Action of Antibacterial Drugs

21.3 Mechanisms of Action of Antibacterial Drugs

Cell wall (peptidoglycan) synthesis b-lactam drugs Vancomycin Bacitracin

473

Nucleic acid synthesis Fluoroquinolones Rifamycins

Focus Points Compare and contrast the antimicrobial drugs that inhibit cell wall synthesis. Compare and contrast the antimicrobial drugs that inhibit protein synthesis. Compare and contrast the antimicrobial drugs that inhibit nucleic acid synthesis.

A

Compare and contrast the antimicrobial drugs that inhibit metabolic pathways. Describe the antimicrobial drugs that interfere with cell membrane integrity. Describe the antibacterial medications used to treat infections caused by Mycobacterium tuberculosis.

A number of bacterial processes utilize enzymes or structures that are different or absent, or are not commonly found in eukaryotic cells. Several microbial processes, including the synthesis of bacterial cell walls, proteins, and nucleic acids, metabolic pathways, and the integrity of the cytoplasmic membrane, are the targets of most antimicrobial drugs (figure 21.2). This section will discuss the bacterial processes commonly targeted by antimicrobial medications. To illustrate how these

Cell membrane integrity Polymyxin B Daptomycin

B

Metabolic pathways (folate biosynthesis) Sulfonamides Trimethoprim

Protein synthesis Aminoglycosides Tetracyclines Macrolides Chloramphenicol Lincosamides Oxazolidinones Streptogramins

FIGURE 21.2 Targets of Antibacterial Medications

targets are affected, the mechanism of action of some of the most widely used antimicrobials will be described (table 21.1). A group of antibiotics called b-lactam drugs will be covered in the greatest detail, because they serve as excellent examples of some of the important features of antimicrobials.

TABLE 21.1 Characteristics of Antibacterial Drugs Target/Drug

Comments/Characteristics

Cell Wall Synthesis b-lactam drugs Penicillins

Bactericidal against a variety of bacteria; inhibits penicillin-binding proteins. Resistance is due to synthesis of b-lactamases, decreased affinity of penicillin-binding proteins, or decreased uptake. A family of antibacterial medications; different groups vary in their spectrum of activity and their susceptibility to b-lactamases.

Natural penicillins: penicillin G, penicillin V

Active against Gram-positive and a few Gram-negative bacteria. Penicillin G is destroyed by stomach acid, and so it usually must be administered by injection. Penicillin V can be taken orally.

Penicillinase-resistant: methicillin, dicloxicillin

Similar to natural penicillins, but resistant to inactivation by the penicillinase of staphylococci.

Broad-spectrum: ampicillin, amoxicillin

Similar to the natural penicillins, but more active against Gram-negative organisms.

Extended-spectrum: ticarcillin, piperacillin

Increased activity against Gram-negative rods, including Pseudomonas species.

Cephalosporins Cephalexin, cephradine, cefaclor, cefprozil, cefixime, cefibuten, cefepime Carbapenems Imipenem, meropenem

A family of antibacterial medications. The later generations are generally more effective against Gram-negative bacteria and less susceptible to destruction by b-lactamases.

Resistant to inactivation by b-lactamases. Imipenem must be given in combination with a drug that inhibits certain kidney enzymes in order to avoid its inactivation. (continued)

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TABLE 21.1 Characteristics of Antibacterial Drugs (continued) Target/Drug

Comments/Characteristics

Cell Wall Synthesis (continued) Monobactams Aztreonam

Resistant to b-lactamases; can be given to patients who are allergic to penicillin. Primarily active against members of the family Enterobacteriaceae.

Vancomycin

Bactericidal against Gram-positive bacteria; binds to the peptide side chain of N-acetylmuramic acid. Used to treat serious systemic infections and antibiotic-associated colitis. In enterococci, resistance is due to a plasmid-encoded altered target.

Bacitracin

Bactericidal against Gram-positive bacteria; interferes with the transport of peptidoglycan precursors. Common ingredient in non-prescription antibiotic ointments.

Protein Synthesis Aminoglycosides Streptomycin, gentamicin, tobramycin, amikacin, neomycin Tetracyclines Tetracycline, doxycycline, glycylcyclines Macrolides Erythromycin, clarithromycin, azithromycin

Bactericidal against aerobic and facultative bacteria; binds to the 30S ribosomal subunit, blocking the initiation of translation and causing the misreading of mRNA. Toxicity limits the use. Resistance is due to a plasmidencoded inactivating enzyme, alteration of the target molecule, or decreased uptake by a cell. Neomycin is commonly used in non-prescription topical antibiotic ointments. Bacteriostatic against some Gram-positive and Gram-negative bacteria; binds to the 30S ribosomal subunit, blocking the attachment of tRNA. Resistance is generally due to decreased accumulation, either through decreased uptake or increased efflux. Bacteriostatic against many Gram-positive bacteria as well as the most common causes of atypical pneumonia; binds to the 50S ribosomal subunit, preventing the continuation of protein synthesis. Used for treating patients who are allergic to b-lactam drugs. Resistance is due to an inactivating enzyme, alteration of the target molecule, or decreased uptake by a cell.

Chloramphenicol

Bacteriostatic and broad-spectrum; binds to the 50S ribosomal subunit, preventing peptide bonds from being formed. Generally used only as a last resort for life-threatening infections. Resistance is often due to a plasmidencoded inactivating enzyme.

Lincosamides

Bacteriostatic against a variety of Gram-positive and Gram-negative bacteria, including the anaerobe Bacteroides fragilis. Binds to the 50S ribosomal subunit, preventing the continuation of protein synthesis. Associated with an even greater risk of developing antibiotic-associated colitis.

Lincomycin, clindamycin Oxazolidinones Linezolid Streptogramins Quinupristin, dalfopristin

Bacteriostatic against a variety of Gram-positive bacteria. Binds to the 50S ribosomal subunit, interfering with the initiation of protein synthesis. A synergistic combination of two drugs that bind to two different sites on the 50S ribosomal subunit, inhibiting distinct steps of protein synthesis. Individually each drug is bacteriostatic, but together they are bacteriocidal. Effective against a variety of Gram-positive bacteria.

Nucleic Acid Synthesis Fluoroquinolones Ciprofloxacin, moxifloxacin Rifamycins Rifampin

Bactericidal against a wide variety of Gram-positive and Gram-negative bacteria; inhibits topoisomerases. Resistance is most often due to structural alterations in the topoisomerase target. Bactericidal against Gram-positive and some Gram-negative bacteria. Binds RNA polymerase, blocking the initiation of RNA synthesis. Primarily used to treat infections caused by Mycobacterium tuberculosis and as prophylaxis for patients who have been exposed to Neisseria meningitidis.

Folate Biosynthesis Sulfonamides

Bacteriostatic against a variety of Gram-positive and Gram-negative bacteria. Structurally similar to paraaminobenzoic acid (PABA) and therefore inhibits the enzyme for which PABA is a substrate. Resistance is most commonly due to a plasmid-encoded alternative enzyme.

Trimethoprim

Often used in combination with a sulfa drug for a synergistic effect; inhibits the enzyme that catalyzes a step following the one inhibited by the sulfonamides. Resistance is commonly due to a plasmid-encoded alternative enzyme; the genes that encode resistance to sulfa drugs are often carried on the same plasmid.

Cell Membrane Integrity Polymyxin B

Bactericidal against Gram-negative bacteria by damaging cell membranes. Its toxicity limits its use primarily to topical applications, but it is a common ingredient in non-prescription antibiotic ointments.

Daptomycin

Bactericidal against Gram-positive bacteria by damaging the cytoplasmic membrane.

Mycobacterium tuberculosis Ethambutol

Inhibits the synthesis of a component of the mycobacterial cell wall.

Isoniazid

Inhibits synthesis of mycolic acid, a major component of the mycobacterial cell wall.

Pyrazinamide

Mechanism unknown.

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21.3 Mechanisms of Action of Antibacterial Drugs

Antibacterial Medications That Inhibit Cell Wall Synthesis

475

(a) Penicillin O

Bacterial cell walls are unique in that they contain peptidoglycan (see figures 3.33 and 3.34). Because of this, antimicrobial medications that interfere solely with synthesis of this cell wall component do not affect eukaryotic cells, generally resulting in a very high therapeutic index (figure 21.3).

R

C

S NH

CH

CH

CH3 C CH3

C

N

CH

COOH

O

Penicillins, Cephalosporins and Other b-Lactam Drugs Penicillins and cephalosporins are members of a group of antimicrobial medications collectively referred to as b-lactam drugs. This group, which also includes the monobactams and carbapenems, all have a shared chemical structure called a b-lactam ring (figure 21.4). The b-lactam drugs competitively inhibit a group of enzymes that catalyze formation of peptide bridges between adjacent glycan strands, an essential step in the final stages of peptidoglycan synthesis (see figure 3.32). These enzymes are commonly called penicillin-binding proteins (PBPs), reflecting the fact that they bind penicillin and were initially discovered during experiments to study the effects of the medication. The disruption in cell wall biosynthesis leads to weakening of the wall and ultimately results in cell lysis (figure 21.5). Because cell walls are synthesized only in actively multiplying cells, the b-lactam drugs are effective only against growing bacteria. ■ competitive enzyme inhibition, p. 138 The different b-lactam drugs vary in their spectrum of activity. Some are more active against Gram-positive bacteria,

b-lactam drugs Interfere with the formation of the peptide side chains between adjacent strands of peptidoglycan by inhibiting penicillin-binding proteins

Vancomycin Binds to the amino acid side chain of NAM molecules, interfering with peptidoglycan synthesis

Peptidoglycan (cell wall)

b-lactam ring (b) Cephalosporin O R

C

S NH

CH

CH

C

N

CH2

C

O

R b-lactam ring

COOH

FIGURE 21.4 The b-Lactam Ring of Penicillins and Cephalosporins The core chemical structure of (a) a penicillin; (b) a cephalosporin. The b-lactam rings are marked by an orange circle. The R groups vary among different penicillins and cephalosporins.

whereas others are more active against Gram-negative organisms. One reason for this difference arises from the architecture of the cell wall. The peptidoglycan layer of Gram-positive organisms directly contacts the outside environment, making the enzymes that synthesize it readily accessible to drugs. In contrast, the outer membrane of Gram-negative bacteria excludes many antimicrobials, making many of these organisms innately resistant to many medications, including certain b-lactam drugs. Another difference is the affinity of an organism’s penicillin-binding proteins for a particular b-lactam drug. The PBPs of Gram-positive bacteria differ somewhat from those of Gram-negative bacteria, and the PBPs of obligate anaerobes differ from those of aerobes. Differences in affinity can even exist among related organisms such as Gram-positive cocci.

Cytoplasmic membrane NAG NAM

Bacitracin Interferes with the transport of peptidoglycan precursors across the cytoplasmic membrane

FIGURE 21.5 Effect of a b-Lactam Drug on a Cell The drug disrupts FIGURE 21.3 Antibacterial Medications that Interfere with Cell Wall Synthesis

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cell wall synthesis, leading to weakening of the cell wall, ultimately causing the cells to lyse.

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Some bacteria can resist the effects of certain b-lactam drugs by synthesizing an enzyme, a b-lactamase, that breaks the critical b-lactam ring, destroying the activity of the antibiotic. Just as there are many b-lactam drugs, there are various b-lactamases; these differ in the range of drugs they destroy. A b-lactamase that was originally detected in some strains of staphylococci only inactivates members of the penicillin family. To reflect this fact, it is often called a penicillinase. In contrast, some of the b-lactamases produced by Gram-negative organisms inactivate a wide variety of b-lactam drugs. The extended-spectrum b-lactamases inactivate both the penicillins and the cephalosporins. As a whole, Gram-negative bacteria can produce a much more extensive array of b-lactamases than can Gram-positive organisms. The Penicillins All members of the family of penicillins share a common basic structure. Only the side chain has been modified in the laboratory to create penicillin derivatives, each with unique characteristics (figure 21.6). Currently the family of penicillins can be loosely grouped into several categories, each of which consists of several different drugs: Natural penicillins. These are the original penicillins produced naturally by the mold Penicillium chrysogenum. Natural penicillins are narrow-spectrum antibiotics, effective against Gram-positive and a few Gram-negative bacteria. Strains of bacteria that produce penicillinase are resistant to the natural penicillins. Penicillin V is more stable in acid and, therefore, better absorbed than penicillin G when taken orally. Pencillinase-resistant penicillins. These drugs were developed in the laboratory as a response to the problem of penicillinase-producing staphylococci. Side chains of the drugs prevent penicillinase from inactivating them. Unfortunately, some strains of penicillinase-producing Staphylococcus aureus synthesize altered PBPs to which b-lactam drugs, including the penicillins, no longer bind. Penicillinaseresistant penicillins include methicillin and dicloxicillin. Broad-spectrum penicillins. The modified side chains of these drugs give them a broad spectrum of activity. They retain their activity against penicillin-sensitive, Gram-positive bacteria, yet they are also active against Gram-negative organisms. Unfortunately, they can be inactivated by many b-lactamases. Broad-spectrum penicillins include ampicillin and amoxicillin. Extended-spectrum penicillins. These have greater activity against Pseudomonas species—Gram-negative bacteria that are unaffected by many conventional antimicrobial drugs. The extended-spectrum penicillins, however, have less activity against Gram-positive organisms. Like the other broad-spectrum penicillins, they are destroyed by many b-lactamase-producing organisms. Extended-spectrum penicillins include ticarcillin and piperacillin. Penicillins+b-lactamase inhibitor. Rather than a new drug, this is a novel combination of therapeutic agents. b-lactamase inhibitors are chemicals that interfere with the activity of some types of b-lactamases. When a b-lactamase inhibitor is administered with one of the penicillins, the medication is protected against enzymatic destruction. An example is Augmentin®, a combination of amoxicillin and clavulanic acid.

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Basic Structure

Side Chain

O CH 2

C

CH 3

S NH

CH C

CH

C

N

CH 3 CH COOH

Penicillin G

O b-lactam ring

OCH 2

Penicillin V (acid-resistant)

OCH 3 Methicillin (penicillinase-resistant) OCH 3 Cl Dicloxacillin (acid- and penicillinase-resistant) N Cl

O

CH 3

Ampicillin (broad spectrum and acid-resistant)

CH NH 2

Amoxicillin (like ampicillin but more active and requiring less frequent doses)

CH

HO

NH 2

CH S

COONa

Ticarcillin (more activity against Gram-negative rods, including Pseudomonas, but not as effective against some Gram-positive organisms)

CH NH C

O

N

O

N

O

Piperacillin (like ticarcillin but a broader spectrum of activity)

C 2H 5

FIGURE 21.6 Chemical Structures and Properties of Representative Members of the Penicillin Family The entire structure of penicillin G and the side chains of other penicillins are shown.

The Cephalosporins The cephalosporins are derived from an antibiotic produced by the fungus Acremonium cephalosporium (formerly called Cephalosporium acremonium). Generally included in this family of drugs is a closely related group of antibiotics made by members of a genus of filamentous bacteria related to Streptomyces.

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21.3 Mechanisms of Action of Antibacterial Drugs

The chemical structure of the cephalosporins makes them resistant to inactivation by certain b-lactamases, but some have a low affinity for penicillin-binding proteins of Gram-positive bacteria, thus limiting their effectiveness against these organisms. Like the penicillins, the cephalosporins have been chemically modified to produce a family of various related antibiotics. They are grouped as the first-, second-, third-, and fourth-generation cephalosporins. These include cephalexin and cephradine (first generation), cefaclor and cefprozil (second generation), cefixime and cefibuten (third generation), and cefepime (fourth generation). The later generations are generally more effective against Gram-negative bacteria and are less susceptible to destruction by b-lactamases. Other b-Lactam Antibiotics Two other groups of b-lactam drugs, carbapenems and monobactams, are very resistant to blactamases. The carbapenems are effective against a wide range of Gram-negative and Gram-positive bacteria. Two types are available—imipenem and meropenem. Imipenem is rapidly destroyed by a kidney enzyme and is therefore administered in combination with a drug that inhibits that enzyme. The only monobactam used therapeutically, aztreonam, is primarily effective against members of the family Enterobacteriaceae, which are Gram-negative rods. Structurally, it is slightly different from other b-lactam drugs; this characteristic is important because aztreonam can be given to patients who have developed an allergy to penicillin. ■ Enterobacteriaceae, p. 262

Vancomycin Vancomycin binds to the terminal amino acids of the peptide side chain of NAM molecules that are being assembled to form glycan chains. By doing so, it blocks synthesis of peptidoglycan, resulting in weakening of the cell wall and, ultimately, cell lysis. Vancomycin does not cross the outer membrane of Gram-negative bacteria; consequently, these organisms are innately resistant. Although vancomycin resistance is increasing, it is still a very important medication for treating infections caused by Gram-positive bacteria that are resistant to b-lactam drugs. In addition, it is sometimes the preferred drug for treating severe cases of antibiotic-associated colitis. Because vancomycin is poorly absorbed from the intestinal tract, it must be administered intravenously except when used to treat intestinal infections. Acquired resistance to vancomycin is most often due to an alteration in the peptide side chain of the NAM molecule that prevents vancomycin from binding.

Bacitracin Bacitracin inhibits cell wall biosynthesis by interfering with the transport of peptidoglycan precursors across the cytoplasmic membrane. Its toxicity limits its use to topical applications; however, it is a common ingredient in non-prescription first-aid ointments.

Antibacterial Medications That Inhibit Protein Synthesis Several types of antibacterial drugs inhibit prokaryotic protein synthesis (figure 21.7). While all cells synthesize proteins, the

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Aminoglycosides Block the initiation of translation and cause the misreading of mRNA

Tetracyclines Block the attachment of tRNA to the ribosome

Macrolides Prevent the continuation of protein synthesis Chloramphenicol Prevents peptide bonds from being formed 30S 50S

Streptogramins Each interferes with a distinct step of protein synthesis.

477

Lincosamides Prevent the continuation of protein synthesis

Oxazolidinones Interfere with the initiation of protein synthesis

FIGURE 21.7 Antibacterial Medications that Inhibit Prokaryotic Protein Synthesis These medications bind to the 70S ribosome.

structure of the prokaryotic 70S ribosome, which is composed of a 30S and a 50S subunit, is different enough from the eukaryotic 80S ribosome to make it a suitable target for selective toxicity. The mitochondria of eukaryotic cells also have 70S ribosomes, however, which may partially account for the toxicity of some of these drugs. ■ ribosome structure, p. 68 ■ protein synthesis, p. 164

The Aminoglycosides The aminoglycosides are bactericidal drugs that irreversibly bind to the 30S ribosomal subunit, causing it to distort and malfunction. This blocks the initiation of translation and causes misreading of mRNA by ribosomes that have already passed the initiation step. Aminoglycosides are actively transported into bacterial cells by a process that requires respiratory metabolism. Consequently, they are generally not effective against anaerobes, enterococci, and streptococci. To extend their spectrum of activity, the aminoglycosides are sometimes used in a synergistic combination with a b-lactam drug. The b-lactam drug interferes with cell wall synthesis, which, in turn, allows the aminoglycoside to more easily enter cells that would otherwise be resistant. Examples of aminoglycosides include streptomycin, gentamicin, tobramycin, and amikacin. Unfortunately, these all can cause severe side effects including hearing loss and kidney damage; consequently, they are generally used only when other alternatives are not available. A form of tobramycin that can be administered through inhalation rather than injection makes treatment of lung infections in cystic fibrosis patients caused by Pseudomonas aeruginosa safer and more effective. Another aminoglycoside, neomycin, is too toxic for systemic use; however, it is a common ingredient in non-prescription topical ointments. ■ active transport, p. 58

The Tetracyclines The tetracyclines reversibly bind to the 30S ribosomal subunit, blocking the attachment of tRNA to the ribosome and preventing the continuation of protein synthesis. These bacteriostatic drugs are actively transported into prokaryotic but not animal cells, which effectively concentrates them inside bacteria. This, in part, accounts for their selective toxicity. The tetracyclines

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are effective against certain Gram-positive and Gram-negative bacteria. Tetracyclines such as doxycycline have a longer halflife, allowing less-frequent doses. The glycylcyclines are a new group of semisynthetic tetracycline derivatives. They have a wide spectrum of activity and are effective against some bacteria that have acquired resistance against tetracycline. Tigecycline is the only example currently approved. Resistance to the tetracyclines is primarily due to a decrease in their accumulation by the bacterial cell, either by decreased uptake or increased excretion. Tetracyclines can cause discoloration in teeth when used by young children.

The Macrolides The macrolides reversibly bind to the 50S ribosomal subunit and prevent the continuation of protein synthesis. Macrolides as a group are bacteriostatic against a variety of bacteria, including many Gram-positive organisms as well as the most common causes of atypical pneumonia (“walking pneumonia”). They often serve as the drug of choice for patients who are allergic to penicillin. Macrolides are not effective against members of the family Enterobacteriaceae, however, because the outer membrane of these organisms excludes the drug. Examples of macrolides include erythromycin, clarithromycin, and azithromycin. Both clarithromycin and azithromycin have a longer half-life than erythromycin, so that they can be taken less frequently. Resistance to all the macrolides can occur through modification of the ribosomal RNA target. Other mechanisms of resistance include the production of an enzyme that chemically modifies the drug and alterations that result in decreased uptake of the drug. ■ walking pneumonia, p. 511

Chloramphenicol Chloramphenicol binds to the 50S ribosomal subunit, preventing peptide bonds from being formed and, consequently, blocking protein synthesis. Although it is bacteriostatic against a wide range of bacteria, it is generally only used as a last resort for lifethreatening infections in order to avoid a rare but lethal side effect. This complication, aplastic anemia, can occur in response to even a small amount of chloramphenicol and is characterized by the inability of the body to form white and red blood cells.

The Lincosamides The lincosamides bind to the 50S ribosomal subunit and prevent the continuation of protein synthesis, inhibiting a variety of Gram-negative and Gram-positive bacteria. They are particularly useful for treating infections resulting from intestinal perforation because they inhibit Bacterioides fragilis, a member of the normal intestinal microbiota that is frequently resistant to other antimicrobials. Unfortunately, the risk of developing antibioticassociated colitis for people taking lincosamides is greater than for some other antimicrobials because Clostridium difficile is generally resistant to these drugs. The most commonly used lincosamide is clindamycin.

The Oxazolidinones The oxazolidinones also bind to the 50S ribosomal subunit and interfere with the initiation of protein synthesis. They are bacterio-

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static against a variety of Gram-positive bacteria and are useful in treating infections caused by bacteria that are resistant to b-lactam drugs and vancomycin. Linezolid is an example.

The Streptogramins Two streptogramins, quinupristin and dalfopristin, are administered together in a medication called Synercid®. These act as a synergistic combination, binding to two different sites on the 50S ribosomal subunit and inhibiting distinct steps of protein synthesis. Individually, each drug is bacteriostatic but together they are bactericidal. Synercid® is effective against a variety of Grampositive bacteria, including some that are resistant to b-lactam drugs and vancomycin.

Antibacterial Medications That Inhibit Nucleic Acid Synthesis Enzymes required for nucleic acid synthesis are the targets of some groups of antimicrobial drugs. These groups include the fluoroquinolones and the rifamycins.

The Fluoroquinolones The synthetic drugs called the fluoroquinolones inhibit one or more of a group of enzymes called topoisomerases, which maintain the supercoiling of closed circular DNA within the bacterial cell. One type of topoisomerase, called DNA gyrase, or topoisomerase II, breaks and rejoins strands to relieve the strain caused by the localized unwinding of DNA during replication and transcription. Consequently, inhibition of this enzyme prevents these essential cell processes. The fluoroquinolones are bactericidal against a wide variety of bacteria, including both Gram-positive and Gram-negative organisms. Examples of fluoroquinolones include ciprofloxacin and moxifloxacin. Acquired resistance is most commonly due to an alteration in the DNA gyrase target. ■ supercoiled DNA, p. 67

The Rifamycins The rifamycins block prokaryotic RNA polymerase from initiating transcription. Rifampin, which is the most widely used rifamycin, exhibits bactericidal activity against many Gram-positive and some Gram-negative bacteria as well as members of the genus Mycobacterium. It is primarily used to treat tuberculosis and Hansen’s disease (leprosy) and to prevent meningitis in people who have been exposed to Neisseria meningitidis. In some patients, a reddish-orange pigment appears in urine and tears. Resistance to rifampin develops rapidly and is due to a mutation in the gene that encodes RNA polymerase.

Antibacterial Medications That Inhibit Metabolic Pathways Relatively few antibacterial medications interfere with metabolic pathways. Among the most useful are the folate inhibitors—sulfonamides and trimethoprim. These each inhibit different steps in the pathway that leads initially to the synthesis of folic acid and ultimately to the synthesis of a coenzyme

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21.3 Mechanisms of Action of Antibacterial Drugs Para-aminobenzoic acid (PABA)

H2N

Enzyme #1

PABA

Sulfa drugs

Precursor #2

Sulfanilamide H2N

Antibacterial Medications That Interfere with Cell Membrane Integrity

Precursor #1

COOH

SO2NH2

Glutamate

Enzyme #2

Dihydrofolate (a) Enzyme #3

Trimethoprim

Tetrahydrofolate Multiple enzymes and reactions Thymine, guanine, and adenine nucleotides (b)

FIGURE 21.8 Inhibitors of the Folate Pathway (a) The chemical structure of PABA and a sulfa drug (sulfanilamide). (b) The sulfonamides and trimethoprim interfere with different steps of the pathway that leads initially to the synthesis of folic acid and ultimately to the synthesis of a coenzyme required for nucleotide biosynthesis.

required for nucleotide biosynthesis (figure 21.8). Animal cells lack the enzymes in the folic acid synthesis portion of the pathway, which is why folic acid is a dietary requirement. ■ coenzyme, p. 135

The Sulfonamides Sulfonamides and related compounds, collectively referred to as sulfa drugs, inhibit the growth of many Gram-positive and Gram-negative bacteria. They are structurally similar to paraaminobenzoic acid (PABA), a substrate in the pathway for folic acid biosynthesis. Because of this similarity, the enzyme that normally binds PABA binds sulfa drugs instead, an example of competitive inhibition (see figure 6.13). Human cells lack this enzyme, providing the basis for the selective toxicity of the sulfonamides. Resistance of bacteria to the sulfonamides is often due to the acquisition of a plasmid-encoded enzyme that has a lower affinity for the drug. ■ competitive inhibition, p. 138

Trimethoprim Trimethoprim inhibits the bacterial enzyme that catalyzes a metabolic step following the one inhibited by sulfonamides. Fortunately, the drug has little effect on the analogous enzyme in human cells. The combination of trimethoprim and a sulfonamide has a synergistic effect, and they are often used together to treat urinary tract infections. The most common mechanism of resistance is a plasmid-encoded alternative enzyme that has a lower affinity for the drug. Unfortunately, the genes encoding resistance to trimethoprim and sulfonamide are often carried on the same plasmid.

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A few antimicrobial drugs damage bacterial membranes. Polymyxin B, a common ingredient in first-aid skin ointments, binds to the membranes of Gram-negative cells and alters the permeability, leading to leakage of cellular contents and eventual death of the cells. Unfortunately, these drugs also bind to eukaryotic cells, though to a lesser extent, which generally limits their use to topical applications. Daptomycin inserts into the bacterial cytoplasmic membrane, resulting in death of the cell. Its approval increases the arsenal of antimicrobial medications available for treating infections caused by Gram-positive bacteria resistant to other drugs. It is not effective against Gram-negative bacteria, however, because it cannot penetrate the outer membrane.

Antibacterial Medications That Interfere with Processes Essential to Mycobacterium tuberculosis Only a limited range of antimicrobials can be used to treat infections caused by Mycobacterium tuberculosis and related species. This is due to several factors, including the chronic nature of the disease caused by these organisms, their slow growth, and their waxy cell wall, which is impervious to many drugs. A group of five medications, called the first-line drugs, are preferred because they are the most effective as well as the least toxic. These are generally given in combination of two or more to patients who have active tuberculosis. This combination therapy prevents the development of resistant mutants; if some cells in the infecting population spontaneously develop resistance to one drug, the other drug will eliminate them. The second-line medications are used if the first-line drugs are not an option because of resistance; however, they are either less effective or have greater risk of toxicity. ■ Mycobacterium tuberculosis, p. 515 Of the first-line medications, some specifically target the unique cell wall that characterizes the mycobacteria. Isoniazid inhibits the synthesis of mycolic acids, a primary component of the cell wall. Ethambutol inhibits enzymes that are required for synthesis of other mycobacterial cell wall components. The mechanism of pyrazinamide is unknown. Other first-line drugs include rifampin and streptomycin, which have already been discussed.

MICROCHECK 21.3 Bacterial processes that utilize enzymes or structures that are different, absent, or not commonly found in eukaryotic cells are the targets of most medically useful antimicrobial drugs. The targets of antimicrobial drugs include biosynthetic pathways for peptidoglycan, protein, nucleic acid, and folic acid and the integrity of membranes. Drugs used to treat tuberculosis often interfere with processes unique to Mycobacterium tuberculosis. ✓ Explain the normal biological role of penicillin-binding proteins. ✓ What is the target of the macrolides? ✓ Why would co-administration of a bacteriostatic drug interfere with the effects of penicillin?

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21.4 Determining the Susceptibility of a Bacterial Strain to an Antimicrobial Drug

overgrowth of pathogens resistant to the drug. A better approach is to determine the susceptibility of the specific pathogen to various antimicrobial drugs and then choose the drug that acts against the offending organism but against as few other bacteria as possible.

Determining the Minimum Inhibitory and Bactericidal Concentrations

Focus Points Describe how the minimum inhibitory concentration (MIC) and the minimum bactericidal concentration (MBC) of an antimicrobial drug are determined. Compare and contrast the Kirby-Bauer disc diffusion test with commercial modifications of antimicrobial susceptibility testing.

In many cases, susceptibility of a pathogenic organism to a specific antimicrobial drug is unpredictable. Unfortunately, it has often been the practice to try one drug after another until a favorable response is observed or, if the infection is very serious, to give several together. Both approaches are undesirable. With each unnecessary drug given, needless risks of toxic or allergic effects arise and the normal microbiota may be altered, permitting the

The minimum inhibitory concentration (MIC) is the lowest concentration of a specific antimicrobial drug needed to prevent the growth of a given organism in vitro. It is determined by examining the test bacterial strain’s ability to grow in broth cultures containing different concentrations of the antimicrobial. Serial dilutions generating decreasing concentrations of the drug are first prepared in tubes containing a suitable growth medium (figure 21.9). Then, a fixed concentration of the organism is added to each tube. The tubes are incubated for at least 16 hours and then examined for visible growth or turbidity. The lowest concentration of the drug that prevents growth of the microorganism is the minimum inhibitory concentration. The fact that a strain is inhibited by a given concentration of drug, however, does not necessarily mean that an infection caused by that

Decreasing Concentration of the Antimicrobial Drug

Organism A

Control (no bacteria)

16 µg/ml

8

4

2

1

0.5

0.25

0.12

0.06

0.03

Control

Result: MIC = 0.12 µg/ml Organism B

Control (no bacteria)

16 µg/ml

8

4

2

1

0.5

0.25

0.12

0.06

0.03

Control

Result: MIC = 1.0 µg/ml Organism C

Control (no bacteria)

16 µg/ml

8

4

2

1

0.5

0.25

0.12

0.06

0.03

Control

Result: MIC = 16 µg/ml

FIGURE 21.9 Determining the Minimum Inhibitory Concentration (MIC) of an Antimicrobial Drug The lowest concentration of drug that prevents growth of the culture is the MIC.

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PERSPECTIVE 21.1 Measuring the Concentration of an Antimicrobial Drug in Blood or Other Body Fluids 6.25

C 1.25

0.25

Concentration (µg/ml)

Logarithm of concentration

There are many situations in which it is necessary to determine the concentration of an antimicrobial drug in a patient’s blood or other body fluid. For example, patients who are being administered an aminoglycoside must often be carefully monitored to ensure that the concentration of drug in their blood does not reach an unsafe level, particularly if they have kidney or liver dysfunction that interferes with normal elimination. Likewise, new drugs must be tested to determine achievable levels in the blood, urine, or other body fluids. A technique called the diffusion bioassay is used to measure the concentration of an antimicrobial drug in a fluid specimen. The test relies on the same principle as the Kirby-Bauer test, except in this case it is the concentration of drug, not the sensitivity of organism, being assayed. A culture of a stock organism highly susceptible to the drug is added to melted cooled agar, and the mixture poured into an agar plate and allowed to solidify. This results in a solid medium uniformly inoculated throughout with the sensitive organism. Cylindrical holes are then punched out of the agar, creating wells. Standards, or fluids containing known concentrations of the drug, are then added to some of the wells, while others are filled with the body fluid being tested. Following overnight incubation, zones of inhibition form around the agar wells, the sizes of which correspond to the concentrations of the drug (figure 1). The higher the concentration of the antimicrobial drug, the larger the zone of inhibition. The zone

10 20 D Zone diameter (mm) (a) Standards and patient’s serum are added to agar that has been seeded with susceptible strain of bacteria.

30

(b) A standard curve that correlates the size of the zone with the concentration of antibiotic is constructed. The concentration of the antimicrobial drug in the body fluid can be read from the line relating zone size to concentration.

FIGURE 1 Biological Assay to Determine the Concentration of an Antimicrobial Drug in a Patient’s Body Fluid sizes around the standards are measured, and from this a standard curve is constructed by plotting the zone sizes against the corresponding drug concentra-

strain can be successfully treated with the drug. For example, an organism with an MIC of 16 mg/ml of a drug is sensitive to that concentration in vitro. Nevertheless, the organism would be considered resistant for the purposes of treatment if the level that can be achieved in a person’s blood were less than that. Microbes that have an MIC on the borderline between susceptible (treatable) and resistant (untreatable) are called intermediate. The minimum bactericidal concentration (MBC) is the lowest concentration of a specific antimicrobial drug that kills 99.9% of cells of a given bacterial strain. The MBC is determined by assaying for live organisms in tubes from the MIC test that showed no growth. A small sample from each of those tubes is transferred to fresh, antibiotic-free medium. If growth occurs, then living organisms remained in the original tube. Conversely, if no growth occurs, then no living organisms remained, indicating that the antibiotic was bactericidal at that concentration. Determining the MIC and MBC using these conventional methods gives precise information regarding an organism’s susceptibility. The techniques, however, are labor-intensive and consequently expensive. In addition, individual sets of tubes must be inoculated to determine susceptibility to each different antimicrobial tested.

tion. A line relating zone size to concentration is obtained, from which the concentration of the antimicrobial drug in the body fluid can be read.

tery of antimicrobial drugs. A standard concentration of the strain is first uniformly spread on the surface of an agar plate. Then 12 or so discs, each impregnated with a specified amount of a selected antimicrobial drug, are placed on the surface of the medium (figure 21.10). During incubation, the various drugs diffuse outward

Conventional Disc Diffusion Method

FIGURE 21.10 Kirby-Bauer Method for Determining Drug Susceptibility The size of the zone of inhibition surrounding the disc reflects, in part,

The Kirby-Bauer disc diffusion test is routinely used to qualitatively determine the susceptibility of a given bacterial strain to a bat-

the sensitivity of the bacterial strain to the drug. Because zone size is influenced by characteristics of the drug such as molecular weight, however, a chart must be consulted that correlates zone size to susceptibility.

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from the discs, forming a concentration gradient around each disc. Meanwhile the bacterial cells multiply, eventually forming a film of growth on the plate, except in regions around the discs where antimicrobial drugs kill the cells or inhibit their growth. A clear zone of inhibition around an antimicrobial disc reflects, in part, the degree of susceptibility of the organism to the drug. The zone size is also influenced by characteristics of the drug including its molecular weight and stability, as well as the amount in the disc. Special charts have been prepared correlating the size of the zone of inhibition to susceptibility of bacteria to the drug. Based on the size of the zone, organisms can be described as susceptible, intermediate, or resistant to the drug.

Commercial Modifications of Antimicrobial Susceptibility Testing Commercial modifications of the conventional methods offer certain advantages. They are less labor-intensive, and the results can be obtained in as little as 4 hours. One system utilizes a small card with miniature wells containing specific antimicrobial concentrations. The highly automated system inoculates and incubates the cards, determines the growth rate by reading the turbidity, and uses mathematical formulas to interpret the results and derive the MICs in 6 to 15 hours (figure 21.11). The E test, a modification of the disc diffusion test, utilizes a strip impregnated with a gradient of concentrations of an antimicrobial drug. Multiple strips, each containing a different drug, are placed on the surface of an agar medium that has been uniformly inoculated with the test organism. During incubation the test organism will grow, and a zone of inhibition will form around the strip, but because of the gradient of drug concentrations, the zone of inhibition will be shaped somewhat like a teardrop that intersects the strip at some point (figure 21.12). The MIC is determined by reading the printed number at the point where the bacterial growth intersects the strip.

(a)

(b)

FIGURE 21.12 The E Test The strip is impregnated with a gradient of concentrations of a given antimicrobial drug. The MIC is determined by reading the number on the strip at the point at which growth intersects the strip.

MICROCHECK 21.4

FIGURE 21.11 Automated Tests Used to Determine Antimicrobial Susceptibility The miniature wells in the card contain specific concentrations of an antimicrobial drug. An automated system inoculates and incubates the cards, determines the growth rate by reading turbidity, and uses mathematical formulas to interpret the results and derive the MICs.

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The minimum inhibitory concentration and minimum bactericidal concentration are quantitative measures of a bacterial strain’s susceptibility to an antimicrobial drug. Disc diffusion tests can determine whether an organism is sufficiently susceptible to a specific drug for it to successfully be used in treatment. Commercial tests for determining antimicrobial sensitivity are less labor-intensive and often more rapid. ✓ Explain the difference between the MIC and the MBC. ✓ List two factors other than an organism’s sensitivity to a drug that can influence the size of the zone of inhibition around an antimicrobial disc. ✓ Why would it be important for the Kirby-Bauer disc diffusion test to use a standard concentration of the bacterial strain being tested?

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S

S S

S

Focus Points R

Describe four general mechanisms of antimicrobial resistance. Describe how antimicrobial resistance can be acquired.

S

S

List four examples of emerging antimicrobial resistance. Antimicrobial drug is added; sensitive organisms are killed or inhibited.

Describe how the emergence and spread of antimicrobial resistance can be slowed.

After the introduction of sulfa drugs and penicillin, there was great hope that such drugs would soon eliminate most bacterial diseases. It is now recognized, however, that resistance to antimicrobial medications limits the usefulness of all known antimicrobials. As these drugs are increasingly used and misused, the resistant bacterial strains have a selective advantage over their sensitive counterparts (figure 21.13). For example, when penicillin G was first introduced, less than 3% of Staphylococcus aureus strains were resistant to its effects. Heavy use of the drug, measured in hundreds of tons per year, progressively eliminated sensitive strains, so that 90% or more are now resistant. This development is understandably of great concern to health professionals because of the impact on the cost, complications, and outcomes of treatment. Understanding the mechanisms and the spread of antimicrobial resistance is an important step in curtailing the problem, and it may also allow pharmaceutical companies to develop new drugs that foil common resistance mechanisms.

S S S

S R S S

Resistant survivors can multiply without competition.

R

R

R

Mechanisms of Acquired Resistance Bacteria can resist the effects of antimicrobial drugs through a variety of mechanisms. In some cases this resistance is innate, but oftentimes it is acquired. Figure 21.14 depicts the most common mechanisms of acquired resistance to antimicrobial drugs.

R

R

R

R

FIGURE 21.13 The Selective Advantage of Drug Resistance When antimicrobial drugs are used, bacterial strains that are resistant (R) to their effects have a selective advantage over their sensitive (S) counterparts.

Drug-Inactivating Enzymes Some organisms produce enzymes that chemically modify a specific drug in such a way as to render it ineffective. Recall that bacteria that synthesize the enzyme penicillinase are resistant to penicillin. As another example, the enzyme chloramphenicol acetyltransferase chemically alters the antibiotic chloramphenicol, making it ineffective.

Alteration in the Target Molecule An antimicrobial drug generally acts by recognizing and binding to a specific target molecule in a bacterium, interfering with its function. Minor structural changes in the target can prevent the drug from binding. Alterations in the penicillin-binding proteins prevent b-lactam drugs from binding to them. Similarly, a change in the ribosomal RNA, the target for the macrolides, prevents those drugs from interfering with ribosome function.

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Decreased Uptake of the Drug The porin proteins in the outer membrane of Gram-negative bacteria selectively permit small hydrophobic molecules to enter a cell. Alterations in these proteins can therefore alter permeability and prevent certain drugs from entering the cell. By excluding entry of a drug, an organism avoids its effects. ■ porins, p. 61

Increased Elimination of the Drug The systems that bacteria use to transport detrimental compounds out of a cell are called efflux pumps. Alterations that result in the increased expression of these pumps can increase the overall capacity of a cell to eliminate a drug, thus enabling the organism to resist higher concentrations of that drug. In addition, structural changes influence the array of drugs that can be actively pumped

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required to prevent binding of the drug. Unlike streptomycin, the newer aminoglycosides bind to several sites on the ribosome, making resistance due to spontaneous mutation less likely. Drugs such as streptomycin to which single point mutations can confer resistance are sometimes used in combination with one or more other drugs to prevent survival of resistant mutants. If any organism spontaneously develops resistance to one drug, another drug will still kill it. The chance of an organism simultaneously developing mutational resistance to multiple drugs is extremely low.

NON-RESISTANT CELL

Target Drug Drug binds target.

RESISTANT CELL

Increased elimination Drug enters cell but efflux pump ejects it.

Drug-inactivating enzyme Enzyme modifies drug, inactivating it. Alteration in target molecule Drug cannot bind target.

Decreased uptake Porin proteins prevent entry into the cell.

FIGURE 21.14 Common Mechanisms of Acquired Antimicrobial Drug Resistance

out. Resistance that develops by this mechanism is particularly worrisome because it potentially enables an organism to become resistant to several drugs simultaneously. ■ efflux pumps, p. 58

Acquisition of Resistance Antimicrobial resistance can be due to either spontaneous mutation, which alters existing genes, or acquisition of new genes (see figure 8.1).

Spontaneous Mutation As cells replicate, spontaneous mutations occur at a relatively low rate. Even at a low rate, however, such mutations can ultimately have a profound effect on the resistance of a bacterial population to an antimicrobial drug. For instance, resistance to the aminoglycoside streptomycin results from a single base-pair change in the gene encoding the ribosomal protein to which streptomycin binds; that point mutation alters the target sufficiently to render the drug ineffective. When a streptomycin-sensitive bacterium is grown in streptomycin-free medium to a population of 109 cells, it is probable that at least one cell in the population has that particular mutation in its genome. Through spontaneous mutation, that particular cell has acquired resistance to streptomycin. If streptomycin is then added to the medium, only that cell and its progeny will be able to replicate, generating a population of streptomycin-resistant clones. When an antimicrobial drug has several different potential targets or has multiple binding sites on a single target, it is more difficult for an organism to develop resistance through spontaneous mutation. This is because several different mutations are

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Gene Transfer Given the mobility of DNA, genes encoding resistance to an antimicrobial drug can spread to different strains, species, and even genera. The most common mechanism of transfer of resistance is through the conjugative transfer of R plasmids. R plasmids frequently carry several different resistance genes, each one mediating resistance to a specific antimicrobial drug. Thus, when an organism acquires an R plasmid, it acquires resistance to several different medications simultaneously. ■ R plasmid, p. 205 ■ conjugation, p. 202 In some cases, the resistance gene that was transferred from one organism to another originated through spontaneous mutation of a common bacterial gene, such as one encoding the target of the drug. In other cases, the gene may have originated from the soil microbe that naturally produces that antibiotic. For example, a gene coding for an enzyme that chemically modifies an aminoglycoside likely originated from the Streptomyces species that produces that aminoglycoside.

Examples of Emerging Antimicrobial Resistance Some of the problems associated with the increasing resistance of bacteria to antimicrobial drugs are highlighted by the following examples.

Enterococci One of the most dramatic examples of antimicrobial resistance is the enterococci, a group of bacteria that is part of the normal intestinal microbiota and a common cause of healthcare-associated infections. Enterococci are intrinsically less susceptible to many common antimicrobials. For example, their penicillin-binding proteins have low affinity for certain b-lactam antibiotics. In addition, many enterococci have plasmid-borne resistance genes. Some strains, called vancomycin-resistant enterococci (VRE), are even resistant to vancomycin. This drug is usually reserved as a last resort for treating life-threatening infections caused by Gram-positive organisms that are resistant to all b-lactam drugs. Because vancomycin resistance in these strains is encoded on a plasmid, the resistance is transferable to other organisms. ■ healthcare-associated infections, p. 462

Staphylococcus aureus Staphylococcus aureus, another common cause of healthcareassociated infections, is becoming increasingly resistant to antimicrobials. Over the past 50 years, most strains have acquired resistance to penicillin due to their acquisition of a gene encoding

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the enzyme penicillinase. Until recently, infections caused by these strains could be treated with methicillin or other penicillinaseresistant penicillins. New strains have emerged, however, that not only produce penicillinase, but also have penicillin-binding proteins with low affinity for all b-lactam drugs. These strains, called methicillin-resistant Staphylococcus aureus, or MRSA, are resistant to methicillin as well as all other b-lactam drugs. Healthcare-associated infections caused by these strains are generally treated with vancomycin. A few hospitals, however, have reported isolates that are no longer susceptible to normal levels of vancomycin. So far, strict hospital guidelines designed to immediately halt the spread of these vancomycin-intermediate S. aureus (VISA) and vancomycin-resistant S. aureus (VRSA) strains have been successful. MRSA strains that cause community-acquired infections are generally susceptible to antibiotics other than b-lactam drugs. ■ Staphylococcus aureus, p. 535

have been identified. These are defined as M. tuberculosis strains that are resistant to isoniazid and rifampin, plus three or more of the second-line drugs.

Streptococcus pneumoniae

Physicians and other healthcare workers need to increase their efforts to identify the specific causative agent of a given infection and only if appropriate, prescribe suitable antimicrobials. They must also educate their patients about the proper use of prescribed drugs in order to increase patient compliance. While these efforts may be more expensive in the short term, they will ultimately save both lives and money.

Until recently, Streptococcus pneumoniae, the leading cause of pneumonia in adults, has remained exquisitely sensitive to penicillin. Some isolates, however, are now resistant to the drug. This acquired resistance is due not to the production of a b-lactamase, but rather to modifications in the chromosomal genes coding for four different penicillin-binding proteins, decreasing their affinities for the drug. The nucleotide changes do not appear to have arisen through a series of point mutations as one might expect; instead, they are due to the acquisition of chromosomal DNA from other species of Streptococcus. As you may recall from earlier reading, S. pneumoniae can acquire DNA through DNA-mediated transformation. ■ Streptococcus pneumoniae, p. 509 ■ DNA-mediated transformation, p. 199

Mycobacterium tuberculosis Treatment of Mycobacterium tuberculosis active infections has always been a long and complicated process, requiring a combination of two or more different drugs taken for a period of 6 months or more. Unfortunately, the first-line drugs (the preferred therapeutic agents) are often those to which spontaneous mutations readily occur. Because large numbers of bacterial cells are found in an active infection, the probability that one has developed spontaneous resistance to a single drug is likely, which is why multiple drug therapy is required. The length of treatment is due to the tediously slow growth of M. tuberculosis. ■ Mycobacterium tuberculosis, p. 514

Many tuberculosis patients do not comply with the complex treatment regime, skipping doses or stopping treatment too soon, and as a consequence, strains of M. tuberculosis are developing resistance to the first-line drugs. This results in even lengthier, more costly treatments that are also less effective. Strains that are resistant to two of the favored drugs for tuberculosis treatment, isoniazid and rifampin, are called multiple-drug-resistant M. tuberculosis, or MDR-TB. To prevent the emergence of these strains, some cities are utilizing directly observed therapy in which healthcare workers routinely visit patients in the community and watch them take their drugs to ensure they comply with their prescribed antimicrobial treatment. Of even greater concern, extensively-drug-resistant M. tuberculosis, or XDR TB, strains

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Slowing the Emergence and Spread of Antimicrobial Resistance To reverse the alarming trend of increasing antimicrobial drug resistance, everyone must cooperate. On an individual level, physicians as well as the general public must take more responsibility for the appropriate use of these life-saving medications. On a global scale, countries around the world need to make important policy decisions about what is, and what is not, an appropriate use of these drugs.

The Responsibilities of Physicians and Other Healthcare Workers

The Responsibilities of Patients Patients need to carefully follow the instructions that accompany their prescriptions, even if those instructions seem inconvenient. It is essential to maintain the concentration of the antimicrobial in the blood at the required level for a specific time period. When a patient skips a scheduled dose of a drug, the blood level of the drug may not remain high enough to inhibit the growth of the least-sensitive members of the population. If these less-sensitive organisms then have a chance to grow, they will give rise to a population that is not as sensitive as the original. Likewise, failure to complete the prescribed course of treatment may not kill the least-sensitive organisms, allowing their subsequent multiplication. Misusing antimicrobials by skipping doses or failing to complete the prescribed duration of treatment promotes the gradual emergence of resistant organisms. In essence, the patient is selecting for the step-wise development of resistant mutants.

The Importance of an Educated Public A greater effort must also be made to educate the public about the appropriateness and limitations of antibiotics in order to ensure they are utilized wisely. First and foremost, people need to understand that antibiotics are not effective against viruses. Taking antibiotics will not cure the common cold or any other viral illness. A few antiviral drugs are available, but they are effective against only a limited group of viruses such as HIV or herpesviruses. Unfortunately, surveys indicate that far too many people erroneously believe that antibiotics are effective against viruses and often seek prescriptions to “cure” viral infections. This misuse only selects for antibiotic-resistant bacteria in the normal microbiota. Even though these organisms are not pathogenic themselves, they can serve as a reservoir for R plasmids, eventually transferring their resistance genes to an infecting pathogen.

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Global Impacts of the Use of Antimicrobial Drugs Worldwide, there is growing concern about the overuse of antimicrobial drugs. Countries may vary in their laws and social norms, but antimicrobial resistance recognizes no political boundaries. An organism that develops resistance in one country can quickly be transported globally. In many parts of the world, particularly in developing countries, antimicrobial drugs are available on a non-prescription basis. Because of the consequences of inappropriate use, there is a growing opinion that over-the-counter availability of these drugs should be curtailed or eliminated. Another worldwide concern is the use of antimicrobial drugs in animal feeds. Low levels of these drugs in feeds result in larger, more economically productive animals, and therefore, less expensive meat, a seemingly attractive option. This use, like any other, however, selects for drug-resistant organisms, which has caused some scientists to question its ultimate wisdom. In fact, infections caused by drug-resistant Salmonella strains have been linked to animals whose feed was supplemented with those drugs. In response to these concerns, there is growing pressure worldwide to ban the use of antimicrobial drugs in animal feeds.

Entry inhibitors (effective against HIV) Entry

Eukaryotic host cell Uncoating Nucleic acid synthesis (viral enzyme directed)

Integrase inhibitors (effective against HIV)

Viral particle production

Exit Viral uncoating (effective against influenza A virus) Amantadine Rimantadine

Assembly and release of viral particles (effective against HIV) Protease inhibitors (effective against influenza viruses) Neuraminidase inhibitors

Nucleic acid synthesis (effective primarily against herpesviruses and HIV) Nucleoside analogs Non-nucleoside polymerase inhibitors Non-nucleoside reverse transcriptase inhibitors

FIGURE 21.15 Targets of Antiviral Drugs

MICROCHECK 21.5 Mutations and transfer of genetic information have enabled microorganisms to develop resistance to each new antimicrobial drug developed. Drug resistance affects the cost, complications, and outcomes of medical treatment. Slowing the emergence and spread of resistant microbes involves the cooperation of health care personnel, educators, and the general public. ✓ Explain how using a combination of two antimicrobial drugs helps prevent the development of spontaneously resistant mutants. ✓ Explain the significance of a member of the normal flora that harbors an R plasmid. ✓ A student argued that “spontaneous mutation” meant that a drug could cause mutations. Is the student correct? Why or why not?

21.6 Mechanisms of Action of Antiviral Drugs Focus Points

targets of antiviral drugs (figure 21.15). Relatively few other targets have been discovered. Many researchers and pharmaceutical companies are currently trying to develop more effective antiviral drugs, medications that interfere with viral replication. The relatively few drugs available are generally effective against only a specific type of virus; none can eliminate latent viral infections. Table 21.2 summarizes the characteristics of the most common antiviral drugs. ■ latent viral infections, p. 330

Entry Inhibitors A new group of drugs in the anti-HIV arsenal are the entry inhibitors, which prevent the virus from entering host cells. Enfuvirtide does this by binding to an HIV protein that mediates fusion of the viral envelope with the cell membrane. Maraviroc blocks the HIV coreceptor CCR5. ■ HIV attachment and entry, p. 702

Viral Uncoating

Describe the antiviral drugs that interfere with nucleic acid synthesis.

After a virus enters a host cell, the protein coat must dissociate from the nucleic acid in order for replication to occur. Drugs that interfere with the uncoating step thus prevent viral replication. The only effective drugs that target this step, however, are those that block influenza A viruses. ■ influenza A virus, p. 519

Describe the antiviral drugs that interfere with the assembly and release of viral particles.

Amantadine and Rimantadine

Describe the antiviral drugs that interfere with viral uncoating.

Viruses rely almost exclusively on the host cell’s metabolic machinery for their replication, making them extremely difficult targets for selective toxicity. Viruses have no cell wall, ribosomes, or any other structure targeted by commonly used antibiotics. Thus, they are completely unaffected by antibiotics. Some viruses encode their own polymerases, however, and these are potential

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Two drugs, amantadine and rimantadine, which are similar in both their chemical structure and mechanism of action, block the uncoating of influenza A virus after it enters a cell. Consequently, they prevent or reduce the severity and duration of the disease. The drugs are only used until active immunization can be achieved, since immunization is important for long-term protection. Unfortunately, resistance develops frequently and limits the usefulness of the drugs.

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TABLE 21.2 Characteristics of Antiviral Drugs Target/Drug Examples

Comments/Characteristics

Entry Inhibitors Enfuvirtide, Maraviroc

Used to treat HIV infections.

Viral Uncoating Amantadine and rimantadine

Reduces severity and duration of influenza A infections, but resistance limits their use.

Nucleic Acid Synthesis Nucleoside analogs Acyclovir, ganciclovir, ribavirin, zidovudine (AZT), didanosine (ddl), lamivudine (3TC)

Non-nucleoside polymerase inhibitors Foscarnet Non-nucleoside reverse transcriptase inhibitors Nevirapine, delavirdine, efavirenz

Primarily used to treat infections caused by herpesviruses and HIV; they do not cure latent infections. The drugs are converted within eukaryotic cells to a nucleotide analog; virally encoded enzymes are prone to incorporate these, resulting in premature termination of synthesis or improper base-pairing of the viral nucleic acid. Acyclovir is used to treat herpes simplex virus (HSV) and varicella-zoster virus (VZV) infections. Ganciclovir is used to treat cytomegalovirus infections in immunocompromised patients. Ribavirin is used to treat respiratory syncytial virus (RSV) infections in newborns. Combinations of nucleoside analogs such as zidovudine (AZT), didanosine (ddl), and lamivudine (3TC) are used to treat HIV infections. Primarily used to treat infections caused by herpesviruses. They inhibit the activity of viral polymerases by binding to a site other than the nucleotide-binding site. Foscarnet is used to treat ganciclovir-resistant cytomegalovirus (CMV) and acyclovir-resistant herpes simplex virus (HSV). Used to treat HIV infections. They inhibit the activity of reverse transcriptase by binding to a site other than the nucleotide-binding site and are often used in combination with nucleoside analogs.

Integrase Inhibitors Raltegravir

Used to treat HIV infections.

Assembly and Release of Viral Particles Protease inhibitors Indinavir, ritonavir, saquinavir, nelfinavir Neuraminidase inhibitors

Used to treat HIV infections. They inhibit protease, an essential enzyme of HIV, by binding to its active site. Used to treat influenza virus infections.

Zanamivir, oseltamivir

Nucleic Acid Synthesis Many of the most effective antiviral drugs exploit the error-prone, virally encoded enzymes used to replicate viral nucleic acid. With few exceptions, however, the use of these drugs is generally limited to treating infections caused by the herpesviruses and HIV.

Nucleoside Analogs A growing number of antiviral drugs are nucleoside analogs, compounds similar in structure to a nucleoside. These analogs can be phosphorylated in vivo by a virally encoded or normal cellular enzyme to form a nucleotide analog, a chemical structurally similar to the nucleotides of DNA and RNA. In some cases, incorporation of the nucleotide analog results in termination of the growing nucleotide chain. In other cases, incorporation of the analog results in a defective strand with altered base-pairing properties. ■ nucleotide, p. 32 The basis for the selective toxicity of most nucleoside analogs is the fact that virally encoded enzymes are much more prone to incorporating nucleotide analogs than are host polymerases. Thus, more damage is done to the rapidly replicating viral genome than to host cells. The analogs, however, are only effective against replicating viruses. Because viruses such as herpesvirus and HIV can remain latent in cells, the drugs do not cure these infections; they

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simply limit the duration of the active infection. Latent virus can still undergo reactivation, causing a reoccurrence of symptoms. Most nucleoside analogs are reserved for severe infections because of their significant side effects. An important exception to this principle is acyclovir, a drug used to treat herpesvirus infections. This drug causes little harm to uninfected cells because the conversion of acyclovir to a nucleotide analog does not utilize a normal cellular enzyme but instead requires a virally encoded enzyme. The enzyme is only present in cells infected by herpesviruses such as herpes simplex virus (HSV) and varicella-zoster virus (VZV). Thus, acyclovir does not get converted to a nucleotide analog in uninfected cells. Other nucleoside analogs include ganciclovir, which is used to treat life-threatening or sight-threatening cytomegalovirus (CMV) infections in immunocompromised patients, and ribavirin, which is used to treat respiratory syncytial virus infections (RSV) in newborns. ■ herpes simplex virus, pp. 592, 638 ■ varicella-zoster, p. 546

A number of different nucleoside analogs are used to treat HIV infection by interfering with the activity of reverse transcriptase. Unfortunately, the virus rapidly develops mutational resistance against these drugs, which is why they are often used in combination with other anti-HIV drugs. Nucleoside analogs that interfere with reverse transcription include zidovudine (AZT), didanosine (ddI), and lamivudine (3TC). Two of these are often used in combination for HIV therapy.

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21.7 Mechanisms of Action of Antifungal Drugs

Non-Nucleoside Polymerase Inhibitors Non-nucleoside polymerase inhibitors are compounds that inhibit the activity of viral polymerases by binding to a site other than the nucleotide-binding site. One example, foscarnet, is used to treat infections caused by ganciclovir-resistant CMV and acyclovir-resistant HSV.

Non-Nucleoside Reverse Transcriptase Inhibitors Non-nucleoside reverse transcriptase inhibitors inhibit the activity of reverse transcriptase by binding to a site other than the nucleotide-binding site. They are often used in combination with nucleoside analogs to treat HIV infections. The medications include nevirapine, delavirdine, and efavirenz.

Integrase Inhibitors Integrase inhibitors offer a new option for treating HIV infections. They inhibit the HIV-encoded enzyme integrase, thereby preventing the virus from inserting the DNA copy of its genome into that of the host cell. Raltegravir is the first approved drug of this class. ■ HIV integrase, p. 701

Assembly and Release of Viral Particles Virally encoded enzymes required for the production and release of viral particles are the targets of medications used to treat certain viral infections.

Protease Inhibitors Protease inhibitors are used to treat HIV infections. These medications inhibit the HIV-encoded enzyme protease, which plays an essential role in the production of viral particles. When HIV replicates, several of its proteins are translated as a single amino acid chain, or polyprotein; protease then cleaves the polyprotein into individual proteins. The various protease inhibitors, including indinavir, ritonavir, saquinavir, and nelfinavir, differ in several aspects including dosage and side effects. ■ HIV protease, p. 701

Neuraminidase Inhibitors

Focus Points Describe the antifungal drugs that interfere with plasma membrane synthesis and function. Describe the antifungal mechanisms of echinocandins, griseofulvin, and flucytosine.

Eukaryotic pathogens such as fungi more closely resemble human cells than do bacteria. It is not surprising, therefore, that relatively few drugs are available for systemic use against fungal pathogens. The targets of antifungal drugs are illustrated in figure 21.16. Table 21.3 summarizes the characteristics of the most common antifungal drugs.

Plasma Membrane Synthesis and Function The target of most antifungal drugs is ergosterol, a sterol found in the plasma membrane of fungal but not human cells. ■ sterol, p. 36

Polyenes The polyenes, a group of antibiotics produced by certain species of Streptomyces, bind to ergosterol. This disrupts the fungal membrane, causing leakage of the cytoplasmic contents and leading to cell death. Unfortunately, the polyenes are quite toxic to humans, which limits their systemic use to life-threatening infections. Amphotericin B causes severe side effects, but it is the most effective drug for treating many systemic infections. Newer lipid-based emulsions are less toxic but are more expensive. Nystatin is too toxic to be given systemically, but is used topically. Plasma membrane synthesis/function Polyenes Azoles Allylamines

Cell division Griseofulvin

Neuraminidase inhibitors inhibit neuraminidase, an enzyme encoded by influenza viruses that is essential for the release of infectious viral particles from infected cells. Two neuraminidase inhibitors are currently available—zanamivir, which is administered by inhalation, and oseltamivir, which is administered orally. Both limit the duration of influenza infections when taken within two days of the onset of symptoms.

Fungal cell

Cell wall

Cell wall synthesis Echinocandins

MICROCHECK 21.6 Viral replication generally uses host cell machinery; because of this there are few targets for selectively toxic antiviral drugs. Available antiviral drugs are virus-specific; targets include viral entry, viral uncoating, nucleic acid synthesis, integrase, and the assembly and release of viral particles. ✓ Explain why acyclovir has fewer side effects than do other nucleoside analogs. ✓ Why are nucleoside analogs active only against replicating viruses?

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Nucleus

Nucleic acid synthesis Flucytosine

Plasma membrane

FIGURE 21.16 Targets of Antifungal Drugs

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489

TABLE 21.3 Characteristics of Antifungal Drugs Drug Target/Drug

Comments

Plasma Membrane Polyenes Amphotericin B, nystatin Azoles Imidazoles: ketoconazole, miconazole, clotrimazole

Bind to ergosterol, disrupting the plasma membrane and causing leakage of the cytoplasm. Amphotericin B is very toxic but the most effective drug for treating life-threatening infections; newer lipid-based emulsions are less toxic but very expensive. Nystatin is too toxic for systemic use, but can be used topically. Interfere with ergosterol synthesis, leading to defective cell membranes; active against a wide variety of fungi. Used to treat a variety of systemic and localized fungal infections. Triazoles are less toxic than imidazoles.

Triazoles: fluconazole, itraconazole Allylamines Naftifine, terbinafine

Inhibit an enzyme in the pathway of ergosterol synthesis. Administered topically to treat dermatophyte infections. Terbinafine can be taken orally.

Cell Wall Synthesis Echinocandins Capsofungin

Interfere with b-1,3 glucan synthesis. Used to treat Candida infections as well as invasive aspergillosis that resists other treatments.

Cell Division Griseofulvin

Used to treat skin and nail infections. Taken orally for months; concentrates in the dead keratinized layers of the skin; taken up by fungi invading those cells and inhibits their division. Active only against fungi that invade keratinized cells.

Nucleic Acid Synthesis Flucytosine

Used to treat systemic yeast infections; enzymes within yeast cells convert the drug to 5-fluorouracil, which inhibits an enzyme required for nucleic acid synthesis; not effective against most molds; resistant mutants are common.

Azoles The azoles are a large family of chemically synthesized drugs, some of which have antifungal activity. They include two classes—the imidazoles and the newer triazoles; the latter are generally less toxic. Both classes inhibit the synthesis of ergosterol, resulting in defective fungal membranes that leak cytoplasmic contents. Fluconazole and itraconazole, which are triazoles, are increasingly being used to treat systemic fungal infections. Ketoconazole, an imidazole, is also used systemically, but it is associated with more severe side effects. Other imidazoles, including miconazole and clotrimazole, are commonly used in nonprescription creams, ointments, and suppositories to treat vaginal yeast infections. They are also used topically to treat dermatophyte infections. ■ dermatophyte, p. 554

Allylamines The allylamines inhibit an enzyme in the pathway of ergosterol synthesis. Naftifine and terbinafine can be administered topically to treat dermatophyte infections. Terbinafine can also be taken orally.

Caspofungin, the first member to be approved, is used to treat Candida infections as well as invasive aspergillosis that resists other treatments.

Cell Division The target of one antifungal drug, griseofulvin, is cell division.

Griseofulvin Griseofulvin interferes with the action of tubulin, a necessary factor in nuclear division. Because tubulin is a part of all eukaryotic cells, the selective toxicity of this drug may be due to its greater uptake by fungal cells. When the drug is taken orally for months, it is absorbed and eventually concentrated in the dead keratinized layers of the skin. The fungi that then invade keratin containing structures such as skin and nails take up the drug, which prevents their multiplication. It is only active against fungi that invade keratinized cells and is used to treat skin and nail infections. ■ tubulin, p. 74 ■ keratin, p. 532

Nucleic Acid Synthesis

Fungal cell walls contain some components not produced by animal cells. Synthesis of these is a target for some antifungal medications.

Nucleic acid synthesis is a common feature of all eukaryotic cells, which generally makes it a poor target for antifungal drugs. The drug flucytosine, however, is taken up by yeast cells and then converted by yeast enzymes to an active, inhibitory form.

Echinocandins

Flucytosine

Echinocandins are a family of antifungal agents that interfere with synthesis of the b-1, 3 glucan component of fungal cell walls.

Flucytosine is a synthetic derivative of cytosine, one of the pyrimidines found in nucleic acids. Enzymes within infecting

Cell Wall Synthesis

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yeast cells convert flucytosine to 5-fluorouracil, which inhibits an enzyme required for nucleic acid synthesis. Unfortunately, resistant mutants are common, and therefore, flucytosine, is used mostly in combination with amphotericin B or as an alternative drug for patients with systemic yeast infections who are unable to tolerate amphotericin B. Flucytosine is not effective against molds.

MICROCHECK 21.7 Because fungi are eukaryotic cells, there are relatively few targets for selectively toxic antifungal drugs. Most antifungal drugs interfere with the function or synthesis of ergosterol, which is found in the membrane of fungal but not human cells. Other targets of antifungal drugs include cell wall synthesis, cell division, and nucleic acid synthesis. ✓ Why is amphotericin B, a polyene, used only for treating lifethreatening infections? ✓ Why is flucytosine generally used only in combination with other drugs? ✓ If griseofulvin were not concentrated in keratin containing structures, would it still be toxic to fungi that invade these structures? Why or why not?

21.8 Mechanisms of Action of Antiprotozoan and Antihelminthic Drugs Focus Point Describe five antiprotozoan drugs and four antihelminthic drugs.

Most antiparasitic drugs probably interfere with biosynthetic pathways of protozoan parasites or the neuromuscular function of worms. Unfortunately, compared with antibacterial, antifungal, and antiviral drugs, little research and development goes into these drugs, because most parasitic diseases are concentrated in the poorer areas of the world where people simply cannot afford to spend money on expensive medications. Some of the most important antiparasitic drugs and their characteristics are summarized in table 21.4.

TABLE 21.4 Characteristics of Some Antiprotozoan and Antihelminthic Drugs Causative Agent/Drug

Comments

Intestinal protozoa Iodoquinol

Mechanism unknown; poorly absorbed but taken orally to eliminate amebic cysts in the intestine.

Nitroimidazoles

Activated by the metabolism of anaerobic organisms. Interferes with electron transfer and alters DNA. Does not reliably eliminate the cyst stage. Metronidazole is also used to treat infections caused by anaerobic bacteria.

Metronidazole Quinacrine

Mechanism of action is unknown, but may be due to interference with nucleic acid synthesis.

Plasmodium (Malaria) and Toxoplasma Folate antagonists

Interferes with folate metabolism; used to treat toxoplasmosis and malaria.

Pyrimethamine, sulfonamide Malarone®

A synergistic combination of atovaquone and proguanil hydrochloride used to treat malaria. Atovaquone interferes with mitochondrial electron transport while proguanil disrupts folate synthesis. The combination is active against both the blood stage and early liver stage of Plasmodium species.

Quinolones

The mechanism of action is not completely clear. Chloroquine is concentrated in infected red blood cells and is the drug of choice for preventing or treating the red blood cell stage of the malarial parasite. Its effects may be due to inhibition of an enzyme that protects the parasite from the toxic byproducts of hemoglobin degradation. Primaquine and tafenoquine destroy the liver stage of the parasite and are used to treat relapsing forms of malaria. Mefloquine is used to treat infection caused by chloroquine-resistant strains of the malarial parasite.

Chloroquine, mefloquine, primaquine, tafenoquine

Trypanosomes and Leishmania Eflornithine

Used to treat infections caused by some types of Trypanosoma; inhibits the enzyme ornithine decarboxylase.

Heavy metals

These inactivate sulfhydryl groups of parasitic enzymes, but are very toxic to host cells as well. Melarsoprol is used to treat trypanosomiasis, but the treatment can be lethal. Sodium stibogluconate and meglumine antimonate are used to treat leishmaniasis.

Melarsoprol, sodium stibogluconate, meglumine antimonate Nitrofurtimox

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Widely used to treat acute Chagas’ disease; forms reactive oxygen radicals that are toxic to the parasite as well as the host.

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Summary

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TABLE 21.4 Characteristics of Some Antiprotozoan and Antihelminthic Drugs (continued) Causative Agent/Drug

Comments

Intestinal and Tissue Helminths Avermectins Ivermectin Benzimidazoles Mebendazole, thiabendazole, albendazole Phenols

Ivermectin causes neuromuscular paralysis in parasites; used to treat infections caused by Strongyloides and tissue nematodes. Mebendazole binds to tubulin of helminths, blocking microtubule assembly and inhibiting glucose uptake. It is poorly absorbed in the intestine, making it effective for treating intestinal, but not tissue, helminths. Thiabendazole may have a similar mechanism, but it is well absorbed and has many toxic side effects. Albendazole is used to treat tissue infections caused by Echinococcus and Taenia solium. Absorbed by cestodes in the intestinal tract, but not by the human host.

Niclosamide Piperazines Piperazine, diethylcarbamazine Pyrazinoisoquinolines Praziquantel Tetrahydropyrimidines Pyrantel pamoate, oxantel

Piperazine causes a flaccid paralysis in worms and can be used to treat Ascaris infections. Diethylcarbamazine immobilizes filarial worms and alters their surface, which enhances killing by the immune system. The resulting inflammatory response, however, causes tissue damage. A single dose of praziquantel is effective in eliminating a wide variety of trematodes and cestodes. It is taken up but not metabolized by the worm, ultimately causing sustained contractions of the worm. Pyrantel pamoate interferes with neuromuscular activity of worms, causing a type of paralysis. It is not readily absorbed from the gastrointestinal tract and is active against intestinal worms including pinworm, hookworm, and Ascaris. Oxantel can be used to treat Trichuris infections.

FUTURE CHALLENGES War with the Superbugs With respect to antimicrobial drugs, the future challenge is already upon us. The challenge is to maintain the effectiveness of antimicrobials by (1) preventing the continued spread of resistance, and (2) developing new drugs that have even more desirable properties. New ways must be developed to fight infections caused by the ever greater numbers of bacterial strains that are resistant to the effects of conventional antimicrobial drugs. Several strategies are being used to develop potential weapons against these “superbugs.” One way to combat resistance is to continue developing modifications of existing antimicrobial drugs. Researchers constantly work to modify drugs chemically,

trying to keep at least one step ahead of bacterial resistance. Another method to foil drug resistance is to interfere with the resistance mechanisms, as is done currently in using b-lactamase inhibitors in combination with b-lactam drugs to protect the antimicrobial drug from enzymatic destruction. Likewise, it may be possible to thwart resistance using other mechanisms—for example, developing chemicals that can be used to inactivate or interfere with bacterial efflux systems. Other researchers are focusing on developing medications entirely unrelated to conventional antimicrobials. One example is a class of compounds called defensins, which are short peptides, approximately

29 to 35 amino acids in length, produced naturally by a variety of eukaryotic cells to fight infections. Various defensins and related compounds are being intensively studied as promising antimicrobials. Accumulating knowledge of the genetic sequences of pathogens and identification of genes associated with pathogenicity may allow development of antimicrobials that interfere directly with those processes. The “master switch” that controls expression of virulence determinants is one such potential target. Nucleotide sequence information and determination of the three-dimensional conformation of proteins may uncover new targets for antimicrobial drug therapy.

SUMMARY 21.1 History and Development of Antimicrobial Drugs

21.2 Features of Antimicrobial Drugs

Discovery of Antimicrobial Drugs Salvarsan, developed by Paul Ehrlich, was the first documented example of an antimicrobial medication.

Most modern antibiotics come from species of Streptomyces and Bacillus (bacteria) and Penicillium and Cephalosporium (fungi).

Discovery of Antibiotics Alexander Fleming discovered that a species of the fungus Penicillium produces penicillin, which kills some bacteria. Development of New Generations of Drugs Antimicrobial drugs can be chemically modified to give them new properties.

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Selective Toxicity Medically useful antimicrobials are selectively toxic; the relative toxicity of a drug is expressed as the therapeutic index. Antimicrobial Action Bacteriostatic drugs inhibit the growth of bacteria; drugs that kill bacteria are bactericidal.

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Spectrum of Activity Broad-spectrum antimicrobials affect a wide range of bacteria; those that affect a narrow range are called narrow-spectrum. Effects of Combinations of Antimicrobial Drugs Combinations of antimicrobial drugs can be synergistic, antagonistic, or additive. Tissue Distribution, Metabolism, and Excretion of the Drug Some antimicrobials cross the blood-brain barrier into the cerebrospinal fluid; these can be used to treat meningitis. Drugs that are unstable in acid must be administered through injection. Drugs that have a long half-life need to be administered less frequently. Adverse Effects Some people develop allergies to certain antimicrobials. Some antimicrobials can have potentially damaging side effects such as kidney damage. When the composition of the normal microbiota is altered, which happens when a person takes antimicrobials, pathogens normally unable to compete may grow to high numbers. Resistance to Antimicrobials The resistance of certain types of bacteria to a particular drug is intrinsic or innate. Previously sensitive microorganisms can develop resistance through spontaneous mutation or the acquisition of new genetic information.

21.3 Mechanisms of Action of Antibacterial Drugs (table 21.1, figure 21.2)

Antibacterial Medications That Inhibit Cell Wall Synthesis (figure 21.3)

The b-lactam drugs, which include the penicillins, cephalosporins, carbapenems, and monobactams, irreversibly inhibit penicillin-binding proteins (PBPs), ultimately leading to cell lysis (figure 21.4). Vancomycin binds to the terminal amino acids of the peptide side chain of NAM, blocking peptidoglycan synthesis. Bacitracin interferes with the transport of peptidoglycan precursors across the cytoplasmic membrane; it is a common ingredient in non-prescription ointments. Antibacterial Medications That Inhibit Protein Synthesis (figure 21.7) Antibiotics that inhibit protein synthesis by binding to the 70S ribosome include the aminoglycosides, the tetracyclines, the macrolides, chloramphenicol, the lincosamides, the oxazolidinones, and the streptogramins. Antibacterial Medications That Inhibit Nucleic Acid Synthesis The fluoroquinolones interfere with DNA replication and transcription by inhibiting one or more topoisomerases. The rifamycins block prokaryotic RNA polymerase from initiating transcription. Antibacterial Medications That Inhibit Metabolic Pathways (figure 21.8)

Sulfa drugs competitively inhibit an enzyme in the metabolic pathway that leads to folic acid synthesis. Trimethoprim inhibits the enzyme that catalyzes a metabolic step following the one inhibited by sulfonamides. Antibacterial Medications That Interfere with Cell Membrane Integrity Polymyxin B damages membranes of Gram-negative bacteria. Daptomycin damages the cytoplasmic membrane.

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Antibacterial Medications That Interfere with Processes Essential to Mycobacterium tuberculosis First-line medications that specifically target Mycobacterium species include isoniazid, ethambutol, and pyrazinamide.

21.4 Determining the Susceptibility of a Bacterial Strain to an Antimicrobial Drug Determining the Minimum Inhibitory and Bactericidal Concentrations (figure 21.9) The minimum inhibitory concentration (MIC) is the lowest concentration of a specific antimicrobial drug needed to prevent the growth of a bacterial strain in vitro. The minimum bactericidal concentration (MBC) is the lowest concentration of a specific antimicrobial drug that kills 99.9% of cells of a given strain of bacterial in vitro. Conventional Disc Diffusion Method (figure 21.10) The Kirby-Bauer disc diffusion test qualitatively determines the susceptibility of a bacterial strain to a battery of antimicrobial drugs. Commercial Modifications of Antimicrobial Susceptibility Testing (figure 21.11)

Automated methods can determine antimicrobial susceptibility in as little as 4 hours.

21.5 Resistance to Antimicrobial Drugs (figure 21.13) Mechanisms of Acquired Resistance (figure 21.14) Enzymes that chemically modify a drug render it ineffective. Structural changes in the target can prevent the drug from binding. Altered porin proteins prevent drugs from entering cells. Efflux pumps actively pump drugs out of cells. Acquisition of Resistance Resistance can be acquired through spontaneous mutation or horizontal gene transfer. The most common mechanism of transfer of antibiotic resistance genes is through the conjugative transfer of R plasmids. Examples of Emerging Antimicrobial Resistance Vancomycin-resistant enterococci (VRE), methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-intermediate S. aureus (VISA), vancomycin-resistant S. aureus (VRSA), penicillin-resistant Streptococcus pneumoniae, multiple-drug-resistant Mycobacterium tuberculosis (MDR-TB), and extensively drug resistant Mycobacterium tuberculosis (XDR-TB) are all examples of emerging antimicrobial resistance. Slowing the Emergence and Spread of Antimicrobial Resistance Physicians should prescribe antimicrobial medications only when appropriate. The public must be educated about the appropriateness and limitations of antimicrobial therapy. Patients need to carefully follow prescribed instructions when taking antimicrobials.

21.6 Mechanisms of Action of Antiviral Drugs (figure 21.15, table 21.2)

Entry Inhibitors Enfuvirtide and maraviroc prevents HIV from entering cells. Viral Uncoating Amantadine and rimantadine block the uncoating of influenza A virus after it enters a cell.

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Review Questions Nucleic Acid Synthesis Most antiviral drugs take advantage of the error-prone virally encoded enzymes used to replicate viral nucleic acid. Nucleoside analogs are phosphorylated in vivo to form nucleotide analogs; when these are incorporated into viral DNA they interfere with replication. Integrase Inhibitors Raltegravir inhibits HIV integrase. Assembly and Release of Viral Particles Protease inhibitors bind to and inhibit protease, the enzyme required for the production of infectious HIV particles. Neuraminidase inhibitors interfere with the release of influenza virus particles from a cell.

21.7 Mechanisms of Action of Antifungal Drugs (figure 21.16,

493

Cell Wall Synthesis Echinocandins interfere with the synthesis of b-1, 3 glucan. Cell Division Griseofulvin is concentrated in keratinized skin cells, where it inhibits fungal cell division. Nucleic Acid Synthesis Flucytosine is taken up by yeast cells and converted by yeast enzymes to an active form.

21.8 Mechanisms of Action of Antiprotozoan and Antihelminthic Drugs (table 21.4) Most antiparasitic drugs are thought to interfere with biosynthetic pathways of protozoan parasites or the neuromuscular function of worms.

table 21.3)

Plasma Membrane Synthesis and Function The polyenes disrupt fungal cell membranes by binding to ergosterol. The azoles inhibit the synthesis of ergosterol. The allylamines inhibit an enzyme in the pathway of ergosterol synthesis.

REVIEW QUESTIONS Short Answer 1. Describe the difference between the terms antibiotic and antimicrobial. 2. Define therapeutic index and explain its importance. 3. Explain the role of penicillin-binding proteins in drug susceptibility. 4. Name three of the first-line drugs used to treat tuberculosis. 5. Name three antimicrobial medications that target ribosomes. 6. Compare and contrast the method for determining the minimum inhibitory concentration of an antimicrobial drug with the Kirby-Bauer disc diffusion test. 7. Name three targets that can be altered sufficiently via spontaneous mutation to result in resistance to an antimicrobial drug. 8. What is MRSA? Why is it significant? 9. Why is it difficult to develop antiviral drugs? 10. Explain the difference between the mechanism of action of an azole and that of a polyene.

Multiple Choice 1. Which of the following targets would you expect to be the most selective with respect to toxicity? a) Cytoplasmic membrane function b) DNA synthesis c) Glycolysis d) Peptidoglycan synthesis e) 70S ribosome 2. Penicillin has been modified to make derivatives that differ in all of the following, except a) spectrum of activity. b) resistance to b-lactamases.

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3.

4.

5.

6.

7.

c) potential for allergic reactions. d) A and C. Which of the following is the target of b-lactam antibiotics? a) Peptidoglycan synthesis b) DNA synthesis c) RNA synthesis d) Protein synthesis e) Folic acid synthesis Which of the following statements is false? a) A bacteriostatic drug stops the growth of a microorganism. b) The lower the therapeutic index, the less toxic the drug. c) Broad-spectrum antibiotics are associated with the development of antibiotic-associated colitis. d) Azithromycin has a longer half-life than does penicillin V. e) Chloramphenicol can cause a life-threatening type of anemia. All of the following interfere with the function of the ribosome, except a) fluoroquinolones. b) lincosamides. c) macrolides. d) streptogramins. e) tetracyclines. The target of the sulfonamides is a) cytoplasmic membrane proteins. b) folic acid synthesis. c) gyrase. d) peptidoglycan biosynthesis. e) RNA polymerase. Routine antimicrobial therapy to treat tuberculosis involves taking a) one drug for 10 days. b) two or more drugs for 10 days. c) one drug for at least 6 months. d) two or more drugs for at least 6 months. e) five drugs for 2 years.

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8. Strains of Staphylococcus aureus referred to as MRSA are sensitive to a) methicillin. b) penicillin. c) cephalosporin. d) vancomycin. e) none of the above. 9. Acyclovir is a) a nucleoside analog. b) a non-nucleoside polymerase inhibitor. c) a protease inhibitor. d) none of the above. 10. The antifungal drug griseofulvin is used to treat a) vaginal infections. b) systemic infections. c) nail infections. d) hair infections.

Applications 1. A physician was treating one young woman and one elderly patient for urinary tract infections caused by the same type of bacterium.

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Although the patients had similar body dimensions and weight, the physician gave a smaller dose of drug to the older patient. What was the physician’s rationale for this decision? 2. An advocacy group in Washington, D.C., is petitioning the United States Department of Agriculture (USDA) to stop the use of lowdosage antimicrobial agents used to enhance the growth of cattle and chickens. Why is the group against this practice? Why does the USDA permit it?

Critical Thinking 1. Figure 21.12 shows the E-test procedure for determining an MIC value. How would the zone of inhibition appear if the drug concentrations in the strip were decreased slightly? 2. Why is acyclovir converted to a nucleotide analog only in cells infected with herpes simplex virus?

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22 Individual with streptococcal pharyngitis.

Respiratory System Infections A Glimpse of History Rebecca Lancefield’s mother was a direct descendent of Lady Mary Wortley Montagu, who promoted smallpox variolation in England more than 75 years before Jenner. Lancefield was educated in various schools as her parents moved from one army base to another. In 1912, she entered Wellesley College and became interested in biology. She was awarded a scholarship to Columbia University and studied under the famous microbiologist Hans Zinsser, a pioneer in the science of immunology. She received a Master’s degree, but her studies were interrupted when her husband was drafted into the armed services in World War I. Fortunately he was assigned to the Rockefeller Institute, where Rebecca got a job as a laboratory technician for the distinguished microbiologists O. T. Avery and A. R. Dochez. Well known for their studies of pneumococci, Avery and Dochez had been commissioned to study streptococcal cultures from personnel at army camps. At that time, classification of the numerous kinds of streptococci was based largely on whether their colonies on blood agar produced b-hemolysis or a green discoloration. By using different streptococcal strains to immunize mice and produce antisera, Avery and Dochez showed that their cultures could be divided into groups based on their antigens. Later, the Lancefields returned to Columbia, where Lancefield received her Ph.D. in 1925 for her studies of a-hemolytic streptococci. At that time, a-hemolytic streptococci were considered a possible cause of rheumatic fever, a common cause of serious heart disease, but she showed that these streptococci occurred just as often in healthy people as in those with rheumatic fever. Thereafter, Lancefield returned to the Rockefeller Institute where she spent the remainder of her scientific career studying streptococci. Building on the discoveries of others, she showed that almost all the strains of b-hemolytic streptococci from human infections had the same cell wall carbohydrate “A.” Streptococci from other sources had different carbohydrates: “B” from cattle infections; “C” from cattle, horses, and guinea pigs; “D” from cheese and human normal flora; and so forth. The grouping of streptococci by their cell wall carbohydrates,

now referred to as “Lancefield grouping,” proved to be a much better predictor of pathogenic potential than hemolysis on blood agar. Lancefield, in 1960, became the first woman president of the American Association of Immunologists. In 1970, Lancefield was elected to the prestigious National Academy of Sciences. She died in 1981 at the age of 86. ■ Mary Wortley Montagu, p. 431

R

espiratory infections encompass an enormous variety of illnesses ranging from the trivial to the fatal. For convenience, they can be divided into infections of the upper part of the respiratory system, primarily the head and neck, and infections of the lower respiratory system, in the chest. Most upper respiratory infections are uncomfortable, but not life threatening and go away without treatment in about a week. However, they are so common that they far outweigh other infections in terms of the cumulative misery they cause. Some illnesses, such as the childhood rashes discussed in chapter 23, have a minor upper respiratory component but injure the skin, lung, nervous system, or other parts of the body. Still others cause major symptoms involving the eye, nose, throat, middle ear, sinuses, and other body systems. The lower respiratory system is usually sterile, well protected from colonization by microorganisms. However, pathogens sometimes evade the body’s defenses and cause serious diseases, such as pneumonia, tuberculosis, and whooping cough.

22.1 Anatomy and Physiology Focus Points Outline the functions of the upper respiratory tract. Describe the mucociliary escalator. 495

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KEY TERMS

often resulting from respiratory syncytial or other viral infection.

Otitis Media Infection of the middle ear.

Antigenic Drift Slight changes that occur in the antigens of a virus that reduce its susceptibility to antibodies existing before the antigenic changes.

Directly Observed Therapy (DOT) Method used to ensure that patients comply with their treatment; the healthcare worker watches while the patient takes each dose.

Pneumonia Inflammation of the lungs accompanied by filling of the air sacs with fluids such as pus and blood.

Antigenic Shift Major changes in the antigens of a virus that make antibodies that existed before the changes ineffective against the virus. Autolysis Spontaneous disintegration as a result of enzymes within a cell. Conjunctivitis Inflammation of the outer surface of the eye. Croup Acute obstruction of the larynx occurring mainly in infants and young children,

Granuloma Found in a chronic inflammatory response, collections of lymphocytes and macrophages; an attempt by the body to wall off and contain persistent organisms and antigens. Mucociliary Escalator Moving layer of mucus and cilia lining the respiratory tract that traps bacteria and other particles and moves them into the throat.

Microorganisms that colonize the respiratory system enter hot, humid, dark caverns and tortuous passages of the respiratory system. The atmosphere contains less oxygen and more carbon dioxide than occurs in air. The eyes and the nose are the two main “portals of entry” to the respiratory system. Respiratory infections often first establish themselves there and then spread to other parts of the system. ■ portals of entry, p. 455 Structures commonly involved in infections of the upper respiratory system (figure 22.1) are: the conjunctiva, composing the moist surfaces of the eyes and eyelids. Infection of the conjunctiva is called conjunctivitis; the nasolacrimal, or tear ducts, from the eyes to the nasal chamber. Infection of the tear ducts is called dacryocystitis; the middle ear. Infection of the middle ear is called otitis media. The external ear canal is not part of the respiratory system. It is a blind tunnel lined with skin and is part of the skin ecosystem; infection there is called external otitis; the air-filled chambers of the skull, the sinuses and mastoid air cells. Infections of these chambers are called sinusitis and mastoiditis, respectively; the nose. Infection of the nose is called rhinitis; the throat, or pharynx. Infections of the throat are called pharyngitis; the epiglottis is a little muscular flap that covers the opening to the lower respiratory system during swallowing, thereby preventing material from entering. Infection of the epiglottis is called epiglottitis. The tonsils are secondary lymphoid organs, strategically located to come into contact with incoming microorganisms. The tonsils are important in the immune response but paradoxically they can also be the sites of infection, resulting in tonsillitis. Enlargement of the pharyngeal tonsil, also called adenoids, can contribute to ear infections by interfering with normal drainage from the eustachian tubes. These tubes, which extend from the middle ear to the nasopharynx, equalize the pressure in the middle ear and drain normal mucous secretions. ■ lymphoid system, p. 369

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Pharyngitis Inflammation of the throat.

Pyrogenic Fever-causing. Sputum Material coughed up from the lungs. Tubercle Granuloma formed in tuberculosis. Virulence Relative ability of a pathogen to overcome body defenses and cause disease.

A person normally breathes about 16 times per minute, inhaling about 0.5 liters of air with each breath, or more than 11,500 liters of air per day, with any accompanying microorganisms or other pollutants. The air enters the respiratory system at the nostrils, flows into the nasal cavity, and is deflected downward through the throat. One of the main functions of the upper respiratory tract is to regulate the temperature and water content of inspired air. When cold air enters the upper respiratory tract, nervous reflexes immediately increase the blood flow to the spongy tissues in the nose, thereby transferring heat to the air. This mechanism usually adjusts the temperature to within 2 to 3 degrees of body temperature by the time it reaches the lungs. Inspired air also becomes saturated with water vapor, the nasal tissues giving up as much as a quart of water per day to keep the air humidified. The warmth and moisture provide optimum conditions for the body’s defenses against infection. The air then enters the lower respiratory tract below the epiglottis. Structures commonly involved in lower respiratory system infections include: the voice box, or larynx (see figure 22.1). Inflammation of the larynx is called laryngitis, and is manifest as hoarseness. The larynx is continuous with the windpipe, or trachea, which branches into two bronchi. Inflammation of the bronchi is called bronchitis, commonly the result of viral infection or smoking tobacco. The bronchi branch repeatedly, becoming bronchioles, site of an important viral infection called bronchiolitis. The smallest branches of the bronchioles end in the tiny, thin-walled air sacs called alveoli that comprise the bulk of lung tissue. Inflammation of the lungs is called pneumonitis, often the result of viral infections. Pneumonitis that results in the filling of alveoli with pus and fluid is called pneumonia. Macrophages are numerous in the lung tissues and readily move into the alveoli and airways to engulf infectious agents, thus helping to prevent pneumonia from developing.

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Anatomy and Physiology

497

Columnar epithelium Secretory (goblet) cell Cilia Flow of mucus

Frontal sinus

Adenoviral pharyngitis Common cold Diphtheria Ear infections Epiglottitis Laryngitis Strep throat Tonsillitis

Sphenoid sinus

Adenoids Eustachian tube opening Opening of maxillary sinus

Nasolacrimal duct opening

Nasopharynx (shaded area) Tonsil Pharynx Epiglottis Larynx Frontal sinus Nasal chamber

(a)

Nasolacrimal duct Middle ear Mastoid air cell

Upper Respiratory System

Eustachian tube Maxillary sinus Throat Bronchioles Trachea Alveoli (air sacs) Bronchi Bronchitis Pleura Pleurisy

Lower Respiratory System

Capillaries

(b)

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Lungs Bronchiolitis Bronchitis Coccidioidomycosis Hantavirus pulmonary syndrome Histoplasmosis Influenza

Legionnaires’ disease Pleurisy Pneumonia RSV infections Tuberculosis Whooping cough

FIGURE 22.1 Anatomy and Infections of the Respiratory System (a) Lateral view, upper respiratory system, showing the inside of the nasal chamber and its connections with the eyes, middle ears, and sinuses, and details of the respiratory epithelium. (b) Frontal view of the upper and lower respiratory system, including details of the alveoli.

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The lungs are surrounded by two membranes: One adheres to the lung and the other to the chest wall and diaphragm. These membranes, termed pleura, normally slide against each other as the lung expands and contracts. Inflammation of the pleura is called pleurisy, characterized by severe chest pain aggravated by breathing or coughing.

22.2 Normal Microbiota Focus Points List the parts of the respiratory system that are normally free of bacteria.

The Mucociliary Escalator The moist membranes of the respiratory system are coated with a slimy glycoprotein material called mucus, which is produced by specialized unicellular glands called goblet cells. Goblet cells, so called because of their shape, narrow at the base and wide at surface, are sprinkled among the other cells composing the membrane. Most of the mucous membranes of the respiratory system are composed of ciliated epithelium. Ciliated cells have tiny, hair-like projections called cilia along their exposed free border. The cilia beat synchronously at a rate of about 1,000 times a minute, continually propelling the mucous film out of the mastoids, middle ear, nasolacrimal duct, sinuses, and the lungs. The mucus is then swallowed, and any entrapped microorganisms and viruses are exposed to the killing action of stomach acid and enzymes. This mechanism, called the mucociliary escalator, normally keeps the middle ears, sinuses, mastoids, and lungs completely free of microorganisms. Viral infection, tobacco smoke, alcohol, and narcotics, however, impair ciliary movement and increase the chance of infection. ■ cilia, p. 74

MICROCHECK 22.1 The respiratory system provides a habitat for microorganisms that is warm and moist, with an atmosphere containing less oxygen and more carbon dioxide than the external environment. It is guarded by tonsils and adenoids representing the immune system, and by the mucociliary escalator. ✓ What is the normal function of the tonsils and adenoids? ✓ Why would the respiratory passages contain less oxygen than air?

Describe the important opportunistic pathogen that commonly inhabits the nose.

The mastoid air cells, middle ear, sinuses, trachea, bronchi, bronchioles, and alveoli are normally sterile. The nasal cavity, nasopharynx, and pharynx are colonized by numerous bacterial species. Aerobes, facultative anaerobes, aerotolerant organisms, and anaerobes are all represented. Although generally harmless, members of the normal bacterial microbiota are opportunists and can cause disease when host defenses are impaired. ■ oxygen requirements, p. 91 ■ opportunists, p. 394 Surprisingly, even though the eyes are constantly exposed to a multitude of microorganisms, normal healthy people commonly have no bacteria on their conjunctivae, the moist membrane covering the eye and inner surfaces of the eyelids. Presumably, this results from the frequent automatic washing of the eye with lysozyme-rich tears and from the eyelid’s blinking reflex, which cleans the eye surface like a windshield wiper sweeps a windshield. Unless they are able to attach to the epithelium, the viruses and microorganisms that impinge on the conjunctiva are swept into the nasolacrimal duct and into the nasopharynx. Organisms recovered from the normal conjunctiva are usually few in number and originate from the skin flora. They are adapted to live in a different environment and are generally unable to colonize the respiratory system. ■ lysozyme, p. 62 Some of the bacterial genera that inhabit the upper respiratory system are listed in table 22.1. The secretions of the nasal entrance usually contain diphtheroids and staphylococci. About 20% of healthy people constantly carry Staphylococcus aureus in their noses, and an even higher percentage of hospital personnel are likely to be carriers of these important opportunistic patho-

TABLE 22.1 Normal Microbiota of the Respiratory System Genus

Characteristics

Comments

Staphylococcus

Gram-positive cocci in clusters

Commonly includes the potential pathogen Staphylococcus aureus, inhabiting the nostrils. Facultative anaerobes.

Corynebacterium

Pleomorphic, Gram-positive rods; non-motile; non-spore-forming

Aerobic or facultatively anaerobic. Diphtheroids include anaerobic and aerotolerant organisms.

Moraxella

Gram-negative diplococci and diplobacilli

Aerobic. Some microscopically resemble pathogenic Neisseria species such as N. meningitidis.

Haemophilus

Small, Gram-negative rods

Facultative anaerobes. Commonly include the potential pathogen H. influenzae.

Bacteroides

Small, pleomorphic, Gram-negative rods

Obligate anaerobes.

Streptococcus

Gram-positive cocci in chains

a (especially viridans, meaning green hemolysis), b (clear hemolysis), and g (non-hemolytic) types; the potential pathogen, S. pneumoniae is often present. Aerotolerant (obligate fermenters).

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gens. Farther inside the nasal passages, the microbial population increasingly resembles that of the nasopharynx (the part of pharynx behind the nose). The nasopharynx contains mostly a-hemolytic viridans streptococci, non-hemolytic streptococci, Moraxella catarrhalis, and diphtheroids. Anaerobic Gram-negative bacteria, including species of Bacteroides, are also present in large numbers in the nasopharynx. In addition, commonly pathogenic bacteria such as Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis are often found, especially during the cooler seasons of the year. ■ viridans streptococci, p. 97

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MICROCHECK 22.2 Except in parts of the upper respiratory tract, the respiratory system is free of a normal microbiota. The upper respiratory tract microbiota is highly diverse, including aerobes, anaerobes, facultative anaerobes, and aerotolerant bacteria. Although most of them are of low virulence, these organisms can sometimes cause disease. ✓ What are some possible advantages to the body of providing a niche for normal flora in the upper respiratory tract? ✓ How can strict anaerobes exist in the upper respiratory tract?

INFECTIONS OF THE UPPER RESPIRATORY SYSTEM

22.3 Bacterial Infections of the Upper Respiratory System Focus Points Compare the distinctive characteristics of strep throat and diphtheria. List the parts of upper respiratory system commonly infected by Streptococcus pneumoniae and Haemophilus influenzae.

A number of different species of bacteria can infect the upper respiratory system. Some, such as Haemophilus influenzae and b-hemolytic streptococci of Lancefield group C, can cause sore throats but generally do not require treatment because the bacteria are quickly eliminated by the immune system. Other infections require treatment because they are not so easily eliminated and can cause serious complications.

Causative Agent Streptococcus pyogenes, the cause of strep throat, is a Gram-positive coccus that grows in chains of varying lengths (figure 22.2). It can be differentiated from other streptococci that normally inhabit the throat by its characteristic colonial morphology when grown on blood agar. Streptococcus pyogenes produces hemolysins, enzymes that lyse red blood cells, which result in the colonies being surrounded by a zone of b-hemolysis (figure 22.3). Because of their characteristic hemolysis, S. pyogenes and other streptococci that show a similar phenotype are called b-hemolytic streptococci. In contrast, species of Streptococcus that are typically part of the normal throat microbiota are either non-hemolytic, or they produce a-hemolysis, characterized by a zone of incomplete, often greenish clearing around colonies grown on blood agar. ■ streptococcal hemolysis, p. 97 Streptococcus pyogenes is commonly referred to as the group A streptococcus. The group A carbohydrate in the cell wall of S. pyogenes differs antigenically from that of most other streptococci and serves as a convenient basis for identification (see figure 19.9). Lancefield grouping uses antibodies to differentiate the various

Strep Throat (Streptococcal Pharyngitis) Sore throat is one of the most common reasons that people in the United States seek medical care, resulting in about 27 million doctor visits per year. Many of these visits are due to a justifiable fear of streptococcal pharyngitis, commonly known as strep throat.

Symptoms Streptococcal pharyngitis typically is characterized by pain, difficulty swallowing, and fever. The throat is red, with patches of adhering pus and scattered tiny hemorrhages. The lymph nodes in the neck are enlarged and tender. Abdominal pain or headache may be prominent in older children and young adults. Not usually present are red, weepy eyes, cough, or runny nose, common symptoms with viral pharyngitis. Most patients with streptococcal sore throat recover spontaneously after about a week. In fact, many infected people have only mild symptoms or no symptoms at all.

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10 mm

FIGURE 22.2 Streptococcus pyogenes Chain formation in fluid culture as revealed by fluorescence microscopy.

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TABLE 22.2 Virulence Factors of Streptococcus pyogenes

FIGURE 22.3 Streptococcus pyogenes Growing on Blood Agar

The colonies are small and surrounded by a wide zone of b-hemolysis.

species of streptococci based on their cell wall carbohydrate. These antibodies are also the basis for many of the rapid diagnostic tests done on throat specimens in a physician’s office. Other rapid tests utilize a DNA probe. ■ DNA probe, p. 227

Product

Effect

C5a peptidase

Inhibits attraction of phagocytes by destroying C5a

Hyaluronic acid capsule

Inhibits phagocytosis; aids penetration of epithelium

M protein

Interferes with phagocytosis by causing breakdown of C3b opsonin

Protein F

Responsible for attachment to host cells

Protein G

Interferes with phagocytosis by binding Fc segment of IgG

Streptococcal pyrogenic exotoxins (SPEs)

Superantigens responsible for scarlet fever, toxic shock, “flesh-eating” fasciitis

Streptolysins O and S

Lyse leukocytes and erythrocytes

Tissue degrading enzymes

Enhance spread of bacteria by breaking down DNA, proteins, blood clots, tissue hyaluronic acid

Pathogenesis Streptococcus pyogenes causes a wide variety of illnesses, which is not surprising considering its vast arsenal of virulence factors. Some of these disease-causing mechanisms are structural components of the outer cell wall that enable the bacterium to foil host defenses (figure 22.4), while others are destructive enzymes and toxins released by the bacterial cell. Some of the virulence factors of S. pyogenes are listed here and summarized in table 22.2: C5a peptidase is an enzyme released by S. pyogenes. This enzyme destroys the complement system component C5a, a substance responsible for attracting phagocytes to the site of a bacterial infection. ■ complement system, p. 355 ■ C5a Peptidase, p. 401 A capsule composed of hyaluronic acid, present on only some strains of S. pyogenes, inhibits phagocytosis and aids penetration of tissues by causing epithelial cells to separate. Hyaluronic acid is a normal component of human tissue, and its presence as a S. pyogenes capsule may impair recognition of the bacterium by the body’s immune system.

M protein facilitates the degradation of complement system component C3b, an opsonin that would otherwise promote phagocytosis of the bacteria. M protein is essential for the virulence of S. pyogenes, because antibody to it prevents infection from occurring. Unfortunately, more than 80 different kinds of M protein exist among the many strains of S. pyogenes, and antibody to one type of M protein does not prevent infection by a S. pyogenes strain that has another kind of M protein. ■ opsonins, p. 373 ■ M protein, p. 402 Protein F of the cell wall mediates attachment of S. pyogenes to the throat by adhering to a protein found on the surface of epithelial cells. Protein G of the S. pyogenes cell wall is an Fc receptor (see figure 17.11). It has a function like that of the protein A of Staphylococcus aureus in binding the Fc segment of immunoglobulin G. This prevents phagocytosis mediated by specific antibody against the bacterium. ■ staphylococcal protein A, p. 402

FIGURE 22.4 Components of the Cell Envelope of Streptococcus pyogenes The M protein is essential for virulence, while the group carbohydrate helps identify the species. Protein F binds the bacterium to epithelial cells, while protein G helps interfere with phagocytosis by binding to the Fc portion of antibodies. Hyaluronic acid interferes with phagocytosis and may aid penetration of epithelium.

M protein Protein G

Lipoteichoic acid

Protein F

Group A carbohydrate Hyaluronic acid capsule Peptidoglycan Cytoplasmic membrane

N-acetylmuramic acid

N-acetylglucosamine

Streptococci

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Streptococcal pyrogenic exotoxins (SPEs) are a family of genetically similar exotoxins produced by strains of S. pyogenes that cause severe streptococcal diseases frequently unrelated to strep throat. These diseases include scarlet fever, streptococcal toxic shock syndrome, and “flesh-eating” necrotizing fasciitis. Only scarlet fever is usually preceded by strep throat symptoms. These exotoxins are superantigens, causing massive activation of T cells. The resulting uncontrolled release of cytokines is probably responsible for the seriousness of these infections. ■ superantigens, p. 406 ■ cytokines, p. 353 ■ necrotizing fasciitis, p. 563

Streptolysins O and S are the proteins responsible for b-hemolysis. These hemolysins lyse erythrocytes and leukocytes by making holes in their cell membranes and probably help to liberate iron from hemoglobin. ■ membrane-damaging toxins, p. 405 A number of other enzymes produced by S. pyogenes, including DNase, protease, and hyaluronidase, degrade tissue and probably enhance the spread of the bacterium. Streptokinase, responsible for dissolving clots, aids spread into tissue and bloodstream. ■ streptokinase, p. 420 Complications of strep throat are uncommon in Western industrialized nations because of prompt identification of Streptococcus pyogenes and treatment with penicillin. However, complications can be serious if overlooked. Globally, they occur much more frequently. Some of the complications that can occur during the acute illness include: Scarlet fever is characterized by a roughening of the skin and red rash that spares the area around the mouth and causes the tongue to look like the surface of a ripe strawberry. The rash is caused by erythrogenic toxin, an SPE released by certain strains of S. pyogenes at the site of infection. The toxin enters the bloodstream and is carried throughout the body. Peritonsilar abscess causes a painful swelling in the area of one of the tonsils, often with fever and difficulty swallowing. Without prompt treatment the abscess can erode into the structures of the neck including blood vessels, potentially causing massive blood loss. Other pyogenic complications include sinusitis, otitis media, mastoiditis, pneumonia, and meningitis. Post-streptococcal sequelae are complications that occur a week to several months after recovery from the symptoms of acute pharyngitis. They are all considered to be the result of immune responses to Streptococcus pyogenes. The most important sequelae are: Acute glomerulonephritis usually begins abruptly about 10 days after strep throat, with fever, fluid retention, high blood pressure, and blood and protein in the urine. The symptoms arise from inflammation of structures within the kidneys, glomeruli (singular, glomerulus), small tufts of tiny blood vessels, and nephrons, responsible for the formation and composition of urine. Only a few of the many strains of S. pyogenes cause the condition, so it is rare to get glomerulonephritis twice. The streptococci are absent from the urine and the diseased kidney tissues. Indeed, S. pyogenes has generally been eliminated from the throat by the body’s immune response by the time the symptoms of glomerulonephritis appear. The damage to the kidneys is due to immune complexes that are deposited in the glomeruli and provoke an inflammatory reaction.

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Acute rheumatic fever usually begins about 3 weeks after recovery from strep throat, with fever, joint pains, chest pains, rash, and nodules under the skin. Acute behavioral changes and uncontrollable movement of various parts of the body can occur and, when present, are major criteria for diagnosing acute rheumatic fever. These symptoms result from an inflammatory process involving various tissues, especially the joints, heart, skin, and brain. Heart failure and death can occur during acute rheumatic fever, but usually symptoms subside with rest and anti-inflammatory medicines such as aspirin. Rheumatic fever often results in damage to the heart valves, causing one or more to leak and lead to heart failure later in life. Indeed, acute rheumatic fever is the major cause of acquired heart valve disease worldwide. The damaged valves are also subject to infection, usually by bacteria from the normal skin or mouth flora, causing subacute bacterial endocarditis. ■ inflammation, p. 360 ■ subacute bacterial endocarditis, p. 677 Acute rheumatic fever is generally a complication of throat, not skin, S. pyogenes infections. Despite many years of study, its pathogenesis is not understood. Symptoms usually begin about 3 weeks after the onset of untreated streptococcal pharyngitis. Cultures of the blood, heart, and joint tissues are negative for S. pyogenes, and antibodies against the bacterium are present in the blood of the patient. A popular idea is that these antibodies attack tissue antigens that are similar to S. pyogenes antigens, starting a self-limited autoimmune process. Another hypothesis is that some streptococcal product, present in only a small percentage of strains, damages the tissue directly or makes it susceptible to attack by the immune system. Genetic factors probably play a role in the development of rheumatic fever, because it occurs more commonly in individuals with certain MHC types. Overall, the risk of developing acute rheumatic fever after severe, untreated streptococcal pharyngitis is 3% or less. Those with untreated mild pharyngitis have a lower risk. Mild infections result in many cases of rheumatic fever, however, because they are common and much more likely to go untreated. Although outbreaks still occur in the United States, rheumatic fever has generally declined in incidence over many years, probably as a result of timely treatment of streptococcal pharyngitis with antibiotics, and a decline in the streptococcal strains associated with the disease. Globally, 10 to 20 million new cases occur each year, mostly in economically disadvantaged countries. ■ major histocompatibility complex (MHC), p. 380

Epidemiology Streptococcus pyogenes infects only humans under natural conditions, probably because streptokinase reacts specifically with a human clotting factor. Streptococcal infections spread readily by respiratory droplets generated by yelling, coughing, and sneezing, especially in the range of about 2 to 5 feet from an infected individual. If strep throat is untreated, the person may be an asymptomatic carrier for weeks. People who carry the organism in their nose spread the streptococci more effectively than do pharyngeal carriers. Anal carriers are not common but can be a dangerous source of nosocomial infections. Epidemics of strep throat can originate from food contaminated by S. pyogenes carriers. Some people become longterm carriers of S. pyogenes. In these cases, the infecting strain usually becomes deficient in M protein and is not a threat to the carrier

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TABLE 22.3 Strep Throat (Streptococcal Pharyngitis) ➀ Streptococcus pyogenes enters by

6

inhalation (nose), or by ingestion (mouth).

➁ Pharyngitis, fever, enlarged lymph nodes; sometimes tonsillitis, abcess; scarlet fever with strains that produce erythrogenic toxin.

Sore, red throat, with pus and tiny hemorrhages, enlargement and tenderness of lymph nodes in the neck; less frequently, abscess formation involving tonsils; occasionally, rheumatic fever and glomerulonephritis as sequels

Incubation period

2 to 5 days

Causative agent

Streptococcus pyogenes, Lancefield group A b-hemolytic streptococci

Pathogenesis

Virulence associated with hyaluronic acid capsule and M protein, both of which inhibit phagocytosis; protein G binds Fc segment of IgG; protein F for mucosal attachment; multiple enzymes.

Epidemiology

Direct contact and droplet infection; ingestion of contaminated food.

Prevention and treatment

Avoidance of crowding; adequate ventilation; daily penicillin to prevent recurrent infection in those with a history of rheumatic heart disease. Treatment: 10 days of penicillin or erythromycin.

1 3

2

2

Symptoms go away.

➂ S. pyogenes exits by nose and

Symptoms

5 7

mouth.

Late complications appear:

5

➃ glomerulonephritis ➄ rheumatic fever

4

➅ neurological abnormalities Complications subside.

➆ Damaged heart valves leak, heart failure develops.

5

or to others. The peak incidence of strep throat occurs in winter or spring and is highest in grade school children. Among students visiting a clinic because of sore throat at a large West Coast university, less than 5% had strep throat. With some groups of military recruits, however, the incidence has been above 20%.

Prevention and Treatment Adequate ventilation and avoidance of crowding help to control the spread of streptococcal infections. No vaccine is available despite many years of studies. However, genome sequencing has revealed some new possibilities. Persons with fever and sore throat should have a throat culture for S. pyogenes so that antibiotic treatment can be given promptly and complications prevented. Individuals with a history of having had acute rheumatic fever with cardiac damage take penicillin daily for years to prevent recurrence of the disease. Confirmed streptococcal pharyngitis is treated with a full 10 days of therapy with penicillin or erythromycin, which

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eliminates the organism in about 90% of the cases. Treatment given as late as 9 days after the onset prevents rheumatic fever from developing. Table 22.3 summarizes some important facts about streptococcal pharyngitis.

Diphtheria Diphtheria, a deadly toxin-mediated disease, is now rare in the United States because of childhood immunization. Events in other parts of the world, however, are a reminder of what can happen when public health is neglected. In 1990, a diphtheria epidemic began in the Russian Federation. Over the next 5 years, it spread to all the newly independent states of the former Soviet Union. By the end of 1995, 125,000 cases and 4,000 deaths had been reported. The social and economic disruption following the breakup of the Soviet Union had allowed diphtheria to

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22.3 Bacterial Infections of the Upper Respiratory System

reemerge after being well controlled over the previous quarter of a century.

Symptoms Diphtheria usually begins with a mild sore throat and slight fever, accompanied by a great deal of fatigue and malaise. Swelling of the neck is often dramatic. A whitish gray membrane forms on the tonsils and the throat or in the nasal cavity. Heart and kidney failure and paralysis may follow these symptoms.

Causative Agent Diphtheria is caused by Corynebacterium diphtheriae, a variably shaped, non-motile, non-spore-forming, Gram-positive rod that often stains irregularly. Slide preparations of C. diphtheriae commonly show the organisms arranged in “Chinese letter” patterns (figure 22.5) or side by side in “palisades.” Different colony types can be identified—a property that is useful in tracing epidemic spread of the organisms. These bacteria require special media and microbiological techniques to aid their recovery from the mixture of bacteria present in throat material. It is unlikely that they would be recovered by the usual methods for culturing S. pyogenes from sore throats. Most but not all strains of C. diphtheriae release diphtheria toxin, a powerful exotoxin responsible for the seriousness of diphtheria. Production of this toxin requires that the bacterium be lysogenized by a specific bacteriophage, an example of lysogenic conversion. Strains that are non-toxigenic become toxin producers when lysogenized with the bacteriophage. Toxin production can be demonstrated in vitro, using immunoasays. The toxin is produced only when the medium on which C. diphtheriae is growing has too little iron for optimal growth. The gene for toxin production is under the control of a repressor that is only active when bound to iron. In a medium containing adequate iron, the repressor shuts down toxin production; when the concentration of iron is very low, the iron molecule leaves the repressor and the toxin gene is expressed. ■ lysogenic conversion, p. 310 ■ repressors, p. 177 ■ immunoassays, p. 438

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Pathogenesis Corynebacterium diphtheriae has little invasive ability, rarely entering the blood or tissues, but the powerful exotoxin it releases is absorbed by the bloodstream. The gray-white pseudomembrane that forms in the throat of people with diphtheria is made up of clotted blood along with dead epithelial cells of the host mucous membrane and the leukocytes that congregate during inflammation. The cells are killed by exotoxin released from C. diphtheriae. This membrane may come loose and obstruct the airways, causing the patient to suffocate. Entry of the toxin into the bloodstream results in damage to the heart, nerves, and kidneys. The diphtheria toxin is a large protein released from the bacterium in an inactive form. It is cleaved extracellularly into two chains, A and B, which remain joined by a disulfide bond. The B chain attaches to specific receptors on a host cell membrane, and the entire molecule is taken into the cell by endocytosis (figure 22.6). Cells that lack the appropriate receptors do not take up the toxin and are unaffected by it. This receptor specificity explains why some tissues of the body are not affected in diphtheria, while others such as the heart, kidneys, and nerves are severely damaged. ■ endocytosis, p. 73 Once the toxin molecule is inside the cell, the A chain separates from the B chain and becomes an active enzyme. This enzyme catalyses a chemical reaction that inactivates elongation factor 2 (EF-2), a substance required for movement of the eukaryotic ribosome on mRNA (see figure 22.6). This halts protein synthesis, and the cell dies. Since the toxin A chain is an enzyme, it is not consumed in the process, so one or two molecules of toxin can inactivate essentially all the cell’s elongation factor 2. This explains the extreme potency of diphtheria toxin. ■ A-B toxins, p. 405 ■ elongation factor, p. 173

Epidemiology Humans are the primary reservoir for C. diphtheriae. Sources of infection include carriers who have recovered from an infection, new cases not yet exhibiting symptoms, people with active disease, and contaminated articles. The bacterium is carried in chronic skin ulcers—cutaneous diphtheria—in some indigent populations. Typically, the organisms are spread by air and acquired by inhalation.

Prevention and Treatment

FIGURE 22.5 Corynebacterium diphtheriae Note the “Chinese letter” pattern.

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Because diphtheria results primarily from toxin absorption rather than microbial invasion, its control can be accomplished most effectively by immunization with toxoid. Toxoid, prepared by formalin treatment of diphtheria toxin, causes the body to produce antibodies that specifically neutralize the diphtheria toxin. The well-known childhood vaccination DPT consists of diphtheria and tetanus toxoids and pertussis vaccine, all three generally given together. Unfortunately, these immunizations have often been neglected, particularly among socioeconomically disadvantaged groups, and serious epidemics of the diseases have occurred periodically. Since the 1980s, there has been an active campaign in most of the United States to ensure that children who are entering school are immunized against diphtheria. As a result, today only a few cases of diphtheria are reported annually in the United States, as compared with 30,000 cases reported in 1936. Of concern is the finding that widespread childhood immunization against

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Toxin precursor (inactive)

A chain

A

B chain

B

B

A

Disulfide bond

B chain attaches to receptor.

A

B chain cannot attach.

B

Binding site

Resistant cell membrane

Cell membrane (susceptible cell)

Endocytosis begins.

B

A

Symptoms B

Acidification of vacuole

A Active enzyme leaves vacuole. B A NAD

+ EF-2

Pinkeye, Earache, and Sinus Infections Bacterial infection of the eye’s surface, generally known as conjunctivitis or “pinkeye,” and infections of the middle ear (otitis media) and sinuses are very common, often occur together, and frequently have the same causative agent. This is not surprising in view of their intimate association with the nasal chamber and nasopharynx (see figure 22.1). Otitis media is a formidable problem, especially in children, and is responsible for 30 million doctor visits per year in the United States, at an estimated cost of $1 billion. Pinkeye, because of its high communicability, is a frequent source of panic when it appears in a day care facility or classroom. Sinusitis, inflammation of the sinuses, is common in both adults and children.

A

Endocytic vacuole

diphtheria has shifted susceptibility to the disease to adolescents and adults. Immunity wanes after childhood because of lack of exposure to now scarce C. diphtheriae to boost immunity. To prevent buildup of a large population of susceptible older individuals, booster injections should be given every 10 years following childhood immunization. Effective treatment of diphtheria depends on injecting antiserum against diphtheria toxin into the patient as soon as possible. If the disease is suspected, antiserum must be administered without waiting several days for culture results, because the delay could be fatal. The bacteria are sensitive to antibiotics such as erythromycin and penicillin, but such treatment only stops transmission of the disease; it has no effect on toxin that has already been absorbed. Even with treatment, about 1 of 10 diphtheria patients dies. Table 22.4 summarizes some important facts about diphtheria.

ADP ribose–EF-2 + nicotinamide (inactivated)

FIGURE 22.6 Mode of Action of Diphtheria Toxin The toxin precursor released from the bacterium is cleaved extracellularly into A and B chains joined only by a disulfide bond; the B chain attaches to a specific receptor on the cell membrane of a susceptible cell. The toxin enters the cell by endocytosis. With acidification of the endocytic vacuole, the A chain separates from the B chain and then enters the cytoplasm as an active enzyme that inactivates EF-2 (elongation factor 2) by ADP ribosylation. Since EF-2 is required for moving the ribosome on mRNA, protein synthesis ceases and the cell dies.

The symptoms of acute bacterial conjunctivitis include increased tears, redness of the conjunctiva, swelling of the eyelids, sensitivity to bright light, and large amounts of pus (figure 22.7). Acute bacterial conjunctivitis must be distinguished from conjunctivitis caused by a large number of viruses. In the latter cases, eyelid swelling and pus are usually minimal. In a typical case of otitis media, a young child wakes from sleep screaming with earache pain. Fever is generally mild or absent. Vomiting often occurs at the height of the pain. Sometimes the pain ends abruptly because the eardrum has ruptured, and drainage of fluid appears in the external ear canal. In sinusitis, pain and a pressure sensation characteristically occur in the region of the involved sinus. Tenderness is also present over the sinus in many instances. Sinus infections are commonly associated with a headache and severe malaise.

Causative Agents In all three conditions the most common bacterial pathogens are Haemophilus influenzae, a tiny Gram-negative rod, and Streptococcus pneumoniae, the Gram-positive encapsulated diplococcus known as the pneumococcus. Strains that infect the conjunctiva have adhesins that allow firm attachment to the epithelium. ■ adhesins, p. 398 ■ Streptococcus pneumoniae, p. 509 ■ Haemophilus influenzae, pp. 373, 650

Less commonly, Moraxella lacunata, enterobacteria, Neisseria gonorrhoeae, and many others infect the conjunctiva. Among these are agents that can contaminate eye medications

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22.3 Bacterial Infections of the Upper Respiratory System

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TABLE 22.4 Diphtheria ➀ Corynebacterium diphtheriae enters

Symptoms

by inhalation.

➁ Infection established in nasal cavity and/or throat.

➂ Toxin released, pseudomembrane forms.

1

3 5

6 4

2

Incubation period

2 to 6 days

Causative agent

Corynebacterium diphtheriae, a toxin-producing, non-spore-forming Gram-positive rod

Pathogenesis

Infection in upper respiratory tract; exotoxin released and absorbed by bloodstream; toxin kills cells by interfering with protein synthesis; effect is on cells that have receptors for the toxin—mainly heart, kidney, and nerve tissue.

Epidemiology

Inhalation of infectious droplets; direct contact with patient or carrier; indirect contact with contaminated articles.

Prevention and treatment

Immunization with diphtheria toxoid; given to children at 6 weeks, 4 months, 6 months, 18 months, and 4 to 6 years; boosters every 10 years. Treatment: antitoxin; erythromycin to prevent transmission.

➃ Toxin causes paralysis, damages heart muscle, kidneys, nerves.

➄ Membrane may come loose and obstruct breathing.

4

➅ Exit from body by respiratory secretions.

4

and contact lens solutions such as Bacillus sp. (free-living aerobic Gram-positive spore-forming rods), Pseudomonas sp. (free-living Gram-negative aerobic rods), and Acanthamoeba sp. (free-living protozoa that live in soil, and fresh and salt water that have a cyst form carried by dust). Infections caused by these organisms are very uncommon, but when they occur they are usually serious and can lead to destruction of the eye. Contact lens wearers need to be

Sore throat, fever, fatigue, and malaise; membrane forms on tonsils and throat or in nose; paralysis, heart and kidney failure

very careful to follow exactly the instructions on use of cleansing solutions, and cloudy or outdated solutions and eye medications should be discarded. Besides Streptococcus pneumoniae and Haemophilus influenzae, Mycoplasma pneumoniae, Streptococcus pyogenes, Moraxella catarrhalis, and Staphylococcus aureus can cause otitis media. About one-third of the cases are caused by respiratory viruses. This helps explain why some infections fail to respond to antimicrobial medications, which have no effect on viruses. The same infecting agents are often involved in sinusitis.

Pathogenesis

FIGURE 22.7 Bacterial Conjunctivitis Redness, swollen eyelids and pus, characteristic of bacterial conjunctivitis.

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Few details are known about the pathogenesis of acute bacterial conjunctivitis. Probably, the organisms are inoculated directly onto the conjunctiva from airborne respiratory droplets or rubbed in from contaminated hands. Like most bacterial pathogens, they resist destruction by lysozyme. Otitis media is sometimes developing at the time conjunctivitis is diagnosed. Generally, otitis media and sinusitis are preceded by infection of the nasal chamber and nasopharynx. Probably, infection spreads upward through the eustachian tube to the middle ear (figure 22.8). The infection damages the ciliated cells, resulting in inflammation and swelling. Because the damaged eustachian tube cannot move secretions from the middle ear, pressure builds up from fluid and pus collecting behind the eardrum. The throbbing ache of a middle ear infection is produced by pressure on nerves supplying the

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INFECTED (MIDDLE) EAR

Eardrum (bulging)

External ear canal

Inflammatory exudate Eustachian tube (inflamed)

FIGURE 22.8 Otitis Media A stylized view of the infected middle ear showing accumulation of fluid, swelling of the eustachian tube, and outward bulging of the eardrum. The inset shows a ventilation tube placed in the eardrum to equalize middle ear pressure in individuals with chronically malfunctioning eustachian tubes.

middle ear. Bacterial infections of the middle ear can cause the eardrum to perforate, giving discharge of blood or pus from the ear and immediate relief from pain. With treatment, the eardrum perforations usually heal promptly. The pressure in the middle ear can force infected material into the mastoid air cells, resulting in mastoiditis. The fluid behind the eardrum impairs movement of the drum, thereby decreasing ability to hear. Because of the fluid, some young children cannot hear clearly and show a delay in normal speech development. Spread of infection from the nasopharynx to the sinuses probably occurs by a mechanism similar to that in otitis media. Both middle ear and sinus infections sometimes spread to the coverings of the brain, causing meningitis. ■ lysozyme, p. 62

Epidemiology The carrier rates for H. influenzae and S. pneumoniae can sometimes reach 80% in the absence of disease, and the ecological factors involved in the appearance and spread of the diseases caused by these organisms are largely unknown. Epidemics of bacterial conjunctivitis commonly occur among schoolchildren. Probably the virulence of the bacterium, crowding of susceptible children, and the presence of respiratory viruses all play important roles. A preceding or concomitant viral illness is common in otitis media and sinusitis; probably the virus damages the mucociliary mechanism that would normally protect against bacterial infection. Although

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otitis media is rare in the first month of life, it becomes very common in early childhood. Older children develop immunity to H. influenzae, and it becomes an increasingly uncommon cause of otitis media after about five years of age. Sinusitis tends to involve adults and older children in whom the sinuses are more fully developed.

Prevention and Treatment Individuals suspected of having bacterial conjunctivitis are removed from school or day care settings for diagnosis and start of treatment. General preventive measures include handwashing, and avoidance of rubbing or touching the eyes and sharing towels. Use of pacifiers beyond the age of 2 years is associated with a substantial increase in otitis media. Viral infections and other conditions that cause inflammation of the nasal mucosa play a role in some cases. Nasal allergies and exposure to air pollution and cigarette smoke are examples of nasal irritants. Administration of influenza vaccine to infants in day care facilities substantially decreases the incidence of otitis media during the “flu” season. Ampicillin or sulfasoxazole given continuously over the winter and spring are useful preventives in people who have three or more bouts of otitis media within a six-month period. Surgical removal of enlarged adenoids improves drainage from the eustachian tubes and can be helpful in preventing recurrences in certain patients. In those with chronically malfunctioning eustachian tubes and hearing loss, plastic ventilation tubes are often installed in the eardrums so that pressure can equalize on both sides of the drum (see figure 22.8). Widespread use of pneumococcal and Haemophilus conjugate vaccines has resulted in only a modest overall decrease in otitis media cases. There are no proven preventive measures for sinusitis. ■ conjugate vaccines, p. 435 Bacterial conjunctivitis is effectively treated with eyedrops or ointments containing an antibacterial medicine to which the infecting strain is sensitive. Antibacterial therapy with amoxacillin is generally effective against otitis media; alternative medications are available for communities where antibioticresistant strains of H. influenzae and S. pneumoniae are common. In general, antibiotics have been used indiscriminately in treating otitis media. However, properly used, they decrease the risk of serious complications such as mastoiditis and meningitis. Decongestants and antihistamines generally are ineffective and can be harmful.

MICROCHECK 22.3 Untreated Streptococcus pyogenes infections can sometimes cause injury to other parts of the body that appear long after the infections have healed. In diphtheria, toxin is absorbed into the bloodstream and circulates throughout the body, selectively damaging certain tissues that have appropriate receptors such as heart, kidneys, and nerves. Viral infections often pave the way for bacterial infections. ✓ Name two post-streptococcal sequlae. ✓ How does diphtheria toxin kill cells? ✓ What purpose would adequate ventilation serve in preventing the spread of streptococcal infections?

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22.4 Viral Infections of the Upper Respiratory System

22.4 Viral Infections of the Upper Respiratory System Focus Points List the strategies helpful in avoiding common colds. Give the distinctive characteristics of adenoviral pharyngitis.

The average person in the United States suffers two to five episodes of viral upper respiratory infections each year. They generally subside without any treatment and rarely cause permanent damage. Most of the causative agents are highly successful parasites, using us to replicate themselves to astronomical numbers, then moving on without killing us or even leaving long-standing immunity. Although hundreds of kinds of viruses are involved, the range of symptoms they produce is similar. Their major importance to health is that they damage respiratory tract defenses and thus pave the way for more serious bacterial diseases.

The Common Cold Medical practitioners have been taught for generations that the symptoms of the common cold, “if treated vigorously, will go away in seven days, whereas if left alone, they will disappear over the course of a week.” This pessimistic outlook may now be changing with development of new antiviral medications. On average, a person in the United States has two to three colds per year. Colds are the leading cause of absences from school, and result in loss of about 150 million work days per year. Immunity generally lasts less than a few years.

Symptoms Colds generally begin with malaise, followed by a scratchy or mildly sore throat, runny nose, cough, and hoarseness. The nasal secretions, initially profuse and watery, thicken in a day or two, then become cloudy and greenish. Unless secondary bacterial infection occurs, there is no fever; symptoms are mostly gone within a week, but a mild cough sometimes continues for longer periods of time.

Causative Agents Between 30% and 50% of colds are caused by the 100 or more types of rhinoviruses (rhino means “nose,” as in rhinoceros, or “horny nose”), members of the picornavirus family (pico is Italian for “small” and rna is ribonucleic acid [RNA]; thus, “small RNA viruses”) (figure 22.9). The viruses are non-enveloped and their RNA is single-stranded. The rhinoviruses can usually be cultivated in cell cultures incubated at 33°C instead of at body temperature (37°C) and at a slightly acid pH instead of at the alkaline pH of body tissues. These conditions of lower temperature and pH normally exist in the upper respiratory tract. Rhinoviruses, however, are killed if the pH drops below 5.3, and therefore, they are usually destroyed in the human stomach. Many other viruses and some bacterial species can also produce the symptoms of a cold.

507

virions are released and infect other cells. Infected cells cease ciliary motion and may slough off. The injury causes the release of inflammatory mediators and stimulates nervous reflexes. The result is an increase in nasal secretions, sneezing, and swelling of the tissue. This swelling partially or completely obstructs the airways. Later, in the inflammatory response, dilation of blood vessels, oozing of plasma, and congregation of leukocytes in the infected area occur. Secretions from the area may then contain pus and blood. The infection is eventually halted by the inflammatory response, interferon release, and cellular and humoral immunity, but it can extend into the ears, sinuses, or even the lower respiratory tract before it is stopped. Rhinoviruses can even cause lifethreatening pneumonia in individuals with AIDS. ■ interferon, p. 357

Epidemiology Humans are the only source of cold viruses, and close contact with an infected person is generally necessary for viruses to be transmitted. A person with severe symptoms early in the course of a cold is much more likely to transmit the viruses than is someone whose symptoms are mild or who is in the late stage of a cold. Very high concentrations of virus are found in the nasal secretions and often on the hands of infected people during the first 2 or 3 days of a cold. By the fourth or fifth day, virus levels are often undetectable, but low levels can be present for 2 weeks. A few virions are sufficient to infect the nasal mucosa, but the mouth is quite resistant to infection. In adults the disease is usually contracted when airborne droplets containing virus particles are inhaled. Transmission can also occur when virus-containing secretions are unwittingly rubbed into the eyes or nose by contaminated hands. Virus introduced into the eye is promptly transmitted to the nasal passage via the nasolacrimal duct. With reasonable caution, however, colds are not highly contagious. In a study of non-immune adults exposed in a family or dormitory setting, less than half contracted colds. Young children, however, transmit cold and other respiratory viruses very effectively because they are often careless with their respiratory secretions. Experimental and epidemiological studies show that there is no relationship between exposure to cold temperature and development of colds, contrary to popular belief. Emotional stress, however, can almost double the risk of catching a cold.

Prevention and Treatment Because such a large number of immunologically different viruses cause colds, vaccines are impractical. Rhinoviruses, like all other FIGURE

22.9 Rhinovirus

Transmission electron micrograph. The red spheres are the rhinovirus virions, and the blue object is the cell in which they are replicating.

Pathogenesis Rhinoviruses attach to specific receptors on respiratory epithelial cells and infect them. After replicating, large numbers of

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viruses, are not affected by antibiotics and other antibacterial medications. Prevention of the spread of rhinoviruses includes handwashing, even in plain water, which readily removes rhinoviruses, and keeping hands away from the face. In addition, one should avoid crowds and crowded places such as commercial airplanes when respiratory diseases are prevalent, and especially avoid people with colds during the first couple of days of their symptoms. In experimental rhinovirus infections, both aspirin and acetaminophen somewhat prolonged symptoms and duration of virus excretion and delayed antibody production. Table 22.5 summarizes some facts about the common cold.

TABLE 22.5 The Common Cold Symptoms

Incubation period 1 to 2 days Causative agent

Mainly rhinoviruses—more than 100 types; many other viruses, some bacteria

Pathogenesis

Viruses attach to respiratory epithelium, starting infection that spreads to adjacent cells; ciliary action ceases and cells slough; mucus secretion increases, and inflammatory reaction occurs; infection stopped by interferon release, cellular and humoral immunity.

Epidemiology

Inhalation of infected droplets; transfer of infectious mucus to nose or eye by contaminated fingers; children initiate many outbreaks in families because of lack of care with nasal secretions.

Prevention and treatment

Handwashing; avoiding people with colds and touching face. No generally accepted treatment except for control of symptoms.

Adenoviral Pharyngitis Adenoviruses are widespread and can cause epidemics of febrile upper respiratory illness throughout the year. Although they typically produce sore throat and enlarged lymph nodes with or without conjunctivitis, they can sometimes also cause pneumonia or diarrhea. They are representative of the many viruses that cause upper respiratory symptoms with fever.

Scratchy throat, nasal discharge, malaise, headache, cough

Symptoms Adenoviral infections often cause a runny nose, but unlike the common cold, fever is commonly present. Typically, the throat is sore, and gray-white pus present on the pharynx and tonsils can cause confusion with strep throat. The lymph nodes of the neck enlarge and become tender. In some epidemics, conjunctivitis is a prominent symptom, sometimes showing multiple conjunctival nodules composed of infiltrating lymphocytes, and long-lasting opacities in the cornea, the clear central portion of the eye. Other strains of the virus cause epidemics of hemorrhagic conjunctivitis. A mild cough is common; sometimes a severe cough develops, indicating possible pneumonia or whooping cough, or chest pain indicating pleurisy. With or without treatment, recovery usually occurs in 1 to 3 weeks.

Causative Agent More than 45 antigenic types of adenoviruses infect humans. The viruses are non-enveloped, 70 to 90 nm in diameter, with doublestranded DNA. They can remain infectious in the environment for long periods of time and can be transferred readily from one patient to another on medical instruments. They are easily inactivated, however, by heat at 56°C, chlorine, and various other disinfectants.

of the viruses in inadequately chlorinated swimming pools. These cases typically have fever, conjunctivitis, pharyngitis, enlargement of the lymph nodes of the neck, a rash, and diarrhea. Adenoviral disease is spread by respiratory droplets and is likely to occur in groups of young people living together in crowded conditions. It has been a big problem in military recruits. Epidemic spread is fostered by a high percentage of asymptomatic infections. The viruses are shed from the upper respiratory tract during the acute illness and continue to be eliminated in the feces for months thereafter.

Prevention and Treatment Formerly, an attenuated vaccine administered orally was helpful for preventing acute respiratory disease in military recruits, but the vaccine program was abandoned in 1996 because of cost. Now, with more than 2,500 adenoviral illnesses monthly with some deaths, reinstitution of adenoviral vaccination of recruits is planned. As with colds, there is no treatment, and most immunocompetent patients get well on their own. Secondary bacterial infections, however, may occur and require antibacterial medication. Table 22.6 summarizes some important facts about adenoviral pharyngitis.

Pathogenesis Adenoviruses infect epithelial cells by attaching to receptors near the basement membrane. Inside the cells of the host, the virus multiplies in the nuclei. The virus escapes to the epithelial surface by overproducing its attachment protein, causing the epithelial cells to separate from each other. In severe infections, extensive cell destruction and inflammation occur. Different types of adenoviruses vary with respect to the tissues they affect. For example, some cause illness characterized by sore throat and enlarged lymph nodes, whereas others cause eye infection. ■ basement membrane, p. 348

TABLE 22.6 Adenoviral Pharyngitis Symptoms

Fever, very sore throat, severe cough, swollen lymph nodes of neck, pus on tonsils and throat, sometimes conjunctivitis; less frequently, pneumonia

Incubation period 5 to 10 days Causative agent

Adenoviruses—more than 45 types

Pathogenesis

Virus multiplies in host cells; cell destruction and inflammation occur; different types produce different symptoms.

Epidemiology

Epidemiology

Humans are the only source of infection. Adenoviral illness is prevalent among schoolchildren, usually in sporadic cases, but occasionally occurring as outbreaks of respiratory sickness in winter and spring. Summertime epidemics occur as a result of transmission

Inhalation of infected droplets; possible spread from gastrointestinal tract.

Prevention and treatment

Live virus vaccine formerly used by the military is no longer produced. No treatment except for relief of symptoms.

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22.5 Bacterial Infections of the Lower Respiratory System

509

MICROCHECK 22.4 Many different kinds of infectious agents can produce the same symptoms and signs of respiratory disease. Emotional stress significantly increases the risk of contracting a cold, but exposure to cold temperatures probably does not. Persons suffering a cold are most likely to transmit it if symptoms are severe, and during the first few days of illness. Adenovirus infections can mimic colds, pinkeye, strep throat, and whooping cough.

✓ How is an adenovirus infection treated? ✓ People who staff polar ice stations where they are isolated from other human contact for long periods often do not develop colds. Is this an expected observation? Why or why not?

INFECTIONS OF THE LOWER RESPIRATORY SYSTEM

22.5 Bacterial Infections of the Lower Respiratory System Focus Points Compare the distinctive features of pneumococcal, Klebsiella, and mycoplasmal pneumonia. Outline the pathogenesis of pertussis. List the main steps in the pathogenesis of tuberculosis. Describe the epidemiology of Legionnaires’ disease.

Bacterial infections of the lower respiratory system are less common than those of the upper system, largely because they are stopped by body defenses at the portal of entry. Lower tract infections, however, are generally much more serious. An earache or sore throat is unlikely to be life threatening, but the causative organisms of both can endanger life when they infect the lung. Distinctive patterns of signs and symptoms are produced by the different kinds of organisms that infect the lower respiratory system. The pneumonias are inflammatory diseases of the lung in which fluid fills the alveoli. They top the list of infectious killers in the general population of the United States, and they are important as nosocomial infections. Whooping cough, tuberculosis, and Legionnaires’ disease are other distinctive types of infection. ■ nosocomial infection, p. 462

the pain, breathing becomes shallow and rapid. The patient becomes short of breath and develops a dusky color because of poor oxygenation. Without treatment, after 7 to 10 days people who survive show profuse sweating and a rapid fall in temperature to normal.

Causative Agent Streptococcus pneumoniae, the pneumococcus, is a Gram-positive diplococcus (figure 22.10). The most striking characteristic of S. pneumoniae is its thick polysaccharide capsule, which is responsible for the organism’s virulence. There are 90 different types of S. pneumoniae, as determined by differing capsular antigens. ■ capsules, p. 64

Pathogenesis Pneumococcal pneumonia develops when encapsulated pneumococci, the virulent form, are inhaled into the alveoli of a susceptible host, multiply rapidly, and cause an inflammatory response. The bacteria are resistant to phagocytosis because their capsules interfere with the action of C3b, the fraction of complement system component responsible for opsonization. A surface protein, PspA, also interferes with complement-mediated opsonization. A hemolysin called pneumolysin, antigenically related to streptolysin O of S. pyogenes, is released by autolysis, spontaneous enzymatic disintegration, and is

Pneumococcal Pneumonia Pneumococci are an important cause of pneumonia acquired in the community, accounting for about 60% of the adult pneumonia victims requiring hospitalization.

Symptoms The typical symptoms of pneumococcal pneumonia are cough, fever, chest pain, and sputum production. These symptoms are usually preceded by a day or two of runny nose and upper respiratory congestion, ending with an abrupt rise in temperature and a single body-shaking chill. The sputum quickly becomes pinkish or rust colored, and severe chest pain develops, aggravated by each breath or cough. As a result of

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FIGURE 22.10 Streptococcus pneumoniae Gram stain of sputum from a person with pneumococcal pneumonia showing Gram-positive diplococci and polymorphonuclear neutrophils (PMNs).

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stream from the inflamed lung are responsible for three often fatal complications: septicemia, a symptomatic infection of the bloodstream; endocarditis, an infection of the heart valves; and meningitis, an infection of the membranes covering the brain and spinal cord. Individuals who do not develop such complications usually develop sufficient specific anticapsular antibodies within about a week to permit phagocytosis and destruction of the infecting organisms. Complete recovery usually results. Most pneumococcal strains do not destroy lung tissue.

Epidemiology

(b)

(a)

FIGURE 22.11 Chest X-Ray Appearance in Pneumococcal Pneumonia (a) Pneumonia. The left lung (right side of figure) appears white because fluid-filled alveoli stop the X-ray beam from reaching the X-ray film and turning it black. (b) Normal X-ray film after recovery. The X-ray beam passes through air-filled alveoli and turns the film black.

toxic to ciliated epithelium. Serum and phagocytic cells pour into the air sacs of the lung, causing difficulty breathing. This increase in fluid produces abnormal shadows on chest X-ray films of patients with pneumonia (figure 22.11). Material coughed from the lungs, called sputum, increases in amount and contains pus, blood, and many pneumococci. ■ opsonization by C3b, p. 356 The inflammatory response to the infection often involves nerve endings, causing pain; the condition in which pain arises from an inflamed pleura is called pleurisy. Pneumococci that enter the blood-

Up to 30% of healthy people carry encapsulated pneumococci in their throat. Because of the effectiveness of the mucociliary escalator, these bacteria rarely reach the lung. The risk of pneumococcal pneumonia rises dramatically when this defense mechanism is impaired, however, as it is with alcohol and narcotic use, and with respiratory viral infections such as influenza. There is also an increased risk of the disease with underlying heart or lung disease, diabetes, and cancer, and with age over 50.

Prevention and Treatment A vaccine is available that stimulates production of anticapsular antibodies and gives immunity to 23 strains that account for over 90% of serious pneumococcal disease. A conjugate vaccine against seven types is available for infants and children up to the age of 5 years. Most pneumococcal infections can be cured if penicillin or erythromycin is given early in the illness. Strains of pneumococci resistant to one or more antibiotics, however, are increasingly being encountered. ■ conjugate vaccine, p. 383 See table 22.7 for a description of some features of pneumococcal pneumonia.

TABLE 22.7 Pneumococcal, Klebsiella, and Mycoplasmal Pneumonias Compared Pneumococcal Pneumonia

Klebsiella Pneumonia

Mycoplasmal Pneumonia

Cough, fever, single shaking chill, rustcolored sputum from degraded blood, shortness of breath, chest pain

Chills, fever, cough, chest pain, and grossly bloody, mucoid sputum

Gradual onset of cough, fever, sputum production, headache, fatigue, and muscle aches

Incubation period 1 to 3 days

1 to 3 days

2 to 3 weeks

Causative agent

The pneumococcus, Streptococcus pneumoniae, encapsulated strains

Klebsiella pneumoniae, an enterobacterium

Mycoplasma pneumoniae; lacks cell wall

Pathogenesis

Inhalation of encapsulated pneumococci; colonization of the alveoli incites inflammatory response; plasma, blood, and inflammatory cells fill the alveoli; pain results from involvement of nerve endings.

Aspiration of colonized mucus droplets from the throat. Destruction of lung tissue and abscess formation common; infection spreads via blood to other body tissues.

Cells attach to specific receptors on the respiratory epithelium; inhibition of ciliary motion and destruction of cells follow.

Epidemiology

High carrier rates for S. pneumoniae. Risk of pneumonia increased with conditions such as alcoholism, narcotic use, chronic lung disease, and viral infections that impair the mucociliary escalator. Other predisposing factors are chronic heart disease, diabetes, and cancer.

Often resistant to antibiotics, and colonize individuals who are taking them. Klebsiella sp. and other Gram-negative rods are common causes of fatal nosocomial pneumonias.

Inhalation of infected droplets; mild infections common and foster spread of the disease.

Prevention and treatment

Capsular vaccine available contains 23 capsular antigens; conjugate vaccine for infants. Treatment: penicillin, erythromycin, and others.

No vaccine available. A cephalosporin with an aminoglycoside.

No vaccine available; avoidance of crowding in schools and military facilities advisable; tetracycline or erythromycin for treatment.

Symptoms

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22.5 Bacterial Infections of the Lower Respiratory System

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Pathogenesis

Polymorphonuclear neutrophil (PMN)

Klebsiellas

(a)

10 µm

Inhaled organisms first colonize the throat and then are carried to the lung by inspired air or aspirated mucus. Specific adhesins aid colonization, but their exact nature is not yet known. The capsule is an essential virulence factor, probably functioning like the pneumococcal capsule in interfering with the action of C3b, a critically important opsonin before the appearance of antibody. Unlike Streptococcus pneumoniae, K. pneumoniae causes death of tissue and rapid formation of lung abscesses. The infection often enters the bloodstream, causing abscesses in other tissues, and endotoxic shock. Therefore, even with effective antibacterial medication, the lung can be permanently damaged and death may occur. ■ endotoxic shock, p. 407 ■ abscess, p. 560

Epidemiology Klebsiellas are part of the normal flora of the intestine in a small percentage of individuals. Colonization of the mouth and throat is common in debilitated individuals, especially in an institutional setting. In hospitals and nursing homes, the organisms are often resistant to antimicrobial medications, and they readily colonize patients taking the medications. Klebsiella resistance to antimicrobial medications can be chromosomal or plasmid-mediated. The organisms easily acquire and are a source of R factors, all of which contain transposons. This allows resistance genes to spread readily to other species and genera when antibacterial medications are used. ■ R plasmids and transposons, pp. 189, 205

Prevention and Treatment (b)

FIGURE 22.12 Klebsiella pneumoniae (a) In sputum from a pneumonia victim. (b) Colonies. When the colony is touched with a microbiological loop, it “strings out.”

There are no specific preventive measures. Disinfection of the environment, use of sterile respiratory equipment, and use of antimicrobial medications only when necessary help control the organisms in hospitals. See table 22.7 for a description of the main features of this disease.

Mycoplasmal Pneumonia Klebsiella Pneumonia Enterobacteria such as Klebsiella sp., and other Gram-negative rods, can cause pneumonia, especially if host defenses are impaired. These pneumonias attack the very old, the very young, alcoholics, nursing home patients, those debilitated by other diseases, and immunocompromised persons. Pneumonias caused by Gram-negative rods such as Klebsiella sp., cause most of the deaths from nosocomial infections. ■ enterobacteria, p. 262

Symptoms In general, the symptoms of Klebsiella pneumonia—cough, fever, and chest pain—are indistinguishable from those of pneumococcal pneumonia. Klebsiella pneumonia patients typically have repeated chills, however, and their sputum is red and gelatinous, resembling currant jelly. Their mortality rate without treatment is 50% to 80%, and they tend to die sooner than other pneumonia patients.

Causative Agent Several species of Klebsiella cause pneumonia, but Klebsiella pneumoniae is the best known. It is a Gram-negative rod with a large capsule and big, strikingly mucoid colonies (figure 22.12).

nes95432_Ch22_495-530.indd 511

Mycoplasmal pneumonia is the leading kind of pneumonia in college students and is also common among military recruits. The disease is generally mild, is often referred to by the popular name, “walking pneumonia,” and usually does not require hospitalization.

Symptoms The onset of mycoplasmal pneumonia is typically gradual. The first symptoms are fever, headache, muscle pain, and fatigue. After several days, a dry cough begins, but later mucoid sputum may be produced. About 15% of cases also have middle ear infections.

Causative Agent The causative agent of mycoplasmal pneumonia is Mycoplasma pneumoniae, a small (0.2 mm diameter), easily deformed bacterium that has no cell wall (see figure 3.35). Distinguishing characteristics are slow growth and aerobic metabolism. As with other mycoplasmas, the central portion of M. pneumoniae colonies grows down into the medium, producing a fried egg appearance (see figure 11.27). ■ mycoplasmas, p. 273

Pathogenesis Only a few inhaled M. pneumoniae cells are necessary to start an infection. The organisms attach to specific receptors on the respiratory

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PERSPECTIVE 22.1 Terror by Mail: Inhalation Anthrax During October and November 2001, 22 human cases of anthrax were reported in the United States, half due to inhalation of Bacillus anthracis spores (inhalation anthrax) and half due to skin infections (cutaneous anthrax). Five deaths occurred, all among the inhalation cases, and more than 30,000 individuals potentially exposed to the spores were given antibiotic treatment as a preventive. Most of the anthrax cases could reasonably be linked to four envelopes containing purified spores of B. anthracis, which contaminated people, air, and surfaces during their journey through the postal system to their destinations. Only 18 cases of inhalation anthrax were identified in the United States during the entire twentieth century. Sometimes called “anthrax pneumonia,” inhalation anthrax victims generally fail to show the hallmarks of pneumonia. Inhaled B. anthracis spores are quickly taken up by lung phagocytes and carried to the regional lymph nodes, where they germinate, kill the phagocytes, and invade the bloodstream. Although the organisms are susceptible to various antibacterial medications, treatment must be given as soon as possible after infection, because the bacteria produce a powerful toxin that usually kills the victim within a day or two after bloodstream invasion occurs. Cutaneous anthrax and anthrax acquired by ingesting contaminated meat are much less likely to be fatal. Bacillus anthracis endospores have long been considered for use in biological warfare. The organism is readily available; anthrax is endemic in livestock in

most areas of the world including the United States and Canada. The spores are easy to produce and remain viable for years. When anthrax is acquired by inhalation, the fatality rate approaches 90%, yet the disease is easily confined to the attack area because it does not spread person-to-person. Bacillus anthracis spores were employed as a weapon as early as World War I, although ineffectively, in an attack on livestock used for food. Just prior to World War II, Japan, the United States, USSR, Germany, and Great Britain secretly began to develop and perfect anthrax weapons, but they were not used during the war. During the “cold war” that followed, both the United States and the USSR developed massive biological warfare programs that employed many thousands of people, perfecting techniques for preparing the spores and delivering them to enemy targets. An executive order by President Nixon ended the U.S. program in 1969, and the stockpiled weapons were ordered destroyed, but other countries continued weapon development. In 1979, an accidental discharge of B. anthracis spores, a weight equaling about two paper clips, from a biological warfare plant at Sverdlovsk, USSR, caused more than 90 deaths downwind of the facility. The 1990 war with Iraq exposed their sizeable anthrax weapon program, and several times during the 1990s a Japanese terrorist group tried ineffectively to attack Tokyo institutions with anthrax spores. During this long history of anthrax weapon development, remarkably little was accomplished that would

epithelium (figure 22.13), interfere with ciliary action, and cause the ciliated cells to slough off. An inflammatory response characterized by infiltration of lymphocytes and macrophages causes the walls of the bronchial tubes and alveoli to thicken.

help defend against an attack, presumably because the best defense was considered an opponent’s fear of counterattack. As a result of the 2001 anthrax-by-mail incident a number of questions came into focus. How do you diagnose anthrax quickly, by history, physical examination, and X-ray, and what is the best way to teach and organize medical practitioners to meet an anthrax attack? What tests are available to identity B. anthracis rapidly and reliably, and what is the best way to sample people and the environment? How can decontamination of buildings and other objects be accomplished? Is there sufficient vaccine available, can better vaccines be developed, and what is their role before or after exposure to B. anthracis? What is the best antimicrobial treatment, is there enough of it, is it readily accessible, and how long should it be given to exposed individuals? Are other potential treatments such as antitoxins and designer medications to block the lethal effect of B. anthracis toxin being developed? The mail attack has stimulated remarkable progress toward answering these questions, especially in the area of using the latest technology for early detection, and teaching medical personnel about symptoms, signs, and X-ray findings. Antibacterial treatment proves highly effective if given soon after exposure. Approaches to combatting the toxin are under development, using designer drugs and antibodies. More information about anthrax is available at the Online Learning Center at www.mhhe.com/nester6.

M. pneumoniae

Cilia

Attachment site

Epidemiology The mycoplasmas are spread by aerosolized droplets of respiratory secretions. Transmission from person to person is aided by the long time period in which M. pneumoniae is present in respiratory secretions, ranging from about 1 week before symptoms begin to many weeks afterward. Mycoplasmal pneumonia accounts for about one-fifth of bacterial pneumonias, and it has a peak incidence in young people. Immunity after recovery is not permanent, and repeat attacks have occurred within 5 years.

Prevention and Treatment No practical preventive measures exist for mycoplasmal pneumonia, except avoiding crowding in schools and military facilities. Antibiotics that act against bacterial cell walls, such as the penicillins and cephalosporins, are of course not effective. Tetracycline and erythromycin shorten the illness if given early, but they are bacteriostatic, meaning they only inhibit the growth of the bacteria without killing them. Some features of pneumococcal, Klebsiella, and mycoplasmal pneumonias are compared in table 22.7.

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Ciliated respiratory epithelium

0.5 mm

FIGURE 22.13 Mycoplasma pneumoniae Infecting Respiratory Epithelium Transmission electron micrograph. Notice the distinctive appearance of the tips of the mycoplasmas adjacent to the host epithelium. The tips probably represent a site on the microorganism that is specialized for attachment.

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Ciliated epithelial cell

22.5 Bacterial Infections of the Lower Respiratory System

Cluster of B. pertussis

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resulting in small areas of collapsed lung. Others, because of spasm or mucus plugging, let air enter but not escape, causing hyperinflation. Paroxysmal coughing causes hemorrhages in the brain, and seizures can occur. Pneumonia due to B. pertussis or, more commonly, secondary bacterial infection is the chief cause of death. A number of toxic products of B. pertussis probably play a role in its pathogenesis. Pertussis toxin (Ptx), mentioned earlier for its role in colonization, is an A-B toxin. Figure 22.15 shows Ptx toxin B B

B B

A

B

10 µm

Receptors

FIGURE 22.14 Bordetella pertussis Fluorescent antibody stain of respi-

G protein

ratory secretions from an individual with whooping cough. The bacteria stain a greenish-yellow color. The large orange object is a ciliated epithelial cell. Notice the cluster of B. pertussis at one end of the cell, the location of the cell’s cilia.

G

Membrane of host cell

Ptx toxin binds to the host cell surface using the B subunits.

Whooping Cough (Pertussis)

B B

B

Whooping cough is the common name for pertussis, a disease that is now uncommon in the United States because of childhood immunization. The causative bacterium is widespread, however, and remains a threat to those people who lack immunity. Worldwide, the disease causes 300,000 to 500,000 deaths yearly.

B

A

B

G

Symptoms

The A portion of Ptx toxin is activated when transferred into the host cell.

Pertussis typically begins with a number of days of runny nose followed by sudden bouts of violent, uncontrollable coughing. This symptom, termed paroxysmal coughing, is severe enough to rupture small blood vessels in the eyes. The coughing spasm is followed by forceful attempts to inhale—the “whoop.” Vomiting and seizures can occur during this phase of the illness.

B B

B

B

B

A

G

Causative Agent The disease is caused by Bordetella pertussis (figure 22.14), a tiny, encapsulated, strictly aerobic, Gram-negative rod. These organisms do not tolerate drying or sunlight and die quickly outside the host.

The G protein is inactivated by ADP ribosylation. B

Pathogenesis Bordetella pertussis enters the respiratory tract with inspired air and attaches specifically to ciliated cells of the respiratory epithelium. Among the proteins present on the bacterial surface, pertussis toxin (Ptx) and filamentous hemagglutinin (Fha) are probably the main ones involved in attachment. The areas colonized by B. pertussis include the nasopharynx, trachea, bronchi, and bronchioles. The violent symptoms arise because of involvement of the passageways of the lower respiratory tract. The organisms grow in dense masses on the epithelial surface, but they do not invade. Mucus secretion increases markedly, while ciliary action declines precipitously, and patches of ciliated cells slough off. Only the cough reflex remains for clearing the secretions. Some of the bronchioles become completely obstructed,

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B

B

B

B

G Activated ADP ribosylating enzyme

A

A NAD

+

G

ADP • ribose – G + nicotinamide

FIGURE 22.15 Mode of Action of Pertussis Toxin The B portion of this A-B toxin attaches to receptors on the cell membrane. The B portion stays behind as the A portion enters the cell, becoming an enzyme activated by intracellular conditions. Activated A enzyme inactivates a G protein by ADP ribosylation, thereby maximizing cAMP production.

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the steps involved in the toxin’s action. First, the B portion attaches specifically to receptors on the host cell surface. Second, the A portion is transferred through the cytoplasmic membrane of the host cell, becoming an active ribosylating enzyme in the process. The activated A portion of the Ptx toxin inactivates the G protein normally responsible for initiating a decrease in cyclic adenosine monophosphate (cAMP) synthesis, thereby allowing maximum production of cAMP. Unregulated cAMP production causes marked increase in mucus output, decreased killing ability of phagocytes, massive release of lymphocytes into the bloodstream, ineffectiveness of natural killer cells, and low blood sugar. Invasive adenylate cyclase, another B. pertussis toxin, also causes an increase in cAMP production. ■ A-B toxins, p. 405 ■ cAMP, p. 179 Tracheal cytotoxin produced by B. pertussis acts with endotoxin to cause release of nitric oxide (NO) from goblet cells. The NO causes ciliated epithelial cells to die and slough off. Tracheal cytotoxin also causes the release of interleukin-1 (IL-1), a fevercausing cytokine. ■ interleukin-1, p. 353

TABLE 22.8 Pertussis Symptoms

Runny nose followed after a number of days by spasms of violent coughing; vomiting and possible convulsions

Incubation period 7 to 21 days Causative agent

Bordetella pertussis, a tiny Gram-negative rod

Pathogenesis

Colonization of the surfaces of the upper respiratory tract and tracheobronchial system; ciliary action slowed; toxins released by B. pertussis cause death of epithelial cells and increased cAMP; fever, excessive mucus output, and a rise in the number of lymphocytes in the bloodstream result.

Epidemiology

Inhalation of infected droplets; older children and adults have mild symptoms.

Prevention and treatment

Acellular vaccines, for immunization of infants and children; erythromycin, somewhat effective if given before coughing spasms start, eliminates B. pertussis.

Epidemiology

Prevention and Treatment Intensive vaccination of infants with killed B. pertussis cells can prevent the disease in about 70% of individuals. Its widespread administration to young children is responsible for the drop from 235,239 reported cases of pertussis in the United States in 1934 to only 1,248 in 1981. Since then, reported cases have increased in number, reaching a peak of 25,827 cases in 2004. Acellular pertussis vaccine is given along with diphtheria and tetanus toxoids (DTaP) by injection at 2, 4, 6, 12–15 and 18 months of age, with a booster dose between 4 and 6 years. Common reactions to the vaccine include pain and tenderness at the injection site and fever. Acellular vaccines that use only part of the bacterium instead of the whole cells, first approved for use in the United States in 1991, are now advised for all five doses and give good immunity with fewer side effects. A pertussis vaccine with a decreased dose of pertussis antigen (Tdap) is advised at age 11–12 years and for older individuals needing a booster. Erythromycin given for treatment reduces the duration of symptoms if given early in the disease, and the antibiotic usually eliminates B. pertussis from the respiratory secretions. Azithromycin and trimethoprim-sulfamethoxazole are effective alternatives. ■ acellular vaccines, p. 435 The main features of this disease are shown in table 22.8.

Tuberculosis Over the last hundred or more years, tuberculosis gradually declined in industrialized countries in association with improved living standards. In 1985, however, the rate of decline slowed, and then the incidence of tuberculosis began to rise (figure 22.16).

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The rise continued for the next 6 years in association with the expanding AIDS epidemic and increases in treatment-resistant cases. Fortunately, starting in 1993, with better funding of control measures and more aggressive treatment, tuberculosis resumed its slow retreat. In 1989, a Strategic Plan for the Elimination of Tuberculosis in the United States was published by the Centers for Disease Control and Prevention. The plan depends largely on increased efforts in identifying and treating people with the disease among the high-risk groups, particularly poor people, people with AIDS, prisoners, and immigrants from countries with high rates of tuberculosis. Although the decline in the incidence rate of tuberculosis has continued, it is much slower than anticipated by the strategic plan, calling into question the goal of eliminating the disease from the United States by the year 2010. Wide variation exists among different segments of the population—the rate of disease among the foreign born approaches 10 times the

20 Reported cases per 100,000 population

Pertussis spreads via respiratory secretions suspended in air. Patients are most infectious during the runny nose period, the numbers of expelled organisms decreasing substantially with the onset of violent coughing. Pertussis is classically a disease of infants. It can occur in a milder form in older children and adults, however, overlooked as a persistent cold, thus fostering transmission. During 2003 and 2004, small outbreaks in hospitals involving doctors, nurses, and other staff occurred in Kentucky, Oregon, Pennsylvania, Texas, and Washington.

18 16 14 12 10 8 6 4 2 0 1978

1983

1988

1993

1998

2003 ‘05

Year

FIGURE 22.16 Incidence of Tuberculosis, United States, 1978– 2005 Resurgence 1988 to 1994 responded to better funding of control measures.

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22.5 Bacterial Infections of the Lower Respiratory System

M. tuberculosis

10 mm

515

nism that protects them from nitric oxide. Evidence indicates that they leave the phagosome and multiply within the cytoplasm of the macrophages and are carried to nearby lymph nodes. At this stage, there is little inflammatory response to the infection. The organisms continue to multiply, lyse the macrophages, and spread throughout the body. After about 2 weeks, delayed hypersensitivity to the tubercle bacilli develops. An intense reaction then occurs at sites where the bacilli have lodged. Macrophages, now activated, collect around the bacteria, and some macrophages fuse together to form large multinucleated giant cells. Lymphocytes and macrophages then collect around these multinucleated cells and wall off the infected area from the surrounding tissue. The localized collection of inflammatory cells is called a granuloma (figure 22.18), which is the characteristic response of the body to microorganisms and other foreign substances that resist digestion and removal. The granulomas of tuberculosis are called tubercles. Some of the mycobacteria in the tubercles remain

FIGURE 22.17 Myobacterium tuberculosis in Sputum from an Individual with Tuberculosis The sputum has been “digested,” meaning that it has been treated with strong alkali to kill the other bacteria that are invariably present.

rate among the native born, and the rates in some cities such as Washington, D.C., are even higher. Worldwide, it is estimated that one-third of the population is infected with Mycobacterium tuberculosis and two million die of the disease annually.

Symptoms Tuberculosis is a chronic illness characterized by slight fever, progressive weight loss, sweating at night, and chronic cough, often producing blood-streaked sputum.

Causative Agent Today, most cases of tuberculosis are caused by Mycobacterium tuberculosis, although in the years before widespread milk pasteurization, the cattle-infecting species Mycobacterium bovis was a common cause. Mycobacterium tuberculosis, commonly called the tubercle bacillus, is a slender, acid-fast, rod-shaped bacterium (figure 22.17). The organism is a strict aerobe that grows very slowly, with a generation time of 12 hours or more. This slow growth makes it difficult to diagnose tuberculosis quickly. Although easily killed by pasteurization, the tubercle bacillus is unusually resistant to drying, disinfectants, and strong acids and alkali. The bacterium has a Gram-positive cell wall, but bound covalently to the cell wall peptidoglycan is a thick layer composed of complex glycolipids. Up to 60% of the dry weight of the M. tuberculosis cell wall consists of lipids, a much higher percentage than that in most other bacteria. The lipid-containing cell wall is largely responsible for its acid-fast staining, resistance to drying and disinfectants, and its pathogenicity. ■ pasteurization, p. 112 ■ lipids, p. 35

Boundary of necrotic area

1 mm

Pathogenesis

FIGURE 22.18 Stained Lung Tissue Showing a Tubercle A tubercle

Individuals usually contract tuberculosis by inhaling airborne organisms from a person who has tuberculosis. In the lungs, the bacteria are taken up by pulmonary macrophages, where they resist destruction by releasing an enzyme that prevents fusion of the phagosome with lysosomes. They also possess a mecha-

is a kind of granuloma caused by the body’s reaction to Myobacterium tuberculosis. The innumerable dark dots around the outer portion of the picture are nuclei of lung tissue and inflammatory cells. Centrally and extending to the right of the photograph, most of the nuclei have disappeared because the cells are dead and the tissue has begun to liquefy. The photograph depicts a chest X-ray film of an individual with tuberculosis.

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alive, but they are kept from multiplying by conditions in the tubercle including low pH and low available oxygen. They remain alive in this state for many years, causing a latent infection. Individuals with latent tuberculosis infection are asymptomatic. ■ delayed hypersensitivity, p. 422 ■ lysosomes, p. 79 ■ latent infection, p. 330

Sometimes the mycobacteria are not contained by the inflammatory response and cause symptomatic active tuberculosis. Lysis of activated macrophages attacking M. tuberculosis releases their enzymes into the infected tissue. The result is death of tissue, with the formation of a cheesy material by a process called caseous necrosis. If this process involves a bronchus, the dead material may discharge into the airways, causing a large lung defect called a cavity and spread of the bacteria to other parts of the lung. Lung cavities characteristically persist, slowly enlarging for months or years and shedding tubercle bacilli into the bronchi. Coughing and spitting transmit the organisms to other people. Wherever living organisms persist, they can resume growing if the person’s immunity becomes impaired by stress, advanced age, or AIDS. Disease resulting from renewed growth of the organisms is called reactivation tuberculosis.

FIGURE 22.19 Tuberculin Test A positive test is the result of delayed hypersensitivity to Myobacterium tuberculosis antigens injected into the skin, and it gives evidence of past or current infection with the bacterium.

Epidemiology Most of the estimated 10 million Americans who are infected by M. tuberculosis have latent tuberculosis infection and are asymptomatic. However, about 10% of them will develop reactivation tuberculosis at some time during their life. Infection rates are highest among non-whites and elderly poor people. Foreign-born U.S. residents have rates of tuberculosis much higher than those born in the United States. Transmission of tuberculosis occurs almost entirely by the respiratory route; 10 or even fewer inhaled organisms are enough to cause infection. Factors important in transmission include the frequency of coughing, the adequacy of ventilation (transmission is unlikely to occur outdoors), and the degree of crowding. Immunodeficiency can result in activation of latent tuberculosis, and over 5% of AIDS patients have developed active tuberculosis. The tuberculin skin test (TST), also known as the Mantoux (pronounced man-too) test, is an extremely important tool for studying the epidemiology of the disease and in detecting those who are infected with M. tuberculosis. The test is carried out by injecting into the skin a very small amount of a sterile fluid called purified protein derivative, or PPD, derived from cultures of M. tuberculosis. People who are infected with the bacterium develop redness and a firm swelling at the injection site, reaching a peak intensity after 48 to 72 hours (figure 22.19). This reaction is due to the congregation of macrophages and T lymphocytes at the injection site, a manifestation of delayed hypersensitivity to the tubercle bacillus. A positive reaction to the test generally indicates that living M. tuberculosis bacilli are present somewhere in the body of the person tested. A positive TST does not necessarily mean that the person has tuberculosis—only that he or she has been infected by M. tuberculosis at some time in the past. Beside the TST, a blood test (QFT-G) is available for diagnosing M. tuberculosis infection. QFT-G generally gives results similar to TST, but sooner and with greater specificity. It is based on the fact that lymphocytes in the blood of M. tuberculosis-infected indi-

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viduals release INF-gamma when they contact specific M. tuberculosis antigens added to the blood. ■ IFN-gamma, p. 353

Prevention and Treatment Vaccination against tuberculosis has been widely used in many parts of the world with varying success. The vaccinating agent, a living attenuated mycobacterium known as Bacille Calmette-Guérin, or BCG, is derived from M. bovis. Repeated subculture in the laboratory over many years resulted in selection of this strain of M. bovis, which has little virulence in humans but produces some immunity to tuberculosis. Use of the vaccine is discouraged in the United States, because people who receive the vaccine usually develop a positive tuberculin test. By causing a positive test, BCG vaccination eliminates an important way of diagnosing tuberculosis early in the disease when it can most easily be treated. BCG is not safe to use in severely immunocompromised patients because the vaccine bacillus can spread throughout the body and cause disease. Genetically engineered vaccines are under development. Control of tuberculosis is aided by identifying unsuspected cases using skin tests and lung Xrays. Individuals with active disease are then treated, thus interrupting the spread of M. tuberculosis. People whose TST has changed from negative to positive are also treated, as are all high-risk individuals, even when no evidence of active disease exists. Highrisk individuals include babies, young children, and the elderly; those whose TST converted to positive within 2 years; those recently exposed to active tuberculosis; and those with underlying conditions such as HIV infection, drug abuse, and diabetes. Treatment reduces the risk that these people will develop active disease later in life. Mutants resistant to antibacterial medications frequently occur among sensitive M. tuberculosis strains. Because mutants simultaneously resistant to more than one antimicrobial medication occur with a very low frequency, two or more of the medications are always given together in treating tuberculosis. The combination of rifampin and isoniazid (INH) is favored because

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22.5 Bacterial Infections of the Lower Respiratory System

both drugs are bactericidal against actively growing organisms in cavities as well as metabolically inactive intracellular organisms. Because of the long generation times of M. tuberculosis and its resistance to destruction by body defenses, drug treatment of tuberculosis must generally be continued for a minimum of 6 months to cure the disease. During the prolonged treatment, symptoms usually disappear and many individuals become careless about continuing to take their medications. Such negligence allows the rare, resistant mutants to multiply and can lead to high rates of relapse. Up to two-thirds of the M. tuberculosis strains obtained from inadequately treated patients are resistant to one or more antitubercular medications. These resistant strains can infect others in the community. DOTS (directly observed therapy short-course) programs employ three or four antitubercular medications given daily or thrice weekly for 6 months. They have been effective in assuring that medications are taken properly. Nevertheless, the problem of drug-resistant M. tuberculosis strains has reached alarming proportions in some areas. During the 1990s, multiple drug-resistant tuberculosis (MDR-TB) became an increasing problem. These cases resisted treatment with rifampin and isoniazid, the two most effective first-line drugs available, and were often treated with less effective, more toxic, and more expensive second-line medications. By the end of the decade, MDR-TB cases were appearing that also resisted treatment with many of the second-line drugs. These extensively drug-resistant tuberculosis (XDR-TB) cases now threaten tuberculosis-control

517

efforts around the world. Fortunately, promising new antituberculosis medications representing at least five different chemical families are being developed. One entirely new and highly active antitubercular medication, a diarylquinoline (DARQ), is among those under evaluation. ■ antibiotic resistance, p. 483 The main features of tuberculosis are shown in table 22.9.

Legionnaires’ Disease Legionnaires’ disease was unknown until 1976, when a number of people attending an American Legion Convention in Philadelphia developed a mysterious pneumonia that was fatal in many cases. Months of scientific investigation eventually paid off when the cause was discovered to be a previously unknown bacterium commonly present in the natural environment.

Symptoms Legionnaires’ disease typically begins with headache, muscle aches, rapid rise in temperature, confusion, and shaking chills. A dry cough develops that later produces small amounts of sputum, sometimes streaked with blood. Pleurisy, manifest as chest pain brought on by coughing or deep breathing, can also occur. About one-fourth of the cases also have some alimentary tract symptoms such as diarrhea, abdominal pain, and vomiting. Shortness of breath is common, and oxygen therapy is often needed. Recovery is slow, and weakness and fatigue last for weeks.

TABLE 22.9 Tuberculosis ➀ Airborne Mycobacterium

3

tuberculosis bacteria are inhaled and lodge in the lungs.

➁ The bacteria are phagocytized by lung macrophages and multiply within them, protected by lipidcontaining cell walls and other mechanisms.

➂ Infected macrophages are carried

to various parts of the body such as the kidneys, brain, lungs, and lymph nodes; release of M. tuberculosis occurs.

7 5

➅ Intense inflammatory reaction and release of enzymes can cause caseation necrosis and cavity formation.

➆ With uncontrolled or reactive

infection, M. tuberculosis exits the body through the mouth with coughing or singing.

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Chronic fever, weight loss, cough, sputum production

Incubation period

2 to 10 weeks

Causative agent

Mycobacterium tuberculosis; unusual cell wall with high lipid content

3 4

Pathogenesis

Colonization of the alveoli incites inflammatory response; ingestion by macrophages follows; organisms survive ingestion and are carried to lymph nodes, lungs, and other body tissues; tubercle bacilli multiply; granulomas form.

Epidemiology

Inhalation of airborne organisms; latent infections can reactivate.

Prevention and treatment

BCG vaccination, not used in the United States; tuberculin (Mantoux) test for detection of infection, allows early therapy of cases; treatment of all high-risk cases including young people with positive tests and individuals whose skin test converts from negative to positive. Treatment: two or more antitubercular medications given simultaneously long term, such as isoniazid (INH) and rifampin; DOTS.

1 2 6

wherever infected M. tuberculosis has lodged, an intense inflammatory reaction develops. macrophages and lymphocytes; growth of the bacteria ceases.

Symptoms

5

1

➃ Delayed hypersensitivity develops;

➄ The bacteria are surrounded by

4

3 5 4

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TABLE 22.10 Legionnaires’ Disease Symptoms

Muscle aches, headache, fever, cough, shortness of breath, chest and abdominal pain, diarrhea

Incubation period 2 to 10 days

10 mm

FIGURE 22.20 Legionella pneumophila in Lung Tissue Stained with Fluorescent Antibody When present in tissue or sputum, the bacte-

Causative agent

Legionella pneumophila, a Gram-negative bacterium that stains poorly in clinical specimens.

Pathogenesis

Organism multiplies within phagocytes; released with death of the cell; necrosis of cells lining the alveoli; inflammation, and formation of microabscesses.

Epidemiology

Originates mainly from warm water contaminated with other microorganisms, such as found in air conditioning systems.

Prevention and treatment

Avoidance of contaminated water aerosols; regular cleaning and disinfection of humidifying devices. Treatment: erythromycin and rifampin.

rium fails to stain with most of the usual microbiological stains.

Causative Agent The causative agent of Legionnaires’ disease is Legionella pneumophila (figure 22.20). The organism is rod-shaped, Gram-negative, and requires a special medium for laboratory culture, which partly explains why it escaped detection for so long. Also, in tissue, L. pneumophila stains poorly with many of the usual microbiological stains. Genomic studies have revealed genes that aid its survival in protozoa, macrophages, and in adverse environments. The studies also give evidence of horizontal gene transfer. ■ horizontal gene transfer, p. 186

Pathogenesis Legionella pneumophila infection is acquired by breathing aerosolized water contaminated with the organism. Healthy people are quite resistant to infection, but smokers and those with impaired host defenses from chronic diseases such as cancer and heart or kidney disease are susceptible. The organisms lodge in and near the alveoli of the lung, and their porin proteins bind complement component C3b, which aids phagocytosis of L. pneumophila by macrophages. A surface protein of L. pneumophila, macrophage invasion potentiator (Mip), also aids entry into the macrophages. The bacteria survive in the phagocytes by preventing phagosome-lysosome fusion, multiply and are released upon death of the macrophages to infect other tissues. Necrosis (tissue death) of alveolar cells and an inflammatory response result, causing multiple small abscesses, pneumonia, and pleurisy. Bacteremia is often present. Fatal respiratory failure, meaning that the lungs can no longer adequately oxygenate the blood or expel carbon dioxide, occurs in about 15% of hospitalized cases. Curiously, L. pneumophila infections remain confined to the lung in most cases. ■ porin proteins, p. 483

Epidemiology The organism is widespread in warm natural waters where other microorganisms are present, and where it is taken up and multiplies within amebas, protozoa mobile by pseudopods, in the same way it grows in human macrophages. Legionella pneumophila survives well in the water systems of buildings, particularly in hot water systems, where chlorine levels are generally low. However, even increased levels of chlorine fail to decontaminate water systems consistently,

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probably because the bacteria are protected by their growth inside amebas.Legionnaires’ disease cases have originated from contaminated aerosols from air conditioner cooling towers, nebulizers, sprays to freshen produce, and even from showers and water faucets. Direct person-to-person spread, however, does not occur. Monoclonal antibodies against different L. pneumophila strains help trace the source of epidemics. ■ monoclonal antibodies, p. 439 ■ protozoa, p. 285

Prevention and Treatment Most efforts at control have focused on designing equipment to minimize the risk of infectious aerosols and on disinfecting procedures. Environmental surveillance is not practical because of the lack of a simple method for detecting virulent strains. Legionnaires’ disease is treated with high doses of erythromycin, sometimes concurrently with rifampin. Like many other pathogens, L. pneumophila produces b-lactamase, which makes it resistant to many penicillins and cephalosporins. ■ b-lactamase, p. 476 The main features of Legionnaires’ disease are given in table 22.10.

MICROCHECK 22.5 Pneumococcal pneumonia is typically acquired in the community and leads the list of pneumonias in adults requiring hospitalization. Pneumonia due to Klebsiella sp. and other Gram-negative rods is mainly nosocomial and leads the causes of death from nosocomial infections. Mycoplasmal pneumonia usually does not require hospitalization. Whooping cough (pertussis) is mainly a threat to infants; childhood immunization against the disease protects them, but immunity often does not persist to adulthood. Tuberculosis is a chronic disease spread from one person to another by coughing and singing. Most Mycobacterium tuberculosis infections become latent, posing the risk of reactivation throughout life. Legionella pneumophila, the bacterium that causes Legionnaires’ disease, originates from waters containing other microorganisms, where it can grow within protozoa. In the human lung, the bacterium readily multiplies within macrophages. ✓ What feature of the S. pneumoniae cell is responsible for its virulence? ✓ Why isn’t pertussis toxin eliminated by the mucociliary escalator?

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22.6 Viral Infections of the Lower Respiratory System

22.6 Viral Infections of the Lower Respiratory System Focus Points Describe the principal factors driving the epidemiology of influenza. Give the symptoms of respiratory syncytial virus infection of infants. List measures for the prevention of hantavirus pulmonary syndrome.

DNA viruses such as varicella-zoster virus and the adenoviruses sometimes cause serious pneumonias, and some adenovirus infections can mimic pertussis. RNA viruses are of greater overall importance, however, because of the large number of people they infect and their potential for serious outcomes. The following examples come from the orthomyxovirus, paramyxovirus, and bunyavirus families of RNA viruses. ■ RNA viruses, p. 322

Influenza Influenza is a good example of the constantly changing interaction between people and the agents that infect them. Antigenic changes in the influenza viruses are responsible for serious epidemics of the disease that recur in human populations. Epidemics of influenza also occur in animals such as birds, seals, and pigs, and antigenic variability of influenza viruses is partly due to movement of viral genes from one animal species to another. There are three major influenza types, designated A, B, and C, based on differences in their nucleoprotein antigens. Type A, considered here, causes the most severe disease and its epidemics are the most widespread. Outbreaks due to type B strains occur each year, but they are less extensive and the severity of the disease is less. Type C strains are of relatively little importance. Influenza viruses do not cause “stomach flu.”

Symptoms After a short incubation period, averaging 2 days, influenza typically begins with headache, fever, and muscle pain, which reach a peak in 6 to 12 hours. A dry cough worsens over a few days. Usually these acute symptoms go away within a week, leaving the patient with a lingering hacking cough, fatigue, and generalized weakness for additional days or weeks. Infection by influenza viruses is associated with Reye’s syndrome on rare occasions.

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destroys the cell receptor to which the hemagglutinin attaches. This aids in the release of newly formed virions from the infected host cell and fosters the spread of the virus to uninfected host cells.

Pathogenesis Individuals acquire influenza by inhaling aerosolized respiratory secretions from a person who has the disease. The virions attach by their hemagglutinin to specific receptors on ciliated epithelial cells, their envelope fuses with the cell membrane, and the virus enters the cell by endocytosis. Viral RNA is released into the cytoplasm following fusion with the endosomal membrane. Host cell protein and nucleic acid synthesis cease, and rapid synthesis of viral nucleoproteins begins. Regions of the cell membrane become embedded with viral glycoproteins, specifically hemagglutinin and neuraminidase. Within 6 hours, mature virions bud from the host cell, receiving an envelope of cell membrane containing viral hemagglutinin and neuraminidase as they are released. The virus spreads rapidly to nearby cells, including mucus-secreting cells and cells of the alveoli. Infected cells ultimately die and slough off, thus destroying the mucociliary escalator and severely impairing one of the body’s major defenses against infection. The immune response quickly controls the infection in the vast majority of cases, although complete recovery of the respiratory epithelium may take 2 months or more. Usually, only a small percentage of people with influenza die, but even so, epidemics are so widespread that the total number of deaths is high. Influenza virus infection alone can kill apparently normal, healthy people. More often, however, death occurs because of bacterial secondary infections, usually by Staphylococcus aureus, Streptococcus pyogenes, or Haemophilus influenzae. Influenza takes a heavy toll on people whose hearts or lungs are weak.

Epidemiology Outbreaks of influenza occur every year in the United States and are associated with an estimated 10,000 to 40,000 deaths. Figure 20.2 shows the variations in the percentage of total deaths attributed to pneumonia and influenza. Pandemics occur periodically over the years, marked by rapid spread of influenza viruses around the globe and higher than normal morbidity. ■ pandemics, p. 451

Matrix protein RNA, nucleoprotein

■ Reye’s syndrome, p. 546

Causative Agents Influenza A virus belongs to the orthomyxovirus family; its genome consists of eight segments of single-stranded RNA. The virion is surrounded with a lipid-containing envelope derived from the host cell membrane (figure 22.21). Projecting from the envelope are two kinds of glycoprotein spikes—hemagglutinin (H) and neuraminidase (N). Hemagglutinin attaches the virus to specific receptors on ciliated epithelial cells of the host and thus initiates infection. Neuraminadase, on the other hand, is an enzyme that

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Lipid envelope from host membrane Neuraminidase (N) Hemagglutinin (H)

FIGURE 22.21 Diagrammatic Representation of Influenza Virus Note the surface structures, hemagglutinin and neuraminidase, the eightsegment genome, and the nucleoprotein, which distinguishes the three viral types, A, B, and C.

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Genome segments H antigen N antigen

Mutation #1

Mutation #2

Mutation #1 Result of

Mutation #2

ANTIGENIC DRIFT

Human influenza virion Influenza virion from an animal

Reassortment of genome segments

Host cell

ANTIGENIC SHIFT

FIGURE 22.22 Influenza Virus: Antigenic Drift and Antigenic Shift With drift, repeated mutations cause a gradual change in the antigens composing the hemagglutinin, so that antibody against the original virus becomes progressively less effective. With shift, there is an abrupt, major change in the hemagglutinin antigens because the virus acquires a new genome segment, which in this case codes for hemagglutinin. Changes in neuraminidase could occur by the same mechanism.

Although other factors are involved in the spread of influenza viruses, major attention has focused on their antigenic changeability. Two types of variation are seen: antigenic drift and antigenic shift (figure 22.22). Antigenic drift is seen in interepidemic years and consists of minor mutations in the hemagglutinin (H) antigen that make immunity developed during prior years less effective and ensure that enough susceptible people are available for the virus to survive. This type of change is exemplified by A/Texas/77 (H3N2) and A/Bangkok/79 (H3N2), wherein there have been mutations that have altered the H antigen slightly. (The geographic names are the places where the virus was first isolated, the next two numbers represent the year.) The antibody produced by people who have recovered from A/Texas/77 (H3N2) is only partially effective against the mutant H3 antigen of A/Bangkok/79 (H3N2). Thus, the newer Bangkok strain might be able to spread and cause a minor epidemic in a population previously exposed to the Texas strain. ■ antigenic shift and drift, p. 335

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Antigenic shifts are represented by more dramatic changes; virus strains appear that are markedly different antigenically from the strains previously seen. Most likely they arise as a result of genetic reassortment when two different viruses infect a cell at the same time. Animal strains of influenza virus can occasionally infect humans and cause dual infections with human strains. When genetic mixing results in a new virus that is infectious, virulent, and possesses a hemagglutinin for which a population has no immunity, it can cause widespread disease. Ecological studies show that all the known influenza A virus types exist in aquatic birds, generally causing chronic intestinal infections. These bird influenza (avian flu) viruses readily infect domestic fowl, and from them can infect other domestic animals and humans. A well-studied episode in Hong Kong in 1997 involved an H5N1 virus from chickens that caused fatal infections in humans, but fortunately it did not spread easily from person to person. Subsequent outbreaks show that H5N1 viruses are now endemic in a number of Asian communities. ■ genetic reassortment, p. 335

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22.6 Viral Infections of the Lower Respiratory System

Prevention and Treatment Inactivated vaccines can be 80% to 90% effective in preventing disease when the vaccine is produced from the epidemic strain. Subunit vaccines consisting mostly of hemagglutinin are now widely used instead of whole virus vaccines. Attenuated nasally administered vaccines appear to be safe and effective. Because of antigenic drift, vaccines produced from earlier strains having the same H type may be decreasingly effective, so that new vaccines must be produced each year. It takes 6 to 9 months from the appearance of a new influenza strain before adequate amounts of vaccine can be manufactured. A serious reaction was observed during a nationwide immunization program with the swine influenza vaccine produced against the 1976 Fort Dix H1N1 influenza A strain. This reaction, called the Guillain-Barré syndrome, occurred in about 1 of every 100,000 persons vaccinated. It is characterized by severe paralysis, and although most people recover completely, about 5% die of the paralysis. The possibility that this or other side effects will generate lawsuits is one reason vaccine production is a risky business. Medications such as amantadine (Symmetrel) and rimantadine (Flumadine) have been employed for short-term prevention of influenza A disease when vaccine is not available. However, they are not currently recommended because many circulating viruses are resistant. Zanamivir (Relenza) and oseltamivir (Tamiflu), first approved for use in 1999, represent neuraminidase inhibitors, active against both A and B viruses. Some experts have advised stockpiling anti-influenza medications to protect populations faced with a new virulent influenza virus. These medicines

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are generally used in conjunction with vaccination to protect exposed individuals until they can develop immunity. ■ neuraminidase inhibitors, p. 488

The main features of influenza are summarized in table 22.11.

Respiratory Syncytial Virus Infections Respiratory syncytial virus (RSV) infection is first among serious lower respiratory tract infections of infants and young children, causing an estimated 90,000 hospitalizations and 4,500 deaths in the United States each year. It is also responsible for serious disease in elderly people, and for nosocomial epidemics.

Symptoms Symptoms begin after an incubation period of 1 to 4 days with runny nose followed by cough, wheezing, and difficulty breathing. Fever may or may not be present. Victims often develop a dusky color, indicating that they are not getting enough oxygen. Death occurs in 0.5% to 1% of hospitalized infants but is much higher in those with underlying diseases such as heart and lung disease, cancer, and immunodeficiency. RSV is one of the causes of croup, seen commonly in older infants and manifest as a loud high-pitched cough and noisy inspiration due to airway obstruction at the larynx. Infections of healthy older children and adults generally cause symptoms of a bad cold.

Causative Agent Respiratory syncytial virus is a member of the paramyxovirus family and contains a single-stranded RNA genome. Like all

TABLE 22.11 Influenza ➀ Influenza virus is inhaled and carried

Symptoms

to the lungs.

6

➁ Viral hemagglutinin attaches to

specific receptors on ciliated epithelial cells, the viral envelope fuses with the epithelial cell, and the virus enters the cell by endocytosis.

6

1 7

Incubation period

1 to 2 days

Causative agent

Influenza virus, an orthomyxovirus

Pathogenesis

Infection of respiratory epithelium; cells destroyed and virus released to infect other cells. Secondary bacterial infection results from damaged mucociliary escalator.

Epidemiology

Antigenic drift and antigenic shift thwart immunity.

Prevention and treatment

Vaccines usually 80% to 90% effective. Amantadine and rimantadine are sometimes effective for preventing type A but not type B virus disease; neuraminidase inhibitors effective against both A and B viruses. These medications somewhat effective for treatment when given early in the disease.

➂ Host cell synthesis is diverted to synthesizing new virus.

➃ Newly formed virions bud from infected cells, they are released by viral neuraminidase and infect ciliated epithelium, mucussecreting, and alveolar cells. ➄ Infected cells ultimately die and slough off; recovery of the mucociliary escalator may take weeks.

➅ Secondary bacterial infection of the lungs, ears, and sinuses is common.

1 6

Fever, muscle aches, lack of energy, headache, sore throat, nasal congestion, cough

➆ The virus exits with coughing.

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paramyxoviruses, its virion is enveloped. It causes cells in cell cultures to fuse together. The clumps of fused cells are known as syncytia, thus the name of the virus. ■ paramyxovirus family, p. 323

Pathogenesis The virus enters the body by inhalation and infects the respiratory tract epithelium, causing death and sloughing of the cells. Bronchiolitis is a common feature of the disease; the inflamed bronchioles become partially plugged by sloughed cells, mucus, and clotted plasma that has oozed from the walls of the bronchi. The initial obstruction causes wheezing when air rushes through the narrowed passageways, sometimes causing the condition to be confused with asthma. The obstruction often acts like a one-way valve, allowing air to enter the lungs, but not leave them. In many cases the inflammatory process extends into the alveoli, causing pneumonia. There is a high risk of secondary infection because of the damaged mucociliary escalator. ■ mucociliary escalator, p. 498

Epidemiology RSV outbreaks are common from late fall to late spring, peaking in mid-winter. Recovery from infection produces only weak and short-lived immunity, so that infections can recur throughout life. Healthy children and adults usually have mild illness and readily spread the virus to others.

Prevention and Treatment No vaccines are available although there are at least six programs underway to develop a vaccine. Preventing nosocomial RSV illness requires strict isolation technique. Subjects with underlying illnesses can be protected from the disease by monthly injections of immune serum globulin or a monoclonal antibody called palivizumab. There are no effective antiviral medications. ■ monoclonal antibody, p. 439 The main features of RSV infections are summarized in table 22.12.

TABLE 22.12 Respiratory Syncytial Virus (RSV) Infections Symptoms

Runny nose, cough, fever, wheezing, difficulty breathing, dusky color

Incubation period 1 to 4 days Causative agent

RSV, a paramyxovirus that produces syncytia

Pathogenesis

Sloughing of respiratory epithelium and inflammatory response plug bronchioles, cause bronchiolitis; pneumonia results from bronchiolar and alveolar inflammation, or secondary infection.

Epidemiology

Yearly epidemics during the cool months; readily spread by healthy older children and adults who often have mild symptoms; no lasting immunity.

Prevention and treatment

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No vaccine. Preventable by injections of immune serum globulin or a monoclonal antibody; no satisfactory antiviral treatment.

Hantavirus Pulmonary Syndrome In the spring of 1993 a newly emerging disease made a dramatic appearance in the American Southwest near the place where the corners of four states, Arizona, Colorado, New Mexico, and Utah, come together. The initial outbreak of the disease was alarming. It involved less than a dozen people, mostly Navajo, and most were vigorous young adults who started with influenza-like symptoms, but were dead in a few days. Scientists from the Centers for Disease Control and Prevention rushed to join local epidemiologists and health officials investigating the outbreak. Their studies quickly established that the disease was associated with exposure to mice. By allowing the serum from victims to react with many different known viruses, they learned within a month that antibodies in the blood of the victims reacted with a hantavirus that had plagued American troops during the 1950s Korean War. Using the polymerase chain reaction (PCR), the scientists recovered a viral genome from the lungs of patients who had died, and they showed it was identical to one from mice captured in the area. This virus proved to be a close relative of the Korean virus. ■ polymerase chain reaction, p. 223

Symptoms Hantavirus pulmonary syndrome usually begins with fever, muscle aches (especially in the lower back), nausea, vomiting, and diarrhea. Unproductive cough and increasingly severe shortness of breath appear within a few days, followed by shock and death.

Causative Agents The causative agents are the Sin Nombre, Spanish for “no name,” virus and various related hantaviruses that exist at different locations in the Western Hemisphere. The hantaviruses are enveloped viruses of the bunyavirus family. Their genome consists of three segments of single-stranded RNA. In nature these viruses cause lifetime infections, primarily of rodents, without any apparent harm to the animals. ■ bunyavirus family, p. 323

Pathogenesis The virus enters the body by inhalation of air containing dust contaminated with the urine, feces, or saliva of infected rodents. The virus enters the circulation and is carried throughout the body, infecting the cells that line tissue capillaries. Massive amounts of the viral antigen appear in lung capillaries, but the antigen is also demonstrable in capillaries of the heart and other organs. The inflammatory response to the viral antigen causes the capillaries to leak large amounts of plasma into the lungs, suffocating the patient and causing the blood pressure to fall. Shock and death occur in more than 40% of the cases.

Epidemiology Hantavirus pulmonary syndrome (figure 22.23) is another example of a zoonosis. It is called an “emerging disease” because of its recent discovery and apparent increase in frequency. Nevertheless, this zoonosis has undoubtedly existed for centuries, occasionally claiming human victims when mice

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22.6 Viral Infections of the Lower Respiratory System 60 Lived 55

Died

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TABLE 22.13 Hantavirus Pulmonary Syndrome Symptoms

Fever, muscle aches, vomiting, diarrhea, cough, shortness of breath, shock

50

Incubation period 3 days to 6 weeks 45

Causative agent

Sin Nombre and related hantaviruses of the bunyavirus family

Pathogenesis

Viral antigen localizes in capillary walls in the lungs; inflammation.

Epidemiology

Zoonosis likely to involve humans in proximity to booming mouse populations; generally no person-to-person spread.

Prevention and treatment

Avoid contact with rodents; seal access to houses, food supplies; good ventilation, avoid dust, use disinfectants in cleaning rodentcontaminated areas. No proven antiviral treatment.

Number of cases

40 35 30 25 20 15 10 5 0 1996

1997

1998

1999

2000

2001

2002

2003

2004

2005

Year

FIGURE 22.23 Total Hantavirus Pulmonary Syndrome Cases, United States, 1996–2005 (Source: MMWR, CDC 2007 54(53): 2–92).

and humans get too close together. Since the description of the syndrome, cases have been identified from Canada to Argentina, including several hundred cases from the United States. Most of the cases have occurred west of the Mississippi River and were due to Sin Nombre virus carried by deer mice. Others have been caused by related viruses carried by other rodents. Outbreaks of the disease correlate with marked increases in mouse populations adjacent to impoverished communities with substandard housing. The virus spreads more easily when the mouse population density is high. Thirty percent or more of the mice can become carriers of the disease. These mice eagerly and easily invade the houses of the poor. Complex ecological factors control the size of mouse populations. The numbers of foxes, owls, snakes, and other predators play a role. Moreover, two outbreaks of hantavirus pulmonary syndrome occurred in association with El Niño weather patterns, which brought increased rainfall to the area, yielding increased plant growth and seed production for mice to feed on. The emergence of hantavirus pulmonary syndrome is a convincing example of how environmental change can result in infectious human disease. Luckily, despite the large amount of viral antigen in the lung capillaries, few mature infectious virions enter the air passages of the lung; thus, person-toperson transmission occurs rarely, if ever. ■ emerging diseases, p. 461 ■ zoonoses, p. 453

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Prevention and Treatment Prevention of hantavirus pulmonary syndrome is based on minimizing exposure to rodents and dusts contaminated by them. Food for humans and pets should be kept in containers. Buildings should be made mouse-proof if possible, and maximal ventilation is advisable when cleaning a rodent-infested area. Mopping with a disinfectant solution is preferable to use of brooms and vacuum cleaners, because the latter two stir up dust. Lethal traps and poisons may be necessary to decrease the rodent population in the area. Rubber gloves and a mask are advisable for those doing field studies on wild rodents. When camping, a tent with a floor should be used. There is no proven antiviral treatment for this highly fatal disease. The main features of hantavirus pulmonary syndrome are summarized in table 22.13.

MICROCHECK 22.6 Because of the speed with which influenza travels around the world, and the potential for development of virulent influenza virus strains, the disease poses an extremely serious threat to humankind. Most deaths from influenza are caused by secondary bacterial infections. Respiratory syncytial virus is the leading cause of serious respiratory disease in infants and young children. Hantavirus pulmonary syndrome, first recognized in 1993, is often fatal. It is contracted from inhalation of dust contaminated by mice infected with certain hantaviruses. ✓ Why are there so many deaths from influenza when it is generally a mild disease? ✓ What is the source of the virus that causes hantavirus pulmonary syndrome? ✓ Why might you expect an influenza epidemic to be more severe following an antigenic shift in the virus than after antigenic drift?

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PERSPECTIVE 22.2 What to Do About Bird Flu The known antigenic types of influenza A are 16 different hemaglutinins, designated H 1–16, and nine neuraminidases, N types 1–9. All of these are represented among the influenza A viruses infecting wild waterfowl. Generally, only H types 1–3, and N types 1 and 2 viruses have been important in human disease. Occasionally, however, avian viruses infect humans and cause illness. For example, there were 123 known human cases caused by avian viruses between 1996 and 2004, caused by five avian strains—H7N7, H5N1, H9N2, H7N2, and H7N3. There was a high mortality among the 29 cases caused by the H5N1 strains (seven died), whereas only one death occurred among the remaining 103 cases due to the other four avian viruses. The high virulence of the H5N1 strain has been apparent since the first H5N1 outbreak occurred in

United Kingdom of Great Britain and Northern Ireland

1997. Moreover, the virus has spread rapidly from Asia to the Middle East, Europe, and Africa (figure 1), devastating flocks of domestic fowl and causing several hundreds of deaths among humans. Fortunately, so far there have been only a few instances that suggest person-to-person spread of the disease. The H5N1 avian virus concerns us because it has two of the three characteristics required of a pandemic influenza virus: (1) It is infectious for humans who have no herd immunity; and (2) it causes severe disease in humans. The virus does not yet meet the third requirement—easy spread from person to person, but it might acquire this ability through mutation or antigenic shift. The H5N1 virus may never become a pandemic strain, but even if it doesn’t, it is highly likely that other

avian strains will do so sometime in the future. We have a historical example in the 1918-1919 “Spanish flu” that killed 40 to 100 million people. This pandemic was caused by an avian virus. Today, we are using some important tools to defend ourselves that weren’t available in 1918. Rapid viral diagnosis is now possible, and global communication can inform us promptly of outbreaks anywhere in the world so we can take defensive measures. We can also make and stockpile influenza vaccines, and vaccines against bacterial secondary invaders such as Streptococcus pneumoniae and Haemophilus influenzae. We can also place antiviral and antibacterial medications at strategic locations. A lot depends on international cooperation.

Russian Federation

Sweden Denmark Netherlands

Poland

Czech Republic

Germany Slovakia Austria

France Switzerland

Italy

Hungary Romania Serbia Bulgaria

Slovenia Croatia Greece Bosnia and Herzegovina Albania

Spain

Kazakhstan

Ukraine

Mongolia

Georgia Azerbaijan

Republic of Korea

Turkey

Iraq

Islamic Republic of Iran

China

Afghanistan

Japan Pakistan

Egypt

Saudi Arabia

Myanmar Lao People’s Democratic Republic

India Niger

Burkina Faso

Bangladesh

Nigeria

Cote d’Ivore

Thailand

Viet Nam

Cambodia

Sudan Cameroon

Malaysia

Togo Ghana

Indonesia

Areas reporting occurance in poultry Areas reporting occurance only in wild birds

FIGURE 1 Areas Reporting H5N1 Avian Influenza in Poultry and Wild Birds. Confirmed reports since 2003, last updated September 2007. Source: World Organization for Animal Health, World Health Organization

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22.7 Fungal Infections of the Lung

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22.7 Fungal Infections of the Lung Focus Points Describe in general terms the distribution of histoplasmosis in the United States. Outline the epidemiology of coccidioidomycosis

Serious lung diseases caused by fungi are quite unusual in healthy, immunocompetent individuals. Symptomatic and asymptomatic infections that subside without treatment, however, are common. One fungus infects most of us in childhood without causing symptoms. This organism, Pneumocystis jirovecii, will be discussed in chapter 29 on AIDS. Coccidioidomycosis and histoplasmosis are two other examples of widespread mycoses.

20 mm

(a)

Valley Fever (Coccidioidomycosis) In the United States, coccidioidomycosis occurs mainly in California, Arizona, Nevada, New Mexico, Utah, and West Texas. People who are exposed to dust and soil, such as farm workers, are most likely to become infected, but only 40% develop symptoms.

Symptoms “Flu”-like symptoms such as fever, cough, chest pain, and loss of appetite and weight are common symptoms of coccidioidomycosis. About 10% of victims experience symptoms caused by hypersensitivity to the fungal antigens, manifested by tender nodules often localized to the shins and pain in the joints. The majority of people afflicted with coccidioidomycosis recover spontaneously within a month. A small percentage of victims develop chronic disease.

Causative Agent The causative agent of coccidioidomycosis, Coccidioides immitis, is a dimorphic fungus. The mold form of the organism grows in soil. The mold’s hyphae develop numerous barrel-shaped, highly infectious arthrospores (figure 22.24a), which separate easily and become airborne. In infected tissues, the arthrospores develop into thick-walled, spherical spores that may contain several hundred small cells called endospores (figure 22.24b), not to be confused with bacterial endospores. ■ dimorphic fungi, p. 290

Pathogenesis Arthrospores enter the lung with inhaled air and develop into thick-walled spheres that mature and rupture, spilling numerous endospores. The endospores develop into more large, thick-walled spores containing endospores and repeat the process, each time provoking an inflammatory response and subsequent immune response. Symptoms and tissue injury are caused mainly by the host’s immune response to coccidioidal antigens. Usually, the organisms are eliminated by body defenses, but in a small percentage of individuals caseous necrosis occurs and results in a lung cavity mimicking tuberculosis. Rarely, organisms are carried throughout the body by

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(b)

50 mm

FIGURE 22.24 Coccidioides immitis (a) Mold-phase hyphae fragmenting into barrel-shaped arthrospores, the infectious form of the fungus. (b) Spherical spores containing endospores, the form of the fungus found in tissues.

the bloodstream and infect the skin, mucous membranes, brain, and other organs. This disseminated form of the disease occurs more often in people with AIDS or other immunodeficiencies and is fatal without treatment. ■ caseous necrosis, p. 516

Epidemiology Coccidioides immitis grows only in semi-arid desert areas of the Western Hemisphere (figure 22.25). In these areas, infections occur only during the hot, dry, dusty seasons when airborne arthrospores are easily dispersed from the soil. Dust stirred up by earthquakes can result in epidemics. Rainfall promotes growth of the fungus, which then produces increased numbers of spores when dry conditions return. People can contract coccidioidomycosis by simply traveling through the endemic area. Infectious spores have unknowingly been transported to other areas, but the organism apparently is unable to establish itself in moist climates.

Prevention and Treatment Preventive measures include avoiding dust in the endemic areas. Watering and planting vegetation aid in dust control. Medications approved for treatment of the serious cases include amphotericin

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Spelunkers’ Disease (Histoplasmosis) Histoplasmosis, like coccidioidomycosis, is usually benign but occasionally mimics tuberculosis. Rare, serious forms of the disease suggest that AIDS or another immunodeficiency may also be present. The distribution is more widespread than that of coccidioidomycosis and is associated with different soil and climate.

Symptoms Most infections are asymptomatic. Fever, cough, and chest pain are the most common symptoms, sometimes with shortness of breath. Mouth sores may develop, especially in children.

Causative Agent Histoplasmosis is caused by the dimorphic fungus Histoplasma capsulatum. This organism prefers to grow in soils contaminated by bat or bird droppings, but it is not pathogenic for these animals. In pus or tissue from people with active disease, H. capsulatum is a tiny oval yeast that grows within host macrophages Macrophage Macrophage nucleus

FIGURE 22.25 Area of Distribution of Coccidioides immitis

B and fluconazole or itraconazole. They markedly improve the prognosis but must be given for long periods of time, and cause troublesome side effects. Even with treatment, disseminated disease can reactivate months or years later. Table 22.14 describes the main features of coccidioidomycosis.

TABLE 22.14

Coccidioidomycosis (Valley Fever)

Symptoms

Fever, cough, chest pain, loss of appetite and weight; less frequently, painful nodules on extremities, pain in joints; skin, mucous membranes, brain, and internal organs sometimes involved

Incubation period

2 days to 3 weeks

Causative agent

Coccidioides immitis, a dimorphic fungus

Pathogenesis

After lodging in lung, arthrospores develop into spheres that mature and discharge endospores, each of which then develops into another sphere; inflammatory response damages tissue; hypersensitivity to fungal antigens causes painful nodules and joint pain.

Epidemiology

Inhalation of airborne C. immitis spores with dust from soil growing the organism. Occurs only in certain semi-arid regions of the Western Hemisphere.

Prevention and treatment

Dust control methods such as grass planting and watering. Treatment: amphotericin B and fluconazole or itraconazole.

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H. capsulatum

(a)

(b)

10 mm

10 mm

FIGURE 22.26 Histoplasma capsulatum (a) Yeast-phase organisms packing the cytoplasm of a macrophage. (b) Mold phase, showing large conidia with projecting knobs.

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22.7 Fungal Infections of the Lung

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TABLE 22.15 Histoplasmosis (Spelunkers’ Disease)

FIGURE 22.27 Geographical Distribution of Histoplasma capsulatum in the United States as Revealed by Positive Skin Tests Human histoplasmosis has been reported in more than 40 countries besides the United States, including Argentina, Italy, South Africa, and Thailand.

(figure 22.26a). Contrary to its name, the fungus is not encapsulated. The mold form of the organism characteristically produces two kinds of spores: macroconidia, which often have numerous projecting knobs (figure 22.26b) and tiny pear-shaped or spherical microconidia.

Pathogenesis Individuals inhale infectious conidia of H. capsulatum with dust from contaminated soils and the conidia develop into the yeast form. The organisms promptly enter macrophages and grow intracellularly. Granulomas develop in infected areas, closely resembling those seen in tuberculosis, sometimes even showing caseation necrosis. Eventually, the lesions are replaced with scar tissue, and many calcify, meaning that the body deposits calcium compounds in them that show up on X-rays. In rare cases, the disease is not controlled and spreads throughout the body. This suggests AIDS or another immunodeficiency.

Epidemiology The distribution of histoplasmosis is quite different from that of coccidioidomycosis. Figure 22.27 shows the distribution of histoplasmosis in the United States, but the disease also occurs in tropical and temperate zones scattered around the world. Cave explorers, spelunkers, are at risk for contracting the disease because many caves contain soil enriched with bat droppings. Most cases of histoplasmosis in the United States have occurred in the Mississippi and Ohio River drainage area and in South Atlantic states. Skin tests reveal that millions of people living in these areas have been infected.

Prevention and Treatment No proven preventive measures are known other than to avoid areas where soil is heavily enriched with bat, chicken, and bird

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Symptoms

Mild respiratory symptoms; less frequently, fever, chest pain, cough, chronic sores

Incubation period

5 to 8 days

Causative agent

Histoplasma capsulatum, a dimorphic fungus

Pathogenesis

Spores inhaled, change to yeast phase, multiply in macrophages; granulomas form; disease spreads in individuals with AIDS or other immunodeficiencies.

Epidemiology

The fungus prefers to grow in soil contaminated by bird or bat droppings, especially in Ohio and Mississippi River valleys, and in the U.S. Southeast. Spotty distribution in many other countries around the world. Spelunkers are at risk of infection.

Prevention and treatment

Avoidance of soils contaminated with chicken, bird, or bat droppings. Treatment: amphotericin B and itraconazole for serious infections.

droppings, especially if they have been left undisturbed for a long period. Some researchers have recommended that several inches of clay soil be placed over soils containing large quantities of old droppings. Treatment of histoplasmosis is similar to that of coccidioidomycosis. Amphotericin B and itraconazole are used for treating severe disease, but both medications have potentially serious side effects. The main features of histoplasmosis are described in table 22.15.

MICROCHECK 22.7 Coccidioidomycosis and histoplasmosis are two diseases caused by fungi that live in the soil. The body responds to these infections by forming granulomas, mimicking tuberculosis. Each fungus has its own ecological niche, Coccidioides immitis in semi-arid regions of the Western Hemisphere, and Histoplasma capsulatum in moist soils enriched with bird or bat droppings around the world. ✓ Why should an immunodeficient person avoid traveling through hot, dry, dusty areas of the Southwest? ✓ Why might cave exploration increase the risk of histoplasmosis? ✓ In March 2001, 221 students from 37 colleges and universities in 18 states developed one or more of the following symptoms: fever, cough, shortness of breath, and chest pain. Serological tests indicated acute histoplasmosis. Most of the students had just returned from spring break in Mexico where they stayed in a hotel next door to a bulldozing operation. How might the bulldozing explain the epidemic?

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FUTURE CHALLENGES Global Preparedness vs. Emerging Respiratory Viruses In November 2002, a frightening new respiratory disease emerged in Guangdong province, China. Symptoms included cough and fever, and Xrays showed characteristics of viral pneumonia. The disease, labeled “SARS” (severe acute respiratory syndrome), quickly spread around the world, involving 25 countries and causing more than 700 deaths. Many of its victims were medical personnel. It had two characteristics that quickly led to its control—a long incubation of 6 days, and dramatic symptoms that were easily recognized. This allowed healthcare personnel time to identify contacts and institute quarantines to stop the spread of the disease. The causative agent proved to be a previ-

ously unknown coronavirus, and its source was never identified, although it was probably a wild animal sold for meat in the markets. On three occasions, SARS escaped from laboratories where the virus was being studied, and the disease may arise again from its natural source. However, its main importance is that it caused many countries to learn to work together to help forge a more effective global response to emerging pandemic diseases. More details on SARS can be found at www.sarsreference.com. The problem of avian influenza is more difficult to solve than SARS because the avian viruses are carried in the intestines of wild waterfowl that readily infect

domestic flocks, which then infect humans. Epidemic influenza in humans generally has a short incubation period, and many victims have mild, coldlike symptoms not easily recognized as part of an influenza epidemic. Therefore, quarantines are not helpful in disease control. Many experts think we have been lucky that no virus capable of causing a pandemic has appeared. However, thanks to the battles against the H5N1 avian virus and the SARS outbreaks, the world is much closer to being prepared for the next pandemic. The challenge is to sustain and improve advances in cooperative surveillance, and action planning to avoid a global catastrophe.

SUMMARY 22.1 Anatomy and Physiology (figure 22.1) The moist lining of the eyes (conjunctiva), nasolacrimal duct, middle ears, sinuses, mastoid air cells, nose, and throat make up the main structures of the upper respiratory system. The functions of the upper respiratory tract include temperature and humidity regulation of inspired air and removal of microorganisms. The lower respiratory system includes the trachea, bronchi, bronchioles, and alveoli. Pleural membranes cover the lungs and line the chest cavity. The Mucociliary Escalator Ciliated cells line much of the respiratory tract and remove microorganisms by constantly propelling mucus out of the respiratory system (figure 22.1a).

22.2 Normal Microbiota (table 22.1) A wide variety of microorganisms colonize parts of the upper respiratory system, often including the important opportunistic pathogen, Staphylococcus aureus. Viruses and microorganisms are normally absent from the lower respiratory system.

Infections of the Upper Respiratory System 22.3 Bacterial Infections of the Upper Respiratory System Strep Throat (Streptococcal Pharyngitis) (tables 22.2, 22.3) Streptococcus pyogenes causes strep throat, a significant bacterial infection that may lead to scarlet fever, toxic shock, or sequelae due to the immune response, glomerulonephritis, or rheumatic fever (figures 22.2, 22.3).

Diphtheria (table 22.4) Diphtheria, caused by Corynebacterium diphtheriae, is a toxin-mediated disease that can be prevented by immunization (figures 22.5, 22.6). Pinkeye, Earache, and Sinus Infections Conjunctivitis (pinkeye) is usually caused by Haemophilus influenzae or Streptococcus pneumoniae, (pneumococcus) (figure 22.6). Viral causes,

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including adenoviruses and rhinoviruses, usually result in a milder illness. Otitis media and sinusitis develop when infection extends from the nasopharynx (figure 22.7).

22.4 Viral Infections of the Upper Respiratory System The Common Cold (table 22.5) The common cold can be caused by many different viruses, rhinoviruses being the most common (figure 22.8). Adenoviral Pharyngitis (table 22.6) Adenoviruses cause illnesses varying from mild to severe, which can resemble a common cold or strep throat.

Infections of the Lower Respiratory System 22.5 Bacterial Infections of the Lower Respiratory System Pneumococcal Pneumonia (table 22.7, figures 22.9, 22.10) Streptococcus pneumoniae, one of the most common causes of pneumonia, is virulent because of its capsule. Klebsiella Pneumonia (table 22.7) Klebsiella pneumonia, is representative of many nosocomial pneumonias that cause permanent damage to the lung (figure 22.11). Serious complications such as lung abscesses and bloodstream infection are more common than with many other bacterial pneumonias. Treatment is more difficult, partly because klebsiellas often contain R factor plasmids. Mycoplasmal Pneumonia (table 22.7, figure 22.12) Mycoplasmal pneumonia is often called walking pneumonia; serious complications are rare. Penicillins and cephalosporins are not useful in treatment because the cause, M. pneumoniae, lacks a cell wall. Whooping Cough (Pertussis) (table 22.8, figures 22.13, 22.14) Whooping cough is characterized by violent spasms of coughing and gasping. Childhood immunization against the Gram-negative rod, Bordetella pertussis, prevents the disease.

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Review Questions Tuberculosis (table 22.9, figures 22.15, 22.16, 22.17, 22.18) Tuberculosis, caused by the acid-fast rod Mycobacterium tuberculosis, is generally slowly progressive or heals and remains latent, presenting the risk of later reactivation. Legionnaires’ Disease (table 22.10, figure 22.19) Legionnaires’ disease occurs when there is a high infecting dose of the causative microorganisms or an underlying lung disease. The cause, Legionella pneumophila, is a rod-shaped bacterium common in the environment.

22.6 Viral Infections of the Lower Respiratory System Influenza (table 22.11, figure 22.20) Widespread epidemics are characteristic of influenza A viruses. Antigenic shifts and drifts are responsible. Deaths are usually but not always caused by secondary infection. Reye’s syndrome may rarely occur during recovery from influenza and other viral infections but is probably not caused by the virus itself.

529

Respiratory Syncytial Virus Infections (table 22.12) RSV is the leading cause of serious respiratory disease in infants and young children. Hantavirus Pulmonary Syndrome (table 22.13, figure 22.22) Hantavirus pulmonary syndrome is contracted from inhalation of dust contaminated by mice infected with the hantavirus and is often fatal.

22.7 Fungal Infections of the Lung Valley Fever (Coccidioidomycosis) (table 22.14) Coccidioidomycosis occurs in hot, dry areas of the Western Hemisphere and is initiated by airborne spores of the dimorphic soil fungus Coccidioides immitis (figures 22.23 and 22.24). Spelunker’s Disease (Histoplasmosis) (table 22.15) Histoplamosis is similar to coccidioidomycosis but occurs in tropical and temperate zones around the world (figure 22.25). The causative fungus, Histoplasma capsulatum, is dimorphic and found in soils contaminated by bat or bird droppings (figure 22.26).

REVIEW QUESTIONS Short Answer 1. How does contamination of the eye lead to upper respiratory infection? 2. After you recover from strep throat, can you get it again? Explain why or why not. 3. Where is the gene for diphtheria toxin production located? 4. Describe two ways to decrease the chance of contracting a cold. 5. What kinds of diseases are caused by adenoviruses? 6. How do alcoholism and cigarette smoking predispose a person to pneumonia? 7. Give a mechanism by which Klebsiella sp. become antibiotic-resistant. 8. Why does the incidence of whooping cough rise promptly when pertussis immunizations are stopped? 9. Why are two or more antitubercular medications used together to treat tuberculosis? 10. Why did it take so long to discover the cause of Legionnaires’ disease?

Multiple Choice 1. The following are all complications of streptococcal pharyngitis, except a) throat abscess. b) scarlet fever. c) otitis media. d) acute rheumatic fever. e) Reye’s syndrome. 2. All of the following are true of diphtheria, except a) a membrane that forms in the throat can cause suffocation. b) a toxin is produced that acts by ADP ribosylation. c) the causative organism typically invades the bloodstream. d) immunization with a toxoid prevents the disease. e) nerve injury with paralysis is common.

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3. Adenoviral infections generally differ from the common cold in all the following ways, except adenoviral infections are a) not caused by picornaviruses. b) often associated with fever. c) likely to extensively involve the cornea and conjunctiva. d) much more likely to cause pneumonia. e) associated with negative cultures for Streptococcus pyogenes. 4. All are true of mycoplasmal pneumonia, except a) it is a mycosis. b) it usually does not require hospitalization. c) penicillin is ineffective for treatment. d) it is the leading cause of bacterial pneumonia in college students. e) the infectious dose of the causative organism is low. 5. All of the following are true of Legionnaires’ disease, except a) the causative organism can grow inside amebas. b) it spreads readily from person to person. c) it is more likely to occur in long term cigarette smokers than in nonsmokers. d) it is often associated with diarrhea or other intestinal symptoms. e) it can be contracted from household water supplies. 6. Which of the following infectious agents is most likely to cause a pandemic? a) Influenza A virus b) Streptoccus pyogenes c) Histoplasma capsulatum d) Sin Nombre virus e) Coccidioides immitis 7. Respiratory syncytial virus a) is a leading cause of bronchiolitis in infants. b) is an enveloped DNA virus of the adenovirus family. c) attaches to host cell membranes by means of neuraminidase.

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d) poses no threat to elderly people. e) mainly causes disease in the summer months. 8. In the United States, hantaviruses a) are limited to southwestern states. b) are carried only by deer mice. c) infect human beings with a fatality rate above 40%. d) were first identified in the early 1970s. e) are contracted mainly in bat caves. 9. All of the following are true of coccidioidomycosis, except a) it is contracted by inhaling arthrospores. b) it is caused by a dimorphic fungus. c) endospores are produced within a spore. d) it is more common in Maryland than in California. e) it is often associated with painful nodules on the legs. 10. The disease histoplasmosis a) is caused by an encapsulated bacterium. b) is contracted by inhaling arthrospores. c) occurs mostly in hot, dry, and dusty areas of the American Southwest.

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d) is a threat to AIDS patients living in areas bordering the Mississippi River. e) is commonly fatal for pigeons and bats.

Applications 1. A physician is advising the family on the condition of a diphtheria patient. How would the physician explain why the disease affects some tissues and not others? 2. How should a physician respond to a mother who asks if her daughter can get pneumococcal pneumonia again?

Critical Thinking 1. If all transmission of Mycobacterium tuberculosis from one person to another were stopped, how long would it take for the world to be rid of the disease? 2. Medications that prevent and treat influenza by binding to neuraminidase on the viral surface, act against all the kinds of influenza viruses that infect humans. What does this imply about the nature of the interaction between the medications and the neuraminidase molecules?

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23 A dividing Staphylococcus epidermidis cell.

Skin Infections A Glimpse of History Howard T. Ricketts was born in Ohio in 1871. He studied medicine in Chicago, and then specialized in pathology—the study of the nature of disease and its causes. In 1902, he was appointed to the faculty of the University of Chicago, where his research interests turned to Rocky Mountain spotted fever, an often fatal and little understood disease characterized by a dramatic rash. The disease could be transmitted to laboratory animals by injecting them with blood from an infected person, and Ricketts noticed that people and laboratory animals with the disease had tiny bacilli in their blood. Ricketts was sure that these tiny bacteria were the cause of the disease, but he was never able to cultivate them on laboratory media. Based on observations of victims with the disease, Ricketts and others suspected that Rocky Mountain spotted fever was contracted from tick bites, and Ricketts went on to prove that certain species of ticks could transmit the disease from one animal to another. The infected ticks remained healthy but capable of transmitting the disease for long periods of time, and oftentimes the offspring of infected ticks were also infected. Ricketts was able to explain this by showing that the eggs of infected ticks often contained large numbers of the tiny bacilli—an example of transovarial, meaning via the eggs, passage of an infectious agent. Frustrated by his inability to cultivate the bacilli for further studies, Ricketts declined to give them a scientific name and went off to Mexico to study a very similar disease—louse-borne typhus (Rocky Mountain spotted fever is also known as tick-borne typhus). Unfortunately, Ricketts contracted the disease and died at the age of 39. Five years later, a European scientist, Stanislaus Prowazek, studying the same disease in Serbia and Turkey, met the same fate at almost the same age. The martyrdom of the two young scientists struggling to understand infectious diseases is memorialized in the name of the louse-borne agent, Rickettsia prowazekii. Both the genus and species names of the Rocky Mountain spotted fever agent, Rickettsia rickettsii, recognize Howard Ricketts. We now know that these bacteria are obligate intracellular parasites, which explains why they could not be cultivated on ordinary laboratory media. Antibiotics, which could have saved these men, had not yet been discovered.

M

uch of the body’s contact with the outside world occurs at the surface of the skin. As long as skin is intact, this tough, flexible outer covering is remarkably resistant to infection. Because of its exposed state, however, it is frequently subject to cuts, punctures, burns, chemical injury, reactions, and insect or tick bites. These injure the skin and provide a way for pathogens to enter and infect the skin and underlying tissues. For example, Staphylococcus aureus can enter a surgical wound and then invade the bloodstream; sandfly bites can introduce Leishmania species, the cause of leishmaniasis cases seen in Americans returning from Afghanistan, Iraq, and Kuwait (more can be learned about this disease at the Online Learning Center, www.mhhe.com/nester6). Skin infections also occur when microorganisms or viruses are carried to the skin by the bloodstream after entering the body from another site, such as the respiratory or gastrointestinal systems. ■ pediculosis, p. 296 ■ scabies, p. 297

23.1 Anatomy and Physiology Focus Points Explain why the skin is more than a wrapping for the body. Describe the importance of skin glands in health and disease.

The skin is far more than an inert wrapping for the body. Control of body temperature and prevention of loss of fluid from body tissues are among its vitally important functions. It also plays an important role in the synthesis of vitamin D, which is needed for development of normal teeth and bones. Numerous sensory receptors of various types occur in the skin, providing the central nervous system with information about the environment. The skin also produces cytokines that aid the development and function of 531

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KEY TERMS

Skin Infections Exanthem A skin rash, such as measles. Exfoliatin A bacterial toxin that causes sloughing of the outer epidermis.

Abscess A localized collection of pus within a tissue. Carbuncle Painful infection of the skin and subcutaneous tissues; manifests as a cluster of boils. Epidermis The outermost layer of skin.

yellow crusts; caused by Staphylococcus aureus and Streptococcus pyogenes.

Folliculitis Inflammation of a hair follicle.

Pyoderma Any skin disease characterized by production of pus.

Furuncle A boil; a localized skin infection that penetrates into subcutaneous tissue.

Sebaceous Gland Skin glands that produce an oily substance called sebum.

Impetigo A superficial skin infection characterized by thin-walled vesicles, weeping of plasma, and

immunity. In addition, collections of lymphocytes are found in skin-associated lymphoid tissues. Because of its exposed location, the temperature of the skin is generally lower than that of the rest of the body. ■ cytokines, p. 353 ■ skin-associated lymphoid tissue, p. 370 The skin is composed of two main layers—the epidermis and the dermis (figure 23.1). The epidermis, the surface layer,

is stratified squamous epithelium and ranges from 0.007 to 0.12 mm thick (see figure 15.1). The outer portion is composed of scaly material made up of flat cells containing keratin, a durable protein also found in hair and nails. The cells on the skin surface are dead and, along with any resident organisms, continually peel off, replaced by cells from deeper in the epidermis. These cells, in

FIGURE 23.1 Microscopic Anatomy of the Skin Notice that the sebaceous unit, composed of the hair follicle and the attached sebaceous gland, almost reaches the subcutaneous tissue.

Staphylococci Diphtheroids (propionibacteria)

Malassezia (yeast)

Sebum Hair follicle

Hair

Opening of sweat gland Epidermis Nerve Lymphatic vessel Dermis

Sebaceous gland Arrector muscle

Sensory ending Subcutaneous tissue

Sweat gland Nerve Junction of dermis and subcutaneous tissues Blood vessels Fat

Muscle

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23.2 Normal Microbiota of the Skin

turn, become flattened and die as keratin is formed within them. This process results in a complete regeneration of the skin about once a month. Dandruff represents excessive shedding of skin cells, but mostly the shedding process is unnoticed and represents one of the skin’s defenses against infection. The epidermis is supported by the dermis, a deeper layer of skin cells through which many tiny nerves, blood vessels, and lymphatic vessels penetrate. The dermis adheres in a very irregular fashion to the fat and other cells that make up the subcutaneous tissue (see figure 23.1). Fine tubules of sweat glands and hair follicles traverse the dermis and epidermis (see figure 23.1). Since sweat is a salty solution, high concentrations of salt occur as it evaporates. Evaporation of sweat and regulation of the amount of blood flow through the skin’s blood vessels are critically important in controlling body temperature. Sebaceous glands produce an oily secretion called sebum that feeds into the hair follicles. This secretion flows up through the follicles and spreads out over the skin surface, keeping the hair and skin soft, pliable, and water-repellent. The hair follicles provide passage for certain salt-tolerant bacteria to penetrate the skin and reach deeper tissues. The secretions of the sweat and sebaceous glands are essential to the normal microbial population of the skin because they supply water, amino acids, and lipids, which serve as nutrients for microbial growth. Breakdown of the lipids by the microbial residents of normal skin results in fatty-acid by-products that inhibit the growth of many potential disease-producers. The normal acidity of the skin (pH 4.0–6.8) also inhibits some microorganisms. In fact, the normal skin surface is an unfriendly habitat for most potential pathogens, being too dry, salty, unstable because of shedding, acidic, and toxic for their survival.

533

TABLE 23.1 Principal Members of the Normal Skin Microbiota Name

Characteristics

Diphtheroids

Variably shaped, non-motile, Gram-positive rods of the Corynebacterium and Propionibacterium genera

Staphylococci

Gram-positive cocci arranged in packets or clusters; coagulase negative; facultatively anaerobic

Fungi

Small yeasts of the genus Malassezia that require oily substances for growth

and amount of skin moisture, the number of bacteria on the skin surface may range from only about 1,000 organisms per square centimeter on the back to more than 10 million in the groin and armpit, where moisture is more plentiful. The numbers actually increase after a hot shower because of increased flow from the skin glands where many bacteria reside. Most of the microbial skin inhabitants can be categorized in three groups: diphtheroids, staphylococci, and yeasts (table 23.1; see figure 23.1). Although generally harmless, skin organisms are opportunistic pathogens that can only cause disease in people with impaired body defenses. AIDS patients and others with impaired immunity are especially vulnerable. ■ normal microbiota, p. 393 ■ oportunistic pathogens, p. 394

Diphtheroids Diphtheroids are a group of Gram-positive, pleomorphic bacteria named for the fact that their microscopic appearance resembles

MICROCHECK 23.1 The skin is a large, complex organ that covers the external surface of the body. Properties of the skin cause it to resist colonization by most microbial pathogens, pose a physical barrier to infection, provide sensory input from the environment, and assist the body’s regulation of temperature and fluid balance. ✓ Give three routes by which microorganisms invade the skin. ✓ Give four characteristics of skin that help it resist infection. ✓ Would a person living in the tropics or in the desert have larger numbers of bacteria living on the surface of their skin?

23.2 Normal Microbiota of the Skin Focus Points Describe the role of normal skin microbiota in health and disease. Outline the pathogenesis of acne.

The skin represents a distinct ecological habitat, analogous to a cool desert, compared to the warm, moist tropical conditions that exist in other body systems. Depending on the body location

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By permission of John Deering and Creators Syndicate, Inc.

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the bacterium that causes diphtheria, Corynebacterium diphtheriae. Diphtheroids are responsible for body odor, caused by their breakdown of substances in sweat, which is odorless when it is first secreted. A diphtheroid found on the skin in large numbers is Propionibacterium acnes, which is present on virtually all humans. This bacterium grows primarily within the hair follicles, where conditions are anaerobic. Growth of P. acnes is enhanced by the oily secretion of the sebaceous glands, and the organisms are usually present in large numbers only in areas of the skin where these glands are especially large and numerous—on the face, upper chest, and back. These are also the areas of the skin where acne most commonly develops, and the association of P. acnes with acne inspired its name, even though most people who carry the organisms do not have acne. ■ aerotolerance, p. 92

Important functions of the skin’s staphylococci are to prevent colonization by pathogens and to maintain a balance among the microbial inhabitants of the skin ecosystem. These Gram-positive cocci compete for nutrients with other potential skin colonizers, and they also produce antimicrobial substances highly active against P. acnes and other Gram-positive bacteria.

Fungi Tiny lipophilic, meaning oil-requiring, yeasts almost universally inhabit the normal human skin from late childhood onward. Their shape varies with different strains, being round, oval, or sometimes short rods. These yeasts can be cultivated on laboratory media containing fatty substances such as olive oil. They belong to the genus Malassezia and are generally harmless. In some people, however, they cause skin conditions such as a scaly face rash, dandruff, or tinea versicolor (figure 23.2). The latter is a common skin disease characterized by patchy scaliness and increased pigment in light-skin persons, or a decrease in pigment in dark-skin people. Scrapings of the affected skin show large numbers of Malassezia furfur both in its yeast form and as

■ Corynebacterium, p. 262

Acne in its most common form begins at puberty in association with a rise in sex hormones, enlargement of the sebaceous glands, and enhanced secretion of sebum. The hair follicle epithelium thickens and sloughs off in clumps, causing increasing obstruction to the flow of sebum to the skin surface. Continued sebum production by the gland can force a plug of material to the surface, where it is visible as a blackhead. With complete obstruction the follicle becomes distended with sebum, which causes the epidermis to bulge outward, producing a whitish lesion called a whitehead. The P. acnes that normally reside in the gland multiply to enormous numbers in the trapped sebum. Lipases of the bacteria degrade the sebum, releasing fatty acids and glycerol, a growth requirement of the organisms. The metabolic products of the bacteria cause an inflammatory response, attracting leukocytes (white blood cells) whose enzymes damage the wall of the distended follicle. The inflammatory process can cause the follicle to rupture, releasing the follicle contents into the surrounding tissue. The result is an abscess—a collection of white blood cells, bacteria, and cellular debris, that eventually heals and leaves a scar. Squeezing acne lesions is ill-advised, because it promotes rupture of the inflamed follicles and there- (a) fore more acne scars. Usually acne can be controlled until it goes away by itself, by using medications such as antibiotics and benzoyl peroxide that inhibit the growth of P. acnes, or by those such as azelaic acid (Azelex) and isotretinoin (Accutane) that act primarily to reverse the hair follicle abnormalities. The latter medication is reserved for the most serious cases of acne because it has potentially serious side effects. ■

(b)

inflammation, p. 360 ■ leukocytes, p. 350

Staphylococci The second group of microorganisms universally present on the normal skin is composed of members of the genus Staphylococcus. They are salt-tolerant organisms that grow well on the salty skin surface. As with the diphtheroids, most of these bacteria have little virulence, although they can cause serious disease if host defenses are breached. Generally, staphylococci are the most common of the skin bacteria able to grow aerobically. The principal species is Staphylococcus epidermidis. ■ Staphylococcus, p. 270

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(c)

FIGURE 23.2 Tinea Versicolor Appearance in (a) a fair-skin individual and (b) a dark-skin individual. (c) Microscopic appearance of skin scraping showing Malassezia furfur yeast and filamentous forms.

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23.3

short filaments called pseudohyphae. Unknown factors, probably relating to the host, are important in these diseases because most people carry the organism on their skin without any disease. AIDS patients often have a severe rash with pus-filled pimples caused by Malassezia yeasts, and the organisms may even infect internal organs in patients receiving lipid-containing intravenous feedings. ■ yeasts, p. 289

MICROCHECK 23.2 The normal skin microbiota are important because they help protect against colonization by pathogens. Occasionally, they cause disease when body defenses are impaired. They are responsible for body odor, and probably contribute to acne. ✓ Name and describe the three groups of organisms generally present on normal skin. ✓ Under what circumstances is Malassezia furfur most likely to be pathogenic? ✓ Would frequent showering tend to increase or decrease the numbers of Staphylococcus on the surface of the skin? Why?

23.3 Bacterial Skin Diseases Focus Points Name and give a distinctive characteristic of five bacterial skin diseases. Give three mechanisms of pathogenesis seen in bacterial skin diseases.

Only a few species of bacteria commonly invade the intact skin directly, which is not surprising in view of the anatomical and physiological features discussed earlier. Hair follicle infections exemplify direct invasion.

Bacterial Skin Diseases

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Causative Agent Most furuncles and carbuncles, as well as many cases of folliculitis, are caused by Staphylococcus aureus. It is much more virulent than the staphylococci normally found on the skin. The name derives from staphyle, “a bunch of grapes,” referring to the arrangement of the bacteria as seen on stained smears, and aureus, “golden,” referring to the typical color of the S. aureus colonies. This bacterium is an extremely important pathogen and is mentioned frequently throughout this text as the cause of a number of medical conditions (table 23.2). One of the most useful identifying characteristics of S. aureus is that it produces coagulase. Despite its ase ending, coagulase is not an enzyme. This protein product of S. aureus is largely extracellular, meaning it is released from the bacterium. It reacts with a substance in blood called prothrombin. The resulting complex, called staphylothrombin, causes blood to clot by converting fibrinogen to fibrin. Some coagulase is tightly bound to the surface of the bacteria and coats their surface with fibrin upon contact with blood. Fibrin-coated staphylococci resist phagocytosis. Generally, S. aureus also possesses clumping factor, often called “slide coagulase,” because it causes a suspension of the bacteria to clump together when mixed with a drop of blood plasma on a microscope slide. Like coagulase, it is a useful identifying characteristic of S. aureus. The clumping is caused by a cell-fixed protein that attaches specifically to fibrinogen in the plasma. Clumping factor protein is a virulence factor for S. aureus because it attaches to fibrinogen and fibrin present in wounds, thus aiding colonization of wound surfaces. Plastic devices, such as intravenous catheters and heart valves, become coated with fibrinogen shortly after insertion, thus making them, too, a target for colonization. The gene for clumping factor is distinct from the one controlling coagulase. Other virulence factors possessed by S. aureus that aid colonization of wounds include binding proteins for fibronectin, fibrin, fibrinogen, and collagen. Most strains of S. aureus also produce a-toxin, a membrane-damaging toxin that kills cells by attaching to specific receptors

Hair Follicle Infections Infections originating in hair follicles commonly clear up without treatment. In some instances, however, they progress into severe or even life-threatening disease.

TABLE 23.2 Some Diseases Often Caused by Staphylococcus aureus

Symptoms

Disease

Page for More Information

Carbuncles

p. 535

Endocarditis

p. 677

Folliculitis

p. 535

Food poisoning

p. 762

Furuncles

p. 535

Impetigo

p. 538

Osteomyelitis (bone infection)

p. 682

Scalded skin syndrome

p. 537

Toxic shock syndrome

p. 626

Wound infections

p. 562

Folliculitis, furuncles, and carbuncles represent different outcomes of hair follicle infections. In folliculitis, a small red bump, or pimple, develops at the site of the involved hair follicle. Often, the hair can be pulled from its follicle, accompanied by a small amount of pus, and then the infection goes away without further treatment. If, however, the infection extends from the follicle to adjacent tissues, causing localized redness, swelling, severe tenderness, and pain, the lesion is called a furuncle or boil. Pus may drain from the boil along with a plug of inflammatory cells and dead tissue. A carbuncle is a large area of redness, swelling, and pain punctuated by several sites of draining pus. Carbuncles usually develop in areas of the body where the skin is thick, such as the back of the neck. Fever is often present, along with other signs of a serious infection.

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The properties of S. aureus that probably contribute to its virulence are shown in table 23.3. Virtually all strains possess an unusual cell wall component called protein A. This protein, is an Fc receptor that prevents antibody from attaching to Fc receptors on phagocytes (see figure 17.11). Thus, a major effect of protein A is to interfere with phagocytosis. Many strains of S. aureus growing in body tissues synthesize a polysaccharide capsule that also inhibits phagocytosis. The S. aureus genes responsible for capsule formation are activated following invasion of tissue. S. aureus also produces numerous extracellular products that might contribute to virulence. These products include leukocidins, which kill white blood cells; hyaluronidase, which degrades hyaluronic acid, a component of host tissue that helps hold the cells together; proteases, which degrade various host proteins including collagen, the white fibrous protein found in skin, tendons, and connective tissue; and lipases, which degrade lipids. Lipases may assist colonization of the oily hair follicles by strains of S. aureus that cause follicle infections. ■ protein A, p. 402 ■ Fc receptors, p. 373

on host cell membranes and making holes in them. A relatively small percentage of S. aureus strains produce one or more additional toxins. ■ IgG, p. 374 ■ Fc region, p. 371 ■ membrane-damaging toxin, p. 405

Pathogenesis Infection begins when Staphylococcus aureus attaches to the cells of a hair follicle, multiplies, and spreads inward to involve the follicle and sebaceous glands. The infection induces an inflammatory response with swelling and redness, followed by attraction and accumulation of polymorphonuclear leukocytes. If the infection continues, the follicle becomes a plug of inflammatory cells and necrotic tissue overlying a small abscess (figure 23.3). The infectious process spreads deeper, reaching the subcutaneous tissue where a large abscess forms. This subcutaneous abscess is responsible for the painful localized swelling that constitutes the boil. Without effective treatment, pressure within the abscess increases, causing it to expand to other hair follicles, causing a carbuncle. If organisms enter the bloodstream, the infection can spread to other parts of the body, such as the heart, bones, or brain. ■ abscess, p. 560

Staphylococcus aureus infects hair follicle.

Hair

Epidermis

Sebaceous gland

Dermis

White blood cell Blood vessel

Subcutaneous tissue

Plug of necrotic material

Infection spreads to subcutaneous tissue.

Abscess

Accumulation of white blood cells

FIGURE 23.3 Pathogenesis of a Boil (Furuncle) Staphylococcus aureus infects a hair follicle through its opening on the skin surface. The infection produces a plug of necrotic material, a small abscess in the dermis, and, finally, a larger abscess in the subcutaneous tissue.

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Properties of Staphylococcus aureus TABLE 23.3 Implicated in Its Virulence Product

Effect

Capsule

Inhibits phagocytosis

Clumping factor

Attaches the bacterium to fibrin, fibrinogen, plastic devices

Coagulase

May impede progress of leukocytes into infected area by producing clots in the surrounding capillaries

Enterotoxins

Superantigens cause food poisoning if ingested, cause toxic shock if systemic

Exfoliatin

Separates layers of epidermis, causing scalded skin syndrome

Fibronectinbinding protein

Attaches bacterium to acellular tissue substances endothelium, epithelium, clots, indwelling plastic devices

Hyaluronidase

Breaks down hyaluronic acid component of tissue, thereby promoting extension of infection

Leukocidin

Kills neutrophils or causes them to release their enzymes

Lipase

Breaks down fats by hydrolyzing the bond between glycerol and fatty acids

Proteases

Degrade collagen and other tissue proteins

Protein A

Binds to Fc portion of antibody; coats bacteria with host’s immunoglobulin thereby inhibiting phagocytosis

Toxic shock syndrome toxin

Causes rash, diarrhea, and shock

a-toxin

Makes holes in host cell membranes.

Epidemiology Staphylococcus aureus inhabits the nostrils of virtually everyone at one time or another, each nostril containing as many as 108 bacteria. About 20% of healthy adults have continually positive nasal cultures for a year or more, while over 60% will be colonized at some time during a given year. The organisms are mainly disseminated to other parts of the body and to the environment by the hands. Although the nostrils seem to be the preferred habitat of S. aureus, moist areas of skin are also frequently colonized. People with boils and other staphylococcal infections shed large numbers of S. aureus and should not work with food, or near patients with surgical wounds or chronic illnesses. Staphylococci survive well in the environment, which favors their transmission from one host to another. Since S. aureus is so commonplace and there are many different strains in the population, epidemics of staphylococcal disease can generally be traced to their sources only by precise identification of the epidemic strain. Techniques for characterizing strains of S. aureus include determining the antibiogram, phage typing, and genome typing (see section 10.4). ■ characterizing strain differences, p. 243

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Prevention and Treatment Prevention of staphylococcal skin disease is very difficult. Attempts are made to eliminate the carrier state by applying an antistaphylococcal cream to the nostrils, and using soaps containing an antistaphylococcal agent such as hexachlorophene to bathe the skin. Effective treatment of boils and carbuncles often requires that the pus be surgically drained from the lesion and an antistaphylococcal medicine be given. Treatment of staphylococcal infections is complicated because so many strains of S. aureus are resistant to antibacterial medications. When penicillin was first introduced, more than 95% of S. aureus strains were susceptible to it. However, these strains soon largely disappeared with the widespread use of the antibiotic. Now, about 90% of S. aureus strains are resistant to penicillin because they produce a plasmid-encoded b-lactamase. Treatment became much easier with the development of penicillins and cephalosporins resistant to b-lactamase. Soon thereafter, however, strains of S. aureus, referred to as MRSAs, methicillin-resistant Staphylococcus aureus, appeared that were resistant because of modified penicillin-binding proteins. These strains were reliably treated with vancomycin until 1997, when the first vancomycin-resistant strain was identified. Because many MRSAs had R plasmids, making them resistant to most other antistaphylococcal medications, the appearance of vancomycin resistance was an alarming development. Beginning in 1999, several medications active against vancomycin-resistent bacteria were marketed. Quinupristin/dalfopristin (trade name Synercid) is a combination of two substances that act synergistically to block bacterial protein synthesis, and linezolid (trade name Zyvox), which represented a new class of antibacterials, the oxazolidinons, were followed by daptomycin (trade name Cubicin), a lipopeptide. Hopefully, development of new medications will keep pace with the growth of bacterial resistance, but this will depend on humans avoiding overuse of these valuable substances. ■ penicillin-binding proteins, p. 475 Most multiply-resistant S. aureus strains can be traced to hospitals and clinics, but more recently completely different strains have become widespread among healthy carriers in the community. Generally, these community MRSAs are resistant only to methicillin and related b-lactam antibiotics, and the macrolides, but they are highly virulent because they possess a cluster of genes that codes for a leukocyte-destroying leukocidin. In an effort to control the spread of MRSAs, many hospitals are screening patients at admission. If they carry MRSAs, they are isolated and given appropriate antibacterial treatment to limit spread of the strain to other patients or staff. Some hospitals also screen patients for MRSAs, at discharge from the hospital to make sure they don’t take a strain home with them. ■ penicillins and other b-lactam antibiotics, p. 475

Scalded Skin Syndrome Staphylococcal scalded skin syndrome (SSSS), is a potentially fatal toxin-mediated disease that occurs mainly in infants.

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damaged by an earlier infection. Mortality can range up to 40%, depending on how promptly the disease is diagnosed and treated, and the patient’s age and general health. ■ Candida albicans, p. 626

Epidemiology The disease can appear in any age group but occurs most frequently in newborn infants. The elderly and immunocompromised individuals are also at increased risk. Transmission is generally from person-to-person. Staphylococcal scalded skin syndrome usually appears in isolated cases, although small epidemics in nurseries sometimes occur.

Prevention and Treatment There are no preventive measures except to place patients suspected of having SSSS in protective isolation. These measures help to limit spread of the pathogen to others and help prevent secondary infection of the isolated patient. Initial therapy includes a bactericidal antibiotic such as methicillin. Dead skin is removed to help prevent secondary infection. Although scalded skin syndrome can be fatal, prompt therapy usually leads to full recovery. Table 23.4 describes the main features of this disease.

FIGURE 23.4 Staphylococcal Scalded Skin Syndrome (SSSS) A toxin called exfoliatin, produced by certain strains of Staphylococcus aureus, causes the outer layer of skin to separate.

Symptoms

Streptococcal Impetigo Impetigo is the most common type of pyoderma, a skin infection characterized by pus production (figure 23.5). Pyodermas can result from infection of an insect bite, burn, scrape, or other wound. Sometimes, the injury is so slight that it is not apparent.

As the name suggests, the skin appears to be scalded (figure 23.4). SSSS begins as a generalized redness of the skin affecting 20% to 100% of the body. Other symptoms, such as malaise—a vague feeling of discomfort and uneasiness—irritability, and fever are also present. The nose, mouth, and genitalia may be painful for one or more days before the typical features of the disease become apparent. Within 48 hours after the redness appears, the skin becomes wrinkled, and large blisters filled with clear fluid develop. The skin is tender to the touch and looks like sandpaper.

Symptoms

Causative Agent

TABLE 23.4 Staphylococcal Scalded Skin Syndrome

Scalded skin syndrome is caused by Staphylococcus aureus strains that produce a toxin called exfoliatin. Only about 5% of S. aureus strains produce this toxin, which destroys material that binds together the outer layers of epidermis. At least two kinds of exfoliatins exist: one is coded by a plasmid gene, and the other is chromosomal. ■ plasmids, p. 68

Symptoms

Causative agent

Strains of Staphylococcus aureus that produce exfoliatin toxin

Pathogenesis

Pathogenesis

Exfoliatin toxin is produced by staphylococci at an infection site, usually of the skin, and carried by the bloodstream to the epidermis, where it causes a split in a cellular layer; loss of body fluid and secondary infections contribute to mortality.

Epidemiology

Person-to-person transmission; seen mainly in infants, but can occur at any age.

Prevention and treatment

Isolation of the victim to protect from environmental potential pathogens; penicillinase–resistant penicillins; removal of dead tissue.

If an exfoliatin-producing strain of S. aureus is growing in a lesion, even one too small to be readily apparent, the toxin can be carried by the bloodstream to large areas of the skin. In the skin, it causes a split in the cellular layer of the epidermis just below the dead keratinized outer layer. Staphylococcus aureus is usually not present in the blister fluid. Because the outer layers of skin are lost as in a severe burn, there is marked loss of body fluid and danger of secondary infection with Gram-negative bacteria such as Pseudomonas sp., or with fungi such as Candida albicans. Secondary infection means invasion by a new organism of tissues

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Impetigo is a superficial skin infection, involving patches of epidermis just beneath the dead, scaly outer layer. Thin-walled blisters first develop, then break, and are replaced by yellowish crusts that form from the drying of plasma that weeps through the skin. Usually, little fever or pain develop, but lymph nodes near the involved areas often enlarge, indicating that bacterial products

Tender red rash with sandpaper texture, malaise, irritability, fever, large blisters, peeling of skin

Incubation period Variable, usually days

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Glomerulus Streptococcus pyogenes antigen Puffiness around the eyes (fluid retention)

Antibody Complement

Immune complex

Nephron Glomerulus

FIGURE 23.5 Impetigo This type of pyoderma is often caused by Streptococcus pyogenes and may result in glomerulonephritis. Symptoms and Signs Kidney

have entered the lymphatic system and an immune response is occurring. ■ plasma, p. 439

Bladder

• Fluid retention • Fever • High blood pressure

Causative Agent

• Blood and protein in urine

Although Staphylococcus aureus often causes impetigo, many cases, even epidemics, are due to Streptococcus pyogenes. These Gram-positive, chain-forming cocci are b-hemolytic (see figure 22.3) and are frequently referred to as group A streptococci because their cell walls contain a polysaccharide called group A carbohydrate. Like Staphylococcus aureus, Streptococcus pyogenes causes a variety of different diseases and is mentioned in numerous places throughout this text. The most detailed description is in chapter 22. ■ hemolysis, p. 97 ■ Streptococcus pyogenes, p. 499 Table 23.5 compares Staphylococcus aureus and Streptococcus pyogenes.

Pathogenesis Many different strains of Streptococcus pyogenes exist, some of which can colonize the skin. Infection is probably established by scratches or other minor injuries that introduce the bacteria into the deeper layer of epidermis. In impetigo, even though the infection is limited to the epidermis, streptococcal products are absorbed into the circulation. As with Staphylococcus aureus, a number of extracellular products may contribute to the virulence of Streptococcus pyogenes. These products include enzymes such as proteases, nucleases, and hyaluronidase. The enzymes probably contribute to streptococcal pathogenicity. None of them appear to be essential, however,

Swollen ankles (fluid retention)

FIGURE 23.6 Pathogenesis of Post-Streptococcal Acute Glomerulonephritis Immune complexes are deposited in the kidney glomeruli, inciting an inflammatory response.

because antibody against them fails to protect experimental animals. On the other hand, the surface components of S. pyogenes, notably a hyaluronic acid capsule and a cell wall component known as the M protein, are very important in enabling this organism to cause disease because they interfere with phagocytosis. ■ M protein, p. 402 Acute glomerulonephritis is a serious complication of S. pyogenes pyoderma due to the immune response to the organism. This condition may appear abruptly during convalescence from untreated S. pyogenes infections, with fever, fluid retention, high blood pressure, and blood and protein in the urine. Acute glomerulonephritis is caused by inflammation of structures within the kidneys, the glomeruli (singular: glomerulus), small tufts of tiny blood vessels, and the nephrons, responsible for the formation and composition of urine (figure 23.6). Only a few of the many S. pyogenes strains cause the

TABLE 23.5 Streptococcus pyogenes vs. Staphylococcus aureus Streptococcus pyogenes

Staphylococcus aureus

Characteristics

Gram-positive cocci in chains; b-hemolytic colonies; cell wall contains group A polysaccharide, an Fc receptor (protein G), and M protein

Gram-positive cocci in clusters; golden hemolytic colonies; cell wall contains an Fc receptor (protein A)

Extracellular Products

Hemolysins: streptolysins O and S; streptokinase, DNase, hyaluronidase, and others

Hemolysins, leukocidin, hyaluronidase, nuclease, protease, penicillinase, and others

Disease Potential

Causes impetigo, strep throat, wound infections, scarlet fever, puerperal fever, toxic shock, and flesh-eating fasciitis. Complications: glomerulonephritis, rheumatic fever, and neurological involvement

Causes boils, staphylococcal scalded skin syndrome, wound infections, abscesses, bone infections, impetigo, food poisoning, and staphylococcal toxic shock syndrome

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condition. Streptococci are absent from the urine and diseased kidney tissues. Indeed, the bacteria have generally been eliminated from the infection site in the skin by the immune response by the time symptoms of glomerulonephritis appear. Damage to the kidney is caused by immune complexes that settle in the glomeruli and provoke an inflammatory reaction. Both streptococcal skin and throat infections can sometimes cause acute glomerulonephritis. Rheumatic fever, a serious complication of strep throat, is not generally a complication of streptococcal pyoderma. ■ immune complexes, p. 420 ■ rheumatic fever, p. 501

Epidemiology Impetigo is most prevalent among poor children of the tropics or elsewhere during the hot, humid season. Children two to six years are mainly afflicted. Person-to-person contact spreads the disease, as do flies and other insects, and fomites—inanimate objects such as toys or towels. Impetigo patients often become throat and nasal carriers of S. pyogenes.

Prevention and Treatment General cleanliness and avoiding people with impetigo help prevent the disease. Prompt cleansing of wounds and application of antiseptic probably also decrease the chance of infection. So far, S. pyogenes strains remain susceptible to penicillin. In patients allergic to penicillin, erythromycin can be substituted. Table 23.6 summarizes the main features of impetigo.

Rocky Mountain Spotted Fever Rocky Mountain spotted fever was first recognized in the Rocky Mountain area of the United States—thus its name. The disease is representative of a group of serious rickettsial diseases that occur worldwide and are transmitted by certain species of ticks, mites, or lice.

Rocky Mountain spotted fever generally begins suddenly with a headache, pains in the muscles and joints, and fever. Within

TABLE 23.6 Impetigo Symptoms

Blisters that break and “weep” plasma and pus; formation of golden-colored crusts; lymph node enlargement

Incubation period

2 to 5 days

Causative organisms

Streptococcus pyogenes, Staphylococcus aureus

Pathogenesis

Initiated by organisms entering the skin through minor breaks; certain strains of S. pyogenes that are prone to cause impetigo can cause glomerulonephritis.

Prevention and treatment

nes95432_Ch23_531-558.indd 540

a few days, a rash consisting of faint pink spots appears on the palms, wrists, ankles, and soles. This rash spreads up the arms and legs to the rest of the body and becomes raised and hemorrhagic (figure 23.7), meaning that it is due to blood leaking from damaged blood vessels. Bleeding may occur at various other sites, such as the mouth and nose. Involvement of the heart, kidneys, and other body tissues can result in drop in blood pressure with shock and death unless treatment is given promptly.

Causative Agent

Symptoms

Epidemiology

FIGURE 23.7 Rash Caused by Rocky Mountain Spotted Fever Characteristically, the rash begins on the arms and legs, spreads centrally, and as shown in this photo, becomes hemorrhagic.

Spread by direct contact with carriers or patients with impetigo, insects, and fomites. Cleanliness; care of skin injuries. An oral penicillin if cause is known to be S. pyogenes; otherwise, an antistaphylococcal antibiotic orally or topically.

Rocky Mountain spotted fever is caused by Rickettsia rickettsii (figure 23.8), an obligate intracellular bacterium. The organisms are tiny, Gram-negative, non-motile coccobacilli. Rickettsia rickettsii can sometimes be identified early in an infection by demonstrating the organisms in biopsies—bits of tissue removed Rodent cell

Rodent cell nucleus

Rickettsias

10 µm

FIGURE 23.8 The Obligate Intracellular Bacterium Rickettsia rickettsii Growing Within a Rodent Cell

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541

FIGURE 23.9 Rocky Mountain Spotted Fever Number of reported cases, by county— United States, 2005. (Source: Centers for Disease Control and Prevention. MMWR 54(53):2–92, March 30, 2007.)

0 1–14 average cases ≥15

surgically—of skin lesions. Also, their DNA can be amplified by the polymerase chain reaction (PCR) and identified with a probe. ■ the genus Rickettsia, p. 274 ■ PCR, p. 223 ■ probe, p. 227

Pathogenesis Rocky Mountain spotted fever is acquired from the bite of a tick infected with R. rickettsii. The bite is usually painless and unnoticed; the tick remains attached for hours while it feeds on capillary blood. Rickettsias are not immediately released into tick saliva from the tick’s salivary glands. Therefore, the infection is not usually transmitted until the tick has fed for 4 to 10 hours. When the bacteria are released into capillary blood with the tick saliva, they are taken up preferentially by the cells lining the small blood vessels. Following attachment to host cells, R. rickettsii is taken into the cells by endocytosis. Inside the cell, the bacteria leave their phagosome and multiply in both the cytoplasm and nucleus without being enclosed in vacuoles. Early in the infection the bacteria enter and then lyse fingerlike host cell cytoplasmic projections. Eventually, the cell membrane is so damaged by this process, the cell takes in water, lyses, and releases the remaining rickettsias. These seed the blood-stream, infecting even more cells. Infection can also extend into the walls of the small blood vessels, causing an inflammatory reaction, clotting of the blood vessels, and small areas of necrosis, or death of tissue. This process is readily apparent in the skin as a hemorrhagic rash but, more ominously, occurs throughout the body, resulting in damage to vital organs such as the kidneys and heart. Potentially even more serious is the release of endotoxin into the bloodstream from the rickettsial cell walls, causing shock and generalized bleeding because of disseminated intravascular coagulation. ■ endotoxin,

Mexico, and a few countries of South America. The involved areas change over time, but despite the name of the disease, in the United States the highest incidence has generally been in the south Atlantic and south-central states (figure 23.9). Rocky Mountain spotted fever is a zoonotic disease maintained in nature in various species of ticks and mammals. Generally, little or no illness develops in these natural hosts, but humans, being an accidental host, often develop severe disease. Several species of ticks transmit the disease to humans. The main vector in the western United States is the wood tick, Dermacentor andersoni (figure 23.10), while in the East it is the dog tick, Dermacentor variabilis. Once infected, ticks remain infected for life, transmitting R. rickettsii from one generation to the next through their eggs. Ticks are most active from April to September, and it is during this time period that most cases of Rocky Mountain spotted fever occur. ■ zoonotic disease, p. 453

pp. 61, 407 ■ disseminated intravascular coagulation, p. 679

Epidemiology Rocky Mountain spotted fever occurs in a spotty distribution across the contiguous United States and extends into Canada,

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FIGURE 23.10 Dermacentor andersoni, the Wood Tick The wood tick is the principal vector of Rocky Mountain spotted fever in the western United States.

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Prevention and Treatment No vaccine against Rocky Mountain spotted fever is currently available to the public. The disease can be prevented if people take the following precautions: (1) avoid tick-infested areas when possible; (2) use protective clothing; (3) use tick repellents such as dimethyltoluamide; (4) carefully inspect their bodies, especially the scalp, armpits, and groin, for ticks several times daily; and (5) remove attached ticks carefully to avoid crushing them and thereby contaminating the bite wound with their infected tissue fluids. Gentle traction with blunt tweezers applied at the mouthparts is the safest method of removal. Touching the tick with a hot object, gasoline, or whiskey is ineffectual. After removing the tick, the site of the bite should be treated with an antiseptic. The antibiotics doxycycline and chloramphenicol are highly effective in treating Rocky Mountain spotted fever if given early in the disease, before irreversible damage to vital organs has occurred. Without treatment, the overall mortality from the disease is about 20%, but it can be considerably higher in elderly patients. With early diagnosis and treatment, the mortality rate is less than 5%. The main features of Rocky Mountain spotted fever are summarized in table 23.7.

Lyme Disease In the mid-1970s, studies of a group of cases in Lyme, Connecticut, led to the recognition of Lyme disease as a distinct entity. It was not until 1982 that the causative agent was first identified in ticks from New York State by Dr. Willy Burgdorfer at the Rocky Mountain Laboratories in Hamilton, Montana. We now know that Lyme disease was present in many areas of the world long before its recognition at Lyme. The ecology of the disease is complex and still incompletely understood, but we are beginning to get some answers as to why the disease has increased and extended its range. About 20,000 new cases occur

TABLE 23.7 Rocky Mountain Spotted Fever Symptoms

Headache, pains in muscles and joints, and fever, followed by a hemorrhagic rash that begins on the extremities

Incubation period

4 to 8 days

Causative organism

Rickettsia rickettsii, an obligate intracellular bacterium

Pathogenesis

Organisms multiply at site of tick bite; the bloodstream is invaded and endothelial cells of blood vessels are infected; vascular lesions and endotoxin account for pathologic changes.

Epidemiology

A zoonosis transmitted by bite of infected tick, usually Dermacentor sp.

Prevention and treatment

Avoidance of tick-infested areas, use of tick repellent, removal of ticks within 4 hours of exposure. Treatment: doxycycline or chloramphenicol.

nes95432_Ch23_531-558.indd 542

each year, making it the most common vector-borne disease in the United States.

Symptoms Symptoms of Lyme disease can be divided roughly into three stages, although individual patients may lack symptoms in one or more of the three. The first stage typically begins a few days to several weeks after a bite by an infected tick. It is characterized by a skin rash called erythema migrans (figure 23.11) and enlargement of nearby lymph nodes. The rash begins as a red spot or bump at the site of the tick bite and slowly enlarges to a median diameter of 15 cm (about 6 inches). The advancing edge is bright red, leaving behind an area of fading redness as the lesion enlarges. About half of these cases develop smaller satellite lesions that behave similarly. The characteristic rash is the hallmark of Lyme disease but is present in only twothirds of the cases. Most of the other symptoms that occur during this stage are influenza-like—malaise, chills, fever, headache, stiff neck, joint and muscle pains, and backache. Symptoms of the second stage generally begin 2 to 8 weeks after the appearance of erythema migrans and involve the heart and the nervous system. Electrical conduction within the heart is impaired, leading to dizzy spells or fainting, and a temporary pacemaker is sometimes required to maintain a normal heartbeat. Involvement of the nervous system can cause one or more of the following symptoms: paralysis of the face, severe headache, pain when moving the eyes, difficulty concentrating, emotional instability, fatigue, and impairment of the nerves of the legs or arms. The symptoms of the third stage are characterized by arthritis, manifest as joint pain, swelling, and tenderness, usually of a large joint such as the knee. These symptoms develop in 60% of untreated cases, beginning on the average 6 months after FIGURE 23.11 Erythema Migrans, the Characteristic Rash of Lyme Disease The rash usually has a targetlike or bull’s-eye appearance. It generally causes little or no discomfort. While highly suggestive of Lyme disease, many victims of the disease fail to develop the rash.

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widely differing species as mice, lizards, and ticks. ■ spirochetes, p. 269 ■ microaerophilic conditions, p. 98 ■ axial filaments, p. 269

Pathogenesis

10 µm

FIGURE 23.12 Scanning Electron Micrograph of Borrelia burgdorferi, the Cause of Lyme Disease

the skin rash, and slowly disappear over subsequent years. Chronic nervous system impairments such as localized pain, paralysis, and depression can occur.

The spirochetes are introduced into the skin by an infected tick, multiply, and migrate outward in a radial fashion. Their Gram-negative cell walls cause an inflammatory reaction in the skin, which produces the expanding rash. The host’s immune response is initially suppressed, allowing continued multiplication of the spirochete. The organisms then enter the bloodstream and become disseminated to all parts of the body but generally do not cross the placenta of pregnant women. Wide dissemination of the organisms accounts for the influenza-like symptoms of the first stage. After the first few weeks, an intense immune response occurs, and thereafter, it becomes very difficult to recover B. burgdorferi from blood or body tissues. The immune response against the bacterial antigens is probably responsible for the symptoms of the second stage. The third stage of Lyme disease is characterized by arthritis, and the affected joints have high concentrations of reactive immune cells and immune complexes. The joint and chronic nervous system symptoms of the third stage probably result from immune responses against persisting bacterial antigens, but evidence suggests a role for autoimmunity in some cases.

Causative Agent Lyme disease is caused by Borrelia burgdorferi, a large, microaerophilic spirochete (figure 23.12), 11 to 25 mm in length, with a number of axial filaments wrapped around its body and enclosed in the outer sheath of the cell wall. Surprisingly, the Borrelia chromosome is linear and present in multiple copies, completely unlike E. coli and most other prokaryotes, which have a single copy of a circular chromosome. The organism also contains numerous different plasmids both circular and linear, peculiar in that they contain genes usually found on bacterial chromosomes. These findings may lead to an understanding of how B. burgdorferi can infect such

Epidemiology Like Rocky Mountain spotted fever, Lyme disease is a zoonosis, and humans are accidental hosts. The disease is widespread in the United States (figure 23.13), and its incidence depends on complex ecological factors. Several species of ticks have been implicated as vectors, but the most important in the eastern United States is the black-legged (deer) tick, Ixodes scapularis (figure 23.14). In some areas of the East Coast, 80% of these ticks are infected with Borrelia burgdorferi. Because of their small size (1 to 2 mm before feeding; 3 to 5 mm when fully engorged with blood), these ticks FIGURE 23.13 Number of Reported Lyme Disease Cases–2005 (Source: Centers for Disease Control and Prevention. MMWR 54(53):2–92, March 30, 2007.)

0 1–14 average cases ≥15

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Female drops from host and lays uninfected eggs. Spring Eggs

Uninfected larvae hatch.

FIGURE 23.14 The Black-Legged (Deer) Tick, Ixodes scapularis, Adult and Nymph This tick is the most important vector of Lyme disease

Fall

Infected larvae become dormant.

in the eastern and north-central United States.

often feed and drop off their host without being detected, so that two-thirds of Lyme disease patients are unable to recall a tick bite. The ticks mature during a 2-year cycle (figure 23.15). A six-legged larval form emerges from the egg. After growing, it molts, shedding its outer covering to become an eight-legged form called a nymph. After another molt as the tick grows in size, the nymph becomes the sexually mature adult form. The nymph avidly seeks blood meals and is therefore mainly responsible for transmitting Lyme disease. The preferred host of I. scapularis is the white-footed mouse, which acquires Borrelia burgdorferi from an infected tick and develops a sustained bacteremia. The mouse thus becomes a source of infection for other ticks. Passage of the spirochete from adult tick to its offspring via its eggs rarely occurs. Infected ticks and mice constitute the main reservoir of B. burgdorferi, but deer, while not a significant reservoir, are important because they are the preferred host of the adult ticks and the site where mating occurs. Moreover, deer can quickly spread the disease over a wide area. Tick nymphs are the most active from May to September, corresponding to the peak occurrence of Lyme disease cases. Adult ticks sometimes bite humans late in the season and transmit the disease. Infectious ticks can be present in well-mowed lawns as well as in wooded areas. Expanding human populations continually intrude into the zoonotic life cycle. ■ bacteremia, p. 395 ■ reservoirs, p. 453

First year

Larvae feed on infected animal host and acquire Borrelia burgdorferi, the spirochete that causes Lyme disease.

Winter Infected larvae molt, becoming nymphs.

Infected nymphs feed, transmitting Borrelia burgdorferi.

Spring

Infected nymphs molt, becoming adults.

Summer

Second year

2 mm

Summer

Adults feed on animal (deer) host and mate. Fall

Prevention and Treatment General preventive measures for Lyme disease are the same as those for Rocky Mountain spotted fever. There is no available vaccine. Persons are advised to use every other means to avoid infection. Several antibiotics are effective in patients with early disease. In late disease, the response to treatment is less satisfactory, presumably because the spirochetes are not actively multiplying and antibacterial medications are usually ineffective against non-growing bacteria. Nevertheless, prolonged treatment with intravenous ampicillin or ceftriaxone has been curative in many cases. Table 23.8 summarizes some features of Lyme disease.

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Winter Female dormant; male dies.

FIGURE 23.15 Life Cycle of the Black-Legged (Deer) Tick, Ixodes scapularis, the Principal Vector of Borrelia burgdorferi, Cause of Lyme Disease Note that the life cycle covers 2 years, during which the tick obtains three blood meals. The males die soon after mating, the females after depositing their eggs in the following spring. Variations in the life cycle occur, probably dependent on climate and food availability for the natural hosts.

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TABLE 23.8 Lyme Disease ➀ Bite of tick infected with Borrelia

Symptoms

Stage 1: Enlarging, red rash at the site of the bite; fever, malaise, headache, general achiness, enlargement of lymph nodes near bite, joint pains. Stage 2: Acute involvement of heart and nervous system. Stage 3: Chronic arthritis and impairment of the nervous system.

Incubation period

Approximately 1 week

Causative agent

Borrelia burgdorferi, a spirochete

Pathogenesis

Spirochetes injected into the skin by an infected tick multiply and spread radially; the spirochetes enter the bloodstream and are carried throughout the body; the immune reaction to bacterial antigen causes tissue damage.

Epidemiology

Spread by the bite of ticks, Ixodes sp., usually found in association with animals such as white-footed mice and whitetailed deer living in wooded areas.

Prevention and treatment

Protective clothing; tick repellents. Early treatment with doxycycline and others; prolonged antibiotic therapy in chronic cases.

4

burgdorferi introduces the bacteria into the skin.

➁ B. burgdorferi reproduce and

spread radially in the skin, causing an expanding red rash which tends to clear centrally.

➂ The bacteria enter the bloodstream, cause fever, acute injury to the heart and nervous system.

3

➃ Chronic symptoms develop, such

as arthritis and paralysis due to persisting bacteria and the immune response to them.

4

➄ No person-to-person transmission. 1 2

MICROCHECK 23.3 Folliculitis, furuncles, and carbuncles are usually caused by Staphylococcus aureus. Some strains of S. aureus produce exfoliatin and can cause scalded skin syndrome. Impetigo is a kind of pyoderma that is often caused by Streptococcus pyogenes. Acute glomerulonephritis is a possible sequel to streptococcal pyoderma. Rocky Mountain spotted fever is caused by Rickettsia rickettsii and is transmitted by ticks. Lyme disease is caused by Borrelia burgdorferi and is also transmitted by ticks. It is the most common vectorborne disease in the United States. ✓ List four extracellular products of Staphylococcus aureus that contribute to its virulence. ✓ Describe the characteristic rash of Lyme disease. ✓ The existence of extensive scalded skin syndrome does not indicate that Staphylococcus is growing in all the affected areas. Why?

Several childhood diseases are characterized by distinctive skin rashes called exanthems. The viruses that cause these rashes initially infect the upper respiratory tract but are then carried to the skin by the blood. These diseases are usually diagnosed by inspection of the rash and other clinical findings. When the disease is not typical, however, tests can be performed to identify specific antibody against the virus, and the virus can often be cultivated from skin lesions, upper respiratory secretions, or other material.

Chickenpox (Varicella) Chickenpox is the popular name for varicella, a rash that was common in childhood before the introduction of varicella vaccine in 1995. The causative virus is a member of the herpesvirus family and, like others in that group, produces a latent infection that can reactivate long after recovery from the initial illness. ■ latent infections, p. 325

23.4 Skin Diseases Caused by Viruses Focus Points Name and give a distinctive characteristic of six viral skin diseases. Give three reasons why skin diseases controllable by vaccines have not yet been eradicated from the world.

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Symptoms Most cases of chickenpox are mild, sometimes unnoticed, and recovery is usually uncomplicated. The typical case has a rash that is diagnostic. It begins as small, red spots called macules, little bumps called papules, and small blisters called vesicles, surrounded by a narrow zone of redness. The lesions can erupt anywhere on the body, although usually they first appear on the back of the head, then the face, mouth, main body, and arms and legs, ranging from only a few lesions to many

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FIGURE 23.17 Shingles (Herpes Zoster) The rash mimics that of FIGURE 23.16 A Child with Chickenpox (Varicella) Characteristically, lesions in various stages of evolution—macules, papules, vesicles, and pustules—are present.

hundreds. The lesions appear at different times, and within a day or so they go through a characteristic evolution from macule to papule to vesicle to pustule, a pus-filled blister. After the pustules break, leaking virus-laden fluid, a crust forms, and then healing takes place. At any time during the rash, lesions are at various stages of evolution (figure 23.16). The lesions are pruritic, meaning itchy, and scratching may lead to serious, even fatal, secondary infection by Streptococcus pyogenes or Staphylococcus aureus. Symptoms of varicella tend to be more severe in older children and adults. In about 20% of adults, pneumonia develops, causing rapid breathing, cough, shortness of breath, and a dusky skin color. The pneumonia subsides with the rash, but respiratory symptoms often persist for weeks. Varicella is also a major threat to newborn babies if the mother develops the disease within 5 days before delivery to 2 days afterward. Mortality in these babies has been as high as 30%. Also, congenital varicella syndrome develops in a fraction of a percent of babies whose mothers contract varicella earlier in pregnancy. These babies are born with such defects as underdeveloped head and limbs, and cataracts. In addition, the disease is a threat to immunocompromised patients of any age. The virus can damage the lungs, heart, liver, kidneys, and brain, resulting in death in about 20% of the cases. Reactivation of chickenpox results in a disease called shingles, (herpes zoster). It can occur at any age but becomes increasingly common with advancing age. It begins with pain in the area supplied by a nerve of sensation, often on the chest or abdomen but sometimes on the face or an arm or leg. After a few days to 2 weeks, a rash characteristic of chickenpox appears, but unlike chickenpox the rash is usually restricted to an area

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chickenpox, except that it is limited to a sensory nerve distribution on one side of the body.

supplied by the branches of the involved sensory nerve (figure 23.17). The rash generally subsides within a week, but pain may persist for weeks, months, or longer. In people with AIDS or other serious immunodeficiency, instead of being confined to one area the rash often spreads to involve the entire body, as in a severe case of chickenpox. A curious, rare affliction known as Reye’s syndrome occasionally occurs in association with chickenpox and a number of other viral infections, usually within 2 to 12 days of the onset of the infection. The patients begin vomiting and slip into a coma. The syndrome occurs predominantly in children between 5 and 15 years old and is characterized by liver and brain damage and a death rate as high as 30%. Epidemiologic evidence suggesting that aspirin therapy increases the risk of Reye’s syndrome has led physicians to use this drug sparingly in children with fever.

Causative Agent Chickenpox is caused by the varicella-zoster virus, a member of the herpesvirus family. It is an enveloped, medium-sized (150 to 200 nm), double-stranded DNA virus, indistinguishable from other herpesviruses in appearance (figure 23.18).

Pathogenesis The virus enters the body by the respiratory route, establishes an infection, replicates, and disseminates to the skin via the blood-stream. After the living layers of skin cells are infected, the virus spreads directly to adjacent cells, and the characteristic skin lesions appear. Stained preparations of infected cells show intranuclear inclusion bodies where the virus reproduces, visible as pink

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until all the lesions have crusted (usually 4 days after the onset). ■ reservoir, p. 453

The mechanism by which the varicella-zoster virus persists in the body allows it to survive indefinitely in small, isolated populations. By contrast, when a virus such as measles is introduced into an isolated community, it spreads quickly and infects most of the susceptible individuals, who either become immune or die. If susceptible victims are unavailable, the measles virus will disappear from the community. On the other hand, varicella-zoster virus will reappear from cases of shingles whenever sufficient numbers of susceptible children have been born. Shingles occurs in about 1% of elderly people.

Prevention and Treatment 100 nm

FIGURE 23.18 Electron Micrograph of Varicella-Zoster Virus, Cause of Chickenpox and Shingles

staining bodies in the nucleus. Some infected cells fuse together, forming multinucleated giant cells. The infected cells swell and ultimately lyse. The virus enters the sensory nerves, presumably when an area of skin infection advances to involve a sensory nerve ending. Conditions inside the nerve cell do not permit full expression of the viral genome; however, viral DNA is present in the ganglia (singular: ganglion) of the nerves and is fully capable of coding for mature infectious virus. Ganglia are small bulges in sensory nerves located near the spine; they contain the nuclei and cell bodies of the nerves. The mechanism of suppression of viral replication within the nerve cell is not known but is probably under the control of immune cells. Shingles is most likely to occur when cellular immunity declines. With the decline, infectious varicella-zoster virus is presumably produced in the nucleus of the nerve cells and is carried to the skin by the normal circulation of cytoplasm within the nerve cell. With the appearance of the skin lesions, a prompt, intense secondary (memory) response of both cellular and humoral immunity ensues. A marked inflammatory reaction occurs in the ganglion with an accumulation of immune cells, and shingles quickly disappears, although sometimes leaving scars and chronic pain. ■ secondary response, p. 379

Epidemiology The annual incidence of chickenpox in the United States, once estimated at several million, is probably less than one-tenth that number now that immunization is widespread. Reporting the disease is not required, so most cases go unreported and many are so mild that they go unnoticed. Respiratory secretions and skin lesions are both infectious; as with many diseases transmitted by the respiratory route, most cases occur in the winter and spring months. Humans are the only reservoir, and the disease is highly contagious. The incubation period averages about 2 weeks, with a range of 10 to 21 days. Cases are infective from 1 to 2 days before the rash appears

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A safe attenuated chickenpox vaccine has been used in the United States since 1995. The vaccine is given routinely to all healthy children in a two-dose regimen, the first dose at 12 to 15 months of age and the second at 4 to 6 years. All healthy children and adults without a history of chickenpox are also advised to receive two doses of the vaccine. Likewise, asymptomatic, HIV-infected children and adults should receive the vaccine if their immune system is still intact. In general, the vaccine should not be administered to people with immunodeficiencies. Healthy, non-immune contacts of such people, however, should be vaccinated. ■ attenuated vaccines, p. 433

By preventing chickenpox, the vaccine markedly decreases the chance of developing shingles. Another vaccine is available to prevent shingles in individuals 60 years old or older. This vaccine is composed of the same attenuated virus used in the chickenpox vaccine, but in a much higher dose. It is given in a single dose and halves the risk of developing shingles. Increasing numbers of individuals with impaired immunity are at risk of severe disseminated varicella-zoster virus infections. These include persons with cancer, AIDS, and organ transplants and newborn babies whose mothers contracted chickenpox near the time of delivery. They can be partially protected from severe disease if they are passively immunized by injecting them with varicella zoster immune globulin (VZIG) derived from the blood of healthy individuals with a high titer of antibody to varicella-zoster virus. The antiviral medications acyclovir and famciclovir, among others, are helpful in preventing and treating varicella-zoster infections. ■ passive immunity, p. 432 The main features of chickenpox are summarized in table 23.9.

Measles (Rubeola) Measles, “hard measles,” and “red measles” are common names for rubeola. One of the great success stories of the last half of the twentieth century was the dramatic reduction in measles cases as a result of immunizing children with an attenuated vaccine against the disease. Now there is reason to hope that the disease can be entirely eliminated from the world by 2015.

Symptoms Measles begins with fever, runny nose, cough, and swollen, red, weepy eyes. Within a few days, a fine red rash appears on the

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TABLE 23.9 Chickenpox (Varicella) ➀ Varicella-zoster virus is inhaled;

Symptoms

infects nose and throat.

➁ The virus infects nearby lymph

nodes, reproduces, and seeds the bloodstream.

1 7

➂ Infection of other body cells occurs, resulting in showers of virions into the bloodstream.

➃ These virions cause successive

2

crops of skin lesions, which evolve into blisters and crusts.

Incubation period

10 to 21 days

Causative agent

Varicella-zoster virus; enveloped double-stranded DNA virus of the herpesvirus family.

Pathogenesis

Upper respiratory virus multiplication followed by dissemination via bloodstream to the skin; cytopathic effect of virus includes the formation of giant cells.

Epidemiology

Highly infectious. Acquired by the respiratory route; humans, both individuals with chickenpox and those with shingles, the only source; dissemination is from skin lesions and respiratory secretions.

Prevention and treatment

Attenuated vaccine. Passive immunization with zoster immune globulin (ZIG) for immunocompromised individuals; acyclovir or similar antiviral medication for prevention and treatment.

5

6

3

➄ Immune system eliminates the

infection except for some virions inside the nerve cells.

➅ If immunity wanes with age or other

4 7

reason, the virus persisting in the nerve ganglia can infect the skin, causing herpes zoster.

➆ Transmission to others occurs from respiratory secretions and skin.

forehead and spreads outward over the rest of the body (figure 23.19). Unless complications occur, symptoms generally disappear in about 1 week. Unfortunately, many cases are complicated by secondary infections caused mainly by Staphylococcus aureus, Streptococcus FIGURE 23.19 A Child with Measles (Rubeola) The rash is usually accompanied by fever, runny nose, and a bad cough.

Itchy bumps and blisters in various stages of development, fever; latent infections can become manifest as shingles (herpes zoster) years later.

pneumoniae, Streptococcus pyogenes, and Haemophilus influenzae. These opportunistic pathogens readily invade the body because measles damages the normal body defenses. Secondary infections most commonly cause earaches and pneumonia. In about 5% of cases, the rubeola virus itself causes pneumonia, with rapid breathing, shortness of breath, and dusky skin color from lack of adequate oxygen exchange in the lungs. Encephalitis, inflammatory disease of the brain, is another serious complication, marked by fever, headache, confusion, and seizures. This complication occurs in about one out of every 1,000 cases of measles. Permanent brain damage, with mental retardation, deafness, and epilepsy, commonly results from measles encephalitis. Very rarely, rubeola is followed 2 to 10 years later by a disease called subacute sclerosing panencephalitis (SSPE), which is marked by slowly progressive degeneration of the brain, generally resulting in death within 2 years. A defective measles virus can be detected in the brains of these patients, and high levels of measles antibody are present in their blood. This is an example of a “slow virus” disease. It has all but disappeared from the United States with widespread vaccination against measles. ■ slow virus infections, p. 331

Measles that occurs during pregnancy results in an increased risk of miscarriage, premature labor, and low birth weight. Birth defects, however, are generally not seen.

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23.4 Skin Diseases Caused by Viruses

Causative Agent Measles is caused by rubeola virus, a pleomorphic, mediumsized (120 to 200 nm diameter), enveloped, single-stranded RNA virus of the paramyxovirus family. The viral envelope has two biologically active projections. One, H, is responsible for viral attachment to host cells, and the other, M, is responsible for fusion of the viral outer membrane with the host cell. The M antigen also causes adjacent infected host cells to fuse together, producing multinucleated giant cells.

Pathogenesis Rubeola virus is acquired by the respiratory route. It replicates in the upper respiratory epithelium, spreads to lymphoid tissue, and following further replication, eventually spreads to all parts of the body. Mucous membrane involvement is responsible for an important diagnostic sign, Koplik spots (figure 23.20), which are usually best seen opposite the molars, located in the back part of the mouth. Koplik spots look like grains of salt lying on an oral mucosa that is red and rough, resembling red sandpaper. Damage to the respiratory mucous membranes partly explains the markedly increased susceptibility of measles patients to secondary bacterial infections, especially infection of the middle ear and lung. Involvement of the intestinal epithelium may explain the diarrhea that sometimes occurs in measles and contributes to high measles death rates in impoverished countries. In the United States, deaths from measles occur in about one to two of every 1,000 cases, mainly from pneumonia and encephalitis. The skin rash of measles results from the effect of rubeola virus replication in skin cells and the cellular immune response against the viral antigen in the skin. The measles virus temporarily suppresses cellular immunity, causing cold sores to appear and latent tuberculosis to activate. ■ cold sores, p. 592 ■ tuberculosis, p. 514

Epidemiology Humans are the only natural host of rubeola virus. Spread is by the respiratory route. Before vaccination became wide-

549

spread in the 1960s, probably less than 1% of the population escaped infection with this highly contagious virus. Continued use of measles vaccine resulted in a progressive decline in cases, so that endemic measles no longer occurs in the Western Hemisphere. Small outbreaks of the disease, however, continue to be seen as a result of introductions from other countries. These outbreaks occur due to the presence of non-immune populations including (1) children too young to be vaccinated; (2) preschool children never vaccinated; (3) children and adults inadequately vaccinated; and (4) persons not vaccinated for religious or medical reasons. Worldwide, about 750,000 children still die from measles, which ranks among the leading causes of death and disability among the impoverished, where the mortality rate may reach 15% and secondary infections may reach 85%. Measles vaccination was a high priority following the tsunami disaster of 2004.

Prevention and Treatment Measles can be prevented by injecting an attenuated rubeola virus vaccine. At present, less than 100 cases per year are generally reported. In 1980 the worldwide incidence of rubeola was estimated to be 100 million with 5.8 million deaths. Globally, vaccination programs have lowered the number of cases dramatically since then. The measles vaccine is usually given together with mumps, rubella and varicella vaccines (MMRV). The first injection of vaccine is given near an infant’s first birthday. Since 1989, a second injection of vaccine is given at entry into elementary school. The two-dose regimen has resulted in at least 99% of the recipients becoming immune. In an epidemic, vaccine is given to babies as young as 6 months, who are then reimmunized before their second birthday. Students entering high school or college are advised to get a second dose of vaccine if they have not received one earlier. Those at special risk of acquiring rubeola, such as medical personnel, should be immunized regardless of age, unless they definitely have had measles or have laboratory proof of immunity. No antiviral treatment exists for rubeola at present. Some features of rubeola are summarized in table 23.10.

German Measles (Rubella) Koplik spots

German measles and three-day measles are common names for rubella. The term German measles arose because the disease was first described in Germany. In contrast to varicella and rubeola, rubella is typically a mild, often unrecognized disease that is difficult to diagnose. Nevertheless, infection of pregnant women can have tragic consequences.

Symptoms

FIGURE 23.20 Koplik Spots, Characteristic of Measles (Rubeola), Are Usually Transitory They resemble grains of salt on a red base.

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Characteristic symptoms of German measles are slight fever, mild cold symptoms, and enlarged lymph nodes behind the ears and on the back of the neck. After about a day, a faint rash consisting of innumerable pink spots appears over the face, chest, and abdomen

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TABLE 23.10

CHAPTER TWENTY THREE

Skin Infections

Measles (Rubeola)

➀ Airborne rubeola virus infects eyes

Symptoms

4

5

and upper respiratory tract, then the lymph nodes in the region.

➁ Virus enters the bloodstream and

is carried to all parts of the body including the brain, lungs, and skin.

6

1

Incubation period

10 to 12 days

Causative agent

Rubeola virus, a single-stranded RNA virus of the paramyxovirus family

Pathogenesis

Virus multiplies in respiratory tract; spreads to lymphoid tissue, then to all parts of body, notably skin, lungs, and brain; damage to respiratory tract epithelium leads to secondary infection of ears and lungs.

Epidemiology

Acquired by respiratory route; highly contagious; humans only source.

Prevention and treatment

Attenuated virus vaccine after age 12 months; second dose upon entering elementary school or at adolescence. No antiviral treatment available at present.

7

➂ Skin cells infected with the rubeola

virus are attacked by immune T cells, causing a generalized rash.

➃ Virus replicating in the lungs can cause pneumonia; the brain can also be infected.

➄ In rare cases, virus persisting in the brain causes subacute sclerosing panencephalitis, months or years after the acute infection.

4 2 6

3

Rash, fever, weepy eyes, cough, and nasal discharge

➅ Secondary infection of the ears and lungs is common.

➆ Transmission is by respiratory secretions.

(figure 23.21). Unlike rubeola, there are no diagnostic mouth lesions. Adults commonly develop painful joints, with pain generally lasting 3 weeks or less. Other symptoms generally last only a few days. The significance of rubella, however, lies not with these symptoms but rather with rubella’s threat to the fetuses of pregnant women.

Causative Agent German measles is caused by the rubella virus—a member of the togavirus family. It is a small (about 60 nm in diameter), enveloped, single-stranded RNA virus that can readily be cultivated in cell cultures. Surface glycoproteins give the virus in vitro hemagglutinating ability, which is inhibited by specific antibody, allowing serological identification of the virus.

Pathogenesis

FIGURE 23.21 Adult with German Measles (Rubella) Symptoms are often very mild, but the effects on a fetus can be devastating.

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The rubella virus enters the body via the respiratory route. It multiplies in the nasopharynx and enters the bloodstream, causing a sustained viremia (meaning viruses circulating in the bloodstream). The blood transports the virus to various body tissues, including the skin and joints. Humoral and cellular immunity develop against the virus, and the resulting antibodyantigen complexes probably account for the rash and joint symptoms. ■ viremia, p. 395 In pregnant women, the placenta becomes infected during the period of viremia. Early in pregnancy, the virus readily crosses the placenta and infects the fetus, but as the pregnancy progresses, fetal infection becomes increasingly less likely. Virtually all types of fetal cells are susceptible to infection; some cells are killed, whereas others develop a persistent infection in which cell division is impaired and chromosomes are damaged. The result is a characteristic pattern of fetal abnormalities that is referred to as the congenital rubella syndrome. The abnormalities include cataracts and other abnormalities of the eyes, brain damage, deafness, heart defects, and low birth

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CASE PRESENTATION improved. Subsequently, however, his condition deteriorated, and he died of presumed complications of AIDS. 1. Is measles immunization a good idea for people with immunodeficiency? 2. Is it surprising that the vaccine virus was still present in this patient 11 months after vaccination? Explain. 3. Despite the severe infection, there was no rash. Why?

The patient was a 20-year-old asymptomatic man who was immunized against measles as a requirement for starting college. He had received his first dose of measles vaccine at approximately 1 year of age. Past medical history revealed that he was a hemophiliac and had contracted the human immunodeficiency virus from clotting factor (a blood product given to control bleeding) contaminated with the virus. Laboratory tests showed that he had a very low CD4; lymphocyte count, indicating a severely damaged immune system. About a month after his precollege immunization, he developed pneumocystosis, a lung infection characteristic of AIDS, was hospitalized, had a good response to treatment, and was discharged. Ten months later, he was again hospitalized for symptoms of a severe lung infection. He had no rash. Multiple laboratory tests to determine the cause of his infection were negative. Finally, a lung biopsy was performed and revealed “giant cells”—very large cells with multiple nuclei. Cytoplasmic and intranuclear inclusion bodies were also present. This picture was highly suggestive of measles pneumonia, and measles virus subsequently was recovered from cell cultures of the biopsy material. Other studies showed it to be the vaccine strain of measles virus. The patient received intravenous gamma globulin and an antiviral medication—ribavirin—and

Discussion 1. Measles is often disastrous for persons with AIDS or other immunodeficiencies. They should be immunized as soon as possible in their illness, before the immune system becomes so weakened it cannot respond effectively to the vaccine. Also, as this and other cases have shown, the vaccine virus can itself be pathogenic when immunodeficiency is severe. With the worldwide effort to eliminate measles, the risk of exposure to the wild-type measles virus, as opposed to the laboratory-derived vaccine virus, is declining, but outbreaks in colleges and other institutions still occur. A severely immunodeficient individual can

weight despite normal gestation. Babies may be stillborn. Those that live continue to excrete rubella virus in throat secretions and urine for many months. The likelihood of the syndrome varies according to the age of the fetus when infection occurs. Infections occurring during the first 6 weeks of pregnancy result in almost 100% of the fetuses having a detectable injury, most commonly minor deafness. Even infants who are apparently normal, however, excrete rubella virus for extended periods and thus can infect others.

100,000

be passively immunized against measles with immune globulin if exposure to the wild-type virus occurs. 2. Measles is often given as an example of a persistent viral infection, meaning that following infection the virus can persist in the body for months or years in a slowly replicating form. It has been suggested but not proven that this explains the lifelong immunity conferred by measles infection in normal people. Rarely in presumably normal individuals and, more commonly, in malnourished or immunodeficient individuals, persistent infection leads to damage to the brain, lung, liver, and possibly, the intestine. Subacute sclerosing panencephalitis can follow measles vaccination, but at a much lower rate than after wild virus infection. 3. Following acute infection, the measles virus floods the bloodstream and is carried to various tissues of the body, including the skin. The rash that characterizes measles is caused by T lymphocytes attacking measles virus antigen lodged in the skin capillaries. In the absence of functional T lymphocytes, the rash does not occur.

Epidemiology Humans are the only natural host for rubella virus. The disease is highly contagious although less so than rubeola; it is estimated that in the prevaccine era, 10% to 15% of people reached adulthood without being infected. Complicating the epidemiology of rubella is the fact that over 40% of infected individuals fail to develop symptoms, but can spread the virus. People who develop typical rubella can be infectious for as long as 7 days before the rash appears until 7 days afterward. Before widespread use of the vaccine began in 1969, periodic major epidemics arose. One epidemic in 1964 resulted in about 30,000 80 cases of congenital rubella syndrome. Rubella

Prevention and Treatment

CRS 60 1,000 40 100

Number of CRS cases

Number of rubella cases

10,000

20 10

0

0 1966

1970

1974

1978

1982

1986

1990

1994

1998

2002

Year

FIGURE 23.22 Reported Cases of German Measles (Rubella) and Congenital Rubella Syndrome (CRS), United States, 1966–2004 (Source: Centers for Disease Control and Prevention. MMWR 2005: 54(11): 27.)

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Prevention of German measles depends on subcutaneous injection of an attenuated rubella virus administered to babies at 12 to 16 months of age with a second dose at age 4 to 6 years. The vaccine produces long-lasting immunity in about 95% of recipients. The vaccine is not given to pregnant women for fear it might result in congenital defects. As an added precaution, women are advised not to become pregnant for 28 days after receiving the vaccine. Use of the vaccine has markedly reduced the incidence of rubella in the United States to generally less than 50 cases per year (figure 23.22). There were less than 1,000 confirmed cases in the entire Western Hemisphere in 2004.

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TABLE 23.11

CHAPTER TWENTY THREE

Skin Infections

German Measles (Rubella)

➀ Airborne rubella virus infects nose

Symptoms

and throat.

➁ Virus taken up by lymph nodes in the region.

➂ Rubella virus multiples and enters the bloodstream.

1 7 2

➃ Circulating virus reacts with antibodies, resulting in antibodyantigen complexes.

Incubation period

14 to 21 days

Causative agent

Rubella virus, an RNA virus of the togavirus family

Pathogenesis

Following replication in the upper respiratory tract, virus disseminates to all parts of the body and crosses the placenta; surviving fetuses often develop abnormally, and they excrete the virus for months after birth.

Epidemiology

Virus possibly present in nose and throat from 1 week before rash to 1 week after; infection occurs via the respiratory route; humans are the only source.

Prevention and treatment

Attenuated rubella virus vaccine administered to children at 12 to 16 months, repeated at 4 to 6 years of age. No specific antiviral treatment.

3 4

➄ Antibody-antigen complexes lodge in the skin, causing a rash, and in the joints, causing pain.

➅ In women during pregnancy, rubella virus crosses the placenta, infecting the fetus, resulting in congenital rubella syndrome.

Mild fever and cold symptoms, rash beginning on forehead and face, enlarged lymph nodes behind the ears

5 6

➆ Transmission to others is by respiratory secretions.

5

No specific antiviral therapy is available. Some features of German measles are summarized in table 23.11.

Other Viral Rashes of Childhood The kinds of viruses that can cause childhood rashes probably number in the hundreds. One group alone, the enteroviruses, has about 50 members that have been associated with skin lesions. In the early 1900s the causes of the common childhood rashes were largely unknown, and it was the practice to number them 1 to 6 as follows: (1) rubeola, (2) scarlet fever, (3) rubella, (4) Duke’s disease—a mild disease with fever and bright red generalized rash, now thought to have been due to an enterovirus, (5) erythema infectiosum, and (6) exanthem subitum. The causes of two common childhood rashes, erythema infectiosum and exanthem subitum, have only been established in recent years. Fifth disease (erythema infectiosum) occurs in both children and young adults. The illness begins with fever, malaise, and head and muscle aches. A diffuse redness appears on the cheeks, giving the appearance of the face as if it were slapped (figure 23.23a). The rash commonly spreads in a lacy pattern to involve other parts of the body, especially the extremities (figure 23.23b). The rash may come and go for 2 weeks or more before recovery. Joint pains are a prominent feature of some adult

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infections. The disease is caused by parvovirus B-19, a small (18 to 28 nm), non-enveloped, single-stranded DNA virus of the parvovirus family. The virus preferentially infects certain bone marrow cells and is a major threat to persons with sickle cell and other anemias because the infected marrow sometimes stops producing blood cells, a condition known as aplastic crisis. Also, about 10% of women infected with the virus during pregnancy suffer spontaneous abortion. Roseola (exanthem subitum, roseola infantum), is a common disease in infants 6 months to 3 years old. It causes a great deal of parental anxiety because it begins abruptly with fever that may reach 105°F and cause convulsions. The children generally do not appear ill, however. After several days, the fever vanishes and a transitory red rash appears, mainly on the chest and abdomen. The patient has no symptoms at this point, and the rash vanishes in a few hours to 2 days. This disease is caused by herpesvirus, type 6. There is no vaccine against the disease, and no treatment except to reduce the risk of seizures by sponging with lukewarm water and using medication to keep the temperature below 102°F.

Warts Papillomaviruses, cause of warts, can infect the skin through minor abrasions. Warts are small tumors called papillomas that consist

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(a)

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(b)

FIGURE 23.23 Erythema Infectiosum (Fifth Disease) (a) “Slapped cheek” appearance of the rash on the face. (b) Appearance of the rash on the extremities. (Source: CDC Public Health Image Library.)

of multiple nipplelike protrusions of tissue covered by skin or mucous membrane. Warts rarely become cancers, although some sexually transmitted papillomaviruses are strongly associated with cervical cancer. About 50% of the time, warts on the skin disappear within 2 years without any treatment. Papillomaviruses (figure 23.24) belong to the papovavirus family. They are small (about 50 nm diameter), non-enveloped, double-stranded DNA viruses. More than 50 different papillomaviruses are known to infect humans. Warts of other animals are generally not infectious for humans.

Papillomaviruses have been very difficult to study because they grow poorly in cell cultures or experimental animals. The viruses that cause warts can survive on inanimate objects such as wrestling mats, towels, and shower floors, and infection can be acquired from such contaminated objects. The virus infects the deeper cells of the epidermis and reproduces in the nuclei. Some of the infected cells grow abnormally, forming the wart. The incubation period ranges from 2 to 18 months. Infectious virus is present in the wart and can contaminate fingers or objects that pick or rub the lesions. Like other tumors, warts can only be treated effectively by killing or removing all of the abnormal cells. This can usually be accomplished by freezing the wart with liquid nitrogen, by cauterization, meaning burning the tissue usually with an electrically heated needle, or by surgical removal. Virus generally remains in the adjacent normal-appearing skin, however, and may cause additional warts. Warts that grow on the soles of the feet are called plantar warts (often mistakenly called planter’s warts; plantar is a word meaning “referring to the sole of the foot”). These warts are very difficult to treat because the pressure of standing on them causes them to grow wide and deep. ■ cervical cancer, p. 639

MICROCHECK 23.4

1 µm

FIGURE 23.24 Wart Virus The virions appear yellow in this colorenhanced transmission electron micrograph.

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Chickenpox, measles, and rubella can be controlled by vaccines. Viral diseases that may only inconvenience a pregnant woman can be disastrous to her fetus. A viral infection acquired in childhood can remain latent for years only to reactivate in a different form. One group of viruses causes benign skin tumors. ✓ What important diagnostic sign is often present in the mouth of measles (rubeola) victims? ✓ What is the epidemiological significance of shingles? ✓ Why is it a good idea to immunize little boys against rubella?

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PERSPECTIVE 23.1 The Ghost of Smallpox, An Evil Shade Historically, smallpox epidemics have been devastating to the Americas. In the 1500s smallpox virus introduced into Central and South America caused horrendous loss of life and may have contributed to the downfall of the Inca and Aztec nations. An epidemic that swept the Massachusetts coast in the 1600s killed so many Native Americans that in some communities there were not enough survivors to bury the dead. Even in the latter 1700s, during the Revolutionary War, a smallpox epidemic raged through the American colonies. General George Washington suspected that the virus had been deliberately introduced by the British. So many of his men were ill after his defeat at Quebec in 1777 that he ordered the mass variolation of remaining troops. ■ smallpox, pp. 431, 460 ■ variolation, p. 431 Why does the ghost of smallpox concern us now, when the last case, acquired through a laboratory accident, occurred in 1978? The answer is that the smallpox virus still exists, locked in high-security laboratories in the United States and the Russian Federation, and perhaps held in secret locations by countries or individuals that could use it to harm others. A number of factors need to be considered in choosing the smallpox virus as an agent of bioterror. Factors That Might Encourage Its Use: • It spreads easily from person to person, mainly through close contact with respiratory secretions, but

also by airborne virus from the respiratory tract, skin lesions, and contaminated bedding or other objects. • It can be highly lethal, with mortality rates generally above 25%. After the virus establishes infection of the respiratory system, it enters the lymphatics and bloodstream, finally causing lesions of the skin and throughout the body. • The virus is relatively stable, probably remaining infective for hours in the air of a building; viable smallpox has been demonstrated in dried crusts from skin lesions after storage for 10 years at room temperature in ordinary envelopes. • Large numbers of people are highly susceptible to the virus. Routine vaccination against smallpox was discontinued in the United States several decades ago. • The relatively large genome of the smallpox virus probably permits genetic modifications that could enhance its virulence. Factors That Discourage Its Use: • Propagating the smallpox virus is dangerous and requires advanced knowledge and laboratory facilities. • A proven highly effective vaccine (vaccinia virus) is available. A protective antibody response

23.5 Skin Diseases Caused by Fungi Focus Points Explain why dermatophytes usually invade only nails, hair, and outermost skin cells. Describe the role of skin moisture in the pathogenesis of superficial cutaneous mycoses.

Diseases caused by fungi are called mycoses. Earlier in this chapter, we mentioned the role of normal microbiota yeast of the genus Malassezia in causing mild skin diseases. Other fungi are responsible for more serious infections of the skin, although even in these cases the condition of the host’s defenses against infection is often crucial. The yeast Candida albicans (figure 23.25) may live harmlessly among the normal flora of the skin, but in some people it invades the deep layers of the skin and subcutaneous tissues. In many people with candidal skin infections, no precise cause for the invasion can be determined. Certain molds also cause cutaneous mycoses, but they are not as likely as C. albicans to invade the deep skin layers.

Superficial Cutaneous Mycoses Certain species of molds can invade hair, nails, and the keratinized portion of the skin. The resulting mycoses have colorful

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occurs rapidly and prevents fatalities for 10 years or more. Smallpox is prevented even when the vaccine is administered up to four days after exposure to the virus. • Infected persons do not spread the disease during the long incubation period, generally 12 to 14 days; they only become infectious with the onset of fever. • The disease can usually be diagnosed rapidly, by the characteristic appearance of skin lesions that predominate on the face and hands, and by laboratory examination of material from skin lesions. • There is already widespread experience on how to watch for and contain the disease. In a simulated attack on an American city in the summer of 2001, only 24 primary cases of smallpox increased in 2 months to 3 million, with 1 million deaths. This study probably greatly exaggerated the risk. Nevertheless, even though unlikely, the potential danger from a smallpox introduction has caused the United States to begin preparations for this possibility, including markedly expanding its stockpile of smallpox vaccine. More information on smallpox is available at the Online Learning Center, www.mhhe. com/nester6.

names such as jock itch, athlete’s foot, and ringworm, and more traditional latinized names that describe their location: tinea capitis—scalp, tinea barbae—beard, tinea axillaris—armpit, tinea corporis—body, tinea cruris—groin, and tinea pedis—feet, to list a few. Tinea just means “worm,” which probably reflects early erroneous ideas about the cause.

Symptoms Most people colonized by these molds have no symptoms at all. Others complain of itching, a bad odor, or a rash. In ringworm, a rash occurs at the site of the infection and consists of a scaly area surrounded by redness at the outer margin, producing irregular rings or a lacy pattern on the skin. On the scalp, patchy areas of hair loss can occur, with a fine stubble of short hair left behind. Involved nails become thickened and brittle and may separate from the nailbed. Sometimes, a rash consisting of fine papules and vesicles develops distant from the infected area. This rash is referred to as a dermatophytid, or “id” reaction, a reflection of allergy to products of the infecting fungus.

Causative Agents The skin-invading molds belong mainly to the genera Epidermophyton, Microsporum, and Trichophyton and are collectively termed dermatophytes (figure 23.26). They can be cultivated on media especially designed for molds and are identified by their colonial and microscopic appearance, their nutritional requirements, and biochemical tests.

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(a) (a)

(b)

10 µm

FIGURE 23.25 Candida albicans (a) Causing a diaper rash; (b) Gram stain of pus showing C. albicans yeast forms and filamentous forms called pseudohyphae.

(b)

20 µm

FIGURE 23.26 Dermatophytosis (a) Tinea pedis, usually caused by species of Trichophyton. (b) Large boat-shaped spores of Microsporum gypseum, a cause of scalp ringworm in children.

Pathogenesis The normal skin is generally resistant to invasion by dermatophytes. Some species, however, are relatively virulent and can even cause epidemic disease, especially in children. In conditions of excessive moisture, dermatophytes can invade keratinized structures, including the epidermis down to the level of the keratin-producing cells. A keratinase enables them to dissolve keratin and use it as a nutrient. Hair is invaded at the level of the hair follicle because the follicle is relatively moist. Fungal products diffuse into the dermis and provoke an immune reaction, which probably explains why adults tend to be more resistant to infection than children. It also explains why some people develop the allergic “id” reactions.

Epidemiology As mentioned, age, virulence of the infecting strain of mold, and excessive moisture are important factors in causing infections. Common causes of excessive moisture include obesity causing folds of skin to lie together, tight clothing, and plastic or rubber footware. Potentially pathogenic molds may be present in soil and on pets such as young cats and dogs.

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Prevention and Treatment Attention to cleanliness and maintenance of normal dryness of the skin and nails effectively prevent most dermatophyte infections. Powders, open shoes, changing of socks, and application of alcohol after bathing may help prevent toenail infections. Numerous prescription and over-the-counter medications are promoted for treating dermatophytoses, and most are effective for treating superficial skin infections. Nail infections are often very difficult to cure, requiring taking medication by mouth for months, and sometimes surgical removal of the nail.

MICROCHECK 23.5 The causes of skin mycoses commonly colonize skin without causing symptoms. The best protection against fungal skin infections is to maintain normal skin dryness. ✓ What is a mycosis? ✓ What kinds of structures are invaded by dermatophytes? ✓ Would you be surprised if a child contracted ringworm from a pet that showed no signs of the disease? Why, or why not?

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FUTURE CHALLENGES The Ecology of Lyme Disease Lyme disease is often referred to as one of the emerging diseases. Unrecognized in the United States before 1975, it is now the most commonly reported vector-borne disease. Because of the seeming explosion in the numbers of Lyme disease cases, and its apparent extension to new geographical areas, the ecology of Lyme disease is under intense study. In the northeastern United States, large increases in whitefooted mouse populations occur in oak forests during years in which there is a heavy acorn crop, with a

corresponding increase in Ixodes scapularis ticks. Both deer and mice feed on the acorns and subsequently spread the disease to adjacent areas. Variations in weather conditions, and their effect on food supply for these animals, might therefore be an important ecological factor, although it is not clear that weather cycles completely explain the emerging nature of the disease. The presence of animals other than white-footed mice for the ticks to feed on is another factor. Alternative tick hosts usually do not have

a sustained Borrelia burgdorferi bacteremia following infection from a tick, and the blood of a common lizard host along the West Coast even kills the spirochetes. The role of snakes, foxes, and birds of prey that control mouse populations and that of birds, spiders, and wasps that feed on ticks are also under study. The challenge is to define more completely the ecology of Lyme and other tick-borne diseases in order to predict their emergence and find new ways for their prevention.

SUMMARY 23.1 Anatomy and Physiology (figure 23.1) The skin is a large complex organ with many functions, including temperature regulation and vitamin D synthesis, and aiding cellular immunity. The skin repels potential pathogens by shedding and being dry, acidic, and toxic.

23.2 Normal Microbiota of the Skin Skin is inhabited by large numbers of bacteria of little virulence that help prevent colonization by more dangerous species (table 23.1). Diphtheroids Diphtheroids are Gram-positive, pleomorphic, rod-shaped bacteria that play a role in acne and body odor. Fatty acids, produced from their metabolism of the oily secretion of sebaceous glands, keep the skin acidic. Staphylococci Staphylococci are Gram-positive cocci arranged in clusters. Universally present, they help prevent colonization by potential pathogens and maintain the balance among flora of the skin. The principal species, Staphylococcus epidermidis, can sometimes cause disease. Fungi Malassezia sp. are yeasts found on the skin. Usually harmless, they can cause tinea versicolor, probably some cases of dandruff, and serious skin disease in AIDS patients (figure 23.2).

23.3 Bacterial Skin Diseases Hair Follicle Infections (figure 23.3) Folliculitis, boils and carbuncles are caused by Staphylococcus aureus (table 23.3), which is coagulase-positive and often resists penicillin and other antibiotics. A carbuncle is more serious because the infection is more likely to be carried to the heart, brain, or bones. Scalded Skin Syndrome (figure 23.4, table 23.4) Staphylococcal scalded skin syndrome results from exfoliatin produced by certain strains of Staphylococcus aureus. Streptococcal Impetigo (figure 23.5, table 23.6) Impetigo is a superficial skin infection caused by Streptococcus pyogenes and Staphylococcus aureus. Acute glomerulonephritis, a kidney disease, caused by an antibody-antigen reaction, is an uncommon complication of S. pyogenes infections (figure 23.7).

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Rocky Mountain Spotted Fever (figures 23.8, 23.10, table 23.7) Rocky Mountain spotted fever, caused by the obligate intracellular bacterium Rickettsia rickettsii, is an often fatal disease transmitted to humans by the bite of an infected tick (figures 23.9, 23.11). Lyme Disease (figures 23.12, 23.14, table 23.8) Lyme disease can imitate many other diseases. It is caused by a spirochete, Borrelia burgdorferi, transmitted to humans by certain ticks. A target-shaped rash, present in most victims, is the hallmark of the disease (figures 23.12, 23.13, 23.15, 23.16).

23.4 Skin Diseases Caused by Viruses Chickenpox (Varicella) (figure 23.17, table 23.9) Chickenpox, once a common disease of childhood is caused by the varicella-zoster virus (figure 23.19). Shingles, or herpes zoster (figure 23.18), can occur months or years after chickenpox. It is a reactivation of the varicella-zoster virus infection in the distribution of a sensory nerve. Shingles cases can be sources of chickenpox epidemics. Measles (Rubeola) (figures 23.20, 23.21, table 23.10) Measles (rubeola) is a potentially dangerous viral disease that can lead to serious secondary bacterial infections, and fatal lung or brain damage. Measles can be controlled by vaccinating with an attenuated vaccine. German Measles (Rubella) (figure 23.22, table 23.11) German measles (rubella), if contracted by a woman in the first 6 weeks of pregnancy, often results in birth defects making up the congenital rubella syndrome. Immunization with an attenuated virus protects against this disease (figure 23.23). Other Viral Rashes of Childhood Numerous other viruses can cause rashes. Fifth disease (erythema infectiosum) is characterized by a “slapped check” rash. It is caused by parvovirus B-19. It can be fatal to people with certain anemias. Roseola (exanthem subitum) is marked by several days of high fever and a transitory rash that appears as the temperature returns to normal. It occurs mainly in infants six months to three years old. The disease is caused by human herpesvirus, type 6. Warts Warts are skin tumors caused by a number of papillomaviruses (figure 23.24). They are generally benign, but some sexually transmitted papillomaviruses are associated with cancer of the uterine cervix.

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Review Questions

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feed on keratin cause athlete’s foot, ringworm, and invasions of the hair and nails (figure 23.26).

Superficial Cutaneous Mycoses Invasive skin infections, such as diaper rashes, are sometimes caused by the yeast Candida albicans (figure 23.25). Certain species of molds that

REVIEW QUESTIONS Short Answer 1. What is the difference between a furuncle and carbuncle? 2. Why is the blister fluid of staphylococcal scalded skin syndrome free of staphylococci? 3. Give three ways in which Streptococcus pyogenes resembles Staphylococcus aureus, and three ways in which it differs. 4. What is the epidemiological importance of passage through tick eggs by Rickettsia rickettsii? 5. Describe the causative agent of Lyme disease. 6. What is characteristic about the rash of varicella? 7. What is the relationship between chickenpox (varicella) and shingles (herpes zoster)? 8. Why do so many people suffer permanent damage or die from measles? 9. What viral disease might be associated with an aplastic crisis? Describe its characteristic rash. 10. What is the significance of rubella viremia during pregnancy? 11. How does a person contract warts? 12. What is the allergic rash called that appears in response to ringworm and distant to it?

6.

7.

8.

Multiple Choice 1. Which of the following conditions is important in the ecology of the skin? a) Temperature b) Salt concentration c) Lipids d) pH e) All of the above 2. Staphylococcus aureus can be responsible for which of these following conditions? a) Impetigo b) Food poisoning c) Toxic shock syndrome d) Scalded skin syndrome e) All of the above 3. The main effect of staphylococcal protein A is to a) interfere with phagocytosis. b) enhance the attachment of the Fc portion of antibody to phagocytes. c) coagulate plasma. d) kill white blood cells. e) degrade collagen. 4. Which of the following is essential for the virulence of Streptococcus pyogenes? a) Protease b) Hyaluronidase c) DNase d) All of the above e) None of the above 5. Which of the following statements is true of streptococcal acute glomerulonephritis? a) It is a streptococcal infection of the kidneys. b) It is caused by immune complexes containing streptococcal antigen. c) It is caused by most strains of b-hemolytic group A streptococci.

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9.

10.

d) It is the result of a streptococcal toxin directed against the kidneys. e) All of the above. All of the following are true of Rocky Mountain spotted fever, except a) the disease is most prevalent in the western United States. b) it is caused by an obligate intracellular bacterium. c) it is a zoonosis transmitted to human beings by ticks. d) those with the disease characteristically develop a hemorrhagic rash. e) antibiotic therapy is usually curative if given early in the disease. All of the following are true of Lyme disease, except a) it is caused by a spirochete. b) it is transmitted by certain species of ticks. c) it occurs only in the region around Lyme, Connecticut. d) most cases get a rash that looks like a target. e) it can cause heart and nervous system damage. Which of the following statements is more likely to be true of measles (rubeola) than German measles (rubella)? a) Koplik spots are present. b) It causes birth defects. c) It causes only a mild illness. d) Human beings are the only natural host. e) Attenuated virus vaccine is available for prevention. All of the following must be cultivated in cell cultures instead of cell-free media, except a) Rickettsia rickettsii. b) rubella virus. c) varicella-zoster virus. d) Borrelia burgdorferi. e) rubeola virus. All of the following might contribute to development of ringworm or other superficial cutaneous mycoses, except a) obesity. b) playing with kittens. c) rubber boots. d) using skin powder. e) dermatophyte virulence.

Applications 1. A school administrator in a small Iowa community prohibited a child with chickenpox from attending school. He claimed that this was the first case of chickenpox seen in the school in 6 years and that he did not want to have an outbreak at the school. Several parents argued to the school board that an outbreak would benefit the school in the long term. Discuss the pros and cons of allowing this child to attend school. 2. A public health official was asked to speak about immunization during a civic group luncheon. One parent asked if rubella was still a problem. In answering the question, the official cautioned women planning to have another child to have their present children immunized against rubella. Why did the official make this statement to the group?

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Critical Thinking 1. A microbiology instructor stated that the presence of large numbers of Propionibacterium acnes in the same areas where acne develops illustrates that occurrence of a bacterium and a disease together does not necessarily imply cause and effect. Why would the instructor make this statement?

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2. When Lyme disease was first being investigated, the observation that frequently only one person in a household was infected was a clue leading to the discovery that the disease was spread by arthropod bites. Why was this so? 3. Why might it be more difficult to eliminate a disease like Lyme disease or Rocky Mountain spotted fever from the earth than rubeola or rubella?

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24 Shotgun wound of the torso.

Wound Infections A Glimpse of History Spores of Clostridium tetani, the cause of lockjaw (tetanus), are found in soil and dust—thus, virtually everywhere. Before its cause and pathogenesis were understood, the disease was widespread, often ending in agonizingly painful death. Dr. Shibasaburo Kitasato (1856–1931), working in Robert Koch’s laboratory in Germany, was the first to discover how to cultivate C. tetani, and subsequently he made a startling discovery that paved the way for control of the disease. Kitasato was born in a mountainous village in southern Japan in 1856. He was sent by his family to medical schools in Kumamoto and Tokyo. Following his graduation in 1883, Kitasato went to work for the Central Hygienic Bureau in Japan. The Japanese government needed to control epidemics of typhoid, cholera, and black-leg, a clostridial disease of calves, and so in 1885, Kitasato was sent to Germany to study with the famous Dr. Koch. In Koch’s laboratory, Kitasato was given the tetanus problem to study. In the course of his experiments, he discovered that C. tetani would only grow under strictly anaerobic conditions. Once he had isolated the organism in pure culture, he was able to show that it produced tetanus in laboratory animals. He was puzzled, however, by a surprise finding: although the animals died of generalized disease, there was no C. tetani anyplace other than the site where the organism had been injected. By doing experiments in which he injected the tails of mice and then removed the injected tissue at hourly intervals after injection, he showed that the animals only developed tetanus if the organisms were allowed to remain for more than an hour. He further showed that the organisms remained at the site of inoculation; at no time were they found in the rest of the body. Kitasato reasoned that something other than bacterial invasion was causing the disease. About this time, another investigator, Emil von Behring, was busy investigating how Corynebacterium diphtheriae caused the disease diphtheria. Together, Kitasato and von Behring were able to show that both diseases were caused by poisonous substances— toxins—that were produced by the bacteria. The concept that a bacterial toxin could cause disease in the absence of bacterial inva-

sion was an extremely important advance in the understanding and control of infectious diseases. Kitasato published his studies in 1890. In 1892, even though urged to stay in Germany, he returned to Japan. The Japanese government was not prepared to support basic research at that time, and so Kitasato established his own institute for infectious diseases where he worked and trained Japanese scientists for the rest of his life. In 1908, Koch paid a visit to Kitasato in Japan and a Shinto shrine was built in Koch’s honor. During his later years, Kitasato was instrumental in establishing laws regulating health practices in Japan. He died in 1931 at age 75. To honor him, a shrine was erected next to Koch’s.

M

ost people occasionally sustain wounds that produce breaks in the skin or mucous membranes. Almost always, microorganisms contaminate these wounds from the air, fingers, normal microbiota, or the object causing the wound. Whether these microorganisms cause disease depends on (1) how virulent they are, (2) how many there are, (3) the status of host defenses, and (4) the nature of the wound, especially whether it contains crushed tissue or foreign material. Wounds that contain materials such as dirt, leaves, bits of rubber, and cloth usually become infected and do not heal until the foreign material is removed. Often such a wound provides places for microorganisms to multiply and produce injurious substances, out of the reach of phagocytes and other body defenses. Foreign materials may also provide surfaces for biofilms, or the materials reduce available oxygen, thereby impairing phagocytic function and allowing growth of anaerobic pathogens. Clean wounds often heal without treatment despite microbial colonization, but sometimes even a trivial wound can result in a severe, or even fatal, infection by providing an entryway for infection or microbial toxins to spread throughout the body. 559

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KEY TERMS Abscess A localized collection of pus within a tissue. Fasciitis Inflammation of the fascia, bands of fibrous tissue that underlie the skin and surround muscle and body organs. When it leads to death of tissue, it is called necrotizing fasciitis. Granulation Tissue New tissue formed during healing of an injury, consisting of small, red, translucent nodules containing abundant blood vessels.

Wound Infections MRSA Methicillin-resistant Staphylococcus aureus; many strains have acquired R plasmids making them resistant to multiple anti-staphylococcal medications. Neonatal Tetanus Tetanus that develops in newborn babies, often from cutting the umbilical cord with an unsterile instrument; preventable by immunizing the mother before delivery. Pyogenic Pus-producing

Wounds can be classified as: burns; incised, as when produced by a knife or other sharp object, as in surgery; punctured, from penetration of a small sharp object, as when an individual steps on a nail; lacerated, when the tissue is torn; contused, as when caused by a blow that crushes tissue. Burns represent an important category of accidental wounds. In the United States each year, more than 2.5 million people sustain thermal burns severe enough for them to seek medical attention. Of these, more than 100,000 require hospitalization, and 12,000 die from their burns. Burns present special problems. Although initially sterile, thermal burns are often extensive, with a large area of weeping devitalized tissue, representing an enormous and nutritious feast for microorganisms. Intentional wounds inflicted by surgery represent about 23 million cases annually in the United States. From 1% to 9% of them become infected; the percentages vary according to the type of surgery and the status of the patients’ host defenses. Costs related to postoperative wound infections amount to approximately $1.5 billion each year, more than half of the total expense for nosocomial infections. They result in about 13,000 deaths each year. ■ nosocomial infections, p. 462

24.1 Anatomy and Physiology Focus Points Name three tissue components exposed by wounds to which pathogens specifically attach. Describe the potentially beneficial and harmful aspects of abscess formation.

Wounds expose components of tissue normally protected from the outside world by skin or mucous membranes. These exposed tissue components, including collagen, fibronectin,

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Superantigen Molecules that bind to and stimulate T lymphocytes, resulting in activation of many T cells, overproduction of cytokines, severe reactions, and sometimes fatal shock. Synergistic Infection An infection in which two or more species of pathogens act together to produce an effect greater than the sum of effects if each pathogen were acting alone. Toxic Shock Life-threatening drop in blood pressure resulting from certain types of circulating bacterial exotoxins.

fibrin, and fibrinogen, provide receptors to which potential pathogens specifically attach. Collagen is a fibrous material—the main supportive protein of skin, tendons, scars, and other body structures. Fibronectin is a glycoprotein that occurs both as a circulating form and as a component of tissue, where it ties cells and other tissue substances together. Shortly after a wound occurs, the soluble blood protein fibrinogen is converted to the fibrous material fibrin, thereby forming clots in the damaged vessels. This stops the flow of blood as the first step in the repair process. Wound healing begins with the outgrowth of connective tissue cells, called fibroblasts, and capillaries from the surfaces of the wound, producing a nodular, red, translucent material called granulation tissue. In the absence of dirt or infection, granulation tissue fills the void created by the wound, contracts, and is converted to collagen that composes the scar tissue eventually covered by overlying skin or mucous membrane (figure 24.1). Sometimes in the presence of dirt or infection, the granulation tissue overgrows, bulging from the wound to form a pyogenic granuloma.

Wound Abscesses An abscess (figure 24.2) is a localized collection of pus surrounded by body tissue. It is composed of living and dead leukocytes, components of tissue breakdown, and infecting organisms. No blood vessels are in abscesses because they have been destroyed or pushed aside. An area of inflammation and clots in adjacent blood vessels separate the abscess from normal tissue. Consequently, abscess formation helps to localize an infection and prevent its spread. Microorganisms in abscesses often are not killed by antimicrobial medications because the microorganisms cease multiplying, and active multiplication is generally required for microbial killing by the medications. In addition, the chemical nature of pus interferes with the action of some antibiotics, and many antimicrobials diffuse poorly into abscesses because of the absence of blood vessels. Microorganisms in abscesses are a potential source of infection of other parts of the body if they escape the surrounding area of inflammation and enter the blood or lymph vessels. Generally, abscesses must burst to a body surface or be drained surgically in order to effect a cure. ■ antimicrobial medications, p. 469

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24.1 Clots forming Epithelium

Circulating fibrinogen is converted to fibrin, resulting in clots in the severed capillaries.

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Epithelial surface A pathogenic microorganism is deposited in the tissue from a wound or from the bloodstream.

Subepithelial tissue

Cells from the capillaries and subepithelial tissue cells called fibroblasts multiply, forming buds of tissue protruding into the wound.

Leukocytes

Tissue Capillary

Pathogen

Blood vessels dilate, and leukocytes migrate to the area of the developing infection.

The wound is filled with bright red granulation tissue, which differentiates into abundant new capillaries and bleeds easily.

The fibroblasts multiply, producing a dense, strong substance called collagen, the main component of scar tissue. The collagen contracts and may distort the tissue in the process; epithelium covers the repaired wound.

Pus forms, composed of the products of tissue cell breakdown, leukocytes, and bacteria; clotting occurs in the adjacent blood vessels.

Blood clots Pus Dead tissue

Buildup of pressure causes the abscess to expand in the direction of least resistance; if it reaches a body surface, it may rupture and discharge its contents.

FIGURE 24.1 The Process of Wound Repair Blood clots

FIGURE 24.2 Abscess Formation

Anaerobic Wounds An important feature of many wounds is that they are relatively anaerobic, thus allowing colonization by dangerous anaerobic pathogens such as Clostridium tetani. Anaerobic conditions are especially likely in dirty wounds, wounds with crushed tissue, and puncture wounds. Puncture wounds caused by nails, thorns, splinters, and other sharp objects can introduce foreign material and microorganisms deep into the body. Bullets and other projectiles can carry fragments of skin or cloth contaminated with microorganisms into the tissues. Projectiles, although causing relatively small breaks in the skin, often produce extensive tissue damage because of the force with which they enter.

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MICROCHECK 24.1 Wounds expose components of tissue to which pathogens specifically attach. Wounds can be classified as incised, punctured, lacerated, contused, or burns. Healing involves the outgrowth of fibroblasts and capillaries from the sides of the wound to produce granulation tissue that fills the defect. Abscess formation provides a way of isolating infections enclosed by tissue. Anaerobic conditions in wounds are created by the presence of dead tissue and foreign material. ✓ Name two substances in wounds to which pathogens specifically attach. ✓ Give two reasons why an abscessed wound might not respond to antibiotic treatment. ✓ What is the advantage of the contraction of granulation tissue?

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24.2 Common Bacterial Wound Infections Focus Points Give distinctive characteristics of three common wound infections caused by bacteria that grow in the presence of air. Outline the evolution and current significance of MRSA.

The possible consequences of wound infections include (1) delayed healing, (2) formation of abscesses, and (3) spread of the bacteria or their products into adjacent tissues or the bloodstream. Infected surgical wounds often split open as swelling causes the stitches to pull through tissues softened by the infection. Also, the infection can extend to involve devices such as an artificial hip, often requiring that the device be removed pending control of the infection. The following sections present some aspects of wound infections caused by staphylococci, streptococci, and Pseudomonas sp.

Staphylococcal Wound Infections Staphylococci lead the causes of wound infections, both surgical and accidental (figure 24.3). Staphylococci are commonly present in the nostrils or on the skin. Of the 30 or more recognized species of staphylococci, only two account for most human wound infections. ■ the genus Staphylococcus, p. 270

FIGURE 24.4 Staphylococcus aureus in Pus The dark-colored dots are staphylococci; the red objects, leukocytes.

Symptoms Staphylococci are pyogenic, meaning that they characteristically cause the production of a purulent discharge, otherwise known as pus. They usually cause an inflammatory reaction, with swelling, redness, and pain. If the infected area is extensive or if the infection has spread to the general circulation, fever is a prominent symptom. Wound infections by toxin-producing strains can result in toxic shock syndrome, characterized by high fever, muscle aches, and life-threatening shock, sometimes accompanied by a rash and diarrhea. ■ staphylococcal toxic shock syndrome, p. 626

Causative Agents Staphylococci are Gram-positive cocci that grow as clusters (figure 24.4). They grow readily aerobically or anaerobically and are salt tolerant, probably because they evolved on the skin where evaporation concentrates the salt in sweat. The most important species are S. aureus and S. epidermidis. Both species survive well in the environment, making it easy for them to transfer from one person to another. Staphylococcus aureus Characteristics of this common pathogen were discussed in chapter 23. Staphylococcus epidermidis Most strains of S. epidermidis have little or no invasive ability for healthy people but they commonly cause small abscesses of little consequence around the stitches used in surgery. Most strains bind fibronectin, however, and can therefore colonize the plastic intravenous catheters, heart valves, and other devices employed in modern medicine. Following adherence, the bacteria may produce a kind of slime or glycocalyx that cements the growing colony to the plastic in a biofilm, protecting it from attack by phagocytes and other host defense mechanisms, and antibacterial medications. ■ glycocalyx, p. 64 ■ biofilm, p. 85

Pathogenesis FIGURE 24.3 Surgical Wound Infection Due to Staphylococcus aureus The stitches and staples pull through the infected tissue, causing the wound to open.

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Staphylococcus aureus Many years ago, it was shown that it takes more than 100,000 staphylococci injected into the skin to produce a small abscess. When injected along with a suture, however, only about 100 S. aureus are required to produce the same

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24.2 Common Bacterial Wound Infections

lesion. These studies, which used students as human guinea pigs, dramatized the effect of foreign material in the pathogenesis of staphylococcal infections. Studies using genetically engineered strains have indicated that multiple virulence factors act together to produce the usual wound infection. Clumping factor and the other binding proteins attach the organisms to clots and tissue components, fostering colonization. Clumping factor, coagulase, and protein A serve to coat the organisms with host proteins, providing a disguise that hides them from attack by phagocytes and the immune system. This may explain why immunity to staphylococcal infection is generally weak or non-existent. Some protein A is released from the bacterial surface and reacts with circulating immunoglobulin. The resulting complexes activate the complement system and probably contribute to the intense inflammatory response and accumulation of pus. Colonization of plastics and other foreign materials occurs because they quickly become coated with fibrinogen and fibronectin to which the staphylococci attach. Systemic spread of wound infections can lead to abscesses in other tissues, such as the heart and joints. Staphylococcal toxins that enter the circulation are superantigens, causing the widespread release of cytokines, thereby producing toxic shock. ■ superantigens, p. 406 ■ cytokines, p. 353 ■ complement system, p. 355

The bacteria growing as biofilms on indwelling plastic catheters can come loose from and be carried by the bloodstream to the heart and other tissues. This can result in subacute bacterial endocarditis or multiple tissue abscesses in people with impaired host defenses as from cancer, diabetes mellitus, or other causes. Wound infections by S. epidermidis in healthy people are frequently cleared by host defenses alone.

Staphylococcus epidermidis

■ bacterial endocarditis, p. 677

Epidemiology The epidemiology of S. aureus is discussed in chapter 23. Various studies have shown that in the case of surgical wound infections, nasal carriers have a two to seven times greater risk of infection than do those who are not nasal carriers. From 30% to 100% of the infections in different studies were due to a patient’s own staphylococcus strain. Advanced age, poor general health, immunosuppression, prolonged preoperative hospital stay, and infection at a site other than the site of surgery increase the risk of infection.

563

Group A Streptococcal “Flesh Eaters” Streptococcus pyogenes was introduced under “Strep Throat” in chapter 22 and under “Streptococcal Impetigo,” in chapter 23. It is also a common cause of wound infections, which have generally been easy to treat since the bacteria are consistently susceptible to penicillin. Occasionally, however, S. pyogenes infections can progress rapidly, even leading to death despite antimicrobial treatment. These more severe infections are called invasive because they extend beyond the skin into underlying tissues and organs, and include pneumonia, meningitis, puerperal or childbirth fever, necrotizing fasciitis or “flesh-eating” disease, and worst of all, streptococcal toxic shock, which is similar to staphylococcal toxic shock. Deaths from invasive strep infections have caused widespread popular concern as S. pyogenes became the “flesheating” bacterium of the tabloid press. This section will focus on necrotizing fasciitis (figure 24.5), a rare but dramatic complication of S. pyogenes infection. ■ Streptococcus pyogenes, p. 499 ■ staphylococcal toxic shock, p. 626

Symptoms At the site of a surgical wound or accidental trauma, sometimes even without an obvious break in the skin, severe pain develops acutely. Within a short time, swelling becomes apparent, and the injured person develops fever and confusion. The overlying skin becomes stretched and discolored because of the swelling. Unless treatment is initiated promptly, shock and death usually follow in a short time.

Causative Agent Streptococcus pyogenes is a b-hemolytic, aerotolerant, Grampositive, chain-forming coccus with Lancefield group A cell wall polysaccharide. Strains of S. pyogenes that cause invasive disease are more virulent than other strains by virtue of at least two extracellular products: pyrogenic exotoxin A, is a superantigen that causes streptococcal toxic shock, and exotoxin B, a protease that destroys tissue by breaking down protein. ■ aerotolerance, p. 92 ■ b-hemolysis, p. 97 ■ pyrogens, p. 362

■ S. aureus epidemiology, p. 537

Prevention and Treatment Cleansing and removal of dirt and devitalized tissue from accidental wounds minimizes the chance of infection, as does prompt closure of clean wounds by sutures. Trying to eliminate the nasal carrier state with anti-staphylococcal medications is occasionally successful. Infections in surgical wounds can be reduced by half by administering an effective anti-staphylococcal medication immediately before surgery. For unknown reasons, the infection rate is actually increased if the medication is given more than 3 hours before or 2 hours after the surgical incision. As described in the chapter 23, treating staphylococcal infections can often be problematic due to wide spread antibiotic resistance. ■ MRSAs, pp. 485, 537 ■ antibacterial resistance, p. 483

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FIGURE 24.5 Individual with Streptococcus pyogenes “FleshEating” Disease (Necrotizing Fasciitis)

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Pathogenesis Like Staphylococcus aureus, S. pyogenes has a fibronectin-binding protein that aids colonization of wounds. In necrotizing fasciitis, the subcutaneous fascia and fatty tissue are destroyed. Fascia are bands of fibrous tissue that underlie the skin and surround muscle and body organs. In some cases, the fascia surrounding muscle is penetrated, and muscle tissue is also destroyed. Intense swelling occurs as fluid is drawn into the area because of increased osmotic pressure from the breakdown of tissue into small molecules. The organisms continue to multiply and produce toxic products in the mass of dead tissue, using the breakdown products as nutrients. In most cases, toxic products and organisms enter the bloodstream. Superantigens and other streptococcal products cause shock by inducing T cells to release cytokines and other mechanisms.

In hospitals, the bacterium is an important cause of lung infections and a common cause of wound infections, especially of thermal burns. Burns have large exposed areas of dead tissue free of any body defenses and, therefore, are ideal sites for infection by bacteria from the environment or normal microbiota. Almost any opportunistic pathogen can infect burns, but Pseudomonas aeruginosa is among the most common and hardest to treat.

Symptoms In burns and other wounds, P. aeruginosa can often color the tissues green from pigments released from the bacterial cells (figure 24.6a,b). This bacterium is especially dangerous because

Epidemiology “Flesh-eating” infections by S. pyogenes have probably occurred at least since the fifth century b.c. based on descriptions of necrotizing fasciitis by Hippocrates. More than 2,000 cases of this condition were reported among soldiers during the Civil War. Cases in this country are generally sporadic, although small epidemics have occurred such as a 1996 outbreak in San Francisco among injected-drug abusers using contaminated “black tar” heroin. The number of cases with invasive S. pyogenes in the United States was estimated at about 9,000 for 2002, resulting in 1,080 deaths, 135 of which were due to necrotizing fasciitis. There is no firm evidence of a trend toward higher incidence. Underlying conditions that increase the risk of necrotizing fasciitis and other invasive S. pyogenes infections include diabetes, cancer, alcoholism, AIDS, recent surgery, abortion, childbirth, chickenpox, and injected-drug abuse; invasive infections rarely occur in healthy individuals with minor injuries.

(a)

Prevention and Treatment (b)

There are no proven preventive measures. Because of the rapidity with which the toxins spread, urgent surgery is mandatory to relieve the pressure of the swollen tissue and to remove dead tissue. Amputation is sometimes necessary, to promptly rid the patient of the source of toxins. Penicillin is the drug of choice for early infection, but it has little or no effect on streptococci in necrotic tissue and no effect on toxins, and therefore it cannot substitute for surgery.

Pseudomonas aeruginosa Infections Pseudomonas aeruginosa is an opportunistic pathogen that is a major cause of nosocomial infections. In addition, it is an occasional cause of community-acquired infections, meaning infections acquired outside hospital or other medical facilities. Community-acquired infections include skin rashes from contaminated swimming pools and hot tubs, serious infections of the foot bones from stepping on nails, serious eye infections from contaminated contact lens solutions, heart valve infections in injected-drug abusers, external ear canal infections in swimmers and others who fail to dry their ears properly, disfiguring infections from ear piercing, especially of the ear cartilage, and biofilms in the lungs of individuals with the inherited disease cystic fibrosis. ■ Pseudomonas, p. 261

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(c)

10 mm

FIGURE 24.6 Pseudomonas aeruginosa (a) Extensive burn infected with P. aeruginosa. Notice the green discoloration. (b) Culture. The green discoloration of the medium results from water-soluble pigments diffusing from the P. aeruginosa colonies. (c) P. aeruginosa has a single polar flagellum.

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it often invades the bloodstream and causes chills, fever, skin lesions, and shock.

24.2 Common Bacterial Wound Infections

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competing bacteria and helping it acquire iron.

■ Bordetella pertussis,

p. 513 ■ Corynebacterium diphtheriae, p. 503 ■ elongation factor, p. 173 ■ required elements p. 93 ■ Vibrio cholerae, p. 596

Causative Agent Pseudomonas aeruginosa is found in a wide variety of environments such as soil and water. It is motile by means of a single polar flagellum (figure 24.6c). The organisms grow readily and rapidly; some strains can grow in a variety of aqueous solutions, even in distilled water. The bacterium generally utilizes O2 as the terminal electron acceptor in the breakdown of nutrients. Under certain circumstances, however, it can also grow anaerobically, as when nitrate is available. Nitrate substitutes for O2 as a terminal electron acceptor, an example of anaerobic respiration. Strains of P. aeruginosa often produce one or more water-soluble pigments, which can be red, yellow, blue, or dark brown. Commonly they produce a fluorescent yellowish pigment called pyoverdin, which combines with a blue pigment, pyocyanin, to produce the striking green color characteristically seen in infected wounds and in growth media. ■ anaerobic respiration, pp. 133, 354 ■ the genus Pseudomonas, p. 261

Pathogenesis The overall effect of P. aeruginosa infection of burns and other wounds is to produce tissue damage, prevent healing, and increase the risk of septic shock. Virulence depends mainly on production of two extracellular enzymes—exoenzyme S and toxin A. Exoenzyme S modifies various critical processes in the host cells, leading to their death. It functions in a way similar to the toxins of Vibrio cholerae and Bordetella pertussis. Most strains of P. aeruginosa also produce toxin A, an exoenzyme that has a mode of action identical to that of the toxin of Corynebacterium diphtheriae, a Gram-positive rod. The two toxins, however, are antigenically distinct and target different cells. These toxins halt protein synthesis by the host cell and are enhanced by lowering the concentration of iron. Most strains of P. aeruginosa also produce proteases that cause localized hemorrhages and tissue necrosis. Also, many strains produce a heat-labile hemolysin, a phospholipase C, identical in mode of action to the principal toxin of the gas gangrene bacillus Clostridium perfringens to be discussed later in this chapter. Phospholipase C hydrolyses lecithin, an important lipid component of cell membranes. The pigments released from P. aeruginosa may also contribute to pathogenicity by inhibiting

Epidemiology Pseudomonas aeruginosa is widespread in nature. It is introduced into hospitals on shoes, ornamental plants and flowers, and produce. It can persist in most places where there is dampness or water, and it can contaminate soaps, ointments, eye-drops, contact lens solutions, cosmetics, disinfectants, many kinds of hospital equipment, swimming pools, hot tubs, the inner soles of shoes, and illegal injectable drugs, all of which have been sources of infections.

Prevention and Treatment Prevention of P. aeruginosa infections involves elimination of potential sources of the bacterium and prompt care of wounds. Careful removal of dead tissue from burn wounds, followed by application of an antibacterial cream such as silver sulfadiazine, is often effective in preventing infection with P. aeruginosa. Established infections are notoriously difficult to treat because P. aeruginosa is usually resistant to multiple antibacterial medications. Antibiotic susceptibility tests are done to guide the selection of an effective regimen. For systemic infection, antibacterial medications must usually be administered intravenously in high doses. Table 24.1 compares the leading causes of wound infections.

MICROCHECK 24.2 Staphylococcus aureus is the most important cause of wound infections because it is so commonly carried by humans, transfers easily from one person to another, and possesses multiple virulence factors. Staphylococcus epidermidis forms biofilms on foreign materials, protecting the bacteria from body defenses and antibacterial medications. “Flesh-eating” strains of Streptococcus pyogenes are uncommon, but are often life threatening. Pseudomonas aeruginosa, a Gram-negative, pigment-producing rod, is widespread in the environment and is a major cause of nosocomial infections. ✓ Why are antibacterial medications not effective for treating “flesh-eating” disease (necrotizing fasciitis)? ✓ Why do wound infections due to Pseudomonas aeruginosa sometimes produce green pus? ✓ Why is it not surprising that staphylococci are the leading cause of wound infections?

TABLE 24.1 Leading Causes of Wound Infections Causative Organism

Characteristics

Consequences

Staphylococcus aureus

Gram-positive cocci in clusters, coagulase-positive

Delayed healing; abscess formation; extension into tissues, artificial devices, or bloodstream; occasional strains can cause toxic shock syndrome

Streptococcus pyogenes

Gram-positive cocci in chains; Lancefield group A

Same, except occasional strains can cause “flesh-eating” necrotizing fasciitis

Pseudomonas aeruginosa

Aerobic Gram-negative rod, green pigment

Delayed healing; abscess formation; extension into tissues, artificial devices, or bloodstream; septic shock

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24.3 Diseases Due to Anaerobic Bacterial Wound Infections Focus Points Describe the conditions that favor the development of anaerobic wound infections. Outline the special difficulties in treating wounds infected with toxin-producing bacteria.

Wounds that provide anaerobic conditions allow colonization by certain strictly anaerobic species of bacteria—organisms with their own unique pathogenic abilities. This section describes three distinctive diseases that result from anaerobic bacterial wound infections: lockjaw, gas gangrene, and lumpy jaw.

Spores

5 mm

FIGURE 24.8 Clostridium tetani Terminal endospores are characteris-

“Lockjaw” (Tetanus) Tetanus is frequently fatal; fortunately, it is rare in economically advanced countries. There is no reasonable way to avoid exposure to the causative organism because its endospores are widespread in dust and dirt, frequently contaminating clothing, skin, and wounds. Even a trivial wound in a non-immunized person can result in tetanus if the wound provides conditions sufficiently anaerobic to allow germination of the spores. ■ endospores, p. 69

Symptoms Tetanus is characterized by sustained, painful, and uncontrollable cramplike muscle spasms, which are usually generalized (figure 24.7) but can be limited to one area of the body. The spasms often begin with the jaw muscles, giving the disease the popular name “lockjaw.” The early symptoms include restlessness, irritability, difficulty swallowing, contraction of the muscles of the jaw, and sometimes convulsions, particularly in children. As more muscles tense, the pain grows more severe and is similar to that of a severe leg cramp. Breathing becomes labored, and after a period of almost unbearable pain, the infected person often dies of pneumonia or from stomach contents regurgitated into the lung.

tic of this species.

Causative Agent The causative agent, Clostridium tetani, an anaerobic, sporeforming, Gram-positive, rod-shaped bacterium (figure 24.8), shows two striking features: (1) a spherical endospore that forms at the end of the bacillus, in contrast to the oval endospore that develops near the center of the cell in other pathogenic species of Clostridium, and (2) swarming growth that quickly spreads over the surface of solid media, making it easy to obtain pure cultures. Final identification of C. tetani depends on identifying its toxin, which is coded by a plasmid. ■ bacterial toxins, p. 403 ■ Clostridium, p. 254 ■ plasmids, p. 68 ■ C. botulinum spores, figure 27.10, p. 657

Isolation of C. tetani from wounds does not prove that a person has tetanus. This is because tetanus endospores may contaminate wounds that are not sufficiently anaerobic to allow germination and toxin production, or the person may simply be immune to the toxin by prior vaccination. Only vegetative cells, not endospores, synthesize toxin. Conversely, failure to find the organism in a person’s wound cultures does not eliminate the possibility of tetanus.

Pathogenesis

FIGURE 24.7 Infant with Neonatal Tetanus

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Clostridium tetani is not invasive, and colonization is generally localized to a wound. Its pathologic effects are entirely the result of an exotoxin called tetanospasmin, released from the organism during the stationary phase of growth. It is an A-B toxin. The B portion attaches specifically to receptors on motor neurons, which then take up the A portion by endocytosis. The toxin is carried by the neuron to its cell body in the spinal cord. There, the motor neuron is in contact with other neurons that normally control its action. Some of these other neurons function to stimulate the motor nerve cell, thereby producing a muscle contraction, and others make the motor neuron resistant to stimulation, thereby inhibiting muscle contraction. Tetanospasmin blocks the action of the inhibitory neurons, so that the muscles contract without control (figure 24.9).

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24.3 Diseases Due to Anaerobic Bacterial Wound Infections NORMAL (Flexion)

foods contaminated with its spores. Therefore, fecal contamination is a potential source of infection. About half of the cases result from puncture wounds, including stepping on a nail, body piercing, tattooing, animal bites, splinters, injected-drug abuse, and insect stings. Cases also occur following medical procedures such as hemorrhoid removal or knee surgery. Surface abrasions and burns can result in tetanus if the wound is anaerobic by virtue of dirt, dead tissue, or exclusion of air. Ordinarily, about 30 cases are reported annually in the United States, with a mortality rate around 25%. Age is an important factor, probably because many older people fail to get recommended booster injections of vaccine. Due to lack of immunization and proper care of wounds, tetanus occurs much more frequently on a global basis than it does in the economically advanced countries. In some parts of the world, babies commonly die of neonatal tetanus as a result of their umbilical cord being cut with unsterile instruments contaminated with C. tetani.

NORMAL (Extension)

Motor neuron stimulated; this muscle contracts. Motor neuron inhibited; this muscle relaxes.

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Motor neuron inhibited; this muscle relaxes.

TETANUS

Prevention and Treatment

There is no inhibition; both muscles contract.

Active immunization with tetanus toxoid, which is inactivated tetanospasmin, is by far the best preventive weapon against tetanus. Immunization is usually begun during the first year of life. For infants and young children, the tetanus toxoid is given at two, four, six and 18 months of age in combination with diphtheria toxoid and acellular pertussis vaccine. The three together are commonly known as DTaP. A booster dose is given when children enter school. Once immunity has been established by this regimen, additional booster doses of tetanus toxoid are given at 10-year intervals to maintain an adequate level of protection. Any injury, burn, or contemplated surgery is an occasion to make sure immunization is up to date. Updating of booster doses of toxoid more frequently than every 10 years is not recommended because there is danger of an allergic reaction following intensive immunization. This type of reaction can occur when the toxoid is injected into an individual who already has large quantities of antitoxin, meaning antibodies against the toxoid. Individuals who have recovered from tetanus are not immune to the disease and must be immunized. ■ toxoid, p. 435 Even though tetanus is easily prevented by immunization with tetanus toxoid, about 97% of the people who developed tetanus in recent years were never immunized. To help prevent tetanus after a wound has been sustained, active immunization with toxoid, and passive immunization with tetanus immune globulin (TIG), may be indicated (table 24.2). Neonatal tetanus can be prevented by immunizing expectant mothers. Their infants are then protected by antitoxin crossing the

FIGURE 24.9 Tetanus and Inhibitory Neuron Function The exotoxin tetanospasmin blocks the action of inhibitory neurons, allowing all muscles to contract at the same time.

The toxin generally spreads across the spinal cord to the side opposite the wound and then downward. Thus, typically, spastic muscles first appear on the side of the wound, then on the opposite side, and then downward, depending on the amount of toxin. Tetanospasmin released from the infected wound often enters the bloodstream, which carries it to the central nervous system. In these cases, inhibitory neurons of the brain are first affected, and the muscles of the jaw are among the first to become spastic. ■ A-B toxins, p. 405

Neurons exert their effect on other nerve cells by releasing chemicals called neurotransmitters. Tetanospasmin prevents the release of neurotransmitters from inhibitory neurons.

Epidemiology Clostridium tetani occurs not only in dirt and dust, but in the gastrointestinal tract of humans and other animals that have eaten

TABLE 24.2 Tetanus Prevention in the Management of Wounds Clean Minor Wounds Immunization History

All Other Wounds

Toxoid

TIG

Toxoid

TIG

Unknown, or fewer than three injections

Yes

No

Yes

Yes

Fully immunized (three or more injections of toxoid) • 5 years or less since last dose

No

No

No

No

• 5 to 10 years since last dose

No

No

Yes

No

• more than 10 years since last dose

Yes

No

Yes

No

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neutralize tetanospasmin that is already bound to nerve tissue. This explains why tetanus antitoxin is often ineffective in treating the disease. In addition to antitoxin treatment, the wound is thoroughly cleaned of all dead tissue and foreign material that could provide anaerobic conditions. An antibacterial medication such as metronidazole is given to kill any actively multiplying clostridia and thereby prevent the formation of more tetanospasmin. Antibacterials do not kill endospores or nongrowing bacteria, however. Table 24.3 describes the main features of tetanus.

placenta. Since 1989, when almost 30,000 cases were reported, the World Health Organization has been attempting to eliminate neonatal tetanus. By 2006, the number of reported cases had fallen to 8,376. The decrease in cases largely resulted from immunizing millions of expectant mothers in developing countries against tetanus and educating them in the care of the severed umbilical cord. Tetanus is treated by administering tetanus antitoxin, which is antibody against tetanospasmin, to neutralize any of the toxin not yet attached to motor nerve cells. The antitoxin of choice is tetanus immune globulin (TIG), which is prepared from blood of humans immunized with tetanus toxoid. This antitoxin generally does not cause hypersensitivity reactions in humans and is much more effective than the antitoxin formerly used which was derived from the blood of horses immunized with toxoid. TIG, however, cannot

Gas Gangrene (Clostridial Myonecrosis) Almost every sample from soil and dusty surfaces has endospores of Clostridium perfringens, the bacterium that causes gas gan-

TABLE 24.3 “Lockjaw” (Tetanus) ➀ Clostridium tetani spores from dust

3

or dirt enter a wound.

➁ In wounds sufficiently anaerobic,

the spores germinate, vegetative bacteria release an exotoxin called tetanospasmin.

Symptoms

Restlessness, irritability, difficulty swallowing; muscle pain and spasm in jaw, abdomen, back, or entire body

Incubation period

3 days to 3 weeks; average 8 days

Causative agent

Clostridium tetani, an anaerobic, sporeforming, Gram-positive rod

Pathogenesis

Tetanus results from tetanospasmin, an exotoxin produced by the bacterium. The toxin is carried to brain and spinal cord by motor nerve axons or circulating blood; toxin acts against nerve cells that normally inhibit muscle contraction. Other nerves that normally cause muscle contraction then act unopposed, causing muscle spasms.

Epidemiology

Organisms common in soil; spores contaminate wounds, germinate in those having anaerobic conditions, particularly dirty or puncture wounds.

Prevention and treatment

Immunization of children at ages 2 months, 4 months, 6 months, 18 months; booster dose at time of entering school and at 10year intervals after that; tetanus immune globulin (TIG), cleaning wound. Treatment: metronidazole, tetanus antitoxin.

4

➂ Tetanospasmin is carried to the

5

central nervous system by motor nerve axons or by the bloodstream.

6

3

➃ The toxin prevents any inhibitory neurons it reaches from functioning.

➄ The corresponding neurons, which cause muscles to contract, act unopposed by inhibitory neurons.

3

➅ The result is a sustained, painful cramplike muscle spasm.

3

2 1

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24.3 Diseases Due to Anaerobic Bacterial Wound Infections

grene bacillus, and the organism can frequently be recovered from cultures of wounds. Only rarely does contamination of a wound result in gas gangrene, however, because anaerobic conditions are necessary for the disease to develop. Primarily a disease of wartime, gas gangrene occurs mainly in neglected wounds with fragments of bone, foreign material, and extensive tissue damage, as might occur from schrapnel. Gas gangrene is highly unusual in peace-time gunshot wounds, but it occurs occasionally in abdominal and other surgeries, especially in persons with underlying diseases.

Symptoms Gas gangrene (figure 24.10) begins abruptly, with pain rapidly increasing in the infected wound. Increased swelling occurs in the area, and a thin, bloody or brownish fluid leaks from the wound. The fluid may have a frothy appearance due to gas formation by the organism. The overlying skin becomes stretched tight and mottled with black. The victim appears very ill and apprehensive, but remains quite alert until late in the illness when, near death, he or she becomes delirious and lapses into a coma.

Causative Agent Several species of Clostridium can produce life-threatening gas gangrene when they invade injured muscle, but by far the most common offender is C. perfringens. These encapsulated Grampositive rods are shorter and fatter than C. tetani and usually do not exhibit spores in material from wounds or cultures.

Pathogenesis Two main factors foster the development of gas gangrene: (1) the presence of dirt and dead tissue in the wound and (2) long delays before the wound gets medical attention. The toxin implicated in pathogenicity is a-toxin, an enzyme that attacks a vital component of host cell membranes called lecithin. Clostridium perfringens is unable to infect healthy tissue but grows readily in dead and poorly oxygenated tissue,

569

releasing a-toxin. Growth is fostered by anaerobic conditions, as well as by the presence of growth factors and amino acids in dead tissue. Curiously, these infections are generally not ominous until they invade muscle. The toxin diffuses from the area of infection, killing leukocytes and tissue cells. Several enzymes produced by the pathogen, including collagenase and hyaluronidase, break down macromolecules in the dead tissues to smaller ones, thereby promoting swelling. The organisms grow readily in the fluids of the dead tissue, producing hydrogen and carbon dioxide from fermentation of amino acids and muscle glycogen. These gases accumulate in the tissue and contribute to the rise in pressure, thereby fostering spread of the infection. Without prompt surgical treatment, massive amounts of a-toxin diffuse into the bloodstream and destroy red blood cells, tissue capillaries, and other structures throughout the body and cause death. The reason for the rapid onset of severe toxicity when muscle becomes involved is unclear. It is not reversed by administering antibody to a-toxin. ■ growth factors, p. 94 ■ membrane-damaging toxin, p. 405

Epidemiology Besides being widespread in soil, C. perfringens is present in the feces of many animals and humans, and sometimes in the vagina of healthy women. Besides neglected battlefield wounds and occasional surgical wounds, gas gangrene of the uterus is fairly common after self-induced abortions, and rarely, it can occur after miscarriages and childbirth. In other cases, impaired oxygenation of tissue from poor blood flow because of arteriosclerosis, otherwise known as hardening of the arteries, and diabetes are predisposing factors. Cancer patients also have increased susceptibility to gas gangrene.

Prevention and Treatment

Neither toxoid nor vaccine is available for immunization against gas gangrene. Prompt cleaning and removal of dead tissue from wounds, is highly effective in preventing the disease. Treatment of gas gangrene depends primarily on the prompt surgical removal of all dead and infected tissues, and it may require amputations. Some authorities recommend hyperbaric (under increased pressure) oxygen treatment because it inhibits growth of the clostridia, thereby stopping release of toxin, and it also improves oxygenation of injured tissues. In this treatment the patient is placed in a special chamber and breathes pure oxygen under three times normal atmospheric pressure. Some people appear to improve dramatically with hyperbaric oxygen, but others show no benefit and develop complications from the treatment. Antibiotics such as penicillin are given to help stop bacterial growth and toxin production, but they are of minor if any value in treating the disease because they do not diffuse well into large areas of dead tissue and they do not inactivate toxin. FIGURE 24.10 Individual with Gas Gangrene (Clostridial Myonecrosis) Fluid Table 24.4 describes the main features of this seeping from the involved area typically shows bits of muscle digested by Clostridium perfdisease. ringens. Leukocytes are absent because the clostridial toxin kills them.

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TABLE 24.4 Gas Gangrene (Clostridial Myonecrosis) ➀ Clostridium perfringens spores

enter a wound having two essential characteristics: dead tissue and anaerobic conditions.

➁ The spores germinate, and the vegetative bacteria multiplying in dead tissue produce a-toxin. ➂ a-toxin diffuses into normal tissue and kills it. The infection expands into the newly killed tissue, the bacteria utilizing amino acids and growth factors released from the tissue by bacterial enzymes.

Symptoms

Severe pain, gas and fluid seep from wound, blackening of overlying skin; shock and death commonly follow

Incubation period

Usually 1 to 5 days

Causative agent

Usually Clostridium perfringens; other clostridia less frequently

Pathogenesis

Organism grows in dead and poorly oxygenated tissue and releases a-toxin; toxin kills leukocytes and normal tissue cells by degrading the lecithin component of their cell membranes; involvement of muscle causes shock by unknown mechanism.

Epidemiology

Wounds of war; dirt contamination of wounds, tissue death, impaired circulation to tissue as in persons with poor circulation from diabetes and arteriosclerosis; selfinduced abortions.

Prevention and treatment

Prompt cleaning and debridement of wounds is preventive; no vaccine available. Treatment: surgical removal of dirt and dead tissues of primary importance; hyperbaric oxygen of possible value; antibiotics to kill vegetative C. perfringens of marginal value.

5

➃ Swelling and gas produced by fermenting amino acids and muscle glycogen aid rapid progress of the infection.

➄ Massive amounts of a-toxin are produced and diffuse into the bloodstream, destroying blood and other cells throughout the body.

4 1 2

3

“Lumpy Jaw” (Actinomycosis)

Causative Agent

Many wound infections are caused by anaerobes other than clostridia. The main offenders are members of the normal microbiota of the mouth and intestine. Actinomycosis is not a mycosis because it is not caused by a fungus, but its name persists from when it was thought to be a fungal disease.

Most cases of actinomycosis are caused by Actinomyces israelii, a Gram-positive, filamentous, branching, anaerobic bacterium that grows slowly on laboratory media. A number of similar species can cause the disease in animals and humans.

Symptoms

Actinomyces israelii cannot penetrate the normal mucosal surface, but it can establish an infection in association with other organisms of the normal microbiota if introduced into tissue by wounds. The infectious process is characterized by cycles of abscess formation, scarring, and formation of passageways that generally ignore tissue boundaries. The disease usually progresses to the skin where pus is discharged, but occasionally it penetrates into bone, or into the central nervous system. In the tissue, A. israelii grows as dense yellowish colonies

Actinomycosis is characterized by slowly progressive, sometimes painful swellings under the skin that eventually open and intermittantly drain pus. The openings usually heal, only to reappear at the same or nearby areas days or weeks later. Most cases involve the area of the jaw and neck; the resulting scars and swellings gave rise to the popular name “lumpy jaw” (figure 24.11). In other cases the recurrent swellings and drainage develops on the chest or abdominal wall, or in the genital tract of women.

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Pathogenesis

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TABLE 24.5 “Lumpy Jaw” Actinomycosis Symptoms

Chronic disease; recurrent, sometimes painful swellings open and drain pus, heal with scarring; usually involves face and neck; chest, abdomen, and pelvis other common sites

Causative agent

Actinomyces israelii, a filamentous, branching, Gram-positive, slow-growing, anaerobic bacterium

Incubation period

Months (usually indeterminate)

Pathogenesis

Usually begins in a mouth wound, extends without regard to tissue boundaries to the face, neck, or upper chest; sometimes begins in the lung, intestine, or female pelvis. A. israelii always accompanied by normal microbiota. In tissue, grows as dense yellowish colonies called sulfur granules.

Epidemiology

No person-to-person spread. A. israelii commonly part of normal mouth, upper respiratory, intestine, and vagina microbiota. Dental procedures, intestinal surgery, insertion of IUDs can initiate infections.

Prevention and treatment

No proven preventive measures. Because of its slow growth. A. israelii infections require prolonged treatment; a number of antibacterial medications are effective.

FIGURE 24.11 ”Lumpy Jaw” (Actinomycosis) of the Face Abscesses, such as the one shown, form, drain, and heal, and then they recur at the same or different location. Sulfur granules, colonies of Actinomyces israelii, can be found in the drainage.

called sulfur granules (figure 24.12) because they are the color and size of particles of elemental sulfur. Because other more rapidly growing bacteria are invariably present, finding sulfur granules in the sinus drainage is a great aid in establishing the diagnosis. Almost half of the cases originate from wounds in the mouth, the remainder from the lung, intestine, or vagina. The detailed mechanisms by which the organism produces the disease have not yet been established.

Epidemiology Actinomyces israelii can be part of the normal microbiota of the mucosal surfaces of the mouth, upper respiratory tract, intestine, and sometimes the vagina. It is common in the gingival crevice, particularly with poor dental care. Pelvic actinomycosis can complicate use of intrauterine contraceptive devices (IUDs). Other species of Actinomyces responsible for actinomycosis of dogs, cattle, sheep, pigs, and other animals generally do not cause human disease. The disease is sporadic and is not transmitted person to person. ■ gingival crevice, p. 582

Prevention and Treatment There are no proven preventive measures. Actinomycosis responds to treatment with a number of antibacterial medications, including penicillin and tetracycline. To be successful, however, treatment must be given over weeks or months. This need for prolonged therapy probably is due to the slow growth of the organisms and their tendency to grow in dense colonies. The main features of actinomycosis are presented in table 24.5.

MICROCHECK 24.3 PMN nuclei Radiating filaments Sulfur granules

0.25 mm

FIGURE 24.12 Actinomyces israelii Sulfur Granule Microscopic view of a stained smear of pus from an infected person. Filaments of the bacteria can be seen radiating from the edge of the colony.

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Lockjaw (tetanus) is caused by an anaerobic, spore-forming bacterium with essentially no invasive ability, yet it causes death by releasing an exotoxin that is carried to the nervous system. Gas gangrene (clostridial myonecrosis), caused by another anaerobic spore-former, usually arises from neglected wounds containing dead tissue and foreign material and advances into normal muscle tissue. Lumpy jaw (actinomycosis) is caused by a branching, filamentous, slow-growing, anaerobic bacterium, a member of the normal flora of the mouth, upper respiratory tract, intestine, and vagina. The disease is characterized by recurrent abscesses that drain sulfur granules. ✓ Why do many tetanus victims fail to respond to tetanus antitoxin? ✓ What factors favor the development of gas gangrene (clostridial myonecrosis)? ✓ Would babies need to be immunized against lockjaw (tetanus) if their mother had been immunized against the disease? Explain.

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24.4 Bacterial Bite Wound Infections Focus Points Describe two zoonotic wound infections. Explain why human mouth microbiota can cause serious bite wound infections.

Each year, more than 3 million animal bites occur in the United States, the most feared result being the viral disease, rabies. The infection risk following an animal bite depends partly on the type of injury (crushing, lacerated, or puncture), and partly on the kinds of infectious agents in the animal’s mouth. ■ rabies, p. 663

Pasteurella multocida Bite Wound Infections Infections caused by bacteria that live in the mouth of the biting animal are very common. Surprisingly, a single species, Pasteurella multocida, is responsible for bite infections from a number of kinds of animals, including dogs, cats, monkeys, and humans, among others.

Symptoms There are no reliable symptoms or signs that distinguish among most bacterial bite wound infections. Spreading redness and tenderness and swelling of tissues adjacent to the wound, followed by the discharge of pus, are early indications of infection.

Causative Agent Pasteurella multocida is a Gram-negative, facultatively anaerobic coccobacillus that is easily cultivated in the laboratory. Most isolates are encapsulated. There are a number of different antigenic types.

Pathogenesis The details of pathogenesis are not yet known. There is evidence for one or more adhesins. Some strains produce a toxin that kills cells. The capsules of P. multocida are antiphagocytic. When opsonized by specific antibody, the organisms are ingested and killed by phagocytes. Abscesses commonly form. Without prompt treatment, infection can lead to bloodstream invasion or permanent loss of function.

Epidemiology Pasteurella multocida is best known as the cause of a devastating disease of chickens called fowl cholera. This disease is historically significant because while studying it, Pasteur first discovered that the virulence of a pathogen could be attenuated by repeated laboratory culture, and the attenuated organism used as a vaccine. Pasteurella multocida also causes diseases in a number of other animal species. Epidemics of fatal pneumonia and bloodstream infection occur in rabbits, cattle, sheep, and mice. Many healthy animals, however, carry the bacterium among their normal oral and upper respiratory microbiota. Both diseased animals and healthy carriers constitute a reservoir for human infections. Cats are more likely to carry. P. multocida than dogs, and so cat bites are more likely than dog bites to cause the infection.

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Prevention and Treatment No vaccines are available for use in humans. Immediate cleansing of bite wounds and prompt medical attention usually prevent the development of serious infection and possible permanent impairment of function. Unlike many Gram-negative pathogens, P. multocida is susceptible to penicillin. Usually, before the cultural diagnosis is known, amoxicillin plus a b-lactamase inhibitor are administered, available in a single tablet under the trade name Augmentin. This combination is used because amoxicillin is active against P. multocida, and with the addition of the b-lactamase inhibitor, the antibiotic is also active against many strains of b-lactamase-producing Staphylococcus aureus, another common cause of bite wound infections. This and other antibacterial medications are effective if given early in the infection. Table 24.6 gives the main features of Pasteurella multocida bite wound infections.

Cat Scratch Disease In the United States, cat scratch disease is the most common cause of chronic lymph node enlargement at one body site in young children (figure 24.13). Despite its name, this disease can be transmitted by bites, and probably other means. Typically the infection is mild and localized, lasting from several weeks to a few months. Of the estimated 22,000 annual cases, less than 2,000 require hospitalization.

Causative Agent Cat scratch disease is caused by Bartonella (formerly Rochalimaea) henselae, a tiny, slightly curved, Gram-negative rod cultivable on laboratory media.

Symptoms In about half the cases, the disease begins within a week of a scratch or bite with the appearance of a pus-filled pimple at the

TABLE 24.6 Pasteurella multocida Bite Wound Infections Symptoms

Spreading redness, tenderness, swelling, discharge of pus

Incubation period

24 hours or less

Causative agent

Pasteurella multocida, a Gram-negative, facultatively anaerobic, encapsulated coccobacillus

Pathogenesis

Introduced by bite, P. multocida attaches to tissue, resists phagocytes because of its capsule; probable cell-destroying toxin. Extensive swelling, abscess formation. Opsonins develop, allow phagocytic killing, limit spread.

Epidemiology

Carried by many animals in their mouth or upper respiratory tract.

Prevention and treatment

No vaccines to use in humans. Prompt wound care is preventive. Treatment with penicillin, other antibacterials, effective if given promptly.

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CASE PRESENTATION A 63-year-old woman, healthy except for mild diabetes, underwent surgery for a diseased gallbladder. The surgery went well, but within 72 hours the repaired surgical incision became swollen and pale. Within hours the swollen area widened and developed a bluish discoloration. The woman’s surgeon suspected gangrene. Antibiotic therapy was started and she was rushed back to the operating room where the entire swollen area, including the repaired operative incision, was surgically removed. After that, the wound healed normally, although she required a skin graft to close the large skin deficit. Large numbers of Clostridium perfringens grew from the wound culture. Six days later, a 58-year-old woman underwent surgery in the same operating room for a malignant tumor of the colon. The surgery was performed without difficulty, but 48 hours later she developed rapidly advancing swelling and bluish discoloration of her surgical wound. As with the first case, gangrene was suspected and she was treated with antibiotics and surgical removal of the affected tissue. She also required skin grafting. Her wound culture also showed a heavy growth of Clostridium perfringens. Because the surgery department had never had any of its patients develop surgical wound infections with Clostridium perfringens, much less two cases so close together, the hospital epidemiologist was asked to do an investigation. Among the findings of the investigation:

1. Cultures of horizontal surfaces in the operating room grew large numbers of Clostridium perfringens: 2. Unknown to the medical staff, a workman had recently serviced a fan in the ventilation system of the operating room, and for a time air was allowed to flow into the operating room, rather than out of it. 3. Heavy machinery was doing grading outside the hospital, creating clouds of dust. As a result of these findings, the operating room and its ventilating system were cleaned and upgraded. No further cases of surgical wound gangrene developed. 1. Was the surgeon’s diagnosis correct? 2. Many other patients had surgery in the same operation room. Why did only these two patients develop wound gangrene? 3. What could be done to help identify the source of the patients’ infections? Discussion 1. Clostridium perfringens is commonly cultivated from wounds without any evidence of infection. However, in these cases, there was not only a heavy growth of the organism but a clinical picture compatible with gangrene. The surgeon’s diagnosis was undoubtedly correct.

site of injury. Painful enlargement of the lymph nodes of the region develops in 1 to 7 weeks. About one-third of the patients develop fever, and in about half that number the lymph nodes become pus-filled and soften. The disease generally disappears without treatment in 2 to 4 months. About 10% of cases develop irritation of an eye with local lymph node enlargement, epileptic seizures and coma due to encephalitis, or acute or chronic fever associated with bloodstream or heart valve infection.

2. In both cases there was an underlying condition that increased the two patients’ susceptibility to infection—cancer in one, and diabetes in the other. Moreover, both had a recognized source for the organism. Cultures of as many as 20% of diseased gallbladders are positive for Clostridium perfringens, while the organism is commonly found in large numbers in the human intestine— a potential source in the case involving removal of the bowel malignancy. 3. The surgeon favored the idea that the infecting organism came from the patients themselves because such strains tend to be much more virulent than strains that live and sporulate in the soil. One the other hand, the gross contamination of the operating room as revealed by the cultures of its surfaces could indicate a very large infecting dose at the operative site, possibly compensating for lesser virulence. Moreover, no further cases occurred after cleaning the operating room and fixing the ventilation system. Unfortunately, in this case, no cultures of the excised gallbladder or bowel tumor were done, nor were the strains isolated from the wounds and the environment compared. Comparing the antibiotic susceptibility, toxin production, and other characteristics of the different isolates could have helped identify the source of the infections.

Pathogenesis The virulence factors of B. henselae and the process by which it causes disease are not yet known. The organisms can enter the body via a cat bite or scratch, or when cat saliva contaminates a mucous membrane. They are carried to the lymph nodes, and the disease is arrested by the immune system in most cases. Spread by the bloodstream, however, occurs in some individuals. Peliosis hepatis and bacillary angiomatosis are two complicating conditions seen mostly in people with AIDS. In peliosis hepatis, bloodfilled cysts form in the liver. In bacillary angiomatosis, nodules composed of proliferating blood vessels develop in the skin and other parts of the body. Bartonella henselae identifiable with fluorescent antibody is present in these lesions and those of typical cat scratch disease.

Epidemiology

FIGURE 24.13 Individual with Cat Scratch Disease, Showing Enlarged Lymph Node and Wrist Lesion

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Cat scratch disease mainly occurs in people under 18 years old. The disease is a zoonosis of cats, transmitted to humans mainly by kittens. Person-to-person spread does not occur. Bites and scratches represent the usual mode of transmission of B. henselae from cats to people. Asymptomatic bacteremia is common in cats, however, and transmission from cat to cat occurs by cat fleas. The fleas are biological vectors, and they discharge B. henselae in their feces. Cat fleas probably are responsible for transmission in cases where people develop the disease after they handle cats but are not scratched or bitten. The disease occurs worldwide. ■ biological vectors, p. 455

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Prevention and Treatment

Causative Agent

There are no proven preventive measures for cat scratch disease. It is prudent to avoid handling stray cats, however, especially young ones and those with fleas. Any cat-inflicted wound should be promptly cleaned with soap and water and then treated with an antiseptic. If signs of infection develop, or if the cat’s immunization status against rabies is uncertain, prompt medical evaluation is indicated. Severely immunodeficient persons should avoid cats if possible and, if not, control of fleas and abstinence from rough play are advisable. Severe B. henselae infections can usually be treated with antibacterial medications such as ampicillin, but some strains are resistant. The main features of cat scratch disease are presented in table 24.7.

The cause of streptobacillary rat bite fever is Streptobacillus moniliformis, a facultatively anaerobic, Gram-negative rod. Stained smears show a multiplicity of forms ranging from small coccobacilli to unbranched filaments more that 100 mm long. The organism is unique in that it spontaneously develops L-forms. L-forms are cell wall-deficient variants, first identified at the famous Lister Institute (hence, the L in L-form). As might be expected, L-form colonies resemble those of mycoplasmas—bacteria that lack a cell wall. ■ mycoplasmas, p. 273

Streptobacillary Rat Bite Fever Rat bites are fairly common among the poor people of large cities and among workers who handle laboratory rats. In the past, as many as one out of 10 bites resulted in rat bite fever. Currently, the disease is not reportable in any state and the incidence of the disease in the United States is unknown.

Symptoms Usually, the bite wound heals promptly without any problem noted. Two to 10 days later, however, chills and fever, head and muscle aches, and vomiting develop. The fever characteristically comes and goes. A rash usually appears after a few days, followed by pain on motion of one or more of the large joints.

TABLE 24.7 Cat Scratch Disease Symptoms

Pimple appears at the bite or scratch site, followed by local lymph node enlargement, fever; nodes may soften and drain pus; prolonged fever, convulsions, indicate spread to other body parts

Incubation period

Usually less than 1 week

Causative agent

Bartonella henselae, a tiny Gram-negative rod

Pathogenesis

The bacteria enter with cat bite or scratch and reach lymph nodes, where the disease is usually arrested. May spread by bloodstream, cause infections of the heart, brain, or other organs. Peliosis hepatis, bacillary angiomatosis mostly in those with AIDS.

Epidemiology

Prevention and treatment

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A zoonosis of cats, spread from one to another by cat fleas, which are biological vectors and have B. henselae in their feces. Infected cats usually asymptomatic, but often bacteremic. Humans are accidental hosts. No person-toperson spread. Mainly a disease of those under 18 years old. Avoiding rough play. Promptly wash skin breaks, apply antiseptic. Flea control in cats. Most B. henselae susceptible to antibacterial treatment.

Pathogenesis The organisms enter the body through a bite or scratch, and sometimes by ingestion. There is typically little enlargement of the local lymph nodes, and S. moniliformis quickly enters the bloodstream and spreads throughout the body. The majority of cases recover without treatment in about 2 weeks, but some are rapidly fatal, and others develop serious complications such as brain abscesses or infection of the heart valves. About 7% to 10% of untreated cases are fatal.

Epidemiology From 50% to 100% of wild, and 10% to 100% of healthy laboratory rats, as well as mice and other rodents, carry the organism in their nose and throat. Laboratory and pet store workers are at increased risk of contracting the disease. Rat bites and scratches are the usual source of human infections and can occur while the victim is sleeping. However, 30% of rat bite fever victims do not report bites or scratches. Epidemics of the disease have arisen from ingesting milk, water, or food contaminated with S. moniliformis from rodent droppings. The foodborne disease is called Haverhill fever from a 1926 epidemic in Haverhill, Massachusetts. Cases of rat bite fever have also been associated with exposure to animals that prey on rodents, including cats and dogs.

Prevention and Treatment Wild rat control and care in handling laboratory rats and their droppings are reasonable preventive measures. Penicillin, given intravenously, is the treatment of choice for cases of rat bite fever. This shows that either S. moniliformis L-forms do not occur in vivo, or if they do, they are avirulent. The main features of streptobacillary rat bite fever are presented in table 24.8.

Human Bites Wounds caused from human bites, striking the teeth of another person, or resulting from objects that have been in a person’s mouth are common and can result in very serious infections. Rarely, diseases such as syphilis, tuberculosis, and hepatitis B are transmitted this way. Much more commonly, it is the normal mouth microbiota that cause trouble.

Symptoms The wound may appear insignificant at first but then becomes painful and swells massively. Discharged pus often has a foul smell. Most of the wounds are on the extensor surface on the hand, and here the swelling may soon involve the palm also, and movement of some or all of the fingers becomes difficult or impossible.

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PERSPECTIVE 24.1 Infection Caused by a Human “Bite” A 26-year-old man injured the knuckle of the long finger of his right hand during a tavern brawl when he punched an assailant in the mouth. Due to his inebriated condition, a night spent in jail, and the insignificant early appearance of his knuckle, the man did not seek medical help until more than 36 hours later. At that time, his entire hand was massively swollen, red,

and tender. Furthermore, the swelling was spreading to his arm. The surgeon cut open the infected tissues, allowing the discharge of pus. He removed the damaged tissue and washed the wound with sterile fluid. Smears and cultures of the infected material showed aerobic and anaerobic bacteria characteristic of mouth microbiota, including species of Bacteroides and Strep-

Causative Agents Stains and cultures usually show members of the normal mouth microbiota, including anaerobic streptococci, fusiforms, spirochetes, and Bacteroides sp., often in association with Staphylococcus aureus.

Pathogenesis The crushing nature of bite wounds provides suitable conditions for anaerobic bacteria to establish infection. Although most members of the mouth microbiota are harmless alone, together they produce an impressive number of toxins and destructive enzymes. These include leukocidin, collagenase, hyaluronidase, ribonuclease, various proteinases, neuraminidase, and enzymes that destroy proteins of the complement system and antibody. Capsules of some species inhibit phagocytosis. Facultatively anaerobic organisms reduce available oxygen and thus encourage the growth of anaerobes. The result of all these factors is a synergistic infection,

TABLE 24.8 Streptobacillary Rat Bite Fever Symptoms

Chills, fever, muscle aches, headache, and vomiting; later, rash and pain in one or more of the large joints

Incubation period

Usually 2 to 10 days (range, 1 to 22) after a rat bite

Causative agent

Streptobacillus moniliformis, a highly pleomorphic, Gram-negative bacterium that spontaneously produces L-forms

Pathogenesis

Bite wound heals without treatment; S. moniliformis quickly invades bloodstream. Fevers come and go irregularly. Most victims recover without treatment; in others, infection established in various body organs, results in death if treatment is not given.

Epidemiology

Prevention and treatment

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Wild and laboratory rats can carry S. moniliformis. Bites of other rodents and animals that prey on them can transmit the disease to humans. Food or drink contaminated with rodent excreta can also transmit the infection; foodborne disease is called Haverhill fever. Control wild rats and mice, care in handling laboratory animals. Effectively treated with penicillin, other antibacterial medications.

tococcus. The patient was given antibiotics to combat infection, but the wound did not heal well and continued to drain pus. Several weeks later, X-rays revealed that infection had spread to the bone at the base of the finger. To cure the infection, the finger had to be amputated.

meaning that the sum effect of all the organisms acting together is greater than the sum of their individual effects. Irreversible destruction of tissues such as tendons and permanent loss of function can be the result. ■ facultative anaerobes, p. 92

Epidemiology Most of the serious human bite infections occur in association with violent confrontations related to alcohol ingestion, or during forcible restraint, as in law enforcement and in mental institutions. The risk is greatly increased when the biting individual has poor mouth care and extensive dental disease. Bites by little children are usually inconsequential.

Prevention and Treatment Prevention involves avoiding situations that lead to uncivilized behavior such as biting and hitting. Prompt cleansing of wounds followed by application of an antiseptic are advised, and most important is immediate medical attention if there is any suspicion of developing infection. Treatment of infected wounds consists of opening the infected area widely with a scalpel, washing the wound thoroughly with sterile fluid, and removing dirt and dead tissue. The choice of antibacterial medication includes one effective against anaerobes. The main features of human bite wound infections are presented in table 24.9.

TABLE 24.9 Human Bite Wound Infections Symptoms

Rapid onset, pain, massive swelling, drainage of foul-smelling pus

Incubation period

Usually 6 to 24 hours

Causative agent

Mixed mouth flora: anaerobic streptococci, fusiforms, spirochetes, anaerobic Gramnegative rods; sometimes Staphylococcus aureus

Pathogenesis

Various mouth bacteria act synergistically to destroy tissue.

Epidemiology

Alcohol-related violence; forcible restraint; poor mouth care and extensive dental disease.

Prevention and treatment

No proven preventive measures except to avoid altercations. Prompt cleansing of wound and application of antiseptic is advised. Treatment is usually surgical.

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MICROCHECK 24.4 Pasteurella multocida can infect bite wounds caused by a number of different animals, notably cats. Cat bites and scratches can also transmit Bartonella henselae, cause of cat scratch disease, characterized typically by local lymph node enlargement, but the disease may involve other parts of the body. Streptobacillary rat bite fever, caused by Streptobacillus moniliformis, is acquired from bites of rats and mice, and animals that prey on them. It is marked by fever that comes and goes and a rash. The causative bacterium, S. moniliformis, spontaneously develops L-forms. Human bite infections can be dangerous because certain members of the mouth microbiota with little invasive ability when growing alone can invade and destroy tissue when growing together. ✓ What Gram-negative organism commonly infects wounds caused by animal bites? ✓ What is the most common cause of chronic localized lymph node enlargement in young children? ✓ Why would normal mouth flora be a more common cause of serious human bite infections than the causative agents of syphilis, tuberculosis, and hepatitis B, which can also be transmitted by human bites?

24.5 Fungal Wound Infections Focus Points Give distinctive features of two wound infections caused by fungi originating from soil. Give evidence of the role of the immune system in controlling wound infections caused by fungi.

Fungal infections of wounds are unusual in economically developed countries, except that the yeast Candida albicans can be troublesome in severe burns and in those with wounds and underlying diseases such as diabetes and cancer. This yeast, commonly present among the normal microbiota and kept in check by it, becomes pathogenic when the competing microorganisms are eliminated, as

in individuals receiving antibacterial therapy. Other fungal wound infections are much more common in impoverished people around the world. For example, Madura foot, a condition caused by various species of soil fungi, occurs in areas of the world where foot injuries are common, resulting from lack of shoes. Named after the city in India where it was first described, Madura foot is characterized by swellings and draining passageways that discharge yellow or black granules of fungal material. Only a minority of those with foot injuries contract the disease despite exposure to the same fungi, suggesting that other factors such as malnutrition may play a role. Sporotrichosis, another kind of fungal wound infection, occurs worldwide and is not poverty-related.

“Rose Gardener’s Disease” (Sporotrichosis) Sporotrichosis, also known as “rose gardener’s disease,” is widely distributed around the world and is associated with activities that lead to puncture wounds from vegetation. Although many cases are sporadic, the disease can occur in groups of people engaged in the same occupation. Thousands of workers in the warm, humid mines of South Africa have contracted the disease from splinters on mine timbers. Epidemics have occurred in the United States among handlers of sphagnum moss from Wisconsin.

Symptoms In most cases, a hand or arm is involved, but the trunk, legs, and face can also be sites of infection. Typically, a chronic ulcer forms at the wound site, followed by a slowly progressing series of ulcerating nodules that develop sequentially toward the center of the body (figure 24.14). Lymph nodes in the region of the wound enlarge, but patients generally do not become ill. If they have AIDS or other immunodeficiency, however, the disease can spread throughout the body, threatening life.

Causative Agent Sporotrichosis is caused by the dimorphic fungus Sporothrix schenckii (figure 24.15), which lives in soil and on vegetation. ■ dimorphic fungus, p. 290

FIGURE 24.14 Individual with “Rose Gardener’s Disease” (Sporotrichosis) Notice the multiple abscesses along the course of the lymphatic drainage from the hand.

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24.5

Hyphae

25 mm

Symptoms

Painless, ulcerating nodules appearing in sequence in a linear pattern

Incubation period

Usually 1 to 3 weeks

Causative agent

Sporothrix schenckii, a dimorphic fungus

Pathogenesis

Spores multiply at site of introduction by thorn, splinter, or other plant material, causing a small nodule that ulcerates. Spores carried by lymph flow repeat the process along the course of the lymphatic vessel. May spread beneath the skin irrespective of lymphatic vessels.

Epidemiology

Distributed worldwide in tropical and temperate climates. Occupations requiring contact with sharp plant materials at particular risk.

Prevention and treatment

Protective gloves and clothing. Most cases effectively treated with potassium iodide. Generalized infections require amphotericin B or itraconazole.

Yeast forms

(b)

30 mm

FIGURE 24.15 Sporothrix schenckii, Showing the Two Forms of This Dimorphic Fungus (a) Mold form, (b) Yeast form, as seen in infected tissue.

Pathogenesis Sporothrix schenckii spores are usually introduced with an injury caused by plant material. After an incubation period that usually ranges from 1 to 3 weeks but can be much longer, the multiplying fungi cause a small nodule or pimple to form at the site of the injury. This lesion slowly enlarges and ulcerates, producing a red, easily bleeding skin defect. Unless the ulcer becomes secondarily infected with bacteria, there is little or no pus, and the lesion is pain-free. After a week or longer, the process repeats itself—progression of the disease usually follows the flow of a lymphatic vessel. In healthy individuals, the process does not proceed beyond the lymph node. Sometimes, however, satellite lesions appear irrespective of the lymphatic vessels. Without treatment, the disease can go on for years. ■ lymphatic vessel, p. 370

Epidemiology Sporotrichosis is distributed worldwide, mostly in the warmer regions but extending into temperate climates. In the United States, most cases occur in the Mississippi and Missouri river valleys. It is an occupational disease of farmers, carpenters, gardeners, greenhouse workers, and others who deal with plant materials. Public health authorities do not require reporting of cases of sporotrichosis and its incidence is unknown. Risk factors for the disease besides occupation include diabetes, immunosuppression, and alcoholism. Children can contract the disease from playing in baled hay. Individuals with chronic lung disease can contract

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TABLE 24.10 “Rose Gardener’s Disease” (Sporotrichosis)

Spores

(a)

Fungal Wound Infections

S. schenckii lung infections from inhaling dust from hay or cattle feed. Deaths from sporotrichosis are rare.

Prevention and Treatment Protective gloves and a long-sleeved shirt can help prevent sporotrichosis, especially when individuals are handling evergreen seedlings and sphagnum moss. This chronic disease is often misdiagnosed, leading to delayed and inappropriate treatment. Surprisingly, unlike other infections, sporotrichosis can usually be cured by oral treatment with the simple chemical compound potassium iodide (KI). KI is not active against S. schenckii in vitro, but somehow enhances the body’s ability to reject the fungus. Itraconazole or the antibiotic amphotericin B is used in rare cases when the disease spreads throughout the body. Table 24.10 presents some of the main features of sporotrichosis.

MICROCHECK 24.5 Candida albicans, often a member of the normal microbiota, can infect burns and other wounds, especially in individuals with underlying conditions. Madura foot, characterized by draining passageways that discharge colored granules, occurs mainly in areas of the world where shoes are scarce and foot injuries common. Rose gardener’s disease (sporotrichosis), caused by the dimorphic fungus Sporothrix schenckii, is widely distributed around the world, affecting mainly those associated with occupations that expose them to splinters and sharp vegetation. Unlike most invasive fungal infections, sporotrichosis is usually easy to treat. ✓ What fungal disease victimizes people who can’t afford shoes? ✓ What fungus infection is likely to result from thorn or splinter injuries? What is unique about the treatment of the disease? ✓ Why might Candida albicans become pathogenic in an individual receiving antibacterial medications?

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FUTURE CHALLENGES Staying Ahead in the Race with Staphylococcus aureus Over the last half century or so, scientists have generally, but not always, kept us at least one step ahead in the race between Staphylococcus aureus and human health. Today, “staph” seems again poised to challenge us for the lead, but new knowledge from molecular biology promises to help us leave this microscopic menace in the dust. In the past, we have relied heavily on developing antibacterial medications to kill or inhibit the growth of S. aureus but there is continuing investigation of alternative approaches. This search is aided by im-

provement in understanding staphylococcal pathogenesis. We now know in more detail the mechanism by which S. aureus obtains iron from hemoglobin. In another example, the bacterium’s protein A has been shown to attach to TNF receptors, and to recruit enormous numbers of pus cells. There have also been advances in vaccine development. An experimental vaccine composed of staphylococcal capsular material conjugated with a nontoxic form of Pseudomonas exotoxin A has been shown to reduce substantially staphylococcal infections in kidney dialysis patients.

Other options now seem to be within reach. For example, it should be possible to determine the structure of the active portion of toxin molecules and design medications that would bind to that site and inactivate it. Also, working with the staphylococcal genome, it is possible to determine which staphylococcal genes are responsible for virulence. The products of these genes can prove to be unexpected vaccine candidates. The race continues!

SUMMARY 24.1 Anatomy and Physiology Wounds expose components of tissues to which pathogens specifically attach. Wounds heal by forming granulation tissue, which in the absence of dirt and infection, fills the defect, and subsequently contracts to minimize scar tissue (figure 24.1). Thermal burns often present large areas of dead tissue devoid of competing organisms and body defenses, ideal conditions for microbial growth. Wound Abscesses An abscess is composed of a collection of pus, which is composed of leukocytes, components of tissue breakdown, and infecting organisms. Abscess formation localizes an infection within tissue, preventing its spread; inflammatory cells and clotted blood vessels separate the abscesses from normal tissue (figure 24.2). Anaerobic Wounds Anaerobic conditions are likely to occur in wounds containing dead tissue or foreign material, and those with a narrow opening to the air. Anaerobic conditions permit infection by particularly dangerous pathogens.

24.2 Common Bacterial Wound Infections (table 24.1) Possible consequences of wound infections include delayed healing, abscess formation, and extension of infection or toxins into adjacent tissue or the bloodstream. Infections can cause surgical wounds to split open, and they can spread to create biofilms on artificial devices. Staphylococcal Wound Infections (figures 24.3, 24.4) Staphylococci are the leading cause of wound infections, both surgical and accidental; Staphylococcus aureus and S. epidermidis are the most common wound-infecting species. Staphylococcus aureus possesses many virulence factors; occasional strains release a toxin that causes toxic shock syndrome (table 24.1). Staphylococcus epidermidis is less virulent but can form biofilms on blood vessel catheters and other devices. Group A Streptococcal “Flesh Eaters” Streptococcus pyogenes (Group A, b-hemolytic streptococcus) causes strep throat, scarlet fever, wound infections, and other conditions. Necrotizing fasciitis-causing strains of S. pyogenes produce exotoxin B, a protease thought to be responsible for the tissue destruction (figure 24.5).

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Pseudomonas aeruginosa Infections Pseudomonas aeruginosa, an aerobic, Gram-negative rod with a single polar flagellum, is an opportunistic pathogen widespread in the environment, and a cause of both nosocomial infections and those acquired outside the hospital. Production of two pigments by the bacterium often colors infected wounds green (figure 24.6). Toxin A of P. aeruginosa has a mode of action identical to that of diphtheria toxin, but it is antigenically distinct and attaches to different cells.

24.3 Diseases Due to Anaerobic Bacterial Wound Infections “Lockjaw” (Tetanus) (table 24.3) The characteristic symptom of tetanus is sustained, painful, cramplike spasms of one or more muscles (figure 24.7). The disease is often fatal. Tetanus is caused by an exotoxin, tetanospasmin, produced by Clostridium tetani, a non-invasive, anaerobic, Gram-positive rod (figure 24.8). The toxin renders the nerve cells that normally inhibit muscle contraction inactive by blocking release of their neurotransmitter (figure 24.9). The spores of C. tetani are widespread in dust and dirt, and most wounds are probably contaminated with them. Tetanus can be prevented by vaccination with toxoid (inactivated tetanospasmin), and maintaining immunity throughout life. Any wound, including surgeries, no matter how trivial, is an occasion to make sure immunizations are current (table 24.2). Gas Gangrene (Clostridial Myonecrosis) (table 24.4) Usually caused by the anaerobe Clostridium perfringens, symptoms begin abruptly with pain, and swelling; a thin, brown, bubbly discharge; and dark blue mottling of the tightly stretched overlying skin (figure 24.10). The toxin causes tissue necrosis; hydrogen and carbon dioxide gases are produced from fermentation of amino acids and glycogen in the dead tissue. There is no vaccine or toxoid. Prevention depends on prompt medical care of dirty wounds containing dead tissue. Treatment depends on urgent surgical removal of dead and infected tissue, and it may require amputation. “Lumpy law” (Actinomycosis) (table 24.5) Actinomycosis is a chronic, slowly progressive disease characterized by repeated swellings, discharge of pus, and scarring, usually of the face and neck (figure 24.11).

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Review Questions The causative agent is Actinomyces israelii, a member of the normal mouth, intestinal, and vaginal flora that enters tissues with wounds such as those with dental and intestinal surgery (figure 24.12). The organism is slow growing; treatment must be continued for weeks or months.

24.4 Bacterial Bite Wound Infections The kind of bite wound infection depends on the kinds of infectious agents in the mouth of the biting animal, and the nature of the wound— whether punctured, crushed, or torn. Pasteurella multocida Bite Wound Infections (table 24.6) Pasteurella multocida, a small, Gram-negative rod, can infect bite wounds inflicted by a number of animal species. P. multocida causes fowl cholera and diseases in other animals, but many animals are asymptomatic carriers. Cat Scratch Disease (table 24.7, figure 24.13) Cat scratch disease is the most common cause of chronic, localized lymph node enlargement in children. Caused by Bartonella henselae, it begins with a pimple at the site of a bite or scratch, followed by enlargement of local lymph nodes, which often become pus-filled. Most individuals with cat scratch disease recover without treatment, but persons with AIDS are susceptible to two serious conditions caused by B. henselae— peliosis hepatis and bacillary angiomatosis. Streptobacillary Rat Bite Fever (table 24.8) Streptobacillary rat bite fever is characterized by relapsing fevers, head and muscle aches, and vomiting, following a rat bite. A rash and joint pains often develop. It is usually caused by Streptobacillus moniliformis, a highly pleomorphic, Gram-negative rod that characteristically produces

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cell wall deficient variants called L-forms. People who live in rat-infested dwellings and those who handle laboratory rats are at greatest risk of contracting the disease. Human Bites (table 24.9) Human bites, injuries from objects that have been in a person’s mouth, and those from striking a person in the teeth often result in severe infections, with pain, massive swelling, and foul-smelling pus. The infections are usually caused by members of the normal mouth flora acting synergistically, including anaerobic streptococci, fusiforms, spirochetes, and Bacteroides sp., often with Staphylococcus aureus. The crushing nature of bite wounds causes death of tissue and conditions suitable for growth of anaerobes; prompt cleansing and application of an antiseptic are advised.

24.5 Fungal Wound Infections Fungal wound infections are unusual in economically developed countries, except for Candida albicans infections of burns and other wounds in individuals receiving antibacterial therapy. Madura foot occurs in many impoverished areas of the world where people do not wear shoes. “Rose Gardener’s Disease” (Sporotrichosis) (table 24.10) Rose gardener’s disease, also called sporotrichosis, is a chronic fungal disease mainly of people who work with wood or vegetation. The usual case is characterized by painless, ulcerating nodules that develop one after the other along the course of a lymphatic vessel (figure 24.14). The causative organism is the dimorphic fungus, Sporothrix schenckii (figure 24.15), usually introduced into wounds caused by thorns or splinters. The fungus is distributed worldwide in tropical and temperate climates; people at risk include farmers, carpenters, gardeners, and greenhouse workers.

REVIEW QUESTIONS Short Answer 1. Give three undesirable consequences of wound infection. 2. What property of Staphylococcus epidermidis aids its ability to colonize plastic materials used in medical practice? 3. What is the relationship between the superantigens of S. aureus and the organism’s production of toxic shock? 4. Name two underlying conditions that predispose to Streptococcus pyogenes “flesh-eating” disease. 5. Give two sources of Pseudomonas aeruginosa. 6. Outline the pathogenesis of lockjaw. 7. What characteristic of Clostridium tetani aids its isolation when other bacteria are present? 8. Explain why C. tetani can be cultivated from wounds in the absence of tetanus. 9. What characteristics of bite wounds favor anaerobic infections? 10. What is the causative agent of cat scratch disease? Why is it a threat to patients with AIDS? 11. What is a synergistic infection? How might one be acquired? 12. Why is sporotrichosis sometimes called rose gardener’s disease?

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Multiple Choice 1. All of the following are true of Staphylococcus aureus, except a) it is generally coagulase-positive. b) its infectious dose is increased in the presence of a foreign body. c) some strains infecting wounds can cause toxic shock. d) nasal carriage increases the risk of surgical wound infection. e) it is pyogenic. 2. Which of these statements about Streptococcus pyogenes is false? a) It is a Gram-positive coccus occurring in chains. b) Some strains that infect wounds can cause toxic shock. c) Some strains that infect wounds can cause necrotizing fasciitis. d) It can cause puerperal sepsis. e) A vaccine is available for preventing S. pyogenes infections. 3. Choose the one false statement about Pseudomonas aeruginosa. a) It is widespread in nature. b) Some strains can grow in distilled water. c) It is a Gram-positive rod. d) It produces a hemolytic toxin that has the same mode of action as a-toxin of Clostridium perfringens. e) Under certain circumstances it can grow anaerobically.

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4. Which of these statements concerning tetanus is true? a) It can originate from a bee sting. b) Immunization is carried out using tiny doses of tetanospasmin. c) Those who recover from the disease are immune for life. d) Tetanus immune globulin is derived from the blood of immunized sheep. e) It is easy to avoid exposure to spores of the causative organism. 5. Choose the one true statement about gas gangrene. a) There are few or no leukocytes in the wound drainage. b) It is best to rely on antibacterial medications and avoid disfiguring surgery. c) A toxoid is generally used to protect against the disease. d) Only one antitoxin is used for treating all cases of the disease. e) It is easy to avoid spores of the causative agent. 6. All the following statements about actinomycosis are true, except a) it can occur in cattle. b) it is caused by a branching filamentous bacterium. c) it always appears on the jaw. d) it can arise from intestinal surgery. e) its abscesses can burrow into bone. 7. Which of the following statements about Pasteurella multocida is false? a) Infections generally respond to a penicillin. b) It can cause epidemics of fatal disease in domestic animals. c) It is commonly found in the mouths of biting animals, including human beings. d) A vaccine is, in general, used to prevent P. multocida disease in people. e) Cat bites are more likely to result in P. multocida infections than dog bites. 8. Which of these statements about cat scratch disease is false? a) It is a common cause of chronic lymph node enlargement in children. b) It is a serious threat to individuals with AIDS. c) Cat scratches are the only mode of transmission to humans. d) It is a zoonosis of cats transmitted by fleas. e) It can affect the brain or heart valves in a small percentage of cases.

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9. The following statements about Streptobacillus moniliformis are all true, except a) it can be transmitted by food. b) its colonies can resemble those of mycoplasmas. c) it can be transmitted by the bites of animals other than rats. d) human infection is characterized by irregular fevers, rash, and joint pain. e) it is a Gram-positive spore-forming rod. 10. Pick out the statement concerning sporotrichosis that is wrong. a) It is characterized by ulcerating lesions along the course of a lymphatic vessel. b) Person-to-person transmission is common. c) It can occur in epidemics. d) It can persist for years if not treated. e) The causative organism is a dimorphic fungus.

Applications 1. Clinicians become concerned when the laboratory reports that organisms capable of digesting collagen and fibronectin are present in a wound culture. What is the basis of their concern? 2. ABC pharmaceutical company produces a drug that inhibits new blood vessel growth into cancers, thus depriving the cancer cells of the nutrients and hormones needed for growth of the tumor. A researcher in the company laboratory has now isolated a compound having the opposite effect. Do you see any possible role for the new compound in the treatment of wounds? 3. An army field nurse performing triage at a mobile surgical hospital asks this question of all the ambulance drivers: “Was the soldier wounded while in a pasture?” Why did he ask this question?

Critical Thinking 1. In what way would the incidence of tetanus at various ages in an economically disadvantaged country differ from age incidence in western industrialized countries? 2. Could colonization of a wound by a noninvasive bacterium cause disease? Explain your answer. 3. Surgical wound infections are frequently due to Staphylococcus aureus, a bacterium often carried in the nostrils and sometimes on the skin. How would you study the relationship, if any, between carriage of S. aureus and the chance of getting a wound infection?

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25 Yellow color of eye and skin as seen in jaundice.

Digestive System Infections A Glimpse of History “The face was sunken as if wasted by lingering consumption, perfectly angular, and rendered peculiarly ghastly by the complete removal of all the soft solids, in their places supplied by dark leadcolored lines. The hands and feet were bluish white, wrinkled as when long macerated in cold water; the eyes had fallen to the bottom of their orbes, and envinced a glaring vitality, but without mobility, and the surface of the body was cold.” This vivid description of cholera was written by Army surgeon S. B. Smith in 1832 when the disease first appeared in the United States. “Lingering consumption” refers to the marked wasting of the body seen in people with chronic tuberculosis. Cholera is a very old disease and is thought to have originated in the Far East thousands of years ago. Sanskrit writings indicate that it existed endemically in India many centuries before Christianity. With the increased shipping of goods, and the mobility of people during the nineteenth century, cholera spread from Asia to Europe and then to North America. Cholera was a major epidemic disease of the nineteenth century and appeared in almost every part of the world. In 1854, John Snow, a London physician, demonstrated that cholera was transmitted by contaminated water. He observed that almost all people who contracted cholera got their water from a well on Broad Street. When the handle of the Broad Street pump was removed, people were forced to obtain their water elsewhere and the cholera epidemic in that area subsided. Snow’s explanation was not generally accepted by other doctors, mostly because disease-causing “germs” had yet to be discovered. It was not until 1883 that Robert Koch isolated Vibrio cholerae, the bacterium that causes cholera.

In the United States, cholera epidemics occurred in 1832, 1849, and 1866. The disease seemed to affect poorer people— those unfortunate enough to be crowded together in cities where cleanliness was impossible to maintain. Many doctors were of the opinion that not only were the personal habits of these people “rash and excessive,” but also that they insisted on taking the “wrong” medicines. By 1866, however, it was evident that where cholera appeared, the lack of sanitation was at fault. Public health agencies then played a major role in preventing epidemic cholera.

I

n the spring of 1997, an epidemic of severe diarrhea broke out among 90,000 sick and malnourished refugees in the Democratic Republic of Congo. More than 1,500 deaths occurred over a 3-week period. Volunteers from the medical relief organization Medecins Sans Frontieres rushed to set up medical facilities, while people from the World Health Organization, Red Cross, and local health agencies worked to provide a filtered and chlorinated water source, constructed latrines, and educated the people about sanitary measures. Treatments were started using oral and intravenous rehydration fluids. Unfortunately, at that point, the refugees were all scattered and driven away by unidentified soldiers who were afraid of the disease. Fear generated by a diarrhea epidemic, compounded by ignorance, can defeat efforts based on reason and understanding of disease.

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KEY TERMS Bile Yellow-colored fluid produced by the liver that aids in the absorption of nutrients from the intestine. Cariogenic Causing dental caries, tooth decay. Cholera Severe, watery diarrhea caused by Vibrio cholerae. Cirrhosis A condition marked by extensive scarring of the liver. Dysentery Condition characterized by crampy abdominal pain and bloody diarrhea.

Digestive System Infections Gastroenteritis Acute inflammation of the stomach and intestines; the syndrome of nausea, vomiting, diarrhea, and abdominal pain.

Microvilli Tiny tubular processes from the luminal surfaces of cells such as those lining the intestine; increases surface area of the cell.

Gingivitis Inflammation of the gums.

Pseudomembranous Colitis Disease of the colon caused by Clostridium difficile in which patches called pseudomembranes, composed of dead epithelium, inflammatory cells, and clotted blood, form on the intestinal lining.

Glucans Polysaccharides composed of repeating subunits of glucose; involved in formation of dental plaque. Hemolytic Uremic Syndrome (HUS) Serious condition characterized by red cell breakdown and kidney failure; a sequel to infection by certain Shiga toxin-producing strains of Shigella dysenteriae and Escherichia coli. Hepatitis Inflammation of the liver.

25.1 Anatomy and Physiology Focus Points List the functions of the main components of the upper digestive tract.

Reverse Transcriptase Enzyme that synthesizes DNA complementary to an RNA template. Secretion System A mechanism by which bacterial pathogens transfer gene products directly into host cells.

to discharge stomach contents at a controlled rate into the small intestine, where they are digested under alkaline conditions, and nutrients are absorbed into the bloodstream; to move undigested material into the large intestine, where water is absorbed from the intestinal contents along with any remaining vitamins, minerals, or nutrients; and to discharge the waste as feces.

Describe the role of the liver in health and disease.

The digestive tract, sometimes referred to as the alimentary or gastrointestinal (GI) tract, is the passageway that extends from the mouth to the anus. Like the skin, it is one of the body’s boundaries with the environment, and it is one of the major routes into the body for invading microbial pathogens. The digestive tract and its accessory organs—the saliva-producing glands, liver, and pancreas—together compose the digestive system, the main purpose of which is to provide nourishment for the body. The upper part consists of the mouth, salivary glands, esophagus, and stomach, and the lower part includes the intestines, pancreas, and liver. Figure 25.1 illustrates the relationships among the various parts of the digestive system. The main functions of the system are: to grind food in the mouth into small particles that can readily react with digestive juices that break down large, complex molecules into absorbable components; to move the food through the esophagus to the stomach, where it undergoes preliminary treatment with acid and enzymes;

The Mouth The mouth is mainly a grinding apparatus. The tongue and cheeks move bites of food to be ground up by the teeth, which are composed of a calcium compound harder than bone (figure 25.2). The outer portion of the teeth, the enamel, is a hard, protective layer. Pits and crevices normally present on the enamel surfaces of the teeth collect food particles and offer protected sites for microbial colonization. Beneath the enamel lies the dentin, a softer, more easily penetrated layer. The gingival crevice, the space between the tooth and gum, is important because inflammation at this site can lead to loss of the tooth.

Salivary Glands Salivary glands are located under the tongue and laterally in the floor of the mouth. There are two additional saliva-producing glands, called the parotids, one on either side of the face below the ears. About 1,500 ml of saliva is secreted from the salivary glands each day. It moistens and lubricates the mouth, and

FRANK & ERNEST: © Thaves/Dist. By Newspaper Enterprise Association, Inc.

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25.1

Anatomy and Physiology

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(a) Food ground; digestion initiated by saliva

Parotid gland Mumps

Teeth Tongue

(b) Conveyed to stomach

Salivary glands

Upper digestive tract

Esophagus Esophagitis

(c) Acid digestion

Stomach Gastritis Gastric ulcer Pylorus

Liver Hepatitis

Gallbladder Cholecystitis

Pancreas Pancreatitis

Upper small intestine (duodenum) Duodenal ulcer

(d) Alkaline digestion and absorption Lower digestive tract

Small intestine Enteritis Large intestine Dysentery Colitis

(e) Resorption of water and nutrients; elimination of feces

Small intestine joins large intestine. Appendix Appendicitis

Villi Rectum Anal canal

Microvilli

FIGURE 25.1 The Digestive System To the right of the human figure is a schematic representation of the major components of the system. Terms in color under the body part labels name some of the disease conditions that can affect that part. For example, mumps is a viral disease affecting the parotid gland; cholecystitis is an infection of the gallbladder.

Openings of intestinal glands Intestinal gland

contains the enzyme amylase, which begins the breakdown of starches present in food. Saliva is extremely important in protecting the teeth from decay because it is saturated with calcium and contains buffers that help neutralize acids. People with poor saliva production are subject to severe tooth decay. Saliva also contains antibacterial substances including lysozyme, the enzyme that attacks the peptidoglycan of bacterial cell walls; lactoferrin, a substance that binds iron ions critically required

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Epithelial cell

by bacteria; and secretory IgA antibodies that inhibit bacterial attachment. ■ lactoferrin, p. 349 ■ IgA, p. 374 ■ lysozyme, p. 62

The Esophagus The tongue and throat muscles work together in swallowing to propel food from the mouth and throat into the esophagus, a collapsible tube about 10 inches long, located behind the

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Enamel Dentin Crown Pulp Gingival crevice Gingiva (gum)

Bone Periodontal membrane Root Root canal

Nerve Vein Artery

tions. Tiny intestinal glands continuously secrete large amounts of fluid into the lumen, the space enclosed by the walls of the intestine. This fluid is then reabsorbed along with the products of food digestion. Small intestine function depends on active transport of nutrients and electrolytes across the plasma membranes of the epithelial cells. For example, sodium ions (Na;) are taken up by the cell when glucose or amino acids are absorbed; hydrogen ions (H;) and bicarbonate ions (HCO3:) are secreted to adjust the pH of the intestinal contents. Movement of these substances is accompanied by water molecules. Digestion takes place as the cells secrete juices rich in enzymes, such as those that break peptides into amino acids, and disaccharidases that convert complex sugars into simpler ones. The major part of nutrient absorption, including absorption of monosaccharides, amino acids, fatty acids, and vitamins, takes place in the small intestine. Some minerals, such as iron, can only be absorbed there. In addition, the small intestine reabsorbs approximately 9 liters of fluid per day. The lining cells of the small intestine are continuously shed and replaced by new cells, so that cells poisoned by a microbial toxin are soon replaced. Intestinal epithelial cells are completely replaced every 9 days—one of the fastest turnover rates in the body.

The Pancreas FIGURE 25.2 Structure of a Tooth and Its Surrounding Tissues

windpipe. The esophagus has a muscular wall that contracts rhythmically to move food and liquid in a process called peristalsis. The lower portion of the esophagus normally closes to prevent regurgitation of stomach contents. The esophagus rarely becomes infected except in individuals with AIDS or other immunodeficiencies.

The Stomach The lower portion of the esophagus leads into the stomach, an elastic, saclike structure with a muscular wall. Some of the cells that line it produce hydrochloric acid, whereas others produce pepsinogen, which becomes the protein-splitting enzyme pepsin upon contact with acid. The stomach itself is protected from the acid and enzymes by a thick layer of mucus secreted by the stomach lining. Stomach emptying is controlled by a complex system of nerve impulses and hormones acting on a muscular valve, the pylorus, which determines the rate at which the stomach contents enter the intestine.

The Small Intestine Although it is only 8 or 9 feet long, the small intestine has an enormous surface area, about 30 square feet, which facilitates nutrient absorption. The inside surface of the intestine is covered with many small, fingerlike projections called villi, each 0.5 to 1 mm long. Each of these villi is, in turn, covered with cells that have cytoplasmic projections called microvilli (see figure 25.1). Many intestinal digestive enzymes are present as integral parts of the plasma membranes of these microvilli. This epithelial surface has both secretory and absorptive func-

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The pancreas is a large, glandular organ located behind the stomach. Some cells of the pancreas produce hormones, and others produce digestive enzymes. The hormones are released directly into the bloodstream and help regulate various body functions— for example, insulin helps regulate the amount of glucose in the blood. On the other hand, about 2 liters of pancreatic digestive juices discharge directly into the upper portion of the small intestine each day. These fluids, as well as digestive juices of the small intestine itself, are alkaline and neutralize the stomach acid as it passes into the intestine.

The Liver The liver is a large, dark-red, glandular organ located in the upper abdomen on the right side. The liver aids digestion, neutralizes poisons, degrades medications, and removes a normal breakdown product of hemoglobin from the bloodstream. This yellowish product, called bile pigment, is discharged with the bile, the fluid produced by the liver. Each day, about 500 ml of bile flows through a system of tubes into the upper small intestine. Severe liver disease and obstruction of the bile ducts can produce jaundice, a yellow color of the skin and eyes caused by buildup of bile pigment in the blood. The gallbladder is a saclike structure in which bile is concentrated and stored. Substances in the bile called bile salts help the intestine absorb oils and fats and the fat-soluble vitamins A, D, E, and K. The normal brown color of feces results from the action of intestinal bacteria on bile pigment. The liver also inactivates poisonous substances that enter the bloodstream. For example, ammonia produced by intestinal bacteria and absorbed into the bloodstream could poison the body if it were not detoxified by the liver. The liver also chemically alters and excretes many medications; if the liver is damaged, as it might

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25.2

be by a viral infection, lower medication doses might be needed to avoid the buildup of toxic levels of the medication.

The Large Intestine The main function of the large intestine is to recycle water and absorb nutrients. Because the small intestine absorbs so much water, only 300 to 1,000 ml of fluid normally reach the large intestine per day. From this volume of fluid, the large intestine absorbs water, electrolytes, vitamins, and amino acids. The semisolid feces, composed of indigestible material and bacteria, remain. Infection of the large intestine can interfere with absorption and stimulate the painful peristaltic contractions known as “stomach cramps.”

MICROCHECK 25.1 The digestive tract is a major route for pathogenic microorganisms to enter the body. People with poor saliva production risk severe tooth decay. Infections of the esophagus are so unusual in normal people that their occurrence suggests immunodeficiency. The stomach is responsible for acid digestion of food; the small intestine carries out alkaline digestion and absorption of nutrients. Undigested material becomes feces in the large intestine. ✓ What makes the surface area of the small intestine so large, when it is only 8 to 9 feet long? ✓ What is the main function of the large intestine? ✓ What might occur to the blood levels of a medication if another medication interferes with its degradation by the liver?

25.2 Normal Microbiota Focus Points Describe how suppression of the normal microbiota can result in pseudomembranous colitis.

Normal Microbiota

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action of food and the tongue and the flushing action of salivary flow. The fact that the cells lining various parts of the mouth have different receptors accounts for the distribution of the various species of streptococci. The host limits the numbers of bacteria on its mucous membranes by constantly shedding the superficial layers of cells and replacing them with new ones; the rate of this shedding correlates with the number of microorganisms present on the surface. Because teeth are a non-shedding surface, large collections of bacteria can build up on them in a biofilm. These masses of bacteria, called dental plaque (figure 25.3), form because the bacteria attach to specific receptors on each other or on the tooth, and they can be bound together by extracellular polysaccharides. There can be up to 100 billion bacteria per gram of plaque. Metabolic by-products of one species are utilized by another. Plaque organisms consume O2, thereby creating conditions that permit the growth of strict anaerobes. In fact, colonization of the mouth by strictly anaerobic microbes requires the presence of teeth, because only teeth provide sufficiently anaerobic habitats for growth of these organisms. Dental plaque, gingival crevices, and fissures in the teeth are such habitats. ■ lactic acid production, p. 147 ■ biofilms, p. 85

The Intestines Only small numbers of bacteria live in the upper small intestine because they are continually flushed away by the rapid passage of digestive juices. The predominant organisms are usually aerobic and facultatively anaerobic, Gram-negative rods and some streptococci. Lactobacilli and yeasts such as Candida albicans are found in small numbers. The bacterial population increases as the intestinal contents move toward the large intestine. In contrast to the relatively scanty numbers of organisms in the small intestine, the large intestine contains high numbers of microorganisms—approximately 1011 bacteria per gram of feces. These large numbers occur because of the abundance of nutrients

List activities of the normal microbiota potentially of value to the host. This section focuses mainly on microbiota of the oral cavity and intestine. The esophagus has a relatively sparse population, consisting mostly of bacteria from the mouth and upper respiratory tract. When empty of food, the normal stomach has few microorganisms because most are killed by the action of acid and pepsin. ■ normal microbiota, p. 462

The Mouth Of all species of bacteria introduced into the mouth from the time of birth onward, relatively few can colonize the oral cavity. Streptococcal species—Gram-positive, chain-forming cocci that produce lactic acid as a by-product of carbohydrate metabolism— are the most numerous. One species of Streptococcus preferentially colonizes the upper part of the tongue, another colonizes the teeth, and still another colonizes the mucosa of the cheek. Streptococci and other bacteria attach specifically to receptors on host tissues, allowing the microorganisms to resist the scrubbing

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5 mm

FIGURE 25.3 Scanning Electron Micrograph of Dental Plaque The many kinds of bacteria composing the plaque exhibit specific attachments to the tooth and to each other, and may be bound together by extracellular polysaccharides.

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in undigested and indigestible food material. Bacteria make up about one-third of the fecal weight. The numbers of anaerobic bacteria, notably including members of the genus Bacteroides, generally exceed the numbers of other organisms by about 100fold. Of the fecal microorganisms able to grow in the presence of air, facultatively anaerobic, Gram-negative rods, particularly Escherichia coli and other enterobacteria, predominate. Fecal organisms are an important source of opportunistic pathogens, especially for the urinary tract. The enormous population of bacteria comprises species that can work together enzymatically to change numerous materials. The currently recommended high-fiber diets contain substances that are indigestible by the gastric and intestinal juices but are readily degraded by intestinal organisms, which often produce large amounts of carbon dioxide, hydrogen, and methane gas. Abdominal discomfort and discharge of intestinal gas (flatus) from the anus is an unfortunate result. Bacterial enzymes can also convert various substances in food to carcinogens and therefore may be involved, along with diet, in the production of intestinal cancer. ■ opportunistic pathogens, p. 394 ■ enterobacteria, p. 262 Intestinal bacteria synthesize a number of useful vitamins, including niacin, thiamine, riboflavin, pyridoxine, vitamin B12, folic acid, pantothenic acid, biotin, and vitamin K. These vitamins are important when a person’s diet is inadequate.

Antibiotic-Associated Diarrhea The normal microbiota helps prevent colonization of the large intestine by pathogens. Antibiotic treatment, especially with broad-spectrum medications, disrupts the normal microbiota and results in mild to severe diarrhea. A sometimes lifethreatening disease called antibiotic-associated, or pseu-

domembranous, colitis can follow antibiotic therapy. The disease is caused by the toxin-producing, anaerobic bacterium Clostridium difficile, which readily colonizes the intestine of people whose normal intestinal microbiota has been reduced by antimicrobial chemotherapy. The toxins of C. difficile are lethal to intestinal epithelium and cause small patches called pseudomembranes, composed of dead epithelium, inflammatory cells, and clotted blood, to form on the intestine. Fever, abdominal pain, and profuse diarrhea result. Suppression of intestinal microbiota with antibacterial medications can also increase susceptibility to other pathogens such as Salmonella enterica, to be discussed later.

MICROCHECK 25.2 The distribution of bacterial microbiota in the mouth is governed by different receptors on the epithelium. The quantity of microbiota on mouth epithelium is limited by shedding. Because the teeth are a non-shedding surface, enormous populations of bacteria, manifest as dental plaque, form a biofilm on teeth. A properly functioning stomach destroys most microorganisms before they reach the intestine. The normal intestinal microbiota helps protect the body from infection; disruption of the microbiota by antibiotics can lead to infection. Metabolic activity of intestinal microbiota produces vitamins, but it causes gas and can contribute to cancer. ✓ Why must teeth be present in order for anaerobic bacteria to colonize the mouth? ✓ What is the advantage to the body of having pepsin becoming active only on exposure to acid? ✓ Why is it that the tongue and cheek epithelium doesn’t provide sufficiently anaerobic conditions for plaque anaerobes to grow?

UPPER DIGESTIVE SYSTEM INFECTIONS

25.3 Bacterial Diseases of the Upper Digestive System Focus Points Compare and contrast dental caries, periodontal disease, and trench mouth. Give the evidence that Helicobacter pylori infection predisposes people to stomach cancer.

It may be surprising that the most common bacterial disease of human beings occurs in the mouth, and that bacterial infections of the stomach are not only common but can lead to ulcers and cancer. These infections often go unnoticed for years but have consequences both locally and for the rest of the body. Oral microbiota, for example, can enter the blood-

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stream during dental procedures and cause subacute bacterial endocarditis, and some studies suggest that chronic gum infections play a role in hardening of the arteries and arthritis. The most important bacterial diseases of the upper alimentary system concern the teeth, the gums, and the stomach. ■ subacute bacterial endocarditis, p. 677

Tooth Decay (Dental Caries) Dental caries, generally known as tooth decay, is the most common infectious disease of human beings. The cost to restore and replace teeth damaged by this disease is estimated to be about $20 billion per year in the United States. Dental caries is the main reason for tooth loss. Across the United States, from 14% to 47% of people aged 65 or older have lost all their teeth.

Symptoms Dental caries is usually far advanced before any symptoms develop. The severe, throbbing pain of a toothache is often the

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first symptom. Sometimes there is noticeable discoloration, roughness, or defect, and a tooth can break during chewing.

Causative Agent Dental caries is caused principally by Streptococcus mutans and closely related species. These bacteria live only on the teeth and cannot colonize the mouth in the absence of teeth. They produce lactic acid as a by-product of their metabolism of sugars and, unlike many other bacteria, they thrive under acidic conditions below pH 5. Another important feature is that they produce insoluble extracellular glucans from sucrose, but not from other sugars. Glucans—polysaccharides composed of repeating subunits of glucose—are essential for the production of dental caries on smooth tooth surfaces. ■ polysaccharides, p. 37

The first step in the formation of a cariogenic plaque, meaning a plaque that causes tooth decay, is the adherence of oral streptococci to specific receptors on the tooth pellicle. The pellicle is a thin film of proteinaceous material adsorbed on the tooth from the saliva. Other species of bacteria attach specifically to earlier arrivals. Two species that might not attach to each other can attach to a third. If dietary sucrose is present, S. mutans attaches to the bacterial mass and produces glucans from sucrose through the action of extracellular enzymes. Sucrose is split by the enzymes to the monosaccharides glucose and fructose. The glucose is polymerized, yielding glucan, and the fructose is metabolized, producing lactic acid. The glucans bind the organisms together and to the tooth to form a biofilm, making the plaque impenetrable to saliva. When sugar enters the mouth, the pH of cariogenic plaques drops from its normal value of about 7 to below 5 within minutes (figure 25.4). This 100-fold increase in acidity begins dissolving the calcium phosphate of the teeth. The duration of this acidic 7 Glucose rinse

pH

6

5

High acidity in dental plaque

4 10

20 Minutes

30

40

FIGURE 25.4 Increase in Acidity in Cariogenic Dental Plaque After Rinsing the Mouth with a Glucose Solution Tooth enamel begins to dissolve at about pH 5.5, continuing as pH decreases.

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state depends on how long the teeth are exposed to sugars and on the concentration of the sugars. After food leaves the mouth, the pH of the plaque rises slowly to neutrality. The delay in return of the pH to neutrality is due to the ability of S. mutans to store a portion of its food as an intracellular, starchlike polysaccharide that is later metabolized with the production of acid. Cariogenic plaque thus acts as a tiny, acid-soaked sponge closely applied to the tooth. Both S. mutans and a suitable sucrose-rich diet are required to produce dental caries on smooth surfaces of the teeth. In deep fissures or pits in the teeth, plaque can accumulate in the absence of S. mutans but can still be cariogenic as long as lactic acid-producing bacteria and fermentable substances are present.

Epidemiology

Pathogenesis

0

587

Dental caries is worldwide in distribution, but the incidence varies markedly depending mainly on intake of dietary sucrose and access to preventive dental care. Heredity also plays an important role—some individuals inherit resistance to the disease. Young people are generally much more susceptible than older people, probably because the pits and fissures that are sites for dental caries wear down with time.

Prevention and Treatment The most important method for controlling dental caries is restricting sucrose and other refined dietary carbohydrates, thereby reducing Streptococcus mutans colonization of teeth and acid production by cariogenic plaques. Dental caries can be reduced by 90% if sucrose-containing sweets are eliminated from the diet. It is not, however, simply the quantity of sugar in the diet that is important. The frequency of eating and the length of time food stays on the teeth are more critical than the actual quantity of sucrose ingested. Interestingly, chewing paraffin or sorbitol-sweetened gum reduces dental caries, probably because it increases the flow of saliva. Trace amounts of fluoride are required for teeth to resist the acid of cariogenic plaques. Fluoride makes tooth enamel harder and more resistant to dissolving in acid. In the United States, more than 100 million people are currently supplied by fluoridated public drinking water, which has resulted in a 60% reduction in dental caries. In areas where fluoridated drinking water is not available, fluoride tablets or solutions can be used. To have optimum effect, children should begin receiving fluoride before their permanent teeth erupt. Fluoride applied to tooth surfaces in the form of mouthwashes, gels, or toothpaste is generally less effective. Mechanical removal of plaque by toothbrushing and use of dental floss is another important preventive measure, reducing the incidence of dental caries by about 50%. Toothbrush bristles cannot remove plaque from the pits and fissures normally present in children’s teeth, however, because they are too deep and narrow. Caries commonly develops in these pits and fissures and can be prevented by using a sealant—a kind of epoxy glue that seals the fissures, kills the bacteria in plaque, and prevents bacterial recolonization. Older people have less fissure-related caries; however, receding gums can expose root surfaces that become sites for dental caries. Treatment of dental caries requires drilling out the cavity, filling the defect with amalgam (an alloy of mercury and some other metal) or other material, and restoring the contour of the tooth.

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Periodontal Disease Periodontal disease is a chronic inflammatory process involving the gums and tissues around the roots of the teeth. It usually develops slowly over many years, and is an important cause of tooth loss from middle age onward.

Symptoms The majority of individuals with periodontal disease are asymptomatic. Common symptoms are bleeding and sensitive gums, bad breath, and loosening of the teeth. Discoloration, ranging from yellowish to black, occurs at the base of the teeth. The gums generally recede and expose the roots of the teeth to dental caries.

Causative Agent Periodontal disease is caused by dental plaque that forms at the point where the gum joins the tooth. The plaque may or may not be cariogenic. Hundreds of kinds of bacteria have been identified in plaques associated with periodontal disease.

Pathogenesis Plaque forms on teeth at the gum margin, especially in hard-to-clean areas between the teeth. Calcium salts deposited in the plaque result in hard-to-remove dental calculus, often referred to as tartar. Plaque gradually extends into the gingival crevice and bacterial products incite an inflammatory and immune response manifested by swelling and redness of the gingiva (figure 25.5). This gum inflammation is known as gingivitis. If the plaque remains small, neutrophils along with cellular and humoral immunity limit the process at this stage. Large populations of microorganisms, however, release the enzymes

collagenase and hyaluronidase, which weaken the gingival tissue and cause the gingival crevice to widen and deepen. As the plaque enlarges, the proportion of anaerobic, Gram-negative bacteria such as Porphyromonas gingivalis increases. These organisms release endotoxin and a variety of exotoxins that attack leukocytes and host tissue, but they generally do not invade the tissues of the host. The membrane that attaches the root of the tooth to the bone weakens, and the bone surrounding the tooth gradually softens. The tooth becomes loose and may be lost. ■ neutrophils, p. 350

Epidemiology Periodontal disease is mainly a disease of those over 35 years of age. After age 65, almost 90% of individuals have some degree of periodontal disease. Persons with AIDS and other immunodeficiencies, and those with defective neutrophils, often have severe periodontal disease that leads to loss of their teeth.

Prevention and Treatment Careful flossing and toothbrushing can prevent periodontal disease, especially if combined with twice-yearly polishing and removal of calculus at a dental office. Periodontal disease can be treated in its earlier stages by cleaning out the inflamed gingival crevice and removing plaque and calculus. In advanced cases, surgery is usually required to expose and clean the roots of the teeth.

Trench Mouth Trench mouth (figure 25.6), also known as Vincent’s disease or acute necrotizing ulcerative gingivitis (ANUG), is a severe, acute

(a) (a)

(b)

3 mm (b)

FIGURE 25.5 Periodontal Disease (a) Normal gingival. (b) Periodontal

FIGURE 25.6 Trench Mouth (Acute Necrotizing Ulcerative Gingivitis, or ANUG) (a) Red, swollen gingiva with loss of tissue, especially

disease, with plaque, inflammatory changes, bleeding, and shortening of the gingival between the teeth.

between the teeth. (b) Gram stain of exudate showing a spirochete and rodshaped bacteria.

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condition distinct from other forms of periodontitis. The disease was rampant among soldiers living in trenches during World War I because they were unable to attend to mouth care—thus, its name.

Symptoms Trench mouth is characterized by an abrupt onset, fever, bleeding and painful gums, and a foul odor.

Causative Agent The suspected causative agent is an oral, unculturable spirochete of the Treponema genus, antigenically related to T. pallidum, the cause of syphilis. These trench mouth spirochetes probably act synergistically with other anaerobic species, with which they are always associated. ■ the genus Treponema, p. 273 ■ syphilis, p. 633

Pathogenesis The spirochetes and the other anaerobes are presumed to act together to destroy tissue, but the precise mechanisms are unknown. Plaque is always present, but its bacterial composition shows much larger numbers of spirochetes and other anaerobes than present in chronic periodontal disease. The spirochetes invade the tissue, causing necrosis and ulceration, mainly of the gums between the teeth.

Epidemiology The disease can occur at any age in association with poor mouth care, especially with stress, malnutrition, or immunodeficiency. It is not contagious.

589

Prevention and Treatment Prevention begins with daily brushing and flossing, and twiceyearly professional cleaning. Antibacterial treatment directed against the spirochetes and anaerobic rods rapidly relieves the acute symptoms, but this must be followed by extensive removal of plaque and calculus. The main features of teeth and gum infections are presented in table 25.1.

Helicobacter pylori Gastritis Gastritis, meaning inflammation of the stomach, is commonly present in otherwise healthy, asymptomatic people. It was not until the early 1980s that a bacterial cause of this condition was identified and its association with ulcers and gastric malignancy became apparent. These ulcers occur in the stomach and uppermost part of the duodenum. They are localized, roughly circular erosions of the epithelium that can extend deeply into the underlying tissue.

Symptoms The initial infection can cause symptoms ranging from belching to vomiting. Most people, however, have no symptoms except when infection is complicated by ulcers or cancer. Localized abdominal pain, tenderness, and bleeding are manifestations of these complications.

TABLE 25.1 Important Infections of the Teeth and Gums Dental Caries

Periodontal Disease

Trench Mouth

Symptoms

None until advanced disease. Late: discoloration, roughness, broken tooth, throbbing pain

Most cases asymptomatic until advanced disease. Bleeding, sensitive gums, bad breath, loosening of the teeth. Receding gums with exposed discolored tooth roots.

Abrupt onset of fever, painful bleeding gums, and a foul mouth odor

Incubation period

1 to 24 months before cavity is detectable

Months or years

Undetermined

Causative agent

Dental plaque populated with Streptococcus mutans

Dental plaque, cariogenic or not

Probably a spirochete of the genus Treponema acting with Fusobacterium, Prevotella, or other anaerobes

Pathogenesis

Bacteria in plaque produce acid from dietary sugars; slowly dissolves the calcium phosphate crystals composing the tooth; sucrose critical for cariogenic plaque formation.

Plaque forms at the gum margins and gradually extends into the gingival crevices. Bacterial products incite an inflammatory response. The crevices widen and deepen, and the proportion of anaerobes increases. Toxins and enzymes weaken the tissues holding the teeth and cause them to become loose.

The spirochetes and certain other anaerobes act synergistically to cause death of tissue, ulceration, and tissue invasion by spirochetes.

Epidemiology

Worldwide distribution, incidence depending on dietary sucrose, natural or supplemental fluoride. The young are more susceptible than the old.

Primarily a disease of those older than 35 years. Immunodeficient individuals are at increased risk of severe disease.

All ages are susceptible in association with poor mouth care, malnutrition, or immunodeficiency. It is not contagious.

Prevention and treatment

Restriction of dietary sucrose, supplemental fluoride, mechanical removal of plaque, sealing pits and fissures in childhood teeth.

Avoid buildup of plaque. Surgical treatment in severe cases to expose tooth roots and remove plaque and calculus.

Avoid buildup of plaque. Antibiotic treatment acutely, followed by removal of plaque and calculus.

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Sheath Cell wall

Cytoplasmic membrane

Flagella Urease Ammonia Urea Urease CO(NH2)2 + H2O Urea

CO2 + 2NH3 Ammonia

FIGURE 25.7 Helicobacter pylori This bacterium, which has unusual sheathed flagella with terminal knobs, produces a powerful urease that allows it to survive stomach acid by converting urea to ammonia, which neutralizes acidity.

Causative Agent Helicobacter pylori is a short, spiral, Gram-negative, microaerophilic bacterium with multiple unusual-appearing, sheathed polar flagella (figure 25.7). ■ the genus Helicobacter, p. 273

Pathogenesis These remarkable organisms survive the extreme acidity of the stomach because of their powerful urease. This enzyme creates

an alkaline microenvironment by hydrolyzing urea to ammonia. Urea is a waste product of protein catabolism by the body’s cells and is normally present in the gastric juices. Once the bacteria reach the mucus that coats the stomach or duodenal lining, they use their flagella to corkscrew through the mucus to the epithelial cells. In this location, the pH of the mucus is nearly neutral, and the bacteria attach to the mucussecreting epithelium or multiply adjacent to it. Bacterial products incite an inflammatory response in the wall of the stomach, and mucus production decreases. Once infection occurs it persists for years, often for life. From 10% to 20% of infected persons develop ulcers; 65% to 80% of patients with gastric ulcers and 95% of those with duodenal ulcers are infected with H. pylori. The thinning of the protective mucus layer at the site of infection (figure 25.8) probably accounts for the development of peptic (meaning “caused by digestive juices”) ulcers of the stomach and duodenum. A very small percentage of individuals infected with H. pylori develop cancer of the stomach, but more than 90% of those with stomach cancer are infected by the bacterium. Virulent H. pylori strains produce a protein, CagA, which they transfer into host cells, resulting in changes in shape and surface characteristics of the cells. Evidence suggests these changes represent a prelude to malignancy. Another bacterial product, VacA, acts on mucosal cells to promote flow of urea into the stomach.

Epidemiology Infections tend to cluster in families. Transmission of H. pylori probably occurs by the fecal-oral route, and the bacteria have been found in well water. Also, flies are capable of transmitting the organisms. Overall, about 20% of the adult U.S. population is infected with the bacterium, but the incidence progressively

LUMEN OF STOMACH Helicobacter pylori Bacteria invade and multiply. Thinning of mucus layer due to mucosal damage

Mucus layer

Epithelium destroyed by gastric acid

Stomach-lining epithelium Basement membrane Connective tissue Capillary Mucus-secreting cell

Red blood cell

Neutrophil

Plasma cell

Lymphocyte

Red blood cell

Ulcer

Dilated capillary

Cellular response to inflammation

FIGURE 25.8 Gastric Ulcer Formation Associated with Helicobacter pylori Infection Thinning of the protective layer of mucus probably results from an inflammatory and immune response to the bacteria growing on or near the epithelium. The acid and pepsin of the stomach juices can then attack the epithelium. Neutrophils are phagocytic early responders to inflammation: lymphocytes and plasma cells represent the immune response.

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increases with age, reaching almost 80% for those over age 75. Infection rates are highest in low-socioeconomic groups.

TABLE 25.2 Heliobacter pylori Gastritis

Prevention and Treatment

Symptoms

Initial infection: range from belching to vomiting. Localized abdominal pain and tenderness, bleeding when complicated by ulcer or cancer

Incubation period

Usually undetermined

Causative agent

Helicobacter pylori, a spiral, Gram-negative, microaerophilic bacterium, with sheathed flagella

Pathogenesis

Organisms survive the acidity of stomach juices by producing a powerful urease. Upon reaching the layer of mucus, they penetrate to the epithelial surface, where bacterial products incite an inflammatory response. Thinning of the mucus layer occurs, and 10% to 20% of infected individuals develop ulcerations. Only a small percentage develop cancer, but more than 90% of individuals with stomach cancers are infected with H. pylori.

Epidemiology

Probably fecal-oral transmission. Progressive increase with age, reaching almost 80% of those over 75.

Prevention and treatment

No proven preventive. Most infections are cured using two antibiotics together, plus a medication to suppress stomach acid.

There are no proven preventive measures. Helicobacter pylori infections can usually be eradicated by combined treatment with two antibiotics and a medication that inhibits stomach acid production, with complete clearing of the gastritis and healing of any ulcers. The main features of H. pylori gastritis are shown in table 25.2.

MICROCHECK 25.3 The pathogenesis of tooth decay depends on both dietary sucrose and acid-forming bacteria that are adapted to colonize hard, smooth surfaces within the mouth. Periodontal disease is a chronic condition caused by plaque at the gum margin that can lead to loosening of teeth. Trench mouth is an acute illness with destruction of gingival tissue. Chronic infection by Helicobacter pylori is a key factor in the development of gastric and duodenal ulcers and gastric cancer. ✓ Why is loss of teeth so common in people over age 65? ✓ What enzyme produced by Heliobacter pylori assists its survival in stomach acid? ✓ Discuss the pros and cons of the statement “Helicobacter pylori causes stomach cancer.”

CASE PRESENTATION The patient was a 35-year-old man who consulted his physician because of upper abdominal pain. The pain was described as a steady burning or gnawing sensation, like a severe hunger pain. Usually it came on 1* to 3 hours after eating, and sometimes it woke him from sleep. Generally, it was relieved in a few minutes by food or antacid medicines. On examination, the patient appeared well, without evidence of weight loss. The only positive finding was tenderness slightly to the right of the midline in the upper part of the abdomen. A test of the patient’s feces was positive for blood. The remaining laboratory tests were normal. Endoscopy, a procedure that employs a long, flexible fiber-optic device passed through the mouth, showed a patchy redness of parts of the stomach lining. A biopsy was taken. The endoscopy tube was passed through the pylorus and into the duodenum. About 2 cm into the duodenum, there was a lesion 8 mm in diameter that lacked a mucous membrane and appeared to be “punched out.” The base of the lesion was red and showed adherent blood clot. After the endoscopy, a portion of material obtained by biopsy was placed on urea-containing medium. Within a few minutes, the medium began to turn color, indicating a developing alkaline pH. 1. What is the patient’s diagnosis? 2. What would you expect microscopic examination and culture of the gastric mucosa biopsy to show?

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3. Outline the pathogenesis of this patient’s disease. 4. It took a long time for doctors to accept that this condition had an infectious etiology. Why? Discussion 1. This patient had a duodenal ulcer. The ulcer had penetrated deeply beyond the mucosa, involving small blood vessels and causing bleeding. This was apparent from the clot that was visualized at endoscopy and the positive test for blood in the stool. 2. Microscopic examination of the biopsy showed curved bacteria, confirmed by culture to be Helicobacter pylori. 3. Helicobacter pylori enter the gastrointestinal tract by the fecal-oral route. In the stomach, they escape the lethal effect of gastric acid because they produce urease. Highly motile, they enter the gastric mucus and follow a gradient of acidity ranging from pH 2 in the gastric juices to pH 7.4 at the epithelial surface. Mutant strains that lack the ability to produce urease are only infectious if they are introduced directly into the mucus layer. Multiplication occurs just above the epithelial surface, but some of the bacteria attach to the epithelial cells and cause a loss of microvilli and thickening at the site of attachment. An inflammatory reaction develops beneath the affected mucosa. Two genes, vacA and cagA, correlate with virulence. The gene product VacA is a toxin similar to the adenylate cyclase of Bordetella pertussis. The

bacteria inject CagA into host cells, causing the cells to elongate and spread out. CagA also provokes a strong immune response. Once established, H. pylori infections persist for years and often for a lifetime. It is not known why some people develop gastric or duodenal ulcers and others do not. Both host and bacterial factors are almost certainly involved. For example, strains of H. pylori isolated from peptic ulcer patients tend to be more virulent than those from patients who just have gastritis; patients with blood group O have more receptors for the bacterium and a higher incidence of peptic ulcers than do other people. Stomach acid and peptic enzymes probably play a role in ulcer formation by acting on damaged epithelium unprotected by normal mucus. 4. Claude Bernard, a scientist of Pasteur’s time, put it this way: “It is that which we do know which is the greatest hindrance to our learning that which we do not know.” In 1983, when Dr. Barry J. Marshall proclaimed before an international gathering of infectious disease experts that a bacterium caused stomach and duodenal ulcers, everyone “knew” it could not be true because no organism was thought to exist that could survive stomach acidity and enzymes. Indeed, almost everyone already “knew” the cause of ulcers to be psychosomatic. There is much still to be learned about the cause of ulcers, however, and Bernard’s statement remains relevant.

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25.4 Viral Diseases of the Upper Digestive System

Epithelial cells

Cell nuclei

Multinucleated cell Intranuclear inclusion body Epithelial cell Neutrophils

Focus Points Explain why HSV-1 can spread easily from person to person. Give the characteristics of the mumps virus that make it a good candidate for eradication.

Some viral diseases involve the upper alimentary system but produce more dramatic symptoms elsewhere in the body. For example, measles produces Koplik spots in the mouth, respiratory symptoms, and a dramatic skin rash; chickenpox causes oral blisters, ulcers, and a striking skin rash; infectious mononucleosis can cause multiple oral ulcers, bleeding gums, and impressively enlarged lymph nodes and spleen. In this section, we focus on two viruses that produce dramatic symptoms in the upper digestive system, herpes simplex, with its characteristically painful oral ulcers, and mumps, with its enlarged, painful parotid glands. ■ chickenpox, p. 545 ■ infectious mononucleosis, p. 686 ■ measles, p. 547

Herpes Simplex (Cold Sores or Fever Blisters) Herpes simplex is an extremely widespread disease with many manifestations. In its most common form, it begins in the mouth and throat. Involvement of the esophagus is suggestive of AIDS or other immunodeficiency. The infection persists for life; its causative virus is transmissible with saliva. Although the disease is usually insignificant, it can have tragic consequences if it results in infection of newborn infants or people with immunodeficiency.

Symptoms Herpes simplex typically begins during childhood with fever, and blisters and ulcers in the mouth and throat so painful that it is difficult for those infected to eat or drink. The first lesions are small blisters that break within a day or two, leaving superficial, painful ulcers that heal without treatment within about 10 days. Thereafter, the infection becomes latent and the affected person may suffer the recurrent disease, herpes simplex labialis (the word labialis indicates location of the lesions on the lips), otherwise known as “cold sores” or “fever blisters” (figure 25.9). The symptoms of recurrences usually begin on the lips and include a tingling, itching, burning, or painful sensation. Blisters then appear, followed by painful ulcerations. Healing occurs within 7 to 10 days.

Causative Agent Herpes simplex is caused by the herpes simplex virus (HSV), a medium-sized, enveloped virus containing double-stranded, linear DNA. There are two types of the virus—HSV-1 and HSV-2. Most oral infections are due to HSV-1; HSV-2 usually causes genital infections. ■ genital herpes simplex, p. 638

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FIGURE 25.9 Herpes Simplex Labialis, (Cold Sores or Fever Blisters) The photomicrograph is of stained material from a herpes simplex lesion. It shows a multinucleated giant cell and intranuclear inclusion bodies. The pink areas within the epithelial cell nuclei are inclusion bodies, the sites of viral replication.

Pathogenesis The virus multiplies in the epithelium of the mouth or throat, and destroys the cells. Some epithelial cells fuse together, producing large, multinucleated giant cells. Nuclei of infected cells characteristically contain a deeply staining area called an intranuclear inclusion body (see figure 25.9), which is the site of earlier viral replication. The blisters that form contain large numbers of infectious virions. Although an immune response develops and quickly limits the infection, some of the virions enter the sensory nerves in the area. Viral DNA persists in these nerve cells in a noninfectious, non-replicating form. This latent virus can, from time to time, become infectious. It is then carried by the nerves to skin or mucous membranes and produces recurrent disease. Stresses that can precipitate recurrences include menstruation, sunburn, and any illness associated with fever.

Epidemiology HSV is extremely widespread and infects up to 90% of some U.S. inner-city populations, usually resulting in mild, if any, symptoms. An estimated 20% to 40% of Americans suffer recurrent herpes simplex. The virus is transmitted primarily by close physical contact, although it can survive for several hours on plastic and cloth. The greatest risk of infection is from contact with lesions or saliva from patients within a few days of disease onset, because at this time large numbers of virions are present. The saliva of people with no symptoms can be infectious, however, posing a risk to healthcare workers or therapists who have contact with saliva, such as nurses and dental workers. HSV can infect almost any body tissue—for example, herpetic whitlow, a painful finger infection, is not uncommon among nurses; and wrestlers can develop infections at almost any skin site because saliva containing HSV can contaminate wrestling mats and get rubbed into abrasions. Blindness can result if the virus is rubbed into the eye. Although uncommon, HSV is the most frequently identified cause of sporadic, viral encephalitis, a serious brain disease.

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Prevention and Treatment Acyclovir, penciclovir, and similar medications target HSV DNA polymerase and halt the progress of herpes simplex, but they do not affect the latent virus and thus cannot rid the body of HSV infection. These medications are useful for treating severe cases and for preventing disabling recurrences. Because the ultraviolet portion of sunlight can trigger recurrent disease, sunscreens are sometimes a helpful preventive. ■ DNA polymerase, p. 166 ■ acyclovir, p. 487

Some of the main features of herpes simplex are shown in table 25.3.

Mumps Mumps is an acute viral illness that preferentially attacks glands such as the parotids. Formerly common in the United States, the disease is now relatively rare because of routine childhood immunization. However, outbreaks occur due to waning immunity, mostly in college students and other young adults. A large outbreak in 2006 resulted in almost 6,000 reported cases.

Symptoms The onset of mumps is marked by fever, loss of appetite, and headache. Typically these symptoms are followed by painful swelling of one or both parotid glands (figure 25.10). Spasm of the underlying muscle makes it difficult to chew or talk. The

TABLE 25.3 Herpes Simplex Symptoms

Initial infection: fever, severe throat pain, ulcerations of the mouth and throat. Recurrences: itching, tingling or pain usually localized to the lip, followed by blisters that break leaving a painful sore, which usually heals in 7 to 10 days

Incubation period

2 to 20 days

Causative agent

Herpes simplex virus (HSV), usually type 1

Pathogenesis

The virus multiplies in the epithelium, producing cell destruction and blisters containing large numbers of infectious virions. An immune response quickly limits the infection, but noninfectious HSV DNA persists in sensory nerves. This DNA becomes the source of infectious virions that are carried to the skin or mucous membranes, usually of the lip, causing recurrent sores.

Epidemiology

Widespread virus, transmitted by close physical contact. The saliva of asymptomatic individuals is commonly infectious.

Prevention and treatment

Acyclovir, penciclovir, and similar medications that target HSV DNA polymerase can shorten the duration of the illness or prevent recurrences. Sunscreens are helpful in preventing recurrences due to ultraviolet exposure.

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FIGURE 25.10 A Child with Mumps The swelling directly below the earlobe is due to enlargement of the parotid gland.

word mumps probably derives from the verb mump, meaning “to mumble” or “whisper.” Symptoms of mumps usually disappear in about a week. Although painful parotid swelling is characteristic of mumps, up to half of the cases of mumps virus infection show no obvious parotid involvement. Symptoms can arise elsewhere in the body with or without parotid swelling. For example, headache and stiff neck indicate that the virus is causing meningitis—infection of the coverings of the brain, a common manifestation of mumps virus infection. Generally, mumps symptoms are much more severe in individuals past the onset of puberty. For example, about one-quarter of cases of mumps in post-pubertal boys and men are complicated by orchitis—a rapid, intensely painful swelling of one or both testicles to three to four times their normal size. Atrophy, or shrinkage, of the involved testicles commonly develops after recovery from the illness and, in rare cases, sterility results. In women and post-pubertal girls, ovarian involvement occurs in about one of 20 cases, and is manifested by pelvic pain. Pregnant women with mumps commonly miscarry, but birth defects do not result from mumps as they do from rubella. Serious consequences of mumps are rare and are most likely to occur in older people. These consequences include deafness and death from encephalitis (brain infection). ■ rubella, p. 549

Causative Agent Mumps virus has a lipid-containing envelope and is classed in the paramyxovirus family, a group of single-stranded RNA viruses that includes the rubeola and respiratory syncytial viruses. Only one antigenic type of the mumps virus is known.

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Pathogenesis

50

Epidemiology Humans are the only natural host of mumps virus, and natural infection confers lifelong immunity. Individuals sometimes claim to have had mumps more than once, probably because other infectious and non-infectious diseases can cause parotid swelling. The virus is spread by the high percentage, about 30%, of individuals who have asymptomatic infections but secrete mumps virus in their saliva and continue to mingle with other people. In symptomatic patients, the virus can be present in saliva from almost a week before symptoms appear to 2 weeks afterward. Peak infectivity however, is from 1 to 2 days before parotid swelling until the gland begins to return to normal size.

45

Reported cases per 100,000 population

Infection occurs when a person who lacks immunity to mumps inhales virus-laden droplets of saliva. The incubation period is long, generally 15 to 21 days, because the virus reproduces first in the upper respiratory tract, then is spread throughout the body by the bloodstream, and produces symptoms only after infecting tissues such as the parotid glands, meninges, pancreas, ovaries, or testicles. In the salivary glands, the virus multiplies in the epithelium of ducts that convey saliva to the mouth. This destroys the epithelium, which releases enormous quantities of virus into the saliva. The body’s inflammatory response to the infection is responsible for the severe swelling and pain. A similar sequence of events occurs in the testicles, where the virus infects the system of tubules that convey the sperm. The marked swelling and pressure often impair the blood supply, leading to hemorrhages and death of testicular tissue. Kidney tubules are also infected, and the virus can be cultivated from the urine for 10 or more days following the onset of illness.

40 35 30 25 20 15 10 5 0 1973

1978

1983

1988 Year

1993

1998

2002

FIGURE 25.11 Reported Cases of Mumps per 100,000 Population, United States, 1973–2001 Mumps vaccine was licensed in 1967. There were only 236 cases reported for the year 2004 but more than six thousand in 2006 because of an epidemic among college students.

Prevention and Treatment An effective attenuated mumps vaccine has been available in the United States since 1967, usually given in the same injection as measles, mumps, and rubella varicella vaccines (MMRV). Figure 25.11 shows how the incidence of mumps has generally declined, although it increased in the 1980s because of a decline in funding for vaccinations. Because its host range is limited to humans, there is only a single viral serotype, and latent recurrent infections do not occur, mumps is a good candidate for eradication. There is no effective antiviral medication. The main features of mumps are presented in table 25.4.

MICROCHECK 25.4 Herpes simplex is characterized by acute infection followed by lifelong latency and the possibility of recurrent disease. Infectious virus is often present in saliva in the absence of symptoms. Mumps virus infections characteristically cause enlargement of the parotid glands, but they can involve the brain, testicles, and ovaries, and cause miscarriages. Mumps is a good candidate for eradication. ✓ What infections are caused by the two types of herpes simplex viruses? ✓ Why is mumps a good candidate for eradication from the world? ✓ Why would you expect acyclovir to be ineffective against latent HSV infections?

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TABLE 25.4

Mumps

Symptoms

Fever, headache, loss of appetite, typically followed by painful swelling of one or both parotid glands. Painful enlargement of the testicles, pelvic pain in women, and symptoms arising from brain involvement are likely to occur in individuals past the age of puberty.

Incubation period

Generally 15 to 21 days

Causative agent

Mumps virus, a single-stranded RNA virus of the paramyxovirus family

Pathogenesis

The virus initially replicates in the upper respiratory tract, then disseminates to the parotids and other organs of the body via the bloodstream. The Inflammatory response to cell destruction is responsible for the marked swelling and pain.

Epidemiology

Humans are the only source of the virus. Spread is likely because of a high percentage of asymptomatic infections.

Prevention and treatment

An effective attenuated vaccine has been used since 1967. No antiviral therapy is available.

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LOWER DIGESTIVE SYSTEM INFECTIONS

Each year, in developing countries, one out of five children dies of diarrhea before the age of 5 years; most of the 5 million individuals who die of diarrhea each year are infants, but no age group is spared. Fatal cases are less common in the United States than in the developing world, but there are millions of diarrhea cases annually. The all-too-familiar symptoms of lower alimentary system diseases include diarrhea, loss of appetite, nausea and vomiting, and sometimes fever—or any combination of these symptoms can occur. Members of the medical profession often loosely ascribe these symptoms to gastroenteritis (gastro-, “stomach,” entero-, “intestine,” -itis, “inflammation”); others prefer the term “stomach flu.” (Note that “stomach flu” has no relationship to “the flu,” influenza). Diarrhea can be copious and watery with infections of the small intestine, or in smaller amounts containing mucus, pus, and sometimes blood when invasion of the large intestine is involved. The name dysentery is given to diarrheal illnesses when pus and blood are present in the feces. Various causative agents can be responsible for these symptoms, including poisonings by microbial toxins in food (foodborne intoxication) and infections. Chapter 32 gives examples of microbial poisonings; this chapter focuses on infectious causes. Bacterial causes will be described first, and viral and protozoal causes will be discussed later. Pork tapeworm, one of a large number of intestinal helminth infestations, is discussed in chapter 12. Others can be found at the Online Learning Center (www.mhhe. com/nester6). ■ foodborne intoxication, p. 763

25.5 Bacterial Diseases of the Lower Digestive System Focus Points List the mechanisms by which bacterial pathogens cause diarrheal disease. Give the most common sources of bacteria pathogenic for the intestine.

Diarrheal illness is a common result of bacterial infection of the intestine, but bacteria can also use the intestine as an entryway to the rest of the body, thereby causing other types of illness. A minority of bacterial pathogens that invade the body from intestinal infections can cause severe headache, high temperature, abscesses throughout the body, intestinal rupture, shock, and death. This kind of illness, called enteric fever, is generally seen after infection by certain strains of Salmonella. Typhoid fever is an example. Because of the wide variety of bacterial intestinal diseases, we will first consider some generalities.

nes95432_Ch25_581-617.indd 595

The pathogenesis of bacterial intestinal disease involves a number of mechanisms. Different strains within the same species can differ in the way they cause disease, and the same strain can employ more than one mechanism. Moreover, the responsible genes can be transferred from one species to another by conjugation or by bacteriophages. Microbiologists are discovering exciting details at the molecular level of how bacteria cause disease, and finding unexpected complexity in these seemingly simple creatures. Many of these pathogens, upon contact with a host cell, activate a type III secretion system that employs a structure resembling a short flagellum to join the bacterial cytoplasm with that of the host cell. Gene products from pathogenicity islands then pass directly into the host cell and activate endocytosis or other processes to the benefit of the bacterium. ■ secretion system, p. 378 ■ pathogenicity islands, p. 208

The main pathogenic mechanisms can be summarized as: Attachment. Infecting bacteria must have a means of attaching to intestinal cells to avoid being swept away by the flow of intestinal contents. Initial attachment is often by means of pili (see figure 17.4); but other adhesins are usually required for intimate attachment. Secretion systems sometimes transfer substances into the host cell that become receptors for bacterial attachment. ■ adhesins, p. 398 Toxin production. Toxins involved in intestinal infections fall into two groups: (1) toxins that increase secretion of water and electrolytes, as seen with Vibrio cholerae; and (2) toxins that cause cell death by halting protein synthesis, as seen with Shigella dysenteriae. Alterations in the host cells. Some infecting bacteria use type III secretion systems to deliver molecules into intestinal epithelial cells (see figure 17.5), causing the cells to change. For example, certain pathogenic strains of E. coli deliver substances to intestinal epithelial cells that cause rearrangement of the actin filaments in those cells, resulting in loss of microvilli and creation of a platform or pedestal under the bacterium. The secretion system can also transfer substances that become receptors for intimate bacterial attachment. Cell invasion. Some infecting bacteria use a type III secretion system to deliver molecules to intestinal epithelial cells, causing the cells to engulf the bacteria (see figure 17.6). In the example of invasion by Shigella species, the bacteria then multiply in the cell’s cytoplasm, leading to destruction of the cell. The epidemiology of intestinal diseases involves transmission by the fecal-oral route, usually when a person ingests food or drinking water contaminated with animal or human feces. Generally, with certain important exceptions, bacterial intestinal pathogens from animal sources have a high infecting dose and are not transmitted from person to person. Pathogens from a human

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source usually have a low infecting dose and are transmitted from person to person. Regarding prevention and treatment, only a few vaccines are currently available, and they are of limited effectiveness because they fail to elicit a sufficient secretory IgA response on the intestinal mucosa. Sanitary and hygienic measures, and chlorination of drinking water, are important control measures. Antibacterial medications are not helpful for most cases originating from animal sources, and they often prolong the illness because they depress the normal microbiota. On the other hand, antibacterial medications can be life-saving in cases where the bacterium invades beyond the intestine. ■ IgA antibodies, p. 374 Cases of severe, watery diarrhea can cause rapid loss of water and electrolytes, so that the blood becomes reduced in volume and there is insufficient blood flow to keep vital organs, such as the kidneys, working properly. Severe, watery diarrhea can be rapidly fatal unless the lost fluid can be replaced promptly. Fortunately, despite the inability of the small intestine to control fluid secretion, if glucose is supplied it is still able to absorb fluid and electrolytes in most diarrheal diseases. An oral rehydration solution (ORS) that consists of water, glucose, and electrolytes is commercially available, and recipes for homemade ORS have been approved by the World Health Organization. ORS is a highly effective lifesaver in severe diarrheas regardless of cause. Only three kinds of bacteria account for almost all bacterial intestinal infections: Vibrio species, Campylobacter jejuni, and enterobacteria. ■ enterobacteria, p. 262

Cholera There have been seven cholera pandemics since the early 1800s. Between 1832 and 1836, more than 200,000 Americans died when the second and fourth pandemics of cholera swept across North America. The seventh pandemic began in 1961 in Indonesia and spread to South Asia, the Middle East, and parts of Europe and Africa. South America had remained cholera-free for 100 years until January 1991, when the disease abruptly appeared in Peru. Introduction probably occurred when a freighter discharged bilgewater into a Lima harbor. The municipal water supply was not chlorinated and quickly became contaminated. The disease then spread rapidly, so that in 2 years more than 700,000 cases and 6,323 deaths had been reported from South and Central America. Cases also appeared in 14 states in the United States. ■ pandemic

Pathogenesis Vibrio cholerae is killed by acid, and so large numbers of the organism must be ingested before enough survive stomach passage to establish infection. Those that make it to the small intestine adhere to the small intestinal epithelium by means of pili and other surface proteins. The organisms multiply on the epithelial cells (figure 25.12) but do no visible damage to them. The bacteria, however, produce cholera toxin, a potent exotoxin. This enterotoxin causes the epithelial cells to continuously secrete chloride ions into the intestinal lumen. Sodium and other ions and water follow the chloride, resulting in an outpouring of fluid and electrolytes from the cells. Although the large intestine is not affected by the toxin, it cannot absorb the large volume of fluid that rushes through it, and diarrhea results. Cholera toxin is an A-B toxin (figure 25.13). The B portion binds irreversibly to specific receptors on the microvilli of the epithelial cells whereas the A portion enters the intestinal cell and causes the symptoms of cholera. It does this by modifying a protein that normally controls the level of cyclic adenosine monophosphate (cAMP) in the cells, effectively making a key enzyme, adenylate cyclase, continuously active. Adenylate cyclase converts ATP to cAMP and its continuous activity results in maximum levels of cAMP in the intestinal cells, causing the cells to constantly pump water and electrolytes into the intestinal lumen. The normal shedding of intestinal cells eventually gets rid of the toxin. Synthesis of cholera toxin is an example of lysogenic conversion. It is coded by a filamentous bacteriophage that infects Vibrio cholerae via the pili by which the bacteria attach to the intestinal cells. Synthesis of both cholera toxin and the pili is regulated by the same bacterial gene, so that toxin and pili, the two factors required for disease production, are synthesized at the same time. ■ lysogenic conversion, p. 310

Epidemiology Fecally contaminated water is the most common source of cholera infection, although foods such as crab and vegetables fertil-

disease, p. 451

Symptoms Cholera causes the classic example of severe watery diarrhea. The diarrheal fluid can amount to 20 liters a day and because of its appearance, has been described as “rice water stool.” Vomiting also occurs in most people at the onset of the disease, and many people suffer muscle cramps caused by loss of fluid and electrolytes. 10 mm

Causative Agent The causative agent is Vibrio cholerae, a curved, Gram-negative rod able to tolerate strong alkaline conditions and high salt concentrations.

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FIGURE 25.12 Scanning Electron Micrograph of Vibrio cholerae Attached to Small Intestinal Mucosa Attachment occurs by means of pili.

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PERSPECTIVE 25.1 Ecology of Cholera The ecology of cholera is fascinating but still incompletely understood. The O139 Vibrio cholerae strain arose in India in the fall of 1992 from a serotype O1 strain, the same serotype as the pandemic and American Gulf Coast strains. Interestingly, the change in O antigen was accompanied by acquisition of a capsule—these changes probably resulting from genes acquired by transduction or conjugation. Various strains

abundant nutrients cause explosive growth of phytoplankton. These findings could explain (1) how new pandemic strains could arise through genetic interchange; (2) an association between cholera and climatic changes such as El Niño; and (3) the onset and rapid spread of epidemic cholera by ocean currents along coastal areas. ■ zooplankton, p. 286

of V. cholerae, most of which are not pathogenic for humans, live in the coastal seas around the world, largely in association with zooplankton. These zooplankton can sometimes also harbor the V. cholerae strains responsible for pandemic cholera. Moreover, the zooplankton feed on phytoplankton and therefore increase markedly in number when warm seas and

ized with human feces have also been implicated in outbreaks. A person with cholera can discharge a million or more V. cholerae organisms in each milliliter of feces. Although cholera is relatively common worldwide, few cases due to the pandemic strain have been acquired in the United States since the early 1900s. Since 1973, however, sporadic cases have occurred along the Gulf of Mexico. Most of these infections have been traced to consumption of coastal marsh crabs. These cases were due to a strain of V. cholerae different from the pandemic OI strain. Ominously, in September 1992, a new strain of V. cholerae, belonging to a different O group (O139), appeared in India and spread rapidly across South Asia, attacking even those people with immunity to

the seventh pandemic strain. This new strain and its rapid spread suggested it could initiate another pandemic, but after about a year it declined in incidence and remained endemic, causing resurgent localized epidemics. ■ O antigen, pp. 243, 262

Prevention and Treatment Control of cholera depends largely on adequate sanitation and the availability of safe, clean water supplies. Travelers to areas where cholera is occurring are advised to cook food immediately before eating it. Crabs should be cooked for no less than 10 minutes. No fruit should be eaten unless peeled personally by the traveler, and ice should be avoided unless it is known to be made from boiled

(a) B component of toxin attaches to specific receptors on cell membrane; A component penetrates membrane.

B

B

B

B B

FIGURE 25.13 Mode of Action of Cholera Toxin As with other A-B toxins, the B portion attaches the toxin to the host cell, and the A portion penetrates the cell and causes toxicity. In this case, the target of the A portion is a G protein responsible for regulating production of cAMP. By splitting off the ADP-ribose portion of NAD and attaching it to G, the toxin makes it impossible for G to down-regulate cAMP production.

Cytoplasmic membrane of intestinal cell

A (b) Component A causes ADP ribosylation of a G protein that controls activation of adenylate cyclase, locking the G protein in the "active" mode. OFF

ADP Ribose G protein

(c) Adenylate cyclase causes the conversion of ATP to cAMP.

ON ATP K+

Adenylate cyclase

Na+ ClHCO3cAMP H2O

(d) Buildup of cAMP causes water and electrolytes to pour out of the cell.

NAD A nicotinamide • ADP • ribose + G

Locked G protein nicotinamide + G • ADP • ribose

(e) Reaction summary: Active adenylate cyclase ATP

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cAMP

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Pathogenesis

water. Orally administered vaccines are commercially available in a number of countries outside the United States. One consists of a living, genetically altered strain of V. cholerae, and another, killed V. cholerae in combination with the purified recombinant B subunit of cholera toxoid. Treatment of cholera depends on the rapid replacement of electrolytes and water before irreversible damage to vital organs can occur. The prompt administration of intravenous or oral rehydration fluid decreases the mortality of cholera to less than 1%. The main features of cholera are summarized in table 25.5.

Shigella species invasion of intestinal epithelial cells causes a strong inflammatory response. Invasion is accomplished by exploiting the antigen sampling function of M cells (figure 25.14). Recall that M cells normally take in microbes and transfer them to macrophages in Peyer’s patches. Shigella species selectively attach to M cells and are thereby transported across the epithelial barrier. Upon engulfment by macrophages, the bacteria escape from the phagosome and multiply in the cytoplasm of the macrophages. The bacteria are released when the infected macrophages undergo apoptosis. The released bacteria then attach to specific receptors near the bases of the epithelial cells and induce those cells to take them in. Once inside, the Shigella bacteria escape from the endosome and multiply in the cytoplasm. These nonmotile bacteria can nevertheless propel themselves into neighboring intestinal cells by producing a protein that causes the host cell actin to rapidly polymerize at one end of the bacterial cell, forming an “actin tail.” The overall result of infection is death and sloughing of patches of epithelium. The denuded areas become intensely inflamed, covered with pus and blood, accounting for the pus and blood in the diarrhea of dysentery. ■ actin, p. 74 Some strains of Shigella dysenteriae, a species rarely encountered in the United States, produce a potent toxin known as the Shiga toxin, a cytotoxin. It is a chromosomally coded A-B toxin. The B portion binds to endothelial cells of small blood vessels, and the A subunit enters the endothelial cell and reacts with its ribosome, thereby halting protein synthesis. The importance of this toxin is that it is responsible for the hemolytic uremic syndrome (HUS), an often fatal condition that can follow Shigella

Shigellosis Shigellosis is distributed worldwide wherever sanitary practices are lacking. Reported cases in the United States have averaged about 21,500 per year, but the true prevalence is much higher.

Symptoms The classic symptom of shigellosis is dysentery. Other symptoms are headache, vomiting, fever, stiff neck, convulsions, and joint pain. Shigellosis is commonly fatal for infants in developing countries.

Causative Agents There are four species of Shigella—S. flexneri, S. boydii, S. sonnei, and S. dysenteriae. Shigellas are Gram-negative enterobacteria. Virulent strains contain a large plasmid that is essential for the attachment and entry of Shigella into host cells.

TABLE 25.5 Cholera ➀ Vibrio cholerae, the causative

bacterium, enters the mouth with fecally contaminated food or drink.

➁ The bacteria attach to epithelial cells

1

of the small intestine.

Symptoms

Abrupt onset of massive diarrhea, vomiting, muscle cramps

Incubation period

Short, generally 12 to 48 hours

Causative agent

Vibrio cholerae, a curved, alkali and salt tolerant, Gram-negative rod bacterium

Pathogenesis

Heat-labile exotoxin causes excessive secretion of water and electrolytes by the intestinal epithelium; leads to dehydration and shock.

Epidemiology

Ingestion of fecally contaminated food or water; sometimes natural sources associated with marine crustaceans.

Prevention and treatment

Purification of water, careful handwashing; vaccination. Treatment: Rehydration with a solution of electrolytes and glucose, given intravenously in severe cases; or similar electrolyte solution containing a glucose source given by mouth in milder cases.

➂ V. cholerae toxin enters the cells

and prevents them from downregulating secretion of water and electrolytes.

➃ The epithelial cells pump water and

5

electrolytes from the blood into the intestinal lumen, causing watery diarrhea.

➄ Shock and death occur because of fluid loss from the circulatory system, unless the fluid can be replaced.

➅ The bacteria exit the body with

2

4 3

feces.

6

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25.5 Bacterial Diseases of the Lower Digestive System

Epithelial cell

M cell

Macrophage

Intestinal lumen

Shigella

Cell nucleus

(1) Shigellas are taken up by M cells and transported beneath the epithelium. Macrophages take up shigellas, die and release the bacteria. (2) The bacteria enter the inferior and lateral aspects of the epithelial cells by inducing endocytosis. The endosomes are quickly lysed, leaving the shigellas free in the cytoplasm.

(3) Actin filaments quickly form a tail, pushing the shigellas into the next cell.

(4) Shigellas multiply in the cytoplasm, and the infection extends to the next cell.

599

azole are useful against susceptible strains because they shorten the duration of symptoms and the time during which shigellas are discharged in the feces. Almost 20% of Shigella strains, however, are resistant to these two commonly employed medications. R plasmids that convey resistance to several antibacterial medications are often present. Two specimens of feces, collected at least 48 hours after stopping antimicrobial medicines, must be negative for Shigella sp. before a person is allowed to return to a day care center or food-handling job. ■ R plasmids, p. 205 Table 25.6 describes the main features of shigellosis.

Escherichia coli Gastroenteritis Escherichia coli generally ferments lactose, in contrast to most shigellas and salmonellas. It is an almost universal member of the normal intestinal flora of humans and a number of other animals. Long ignored as a possible cause of gastrointestinal disease, certain strains were shown in 1945 to cause life-threatening epidemic gastroenteritis in hospitalized infants. Later, E. coli strains were shown to cause gastroenteritis in adults, notably as agents responsible for traveler’s diarrhea (also called “Delhi belly,” “Montezuma’s revenge,” “ Turkey trots,” etc.). Still later, E. coli strains were identified as causative agents in dysentery, cholera-like illnesses, and diarrheas associated with the hemolytic uremic syndrome.

Symptoms

Neutrophils (5) Infected cells die and slough off. Intense response of acute inflammatory cells (neutrophils), bleeding and abscess formation.

FIGURE 25.14 Pathogenesis of Shigellosis The bacteria do not invade the intestinal epithelium directly, but are transported to the area underneath the epithelial cells by M cells. They then invade the epithelial cells from their inferior and lateral borders. The photomicrograph shows the actin tails (green) that form on intracellular shigellas (orange) and rapidly push these non-motile bacteria from cell to cell.

Symptoms depend largely on the virulence of the infecting E. coli strain. They range from vomiting and a few loose bowel movements, to profuse watery diarrhea, to severe cramps and bloody diarrhea. Fever is not usually prominent and recovery usually occurs within 10 days. Hemolytic uremic syndrome, however, develops after some bloody diarrhea cases.

TABLE 25.6

Shigellosis

dysenteriae dysentery. In this syndrome, red blood cells break up in the tiny blood vessels of the body, resulting in anemia and kidney failure, sometimes accompanied by paralysis or other signs of nervous system injury. Shiga toxin is also produced by strains of Escherichia coli that cause the hemolytic uremic syndrome.

Symptoms

Fever, dysentery, vomiting, headache, stiff neck, convulsions, and painful joints

Incubation period

3 to 4 days

Causative agent

Species of Shigella, Gram-negative, non-motile enterobacteria

Epidemiology

Pathogenesis

Invasion of and multiplication within intestinal epithelial cells; death of cells, intense inflammation and ulcerations of intestinal lining. Some species produce a cytotoxin.

Epidemiology

Transmission via fecal-oral route; sometimes by fecally contaminated food or water; humans generally the only source.

Prevention and treatment

Sanitary measures; surveillance of food handlers and water supplies. Treatment: Antibacterial medications such as ampicillin and cotrimoxazole (trimethoprim plus sulfamethoxazole) shorten duration of symptoms and time shigellas are excreted; multiple R factor resistances may be present.

Shigellosis generally has a human source and is transmitted by the fecal-oral route. The bacteria are not easily killed by stomach acid, so that the infectious dose is small and as few as 10 of the bacterial cells can initiate infection. Transmission occurs most readily in overcrowded populations with poor sanitation. It is a common problem in day care centers and among homosexual men. Fecally contaminated food and water have also caused outbreaks.

Prevention and Treatment The spread of Shigella sp. is controlled by sanitary measures and surveillance of food handlers and water supplies. There is no vaccine. Antimicrobial medications such as ampicillin and cotrimox-

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Causative Agent Escherichia coli are Gram-negative, generally lactose-fermenting rods of the enterobacteria group. Most of the diarrhea-causing E. coli fall into five groups: enterotoxigenic (ETEC), enteroinvasive (EIEC), enteropathogenic (EPEC), enteroaggregative (EAEC), and Shiga toxin-producing E. coli (STEC), also known as enterohemorrhagic E. coli. In contrast to other strains of E. coli, strains in these groups possess virulence factors that cause them to be intestinal pathogens. Other strains of E. coli cause urinary infections, septicemia, and meningitis. Enterotoxigenic E. coli (ETEC) is a common cause of traveler’s diarrhea and diarrhea in infants. Some members of this group are responsible for significant mortality due to diarrhea in young livestock. ETEC strains usually possess adhesins that allow them to attach to and colonize the intestinal epithelium, where they secrete one or more toxins. One such toxin is nearly identical to cholera toxin in action and antigenicity. Enteroinvasive E. coli (EIEC) invade the intestinal epithelium, resulting in a disease closely resembling that caused by Shigella sp. Enteropathogenic E. coli (EPEC) strains cause diarrheal outbreaks in hospital nurseries and in bottle-fed infants in developing countries and can also cause chronic diarrhea in infants. They possess plasmid-encoded adhesins; the bacteria cause loss of microvilli and a thickening of the cell surface at the site where the organisms attach. Enteropathogenic E. coli strains can be distinguished from other E. coli strains by the fluorescent antibodies that identify their somatic and capsular antigens. Enteroaggregative E. coli (EAEC) causes epidemic diarrhea in children, diarrhea in patients with AIDS, and travelers diarrhea. Originally, these strains were identified by their distinctive aggregation on tissue culture cells, but now can best be identified by a DNA probe. Shiga toxin-producing E. coli (STEC), the fifth group of diarrhea-producing strains, was discovered in 1982. Most of these organisms belong to a single serological type, O157:H7. They often produce severe illness, including bloody diarrhea. These strains produce potent cytotoxins that cause the death of intestinal epithelium by interfering with protein synthesis. Some of the toxins are identical to the Shiga toxins of Shigella dysenteriae, mentioned earlier. Unlike shigellas, however, enterohemorrhagic

TABLE 25.7

E. coli generally do not penetrate intestinal epithelial cells. Their toxin production depends on lysogenic conversion by a distinct bacteriophage. About 4% of infected individuals develop hemolytic uremic syndrome, marked by anemia due to lysis of red blood cells, kidney failure, and central nervous system damage. STEC epidemics have been traced to ground beef, sausage, unpasteurized milk, apple juice, spinach, and unchlorinated city water. In most instances, cow manure was the source of the offending strain. ■ enterohemorrhagic E. coli epidemics, p. 244 Characteristics of diarrhea-causing E. coli are summarized in table 25.7.

Pathogenesis Of hundreds of different strains of E. coli, only those possessing certain virulence factors cause gastrointestinal disease. Some of these factors were discussed in the previous section; there is strong evidence that not all factors have been identified. Two important virulence factors, enterotoxin production and the ability to adhere to the small intestine, are coded by plasmids. These plasmids can be transferred to other E. coli organisms by conjugation, thereby conferring virulence on the recipient strain. Gastroenteritis-producing strains of E. coli often have more than one type of virulence plasmid. It is interesting that the heat-labile toxin of E. coli is antigenically closely related to the cholera toxin of Vibrio cholerae. This similarity suggests that the genes responsible for the two toxins have a common ancestry. ■ conjugation, p. 202 ■ plasmids, p. 68

Epidemiology Epidemics occur from person-to-person spread, contamination of foods, unpasteurized milk and juices, and water sources contaminated with feces. Human beings, and domestic and wild animals can all be sources of pathogenic strains. The infecting dose is low—only 200 organisms or less.

Prevention and Treatment Preventive measures include handwashing, pasteurization of drinks, and thorough cooking of food. Treatment of E. coli gastroenteritis includes replacing the fluid lost from vomiting and diarrhea. In addition, infants may require antibiotic treatment for a few days. Traveler’s diarrhea can usually be prevented with bismuth preparations (such

Characteristics of Diarrhea-Causing Escherichia coli

Designation

Characteristic Features

Clinical Picture

Enterotoxigenic E. coli (ETEC)

Can release two kinds at toxin, one similar to cholera toxin; small intestinal location

Nausea, vomiting, abdominal cramps, massive watery diarrhea leading to dehydration

Enteroinvasive E. coli (EIEC)

Entry into and growth in intestinal epithelium, with cell destruction; large intestinal location

Fever, cramps, blood and pus in the feces

Enteropathogenic E. coli (EPEC)

Attachment of the bacterium is followed by loss of microvilli and formation of a platform or pedestal of actin fibrils under the bacterium; small intestinal location

Fever, vomiting, watery diarrhea containing mucus; associated with a limited number of serotypes

Shiga toxin-producing Same as above, except large intestine location and release of E. coli (STEC) Shiga toxin

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Fever, abdominal cramps, bloody diarrhea without pus; 2% to 7% develop hemolytic uremic syndrome; most cases due to serotype O157:H7

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601

severe headache, constipation, and abdominal pain, followed in some cases by intestinal rupture, internal bleeding, shock, and death. Salmonella Typhi, the cause of typhoid fever, is an example.

as Pepto-Bismol). Antibacterial medications such as ciprofloxacin (Cipro) and the non-absorbable rifaximin (Xifaxan) are no longer routinely recommended. The widespread use of an antibiotic to prevent diarrhea has promoted development of resistant strains. Some features of E. coli gastroenteritis are summarized in table 25.8.

Causative Agents Salmonellas are motile, Gram-negative enterobacteria. It is generally recognized that there are only two species of Salmonella—S. enterica and S. bongori, the latter species rarely isolated from humans. The Salmonella are subdivided into more than 2,400 serotypes based on differences in their somatic (O), flagellar (H), and capsular (K) antigens. They are referred to as serotypes because the Salmonella strains are identified by sera that contain antibody against known strains. Formerly, many of these serotypes were assigned species names; for example, Salmonella dublin and Salmonella heidelberg. (In this discussion we will not italicize the serotype name, to distinguish it from a species name, as in Salmonella Dublin.) Salmonella Typhimurium and Salmonella Enteritidis are the serotypes most commonly isolated in the United States. Typhoid fever, an example of enteric fever, is caused by Salmonella Typhi.

Salmonellosis Salmonellosis, a disease caused by bacteria of the Salmonella genus, can be contracted from many animal sources. There are an estimated 1.4 million cases annually in the United States, resulting in 400 deaths. Large outbreaks are usually due to commercially distributed produce contaminated by animal feces. A few Salmonella strains, fortunately now rare in the United States, originate from humans. These human strains generally cause systemic disease, as in typhoid fever.

Symptoms Most cases of salmonellosis have gastroenteritis symptoms, with diarrhea (sometimes with blood in the stool), abdominal cramps, nausea, vomiting, headache, and fever. The symptoms vary depending on the virulence of the strain of Salmonella and the number of infecting organisms. The symptoms are usually short-lived and mild.

Gastroenteritis.

Pathogenesis Most salmonellas are killed by acid, and so a large number must generally be ingested to survive passage through the stomach. Upon reaching the lower small and large intestines, an adhesin on the bacterial surface attaches the bacteria to specific receptors on the surface of the epithelial cells. Contact with intestinal epithelium activates a type III secretion system (see figure 17.6). In only

A few Salmonella strains cause symptoms of enteric fever, with progressively increasing fever over a number of days,

Enteric fever.

TABLE 25.8 Escherichia coli Gastroenteritis ➀ Pathogenic strain of E. coli enters

Symptoms

the body by the fecal-oral route, usually with contaminated food or beverage.

Incubation period 2 hours to 6 days

➁ Most strains colonize the small intestine and produce watery diarrhea.

1

Causative agent

Escherichia coli, certain strains

Pathogenesis

Various mechanisms; attachment to small intestinal cells allows colonization; some strains produce one or more enterotoxins; some strains, resembling shigellas, invade large intestinal epithelium; others cause host cell membrane thickening and loss of microvilli, and may produce Shiga toxin.

Epidemiology

Common in travelers; can be foodborne or waterborne; fecal-oral route transmission, sometimes animal source.

Prevention and treatment

Sanitary precautions including careful handwashing; pasteurization of drinks, thorough cooking of meats; replacement of fluid loss; bismuth compounds for treatment.

➂ Others invade the large intestine and cause dysentery.

➃ Some strains produce Shiga toxin

4

which is absorbed by the bloodstream and causes hemolyticuremic syndrome with damage to red blood cells and the kidneys.

➄ The bacteria exit the body with

Vomiting and diarrhea; sometimes dysentery

4

feces.

2

3

5

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a matter of minutes, transfer of bacterial proteins into the epithelial cell tricks it into taking in the bacterium by endocytosis. The bacteria multiply within a phagosome and are discharged from the base of the cell by exocytosis. In most instances, the bacteria are quickly taken up and killed by macrophages, but the inflammatory response to the infection increases fluid secretion, causing diarrhea. ■ endocytosis, exocytosis, p. 73 ■ type III secretion system, p. 398 Some strains, such as Salmonella Typhi, are not so easily eliminated by host defenses. They cross the mucous membrane via M cells, resist killing by macrophages, multiply within them, and are carried by the bloodstream throughout the body. Released by death of the macrophages, the bacteria can invade tissues, cause prolonged fever, abscesses, septicemia, and shock, often with little or no diarrhea. Salmonella Typhi can also cause destruction of Peyer’s patches, leading to rupture of the intestine and hemorrhage. ■ septicemia, p. 678 ■ Peyer’s patches, p. 370

plasmid-mediated resistance to antibacterial treatment. About 35% of Salmonella Typhimurium isolates are resistant to five or more antibacterial medications. This resistance is partly due to selection of resistant strains of Salmonella by the widespread, ill-advised addition of antibiotics to animal feeds. Antibacterial medications are not advised for treating humans except when there is tissue or bloodstream invasion. An attenuated oral vaccine for preventing typhoid fever is about 50% to 75% effective. An equally effective injectable vaccine composed of Salmonella Typhi capsular polysaccharide is also available. Surgical removal of the gallbladder is often necessary to rid Salmonella Typhi carriers of their infection. Table 25.9 summarizes some of the features of salmonellosis.

Epidemiology

It was not until 1972 that Campylobacter jejuni was isolated from a diarrheal stool. It took another five years for a suitable culture medium to be developed and widely used, which led to recognition of campylobacteriosis as a leading bacterial diarrheal illness in the United States, with an estimated 2.1 to 2.4 million cases per year. There are generally less than 1,000 fatalities per year, mostly in the elderly and those with AIDS or other immunodeficiencies.

Salmonellas survive for months in soil, water, and other environments. Children are commonly infected by seemingly healthy pets, such as turtles, iguanas, baby chickens, and ducks, that discharge salmonellas in their feces. Eggs and poultry are often contaminated with Salmonella strains. Other outbreaks have resulted from contaminated tomatoes, brewer’s yeast, alfalfa sprouts, protein supplements, dry milk, and even a red dye used to diagnose intestinal disease. Most cases of Salmonella gastroenteritis have an animal source rather than a human source. Enteric fever strains such as Salmonella Typhi generally can be traced to long-term human carriers. Although fecal discharge of gastroenteritis-causing strains is usually of short duration, carriers of Salmonella Typhi can eliminate up to 10 billion of the bacteria per gram of their feces for years. The source of these organisms is usually the gallbladder, which Salmonella Typhi colonizes free of competition because much of the normal flora is killed or inhibited by concentrated bile. Mary Mallone, “Typhoid Mary,” a young Irish cook living in New York State in the early 1900s, was a notorious carrier. She was responsible for at least 53 cases of typhoid fever over a 15year period. In her day, about 350,000 cases of typhoid occurred in the United States each year. The low incidence of typhoid fever in the United States today can be attributed to improved sanitation and public health surveillance measures.

Prevention and Treatment Control of Salmonella infections depends on reporting cases of salmonellosis, tracing sources, sanitary handling of animal carcasses, pasteurizing animal products or irradiating them, and testing them for contamination. Adequate cooking effectively kills salmonellas. Note, however, that heat penetration to the center of a carcass may be inadequate to kill salmonellas, especially in frozen fowl, even when the outside appears “well done.” Unfortunately, the number of reported cases of salmonellosis has tended to rise, due in part to mass distributions of food and water that become contaminated from time to time. Most people with salmonellosis recover without antimicrobial treatment; this is fortunate because S. enterica has shown increasing

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Campylobacteriosis

■ Campylobacter, p. 273

Symptoms Fever, vomiting, diarrhea, and abdominal cramps are typical. Dysentery occurs in about half the cases.

Causative Agent Campylobacter jejuni is a motile, curved, Gram-negative rod (figure 25.15) that can be cultivated from feces under microaero-

TABLE 25.9

Salmonellosis

Symptoms

Diarrhea and vomiting; rarely, prolonged fever, headache, abdominal pain, abscesses, and shock

Incubation period

Usually 6 to 72 hours; can be 1 to 3 weeks in typhoid fever

Causative agent

Salmonella enterica, motile, Gram-negative, enterobacteria

Pathogenesis

Invasion of the lining cells of lower small and large intestine, with penetration to underlying tissues; body’s inflammatory response causes increase in fluid secretion. Sometimes survival within macrophages and spread throughout the body, destruction of Peyer’s patches.

Epidemiology

Ingestion of food contaminated by animal feces, especially poultry. Human fecal source in typhoid fever-like illnesses.

Prevention and treatment

Adequate cooking and handling of food; attenuated vaccine against typhoid fever. Usually no antimicrobial advised unless invasion of tissues or blood occurs.

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603

Prevention and Treatment Prevention of outbreaks depends mostly on pasteurization of milk and on chlorination of water. Proper cooking and handling of raw poultry to avoid contamination of hands and kitchen surfaces can prevent most of the other cases. Chicken should be cooked until it is no longer pink. Most cases of C. jejuni gastroenteritis subside without antimicrobial treatment in 10 days or less and leave the infected individual immune to further infection. The antibiotic erythromycin is recommended for severe cases. The main features of campylobacteriosis are shown in table 25.10.

MICROCHECK 25.5 5 mm

FIGURE 25.15 Scanning Electron Micrograph of Campylobacter jejuni C. jejuni is a common bacterial cause of diarrhea in the United States.

philic conditions using a selective medium to suppress the other intestinal organisms. ■ selective media, p. 96

Pathogenesis The number of organisms required to produce symptomatic infection is 500 or less. The bacteria penetrate the intestinal epithelial cells of the small and large intestines, multiply within and beneath the cells, and cause an inflammatory reaction. As with most strains of Shigella and Salmonella, penetration into the bloodstream is uncommon. A mysterious sequel to C. jejuni infections, GuillainBarré syndrome, occurs in about 0.1% of cases. Although C. jejuni infections are probably not a direct cause of this syndrome, almost 40% of all cases are preceded by campylobacteriosis, and most of the rest by viral infections. Evidence suggests that autoimmunity could be responsible for C. jejuni-associated cases. The syndrome begins abruptly within about 10 days of the onset of diarrhea, with tingling of the feet followed by progressive paralysis of the legs, arms, and rest of the body. Most victims require hospitalization, but over 80% recover completely. About 5% of patients die of the syndrome despite treatment. ■ Guillain-Barré

Vibrios, Campylobacter jejuni, and enterobacteria account for most intestinal bacterial infections. Pathogenic mechanisms include attachment, toxin production, cell invasion, and destruction of microvilli. Some microbial toxins alter the secretory function of cells in the small intestine without killing or visibly damaging them. Unsuspected human carriers can remain sources of enteric infections for many years. Most vaccines are of limited value because they induce little secretory IgA production. ✓ Explain how Vibrio cholerae causes cholera without apparent damage to the intestinal epithelium. ✓ How does the epidemiology of Salmonella Typhi differ from that of most other S. enterica? ✓ What makes Campylobacter jejuni a leading cause of bacterial diarrhea in the United States? ✓ How would you devise a selective medium for Vibrio cholerae?

TABLE 25.10 Campylobacteriosis Symptoms

Diarrhea, fever, abdominal cramps, nausea, vomiting, bloody stools

Incubation period

Usually 3 days (range, 1 to 5 days)

Causative agent

Campylobacter jejuni, a curved Gram-negative, microaerophilic rod

Pathogenesis

Low infecting dose. The bacteria multiply within and beneath the epithelial cells and incite an inflammatory response. Bloodstream invasion is uncommon. Complicated by a generalized paralysis, Guillain-Barré syndrome, on rare occasions.

Epidemiology

Large foodborne and waterborne outbreaks originating from chickens, cows and other animals. Person-to-person spread rarely occurs.

Prevention and treatment

Avoiding contamination of hands and food preparation areas with uncooked poultry, and cooking of poultry until it is no longer pink are also effective. Water chlorination and pasteurization of beverages are effective control measures. Most victims recover within 10 days without antibacterial medications.

syndrome, p. 521

Epidemiology Numerous foodborne and waterborne outbreaks of C. jejuni have been reported, involving as many as 3,000 people. Most cases, however, are sporadic. Like the salmonellas, C. jejuni lives in the intestines of a variety of domestic animals. Poultry is a common source of infection, and as many as 89% of raw poultry products have harbored the organism. One drop of juice from raw chicken meat can easily contain an infectious dose. Cats have also been implicated as a source. Epidemics have resulted from ingesting unpasteurized cow and goat milk and from drinking non-chlorinated surface water. Despite its low infectious dose, person-toperson spread of C. jejuni rarely occurs.

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25.6 Viral Diseases of the Lower Digestive System Focus Points Describe measures for the prevention of hepatitis A, B, and C. Outline the significance of hepatitis B viral antigen or antibody in the blood of a hepatitis victim.

Viral infections of the lower digestive system are common in all age groups. The intestines and accessory organs such as the liver can be affected. At least five different groups of viruses can cause epidemic gastroenteritis, resulting in millions of cases each year in the United States. More than six different viruses can cause hepatitis, meaning inflammation of the liver. Hepatitis A virus (HAV), hepatitis B virus (HBV), and hepatitis C virus (HCV) account for most cases of viral hepatitis.

Rotaviral Gastroenteritis Rotaviruses cause most cases of viral gastroenteritis in infants and children. In the United States, almost every child is infected at some time before they reach the age of 5 years. Each year in the United States, rotavirus infections result in 500,000 emergency department or clinic visits, and 49,000 hospital admissions, but few deaths. Worldwide, more than 600,000 deaths are attributed to rotaviruses each year.

Symptoms Illness begins abruptly with vomiting and slight fever, followed in a short time by profuse, watery diarrhea. Symptoms generally are gone in about a week. Unless adequate replacement fluid is given, death can occur from dehydration.

100 nm

FIGURE 25.16 Rotavirus in Human Feces Transmission electron micrograph.

human disease. Experimentally, however, reassortment of genetic segments can occur with dual infections. It is not known whether new human pathogenic rotaviruses arise by this mechanism.

Prevention and Treatment Handwashing, disinfectant use, and other sanitary measures help limit the spread of rotaviruses. An effective attenuated vaccine was approved in 1998, but was withdrawn the next year because it increased the risk of a rare, potentially fatal kind of bowel obstruction. A new, safer attenuated vaccine was approved in 2006 and is administered to infants at ages 2, 4, and 6 months.

Causative Agents

Norovirus Gastroenteritis

Rotaviruses (figure 25.16) are about 70 nm in diameter, have a double-walled capsid, and a double-stranded, 11-segment RNA genome. The viruses represent a major subgroup of the reovirus family. Their name comes from rota, Latin for “wheel.” ■ reovirus

Noroviruses are responsible for an estimated 23 million cases of viral gastroenteritis annually in the United States. Originally they were called “Norwalk viruses,” from Norwalk, Ohio, the place where they were first implicated in an epidemic of gastroenteritis. Because noroviruses tend to cause large, demoralizing outbreaks that affect people of all ages, they have been designated a category B bioterrorism agent. ■ bioterrorism agents, p. 466

family, p. 323

Pathogenesis The viruses infect mainly the epithelial cells that line the upper part of the small intestine, causing cell death and decreased production of digestive enzymes. These changes gradually return to normal over a number of weeks.

Epidemiology Rotaviruses spread by the fecal-oral route. Childhood epidemics generally occur in winter in temperate climates, perhaps because children are more apt to be confined indoors in groups where the viruses can spread easily. Generally, by the age of 4 years, children have acquired some immunity to these viruses. Rotaviruses also cause about 25% of traveler’s diarrhea cases. Rotaviruses that infect a wide variety of young wild and domestic animals do not cause

nes95432_Ch25_581-617.indd 604

Symptoms The symptoms of nausea, vomiting, and watery diarrhea of abrupt onset are identical to those of rotaviruses. Symptoms with norovirus infections, however, generally last only 12 to 60 hours.

Causative Agent Noroviruses are small (about 30 nm diameter), non-enveloped, single-stranded RNA viruses. Their spherical surface is covered with small depressions (figure 25.17). These viruses represent a group of gastroenteritis-producing viruses within the calcivirus family, none of which has been cultivated in the laboratory. ■ calcivirus family, p. 323

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Hepatitis A Hepatitis A, formerly called infectious hepatitis, is endemic around the world. The distribution of reported cases in the United States is shown in figure 25.18, but its true incidence is undoubtedly much higher. With its lack of an animal reservoir for the causative virus, its antigenic simplicity, and the availability of an effective vaccine, the disease could be considered for eradication. Hepatitis A is only one example of viral hepatitis; at least five other kinds of viral hepatitis—B, C, D, E, and G—are known.

Symptoms

Pathogenesis Noroviruses infect the upper small intestinal epithelium and produce changes similar to those of rotaviruses. The epithelium generally recovers fully within about 2 weeks.

Epidemiology Transmission is by the fecal-oral route; the viruses are highly contagious and survive well in the environment. The incubation period is 12 to 48 hours. Although some viral strains cause gastroenteritis in infants, noroviruses typically infect children and adults. Infected individuals generally eliminate virus in their feces for only a few days. Individuals sometimes contract the illness by eating shellfish that have no known exposure to human feces. Norovirus epidemics are common on cruise ships and college dormatories. Calciviruses are widespread among marine and other animals, raising the question whether they could be involved in the ecology of noroviruses.

Prevention and Treatment Handwashing, disinfectants, and other sanitary measures can minimize transmission of noroviruses. Infected foodworkers should be restricted from working for 72 hours after their symptoms subside. There is no vaccine and no proven antiviral medication. Table 25.11 compares noroviruses and rotaviruses and the illnesses they produce.

TABLE 25.11 Rotavirus and Norovirus Compared

Causative Agent Hepatitis A is caused by the hepatitis A virus (HAV), a small (27 nm), single-stranded RNA virus of the picornavirus family. HAV differs from other members of the family and has been given the name hepatovirus. There is only one serotype. ■ picornaviruses, p. 324

Pathogenesis Following ingestion, the virus reaches the liver by an unknown route. The liver is the main site of replication and the only tissue known to be damaged by the infection. The virus is released into the bile and eliminated with the feces.

Epidemiology Hepatitis A virus spreads by the fecal-oral route, principally through fecal contamination of hands, food, or water. Outbreaks

30 Cases per 100,000 population

FIGURE 25.17 Electron Micrograph of a Norovirus

Typical symptoms of hepatitis A are fatigue, fever, loss of appetite, nausea, right-sided abdominal pain, dark-colored urine, claycolored feces, and jaundice. In children less than 6 years old, 70% have no symptoms and those with symptoms rarely have jaundice. Older children and adults usually develop symptomatic infections and most of them develop jaundice. About 20% of adults require hospitalization. Usually patients recover within 2 months, but 10% to 15% require up to 6 months for full recovery.

20

15

Rotavirus

Norovirus

Characteristics

70 nm diameter double-walled capsid; double-stranded RNA

30 nm diameter, single-stranded RNA

5

Incubation period

24 to 48 hrs

12 to 48 hrs

0

Typical symptoms

Vomiting, abdominal cramps, diarrhea, lasting 5 to 8 days

Vomiting, abdominal cramps, diarrhea, lasting 12 to 60 hours

Attenuated vaccine

No vaccine

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Midwest Northeast South West

25

Causative Agent

Prevention

Vaccine available

10

1991

1993

1995

1997

1999

2001

2003

2005

Year

FIGURE 25.18 Acute Hepatitis A Reported Cases, different regions of the United States, 1991–2005. Source: Centers for Disease Control and Prevention 2007. Morbidity and Mortality Weekly Report Surveillance Summary 56 (SS 3).

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of the disease have originated from restaurants because foodhandlers who carried the virus failed to wash their hands. A large 2003 epidemic caused by contaminated green onions imported from Mexico involved 600 people in Pennsylvania and smaller outbreaks in several other states. Consumption of raw shellfish is a frequent source of infection because these animals concentrate the hepatitis A virus from fecally polluted seawater. Other important risk factors are international travel and sexual contact with someone with the disease. Other groups at high risk of hepatitis A include children in day care centers and residents in nursing homes, and homosexual men. Infants and children with hepatitis A can shed the virus in their feces for several months after symptoms begin, but the amount of virus in feces usually drops markedly with the appearance of jaundice.

Prevention and Treatment An effective, inactivated virus vaccine against hepatitis A has been available since 1995. It is indicated for travelers to economically deprived regions, homosexual men, those who work on sewers, healthcare workers, individuals with chronic liver disease, food-handlers, and all persons 12 months to 40 years of age. Since the introduction of vaccination, the number of reported cases of hepatitis A has dropped to historic lows (1.5 acute cases per 100,000). Immune globulin containing antibody to HAV can be given by injection for passive immunization of travelers under the age of 12 months or more than 40 years old, and those at high risk for other reasons. It gives short-term protection against the disease if given within 2 weeks of exposure. No antiviral treatment is available. Victims of the disease are advised to avoid alcohol and other hepatic toxins.

Hepatitis B Hepatitis B, formerly known as serum hepatitis, represents about 40% of the cases of viral hepatitis in the United States. Approximately 50,000 new cases occur each year, and as many as 1% to 6% of the infected adults will become carriers of the

disease. About 1.25 million people in the United States have chronic hepatitis B and therefore have an increased risk of death from cirrhosis and liver cancer. Hepatitis B infects at least 5% of the world’s population and is the ninth-leading cause of death worldwide.

Symptoms Symptoms of hepatitis A and B are similar, except that hepatitis B tends to be more severe than hepatitis A, causing death from liver failure in 1% to 10% of hospitalized cases.

Causative Agent Hepatitis B is caused by hepatitis B virus (HBV) (figure 25.19a), a member of the hepadnavirus family (hepa-, referring to the liver, and -dna- “DNA”). The virus contains double-stranded DNA and has a lipid-containing outer envelope. Three important HBV antigens are (1) surface antigen (HBsAg); (2) core antigen (HBcAg), a protein of the nucleocapsid; and (3) e antigen (HBeAg), a soluble component of the viral core. HBsAg is produced during viral replication in amounts far in excess of that needed for virus production. It occurs in the bloodstream on small spheres and filaments of viral envelope material empty of DNA (figure 25.19b) in quantities often 1,000 or more times as great as complete virions. HBsAg is responsible for the ability of the virus to attach to and infect host cells; antibody to surface antigen (anti-HBsAg) confers immunity.

Pathogenesis Following entry into the body, HBV is carried to the liver by the bloodstream. The mechanism by which HBV causes liver injury is not known but most likely results from the body’s immune system attacking the infected liver cells. After entering the liver cell, the virus replicates by a mechanism involving reverse transcriptase (figure 25.20), unusual for a DNA virus. The double-stranded viral DNA genome is transported to the host cell nucleus, where messenger RNA and a RNA copy of the genome are synthesized. This RNA copy of the genome is

Genomic DNA (double-stranded with partial single strand)

Envelope

Hepatitis B surface antigen (HBsAg)

Nucleocapsid (viral capsid)

Spherical

Envelope lipid (from host cell)

Hepatitis B e antigen (HBeAg) (a) Complete infectious virion

Hepatitis B core antigen (HBcAg)

Elongated (b) Viral envelope particles containing HBsAg

FIGURE 25.19 Hepatitis B Virus Components Found in the Blood of Infected Individuals (a) Complete infectious virion. (b) Smaller spherical and elongated envelope particles lacking DNA.

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25.6 Viral Diseases of the Lower Digestive System

Epidemiology

HBV

Liver cell cytoplasmic membrane

(a) HBV infects liver cell. Cell nucleus (b) Polymerase completes DNA strand. (c) Completed viral genome is transported to cell nucleus, messenger RNA and RNA copy of genome transcribed. (d) Reverse transcriptase and other viral proteins are translated; assembly of viral capsid begun.

mRNA RNA copy of genome

DNA RNA

(e) Reverse transcription of RNA genome copy is packaged in newly forming capsid; RNA strand degraded.

(f) Synthesis of complementary DNA strand begun.

(g) Replication of second DNA strand ceases as virion buds from cell membrane.

From 1965 to 1985, a progressive rise in reported hepatitis B cases occurred. Since then, the incidence of the disease has appeared to plateau and decline (figure 25.21). HBV is spread mainly by blood, blood products, and semen. Persisting viremia, meaning virus circulating in the bloodstream, can follow both symptomatic and asymptomatic cases, and the virus may continue to circulate in the blood for many years. Carriers are of major importance in the spread of hepatitis B because they are often unaware of their infection. If only a minute amount of blood from an infected person is injected into another person’s bloodstream or rubbed into minor wounds, infection can result. Blood and other body fluids can be infectious by mouth, the virus probably infecting the recipient through small scratches or abrasions. Many hepatitis B virus infections result from sharing of needles by drug abusers. Unsterile tattooing and ear-piercing instruments and shared toothbrushes, razors, or towels can also transmit HBV infections. Sexual intercourse is responsible for transmission in nearly half of hepatitis B cases in the United States. HBV antigen is often present in saliva and breast milk, but the quantity of infectious virus and the risk of transmission are low. Five percent or more of pregnant women who are HBV carriers transmit the disease to their babies at delivery, and more than two-thirds of women who develop hepatitis late in pregnancy or soon after delivery do so. Most of these babies have asymptomatic infections and become long-term carriers, but some die of liver failure.

Prevention and Treatment The first vaccine against hepatitis B, approved in the early 1980s, consisted of HBsAg obtained from the blood of chronic carriers; 1 ml of their blood often had enough antigen to immunize eight people! Since 1986, however, a subunit vaccine produced in

35

Hepatitis A, viral, acute Hepatitis B, viral, acute Hepatitis C, viral, acute

HBV

FIGURE 25.20 Replication of Hepatitis B Virus Notice that this DNA virus employs reverse transcriptase in its replication cycle.

subsequently transcribed into DNA by reverse transcriptase, and when a double strand is formed by DNA polymerase, this DNA becomes the genome for the newly forming virions. Doublestrand formation ceases when the virions bud from the host cell, however, generally leaving part of the genome single-stranded. ■ reverse transcriptase, p. 332

HBsAg appears in the bloodstream days or weeks after infection, often long before signs of liver damage are evident. In 1% to 6% of cases, the infection smolders in the liver, unsuspected for years. About 40% of chronically infected people eventually die from cirrhosis, meaning scarring, of the liver, or from liver cell cancer. Evidence indicates that these cancers result from HBV transformation of liver cells. ■ transformed cells, p. 333

Cases per 100,000 population

30

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607

25

20

15

10

5

0 1975

1980

1985

1990 Year

1995

2000

2005

FIGURE 25.21 Incidence of Viral Hepatitis in the United States, 1975–2005 The first hepatitis B vaccine was licensed in 1982, the first hepatitis A vaccine in 1995. A test for hepatitis C antibody became available in 1990. Source: Centers for Disease Control and Prevention, 2007. Summary of Motifiable Diseases-United States–2005, 54(53).

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genetically engineered yeast has been available against hepatitis B and a combined vaccine against both hepatitis A and B has also been approved. It is now recommended that all healthy newborns receive hepatitis B vaccine before they leave the hospital. Infants born to an infected mother are injected at birth with hepatitis B immune globulin (HBIG) containing a high titer of antibody to HBV. Active immunization is also started, with injections of the vaccine at 1 week, 1 month, and 6 months of age. Vaccination against hepatitis B prevents the disease, and it can also help prevent many of the 500,000 to 1 million new liver cell cancers that occur worldwide each year. Education of groups at high risk of contracting hepatitis B can help prevent the disease. Those likely to be exposed to blood are taught to consider all blood to be infectious, to wash their hands contaminated with blood, to wear gloves and protective clothing, and to handle contaminated, sharp objects such as needles and scalpel blades carefully (see Perspective 20.1). Teaching the importance and proper use of condoms also helps limit spread of the infection. Victims are advised to avoid alcohol and other hepatic toxins. There is no curative antiviral treatment yet for hepatitis B. Remarkable improvement can be achieved in many cases, however, by giving injections of genetically engineered interferon along with an antiviral medication such as lamivudine, a reverse transcriptase inhibitor, or adefovir dipivoxil. ■ interferon, p. 357

Hepatitis C Even when blood that tested positive for HBV was excluded from transfusions, post-transfusion hepatitis continued to be common, indicating the presence of another bloodborne hepatitis virus. After a number of years of trying to isolate a non-A, non-B hepatitis virus, scientists in 1989 were able to clone parts of the genome of a transfusion-associated virus, now known as hepatitis C virus (HCV). One of the gene products of these clones proved to be an HCV antigen satisfactory for detecting antibody to HCV in the blood of prospective blood donors. By not using donated blood containing the HCV antibody, the incidence of post-transfusion hepatitis fell from about 8% to very low levels. The antibody test has revealed that more than 3 million Americans are infected with HCV and that about 20,000 new cases occur each year. It is now the most common chronic, blood-borne infection in the United States.

Symptoms The symptoms of hepatitis C are similar to those of hepatitis A and B except they are generally milder. About 65% of infected individuals have no symptoms relating to the acute infection, whereas only about 25% have jaundice.

Causative Agent HCV is an enveloped, single-stranded RNA virus of the flavivirus family. The virus was successfully cultivated in vitro in 2005. There is considerable genetic variability in the viruses from different people, leading to classification into types and subtypes having differing pathogenicity. ■ flavivirus family, p. 323

Pathogenesis Few details are known about the pathogenesis of hepatitis C. Infection generally occurs from exposure to contaminated blood.

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The incubation period averages about 6 weeks (range, 2 weeks to 6 months). Despite the lack of symptoms in most people with acute infection, more than 80% develop chronic infections. The virus infects the liver and incites inflammatory and immune responses. The disease process in the liver waxes and wanes, at times seeming to return to normal, then weeks or months later showing marked inflammation. After months or years, cirrhosis and liver cancer develop in 10% to 20% of patients.

Epidemiology Although transmitted by blood from an infected person, the mechanism of exposure is not always obvious. Sharing toothbrushes, razors, and towels can be responsible. Tattoos and body piercing with unclean instruments have transmitted the disease. Approximately 50% of transmissions in the United States are due to sharing of syringes by illegal drug abusers. Transmission by sexual intercourse is probably uncommon, but those with multiple partners and sexually transmitted diseases are at increased risk for the disease. The risk of contracting the disease from transfusion of a unit of blood is now only about 0.001% because of effective screening of donated blood.

Prevention and Treatment No vaccine is available for preventing hepatitis C although new methods for producing viral proteins have raised hopes for vaccine development. Vaccination against hepatitis A and B is recommended to help avoid dual infections that might severely damage the liver. A combined hepatitis A and B vaccine is available. Avoidance of alcoholic beverages is recommended because of the toxic effect of alcohol on the already damaged liver. There is no satisfactory treatment for the chronic disease, although 30% to 50% of individuals are helped by interferon injections combined with ribavirin, an antiviral nucleoside derivative. Prolonged interferon treatment of the acute illness may prevent the chronic disease. ■ ribavirin, p. 487 Besides HAV, HBV, and HCV, hepatitis can be caused by several other hepatitis viruses, and can also occur as part of viral diseases such as yellow fever and infectious mononucleosis. Table 25.12 compares the known hepatitis viruses—A, B, C, D, E, and G.

MICROCHECK 25.6 Rotaviruses are the leading cause of viral gastroenteritis in infants and children, and they also are a common cause of traveler’s diarrhea. Noroviruses cause almost half the viral gastroenteritis in children and adults. Hepatitis A is transmitted by the fecal-oral route and is preventable by gamma globulin and an inactivated vaccine. Hepatitis B, transmitted by exposure to blood and by sexual intercourse, is preventable by a vaccine produced in yeast. A combination hepatitis A and hepatitis B vaccine is available. Hepatitis C is transmitted by blood and perhaps occasionally by sexual intercourse. Chronic hepatitis often results in cirrhosis and cancer. ✓ What two serious complication can occur late in the course of both chronic hepatitis B and C? ✓ At what stage in the replication of hepatitis B would a reverse transcriptase inhibitor act? ✓ Why might it be more difficult to prepare a vaccine against noroviruses than against rotaviruses?

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TABLE 25.12 Viral Hepatitis Hepatitis A

Hepatitis B

Hepatitis C

Causative agent

Non-enveloped, single-stranded RNA picornavirus, HAV

Enveloped, double-stranded DNA hepadnavirus, HBV

Enveloped, single-stranded RNA flavivirus, HCV

Mode of spread

Fecal-oral

Blood, semen

Blood, possibly semen

Incubation period 3 to 5 weeks (range, 2 to 7 weeks)

10 to 15 weeks (range, 6 to 23 weeks)

6 to 7 weeks (range, 2 to 24 weeks)

Prevention

Inactivated vaccine; immune globulin

Subunit-vaccine; immune globulin

No vaccine

Comments

Usually mild symptoms, but often prolonged; full recovery; no long-term carriers; combined hepatitis A and hepatitis B vaccine available

Symptoms often more severe than hepatitis A; progressive liver damage in 1% to 6% can lead to cirrhosis and cancer, chronic carriers; can cross the placenta; combined hepatitis A and hepatitis B vaccine available

Usually few or no symptoms; progressive liver damage or cancer in 10% to 20% of cases; chronic carriers

Hepatitis D

Hepatitis E

Hepatitis G

Causative agent

Defective single-stranded RNA virus, HDV

Non-enveloped, single-stranded RNA calcivirus, HEV

Single-stranded RNA flavivirus

Mode of spread

Blood, semen

Fecal-oral

Blood, possibly semen

Incubation period 2 to 12 weeks

2 to 6 weeks

Weeks

Prevention

No vaccine

No vaccine

No vaccine

Comments

Prior or concurrent HBV infection necessary; can cause worsening of hepatitis B; can cross the placenta

Similar to hepatitis A, except severe disease in pregnant women, same or related virus in rats

Usually mild symptoms; persistent viremia for months or years

25.7 Protozoan Diseases of the Lower Digestive System Focus Points Describe the causative agents of giardiasis, cryptosporidiosis, cyclosporiasis, and amebiasis. Compare and contrast the epidemiology of these protozoan intestinal diseases.

Symptoms In the usual epidemic of giardiasis, about two-thirds of exposed individuals develop symptoms. The incubation period is generally 6 to 20 days. Symptoms can range from mild (indigestion, “gas,” and nausea) to severe (vomiting, explosive diarrhea, abdominal cramps, fatigue, and weight loss). The symptoms usually disappear without treatment in 1 to 4 weeks, but some cases become chronic. Both symptomatic and asymptomatic persons can become long-term carriers, unknowingly excreting infectious cysts with their feces.

Causative Agent Protozoa are important causes of human intestinal disease. All the major protozoan motility groups are represented: Mastigophora, those with flagella; Ciliophora, those with cilia; Apicomplexa, those that are usually immobile; and Sarcodina, those that move by pseudopods. All are transmitted by the fecal-oral route. ■ protozoa, p. 285

Giardiasis Disease resulting from Giardia lamblia infection, called giardiasis, is the most commonly identified waterborne illness in the United States. It can be contracted from clear mountain streams or from chlorinated city water and can be transmitted by personto-person contact. Giardiasis occurs worldwide and is responsible for many cases of traveler’s diarrhea. In Americans, G. lamblia is the most commonly identified intestinal parasite, and in economically underdeveloped areas of the world, its incidence often exceeds 10%.

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Giardia lamblia is a flagellated protozoan shaped like a pear cut lengthwise, with two side-by-side nuclei that resemble eyes. These features along with an adhesive disc on its undersurface give the organism an unmistakable appearance (figure 25.22). Giardia lamblia can exist in two forms: as a vegetative trophozoite or as a resting form called a cyst. The trophozoite is the actively feeding form, and it colonizes the upper part of the small intestine. Generally, only trophozoites are present in the feces when an infected person is having diarrhea. When trophozoites are carried slowly by intestinal contents toward the large intestine, they develop into cysts. Giardia cysts have thick walls composed of chitin, a tough, flexible, nitrogen-containing polysaccharide. The cyst wall protects the organism from harsh environmental conditions. Because it appeared to lack mitochondria, G. lamblia has been considered to be part of an ancient group that arose before eukaryotes acquired these organelles. More recent evidence appears to refute this idea because the protozoan contains functional remnants of mitochondria. ■ chitin, p. 71

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Although waterborne outbreaks are the most common, person-to-person contact can also transmit the disease. This mode of transmission is especially likely in day care centers where workers’ hands become contaminated in the process of diaper changing. People who promiscuously engage in anal intercourse and fellatio are also prone to contracting the disease. Transmission by fecally contaminated food has also been reported. Good personal hygiene, especially handwashing, decreases the chance of passing on the infection. ■ day care centers, p. 461

Prevention and Treatment

FIGURE 25.22 Giardia lamblia Trophozoites in Human Intestine

Filtration of community water supplies is effective. For hikers, the best way to make drinking water safe from giardiasis is to boil it for 1 minute or use a portable filter of 1 micrometer pore size or smaller. Other methods, such as using a few drops per quart of water of household sodium hypochlorite bleach, tincture of iodine, or commercial water-purifying tablets, are time consuming and considerably less reliable. As in all chemical sterilization procedures, time and temperature are important. Only an hour may be necessary to treat warm water, but many hours are required to kill cysts in cold water. Several medicines, including quinacrine (Atabrine) and metronidazole (Flagyl), effectively treat giardiasis. Table 25.13 describes the main features of giardiasis.

Scanning electron micrograph.

Cryptosporidiosis Pathogenesis The cyst form is responsible for infection because, unlike the trophozoite, it is resistant to stomach acid. Two trophozoites emerge from each cyst when it reaches the small intestine. Some of these trophozoites attach to the epithelium by their adhesive disc, whereas others move freely in the intestinal mucus using their flagella. Some may even migrate up the bile duct to the gallbladder and cause crampy pain or jaundice. The protozoa do not destroy the host epithelium, but in severe infestations they may entirely cover the epithelial surface. They interfere with the ability of the intestine to absorb nutrients and secrete digestive enzymes. The result is malnutrition, bulky feces containing fat, and excessive intestinal gas from bacterial digestion of unabsorbed food material. Some of the intestinal impairment is probably a side effect of the host immune system attacking the parasites.

Epidemiology Transmission of G. lamblia is usually by the fecal-oral route, especially via fecally contaminated water. Known or suspected sources of G. lamblia include beavers, raccoons, muskrats, dogs, cats, and humans. A single human stool can contain 300 million G. lamblia cysts; only 10 cysts are required to establish infection. The cysts are infectious immediately after passage and can remain viable in cold water for more than 2 months. Usual levels of chlorination of municipal water supplies are ineffective against the cysts, and water filtration is necessary to remove them. Hikers who drink from streams, even in remote areas thought to contain safe water, are at risk of contracting giardiasis.

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Cryptosporidiosis, disease of the small intestine caused by the Cryptosporidium genus of protozoa, was recognized in animals in the early 1900s, but not identified as a threat to human beings until the AIDS epidemic struck in the early 1980s. Since then, it has become clear that cryptosporidiosis is a major hazard not only to those with immunodeficiency, but to the public at large. A 1993 waterborne outbreak of the disease in Milwaukee involved more than 403,000 people!

TABLE 25.13

Giardiasis

Symptoms

Mild illness: indigestion, flatulence, nausea; severe: vomiting, diarrhea, abdominal cramps, weight loss

Incubation period

6 to 20 days

Causative agent

Giardia lamblia, a flagellated pear-shaped protozoan with two nuclei

Pathogenesis

Ingested cysts survive stomach passage; trophozoites emerge from the cysts in the small intestine, where some attach to epithelium and others move freely; mucosal function is impaired by adherent protozoa and host immune response.

Epidemiology

Ingestion of fecally contaminated water; personto-person, in day care centers.

Prevention and treatment

Boiling or disinfecting drinking water; filtration of community water supplies. Treatment: quinacrine hydrochloride (Atabrine) or metronidazole (Flagyl).

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25.7 Protozoan Diseases of the Lower Digestive System

Symptoms Cryptosporidiosis is characterized by fever, loss of appetite, nausea, crampy abdominal pain, and profuse watery diarrhea, beginning after an incubation period of 4 to 12 days. The symptoms generally last 10 to 14 days, but in people with immunodeficiency diseases, they can last for months and be life threatening.

Causative Agent Cryptosporidium parvum, a coccidian member of the Apicomplexa, is the causative agent of cryptosporidiosis. Cryptosporidium parvum multiplies intracellularly in the small intestinal epithelium, its entire life cycle occurring in a single host. The oocyst stage is a tiny (4 to 6 mm), acid-fast sphere that contains four banana-shaped sporozoites (figure 25.23). ■ Apicomplexa, p. 273

Pathogenesis Few details are known about the pathogenesis of cryptosporidiosis. Following ingestion, the digestive juices of the small intestine release the sporozoites from the oocysts. The sporozoites invade the epithelial cells of the small intestine, deforming the epithelium and intestinal villi and causing an inflammatory response beneath the cells. Secretion of water and electrolytes increases and absorption of nutrients decreases, but the mechanism is unknown. Cellmeditated immunity is important in controlling the infection.

611

taminate food and drinking water. Epidemics have arisen from drinking water, swimming pools, a water slide, a zoo fountain, day care centers, unpasteurized apple juice, and other food and drink. The organism is responsible for many cases of traveler’s diarrhea.

Prevention and Treatment Effective measures for preventing cryptosporidiosis are limited to careful monitoring of municipal water supplies, with institution of filtration, ultraviolet radiation, and ozone treatments when necessary. Pasteurization of liquids for human consumption and sanitary disposal of human and animal feces are other important control measures. Food-handlers with diarrhea should not handle food until they are symptom-free, and all food-handlers should adhere to handwashing and other sanitary measures. Immunodeficient individuals are advised to avoid contact with animals, to boil or filter drinking water using a 1 mm or smaller pore size filter, and to avoid recreational water activities. No satisfactory treatment exists for cryptosporidiosis, although a combination of two antibiotics, paromomycin and azithromycin, has helped control the disease in some AIDS patients. The main features of cryptosporidiosis are shown in table 25.14.

Epidemiology The oocysts of C. parvum are infectious when eliminated with the feces, and fewer than 30 of them are sufficient to cause an infection. Person-to-person spread readily occurs under conditions of poor sanitation. Infected individuals often have prolonged diarrhea and can continue to eliminate infectious cysts for 2 weeks or more after the diarrhea ceases. Moreover, the cysts can survive for long periods of time in food and water, are even more resistant to chlorine than Giardia, and are too small to be removed from drinking water by some filtration methods. Equally troubling, C. parvum has a wide host range, infecting domestic animals such as dogs, pigs, and cattle. These animals, as well as humans, can con-

10 mm

FIGURE 25.23 Oocysts of Cryptosporidium parvum Acid fast stain of feces. Person-to-person and waterborne transmission are common.

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TABLE 25.14

Cryptosporidiosis

Symptoms

Fever, loss of appetite, nausea, crampy abdominal pain, watery diarrhea, usually lasting 10 to 14 days

Incubation period

Usually about 6 days (range, 4 to 12 days)

Causative agent

Cryptosporidium parvum, a coccidian member of the Apicomplexa. Its life cycle takes place entirely within the epithelial cells of the small intestine.

Pathogenesis

Following ingestion of oocysts, the intestinal juices cause the release of four banana-shaped sporozoites. The sporozoites invade the epithelial cells, causing deformity of the cells and the intestinal villi and inciting an inflammatory response. Secretion of water and electrolytes increases, and absorption of nutrients decreases. The process is brought under control largely by cell-mediated immunity.

Epidemiology

Oocysts of C. parvum are infectious when discharged with the feces. The infectious dose is small, and person-to-person spread readily occurs under unsanitary conditions. Infected individuals can discharge the oocysts for weeks after symptoms subside. The oocysts resist chlorination, and they pass through many municipal water filtration systems. The host range is wide, including cattle, pigs, and dogs.

Prevention and treatment

Pasteurization of beverages such as milk and apple juice, boiling of drinking water, or filtering it using a 1-mm or smaller pore size filter. Sanitary disposal of human and animal feces. No effective treatment exists.

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Cyclosporiasis

Prevention and Treatment

Cyclosporiasis first came to medical attention in the late 1980s, with widely scattered epidemics of severe diarrhea. For several years, the causative organism was known only as a “cyanobacterium-like body.” Later, the bodies were shown to be the oocysts of a coccidian protozoan, Cyclospora cayetanensis.

No preventive measures are available except boiling or filtering drinking water and thoroughly washing produce such as berries and leafy vegetables during an epidemic. Cotrimoxazole (trimethoprim plus sulfamethoxazole) effectively treats most cases of cyclosporiasis. The main features of cyclosporiasis are presented in table 25.15.

■ cyanobacteria, p. 258

Symptoms Cyclosporiasis begins after an average incubation period of about 1 week, with fatigue, loss of appetite, slight fever, vomiting, and watery diarrhea, followed by weight loss. The diarrhea usually subsides in 3 to 4 days, but relapses occur for up to 4 weeks.

Causative Agent Cyclospora cayetanensis is also a coccidian member of the Apicomplexa, and its oocysts are similar to those of Cryptosporidium parvum, except C. cayetanensis oocysts are larger, about 8 to 10 mm in diameter, and when passed in feces do not yet contain sporozoites. After days under favorable conditions outside the body, two sporocysts, each containing two sporozoites, develop within each oocyst, which is then infectious. Structural features place the protozoan within the Cyclospora, a genus described in 1881. Studies of its ribosomal RNA base sequence show that it is closely related to members of the genus Eimeria. This is an example of the turmoil arising from molecular biological findings as the newer science challenges the old on the naming of microorganisms.

Amebiasis Disease resulting from Entamoeba histolytica infection is called amebiasis. In the United States, cases occur mainly among male homosexuals who have many sexual partners, in poverty-stricken areas, and among migrant farm workers. Although usually a mild disease, worldwide it causes about 30,000 deaths per year, most of which occur in Mexico, parts of South America, Asia, and Africa. Life-threatening disease occurs in these areas because of the presence of virulent E. histolytica strains and crowded, unsanitary living conditions.

Symptoms Amebiasis is commonly asymptomatic, but symptoms ranging from chronic, mild diarrhea lasting months or years, to acute dysentery and death, can occur.

Causative Agent The causative organism, Entamoeba histolytica (see figure 25.24 inset), is a member of the Sarcodina, ranging from about 20 to

Pathogenesis Little is known about the pathogenesis of cyclosporiasis because laboratory animals are not susceptible to the disease. Scant information available from small intestinal biopsies of patients infected with C. cayetanensis confirms that both sexual and asexual forms of the protozoan are present in the intestinal epithelium.

Epidemiology The epidemiology of Cyclospora cayetanensis differs in important ways from that of Cryptosporidium parvum. The oocysts of C. cayetanensis are immature when eliminated in the stool and are non-infectious, so that person-to-person spread does not occur. Most infections occur in spring and summer, probably because warm, moist conditions favor maturation of the C. cayetanensis oocysts. Travelers to tropical areas are more likely than others to become infected. So far, no animal source has been identified. Fresh produce, especially imported raspberries, has been implicated in a number of epidemics, but the source of the contaminating organisms is unknown. In most instances, the produce has been imported from a tropical region. The protozoa have been identified in natural waters, but a human source could not be ruled out. Outbreaks have occurred in Canada, the United States, Nepal, Peru, Haiti, and various other countries of South and Central America, Southeast Asia, and Europe.

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TABLE 25.15 Cyclosporiasis Symptoms

Fatigue, loss of appetite, vomiting, watery diarrhea, and weight loss. Symptoms improve in 3 to 4 days, but relapses can occur for up to a month.

Incubation period

Usually about 1 week (range, 1 to 12 days)

Causative agent

Cyclospora cayetanensis, a coccidian

Pathogenesis

Biopsies of human intestine show sexual and asexual stages in the intestinal epithelium. Laboratory animals are not susceptible to the infection.

Epidemiology

The oocysts of C. cayetanensis are not infectious when discharged in the feces, and so person-to-person spread does not occur. Travelers to tropical countries are at risk of infection. Produce, especially raspberries, imported from tropical Central America, has been implicated in most North American outbreaks.

Prevention and treatment

Use of boiled or filtered drinking water is advised in the tropics. Thorough washing of imported berries and leafy vegetables. Most victims are effectively treated with trimethoprimsulfamethoxazole (trade names Bactrim, Septra).

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25.7 Protozoan Diseases of the Lower Digestive System

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FIGURE 25.24 Life Cycle of Entamoeba histolytica Quadrinucleate (a) Infectious quadrinucleate cyst

(c) Trophozoite with ingested bacteria and red blood cells

cysts enter the mouth (a) and pass through the stomach to the lower small intestine (b) Four daughter protozoa are released from each cyst and develop into trophozoites (c), the feeding form (d). Dehydration in the large intestine stimulates progressive stages of cyst development (e). Mature cysts are passed in the feces to contaminate soil, water, hands and food. Trophozoites that burrow into intestinal blood vessels can be carried to the liver or other organs, causing abscesses. The electron micrograph shows amebic cysts and trophozoites on bowel mucosa.

Liver Stomach Large intestine

(d) Immature cyst with single nucleus

(b) Four daughter protozoa are released and develop into trophozoites.

Lower small intestine

(e) Quadrinucleate cyst with chromatoid bodies

Mature cysts contaminate soil, water, hands, and food Life cycle is repeated.

40 mm in diameter. Like Giardia, it has a cyst form with a chitincontaining cyst wall. Immature cysts have a single nucleus. As the cyst matures, the nucleus divides twice to form a cyst with four nuclei—the infectious form for the next host. The life cycle of E. histolytica is shown in figure 25.24.

and tissue destruction in the intestine and in other body tissues can result in amebic abscesses. The irritating effect of the amebas on the cells lining the intestine causes intestinal cramps and diarrhea. Due to intestinal ulceration, the diarrheal fluid is often bloody, and the condition is referred to as amebic dysentery.

Pathogenesis

Epidemiology

Ingested quadrinucleate cysts of E. histolytica survive passage through the stomach. The organisms are released from their cysts in the small intestine, whereupon the cytoplasm and nuclei divide, yielding eight trophozoites. Upon reaching the lower intestine, these trophozoites begin feeding on mucus and intestinal bacteria. Many, but not all, strains produce a cytotoxic enzyme that kills intestinal epithelium on contact, allowing the organisms to penetrate the lining cells and enter deeper tissues of the intestinal wall. Sometimes, they penetrate into blood vessels and are carried to the liver or other body organs. Multiplication of the organisms

Amebiasis is distributed worldwide, but it is more common in tropical areas where sanitation is poor. Humans constitute the only important reservoir. Transmission is fecal-oral. The disease is mainly associated with poverty, male homosexuality, and migrant workers.

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Prevention and Treatment Prevention of amebiasis depends on sanitary measures and avoiding fecal contamination of drinking water. Metronidazole, paromomycin, and other medications are available for treatment. Table 25.16 gives the main features of amebiasis.

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TABLE 25.16

Digestive System Infections

MICROCHECK 25.7

Amebiasis

Symptoms

Diarrhea, abdominal pain, blood in feces

Incubation period

2 days to several months

Causative agent

Entamoeba histolytica; a protozoan of the group Sarcodina

Pathogenesis

Ingested cysts liberate trophozoites in the small intestine; upon reaching the large intestine, trophozoites feed on mucus and cells lining the intestine; enzymes are produced that allow penetration of the intestinal epithelium, sometimes the intestinal wall and blood vessels, and thence to the liver and other organs, resulting in abscesses.

Epidemiology

Ingestion of fecally contaminated food or water; disease associated with poverty, homosexual men, and migrant workers.

Prevention and treatment

Good sanitation and personal hygiene. Treatment: metronidazole, paromomycin.

Giardiasis, caused by the flagellated protozoan Giardia lamblia, is a common waterborne disease, but it can also be transmitted personto-person. Cryptosporidiosis is another waterborne disease that is also transmissible person-to-person, but it is caused by a coccidian member of the Apicomplexa that multiplies within intestinal epithelial cells. There is no satisfactory treatment. Cyclosporiasis is a similar disease, but it is not transmissible person-to-person and it can be effectively treated. Amebiasis is caused by an ameba that ulcerates the large intestinal epithelium, resulting in dysentery. ✓ Explain why person-to-person spread does not occur in cyclosporiasis. ✓ Why might cryptosporidiosis be a threat to AIDS patients? ✓ Would you expect an individual with giardiasis who has diarrhea to be more likely to transmit the disease than an individual with giardiasis who does not have diarrhea? Explain.

FUTURE CHALLENGES Defeating Diarrhea Development of better preventive and treatment techniques for digestive tract diseases has an urgency arising from massive food and beverage production and distribution methods. For example, in 1994, an estimated 224,000 people became ill because a tanker truck used to transport ice cream mix had previously carried liquid eggs. One day’s production from a ground beef factory can yield hundreds of thousands of pounds of hamburgers, which are soon sent to many parts of this or other countries. The challenge is to better educate the producers and transporters, to develop guidelines to help them avoid contamination, to develop fast and accurate ways of identifying pathogens in

food, and to utilize newly approved methods such as meat irradiation. Other challenges include: Exploiting the power of molecular biology techniques to produce effective vaccines against hepatitis C virus and bacterial pathogens. There is special need for bacterial vaccines that can be administered by mouth and evoke long-lasting mucosal immunity. Exploring the influence of global warming on digestive tract diseases. A study of Peruvian children by Johns Hopkins University scientists found an 8% increase in clinic visits for diarrhea

with each 1°C increase in temperature from the normal. Exploring new prevention and treatment options. Scientists at the University of Florida have developed a genetically engineered Streptococcus mutans that does not produce lactic acid but readily displaces wild strains of the dental decaycausing bacterium. Researchers at the University of Alberta have custom-designed a molecule that binds circulating Shiga toxin, potentially preventing hemolytic uremic syndrome. Others work on finding an effective therapy for cryptosporidiosis.

SUMMARY 25.1 Anatomy and Physiology (figures 25.1, 25.2) The digestive tract is composed of the mouth and teeth, saliva-producing glands, esophagus, stomach, small intestine, liver, pancreas, and large intestine. It is a major route for pathogens to enter the body.

The Esophagus The esophagus is a muscular walled tube that conveys food and liquids to the stomach by peristalsis.

The Mouth The cheeks and tongue move food so it can be ground by the teeth to make it more easily digested. Teeth are composed of enamel—a protective, hard, outer layer—and dentin—a softer, more easily penetrated substance. The gingival crevice is a space between the tooth and the gum.

The Stomach The stomach is a distensible sack with a muscular wall and a lining epithelium that produces hydrochloric acid and the digestive enzyme, pepsin. The epithelium is protected by a thick layer of mucus. Emptying of the stomach is regulated by a valve called the pylorus, under the control of nerves and hormones.

Salivary Glands Salivary glands are located under the tongue, and laterally in the floor of the mouth. Two other glands, the parotids, are located in the face below the ears. These glands produce saliva, saturated with calcium, and contain lysozyme, amylase, lactoferrin, and IgA antibodies.

The Small Intestine Villi and microvilli markedly increase the surface area of the intestinal lining, which both secretes digestive enzymes and absorbs fluids and nutrients. The lining cells are continuously shed and replaced, which helps protect against microbial poisons.

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Summary

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The Pancreas The pancreas produces insulin, a regulator of blood glucose levels, directly into the bloodstream. The pancreas also produces a large amount of alkaline fluid that contains digestive enzymes, conveyed via a tube into the upper small intestine.

25.4 Viral Diseases of the Upper Digestive System

The Liver The liver produces a fluid, bile, that is stored in the gallbladder, ultimately flowing through a tube into the upper small intestine. Bile contains a yellowish pigment, bile pigment, a breakdown product of hemoglobin that the liver removes from the blood. Bile helps in the digestion of fats and oils, and the absorption of fat-soluble vitamins, A, D, E, and K. Other functions of the liver include inactivating bloodstream poisons and chemically altering medications.

Mumps (table 25.4, figure 25.10) Mumps is caused by an enveloped RNA virus that infects not only the parotid glands, but the meninges, testicles, and other body tissues. Mumps virus generally causes more severe disease in persons beyond the age of puberty; it can be prevented using an attenuated vaccine (figure 25.11).

The Large Intestine The large intestine absorbs any remaining nutrients and water from the intestinal contents, leaving the residual material, feces, for excretion.

25.2 Normal Microbiota The Mouth The species of bacteria that inhabit the mouth colonize different locations depending on their ability to attach to specific receptors. Dental plaque consists of enormous quantities of bacteria of various species attached to teeth or each other (figure 25.3). The presence of teeth allows for colonization by anaerobic bacteria. The Intestines The normal fasting stomach is devoid of microorganisms. Microorganisms make up about one-third of the weight of feces. The biochemical activities of microorganisms in the large intestine include synthesis of vitamins, degradation of indigestible substances, competitive inhibition of pathogens, chemical alteration of medications, and production of carcinogens.

Upper Digestive System Infections 25.3 Bacterial Diseases of the Upper Digestive System Tooth Decay (Dental Caries) (table 25.1) Dental caries is caused mainly by Streptococcus mutans involved in formation of extracellular glucans from dietary sucrose. Penetration of the calcium phosphate tooth structure depends on acid production by cariogenic dental plaque. S. mutans is not inhibited by plaque acidity and stores fermentable intracellular polysaccharide (figure 25.4). Control of dental caries depends mainly on supplying fluoride and restricting dietary sucrose. Dental sealants fill the pits and crevices in children’s teeth. Periodontal Disease (table 25.1) Periodontal disease is caused by an inflammatory response to the plaque bacteria at the gum line; it is mainly responsible for tooth loss in older people (figure 25.5). Trench Mouth (table 25.1) Trench mouth, or acute necrotizing ulcerative gingivitis (ANUG), can occur at any age in association with poor mouth care (figure 25.6). Helicobacter pylori Gastritis (table 25.2) H. pylori predisposes the stomach and the uppermost part of the duodenum to peptic ulcers (figures 25.7, 25.8). Treatment with antimicrobial medications can cure the infection and prevent peptic ulcer recurrence.

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Herpes Simplex (Cold Sores or Fever Blisters) (table 25.3, figure 25.9) Herpes simplex is caused by an enveloped DNA virus. Infected cells show intranuclear inclusion bodies. HSV persists as a latent infection inside sensory nerves; active disease occurs when the body is stressed.

Lower Digestive System Infections 25.5 Bacterial Diseases of the Lower Digestive System Cholera (table 25.5) Cholera is a severe form of diarrhea caused by a toxin of Vibrio cholerae that acts on the small intestinal epithelium (figures 25.12, 25.13). Shigellosis (table 25.6) Shigellosis is caused by species of Shigella, common causes of dysentery because they invade the epithelium of the large intestine (figure 25.14). One Shigella species produces Shiga toxin, which causes the hemolytic uremic syndrome. Escherichia coli Gastroenteritis (tables 25.7, 25.8) Virulence factors often depend on plasmids, which can transfer virulence to other enteric bacteria. Some E. coli strains, such as O157:H7, originating from wild and domestic animals, can cause the hemolytic uremic syndrome. Salmonellosis (table 25.9) Strains of Salmonella that originate from animals usually cause gastroenteritis. The organisms are often foodborne, commonly with eggs and poultry. Typhoid fever is caused by Salmonella Typhi, which only infects humans. The disease is characterized by high fever, headache, and abdominal pain. Untreated, it has a high mortality rate. An oral attenuated vaccine helps prevent the disease. Campylobacteriosis (table 25.10) Campylobacter jejuni is the most common bacterial cause of diarrhea in the United States; it usually originates from domestic animals (figure 25.15).

25.6 Viral Diseases of the Lower Digestive System Rotaviral Gastroenteritis (table 25.11) Rotaviral gastroenteritis is the main diarrheal illness of infants and young children, but also can involve adults, as in traveler’s diarrhea. Rotaviruses are segmented RNA viruses of the reovirus family (figure 25.16). Norovirus Gastroenteritis (table 25.11) Norovirus gastroenteritis accounts for almost half the cases of viral gastroenteritis in the United States. Noroviruses are small RNA viruses of the calcivirus family (figure 25.17). Hepatitis A (table 25.12, figures 25.18, 25.21) Hepatitis A is usually mild or asymptomatic in children; some cases are prolonged, with weakness, fatigue, and jaundice. Hepatitis A virus (HAV) is a picornavirus spread by fecal contamination of hands, food, or water. An injection of gamma globulin gives temporary protection from the disease; an inactivated vaccine is available actively to immunize against the disease.

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Hepatitis B (table 25.12, figure 25.21) Hepatitis B virus (HBV) is a hepadnavirus spread by blood, blood products, semen, and from mother to baby (figures 25.19, 25.20). Asymptomatic carriers are common and can unknowingly transmit the disease. Chronic infection is common and can lead to scarring of the liver (cirrhosis) and liver cancer.

Cryptosporidiosis (table 25.14) The life cycle of Cryptosporidium parvum, a coccidium, a member of the Apicomplexa, takes place in the small intestinal epithelium. Its oocysts are infectious, resist chlorination, and are too small to be removed by many filters (figure 25.23). It is a cause of many water- and foodborne epidemics, and traveler’s diarrhea.

Hepatitis C (table 25.12, figure 25.21) Hepatitis C virus (HCV) is a flavivirus transmitted mainly by blood; approximately 60% of cases are acquired from needle sharing by injected drug abusers. Hepatitis C is asymptomatic in over 60% of acute infections; more than 80% of infections become chronic.

Cyclosporiasis (table 25.15) Transmission of Cyclospora cayetanensis, a coccidium, is fecal-oral, via water or produce such as berries; it causes traveler’s diarrhea. Oocysts are not infectious when passed in feces, and thus there is no person-to-person spread; no hosts other than humans are known.

25.7 Protozoan Diseases of the Lower Digestive System

Amebiasis (table 25.16) Entamoeba histolytica, a member of the Sarcodina group of protozoa, is an important cause of dysentery; often chronic; infection can spread to the liver and other organs (figure 25.24). The organism exists in ameba and cyst forms; the quadrinucleate cyst is infectious.

Giardiasis (table 25.13) Transmission of Giardia lamblia, a mastigophoran, is usually via drinking water contaminated by feces. It is a common cause of traveler’s diarrhea (figure 25.22). Its cysts survive in chlorinated water and must be removed by filtration.

REVIEW QUESTIONS Short Answer 1. Name a disease caused by Clostridium difficile. 2. Name three characteristics of Streptococcus mutans that contribute to its ability to cause dental caries. 3. Give the pathogenesis of periodontal disease. 4. Give three examples of stressful events that can reactivate herpes simplex. 5. At what stage of maturation in boys is mumps likely to be complicated by swelling of the testicles? 6. What is the hemolytic uremic syndrome? Name an organism that can cause it. 7. What is the usual source of Campylobacter jejuni infections? 8. How can shigellas move from one host cell to another even though they are non-motile? 9. Name four different groups of Escherichia coli based on their pathogenic mechanisms. 10. Contrast the transmission of hepatitis A and hepatitis B. 11. Name two kinds of hepatitis that can be prevented by vaccines. 12. Contrast the cause and epidemiology of giardiasis and amebiasis.

Multiple Choice 1. The following are all true of intestinal bacteria, except a) they produce vitamins. b) they can produce carcinogens. c) they are mostly aerobes. d) they produce gas from indigestible substances in foods. e) they include potential pathogens. 2. All of the following attributes of Streptococcus mutans are important in tooth decay, except a) it attaches specifically to tooth pellicle. b) it can grow at pH below 5. c) it produces lactic acid. d) it synthesizes glucan. e) it stores fermentable polysaccharide.

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3. All of the following are true of Helicobacter pylori, except a) it is a helical bacterium with sheathed flagella. b) it has not been cultivated in vitro. c) it produces a powerful urease. d) it causes stomach infections that last for years. e) it has an important role in the causation of stomach ulcers. 4. All of the following are probably important to the cholera-causing ability of Vibrio cholerae, except a) it attaches firmly to small intestinal epithelium. b) it produces cholera toxin. c) lysogenic conversion. d) acid resistance. e) it survives in the sea in association with zooplankton. 5. Which of the following statements concerning Salmonella Typhi is false? a) It is commonly acquired from domestic animals. b) It can colonize the gallbladder for years. c) It is highly resistant to killing by bile. d) It can destroy Peyer’s patches. e) It causes typhoid fever. 6. Which statement about rotaviral gastroenteritis is false? a) The name of the causative agent was suggested by its appearance. b) Most of the 600,000 deaths occurring worldwide from this disease are due to dehydration. c) Most cases of the disease occur in infants and children. d) The causative agent infects mainly the stomach. e) The disease is transmitted by the fecal-oral route. 7. Which of the following statements about noroviruses is false? a) They cause almost half the cases of viral gastroenteritis in the United States. b) They can be responsible for epidemics of gastroenteritis. c) They generally produce an illness lasting 1 to 2 weeks. d) Similar viruses are widespread among marine animals. e) They typically cause disease in children and adults rather than infants.

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Review Questions 8. Which of the following statements about hepatitis is false? a) Both RNA and DNA viruses can cause hepatitis. b) Some kinds of hepatitis can be prevented by vaccines. c) More than half of the new hepatitis C cases are the result of injected-drug abuse. d) Lifelong carriers of hepatitis A are common. e) At least six different viruses can cause hepatitis. 9. Which of the following statements about hepatitis B virus is false? a) Replication involves reverse transcriptase. b) Infected persons may have large numbers of non-infectious viral particles circulating in their bloodstream. c) In the United States, the incidence of infection has been steadily increasing over the last few years. d) Asymptomatic infections can last for years. e) Infection can result in cirrhosis. 10. Choose the most accurate statement about cryptosporidiosis. a) Waterborne transmission is unlikely. b) The host range of the causative agent is narrow. c) It is prevented by chlorination of drinking water. d) Person-to-person spread does not occur. e) The life cycle of the causative agent occurs within small intestinal epithelial cells.

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617

Applications 1. One reason given by Peruvian officials for not chlorinating their water supply is that chlorine can react with substances in water or in the intestine to produce carcinogens. How do you assess the relative risks of chlorinating or not chlorinating drinking water? 2. A medical scientist is designing a research program to determine the effectiveness of hepatitis B vaccine in preventing liver cell cancer. Because liver cell cancer probably has multiple causes, how would you measure the success of an anticancer vaccination program?

Critical Thinking 1. What might the lack of a brown color of feces indicate? 2. Mutant strains of Helicobacter pylori that lack the ability to produce urease fail to cause infection when they are swallowed. Infection occurs, however, if a tube is used to introduce them directly into the layer of mucus that overlies the stomach epithelium. What does this imply about the role of urease in the bacterium’s pathogenicity?

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26 Color-enhanced electron micrograph of a human papillomavirus.

Genitourinary Infections A Glimpse of History Although some historians argue that syphilis was transported to Europe from the New World by Columbus’s crew, others find convincing evidence, including biblical references, that syphilis existed in the Old World for many years before Columbus returned. History and literature record that kings, queens, statesmen, and heroes degenerated into madness or mental incompetence or were otherwise seriously disabled as a result of the later stages of syphilis. Henry VIII (King of England, 1509–1547), Ivan the Terrible (Czar of Russia, 1547–1584), Catherine the Great (Empress of Russia, 1762–1796), Merriwether Lewis (Lewis and Clark Expedition, 1803–1808), and Benito Mussolini (Premier of Italy, 1883–1945) are a few of the famous people who probably suffered from syphilis. Syphilis was first named the “French pox” or the “Neapolitan disease” because it was believed to have come from France or Italy. In 1530, Girolamo Fracastoro, an Italian physician who suggested the germ theory long before the discovery of microorganisms, wrote a poem about a shepherd named Syphilis who had ulcerating sores covering his body. The description matched the symptoms of syphilis, and from that time on, the disease was known by the shepherd’s name. Initially, the method of transmission was unknown, but gradually it became generally recognized that the disease was sexually transmitted. The symptoms of syphilis were very severe in the early years of the epidemic, often causing death within a few months. Treatment, consisting of doses of mercury, and guaiacum, the resin from a tropical American tree of the genus Guaiacum, had little beneficial effect. As the decades went by, mutations and natural selection resulted in more resistant hosts and a less-virulent microbe, and the disease evolved into the chronic illness known today. In 1905, Fritz Schaudinn, a German protozoologist, examined some fluid from a syphilitic sore and saw a faintly visible organism “twisting, drilling back and forward, hardly different from the dim

nothingness in which it swam.” When Schaudinn used dark-field illumination, he was able to see the organism much more clearly. It appeared very thin and pale, similar to a corkscrew without a handle. The spirochetes appeared in specimens from other cases of syphilis, and Schaudinn later succeeded in staining them. By this time, he felt certain he had discovered the cause of syphilis, but the organism could not be cultivated on laboratory media. Schaudinn named the organisms Spirochaeta pallida, “the pale spirochete.” This organism is now called Treponema pallidum, from treponema, “a turning thread.”

I

nfections of the reproductive and urinary tracts are very common, often uncomfortable or quietly destructive, and sometimes tragic in their consequences. Urinary infections lead the list of infections acquired in hospitals and are the chief source of fatal, nosocomial, bacterial bloodstream invasions. Nosocomial uterine infections—puerperal fever, once a common cause of maternal deaths from childbirth—still require strict medical vigilance to be prevented. Much of this chapter will be devoted to sexually transmitted diseases (STDs). The United States leads the industrialized nations in the reported incidence of STDs. About 1 million unintended pregnancies occur among the estimated 12 million college students each year. Only about 15% of the students have never engaged in sexual intercourse, and almost 35% of the remaining students have had six or more lifetime sexual partners. About 20% of women students say they have been forced to have sexual intercourse against their will. Approximately 70% of sexually active students report that they or their partner rarely or never use a condom. These data suggest a lack of knowledge or concern about the high risk of contracting and transmitting an STD. ■ puerperal fever, p. 450

618

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26.1

KEY TERMS Catheter A flexible tube, usually of plastic or rubber, inserted into the bladder or other body space, usually in order to drain it or instill medication. Chancre Sore resulting from an ulcerating infection. Cystitis Inflammation of the urinary bladder. Fallopian Tube The tubes that convey ova from the ovaries to the uterus.

Ophthalmia Neonatorum Infection of the eyes of newborn babies contracted during passage through the birth canal; often caused by the gonococcus or Chlamydia trachomatis. Papilloma A kind of tumor characterized by nipplelike projections of tissue; warts are an example. Pelvic Inflammatory Disease (PID) Infection of the fallopian tubes. Puerperal Fever Childbed fever; infection of the uterus following childbirth, commonly caused by Streptococcus pyogenes.

26.1 Anatomy and Physiology Focus Points List ways the urinary system protects itself from infection. Discuss the potential consequences of fallopian tube infections.

Anatomy and Physiology

619

Pyelonephritis Infection of the kidneys. Semen Fluid composed of sperm from the testicles and prostate gland secretions. Toxic Shock Collapse of the blood pressure due to a circulating toxin. Trachoma Potentially serious chronic eye disease caused by certain strains of Chlamydia trachomatis. Urethra The tube draining the bladder.

specific antibodies can be found in the urine. Antibody-forming lymphoid cells in the infected kidneys or bladder wall produce protective antibodies locally at the site where they are needed. In addition, during infection an inflammatory response occurs in which phagocytes enter the bladder and are of the utmost importance in engulfing and destroying the invading microorganisms. ■ phagocytes, p. 358

The reproductive and urinary systems are often considered together, and they are referred to as the genitourinary system because of their close proximity to one another. Also, both systems are commonly affected by the same pathogens. The genitourinary system is one of the portals of entry for pathogens.

Left kidney Right kidney

The Urinary System The urinary system consists of the kidneys, the ureters, the bladder, and the urethra (figure 26.1). The kidneys act as a specialized filtering system to cleanse the blood of many waste materials, selectively reabsorbing substances that can be reused. Waste materials are excreted in the urine, which is usually acidic because of excretion of excess hydrogen ions from foods and metabolism. Consistently alkaline urine suggests infection with a urease-producing bacterium that converts the urea in urine to ammonia. Antimicrobial medications are commonly excreted in the urine and reach concentrations higher than those in the bloodstream. Each kidney is drained by a ureter, which connects it with the urinary bladder. The bladder acts as a holding tank. Once filled, it empties through the urethra. Infections of the urinary tract occur far more frequently in women than in men, because the female urethra is short (about 4 cm, or 1.5 inches, compared with 20 cm, or 8 inches, in the male) and is adjacent to openings of the genital and intestinal tracts. Special groups of muscles near the urethra keep the system closed most of the time and help prevent infection. The downward flow of urine also helps clean the system by flushing out microorganisms before they have a chance to multiply and cause infection. The urinary tract is protected from infection by a number of mechanisms besides its anatomy. Normal urine contains antimicrobial substances such as organic acids and small quantities of antibodies. During urinary tract infections, larger quantities of

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Ureters

Bladder

Pelvis

Sphincters

Urethra

Figure 26.1 Anatomy of the Urinary System Urine flows from the kidneys, down the ureters, and into the bladder, which empties through the urethra. Sphincter muscles help to prevent microorganisms from ascending.

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The Genital System The anatomy of the female and male genital systems is shown in figure 26.2. In women during the childbearing years, an egg, or ovum, is expelled from one of the two ovaries each month and swept into the adjacent fallopian tube. Fertilization normally takes place in the fallopian tube; ciliated epithelium of the tube then moves the fertilized ovum to the uterus, where it implants itself in the epithelial lining. If fertilization does not occur, the epithelial lining of the uterus sloughs off, producing a menstrual period. Infection of the fallopian tubes can cause scarring and destruction of the ciliated epithelium, so that ova are not moved efficiently to the uterus. The fallopian tubes are open on both ends, providing a pathway into the abdominal cavity where the liver and other structures can be infected. The uterine cervix is a common site of sexually transmitted infections, and a place where cancer can develop. Except during menstruation, the cervical opening is tiny and filled with mucus. The vagina is a portal of entry for a number of infectious organisms that can advance to the uterus and fallopian tubes at the time of menstruation. The vaginal openFallopian tube

Uterus

Ovary

ing is framed on each side by two labia, or lips. These plus the clitoris and entryway of the vagina constitute the female external genitalia, or vulva. In men, the paired reproductive organs, the testes (testicles), exist outside the abdominal cavity in the scrotum. Sperm from each testis collect in a tightly coiled tubule called the epididymis and are conveyed by a long tube called the vas deferens, which enters the abdomen in the groin to join the prostate gland. The sperm and secretions of the prostate gland compose the semen. The urinary and reproductive systems join at the prostate gland. The prostate can be infected by urinary or sexually transmitted pathogens. In older men it often enlarges and hinders the flow of urine, thus fostering urinary infection.

MICROCHECK 26.1 The genitourinary system is one of the portals of entry for pathogens. Many antimicrobial medications are excreted in the urine in concentrations higher than in the blood. The flushing action of urination is a key defense mechanism against bladder infections. The fallopian tubes can provide a passageway for pathogens to enter the abdominal cavity. The uterine cervix is a common site of infection by sexually transmitted pathogens. Prostate enlargement predisposes men to urinary infection. ✓ Name two kinds of cells that help defend the bladder against infection. ✓ Would ammonia make the urine basic? How?

Bladder

Cervix Pubic bone

26.2 Normal Microbiota of the Genitourinary System

Rectum

Labia

Urethra

Vagina

Focus Points Outline the effects of estrogen on the vaginal epithelium.

(a)

List the parts of the genitourinary system that harbor normal microbiota.

Bladder Vas deferens (duct through which sperm are transported)

Pubic bone

Prostate gland Rectum

Penis

Urethra

Testis Epididymis

(b)

Figure 26.2 Anatomy of the Genital System (a) Female and (b) male.

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Normally, the urine and urinary tract above the entrance to the bladder are essentially free of microorganisms; the lower urethra, however, has a normal resident microbiota. Species of Lactobacillus, Staphylococcus (coagulase-negative), Corynebacterium, Haemophilus, Streptococcus, and Bacteroides are common inhabitants. The normal microbiota of the genital tract of women is influenced by the action of estrogen hormones on the epithelial cells of the vaginal mucosa. When estrogens are present, glycogen is deposited in these cells. The glycogen is converted to lactic acid by lactobacilli, resulting in an acidic pH that inhibits the growth of many potential pathogens. Lactobacilli may also release hydrogen peroxide, a powerful inhibitor of some anaerobic bacteria, as a by-product of metabolism. Thus, the normal microbiota and resistance to infection of the female genital tract vary considerably with the person’s hormonal status. For example, prepubertal girls, having low estrogen levels, are much more susceptible to vaginal infections with Streptococcus pyogenes

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26.3

and Neisseria gonorrhoeae than are women in their childbearing years. ■ lactobacilli, p. 255

MICROCHECK 26.2 Normally the urine and urinary tract are free of microorganisms above the entrance to the bladder, but the lower urethra hosts a number of genera of bacteria. During the childbearing years, a woman’s hormones are important in the vagina’s resistance to infection, because estrogen promotes growth of lactobacilli and acidic conditions. ✓ Which parts of the genitourinary system are normally sterile? ✓ Name two species of pathogenic bacteria to which the vagina is especially susceptible during childhood. ✓ What changes might occur in the vagina if lactobacilli were eliminated?

26.3 Urinary System Infections Focus Points Describe the factors that predispose the urinary tract to infections. Outline the pathogenesis and epidemiology of leptospirosis.

Urinary infections can involve the urethra, the bladder, or the kidneys, alone or in combination. They account for about 7 million visits to the doctor’s office each year in the United States. Any situation in which the urine does not flow naturally increases the chance of infection. After anaesthesia and major surgery, for example, the reflex ability to void urine is often inhibited for a time, and urine accumulates and distends the elastic bladder. Even being too busy to empty the full bladder may predispose to infection. Catheterization of the bladder (meaning inserting a tube, catheter, into the bladder) is another common cause of infection. Most cases of urinary infection, however, occur in otherwise healthy young women without impaired urinary flow. Pathogens infecting other body sites can spread to infect the urinary system. For example, in typhoid fever, Salmonella Typhi organisms disseminate throughout the body, infect the kidneys, and are excreted in the urine starting about 1 to 2 weeks after infection. ■ typhoid fever, pp. 601, 602

Bacterial Cystitis Cystitis, meaning inflammation of the bladder, is the most common type of urinary track infection. Bacterial cystitis is common among otherwise healthy women, and is also a common nosocomial infection. ■ health-care related infections, p. 462

Symptoms The onset of bacterial cystitis is typically abrupt, with a burning pain on urination, an urgent sensation to urinate, and frequent voiding in small amounts. The urine is usually cloudy due to the presence of leukocytes, often smells bad, and sometimes has a pale-red color due to bleeding. Tenderness may be present in the

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Urinary System Infections

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area above the pubic bone due to the underlying inflamed bladder. Some cases, however, are asymptomatic, especially among children and the elderly. Others develop sudden elevation in temperature, chills, vomiting, back pain, and tenderness overlying the kidneys, indicating a potentially serious complication—a kidney infection called pyelonephritis.

Causative Agents Bladder infections usually originate from the normal intestinal microbiota. Specific strains of Escherichia coli cause most cases of bacterial cystitis, accounting for 80% to 90% of cystitis cases in women during the reproductive years and about 70% of all bladder infections. Other enterobacteria such as Klebsiella and Proteus species account for 5% to 10%, and the Gram-positive species, Staphylococcus saprophyticus, accounts for another 5% to 10% of infections in young women. Hospitalized patients are more likely than outpatients to have bladder infections with bacteria such as the Gram-negative rods Serratia marcescens and Pseudomonas aeruginosa and the Gram-positive coccus Enterococcus faecalis, which are resistant to antibacterial medications. Persons with long-standing bladder catheters are often chronically infected with multiple species of intestinal bacteria.

Pathogenesis Generally, the causative agents of cystitis reach the bladder by ascending from the urethra. The process is aided by motility of the organisms. Urine is a good growth medium for many species of bacteria. Strains of E. coli that infect the urinary system possess pili that attach specifically to receptors on the cells that line the bladder. Experimental evidence indicates that attachment is followed by death and sloughing of the superficial layer of epithelium. The bacteria then penetrate the newly exposed cells by endocytosis. Intracellular bacteria encase themselves in a polysaccharide matrix in a kind of biofilm. Bacteria ascend the ureters and cause pyelonephritis in many cases of cystitis. Repeated episodes of pyelonephritis cause scarring and shrinkage of the kidneys and are an important cause of kidney failure. ■ pili, pp. 66, 398 ■ endocytosis, p. 73

Epidemiology About 30% of women develop cystitis at some time during their life. Factors involved in urinary infections in women include: A relatively short urethra. The position of the urethra makes it subject to fecal contamination and colonization with potentially pathogenic intestinal bacteria. From there, the bacteria need only travel a few centimeters to access the bladder. Sexual intercourse. About one-third of urinary tract infections in sexually active women are associated with sexual intercourse. The massaging effect of sexual intercourse on the urethra propels bacteria from the urethra into the urinary bladder. Many women develop their first bladder infections following their first sexual intercourse—a condition referred to as “honeymoon cystitis.” Use of a diaphram to avoid pregnancy. The ring of the diaphragm compresses the urethra and impedes the flow of urine, increasing by two to three times the risk of urinary infection.

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Urinary infections are unusual in men until about age 50, when enlargement of the prostate gland compresses the urethra and makes it difficult to completely empty the bladder. Medical conditions may require a bladder catheter to be inserted for periods ranging from several days to months. Unfortunately, this allows bacteria to reach the bladder and establish urinary tract infections both via the catheter lumen and the mucus between the wall of the catheter and the urethra. Pathogens establish a biofilm on the catheter, making it difficult or impossible to kill them with antibacterial medications. The risk of infection increases about 5% each day the catheter remains in place. In the United States, about 500,000 hospitalized patients develop bladder infections each year, mostly after catheterization. Paraplegics, individuals with paralysis of the lower half of the body, are almost always afflicted with urinary infections. Because they lack bladder control, paraplegics are unable to void normally and require a catheter indefinitely to carry their urine to a container.

TABLE 26.1 Bacterial Cystitis Symptoms

Abrupt onset, burning pain on urination, urgency, frequency, foul smell, red-colored urine; with pyelonephritis, fever, chills, back pain, and vomiting

Incubation period

Usually 1 to 3 days

Causative agents Most due to Escherichia coli; other enterobacteria, Staphylococcus saprophyticus cause some cases; nosocomial infections with antibiotic-resistant strains of Pseudomonas, Serratia, and Enterococcus genera

Pathogenesis

Usually, bacteria ascend the urethra, enter the bladder, and attach by pili to receptors on urinary tract epithelium. Sloughing of cells and an inflammatory response ensue. Spread to the kidneys can occur via the ureters, causing pyelonephritis and potential kidney failure.

Epidemiology

Bacterial cystitis is common in women, promoted by a relatively short urethra, use of a diaphragm, and sexual intercourse. Middleaged men are prone to infection because enlargement of the prostate gland partially obstructs their urethra. Placement of a bladder catheter commonly results in infection.

Prevention and treatment

Taking sufficient fluid to void urine at least four to five times daily, wiping from front to back. Single dose of antimicrobial medication with sexual intercourse may help prevent bacterial cystitis in women. Short-term antimicrobial therapy usually sufficient. Longer treatment for pyelonephritis.

Prevention and Treatment General measures for preventing urinary infections include taking enough fluid to ensure voiding at least four or five times daily, voiding immediately after sexual intercourse, and wiping from front to back after defecation to minimize fecal contamination of the vagina and urethra. Preventing recurrent infections may require taking a dose of antibacterial medication immediately before or after sexual intercourse, or taking daily a small dose of an antibiotic that is concentrated in the urine. Scientific evidence is equivocal regarding the value of cranberry juice in preventing or treating bacterial cystitis. Treatment of cystitis is usually easily carried out with a few days of an antimicrobial medication to which the causative bacterium is susceptible. Pyelonephritis usually requires prolonged treatment and often hospitalization. The main features of bacterial cystitis are presented in table 26.1.

Leptospirosis In leptospirosis, the causative organism infects the urinary system after entering the body through a mucous membrane or wound. It is then carried to the urinary system by the bloodstream rather than by ascending from the urethra. The disease is probably the most widespread of all the zoonoses, but most cases are mild, recover without treatment, and remain undiagnosed. Epidemics have occurred in soldiers serving in tropical areas and in athletes competing in triathlons. Only one or two fatal cases occur in the United States each year and it has not been a reportable disease since 1994. Leptospirosis occurs around the world in all types of climates, although it is more common in the tropics. ■ zoonoses, p. 453

follow a similar course, except after 1 to 3 days of feeling well, symptoms recur accompanied by bleeding from various sites, confusion, and evidence of severe heart, brain, liver, and kidney damage. This biphasic course of the illness is characteristic of most cases that come to medical attention.

Causative Agent Leptospirosis is caused by a slender spirochete with hooked ends, Leptospira interrogans (figure 26.3). Although some of the more

Hook

Symptoms Many infections are asymptomatic. Symptomatic cases of leptospirosis typically begin after an incubation period averaging 10 days, with the abrupt onset of headache, spiking fever, chills, and severe muscle pain. The most characteristic feature of this phase of the disease is the development of redness of the eyes due to dilation of small blood vessels. In mild cases, which are the most common, symptoms usually subside within a week and all signs and symptoms of illness are gone in a month or less. Severe cases

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5 mm

Figure 26.3 Leptospira interrogans, the Cause of Leptospirosis Note the hooked ends of this spirochete.

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26.3

Urinary System Infections

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CASE PRESENTATION The patient was a 32-year-old married woman complaining of 1 week of burning pain on urination, and frequent voiding of small amounts of bloody urine. About 8 days earlier, she completed 3 days of trimethoprim-sulfamethoxazole therapy for similar symptoms. Tests at that time showed that her urine was infected with Escherichia coli, resistant only to amoxicillin. When the symptoms returned, she began drinking 12 ounces of cranberry juice three times daily but had only partial relief. She denied having chills, fever, back pain, nausea, or vomiting. She was approximately 12 weeks pregnant. ■ trimethoprim, p. 479 Her medical history revealed that she had suffered two or three similar episodes of urinary symptoms every year for a number of years. Sometimes the symptoms would go away when she forced herself to take extra fluid, but at other times the symptoms would persist and she would obtain medical evaluation and treatment with an antibacterial medication. On one occasion several years before the present illness, chills, fever, back pain, nausea, and vomiting accompanied her symptoms and she was hospitalized for a “kidney infection.” There was no history suggesting any underlying disease such as diabetes, cancer, or immunodeficiency. On examination the patient appeared well, with no obvious distress. Her temperature was normal, as was the remainder of the physical examination. The results of her laboratory tests included normal leukocyte count and kidney function tests. Microscopic examination of her urine showed numerous red and white blood cells. A Gram-stained smear of the uncentrifuged urine showed numerous rod-shaped, Gramnegative bacteria and polymorphonuclear neutrophils. Culture of the urine revealed more than 100,000

colonies of Escherichia coli per ml. The bacterium was resistant to amoxicillin, but sensitive to the other antibacterials useful for treating urinary infections. ■ polymorphonuclear neutrophils, p. 350

1. 2. 3. 4.

What is the diagnosis? What is the treatment? What is the prognosis? What future preventive measures might be undertaken?

Discussion 1. This woman’s symptoms and signs clearly lead to a diagnosis of bacterial cystitis, but there are a number of clues in the presentation of this case that point to a significant complication. First, most patients with uncomplicated bacterial cystitis are cured by 3 days of an antibacterial medication to which the causative bacterium is susceptible. Her symptoms recurred only 1 day after completing her medication. Second, her symptoms had been present for a full week before she sought medical evaluation. Third, she was pregnant. Fourth, she gave a past history of being hospitalized for pyelonephritis. These clues make it highly likely that she has a condition called subclinical pyelonephritis, in which her bladder infection has spread to her kidneys but has not yet produced the symptoms of pyelonephritis. As many as 30% of patients with cystitis have subclinical pyelonephritis, depending on risk factors such as the clues mentioned in this case. Although contraindicated in this patient because of her pregnancy, the kidney infection can be demonstrated with a

scintogram, an image of the kidneys produced following injection into the bloodstream of a tiny amount of radioactive material, which is removed from the blood by the kidneys and excreted. 2. The patient can be treated with trimethoprimsulfamethoxazole, the same medication that was given before. Because infection in the kidneys takes much longer to cure than bladder infections, however, the treatment must be continued for 2 weeks or longer. This medication diffuses well into vaginal secretions and can eliminate E. coli colonization of the vagina, which may be present. Although this drug is safe to use early in pregnancy, it cannot be used late in pregnancy because it can worsen jaundice in the newborn. A urine culture was done 1 week after completion of treatment to be sure that the infection was truly gone. ■ newborn jaundice, p. 419 3. The outlook is good for a full recovery without any permanent damage to the kidneys. The patient was advised, however, that repeated future infections of the kidneys could lead to kidney failure if not treated promptly. 4. For the future, this patient should employ all the usual methods for preventing urinary infections, including taking enough fluid to ensure voiding urine at least four or five times daily, avoiding delays in emptying the bladder, not using a diaphragm for contraception, urinating promptly after intercourse, and taking a preventive antimicrobial medication. No vaccine for this infection has been approved for use in the United States.

than 200 antigenic types have been given different species names in the past, probably all belong to this single species. Most strains can be cultivated using cell-free media. ■ spirochetes, p. 269

the serious effects of the illness, including kidney failure, the main cause of fatalities.

Pathogenesis

Leptospira interrogans infects numerous species of wild and domestic animals, usually causing little or no apparent illness, but ranging to highly fatal, epidemic disease. Characteristically, the organisms are excreted in the animal’s urine, which provides the principal mode of transmission to other hosts. Spots on the ground where urine has been deposited can remain a source of infection for as long as 2 weeks, while Leptospira in mud or water can survive for several weeks. Warm summer temperatures and neutral or slightly alkaline, moist conditions promote survival of the bacteria. Swimming and getting splashed with urine-contaminated water account for many cases. Infected humans usually excrete the organisms for up to a few weeks, but sometimes excretion can continue for many months. Rodents often excrete Leptospira for a lifetime.

The organisms enter the body through mucous membranes and breaks in the skin. No lesion develops at the site of entry, but the organisms multiply and spread throughout the body by way of the bloodstream, penetrating all tissues, including the eyes and the brain. Severe pain is characteristic of this first (septicemic) phase, and it may lead to unnecessary surgery for suspected appendicitis or gallbladder infection. A lack of inflammatory changes or tissue damage is a striking feature. Within a week, the immune response destroys the organisms present in most tissues, although they continue to multiply in the kidneys. The victim then characteristically enjoys 1 or more days of improvement before symptoms recur. The cause of the recurrent symptoms is presumed to be due to an immune response, and this second phase of the illness is often called the “immune phase.” This phase is characterized by injury to the cells that line the lumen of tiny blood vessels, causing clotting and impaired blood flow in tissues throughout the body. This accounts for most of

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Epidemiology

Prevention and Treatment Because of the ubiquity of the causative organism, there are few effective, preventive measures other than to avoid animal urine.

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Maintaining general sanitary conditions is helpful in the care of domestic animals raised for food. Multivalent vaccines—those that contain a number of different serotypes of L. interrogans— are available for preventing the disease in domestic animals, but they do not consistently prevent the carrier state. In an epidemic situation, small doses of a tetracycline antibiotic can prevent the disease in exposed individuals. A number of antibiotics are effective for treating the disease, but only if started during the first 4 days of the illness. As in a number of other microbial diseases, the onset of treatment is often followed in 4 to 6 hours by a transitory worsening of symptoms due to massive release of antigens from organisms lysed by the antimicrobial medication. The main features of leptospirosis are shown in table 26.2.

MICROCHECK 26.3 Situations that interfere with the normal flow of urine predispose to urinary system infections. Bladder infections are common, especially in women, caused by bowel bacteria ascending from the urethra. Pyelonephritis is a feared complication. In leptospirosis, a widespread zoonosis spread by urine, the kidneys are infected from the bloodstream. Usually mild, the disease can be a severe biphasic illness characterized by tissue invasion and pain in the first phase and tissue destruction in the second. ✓ What organism is the leading cause of bladder infections in otherwise healthy women? Where does this organism come from? ✓ How do people become infected with Leptospira interrogans? ✓ How might insertion of a catheter foster bladder infection?

TABLE 26.2 Leptospirosis ➀ Water or animal urine contaminated with Leptospira sp. splashes onto mucous membrane or abraded skin.

Symptoms

Many mild and asymptomatic cases. Others have a biphasic illness: spiking fever, headache, muscle pain, bloodshot eyes in the first (septicemic) phase, then 1 to 3 days of improvement; second (immune) phase has recurrence of severe symptoms with heart, brain, liver, and kidney damage

Incubation period

Usually about 10 days (range, 2 to 30 days)

Causative agent

Leptospira interrogans, a cultivable spirochete with many serotypes

Pathogenesis

The bacteria penetrate mucous membranes or breaks in the skin, multiply in the bloodstream, and are carried to all parts of the body. Severe pain with penetration of body tissues, but little or no tissue damage. Immune phase: damage to cells that line small blood vessels and clotting of blood. Causes severe damage to the liver, kidneys, heart, brain, and other organs.

Epidemiology

Worldwide distribution. Wide range of animal hosts chronically excrete the bacteria in their urine, causing contamination of natural waters and soils. Organisms remain infectious for long periods of time under warm, moist, neutral or alkaline conditions.

Prevention and treatment

Avoid contact with animal urine. Vaccines prevent disease in domestic animals, may not prevent urinary carriage. Tetracycline antibiotics preventive in epidemics. Various antibacterial medications useful in treatment of leptospirosis, but only if given early in the disease. Symptoms often worsen transiently with effective treatment due to the massive release of leptospiral antigens.

1

➁ The bacteria infect the bloodstream and are carried throughout all the body tissue causing fever, intense pain.

➂ Symptoms subside and bacteria

disappear from blood and tissues, except kidneys.

2

➃ Symptoms recur associated with

severe damage to liver and kidneys.

4

➄ Complete recovery occurs if kidney

3

failure can be effectively treated.

➅ Excretion of Leptospira continues in

4

urine.

5

6

1

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Genital System Diseases

625

26.4 Genital System Diseases Focus Points List the distinctive characteristics of three microbial genital system diseases. Outline prevention of staphylococcal toxic shock syndrome.

The genital tract is the portal of entry for numerous infectious diseases, both sexually and non-sexually transmitted. This section discusses some examples of genital system diseases that are not generally transmitted sexually. Puerperal (“childbed”) fever, which can still occur occasionally following childbirth, is an example of such a genital system infection. Other serious infections are associated with menstruation and spontaneous or induced abortions. Organisms from dirt and dust and from a woman’s own fecal bacteria can attack the traumatized uterus. A much-feared bacterium, Clostridium perfringens, can cause uterine gas gangrene and has been responsible for many fatalities following abortions induced under unclean conditions. Also, the normal vagina can be colonized by various pathogens, producing symptoms that range from annoying to life threatening. ■ puerperal fever, p. 450 ■ Clostridium perfringens, p. 569

Bacterial Vaginosis In the United States, bacterial vaginosis is the most common vaginal disease of women in their childbearing years. It is termed vaginosis rather than vaginitis because inflammatory changes are absent. Pregnant women with this condition have a sevenfold increase in the risk of having a premature baby or other complications. Nevertheless, the risk is small (less than 10%).

Symptoms Bacterial vaginosis is characterized by a thin, grayish-white, slightly bubbly vaginal discharge that has a characteristic pungent, “fishy” odor. For many, the odor is more distressing than the vaginal discharge, which is often slight; half of those with the disease are asymptomatic.

Causative Agent The cause or causes of bacterial vaginosis are unknown. A marked decrease in vaginal lactobacilli is a constant feature, suggesting that conditions supressing lactobacilli, or promoting other microbiota, play a causative role. Gardnerella vaginalis, a small, aerotolerant bacterium with a Gram-positive type of cell wall, is commonly present in large numbers, as are strictly anaerobic bacteria of the Mobiluncus and Prevotella genera, Mycoplasma sp., and anaerobic streptococci. Pure cultures of these species do not consistently produce bacterial vaginosis when healthy people are voluntarily inoculated, although the discharge from people with the condition can produce the disease. Each of these species of bacteria can occur in vaginal secretions of women without the disease, although in much smaller numbers.

Pathogenesis The key changes in this disease are a decrease in the normal acidity of the vagina, a marked derangement of the normal vaginal flora, and a substantial increase in the numbers of clue cells

nes95432_Ch26_618-646.indd 625

Figure 26.4 Clue Cell in an Individual with Bacterial Vaginosis The cells in the photograph are epithelial cells that have sloughed from the vaginal wall, one of which, the clue cell, is a dark color because it is completely covered with adherent anaerobes.

(figure 26.4). Clue cells are epithelial cells that have sloughed off the vaginal wall and are covered with masses of bacteria. The pH of the vaginal secretions is elevated above the normal of 4.5. No inflammation occurs unless there is another, concurrent vaginal infection. The strong, fishy odor is due to metabolic products of the anaerobes, including the amines putrescine and cadaverine.

Epidemiology The cause of bacterial vaginosis is not known, so its epidemiology is not well understood. The disease is most common among sexually active women and sometimes occurs in children who have been sexually abused. Sexual promiscuity, a new sex partner, douching, and using an intrauterine device (IUD) also increase risk of the disease. Virgins rarely get the disease. Proof is lacking, however, that bacterial vaginosis is a sexually transmitted infection.

Prevention and Treatment There are no proven measures to prevent bacterial vaginosis. Studies on the use of yogurt by mouth or vaginally to restore vaginal lactobacilli have given conflicting results. Treatment of the male sex partners of patients with recurrent disease does not prevent recurrences. Most cases respond promptly to treatment with metronidazole, a medication active against anaerobes. The main features of bacterial vaginosis are summarized in table 26.3.

Vulvovaginal Candidiasis Vulvovaginal candidiasis is the second most common cause of vaginal symptoms after bacterial vaginosis. As with bacterial vaginosis, vulvovaginal candidiasis appears to follow a disruption of normal microbiota. As the name indicates, the infection often involves not only the vagina, but the woman’s vulva, or external genitalia, as well.

Symptoms The most common symptoms of vulvovaginal candidiasis are itching and burning that can be intense and unremitting. Typically, the vaginal discharge is scanty and whitish, often occurring in curdlike clumps. The involved area is usually red and somewhat swollen.

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poses an increased risk of the disease, which increases with the duration of treatment.

TABLE 26.3 Bacterial Vaginosis Symptoms

Gray-white vaginal discharge and unpleasant fishy odor

Prevention and Treatment

Incubation period

Unknown

Causative agent

Unknown

Pathogenesis

Uncertain. Marked distortion of the normal microbiota. Increased sloughing of vaginal epithelium in the absence of inflammation. Odor due to metabolic products of anaerobic bacteria. Association with complications of pregnancy, including premature births.

Epidemiology

Associated with many sexual partners or a new partner, but can occur in the absence of sexual intercourse. Probably not a sexually transmitted disease.

Prevention and treatment

No proven preventive measures. Treatment with metronidazole is effective.

Prevention depends on minimizing the use and duration of antibacterial medications, and on effective treatment of underlying conditions such as diabetes. Intra-vaginal treatment of C. albicans infections with antifungal medicines such as nystatin or clotrimazole is usually effective. Fluconazole (Diflucan) given by mouth is generally safe and effective, although some recipients have annoying side effects such as headache and nausea, and it can interact with other medications or cause rare, serious reactions. Self diagnosis and treatment with over-the-counter medications is often in error and can contribute to development of treatment-resistant organisms. Simultaneous treatment of any male sex partners is rarely helpful, except when a Candida infection of the penis is present. The main features of vulvovaginal candidiasis are presented in table 26.4.

Staphylococcal Toxic Shock Syndrome Causative Agent Vulvovaginal candidiasis is caused by Candida albicans (figure 26.5), a yeast that is part of the normal microbiota of the vagina in about 35% of women. Because C. albicans is a fungus, it has a eukaryotic cell structure. ■ yeast, p. 289

Pathogenesis Normally, vaginal colonization by C. albicans causes no symptoms. The large numbers of the normal vaginal lactobacilli keep these fungi in check, probably because they compete for nutrients. When this balance is upset by intensive antibacterial treatment, C. albicans multiplies without restraint, causing an inflammatory response. The symptoms of vulvovaginitis occur within about 10 days. Other predisposing factors to Candida infection are late pregnancy, the use of oral contraceptives, and poorly controlled diabetes with glucose excretion in the urine. However, most patients with vulvovaginal candidiasis have no known predisposing factors.

Toxic shock syndrome was described in the late 1970s in several children with staphylococcal infections. In 1980, it became epidemic in young, healthy, menstruating women in association with use of a brand of high-absorbency tampon that has since been removed from the market (figure 26.6). The term toxic shock syndrome was used to represent the symptoms and signs of the illness. Now that we know its cause, it is appropriately called staphylococcal toxic shock syndrome. This was not a new disease, but one that emerged in a new form and became much more common as a result of changes in technology and human behavior.

Symptoms Staphylococcal toxic shock syndrome is characterized by sudden onset of high temperature, headache, muscle aches, bloodshot eyes, vomiting, diarrhea, a sunburn-like rash, and confusion. Without treatment, dropping blood pressure that can lead to kidney failure and death may result. Typically, the skin peels about a week after the onset.

Epidemiology The disease does not spread from person to person and is generally not transmitted sexually. Treatment with antibacterial medications

Figure 26.5 Candida albicans in the Vaginal Discharge of a Woman with Vulvovaginal Candidiasis

Yeast cell, budding

Pseudomycelium

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Cell nucleus Epithelial cell

20 mm

TABLE 26.4 Vulvovaginal Candidiasis Symptoms

Itching, burning, thick white vaginal discharge, redness and swelling

Incubation period

Usually unknown. Generally 3 to 10 days when associated with antibacterial medications

Causative agent

Candida albicans, a yeast

Pathogenesis

Inflammatory response to overgrowth of the yeast, which is often present among the normal microbiota. Associated with antibacterial therapy, use of oral contraceptives, pregnancy, and uncontrolled diabetes, but most cases have no identifiable predisposing factor.

Epidemiology

Not contagious. Usually not sexually transmitted.

Prevention and treatment

No proven preventive measures. Intravaginal antifungal medications such as clotrimazole usually effective.

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1,400

26.4

Intense publicity; suspect tampon taken off the market.

Total Menstrual Non-menstrual

1,200 Number of cases

Absorbency lowered 1,000 1982 – FDA* requires tampon labeling.

800 600 400

FDA standardizes absorbency labeling.

200 0 1980

1982

1984

1986 1988 Year

1990

1992

1994

1996

*FDA, Food and Drug Administration

Figure 26.6 Staphylococcal Toxic Shock Syndrome, United States A sharp drop in cases occurred when a brand of high-absorbency tampon was taken off the market. Since 1996, only six or fewer total cases have generally been reported per 100,000 population each year. Non-menstrual cases (men, women, and children) have sometimes exceeded the number of cases associated with menstruation (almost all of them tampon users).

Causative Agent Staphylococcal toxic shock syndrome is caused by strains of Staphylococcus aureus that produce one or more of a particular kind of exotoxin. The involved toxins are all superantigens. Toxic shock syndrome toxin-1 (TSST-1) accounts for about 75% of the cases; the remainder are due to other staphylococcal exotoxins. ■ Staphylococcus aureus, p. 535 ■ exotoxins, p. 403 ■ superantigens, p. 406 ■ staphylococcal enterotoxins, p. 763

Pathogenesis Tampon-associated toxic shock usually begins 2 to 3 days after the start of menstruation and use of vaginal tampons. Generally, it is not an infection because the causative staphylococci grow in the menstrual fluid-soaked tampon and rarely spread throughout the body. Staphylococcal toxic shock results from absorption into the bloodstream of one or more of the toxins from the site where the organisms are growing, a situation analogous to staphylococcal scalded skin syndrome. Tampons that abrade the vaginal wall probably promote toxin absorption. Toxic shock syndrome toxin-1 and the other responsible toxins, being superantigens, cause a massive release of cytokines, which in turn cause a drop in blood pressure and kidney failure—the most dangerous aspect of the illness. ■ staphylococcal scalded skin syndrome, p. 537

Epidemiology Staphylococcal toxic shock syndrome can occur after any infection with Staphylococcus aureus strains that produce one of the responsible toxins. It does not spread from person to person. The syndrome can occur after infection of surgical wounds, infections associated with childbirth, and other types of staphylococcal infections. Using tampons increases the risk of staphylococcal toxic shock, and the higher-absorbency tampons may pose a greater risk. Use of intravaginal contraceptive sponges also increases risk. Most of the menstruation-associated cases occur in women under age 30, probably because younger women are less likely to have protective antibody against the toxin. Recovery from the disease does not consistently give rise to immunity. In fact, about 30% of

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those who recover will suffer a recurrence of the disease, although it is usually milder than the original illness. Except for the tampons responsible for the 1980s epidemic, which were removed from the market, the type of absorbent fiber is probably not an important factor in the current incidence of the disease. Since 1990, there has been a slow, steady decline in the incidence of staphylococcal toxic shock syndrome, now estimated to be only one to two cases per 100,000 menstruating women per year. In recent years, the prevalence of non-menstrual toxic shock has been increasing and is generally more prevalent than menstruation-related cases. Close monitoring continues, however, because of the introduction of prolonged-use tampons and those of different fiber composition.

Prevention and Treatment More than 1,100 cases were reported 1980; only 100 to 200 cases have been reported each year since 1994. The improved figures result largely from women better understanding how to use vaginal tampons, and the fact that they no longer use certain highly absorbent types that promoted development of the disease. The incidence of toxic shock syndrome associated with the use of menstrual tampons can be minimized in these ways: Wash hands thoroughly before and after inserting a tampon. Use tampons with the lowest absorbency that is practical. Since 1990, the law requires that absorbency be stated on the package, ranging from less than 6 to 15 ml. Change tampons about every 6 hours and use a pad instead of a tampon while sleeping. Tampons for overnight use introduced in the last few years, however, appear so far to be safe. Avoid trauma to the vagina when inserting tampons. Know and understand the symptoms of staphylococcal toxic shock syndrome, and remove any tampon immediately if symptoms occur. Do not use tampons if you have had staphylococcal toxic shock syndrome previously. Staphylococcal toxic shock syndrome can be effectively treated with an antibacterial medication active against the infecting S. aureus strain, intravenous fluid, and other measures to prevent shock and kidney damage. Most people recover fully in 2 to 3 weeks. With treatment the mortality rate is less than 3%. Table 26.5 describes the main features of staphylococcal toxic shock syndrome.

MICROCHECK 26.4 A marked derangement of the normal vaginal flora characterizes bacterial vaginosis, the most prevalent vaginal disease of women in their childbearing years. Vulvovaginal candidiasis often occurs as a result of antibacterial therapy suppressing normal vaginal flora, but many other cases arise for unknown reasons. Staphylococcal toxic shock syndrome is caused by certain strains of Staphylococcus aureus whose exotoxins are absorbed into the bloodstream, causing the massive release of cytokines responsible for shock. ✓ Why was the incidence of staphylococcal toxic shock syndrome higher in menstruating women than in other people during the early 1980s? ✓ Why is puerperal fever not regarded as a sexually transmitted disease? What spreads the disease?

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TABLE 26.5 Staphylococcal Toxic Shock Syndrome Symptoms

Fever, vomiting, diarrhea, muscle aches, low blood pressure, and a rash that peels

Incubation period

3 to 7 days

Causative agent

Staphylococcus aureus, certain toxin-producing strains

Pathogenesis

Toxin (TSST-1 and others) produced by certain strains of S. aureus; toxins are superantigens, causing cytokine release and drop in blood pressure.

Epidemiology

Associated with certain high-absorbency tampons, leaving tampons in place for long periods of time, and abrasion of the vagina from tampon use. Also as a result of infection by certain toxin-producing S. aureus strains in other parts of the body.

Prevention and treatment

Awareness of symptoms. Prompt treatment of S. aureus infections; frequent change of tampons by menstruating women. Antimicrobial medication effective against the causative S. aureus strain; intravenous fluids.

26.5 Sexually Transmitted Diseases: Scope of the Problem Focus Points List three behaviors that increase the risk of acquiring a sexually transmitted disease.

Figure 26.7 The Possible Risk of Acquiring a Sexually Transmitted Disease in Two Individuals Contemplating Unprotected Sexual Intercourse Each partner had two previous sexual partners, and each of these partners had two previous partners, and so on. This risk of contracting an STD rises with the number of sexual partners. (HSV-2—herpes simplex virus, type 2; HIV—human immunodeficiency virus; HPV—human papillomavirus.)

List three measures that help prevent sexually transmitted diseases.

Despite the expenditure of approximately $8 billion each year for sexually transmitted disease (STD) control, 15 million Americans become infected annually, including 3 million teenagers. An individual who acquires an STD is apt to have acquired others without knowing it, and he or she needs to be tested for that possibility. The risk of acquiring an STD rises steeply with the number of partners with whom an individual has unprotected sexual intercourse, and with the numbers of sexual partners of those partners (figure 26.7). The use of alcohol and other drugs that release inhibitions adds to the risk. Table 26.6 lists some often-overlooked symptoms that can indicate the possibility of a person having a sexually transmitted disease. These warrant clinical evaluation even if they go away without treatment, especially if they appear within a few weeks of sexual intercourse with a new partner. A number of STDs can cause few or no symptoms and yet produce serious effects and be transmissible to other people. Simple measures, although generally not popular, are highly effective in preventing STDs. A small but increasing percentage of students are abstaining from sexual intercourse, or conducting a monogamous relationship with a non-infected person. For others, proper and consistent use of latex or polyurethane condoms, while not an absolute guarantee of protection, markedly reduces the risk of acquiring an STD. The list of diseases that can be transmitted sexually is very long. Shigellosis, giardiasis, scabies, viral hepatitis, and many others that have non-sexual modes of transmission cannot be overlooked. The epidemiology can be obscure, such as when a drug

Each of these agents can give asymptomatic infections: HSV-2 Neisseria gonorrhoeae HIV HPV Chlamydia trachomatis Treponema pallidum

? ? ?

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26.6

1. Abnormal discharge from the vagina or penis

3. Sore or blister, painful or not, on the genitals or nearby; swellings in the groin 4. Abnormal vaginal bleeding or unusually severe menstrual cramps

629

26.6 Bacterial STDs

TABLE 26.6 Symptoms that Suggest STD 2. Pain or burning sensation with urination

Bacterial STDs

Focus Points Compare and contrast gonorrhea and chlamydial genital system infections. Compare and contrast syphilis and chancroid.

5. Itching in the vaginal or rectal area 6. Pain in the lower abdomen in women; pain during sexual intercourse 7. Skin rash or mouth lesions

abuser contracts hepatitis B from sharing a contaminated needle. The disease can smolder unrecognized for years, and then is transmitted to another person by semen during sexual intercourse. ■ shigellosis, p. 598 ■ giardiasis, p. 609 ■ hepatitis, pp. 605–609

Table 26.7 lists some common sexually transmitted diseases discussed in subsequent sections of this chapter.

MICROCHECK 26.5 An individual who acquires an STD may well have acquired others without knowing it. The chance of a person acquiring an STD increases steeply with the number of his or her sexual partners, and with the number of sexual partners of those partners. Symptoms of an STD can sometimes easily be overlooked. Simple measures are highly effective for preventing STDs. ✓ Name two diseases that have both sexual and non-sexual modes of transmission. ✓ Why might an individual with an STD need to be checked for other STDs even though he or she has no symptoms of any others?

Most of the bacteria that cause sexually transmitted diseases survive poorly in the environment. Because of this, transmission from one person to another usually requires intimate physical contact but is highly unlikely to occur via a handshake or contact with a contaminated toilet seat.

Gonorrhea Gonorrhea is not a new problem; it was common among World War I recruits. More than 1 million cases per year were reported during the late 1970s, now down to an average around 342,250 per year. Today’s concerns are its continued prevalence and its slowly increasing resistance to antibacterial treatment.

Symptoms The incubation period of gonorrhea is generally only 2 to 5 days. Asymptomatic infections can occur in both sexes. In men, gonorrhea is characterized by urethritis, with pain during urination, and a thick, pus-containing discharge from the penis (figure 26.8). These symptoms are dramatic and unpleasant, and they usually inspire prompt treatment. In women, the usual symptoms of painful urination and vaginal discharge tend to be mild, and they may be overlooked. Therefore, women become unknowing carriers of gonorrhea.

TABLE 26.7 Common Sexually Transmitted Diseases Cause

Comment

Gonorrhea (“clap”)

Neisseria gonorrhoeae

Average reported cases per year—340,000. True incidence much higher.

Chlamydial infections

Chlamydia trachomatis

Average reported cases per year—800,000. True incidence much higher.

Syphilis

Treponema pallidum

Average reported cases (primary and secondary) per year—6,600.

Chancroid

Haemophilis ducreyi

Average reported cases per year—50. True incidence much higher.

Genital herpes simplex

Herpes simplex virus (HSV)

Not reportable. Estimated 45 million Americans infected; about 85% HSV, type 2.

Papillomavirus infections

Human papillomavirus (HPV)

Not reportable. Estimated 40 million Americans infected.

AIDS

Human immunodeficiency virus (HIV)

Average reported cases per year—40,000.

Trichomona vaginalis

Not reportable. Estimated 5 million Americans infected per year.

Disease Bacterial

Viral

Protozoal Trichomoniasis (“trich”)

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CHAPTER TWENTY SIX

Genitourinary Infections Figure 26.10 Electron Micrograph of a Single Coccus of Neisseria gonorrhoeae Notice the many long pili.

0.5 mm

Pathogenesis

Figure 26.8 Urethral Discharge in a Man with Gonorrhea Gonorrhea in men is usually, but not always, highly symptomatic.

Causative Agent Gonorrhea is caused by Neisseria gonorrhoeae, the gonococcus—a Gram-negative diplococcus that can be cultivated on chocolate agar medium. The organisms are typically found on and within the leukocytes in urethral pus (figure 26.9). Gonococci are parasites of humans only, preferring to live on the mucous membranes of their host. Most strains are susceptible to cold and drying and, hence, do not survive well outside the host. For this reason, gonorrhea is transmitted primarily by direct contact. Because the bacteria mainly live in the genital tract, this contact is almost always sexual. An increasing percentage of strains contain R plasmids that render them resistant to antibiotics such as penicillin and tetracycline. ■ chocolate agar, p. 96 ■ R plasmids, p. 205

Figure 26.9 Stained Smear of Pus from the Urethra Showing Neisseria gonorrhoeae The bacteria are the tiny, Gram-negative, bean-shaped diplococci next to the neutrophils.

White blood cell

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Neisseria gonorrhoeae

15 mm

Gonococci selectively attach to certain non-ciliated epithelial cells of the body, notably those of the urethra, uterine cervix, pharynx, and conjunctiva. Infection begins when pili (fimbriae) (figure 26.10) attach specifically to receptors on host cells. Pili and certain other surface proteins involved in attachment can either be expressed or not, an example of phase variation. Also, a single strain of gonococcus can express many different kinds of pili by antigenic variation, brought about by chromosomal rearrangements within the pili genes. This variation explains why cultures from different body sites in an infected individual and those from his or her sex partner may yield N. gonorrhoeae with different types of pili. The ability of gonococci to express different surface antigens allows it to attach to many different kinds of cell receptors. Also, phase and antigenic variation allow the organism to escape the effects of antibody formed against the bacterium. So far, the large variety of N. gonorrhoeae surface antigens has defeated efforts to develop a vaccine for prevention of gonorrhea. Also, virtually all pathogenic N. gonorrhoeae produce an enzyme that destroys IgA antibody found on mucosal surfaces. ■ phase and antigenic variation, p. 181

Outer membrane proteins called Opa represent another important pathogenicity-associated property of N. gonorrhoeae. Some Opa proteins attach specifically to receptors on CD4 T lymphocytes, thereby preventing activation and proliferation of the lymphocytes and impairing the immune response to the infection. Untreated disease in men can lead to complications. Inflammatory reaction to the infection can cause scar tissue formation that partially obstructs the urethra, predisposing the man to urinary tract infections. The infection may spread to the prostate gland and testes, producing hard-to-treat prostatic abscesses and orchitis (inflammation of the testicle). Sterility can result when scar tissue blocks the tubes that carry the sperm, or if testicular tissue is destroyed by the infection. Gonorrhea follows a different course in women. Besides infecting the urethra, gonococci thrive in the cervix and fallopian tubes, as well as in glands in the vaginal wall and other areas of the genital tract. Some 15% to 30% of untreated infections progress upward through the uterus into the fallopian tubes, causing pelvic inflammatory disease (PID). Occasionally the infection exits the fallopian tube and passes into the abdominal cavity, where it attacks the surface of the liver or other abdominal organ. It is not clear how N. gonorrhoeae (which is non-motile) can traverse the uterus to reach the fallopian tubes. One possibility is that the

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26.6

organisms hitch a ride on sperm, to which the bacteria are known to attach. Scar tissue formed as a result of the infection in the fallopian tubes can block normal passage of the ova through the tubes, causing sterility. Scarring of a fallopian tube can also lead to a dangerous complication—ectopic pregnancy—in which the embryo develops in the fallopian tube or even in the abdominal cavity outside the uterus. Ectopic pregnancy can lead to lifethreatening internal hemorrhaging. Infrequently, Neisseria gonorrhoeae can also cause disseminated gonococcal infection (DGI). Curiously, this complication is not usually preceded by urogenital symptoms. Disseminated gonococcal infections are characterized by one or more of the following: arthritis caused by growth of gonococci within the joint spaces, fever, and rash. Any joint may be affected, especially the larger ones. The heart valves can also be infected and destroyed in DGI. Ophthalmia neonatorum is a destructive N. gonorrhoeae infection of the eyes of newborn babies whose mothers have symptomatic or asymptomatic gonorrhea. The bacteria are transmitted during the infant’s passage through the infected birth canal. This form of gonococcal infection is now unusual in the United States because laws require that an antibiotic ointment such as 0.5% erythromycin be placed directly into the eyes of all newborn infants. This treatment must be given within 1 hour of birth. Some mothers who feel certain that they do not have gonorrhea have challenged these laws, but the long-lasting and asymptomatic nature of gonorrhea in many women makes it risky to omit prophylactic treatment of a baby’s eyes.

Epidemiology Gonorrhea is among the most prevalent of the sexually transmitted diseases. In the United States, its incidence is the highest of any reportable bacterial disease other than Chlamydia infection. A steady rise in reported cases of gonorrhea from about 350,000 in 1966 to more than 1 million cases in 1976 occurred despite the availability of effective treatment. From 1976 through 1980, more than 1 million cases were reported each year, but since then the incidence has progressively declined, probably due largely to increased condom use from fear of AIDS. Factors that influence the incidence of gonorrhea include: Birth control pills. About 35% of sexually active American college and university students say that they or their partner employs a contraceptive pill. Oral contraceptives without use of a condom offer no protection against sexually transmitted diseases and may increase susceptibility to them. Use of oral contraceptives leads to migration of gonorrhea-susceptible epithelial cells from the cervical lumen onto more exposed areas of the outer cervix. Oral contraceptives also tend to increase both the pH and the moisture content of the vagina, favoring infection with gonococci and other agents of sexually transmitted diseases. Besides being more vulnerable to gonorrhea, women taking oral contraceptives are also more likely to develop serious complications from the disease. Carriers. Carriers of gonococci, both male and female, can unknowingly transmit these bacteria over months or even years.

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Lack of immunity. There is little or no immunity following recovery from the disease. Individuals can contract gonorrhea repeatedly.

Prevention and Treatment Prevention depends on abstinence, monogamous relationships, consistent use of condoms, and prompt identification and treatment of sexual contacts. No vaccine is available. Resistance of N. gonorrhoeae to penicillins, tetracyclines, and sulfonamides is now widespread. Fluoroquinolones were formerly recommended but resistance has risen progressively over the past decade reaching 30% or higher in some groups of men who have sex with men. Only a single class of antibiotics, the cephalosporins, is currently recommended for the initial treatment of gonorrhea. ■ fluoroquinolones, p. 478 ■ cephalosporins, p. 475

Table 26.8 describes the main features of the disease.

Chlamydial Genital System Infections Most college men with symptoms suggesting gonorrhea actually have other infections. From 25% to 40% of these students are infected with Chlamydia trachomatis, a common cause of sexually transmitted disease of men and women. Chlamydial infections mimic gonorrhea in several ways, including production of urethritis, and testicle and fallopian tube damage. Like N. gonorrhoeae, C. trachomatis attaches to sperm, and some have speculated that its rapid ascent to the fallopian tubes occurs by hitching a ride on sperm. The main importance of the infection is that it can produce pelvic inflammatory disease (PID) in women, damaging the fallopian tubes and promoting sterility or ectopic pregnancy. Most alarming, tubal damage can occur without symptoms. The infection in men can produce sterility by infecting the epididymis. Chlamydial genital infections have only been reportable nationally since 1995, and they substantially exceed the numbers of reported cases of gonorrhea. ■ Chlamydia, p. 274

Symptoms The symptoms of C. trachomatis infection generally appear 7 to 14 days after exposure. In men, the main symptom is a thin, graywhite discharge from the penis, sometimes with painful testes. Women most commonly develop an increased vaginal discharge, sometimes accompanied by painful urination, abnormal vaginal bleeding, and upper or lower abdominal pain. Many infections of men and women are asymptomatic.

Causative Agent Chlamydia trachomatis is a spherical, obligate intracellular bacterium. Inclusion bodies containing a glycogen-like material form at the site of bacterial replication in the cytoplasm of host cells. These inclusions stain deeply with iodine and can provide a rapid way of identifying C. trachomatis infections. There are a number of different antigenic types of C. trachomatis, and different types may cause different diseases. Approximately eight types are responsible for most C. trachomatis sexually transmitted disease. Three other types cause lymphogranuloma venereum, a rare STD in the United States, in which lymph nodes in the groin swell up and drain pus; after years, gross swelling of

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TABLE 26.8 Gonorrhea ➀ Eyes of adults and children are

susceptible to the gonococcus; serious infections leading to loss of vision are likely in newborns.

Symptoms

Men: no symptoms, pain on urination, discharge; with complication impaired urinary flow, sterility, or arthritis. Women: no symptoms or pain on urination, discharge, fever, pelvic pain, sterility, ectopic pregnancy, arthritis can occur

Incubation period

2 to 5 days

Causative agent

Neisseria gonorrhoeae, a Gramnegative diplococcus

Pathogenesis

Organisms attach to certain nonciliated epithelial cells by pili; phase and antigenic variation in surface proteins allows attachment to different host cells and escape from immune mechanisms. Inflammation, scarring; can spread by bloodstream.

Epidemiology

Transmitted by sexual contact. Asymptomatic carriers. No immunity.

Prevention and treatment

Abstinence, monogamous relationships, condoms, early treatment of sexual contacts. Treatment: intramuscular ceftriaxone.

1

➁ Organisms carried by the

bloodstream infect the heart valves and joints.

➂ The outer covering of the liver is

infected when gonococci enter the abdominal cavity from infected fallopian tubes.

2

➃ Prostatic gonococcal abscesses may be difficult to eliminate.

3

➄ Infection of the fallopian tubes results in scarring, which can lead to sterility or ectopic pregnancy.

5

➅ The cervix is the usual site of primary infection in women.

➆ Urethral scarring from gonococcal

infection can predispose to urinary infections by other organisms.

7

6

➇ Scarring of testicular tubules can cause sterility.

2

7 4 8

male

the genitalia can occur. Four other types cause the chronic eye disease trachoma, an important preventable cause of blindness worldwide. ■ glycogen, p. 32

Pathogenesis The infectious form of C. trachomatis, called an elementary body, attaches specifically to receptors on the surface of the host epithelial cell, thereby inducing the cell to take in the bacterium by endocytosis. In the endocytic vacuole, the bacterium enlarges and becomes a non-infectious form called a reticulate body. The reticulate body divides repeatedly by binary fission, resulting in numerous elementary bodies. These are released from the host cell and infect nearby cells. The infected cells release cytokines that provoke an intense inflammatory reaction. Much of the tissue damage results from the cell-mediated immune response. The infection usually involves the urethra in both men and women. In men, it spreads to the tubules that collect sperm from the testicles, causing acute pain and swelling. In women, the infection

nes95432_Ch26_618-646.indd 632

commonly involves the cervix, making it bleed easily, often with sexual intercourse. The uterus is commonly involved, causing pain and bleeding. From the uterus, the infection spreads to the fallopian tubes (figure 26.11), causing PID, and like gonorrhea, it can exit the fallopian tubes and infect the surface of the liver. Subsequent scar tissue formation is responsible for many of the serious consequences of the disease such as sterility and ectopic pregnancy. ■ endocytosis, p. 73

Epidemiology Chlamydial genital infections lead all reportable bacterial infectious diseases. In contrast to gonorrhea, the number of reported chlamydial infections has tended to rise each year, probably a reflection of increased awareness of the disease and better diagnostic tests. Only a fraction of the total cases, estimated at 4 million per year in the United States, is reported by physicians to public health departments. More than 14% of sexually active high school and college women were asymptomatic carriers of

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TABLE 26.9 Chlamydial Genital System Infections Microvilli

Symptoms

Men: thin, gray-white penile discharge, painful testes. Women: vaginal discharge, vaginal bleeding, lower or upper abdominal pain

Chlamydias

Incubation period

Usually 7 to 14 days

Causative agent

Chlamydia trachomatis, an obligate intracellular bacterium, certain serotypes

Pathogenesis

Elementary body attaches to specific receptors on the epithelial cell, causing endocytosis; transforms to reticulate body in the endocytic vacuole; repeated replication by binary fission and differentiation into elementary bodies; rupture of the vacuole and release of elementary bodies to infect adjacent cells; release of cytokines results in inflammatory response; cellular immune response against infection causes extensive damage; scar tissue formation responsible for ectopic pregnancy and sterility.

Epidemiology

The leading reportable bacterial infection in the United States. Large numbers of asymptomatic men and women carriers. Non-sexual transmission can occur in non-chlorinated swimming pools.

Prevention and treatment

Abstinence, monogamous relationship, condom use. Test sexually active men and women at least once yearly to rule out asymptomatic infection. Treatment: azithromycin, single dose; other antibacterial medications.

Figure 26.11 Scanning Electron Micrograph of Chlamydia trachomatis The bacteria are attached to fallopian tube mucosa.

C. trachomatis in one study. Non-sexual transmission of this agent also occurs, for example, in non-chlorinated swimming pools. Newborn babies of infected mothers often develop chlamydial ophthalmia neonatorum, also called inclusion conjunctivitis, and pneumonia from C. trachomatis infection contracted during passage through the birth canal.

Prevention and Treatment Abstinence, monogamous relationships, and condoms properly used can prevent transmission of the disease. All sexually active women are advised to get tested for Chlamydia each year, or twice yearly if they have multiple partners or if their partner has multiple partners. Several antibiotics offer effective treatment and prevent serious complications if the disease is diagnosed and treated promptly. Azithromycin can be given as a single dose, whereas tetracyclines and erythromycin are less expensive alternatives. The sexual partner is treated at the same time. Chlamydial ophthalmia neonatorum is treated with oral erythromycin. The main features of chlamydial genital infections are summarized in table 26.9.

Syphilis During the first half of the twentieth century, syphilis was a major cause of mental illness and blindness, and a significant contributor to the incidence of heart disease and stroke. Syphilis was common in the United States during World War II, present in about 5% of military recruits, but by the mid-1950s, it was almost eradicated. This was accomplished by aggressively locating syphilis cases and their sexual contacts and treating them with penicillin, which became generally available after the war. A number of factors, however, conspired to cause a resurgence of the disease. Inner-city poverty, prostitution, and drug use were linked to a high incidence of syphilis, which exceeded 100 new cases per 100,000 population in at least seven cities in 1990. Since then, renewed efforts in education, case finding, and treatment have caused a dramatic drop in new cases. The presence of the AIDS epidemic added urgency to syphilis con-

nes95432_Ch26_618-646.indd 633

trol efforts, because syphilis, like other STDs that cause genital sores, promotes the spread of AIDS by increasing the risk of HIV infection. By the end of 1998, the syphilis rate was down to 2.6 per 100,000, the lowest level since reporting began in 1941, surpassing the national health objective for the year 2000 of four or fewer cases per 100,000 population. Unfortunately rates have tended to rise since then and there has been a worrisome increase in the disease among women.

Symptoms Syphilis occurs in so many forms that it is easily confused with other diseases and is often called “the great imitator.” Generally, its manifestations occur in three clinical stages. The characteristic feature of primary syphilis occurs about 3 weeks after infection and consists of a painless, red ulcer with a hard rim called a hard chancre (pronounced “shanker”) that appears at the site of infection (figure 26.12). The local lymph nodes enlarge. Primary syphilis often goes unnoticed in women and homosexual men because the painless chancre is hidden from view in the anus or vagina. After 2 to 10 weeks or longer, the manifestations of secondary syphilis usually appear, including runny nose and watery eyes, aches and pains, sore throat, a rash that includes the palms and soles, and whitish patches on the mucous membranes. After a latent period that can last for many years, manifestations of tertiary syphilis occur and typically include mental illness, blindness, stroke, and other nervous system disorders.

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PERSPECTIVE 26.1 The Demise of Syphilis? For 40 years, 1932 to 1972, the U.S. Public Health Service conducted a study, now known as the Tuskegee Syphilis Experiment, of 399 poor Alabama black men with advanced syphilis. For roughly the first half of the study there was no effective therapy for syphilis, and the study was meant to assess the natural progression of the disease in black men. The men were not told their diagnosis nor educated about the nature of their condition and its transmission. In a blatant union of bad science and raw racism, the study was allowed to continue without giving treatment, even after effective therapy became available. Twenty-eight of the subjects died of the disease, and another hundred died from its complications. Forty wives became infected, and there were 19 children born with congenital syphilis. Nothing of scientific value was learned, and many people to this day remain bitter and distrustful of the U.S. Public Health Service. In 1997, President Clinton, speaking for the government, formally apologized to the surviving eight subjects.

Fortunately, in more recent years, major governmental efforts to conquer the disease have met with some success. In the year 2006, only 9,756 cases of primary and secondary syphilis were reported, down from 50,223 in 1990. The Centers for Disease Control and Prevention (CDC) has even considered the possibility that transmission of the disease could be eliminated in the United States. Syphilis is a tempting target for eradication because it has no animal reservoir, infectious cases can generally be treated with a single injection of penicillin, and the incubation period is long enough so that sexual contacts of an infected person can be found and treated before they spread the disease any further. Moreover, instead of being widely endemic, most syphilis cases are now concentrated in a relatively few areas and certain populations. Also, new techniques are now available for rapid diagnosis, treatment, and epidemiological tracing of the disease. Finally, control of syphilis is closely linked to AIDS control efforts be-

Causative Agent Syphilis is caused by Treponema pallidum, an extremely slender, motile spirochete with tightly wound coils. It ranges in length up to 20 μm. Dark-field microscopy is used to observe T. pallidum (figure 26.13) and its characteristic slow rotational and flexing motions. The organism is difficult to study because it cannot be cultivated in vitro and must be grown in the testicles of laboratory rabbits. Although the organism can be maintained in vitro and its metabolism studied, it undergoes little or no multiplication.

cause the risk of HIV transmission is six times as great if either sex partner has syphilis. One population targeted for treatment is persons detained in county and city jails—representing more than 500,000 individuals at any one time—with a known high incidence of STDs including syphilis. Screening these people for syphilis and getting them treated has proved frustrating because almost half of them are discharged within 48 hours—too soon to get the results of blood tests and arrange for medical evaluation and treatment. After release from jail, these individuals are notoriously hard to find and are often unwilling or unable to reveal the names and locations of their sexual contacts. Studies carried out in Illinois during 1996 showed that by using a screening blood test for syphilis that gave results in 15 minutes, and having a physician’s assistant available for examination and treatment, almost 80% of jail inmates found to have syphilis got treatment the same day. Unfortunately, in the past, few jailers have had the interest or resources to focus on STD control to this extent.

Like most strains of gonococci, T. pallidum is killed by drying and chilling and is therefore transmitted almost exclusively by sexual or oral contact. Normally, T. pallidum is only a parasite of humans. We now know the sequence of nucleotides in its genome, which should give better understanding of its virulence, why it cannot be cultivated in vitro, its evolution, and how to make an effective vaccine. ■ dark-field microscopy, p. 43

5 mm

Figure 26.12 Syphilitic Chancre on the Foreskin of an Uncircumcised Man This is the site where Treponema pallidum entered the man’s

Figure 26.13 Appearance of Treponema pallidum with Dark-Field Illumination This technique readily detects the organism in skin and mu-

body.

cous membrane lesions of syphilis.

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Pathogenesis Like the spirochetes that cause leptospirosis, T. pallidum readily penetrates mucous membranes and abraded skin. The infectious dose is very low—less than 100 organisms. In primary syphilis, T. pallidum grows and multiplies in a localized area of the genitalia, spreading from there to the lymph nodes and bloodstream. The hard chancre represents an intense inflammatory response to the bacterial invasion. Sometimes no chancre develops, only a pimple small enough to go unnoticed. Examination of a drop of fluid squeezed from the chancre reveals that it is teeming with infectious T. pallidum. Whether or not treatment is given, the chancre disappears within 2 to 6 weeks, and the victim may mistakenly believe that recovery from the disease has occurred. The organisms resist destruction by the body’s defenses via an unknown mechanism, however, and progression of the disease can continue for years. Many of the manifestations of secondary syphilis are due to immune complexes that form as specific antibodies bind to circulating T. pallidum. By this time, the spirochetes have spread throughout the body, and infectious lesions occur on the skin and mucous membranes in various locations, especially in the mouth (figure 26.14). Syphilis can be transmitted by kissing during this stage. The secondary stage lasts for weeks to months, sometimes as long as 1 year, and then gradually subsides. About 50% of untreated cases never progress past the secondary stage. After a latent period of from 5 to 20 years or even longer, however, some people with the disease develop tertiary syphilis. ■ immune complexes, p. 420 Tertiary syphilis (the third stage of syphilis) represents a hypersensitivity reaction to small numbers of T. pallidum that grow and persist in the tissues. In this stage, the patient is no longer infectious. The remaining organisms may be present in almost any part of the body, and the symptoms of tertiary syphilis depend on where the hypersensitivity reactions occur. If they occur in the skin, bones, or other areas not vital to existence, the disease is not life threatening. If, however, they occur within the walls of a major blood vessel such as the aorta, the vessel may become

Figure 26.15 A Gumma of Tertiary Syphilis Gummas consist of an inflammatory mass which can perforate, as in this example in the roof of the mouth. Gummas can occur anywhere in the body.

weakened and even rupture, resulting in death. Hypersensitivity reactions to T. pallidum in the eyes cause blindness; central nervous system involvement most commonly manifests itself as a stroke. A granulomatous necrotizing mass called a gumma (figure 26.15), analogous to the tubercle of tuberculosis, can involve any part of the body. A characteristic pattern of symptoms and signs called general paresis develops an average of 20 years after infection. Typical findings include personality change, emotional instability, delusions, hallucinations, memory loss, impaired judgment, abnormalities of the pupils of the eye, and speech defects. ■ tubercle, p. 515

The main characteristics of the three stages of syphilis are summarized in table 26.10. Congenital Syphilis During pregnancy, T. pallidum readily crosses the placenta and infects the fetus. This can occur at any stage of pregnancy, but damage to the fetus does not generally occur until the fourth month. Therefore, if the mother’s syphilis is diagnosed and treated before the fourth month of pregnancy, the fetus will also be treated and will not develop the disease. Without treatment, the risk to the fetus depends partly on the stage of the mother’s infection. Three-fourths or more of the fetuses become infected if the mother has primary or early secondary syphilis; risk decreases with the duration of the mother’s infection but is still significant into the latent period. Fetal infections can occur in the absence of any symptoms of syphilis in the mother. About two out

TABLE 26.10 Stages of Syphilis

Figure 26.14 Appearance of Mucous Patches in the Mouth of an Individual with Secondary Syphilis These lesions are swarming with

Stage of Disease

Main Characteristics

Infectious?

Primary

Firm, painless ulcer (hard chancre) at site of infection; lymph node enlargement

Yes

Secondary

Rash, aches, and pains; mucous membrane lesions

Yes

Tertiary

Gummas; damage to large blood vessels, eyes, nervous system; insanity

No

Treponema pallidum and are highly infectious.

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such as prostitutes, promiscuous homosexual men, and jail inmates, and guarding against reintroduction of the disease from countries where it is still rampant. Effective screening to detect infected individuals can easily be accomplished using a blood test.

Prevention and Treatment No vaccine against syphilis is currently available. Abstinance, monogamous relationships, condoms, and other safer sex practices decrease the risk of contracting the disease. Prompt identification and treatment of sexual contacts are important in limiting spread of the disease. Primary and secondary syphilis are effectively treated with an antibiotic such as penicillin. Treatment must be continued for a longer period for tertiary syphilis, however, probably because most of the organisms are not actively multiplying. Table 26.11 summarizes the main features of syphilis. Figure 26.16 Hutchinson Teeth Notice the notched, deformed incisors, a late manifestation of congenital syphilis.

Chancroid

of every five infected fetuses are lost through miscarriage or stillbirth. The remainder are born with congenital syphilis. Although these infants frequently appear normal at the time of birth, some develop secondary syphilis, which is often fatal, within a few weeks. Others develop characteristic deformities of their face, teeth (figure 26.16), and other body parts later in childhood.

Chancroid is another bacterial sexually transmitted disease that showed a marked increase in frequency, reaching 5,000 reported cases in 1988, followed by a progressive decline to the lowest frequency in decades. Although widespread in the United States, it is not commonly reported. It is another STD with genital sores that promote the spread of HIV, the cause of AIDS.

Epidemiology

Symptoms

There is no animal reservoir. Syphilis is usually transmitted by sexual intercourse, but infection can be contracted from kissing. Elimination of transmission in the United States is within reach, but depends on identifying and treating cases within high-risk groups

Chancroid is characterized by a single or multiple genital sores called soft chancres (figure 26.17a), which are painful, unlike the hard chancre of syphilis. The lymph nodes in the groin enlarge (figure 26.17b); they become tender, and sometimes pus-filled.

TABLE 26.11 Syphilis ➀ Treponema pallidum enters the

6

body through a microscopic abrasion or mucous membrane, usually genitalia, mouth, or rectum.

1 2

➁ A chancre develops at site of entry. ➂ Organisms multiply locally and

4

spread throughout the body by the bloodstream.

➃ Infectious mucous patches and skin

Incubation period

10 to 90 days

Causative agent

Treponema pallidum, a nonculturable spirochete

Pathogenesis

Primary lesion, or chancre, appears at site of inoculation, heals after 2 to 6 weeks; T. pallidum invades the blood vessel system and is carried throughout the body, causing fever, rash, mucous membrane lesions; damage to brain, arteries, and peripheral nerves appears years later.

Epidemiology

Sexual contact with infected partner; kissing; transplacental passage.

Prevention and treatment

Monogamous relationships, use of condoms, treatment of sexual contacts, reporting cases. Treatment: penicillin.

3

4

➄ An asymptomatic latent period

occurs. T. pallidum disappears from blood, skin, and mucous membranes.

2

➅ After months or years, symptoms of

nes95432_Ch26_618-646.indd 636

Chancre, fever, rash, stroke, nervous system deterioration; can imitate many other diseases

6

rashes of secondary syphilis appear. A fetus will become infected, resulting in miscarriage or a live-born infant with congenital syphilis.

tertiary syphilis appear: heart and great vessel defects gummas strokes eye abnormalities general paresis insanity.

Symptoms

1

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(a)

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637

(b)

Figure 26.17 Chancroid (a) Lesions of the penis (“soft chancres”). These ulcerations are soft and painful, in contrast to the chancres of syphilis. (b) Swollen groin lymph nodes. The nodes are tender, often pus-filled, and may break open and drain.

MICROCHECK 26.6

Causative Agent The causative organism of chancroid is Haemophilus ducreyi, a small, pleomorphic, Gram-negative rod that requires X-factor, a blood component called hematin, for growth. ■ Haemophilus, p. 273

Pathogenesis Knowledge of the pathogenesis of chancroid is incomplete. Typically, a small pimple appears, presumably at the site of entry of the organisms. After a few days, this ulcerates and gradually enlarges, reaching an inch or more in diameter, often joining other lesions. Organisms that reach the lymph nodes incite an intense inflammatory response, with congregation of neutrophils, release of proteolytic enzymes, and liquefaction of the lymphoid tissue. The pus-filled nodes enlarge, stretch the skin, and rupture through to the surface, discharging their contents. ■ neutrophils, p. 350

Transmission of bacterial STDs usually requires direct human-tohuman contact. Unsuspected sexually transmitted infections of pregnant women pose a serious threat to fetuses and newborn babies. Even asymptomatic infections can cause genital tract damage and be transmissible to other people. ✓ Can a baby have congenital syphilis without its mother ever having had symptoms of syphilis? Explain. ✓ What, if any, is the relationship between chancroid and development of AIDS? ✓ Why should scarring of a fallopian tube raise the risks of an ectopic pregnancy?

Epidemiology

TABLE 26.12 Chancroid

Epidemics in American cities are associated with prostitution; in some tropical countries, chancroid is second only to gonorrhea in prevalence of the sexually transmitted diseases.

Symptoms

One or more painful, gradually enlarging, soft chancres on or near the genitalia; large, tender regional lymph nodes

Incubation period

3 to 10 days

Causative agent

Haemophilus ducreyi, a small, pleomorphic, Gram-negative rod requiring X-factor for growth

Pathogenesis

A small pimple appears first, which ulcerates and gradually enlarges; multiple lesions may coalesce; lymph nodes enlarge, liquefy, and may discharge to the skin surface.

Epidemiology

Sexual transmission. Common in prostitutes; fosters the spread of AIDS.

Prevention and treatment

Abstinence from sex, monogamous relationships; avoidance of sexually promiscuous partners; proper use of condoms. Treatment: several antibacterial medications effective. Resistance can be a problem.

Prevention and Treatment Abstinence from sexual intercourse, monogamous relationships, and use of condoms help prevent chancroid. The disease usually responds well to treatment with the antibiotics erythromycin, azithromycin, or ceftriaxone. Some strains, however, possess R plasmids that code for resistance to multiple antibacterial medications. Effectiveness of therapy is also sharply reduced if the patient has AIDS. As in a number of bacterial infections, body defenses and antibacterial medications work together to defeat the disease. Table 26.12 gives the main features of chancroid.

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26.7 Viral STDs Focus Points Discuss the distinctive characteristics of genital herpes simplex and human papilloma virus infection. Outline the relationship between HIV infection and AIDS.

Viral sexually transmitted diseases are probably as common or more common than the bacterial diseases, but they are incurable. Their effects can be severe and long-lasting. Genital herpes simplex can cause recurrent symptoms for years, papillomavirus infections can lead to cancer, and untreated HIV infections usually result in AIDS.

Genital Herpes Simplex Genital herpes simplex is among the top three or four most common sexually transmitted diseases. An estimated 45 million Americans are infected with the causative virus and about 500,000 new cases occur each year.

Symptoms Symptoms of genital herpes simplex begin 2 to 20 days (usually about a week) after exposure, with genital itching, burning, and in women, often severe pain. Infection of the urethra may imitate the symptoms of a bladder infection. Clusters of small, red bumps appear on the genitalia, which then become blisters surrounded by redness (figure 26.18). The blisters break in 3 to 5 days, leaving an ulcerated area. The ulcers slowly dry and become crusted and then heal without a scar. Symptoms are the worst in the first 1 to 2 weeks and disappear within 3 weeks. They recur in an irregular pattern; about 75% of patients will have at least one recurrence within a year, and the average is about four. The recurrent symptoms are usually not quite as severe as those of the first episode, and recurrences generally decrease in frequency with time. Some individuals may have recurrences for life.

Causative Agents The causative agent of genital herpes is usually herpes simplex virus type 2 (HSV-2), a medium-sized, enveloped, double-stranded DNA virus. On electron micrographs it looks like herpes simplex virus type 1 (HSV-1), the cause of “cold sores” (“fever blisters,” herpes simplex labialis), and the genomes of the two viruses are about 50% homologous. This disease, like cold sores, often recurs because the virus becomes latent. Either virus can infect the mouth and the genitalia, but the type 2 virus causes more severe genital lesions whose frequency of recurrence is greater than that of the type 1 virus. During initial infection and for as long as 1 month after, the virus is found in genital secretions. During recurrence, the virus is usually present in large numbers for less than a week. ■ HSV-1, p. 592

Pathogenesis Lesions begin with infection of a group of epithelial cells that lyse following viral replication, creating small, fluid-filled blisters (vesicles) containing large numbers of infectious virions. Rupture of the vesicles produces painful ulcerations. Latency of the disease is incompletely understood. The viral DNA exists within nerve cells in a circular, non-infectious form during times when there are no symptoms. In this state, only a single gene is expressed and it encodes for a small segment of RNA called a microRNA (miRNA). HSV miRNA is probably responsible for latency of the virus. At times, however, the entire viral chromosome can be transcribed and complete infectious virions replicated. These reinfect the area supplied by the nerve and cause a recurrence. The mechanisms by which the latent infection is maintained or reactivated are not known in detail, but they probably depend on cellular immunity. ■ latent infections, p. 330 ■ miRNA, p. 180 Genital herpes can pose a serious risk to newborn babies. If the mother has a primary infection near the time of delivery, the baby has about a one in three risk of acquiring the infection. The baby often dies from overwhelming infection or is permanently disabled by it. To prevent contact with the infected birth canal, these babies must be delivered by cesarian section. If the mother has recurrent disease, the risk to the baby is very low, presumably because transplacental anti-HSV antibody from the mother protects the baby, but physicians will often do a cesarian section to minimize the risk.

Epidemiology There are no animal reservoirs. The virus can survive for short periods on fomites or in bathwater, but non-sexual transmission is rare. Sexual transmission of HSV is most likely to occur during the first few days of symptomatic disease, but it can happen in the absence of symptoms or signs of the disease. Once infected, an individual poses a life-long risk of transmitting the virus to another person. Herpes simplex, like other ulcerating genital diseases, promotes the spread of AIDS by increasing the risk of HIV infection.

Prevention and Treatment Figure 26.18 Genital Herpes Simplex on the Shaft of the Penis The lesions typically begin as a group of small vesicles surrounded by redness. Within 3 to 5 days, they break, leaving the small superficial ulcers as shown. The lesions can be very painful, especially in women.

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Avoidance of sexual intercourse during active symptoms and the use of condoms with a spermicide reduce, but do not eliminate, the chance of transmission. Spermicidal jellies and creams can

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26.7

inactivate herpes simplex viruses. There is no cure for genital herpes, although medications such as acyclovir and famciclovir can decrease the severity of the first attack and the incidence of recurrences. The main features of genital herpes simplex are presented in table 26.13.

Papillomavirus STDs: Genital Warts and Cervical Cancer Sexually transmitted human papillomaviruses (HPVs) are among the most common of the sexually transmitted disease agents, infecting an estimated 40 million Americans. Although they cannot be cultivated in the laboratory, their presence in human tissues can be studied by using nucleic acid probes. Some HPVs are responsible for papillomas—warty growths of the external and internal genitalia; others cause non-warty lesions of mucosal surfaces such as the uterine cervix and are a major factor in the development of cervical cancer. Invasive cervical cancer strikes about 12,500 Americans each year and kills more than 4,500 of them. ■ nucleic acid probes, p. 227

Viral STDs

639

Symptoms Warts are the most easily recognized manifestation of infection, with about 750,000 new cases in the United States each year. They often appear on the head or shaft of the penis (figure 26.19), at the vaginal opening, or around the anus. Occasionally, the warts become inflamed or bleed. These warts rarely, if ever, become cancerous but they can have a large emotional impact because of the embarrassment of having such an obvious STD. Important precancerous lesions of the cervix are generally asymptomatic and can only be detected by vaginal examination.

Causative Agents Human papillomaviruses are small, non-enveloped, doublestranded DNA viruses of the papovavirus family. There are more than 100 types of HPV based on DNA homology, and at least 30 of them are transmitted by sexual contact. Approximately 15 types are strongly associated with cancer of the cervix and other cancers. The different papillomavirus types infect different kinds of epithelium. For example, HPVs that cause the common warts of the hands and plantar warts of the feet generally do not infect the genitalia. The HPVs that cause genital warts may infect the cervix, but they do not generally predispose to cancer.

Pathogenesis TABLE 26.13 Genital Herpes Simplex Symptoms

Itching, burning pain at the site of infection, painful urination, tiny blisters with underlying redness. The blisters break, leaving a painful superficial ulcer, which heals without scarring. Recurrences are common.

Incubation period

Usually 1 week (range, 2 to 20 days)

Causative agent

Usually herpes simplex virus, type 2. The cold sore virus, herpes simplex type 1, can also be responsible. Herpesviruses are enveloped and contain double-stranded DNA.

Pathogenesis

Lysis of infected epithelial cells results in fluidfilled blisters containing infectious virions. Rupture of these vesicles causes a painful ulceration. The acute infection is controlled by body defenses; genome persists within nerve cells in a non-infectious form beyond the reach of body defenses. Replication of infectious virions can occur and cause recurrent symptoms in the area supplied by the nerve. Newborn infants can contract fatal generalized herpetic infection if their mother has a primary infection at the time of delivery.

Epidemiology

No animal reservoirs. Transmission by sexual intercourse, oral-genital contact. Transmission risk greatest first few days of active disease. Transmission can occur in the absence of symptoms. Herpes simplex increases the risk of contracting HIV.

Prevention and treatment

Abstinence, monogamy, and condoms help prevent transmission. Medications help prevent recurrences, shorten duration of symptoms. No cure.

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HPVs are thought to enter and infect the deeper layers of epithelium through microscopic abrasions. A latent infection, without

Figure 26.19 Genital Warts on the Penis, a Manifestation of Human Papillomavirus Infection

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warts or microscopic lesions, is the most common result of infection. Latent infection can last for years, but studies in college-age women reveal that about 90% of HPV infections are eliminated by body defenses within 2 years. Viral replication and release are intermittent and require that the deeper layer of epithelial cells begins the normal process of changing to surface layer cells. Different kinds of lesions develop depending on the virus type and the location of the infection. Lesions can be flat, raised or unraised, cauliflower-like, or hidden within the epithelium. The mechanism giving rise to warts is unknown. The viral genome exists in infected cells as extrachromosomal, closed DNA circles. Warts usually appear about 3 months after infection (range, 3 weeks to 8 months). Following removal or destruction of warts, HPV persists in surrounding normal-appearing epithelium and can give rise to additional warts. Warts can occasionally partly obstruct the urethra or, if very large, the birth canal. Newborn infants can become infected with HPV at birth and develop warts that obstruct their respiratory tract, a serious condition that occurs in less than one out of every 100,000 births. Worldwide, cancer of the cervix is second in frequency only to breast cancer among the malignant tumors of women. Most of these cancers are associated with certain HPV types. Cancer-associated HPV types differ from wart-causing HPV types in that the former can integrate into the chromosome of a host cell and code for a protein that permits excessive cell growth. These oncogenic types of HPV tend to cause infections that persist longer than other HPV types, and to cause precancerous lesions. A cancer-associated HPV is present in almost 100% of cervical cancers, but only a small percentage of infections by these viruses result in cancer. This indicates that other unknown factors must be present for cancer to develop. Cervical cancer-associated HPVs have also been found in vaginal cancers, cancers of the penis, and in anal cancers of men and women who engage in receptive anal intercourse. ■ oncogenes, p. 333

Epidemiology HPVs are readily spread by sexual intercourse; a single sexual exposure to an infected person transfers the infection 60% of the time. Asymptomatic individuals infected with HPV can transfer the virus to others. Forty-six percent of women university students seeking routine gynecological examinations were found to be infected with HPV in one study. HPV infection is the most common reason for an abnormal Papanicolaou (Pap) test in teenage women (see next section). A history of having multiple sex partners is the most important risk factor for acquiring genital HPV infection. Warts can develop in the mouth from HPV infection transferred by oral sex.

Prevention and Treatment HPV-infected individuals are advised to use condoms to help decrease the chance of transmission. Women should have a Papanicolaou smear every 12 months. The “Pap test” consists of removing cells from the cervix with a small brush or spatula, staining them on a microscope slide, and examining them for any abnormal cells (figure 26.20). Cervical cancer is generally preceded by precancerous lesions—areas of abnormal cell growth that can be detected by the Papanicolaou test. The abnormal growth can be removed, thereby preventing development of a cancer. Currently available vaccines are designed to protect against infection by HPV types 16 and 18,

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Figure 26.20 Abnormal Papanicolaou Smear The pink and blue objects are squamous epithelial cells; abnormalities include doubling of the nuclei and a clear area around them. Most abnormal smears in young women are due to human papillomavirus infection, that when persistent are an important factor in the development of cancer of the cervix.

which are responsible for about 70% of cancers, and types 6 and 11, which are responsible for more than 90% of genital warts. The vaccine is given in a three-dose series, and is recommended for girls and young women ages 9 to 26. A vaccine will probably soon be approved for men. Warts on the skin can be removed by laser treatment or freezing with liquid nitrogen, but these measures do not cure the infection. Imiquimod (Aldara Cream), an immune modifier, can be effective for anal and genital warts. Table 26.14 summarizes some important features of papillomavirus STDs.

AIDS AIDS, acquired immunodeficiency syndrome, unquestionably the most important sexually transmitted disease of the twentieth century, is covered briefly here and more fully in chapter 29. The AIDS epidemic was first recognized in the United States in 1981. Over the first decade and a half of the epidemic, 500,000 Americans developed AIDS and 300,000 died of the disease. With major advances in prevention and treatment of the disease, and expenditures of huge amounts of money, the epidemic shows signs of leveling off. Nevertheless, in 2007, an estimated 33.2 million people around the world were living with human immunodeficiency virus (HIV) infection, the causative agent of AIDS, and more than 2 million died of AIDS. There were an estimated 1.7 million new infections in sub-Saharan Africa alone. The advances in prevention and treatment of AIDS are not uniformly available to many of those around the world who suffer because of the disease. ■ AIDS, p. 698

Symptoms AIDS is the end stage of what is more properly called HIV disease. Six days to 6 weeks after contracting the virus, some individuals develop a fever, head and muscle aches, enlarged lymph nodes, and a rash. These symptoms are often mild, attributed to the flu, and go

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26.7

TABLE 26.14 Papillomavirus STDs Symptoms

Many have no symptoms. Warts of the external and internal genitalia the most common symptom.

Incubation period

Usually 3 months (range, 3 weeks to 8 months)

Causative agents Human papillomaviruses, many types, small, non-enveloped, double-stranded DNA viruses of the papovavirus family. Different types infect different tissues and produce different lesions.

Pathogenesis

Virus enters epithelium through abrasions, infects deep layer of epithelium; establishes latency; cycles of replication occur when host cell begins maturation; cancer-associated viral types can integrate into the host cell chromosome and can cause precancerous lesions.

Epidemiology

Asymptomatic individuals can transmit the disease; 60% transmission with a single sexual contact; multiple sex partners the greatest risk factor; warts can be transmitted to the mouth with oral sex, and to newborn babies.

Prevention and treatment

Latex condoms advised to minimize transmission and avoidance of sexual contact with those having multiple sex partners. Pap tests at least yearly for sexually active women. Wart removal by multiple techniques, does not cure the infection. Imiquimod useful in treating multiple warts about anus and external genitalia.

away by themselves. Many individuals have no symptoms at all. The typical case of HIV disease then smolders unnoticed for almost 10 years before immunodeficiency develops, as evidenced by certain malignancies and unusual microbial infections that often attack the lungs, intestines, skin, eyes, or the central nervous system.

Causative Agents Most AIDS cases are caused by human immunodeficiency virus type 1 (HIV-1), an enveloped, single-stranded, RNA virus of the retrovirus family. Each virion contains reverse transcriptase and two copies of the viral genome. In parts of western Africa, another retrovirus, HIV-2, is a common cause of AIDS; it is rarely a cause in the United States. ■ retroviruses, pp. 323, 332

Pathogenesis HIV can attack a variety of types of cells in the human body, but most critically a subset of lymphocytes—the helper T (TH) cells. These cells possess the CD4 surface protein to which the virus attaches, and they are referred to as CD4 ; cells. In order for the virus to enter the cell, it must also attach to certain cytokine receptors on the cell surface. Following entry of the virus, a DNA copy is made using reverse transcriptase. This copy integrates itself into the cell’s genome and hides there, inaccessible to antiviral chemotherapy. If the cell becomes activated, however, the virus leaves the cell genome, replicates, and destroys the cell, releasing virions to infect additional cells. Despite the body’s ability to replace hundreds of billions of CD4; lymphocytes, the number of these lymphocytes slowly declines over many months or years.

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Viral STDs

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Infection of macrophages contributes to the decline in cellular immunity. Macrophages, also vitally important to the immune system, are also CD4 ; cells. Although they are generally not killed, their function is impaired both by the viral infection and the lack of interaction with TH lymphocytes. Eventually, the immune system becomes so impaired it can no longer respond to infections or cancers. ■ helper T cells, p. 368 ■ macrophages, p. 350

Epidemiology HIV is present in blood, semen, and vaginal secretions in symptomatic and asymptomatic infections. HIV disease spreads mainly by sexual intercourse, sharing hypodermic needles, or from mother to newborn. The virus is not highly contagious, and most transmissions could be halted by simple changes in human behavior.

Prevention and Treatment One of the most important developments in the prevention of AIDS has been the finding that transmission from mother to newborn can be interrupted by chemotherapy in about two-thirds of the cases. Supplying injected-drug abusers with sterile needles and syringes in exchange for used ones decreases transmissions of the virus without encouraging addiction. Specifically designed educational programs targeting certain groups of people have also shown short term success in decreasing risky sexual practices. Lastly, identification and treatment of other STDs decreases the risk of contracting HIV disease, as does consistent use of latex condoms. Treatment is designed to block replication of HIV, but it does not affect viral nucleic acid already integrated in the host genome. Four kinds of medications are currently available—(1) those that block reverse transcriptase activity; (2) those that act against viral protease; (3) those that block viral integrase; and (4) those that interfere with attachment to host cells. The first three block enzymes essential at different stages of viral replication. The fourth type is represented by a drug that interferes with HIVattachment to the cytokine receptor CCR5. Viral mutants resistant to a single medication, however, quickly arise. To help prevent the selection of resistant variants, a “cocktail” of several medications, each acting in a unique way is given. In many cases this therapy can clear the patient’s blood of detectable viral nucleic acid (but does not affect HIV integrated in the genome of cells), halt the progress of the disease, and even allow partial recovery of immune function. Therapy is very expensive and the medications often have serious side effects, two features that preclude use of the regimen in many of the world’s HIV disease sufferers. While not curative, chemotherapy can markedly prolong and improve the quality of life. ■ HIV replication, p. 703 Each person has a role to play in controlling the AIDS pandemic by studying the disease and doing his or her part in preventing spread from one person to another. About 25% of the estimated 900,000 people in the United States infected with HIV are unaware of their infection. Individuals who, since the 1980s, have engaged in injected drug use or risky sexual behavior, and anyone having had unprotected sexual intercourse with them, should consider obtaining a blood or saliva test to rule out HIV infection. Persons who learn that their HIV test is positive can receive optimum treatment sooner and also prevent transmission of the virus to others. Table 26.15 presents the main features of HIV disease and AIDS.

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TABLE 26.15 HIV Disease and AIDS Symptoms

No symptoms, or “flu”-like symptoms early in the illness; an asymptomatic period typically lasting years; symptoms of lung, intestine, skin, eyes, brain, and other infections, and certain cancers

Incubation period

About 6 days to 6 weeks for “flu”-like symptoms; many months or years for cancers and unusual infections

Causative agents

Generally human immunodeficiency virus, type 1 (HIV-1)

Pathogenesis

The virus infects CD4; lymphocytes and macrophages, thereby slowly destroying the ability of the immune system to fight infections and cancers.

Epidemiology

HIV present in blood, semen, and vaginal secretions in symptomatic and asymptomatic infections; spread usually by sexual intercourse, sharing of needles by injected-drug abusers, and from mother to infant at childbirth. Other STDs foster transmission.

Prevention and treatment

Abstinence from sexual intercourse and drug abuse; monogamy; consistent use of latex condoms; avoidance of sexual contact with injected-drug abusers, those with multiple partners or history of STDs. Anti-HIV medication for expectant mothers and their newborn infants. Treatment: reverse transcriptase and protease inhibitors in combination.

by the fecal-oral route in individuals who engage in oral-genital and -anal contact as part of sexual activity. By contrast, trichomoniasis is a sexually transmitted protozoan disease that involves the genital system. ■ protozoa, p. 285 ■ cryptosporidiosis, p. 610

“Trich” (Trichomoniasis) Trichomoniasis is caused by Trichomonas vaginalis. It ranks third after bacterial vaginosis and candidiasis among the diseases that commonly cause vaginal symptoms. Infected men usually are asymptomatic carriers of the organism. An estimated 5 million Americans contract this STD each year. An African study indicated that trichomoniasis can cause a two to three fold increase in HIV transmission.

Symptoms Most symptomatic T. vaginalis infections occur in women and are characterized by itching of the vulva and inner thighs; itching and burning of the vagina; and a frothy, sometimes malodorous, yellowish-green vaginal discharge, at times accompanied by burning discomfort with urination. Although most infected men are free of symptoms, some have penile discharge, burning pain with urination, painful testes, or a tender prostate gland.

Causative Agent Trichomonas vaginalis is a protozoan measuring about 10 by 30 μm. It has four anterior flagella and a posterior flagellum attached to an undulating membrane (figure 26.21). It also has a slender, posteriorly protruding, rigid rod called an axostyle. Trichomonas vaginalis

MICROCHECK 26.7 Viral STDs are at least as common as bacterial STDs, but so far they are incurable. Genital herpes simplex is widespread and, like most other STDs, can be transmitted in the absence of symptoms. Human papillomaviruses cause genital warts; some play an important role in cancer of the cervix and probably cancers of the vagina, penis, and rectum. HIV disease generally ends in AIDS, but treatment can markedly improve longevity and quality of life. ✓ What are the possible consequences of sexually transmitted papillomavirus infections for men, women, and babies? ✓ What kinds of sex partners present a high risk of transmitting human immunodeficiency virus? ✓ Why should a person be concerned about genital herpes simplex—is it not just a cold sore on the genitals? Explain.

Anterior flagella

Undulating membrane T. vaginalis

Nucleus Nucleus Axostyle Polymorphonuclear leukocyte

Cytoplasm

26.8 Protozoal STDs Focus Points List the distinctive characteristics of the organism that causes trichomoniasis. Outline the epidemiology of trichomoniasis.

A number of protozoan diseases are frequently transmitted sexually even though they do not infect the genital system. For example, giardiasis and cryptosporidiosis are intestinal diseases transmitted

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5 mm

Figure 26.21 Trichomonas vaginalis, a Common Sexually Transmitted Cause of Vaginitis Diagram shows the relative sizes of the protozoan and a polymorphonuclear leukocyte. Although it is a flagellated protozoan, T. vaginalis often exhibits pseudopodia.

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26.8

has an unmistakable, jerky motility on microscopic examination of the vaginal drainage. Unlike most other pathogenic protozoa, T. vaginalis lacks a cyst form to aid its survival in the environment away from the host’s body. The organism is a eukaryote, but it lacks mitochondria. Trichomonas vaginalis has interesting cytoplasmic organelles called hydrogenosomes. Enzymes within these double membrane-bounded organelles remove the carboxyl group (COOH) from pyruvate and transfer electrons to hydrogen ions, thereby producing hydrogen gas. ■ mitochondria, p. 76

Pathogenesis The pathogenesis of trichomoniasis is not fully understood. The vulva and walls of the vagina are diffusely red and slightly swollen. Often there are scattered pinpoint hemorrhages. These changes have been attributed to mechanical trauma by the moving protozoa, but toxins or exoenzymes have not been ruled out. The frothy discharge is probably due to gas produced by the organisms.

Epidemiology Trichomonas vaginalis is distributed worldwide as a human parasite and has no other reservoirs. Because it lacks a cyst form, it is easily killed by drying. Therefore, transmission is usually by sexual contact. The organism can survive for a time on moist objects such as towels and bathtubs, so that it can occasionally be transmitted non-sexually. Nevertheless, T. vaginalis infections in children should at least raise the question of sexual abuse and possible exposure to other sexually transmitted diseases. Newborn infants can contract the infection from infected mothers at birth. There is a high percentage of asymptomatic carriers, especially among men, and this fosters transmission of the disease. Infection rates are highest in men and women with multiple sex partners.

Prevention and Treatment Transmission is prevented by abstinence, monogamy, and the use of condoms. Most strains of T. vaginalis respond quickly to metronidazole treatment, but a few are resistant. Table 26.16 gives the main features of trichomoniasis.

TABLE 26.16

Protozoal STDs

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Trichomoniasis

Symptoms

Women: itching, burning, swelling, vaginal redness, frothy, sometimes malodorous, yellowgreen discharge, and burning on urination. Men: discharge from penis, burning on urination, painful testes, tender prostate. Many women, most men asymptomatic

Incubation period

4 to 20 days

Causative agent

Trichomonas vaginalis, a protozoan with four anterior flagella, and a posterior flagellum attached to an undulating membrane; a rigid rodlike structure called an axostyle protrudes posteriorly; unmistakable jerky motility; no mitochondria; hydrogenosomes are present

Pathogenesis

Unexplained. Inflammatory changes and pinpoint hemorrhages suggest mechanical trauma from the motile organisms.

Epidemiology

Worldwide distribution; asymptomatic carriers foster spread; easily killed by drying due to lack of cyst form, transmission by intimate contact; high rate of infection with multiple sex partners. Newborn infants of infected mothers can acquire the infection at birth.

Prevention and treatment

Abstinence, monogamy, and consistent use of condoms prevent the disease. Treatment: metronidazole.

MICROCHECK 26.8 Trichomoniasis is a protozoan STD that involves the genital tract (other protozoan STDs involve the intestine). The causative agent is a peculiar, flagellated protozoan that does not form cysts and lacks mitochondria. Organelles called hydrogenosomes produce hydrogen gas from pyruvate. ✓ What significance does the lack of a cyst form of Trichomonas vaginalis have on the epidemiology of trichomoniasis? ✓ Why is there a strong relationship between being “easily killed by drying” and “transmission usually by sexual contact”?

FUTURE CHALLENGES Getting Control of Sexually Transmitted Diseases Few problems are as complicated as getting control of sexually transmitted diseases because of the psychological, cultural, religious, and economic factors that are involved—factors that vary from one population and culture to another. Gaining control means focusing on diagnosis, interruption of transmission, education, and treatment. The challenge is to develop innovative approaches in each of these areas and to apply them worldwide on a sustained basis. In the area of diagnosis, the challenge is to use molecular biological techniques to identify and produce specific antigens and antibodies that can be used to quickly identify causative agents and determine the extent of their spread. The development of nucleic acid

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probes to identify genes coding for resistance to therapeutic agents assists in choosing prompt treatment. Interruption of transmission by the consistent use of condoms can be highly effective, but in practice their use presents a number of problems. When infected college students are asked why they did not use a condom, they often state that “it takes away the romance,” “it decreases pleasurable sensation,” or “that’s for sissies.” Also, many individuals are allergic to latex, and the alternatives, perhaps except for polyurethane, are unreliable for preventing disease transmission. Worldwide, as many as one out of three condoms is defective, and the poorest countries cannot even afford them. The challenge is to develop cheaper,

more reliable, and more acceptable barrier methods, perhaps using new space-age polymers or antimicrobial vaginal gels. Effective vaccines could block the spread of STDs, but their development has been extremely problematic and remains a long-term goal. Sequencing the genomes of the causative agents is helping to identify appropriate antigens to include in vaccines, but using them to stimulate a protective immune response is a continuing challenge. Educational efforts focusing on groups at high risk for STDs have had mixed success. Education can be a useful tool for gaining control of STDs, and the challenge is to better understand the reasons for its failures.

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SUMMARY 26.1 Anatomy and Physiology The genitourinary system is one of the portals of entry for pathogens to invade the body. The Urinary System (figure 26.1) The kidneys, ureters, bladder, and urethra compose the urinary system. Frequent, complete emptying is an important bladder defense mechanism against infection. Infections occur more frequently in women than in men because of the shortness of the female urethra and its closeness to openings of the genital and intestinal tracts. The Genital System (figure 26.2) The fallopian tube, which is open on both ends, provides a passageway for infection to enter the abdominal cavity. The uterine cervix is a frequent site of infection and a place where cancer can develop. The vagina is a portal of entry for a number of infections. In men, the prostate can enlarge and partially obstruct urinary flow.

26.2 Normal Microbiota of the Genitourinary System The distal urethra is inhabited by various microorganisms, sometimes including potential pathogens. The normal vaginal microbiota is influenced by estrogen hormones, which cause deposition of glycogen in the cells lining the vagina. Vaginal lactobacilli release lactic acid and hydrogen peroxide when they metabolize the glycogen, making the vagina more resistant to colonization by pathogens.

26.3 Urinary System Infections Any condition that impairs normal bladder emptying increases the risk of infection. The urinary system usually becomes infected by organisms ascending from the urethra, but it can also be infected from the bloodstream. Bacterial Cystitis (table 26.1) Urine is a nutritious medium for many bacteria. Kidney infection— pyelonephritis—may complicate untreated bladder infection when pathogens ascend through the ureters and involve the kidneys. Most urinary tract infections in healthy people are caused by Escherichia coli or other enterobacteria from the person’s own normal intestinal flora. Nosocomial urinary infections are common and caused by Pseudomonas aeruginosa, Serratia marcescens, and Enterococcus faecalis—organisms that are generally resistant to many antibiotics. Leptospirosis (table 26.2) In leptospirosis, the urinary system is infected by Leptospira interrogans from the bloodstream (figure 26.3). This biphasic illness causes fever, bloodshot eyes, and pain in the septicemic phase. Improvement occurs, then recurrent symptoms emerge, with damage to multiple organs during the immune phase. Many species of animals are chronically infected with L. interrogans and excrete the organism in their urine.

26.5). Antibacterial treatment, uncontrolled diabetes, and oral contraceptives are predisposing factors, but in most cases no such factor can be identified.

Staphylococcal Toxic Shock Syndrome (table 26.5) First described in children, it became widely known with a 1980 epidemic in menstruating women who used a certain kind of vaginal tampon that has since removed from the market (figure 26.6). Symptoms include sudden fever, headache, muscle aches, bloodshot eyes, vomiting, diarrhea, a sunburn-like rash that later peels, and confusion. The blood pressure drops, and without treatment, kidney failure and death may occur.

26.5 Sexually Transmitted Diseases: Scope of the Problem (tables 26.6, 26.7)

In the United States, 15 million new sexually transmitted infections occur each year, including 3 million in teenagers. Simple measures exist for controlling STDs: abstinence from sexual intercourse, a monogamous relationship with an uninfected person, and consistent use of latex or polyurethane condoms (figure 26.7).

26.6 Bacterial STDs Most of the bacteria that cause STDs survive poorly in the environment and require intimate contact for transmission. Gonorrhea (table 26.8) Gonorrhea, caused by Neisseria gonorrhoeae, has been generally declining in incidence, but it is still one of the most commonly reported bacterial diseases (figures 26.9, 26.10). Men usually develop painful urination and thick pus draining from the urethra; women may have similar symptoms, but they tend to be milder and are often overlooked (figure 26.8). Expression of different surface antigens allows attachment of N. gonorrhoeae to different types of cells, and frustrates development of a vaccine. Inflammatory reaction to the infection causes scarring, which can partially obstruct the urethra or cause sterility in men and women. Chlamydial Genital System Infections (table 26.9, figure 26.11) Chlamydial genital infections, caused by Chlamydia trachomatis, are reported more often than any other bacterial disease. Symptoms and complications of chlamydial infections are very similar to those of gonorrhea, but milder; asymptomatic infections are common and readily transmitted. Sexually active individuals should be tested at least once a year so that transmission can be halted and complications prevented.

Bacterial Vaginosis (table 26.3, figure 26.4) Bacterial vaginosis is the most common cause of vaginal symptoms, including a gray-white discharge from the vagina and a pungent fishy odor; there is no inflammation. The causative agent or agents are unknown.

Syphilis (tables 26.10, 26.11) Syphilis, caused by Treponema pallidum, is called “the great imitator” because its many manifestations can resemble other disease (figure 26.13). Primary syphilis is noted by a painless, firm ulceration called a hard chancre; the organisms multiply and spread throughout the body (figure 26.12). In secondary syphilis, skin and mucous membranes show lesions that teem with the organisms; a latent period of months or years separates secondary from tertiary syphilis (figure 26.14). Tertiary syphilis is not contagious. It is manifest mainly by damage to the eyes and the cardiovascular and central nervous systems. An inflammatory, necrotizing mass called a gumma can involve any part of the body (figure 26.15). Syphilis in pregnant women can spread across the placenta to involve the fetus, resulting in congenital syphilis (figure 26.16).

Vulvovaginal Candidiasis (table 26.4) Vulvovaginal candidiasis is second among causes of vaginal disorders. Symptoms include itching, burning, vulvar redness and swelling, and a thick, white discharge. The causative agent is a yeast, Candida albicans, that is commonly part of the normal vaginal flora (figure

Chancroid (table 26.12) Chancroid is another widespread bacterial STD, but it is not commonly reported because of difficulties in making a bacterial diagnosis. Epidemics in the United States have been associated with prostitution. Caused by Haemophilus ducreyi, chancroid is characterized by single or multiple

26.4 Genital System Diseases

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Review Questions soft, tender genital ulcers, and enlarged, painful groin lymph nodes (figure 26.17). Some strains of H. ducreyi possess R factors, making treatment more difficult.

26.7 Viral STDs Viral STDs are at least as common as bacterial STDs, but they are not yet curable. Genital Herpes Simplex (table 26.13, figure 26.18) It is a very common disease, important because of the discomfort and emotional trauma it causes, its potential for causing death in newborn infants, its association with cancer of the cervix, and the increased risk it poses of transmitting HIV infection and AIDS. Symptoms may include a group of vesicles with itching, burning, or painful sensations; these break, leaving a tender, superficial ulcer. Local lymph nodes enlarge. Many infections have few or no symptoms; some have painful recurrences. The virus establishes a latent infection in sensory nerves and cannot be cured. It can be transmitted in the absence of symptoms, but the risk is greatest when lesions are present. Papillomavirus STDs: Genital Warts and Cervical Cancer (table 26.14) Papillomavirus STDs are probably more prevalent than any other kind of STD; HPVs are the main cause of abnormal Pap smears in young women (figure 26.20). They are manifest in two ways—as warts on or near the genitalia (figure 26.19) and as precancerous lesions. The latter are asymptomatic and can only be detected by medical examination. The causative agents, human papillomaviruses, are small DNA viruses that have not been cultivated in the laboratory.

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AIDS (table 26.15) AIDS is the end stage of disease caused by human immunodeficiency virus (HIV). Worldwide, millions of new HIV infections and deaths from AIDS occur each year. Advances in treatment, available to HIV disease victims in some countries, are not available to many of the world’s HIV victims. HIV disease is usually first manifest as a “flu”-like illness that develops about 6 days to 6 weeks after an individual contracts the virus. An asymptomatic interval follows that typically lasts almost 10 years, during which the immune system is slowly and progressively destroyed. Unusual cancers and infectious diseases then herald the onset of AIDS. No vaccine or medical cure is yet available, but spread of infection can be slowed significantly by consistent use of condoms and employment of sterile needles by injecteddrug abusers. A marked reduction in mother-to-newborn transmission can be achieved with medication.

26.8 Protozoal STDs Intestinal protozoan disease such as giardiasis and cryptosporidiosis are transmitted by the fecal-oral route in those individuals who engage in oral-genital and -anal contact as part of sexual activity. “Trich” (Trichomoniasis) (table 26.16) Symptoms include itching, burning, swelling, and redness of the vagina, with frothy, sometimes smelly, yellow-green discharge, and burning on urination. Men may have discharge from the penis, burning on urination, sometimes accompanied by painful testes and a tender prostate gland. Many women and most men are asymptomatic. The causative agent is Trichomonas vaginalis, a protozoan with four anterior flagella, and a posterior flagellum attached to an undulating membrane (figure 26.21).

REVIEW QUESTIONS Short Answer 1. Name two substances released by lactobacilli that help protect the vagina from potential pathogens. 2. List four things that predispose to the development of infection of the urinary bladder. 3. Name two genera of bacteria that infect the kidneys from the bloodstream. 4. What possible danger lurks in a spot on the ground where an animal has urinated 1 week earlier? 5. What is a clue cell? 6. What is ophthalmia neonatorum? 7. List three diseases caused by different antigenic types of Chlamydia trachomatis. 8. Which bacterium leads all others as a cause of reportable infectious disease? 9. Why is dark-field microscopy used to view Treponema pallidum? 10. Give two ways in which the chancre of chancroid differs from the chancre of syphilis. 11. What is the relationship between AIDS and HIV disease? 12. What is the reservoir of Trichomonas vaginalis?

Multiple Choice 1. All of the following are true of bacterial cystitis, except a) about one-third of all women will have it at some time during their life.

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b) catheterization of the bladder markedly increases the risk of contracting the disease. c) individuals who have a bladder catheter in place indefinitely risk bladder infections with multiple species of intestinal bacteria at the same time. d) bladder infections occur as often in men as they do in women. e) bladder infections can be asymptomatic. 2. Choose the one correct statement about leptospirosis. a) Humans are the only reservoir. b) Most infections produce severe symptoms. c) Transmission is by the fecal-oral route. d) It can lead to unnecessary abdominal surgery. e) Effective vaccine is generally available for preventing human disease. 3. Which one of the following statements about bacterial vaginosis is false? a) It is the most common vaginal disease in women of childbearing age. b) In pregnant women it is associated with a seven-fold increased risk of obstetrical complications. c) Inflammation of the vagina is a constant feature of the disease. d) The vaginal microbiota shows a marked decrease in lactobacilli and a marked increase in anaerobic bacteria. e) The cause is unknown. 4. Pick the one false statement about vulvovaginal candidiasis. a) It often involves the external genitalia.

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5.

6.

7.

8.

9.

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b) It is readily transmitted by sexual intercourse. c) It is caused by a yeast present among the normal vaginal microbiota in about one-third of healthy women. d) It is associated with prolonged antibiotic use. e) It involves increased risk late in pregnancy. All of the following statements about staphylococcal toxic shock are true, except a) it can quickly lead to kidney failure. b) the causative organism usually does not enter the bloodstream. c) it occurs only in vaginal tampon users. d) almost one-third of victims of the disease will suffer a recurrence sometime after recovery. e) person-to-person spread does not occur. Which of the following statements about gonorrhea is false? a) The incubation period is only a few days. b) Disseminated gonococcal infection (DGI) is almost invariably preceded by prominent urogenital symptoms. c) DGI can result in arthritis of the knee. d) Phase variation helps the causative organism evade the immune response. e) Pelvic inflammatory disease (PID) is common in untreated women. Which one of these statements about chlamydial genital infections is false? a) The incubation period is usually shorter than in gonorrhea. b) Infected cells develop inclusion bodies. c) Pelvic inflammatory disease (PID) can be complicated by infection of the surface of the liver. d) Tissue damage largely results from cell-mediated immunity. e) Fallopian tube damage can occur in the absence of symptoms. Which symptom is least likely to occur as a result of tertiary syphilis? a) Gummas d) Stroke b) White patches on mucous membranes e) Blindness c) Emotional instability During the first 15 years of the AIDS epidemic, approximately how many Americans died of the disease? a) 10,000 d) 5 million b) 50,000 e) 50 million c) 300,000

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10. All of the following are true of “trich” (trichomoniasis), except a) it can cause burning pain on urination and painful testes in men. b) it occurs worldwide. c) asymptomatic carriers are rare. d) transmission can be prevented by proper use of condoms. e) individuals with multiple sex partners are at high risk of contracting the disease.

Applications 1. Religious restrictions of a small North African community are preventing a World Health Organization project from reducing the incidence of gonorrhea. The community will not permit the testing of females for the disease. They can be treated, however, if they show outward evidence of the disease. Only males are allowed to participate fully in the project, with testing for the disease and treatment. The village elders argue that eradicating the disease from males would eventually remove it from the population. What would be the impact of these restrictions on the success of the project? 2. Former president Ronald Reagan once commented at a press conference that the best way to combat the spread of AIDS in the United States was to prohibit everyone from having sexual contact for 5 years. What would be the success of such a program if it were possible to carry it out?

Critical Thinking 1. The middle curve of figure 26.6 shows the occurrence of staphylococcal toxic shock syndrome in menstruating women from 1979 to 1996. What aspect of these data argue that high-absorbency tampons were not the only cause of staphylococcal toxic shock syndrome associated with menstruation? 2. In early attempts to identify and isolate the cause of syphilis, various bacteria in the discharge from syphilitic lesions in experimental animals were isolated in pure culture. None of them, however, would cause the disease when used in attempts to infect healthy animals. Why was it considered a critical step to have the cultivated bacteria reproduce the disease in the healthy animals?

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27 TEM of West Nile virus, a virus introduced into the United States in 1999.

Nervous System Infections A Glimpse of History Today it is hard to appreciate the fear and loathing formerly attached to leprosy. In the Greek translation of the Bible from Hebrew, a variety of disfiguring skin diseases, including leprosy, are covered by the word lepros, meaning “scaly,” but having the connotation of being disgustingly filthy, outcast, condemned by God for sin. In the Bible, Moses calls lepers “unclean” and proclaims that they must live away from others. In the Middle Ages, lepers wore bells to warn others of their presence, and attended a symbolic burial of themselves before being sent away. Gerhard Henrik Armauer Hansen (1841–1912) was a burly Norwegian physician who lived in the southern part of that country in the bustling seaport of Bergen. He was a man of many interests, ranging from music, religion, and polar exploration to marine biology. A vigorous trade of goods and ideas with other countries was going on at the time, especially with Germany and England and, like many of the city’s inhabitants, Dr. Hansen was fluent in several languages. He was well aware of the scientific advances of the day, including Darwin’s studies, and Pasteur’s proof that bacteria could cause fermentation. His Norwegian contemporaries included such luminaries as his friend, Edvard Grieg, the famous composer, and Henrik Ibsen, a world-renowned playright. When he was 32 years old, Hansen decided to go into medical research, and was named assistant to Dr. Daniel C. Danielson, a leading authority on leprosy. Danielson had developed the hypothesis that leprosy was a disease of the blood that once acquired, was hereditary. He had discarded the idea that the disease was contagious as a “peasant superstition.” To “dispose of this foolish notion,” he injected himself with material from leprosy patients. Fortunately for him and others who had done the same thing, no disease developed, because effective treatment of leprosy did not become available for another three-quarters of a century. Luckily, Danielson and Hansen had great mutual respect, because Hansen, in a meticulous series of 58 studies over a number of years, disproved Danielson’s hypothesis and showed that a unique bacillus was associated with

the disease in every leprosy patient he studied. His findings, finally reported in 1873, almost a decade before Koch’s proof of the cause of tuberculosis, linked for the first time a specific bacterium to a disease. His studies forever changed the way people looked at leprosy, and helped overturn a viewpoint held by many people, one that had existed for many centuries. In the United States, even during the first half of the twentieth century, persons diagnosed with leprosy risked having their houses burned to destroy contagion. Their names were changed to avoid embarrassing their family, and they were whisked off to a leprosarium such as the one at Carville, Louisiana, surrounded by a 12-foot fence topped with barbed wire. They were separated from spouses and children, and denied the right to marry or to vote. Those who attempted to escape were captured and brought back in handcuffs. The story of the Carville leprosarium is told by one who did escape, Betty Martin, in her wonderful book, Miracle at Carville. The leprosarium was finally closed and converted to a military-style academy for high school dropouts in 1999. Because the English word leprosy carries these innuendoes from earlier days, many people prefer to use the term Hansen’s disease, so named after the discoverer of the causative organism.

I

nfections of the nervous system are apt to be serious because they threaten a person’s ability to move, to feel, and to think normally. Just consider poliomyelitis, in which nerve cells are destroyed, leaving the victim with a paralyzed arm or leg, or unable to breathe without mechanical assistance. In Hansen’s disease, nerve damage can result in complete loss of fingers or toes, or deformity of the face. Infections of the brain or its covering membranes can render a child deaf or mentally retarded. Fortunately, nervous system infections are uncommon. Examples given in this chapter, however, reveal a multiplicity of causes, including bacteria, viruses, fungi, and even some protozoa. 647

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KEY TERMS Arbovirus Arthropod-borne virus. One of a large group of RNA viruses carried by insects and mites that act as biological vectors. Axon The long, thin extension of a nerve cell. Blood-Brain Barrier Property of the central nervous system blood vessels that restricts passage of infectious agents and certain molecules (such as medications) into the brain and spinal cord. Botulism A paralytic illness caused by a toxin produced by Clostridium botulinum.

Nervous System Infections Creutzfeld-Jakob Disease A rare, degenerative brain disease of humans caused by prions.

Neurotoxin A toxin that damages the nervous system.

Ganglion (pl., ganglia) Small body near the spinal column representing a bulge in a peripheral nerve at the site where the sensory nerve cells are located.

Parasitemia Parasites (such as protozoan pathogens) circulating in the bloodstream.

Meninges Membranes covering the brain and spinal cord. Meningoencephalitis Inflammation of the brain and its covering membranes. Negri Body Viral inclusion body characteristic of rabies.

27.1 Anatomy and Physiology Focus Points List the main components of the nervous system. Describe the routes a pathogen can take to enter the central nervous system.

The brain and spinal cord make up the central nervous system (CNS). Both are enclosed by bone—the brain by the skull and the spinal cord by the vertebral column (figure 27.1). The network of nerves throughout the body is called the peripheral nervous system. All nerves are made up of cells with very long, thin extensions called axons, which transmit electrical impulses. The peripheral nervous system is connected with the CNS by bundles of axons that penetrate the protective bony covering. Nerves can be damaged if the bones are infected at sites of nerve penetration. Motor nerves carry messages from the CNS to different parts of the body and cause them to act; sensory nerves transmit sensations like heat, pain, light, and sound from the periphery to the central nervous system. The sensory nerve cells are located in small bodies called ganglia (singular, ganglion) located near the vertebral column; motor nerve cells are located in the central nervous system. Nerves can sometimes regenerate if severed or damaged, but they cannot be repaired if the nerve cells are killed, as occurs, for example, in poliomyelitis. Some viruses and toxins can move through the body within the cytoplasm of the axons, and some herpesviruses can remain latent in nerve cells for many years. The brain is a very complex structure—distinct parts have different functions. This means that if an individual has symptoms from a brain abscess, for example, physicians will know in which part of the brain the abscess is located. Generalized inflammation or infection of the brain is termed encephalitis. Deep inside the brain are four cavities called ventricles that are filled with a clear fluid called cerebrospinal fluid (CSF). This fluid is continually produced by structures in the wall of ventricles, and it flows out through a small opening at the base of the brain. It then spreads over the surface of the brain and spinal cord, and is reabsorbed into the bloodstream at specialized sites between the skull and the brain (figure 27.2a).

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Petechia (Petechiae) Small, purplish spot on the skin or mucous membrane caused by a hemorrhage. Spongiform encephalopathy Central nervous disease in which the brain has the appearance of a sponge; caused by prions. Viremia Viruses circulating in the bloodstream.

Three membranes called meninges cover the surface of the brain and spinal cord. Inflammation or infection of these membranes is called meningitis. The outer membrane, or dura, is tough and fibrous and adheres closely to the skull and vertebrae. It provides a barrier to the spread of infection from bones surrounding the central nervous system. The two inner membranes, the arachnoid and pia, are separated by a space through which the cerebrospinal fluid flows. Blood vessels and nerves that pass through the meninges and cerebrospinal fluid can become damaged by meningitis. Sometimes both the meninges and the brain

Brain Encephalitis Rabies Skull

Meninges Meningitis

Spinal cord Poliomyelitis

Vertebral column

Vertebrae

FIGURE 27.1 The Central Nervous System Terms in color indicate diseases associated with that area.

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Anatomy and Physiology

649

(a)

Spinal cord Cerebrospinal fluid reabsorbed into bloodstream (b) Subarachnoid space

Subarachnoid space Lumbar vertebrae

Cerebrospinal fluid formed

Dura

Arachnoid Pia Pia

Spinal fluid

Dura

Arachnoid

Ventricles

Spinal cord

(a)

(b)

FIGURE 27.2 Cerebrospinal Fluid (a) The fluid is formed in the ventricles, flows out over the surface of the brain and spinal cord, and is reabsorbed by structures at the top of the brain. (b) A sample of cerebrospinal fluid can be withdrawn from the subarachnoid space.

are involved by an infection—a condition called meningoencephalitis. To determine if a person has meningitis, a needle can be safely inserted between the vertebrae in the small of the back and a sample of cerebrospinal fluid withdrawn and examined. In this anatomical region, the spinal cord has tapered to only a threadlike structure (see figure 27.2b). The causative agent of a central nervous system infection can thus be identified microscopically and cultivated on laboratory media. Once the cause of the disease is known, it can usually be treated effectively with an appropriate antimicrobial medication.

Pathways to the Central Nervous System Because the nervous system lies entirely within body tissues, it has no normal flora. It is sterile, and no viruses or microorganisms are normally found there. Also, its well-protected environment prevents infectious agents from getting to it readily. Most microorganisms that infect the nervous system infect other parts of the body much more frequently. The routes that pathogenic microor-

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ganisms and viruses take to reach the brain and spinal cord include the bloodstream, the nerves, and extensions from bone.

The Bloodstream The bloodstream is the chief source of CNS infections, although it is very difficult for infectious agents to cross from it to the brain. This barrier to the passage of harmful agents is called the blood-brain barrier. It depends on special cells lining the central nervous system capillaries. These cells, only a single layer thick, are so close to each other that except for essential nutrients that are actively taken up, most molecules cannot pass through them. Consequently, many medications, including penicillin, cannot cross the barrier unless their concentrations in the blood are very high; antimicrobial medications must be able to cross the barrier in order to treat CNS infections. The blood-brain barrier generally prevents pathogens from entering nervous tissue except in rare cases when a high concentration of the infectious agent circulates for a long time in the bloodstream. Infections of the face above the level of the mouth can involve veins that communicate through bone with veins on the

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brain surface. These communicating veins can provide a direct avenue for spread of infection to the central nervous system. A good rule, therefore, is to never squeeze pimples situated on the upper part of the face.

The Nerves Some pathogenic agents penetrate the CNS by traveling up the nerves, probably within the cytoplasm of the axons. Examples of such agents are the rabies and herpes simplex viruses and the tetanus toxin. ■ rabies, p. 663 ■ herpes simplex, p. 592 ■ tetanus, p. 566

Extensions from Bone To reach the CNS, microorganisms must penetrate not only the protecting bone of the skull or spine, but also the tough membrane that surrounds all bones, and the dura. Only rarely do infections in the bone surrounding the CNS succeed in reaching the brain or spinal cord. Sometimes, however, they extend through bone from the sinuses, mastoids, or middle ear. Skull fractures commonly produce non-healing injuries that predispose a person to recurring infection of the CNS. ■ mastoids, p. 496 ■ middle ear, p. 505

MICROCHECK 27.1 The brain and spinal cord make up the central nervous system (CNS). The peripheral nervous system includes sensory nerves, which convey sensations to the CNS, and motor nerves, which carry messages from the CNS to parts of the body, causing those parts to act. The cerebrospinal fluid fills cavities within the brain and flows out over the brain and spinal cord. Inflammation of the meninges is called meningitis. Infection can reach the CNS via the bloodstream, via the nerves, or by extension from bone. Antimicrobial medicines are effective in central nervous system infections only if they can cross the blood-brain barrier. ✓ Describe the flow of cerebrospinal fluid in the central nervous system. ✓ Why is it uncommon that infectious agents pass from the bloodstream to the CNS? ✓ Why can an infection in the brain’s ventricles usually be detected in spinal fluid obtained from the lower back?

27.2 Bacterial Nervous System Infections Focus Points Outline the pathogenesis of meningococcal meningitis. Give reasons why listeriosis is often contracted from contaminated food or drink. Explain why botulism generally is not an infectious disease.

Bacteria can infect the brain and spinal cord, causing abscesses. Or they can infect the peripheral nerves, as in Hansen’s disease. More commonly, bacteria infect the meninges and cerebrospinal fluid, causing meningitis. Meningitis provokes an intense inflammatory response, with a marked accumulation of white blood cells in the cerebrospinal fluid and swelling of brain tissue. The incidence of the disease

nes95432_Ch27_647-673.indd 650

is, on average, fewer than 10 cases per 100,000 population per year. A large number of bacterial species can infect the meninges. In many cases, these organisms are carried in the upper respiratory tract of healthy people, are transmitted by inhalation, and only produce meningitis in a small percentage of people who are infected. Organisms in this category include three important causes of bacterial meningitis—Haemophilus influenzae, Neisseria meningitidis, and Streptococcus pneumoniae. Age plays an important role in susceptibility to these bacteria. Streptococcus pneumoniae, H. influenzae, and N. meningitidis are uncommon causes of meningitis in newborn babies, because most mothers have antibodies against them. The mother’s antibodies cross the placenta and protect her baby. ■ Streptococcus pneumoniae, p. 509 Meningitis in infants during the first month of life is usually caused by bacteria that colonize the mother’s birth canal. For example, newborn babies become infected during labor and delivery by Gram-negative rods such as certain encapsulated strains of E. coli originating from the mother’s intestinal tract. The reason that the newborn is susceptible to Gram-negative rod infections is that its mother’s antibodies to the organisms are of the IgM class, which do not cross the placenta and therefore cannot confer immunity to the infant. ■ IgM antibody, p. 374 Streptococcus agalactiae, a Lancefield group B streptococcus, which colonizes the vagina in 15% to 40% of pregnant women, exceeds E. coli as a cause of meningitis in newborn infants. Babies also acquire this infection from the mother’s genital tract around the time of birth. The American Academy of Pediatrics recommends that cultures selective for group B streptococci be obtained from the vagina and rectum late in pregnancy. Women with positive cultures can then be treated with an appropriate antibacterial medication shortly before or during labor. Evidence indicates that by using this screening procedure, doctors can decrease the incidence of serious group B streptococcal disease by more than 75%. ■ Lancefield grouping, p. 495

Of the six antigenic types of Haemophilus influenzae, labeled a through f, type b is responsible for most cases of serious disease. Starting in the late 1980s, children in the United States have been routinely immunized using a T-cell-dependent antigen consisting of H. influenzae b polysaccharide joined covalently to a bacterial protein such as diphtheria toxoid. The result of using these conjugate vaccines has been a dramatic decline in meningitis and other serious infections caused by H. influenzae type b (figure 27.3). The decline in meningitis due to H. influenzae has resulted in a marked overall decrease in bacterial meningitis and a shift in the peak incidence to older age groups. ■ T-dependent antigen, p. 377 ■ conjugate vaccines, pp. 383, 435

Streptococcus pneumoniae (figure 27.4) is the leading cause of meningitis in adults. The organism is a prominent cause of otitis media, sinusitis, and pneumonia—conditions that often precede pneumococcal meningitis. Neisseria meningitidis, the meningococcus, differs from the other causes in that it is often responsible for epidemics of meningitis. ■ otitis media, p. 504

Meningococcal Meningitis Meningococcal meningitis occurs most commonly in children aged 6 to 11 months, but it also occurs frequently in older children and adults. It is greatly feared because it can sometimes

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27.2 Bacterial Nervous System Infections

651

25

Incidence

20

15

10

5

0 1990

1992

1994

1996

1998

2000

2002

2004

Year

FIGURE 27.3 Rate of Serious Haemophilus influenzae Disease per 100,000 Children Less than Age Five, United States, 1990 Through 2004 Before the availability of conjugate vaccines in late 1987, H. influenzae type b was the most common cause of bacterial meningitis in preschool children.

20 mm

(Source: CDC, Vaccine Information Statements.)

FIGURE 27.4 Streptococcus pneumoniae (Pneumococci) in the Spinal Fluid of a Person with Pneumococcal Meningitis This Gram-

progress to death within a few hours, but most patients respond well to treatment and recover without permanent nervous system damage.

Symptoms The first symptoms of bacterial meningitis are similar regardless of the causative agent. They usually begin with a mild cold; fol-

stained smear shows large numbers of the Gram-positive diplococci; the large red objects are polymorphonuclear leukocytes that have entered the spinal fluid in response to the infection.

lowed by the sudden onset of a severe, throbbing headache; fever; pain and stiffness of the neck and back; nausea; and vomiting. Deafness and alterations in consciousness progressing to coma

CASE PRESENTATION The patient was a 31-month-old girl admitted to the hospital because of fever, headache, drowsiness, and vomiting. She had been previously well until 12 hours before admission, when she developed a runny nose, malaise, and loss of appetite. Her birth and development were normal. There was no history of head trauma. Her routine immunizations had been neglected. On examination, her temperature was 40°C (104°F), her neck was stiff, and she did not respond to verbal commands. Her white blood cell count was elevated and showed a marked increase in the percentage of polymorphonuclear neutrophils (PMNs). Her blood sugar was in the normal range. A spinal tap was performed, yielding cloudy cerebrospinal fluid under increased pressure. The fluid contained 18,000 white blood cells per microliter (normally, there are few or none), a markedly elevated protein, and a markedly low glucose. Gram stain of the fluid showed many tiny, Gram-negative coccobacilli, most of which were outside the white blood cells. 1. What is the diagnosis and what is the causative agent? 2. What is the prognosis in this case? 3. What age group is most susceptible to this illness?

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4. Compare the pathogenesis of this disease in children and adults. Discussion 1. The patient had bacterial meningitis caused by Haemophilus influenzae, serotype b. The fact that she had been healthy prior to her illness makes it highly unlikely that other serotypes could be responsible. 2. With treatment, the fatality rate is approximately 5%. Formerly, ampicillin was effective in most cases, but beginning in 1974, an increasing number of strains possessed a plasmid coding for b-lactamase. So far, however, these strains have been susceptible to the newer cephalosporin-type antibiotics. Unfortunately, about one-third of those who are treated and recover from the infection are left with permanent damage to the nervous system, such as deafness or paralysis of facial nerves. Prompt diagnosis and correct choice of antibacterial treatment minimize the chance of permanent damage. 3. The peak incidence of this disease is in the age range of 6 to 18 months, corresponding to the time when protective levels of transplacental antibody are lacking and adaptive active immunity has not yet developed. Since 1987, vaccines

consisting of type b capsular antigen conjugated with a protein, such as the outer membrane protein of Neisseria meningitidis or diphtheria toxin, have been used to immunize infants and thus eliminate the immunity gap. As a result, meningitis caused by H. influenzae type b is now rare. It is important to know, however, that strains other than type b can sometimes cause meningitis. So far, such strains are uncommon, although they represent an increasing percentage as type b strains decline in importance. 4. Haemophilus influenzae type b strains are referred to as “invasive” strains because they establish infection of the upper respiratory tract, pass the epithelium, and enter the lymphatic vessels and bloodstream. In this way, they gain access to the general circulation and are carried to the central nervous system. Most strains of H. influenzae, unlike type b, are non-invasive. Although they can cause infections of respiratory epithelium, they usually do not enter the circulation. Most adults are immune to type b strains, but some adults develop meningitis from noninvasive H. influenzae strains that gain access to the nervous system because of a skull fracture or by direct extension to the meninges from an infected sinus or middle ear.

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CHAPTER TWENTY SEVEN

Nervous System Infections Polymorphonuclear neutrophils (PMNs)

FIGURE 27.5 Petechiae of Meningococcal Disease Neisseria meningitidis is present in these skin lesions. Meningococci

may develop. Especially likely in meningococcal meningitis, purplish spots called petechiae, resulting from small hemorrhages, may appear on the skin (figure 27.5). The infected person can develop endotoxic shock and die within 24 hours. Usually, though, progression of the illness is slower, allowing time for effective treatment. ■ endotoxic shock, p. 407

Causative Agent The causative organism of meningococcal meningitis is the Gramnegative diplococcus, Neisseria meningitidis. Although there are 13 antigenic groups of N. meningitidis, most serious infections are due to A, B, C, Y, and W135. The process of identifying the different strains, called serogrouping, employs serum containing specific antibody, obtained from the blood of laboratory animals that have been immunized with known strains of meningococci.

Pathogenesis Individuals acquire the infection by inhaling airborne droplets from the respiratory tract of another person. The meningococci attach to the mucous membrane by pili and multiply. They are then taken in by the respiratory tract epithelial cells, pass through them, and invade the bloodstream. The blood carries the organisms to the meninges and cerebrospinal fluid. There they multiply faster than they can be engulfed and destroyed by the polymorphonuclear neutrophils (PMNs) that enter the fluid in large numbers in response to the infection (figure 27.6). The bacteria and leukocytes degrade glucose and thereby cause a marked drop in the glucose concentration normally present in the cerebrospinal fluid. The inflammatory response, with its formation of pus and clots, may cause brain swelling and infarcts—death of tissue resulting from loss of blood supply. It can also lead to obstruction of the normal outflow of cerebrospinal fluid, causing the brain to be squeezed against the skull by the buildup of internal pressure. The infection can damage the nerves of hearing or vision or the motor nerves, producing paralysis. Moreover, N. meningitidis circulating in the bloodstream releases endotoxin, causing a drop in blood pressure that can lead to shock. Shock is a state in which there is not enough blood pressure to circulate the blood adequately to meet the oxygen requirements of vital body tissues such as the

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20 mm

FIGURE 27.6 Meningococcal Meningitis Stained smear of spinal fluid showing polymorphonuclear neutrophils and meningococci. This case is somewhat unusual because so many of the meningococci can be seen outside the leukocytes.

kidneys and central nervous system. The smaller blood vessels of the skin are also damaged by the circulating meningococci, causing the petechiae. ■ pili, pp. 66, 398 ■ endotoxin, pp. 61, 407 The organism’s endotoxin also increases the body’s sensitivity to repeated endotoxin exposure. This strikingly increased sensitivity is probably responsible for the rapidly fatal outcome in some cases of meningococcal meningitis. The tendency of meningococci to autolyse—to rupture spontaneously—may enhance their release of endotoxin.

Epidemiology The reasons are unknown why N. meningitidis, unlike Haemophilus influenzae and Streptococcus pneumoniae, is prone to cause epidemics of meningitis. Meningococcal meningitis can spread rapidly in crowded and stressed populations such as military recruits (figure 27.7), and outbreaks also occur in college dormitories. More typically, however, it appears at widely separate locations and occurs throughout the year. Humans are the only source of the infection, and transmission can occur with exposure to a person with the disease or an asymptomatic carrier of N. meningitidis. The majority of meningococcal infections are limited to the nose and throat and pass unnoticed. If a selective medium is used to suppress the growth of other nasopharyngeal microbiota, meningococci can be recovered from the throats of 5% to 15% of apparently healthy people.

Prevention and Treatment A vaccine composed of purified A, C, Y, and W135 capsular polysaccharides has been available for many years to control epidemics caused by these groups and to immunize people at high risk for the disease. A conjugate vaccine for the same four serogroups was approved in 2005 for ages 11 to 55 years. It is now recommended for routine administration to all preadolescents and those entering high school, and to college freshmen who will live in dormatories.

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27.2 Bacterial Nervous System Infections

gococcal strains from patients with active disease might be more virulent than other strains, people intimately exposed to cases of meningococcal disease are routinely given prophylactic treatment with the antibiotic rifampin. Meningococcal meningitis can usually be cured with penicillin or ceftriaxone unless severe brain injury or shock is present. The mortality rate is less than 10% in treated cases. Table 27.1 gives the main features of this disease.

15

Cases per 100,000 population

653

10

Listeriosis Meningitis is a common manifestation of listeriosis, a foodborne disease caused by Listeria monocytogenes. Although this organism generally causes only a small percentage of meningitis cases in the United States, epidemics sometimes occur.

5

■ foodborne illness, p. 762

0 1935 1940 1945 1950 1955 1960 1965 1970 1975 1980 1985 1990 1995 2000 Year

FIGURE 27.7 Meningococcal Disease in the United States, 1935 to 1998 Notice the high incidence during World War II, when epidemics occurred among military recruits crowded in barracks. Outbreaks also occur in college dormitories.

Group B strains possess a poorly immunogenic polysaccharide and, as yet, no vaccine is available for their control. Mass prophylaxis with an appropriate antibacterial medication, however, can be useful in controlling epidemics in small, confined groups such as people in jails, nursing homes, and schools. Because menin-

Symptoms The vast majority of healthy people have asymptomatic infections or trivial symptoms. Symptomatic infections are usually characterized by fever and muscle aches, and sometimes nausea or diarrhea. About three-quarters of the cases coming to medical attention have meningitis, heralded by fever, headache, stiff neck, and vomiting, that may or may not be preceded by other symptoms. Pregnant women who become infected often miscarry, or deliver terminally ill premature or full-term infants.

Causative Agent Listeria monocytogenes is a motile, non-spore-forming, facultatively anaerobic, Gram-positive rod that can grow at 4°C.

TABLE 27.1 Meningococcal Meningitis ➀ Neisseria meningitidis inhaled,

4

infects upper airways.

➁ Bacteria enter the bloodstream and are circulated throughout the body.

➂ The bacteria lodge in the skin and

Symptoms

Mild cold followed by headache, fever, pain, stiff neck and back, vomiting, petechiae

Incubation period

1 to 7 days

Causative agent

Neisseria meningitidis, the meningococcus; a Gram-negative diplococcus

Pathogenesis

Meningococci adhere by pili, colonize upper respiratory tract, enter bloodstream; carried to meninges and spinal fluid; inflammatory response obstructs normal outflow of fluid; increased pressure caused by obstructed flow impairs brain function; damage to motor nerves produces paralysis; endotoxin release causes shock.

Epidemiology

Close contact with a case or carrier; inhalation of infectious droplets; crowding and fatigue predispose to the disease.

Prevention and treatment

Conjugate vaccine against serogroups A, C, W135, and Y used to immunize ages 11–55 years; rifampin given to those exposed. Penicillin, ceftriaxone, for treatment.

6

1 7

cause petechiae.

➃ Bacteria on the meninges causes meningitis.

➄ Lysing bacteria in the circulation release endotoxin, producing shock.

2

5

➅ Inflammatory response in meninges

can damage nerves of hearing causing deafness and obstruct the flow of cerebrospinal fluid causing increased pressure inside the brain.

➆ Bacteria exit with respiratory secretions.

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3

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Pathogenesis

Prevention and Treatment

The mode of entry in isolated cases is usually obscure, but it is generally via the gastrointestinal tract during epidemics. Gastrointestinal symptoms may or may not occur, but the bacteria promptly penetrate the intestinal mucosa and enter the bloodstream. The resulting bacteremia is usually associated with fever and muscle aches, and it is the source of meningeal infection. In pregnant women, L. monocytogenes crosses the placenta and produces widespread abscesses in tissues of the fetus. Babies infected at the time of childbirth usually develop meningitis after an incubation period of 1 to 4 weeks.

Preventive measures reflect the epidemiology of listeriosis. Poultry, pork, beef, and other meats should be thoroughly cooked. Contamination of countertops and kitchenwares with uncooked meats and produce should be avoided. Raw vegetables need to be thoroughly washed before eating them. Those who are pregnant or have underlying diseases are advised to avoid Mexican-style soft cheeses, and to reheat cold cuts, hot dogs, and refrigerated leftovers before eating. In 2006, the U.S. Food and Drug Administration approved a food additive consisting of a number of different of bacteriophage strains that lyse food-contaminating strains of L. monocytogenes. The additive can be sprayed on a variety of meats normally eaten without being cooked, and its presence is recorded on the food label. Hopefully, use of this bacteriophage additive will substantially increase the safety of these foods. ■ bacterio-

Epidemiology Listeria monocytogenes is widespread in natural waters and vegetation, and it can be carried in the intestines of asymptomatic animals and humans. It occurs on all continents except Antarctica. Pregnant women, the elderly, and those with underlying illnesses such as immunodeficiency, diabetes, cancer, and liver disease are especially susceptible to listeriosis. Epidemic disease has resulted from L. monocytogenes contamination of foods including coleslaw, non-pasteurized milk, pork tongue in jelly, some soft cheeses, and hot dogs. The fact that the organisms can grow in commercially prepared food at refrigerator temperatures has resulted in thousands of infections originating from a single food-processing plant.

phages, p. 303

So far, most strains of L. monocytogenes have remained susceptible to antibacterial medications such as penicillin. Even though the disease is often mild in pregnant women, prompt diagnosis and treatment are important to protect the fetus. Some of the main features of listeriosis are presented in table 27.2. The main causes of acute bacterial meningitis are compared in table 27.3.

TABLE 27.2 Listeriosis ➀ Causative organism Listeria

monocytogenes is ingested with food such as Mexican cheese, soft cheeses, non-pasteurized milk, hot dogs, or coleslaw.

4

1

➁ The bacteria rapidly penetrate the intestinal epithelium and establish bacteremia, especially in pregnant women, the elderly, and the immunodeficient.

2

➂ In pregnant women, circulating

L. monocytogenes crosses the placenta and fatally infects the fetus or bacteria transmitted to the baby at birth cause meningitis in one to four weeks. The mother usually does not have a serious illness.

2

Symptoms

Fever and muscle aches, with or without gastrointestinal symptoms; headache and stiff neck mark the onset of meningitis

Incubation period

A few days to 2 to 3 months; in newborn babies, 1 to 4 weeks

Causative agent

Listeria monocytogenes, a nonspore-forming Gram-positive rod able to grow at 4°C

Pathogenesis

Ingested L. monocytogenes penetrate the intestinal epithelium and enter the bloodstream; the resulting bacteremia seeds the meninges, causing meningitis.

Epidemiology

Epidemics from contaminated soft cheeses, non-pasteurized milk, coleslaw, hot dogs. Pregnant women get bacteremia, fetal infection, miscarriage. Infants contract infection at birth, develop meningitis in the first month of life. Elderly and those with immunodeficiency, cancer, and diabetes also at high risk.

Prevention and treatment

Care in handling, cooking of raw meats; thorough washing of vegetables; reheating of cold cuts, hot dogs, and refrigerated leftovers. Antibacterial medications such as penicillin, given promptly, are effective treatment.

3

➃ In older people and those with underlying diseases L. monocytogenes attacks brain and meninges, causes meningitis, brain abscesses.

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655

TABLE 27.3 Main Causes of Acute Bacterial Meningitis Compared Agent

Characteristics

Source

Vaccine ?

Usual Victims

H. influenzae

Tiny, Gram-negative coccobacilli

Human respiratory system

Yes, type b

Young children

N. meningitidis

Gram-negative diplococci

Human respiratory system

Yes, four types

Mostly ages 2–20 years; can cause epidemics

S. pneumoniae

Encapsulated, Grampositive diplococci

Human respiratory system

Yes, multiple types

Mostly late teens and adults

S. agalactiae

Gram-positive cocci in chains

Bowel, vagina

No

Mostly neonates; others with underlying diseases

E. coli

Gram-negative rods; usually Bowel a specific encapsulated type

No

Mostly neonates

L. monocytogenes

Gram-positive motile rods; multiply at refrigerator temperatures

No

Pregnant women, neonates; elderly

Environment; contaminated cheeses, coldcuts, other foods

Hansen’s Disease (Leprosy) Although Hansen’s disease, also known as leprosy, is now a relatively minor problem in the Western world, it was once common in Europe and America. Like tuberculosis, the disease began to recede for unknown reasons even before an effective treatment was discovered. Today, it is chiefly a problem in tropical and economically underdeveloped countries, with an estimated worldwide occurrence of about 600,000 active cases. Most cases are concentrated in India, Nepal, Myanmar, Madagascar, Mozambique, and Brazil. In recent years, reported new cases in the United States have averaged about 150 per year; most were acquired outside the country.

to be susceptible. Mycobacterium leprae grows very slowly, with a generation time of about 12 days. A clone bank of the genome of M. leprae has been made in E. coli, thus making large quantities of the organism’s antigens available for study. ■ acid-fast stain, p. 50 ■ Mycobacterium, p. 261 ■ cloning, p. 215

Pathogenesis The earliest detectable finding in human infection with M. leprae is generally the invasion of the small nerves of the skin demonstrated by biopsy of skin lesions. Indeed, M. leprae is the only known human pathogen that preferentially attacks the peripheral nerves. The bacterium also initially grows very well within macrophages, before cellular immunity develops. The

Symptoms Hansen’s disease begins gradually, usually with the onset of increased or decreased sensation in certain areas of skin. These areas typically have either increased or decreased pigmentation. Later, they enlarge and thicken, losing their hair, sweating ability, and all sensation. The nerves of the arms and legs become visibly enlarged with accompanying pain, later changing to numbness, muscle wasting, ulceration, and loss of fingers or toes (figure 27.8). In some patients the skin lesions are not sharply defined, but slowly enlarge and spread. Changes are most obvious in the face, with thickening of the nose and ears and deep wrinkling of the facial skin. Collapse of the supporting structure of the nose occurs with accompanying congestion and bleeding.

Causative Agent Mycobacterium leprae (figure 27.9) is identical in appearance to M. tuberculosis. It is aerobic, acid-fast, rod-shaped, and typically stains in a beaded manner. Despite many attempts, M. leprae has not been grown in the absence of living cells. In the 1960s, it was successfully cultivated to a limited degree in the footpads of laboratory mice, and in 1971, in a major advance, Dr. Eleanor E. Storrs and colleagues demonstrated that the organisms can be grown in armadillos. Later, mangabey monkeys were also found

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FIGURE 27.8 A Person with Leprosy Notice the absence of her fingers and sunken nose as a result of the disease.

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The very long generation time of this bacterium most likely accounts for the lengthy incubation period of Hansen’s disease, usually about 3 years (range, 3 months to 20 years). ■ generation time, p. 84

Epidemiology

M. leprae

10 mm

FIGURE 27.9 Mycobacterium leprae in a Biopsy Specimen The red areas are dense masses composed of millions of the bacteria, a typical finding in lepromatous leprosy.

course of the infection depends on the immune response of the host. In most cases, cellular immunity develops against the invading bacteria. Activated macrophages limit the growth of M. leprae, and therefore the bacteria do not become numerous. The attack of immune cells against chronically infected nerve cells can progressively damage the nerves, however, which leads to disabling deformity, resorption of bone, and skin ulceration. The disease often spontaneously stops progressing, and thereafter the nerve damage, although permanent, does not worsen. This limited type of Hansen’s disease in which cellular immunity suppresses proliferation of the bacilli is called tuberculoid leprosy. People with tuberculoid leprosy rarely, if ever, transmit the disease to others. In many cases of tuberculoid leprosy, however, the immune system is gradually overwhelmed by the growth of M. leprae, leading in multiple stages to the more serious lepromatous form of the disease discussed in detail next. These stages are distinguished largely by the quantity of the bacteria in the patient’s tissues. Early treatment is important to prevent the disease from progressing. ■ macrophage, pp. 350, 358 ■ cellular immunity, p. 367

When cellular immunity to M. leprae fails to develop or is suppressed, unrestricted growth of M. leprae first occurs in the cooler tissues of the body, notably in skin macrophages and peripheral nerves, and later throughout the body. This relatively uncommon form of Hansen’s disease is called lepromatous leprosy. The tissues and mucous membranes contain billions of M. leprae, but there is almost no inflammatory response to them. The mucus of the nose and throat is loaded with the bacteria, which can readily be transmitted to others. Lymphocytes are present in the lesions but there is little or no evidence of macrophage activation. In lepromatous leprosy, cell-mediated immunity to M. leprae is absent, although immunity and delayed hypersensitivity to other infectious agents are usually normal. Normal immune function against M. leprae tends to return when the disease is controlled by medication.

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Transmission of M. leprae is by direct human-to-human contact. The source of the organisms is mainly nasal secretions of a lepromatous case, which transport M. leprae to mucous membranes or skin abrasions of another individual. Although leprosy bacilli readily infect people exposed to a case of lepromatous leprosy, the disease develops in only a tiny minority, being controlled by body defenses in the rest. Hansen’s disease is no longer a much-feared contagious disease, and the morbid days when lepers were forced to carry a bell or horn to warn others of their presence are fortunately past. Natural infections with M. leprae occur in wild nine-banded armadillos and in mangabey monkeys. An epidemiological study appears to exclude armadillos as an important source of human leprosy, but occasional transmissions to humans have not been ruled out.

Prevention and Treatment No proven vaccine to control leprosy is yet available. Tuberculoid leprosy can be arrested by treatment with the antimicrobials dapsone and rifampin administered in combination for 6 months. Lepromatous leprosy is generally treated for a minimum of 2 years, with a third drug, clofazimine, included in the treatment regimen. As in tuberculosis, multiple drug therapy is required to minimize the development of strains resistant to the antimicrobials. Some features of Hansen’s disease are summarized in table 27.4.

TABLE 27.4 Hansen’s Disease (Leprosy) Symptoms

Skin lesions that lack sensation, deformed face, loss of fingers or toes

Incubation period

3 months to 20 years; usually 3 years

Causative agent

Mycobacterium leprae, an acid-fast, nonculturable rod

Pathogenesis

Invasion of small nerves of skin; multiplication in macrophages; course of disease depends on immune response of host; activated macrophages limit growth of bacterium; attack of immune cells against infected nerve cells produces nerve damage, leading to deformity; in lepromatous leprosy, lymphocytes fail to react to the bacteria, allowing unrestrained growth of M. leprae.

Epidemiology

Direct contact with M. leprae from mucous membrane secretions.

Prevention and treatment

No vaccine. Treatment: dapsone plus rifampin for months or years; clofazimine added for lepromatous disease.

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27.2 Bacterial Nervous System Infections

Botulism Botulism, classically a severe form of food poisoning, is not a nervous system infection. It is considered here because its principal symptom is paralysis, but it is also discussed in chapter 32, which covers foodborne illness. It is one of the most feared of all diseases because it strikes without warning and is often fatal. The name “botulism” comes from botulus, meaning “sausage,” chosen because some of the earliest recognized cases occurred in people who had eaten contaminated sausage. The majority of cases worldwide are foodborne botulism, which individuals contract by eating food in which the organism has grown and released a poisonous substance. A small percentage of cases occur when the organisms colonize the intestine or a wound, however, causing intestinal botulism and wound botulism, respectively. Botulism does not involve the central nervous system. ■ foodborne botulism, p. 763

Symptoms Symptoms usually begin 12 to 36 hours after ingestion of improperly canned, non-acidic food. Most cases begin with dizziness, dry mouth, and blurred or double vision, indicating eye muscle weakness. Abdominal symptoms, including pain, nausea, vomiting, and diarrhea or constipation, are present in 30% to more than 90% of cases, depending on the strain of the causative organism. Progressive paralysis then ensues, generally involving all voluntary muscles, but respiratory paralysis is the most common cause of death. Paralysis distinguishes botulism from most other forms of food poisoning

Causative Agent Botulism is caused by the strictly anaerobic, Gram-positive, spore-forming, rod-shaped bacterium Clostridium botulinum. Its endospores (figure 27.10), generally resist boiling for hours, but they are killed by autoclaving. Different strains of C. botulinum vary markedly in their biochemical activity, but all produce an exotoxin called botulinum toxin, which causes paralysis. Eight antigenically distinct types of botulinum toxin are synthesized by different strains of C. botulinum. Types A, B, and E are responsible for most human cases, whereas other types such as C and

FIGURE 27.10 Clostridium botulinum Notice the spores. These spores are not reliably killed by the temperature of boiling water.

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657

D affect only birds and other animals. In strains C and D, toxin production results from lysogenic conversion. Botulinum toxin is released in an inactive form upon lysis of the bacterial cells, and it is then activated by proteolytic enzymes. ■ exotoxin, p. 403 ■ lysogenic conversion, p. 310

Pathogenesis Like other clostridia, C. botulinum produces endospores that are generally highly resistant to heat. These endospores can persist in foods such as vegetables, fruit, meat, seafood, and cheese despite cooking and some home-canning processes. The spores germinate if the environment is favorable—such as having a suitable nutrient, anaerobic conditions, a pH above 4.5, and a temperature above 39°F (4°C). Growth of the bacteria results in the release of botulinum toxin into the food. When a person eats the food, the toxin resists digestion by stomach enzymes and acid, is absorbed by the small intestine, and can circulate in the bloodstream for 3 weeks or more. Botulinum toxin is a neurotoxin—it acts against the nervous system and is one of the most powerful poisons known. A few milligrams of the toxin would be sufficient to kill the entire population of a large city. Indeed, cases of botulism have resulted from a person eating a single, contaminated string bean, and from licking a finger in unknowingly tasting a food contaminated with botulinum toxin. Circulating botulinum toxin attaches to motor nerves, blocking transmission of nerve signals to the muscles, and thereby producing paralysis. Normally, nerve signals are transmitted by a type of chemical known as a neurotransmitter, present in the nerve in tiny vesicles. The neurotoxin probably acts by preventing the vesicles from attaching to the cytoplasmic membrane of the nerve cell, thereby preventing discharge of the neurotransmitter by exocytosis. Like a number of other bacterial exotoxins, botulinum toxin is composed of two portions—A and B. The B portion attaches to specific receptors on motor nerve endings, and the A portion enters the nerve cell. The A portion then becomes an active peptidase enzyme that degrades the protein on the vesicle surface responsible for attachment to the cytoplasmic membrane. ■ A-B toxins, p. 405 Intestinal botulism occurs occasionally when C. botulinum colonizes the intestine, especially in infants 6 months of age or less, and produces a mild form of the disease characterized by constipation followed by generalized paralysis that can range from mild lethargy to respiratory insufficiency. In infants, C. botulinum and its toxin are often demonstrable in their feces, but the toxin levels are too low to be detectable in their blood. Most recover without receiving antitoxin treatment, although respiratory support and tube feeding may be needed until the organisms are replaced by normal intestinal microbiota. These infections arise from ingestion of C. botulinum spores, which are commonly present in dust and contaminate foods such as honey. Indeed, ingestion of honey has been implicated in 10% to 30% of infant botulism cases. Intestinal botulism also occurs in adults, particularly in immunodeficient patients whose normal intestinal microbiota has been suppressed by antibiotic treatment. Clostridium botulinum can also colonize dirty wounds, especially those containing dead tissue. The bacteria do not invade, but they can multiply in dead tissue. Botulinum toxin then diffuses into the bloodstream. Many cases have been due to wounds caused by abuse of injected drugs.

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Botulinum toxin can be used to treat people with certain chronic, spastic conditions. Minute amounts of the toxin injected into the area of spasm give prolonged relief of symptoms. In the United States, only one company is licensed to market botulinum toxin for human use (Botox); severe paralysis has resulted when other sources were used for cosmetic treatments. ■ Botox, p. 764

Epidemiology Clostridium botulinum is widely distributed in soils and aquatic sediments around the world. Foodborne botulism, formerly the most common and most severe of the three types of botulism, was first recognized in the late eighteenth century. In the early part of the twentieth century, outbreaks of foodborne botulism were common in the United States, often traceable to commercially canned foods. Strict controls were then placed on commercial canners to ensure adequate sterilizing methods. Since then, outbreaks caused by commercially canned foods have been infrequent. Today, in the United States, intestinal botulism is much more common than foodborne botulism.

TABLE 27.5 Botulism Symptoms

Blurred or double vision, weakness, nausea, vomiting, diarrhea; generalized paralysis and respiratory insufficiency

Incubation period

Usually 12 to 36 hours

Causative agent

Clostridium botulinum, an anaerobic, Grampositive, spore-forming, rod-shaped bacterium

Pathogenesis

Clostridium botulinum endospores germinate in food and release neurotoxin. Toxin is ingested, survives stomach acid and enzymes, is absorbed by the small intestine, and is carried by the bloodstream to motor nerves; toxin acts by blocking the transmission of nerve signals to the muscles, producing paralysis; C. botulinum can also colonize intestine or wounds, and cause generalized weakness or paralysis.

Epidemiology

Ingestion of contaminated, often home-canned, non-acid food that was not heated enough to kill C. botulinum spores. Spores widespread in soil, aquatic sediments, and dust. Can result in colonization of the intestine of adults and infants with deficiencies in normal microbiota, and wounds containing dirt and dead tissue, including those caused by injected-drug abuse.

Prevention and treatment

Education in proper home-canning methods; heating food to boiling for 15 minutes just prior to serving. Treatment: enemas and stomach washing to remove toxin, cleaning infected wounds of dirt and dead tissue, intravenous administration of antitoxin, and artificial respiration.

Prevention and Treatment Prevention of botulism depends on proper sterilization and sealing of food at the time of canning. Fortunately, the toxin is heatlabile, and it is recommended that home-canned, low-acid foods be heated to 100°C for 15 minutes just prior to serving to ensure that they are safe to eat. One cannot rely on a spoiled smell, taste, or appearance to detect contamination because such changes are not always present. The disease is treated by the intravenous administration of antitoxin as soon as possible after the diagnosis is made. The antitoxin, however, only neutralizes toxin circulating in the bloodstream, and the nerves already affected by it recover slowly, over weeks or months. Enemas, gastric washing, and surgical removal of dirt and dead tissue from infected wounds help to remove any unabsorbed toxin. Artificial respiration with a mechanical ventilator may be required for prolonged periods. The main features of botulism are presented in table 27.5.

MICROCHECK 27.2 Bacterial meningitis is uncommon. Most cases occur in children under 5 years of age. Organisms from the mother’s birth canal are responsible in infants less than 1 month old. Bacteria commonly carried in the upper respiratory tract cause most other cases. Meningococcal meningitis sometimes occurs in epidemics and occasionally causes death within 24 hours. Meningitis is a common complication of listeriosis, caused by a Gram-positive rod that can multiply at refrigerator temperatures and is usually foodborne. Hansen’s disease (leprosy) is caused by an acid-fast, unculturable bacterium; the disease exists in two forms, depending on the immune status of the victim. Botulism is a toxin-mediated disease characterized by generalized paralysis. It is not a nervous system infection. ✓ Why are most newborn babies unlikely to contract meningococcal, pneumococcal, or Haemophilus meningitis? ✓ Describe the only bacterial pathogen that preferentially invades peripheral nerves. ✓ Why is such a high percentage of infant botulism cases associated with honey?

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27.3 Viral Diseases of the Nervous System Focus Points Name the main causative agents for viral meningitis. Describe the difference between sporadic and epidemic viral encephalitis. Explain why the biggest impact of poliomyelitis in the 1950s occurred in countries with good sanitation. Outline the steps in the pathogenesis of rabies.

Many different kinds of viruses can infect the central nervous system, including the Epstein-Barr virus of infectious mononucleosis; the mumps, rubeola, varicella-zoster, and herpes simplex viruses; and, more commonly, human enteroviruses and the viruses of certain zoonoses. In most cases, nervous system involvement occurs in only a very small percentage of people infected with the viruses. The next section discusses four kinds of illness resulting from viral central nervous system infections: meningitis, encephalitis, poliomyelitis, and rabies.

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27.3 Viral Diseases of the Nervous System

Viral Meningitis Viral meningitis is much more common than bacterial meningitis. It is usually a mild disease that does not require specific treatment, and patients generally recover in 7 to 10 days. Viruses are responsible for most cases of “aseptic meningitis,” meaning those with symptoms and signs of meningitis but with negative tests for bacterial pathogens.

TABLE 27.6

Abrupt onset, fever, severe headache, stiff neck, often vomiting; sometimes sore throat, large parotid glands, rash, or chest pain

Incubation period

Usually 1 to 2 weeks for enteroviruses, 2 to 4 weeks for mumps

Causative agents Most cases: small non-enveloped RNA enteroviruses of the picornavirus family, usually coxsackie or echoviruses. Mumps virus common in unimmunized populations

Pathogenesis

Viremia from primary infection seeds the meninges. Fewer leukocytes enter cerebrospinal fluid than with bacterial infections, and many are mononuclear, usually no decrease in CSF glucose.

Epidemiology

Enteroviruses transmitted by the fecal-oral route, mumps by respiratory secretions and saliva. Enteroviruses transmission mainly summer and early fall; mumps in fall and winter.

Prevention and treatment

Handwashing, avoiding crowded swimming pools during enterovirus epidemics; mumps vaccine for mumps prevention. No specific treatment.

Causative Agents Small, non-enveloped RNA viruses—members of the enterovirus subgroup of picornaviruses—are responsible for at least half of the cases of viral meningitis. Of these, the most common offenders are coxsackie viruses, which can cause throat or chest pain, and echoviruses, which can cause a rash. The mumps virus, formerly common, is now an infrequent cause because of widespread immunization against the disease. ■ picornaviruses, p. 324 ■ mumps, p. 593

Viral Meningitis

Symptoms

Symptoms The onset of viral meningitis is typically abrupt, with fever and severe headache above or behind the eyes, sensitivity of the eyes to light, and a stiff neck with increased pain on bending the head forward. Nausea and vomiting are common. In addition, depending on the causative agent, there may be a sore throat, chest pain with inspiration, swollen parotid glands, or a skin rash. ■ parotid glands, p. 582

659

Pathogenesis

Viral Encephalitis

Enteroviruses characteristically infect the throat and intestinal epithelium and lymphoid tissue, and then seed the bloodstream. The viremia—viruses circulating in the bloodstream—results in meningeal infection and sometimes rashes or chest infection. The inflammatory response in the meninges differs from bacterial meningitis in that fewer cells usually enter the cerebrospinal fluid, and a high percentage of them are mononuclear rather than polymorphonuclear neutrophils (PMNs). Typically, the cerebrospinal fluid glucose remains normal.

Whereas viral meningitis is usually a benign illness, viral encephalitis is much more likely to cause death or permanent disability. Viral encephalitis can be sporadic—there are generally a few widely scattered cases occurring all the time; or it can be epidemic—a number of cases appear in a limited period of time in a given geographical area. Sporadic encephalitis is usually due to herpes simplex virus, but other viruses, including those that cause mumps, measles, and infectious mononucleosis, can occasionally cause encephalitis. Two mechanisms have been proposed to explain herpes simplex encephalitis. Most occurrences are thought to be due to activation of latent virus—the result of primary infection in the past. In about one-fourth of the cases, however, the encephalitis strain differs from latent virus in the person’s ganglia, suggesting that the infection causing the encephalitis is newly acquired; the virus probably entering the CNS via the nerves of smell. Most people recover from the disease but are left with permanent impairment, such as epilepsy, paralysis, deafness, or difficulty thinking. The yearly incidence of herpes simplex encephalitis is estimated to be two to three cases per million people. The disease occurs throughout the year, mostly affecting those under age 30 and the elderly. Cases in newborn infants are usually acquired from the mother’s birth canal and are due to herpes simplex type 2, but more than 95% of cases in children and adults are caused by herpes simplex type 1. No proven preventive measures for herpes simplex encephalitis exist except for the newborn, for whom cesarian section can be performed to prevent exposure of the baby to a type 2 herpes simplex infection. Medication given promptly can shorten the illness and improve the outcome. ■ herpes simplex virus, pp. 592, 638

Epidemiology Enteroviruses are relatively stable in the environment, and they can sometimes even survive in chlorinated swimming pools. Infected individuals, including those with asymptomatic infections, often eliminate the viruses in their feces for weeks. Enteroviral meningitis is transmitted by the fecal-oral route, and the peak incidence occurs in the late summer and early fall in temperate climates. Mumps virus is transmitted by the respiratory route, and mumps meningitis is generally most common in the fall and winter months.

Prevention and Treatment Handwashing and avoidance of crowded swimming pools are reasonable preventive measures when cases of aseptic meningitis are present in the community. There are no vaccines against coxsackie and echoviruses. Mumps virus disease can be prevented by immunization. No specific treatment is available. The main features of viral meningitis are presented in table 27.6.

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Epidemic viral encephalitis is a bigger problem because of the numbers of people that can be affected. Although its symptoms are quite similar to those of sporadic encephalitis, the causative agents, pathogenesis, epidemiology, prevention, and treatment are different.

Symptoms The onset is usually abrupt, with fever, headache, vomiting, and one or more nervous system abnormalities such as disorientation, localized paralysis, deafness, seizures, or coma.

Causative Agents Epidemic viral encephalitis is usually caused by arboviruses (arthropod-borne viruses), a diverse group of viruses transmitted by insects, mites, or ticks. The four leading causes of epidemic encephalitis in the United States are all arboviruses transmitted by mosquitoes. The West Nile virus, also mosquitoborne, was introduced into New York from the Middle East in the summer of 1999. Migrating birds soon spread the virus to 20 eastern states from Maine to Florida, and then across the country (figure 27.11). The arboviruses are enveloped, single-stranded RNA viruses that are classified in different families: LaCrosse encephalitis virus, bunyavirus family; St. Louis and West Nile encephalitis viruses, flavivirus family; and the Eastern and western equine encephalitis viruses, togavirus family. ■ mosquitoes, p. 296

Pathogenesis Knowledge of the pathogenesis of arboviral encephalitis is incomplete. The viruses multiply at the site of a mosquito bite and in local lymph nodes, producing viremia. Levels of viremia are very low and transitory, yet the ratio of overt encephalitis to mild or inapparent infection can be 1:25 or greater. It is not known how these viruses cross the blood-brain barrier so readily. The viruses replicate in nerve cells and cause extensive destruction of brain tissue in severe cases. The process is halted with the appear-

ance of neutralizing antibody. Mortality ranges from about 2% with LaCrosse, to 35% to 50% with eastern equine encephalitis. Disabilities occur in those who recover, ranging from 5% to more than 50% of cases, depending largely on the kind of virus and the age of the patient—the very young and the elderly suffer the most. The kinds of disability include emotional instability, mental retardation, epilepsy, blindness, deafness, and paralysis of one side of the body.

Epidemiology During epidemic viral encephalitis, only a minority of those infected develop encephalitis. Others develop viral meningitis, fever and headache only, or no symptoms at all. These diseases are all zoonoses maintained in nature in birds or rodents; humans are an accidental host. In the eastern half of the United States, LaCrosse encephalitis virus usually causes most of the reported encephalitis cases. In its natural cycle (figure 27.12), the LaCrosse virus infects Aedes mosquitoes, which pass it directly from one mosquito to another in semen. It can survive the winter in the mosquito’s eggs. These mosquitoes feed on and infect squirrels and chipmunks, which markedly amplify the amount of virus and spread it to uninfected female mosquitoes feeding on the rodents’ blood. These mosquitoes are forest dwellers that normally breed in water-containing cavities in hardwood trees or in discarded tires. The natural cycle of other encephalitis-causing viruses involves wild birds rather than rodents, and involves different mosquitoes with various habitats and feeding habits. There is still much to be learned about the ecological factors responsible for the spread of these viruses to humans, but the proximity of humans to their natural cycles, rainfall, winter and summer temperatures, numbers and range of amplifying hosts, and predators could all be important.

Prevention and Treatment As equine encephalitis viruses spread from their natural hosts, they generally infect horses 1 or 2 weeks before the first human cases appear. Cases in horses provide a warning to increase protection against mosquitoes. Sentinel chickens serve the same function. They are stationed in cages with free access to mosquitoes, and their blood

FIGURE 27.11 Areas Reporting West Nile Virus Infection United States, 2007 (as of November 13, 2007)

PR

Human WNV illness Nonhuman WNV infection only

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27.3 Viral Diseases of the Nervous System Eggs Semen

Mosquito-tomosquito cycle

661

The main features of epidemic viral encephalitis are presented in table 27.7.

FIGURE 27.12 LaCrosse Encephalitis Virus, Natural Cycles The virus is maintained both by mosquito-to-mosquito transmission through semen and eggs, and by mosquito-to-squirrel (or chipmunk)-to-mosquito transmission. Infection of the rodent markedly increases the quantity of virus and the potential to infect many mosquitoes.

Infantile Paralysis, Polio (Poliomyelitis) The characteristic feature of poliomyelitis is selective destruction of motor nerve cells, usually of the spinal cord, resulting in permanent paralysis of one particular group of muscles, such as those of an arm or leg. The two individuals most responsible for control of this terrifying disease will not see its imminent elimination from the world—Albert Sabin died in 1992; Jonas Salk in 1995. The two men were bitter rivals, both of whom expected, but did not receive, the Nobel Prize.

Mosquito-to-squirrel-tomosquito amplifying cycle

Symptoms Poliomyelitis usually begins with the symptoms of meningitis: headache, fever, stiff neck, and nausea. In addition, pain and spasm of some muscles generally occur, later followed by paralysis. Over the ensuing weeks and months, muscles shrink and bones do not develop normally in the affected area (figure 27.13). In more severe cases, the muscles of respiration are paralyzed, and the victim requires an artificial respirator—a machine to pump air in and out of the lungs. Some recovery of function is the rule if the person survives the acute stage of the illness. The nerves of sensation, touch, pain, and temperature are not affected.

is tested periodically for evidence of arbovirus infection. A positive test would trigger an encephalitis alert, as for St. Louis encephalitis in Florida: “Avoid outdoor activity during evening and night, the peak hours of biting for the Culex mosquito vector. If outdoors, wear long sleeves and pants. Make sure windows and porches are properly screened. Use insect repellents and insecticides.” A vaccine against eastern equine encephalitis is approved for use in horses and has also been used to protect emus—a large, domesticated, meat-producing fowl that is highly susceptible to this virus. There is no proven antiviral therapy for arbovirus encephalitis.

Causative Agent Poliomyelitis is caused by three types of polioviruses, designated 1, 2, and 3, that are distinguished by using antisera. These small,

TABLE 27.7 Epidemic Viral Encephalitis ➀ Infected mosquito introduces encephalitis virus.

3

Symptoms

Abrupt onset, fever, headache, vomiting, disorientation, paralysis, seizures, deafness, coma

Incubation period

First symptoms within a few days; encephalitic symptoms often within the first week

Causative agent

Usually caused by one of four arboviruses, LaCrosse, St. Louis, western equine, or eastern equine

Pathogenesis

Replication of virus at the site of the mosquito bite, further replication in lymph nodes, then viremia that seeds brain tissue. Nerve cells in the brain invaded, destroyed. Process halted by neutralizing antibody.

Epidemiology

Viruses transmitted to humans from birds or rodents by mosquitoes.

Prevention and treatment

Chicken sentinels to warn of arbovirus epidemics. Insecticides and other anti-mosquito preventive measures. No accepted treatment for arboviral encephalitis.

4

➁ Virus multiplies locally, establishes brief low-level viremia.

➂ Virus crosses blood-brain barrier

and preferentially attacks the brain.

➃ Destruction of brain tissue causes

death or permanent disabilities such as emotional instability, mental retardation, paralysis of face, arm, leg.

2

➄ Due to brief viremia, there is no exit for the virus, thus humans are the final host.

1 4

2

4

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Even though poliomyelitis transmission no longer occurs in the United States, there are about 300,000 survivors of the disease, most of whom recovered years ago. Some of them develop muscle pain, increased weakness, and muscle degeneration 15 to 50 years after they had acute poliomyelitis. This condition, called the post-polio syndrome, sometimes involves muscles not obviously affected by the original illness. The late progression of muscle weakness is not due to recurrent multiplication of polio viruses. During recovery from acute poliomyelitis, surviving nerve cells branch out to take over the functions of the killed nerve cells. The late appearance of symptoms is probably due to the death of these nerve cells that have been doing double duty for so many years.

FIGURE 27.13 Atrophy of the Left Leg Due to Poliomyelitis

Epidemiology

non-enveloped, single-stranded RNA viruses are members of the enterovirus subgroup of the picornavirus family. They can be grown in vitro in cell cultures, where they cause cell destruction. With low concentrations of virus, the areas of cell destruction, termed plaques, are separated from one another and are readily seen with the unaided eye (figure 27.14). ■ plaques, p. 337

Pathogenesis Polioviruses enter the body orally, infect the throat and intestinal tract, and then invade the bloodstream. In most people, the immune system conquers the infection and recovery is complete. Only in a small percentage of people does the virus enter the nervous system and attack motor nerves. The viruses can infect a cell only if the surface of that cell possesses specific receptors to which the virus can attach. This specificity of receptor sites helps explain the fact that polioviruses selectively infect motor nerve cells of the brain and spinal cord, while sparing many other kinds of cells. The infected cell is destroyed when the mature virus is released.

Because only a small percentage of infected individuals develop nervous system involvement, even one case of poliomyelitis indicates that the virus is widespread in the community. Poliomyelitis has had its greatest impact in countries when the level of sanitation is improved. In areas where sanitation is poor, the polioviruses are widespread, transmitted by the fecaloral route. Very few people in areas with poor sanitation escape childhood without becoming infected and developing immunity to the disease. Therefore, most babies have received antibodies against polio from their mothers, the antibodies having crossed the placenta and entered the circulation of the fetus. Newborn infants in these nations thus are partially protected against nervous system invasion by poliomyelitis virus for as long as their mothers’ antibodies persist in the babies’ bodies—usually about 2 or 3 months. During this time, because of exposure to the poliovirus through crowding and unsanitary conditions, infants are likely to develop mild infections of the throat and intestine, thereby achieving lifelong immunity with little chance of paralysis. In contrast, in areas with efficient sanitation, the poliomyelitis virus sometimes cannot spread to enough susceptible people to sustain itself, and it disappears from the community. When it is reintroduced, people of all ages may lack antibody and be susceptible, and a high incidence of paralysis will result. This situation occurred in the United States in the 1950s, resulting in many cases of respiratory paralysis (figure 27.15) and death. With most people now routinely immunized against the disease, however, and the likelihood of imported disease rapidly waning, this scenario should no longer occur.

Prevention and Treatment

8 mm

FIGURE 27.14 Plaques Produced by Poliomyelitis Virus in a Cell Culture Monolayer Each plaque represents an area of the monolayer that has been destroyed by replicating poliovirus.

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Like other enteroviruses, polioviruses are quite stable under natural conditions, often surviving in swimming pools, but are inactivated by pasteurization and properly chlorinated drinking water. Control of poliomyelitis using vaccines represents one of the greatest success stories in the battle against infectious diseases (figure 27.16). Ironically, all cases of paralytic polio acquired in the United States since 1980 were caused by Sabin’s oral, attenuated polio vaccine, which was introduced in 1961. These cases arise because in rare instances the vaccine strain can mutate and become virulent. This small risk of developing paralytic poliomyelitis from the vaccine virus, approximately one case per 2.4 million doses given, led to discontinuing routine use of the live vaccine in the United States in mid-1999. However, despite its drawback, the Sabin oral vaccine remains key to controlling polio in areas of the world where

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TABLE 27.8 Poliomyelitis Symptoms

Headache, fever, stiff neck, nausea, pain, muscle spasm, followed by paralysis

Incubation period

7 to 14 days

Causative agents Polioviruses 1, 2, 3, members of the picornavirus family

Pathogenesis

Virus infects the throat and intestine, circulates via the bloodstream, and enters some motor nerve cells of the brain or spinal cord; infected nerve cells lyse upon release of mature virus.

Epidemiology

Spreads by the fecal-oral route; asymptomatic and nonparalytic cases common.

Prevention and treatment

Prevented by injecting Salk’s inactivated vaccine, or by Sabin’s orally administered attenuated vaccine in areas of epidemic or endemic disease. Treatment: artificial ventilation for respiratory paralysis; physical therapy and rehabilitation.

FIGURE 27.15 The Horror of Poliomyelitis These tanklike respirators (“iron lungs”) were used during the 1950s epidemics of poliomyelitis to keep alive people whose respiratory muscles were paralyzed by the disease. Now we can hope to see polio forever banished from the earth!

100

Inactivated virus (Salk) vaccine

Cases per 100,000 population

10

Cases reported

transmission of the wild virus still occurs. It produces better local immunity in the throat and intestine, can spread from person to person, does not require an injection, provides herd immunity, and is less expensive. In the 15 years following 1988, when the World Health Organization resolved to eradicate poliomyelitis, the number of countries with endemic disease was reduced from 125 to only six. ■ herd immunity, p. 456 ■ campaign to eliminate poliomyelitis, p. 436 Poliomyelitis is summarized in table 27.8.

20 15 10 5 0 1980

1983

1

0.1

1988 Year

1993

1998

Attenuated oral (Sabin) vaccine

0.01

Rabies In the United States, immunization of dogs and cats against rabies has practically eliminated them as a source of human disease. The rabies virus remains rampant among wildlife, however—a constant threat to non-immunized domestic animals and humans. Many questions remain about the pathogenesis of rabies, and no effective treatment exists for the disease.

Symptoms Rabies is one of the most feared of all diseases because its terrifying symptoms almost invariably end with death. Like many other viral diseases, it begins with fever, head and muscle aches, sore throat, fatigue, and nausea. The characteristic symptom that strongly suggests rabies is a tingling or twitching sensation at the site of viral entry, usually an animal bite. These early symptoms generally begin 1 to 2 months after viral entry and progress rapidly to symptoms of encephalitis, agitation, confusion, hallucinations, seizures, and increased sensitivity to light, sound, and touch. The body temperature then rises steeply, and increased salivation combined with difficulty swallowing result in frothing at the mouth. Hydrophobia—painful spasm of the throat and respiratory muscles provoked by swallowing or even upon seeing liquids—occurs in half the cases. Coma develops, and about 50% of patients die within 4 days of the first appearance of symptoms, the rest soon after.

Causative Agent 0.001 1951 1955

1960

1965

1970

1975

1980

1985

1990

Year

FIGURE 27.16 Incidence of Poliomyelitis in the United States, 1951 to 1998 Ironically, since 1980, all cases acquired in the United States have been caused by the oral attenuated (Sabin) vaccine. Endemic poliomyelitis was eliminated from the United States by 1980, and the entire Western Hemisphere by 1991.

nes95432_Ch27_647-673.indd 663

The cause of rabies is the rabies virus (figure 27.17a), a member of the rhabdovirus family. This virus has a striking bullet shape, is enveloped, and contains single-stranded, negative-sense RNA. It buds from the surface of infected cells.

Pathogenesis The principal mode of transmission of rabies to humans is via the saliva of a rabid animal (figure 27.17b) introduced into

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(a)

Nervous System Infections

75 nm

20 mm

FIGURE 27.18 Stained Smear of Brain Tissue from a Rabid Dog The arrows point to one of several Negri bodies within the triangularshaped nerve cell. The Negri bodies represent the sites of rabies virus replication.

(b)

FIGURE 27.17 Rabies Virus (a) Color-enhanced transmission electron micrograph of rabies virus. Notice the bullet shape. (b) Rabid raccoon caged in a Virginia animal shelter. Rabies virus is usually transmitted in the saliva of a biting animal.

bite wounds or abrasions of the skin. Individuals can also contract rabies by inhaling aerosols containing the virus, such as from bat feces. Only a few details of the events that follow introduction of the virus into the body are known. During the incubation period of the disease, the virus multiplies in muscle cells and probably other cells at the site of infection. Knoblike projections on the viral surface attach to receptors in the region where the nerve joins the muscle. At some point, the virus enters an axon and is carried along the nerve by the normal flow of the axon’s cytoplasm, eventually reaching the brain. The long incubation period, usually 1 to 2 months but sometimes exceeding a year, is partly determined by the length of the journey to the brain. Patients with head wounds into which the virus is introduced tend to have a shorter incubation period than those with extremity wounds. Severe wounds and those with a large amount of introduced rabies virus also generally result in short incubation periods. The virus then multiplies extensively in brain tissue, causing the symptoms of encephalitis. Characteristic inclusion bodies, called Negri bodies (figure 27.18), form at the sites of viral replication in the brain, but the cells are not lysed. The virus spreads outward from the brain via the nerves to various body tissues, notably the salivary glands, eyes, and fatty tissue under the skin, as well as to the heart and other vital organs. The presence of the virus in the eyes is of some practical significance, because victims can be

nes95432_Ch27_647-673.indd 664

diagnosed before their death by identifying rabies in stained smears made from the surface of their eyes. Moreover, several cases of rabies have occurred in individuals who received corneal transplants from donors who died of an atypical form of rabies that escaped diagnosis (the cornea is the clear middle part of the eye in front of the lens).

Epidemiology Rabies is widespread in wild animals; about 5,000 wild animal cases are generally reported each year in the United States. This represents an enormous reservoir from which infection can be transmitted to domestic animals and humans. In the United States, skunks, raccoons, and bats constitute the chief reservoir hosts. Raccoons lead the list of wildlife cases, but almost all human cases are due to contact with infected bats. The virus can remain latent in bats for long periods, and healthy-looking bats can have the virus in their salivary glands. Until the mid-twentieth century, most rabies cases in the United States resulted from dog bites, which is the primary mode of transmission in the non-industrialized world. Fortunately, since World War II, the incidence of dog rabies has dropped dramatically in the United States, and now more than 85% of reported rabies infections are in wild, as opposed to domestic, animals. The incidence of rabies in people has declined because dogs and cats have been immunized against rabies infection, in effect creating a partial barrier to the spread of the rabies virus from wild animal reservoirs to humans. Because pets vary in their tolerance to rabies vaccines depending on their age and species, several kinds of vaccines are available. About three-quarters of dogs that develop rabies excrete rabies virus in their saliva, and about one-third of these begin excreting it 1 to 3 days before they get sick. Therefore, when a person is bitten

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665

PERSPECTIVE 27.1 A Rabies Survivor! In October 2004, a 15-year-old girl was admitted to the hospital with typical signs and symptoms of rabies. A month earlier, while in church, she picked up a bat that had fallen to the floor. The bat bit her left index finger and she carried it outside and released it. The bite wound, which was small and showed a small amount of bleeding, was cleaned with hydrogen peroxide, and healed uneventfully. Because most rabies deaths result from respiratory failure, a tube was placed in the patient’s trachea and hooked to a respirator. She was given medication to put her into a coma to rest her nervous system, and she was given the antiviral medication ribavirin, according to an experimental protocol. After 7 days,

the coma-inducing medication was reduced and the girl was allowed to wake up. A little more than a month after her illness began, her breathing tube was removed, she regained speech, solved mathematics problems, and walked with assistance. Slow, steady improvement continued after she returned home. Survival after the onset of rabies symptoms is known to have occurred in only five individuals prior to this case, and all five had received anti-rabies vaccine either before they were exposed to rabies or before they showed signs or symptoms of the disease. All but one of them suffered persisting neurological damage, unlike the present patient, who made a complete recovery. Over the years, many treatments have been

by an unvaccinated, apparently healthy dog, the animal should be confined for 10 days to see if symptoms of rabies appear. Some dogs become irritable and hyperactive with the onset of rabies, produce excessive saliva, and attack people, animals, and inanimate objects. Perhaps more common is the “dumb” form of rabies, in which an infected dog simply stops eating, becomes inactive, and suffers paralysis of throat and leg muscles. Obviously, one should not be tempted to try to remove a suspected foreign body from the throat of a sick, choking, non-vaccinated dog! The reported number of rabies cases in humans now generally ranges from zero to four per year in the United States. Only about onefourth of the cases have a history of animal bites or exposure to sick animals. Some of them possibly contracted the infection by inhaling dust contaminated by rabies virus. The long incubation period, however, reportedly up to 6 years, and the patients’ illness make the animal bite history unreliable.

Prevention and Treatment A person who has been bitten by an animal should wash the wound immediately and thoroughly with soap and water and then apply an antiseptic. In people bitten by dogs having rabies virus in their saliva, the risk of developing rabies is about 30%. Louis Pasteur discovered that this risk can be lowered considerably by administering rabies vaccine as soon as possible after exposure to the virus. Presumably, the vaccine provokes a better immune response than the natural infection, neutralizing free virus and killing infected cells during the long incubation period before the virus enters the nerves. Pasteur’s vaccine was made from dried spinal cords of rabies-infected rabbits. Unfortunately, the rabbit nervous system tissue in the vaccine sometimes stimulated an immune response against the patient’s own brain, causing allergic encephalitis. Current vaccines are essentially devoid of nervous tissue and the risk of serious side effects is very low. If there is a reasonable possibility that the animal is rabid, the bitten individual should then receive a series of five injec-

nes95432_Ch27_647-673.indd 665

tried without benefit, including hyperimmune human anti-rabies serum, anti-rabies vaccines, and interferon. The current patient did not receive any of these. What is to be learned from the survival of this patient? Perhaps her survival had nothing to do with her treatment, but was due to her own immune system fighting a small infectious dose or a rabies viral strain of low virulence. Is there some cIue in her survival that will perhaps lead to the first effective rabies treatment in the 3,000 years the disease has been recognized? So far, attempts to cure other patients using the treatment used in this case have been unsuccessful.

tions of vaccine intramuscularly. Anti-rabies antibody is also injected at the wound site and intramuscularly to provide passive immunity. The anti-rabies antibody is obtained from humans who have been immunized against rabies. In the United States, about 30,000 people annually receive rabies vaccine to prevent rabies after having been bitten by suspected rabid animals. ■ passive immunity, p. 432

There is no effective treatment for rabies, and only six people are known to have ever recovered from the disease (see Perspective 27.1). Some features of rabies are summarized in table 27.9.

TABLE 27.9 Rabies Symptoms

Fever, headache, nausea, vomiting, sore throat, cough at onset; later, spasms of the muscles of mouth and throat, coma, and death

Incubation period

Usually 30 to 60 days; sometimes many months or years

Causative agent

Rabies virus, single-stranded RNA, rhabdovirus family; has an unusual bullet shape

Pathogenesis

During incubation period, virus multiplies at site of bite, then travels via nerves to the central nervous system; here it multiplies and spreads outward via multiple nerves to infect heart and other organs.

Epidemiology

Bite of rabid animal, usually a bat. Inhalation is another possible mode.

Prevention and treatment

Avoid suspect animals; immunize pets. Effective post-exposure measures: immediately wash wound with soap and water and apply antiseptic; inject rabies vaccine and human rabies antiserum as soon as possible. No effective treatment once symptoms begin.

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MICROCHECK 27.3 Many different kinds of viruses can attack the nervous system, but they generally do so in only a small percentage of the people they infect. At least half of viral meningitis cases are caused by the enterovirus subgroup of picornaviruses, which are generally spread by the fecal-oral route. Viral meningitis is usually benign, but viral encephalitis often causes permanent disability. Arboviruses maintained in nature in a mosquito-bird or mosquito-rodent cycle are a leading cause of epidemic viral encephalitis. Sporadic viral encephalitis is usually due to herpes simplex virus. Poliomyelitis, characterized by paralysis of one or more muscle groups, is caused by three other enteroviruses. Rabies is a widespread zoonosis, almost uniformly fatal for humans, usually transmitted by animal bites. ✓ Name one cause of viral meningitis preventable by vaccination. ✓ Why is rabies now rare in humans when it is still so common in wildlife? ✓ Why is the Sabin vaccine against poliomyelitis the preferred vaccine to use in countries where polio is still prevalent?

27.4 Fungal Diseases of the Nervous System Focus Point Discuss the main steps in the development of cryptococcal meningoencephalitis.

Fungi rarely invade the central nervous system of healthy people, but patients with cancer, diabetes, and AIDS, as well as those receiving immunosuppressive medications, risk serious disease. Common fungi from the soil and decaying vegetation sometimes infect the nose and sinuses of these patients; from there, they penetrate to the brain and cause the patient’s death. These infections are dangerous because they are difficult to treat with antimicrobial medication. Cryptococcal meningoencephalitis differs somewhat from this general pattern—about half the cases occur in otherwise healthy people, and many cases are cured by medication.

Causative Agent Cryptococcal meningoencephalitis is an infection of the meninges and brain by the encapsulated yeast, Cryptococcus neoformans, a member of the basidiomycetes. Different antigenic varieties labeled by capital letters are distinguished using antisera; varieties A and D are opportunistic pathogens, whereas varieties B and C can attack otherwise healthy people. The latter two antigenic varieties are also known as C. neoformans var gattii. In nature, C. neoformans probably can produce tiny spores (basidiospores), but this has been difficult to study in the laboratory. As seen in infected material from patients, the organism is a small, spherical yeast generally 3 to 7 mm in diameter surrounded by a large capsule (figure 27.19). ■ basidiomycetes, p. 288

Pathogenesis Presumably, basidiospores of C. neoformans become airborne and enter the human body by inhalation. Infection is established in the lung, usually producing mild or no symptoms. Body defenses of healthy people can often eliminate the infection, but phagocytic killing is slow and inefficient. In some cases, particularly in immunocompromised individuals, the organisms continue to multiply, enter the bloodstream, and are then distributed throughout the body. The capsule is essential to pathogenicity; non-encapsulated strains do not cause disease. Capsular material inhibits phagocytosis of the organisms despite their being coated with opsonin from the complement system. Migration of leukocytes to the site of infection is impaired. Capsular material diffuses from the organisms and can be detected in spinal fluid and urine, aiding diagnosis. Progressive infection and dissemination are likely to occur when a person’s cellular immunity is impaired, as in AIDS and certain cancers. Meningoencephalitis is the most common infection outside of the lung, but organisms spread by the bloodstream can also infect skin, bones, and other body tissues. In meningoencephalitis, the organisms typically cause thickening of the meninges, sometimes impeding the flow of cerebrospinal fluid, thereby increasing the pressure within the brain. They also

Cryptococcal Meningoencephalitis Cryptococcal meningoencephalitis was an uncommon disease until the onset of the AIDS epidemic. Now 2 to 4 cases occur among every 1,000 AIDS patients, as opposed to 0.2 to 0.9 cases per 100,000 in the general population. The disease is among the top four life-threatening infectious complications in AIDS.

Symptoms In apparently healthy people, symptoms of cryptococcal meningoencephalitis develop very gradually in most cases and generally consist of difficulty in thinking, dizziness, intermittent headache, and slight or no fever. After weeks or months of slow progression of these symptoms, vomiting, weight loss, paralysis, seizures, and coma may appear. In people with immunodeficiency, the disease generally progresses much faster; without treatment death can occur in as little as 2 weeks.

nes95432_Ch27_647-673.indd 666

20 mm

FIGURE 27.19 Cryptococcus neoformans in the Spinal Fluid of an Individual with Cryptococcal Meningoencephalitis India ink has been added to the fluid to outline the organism’s capsule.

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27.5 Protozoan Diseases of the Nervous System

invade the brain tissue, producing multiple abscesses. The sites of infection often show little inflammatory response. ■ opsonins, pp. 356, 373

Epidemiology Cryptococcus neoformans is distributed worldwide in soil and vegetation, but infections have been linked only to sites of welldecomposed pigeon droppings (varieties A and D), and to flowering of certain trees (B variety of C. neoformans). For every case of cryptococcal meningoencephalitis, millions of people are infected by the organism without harm. Symptomatic infection is often, but not always, the first indication of AIDS. Person-to-person transmission of the disease does not occur.

667

MICROCHECK 27.4 Fungi rarely invade the CNS of healthy people, but even common soil fungi are a serious threat to individuals with diabetes, cancer, or immunodeficiency. Cryptococcal meningoencephalitis occurs rarely in healthy people, but it is among the leading life-threatening complications in AIDS. The causative organism is a small yeast with a large capsule, often found in soil contaminated with pigeon droppings. ✓ What underlying condition should a physician immediately suspect when confronted with a patient with cryptococcal meningoencephalitis? ✓ Why might it be a good idea for persons with immunodeficiency to avoid soil contaminated with decomposed pigeon droppings? ✓ Why is it so difficult to cure AIDS victims of cryptococcal meningoencephalitis?

Prevention and Treatment There is no vaccine or other preventive measure available. Treatment with the antibiotic amphotericin B is often effective, particularly if given concurrently with flucytosine (5fluorocytosine) followed by the oral medicine, fluconazole. Amphotericin B must be given intravenously and the dose carefully regulated to minimize the toxic effects of the antibiotic, mainly against the kidneys. Because amphotericin B does not reliably cross the blood-brain barrier, it is often necessary to administer it through a plastic tube inserted through the skull into a lateral ventricle of the brain. Except in AIDS patients, treatment is successful in about 70% of cases. AIDS patients respond poorly to treatment, most likely because they lack Tcell-dependent killing of C. neoformans that normally assists the action of the antifungal medications. Unless their T-cell function can be restored by treatment, AIDS patients are rarely cured of their infection and must remain on antifungal medication for life. ■ antifungal medicines, p. 488 The main features of cryptococcal meningoencephalitis are summarized in table 27.10.

TABLE 27.10 Cryptococcal Meningoencephalitis Symptoms

Headache, vomiting, confusion, and weight loss; slight or no fever; symptoms may progress to seizures, paralysis, coma, and death

Incubation period

Widely variable, few to many weeks

Causative agent

Cryptococcus neoformans, an encapsulated yeast

Pathogenesis

Infection starts in lung; encapsulated organisms multiply, enter bloodstream, and are carried to various parts of the body; phagocytosis inhibited and opsonins neutralized; meninges and adjacent brain tissue become infected.

Epidemiology

Inhalation of dust containing dried pigeon droppings contaminated with the fungus; other sources; most people resistant to the disease.

Prevention and treatment

No preventive measures. Treatment; amphotericin B with flucytosine or itraconazole.

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27.5 Protozoan Diseases of the Nervous System Focus Point Outline the pathogenesis of African sleeping sickness.

Only a few species of protozoa are important central nervous system pathogens for humans. One interesting example, Naegleria fowleri, causes primary amebic meningoencephalitis after penetrating the skull along the nerves responsible for the sense of smell. The protozoan occurs worldwide, but less than 200 cases have been reported, almost all rapidly fatal. The disease is usually acquired when individuals swim in or are splashed with warm, fresh water, with or without chlorine. Apparently it can also be contracted by inhaling dust laden with cysts of the protozoa. For every case of Naegleria meningoencephalitis, many millions of people are exposed to the organism without harm. Naegleria fowleri can exist in three forms: ameba, flagellate, and cyst (see figure 12.7). It is one of only a few free-living protozoa pathogenic for humans. In contrast, African sleeping sickness is a quite different protozoan disease. ■ protozoa, p. 285

African Sleeping Sickness African sleeping sickness, also known as African trypanosomiasis, is transmitted by its biological vector—the daytime-biting tsetse fly. The disease is important because it can be contracted by residents and visitors in a wide area across the middle of the African continent. The causative protozoan has an interesting way of protecting itself against the host’s immune system. ■ biological vector, p. 455

Symptoms The first symptoms of African trypanosomiasis appear within a week after a person is bitten by an infected tsetse fly. A tender nodule develops at the site of the bite. The regional lymph nodes might enlarge, but symptoms may all disappear spontaneously. Weeks to several years later, recurrent fevers develop that can continue for months or years. Involvement of the central nervous system is

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CHAPTER TWENTY SEVEN

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marked by gradual loss of interest in everything, decreased activity, and indifference to food. The eyelids droop, the individual falls asleep while eating or even standing, the speech becomes slurred, coma develops, and eventually death ensues.

Causative Agent African sleeping sickness is caused by the flagellated protozoan, Trypanosoma brucei. These organisms are slender, and have a wavy, undulating membrane and an anteriorly protruding flagellum (figure 27.20). There are two subspecies that are morphologically identical—T. brucei rhodesiense and T. brucei gambiense. The rhodesiense subspecies occurs mainly in the cattle-raising areas of East Africa, whereas the gambiense subspecies occurs mainly in forested areas of Central and West Africa. Both are transmitted by tsetse flies, a group of biting insects of the genus Glossina.

Pathogenesis When an infected tsetse fly bites its victim, the protozoan enters the bite wound in the fly’s saliva. The organism multiplies at the skin site and within a few weeks enters the lymphatics and blood circulation. The patient responds with fever and production of antibody against the protozoa, and symptoms improve. Within about a week and at roughly weekly intervals thereafter, however, there are recurrent increases in the number of parasites in the blood. Each of these bursts of increased parasitemia, meaning parasites in the circulating blood, coincides with the appearance of a new glycoprotein on the surface of the trypanosomes. More than a thousand genes, each coding for a different surface glycoprotein, are present in the protozoan chromosome. Only one of these genes is activated at a time, and the patient’s immune system must respond to each gene product with production of a new specificity of antibody. The recurrent cycles of parasitemia and antibody production continue until the patient is treated or dies. In T. brucei rhodesiense infections, the disease tends to progress rapidly—the heart and brain are invaded within 6 weeks of infection. Irritability, personality changes, and mental dullness result from brain involvement, but the patient usually dies from heart failure

25 mm

FIGURE 27.20 Trypanosoma brucei in a Blood Smear Notice the slender protozoa among the blood cells of an individual with African sleeping sickness (African trypanosomiasis)

nes95432_Ch27_647-673.indd 668

within 6 months. With T. brucei gambiense, progression of infection is much slower—years may pass before death occurs, often from secondary infection. Much of the damage to the host is due to immune complexes formed when antibody reacts with complement and high levels of protozoan antigen. ■ immune complexes, p. 420

Epidemiology African sleeping sickness occurs on the African continent within about 15° of the equator, with 10,000 to 20,000 new cases each year, including a number of American tourists. The occurrence of the disease is determined by the distribution of the tsetse fly vectors. The severe Rhodesian form of the disease is a zoonosis and the main reservoirs are wild animals; for the milder Gambian form, humans are the main reservoir and human-to-human transmission is more common than animal-to-human. Bites of the infected tsetse fly transmit the disease, but less than 5% of the flies are infected. ■ reservoir, p. 453

Prevention and Treatment Preventive measures directed against tsetse fly vectors include use of insect repellents and wearing protective clothing to prevent bites, use of traps containing bait and insecticides, and clearing of brush that provides breeding habitats for the flies. Populations can be screened for T. brucei infection by examining blood specimens. Treatment of infected people helps reduce the protozoan’s reservoir. A single, intramuscular injection of the medication pentamidine prevents the Gambian form of the illness for a number of months, although it will not necessarily prevent an infection that could progress at a later time. As with other eukaryotic pathogens, treatment is problematic because of toxic side effects of the available medications. Suramin can be used if the disease has not progressed to involve the central nervous system; melarsoprol and eflornithine cross the blood-brain barrier and can be used when the central nervous system is involved. ■ antiprotozoan medications, p. 490 The main characteristics of African sleeping sickness are presented in table 27.11.

TABLE 27.11 African Sleeping Sickness Symptoms

Tender nodule at site of tsetse fly bite; fever, enlargement of lymph nodes; later, involvement of the central nervous system, uncontrollable sleepiness, headache, poor concentration, unsteadiness, coma, death

Incubation period

Weeks to several years

Causative agent

Trypanosoma brucei, a flagellated protozoan

Pathogenesis

The protozoa multiply at site of a tsetse fly bite, then enter blood and lymphatic circulation; as new cycles of parasites are released, their surface protein changes and the body is required to respond with a new antibody.

Epidemiology

Bites of infected tsetse flies transmit the trypanosomes through fly saliva; wild animal reservoir for T. brucei rhodesiense.

Prevention and treatment

Protective clothing, insecticides, clearing of brush where flies breed, pentamidine. Treatment: suramin; when central nervous system is involved, melarsoprol or eflornithine.

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27.6

MICROCHECK 27.5 Only on rare occasions can free-living amebas such as Naegleria fowleri cause meningoencephalitis in human beings. Residents and visitors to a wide swath of tropical Africa, however, are at risk of contracting African sleeping sickness, caused by the flagellated protozoan parasite Trypanosoma brucei, and transmitted by a biting insect, the tsetse fly. These protozoa can circulate in the bloodstream for extended periods by changing their surface antigens to escape the host’s antibodies. Eventually they are able to penetrate the CNS, causing indifference, sleepiness, coma, and death. ✓ How likely is it that a person who swims in warm, fresh water will contract primary amebic meningoencephalitis? ✓ How can one explain repeated, abrupt increases in T. brucei in the blood of African sleeping sickness victims?

27.6 Transmissible Spongiform Encephalopathies Focus Point

Transmissible Spongiform Encephalopathies

669

ognized spongiform encephalopathy in humans, variant CreutzfeldJakob disease, appeared during a mad cow disease epidemic in the United Kingdom. ■ mad cow disease, p. 320

Transmissible Spongiform Encephalopathy in Humans Transmissible spongiform encephalopathy is rare in humans, occurring in only 0.5 to 1 case per million people. Most cases occur sporadically as Creutzfeld-Jakob disease, although there are other forms of the disease that run in families. Another form, kuru, is associated with cannibalism, as formerly practiced by some New Guinea natives.

Symptoms Early symptoms include vague behavioral changes, anxiety, insomnia and fatigue, which progress over weeks or months to the hallmarks of the disease, muscle jerks, lack of coordination, and dementia. Individuals suffer deteriorating intellectual function, impaired judgment, memory loss, and loss of normal muscle function, ending in death, generally within a year.

Causative Agent

List the ways in which the transmissible spongiform encephalopathies differ from the infectious diseases discussed earlier in this chapter.

The causative agents of these diseases are called proteinaceous infectious particles, or prions (PrP). Prions appear to be a misfolded form of a normal cellular protein (PrPc). ■ prions, p. 341 The main characteristics of prions are:

A mysterious group of chronic, degenerative brain diseases involves wild and domestic animals and humans. Mink, elk, mule deer, sheep, goats, and cattle are among the animals that can be afflicted (figure 27.21). Microscopically, brain tissue affected by these diseases has a spongy appearance due to the loss of nerve cells and other changes— this is why these diseases are referred to as spongiform encephalopathies. Brain and other tissues from affected animals can transmit the disease to normal animals of the same, and sometimes different, species. Some of these encephalopathies can be transmitted to small laboratory animals such as mice, allowing scientific studies. These diseases assumed new prominence when, in 1996, a previously unrec-

They increase in quantity during the incubation period of the disease. They resist inactivation by ultraviolet and ionizing radiation. They resist inactivation by formaldehyde and heat. They are not readily destroyed by proteases. They are not destroyed by nucleases. They are much smaller than the smallest virus. They are composed of protein coded by a normal cellular gene but modified after transcription.

Pathogenesis In the normal course of infection, multiplication (see figure 14.21) first occurs in the spleen and other lymphoid tissues. Immune cells and proinflammatory cytokines are required for prion multiplication at these sites. The prions are then transported to the central nervous system by B lymphocytes, and probably by other means. There they aggregate in insoluble masses (plaques) outside the nerve cells. Malfunction and nerve cell death probably result from abnormal PrP replacing normal PrPc protein anchored to the cell surface. But not all prions act the same. They differ in host range, incubation period, and the areas of the nervous system that are attacked.

Epidemiology

FIGURE 27.21 A Captive Elk With Chronic Wasting Disease, A Kind of Transmissible Spongiform Encephalopathy Afflicted animals develop incoordination and weight loss, ending in death.

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Creutzfeld-Jakob disease generally occurs in individuals older than 45 years. It can be transmitted experimentally to chimpanzees, and from human to human with corneal transplants and contaminated surgical instruments. Spongiform encephalopathy of sheep, scrapie, has been known for more than two centuries, without any evidence that it is

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directly transmissible to humans. Current evidence indicates that cattle in the United Kingdom became infected with scrapie prions in protein food supplements made from sheep carcasses, giving rise to “mad cow disease.” Based on laboratory and epidemiological evidence, the cattle prions can be transmitted to humans and cause a variant Creutzfeld-Jakob disease marked by differences in symptoms, brain pathology, and age of onset. The median age of individuals with the variant disease is only 28 years.

TABLE 27.12 Transmissible Spongiform Encephalopathy Symptoms

Behavioral changes, anxiety, insomnia, fatigue, progressing over weeks or months to muscle jerks, lack of coordination, dementia

Incubation period

Usually many years

Causative agents Proteinaceous infectious particles known as

Prevention and Treatment Prions are highly resistant to disinfectants including formaldehyde. They can be inactivated by autoclaving in 1N sodium hydroxide. There is no treatment for the spongiform encephalopathies, and they are invariably fatal. The main features of transmissible spongiform encephalopathies are presented in table 27.12.

prions; lack nucleic acids; identical amino acid sequence to a normal protein, but folded differently, and relatively resistant to proteases; resistant to heat, radiation and disinfectants

Pathogenesis

Prions replicate in dendritic cells in various parts of the body by converting normal protein to more prions; transmission to the brain; aggregation into masses outside the nerve cells; cell malfunction and death.

Epidemiology

Human-to-human transmission by corneal transplantation and by contaminated surgical instruments; probable transmission of cattle prions to humans by eating contaminated beef; sporadic Creutzfeld-Jakob disease in those over age 45 years; median age of variant Creutzfeld-Jakob cases only 28 years.

Prevention and treatment

Prions are inactivated by autoclaving in concentrated sodium hydroxide; no treatment, invariably fatal.

MICROCHECK 27.6 Transmissible spongiform encephalopathies are degenerative nervous system diseases that occur in a variety of wild and domestic animals. They are rare in humans, but the appearance of a new form of the disease during an epidemic of mad cow disease in the United Kingdom strongly suggests the possibility that epidemic disease in humans could originate from animals, transmitted via ingested meat. These diseases appear to be caused by prions—infectious agents consisting only of protein and highly resistant to inactivation by heat, radiation, and disinfectants. ✓ By what route might scrapie prions from sheep infect cattle? ✓ If you were a famous American eye surgeon about to transplant a cornea to restore the vision of a woman, would you rather the donor be under 35 or over 45 years of age?

FUTURE CHALLENGES Eradicate Polio: Then What? It is hoped that poliomyelitis will be among the next ancient scourges to follow smallpox down the road to eradication. However, for a variety of political and scientific reasons, the causative virus of smallpox still exists many years after the last naturally acquired case of the disease. Will it be any easier to rid the world of the polioviruses after the last case of poliomyelitis occurs? Dramatic progress toward polio eradication has mainly been accomplished using “immunization days,” when the entire population in a given area is immunized using attenuated (Sabin) vaccine, often with one or more follow-up days to immunize individuals missed

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earlier. The vaccine viruses then disappear from the population within a few months. Although a small percentage of the population suffers paralytic illness from the vaccine, the population is protected from virulent polioviruses until new generations are born. If there were no polioviruses left in the world, there would be no need to immunize the new generations. Potential sources of virulent polioviruses include wild viruses circulating in remote populations, individuals with mild or atypical illness, long-term carriers (especially those with immunodeficiency, who excrete the viruses for months or years), and laboratory freezers around the world that are known to harbor the

viruses, as well as frozen specimens such as feces that could harbor them. It is even possible to synthesize a poliovirus in the laboratory. Lastly, vaccine viruses can change genetically and acquire full virulence, as occurred in the Hispaniola polio epidemic of 2000– 2001. The challenge is to have a continuous, reliable, global polio surveillance system, and maintain immunizations and strategically located stockpiles of vaccine during what is likely to be a long time after the last case of paralytic polio occurs.

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Summary

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SUMMARY 27.1 Anatomy and Physiology (figure 27.1)

27.3 Viral Diseases of the Nervous System

The brain and spinal cord make up the central nervous system (CNS); the peripheral nervous system is composed of motor nerves and sensory nerves. Cerebrospinal fluid is produced by structures in cavities inside the brain and flows out over the brain and spinal cord (figure 27.2). Meninges are the membranes that cover the surface of the brain and spinal cord.

Most viral nervous system infections are caused by human enteroviruses or by the viruses of certain zoonoses. Many common viruses of human beings can occasionally infect the nervous system, including those that cause infectious mononucleosis, mumps, measles, chickenpox, and herpes simplex (“cold sores,” genital herpes).

Pathways to the Central Nervous System Infectious agents can reach the CNS by way of the bloodstream when they penetrate the blood-brain barrier, via the cytoplasm of nerve cell axons, and by direct extension through bone.

Viral Meningitis (table 27.6) Viral meningitis is much more common than bacterial meningitis. It is generally a mild disease for which there is no specific treatment.

27.2 Bacterial Nervous System Infections Bacteria can infect the brain, spinal cord, and peripheral nerves, but more commonly they infect the meninges and cerebrospinal fluid, causing meningitis (figure 27.4). Bacterial meningitis is uncommon; formerly most victims were children, but childhood immunization has decreased the incidence in these age groups. In most but not all of the victims, the causative bacterium is one commonly found among the normal upper respiratory flora of healthy people. Haemophilus influenzae, a tiny, pleomorphic, Gram-negative rod, once the leading cause of childhood bacterial meningitis, is now mostly controlled by a vaccine (figure 27.3). Meningococcal Meningitis (table 27.1) Meningococcal meningitis is greatly feared because it can result in shock and death, and it can occur in both childhood and adult epidemics. Symptoms are similar to other forms of meningitis: cold symptoms followed by abrupt onset of fever, severe headache, pain and stiffness of the neck and back, nausea, and vomiting. Small hemorrhages into the skin (figure 27.5), deafness, and coma can occur. The bacterium Neisseria meningitidis causes a massive PMN response (figure 27.6); metabolic activity of the leukocytes and bacteria consumes glucose normally present in the cerebrospinal fluid; shock results from the release of endotoxin into the bloodstream. Listeriosis (table 27.2) Listeriosis is caused by Listeria monocytogenes, a non-spore-forming, Gram-positive rod; it is a foodborne illness often manifest as meningitis in newborn infants and others. The bacterium is widespread, commonly contaminates foods such as non-pasteurized milk, cold cuts, and soft cheeses, and can grow in the refrigerator. The bacteria readily penetrate the intestinal epithelium, enter the bloodstream, and infect the meninges. Hansen’s Disease (Leprosy) (table 27.4, figure 27.8) Hansen’s disease is characterized by invasion of peripheral nerves by the acid-fast bacillus Mycobacterium leprae, which has not been cultivated in vitro (figure 27.9). The disease occurs in two main forms—tuberculoid and lepromatous, depending on the immune status of the patient. Botulism (table 27.5) Botulism is not a nervous system infection, but is an often-fatal type of food poisoning that causes severe generalized paralysis. The causative bacterium, Clostridium botulinum, is an anaerobic, Gram-positive rod that forms heat-resistant spores (figure 27.10). Spores that survive canning or other heat treatment of foods germinate, and the bacteria multiply, releasing a powerful toxin into the food. Because of strict controls on food processing, intestinal botulism is now the most common form of the disease in the United States. Relatively mild symptoms result from C. botulinum colonization of the intestine of infants and some adults. Wound botulism, caused when C. botulinum colonizes dirty wounds containing dead tissue, is rare.

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Viral Encephalitis (table 27.7) Viral encephalitis has a high fatality rate and often leaves survivors with permanent disabilities. It can be sporadic or epidemic. Herpes simplex virus is the most important cause of sporadic encephalitis; epidemic encephalitis is usually caused by arboviruses. LaCrosse encephalitis virus, maintained in Aedes mosquitoes and squirrels and chipmunks, is usually the most frequently reported (figure 27.12). Infantile Paralysis, Polio (Poliomyelitis) (table 27.8, figure 27.16) Destruction of motor nerve cells of the brain and spinal cord leads to paralysis, muscle wasting, and failure of normal bone development (figures 27.13, 27.15). Post-polio syndrome occurs years after poliomyelitis, and it is probably caused by the death of nerve cells that had taken over for those killed by poliomyelitis virus. Rabies (table 27.9) Rabies is a widespread zoonosis transmitted to humans mainly through the bite of an infected animal (figure 27.17). Once symptoms appear in an infected human being, the disease is almost uniformly fatal. Because of the long incubation period, prompt immunization with inactivated vaccine begun after a rabid animal bite is effective in preventing the disease. Passive immunization given at the same time increases the protection.

27.4 Fungal Diseases of the Nervous System Fungi rarely invade the nervous system of healthy people, but they can be a threat to the life of individuals with underlying diseases such as diabetes, cancer, and immunodeficiency. Treatment of these infections is usually very difficult. Cryptococcal Meningoencephalitis (table 27.10) Infection originates in the lung after a person inhales dust laden with spores of Cryptococcus neoformans, an encapsulated yeast, which resists phagocytosis because of its large capsule (figure 27.19). Some varieties of this organism are associated with soil contaminated with decomposed pigeon droppings.

27.5 Protozoan Diseases of the Nervous System Only a few free-living protozoa infect the human nervous system. Certain parasitic protozoa are a much more widespread threat. African Sleeping Sickness (table 27.11) African sleeping sickness is a major health problem in a wide area across equatorial Africa. In its late stages, it is marked by indifference, sleepiness, coma, and death. The disease is caused by Trypanosoma brucei (figure 27.20), a flagellated protozoan that lives in the blood of its victims and in its biological vector, the tsetse fly. During infection, the organism shows bursts of growth, each appearing with different surface proteins. The organism has more than a thousand genes coding for these antigens, but only expresses one at a time. Each antigen requires that the body respond with a new antibody.

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27.6 Transmissible Spongiform Encephalopathies The spongiform encephalopathies are a group of rare diseases characterized by a spongelike appearance of brain tissue caused by loss of nerve cells. They afflict a variety of wild and domestic animals as well as humans (figure 27.21). Mad cow disease is an example. Brain and other tissues from afflicted animals can transmit the disease to the same, or sometimes other, species. A new form of the disease appeared in humans during an epidemic of mad cow disease in the United Kingdom. Transmissible Spongiform Encephalopathies in Humans (table 27.12) The main symptoms are progressive loss of muscle control, and dementia. The diseases are caused by prions—abnormal proteins that are resistant to heat, radiation, and disinfectants. They appear to be identical to a normal

protein except they are folded differently. Prions convert the normal protein into copies of themselves. In the brain they aggregate in masses and kill nerve cells. There is no apparent inflammatory or immune response. The most common form of the disease in humans, Creutzfeld-Jakob disease, occurs in only about one in a million people, generally in those over 45 years of age. It can be transmitted from one person to another by corneal transplants and by contaminated instruments. The variant of this disease that appeared during the mad cow disease epidemic affected much younger people. Evidence indicates that scrapie prions, from protein supplements made from sheep carcasses, infected cattle; humans then became infected by eating beef. Prions can be inactivated by autoclaving them in strong alkali. So far, there is no treatment for these diseases and they are invariably fatal.

REVIEW QUESTIONS Short Answer 1. How can the incidence of meningitis due to Lancefield group B streptococci be reduced? 2. Name and describe the organism that is the leading cause of bacterial meningitis in adults. 3. What cell wall component of Neisseria meningitidis is probably responsible for the shock and death that sometimes occur with infections by this bacterium? 4. What measures can be undertaken to prevent meningococcal meningitis? 5. Why is listeriosis so important to pregnant women even though it usually causes them few symptoms? 6. Describe the differences between tuberculoid and lepromatous leprosy. 7. What is the difference between sporadic encephalitis and epidemic encephalitis? Name one cause of each. 8. Give two ways in which viral meningitis usually differs from bacterial meningitis. 9. Give an example of an enterovirus. 10. What are arboviruses? Give an example. 11. Why does poliomyelitis virus attack motor but not sensory neurons? 12. Can a dog infected with rabies virus transmit the disease while appearing well? Explain.

Multiple Choice 1. Which is the best way to prevent meningococcal meningitis in individuals intimately exposed to the disease? a) Vaccinate them against Neisseria meningitidis. b) Treat them with the antibiotic rifampin. c) Culture their throat and hospitalize them for observation. d) Withdraw a sample of spinal fluid and begin antibacterial treatment if the cell count is high and the glucose is low. e) Have them return to their usual activities, but seek medical evaluation if symptoms of meningitis occur.

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2. Which of these statements concerning the causative agent of listeriosis is false? a) It can cause meningitis during the first month of life. b) It is a Gram-positive rod that can grow in refrigerated food. c) It is usually transmitted by the respiratory route. d) Infection commonly results in bacteremia. e) It is widespread in natural waters and vegetation. 3. Of the following statements about Hansen’s disease, which one is false? a) It was once common in the United States. b) An early symptom is loss of sensation, sweating, and hair in a localized patch of skin. c) The incubation period is usually less than 1 month. d) Treatment should include more than one antimicrobial medication given at the same time. e) The form the disease takes depends on the immune status of the victim. 4. Pick the one false statement about foodborne botulism. a) It is not a central nervous system infection. b) Pathogenicity of some strains of the causative agent is the result of lysogenic conversion. c) Food can taste normal but still cause botulism. d) Treatment is based on choosing the correct antibiotic. e) Control of the disease depends largely on proper food-canning techniques. 5. Which of the following statements about enteroviral meningitis is true? a) Vaccines are generally available to protect against the disease. b) The main symptom is muscle paralysis. c) Transmission is usually by the fecal-oral route. d) The causative agents do not survive well in the environment. e) Recovery is rarely complete. 6. Choose the one false statement about arboviral encephalitis. a) It is likely to occur in epidemics. b) Mosquitoes can be an important vector.

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Review Questions c) Epilepsy, paralysis, and thinking difficulties are among the possible sequels to the disease. d) Use of sentinel chickens helps warn about the disease. e) In the United States, the disease is primarily a zoonosis involving cattle. 7. Which one of the following statements about poliomyelitis is false? a) The nerves of sensation are usually involved. b) It can be caused by any of three specific enteroviruses. c) Only a small fraction of those infected will develop the disease. d) The disease is transmitted via the fecal-oral route. e) A postpolio syndrome can develop years after recovery from the original illness. 8. Choose the one false statement about rabies. a) It is widespread in wildlife. b) Vaccines are available to protect humans and domestic animals. c) Hydrophobia is a characteristic symptom. d) Animals that do not bite do not get the disease. e) The incubation period is often a month or more. 9. Which statement concerning cryptococcal meningoencephalitis is true? a) It is caused by a yeast with a large capsule. b) It is a disease of pigeons transmissible to humans. c) Typically it attacks the meninges, but spares the brain. d) Person-to-person transmission commonly occurs. e) Cell-mediated immunity is of little importance in the body’s struggle against the disease.

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10. Which of the following statements about African sleeping sickness is true? a) It is transmitted by a species of night-time-biting mosquito. b) It is a threat to visitors to tropical Africa. c) The onset of sleepiness is usually within 2 weeks of contracting the disease. d) It is caused by free-living protozoa. e) Distribution of the disease is determined mainly by the distribution of standing water.

Applications 1. An outbreak of viral meningitis in a small eastern city was linked epidemiologically to a group who swam a non-chlorinated pool in an abandoned quarry outside of town. What might public health officials surmise about the probable cause of the outbreak? 2. Two microbiologists are trying to write a textbook, but they cannot agree where to place the discussion of botulism. One favored the chapter on nervous system infections, whereas the other insisted on the chapter covering digestive system infections. Which microbiologist is correct?

Critical Thinking 1. A pathologist stated that it was much easier to determine the causative agent of meningitis than of an infection of the skin or intestine. Is her statement valid? Why or why not? 2. Why is it important to learn about rabies when only a few cases occur in the entire United States each year?

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28 SEM of the tip of the mouthparts of a female mosquito.

Blood and Lymphatic Infections A Glimpse of History Alexandre Emile John Yersin (1863–1943) is one of the most interesting, though relatively unknown, contributors to the conquest of infectious diseases. He was born in 1863 in the Swiss village of Lavaux, where his family lived in a gunpowder factory. His father, director of the factory and a self-taught insect expert, died unexpectedly 3 weeks before Yersin’s birth. Alexandre developed an interest in science when, as a young boy, he discovered in an attic trunk the microscope and dissecting instruments of the father he never knew. A local public health physician befriended the family and influenced Yersin to study medicine, and at age 20 he began pre-med studies in Lausanne. Later, while a medical student in Paris, Yersin volunteered to help at the Pasteur Institute, and in his fourth year of medical training, he was hired by Emile Roux, a coworker of Pasteur. Yersin became increasingly recognized for his work at the Institute, but he was bored with research, and he did not want to practice medicine because he felt it was wrong for physicians to make a living from sickness. He abruptly left the Pasteur Institute and was employed as a physician on a ship sailing from Marseilles to Saigon. Most of Indochina was under French control and was largely unexplored and undeveloped. Yersin became enchanted with the land and its peoples, exploring crocodile-infested rivers in a dugout canoe and making expeditions on elephant into jungles where tigers roared. For the rest of Yersin’s life, Vietnam was his home. His many contributions to the region included the introduction of improved breeds of cattle, cultivation of rubber and quinine-producing trees, and the establishment of a medical school. Yersin also studied the diseases that affected the Vietnamese people. One of them, plague, was a horrifying recurring problem. The disease had killed millions in Europe in medieval times and had struck France as recently as 1720. This great killer, an incurable disease, came and went unpredictably, its cause and transmission completely unknown.

In 1894, Yersin went to study a Hong Kong outbreak of plague because the facilities for studying the disease were better in Hong Kong than in Vietnam. Unfortunately for Yersin, Shibasaburo Kitasato, the famous colleague of Robert Koch and Emil von Behring, had arrived 3 days earlier with a large team of Japanese scientists. British authorities had given them access to patients and laboratory facilities. Yersin did not speak English, so it was difficult for him to communicate with the authorities. Moreover, although both he and the Japanese scientists spoke fluent German, the Japanese team treated him coolly, perhaps as a reflection of the intense rivalry between Pasteur and Koch. Yersin was reduced to setting up a laboratory in a bamboo shack. He bribed British sailors responsible for disposing of the bodies of plague victims to allow him to get samples of material from their swollen, pus-filled lymph nodes (called buboes). A week after his arrival in Hong Kong in the summer of 1894, Yersin reported to the British authorities his discovery of a bacillus of characteristic appearance, invariably present in the buboes of plague victims. The bacterium could be cultivated, and it caused plaguelike disease when injected into rats. Later, he showed that the disease was transmitted from one rat to another. Yersin’s plague bacillus, now known as Yersinia pestis, was used to make an antiplague vaccine, and in 1896, antiserum prepared against the organism provided the world’s first cure of a patient with plague. Not long afterward, another Pasteur Institute scientist proved that the rat flea was crucial in transmission. ■ Robert Koch, p. 83 ■ Shibasaburo Kitasato, p. 559

Kitasato, working with blood from the hearts of plague victims, announced shortly after his arrival in Hong Kong that he had isolated the bacterium that caused plague. Although subsequently it proved to be only a laboratory contaminant, Kitasato was named co-discoverer of the plague bacillus because of his great prestige.

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28.1

KEY TERMS

Endocarditis Inflammation of the heart valves or lining of the heart chambers.

Aneurysm Localized, abnormal enlargement of a blood vessel resulting from disease of the blood vessel wall.

Lymphangitis Inflammation of lymphatic vessels.

Bubo An enlarged, tender lymph node characteristic of plague and some venereal diseases.

Osteomyelitis Inflammation of the bone marrow and adjacent bone.

Necrosis Death of tissue.

Disseminated Intravascular Coagulation (DIC) Condition in which clots form in small blood vessels throughout the body, leading to failure of vital organs.

Petechiae Small, purple spots on the skin and mucous membranes caused by hemorrhage from small blood vessels.

Embolus (pl., Emboli) An abnormal object such as an air bubble or blood clot that enters the blood circulation.

Septicemia Acute illness caused by infectious agents or their products circulating in the bloodstream: “blood poisoning.”

Pneumonic Referring to the lung.

Anatomy and Physiology

Septic Shock An array of effects that results from infection of the bloodstream or circulating endotoxin; includes fever, drop in blood pressure, and disseminated intravascular coagulation. Subacute Bacterial Endocarditis A chronic illness caused by infection of the heart lining or valves, generally caused by bacteria of low virulence. Zygote A diploid cell formed by the fusion of two haploid cells (gametes) during sexual reproduction.

T

he circulation of blood and lymph fluids supplies nutrients and oxygen to the body’s tissue cells and carries away the cells’ waste products. The circulatory system also heats and cools body tissues to maintain an optimum temperature. Infection of the system can have devastating effects because infectious agents become systemic, meaning they can be carried to all parts of the body, producing disease in one or more vital organs or causing the circulatory system itself to stop functioning. Thus, even a small scratch can cause considerable harm if it results in a pathogen entering the bloodstream. The circulation of an agent in the bloodstream is given a name ending in -emia that specifies the nature of the agent, as with bacteremia, viremia, and fungemia. In many cases, there are no symptoms associated with the circulating agent. When illness results from a circulating agent or its toxins, the condition is referred to as septicemia, or blood poisoning. When, as a result of septicemia, the blood pressure falls to such low levels that blood flow to vital organs is insufficient to maintain their functioning, the condition is called septic shock.

28.1 Anatomy and Physiology Focus Points

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Capillaries of head, upper body, and other tissues

Right lung capillaries

Left lung capillaries

Pericardium Pericarditis

Left atrium Valves Endocarditis

Left ventricle

Heart muscle Myocarditis

Venous system

Lymphatic system Lymphangitis

Lymph node Arterial system

Outline the function of valves in the circulatory system. List the functions of the lymphatic system.

The Heart The heart, a muscular double pump enclosed in a fibrous sac called the pericardium, supplies the force that moves the blood. As shown schematically in figure 28.1, the heart is divided into right and left sides separated by a septum—a wall of tissue through which blood

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Capillaries of body organs and other tissues

FIGURE 28.1 The Blood and Lymphatic Systems Disease conditions are indicated in red type. For simplicity, the spleen is not shown. It is a fistsized, blood-filled lymphoid organ located high in the left side of the abdomen, behind the stomach.

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PERSPECTIVE 28.1 Arteriosclerosis: The Infection Hypothesis Arteriosclerosis, the main cause of heart attacks and strokes, is characterized by lipid-rich deposits that develop in arteries and can impair or stop the flow of blood. In 1988, researchers in Helsinki, Finland, reported that patients with coronary artery disease—meaning arteriosclerosis of the arteries that supply the heart muscle—commonly had antibodies against Chlamydia pneumoniae. This organism is a tiny, obligate, intracellular bacterium that is responsible for a variety of upper and lower respiratory infections including sinusitis and pneumonia. The infections are common, and most

people have been infected by C. pneumoniae by the time they reach adulthood. What was intriguing about the antibody studies was that the higher the titer of antibody, the greater the risk of coronary disease. Then, in 1996, viable C. pneumoniae were shown to be present in many arteriosclerotic lesions, and other studies conclusively established that there was an association between the bacterium and arteriosclerotic lesions of both heart and brain arteries. Does C. pneumoniae cause arteriosclerosis, does it worsen the effects of arteriosclerosis, or does it merely exist harmlessly in the lesions? How can the

normally does not pass after birth. The right and left sides of the heart are both divided into two chambers—the atrium, which receives blood, and the ventricle, which discharges it. Blood from the right ventricle flows through the lungs and into the atrium on the left side of the heart. From the atrium, the blood passes into the left ventricle and is then pumped through the aorta to the arteries and capillaries that supply the tissues of the body. Blood that exits the capillaries is returned to the right atrium by the veins. The heart valves are situated at the entrance and exit of each ventricle and ensure that the blood flows in only one direction. Although not common, infections of the heart valves, muscle, and pericardium can be disastrous because they affect the vital function of blood circulation.

Arteries Arteries have thick muscular walls to withstand the high pressure of the arterial system. The blood in arteries is bright red, the color of oxygenated hemoglobin. Infection of the arteries is unusual, although the aorta can be dangerously weakened by infection in syphilis. Arteries are subject to arteriosclerosis—“hardening of the arteries”—a process that begins in teenage years or before and progresses through life, ultimately putting individuals at risk for heart attacks and strokes. A possible role of bacteria and viruses in arteriosclerosis has been considered for some years. ■ syphilis, p. 633

Veins Blood becomes depleted of O2 in the capillaries, causing it to assume the dark color characteristic of venous blood. Because pressure in the veins is low, one-way valves help keep the blood flowing in the right direction. Veins are easily compressed, so the action of muscles aids the flow of venous blood. Thus, as the blood flows around the circuit, it alternately passes through the lungs and through the tissue capillaries. During each circuit, a portion of the blood passes through organs such as the spleen, liver, and lymph nodes, all of which, like the lung, contain phagocytic cells of the mononuclear phagocyte system. These phagocytes help cleanse the blood of foreign material, including infectious agents, as the blood passes through these tissues.

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hypothesis that C. pneumoniae contributes to heart attacks and strokes be tested? Some studies of coronary patients treated with antibiotics effective against the bacterium have suggested a beneficial effect, and others have not. It now appears that many inflammatory conditions, not just C. pneumoniae infections, increase the risk of heart attacks and strokes. The risk correlates with the level of acute-phase proteins arising from the release of pro-inflammatory cytokines. Undoubtedly there will be more to come in determining the relationship, if any, between arteriosclerosis and acute-phase proteins. ■ acute-phase proteins, p. 360

Lymphatics (Lymphatic Vessels) The system of lymphatic vessels (see figure 16.2) begins in tissues as tiny tubes that resemble blood capillaries but differ from them in having closed (“blind”) ends and in being somewhat larger. Lymph, an almost colorless fluid, is conveyed within these lymphatic vessels. It originates from plasma, the non-cellular portion of the blood, that has oozed through the walls of the blood capillaries to become the interstitial fluid that surrounds tissue cells. This fluid bathes and nourishes the tissue cells and then enters the lymphatics. Unlike the blood capillaries, the readily permeable lymphatic vessels take up foreign material such as invading microbes and their products, including toxins and other antigens. The tiny lymphatic capillaries join progressively larger lymphatic vessels. Many one-way valves in the lymphatic vessels keep the flow of lymph moving away from the lymphatic capillaries. Both contraction of the vessel walls and compression by the movements of the body’s muscles force the lymph fluid along. ■ lymphatic vessels, p. 370

At many points in the system, lymphatic vessels drain into small, bean-shaped bodies called lymph nodes. These nodes are constructed so that foreign materials such as bacteria are trapped in them; the nodes also contain phagocytic cells and antibodyproducing cells. Generally, lymph flows out of the nodes through vessels that eventually unite into one large tube (thoracic duct), which then discharges into a large vein (subclavian vein) behind the left collarbone, and thus back into the main blood circulation. ■ lymphoid system, p. 369 ■ phagocytic cells, p. 358

When a hand or a foot is infected, a visible red streak may spread up the limb from the infection site (figure 28.2). This streak represents the course of lymphatic vessels that have become inflamed in response to the infectious agent. This condition is called lymphangitis. It may stop abruptly at a swollen and tender lymph node, only to continue later to yet another lymph node. This pause in the progression of lymphangitis demonstrates the ability, even though sometimes temporary, of the lymph nodes to clear the lymph of an infectious agent. Blood and lymph carry infection-fighting leukocytes and such antimicrobial proteins as antibodies, complement, lysozyme, b-lysin,

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28.2 Bacterial Diseases of the Blood Vascular System

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28.2 Bacterial Diseases of the Blood Vascular System Focus Points Outline the pathogenesis of subacute bacterial endocarditis. List the effects of endotoxemia.

FIGURE 28.2 Lymphangitis Notice the red streak extending up the arm. The streak represents an inflamed lymphatic vessel.

and interferon. An inflammatory response may cause lymph and blood to clot in vessels that are close to areas of infection or antibody-antigen reactions—one of the ways the body has to localize an infection from the rest of the body. As with the nervous system, the blood and lymphatic systems lie deep within the body and are normally sterile. ■ antimicrobial substances, p. 348 ■ inflammatory response, p. 360

Spleen The spleen is a fist-sized organ situated high up on the left side of the abdominal cavity, behind the stomach. It is composed of two kinds of tissue—one consists of multiple blood-filled passageways, and the other, of lymphoid tissue. One of its functions is to cleanse the blood, much as the lymph nodes cleanse the lymph. Large numbers of phagocytes located in the spleen remove aging or damaged erythrocytes, bacteria, and other foreign materials from the blood. Another function, carried on by the lymphoid tissue, is to provide an immune response to microbial invaders. A third function is to produce new blood cells in rare situations where the bone marrow is unable to meet the demand. The spleen enlarges in a number of infectious diseases, such as infectious mononucleosis and malaria, in which its immune and filtering functions are challenged.

MICROCHECK 28.1 The heart can be thought of as two pumps that work together to move the blood around a circular course. The main function of the lymphatic system is to cleanse interstitial fluid and to return it to the bloodstream. Systemic infections threaten the transportation of oxygen and nutrients to body tissues and removal of waste products. The circulatory system can expose all of the body’s tissues to infectious agents and their toxins. ✓ What are the functions of the spleen? ✓ Which side of the heart—right or left—do bacteria in infected lymph reach first? Where do they go from there?

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Bacterial infections of the vascular system can be rapidly fatal, or they can smolder for months, causing a gradual decline in health. They are not common, but they are always dangerous. Usually the bacteria are carried into the bloodstream by the flow of lymph from an area of infection in the tissues. Some pathogens multiply in the bloodstream, and they may colonize and form biofilms on structures such as the heart valves or abnormalities in the heart or major arteries. ■ biofilm, p. 85 Endocarditis is the term used for infections of the heart valves or the inner, blood-bathed surfaces of the heart, and it can be acute or subacute. Acute bacterial endocarditis starts abruptly with fever, and usually an infection such as pneumonia is present somewhere else in the body or there is evidence of injecteddrug abuse. Virulent species such as Staphylococcus aureus and Streptococcus pneumoniae are usually the cause, and they infect both normal and abnormal heart valves. They can often produce a rapidly progressive disease, often with valve destruction and formation of abscesses in the heart muscle, leading to heart failure. By contrast, subacute bacterial endocarditis is usually caused by organisms with little virulence, and it has a much more protracted course. ■ Staphylococcus aureus, p. 535 ■ Streptococcus pneumoniae, p. 509 Septicemia is caused by both Gram-negative and Grampositive bacteria, as well as other infectious agents.

Subacute Bacterial Endocarditis Subacute bacterial endocarditis (SBE) is usually localized to one of the valves on the left side of the heart. It commonly occurs on valves that are deformed as a result of a birth defect, rheumatic fever, or some other disease. ■ subacute bacterial endocarditis, p. 677 ■ rheumatic fever, p. 501

Symptoms People with subacute bacterial endocarditis usually suffer from marked fatigue and slight fever. They typically become ill gradually and slowly lose energy over a period of weeks or months. They may abruptly develop a stroke.

Causative Agent The causative organisms of SBE are usually members of the normal bacterial microbiota of the mouth or skin, notably a-hemolytic viridans streptococci and Staphylococcus epidermidis. The infecting organisms are usually shed from the infected heart valve into the circulation and can be found by culturing samples of blood drawn from an arm vein. In 5% to 15% of cases, however, culturing the blood from an arm vein fails to yield the causative bacteria. This is especially likely to occur when the

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infection is on the right side of the heart, and blood from the infected site must pass through the lung, which is richly supplied with phagocytes, before entering the left side of the heart, traversing the capillaries, and reaching the arm vein. Also, some bacteria that cause endocarditis, such as Coxiella burnetii, the cause of Q fever, cannot be cultivated on cell-free media. At least one, Tropheryma whippelii, the cause of Whipple’s disease, can be identified at the time of valve surgery by using the polymerase chain reaction and a nucleic acid probe. Cultivation of the bacterium requires a special medium. ■ Q fever, p. 274 ■ Whipple’s disease, p. 243 ■ polymerase chain reaction, p. 223 ■ nucleic acid probes, p. 227

Pathogenesis The bacteria that cause SBE can gain entrance to the bloodstream during dental procedures, toothbrushing, or other trauma. In an abnormal heart, a thin blood clot may form in areas where there is turbulent blood flow around a deformed valve or other defect. This clot traps circulating organisms; these multiply and can form a biofilm that makes them inaccessible to phagocytic killing, and tends to protect them from antimicrobial treatment. People with bacterial endocarditis often have high levels of antibodies, which are of little value in eliminating the bacteria and may even be harmful because they make the bacteria clump together and adhere to the clot. As the organisms multiply, more clot is deposited around them, gradually building up a fragile mass. Bacteria continually wash off the mass into the circulation, and pieces of infected clot (septic emboli) can break off. If large enough, these clots can block important blood vessels and lead to death of the tissue (infarction) supplied by the vessel, as occurs in a stroke. They can also cause a vessel to weaken and balloon out, forming an aneurysm. Circulating immune complexes may lodge in the skin, eyes, and other body structures. In the kidney, they produce a kind of glomerulonephritis by their inflammatory effects. Even though the organisms normally have little invasive ability, great masses of them growing in the heart are sometimes able to burrow into heart tissue to produce abscesses or damage valve tissue, resulting in a leaky valve. This is a good example of how pathogenicity depends on both host factors and the virulence of the microorganism. ■ immune complexes, p. 420 ■ virulence, p. 394

Epidemiology In recent years, viridans streptococci have accounted for a smaller percentage of SBE cases than previously; an increasing percentage of cases are caused by more antibiotic-resistant organisms. This may be an unintended effect of giving antibiotic treatment before dental procedures to patients with prominent heart murmurs. A heart murmur is an abnormal sound the physician hears when listening to the heart, often indicative of a deformed valve or other structural abnormality. Also, more SBE cases occur in injected-drug abusers, in hospitalized patients who have plastic intravenous catheters for long periods, and in those with artificial heart valves. These people are usually infected with S. epidermidis or a wide variety of species other than viridans streptococci.

Prevention and Treatment No scientifically proven preventive methods are available. In people with known or suspected defects in their heart valves,

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however, the accepted practice is to give an antibacterial medication shortly before dental or other bacteremia-causing procedures. The medication is chosen according to the expected species of bacterium and its likely susceptibility to antimicrobials. To prevent nosocomial SBE, rigorous attention to sterile technique when inserting plastic intravenous catheters, changing the catheters to new locations every several days, and discontinuing their use as soon as possible probably helps prevent colonization of the catheters and consequent bacteremia that could lead to heart valve infection. For treatment, antibacterial medications are chosen according to the susceptibility of the causative organism. Only bactericidal medications are effective, and usually two or more antimicrobials are used together. Prolonged treatment such as penicillin and gentamicin over 1 or more months is usually required. Infection of foreign material such as an artificial heart valve is almost invariably associated with biofilm formation and the object must often be replaced to effect a cure. Sometimes, it is necessary to perform surgery to remove the mass of infected clot or to drain abscesses. ■ nosocomial infections, p. 462 The main characteristics of SBE are presented in table 28.1.

Gram-Negative Septicemia Septicemia is a common nosocomial illness, with an estimated 400,000 cases occurring in the United States each year. Approximately 30% of the cases are caused by Gram-negative bacteria. Endotoxin release by Gram-negative bacteria can lead to shock and death. ■ endotoxic shock, p. 407

Symptoms The symptoms of septicemia include violent shaking, chills, and fever, often accompanied by anxiety and rapid breathing. If

TABLE 28.1 Subacute Bacterial Endocarditis Symptoms

Fever, loss of energy over a period of weeks or months; sometimes, a stroke

Incubation period

Poorly defined, usually weeks

Causative agents Usually oral a-hemolytic viridans streptococci or Staphylococcus epidermidis

Pathogenesis

Normal microbiota gain entrance to bloodstream through dental procedures, other trauma; in an abnormal heart, turbulent blood flow causes formation of a thin clot that traps circulating organisms; a biofilm forms, makes them inaccessible to phagocytic killing; pieces of clot break off, block important blood vessels, leading to tissue death.

Epidemiology

Persons at risk are mainly those with hearts that have congenital defects or are damaged by disease such as rheumatic fever; situations that cause bacteremia.

Prevention and treatment

Administration of an antibiotic immediately prior to anticipated bacteremia, such as before dental work. Treatment: Bactericidal antibiotics given together, such as penicillin and gentamicin.

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28.2 Bacterial Diseases of the Blood Vascular System

septic shock develops, urine output drops, respiration and pulse become more rapid, and the arms and legs become cool and dusky-colored.

SHOCK IMPAIRED O2 EXCHANGE Fever

Causative Agents

Cytokines released

Macrophages activated

Pathogenesis

receptors, p. 355

Interleukin-1 (IL-1) is another cytokine released from macrophages. Besides acting with TNF to cause fever and the release of leukocytes from bone marrow, it has many other effects. One potentially harmful action is to cause the release of proteolytic enzymes from neutrophils.

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Increased adhesiveness of PMNs

Increased leakage of plasma from blood vessels

Decreased muscle tone of heart and arteries

Probably because they possess endotoxin, Gram-negative bacteria are more likely to cause fatal septicemias than are other infectious agents. Shock is common, and despite treatment, only about half of all people afflicted with this kind of infection survive. Cultures of blood from these patients usually reveal facultative anaerobes such as Escherichia coli. Among the aerobic, Gram-negative, rodshaped bacteria encountered in septicemia are organisms commonly found in the natural environment, such as Pseudomonas aeruginosa. Some of the Gram-negative organisms that cause septicemia are anaerobes. For example, Bacteroides sp., which make up a sizable percentage of the normal microbiota of the large intestine and the upper respiratory tract, cause many septicemia cases. ■ enterobacteria, p. 262 ■ Pseudomonas, p. 261

Septicemia almost always originates from an infection somewhere in the body other than the bloodstream—a kidney infection, for example. Alterations in normal body defenses as the result of medical treatments, such as surgery, placement of catheters, and medications that interfere with the immune response, may allow microorganisms that normally have little invasive ability to infect the blood. Endotoxin is released from the outermost cell walls of Gram-negative bacteria growing in a localized infection or in the bloodstream. Unfortunately, antibiotics that act against the bacterial cell wall can also enhance the release of endotoxin from the organisms. These antibiotics are typically used in treating Gramnegative bacterial infections. ■ endotoxin, p. 407 The response of the body cells to endotoxin is appropriate for localizing Gram-negative bacterial infections in tissues and killing the invaders. When localization fails and endotoxin enters the circulation, however, it causes the nearly simultaneous triggering of macrophages throughout the body and a cascade of harmful events (figure 28.3). Although macrophages normally are of central importance in body defense, they also play a key role in septic shock. The interaction of endotoxin with toll-like receptors in macrophage cell membranes causes the cell to synthesize and release pro-inflammatory cytokines. For example, tumor necrosis factor (TNF) is released from macrophages within minutes of exposure to endotoxin. TNF has diverse effects, one of which is a change in the setting of the body’s thermostat, causing the temperature to rise. TNF also causes circulating polymorphonuclear neutrophils (PMNs) to adhere to capillary walls, leading to large accumulations of these cells in tissues such as the lung, which have large populations of macrophages. Experimentally, antibody against TNF gives substantial protection against endotoxic shock but its use in humans has been disappointing. ■ cytokines, p. 353 ■ toll-like

679

Gram-negative bacterial infection Complement activated

Clotting activated Endotoxin in bloodstream

Complement components

Leukocytes attracted to lung tissue

Lysosomal enzymes released from leukocytes

Disseminated intravascular coagulation

Depletion of clotting proteins

Tissue damage from clots in capillaries

Increased capillary leakage of plasma LUNG TISSUE DAMAGE

HEMORRHAGE

FIGURE 28.3 Events in Gram-Negative Septicemia

Macrophages also synthesize and secrete complement system proteins. Components of activated complement attract leukocytes and cause them to release tissue-damaging lysosomal enzymes. Activated complement also causes capillaries to leak excessive amounts of plasma. ■ complement system, p. 355 The circulating proteins responsible for blood clotting are also activated by endotoxin. Activation causes small clots to form, plugging capillaries, cutting off blood supply, and causing tissue necrosis. Paradoxically, this condition, called disseminated intravascular coagulation (DIC), is often accompanied by hemorrhage, bleeding. This is because not enough clotting proteins are left to stop blood from flowing out of damaged blood vessels. These harmful effects of endotoxemia—endotoxin circulating in the bloodstream—are made worse by the hypotension (low blood pressure) that usually is present. The hypotension is caused by decreased muscular tone of the heart and blood vessel walls, and the low blood volume that results from leakage of plasma out of the blood vessels. Current evidence indicates that the release

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of cytokines and their effects on the heart and blood vessels play a key role in causing hypotension in Gram-negative septicemia. Shock results when the blood pressure falls so low that vital organs are no longer supplied with adequate amounts of blood to maintain their function. Although multiple organs are affected by endotoxemia, the lung is particularly vulnerable to serious, irreversible damage because of its high concentrations of tissue macrophages. Cytokines released from these macrophages in response to endotoxin attract leukocytes, which in turn discharge tissue-destroying enzymes. The resulting damage to lung tissue often results in death despite successful cure of the individual’s infection and correction of shock.

Epidemiology Gram-negative septicemia is mainly a nosocomial disease, reflecting the high incidence of Gram-negative bacteremia in hospitalized patients with impaired host defenses. Patients with cancers and other malignancies, diabetes, and organ transplants are particularly vulnerable. There is a general trend toward an increasing incidence of the disease that relates to longer life span, antibiotic suppression of normal microbiota, immunosuppressive medications, and medical equipment where biofilms readily develop, such as respirators, and catheters placed in blood vessels and the urinary system.

Prevention and Treatment Prevention of septicemia depends largely on the prompt identification and effective treatment of localized infections, particularly in people whose host defenses are impaired. Also, conditions such as bedsores and pyelonephritis, which commonly lead to septicemia in patients with cancer and diabetes, can usually be prevented. For treatment, antimicrobial medications directed against the causative organism are given. Measures are taken to correct shock and poor oxygenation. Despite these treatments, the mortality rate remains high, generally 30% to 50%, partly because most of the patients have serious underlying conditions. Treatment with monoclonal antibody directed against endotoxin or TNF has shown some benefit when given early in the illness before shock develops. Drotrecogin alpha, another medication being evaluated, is activated human protein C produced by recombinant technology. Protein C normally acts to oppose the effects of cytokines such as TNF and IL-1. Evaluation of these kinds of treatments is difficult because many of the patients have underlying life-threatening illnesses in addition to their septicemia. ■ pyelonephritis, p. 621 ■ monoclonal antibodies, p. 439

MICROCHECK 28.2 Bacteria of low virulence can cause serious, even fatal, infections in individuals whose only defect is a structural abnormality of the heart. A systemic infection represents failure of the body’s mechanisms for keeping infections localized to one area. The inflammatory response, although vitally important in localizing infections, can be life-threatening if generalized. People die of Gram-negative septicemia despite antibacterial therapy because of the endotoxin-mediated release of cytokines in the lung and bloodstream. ✓ What is a “systemic” infection? ✓ What is the difference between bacteremia and septicemia? ✓ Why might clots on the heart valves make microorganisms inaccessible to phagocytic killing?

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28.3 Bacterial Diseases of the Lymph Nodes and Spleen Focus Points Compare and contrast the epidemiology of tularemia and brucellosis. Give reasons why plague is listed as a category A bioterrorism disease.

Enlargement of the lymph nodes and spleen is a prominent feature of diseases that involve the mononuclear phagocyte system. Three examples of these diseases—tularemia, brucellosis, and plague—are discussed next. All three are now uncommon human diseases in the United States, but they represent a constant threat because of their widespread existence in animals. Understanding these diseases is the best protection against contracting them. ■ mononuclear phagocyte system, p. 350

“Rabbit Fever” (Tularemia) Tularemia is widespread among wild animals in the United States, involving species as diverse as rabbits, muskrats, and bobcats. Many human cases are acquired when people are skinning animals that appear to be free of disease. The causative organism enters through unnoticed scratches or by penetration of a mucous membrane. The disease can also be acquired from the bites of flies and ticks and by inhalation of the causative organism. It is potentially a disease transmitted by bioterrorism.

Symptoms Tularemia is characterized by development of a skin ulceration and enlargement of the regional lymph nodes 2 to 5 days after a person is bitten by a tick or insect or handles a wild animal. The usual symptoms of fever, chills, and achiness that occur in many other infectious diseases are also present in tularemia. When contracted by inhalation, there is also a dry cough and pain beneath the sternum (breastbone) due to enlarged lymph nodes. Symptoms usually clear in 1 to 4 weeks, but sometimes they last for months.

Causative Agent Tularemia is caused by Francisella tularensis, a non-motile, aerobic, Gram-negative rod that derives its name from Edward Francis, an American physician who studied tularemia in the early 1900s, and from Tulare County, California, where it was first studied. The organism is unrelated to other common human pathogens and is unusual in that it requires a special medium enriched with the amino acid cysteine in order to grow.

Pathogenesis Typically, F. tularensis causes a steep-walled ulcer where it enters the skin (figure 28.4). Lymphatic vessels draining the area carry the organisms to the regional lymph nodes. These nodes then become large and tender, and they may become filled with pus and

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28.3 Bacterial Diseases of the Lymph Nodes and Spleen

681

Hemisphere, including all the states of the United States except Hawaii. In the eastern United States, human infections usually occur in the winter months, as a result of people skinning rabbits. Hence, the common name, “rabbit fever.” Hunters and trappers in various parts of the country, however, have contracted the disease from muskrats, beavers, squirrels, deer, and other wild animals. The animals are generally free of illness. In the West, infections mostly result from the bites of infected ticks and deer flies and, thus, usually occur during the summer. Generally, 150 to 250 cases of tularemia are reported each year from counties across the United States (figure 28.5). Especially in Europe, epidemics of inhalation tularemia have occurred from dust arising from mowing lawns or rodent-infested buildings. Because of its very low infecting dose, it has long been included among biological warfare agents, and in the United States F. tularensis is listed among the category A (highest risk) agents of biological terrorism. FIGURE 28.4 Tularemic Ulcer of the Thumb This kind of lesion is

Prevention and Treatment

generally acquired through skinning rabbits or other wild game. Tularemia can also be contracted from insect or tick bites, and by inhalation.

Rubber gloves and goggles or face shields are advisable for people skinning wild animals; remember that the bacteria can enter the body via mucous membranes. Insect repellants and protective clothing help guard against insect and arachnid vectors. It is a good practice to inspect routinely for ticks after exposure to the out-of-doors and to remove them carefully. A vaccine is available for laboratory workers, veterinarians, trappers, game wardens, and others at high risk for infection. Most cases of tularemia are effectively treated with ciprofloxacin or gentamicin. The main features of this disease are summarized in table 28.2.

drain spontaneously. Later, the organisms spread to other parts of the body via the lymphatics and blood vessels. Pneumonia, which occurs in 10% to 15% of the cases, occurs when the organisms infect the lung from the bloodstream or by inhalation. Without treatment, tularemic pneumonia has a mortality rate as high as 30%. Francisella tularensis is ingested by phagocytic cells and grows within them. This may explain why tularemia persists in some people despite the high titers of antibody in their blood. Cell-mediated immunity is responsible for ridding the host of this infection, as it is with other pathogens that can live intracellularly. Both delayed hypersensitivity and serum antibodies quickly arise during infection, so that even without treatment over 90% of infected people survive. ■ cell-mediated immunity, p. 367 ■ delayed

“Undulant Fever” (Brucellosis, “Bang’s Disease”) Only about 150 cases of human brucellosis are reported each year in the United States. Between 10 and 20 times that number of cases, however, go unreported annually. Brucellosis is often called “undulant fever,” or “Bang’s disease,” after Frederik Bang (1848–1932), a Danish veterinary professor who discovered the cause of cattle brucellosis.

hypersensitivity, p. 422

Epidemiology Tularemia has been contracted from the bite of a pet hampster. It occurs among wild animals in many areas of the Northern

9

2

1

FIGURE 28.5 Reported Cases of Tularemia, United States, 2005 About 60% of the cases were reported

8

from Arkansas, Massachusetts (Martha’s Vineyard), Missouri, and Oklahoma.

2

2

2

2

8 1 1

5

5

27

3

3 20 2

2

12

2

1

2

9 19 1 1

1 1 1

Reported cases 0 1 or more

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CHAPTER TWENTY EIGHT Blood and Lymphatic Infections

TABLE 28.2 “Rabbit Fever” (Tularemia) Symptoms

Ulcer at site of entry, enlarged lymph nodes in area, fever, chills, achiness

Incubation period

1 to 10 days; usually 2 to 5 days

Causative agent

Francisella tularensis, an aerobic, Gramnegative rod

Pathogenesis

Organisms are ingested by phagocytic cells, grow within these cells, and then spread throughout body.

Epidemiology

Present among wildlife in most states of the United States. Risk mainly to hunters, trappers, game wardens, and others who handle wildlife. Mucous membrane or broken skin penetration of the organism, as with skinning rabbits, for example; bite of infected insect or tick. Occasionally, inhalation.

Prevention and treatment

Vaccination for high-risk individuals; avoiding bites of insects and ticks; wearing rubber gloves, goggles, when skinning rabbits; taking safety precautions when working with organisms in laboratory. Treatment: gentamicin or ciprofloxacin.

Symptoms The onset of brucellosis is usually gradual, and the symptoms are vague. Typically, patients complain of mild fever, sweating, weakness, aches and pains, enlarged lymph nodes, and weight loss. The recurrence in some cases of fevers over weeks or months gave rise to the alternative name, “undulant fever.” Even without treatment, most cases recover within 2 months, and only 15% will be symptomatic for more than 3 months.

Causative Agent Brucella sp. are small, aerobic, nonmotile, Gram-negative rods with complex nutritional requirements. Four varieties of the genus Brucella cause brucellosis in humans. DNA studies show that all members of the genus fall into a single species, Brucella melitensis, but traditionally, the different varieties were assigned species names depending largely on their preferred host: B. abortus invades cattle; B. canis, dogs; B. melitensis, goats; and B. suis, pigs. The distinctions between the various strains are mainly useful epidemiologically and generally have little pathogenic significance.

Pathogenesis As with tularemia, the organisms responsible for brucellosis penetrate mucous membranes or breaks in the skin and are disseminated via the lymphatic and blood vessels to the heart, kidneys, and other parts of the body. The spleen enlarges in response to the infection. Like Francisella tularensis, Brucella sp. are not only resistant to phagocytic killing but also can grow intracellularly in phagocytes, where they are inaccessible to antibody and some antibiotics. Mortality, generally due to endocarditis, is about 2%. Bone infection—osteomyelitis—is the most frequent serious complication.

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Epidemiology Brucellosis is typically a chronic infection of domestic animals involving the mammary glands and the uterus, thereby contaminating milk and causing abortions in the affected animals. Abortion is not a feature of human disease. Sixty percent of the cases of brucellosis occur in workers in the meat-packing industry; less than 10% arise from ingesting raw milk or other unpasteurized dairy products. Worldwide, brucellosis is a major problem in animals used for food, causing yearly losses of many millions of dollars. In the United States, hunters have acquired infections from elk, moose, bison, caribou, and reindeer. About 20% of the Yellowstone Park bison herd is infected, and more than 1,000 have been killed when they wander outside the park because of fear that they will transmit the disease to cattle. B. melitensis is listed as a category B (intermediate risk to national security) bioterrorism agent.

Prevention and Treatment The most important control measures against brucellosis are pasteurization of dairy products and inspection of domestic animals for evidence of the disease. The use of goggles or face shield and rubber gloves helps protect veterinarians, butchers, and slaughterhouse workers; remember, the bacterium can penetrate mucous membranes. An attenuated vaccine effectively controls the disease in domestic animals. Treatment using tetracycline with rifampin for 6 weeks is usually effective. ■ pasteurization, p. 112 Table 28.3 gives the main features of brucellosis.

“Black Death” (Plague) Plague, once known as the “black death,” was responsible for the death of approximately one-fourth of the population of Europe between 1346 and 1350. Crowded conditions in the cities and a large rat population undoubtedly played major roles in the spread of the disease. Plague is a potential bioterrorism disease, listed as category A.

Symptoms The symptoms of plague develop abruptly 1 to 6 days after an individual is bitten by an infected flea. The person characteristically develops markedly enlarged and tender lymph nodes called buboes—hence the name bubonic plague—in the region that receives lymph drainage from the area of the flea bite. High fever, shock, delirium, and patchy bleeding under the skin quickly develop. Some victims develop cough and bloody sputum indicating lung involvement; these cases are called pneumonic plague.

Causative Agent Plague is caused by Yersinia pestis, which, like other enterbacteria, is a facultatively anaerobic, Gram-negative rod. It is non-motile and grows best at 28°C. The organism resembles a safety pin in stained preparations of material taken from infected lymph nodes because the ends of the bacterium stain more intensely than does the middle (figure 28.6). Extensive study has revealed some of the complex mechanisms by which Y. pestis achieves its impressive virulence. The bacterium has plasmids that code for virulence factors. One plasmid codes

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28.3 Bacterial Diseases of the Lymph Nodes and Spleen

TABLE 28.3

“Undulant Fever” (Brucellosis, “Bang’s Disease”)

➀ Causative organism Brucella

melitensis enters the body through mucous membranes, skin abrasions or ingestion of unpasteurized milk.

➁ The bacteria are taken up by

➂ The bacteria enter the lymphatics and bloodstream and are carried throughout the body.

Symptoms

Fever, body aches, weight loss, enlargement of lymph nodes; symptoms may subside without treatment but then recur

Incubation period

Usually 5 to 21 days

Causative agent

Brucella melitensis, a small, aerobic, Gram-negative rod

Pathogenesis

Organisms penetrate mucous membranes and are carried to heart, kidneys, and other parts of the body via the blood and lymphatic system; they are resistant to phagocytic killing and grow within these cells.

Epidemiology

Main sources of human infections: domestic animals. Disease also occurs in wild animals such as moose, caribou, bison; butchers, farmers, veterinarians, those who drink unpasteurized milk are at risk.

Prevention and treatment

Vaccination of domestic animals; pasteurization of milk and milk products; gloves and face protection. Treatment: tetracycline with rifampin.

1 1

phagocytes but resist digestion and grow within cells.

3 4 5

➃ Infection is established in other

body tissues, such as the heart valves, kidneys, and bones.

➄ Osteomyelitis is the most common

4

serious complication. Most deaths are due to endocarditis.

1 4 5

5 mm

FIGURE 28.6 Yersinia pestis Each pole of the organism is stained intensely by certain dyes, producing a safety pin appearance.

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683

for a virulence factor called Pla, an important protease that causes blood clots to dissolve by activating a substance in the body called plasminogen activator. Another activity of the Pla protease is that it destroys the C3b and C5a components of the complement system. ■ plasmids, pp. 68, 205 Another plasmid codes for a group of proteins that interfere with phagocytosis. These proteins are referred to as Yops, for Yersinia outer membrane proteins. The bacterium loses its virulence if this plasmid is lost. Yops are injected into host cells by a type III secretion system. They are responsible for several kinds of actions, the sum of which is to interfere with the phagocytes that normally would kill Y. pestis and initiate an immune response to the bacterium. A plasmid-coded protein, V (for virulence), regulates the type III secretion system. ■ secretion systems, p. 398 Yet another plasmid codes for an important antigen, F1. This protein becomes part of an antiphagocytic capsule and is an important component of a plague vaccine. The stimulus for capsule production is the relatively increased temperature of a

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CHAPTER TWENTY EIGHT Blood and Lymphatic Infections

mammalian host (37°C for humans) compared with that of a flea (about 26°C). The genes for some other Y. pestis virulence factors reside on the bacterial chromosome. These encode resistance to the lytic action of activated complement, mechanisms for storing hemin and using it as an iron source, and production of a pilus adhesion (PsaA). These genes are probably activated as a result of intracellular growth. ■ iron requirement, p. 93 ■ adhesins, p. 398 A summary of these virulence factors is presented in table 28.4. (a)

Pathogenesis Masses of Y. pestis partially obstruct the digestive tract of infected rat fleas (figure 28.7). Consequently, not only is the flea ravenously hungry, causing it to bite repeatedly, but it also regurgitates infected material into the bite wounds. Chronically infected fleas do not have their digestive tract obstructed but discharge Y. pestis in their feces; the organisms can then be introduced into human tissue when a person scratches the flea bite. The Y. pestis protease Pla is essential for the spread of the organisms from the site of entry of the bacteria by clearing the lymphatics and capillaries of clots. The organisms are carried to the regional lymph nodes, where they are taken up by macrophages. The bacteria are not killed by the macrophages and instead multiply and produce F1 capsular material and other virulence factors in response to the intracellular growth conditions. The macrophages die and release the bacteria, which now are encapsulated and express Yops, pilus adhesin, complement resistance, and heme storage. After several days, an acute inflammatory reaction develops in the nodes, producing enlargement and marked tenderness. The lymph nodes become necrotic, allowing large numbers of virulent Y. pestis to spill into the bloodstream. This stage of the disease is called septicemic plague, and endotoxin release results in shock and disseminated intravascular coagulation (DIC). Infection of the lung from the bloodstream occurs in 10% to 20% of the cases, resulting in pneumonic plague. Organisms transmitted to another person from a case of pneumonic plague are already fully virulent and, therefore, are especially dangerous. The dark hemorrhages into the skin from DIC and the dusky color of skin and mucous membranes probably inspired the name “black death” for the plague. The mortality rate for persons with untreated bubonic plague is between 50% and 80%. Untreated pneumonic plague progresses rapidly and is nearly always fatal within a few days.

(b)

FIGURE 28.7 Fleas Following a Blood Meal (a) Healthy flea; (b) flea with obstruction due to Yersinia pestis infection.

Epidemiology Plague is endemic in rodent populations of all continents except Australia. In the United States, the disease is mostly confined to wild rodents in about 15 states in the western half of the country. Prior to 1974, only a few cases of plague were reported each year. Over the last few decades, however, the number of cases has generally been higher, averaging about 15 reported cases per year, as towns and cities expand into the countryside. Prairie dogs, rock squirrels, and their fleas constitute the main reservoirs, but rats, rabbits, dogs, and cats are potential hosts. Hundreds of species of fleas can transmit plague, and the fleas can remain infectious for a year or more in abandoned rodent burrows. Epidemics in humans, initiated by infected rodent fleas, can spread from one person to another by household fleas, as well as by respiratory droplets produced by coughing patients with pneumonic plague. Pneumonic plague is the most dangerous because Y. pestis is fully virulent at the time of transmission. ■ endemic disease, p. 451 ■ reservoir, p. 453

TABLE 28.4 Virulence Factors of Yersinia pestis Factor

Coded by

Action

Pla (protease)

9.5-kbp plasmid

Activates plasminogen activator; destroys C3b, C5a

Yops (proteins)

72-kbp plasmid

Interferes with phagocytosis and the immune response by differing mechanisms

V antigen

Plasmid

Controls type III secretion system

F1

110-kbp plasmid

Forms antiphagocytic capsule at 37°C

PsaA (adhesin)

Chromosome

Role in attachment to host cells

Complement resistance

Chromosome

Protects against lysis by activated complement

Iron acquisition

Chromosome

Traps hemin and other iron-containing substances; stores iron compounds intracellularly

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685

MICROCHECK 28.3

Prevention and Treatment Plague epidemics can be prevented by rat control measures such as proper garbage disposal, constructing rat-proof buildings, installing guards on the ropes that moor ocean-going ships to keep rats from entering, and rat extermination programs. The latter must be combined with the use of insecticides to prevent the escape of infected fleas from dead rats. The killed whole cell vaccine used for many years is no longer available commercially. It did not provide protection against pneumonic plague, the primary concern in the event of biological warfare. New, genetically engineered vaccines containing the F1 and V antigens are being evaluated under a joint agreement among the United States, Canada, and the United Kingdom. The antibiotic tetracycline can be given as a preventive for someone exposed to plague, and is useful in controlling epidemics because of its immediate effect. Treatment with gentamicin, ciprofloxacin, or doxycycline is effective, especially if given within 24 hours

Generally, tularemia is a bacteremic disease of wild animals transmitted to humans by exposure to their blood or tissues, or by biting insects. Brucellosis is most commonly a disease of domestic animals transmitted to humans when individuals handle the animals’ flesh or drink unpasteurized milk. Plague is endemic in rodents in the western United States and is transmitted to humans by flea bites. Unlike tularemia and brucellosis, plague has the potential to spread rapidly from human to human by coughing, with a high fatality rate. ✓ Workers in what industry are especially likely to contract brucellosis? How can they protect themselves from the disease? ✓ How would growth within phagocytes protect Francisella tularensis from destruction by antibodies? ✓ How would crowded conditions in cities favor spread of plague?

of the onset of symptoms of the disease. The main features of plague are presented in table 28.5.

TABLE 28.5 “Black Death” (Plague) ➀ Causative organism Yersinia pestis is contracted from the bite of an infected flea or scratching skin contaminated by the flea’s feces.

➁ The bacteria are carried by the lymphatics to regional lymph nodes. ➂ Phagocytes ingest the bacteria but the intracellular conditions activate capsule production and other genes responsible for virulence.

7

6

5

➃ Fully virulent bacteria break out of the phagocytes, infect the nodes, producing buboes, bubonic plague.

Symptoms

Sudden onset of high fever, large lymph nodes called buboes, skin hemorrhages; sometimes bloody sputum

Incubation period

Usually 1 to 6 days

Causative agent

Yersinia pestis, a Gram-negative rod; an encapsulated enterobacterium with multiple plasmid- and chromosomecoded virulence factors

Pathogenesis

Enters the body with bite of infected flea. Bacteria taken up by macrophages. Intracellular environment triggers them to transform into encapsulated organisms capable of elaborating multiple virulence factors that allow attachment to host cells, and provide defense against phagocytes and the immune system.

Epidemiology

Endemic in rodents and other wild animals, and their fleas, particularly in the western states of the United States. Can be introduced into human habitations by pets, transmitted from human to human by fleas; with pneumonic plague, by coughing. Pneumonic plague is the most dangerous because Y. pestis is fully virulent at the time of transmission.

Prevention and treatment

Currently no vaccine available; new vaccines are under evaluation. Avoid contact with wild rodents and their burrows. Insecticides and rat control. Prompt diagnosis and antibacterial treatment necessary to prevent high mortality.

➄ The bacteria may be carried into the bloodstream, causing septicemic plague.

➅ The lungs can become infected, producing the highly contagious and lethal pneumonic plague.

➆ Bacteria exit with coughing.

2 4 3

1

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28.4 Viral Diseases of the Lymphoid and Blood Vascular Systems Focus Points Outline the pathogenesis of infectious mononucleosis. Describe how infectious mononucleosis is transmitted. Explain why yellow fever has not been eradicated despite the availability of an effective vaccine.

A number of viral illnesses mainly involve the lymphoid system and blood vessels. Two notable examples discussed in chapter 29 are the human immunodeficiency virus (HIV), the cause of AIDS; and cytomegalovirus, which causes lymph node enlargement in healthy adults and more serious disease in infants. Infectious mononucleosis has similar symptoms, but it is a much more familiar disease. Yellow fever more prominently involves the circulatory system. ■ human immunodeficiency virus disease, p. 699 ■ cytomegalovirus disease, p. 715

“Kissing Disease” (Infectious Mononucleosis, “Mono”) Infectious mononucleosis (“mono”) is a disease familiar to many students because of its high incidence among people between the ages of 15 and 24 years. The term mononucleosis refers to the fact that people afflicted with this condition have an increased number of mononuclear leukocytes in their blood. ■ leukocytes, p. 350

Symptoms Typically, symptoms of infectious mononucleosis appear after a long incubation period, usually 30 to 60 days. They consist of fever, a sore throat covered with pus, marked fatigue, and enlargement of the spleen and lymph nodes. In most cases, the fever and sore throat are gone in about 2 weeks; the enlarged lymph nodes in 3. Persons can usually return to school or work within 4 weeks, but some suffer severe exhaustion and difficulty concentrating that prohibits return to normal activities for months.

Causative Agent Infectious mononucleosis is caused by the Epstein-Barr (EB) virus, named after its discoverers, M. A. Epstein and Y. M. Barr. It is a double-stranded DNA virus of the herpesvirus family, and although identical in appearance to the other known herpesviruses that cause human disease, it is not closely related to any of them. This interesting virus was discovered in the early 1960s when it was isolated from Burkitt’s lymphoma, a malignant tumor derived from B lymphocytes, common in parts of Africa. Subsequent studies showed that EB virus is the cause of infectious mononucleosis. ■ B lymphocytes, p. 352

Pathogenesis Primary infection with EB virus is analogous to throat infections with the herpes simplex virus in that both viruses initially infect the mouth and throat and then become latent in

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another cell type. The probable sequence of events is shown in figure 28.8. Following replication in epithelium of the mouth, saliva-producing glands, and throat, the Epstein-Barr virus is carried by the lymphatics to the lymph nodes. There it infects B lymphocytes, which have specific surface receptors for the virus. During the illness, up to 20% of the circulating B lymphocytes are infected with the virus. The B-cell infection can be (1) productive, in which the virus replicates and kills the B cell; or (2) non-productive, in which the virus establishes a latent infection, existing as either extrachromosomal circular DNA or integrated into the host cell chromosome at random sites. For most of these cells, the infection is non-productive, but profound changes in the cells result from the infection. The virus activates the B cells, causing multiple clones of B lymphocytes to proliferate and produce immunoglobulin. The infected cells are also “immortal,” meaning that they can reproduce indefinitely in laboratory cultures. The T lymphocytes respond actively to the infection and destroy B cells with productive infections because these B cells display viral antigens on their surfaces. The abnormal-appearing lymphocytes characteristically seen in smears of the patient’s blood are effector cytotoxic T cells responding to the infected B cells (figure 28.9). The proliferating lymphocytes are responsible for the large numbers of mononuclear cells that give the disease its name. Their numbers and appearance sometimes mistakenly suggest the diagnosis of leukemia, which is disproved when the patient spontaneously recovers. In many cases, a consequence of B-cell infection is the appearance of an IgM antibody that will react with an antigen on the red blood cells of certain animal species, notably sheep, horses, and oxen. This kind of antibody arising against antigens of another animal is called a heterophile antibody. It generally has no pathologic significance, but its presence helps in diagnosing infectious mononucleosis. The antibody does not react specifically with EB virus. Enlargement of the lymph nodes and spleen reflects the active replication of lymphocytes. Hemorrhage from rupture of the enlarged spleen is the chief cause of the rare deaths due to infectious mononucleosis. It is most likely to occur within 3 to 4 weeks of the onset of illness. Patients are instructed to avoid exertion and contact sports, but almost half of the cases of splenic rupture occur in the absence of trauma. The possibility that EB virus could play a role in causing certain malignant tumors has been intensely investigated. The malignancies most closely related to EB virus infection—Burkitt’s lymphoma and nasopharyngeal carcinoma—cluster dramatically in certain populations. This suggests that factors other than simple EB viral infection must be present for these malignancies to develop. EB virus-associated Burkitt’s lymphoma cases occur mainly in children in East Africa and New Guinea, whereas nasopharyngeal carcinoma is common in Southeast China. The EB virus genome is detectable in 90% to 100% of these two malignancies. Infectious mononucleosis has not been shown to increase risk of malignant tumors in otherwise healthy American college students. Evidence suggests that EB virus may be a factor, however, in some malignancies in patients with immunodeficiency from AIDS or organ transplantation.

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28.4 Viral Diseases of the Lymphoid and Blood Vascular Systems EB virus

Epithelium

687

Activated lymphocyte EB virus attaches to and infects epithelium of the throat, where it replicates and causes pharyngitis.

The infected B lymphocytes actively replicate and differentiate into cells producing random immunoglobulins, including heterophile antibody.

Lymphatic vessel Blood vessel

Plasma cells

Lymphatic vessel

Virions enter the lymphatic vessels and are carried to the lymph nodes. Some virions escape the lymph node trap and are carried to the bloodstream.

Heterophile antibody Productively infected B cell

T cells respond to infection and destroy the lymphocytes replicating EB virus.

Lymph node Lysed B cell Virions attach specifically to B lymphocytes and infect them, producing either latent or productive infections.

Effector cytotoxic T cell Latently infected B cell Latently infected B lymphocytes become immortal. They are not attacked by T cells.

Viral genome Productively infected B cell

Latently infected B cell

FIGURE 28.8 Pathogenesis of Infectious Mononucleosis

Epidemiology The EB virus is distributed worldwide and infects individuals in crowded, economically disadvantaged groups at an early age without producing significant illness. In such populations, the characteristic infectious mononucleosis syndrome is quite rare. More affluent populations such as students entering col-

(a)

lege in the United States often have escaped past infection with the agent and lack immunity to EB virus. In any year, an estimated 1.5 million college students will either have had the disease or will get it during the college year. Infectious mononucleosis occurs almost exclusively in adolescents and adults who lack antibody to the virus. Even in the age group of 15 to

(b)

FIGURE 28.9 Normal and Infectious Mononucleosis Blood Smears Photomicrographs of (a) a normal blood smear showing two polymorphonuclear neutrophils (PMNs), a lymphocyte and a monocyte and (b) an infectious mononucleosis blood smear showing an abnormal lymphocyte.

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CASE PRESENTATION The patients were two American boys, 7 and 9 years old, living in Thailand, who almost simultaneously developed irritated eyes and slightly runny noses, progressing to fever, headache, and severe muscle pain. It hurt them to move their eyes, and they refused to walk because of pain in their legs. The symptoms subsided after a couple of days, only to recur at lesser intensity. No treatment was given, and they were completely back to normal within a week. Their illness was diagnosed as dengue (pronounced DEN-gay), also known as “breakbone fever.” 1. What causes dengue and where does it occur? 2. Why is dengue important? 3. What is known about the pathogenesis of dengue? 4. What can be done to prevent dengue? Discussion 1. Dengue is caused by any of four closely related flaviviruses—dengue 1, 2, 3, and 4. The disease occurs in large areas of the tropics and subtropics around the world. In the Americas, the disease is transmitted mainly by Aedes aegypti mosquitoes, which have staged a comeback after being almost eradicated in the 1960s. This vector now occurs year-round along the Gulf of Mexico. Serious

dengue epidemics occurred in Brazil and Cuba in 2002. 2. The two individuals presented here had a mild form of the disease that characteristically involves newcomers to an area where the disease commonly occurs. In endemic areas, the disease is characterized by fever, headache, muscle aches, rash, nausea, and vomiting. In a small percentage of cases, however, the effects of dengue infection are much more serious, resulting in dengue hemorrhagic fever. This form of the disease is characterized by bleeding and leakage of fluid from the capillaries. An important result is that the blood pressure drops and the blood thickens. With expert treatment, the mortality is about 1% to 2%. Dengue shock syndrome is another potential development. It is characterized by profound shock and disseminated intravascular coagulation (DIC) and has a mortality above 40%. 3. About 90% of the cases of hemorrhagic fever or shock occur in subjects who have previously been infected by a dengue virus and have antibody to it. The remaining cases occur largely in infants who still have transplacentally acquired maternal antibody against dengue viruses. These antibodies, whether from earlier infection or from the

24 years, however, only about half of the EB virus infections produce infectious mononucleosis; the remainder develop few or no symptoms. EB virus is present in the saliva for up to 18 months after infectious mononucleosis, and thereafter it occurs intermittently for life. Continuous salivary shedding of virus is common in people with AIDS or other immunodeficiencies. Mouth-tomouth kissing is an important mode of transmission of infectious mononucleosis in young adults, giving rise to the name “kissing disease.” The donor of the virus is usually asymptomatic and may have been infected in the past without developing symptoms of infectious mononucleosis. By middle age, most people have demonstrable antibody to the virus, indicating past infection. There is no animal reservoir.

Prevention and Treatment Prevention is aided by avoiding the saliva of another person, as well as objects such as toothbrushes or drinking glasses possibly contaminated with another’s saliva. No vaccine for infectious mononucleosis is available. Antiviral medications such as acyclovir and famciclovir inhibit productive infection by the virus and are of value in rare serious cases; however, they have no activity against the latent infection. Cortisonelike medication is sometimes useful in relieving airway obstruction from swollen tissue. Table 28.6 gives the main features of infectious mononucleosis.

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TABLE 28.6

mother, attach to the infecting dengue virus strain and thereby promote its uptake by macrophages. The virus, instead of being killed, reproduces in the macrophage. This results in the death of the macrophage and release of chemicals that cause leaky capillaries and shock. T lymphocytes may also play a role in this process in older children and adults. Evidence also exists that the virus causes a depression of the bone marrow, accounting for the very low white blood cell and platelet counts seen in dengue. 4. Scientists at Mahidol University in Bangkok and other research centers around the world are working on vaccines designed to bring dengue under control. At present, control efforts are largely directed at killing mosquitoes and their larvae and eliminating water containers around houses where the mosquitoes breed. Scientists at Colorado State University have successfully genetically engineered mosquitoes to render their cells incapable of reproducing dengue virus. This was accomplished by using another virus to introduce an antisense segment of the dengue genome into the mosquito cells. This was a dramatic accomplishment, but years of work remain before it can play a role in the control of dengue.

“Kissing Disease” (Infectious Mononucleosis, “Mono”)

Symptoms

Fatigue, fever, sore throat, and enlargement of lymph nodes

Incubation period

Usually 1 to 2 months

Causative agent

Epstein-Barr (EB) virus, a DNA virus of the herpesvirus family

Pathogenesis

Productive infection of epithelial cells of throat and salivary ducts; latent infection of B lymphocytes; activation of B and T lymphocytes; hemorrhage from enlarged spleen is a rare but serious complication.

Epidemiology

Spread by saliva; lifelong recurrent shedding of virus into saliva of asymptomatic, latently infected individuals.

Yellow Fever Yellow fever was first recognized with an epidemic in the Yucatan of Mexico, in 1648, probably introduced there from Africa. One of the worst outbreaks of yellow fever in the twentieth century occurred in Ethiopia in the 1960s, producing 100,000 cases and 30,000 deaths. In 1989, an epidemic of yellow fever occurred in

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689

Bolivia among poor people who moved into the jungle to try to make a living growing coca. There have been no outbreaks in the United States since 1905, but the vector mosquito has reappeared in the Southeast, raising the possibility of outbreaks of the disease if the virus is again introduced.

Symptoms The symptoms of yellow fever can range from very mild to severe. Symptoms of mild disease, the most common form, may be only fever and a slight headache lasting a day or two. Patients suffering severe disease, however, may experience a high fever, nausea, bleeding from the nose and into the skin, “black vomit” (from gastrointestinal bleeding), and jaundice (hence, the name yellow fever). The mortality rate of severe yellow fever cases can reach 50% or more. The reasons for the wide variation in severity of symptoms are unknown, but probably have more to do with the size of the infecting dose and the status of human host defenses than with differences among strains of the causative virus.

Causative Agent Yellow fever is caused by an enveloped, single-stranded, positivesense RNA arbovirus of the flavivirus family. The virus multiplies in species of mosquitoes, apparently without harming them, and the mosquitoes transmit the infection to humans.

Yellow fever endemic zones in South America (a)

Pathogenesis The yellow fever virus is introduced into humans by the bite of an Aedes mosquito, the biological vector. It multiplies, enters the bloodstream, and is carried to the liver and other parts of the body. Viral liver damage results in jaundice and decreased production of clotting proteins, and injury to small blood vessels produces petechiae—tiny hemorrhages—throughout the body. The virus affects the circulatory system by directly damaging the heart muscle, by causing bleeding from blood vessel injury in various tissues, and by causing disseminated intravascular coagulation (DIC). Kidney failure is a common consequence of loss of circulating blood and low blood pressure. ■ biological vector, p. 455 ■ disseminated intravascular coagulation, p. 679

Epidemiology The reservoir of the virus is mainly infected mosquitoes and primates living in the tropical jungles of Central and South America and in Africa (figure 28.10). Periodically, the disease spreads from the jungle reservoir to urban areas, where it is transmitted to humans by Aedes mosquitoes.

Yellow fever endemic zones in Africa

Prevention and Treatment In urban areas, control of yellow fever is achieved by spraying insecticides and eliminating the breeding sites of its principal vector, Aedes aegypti. In the jungle, control of yellow fever is almost impossible because the mosquito vectors live in the forest canopy and transmit the disease among canopy-dwelling monkeys. A highly effective attenuated vaccine is available to immunize people who might become exposed, including foreign

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(b)

FIGURE 28.10 Distribution of Endemic Yellow Fever (a) South America (b) Africa. (Source: CDC Health Information for International Travel 2008.)

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CHAPTER TWENTY EIGHT Blood and Lymphatic Infections

PERSPECTIVE 28.2 Walter Reed and Yellow Fever Walter Reed was born in Virginia in 1851. After receiving medical degrees, he entered the Army Medical Corps. He was appointed professor of bacteriology at the Army Medical College in 1893, and in 1900, Reed was named president of the Yellow Fever Commission of the U.S. Army. Although improved sanitation had effectively controlled other diseases, the incidence of yellow fever remained high and its cause and transmission were unknown. Reed suspected that an insect was the vector of yellow fever. As early as 1881, Dr. Carlos Finlay of Havana, Cuba, had suggested that a mosquito might be the carrier of this disease, but he was unable to prove his hypothesis. Beginning with mosquitoes raised from eggs, Reed and the others in his commission proceeded with a series of experiments. First, the laboratory-raised mosquitoes were allowed to feed on patients with yellow fever and, second, on members of the commission. After initial failures to transmit the disease by mosquitoes, one member of the commission, Dr. James Carroll, came down with classic yellow fever 3 days

after an experimental mosquito bite. Dr. Jesse Lazear, another commission member, noted that the yellow fever patient on which the mosquito had originally fed was in his second day of the disease and that 12 days had elapsed before it bit Carroll. This timing was critical for the transmission of the disease because, as we now know, the mosquito can only contract the infection during a brief period when the patient is viremic. Then, the mosquito can only transmit the infection to another individual after the virus has replicated to a high level in the mosquito. Later, Lazear was bitten by a mosquito while working in a hospital yellow fever ward. He developed yellow fever and died. He was the only yellow fever fatality among commission members, although other volunteers lost their lives before the mysteries of this potentially fatal disease were resolved. The commission had a mosquito-proof testing facility constructed, called Camp Lazear in honor of their deceased colleague, to house volunteers for their experiments. As a result of their studies, Dr. Reed and his colleagues made the following conclusions: (1) mosqui-

travelers to the endemic areas. There is no proven antiviral treatment. ■ attenuated vaccine, p. 433 The main features of yellow fever are presented in table 28.7.

TABLE 28.7

Yellow Fever

Symptoms

Often only headache and fever. Severe cases characterized by high fever, jaundice, black vomit, and hemorrhages into the skin

Incubation period

Usually 3 to 6 days

Causative agent

Yellow fever virus, an enveloped, singlestranded RNA virus of the flavivirus family

Pathogenesis

Virus multiplies locally at site of introduction by an infected mosquito; spreads to the liver and throughout the body by the bloodstream. Virus destroys liver cells, causing jaundice and decreased production of blood-clotting proteins. Hemorrhages and decreased strength of the heart result in circulatory failure and kidney failure.

Epidemiology

Prevention and treatment

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Virus persists in forest primates and the mosquitoes that feed on them, in Africa and Central and South America; human epidemics occur when the virus infects household mosquitoes that feed on humans. There is a highly effective attenuated viral vaccine. No proven antiviral therapy is available.

toes are the vectors of the disease; (2) an interval of about 12 days must elapse between the time the mosquito ingests the blood of an infected person and the time it can transmit the disease to an uninfected person; (3) yellow fever can be transmitted from a person acutely ill with the disease to a person who has never had the disease by injecting a small amount of the ill person’s blood; (4) yellow fever is not transmitted by soiled linens, clothing, or other items that have come into contact with infected persons; and (5) yellow fever is caused by an infectious agent so small that it passes through a filter that excludes bacteria. Armed with these findings, Major William C. Gorgas, the chief sanitary officer for Havana, instituted mosquito control measures that resulted in a dramatic reduction in yellow fever cases. Later, Gorgas used mosquito control in the Panama Canal Zone to allow construction of the Panama Canal. Previously, French workers had tried to build the canal but had failed because of heavy losses from yellow fever and malaria.

MICROCHECK 28.4 Infectious mononucleosis occurs worldwide and is transmitted from person to person by saliva. Curiously, the causative virus is associated with different malignancies, but only in certain geographic areas or in AIDS patients. Yellow fever virus infects monkeys that live in tropical forests of Africa and South and Central America, and the mosquitoes that bite them. Transmission of the virus among human beings can occur wherever there is a human-biting mosquito species that is susceptible to the virus. ✓ What characteristic changes occur in the blood of patients with infectious mononucleosis? ✓ What is the name of the tumor from which EB virus was first isolated? ✓ Why does it take more than a week before a mosquito just infected with yellow fever virus can transmit the disease?

28.5 Protozoan Diseases Focus Points Outline the Plasmodium vivax life cycle. Discuss why malaria has been so difficult to control.

Protozoa infect the blood vascular and lymphatic systems of millions of people worldwide. One example, discussed in an earlier chapter, is Trypanosoma brucei, fundamentally a bloodstream

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28.5

parasite of African animals and cause of African sleeping sickness in humans. Another trypanosome, T. cruzi, causes chagas disease (American trypanosomiasis), often manifest as a chronic heart infection. Protozoans of the genus Leishmania cause visceral leishmaniasis, with enormous splenic enlargement, and a problem for American troops involved in war in the Middle East. (There is more information about leishmaniasis at the Online Learning Center www.mhhe.com/nester6.) Malaria, another protozoan disease, is much more widespread and is a leading cause of morbidity and mortality, meaning illness and death, worldwide. An estimated 300 to 500 million people become ill with malaria each year, and a child dies of the disease every 40 seconds. ■ protozoa, p. 285 ■ African sleeping sickness, p. 667

Malaria Malaria is an ancient scourge, as evidenced by early Chinese and Hindu writings. During the fourth century b.c., the Greeks noticed its association with exposure to swamps and began drainage projects to control the disease. The Italians gave the disease its name, malaria, which means “bad air,” in the seventeenth century. In early times, malaria ranged as far north as Siberia and as far south as Argentina. In 1902, Ronald Ross received a Nobel Prize for demonstrating the life cycle of the protozoan cause of malaria. Malaria is the most common serious infectious disease worldwide. In 1955, the World Health Organization (WHO) began a program for the worldwide elimination of malaria. Initially there was great success, as WHO employed insecticides such as DDT against the mosquito vector, detected infected patients by obtaining blood smears, and provided treatment for those who were infected. Fifty-two nations undertook control programs and, by 1960, 10 of them had eradicated the disease. Unfortunately, strains of Anopheles mosquitoes resistant to insecticides began to appear, and in cooperation with bureaucracy and complacency, malaria began a rapid resurgence. In 1976, the World Health Organization acknowledged that the eradication program was a failure. Today, over 300 million people are infected with malaria annually worldwide and it causes more than 1 million deaths per year. More people are dying of the disease than when the eradication programs first began. ■ DDT, p. 749

Symptoms The first symptoms of malaria are “flu”-like, with fever, headache, and pain in the joints and muscles. These symptoms generally begin about 2 weeks after the bite of an infected mosquito, but in some cases they can begin many weeks afterward. After 2 or 3 weeks of these symptoms, the pattern changes abruptly and symptoms tend to fall into three phases highly suggestive of malaria: (1) The patient feels cold and develops shaking chills that can last for as much as an hour (cold phase): (2) following the chills, the temperature begins to rise steeply, often reaching 40°C (104°F) or more (hot phase); and (3) after a number of hours of fever, the patient’s temperature falls, and drenching sweating occurs (wet phase). These abrupt changes in symptoms are referred to as paroxysms—a sudden intensification of symptoms. Except for fatigue, the patient feels well until 24 or 48 hours later, depending on the causative species, when the next paroxysm occurs.

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Protozoan Diseases

691

Causative Agent Human malaria is caused by protozoa of the genus Plasmodium. Four species are involved—P. vivax, P. falciparum, P. malariae, and P. ovale. These species differ in microscopic appearance and, in some instances, life cycle, type of disease produced, severity, and treatment. In recent years, the majority of returning travelers and immigrants diagnosed with malaria in the United States have been infected with P. vivax, but up to 30% have been infected with the more dangerous species, P. falciparum. The Plasmodium life cycle is complex (figure 28.11), with a number of different forms that differ in microscopic appearance and antigenicity. In the human host, sporozoites—the infectious form injected by the mosquito—are carried by the bloodstream to the liver, where they infect liver cells. In these cells, each parasite enlarges and subdivides, producing thousands of merozoites. These merozoites are then released into the bloodstream and establish the cycle involving the erythrocytes. The parasite grows and divides in the erythrocytes of the host. The earliest form resembles a ring, with a large, pale food vacuole in the central area, and the nucleus and cytoplasm pushed to the periphery. This develops into a larger, motile trophozoite, which goes on to subdivide, producing a schizont. The infected erythrocyte then breaks open, and the offspring of the division, also called merozoites, are released into the plasma. The merozoites then enter new erythrocytes and multiply, repeating the cycle. Some merozoites that enter erythrocytes develop into gametocytes, which are specialized sexual forms. These are different from the other circulating plasmodia in both their appearance and susceptibility to antimalarial medicines. These sexual forms do not rupture the red blood cells. They cannot develop further in the human host and are not important in causing the symptoms of malaria. They are, however, infectious for certain species of Anopheles mosquitoes and are thus ultimately responsible for the transmission of malaria from one person to another. When a mosquito dines on a person’s blood (see figure 28.11), it digests the erythrocytes and liberates the gametocytes. Shortly after entering the intestine of the mosquito and stimulated by the drop in temperature, the male and female gametocytes change in form to become gametes. The male gametocyte transforms into about a half dozen tiny, whiplike gametes that swim about until they unite with the female gamete in much the same way as the sperm and ovum unite in higher animals. The resulting zygote transforms into a motile form that burrows into the wall of the midgut of the mosquito and forms a cyst. The cyst enlarges as the diploid nucleus undergoes meiosis, dividing asexually into numerous offspring. The cyst then ruptures into the body cavity of the mosquito, and the released parasites, called sporozoites, find their way to the mosquito’s salivary glands and saliva, from which they may be injected into a new human host.

Pathogenesis The characteristic feature of malaria—recurrent paroxysms of fever followed by feeling healthy again—results from the erythrocytic cycle of growth and release of merozoites. Interestingly, the infections in all the millions of different red blood cells become nearly synchronous. Thus, cell rupture and release of daughter protozoa occur at roughly the same time for all infected cells, and each release causes a fever. For P. malariae, the growth cycle

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CHAPTER TWENTY EIGHT Blood and Lymphatic Infections

7

1

5 6

Zygote

8 Oocyst

9 4

Blood channel

2

Gametocytes ingested by mosquito

Liver cells Cell nucleus Sporozoite Merozoites

3

takes 72 hours, so that fever recurs every third day. For the other species, fevers generally occur every other day. Infections by P. falciparum tend to be very severe, probably because all erythrocytes are susceptible to infection, whereas other Plasmodium species infect only young or old erythrocytes. Thus, very high levels of parasitemia—parasites in the bloodstream—can develop with P. falciparum infections. The infected red blood cells become rigid, in contrast to normal red cells, which are flexible. Also, they adhere to each other and to the walls of capillaries. These tiny blood vessels therefore become plugged, and the affected tissue becomes deprived of oxygen as a result. Involvement of the brain, or cerebral malaria, is particularly devastating, but almost any organ can be severely affected. Plasmodium vivax and P. ovale malaria often relapse after treatment of the blood infection because treatment-resistant forms of the organisms (hypnozoites) continue to reside in the liver in a dormant state. Months or even years later, hypnozoites can begin multiplying in an exoerythrocytic stage (exo- means “outside of,” -erythrocytic refers to red blood cells). The exoerythrocytic stage

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FIGURE 28.11 Life Cycle of Plasmodium vivax (1) Infected Anopheles mosquito introduces Plasmodium vivax sporozoites into a capillary. (2) Sporozoites are carried to the liver and infect liver cells. They multiply, rupture the infected cell, and discharge thousands of merozoites into the blood channels of the liver. (3) The merozoites infect and differentiate in red blood cells (RBCs), becoming first a ring form, then a trophozoite, then a schizont. The schizont separates into merozoites, which break out of the cell and infect new RBCs. Some of the new infections repeat the previous sequence; in others, the infecting merozoite merely differentiates into a gametocyte. (4) An uninfected mosquito ingests gametocytes along with its blood meal. (5) In the mosquito digestive tract, the gametocytes are released from their RBC; other forms are digested. (6) The gametocytes develop into gametes, and fertilization takes place. (7) The resulting zygote develops into a motile form and penetrates the gut wall. (8) In the gut wall, the zygote forms an oocyst and multiplies asexually. (9) The oocyst releases sporozoites that infect the mosquito’s salivary glands.

can initiate new erythrocytic cycles of infection after the earlier bloodstream infection has been cured. The spleen characteristically enlarges in malaria to cope with the large amount of foreign material and abnormal red blood cells, which it removes from the circulation. Malaria is the most common cause of splenic rupture, which can occur with or without trauma. Especially with P. falciparum, the parasites cause anemia by destroying red blood cells and converting the iron in hemoglobin to a form not readily recycled by the body. The large amount of foreign material in the bloodstream strongly stimulates the immune system. In some cases, the overworked immune system fails and immunodeficiency results. Those who live continuously in areas where malaria is endemic develop some immunity from repeated infections, and this protects them from the lethal effects of the disease. This immunity crosses the placenta and gives partial protection to the newborn. The greatest risk of death from malaria is to children over 6 months of age as this immunity wanes. Currently, worldwide, a child dies of malaria about every 40 seconds. Others at

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28.5

high risk of death are women in their first pregnancy, and individuals who move into an endemic area.

Epidemiology Malaria was once common in both temperate and tropical areas of the world, and endemic malaria was only eliminated from the continental United States in the late 1940s. Today, malaria is predominantly a disease of warm climates, but 41% of the world’s population lives in endemic areas. Certain human-biting mosquito species of the genus Anopheles are biological vectors of malaria. Because suitable vectors are abundant in North America, the potential exists for the spread of malaria whenever it is introduced. Infected mosquitoes and humans constitute the reservoir for malaria. Besides mosquitoes, malaria can be transmitted by blood transfusions or the sharing of syringes among drug users. Malaria contracted in this manner is easier to treat because it involves only red blood cells and not the liver—only sporozoites from mosquitoes can infect the liver. Some people of black African heritage are genetically resistant to P. vivax malaria because their red blood cells lack the receptors for the parasite. Also, some genetically determined blood diseases such as sickle cell anemia have survived over the eons, despite their negative effect on health, because they provide partial protection against malaria. ■ biological vector, p. 455

Prevention and Treatment Treatment of malaria is complicated by the fact that different stages in the life cycle of the parasite respond to different medications. Chloroquine, and the newer, chemically related mefloquine, are effective against the erythrocytic stages of sensitive strains, but will not cure the liver infection with P. vivax or kill the gametocytes of P. falciparum. Primaquine or a newer derivative, tafenoquine, is generally effective against the hypnozoites and the P. falciparum gametocytes. In 1998, a new initiative called Roll Back Malaria was begun, linking the World Health Organization, the United Nations

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Childrens Fund (UNICEF), the United Nations Development Program, and the World Bank in the fight against malaria. The program’s goal is to reduce malaria deaths by 50% by the year 2010, and again by 2015. The initial focus was on detailed mapping of malarious areas using satellite imagery and climate information, and documenting the level of malaria treatment and prevention at the village level. The aim was to organize and fund a sustained effort to improve access to medical care, strengthen local health facilities, and promote the delivery of medications and insecticide impregnated mosquito netting. There was a better understanding that malaria control must be part of overall economic development because it is difficult for one to move forward without the other. Unfortunately, the rate of malaria continued to increase under this initiative largely because chloroquine, the main antimalarial medication used for many years, is no longer effective in many areas of the world. Resistance has also quickly developed to newer medications such as mefloquine and sulfadoxine/ pyrimethamine (figure 28.12). By 2004, it was generally agreed that for malaria to be controlled, it is necessary to turn to more effective, although much more costly, medications. Derivatives of artemisinin, the active ingredient of an ancient Chinese herbal medicine, are now used in combination with another medication to minimize the risk of developing resistance. With better funding, these combinations, called ACTs (artemisinin-based combination therapies), are now widely available and are helping to reverse the resurgence of malaria. Other highly active antimalarial medications are being evaluated, and a number of potential vaccines are being tested. The most promising vaccine, so far, gives only 30% protection to children. It consists of a sporozoan coat protein attached to a hepatitis B vaccine protein, and is administered with an adjuvant. Judicious indoor spraying of DDT, the use of insecticide-impregnated bed nets, and elimination of mosquito breeding areas are also being emphasized. Adequate funding of malaria control is a continuing problem. Table 28.8 gives the main features of malaria.

FIGURE 28.12 Distribution of Drug-Resistant Malaria (Source: Roll Back Malaria, World Malaria Report 2005.)

No endemic malaria Melfloquine-resistant Chloroquine-sensitive Chloroquine-resistant

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TABLE 28.8

Malaria

MICROCHECK 28.5

Symptoms

Recurrent bouts of violent chills and fever alternating with feeling healthy

Incubation period

Varies with species; 6 to 37 days

Causative agent

Four species of protozoa of the genus Plasmodium

Pathogenesis

Cell rupture, release of protozoa causes fever; infected red blood cells adhere to each other and to walls of capillaries; in the case of falciparum malaria; vessels plug up, depriving tissue of oxygen; spleen enlarges in response to removing large amount of foreign material and many abnormal blood cells from the circulation.

Epidemiology

Transmitted from person to person by bite of infected anopheline mosquito. Some individuals genetically resistant to infection.

Prevention and treatment

For prevention, weekly doses of chloroquine if in chloroquine-sensitive malarial areas; doxycycline, mefloquine, or other alternative if in chloroquine-resistant areas; after leaving, primaquine is given for liver stage; ACTs or other medicines for resistant strains; eradication of mosquito vectors; mosquito netting impregnated with insecticide; vaccines under development. Treatment: usually ACTs; other medicines if sensitivity known.

There are a number of different stages in the life cycles of the protozoa that cause malaria, and they have differing microscopic appearance, antigenicity, and susceptibility to antimalarial medications. Malaria is a major hindrance to economic improvement in many countries. It is a leading serious, infectious disease worldwide, and unless sustained, well-funded control measures are undertaken, it is expected to advance into new geographic areas. ✓ Why is malaria contracted from a blood transfusion easier to treat than if contracted from a mosquito? ✓ Why did insecticide-resistant mosquitoes begin to appear? ✓ Are sporozoites diploid or haploid?

FUTURE CHALLENGES Rethinking Malaria Control Previous attempts at malaria control have relied heavily on the use of DDT, a non-biodegradable insecticide. Use of this substance was banned in the United States in 1972 because of its accumulation in the environment and its damaging effects on fowl, notably the peregrine falcon and the bald eagle. Many other concerns have been raised about its possible carcinogenicity and potential effects on human fetuses. Although DDT is not generally used in agriculture, more than 20

countries still use it for malaria control, and more would use it if it were affordable. Biodegradable insecticides are available, but they are more expensive than DDT, and not without toxicity. With children dying of malaria every minute worldwide, the options for rapid relief from malaria all seem bad, and a choice has to be made of which ones are the least bad. Insecticides may be necessary short term, but other options, including education, economic development, vaccines, biological

control of the Anopheles vectors, and mosquito habitat alteration, may prove more important in achieving sustained relief from the disease. The challenge for the future is to better understand the ecology of malaria as it applies in each location, with the aim of minimizing insecticide use and discovering new options for maintaining long-term control.

SUMMARY 28.1 Anatomy and Physiology (figure 28.1) The Heart The left side of the heart receives oxygenated blood from the lungs and pumps it into thick-walled arteries; the right side of the heart receives blood depleted of oxygen from the veins and pumps it through the lungs. Arteries Arteries have thick, muscular walls. People begin to develop arteriosclerosis in the teenage years or before. The possible role of bacteria and viruses in the formation of arteriosclerotic lesions is under investigation.

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Veins The blood in veins is a dark color because it is depleted of O2. The pressure is much lower than in arteries. Blood flow is aided by contracting muscles compressing the veins. Direction of flow is maintained by one-way valves. Lymphatics Lymphatics—lymph vessels—are blind-ended tubes that take up fluid that leaks from capillaries. They also take up bacteria, which are normally trapped by lymph nodes distributed along the course of the lymphatics.

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Review Questions Spleen The spleen filters unwanted material such as bacteria and damaged erythrocytes from the arterial blood. It becomes enlarged in diseases such as infectious mononucleosis and malaria.

28.2 Bacterial Diseases of the Blood Vascular System Bacteria circulating in the bloodstream can colonize the inside of the heart, and they can cause collapse of the circulatory system and death. Infections of the heart valves and lining of the heart are called endocarditis; illness resulting from circulating pathogens is called septicemia. Acute bacterial endocarditis is caused when virulent bacteria enter the bloodstream from a focus of infection elsewhere in the body, or when contaminated material is injected by drug abusers; normal heart valves are commonly infected and destroyed. Subacute Bacterial Endocarditis (table 28.1) Subacute bacterial endocarditis (SBE) is commonly caused by organisms of little virulence, including oral streptococci and Staphylococcus epidermidis, and infection usually begins on structural abnormalities of the heart. Biofilm formation may complicate treatment. Gram-Negative Septicemia (figure 28.3) Gram-negative septicemia is commonly a nosocomial illness; many afflicted individuals have serious underlying illnesses such as cancer and diabetes. Shock precipitated by release of endotoxin from the bacteria is a common complication; it is the result of an exaggerated response to endotoxin in which massive release of cytokines occurs in the circulation.

28.3 Bacterial Diseases of the Lymph Nodes and Spleen Tularemia, brucellosis, and plague involve the mononuclear-phagocyte system and are characterized by enlargement of the lymph nodes and spleen. The causative organisms grow within phagocytes, protected from antibody. “Rabbit Fever” (Tularemia) (table 28.2, figure 28.4) Tularemia is usually transmitted from wild animals to humans by exposure to the animals’ blood or via insects and ticks. The cause is the Gramnegative aerobe Francisella tularensis, which is found throughout the United States except Hawaii (figure 28.5). “Undulant Fever” (Brucellosis, “Bang’s disease”) (table 28.3) Brucellosis, caused by Brucella melitensis, is usually acquired from cattle or other domestic animals, less often from wild animals such as elk, moose, and bison. Hunters, butchers, and those who drink unpasteurized milk or milk products are at increased risk for the disease. The organisms can infect via mucous membranes and minor skin injuries.

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“Black Death” (Plague) (table 28.5) Plague, once pandemic, now persists endemically in rodent populations, including those in many western states of the United States. It is caused by Yersinia pestis, an enterobacterium with many virulence factors, chromosomally or plasmid coded, that interfere with phagocytosis and immunity (table 28.4, figure 28.6). Bubonic plague is transmitted to humans by fleas (figure 28.7). Pneumonic plague is transmitted from person to person. Untreated, bubonic plague mortality is 50% to 80%; pneumonic plague, almost 100%.

28.4 Viral Diseases of the Lymphoid and Blood Vascular Systems “Kissing Disease” (Infectious Mononucleosis, “Mono”) (table 28.6) The incidence is high in 15- to 24-year-olds; most individuals with the disease become lifelong carriers, capable of transmitting the disease by their saliva. The causative agent is Epstein-Barr virus, which establishes a lifelong latent infection of B lymphocytes; the disease is called mononucleosis because victims have an increased number of mononuclear cells in their blood (figure 28.9). The disease is confirmed by the presence of a heterophile antibody. Yellow Fever (table 28.7) Yellow fever is a zoonosis of mosquitoes and monkeys that exists mainly in tropical jungles; it can become epidemic in humans where a suitable Aedes mosquito vector is present (figure 28.10). The disease involves the heart and blood vessels throughout the body and is characterized by fever, jaundice, and hemorrhaging. A highly effective attenuated vaccine is available for preventing the disease.

28.5 Protozoan Diseases African sleeping sickness is present over much of tropical Africa; of the protozoan blood and lymphatic diseases, however, malaria is the most widespread. Malaria (table 28.8) Malaria is caused by four species of Plasmodium and is transmitted from person to person by the bite of certain species of Anopheles mosquitoes, its biological vector. Now confined mainly to impoverished warm regions of the world, malaria survives despite massive eradication programs; it is the most widespread of all serious infectious diseases (figure 28.12). The life cycle is complex; different forms of the organism invade different body cells and have different susceptibility to anti-malarial medication (figure 28.11). Replication of the organism inside red blood cells results in the almost simultaneous rupture of the infected cells and release of the progeny protozoa to infect new red cells.

REVIEW QUESTIONS Short Answer 1. 2. 3. 4. 5.

What is the significance of immune complex formation in SBE? What is disseminated intravascular coagulation (DIC)? What activities of humans are likely to expose them to tularemia? Why is brucellosis a threat to big game hunters? Why might the Yersinia pestis bacteria from a patient with pneumonic plague be more dangerous than the bacteria from fleas?

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6. Why might rodent burrows be a source of plague months after they are abandoned? 7. What type of leukocytes does EB virus infect and immortalize? 8. Name a viral disease that can be complicated by disseminated intravascular coagulation. 9. Travelers to and from which areas of the world should have certificates of yellow fever vaccination? 10. Which microorganism causes the most dangerous form of malaria?

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Multiple Choice 1. Which of the following infection fighters are found in lymph? a) Leukocytes d) Interferon b) Antibodies e) All of the above c) Complement 2. All the following are true of the spleen, except a) it is located low on the right side of the abdomen. b) it cleanses the blood of foreign material and damaged cells. c) it provides an immune response to circulating pathogens. d) it can help produce new blood cells. e) it enlarges in a number of infectious diseases. 3. Which one of the following statements about SBE is false? a) It is generally a chronic illness characterized by fatigue and slight fever. b) Kidney involvement can be one complication. c) Infection occurs exclusively on the left side of the heart. d) Injected-drug abuse can be responsible for the disease. e) It can result in aneurysm formation. 4. Choose the one true statement about Gram-negative bacterial septicemia. a) It is a rare nosocomial disease. b) The output of urine increases if shock develops. c) It can only be caused by anaerobic bacteria. d) An antibiotic that kills the causative organism can be depended on to cure the disease. e) Lung damage is an important cause of death. 5. Which of these statements about tularemia is false? a) It can be contracted from muskrats and bobcats. b) Biting insects and ticks can transmit the disease. c) The causative organism is closely related to E. coli. d) A steep-walled ulcer at the site of entry of the bacteria and enlargement of nearby lymph nodes is characteristic. e) Without treatment, 9 out of 10 people can be expected to survive. 6. All of the following statements about brucellosis are true, except a) fevers that come and go over a long period of time gave it the name “undulant fever.” b) the causative agent can infect via mucous membranes. c) the causative agent is readily killed by phagocytes. d) the disease in cattle is characterized by chronic infection of the mammary glands and uterus. e) butchers are advised to wear goggles or a face shield to help protect against the disease. 7. Pick out the one false statement about Yersinia pestis. a) Growth conditions inside human phagocytes activate virulence genes. b) The bacterium can multiply in the flea digestive system. c) The code for YOPs exists on the bacterial chromosome. d) The organism resembles a safety pin in certain stained preparations. e) It was responsible for the “black death” in Europe during the 1300s. 8. Which of the following statements about yellow fever is false? a) There is no animal reservoir. b) The name “yellow” comes from the fact that many victims have jaundice.

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c) Certain mosquitoes are biological hosts for the causative agent. d) Outbreaks of the disease could occur in the United States because a suitable vector is present. e) An attenuated vaccine is widely used to prevent the disease. 9. The malarial form infectious for mosquitoes is called a a) gametocyte. d) schizont b) trophozoite. e) merozoite c) sporozoite. 10. Choose the one true statement concerning malaria. a) Transmission cannot occur in temperate climates b) Transmission usually occurs with the bite of a male Anopheles mosquito. c) The disease is currently well controlled in tropical Africa. d) P. falciparum infects only old erythrocytes and therefore causes milder disease than other Plasmodium species. e) The characteristic recurrent fevers are associated with release of merozoites from erythrocytes.

Applications 1. Some years ago, dentists and doctors began noticing an association between subacute bacterial endocarditis and prior dental work, and they began advising that an antibiotic be administered at the time of dental procedures to those with known or suspected heart defects. What was the rationale for this advice? 2. Several children attending a New Mexico school developed a serious illness characterized by high fever and enlarged, tender lymph nodes. Their physicians diagnosed their illnesses as plague, but were mystified because the children all lived and played in town and denied seeing any rodents. Health officials checked and found no evidence of rodents at their homes or school. What other investigations should they carry out to try to establish the source of the disease? 3. A health worker in Honduras is concerned about a potential outbreak of yellow fever in his town. A laborer from a jungle area known to be endemic for the disease had come to the town 2 weeks earlier to work and subsequently developed yellow fever. Several coworkers reported getting mosquito bites while working with him. Why is it important that the health worker determine how long it is since the workers were bitten by the mosquitoes?

Critical Thinking 1. The finding that there is an association between Chlamydia pneumoniae infection and arteriosclerotic lesions raised hopes that new methods to combat arteriosclerosis could be developed. An investigator reviewing this research, however, stated that even a perfect correlation between infection and lesion formation would not prove that infection causes arteriosclerosis. Moreover, even showing that therapeutic antibiotics could prevent infection and lesion formation would not be definitive proof. Is the investigator justified in making this argument? Why or why not? 2. Distinguish between EB virus infection and infectious mononucleosis. 3. Even though genetically engineered mosquitoes might be developed that do not allow the reproduction of malaria protozoa, these mosquitoes would have little, if any, immediate effect on the spread of the disease. Why should this be so? What would have to happen for these mosquitoes to significantly affect the spread of malaria?

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29 Color-enhanced TEM of human immunodeficiency virus (HIV).

HIV Disease and Complications of Immunodeficiency A Glimpse of History In 1981, five reports described an illness in previously healthy, young, homosexual men characterized by unusual infections, certain malignant tumors, and immunodeficiency. This illness came to be known as AIDS, an acronym for acquired immunodeficiency syndrome. Initially, there was wild speculation about the cause of AIDS, but by 1982, the Centers for Disease Control had convincing epidemiological evidence that AIDS was caused by a new infectious agent. Scientists around the world scrambled to identify it. Fortunately, the scientists were able to build on some important scientific advances of the 1960s and 1970s—specifically, the discovery of subsets of lymphocytes, the functions of T cells, and the role of cytokines. In 1975, the Nobel Prize was awarded to H. Temin and D. Baltimore for discovering reverse transcriptase. Also, in early 1978, Dr. Robert Gallo’s laboratory at the National Cancer Institute discovered the first human retrovirus, human T-lymphotrophic virus (HTLV). Dr. Gallo developed a technique for cultivating retroviruses in normal lymphocytes activated with interleukin-2 (IL-2). ■ lymphocytes, p. 352 ■ cytokines, p. 353 ■ reverse transcriptase, p. 332 ■ interleukins, p. 353 ■ retroviruses, p. 332

In January 1983, an important scientific breakthrough occurred in the laboratory of Dr. Luc Montagnier at the famous Pasteur Institute. Using techniques developed earlier by Gallo for cultivating HTLV, Montagnier recovered a new virus from a patient with lymphadenopathy syndrome, an AIDS-associated condition. Because the IL-2 activated lymphocyte cultures died out quickly, he was only able to obtain small quantities of the new virus, named LAV, an acronym for lymphadenopathy virus, but enough to use as antigen in a blood test that showed that AIDS patients were infected with the virus. He sent a sample of this virus to Gallo at the National Cancer Institute, and the two exchanged material from other patients. He also made application to the U.S. Patent Office for a patent on his blood test. Meanwhile, Gallo’s laboratory began recovering a virus from AIDS patients, and reported the finding in the same issue of the jour-

nal Science in which Montagnier reported his finding. A number of these viral isolates were introduced together in cell cultures to see if a strain of the virus could replicate in the cells. One did replicate well, enabling Gallo to obtain large quantities of the virus. Gallo named the virus HTLV-III because it resembled human T-lymphotrophic viruses discovered earlier, but it soon became clear that the new virus was a lentivirus. Using “HTLV-III,” Gallo perfected a blood test for AIDS and, like Montagnier, applied for a patent. These conflicting patent claims caused a bitter scientific and legal battle that raged for years. Under pressure from President Reagan, a settlement was negotiated in 1987 wherein Gallo and Montagnier were named codiscoverers of the test. Eighty percent of the royalties were to go to an AIDS foundation, the remainder to be divided equally between the National Institutes of Health (NIH) and the Pasteur Institute. The settlement did not end the conflict. Genetic analysis showed that HTLV-III was actually Montagnier’s LAV, introduced into Gallo’s cultures as described earlier. Later, the Pasteur Institute suffered its own embarrassment, acknowledging that due to a laboratory mixup of its own, LAV actually came from a different patient than stated in its publications. In 1994, the earlier settlement was modified, NIH admitting that HTLV-III and LAV were the same and giving the French side a larger share of the royalties. The American share of the royalties has generated many millions of dollars for the NIH over the years, but the value of the blood test far exceeded any monetary figure. It helped prove that HTLV-III/LAV—renamed HIV for human immunodeficiency virus—caused AIDS. It also showed that many infected people were asymptomatic, that they could transmit the virus, and that the epidemic was far more extensive than previously suspected. These findings helped generate support for controlling the disease. By 1985, the blood test was generally available for routine testing of donated blood, thus markedly improving the safety of blood transfusions and blood products.

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KEY TERMS Carcinoma A malignant tumor that arises from epithelium. Clade A group of organisms or viruses that have the same ancestor; subtype of a virus such as human immunodeficiency virus (HIV) defined by similar amino acid sequences of their envelope proteins. Hemophiliac An individual with an inherited bleeding disorder caused by failure of the blood to clot normally.

Integrase Enzyme of human immunodeficiency virus that integrates its linear DNA form into the host chromosome. Lymphoma A malignant tumor that arises from lymphatic tissue. Metastasize To spread to another area of the body, as with tumors or infections. Nucleoside A compound composed of a purine or pyrimidine base covalently bound to ribose or deoxyribose.

Reverse Transcriptase Enzyme that synthesizes double-stranded DNA complementary to an RNA template; target of a number of anti-HIV medications. Sarcoma A malignant tumor that arises from connective tissue, bone, cartilage, or muscle. Therapeutic Vaccine A vaccine administered after infection occurs with the hope of activating immunity in time to prevent or ameliorate a disease; effective in preventing rabies.

Protease Enzyme that degrades protein; the protease that is encoded by HIV is the target of several anti-HIV medications.

AIDS

A

t the end of the second decade after its recognition in 1981, the disease AIDS had killed more American citizens than the Korean and Vietnam wars combined. By 1994, it had become the leading cause of death among those 25 to 44 years of age in the United States. The total number of individuals alive and infected with HIV exceeded 850,000 and the numbers were increasing by more than 40,000 each year. Initially introduced into a population of homosexual men, the virus increasingly infected heterosexuals, especially among economically disadvantaged, racial and ethnic minorities. Western and Central Europe 31,000 760,000

Eastern Europe/ Central Asia 150,000 1.6 million East Asia 92,000 800,000

North America 46,000 1.3 million

Worldwide, at the end of the second decade of the epidemic, an estimated 40 million people were living with HIV infection and more people had died of AIDS than were killed by the “black death” of Europe in the Middle Ages. It became the number one killer in Africa south of the Sahara, surpassing malaria, and the disease spread rapidly into India and China. Millions of children lost one or both parents to the disease. ■ black death, p. 682 Billions of dollars have been spent trying to control the AIDS pandemic, with the result that new HIV infections have declined (figure 29.1). Nevertheless, AIDS is far from conquered.

29.1 Human Immunodeficiency Virus (HIV) Infection and AIDS Focus Points Outline the pathogenesis of HIV disease. Explain the importance of the three main modes of transmission of HIV.

Caribbean 17,000 230,000

North Africa/ Middle East 35,000 380,000 Latin America 100,000 1.6 million

South/ Southeast Asia 340,000 4 million Sub-Saharan Africa 1.7 million 22.5 million

Oceania 14,000 75,000

FIGURE 29.1 The Global HIV/AIDS Epidemic at the End of 2007 An estimated 2.5 million people (figure in red) were newly infected during the year. Altogether, 33.2 million people (figures in black) were living with HIV/AIDS. The arrows indicate an increase (≠) or decrease (Ø) in the numbers of cases as compared with 2001 using an updated statistical method over the 7-year period. (Source: UNAIDS and WHO ’07 AIDS Epidemic update.)

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Microorganisms such as Pneumocystis jirovecii (formerly Pneumocystis carinii) are common, but of such low virulence that they only cause disease in individuals with immunodeficiency disorders. When such a disease appears, it strongly suggests that the victim is immunodeficient. In the United States in 1981, a number of cases of P. jirovecii pneumonia in previously healthy homosexual men first led to the recognition of AIDS. The acronym AIDS, for “acquired immunodeficiency syndrome,” was first used in 1982 by the Centers for Disease Control for diseases that were at least moderately predictive of a defect in cellular immunity in subjects with no apparent cause for low resistance to the diseases. These “AIDS-defining conditions” (table 29.1) were useful in studying the AIDS epidemic before its cause was known, and still alert physicians to the possibility of AIDS. Immunodeficiency, however, is the end stage of a disease with many

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29.1 Human Immunodeficiency Virus (HIV) Infection and AIDS

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TABLE 29.1 “AIDS-Defining Conditions” Cancer of the uterine cervix, invasive

Kaposi’s sarcoma

Candidiasis involving the esophagus, trachea, bronchi, or lungs

Lymphomas, such as Burkitt’s, or arising in the brain

Coccidioidomycosis, of tissues other than the lung

Mycobacterial diseases, including tuberculosis

Cryptococcosis, of tissues other than the lung

Pneumocystosis (pneumonia due to Pneumocystis jirovecii)

Cryptosporidiosis of duration greater than 1 month

Pneumonias occurring repeatedly

Cytomegalovirus disease of the retina with vision loss or other involvement outside liver, spleen, or lymph nodes

Progressive multifocal leukoencephalopathy (a brain disease caused by the JC polyomavirus)

Encephalopathy (brain involvement with HIV)

Salmonella infection of the bloodstream, recurrent

Herpes simplex virus causing ulcerations lasting 1 months or longer or involving the esophagus, bronchi, or lungs

Toxoplasmosis of the brain

Histoplasmosis of tissues other than the lung

Wasting syndrome (weight loss of more than 10% due to HIV); also known as slim disease

Isosporiasis (a protozoan disease of the intestine) of more than 1 month’s duration

other manifestations. AIDS is therefore more appropriately called HIV disease, after its causative agent, human immunodeficiency virus (HIV). In this chapter, the term HIV disease implies that replication of the virus is causing symptoms or demonstrable damage to the body, whereas HIV infection means only that the virus has entered the body and is replicating, whether or not disease has occurred. The term AIDS refers to the end stage of HIV disease characterized by unusual tumors and immunodeficiency. ■ immunodeficiency disorders, p. 426

HIV Disease Almost everyone who becomes infected with HIV develops HIV disease, marked by slow destruction of their immune system and eventually ending in AIDS.

Symptoms The first symptoms of HIV disease appear after an incubation period of 6 days to 6 weeks and usually consist of fever, headache, sore throat, muscle aches, enlarged lymph nodes, and a generalized rash. Some people develop central nervous system symptoms ranging from moodiness and confusion to seizures and paralysis. These symptoms constitute the acute retroviral syndrome (ARS), and they typically subside within 6 weeks. Many HIV infections are asymptomatic, however, or the symptoms are mild and attributed to the “flu.” Following the acute illness, if any, there is an asymptomatic period that typically lasts for years, even though the disease advances in the infected person and can be transmitted to others. The asymptomatic period may end with persistent enlargement of the person’s lymph nodes, a condition known as lymphadenopathy syndrome (LAS). In some cases, symptoms heralding immunodeficiency include fever, weight loss, fatigue, and diarrhea. These symptoms are referred to as the AIDS-related complex (ARC), and indicate a poor prognosis. The first symptoms in many cases are those due to tumors or opportunistic infections resulting from severe immunodeficiency. As one might expect, symptoms at this stage of the disease vary widely according to the kind of infection. For example, a frequently encountered symptom is a fuzzy white patch on the tongue—hairy leukoplakia

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(figure 29.2)—a result of latent Epstein-Barr virus (EBV) reactivation. Severe skin rashes, cough and chest pain, stiff neck, confusion, visual problems, and diarrhea are manifestations of other infections. ■ Epstein-Barr virus, p. 686

Causative Agent In the United States, and in most other parts of the world, AIDS is usually caused by human immunodeficiency virus, type 1 (HIV-1), a single-stranded RNA virus of the retrovirus family. There are many kinds of retroviruses that naturally infect hosts as diverse as fish and humans. HIV-1 belongs to the lentivirus subgroup of the retroviruses, which characteristically infect mononuclear phagocytes. HIV-1 viruses can be classified into subtypes based on nucleic acid sequences. In the M (for “major”) group of HIV-1 viruses, 10 subtypes—clades—have been described, designated A through J. Members of each clade are closely related, as determined by sequencing their genomes. Infection by two different subtypes can give rise to “hybrids” that have properties of both. Other HIV-1

FIGURE 29.2 Hairy Leukoplakia This AIDS-related condition is probably due to activation of latent Epstein-Barr virus infection.

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groups such as O (for “outlier”) and N differ from M group viruses. The importance of being able to recognize all of these different strains of HIV-1 viruses is to aid epidemiological studies and to ensure that the tests for HIV reliably detect infection. Human immunodeficiency viruses, type 2 (HIV-2), are lentiviruses similar in structure to HIV-1, but antigenically distinct, their genomes differing from HIV-1 by more than 55%. They are a prominent cause of AIDS in parts of West Africa and India, and

have appeared in the United States and other countries. HIV-2 transmission has generally been less efficient than that of HIV-1, and disease progression is slower. Otherwise, the biology of HIV-2 is quite similar to that of HIV-1. For the remainder of this chapter, we will use the term HIV to indicate HIV-1. The structure of HIV is shown schematically in figure 29.3a. The locations of its important antigens are indicated. The numerous knobs projecting from the surface of the virion represent SU

Lipid envelope

Surface glycoprotein (SU) gp120

Reverse transcriptase (RT)

Transmembrane glycoprotein (TM) gp41

Integrase (IN) Protease (PR)

Matrix protein (MA) p17

Nucleocapsid (NC) RNA

Capsid protein (CA) p24

HLA antigens from host cell membrane

(a)

gag

vif pol

5'

tat vpr

vpu

rev

nef

env

LTR

LTR tat

gag is transcribed and the mRNA is translated as a unit; the resulting protein is cleaved by viral protease into MA, CA, and NC.

MA

rev

gag and pol are transcribed together and the mRNA is translated; resulting protein is cleaved by viral protease into MA, CA, PR, RT and IN.

(b)

CA

3'

env is transcribed as a unit and the mRNA is translated; resulting protein is cleaved by cellular protease into SU and TM.

NC

SU

TM

FIGURE 29.3 Human Immunodeficiency Virus, Type 1 (HIV-1) MA (c)

nes95432_Ch29_697-720.indd 700

CA

PR

RT

IN

(a) Diagrammatic representation of the virus showing important antigens. (b) Map of the HIV-1 genome showing its nine genes and flanking long terminal repeats (LTRs). The LTRs contain regulatory sequences recognized by the host cell. (c) HIV-1 gene products. The accessory gene products are translated into proteins of final size, while gag and pol products must be cleaved by viral protease, and env products by host cell protease. The small arrows indicate the sites of cleavage.

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29.1 Human Immunodeficiency Virus (HIV) Infection and AIDS

701

and integrase are the targets of the medicines currently available for treating AIDS. The env gene is translated from a spliced messenger RNA, yielding a precursor protein that is processed by host cell enzymes to give the gp120 (SU) surface glycoprotein and the gp41 (TM) transmembrane glycoprotein. ■ RNA splicing, p. 175 There are six additional genes, known as accessory genes, all translated from spliced messenger RNAs. These genes—tat, rev, nef, vif, vpr, and vpu—code for the proteins Tat, Rev, Nef, Vif, Vpr, and Vpu. These gene products interact with host cell proteins in complex ways to regulate HIV replication and release from the cell.

(for “surface”) antigen, which is partly responsible for attachment of the virus to the host cell. The “gp120” indicates that SU is a glycoprotein and the relative weight and size of its molecule is 120. The TM (for “transmembrane”) antigen is also a glycoprotein (gp41). It traverses the viral envelope, is closely associated with SU and plays a role in entry of the virus into the host cell. The MA (for matrix protein) is a protein, p17, located inside the viral envelope. It helps to maintain viral structure and transports the viral genome to the host cell nucleus for assembly of new virions. The core of the virion is composed of the p24 CA (for capsid) antigen, two copies of the single-stranded RNA viral genome, and various other protein antigens, including nucleocapsid (NC) and three important viral enzymes—reverse transcriptase (RT), protease (PR), and integrase (IN). The HIV genome is shown schematically in figure 29.3b. The first two genes, gag (from “group antigen”) and pol (from “polymerase”), can be translated as a unit from the full-length viral messenger RNA (figure 29.3c). The resulting protein is split into functional segments by viral protease. This enzyme releases itself from the large protein and enzymatically splits the remaining protein into functional enzymes and structural units. The final yield is three enzymes: protease, reverse transcriptase, and integrase, and a number of other proteins, including p24 (CA) capsid and p17 (MA) matrix. The virus, however, has a greater need for structural proteins MA, CA, and NC than for the enzymes PR, RT, and IN, and so gag is usually expressed by itself, only rarely joining pol through a frameshift. Reverse transcriptase, protease,

Pathogenesis HIV virions enter the body and attach to and infect certain types of cells. Which cells are affected and their response to infection vary with the particular viral strain and the type of host cell. Some of the cell types and the consequences of infection are shown in figure 29.4. Infection of intestinal epithelium is partly responsible for the chronic diarrhea and weight loss, and infection of brain cells for HIV dementia. Infected macrophages and other antigen-presenting cells are a continuing source of infectious virus and show impairment of chemotaxis, phagocytosis, and antigen presentation. They and the TH (helper T) lymphocytes are exceedingly important targets of HIV because of their central role in the body’s specific immune response. The cytokines of TH lymphocytes regulate cytotoxic action of TC cells, immunoglobulin production by B cells, and chemotaxis of antigen-presenting cells such as macrophages. FIGURE 29.4 Some of HIV’s Cellular Targets

Infection of intestinal epithelium and lymphoid tissue probably contributes to chronic diarrhea and weight loss.

Infection of several types of brain cells probably contributes to lethargy and HIV dementia.

HIV (not drawn to scale)

CD4+ TH1 inflammatory cells are normally responsible for macrophage activation and cell-mediated immunity through CD8 cytotoxic cell activation.

CD4+ macrophages, dendritic and other antigen-presenting cells harbor HIV but are not usually killed by it. The cells are a continuing source of the virus and can carry it into the brain.

CD4+ TH2 helper cells normally control antibody production by B cells.

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CHAPTER TWENTY NINE HIV Disease and Complications of Immunodeficiency

HIV must attach to and enter the body’s cells to establish infection. Like most other cells susceptible to HIV, TH lymphocytes and macrophages are CD4+—they possess the CD4 surface antigen. HIV attaches to CD4 by its surface gp120 (SU) antigen. The presence of the CD4 antigen, however, is by itself not sufficient to cause entry of HIV. In addition, there must be a host cell co-receptor specific for HIV in order for viral entry to occur (figure 29.5). The co-receptor differs for different cell types. CXCR-4, a chemokine receptor, is an HIV co-receptor. CCR5, a chemokine receptor on macrophages, is also an HIV co-receptor. The nature of HIV attachment and entry into the host cell has been a mystery subject to intense study because antibodies and other substances designed to block SU and CD4 have not been FIGURE 29.5 Attachment and Entry of HIV into a Host Cell, Schematic Representation Step 1: Virion in close proximity to the cell membrane; blowup showing gp120 protein and sites of reaction with host cell receptors. Step 2: Initial contact of gp120 (SU) is with CD4. Attachment to a chemokine receptor such as CCR5 must occur before membrane fusion and entry of the viral genome can take place. Step 3: Membrane fusion probably is mediated by gp41 (TM).

Step 1

very successful in preventing infection. SU is known to be flexible, irregular in shape, and divided into two parts connected by peptide strands. The main binding sites for CD4 and the co-receptor are only exposed after initial contact of the virus with CD4. Penetration into the host cell probably involves gp41 (TM). Once HIV enters the host cell, its reverse transcriptase makes a DNA copy of the viral RNA genome. A complementary DNA strand is then added, and the ends of the resulting double-stranded DNA segment are joined non-covalently. The resulting circular DNA is then moved to the nucleus and is inserted into the host cell chromosome by the viral integrase (IN) enzyme. The viral segment thus becomes a provirus, a step necessary for efficient replication of HIV. No specific location is required for the inser-

gp41 HIV

gp120

HIV envelope

gp41

Host cell membrane

gp120 CCR5 Fusion site

CD4 Host cell membrane

Step 2 Attachment

Binding occurs at CD4 and CCR5

Step 3 Membrane fusion and entry of HIV

Viral genome

HIV envelope

Displacement of gp120; attachment of gp41

Host cell membrane

nes95432_Ch29_697-720.indd 702

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29.1 Human Immunodeficiency Virus (HIV) Infection and AIDS

tion into the host chromosome. Following integration, spliced mRNA segments appear, mainly transcribed from the regulatory genes: tat, rev, and nef, and are translated into proteins that are involved in HIV gene expression. High levels of Tat are associated with replication of infectious virions. Nef protein, despite the name derivation from negative factor, may cause increased virion production and other effects that increase pathogenicity, depending on the viral strain and type of cell infected. In the case of TH lymphocytes, replication of mature virions results in lysis of the cells and release of infectious HIV. Macrophages, on the other hand, usually release infectious virus over long periods of time without death of the cells. The life cycle of HIV is shown schematically in figure 29.6, but in an infected person, at any one time, the vast majority of infected cells show neither lysis nor latency. Instead, most of the HIV-infected cells show accumulations of various viral products that impair the normal functioning of the cells. ■ provirus, p. 332 HIV is genetically highly variable. The variant viruses show differences in their preferred host cell, rates of replication, response to host immunity, and other characteristics. The variability is due to a high rate of “error” when reverse transcriptase copies the viral genome. Some regions of the genome are highly conserved, meaning they do not change much from one strain of virus to another.

Site of action of AZT and other reverse transcriptase inhibitors

RNA DNA

(3) RNA degraded; second DNA strand synthesized DNA DNA

(4) DNA circularizes (unintegrated provirus) or integrase functions to incorporate DNA into host cell genome (integrated provirus). Site of action of antiretroviral drugs under development

Other regions are highly variable. This is reflected for example in the glycoprotein gp120 (SU), which has conserved and variable regions (figure 29.7). The V3 variable region is important because it plays a role in the virulence of HIV. This antigenic variability of HIV enormously complicates the task of developing an effective vaccine against the virus. ■ reverse transcriptase, p. 332 Destruction of immune system TH cells by HIV can occur via multiple mechanisms: Lysis following HIV replication. Lysis of activated helper CD4; T lymphocytes during replication of infectious virus is one mechanism, but by itself it cannot account for the devastation that results from HIV disease. Attack by HIV-specific cytotoxic CD8; T lymphocytes. The earliest detectable immune response to HIV infection involves HIV-specific CD8; T lymphocytes, which attack and lyse infected cells. Natural killer (NK) cells. NK cells probably also play a role in cell destruction. ■ natural killer cells, p. 384 Antibody-dependent cellular cytotoxicity. Humoral antibody may also play a role through antibody-dependent cytotoxicity. ■ antibody-dependent cellular cytotoxicity, p. 372

(1) Viral genome and reverse transcriptase enter cell.

(2) DNA copy synthesized by reverse transcriptase

703

(8) Final viral assembly and budding take place.

Host cell nucleus

Host cell genome (7) Viral membrane proteins are transported to host cell membrane.

(6) Viral RNAs are translated, yielding viral enzymes (including protease) and structural proteins.

(5) With host cell activation, viral DNA is transcribed, yielding messenger RNAs and viral genome RNA.

Site of action of protease inhibitors

FIGURE 29.6 The Steps in HIV Replication In step 4, the enzyme, integrase, mediates integration of the provirus into the host cell genome. This enzyme is potentially a target of new anti-HIV medications. In step 7, the accessory gene product Vpr and MA transport viral proteins to the cell membrane.

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CHAPTER TWENTY NINE HIV Disease and Complications of Immunodeficiency V3

V2 V4 C2

C3

Disulfide bond

C4 V1 V5 C1 C5

FIGURE 29.7 Diagram of the SU Glycoprotein There are five “constant” segments (blue) that are conserved in different HIV strains. The segments in orange, labeled V1 to V5, are “variable” and differ from strain to strain, frustrating attempts to develop a vaccine. Note the V3 loop, implicated in pathogenicity.

Autoimmune process. Autoimmunity could be responsible because HIV envelope proteins show some homology with MHC class II molecules. ■ major histocompatibility complex, class II (MHC-II), p. 380 Fusion of infected and uninfected cells. In cell fusion, a large number of uninfected cells fuse with an infected cell, whereupon the resulting syncytium is destroyed. Apoptosis. Also called programmed cell death, apoptosis is accelerated in HIV infections by a number of mechanisms, including induction by Tat, SU interaction with CD4, and certain cytokines. ■ apoptosis, p. 362 FIGURE 29.8 Natural History of HIV Disease Blood

Infection

ASYMPTOMATIC INTERVAL

“Flu”-like symptoms may occur; HIV infection spreads throughout the body

AIDS

Lymph node enlargement, fever, weight loss, fatigue, diarrhea, etc.

Clinical well-being

Death

Opportunistic infections, malignant tumors CD4 lymphocytes Circulating HIV RNA

Blood levels

levels of infectious virus are very high at the beginning, during the acute retroviral syndrome, and at the end of the disease when AIDS ensues. Antibody tests for diagnosing the disease are often negative in the early stage of the disease even though infected people are highly infectious. The disease steadily progresses in the absence of symptoms, as shown by the rising levels of plasma viral RNA and falling CD4; cell count.

ACUTE RETROVIRAL SYNDROME

Accumulation of viral products such as viral RNA and unintegrated viral DNA inside the cytoplasm of the infected cell can also result in its death. An acute retroviral syndrome (ARS) begins in 50% to 70% of HIV-infected subjects after an incubation period of 6 days to 6 weeks, with sore throat, fever, muscle and headaches, enlarged lymph nodes, and a rash. These symptoms generally last 1 to 4 weeks and disappear without treatment. Whether or not symptoms occur, the concentration of HIV in the blood rises to high levels as the newly infected cells release their progeny virus (figure 29.8). The marked viremia usually subsides as the supply of uninfected cells dwindles and anti-HIV CD8; cytotoxic T cells appear. The CD4; T-cell level falls initially, then slowly rises but does not reach the preinfection level. Following the acute episode, the HIV-infected individual generally enters an asymptomatic period ranging from months to many years. Regardless of the lack of symptoms, a silent struggle goes on between HIV and the immune system for the rest of the person’s life. Infectious virus, a threat to others, continues to be present in the blood and body secretions. In the typical case, as seen in approximately 80% of HIVinfected people, the immune system slowly loses ground to HIV even though the body can normally replace over a billion CD4; cells per day. The peripheral blood CD4; count (normally about 1,000 cells per microliter) steadily falls at a rate of roughly 50 cells per microliter per year. Symptoms of AIDS usually appear when CD4; counts fall below 200 cells per microliter. Levels of infectious virus again rise dramatically. At this point in the illness, the pathology is dominated by malignant neoplasms or opportunistic infections. Half of untreated patients reach this stage of the illness within 9 to 10 years; the rest take longer. The typical course of HIV disease is summarized in figure 29.8. Atypical progression to AIDS occurs in about 10% of persons with HIV disease who have high virus levels with the acute infection that do not fall dramatically within a few months. These

Circulating culturable HIV

1

2 Months

nes95432_Ch29_697-720.indd 704

3

1

2

3

4

5

6

7

8

9

10

11

12

Years

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29.1 Human Immunodeficiency Virus (HIV) Infection and AIDS

705

PERSPECTIVE 29.1 Origin of AIDS-Causing Viruses Where did the AIDS-causing viruses come from? Genetic evidence indicates that the HIV-1 virus mutated to its present form fairly recently, between 50 and 150 years ago. Although it first appeared in the United States in the 1970s, serological evidence indicates that it was present in Africa in only a few individuals in the 1950s. Viruses similar to HIV exist in a number of wild and domestic animals, including cats, dairy cattle, and monkeys. A virus closely related to HIV-1 has been found in animals belonging to a single West African subspecies of chimpanzees. The virus does not appear to harm the chimpanzees, suggesting that they have been living together for eons. Another virus, closely related to HIV-2, is present in a species of large monkey, the sooty mangabey. A likely theory is that the

AIDS-causing viruses “jumped” to humans from these simian relatives, presumably through contact with their blood. Indeed, in Africa, chimps and mangabeys are often killed for food, exposing humans to their blood, and incidentally, driving some species nearly to extinction. Also, a number of humans were intentionally injected with chimpanzee and mangabey blood in the course of research on malaria carried out between 1922 and 1955. Genetic comparisons of a large number of simian lentiviruses and AIDS-causing viruses from humans support the idea that the simian viruses can jump to humans. In the case of HIV-1, a jump to humans probably occurred only once, between 1910 and 1950. It is unlikely that HIV was transferred to humans by inade-

subjects progress rapidly to AIDS within a few years. Another 5% to 10% of HIV-infected individuals show no fall in CD4; cells. They maintain high levels of anti-HIV antibody and HIV-specific CD8; cytotoxic T cells. Estimates suggest that, with these cases and the more slowly progressing typical cases, 10% to 17% of HIV-infected persons will not have progressed to AIDS 20 years after becoming infected with HIV.

Epidemiology Sexual intercourse with multiple partners without the use of condoms is a major factor in the spread of HIV disease. In the United States, initially, promiscuous homosexual men were the hardest hit by the epidemic. An estimated 1.4% to 10% of American men are homosexuals. An additional number of men are bisexual, meaning they have sexual intercourse with both men and women. A survey done before the arrival of AIDS found that 33% to 40% of homosexual men had more than 500 lifetime sexual partners. By 1984, two-thirds of one group of homosexual men in San Francisco were infected with HIV and almost one-third had developed AIDS. In the 1-year period ending in mid-1999 there were more than 22,000 new AIDS cases reported among men who had sex with men, and these accounted for an estimated 45% of new HIV infections over the same period. A newer study carried out between 2001–2006 indicated that men who have sex with men continue to lead all other groups in the incidence of HIV infection and AIDS. Heterosexual spread of HIV is increasing and promises to become the dominant mode of transmission, as it is in many African countries. Sex with multiple partners; sex with a person who has had multiple partners; being the receptive partner, especially receptive anal sex; traumatic sex; and any irritation or inflammatory process as from another sexually transmitted disease—all increase the risk of sexual HIV transmission. Contrary to popular notion, the disease can be contracted by the insertive partner during vaginal or rectal intercourse with an infected person. Saliva is very unlikely to transmit the disease, but there is evidence that oral-genital contact may be risky.

nes95432_Ch29_697-720.indd 705

quately sterilized Salk polio vaccine grown in simian kidney cell cultures. There is no credible evidence for another popular theory that the viruses resulted from botched biological warfare experiments by Russia or the United States. It is possible that AIDS-causing viruses have existed for many years in people living in isolated African villages, perhaps even for centuries. According to this idea, population increases and migration to big, crowded cities allowed the viruses to spread rapidly, becoming more virulent in the process. The answer to the question about the origins of AIDS-causing viruses might never be known precisely, but the question is intriguing and may lead to better understanding of the emergence of new infectious diseases.

The next most important mode of transmission of HIV is through blood and blood products. Individuals infected with HIV who donated blood before a screening test became available in 1985 unknowingly infected thousands of transfusion recipients. One of the products from pooled donated blood, clotting factor VIII, was used to treat bleeding episodes among hemophiliacs. By 1984, over half of the hemophiliacs in the United States and 10% to 20% of their sexual partners were HIV positive. Fortunately, the risk of HIV transmission by factor VIII was eliminated in 1992 when recombinant factor VIII was licensed. However, transmission by blood is still a major factor in the HIV disease pandemic because of needle sharing by those who abuse injected drugs. In the United States, the population of abusers of injected drugs is estimated to be 1.5 million. Many of them, both men and women, support their drug habits with prostitution, thereby furthering the spread of HIV. Because HIV is acquired and spread through sexual intercourse and through the sharing of hypodermic needles, drug abusers and their sexual partners have been a big factor in spreading the virus. A study of the first 640,000 AIDS cases revealed that more than onethird were directly or indirectly related to injected-drug abuse. The third most important mode of HIV spread is from mother to infant. Women represent an increasing percentage of the total AIDS cases as heterosexual spread of HIV increases (figure 29.9). An estimated estimated 70% of new HIV infections in women in the 1-year period ending in mid-1999 were acquired heterosexually. If untreated, about 1 out of 10 pregnant HIV-positive women will miscarry, and of live-born babies, 15% to 40% will develop AIDS. Remarkably, however, in a study of 219 newborn babies positive for HIV by culture or PCR, almost 3% appeared to clear their infection without any treatment. Breast feeding carries a significant risk of mother-infant transmission, especially if the mother has high levels of HIV in her blood as a result of an acute HIV infection.

Prevention and Treatment There is no approved vaccine against HIV infection, and current clinical vaccine trials do not look promising. Many people with HIV

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CHAPTER TWENTY NINE HIV Disease and Complications of Immunodeficiency

35

TABLE 29.2 Behaviors that Help Control the AIDS Epidemic

Percentage of AIDS cases

30

1. Not engaging in sexual intercourse. 25

2. Staying in a mutually monogamous relationship.

20

3. Avoiding sexual intercourse with persons at risk for HIV infection (see table 29.3).

15

4. Avoiding trauma to the genitalia and rectum. Small breaks in the skin and mucous membranes allow HIV to infect.

10

5. Not engaging in sexual intercourse when sores from herpes simplex or other causes are present. They represent sites where HIV can infect.

2005

2003

2001

1999

1997

1995

1993

1991

1989

5

Year

FIGURE 29.9 After steadily rising during the 1990s, the percentage of AIDS cases in women appears to be leveling off.

disease do not know they are infected, and it is advisable to consider all blood as potentially containing the virus. Infectious HIV persists in samples of blood plasma for at least 1 week after they are taken from AIDS patients. HIV on objects and surfaces contaminated by body fluids is easily inactivated by commercially available, highlevel disinfectants and heat at 56°C or more for 30 minutes. Freshly opened household sodium hypochlorite 5.25% bleach, diluted 1:10, is a cheap and effective disinfectant for general use. Virus present in dried blood or pus, however, may be difficult to inactivate. Knowing how HIV is transmitted is a powerful weapon against the AIDS epidemic. This weapon can be far more effective than any vaccine or treatment now on the horizon. HIV is not highly contagious, and the risk of contracting and spreading it can be eliminated or markedly reduced by assuming behaviors that prevent transmission of the virus (table 29.2). Some groups of homosexual men lowered the incidence of new HIV infections from 10% to 20% annually to only 1% to 2% annually by using condoms and avoiding practices that favor HIV transmission. The improvement in infection rates has not always been sustained, however. Since 1985, the risk of acquiring HIV from blood transfusions has been lowered dramatically by screening potential donors for HIV risk factors and testing their blood for antibody to HIV. The risk is now estimated to be less than 1 in 400,000 transfused units. Newer tests for HIV antibody and nucleic acid give positive results within 1 month of infection in most but not all cases. Screening tests used for infection have also markedly reduced the risk of HIV transmission from artificial insemination and organ transplantation. Education about how HIV is transmitted can be a very effective tool in helping to bring the worldwide epidemic of HIV disease under control. Education of schoolchildren has been shown effective in decreasing risky sexual behavior among teenagers. Videotapes and written material developed for one group of people, however, can be completely ineffective and even offensive to another group.

nes95432_Ch29_697-720.indd 706

6. Not engaging in anal intercourse. Receptive anal intercourse carries a high risk of HIV transmission. 7. Using latex condoms from beginning to end of sexual intercourse. Polyurethrane condoms are a reasonable alternative for those allergic to latex. Condoms made from other materials are not reliable for disease prevention, nor are those marketed in many African and other countries outside the United States. Oil-based lubricants are not compatible with latex. Condoms for women are available. 8. Postponing pregnancy indefinitely if you are a woman infected with HIV. If you are not sure of your HIV status, blood tests to rule out HIV disease before considering pregnancy. 9. Using extreme care to avoid needles, razors, toothbrushes, etc., that could be contaminated with someone else’s blood.

All persons unsure of their HIV status and especially those at increased risk of HIV disease (table 29.3) are advised to get tested for HIV. With this knowledge, those with HIV disease can receive prompt preventive treatment for the infections and cancers that complicate the disease. Antiretroviral treatment of HIV disease shows promise of preventing the complications of immunodeficiency for decades, and it may also reduce transmissibility. Also, HIV-positive individuals who know their status are able to do their part in preventing transmission. Federally approved home test kits coupled with counseling are reliable and commercially available. ■ sexually transmitted diseases, p. 628

TABLE 29.3 Persons at Increased Risk for HIV Disease 1. Injected-drug abusers who have shared needles. 2. Persons who received blood transfusions or pooled blood products between 1978 and 1985. 3. Sexually promiscuous men and women, especially prostitutes, drug abusers, and homosexual and bisexual men. 4. People with history of hepatitis B, syphilis, gonorrhea, or other sexually transmitted diseases that may be markers for unprotected sexual intercourse with multiple partners. 5. People who have had blood or sexual exposure to any of the people listed.

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29.1 Human Immunodeficiency Virus (HIV) Infection and AIDS 60,000 50,000 40,000 Deaths

HIV transmission from infected mother to newborn can safely be prevented in two-thirds of cases by administering zidovudine (AZT) to the mother during pregnancy and to the newborn infant for 12 weeks. Newer, more potent combinations of AZT and other antiretroviral therapies are widely employed and may be more effective, but their long-term safety is still being evaluated. Elective cesarian section significantly reduces the risk of HIV transmission to the newborn baby, perhaps by avoiding HIV-containing fluids in the birth canal. Also, medications are effective for preventing AIDS acquired from HIV-contaminated instruments, including bloody hypodermic needles. Hundreds of needle and syringe exchange programs, operating in at least 30 states and the District of Columbia, help prevent the spread of HIV and other blood-borne diseases among injecteddrug abusers and to their sexual partners and children. In these programs, sterile syringes and needles are exchanged for used ones. Programs also provide drug rehabilitation efforts and education about use of condoms and other safer sexual practices. Better prevention and treatment of opportunistic infections and better antiviral therapy against HIV have significantly lengthened the asymptomatic stage of the disease and prolonged life once AIDS develops (figure 29.10). Advances in antiviral treatment mainly result from the development of new medications with different modes of antiviral action. Use of these medications in “cocktails,” such as combinations of reverse transcriptase and pro-

707

30,000 20,000 10,000 0 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 Year

FIGURE 29.10 Deaths Due to AIDS, United States, 1995 to 2005 Notice the marked drop in deaths after HAART became available in late 1995. (Source: CDC HIV/AIDS Surveillance Report v.17 revised June 2007; earlier volumes.)

tease inhibitors, is referred to as HAART—“highly active antiretroviral therapy.” Other important advances include the combining of medications in a single dosage form, and developing “once-aday therapy.” The effectiveness of HAART probably stems from the fact that each of the medications act on the replicating virus at different parts of the virus life cycle. Despite the high mutation rate of HIV, it is much less likely that any one mutant could develop resistance to all the medications at the same time.

CASE PRESENTATION The patient was a young woman from West Africa presenting with the complaint of generalized enlargement of her lymph nodes. She had recently moved to the United States. She had no history of drug abuse or of receiving blood transfusions. She had had three sex partners in her life. Her single pregnancy the year before her arrival was delivered by emergency cesarian section. She and the baby’s father had routine tests for HIV at that time, and both tests were negative. The baby and the father remained well. Ten years before her evaluation, she was treated for a fever by scarification deliberately making superficial cuts in the skin, and this was repeated for an unrelated complaint 4 years before her evaluation. The native healer performing the scarification used a razor blade, the sterility of which is unknown to the patient. Her initial test results included non-diagnostic lymph node biopsies and a negative HIV test (enzymelinked immunosorbent assay, ELISA). A repeat HIV test some months later was weakly positive by ELISA, and the confirmatory Western blot showed only questionable reactions of the patient’s serum with gp41 and two other HIV antigens. A test for HIV-2 was negative. A CD4; T lymphocyte cell count was very low. A test to detect HIV1 using the polymerase chain reaction was negative. 1. Could this patient have HIV disease? If so, how could the negative tests be explained? 2. Does the history give any possible ways in which she could have contracted HIV disease?

nes95432_Ch29_697-720.indd 707

3. How could the diagnosis be established? 4. Could her baby and the baby’s father have the disease? 5. Does this case suggest that any changes should be made in the way HIV disease is diagnosed? Discussion 1. This patient could well have had HIV disease/AIDS because of her persistent, generalized lymphadenopathy and very low CD4; cell count. Her HIV strain might have differed enough from the pandemic group M HIV-1 strains so that the usual laboratory tests did not detect antibody to it. 2. The woman could have contracted an AIDScausing virus during sexual intercourse, or from a blood-contaminated razor blade used for scarification. Contracting such a virus from unsterile instruments during her emergency cesarian is a possibility, but this seems less likely because of the short time span before presenting with severe immunodeficiency. 3. The Centers for Disease Control and Prevention have a global surveillance system designed to detect cases like this because they raise the possibility of new or rare AIDS-causing viruses being introduced into a population. In the present case, samples of the patient’s blood were examined by the CDC and she was shown to be infected

with a group O HIV-1 virus. The patient’s serum reacted with peptides specific to group O strains, and the virus was isolated from her blood. Nucleic acid sequences of the env, gag, and pol genes matched those of previously isolated group O strains. Group O strains of HIV-1 were first found in Cameroon, a country on the West African coast, where they account for 6% of HIV infections. 4. Despite the absence of symptoms, both her baby and the baby’s father could have the disease. The baby’s risk of infection was reduced but not eliminated by the emergency cesarian section, and infection could have occurred subsequently if it were breast fed. The mother’s very low CD4; cell count suggests a high level of viremia and, therefore, increased risk of transmitting the disease. She could have infected the baby’s father during sexual intercourse, or he could have infected her. 5. This patient was the first case of group O HIV disease identified in the United States. Studies indicate that previous introductions, if any, were not accompanied by spread of the virus. Nevertheless, federal agencies worked with manufacturers of HIV tests to increase sensitivity of the tests to group O strains.

Source: Centers for Disease Control and Prevention. 1996. Morbidity and Mortality Weekly Report 45(6): 122.

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Presently available medications fall into four groups: inhibitors of reverse transcriptase, inhibitors of viral protease, inhibitors of viral integrase, and a fusion inhibitor. Other types of medications being developed are fusion inhibitors to prevent viral entry into host cells, and medications that interfere with other polyproteins. Medications that interfere with reverse transcriptase fall into two categories: nucleoside reverse transcriptase inhibitors (NRTIs), and non-nucleoside reverse transcriptase inhibitors (NNRTIs). Zidovudine (AZT), stavudine (D4T), and lamivudine (3TC) are among the half dozen NRTIs in wide use, and a number of others are undergoing clinical trials. All are nucleoside analogs, but they differ chemically and in their site of action on the enzyme. These substances owe their effectiveness to their resemblance to the normal purine and pyrimidine building blocks of nucleic acids. During nucleic acid synthesis, the viral reverse transcriptase enzyme incorporates the medication molecule into the growing DNA chain, thereby blocking completion of the DNA strand. This process for AZT is illustrated in figure 29.11. ■ nucleosides, figure 2.22, p. 33

The non-nucleoside inhibitors of reverse transcriptase— nevirapine, efavirenz, and delavirdine—are among those in wide use, and at least five newer NNRTIs are in clinical trials. Generally, the NNRTIs are not nucleoside analogs, and they act in a completely different manner from NRTIs, by binding tightly to reverse transcriptase in an example of non-competitive inhibition.

CH 2 O

O Growing ends of two DNA strands

O

O

O

P

O O

CH 2

nes95432_Ch29_697-720.indd 708

O

CH 2

C

OH

C

OH

O O

O

P

O

Adenine nucleotide is added to part (a), and AZT is added to part (b).

T

O

O O

O

P

AZT O

P O

O O

CH 2

CH 2 O

A

OH

T

N3 Reverse transcriptase catalyzes the reaction

■ non-competitive inhibition, p. 138

Protease inhibitors were a major addition to the anti-HIV arsenal. The first protease inhibitor, saquinavir, was approved for therapy in December 1995. Currently, there are at least six protease inhibitors approved for use, and more in clinical trials. Unlike the reverse transcriptase inhibitors, the protease inhibitors act late in HIV replication to prevent packaging of viral proteins in the virion. The introduction of integrase inhibitors, with raltegravir in 2007, represented another important advance in treatment options that is very welcome in view of increasing resistance to older agents. Fusion inhibitors are a useful addition to therapy with the three types of enzyme inhibitors just mentioned. They act by interfering with viral attachment to the host cell. The first one to be approved, enfuvirtide (Fuzeon), in 2003, acts by blocking gp41attachment; maraviroc, approved in 2007, blocks the CCR5 co-receptor. HAART does not cure AIDS. Viremia becomes undetectable in only about half the cases, and even then, the viremia returns if the medications are discontinued. While it stops production of virions, it does not eliminate HIV provirus hidden in host cell genomes. In successful HAART, production of infectious virus is largely halted, many fewer CD4; lymphocytes are killed, and so the CD4; cell count rises. When the medications are stopped, persistently infected cells release infectious virions that can infect a new population of CD4; cells, resulting in a quick rise in viremia. Many authorities now feel that the secret to controlling HIV disease lies ultimately in minimizing or eliminating body cells containing the hidden HIV genomes. These authorities are advocating HAART for the acute retroviral syndrome to prevent the buildup in the body of cells containing HIV provirus.

CH 2 O

T

CH 2 O

CH 2 O

T

O O

O O

O

P

O

CH 2

O

CH 2 O

C

O O

P

C

O O

O

P

O

O

O CH 2 O

CH 2 O

A

OH (a)

O

P

O DNA strand in part (a) ends in OH and continues to grow; DNA strand in part (b) ends in N3 and cannot grow.

T

T

N3 (b)

FIGURE 29.11 Mode of Action of Zidovudine (AZT) (a) Normal elongation process of DNA in which reverse transcriptase catalyzes the reaction between the OH group on the chain with the phosphate group of the nucleotide being added. (b) Reverse transcriptase catalyzes the reaction of zidovudine with the growing DNA chain. Since zidovudine lacks the reactive OH group, no further additions to the chain can occur, and DNA synthesis is halted. T=thymine, C=cytosine, A=adenine. (It should be noted that zidovudine is a nucleoside. It becomes phosphorylated after entry into the cell.)

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29.1 Human Immunodeficiency Virus (HIV) Infection and AIDS

Many strains of HIV fail to respond to HAART because they have become resistant to the medications during past treatment. These resistant strains of HIV are transmissible to other persons. Toxic effects of the medications are another limitation of anti-HIV therapy. For example, AZT can cause anemia, low white blood cell count, vomiting, fatigue, headache, and muscle and liver damage. Painful peripheral nerve injury, inflammation of the pancreas, rash, mouth and esophagus ulceration, and fever are side effects of other NRTIs. Also, indinavir may be responsible for kidney stone formation, and ritonavir, another protease inhibitor, causes nausea and diarrhea. Diabetes mellitus is another potential side effect of protease inhibitors. Finally, a big limitation of the use of anti-HIV medications is their cost. The cost of a combination of these medications can easily exceed $1,000 per month for either an asymptomatic or a symptomatic individual and is expected to be required for life. While not considered excessive for a serious chronic disease in the United States, the cost of medications puts them out of reach for many of the world’s HIV victims. Negotiated price decreases and the early 2005 approval of three generic drugs by the U.S. Food and Drug Administration have made treatment available to many more HIV victims worldwide. The main features of HIV disease are presented in table 29.4.

HIV Vaccine Prospects There are no approved vaccines for preventing HIV disease. Development of potential HIV vaccines began soon after the discovery of the causative agent. In theory, a vaccine could be used in either of two ways. One, “preventive vaccine,” would be to immunize uninfected individuals against the disease. The other “therapeutic vaccine,” would be to boost the immunity of those already infected with HIV before they become severely immunodeficient. The latter approach would be similar to the post-exposure treatment of rabies infections. A successful vaccine must induce both mucosal and bloodstream immunity, because HIV disease is primarily sexually transmitted. The vaccine must also get around the problem of HIV antigenic variability and stimulate cellular and humoral responses against virulence determinants. Moreover, the vaccine has to be safe. An attenuated agent must not be capable of becoming a disease-causing strain, and it must not be oncogenic, meaning cancer-causing. Additionally, the vaccine must not stimulate an autoimmune response, and it must not cause production of “enhancing antibodies” that could aid the passage of HIV into the body’s cells. The vaccine should induce neutralizing antibodies against cell-free virions and also prevent direct spread of HIV from a cell to neighboring cells. ■ rabies, p. 663 Despite enormous difficulties, HIV vaccine research continues to offer the best hope for eventually controlling a worldwide epidemic that every year produces tens of thousands of new HIV infections in the United States alone. Findings that have encouraged vaccine researchers include failure of some African prostitutes to develop AIDS although repeatedly exposed to HIV. Also, HIVinfected pregnant women that have high titers of HIV-neutralizing antibodies are less likely to transmit the infection to their offspring than women with low antibody titers. Finally, infection by some strains of HIV apparently progresses to AIDS very slowly.

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TABLE 29.4 HIV Disease Symptoms

Over half develop fever, sore throat, head and muscle aches, rash, enlarged lymph nodes early in the infection. After an asymptomatic period symptoms from unusual malignant tumors, pneumonia, meningoencephalitis, diarrhea, etc.

Incubation period

Usually 6 days to 6 weeks for acute symptoms; immunodeficiency symptoms within 10 years in half the infections (10% within 5 years and 90% within 17 years)

Causative agent

Human immunodeficiency virus, type 1 (HIV-1), many subtypes and strains. HIV-2 mainly in West Africa.

Pathogenesis

HIV infects various body cells, notably those vital to specific immunity, CD4; T lymphocytes and antibody-presenting cells. T cells killed, numbers slowly decline until the immune system can no longer resist infections or development of tumors.

Epidemiology

Three main routes of transmission of HIV: intimate sexual contact, via transfer of blood or blood products, and from mother to child around the time of childbirth. Risk of transmission by breast milk, and possibly by oral-genital contact.

Prevention and treatment

No vaccine yet available. Medications and vaccines can prevent many of the infections that can complicate HIV disease. Anti-HIV medications and cesarian section decrease mother-to-newborn transmission. Effective preventive measures: sex education of schoolchildren, needle exchange programs for drug addicts, use of condoms. Treatment: HAART therapy, consisting of combinations of several anti-HIV medications, effective for many AIDS victims, and delays progression of HIV disease to AIDS. Not a cure, and too expensive for most of the world’s HIV disease victims.

Candidate vaccines undergo an extensive evaluation for safety and immunogenicity in experimental animals before they are tested in humans. Some of the many substances in this preclinical stage of development are inactivated HIV, various viruses and bacteria carrying parts of the HIV genome, HIV peptides and proteins, HIV proteins with adjuvants, and naked DNA containing HIV genes. ■ DNA-based vaccines, p. 437 Vaccine trials in humans have been undertaken for at least 10 experimental vaccines. Vaccine evaluations in humans progress from phase I (testing safety and ability to provoke an immune response), to phase II (determining optimum dose, and characteristics and duration of immune response), to phase III (testing effectiveness in preventing HIV infection or AIDS). Substances that have entered human trials include recombinant gp120 and gp160; vaccinia virus containing HIV envelope genes; canary poxvirus containing HIV genes env, gag, and pol; a synthetic lipopeptide; a DNA vaccine containing HIV envelope genes; a Salmonella typhi strain engineered to express HIV gp120; and

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CHAPTER TWENTY NINE HIV Disease and Complications of Immunodeficiency

purified p17 (MA). Phase III trial employing gp120 from subtypes B and E gave negative results as did a later trial of prime-boost vaccine. The “prime-boost” technique employs an initial injection of a virus such as genetically engineered vaccinia containing HIV surface and core genes, followed later by an injection of recombinant viral surface antigen, gp120. The first injection gives primarily a cytotoxic T-lymphocyte response, and the second injection boosts the production of neutralizing antibodies. ■ poxviruses, p. 327 ■ vaccinia, pp. 324, 554, 709

The potential of synthetic peptides in immunization against HIV is also being explored. The amino acid sequence of the surface proteins of HIV is known; thus, peptides that exactly mimic immunologically important segments such as the V3 loop (see figure 29.7) can be synthesized. ■ peptide, p. 28 ■ peptide vaccines, p. 437

MICROCHECK 29.1 The signs and symptoms of persons with AIDS are mainly due to the opportunistic infections and tumors that complicate HIV disease. HIV is not highly contagious, and the AIDS worldwide epidemic could be stopped by changes in human behavior. Highly active antiretroviral therapy has given many patients with AIDS miraculous improvement. ✓ What is hairy leukoplakia? ✓ How would the ability to recognize differing strains of HIV-1 aid in epidemiological studies? ✓ If AIDS was present in Africa in the 1950s, why did it not appear in the United States until the 1970s?

29.2 Malignant Tumors That Complicate Acquired Immunodeficiencies Focus Points

Kaposi’s Sarcoma Kaposi’s sarcoma (figure 29.12) is an unusual tumor arising from blood or lymphatic vessels in multiple locations. Formerly, it was seen rarely and afflicted mainly older men of Mediterranean and Eastern European origin. It also occurs among all age groups in certain parts of tropical Africa. It is not associated with immunodeficiency in any of these varieties. Coincident with the spread of HIV, the tumor began to appear in young men with HIV disease and its incidence rose dramatically. Among a group of never-married San Francisco men, the incidence of Kaposi’s sarcoma was 2,000 times as high in 1984 as it was in the period before HIV became widespread. The tumor was so common among AIDS patients that it became an AIDSdefining condition, even though it generally appeared before the development of severe immunodeficiency. One of the many unsolved mysteries about this tumor is that its incidence among AIDS patients has fallen dramatically since the adoption of condom use and safer sex practices. Besides HIV disease, Kaposi’s sarcoma is often associated with the use of medications to suppress the immune system in organ transplant patients. Indeed, the incidence of Kaposi’s sarcoma is more than 400 times as high in transplant patients as in the general public. Another peculiarity of the tumor is that it can sometimes disappear if a patient’s organ graft is rejected, suggesting a strong influence for cellular immunity. In 1994, scientists at Columbia University detected a previously unknown herpesvirus in Kaposi’s sarcomas, named Kaposi’s sarcoma-associated herpesvirus (KSHV), or human herpesvirus-8 (HHV-8). The virus can be detected in essentially all cases of Kaposi’s sarcoma, whether associated with immunodeficiency or not. It is also strongly associated with certain malignant tumors, including multiple myeloma. Serological evidence of infection is present in about 25% of the healthy adult U.S. population. HHV-8 has been detected in the saliva of patients with HIV disease and Kaposi’s sarcoma, and in semen of healthy men. Although there is still much to be learned about the role HHV-8 plays in Kaposi’s

Explain how HIV disease might increase the risk of malignant tumors. Outline the relationship between Kaposi’s sarcoma and human herpesvirus-8.

Certain malignant tumors are associated with HIV disease, organ transplantation, and other acquired immunodeficiency states. Most of these malignancies fall into one of only three types: Kaposi’s sarcoma, lymphomas, and carcinomas arising from anal or cervical epithelium. They tend to metastasize, meaning jump to new areas, and are difficult to treat. Evidence indicates that viruses are a factor in their causation. A popular theory is that certain viral antigens, perhaps with the aid of cytokines, cause rapid multiplication of a host cell. A mutation to malignancy then occurs among the rapidly dividing cells, the result of insertion of viral DNA into their genome or other carcinogen. Finally, the malignant cell escapes detection and destruction by immune surveillance because of defective cellular immunity, and it is able to multiply without restraint.

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FIGURE 29.12 Kaposi’s Sarcoma Two lesions on a person’s foot are shown.

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29.2 Malignant Tumors That Complicate Acquired Immunodeficiencies

sarcoma, the virus appears to be necessary for formation of the tumor, but additional factors must be present for the tumor to develop. ■ multiple myeloma, p. 427 In Kaposi’s sarcoma, HHV-8 infects the endothelial cells that line blood and lymphatic vessels and persists there mostly in a latent form; only a small percentage of the infected cells evidence a lytic infection at any one time. Presence of the virus is associated with two dramatic changes that result in tumor formation: (1) The cells assume a spindle shape and proliferate; and (2) extensive formation of new blood vessels occurs. These changes are probably due to release from the host cells of the cytokines normally responsible for stimulating cell growth and new vessel formation. This release of cytokines appears to be due largely to a gene product of latent HHV-8. The changes typically seen in cancers and other malignant tumors are usually not present—namely, proliferation of a single clone of microscopically abnormal cells with abnormal chromosomes, and origin in a single location with later distant metastases. When malignant changes occur in Kaposi’s sarcoma, as they do occasionally, the abnormal clone of cells does not contain the HHV-8 genome, showing that a factor other than the virus is responsible for the transformation. Only a fraction of individuals infected with both HHV-8 and HIV-1 develop Kaposi’s sarcoma, but that fraction is enormously greater than that seen in people infected only with HHV-8. Why is HHV-8 infection so much more likely to result in Kaposi’s sarcoma in patients with HIV-1 disease? Scientists around the world, hard at work on this question, have discovered some clues. Tat, the protein product of the HIV tat gene, is released from infected T lymphocytes and enhances proliferation of endothelial cells. The Tat of HIV-2 does not have the same effect, and there is no increase in Kaposi’s sarcoma in patients with HIV-2 disease. Many of the molecular details of the interaction of the two viruses are now known and undoubtedly will lead to new treatment options and better understanding of how malignancy develops.

B-Lymphocytic Tumors of the Brain Lymphomas are a group of malignant tumors that arise from lymphoid cells. Most of these tumors arise from B lymphocytes, although T-lymphocytic lymphomas also occur. B-cell lymphomas are 60 to 100 times as common in AIDS patients as in the general public, and 60 times as frequent in individuals with organ transplants. Intense, sustained replication of lymphoid cells is a constant feature of HIV. As stated at the beginning of this chapter, HIV was first isolated from a patient with the lymphadenopathy syndrome, a condition in which the lymph nodes are markedly enlarged for 3 months or more, now known to be a prelude to AIDS. The lymph node enlargement reflects proliferation of lymphoid cells in response to high-level, unregulated cytokine release and to the HIV gp41 (TM) antigen. Also in HIV disease, sustained replication of T cells occurs as billions of new cells are produced each day to replace those destroyed by HIV. In contrast to Kaposi’s sarcoma, with B-lymphocytic tumors there is no epidemiologic evidence of involvement of a sexually transmitted infection.

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711

Epstein-Barr virus (EBV), however, plays a role in many of the B-cell lymphomas associated with AIDS. EBV is present in essentially all cases that involve the brain. Lymphomas rarely arise in the brain except in AIDS patients. EBV is also present in all the B-cell lymphomas that occur in transplant patients. The EBV-related tumor, Burkitt’s lymphoma, is at least 1,000 times as frequent among AIDS patients as in the general public, representing about one-fourth of all the lymphomas associated with AIDS. EBV probably plays an indirect role in B-cell lymphoma formation rather than being the direct cause. HIV infection causes activation of latent EBV infection, with release of the virus to infect new B lymphocytes. This, in turn, causes polyclonal B-cell proliferation and increased life span. Malignant B-cell clones are thought to arise from this population of rapidly dividing cells. ■ Epstein-Barr virus, Burkitt’s lymphoma, p. 686

Cervical and Anal Carcinoma Carcinoma (cancer) of the uterine cervix in women and carcinoma of the anus in women and homosexual men are strongly associated with human papillomaviruses (HPV) types 16 and 18. The cells involved in these cancers are epithelial cells and, therefore, differ from those in Kaposi’s sarcomas and lymphomas. HPV is transmitted during sexual activity and infects the cervical and anal epithelium, appearing to cause increased replication of the cells by blocking expression of a cellular gene responsible for controlling cell growth. In HIV disease, organ transplantation, and other immunodeficient conditions, HPV replication increases with the decline of the host’s cellular immunity. Precancerous changes can be demonstrated in the anal cells of HIV-positive homosexual men twice as frequently as in homosexual men who are HIV negative, and six times as frequently among HIV-positive homosexual men with low CD4; T-cell counts as in HIV-positive homosexual men with high CD4; T-cell counts. Interestingly, even before the arrival of HIV, the incidence of anal carcinoma in homosexual men exceeded the incidence of cervical carcinoma in women. One important implication of these findings is that women who engage in anal intercourse should be screened for precancerous lesions of the cervix and anus, and homosexual men for lesions of the anus, at least twice yearly if they are HIV positive. ■ human papillomavirus infections, p. 638

MICROCHECK 29.2 Certain DNA viruses are strongly associated with development of malignant tumors in patients with HIV disease. These viruses are not sufficient by themselves to cause malignancy, but require the presence of other conditions. The tumors all arise in a setting of increased cell proliferation caused in part by the viruses. Many of these tumors are preventable by practicing safer sex practices and screening for premalignant lesions. ✓ What HIV gene product appears to play a role in development of Kaposi’s sarcoma? ✓ What member of the herpesvirus family is associated with almost all of the B-cell lymphomas of the brain in AIDS patients? ✓ What measure is important to prevent cervical and anal carcinomas in persons with HIV disease? ✓ Would rapidly dividing cells favor mutation?

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29.3 Infectious Complications of Acquired Immunodeficiency Focus Points Describe the significance of Pneumocystis jirovecii infection as it relates to HIV disease.

Symptoms The symptoms of pneumocystosis typically begin slowly, with gradually increasing shortness of breath and rapid breathing. Fever is usually slight or absent, and only about half of the patients have a cough, which is non-productive. As the disease progresses, a dusky coloration of the skin and mucous membranes appears and gradually worsens—a reflection of poor oxygenation of the blood, which can become fatal.

Outline the epidemiology of toxoplasmosis.

Causative Agent

Discuss the relationship between CMV disease and HIV disease.

Pneumocystosis is caused by Pneumocystis jirovecii (figure 29.13), a tiny fungus belonging to the phylum Ascomycota, class Archiascomycetes. Formerly the organism was classified as P.carinii and it is still widely known by that name. It differs from many fungi in the chemical make-up of its cell wall, which makes it resistant to medications often used against fungal pathogens. The organism has not reliably been cultivated in vitro. ■ ascomycetes, p. 288

Outline the pathogenesis of Mycobacterium avium complex infection in individuals with immunodeficiency.

Immunodeficient individuals are susceptible to the same infectious diseases as other people. In addition, infections that pose no threat to immunologically normal people can cause severe, even fatal disease in those with impaired immune systems. Prevention of infectious diseases is key to the care of these people. Table 29.5 shows some immunizations that are advisable; they should be given as early as possible in HIV disease. Except for measlesmumps-rubella, attenuated vaccines are generally unsafe to use in HIV disease. Bacteria, viruses, fungi, protozoa, and even parasitic worms such as Strongyloides stercoralis can be life threatening. The geographical area may determine which infectious complications are most important. For example, the mold Penicillium marneffei is the third most common opportunistic agent among AIDS patients in Thailand but is almost unheard of elsewhere. This section will present some examples of infectious diseases common in patients with immunodeficiency.

Pneumocystosis

Pathogenesis The small spores of P. jirovecii, measure only 1 to 3 mm and are easily inhaled into lung tissue. In experimental infections, the spores attach to the alveolar walls, and the alveoli fill with fluid, mononuclear cells, and masses of P. jirovecii cells in various stages of development. Later, the alveolar walls become thickened and scarred, preventing the free passage of oxygen.

Epidemiology Various species of Pneumocystis are widespread among animals, including dogs, cats, horses, and rodents, persisting in their lungs as a latent infection. Although identical in appearance to P. jirovecii, they are genetically distinct and play no role in human disease. Most children are infected with P. jirovecii by age 2 and a half. The infection is asymptomatic and is generally

Pneumocystosis, a severe, infectious lung disease, was recognized just after World War II in Europe when it caused deaths among hospitalized, malnourished, premature infants. Subsequently, scattered cases were recognized among immunodeficient patients until the onset of the AIDS epidemic, when the incidence soared. By 1995, almost 128,000 cases had been reported to the Centers for Disease Control and Prevention. Even today it remains the leading opportunistic infection in AIDS patients.

TABLE 29.5 Immunizations in Individuals with HIV Disease Advised

Not Advised

Measles-mumps-rubella

Oral poliomyelitis

Pneumococcal polysaccharide

Oral typhoid

Influenza

BCG (tuberculosis vaccine)

Hepatitis A

Varicella-zoster

Hepatitis B

Yellow fever

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30 µm

FIGURE 29.13 Fluorescent Antibody Stain of Pneumocystis jirovecii The yellow circles are P. jirovecii cysts.

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29.3 Infectious Complications of Acquired Immunodeficiency

eliminated within a year. The source and transmission of human infections are unknown. Most cases of pneumocystosis occur in persons with immunodeficiency, but it is uncertain whether their disease is caused by activation of latent infection, or infection newly acquired from inhalation of airborne spores. Epidemics among hospitalized malnourished infants and elderly nursing home residents suggest airborne spread, and P. jirovecii has been detected in indoor and outdoor air by using the polymerase chain reaction.

Prevention and Treatment Pneumocystosis used to occur in about four-fifths of AIDS patients and was the leading cause of death. The disease is now largely prevented by starting regular doses of a medication such as trimethoprim-sulfamethoxazole to persons with HIV disease as soon as their CD4; T-cell count falls below 200 per ml, or if other hallmarks of immunodeficiency appear, such as thrush, a Candida infection of the mouth and throat. Trimethoprim-sulfamethoxazole is also among the best medications for treating pneumocystosis and, along with oxygen and other measures, can reduce mortality from nearly 100% to about 30%. Alternative medications are available for treating those who cannot tolerate trimethoprim-sulfamethoxazole because of its side effects—mainly rash, nausea, and fever. For unknown reasons, people with HIV disease are more likely to develop these side effects than others. After treatment for pneumocystosis, individuals with HIV disease must receive preventive medication indefinitely, or until they have a sustained rise in CD4; T-cell count to above 200 cells/ml. The main features of pneumocystosis are presented in table 29.6.

713

TABLE 29.6 Pneumocystosis Symptoms

Gradual onset, shortness of breath, rapid breathing, non-productive cough, slight or absent fever, dusky color of skin and mucous membranes

Incubation period

4 to 8 weeks

Causative agent

Pneumocystis jirovecii, a tiny fungus related to the ascomycetes

Pathogenesis

Pneumocystosis can result from reactivation of latent infection or be newly acquired. Spores of P. jirovecii escape body defenses, enter the lungs with inspired air, attach to alveolar walls, multiply. Alveoli fill with fluid, macrophages, and P. jirovecii. The walls thicken, impairing oxygen exchange.

Epidemiology

Pneumocystis carinii widespread in domestic and wild animals as a latent lung infection, but the source of animal and human infections is unknown. Most humans become infected in early childhood. Disease arises in individuals with immunodeficiency; epidemics can occur in hospitalized premature infants and elderly nursing home residents.

Prevention and treatment

Formerly leading cause of death in those with AIDS, now usually prevented by medication (e.g., trimethoprim-sulfamethoxazole) as soon as the CD4; lymphocyte count drops to 200 cells per ml. Same medication is used for treatment; alternatives available. Medication is continued for life, or until the CD4; cell count rises and remains above 200 as a result of HAART or other treatment of the underlying immunodeficiency.

Toxoplasmosis Toxoplasmosis is a protozoan disease that rarely develops among healthy people but can be a serious problem for those with malignant tumors, recipients of organ transplantation, the unborn child, and people with HIV disease.

Symptoms The disease presents itself differently in the three main categories of patients: (1) the immunologically normal, (2) unborn children, and (3) those with immunodeficiency. Toxoplasmosis can be acquired by immunocompetent individuals who eat raw or undercooked meat or who are exposed to cat feces. Most infections are asymptomatic, but 10% to 20% develop symptoms similar to those of infectious mononucleosis. They usually consist of sore throat, fever, enlarged lymph nodes and spleen, and sometimes a rash. These symptoms subside over weeks or months and do not require treatment. Rarely, a severe, even life-threatening illness develops, due to involvement of the heart or central nervous system. ■ infectious mononucleosis, p. 686 Toxoplasmosis of the unborn results from almost half of maternal infections that occur during pregnancy. Fetal toxoplasmosis during the first trimester of pregnancy is the least common but most severe, often resulting in miscarriage or stillbirth. Babies born live may have severe birth defects including small or enlarged heads, and their lungs and liver may also be damaged by

nes95432_Ch29_697-720.indd 713

the disease. Later, these babies can develop seizures or manifest mental retardation. Almost two-thirds of fetal toxoplasmosis cases occur during the last trimester of pregnancy, however, and the effects on the fetus are usually less severe. Most of these infants appear normal at birth, although later in life, retinitis—infection of the retina, the light-sensitive part of the eye—can be a big problem for them. This manifests itself as recurrent episodes of pain, sensitivity to light, and blurred vision, usually involving only one eye. Less common late consequences of congenital toxoplasmosis include mental retardation and epilepsy. Toxoplasmosis that complicates immunodeficiency is commonly life threatening. Brain involvement in the form of encephalitis occurs in more than half the cases, manifested by confusion, weakness, impaired coordination, seizures, stiff neck, paralysis, and coma. Involvement of the brain, heart, and other organs often results in death.

Causative Agent Toxoplasmosis is caused by Toxoplasma gondii, a tiny (3 by 7 mm), banana-shaped protozoan (figure 29.14a) that has a worldwide distribution and infects most warm-blooded animals, including household pets, pigs, sheep, cows, rodents, and birds. Its species name derives from the fact that the protozoan was first

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CHAPTER TWENTY NINE HIV Disease and Complications of Immunodeficiency

(a)

15 µm

Animals with cysts in tissue Immature oocyst Sporocysts

Sporozoite

Changing litter box

Mature oocyst

discovered in the gondi, an African desert rodent. The life cycle of T. gondii is shown in figure 29.14b. The definitive host, the one in which sexual reproduction occurs, is the cat or other feline (ocelot, puma, bobcat, Bengal tigers, and so on). The organism reproduces in the cat’s intestinal lining, resulting in numerous progeny, some of which spread throughout the body and others that differentiate into male and female gametes (sexual forms). Union of gametes results in the formation of a thick-walled, oval structure (oocyst) about 12 mm in diameter that is shed in the cat’s feces. Millions of the oocysts are shed each day, generally over a period of 1 to 3 weeks. In the soil, the oocysts undergo further development over 1 to 5 days into an infectious form containing two sporocysts, each with four sporozoites. These can remain viable for up to a year, contaminating soil and water and, secondarily, hands and food. In general, the cats recover from the acute infection and do not shed oocysts again. The oocysts are infectious for cats and other animals, including humans. When non-feline animals ingest the oocysts, usually from contaminated food or water, the sporozoites emerge from the oocysts and invade the cells of the small intestine, especially its lower part, the ileum, but there is no sexual cycle. The intestinal infection spreads by the lymphatics and blood vessels throughout the tissues of the host, infecting cells of the heart, brain, and muscles. As host immunity develops, multiplication slows, and a tough, fibrous capsule forms, surrounding large numbers of a smaller form of T. gondii. These capsules packed with organisms are called cysts (figure 29.14c), and they remain viable for months or years. The life cycle is completed when a cat becomes infected by eating an animal with cysts in its tissues.

Pathogenesis Infected raw or undercooked meat

Congenital infection

(b)

Cyst wall

The organisms enter the body by ingestion of oocysts or inadequately cooked meat containing tissue cysts. Toxoplasma gondii is infectious for any kind of warm-blooded animal cell except non-nucleated red blood cells. Entry into the host cell is aided by an enzyme produced by the organism, which alters the host cell membrane. Proliferation of T. gondii in cells of the host causes destruction of the cells. Unless the infecting dose of the organism is very high, this process is normally brought under control by the immune response of the host, tissue cysts develop, and infected humans usually show few, if any, symptoms. In patients with immunodeficiency, however, infection can be widespread and uncontrolled, producing many areas of tissue necrosis. The disease process can result from a newly acquired infection, or declining immunity can allow reactivation of latent infection with escape of T. gondii from a person’s tissue cysts.

T. gondii

Epidemiology (c)

10 µm

FIGURE 29.14 Toxoplasma gondii (a) Invasive forms. (b) Life cycle. Oocysts from cat feces and cysts from raw or inadequately cooked meat can infect humans and many other animals. (c) Cyst in tissue.

nes95432_Ch29_697-720.indd 714

Toxoplasma gondii is distributed worldwide, but it is less common in cold and in hot, dry climates. Human infection is widespread. Serological surveys show the infection rate increases with age, ranging from 10% to 67% among those over age 50. Most infections are acquired when a person ingests oocysts that contaminate fingers, food, or drink or inhales contaminated dust in an enclosed space such as a barn. Young, homeless cats that commonly eat

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29.3 Infectious Complications of Acquired Immunodeficiency

rodents and birds are likely sources of the organism. Small epidemics have occurred from drinking water contaminated with oocysts. Gardening in areas frequented by cats can result in T. gondii contamination of hands or vegetables. Eating rare meat poses a definite risk. Tissue cysts are present in about 25% of pork, in 10% of lamb, and less commonly in beef and chicken.

TABLE 29.7 Toxoplasmosis Symptoms

In healthy individuals: sore throat, fever, enlarged lymph nodes, rash; with fetal infections: miscarriage, stillbirth, birth defects, epilepsy, mental retardation, retinitis; in immunodeficient individuals: confusion, poor coordination, weakness, paralysis, seizures, coma

Incubation period

Usually indeterminate

Causative agent

Toxoplasma gondii, a protozoan infectious for most warm-blooded animals. Sexual reproduction occurs in the intestinal epithelium of cats, the definitive hosts. Infected cats discharge oocysts with their feces. Ingested organisms are released from the oocysts, multiply rapidly, spread throughout the body. As immunity develops, infected cells become filled with the organisms, resulting in tissue cysts, which remain viable and infectious for the lifetime of the animal.

Pathogenesis

Organisms penetrate host cells causing necrosis. With development of immunity cell destruction stops, tissue cysts develop. Most healthy individuals have few or no symptoms unless the numbers of ingested organisms is very large. Organisms released from tissue cysts if immunity becomes impaired.

Epidemiology

Occurs worldwide, less common in cold or dry locations. Infection acquired by ingesting oocysts from cat feces, or eating inadequately cooked meat.

Prevention and treatment

Prevention: avoiding foods potentially contaminated with oocysts from cat feces, and not consuming inadequately cooked meat. Trimethoprim-sulfamethoxazole is given to immunodeficient persons with CD4; T lymphocyte counts below 100 cells per ml if they have antibodies to T. gondii indicating latent infection. Treatment: pyrimethamine with sulfadiazine, or alternative medication.

Prevention and Treatment General measures for preventing T. gondii infection include washing hands after handling raw meat, coming in contact with soil, and changing cat litter. Litterboxes should be changed frequently, before oocysts have a chance to mature. Meat, especially lamb, pork, and venison, should be cooked until the pink color is lost from its interior. Fruits and vegetables should be washed before eating. Cats should not be allowed to hunt birds and rodents, nor should they be fed undercooked or raw meat. Children’s sandboxes should be kept tightly covered when not in use. These measures are especially important for pregnant women and persons with immunodeficiency. HIV-infected patients and those about to receive immunosuppressant medications are tested for antibody to T. gondii. A positive test indicates they have latent infection. Therefore, those with positive tests are given prophylactic trimethoprim-sulfamethoxazole if they have fewer than 100 CD4; T cells per microliter. Treatment of toxoplasmosis employs related medications—pyrimethamine with sulfadiazine. Alternatives are available. The main features of toxoplasmosis are presented in table 29.7.

Cytomegalovirus Disease Cytomegalovirus (CMV) is a member of the herpesvirus family, which includes herpes simplex virus, Epstein-Barr virus, and varicella-zoster virus, any of which can cause troublesome symptoms in patients with immunodeficiency. CMV, like other herpesviruses, is commonly acquired early in life and then remains latent. With impairment of the immune system, the infection activates and can cause severe symptoms.

Symptoms Symptoms of cytomegalovirus disease follow a pattern similar to that of toxoplasmosis. Acute infections in immunocompetent individuals are usually without symptoms, but adolescents and young adults sometimes develop illness that resembles infectious mononucleosis, with fever, fatigue, and enlarged lymph nodes and spleen for weeks or months. Severe damage can occur to the fetus if the mother develops an acute infection during pregnancy. This condition is known as congenital cytomegalic inclusion disease and is characterized by jaundice, large liver, anemia, eye inflammation, and birth defects. The vast majority of infected infants appear normal at birth, but 5% to 25% manifest hearing loss, mental retardation, or other abnormalities later in life. Blindness is one of the most feared complications of cytomegalovirus disease in immunodeficient individuals. Other symptoms include fever, loss of appetite, painful joints and muscles, rapid and difficult breathing, ulcerations of the gastrointestinal tract with bleeding, lethargy, paralysis, dementia, coma, and death.

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Causative Agent Human cytomegalovirus is an enveloped, double-stranded DNA virus that looks like other herpesviruses on electron micrographs but has a larger genome. Its name (cyto for “cell” and megalo for “large”) derives from the fact that cells infected by the virus are two or more times the size of uninfected cells. Infected cells show a large, intranuclear inclusion body surrounded by a clear halo, inspiring its description as an “owl’s eye” (figure 29.15). The envelope is acquired as the virion buds from the Golgi apparatus membrane. ■ Golgi apparatus, p. 78 There are many different strains of the virus detected by the patterns of endonuclease digests, and antigenic differences also occur. Like other herpesviruses, CMV can cause lysis of the infected cell or become latent and subject to later reactivation. ■ genomic typing, p. 243

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20 µm

FIGURE 29.15 Cytomegalovirus Infection Infected cells are two to four times normal size; their nuclei contain large inclusions and are surrounded by a clear zone suggesting an “owl’s eye” appearance.

Pathogenesis In cytomegalovirus disease, a wide variety of tissues, including eye (figure 29.16), central nervous system, lung, and liver, are susceptible to infection. Once cell entry has occurred, the viral genome can exist in a latent, non-infectious form, in a slowly replicating form, or as a fully productive infection. Control of viral gene expression depends partly on the type of cell infected. Monocytes allow low levels of infectious virus production. The CMV genome is ordinarily quiescent in T and B lymphocytes, expressing some viral genes but not producing viral DNA. Integration of viral DNA into the host cell genome probably does not occur. If CMV-infected T cells are also infected with HIV, productive CMV infection occurs. Fully productive infection of a wide variety of tissues occurs during acute infections, causing tissue necrosis. Transplanted organs and blood transfusions can transmit the disease, indicating that virus-producing cells are present or that non-producing cells in the blood or organ start producing infectious CMV under conditions of immune suppression. Cellular immunity probably plays a role in suppressing production of infectious virus as well as in lysis of infected cells. In cells infected with CMV, however, transfer of MHC molecules to the cell surface is impaired and, therefore, CMV antigens are not recognized as being “foreign.” CMV infection is associated with an increase in CD8; cells and a decrease in CD4; cells, thus enhancing the effect of HIV infection. Latent infections activate with AIDS, organ transplants, and other immunodeficient states. Also, immunodeficient subjects are highly susceptible to newly acquired infection. ■ MHC molecules, p. 380

Epidemiology CMV is found worldwide. One U.S. study found that more than 50% of adults, ages 18 to 25 years, and more than 80% of people over age 35 had been infected. Infection is lifelong. Infants born with CMV infection and those who acquire it shortly after birth excrete the virus in their saliva and urine for months or years. Virus is found in saliva, semen, and cervical secretions in the absence of symptoms, and sexual

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FIGURE 29.16 Cytomegalovirus (CMV) Retinitis, a Common Cause of Blindness in Persons with AIDS Photograph of a CMV-infected retina as it appears when viewed through the eye’s pupil using an ophthalmoscope.

intercourse is a common mode of transmission in young adults. Up to 15% of pregnant women secrete the virus, and 1% of newborn infants have CMV in their urine. Breast milk, blood, and tissue transplants may contain CMV and can be responsible for transmission. Almost all prostitutes and promiscuous gay men are infected with CMV. CMV spreads readily in day care centers.

Prevention and Treatment There is no approved vaccine for preventing cytomegalovirus disease. The use of condoms is effective in decreasing the risk of sexual transmission. People with HIV disease or other immunodeficiency syndromes or those who lack CMV antibody should avoid contact with day care centers if possible and, in any case, should wash their hands if exposed to saliva, urine, or feces. Tissue and blood donors can be screened for antibody to CMV. Those who have anti-CMV antibody are assumed to be infected and should not donate to those lacking antibody to CMV. The anti-herpesviral medication ganciclovir, given orally, halves the incidence of CMV retinitis in HIV disease patients with low CD4; cell counts and positive tests for CMV antibody. A ganciclovir implant designed to release the medication into the eye over a long period also delays the progression to blindness. Combination drug therapy with the antiviral drugs ganciclovir and foscarnet can reduce the severity of CMV disease. They inhibit CMV DNA polymerase, the enzyme responsible for assembling viral DNA, at different sites. Both medications have serious side effects,

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29.3 Infectious Complications of Acquired Immunodeficiency

mainly bone marrow suppression with ganciclovir and kidney impairment with foscarnet. ■ DNA polymerase, p. 192 The main features of cytomegalovirus disease are presented in table 29.8.

Mycobacterial Diseases Initial exposure to Mycobacterium tuberculosis, the cause of tuberculosis, usually causes an asymptomatic infection that is controlled by the immune system and becomes latent. As might be expected, defects in cellular immunity are associated with reactivation of latent tuberculosis, which commonly results in unrestrained disease in AIDS and other immunodeficiencies. Mycobacterium tuberculosis is not the only mycobacterium that causes disease in immunodeficient people. Disease has been reported due to M. kansasii, M. scrofulaceum, M. xenopi, M. szulgai, M. ganavense, M. haemophilum, M. celatum, BCG vaccine, and others. This section discusses disease caused by organisms of Mycobacterium avium complex, which, next to M. tuberculosis, is the most common mycobacterial opportunists that complicate immunodeficiency diseases.

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Symptoms The vast majority of Mycobacterium avium complex (MAC) infections in immunologically normal people are asymptomatic. Elderly people, especially those with underlying lung disease from smoking and those with alcoholism, develop a chronic cough productive of sputum and sometimes lesions in the lungs resembling tuberculosis. Children sometimes develop chronic enlargement of lymph nodes on one side of their neck, easily treated by surgical removal of the affected nodes. Patients with AIDS and other severe immunodeficiencies have slowly progressing symptoms ranging from chronic cough productive of sputum to fever, drenching sweats, marked weight loss, abdominal pain, and diarrhea.

Causative Agent Mycobacterium avium complex is a group of mycobacteria consisting of two closely related species—M. avium and M. intracellulare. More than two dozen strains of these acid-fast rods fall into the MAC, distinguishable by serological tests, optimum growth temperature, and host range. Their growth rate is almost as slow as that of M. tuberculosis, but they are easily distinguished by using biochemical tests and nucleic acid probes. ■ tuberculosis, p. 514

TABLE 29.8 Cytomegalovirus Disease

Pathogenesis

Symptoms

Symptoms rare in immunocompetent individuals, but sometimes an infectious mononucleosis-like illness develops. Infection of the mother during pregnancy can result in disease of the newborn. Immunocompromised individuals may experience blindness, lethargy, dementia, coma and brain damage

Incubation period

In immunocompetent adults, 20 to 60 days

Causative agent

Cytomegalovirus, a member of the herpesvirus family

Pathogenesis

Many tissues susceptible to infection, damage, especially eyes, brain, and liver. CMV latent infection can reactivate, produce infectious virions, tissue necrosis. CD4; T lymphocyte count is depressed and thus can enhance HIV disease.

Epidemiology

Common worldwide; lifelong infection. More than 50% of 18- to 25-year-olds are infected. Infants with congenital infections and those infected shortly after birth shed the virus for months or years. Body fluids, including breast milk, blood, urine, semen, and vaginal secretions, can transmit the disease. Almost all prostitutes and promiscuous homosexual men are infected with CMV.

MAC organisms enter the body via the lungs and the gastrointestinal tract. They are phagocytized by macrophages, but resist destruction because they inhibit acid production in the phagosome. Surviving organisms multiply within phagocytes and are carried by the bloodstream to all parts of the body. When cellular immunity is intact, most organisms are destroyed, and disease is localized. With profound immunodeficiency, the disease spreads throughout the body. In these patients, there is persistent bacteremia, occasionally with counts as high as 1 million per milliliter of blood. The small intestine contains macrophages packed with the bacteria, and infected tissues (figure 29.17) may resemble leprosy, sometimes containing more than 100 billion of the acid-fast bacteria per gram of tissue. Despite the presence of enormous numbers of the bacteria, there is little or no inflammatory reaction, and the clinical effect is a slow decline in the patient’s wellbeing rather than a quickly lethal effect. One cause of deterioration may be activation of HIV replication when HIV-infected macrophages are infected with MAC. ■ leprosy, p. 655

Prevention and treatment

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No vaccine available. Condoms decrease transmission. CMV-negative immunodeficient persons advised to avoid day care centers, wash their hands following contact with bodily fluids of infants. Blood and tissue transplants are tested for CMV before being given to CMVnegative individuals. The antiviral medication ganciclovir is considered for immunodeficient individuals who have antibody to CMV and whose CD4; T lymphocyte count falls below 50 cells per ml. Treatment: ganciclovir plus foscarnet.

Epidemiology MAC organisms are widespread in natural surroundings and have been found in food, water, soil, and dust. In the United States, they are most prevalent in the Southeast, parts of the Pacific Coast, and the North Central region. Some strains are important pathogens of chickens and pigs. In AIDS patients, they are the most common bacterial cause of generalized infection. It is not known whether infection in AIDS patients is mostly newly acquired or a reactivation of latent disease. Most infections are from environmental sources rather than from person-to-person spread.

Prevention and Treatment No effective measures are available to prevent exposure to MAC organisms. For HIV patients whose CD4; count is below 50 cells/ ml, the antibacterial medication clarithromycin is recommended to help prevent MAC disease. If MAC bacteremia develops, patients

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CHAPTER TWENTY NINE HIV Disease and Complications of Immunodeficiency MAC bacteria

TABLE 29.9 MAC Disease Symptoms

Usually asymptomatic in healthy people. Children can develop chronic localized enlargement of lymph nodes. Can cause chronic cough similar to tuberculosis in the elderly. Cough, fever, sweating, marked weight loss, abdominal pain, and diarrhea in those with severe immunodeficiencies.

Incubation period

Usually indeterminate

Causative agents A group of mycobacterial strains in the species M. avium and M. intracellulare

Pathogenesis

MAC bacteria enter the body via lungs or gastrointestinal tract, are taken up by macrophages. In immunocompetent individuals, most are destroyed and infection controlled by cellular immunity. In severe immunodeficiency the bacteria multiply without restraint, are carried by macrophages throughout the body, and grow to enormous numbers in tissues but cause little or no inflammatory reaction.

Epidemiology

MAC organisms are widespread in food, water, soil, and dust. MAC disease of immunodeficient persons could result from environmental sources, or activation of latent infection.

Prevention and treatment

No proven measures to prevent exposure to MAC bacteria. The antibiotic clarithromycin is used to prevent MAC disease in severe immunodeficiency. If MAC bacteremia develops, two or more medications, such as clarithromycin plus ethambutal, are effective.

10 µm

FIGURE 29.17 MAC Infection Acid-fast stain showing massive numbers of MAC bacteria infecting cells.

must be given two or more medications together, such as clarithromycin plus ethambutal. The main features of MAC disease are presented in table 29.9.

MICROCHECK 29.3 Infectious diseases are a major threat to individuals with immunodeficiency. They get the same infectious diseases that afflict healthy people and, in addition, they are much more susceptible to reactivation of latent infections and organisms of low virulence that are generally harmless to others. Prevention of infectious diseases in AIDS patients is key to improving the quality and duration of their lives. ✓ Bacteria, fungi, protozoa, and viruses can all cause lifethreatening diseases in AIDS patients. Name a fifth kind of infectious agent that can do the same. ✓ The disease pneumocystosis mainly involves which part of the body? ✓ Why should raw or uncooked meat not be eaten?

FUTURE CHALLENGES AIDS and Poverty In the United States and other economically advanced countries, antiviral medications have contributed significantly to the lessening of mother-child transmission of HIV, to delaying progression of HIV disease to AIDS, and to improving the quality and duration of life of AIDS sufferers. Newer drugs have also decreased transmission of HIV somewhat, thereby slowing the progress of the epidemic. The cost in the United States, while high, amounts to less than 1% of the country’s total healthcare expenditure. Antiviral medications have provided little benefit to most of the world’s AIDS sufferers because they cannot afford them. Only an estimated 440,000 of the 5.5

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million people needing anti-HIV medications are actually receiving them. Although HIV disease is spreading rapidly in India and China—two countries that together contain more than one-third of the world’s population— and in the Caribbean, Southeast Asia, and Eastern Europe, the situation is the most desperate in African countries south of the Sahara desert. Only 10% of the world’s population, but two-thirds of all those infected with HIV, lives in this area. About 75% of the region’s young people (ages 15 to 24) infected with HIV are girls or young women. Vitally important research is underway to develop a procedure that would give young

women an option within their control for preventing HIV infection. The humanitarian, social, and economic implications of uncontrolled HIV disease are enormous. Unimaginable suffering; large numbers of starving, uneducated street children; loss of productive work years; spread of other infectious diseases; breakdown of public health; and setbacks for economic development are possible consequences that can affect neighboring countries and the rest of the world. The challenge is urgent: to find effective HIV control measures, especially for the world’s poor.

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Summary

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SUMMARY AIDS Since AIDS was first recognized in 1981 in sexually promiscuous homosexual men, it has claimed millions of lives in the United States, and is a leading cause of death in people 25 to 44 years of age. Worldwide, over 30 million people are infected with an AIDS-causing virus (figure 29.1); it is estimated that a new infection occurs about every 6 seconds, and a person dies of AIDS every 5 minutes. In Africa south of the Sahara, AIDS is now the number one cause of death, surpassing malaria; it is spreading rapidly in India and into China.

29.1 Human Immunodeficiency Virus (HIV) Infection and AIDS “AIDS-defining conditions,” such as unusual tumors or serious infections by agents that normally have little virulence, usually reflect immunodeficiency and were especially useful “markers” in early studies of the AIDS epidemic (table 29.1). HIV Disease (table 29.4, figure 29.8) Acquired immunodeficiency syndrome (AIDS) is a late manifestation of human immunodeficiency virus (HIV) disease. “Flu”-like or infectious mononucleosis-like symptoms representing the acute retrovirus syndrome often occur 6 days to 6 weeks after infection by HIV; these symptoms subside without treatment. Despite the absence of symptoms, HIV disease progresses and can be transmitted to others for years. The asymptomatic period ends with the appearance of certain tumors, or the onset of immunodeficiency (AIDS) as marked by LAV, ARC, and opportunistic or reactivated infections. Human immunodeficiency virus, type 1 (HIV-1), possesses single-stranded RNA. It belongs to the lentivirus genus of the retrovirus family, and is the main cause of AIDS (figure 29.3). The disease is spread mainly by sexual intercourse, by blood or contaminated hypodermic needles, and from mother to fetus or newborn (tables 29.2, 29.3). Different kinds of cells can be infected by HIV, notably two kinds vital to the immune system—helper T (TH) lymphocytes and macrophages (figures 29.4, 29.5). Inside the host cell, a DNA copy of the viral genome is made through the action of reverse transcriptase, a complementary DNA strand is made, and the resultant double-stranded DNA is inserted into the host genome as a provirus by viral integrase (IN) (figure 29.6). Antimicrobial medications are used to prevent and treat opportunistic infections, and combinations of antiretroviral medications (HAART) are used to treat HIV disease (figure 29.11). HIV Vaccine Prospects No approved vaccine is currently available, but a number of prospects have moved from animal to human trials.

29.2 Malignant Tumors that Complicate Acquired Immunodeficiencies Kaposi’s Sarcoma (figure 29.12) Kaposi’s sarcoma is a tumor that arises from blood or lymphatic vessels. The incidence of the tumor is markedly increased among immunodeficient individuals. Infection by human herpesvirus-8 appears to be required for the tumor to develop. B-Lymphocytic Tumors of the Brain Lymphomas are malignant tumors that arise from lymphoid cells. Both B and T lymphocytes can give rise to lymphomas in individuals with immunodeficiencies, but B-cell lymphomas are more common. In contrast to non-immunodeficient cases, B-cell tumors often arise in the brain. Strong evidence exists that Epstein-Barr virus plays a causative role in these tumors.

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Cervical and Anal Carcinoma There is an increased rate of anal, genital, and cervical carcinoma in people with HIV disease. These tumors arise from squamous epithelial cells, thus differing from Kaposi’s sarcoma and lymphomas. These cancers are strongly associated with human papillomaviruses (HPV), transmitted by sexual intercourse.

29.3 Infectious Complications of Acquired Immunodeficiency Infections that occur in healthy individuals also occur and produce more severe disease in those with immunodeficiency. Latent infections such as those by Mycobacterium tuberculosis and herpesviruses commonly activate, and organisms rarely capable of causing disease in healthy individuals can be life threatening. Pneumocystosis (table 29.6) Before effective preventive regimens were developed, the disease was one of the most common causes of death among AIDS sufferers. Symptoms develop slowly, with gradually increasing shortness of breath and rapid breathing; patients can die from lack of oxygen. The causative agent, Pneumocystis jirovecii, a tiny fungus, is widespread in humans and other animals, generally causing asymptomatic infections that become latent. Toxoplasmosis (table 29.7) Toxoplasmosis is rare among healthy people but can be a serious problem for those with cancer, organ transplants, and HIV disease. The disease can also be congenital. Although infection is common in healthy people, only about 10% develop symptoms of sore throat, fever, and enlarged lymph nodes and spleen, sometimes with a rash. Symptoms usually disappear without treatment. With infections early in pregnancy, miscarriage can occur due to toxoplasmosis or babies can be born with birth defects or lung and liver damage. Infections later in pregnancy are usually milder but can result in epilepsy, mental retardation, or recurrent retinitis in the child. More than half of the cases with toxoplasmosis and AIDS develop encephalitis, and death often occurs because of involvement of the brain, heart, and other organs. Toxoplasma gondii is a tiny, banana-shaped protozoan that undergoes sexual reproduction in the intestinal epithelium of cats but can infect humans and many other vertebrates. Oocysts discharged in the feces of acutely infected cats become infectious in soil and contaminate food, water, and fingers (figure 29.14). T. gondii is present worldwide, and most people become infected from oocysts. Epidemics have resulted from contaminated drinking water. Eating rare meat can also cause infection. Cytomegalovirus Disease (table 29.8) Cytomegalovirus is a common cause of impaired vision in people with AIDS (figure 29.16). Normal individuals generally have asymptomatic infections; fetuses may develop cytomegalic inclusion disease or appear normal at birth but show mental retardation or hearing loss later; immunodeficient individuals develop fever, gastrointestinal bleeding, mental dullness, and blindness. Cytomegalovirus (CMV) is an enveloped, double-stranded DNA virus; infected cells are enlarged and have an “owl’s eye” appearance (figure 29.15). The virus can exist in a latent form, a slowly replicating form, or a fully replicating form. Co-infection with HIV results in fully productive infection and tissue death. The virus occurs worldwide in breast milk, semen, and cervical secretions, and in saliva and urine of infected infants. No vaccine is available. Condoms decrease the risk of sexual transmission. The antiviral medication ganciclovir can be given to prevent CMV retinitis. Mycobacterial Diseases (table 29.9) Mycobacterium tuberculosis and Mycobacterium avium complex (MAC) organisms are most commonly responsible for infection. Normal people

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usually get asymptomatic or mild infections with MAC organisms, but immunodeficient patients may have fever, drenching sweats, severe weight loss, diarrhea, and abdominal pain. MAC organisms enter the body via the lungs and gastrointestinal tract, are taken up by macrophages but resist destruction, and are carried to all parts of the body. In immunodefi-

ciency, MAC organisms multiply without restriction, producing massive numbers of the organisms in blood, intestinal epithelium, and other tissues (figure 29.17). No generally effective measures are available for preventing exposure to MAC bacteria. Prophylactic medication is advised for severely immunodeficient patients, but it can fail to prevent infection.

REVIEW QUESTIONS Short Answer 1. What is the main symptom of patients with lymphadenopathy syndrome (LAS)? 2. Which cells of the immune system are prime targets of HIV? 3. What role do asymptomatic people with HIV disease play in the epidemiology of AIDS? 4. Why might the infant son of a hemophiliac man develop AIDS when the son’s parents were strictly monogamous non-abusers of drugs? 5. Give two reasons it is a good idea to know whether you are infected with HIV. 6. What are four requirements of an acceptable HIV vaccine? 7. What is a phase III vaccine trial? 8. What are the three main types of malignant tumors that complicate HIV disease? 9. How do physicians prevent pneumocystosis in AIDS patients? 10. In AIDS patients with toxoplasmosis, which part of the body is affected in more than half the cases? 11. Name a feared complication of cytomegalovirus infection in AIDS patients. 12. Where in an AIDS patient’s surroundings might MAC organisms be found?

7.

8. 9.

10.

d) invasive cancer of the uterine cervix. e) Kaposi’s sarcoma. Which of the following types of cells can be infected by HIV? a) TH cells b) Intestinal epithelium c) Antigen-presenting cells d) Brain cells e) All of the above All of the following are HIV antigens, except a) CD4. b) TM. c) RT. d) MA. e) CA. Which of the following is a cause of TH cell death in HIV disease? a) Replication of HIV lyses the cell. b) Infected cells are destroyed by cytotoxic T cells (TC). c) Infected cells are attacked by natural killer cells. d) Cells are killed by fusion and syncytium formation. e) All of the above. Highly active antiretroviral therapy (HAART) is less than ideal because a) it does not eliminate latent HIV infection. b) its cost is too great for 90% of AIDS sufferers. c) it often has severe side effects. d) some HIV strains are resistant to it. e) All of the above.

Multiple Choice 1. About how many people died of AIDS in the United States in the first 10 years after the introduction of HAART? a) 4,000,000 b) 4,100 c) 42,000 d) 250,000 e) 120,000 2. All of the following symptoms are characteristic of the AIDS related complex (ARC), except a) fever. b) fatigue. c) diarrhea. d) blindness. e) weight loss. 3. Which one of the following is true of Kaposi’s sarcoma? a) HHV-8 is necessary for development of the tumor. b) HIV-1 is necessary for development of the tumor. c) Both HHV-8 and HIV-1 are necessary for development of the tumor. d) HHV-8 alone is sufficient for development of the tumor. e) Both HHV-8 and HIV-1 together are sufficient for the tumor to develop. 4. All of the following are HIV accessory genes, except a) tat. b) env. vpr. d) rev. e) vpu. 5. When was AIDS first recognized as representing a new disease? a) 1973 b) 1959 c) 1981 d) 1989 e) 1999 6. All of the following are AIDS-defining conditions, except a) influenza. b) herpes simplex of the esophagus. c) Pneumocystis jirovecii pneumonia.

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Applications 1. An epidemiologist from the Centers for Disease Control and Prevention was presenting a report on the status of AIDS to a congressional committee. In concluding her remarks, she noted that from an epidemiological perspective it was more important to focus on HIV infection than on AIDS, and urged that the Congress consider redirecting funding of AIDS research to reflect this fact. What was the rationale for her request? 2. A historian researching the influence of society on the spread of communicable disease began to speculate on what it would be like if AIDS had appeared at a different time. What differences might one expect, for example, if AIDS had appeared in 1928 instead of 1978? 3. A newly emerging virus lethal for all felines is rapidly killing off household cats and related zoo animals. The CDC urgently appeals for funds to develop a vaccine against the virus, but a scientific adviser to Congress states that it would be very expensive and may not be possible. Moreover, she states that getting rid of cats would have the side benefit of ridding the world of toxoplasmosis. Is she correct? If so, how long would it take?

Critical Thinking 1. Vaccines have effectively prevented many viral diseases—witness smallpox and poliomyelitis. Attempts over many years to develop an effective vaccine against HIV disease and AIDS, however, have so far met with little success. Why might this be so? 2. Why is reverse transcriptase needed in order for HIV to become a provirus?

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30 Farming relies on the activities of microorganisms.

Microbial Ecology A Glimpse of History For centuries, farmers have understood they could not continue growing the same crop on the same piece of land year after year without reducing the crop’s yield. They knew that allowing a field to lie unplanted for one or more seasons enables it to recover its productivity. The wild plants that grow on the field for a year or two appear to rejuvenate the soil. It was not until the late nineteenth century that scientists began to discover why this was so. They isolated soil microorganisms that could take nitrogen from the air and transform it into forms plants could use. This process is called nitrogen fixation and the nitrogen is said to be “fixed.” Although many scientists have worked for years to understand how microorganisms fix nitrogen, one scientist from the Netherlands, Martinus Willem Beijerinck, stands out as an early contributor in these studies. In 1887 Beijerinck reported on the properties of the root nodule bacterium, which he called Bacterium radicola. (The genus name of this bacterium was later changed to Rhizobium.) He showed in 1890 that root nodules were formed when B. radicola was incubated with legume seedlings. Russian microbiologist Sergei Winogradsky then showed that the bacterium formed a symbiotic relationship with the roots of the legumes. We now know that the bacterial cells in the nodules fix nitrogen. Beijerinck also made major contributions to other areas of microbiology. He worked on yeasts, plant viruses such as tobacco mosaic virus, and plant galls. Beijerinckia, a group of Gram-negative aerobic rods, is named for him. The genera Azotobacter and Beijerinckia include bacteria that can fix nitrogen under aerobic conditions in the absence of plants. Beijerinck was described as a “keen observer,” a person who was able “to fuse results of remarkable observations with a profound

and extensive knowledge of biology and the underlying sciences.” This ability was undoubtedly partly responsible for the great success of his work.

M

icrobes cycle nutrients, maintain fertile soil, and decompose wastes and other pollutants. Without microbial activities, life on earth could not survive. People would quickly become buried by the tons of wastes they generate, and nutrients would be depleted, halting growth and reproduction. In view of the crucial functions microorganisms perform, it would seem we should know a great deal about the diverse microbial species that inhabit our surroundings. Quite the opposite is true, however, as less than a mere 1% have been successfully grown in culture. Even if all microorganisms could be cultivated in the laboratory, the information gained might not accurately reflect their role in the environment. In the laboratory, organisms are grown as pure cultures under controlled conditions that ensure the optimal growth. In nature, however, organisms generally grow as members of heterogeneous communities in poorly defined and often changing conditions. Nutrients are normally in short supply, limiting microbial growth. Thus, with respect to environmental microbiology, results obtained in the artificial setting of the laboratory, although useful, must be interpreted with caution. ■ bacterial growth in nature, p. 85

Chapters 4 and 11 discussed bacterial growth in nature, and microbial diversity. This chapter will expand on some of those concepts, focusing on activities of microorganisms that make them essential in the biosphere.

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CHAPTER THIRTY

Microbial Ecology

KEY TERMS

Hydrothermal Vents Undersea geysers that spew out mineral-laden hot water.

Nitrogen Fixation Conversion of nitrogen gas to ammonia.

Consumers Organisms that consume organic material and rely on the activities of primary producers.

Hypoxic An environment very low in dissolved oxygen.

Oligotrophic A nutrient-poor environment.

Decomposers Organisms that digest the remains of primary producers and consumers. Denitrification Reduction of nitrate to gaseous nitrogen by anaerobic respiration. Eutrophic An environment that is nutrient rich, supporting the excessive growth of algae and other organisms.

Microbial Mat A type of microbial community characterized by distinct layers of different groups of microbes that together make up a thick, dense, highly organized structure.

Primary Producers Organisms that convert CO2 into organic compounds, sustaining other life forms. Rhizosphere Zone around plant roots containing organic materials exuded by the roots.

Nitrification Oxidation of ammonia (NH3) to nitrate (NO3:).

30.1 Principles of Microbial Ecology Focus Points Describe the roles of primary producers, consumers, and decomposers. Describe how some microbes are able to grow in low-nutrient environments and adapt to environmental changes. Compare and contrast microbial competition and antagonism. Describe the structural organization of a microbial mat.

biofilm can deplete oxygen and create microzones that will support the survival of obligate anaerobes. Fermenters can produce organic acids that may then be metabolized by other organisms in the film. Various growth factors can be transferred directly within the microenvironment of the biofilm. Thus, certain microorganisms that might seem unexpected in a given macroenvironment actually thrive there because of microenvironments. ■ biofilm, p. 85 ■ growth factor, p. 95

Nutrient Acquisition

Describe FISH and DDGE, focusing on how each enables researchers to better understand complex microbial communities.

Organisms are categorized according to their trophic level, or their source of food, which is intimately related to the cycling of nutrients. There are three general trophic levels: primary producers, consumers, and decomposers (figure 30.1):

Ecology is the study of the relationships of organisms, plant and animal, to each other and to their environment. Likewise, microbial ecology is the study of the relationships of microorganisms to each other and to their environment. Living organisms interact with one another in symbiotic relationships, such as commensalism, mutualism, and parasitism, described in chapter 17. Organisms in a given area, the community, interact with each other and the non-living environment, forming an ecological system, or ecosystem. Major ecosystems include the oceans, rivers and lakes, deserts, marshes, grasslands, forests, and tundra. Each ecosystem possesses a certain spectrum of organisms and characteristic physical conditions. The region of the earth inhabited by living organisms is called the biosphere. Within the biosphere, ecosystems vary both in biodiversity (number and variety of species present and their evenness of distribution) and biomass (the weight of all organisms present). ■ symbiotic relationships, p. 392 Microorganisms play a major role in most ecosystems, and many ecosystems host microbes unique to themselves. The role an organism plays in a particular ecosystem is called its ecological niche. The environment immediately surrounding an individual microorganism, the microenvironment, is most relevant to that cell, but because microbes are so small the microenvironment is difficult to identify and measure. The more readily measured gross environment, or macroenvironment, may be very different from the microenvironment. Consider a bacterial cell living within a biofilm (see figure 4.3); growth of aerobic organisms in the

Primary producers are autotrophs; they convert carbon dioxide into organic materials. Producers include both photoautotrophs, which use sunlight for energy, and chemolithoautotrophs, which oxidize inorganic chemicals for energy. Primary producers serve as a food source for consumers and decomposers. ■ photoautotroph, p. 95 ■ chemolithoautotroph, p. 95 Consumers are heterotrophs. Because they utilize organic materials, they rely on the activities of primary producers. Herbivores, which eat plants or algae, are primary consumers. Carnivores that eat herbivores are secondary consumers; carnivores that eat other carnivores are tertiary consumers. This chain of consumption is called a food chain. Interacting food chains are called a food web. Decomposers are heterotrophs that digest the remains of primary producers and consumers. The fresh or partially decomposed organic matter used as a food source, including carcasses, excreta, and plant litter, is called detritus. Decomposers specialize in digesting complex materials such as cellulose, converting them into small molecules that can more readily be reused by other organisms. The complete breakdown of organic molecules into inorganic molecules such as ammonia, sulfates, phosphates, and carbon dioxide is called mineralization. Microorganisms, particularly bacteria and fungi, play a major role in decomposition processes owing to their ubiquity and unique metabolic capabilities.

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ments that depend on water purity. Organisms that grow in dilute environments contain highly efficient transport systems for moving nutrients inside the cell. Other mechanisms that bacteria use to thrive in dilute aquatic environments are described in chapter 11.

H2S, NH3 and other reduced inorganic chemicals

■ transport systems, p. 58 ■ thriving in aquatic environments, p. 266

Chemical energy

Radiant energy

Microbial Competition and Antagonism

Primary producers CO2

Organic (CH2O) Dead organic matter

Consumers

CO2

Dead organic matter

Perhaps nowhere in the living world is competition more fierce and the results of competition more quickly evident than among microorganisms. The ability of an organism to compete successfully for a habitat is generally related to the rate at which the organism multiplies, as well as to its ability to withstand adverse environmental conditions. Because bacteria multiply logarithmically, any small differences in their generation times will result in a very large difference in the total number of cells of each species after a relatively short time (figure 30.2). Antagonism among groups of organisms also helps determine the make-up of a community. In the soil, for example, some microbes resort to a type of chemical warfare, producing antimicrobial compounds. Bacteriocins, proteins produced by bacteria that kill closely related strains, are an example of antagonistic chemicals that play an important role in microbial ecosystems, promoting biodiversity through competition. It is tempting to speculate that antibiotics produced by Streptomyces species share a similar function, but their natural role is still poorly understood. ■ the genus Streptomyces, p. 265

Decomposers

Microorganisms and Environmental Changes Environmental changes often result in alterations in a community. Those organisms that have adapted to live several inches beneath the surface of an untilled field will probably not be well suited

Small molecules (including CO2)

FIGURE 30.1 Relationship Among Primary Producers, Consumers, and Decomposers in an Ecosystem

Bacteria in Low-Nutrient Environments Growth

Because low-nutrient environments are common in nature, microorganisms capable of growth in dilute aqueous solutions are also common. Most microbial growth in these environments is in biofilms, and the organisms are shed from the film into the aqueous solution. These organisms are by no means restricted to lakes, rivers, and streams. Indeed, microorganisms even grow in distilled-water reservoirs such as those found in research laboratories and pulmonary mist therapy units used in hospitals. In these environments, the microbes can extract trace amounts of nutrients absorbed by the water from the air or adsorbed onto the biofilm. Although the organisms grow slowly, they can reach concentrations as high as 107 per milliliter. This cell concentration is not high enough to result in a cloudy solution, so the growth usually goes unnoticed. This can have serious consequences for the health of hospitalized patients and for the success of laboratory experi-

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Coccus

Transfers and more growth

Rod

FIGURE 30.2 Competition The bacterium that multiplies faster yields the larger population.

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to growth in that field if it is plowed, fertilized, and irrigated. In addition to external sources of environmental change, the growth and metabolism of organisms themselves can alter the environment dramatically. Nutrients may become depleted, and a variety of waste products, many of which are toxic, may accumulate. In some environments, the changing conditions bring about a highly ordered and predictable succession of bacterial species. An example of such a microbial succession occurs in unpasteurized milk, which usually contains various species of microbes derived mainly from the immediate environment around the cow. Initially, the dominant organism is the bacterium Lactococcus lactis, which breaks down the milk sugar lactose, forming lactic acid as an end product (figure 30.3). This inhibits most other organisms in the milk, and eventually enough acid is produced to inhibit L. lactis. The acid sours the milk and also curdles it, a result of denaturation of the milk proteins. Members of the genus Lactobacillus can multiply in this highly acidic environment. These metabolize any remaining sugar, forming more acid until their growth is also inhibited. Yeasts and molds, which grow very well in this highly acidic environment, then become the dominant group and convert the lactic acid into non-acidic products. Because most of the sugar has already been used, the streptococci and lactobacilli cannot resume multiplication. Milk protein (casein) is still available and can be utilized for energy by bacteria of the spore-forming genus Bacillus, and some other bacteria, all of which secrete proteolytic enzymes that digest the protein. This breakdown of protein, known as putrefaction, yields a completely clear and very odorous product. The milk thus goes through a succession of changes with time, first souring and finally putrefying.

Microbial Communities

described in detail in chapter 4. In this section, we focus on a specific type of biofilm—a microbial mat. ■ biofilms, p. 85 A microbial mat is a thick, dense, highly organized structure composed of distinct layers. Frequently they are green, pink, and black, which indicate the growth of different groups of microorganisms (figure 30.4). The green layer is the uppermost and is typically composed of various species of cyanobacteria. The color is due to the photosynthetic pigments of these microbes. The pink layer directly below consists of purple sulfur bacteria. The light-harvesting pigments of these anoxygenic phototrophs can use wavelengths of light not collected by the cyanobacteria. The black layer at the bottom results from iron molecules reacting with hydrogen sulfide produced by a group of bacteria called sulfate-reducers. These obligate anaerobes oxidize the organic compounds produced by the photosynthetic bacteria growing in the upper layers of the mat, using sulfate as a terminal electron acceptor. ■ cyanobacteria, p. 258 ■ photosynthetic pigments, p. 152 ■ purple sulfur bacteria, p. 256 ■ sulfate-reducers, p. 254 ■ terminal electron acceptor, p. 131

Although microbial mats can be found in a variety of areas, those near hot springs in Yellowstone National Park are some of the most intensively studied. The mats in these extreme areas are undisturbed by grazing eukaryotic organisms and, consequently, they provide an important model for the study of microbial interactions.

Studying Microbial Ecology Because so few microorganisms can be successfully cultivated in the laboratory, investigating only those that have been isolated often does not portray an accurate picture of what actually occurs in nature. Molecular techniques are now complementing the traditional methods such as culture and microscopy, enabling researchers to better understand complex microbial communities.

Microorganisms most often grow as biofilms attached to solid substrates or at air-water interfaces. General aspects of biofilms were

Acidity (pH) 6.8

Most acidic 4.0

3.0

4.0

Lactobacillus sp.

5.5 Yeasts and molds

6.8 Putrefying bacteria

Number of organisms

Lactococcus lactis

0

7 Time (days)

14

FIGURE 30.3 Growth of Microbial Populations in Unpasteurized Raw Milk at Room Temperature Production of acid causes souring and encourages growth of fungi. Eventually bacteria digest the proteins, causing putrefaction.

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FIGURE 30.4 A Microbial Mat A microbial mat is a thick, dense, highly organized structure composed of distinct layers of different groups of microorganisms.

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30.2

Microscopic methods can now be used to examine the composition of microbial populations. For example, certain dyes are made fluorescent by metabolic activities carried out only by living cells, and therefore can be used to observe only those cells that are viable (see figure 3.19a). A different technique, fluorescence in situ hybridization (FISH), uses nucleic acid probes that are labeled with a fluorescent molecule to observe only cells that contain specific nucleotide sequences (see figure 9.20). Confocal scanning laser microscopes enable researchers to observe sectional views of a three-dimensional specimen such as a biofilm (see figure 3.8). ■ fluorescent dyes, p. 51 ■ FISH, p. 228 ■ confocal scanning laser microscope, p. 46

Polymerase chain reaction (PCR) can be used to detect certain organisms and assess population characteristics. To detect a specific organism, primers are selected that amplify only DNA unique to that organism (see figure 9.14). To study the composition of a population, total 16S rRNA gene segments can be amplified. Individual fragments can then be cloned and studied. Alternatively, the set of amplified sequences can be separated and examined using a technique called denaturing gradient gel electrophoresis (DGGE). This procedure gradually denatures double-stranded nucleic acid during gel electrophoresis and, as a consequence, separates fragments of similiar size according to their melting point, which is related to the nucleotide sequence. Using DGGE, a mixture of 16S rRNA fragments with different sequences will resolve into a distinct pattern of bands. PCR and DDGE studies have confirmed that standard culture techniques can be poor indicators of the composition of natural microbial populations. Based on these molecular techniques that can show the relative abundance of specific nucleotide sequences in the sample, the species that predominate in laboratory culture often represent only a minute portion of the total population. ■ polymerase chain

Aquatic Habitats

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30.2 Aquatic Habitats Focus Point Compare and contrast the habitats provided by marine, freshwater and specialized aquatic environments.

Oceans, covering more than 70% of the earth’s surface, are the most abundant aquatic habitat, representing about 95% of the global water. They compose the marine environment. Lakes and rivers, the freshwater environments, represent only a small fraction of the total water. Deep lakes and oceans have characteristic zones that influence the distribution of microbial populations. The uppermost layer, where sufficient light penetrates, supports the growth of photosynthetic microorganisms, including algae and cyanobacteria. The organic material synthesized by these primary producers gradually descends and is then metabolized by heterotrophs. In oligotrophic waters, meaning nutrient poor, the growth of photosynthetic organisms and other autotrophs is limited by the lack of certain inorganic nutrients, particularly phosphate, nitrate, and iron. When waters are eutrophic, or nutrient rich, photosynthetic organisms flourish, sometimes forming a visible layer on the surface (figure 30.5). In turn, the photosynthetic activities of FIGURE 30.5 Eutrophication in a Polluted Stream Photosynthetic organisms flourish in the nutrient-rich water. The organic compounds they produce permit luxuriant growth of heterotrophs in lower layers.

reaction, p. 223 ■ gel electrophoresis, p. 214

Genomics is also advancing the study of microbial ecology because sequence information gleaned from one species can be applied to others. For example, researchers found that variations of a gene coding for bacterial rhodopsin, a light-sensitive pigment that provides a mechanism for harvesting the energy of sunlight, are widespread in marine bacteria. This gene provides bacteria with a mechanism for phototrophy that does not require chlorophyll and might be an important mechanism for energy accumulation in ocean environments. Scientists are also using metagenomics, the study of total genomes in a sample, to study microbial populations in their natural environment. ■ genomics, p. 181 ■ bacterial rhodopsin, p. 275 ■ metagenomics, p. 221

MICROCHECK 30.1 Microorganisms play a major role in most ecosystems. Organisms are categorized as primary producers, consumers, or decomposers. Competition among microorganisms in a habitat can be intense. Microbial mats have distinct layers. Molecular techniques are enabling researchers to better understand natural microbial communities. ✓ What are the roles of primary producers, consumers, and decomposers? ✓ What microorganisms live within the green, pink, and black layers of a microbial mat? ✓ How could FISH (fluorescence in situ hybridization) be used to determine the relative proportions of Archaea and Bacteria in a population?

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these organisms produce organic compounds that permit luxuriant growth of heterotrophs in lower layers. The heterotrophs consume dissolved O2 as they metabolize the organic material. Because O2 consumption can outpace the slow rate of diffusion of atmospheric O2 into the waters, the environment can become very low in dissolved oxygen, or hypoxic. Lack of sufficient O2 leads to the death of resident fish and other aquatic animals.

Algae and cyanobacteria flourish, using photosynthesis to produce organic compounds. Nutrient-rich water

Marine Environments Marine environments range from the deep sea, where nutrients are scarce, to the shallower coastal regions, where nutrients may be abundant due to runoff from the land. Seawater contains about 3.5% salt, compared with about 0.05% for fresh water. Consequently, it supports the growth of halophilic organisms, which prefer or require high salt concentrations, and halotolerant ones. Temperatures may vary widely at the surface, depending upon locale and other factors, but decrease with depth until reaching about 2°C in the deeper waters; an exception is the areas around hydrothermal vents, which will be described later. ■ hydro-

organic compounds

Aerobic decomposition of organic compounds by heterotrophic microbes depletes O 2

thermal vents, p. 732

Ocean waters are typically oligotrophic, limiting the growth of microorganisms. The little organic material produced by photosynthetic organisms is consumed as it descends, so that only scant amounts reach the sediments below. Even in the deep sea, marine water is O2-saturated due to mixing associated with tides, currents, and wind action. The ecology of inshore areas is not as stable as the deep sea, and can be dramatically affected by nutrient-rich runoff. An unfortunate example is a region devoid of fish and other marine life—a dead zone—that forms in the Gulf of Mexico as well as other areas (figure 30.6). The Mississippi River, carrying nutrients accumulated as it runs through agricultural, industrial, and urbanized regions, feeds into the Gulf. As a consequence of this nutrient-enrichment, populations of algae and cyanobacteria flourish in the Gulf waters in the spring and summer when sunlight is also plentiful. Heterotrophic microbes then metabolize the organic compounds synthesized by these primary producers, consuming dissolved O2 in the process. This causes a large region in the Gulf, sometimes in excess of 7,000 square miles, to become hypoxic. Animals in the area either flee or die. Enrichment of coastal waters also contributes to blooms of toxic algae. ■ toxic algae, p. 284

Animals flee hypoxic environment or die

FIGURE 30.6 Dead Zone Formation

sumption of O2 by heterotrophs. Separating these two layers is the thermocline, a zone of rapid temperature change. As the weather cools, the waters mix, providing O2 to the deep water. Rapidly moving waters, such as rivers and streams, are very different from lakes. They are usually shallow and turbulent, facilitating O2 circulation, so they are generally aerobic. Light may penetrate to their bottom, making photosynthesis possible. Sheathed bacteria such as Sphaerotilus and Leptothrix species commonly adhere to rocks and other solid structures, enabling the microbes to remain stationary, utilizing nutrients that flow by. ■ sheathed bacteria, p. 266

Freshwater Environments

Specialized Aquatic Environments

As with marine environments, the types and relative numbers of microbes inhabiting fresh waters depend on multiple factors including light, concentration of dissolved O2 and nutrients, and temperature. Oligotrophic lakes in temperate climates may have anaerobic layers due to thermal stratification resulting from seasonal temperature changes. During the summer months, the surface water warms. This decreases the density of the water, causing it to form a distinct layer that does not mix with the cooler, denser water below. The upper layer, called the epilimnion, is generally oxygen-rich due to the activities of photosynthetic organisms. In contrast, the lower layer, the hypolimnion, may be anaerobic due to the con-

Specialized aquatic environments include salt lakes, such as the Great Salt Lake in Utah, which have no outlets. Water in these lakes evaporates, leaving concentrations of salt much higher than that in seawater. Extreme halophiles thrive in this environment. Other specialized habitats include iron springs that contain large quantities of ferrous ions; these springs are habitats for species of Gallionella and Sphaerotilus. Sulfur springs support the growth of both photosynthetic and non-photosynthetic sulfur bacteria. There are many other aquatic environments, both natural and humanmade, ranging from groundwater to stagnant ponds and swimming pools to drainage ditches, each offering its own opportunity for bacterial growth. ■ extreme halophiles, p. 275

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30.3

MICROCHECK 30.2 Aquatic habitats include marine, freshwater, and specialized environments. Nutrient-rich waters can become hypoxic. Lakes often exhibit thermal stratification during summer months. ✓ Compare the salt content of seawater with that of fresh water and salt lakes. ✓ Explain how nutrient-rich runoff can cause waters to become hypoxic. ✓ Why would the nutrient content of a body of water be more homogeneous than that of a terrestrial environment?

30.3 Terrestrial Habitats Focus Point Describe soil as a microbial habitat.

Although microbes can adhere to and grow on a variety of objects on land, the focus in this section is soil—a critical component of terrestrial ecosystems. Extreme terrestrial habitats, such as volcanic vents and fissures, and some of the extremophiles that inhabit them are described in chapter 11. ■ archaea that thrive in extreme conditions, p. 275

Human interest in the microbiology of soil stems partly from the ability of microbes to synthesize a variety of useful chemicals. For example, over 500 different antibiotic substances are produced by Streptomyces species, at least 50 of which have useful applications in medicine, agriculture, and industry. The pharmaceutical industry has tested many thousands of soil microorganisms in search of those that produce useful antibiotics. In addition, soil microbes are being investigated for their ability to degrade toxic chemicals, an application of environmental microbiology called bioremediation, which will be discussed in chapter 31. Probably in no other habitat can one hope to find a greater range of biosynthetic and biodegradative capabilities than are represented in the soil. ■ bioremediation, p. 749

Characteristics of Soil Soil is composed of pulverized rock, decaying organic material, air, and water. It teems with life, including bacteria, fungi, algae, protozoa, worms, insects, and plant roots. Soil communities may contain more than 4,000 different species per gram of soil. The top 6 inches of fertile soil may harbor more than 2 tons of bacteria and fungi per acre! Soil represents an environment that can fluctuate abruptly and dramatically. Heavy rains, for example, can cause a soil to rapidly become waterlogged. Trees dropping their leaves can suddenly enrich the soil with organic nutrients. Farmers and gardeners can rapidly change the nutrient mix by applying fertilizers. Soil forms as rock weathers. Water, temperature changes, wind-blown particles, and other physical forces gradually lead to cracking and fragmentation of the rock. Photosynthetic organisms including algae, mosses, and lichens growing on the surfaces of

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Terrestrial Habitats

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rocks synthesize organic compounds. Various chemoorganoheterotrophic bacteria and fungi then use these compounds as carbon and energy sources. Their metabolism results in the production of acids and other chemicals, which gradually decompose the rocks. As soil slowly forms, some plants begin to grow. When these die and decay, the residual organic material functions as a sponge, retaining water and thus enabling more plants to grow. Over time, more organic compounds accumulate, forming a slowly degrading complex polymeric substance called humus. ■ lichens, p. 292 ■ chemoorganoheterotroph, p. 95

The texture of the soil influences its porosity, which in turn impacts the amount of air exchange and how much water can flow through. Finely textured soils, such as clay soils, are more apt to become waterlogged and anaerobic. In contrast, sandy soils that dry quickly allow water to pass through and are generally aerobic.

Microorganisms in Soil The density and composition of the microbiota of the soil are dramatically affected by environmental conditions. Wet soils, for example, are unfavorable for aerobic microbes because the spaces in the soil fill up with water, thus diminishing the amount of air in the soil. When the water content of soil drops to a very low level, as during a drought or in a desert environment, the metabolic activity and number of soil microorganisms decrease. Many species of soil organisms produce survival forms such as endospores and cysts that are resistant to drying. Other environmental influences that impact soil microbes include acidity, temperature, and nutrient supply. For example, acidity suppresses the growth of bacteria, allowing fungi to thrive with less competition for nutrients. This is why mushrooms often appear in a lawn fertilized with an acid-producing fertilizer such as ammonium chloride. Prokaryotes are the most numerous soil inhabitants. Their physiological diversity allows them to colonize all types of soil. In general, Gram-positive bacteria are more abundant in soils than Gram-negative bacteria. Among the most common Grampositive bacteria are members of the genus Bacillus. These form endospores, enabling them to survive prolonged periods of adverse conditions such as drought or extreme heat. Streptomyces species produce conidia, which are dessication-resistant structures. They also produce metabolites called geosmins, which give soil its characteristic musty odor. As discussed earlier, Streptomyces species produce many medically useful antibiotics. Some of the other bacteria adapted to thrive in terrestrial environments, including myxobacteria and species of Clostridium, Azotobacter, Agrobacterium, and Rhizobium, were discussed in chapter 11. ■ endospore-formers, p. 264 ■ the genus Streptomyces, p. 265 ■ thriving in terrestrial

environments, p. 263

While prokaryotes are the most numerous in soil, the biomass of fungi is much greater. Because most fungi are aerobes, they are usually found in the top 10 cm of soil. The soil fungi are crucial in decomposing plant matter—degrading and using complex macromolecules such as lignin, the major component of cell walls of woody plants, and cellulose. Some soil fungi are free-living, and others live in symbiotic relationships. The latter include mycorrhizae, fungi growing in a symbiotic relationship with certain plant roots. ■ mycorrhizae, p. 733

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In addition to bacteria and fungi, various algae and protozoa are found in most soils. Because algae depend on sunlight for energy, they mostly live on or near the soil surface. Most protozoa require oxygen, so they too are found near the surface. They may be found in higher numbers in areas where microbes on which they feed are plentiful.

The Rhizosphere The rhizosphere is the zone of soil that adheres to plant roots. The root cells excrete organic molecules including sugars, amino acids, and vitamins. The enriched soil in this zone fosters the growth of microorganisms. As a result, the concentration of microbes, particularly Gram-negative bacteria, is generally much higher than that of the surrounding soil. Particular bacterial species appear to preferentially interact with certain plants. For example, the rhizosphere of certain grasses is enriched with Azospirillum species, which fix nitrogen. ■ nitrogen fixation, p. 730

MICROCHECK 30.3 The density and composition of the soil are dramatically affected by environmental conditions. The concentration of microbes in the rhizosphere is generally much higher than that of the surrounding soil. ✓ Why are wet soils unfavorable for aerobic organisms? ✓ What is the significance of the rhizosphere? ✓ How can the biomass of fungi in soil be greater considering that bacteria are more numerous?

30.4 Biogeochemical Cycling and Energy Flow Focus Points Diagram the carbon, nitrogen, sulfur, and phosphorus cycles, and describe some of the important microbial contributors to these cycles. Compare and contrast energy cycling in environments with sunlight versus those far removed from sunlight.

Biogeochemical cycles are the cyclical paths that elements take as they flow through living (biotic) and non-living (abiotic) components of ecosystems. These cycles are important because a fixed and limited amount of the elements that make up living cells exists on the earth and in the atmosphere. Thus, in order for an ecosystem to sustain its characteristic life forms, elements must continuously be recycled. For example, if the organic carbon that animals use as an energy source and exhale as carbon dioxide (CO2) were not eventually converted back to an organic form, we would run out of organic carbon to build cells. The carbon and nitrogen cycles are particularly important because they involve stable gaseous forms (carbon dioxide and nitrogen gas), which enter the atmosphere and thus have global impacts.

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While elements continually cycle in an ecosystem, energy does not. Instead, energy must be continually added to an ecosystem, fueling the activities required for life. Understanding the cycling of nutrients and the flow of energy is becoming increasingly important as the burgeoning human population impacts the environment in a major way. For example, industrial processes that convert nitrogen gas (N2) into ammoniacontaining fertilizers have increased food production substantially, but they have also altered the nitrogen cycle by increasing the amount of fixed nitrogen, such as ammonium and nitrate, in the environment. Pollution of lakes and coastal areas with these nutrients has far-reaching effects, including depletion of dissolved O2, which leads to the death of aquatic animals. It also decreases the biodiversity in terrestrial ecosystems. Excavation and burning of coal, oil, and other carbon-rich fossil fuels provides energy for our daily activities, but releases additional CO2 and other carboncontaining gases into the atmosphere. Fossil fuels, the ancient remains of partially decomposed plants and animals, are nutrient reservoirs that are unavailable without human intervention, and therefore would not normally participate in biogeochemical cycles. The increase of carbon-containing gases in the atmosphere raises global temperatures because the gases absorb infrared radiation and reflect it back to earth. When studying biogeochemical cycles, it is helpful to bear in mind the role of a given element in a particular organism’s metabolism. Elements are used for three general purposes: Biomass production. As an example, all organisms require nitrogen to produce amino acids. Plants and many prokaryotes assimilate nitrogen by incorporating ammonia (NH3) to synthesize the amino acid glutamate (see figure 6.28a). Some prepare for this step using the process of assimilatory nitrate reduction, which converts nitrate (NO3:) to ammonia. Once glutamate has been synthesized, the amino group can then be transferred to other carbon compounds in order to produce the necessary amino acids. Animals cannot incorporate ammonia and instead require amino acids in their diet. Some prokaryotes can reduce atmospheric nitrogen to form ammonia—the process of nitrogen fixation. The ammonia can then be incorporated into cellular material. ■ amino acid synthesis, p. 156 Energy source. For example, reduced carbon compounds such as sugars, lipids, and amino acids are used as energy sources by chemoorganotrophs. Chemolithotrophs can use reduced inorganic molecules such as hydrogen sulfide (H2S), ammonia (NH3), and hydrogen gas (H2) (see table 4.5). ■ energy source, p. 130

Terminal electron acceptor. In aerobic conditions, O2 is used as a terminal electron acceptor. In anaerobic conditions, some prokaryotes can use nitrate (NO3), nitrite (NO2), sulfate (SO4), or carbon dioxide (CO2) as a terminal electron acceptor. ■ terminal electron acceptor, p. 131

Carbon Cycle All organisms are composed of organic molecules including proteins, lipids, and carbohydrates. Consumers eat plants as well as other consumers to acquire organic carbon for building biomass

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30.4 Biogeochemical Cycling and Energy Flow

and as a source of energy. Decomposers use the remains of primary producers and consumers for the same purposes. As the organic carbon is degraded, respiration and some fermentations release CO2, which must then be converted back to an organic form to complete the cycle (figure 30.7). A fundamental aspect of the carbon cycle is carbon fixation, the defining characteristic of primary producers. These organisms all convert CO2 into an organic form. The mechanisms used are described in chapter 6. Without the activities of the primary producers, no other organisms, including humans, could exist. We depend on them to generate the organic carbon we require. ■ carbon fixation, p. 154

The organic carbon travels through the food chain as primary producers are eaten by primary consumers, which are then eaten by secondary consumers. Through these events, one form of biomass is transformed into another. Not all of the organic material consumed is employed to create biomass, however; some is used as an energy source, generating carbon dioxide as a product. As plants lose their leaves, and as members of the food web die, various decomposers degrade the resulting detritus, using it both as an energy source and to create biomass. The type of organic material helps dictate which species are involved in the degradation. For example, a wide variety of organisms

729

utilize the more readily decomposable organic substances such as sugars, amino acids, and proteins. Bacteria, which usually multiply rapidly, generally play the dominant role in the decomposition of animal flesh. In contrast, only certain fungi can break down lignin, a major component of wood (figure 30.8). Aerobic conditions are required for this degradation, which is why water-saturated wood in anaerobic conditions such as a marsh resists decay. The supply of oxygen has a profound influence on the carbon cycle. Not only does oxygen allow the degradation of certain compounds such as lignin, it also helps determine the types of carboncontaining gases produced. During the aerobic decomposition of organic matter, a great deal of carbon dioxide is produced through aerobic respiration. When the level of oxygen is low, however, as is the case in wet rice-paddy soil, marshes, swamps, and manure piles, the degradation is incomplete, generating some CO2 and a variety of other products. Some of the CO2 produced is used by the methanogens, anaerobic members of the Domain Archaea. These prokaryotes gain energy by oxidizing hydrogen gas, using carbon dioxide as a terminal electron acceptor, generating methane (CH4). Methane that enters the atmosphere is oxidized by ultraviolet light and chemical ions to carbon monoxide (CO) and carbon dioxide. ■ methanogens, p. 254

FIGURE 30.7 Carbon Cycle

(CH2O)n Organic compounds

Aerobic respiration

Combustion of organic material

Aerobic Carbon fixation

Methane-oxidizing bacteria

CO2 Oxidized carbon

CH4 (Methane) Reduced carbon

CO2

Methanogens Carbon fixation

Anaerobic respiration Anaerobic Fermentation

(CH2O)n Organic compounds

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FIGURE 30.8 Wood-Degrading Fungus Growing on a Dead Tree These fungi thrive in wet conditions. They digest lignin, the major cell wall component of woody plants, and consequently degrade the wood.

Nitrogen Cycle Nitrogen is an essential constituent of proteins and nucleic acids. As consumers ingest plants and animals to fill their carbon and energy needs, they also obtain their required nitrogen, using it solely to build biomass. Prokaryotes, as a group, are far more diverse in their use of nitrogen-containing compounds. Some use oxidized nitrogen compounds such as nitrate (NO3:) and nitrite (NO2:) as a terminal electron acceptor; others used reduced nitrogen compounds such as ammonium (NH4;) as an energy source. These metabolic activities represent essential steps in the nitrogen cycle (figure 30.9).

Nitrogen Fixation Nitrogen fixation is the process in which nitrogen gas (N2) is reduced to form ammonia (NH3), which can then be incorporated

Organic N (animals)

Animals eat plants.

Decomposition

Organic N (plants, microorganisms) Nitrogen fixation (symbiotic and free-living) Plants take up nitrogen.

Ammonification Lightning N 2 Chemical fixation

NO 3–

Denitrification (anaerobic bacteria)

Nitrification (Nitrobacter, Nitrospira)

Nitrification (Nitrosomonas) NO 2–

FIGURE 30.9 Nitrogen Cycle

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NH 3 + H 2O NH 4+ + OH –

into cellular material. The process, which is mediated by the enzyme complex nitrogenase, requires a tremendous expenditure of energy. At least 16 molecules of ATP must be expended for every molecule of nitrogen fixed, because N2 has a very stable triple bond. Although the atmosphere consists of approximately 79% N2, relatively few organisms, all of which are prokaryotes, can reduce this gaseous form of the element. Thus, just as animals, including humans, depend on other organisms to fix carbon, they rely on prokaryotes to convert atmospheric nitrogen to a form they can assimilate to create biomass. Nitrogen-fixing prokaryotes, or diazotrophs, may be freeliving, or they may live in symbiotic association with higher organisms, particularly certain plants. Those that form symbiotic relationships will be discussed later. Among the free-living examples are members of the genus Azotobacter. These heterotrophic, aerobic, Gram-negative rods may be the chief suppliers of fixed nitrogen in grasslands and other similar ecosystems that lack plants with nitrogen-fixing symbionts. Certain cyanobacteria species are also diazotrophs, enabling these photosynthetic organisms to use both nitrogen and carbon from the atmosphere. The dominant free-living, anaerobic, nitrogen-fixing organisms of soil are certain members of the genus Clostridium, which are distributed widely in nature. ■ symbiotic nitrogen-fixers and plants, p. 734 ■ the genus Azotobacter, p. 264 ■ nitrogen-fixing cyanobacteria, p. 258 ■ the genus

Clostridium, p. 254

Energy-expensive chemical processes developed to fix nitrogen are widely used to make fertilizers. These synthetic compounds are playing an increasingly larger role in the nitrogen cycle. In fact, fixed nitrogen sources associated with human intervention, including fertilizer production and planting crops that foster the growth of symbiotic nitrogen-fixers, now appear to surpass natural biological nitrogen fixation.

Ammonification Ammonification is the decomposition process that converts organic nitrogen into ammonia (NH3). In neutral environments, ammonium (NH4;), a positively charged ion that adheres to negatively charged particles, is formed; in alkaline environments, such as heavily limed soil, the gaseous ammonia may enter the atmosphere. A wide variety of organisms, including aerobic and anaerobic bacteria as well as fungi, can degrade proteins, which are among the most prevalent nitrogen-containing organic compounds. The microbes do this initially through the action of extracellular proteolytic enzymes that break down proteins into short peptides or amino acids. After transport of the breakdown products into the cell, the amino groups are removed, releasing ammonium. The decomposer will assimilate much of this compound to create biomass. Some, however, will be released into the environment, where it can then be assimilated by other organisms such as plants. ■ deamination, p. 150

Nitrification Nitrification is the process that oxidizes ammonium (NH4;) to nitrate (NO3:). A group of bacteria known collectively as nitrifiers do this in a cooperative two-step process, using ammonium and an intermediate, nitrite (NO2:), as energy sources. They are obligate

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30.4 Biogeochemical Cycling and Energy Flow

aerobes, using molecular oxygen as a terminal electron acceptor. Consequently, nitrification does not occur in waterlogged soils or in anaerobic regions of aquatic environments. ■ nitrifiers, p. 260 Nitrification has some important consequences with respect to agricultural practices and pollution. Farmers often apply ammonium-containing compounds to soils as a source of nitrogen for plants. The ammonium is retained by soils, because its positive charge enables it to adhere to negatively charged soil particles. Nitrification converts the ammonium to nitrate, a form of nitrogen more readily used by plants, but rapidly leached from soil by rainwater. To impede nitrification, certain chemicals can be added to ammonium-fertilized soils. Another negative aspect of ammonium oxidation is that nitrite can accumulate in soil if insufficient numbers of nitrite oxidizers are present. If the nitrite leaches into groundwater, it might contaminate wells used for drinking water. Nitrite is toxic because it combines with hemoglobin of the blood, reducing blood’s O2-carrying capacity. Even nitrate, which in itself is not very toxic, can be dangerous if high levels contaminate groundwater. When ingested, it can be converted to nitrite by intestinal bacteria that use it as a terminal electron acceptor.

731

Organic S (animals)

Animals eat plants.

Organic S (plants, microorganisms)

Sulfate incorporated into plants

SO 42

Sulfate reduction (bacteria)

Decomposition (microorganisms)

-

S oxidation (photosynthetic and non-photosynthetic sulfur bacteria)

H2S

S

H 2S oxidation (photosynthetic and non-photosynthetic sulfur bacteria)

FIGURE 30.10 Sulfur Cycle

Denitrification Denitrification is the process that converts nitrate (NO3:) to gaseous nitrogen. Nitrate (NO3:) represents fully oxidized nitrogen. Some Pseudomonas species and a variety of other bacteria can use nitrate as a terminal electron acceptor when molecular oxygen is not available; this is the process of anaerobic respiration. The nitrate is reduced to gaseous forms of nitrogen such as nitrous oxide (N2O) and molecular nitrogen (N2). Release of these gases to the atmosphere represents a loss of nitrogen from an ecosystem. In addition, nitrous oxide contributes to global warming. ■ anaerobic respiration, pp. 133, 145

Under anaerobic conditions in wet soils, denitrifying bacteria can use the oxidized nitrogen compounds of expensive fertilizers, resulting in the release of gaseous nitrogen to the atmosphere and consequent economic loss to the farmer. In some areas, this process may represent 80% of nitrogen lost from fertilized soil. Denitrification is not always undesirable, however. The process can be actively fostered in certain steps of wastewater treatment as a means to remove nitrate. This compound could otherwise act as a fertilizer in the waters to which the wastewater is discharged, thereby promoting algal growth. ■ microbiology of wastewater treatment, p. 739

Anammox Certain bacteria oxidize ammonium under anaerobic conditions, using nitrate as a terminal electron acceptor. This reaction, called anammox (for anoxic ammonia oxidation), forms N2 and might provide an economical means of removing nitrogen compounds during wastewater treatment.

Sulfur Cycle Sulfur occurs in all living matter, chiefly as a component of the amino acids methionine and cysteine. Like the nitrogen cycle, key steps of the sulfur cycle depend on the activities of prokaryotes (figure 30.10). Some prokaryotes use the reduced form of sul-

nes95432_Ch30_721-737.indd 731

fur, hydrogen sulfide (H2S), and elemental sulfur (S0) as energy sources or electron donors; others use oxidized sulfur compounds such as sulfate (SO4:2) as terminal electron acceptors. Most plants and microorganisms assimilate sulfur as sulfate (SO4:2), reducing it to form biomass. Like nitrogen, organic sulfur is present chiefly as a part of proteins. These organic compounds are first degraded into their constituent amino acids by proteolytic enzymes secreted by a wide variety of microorganisms. Decomposition of the sulfur-containing amino acids releases hydrogen sulfide, a gas.

Sulfur Oxidation Hydrogen sulfide (H2S) and elemental sulfur (S0) can both serve as an energy source for certain chemolithotrophs. Sulfur-oxidizing prokaryotes, including Beggiatoa, Thiothrix, and Thiobacillus species, oxidize these molecules to sulfate (SO4:2). Certain bacteria in anaerobic marine environments can oxidize elemental sulfur, using nitrate as a terminal electron acceptor. As discussed in chapter 11, these organisms, including Thioploca species and the largest known bacterium, Thiomargarita namibiensis, have unusual mechanisms to cope with the fact that their energy source and terminal electron acceptor are found in two different environments. ■ sulfur-oxidizing bacteria, p. 259 ■ sulfur-oxidizing, nitrate-reducing marine bacteria, p. 270

Hydrogen sulfide and elemental sulfur are oxidized anaerobically by photosynthetic green and purple sulfur bacteria. These bacteria use sunlight for energy, but require reduced molecules as a source of electrons to generate reducing power. Like the chemolithotrophs that use hydrogen sulfide and elemental sulfur, the photosynthetic sulfur oxidizers produce sulfate. ■ green sulfur bacteria, p. 257 ■ purple sulfur bacteria, p. 256

Sulfur Reduction Under anaerobic conditions, sulfate generated by the sulfuroxidizers can then be used as a terminal electron acceptor by

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certain organisms. The sulfur- and sulfate-reducing bacteria and archaea use sulfate in the process of anaerobic respiration, reducing it to hydrogen sulfide (H2S). In addition to its unpleasant odor, the H2S is a problem because it reacts with metals, resulting in corrosion. ■ sulfur- and sulfate-reducing bacteria, p. 254

Phosphorus Cycle and Other Cycles Phosphorus is a component of several critical biological compounds including nucleic acids, phospholipids, and ATP. Most plants and microorganisms readily take up phosphorus as orthophosphate (PO4:3), assimilating it into biomass. From there, the phosphorus is passed along the food web. When plants and animals die, decomposers convert organic phosphate back to inorganic phosphate. In many aquatic habitats, growth of algae and cyanobacteria, the primary producers, is limited by low concentrations of phosphorus. Addition of phosphates from sources such as agricultural runoff, phosphate-containing detergents, and wastewater can result in eutrophication. Other important elements, including iron, calcium, zinc, manganese, cobalt, and mercury, are also recycled by microorganisms. Many prokaryotes contain plasmids coding for enzymes that carry out oxidation of metallic ions.

(a)

Energy Sources for Ecosystems All chemotrophs, including animals, harvest the energy trapped in chemical bonds to generate ATP. This energy cannot be totally recycled, however, since a portion is always lost as heat when bonds are broken. Thus, energy is continually lost from biological systems. To compensate for this outflow, energy must be added to ecosystems. Photosynthesis, carried out by chlorophyll-containing plants and microorganisms, converts radiant energy (sunlight) to chemical energy in the form of organic compounds, which can be used by chemoorganotrophs. The requirement for radiant energy has traditionally been used to explain why life is not equally abundant everywhere. The discovery of different types of communities far removed from sunlight, including those near hydrothermal vents and within rocks, however, has dramatically altered these ideas. These communities rely on chemolithoautotrophs, which harvest the energy of reduced inorganic compounds and use it to form organic compounds. ■ chemolithoautotroph, pp. 95, 150 A number of hydrothermal vents have been discovered, some thousands of meters below the ocean surface. These vents form when water seeps into cracks in the ocean floor and becomes heated by the molten rock, finally spewing out in the form of mineral-laden undersea geysers. The hydrogen sulfide discharged supports thriving deep-sea communities, oases in the otherwise desolate ocean floor (figure 30.11). Large numbers of sulfuroxidizing chemolithoautotrophs (bacteria and archaea) are found in and around the vents. Many are free-living but some live in symbiotic association with the large tube worms and clams that inhabit the areas. The chemolithoautotrophs harvest energy from oxidation of hydrogen sulfide, and they fix CO2, providing the animals with both a carbon and energy source.

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H2S

H2S H2S

H2S H2S

CO 2

H2S

bacteria and archaea

H2S Organic compounds

H2S SO 42:

(b)

FIGURE 30.11 Hydrothermal Vent Community (a) This diverse community is supported by the metabolic activities of chemolithoautotrophs. (b) Water escaping from the vent is rich in minerals and dissolved gases, including hydrogen sulfide.

In 1994, microbial populations were reported living almost 3 km under the ground. Then, in 1995, scientists found large populations of microbes thriving in iron-rich volcanic rocks from nearly a thousand meters below the surface of the Columbia River (see Perspective 4.1). These organisms gain energy from hydrogen (H2) produced in the subsurface. It has been estimated that if (and it is a big “if” at this point) most similar rocks contain microbes,

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30.5 Mutualistic Relationships between Microorganisms and Eukaryotes

there could be as much as 2!1014 tons of underground microorganisms—equivalent to a layer 1.5 meters thick over the entire land surface of the earth!

Root cells of plants (cross-section)

733 Ectomycorrhizae

MICROCHECK 30.4 Recycling of elements occurs as organisms incorporate them to produce biomass, oxidize reduced forms as energy sources, and reduce oxidized forms as terminal electron acceptors. Carbon fixation utilizes atmospheric CO2 to produce organic material; the CO2 is regenerated during respiration and some fermentations. Prokaryotes are essential for several steps of the nitrogen cycle including nitrogen fixation, nitrification, denitrification, and anammox. Prokaryotes are also essential for several steps of the sulfur cycle, including sulfur reduction and sulfate oxidation. ✓ What is a diazotroph? ✓ Why do farmers try to impede nitrification? ✓ Although chemoautotrophs serve as the primary producers near hydrothermal vents, animals in that environment still ultimately depend on the photosynthetic activities of plants and cyanobacteria. Why?

Endomycorrhizae (a) Diagram of Mycorrhizae

30.5 Mutualistic Relationships between Microorganisms and Eukaryotes Focus Point Describe the mutalistic relationships between fungi and plant roots, symbiotic nitrogen-fixers and plants, and microorganisms and herbivores.

As described in chapter 19, mutualism is a symbiotic association in which both partners benefit. A variety of other ecologically important symbiotic relationships exist, but mutualistic relationships highlight the vital role of microorganisms to life on this planet. This section will describe three important mutualistic relationships between microbes and eukaryotes—mycorrhizae and plants, symbiotic nitrogen-fixers and plants, and microorganisms and herbivores. ■ symbiotic relationships, p. 392

(b) Endomycorrhiza

Mycorrhizae Mycorrhizae are fungi growing in symbiotic relationships with plant roots (figure 30.12). They enhance the competitiveness of plants by helping them take up phosphorus and other substances from the soil. In turn, the fungi gain nutrients for their own growth from root secretions. It is estimated that over 85% of vascular plants (plants with specialized water and food conducting tissues) have mycorrhizae. There are two common types of mycorrhizal relationships: Endomycorrhizae. The fungi penetrate root cells, growing as coils or tight, bushlike masses within the cells. These are by far the most common mycorrhizal relationships, and are found in association with most herbaceous plants. Relatively

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(c) Ectomycorrhiza

FIGURE 30.12 Mycorrhizae (a) Diagram illustrating the two types of mycorrhizae. (b) In an endomycorrhizal relationship, the fungi penetrate root cells growing within the cells. (c) In an ectomycorrhizal relationship, the fungi grow around the plant root cells, forming a fungal sheath around the root.

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few species of fungi are involved, perhaps only 100 or so, and most appear to be obligate symbionts. The relationship for some plants is also obligate; for example, most orchid seeds will not germinate without the activities of a fungal partner. Ectomycorrhizae. The fungi grow around the plant cells, forming a fungal sheath around the root. These fungi mainly associate with certain trees, including conifers, beeches, and oaks. Over 5,000 species of fungi are involved in ectomycorrhizal relationships, but many are restricted to a single type of plant. Chanterelles and truffles are examples of commercially valuable ectomycorrhizal fungi.

Symbiotic Nitrogen-Fixers and Plants Although free-living bacteria are potentially capable of adding a considerable amount of fixed nitrogen to the soil, symbiotic nitrogen-fixing organisms are far more significant in benefiting plant growth and crop production. They are important in both terrestrial and aquatic habitats. Members of several genera, including Rhizobium, Bradyrhizobium, Sinorhizobium, and Azorhizobium, collectively referred to as rhizobia, are the most agriculturally important symbiotic nitrogen-fixing bacteria. These organisms associate with leguminous plants including alfalfa, clover, peas, beans, and peanuts.

Rhizobium cells attach specifically to cells of root hair and enter the cells.

The Rhizobium cells invade other cells through an infection thread synthesized by the root hair.

The input of soil nitrogen from the microbial symbionts of these plants may be roughly 10 times the annual rate of nitrogen fixation attainable by non-symbiotic organisms in a natural ecosystem. To encourage plant growth, people often plant the seeds of certain legumes together with inocula of the appropriate symbionts. The symbiotic association between rhizobia and plants involves chemical communication between the partners. First, root exudates of the leguminous plant attract the appropriate bacterial species, which then attach to and colonize the root cells (figure 30.13). Substances secreted by the root cells cause the bacteria to produce chemical signals called nod factors, which in turn, induce the root hairs to curl. The bacteria then invade the root hair, multiplying and moving into the root cells by means of an infection thread, a tube produced by the plant cells in response to infection, through which the bacteria invade. Once inside the root, the bacterial cells change in appearance, forming a cell type called a bacterioid. Repeated division of both root cells and bacteroids leads to the development of root nodules (figure 30.13b). The plant cells synthesize a special oxygen carrier called leghemoglobin, which binds to O2 and regulates its concentration in the nodule. This protects the O2-sensitive nitrogenase by keeping free O2 at a low level. The bacterioids in the nodule fix nitrogen, releasing ammonia that then diffuses into the root cell.

Rhizobium cells develop into bacteroids, which pack the enlarged plant cells.

Nodule consists of enlarged plant cells packed with bacteroids.

(a)

FIGURE 30.13 Symbiotic Nitrogen Fixation (a) The major steps lead(b)

nes95432_Ch30_721-737.indd 734

ing to the formation of a root nodule in leguminous plants by Rhizobium species. (b) Root nodules.

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Summary

There it is assimilated into amino acids for use by the plant. In return, the bacteria receive nutrients from the plant. Although the relationship between the plant and bacterium is not obligate, it offers a distinct competitive advantage to both partners. The rhizobia do not fix nitrogen in soils lacking leguminous plants, and they compete poorly with other environmental organisms, slowly disappearing from soils in which leguminous plants are not grown. Likewise, leguminous plants compete poorly against other plants in heavily fertilized soils. Several genera of non-leguminous trees, including alder and gingko, possess nitrogen-fixing root nodules at some stages of their life cycle. The bacteria involved in the symbiosis are members of the genus Frankia. In aquatic environments, the most significant nitrogen-fixers are cyanobacteria. They are especially important in flooded soils such as rice paddies. In fact, rice has been cultivated successfully for centuries without the addition of nitrogen-containing fertilizer because of the symbiotic relationship between the cyanobacterium Anabaena azollae and the aquatic fern Azolla. The bacterium grows in specialized sacs in the leaves of the fern, providing nitrogen to the fern. Before planting rice, the farmer allows the flooded rice paddy to overgrow with Azolla ferns. Then, as the rice grows, it eventually crowds out the ferns. As the ferns die and decompose, their nitrogen is released into the water.

Microorganisms and Herbivores Another mutualistic relationship occurs between microbes and certain herbivores. In order to subsist on grass and other plant material, herbivores such as cattle and horses rely on a community of microbes that inhabit a specialized digestive compartment. The microbes digest cellulose and hemicellulose, two of the major components of plant material, releasing compounds that can then serve as a nutrient source for the animal. In ruminants such as cattle, sheep, and deer, the digestive compartment, called the rumen, precedes the true stomach; in non-ruminant herbivores such as horses and rabbits, the cecum, which lies between the small intestine and the large intestine, serves a similar purpose. ■ cellulose, p. 32

The rumen functions as an anaerobic fermentation vessel to which nutrients in the form of plant materials are intermittently

735

added. In some cases the animal produces over 150 liters of saliva per day. In addition to providing water, the saliva also contains bicarbonate, a buffer, which helps maintain the pH. A remarkably complex variety of microorganisms degrade the ingested material, liberating sugars that are then fermented, producing various organic acids. Each milliliter of rumen content contains approximately 1010 bacteria, 106 protozoa, and 103 fungi. Of the over 200 species identified in the rumen, no single one accounts for more than 3% of the total flora. The organic acids released during fermentation are absorbed by the cells that line the rumen, providing the animal with an energy and nutrient source. Copious quantities of gas are produced as a result of fermentation, which are discharged when the animal belches. The contents of the rumen then enter another compartment (the omasum), eventually reaching the acidic true stomach (abomasum). There, more organic acids are absorbed. In addition, lysozyme is secreted, enabling the animal to lyse and then digest members of the microbial population, providing even more nutrients. A critical aspect of the anatomy of ruminants is that the microbial population gets the first opportunity to use the nutrients that are ingested. The animal then uses the end products of microbial metabolism as well as the microbial cells themselves. The cecum of non-ruminant herbivores serves a similar function as a rumen, but because it follows the stomach, there is no anatomical mechanism to utilize the microbes as a food source. The benefit of this arrangement, however, is that the animal can digest and absorb readily available nutrients without competition from microbes.

MICROCHECK 30.5 Mycorrhizal fungi gain nutrients from plant root secretions while helping plants take up substances from soil. Symbiotic nitrogen-fixers provide plants with a source of usable nitrogen while being provided with an exclusive habitat. Microorganisms in the rumen and cecum of herbivores digest cellulose and hemicellulose, enabling the animal to subsist on plant material. ✓ Describe the differences between endomycorrhizae and ectomycorrhizae. ✓ Describe the differences between a rumen and a cecum. ✓ Gardeners sometimes plant clover between productive growing seasons. Why would this practice be beneficial?

SUMMARY 30.1 Principles of Microbial Ecology Within the biosphere, ecosystems vary in their biodiversity and biomass. The microenvironment immediately surrounding a microorganism is most relevant to its survival and growth. Nutrient Acquisition Primary producers convert carbon dioxide into organic material; consumers utilize the organic materials, directly or indirectly, produced by plants; decomposers digest the remains of primary producers and consumers (figure 30.1). Bacteria in Low-Nutrient Environments Microorganisms capable of growing in dilute aqueous solutions are common in nature; often they grow in biofilms.

nes95432_Ch30_721-737.indd 735

Microbial Competition and Antagonism Microorganisms in the environment vie for the same limited pool of nutrients. A species can competitively exclude others, or produce compounds that inhibit others. Microorganisms and Environmental Changes External and internal sources of environmental fluctuations are common. As a result, different species can become dominant (figure 30.3). Microbial Communities A microbial mat is a thick, dense, highly organized biofilm composed of distinct layers of different groups of microbes, often green, pink, and black (figure 30.4).

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Studying Microbial Ecology Microbial ecology has been difficult to study because so few environmental prokaryotes can be successfully grown in the laboratory. Molecular techniques, including fluorescence in situ hybridization (FISH), polymerase chain reaction (PCR), denaturing gradient gel electrophoresis (DGGE), and DNA sequencing are enabling researchers to better understand complex microbial communities.

30.2 Aquatic Habitats Oligotrophic waters are nutrient poor; eutrophic waters are nutrient rich (figure 30.5). Excessive growth of aerobic heterotrophs may cause an aquatic environment to become hypoxic, resulting in the death of fish and other aquatic animals. Marine Environments Ocean waters are generally oligotrophic and aerobic, but inshore areas can be dramatically affected by nutrient-rich runoff (figure 30.6).

Carbon Cycle (figure 30.7) One of the fundamental aspects of the carbon cycle is carbon fixation. As consumers and decomposers degrade organic material, respiration and some fermentations release CO2. Nitrogen Cycle (figure 30.9) The steps of the nitrogen cycle include nitrogen fixation, ammonification, nitrification, denitrification, and anammox. Sulfur Cycle (figure 30.10) Certain steps of the sulfur cycle—sulfur reduction and sulfate oxidation— depend on the activities of prokaryotes. Phosphorus Cycle and Other Cycles Most plants and microorganisms take up orthophosphate, assimilating it into biomass. Iron, calcium, zinc, manganese, cobalt, and mercury are recycled by microorganisms.

Freshwater Environments Oligotrophic lakes may have anaerobic layers due to thermal stratification. Shallow, turbulent streams are generally aerobic.

Energy Sources for Ecosystems Photosynthetic organisms convert radiant energy to chemical bond energy in the form of organic compounds. Chemolithoautotrophs harvest energy from reduced inorganic chemicals (figure 30.11).

Specialized Aquatic Environments Salt lakes and mineral-rich springs support the growth of microbes specifically adapted to thrive in these specialized environments.

30.5 Mutualistic Relationships between Microorganisms and Eukaryotes

30.3 Terrestrial Habitats Characteristics of Soil Soil represents an environment that can fluctuate abruptly and dramatically. Microorganisms in Soil The environmental conditions affect the density and composition of the flora of the soil. The Rhizosphere The concentration of microbes in the rhizosphere is generally much higher than that of the surrounding soil.

30.4 Biogeochemical Cycling and Energy Flow Organisms use elements to produce biomass, as sources of energy, and as terminal electron acceptors.

Mycorrhizae Mycorrhizae help plants take up phosphorus and other substances from soil; in turn the fungal partners gain nutrients for their own growth (figure 30.12). Endomycorrhizal fungi penetrate root cells; ectomycorrhizal fungi grow around root cells. Symbiotic Nitrogen-Fixers and Plants Rhizobia fix nitrogen in nodules of leguminous plants (figure 30.13). Frankia species fix nitrogen in nodules of alder and gingko. A species of cyanobacteria fixes nitrogen in specialized sacs in the leaves of the Azolla fern. Microorganisms and Herbivores In order to subsist on grass and other plant material, herbivores rely on a community of microbes that inhabit a specialized digestive compartment, either a rumen or a cecum.

REVIEW QUESTIONS Short Answer 1. 2. 3. 4. 5. 6. 7. 8. 9.

Describe why a microbial mat has green, pink, and black layers. Why do lakes in temperate regions stratify during the summer months? Why is there a high concentration of microbes in the rhizosphere? What dictates whether a form of an element is suitable for use as an energy source versus a terminal electron acceptor? Why does wood resting at the bottom of a bog resist decay? What is the importance of nitrogen fixation? Describe the relationship between ammonia oxidizers and nitrite oxidizers. How do hydrothermal vents support a thriving community of microbes, clams, and tube worms? Give examples of free-living and symbiotic nitrogen-fixing microorganisms. Are these prokaryotic or eukaryotic?

nes95432_Ch30_721-737.indd 736

10. Describe the steps that lead to the formation of the symbiotic relationship between rhizobia and leguminous plants.

Multiple Choice 1. Cyanobacteria are a) primary producers. b) consumers. c) herbivores. d) decomposers. e) more than one of the above. 2. Which of the following is false? a) Culture techniques provide an accurate way of determining the predominant members of a microbial community such as a biofilm. b) Fluorescence in situ hybridization (FISH) can be used to distinguish subsets of prokaryotes that contain a specific nucleotide sequence. c) Polymerase chain reaction (PCR) can be used to distinguish subsets of prokaryotes based on their 16S rRNA sequences.

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Review Questions

3.

4.

5.

6.

7.

8.

9.

10.

d) Denaturing gradient gel electrophoresis (DGGE) can be used to separate PCR products. e) Studying the genome of one organism can give insights into the characteristics of another. The decomposition of organic matter a) is carried out by only a few bacterial species. b) produces oxygen. c) involves all the biogeochemical cycles discussed. d) involves primarily photosynthesis. e) is largely symbiotic. Which of the following pairs that relate to aquatic environments does not match? a) Oligotrophic—nutrient poor b) Hypoxic—oxygen poor c) Hypolimnion—lower layer d) Epilimnion—oxygen poor e) Eutrophic—nutrient rich Which of the following pairs that relate to terrestrial environments does not match? a) Soil—minimal biodiversity b) Bacillus—endospores c) Streptomyces—geosmin production d) Fungi—lignin degradation e) Rhizosphere—soil that adheres to plant root Atmospheric nitrogen can be used a) directly by all living organisms. b) only by aerobic bacteria. c) only by anaerobic bacteria. d) in symbiotic relationships between rhizobia and plants. e) in photosynthesis. Which process converts ammonium (NH4;) into nitrate (NO3:)? a) Nitrogen fixation b) Ammonification c) Nitrification d) Denitrification e) Anammox Energy for ecosystems can come from a) sunlight via photosynthesis. b) oxidation of reduced inorganic chemicals by chemoautotrophs. c) both A and B. Mycorrhizae represent associations between plant roots and microorganisms that a) are antagonistic. b) help plants take up phosphorus and other nutrients from soil. c) involve algae in the association with plant roots. d) form nodules on the plant’s leaves. e) lead to the production of antibiotics. In symbiotic nitrogen fixation by rhizobia and legumes a) the amount of nitrogen fixed is much greater than by non-symbiotic organisms.

nes95432_Ch30_721-737.indd 737

737

b) neither the bacteria nor the legume can exist independently. c) the bacteria enter the leaves of the legume. d) the bacteria operate independently of the legume.

Applications 1. A farmer who was growing soybeans, a type of legume, saw an Internet site advertising an agricultural product for safely killing soil bacteria. The ad claimed that soil bacteria were responsible for most crop losses. The farmer called the agricultural extension office at a local university for advice. Explain what the extension office crop adviser most likely told the farmer about the usefulness of the product. 2. Recent reports suggest that human activities, such as the generous use of nitrogen fertilizers, have doubled the rate at which elemental nitrogen is fixed, raising concerns of environmental overload of nitrogen. What problems could arise from too much fixed nitrogen, and what could be done about this situation?

Critical Thinking 1. Each colony growing on an agar plate arises from a single cell (see photo). Colonies growing close together are much smaller than those that are well separated. Why would this be so? 2. An entrepreneur found an economically feasible way of collecting large amounts of sulfur from underwater hot vents in the Pacific Ocean. The sulfur will be harvested from the microorganisms found in the vent areas. A group of ecologists argued that the project would destroy the fragile ecosystem by depleting it of usable sulfur. The entrepreneur argued that the environment would not be harmed because the vents produce an unlimited source of sulfur for the clams and tube worms in the area. Explain who is correct.

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31 A pristine mountain lake.

Environmental Microbiology: Treatment of Water, Wastes, and Polluted Habitats A Glimpse of History Delivering fresh water to urban areas and removing human wastes have been practiced at least since Roman times. The ruins of aqueducts that delivered fresh water long distances can be seen today in many parts of Europe. Ridding cities of human wastes has been more difficult, and the sewers that were used until the mid-nineteenth century were not much more than large, open cesspools. Long before the discovery of the microbial world, it was recognized that some diseases are associated with water supplies. As early as 330 B.C., Alexander the Great had his armies boil their drinking water, a habit that probably contributed to his huge successes. Certainly, many battles have been lost over the years as a result of waterborne diseases that decimated the combatants. Years before the cholera-causing Vibrio cholerae was identified, it was obvious that cholera epidemics were associated with drinking water. The desire for clean, clear water led to the use of a sand filtration system in London and elsewhere in the early nineteenth century. Late in that century, Robert Koch showed that not only did this kind of filtration yield clear water, it also removed more than 98% of bacteria from the water. As early as the 1840s, Edwin Chadwick, an English activist, championed a new idea on how wastes could be removed. His idea was to construct a system of narrow, smooth ceramic pipes through which water could be flushed along with solid waste materials. This system would carry the waste materials away from the inhabited part of the city to a distant collection site. There, he hoped to collect the waste materials and turn them into fertilizer to sell to farmers. The system he envisioned required the installation of new water and sewer pipes along with pumps to deliver water under pressure to houses. With the water under pressure and smooth narrow pipes, the system could be kept well flushed. In 1848, with the threat of a cholera epidemic imminent, the Board of Health in England instituted widespread reforms and began installing a sewage system along the lines envisioned by Chadwick. New York City did not establish its Board of Health and a proper,

sewage disposal system until 1866, again in response to a threatened cholera epidemic. By the end of the nineteenth century, most large European and U.S. cities had established water-sewer systems to deliver safe drinking water and remove and treat waste materials. Cholera in the industrialized nations of Europe and North America virtually disappeared.

M

ost people living in developed countries take for granted that their tap water is safe to drink, their wastes will reliably disappear into sewers or landfills for proper disposal, and pollutants, substances that are harmful or injurious, will not accumulate in the environment. They seldom consider the role that microbes play in these essential aspects of modern life. Microorganisms are important in the treatment of water, waste, and polluted environments for two very distinct reasons. First, we benefit from the fact that microbes are the ultimate recyclers, playing an essential role in the decomposition of our wastes. At the same time, pathogenic microorganisms and viruses must be eliminated from sewage before it is discharged, and removed from drinking water before it is deemed potable, or safe for human consumption. Recreational waters such as swimming pools, water parks, lakes, rivers, and shorelines are also monitored to ensure they do not contain or accumulate harmful levels of certain pathogens. Treatment of water, waste, and polluted habitats is a formidable challenge, particularly in densely populated areas. Consider that every day the average American uses about 150 gallons of water, and produces 120 gallons of wastewater and 5 pounds of trash. This means that a city with only 1 million inhabitants is faced with the disposal of approximately 44 billion gallons of wastewater and a million tons of trash each year!

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31.1 Microbiology of Wastewater Treatment

KEY TERMS Advanced Treatment Any physical, chemical, or biological purification process beyond secondary treatment of wastewater. Anaerobic Digestion Process that uses anaerobic microbes to degrade the sludge obtained during wastewater treatment. Biochemical Oxygen Demand (BOD) The amount of O2 required for the microbial decomposition of organic matter in a sample. Bioremediation Process that uses microorganisms to degrade harmful chemicals.

Effluent The liquid portion of treated wastewater. Indicator Organisms Microbes commonly found in the intestinal tract whose presence in other environments suggests fecal contamination. Primary Treatment A physical wastewater treatment process designed to remove materials that will settle out of sewage. Sanitary Landfill A site used for disposal of non-hazardous solid wastes in a manner that minimizes damage to human health and the environment.

31.1 Microbiology of Wastewater Treatment Focus Points Describe the concept of BOD. Compare and contrast primary treatment, secondary treatment, advanced treatment, and anaerobic digestion. Describe how a septic tank functions.

Wastewater, or sewage, is composed of all the material that flows from household plumbing systems, including washing and bathing water and toilet wastes. Municipal wastewater also includes business and industrial wastes. In many cities, storm water runoff that flows into street drains enters the system as well. The most obvious reason that wastewater must be treated before discharge is that pathogenic microbes can be transmitted in feces, including those that cause diarrheal diseases and hepatitis. If untreated sewage is released into a river or lake that is then used as a source of drinking water, disease can easily spread. In a similar manner, if marine waters become contaminated with untreated sewage, consumption of the shellfish grown there can result in disease. Shellfish are filter feeders and they concentrate microbes from the waters in which they live. A less obvious problem is the impact that the high nutrient content of wastewater has on the receiving water. When any nutrientrich substance is added to an aqueous environment, microorganisms quickly utilize the compounds as energy sources, employing metabolic pathways such as glycolysis and the TCA cycle (see figure 6.8). As a result, microbes that use aerobic respiration consume available O2 in the water, using it as a terminal electron acceptor (see figure 6.18). The amount of dissolved O2 in lakes and rivers is limited and can easily be depleted during the microbial breakdown of nutrients. Fish and other aquatic animals in the environment die because they require O2 for respiration (see figure 30.6). Thus, effective treatment of wastewater must decrease the level of organic compounds substantially, in addition to eliminating pathogens, toxic materials, and other pollutants. ■ aerobic respiration, pp. 133, 144

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Secondary Treatment A biological wastewater treatment process in which microbial growth is actively encouraged, allowing the microbes to convert most of the suspended solids to inorganic compounds and removable cell mass. Septic Tank A large tank used for individual wastewater treatment systems. Sludge The solid portion of wastewater that settles to the bottom of sedimentation tanks during primary and secondary treatment. Wastewater (Sewage) Material that flows from household plumbing systems; municipal wastewater also include business and industrial wastes and storm water runoff.

Biochemical Oxygen Demand (BOD) An important goal of wastewater treatment is to lessen the environmental impact of sewage by reducing the biochemical oxygen demand (BOD), the amount of O2 required for the microbial decomposition of organic matter in a given sample. The BOD is roughly proportional to the amount of degradable organic material present in a sample. To determine the BOD, the O2 level in a well-aerated sample of microbe-containing test water is first measured. The sample is then incubated in a sealed container in the dark under standard conditions of time and temperature, usually 5 days at 20°C. The O2 level is then determined again. The difference between the dissolved O2 at the beginning of the test and at the end reflects the BOD of the sample. In many cases the sample must be diluted first in order to accurately determine the BOD. High BOD values indicate that large amounts of degradable materials were present in the test water, resulting in correspondingly large amounts of O2 being used during its biological degradation. The BOD of raw sewage is approximately 300 to 400 mg/liter, which could easily deplete the dissolved O2 in the receiving water. The dissolved O2 content of natural waters is generally 5 to 10 mg/liter.

Municipal Wastewater Treatment Methods Large-scale wastewater treatment plants in the United States use a series of two processes—primary and secondary treatment—as mandated by the 1972 Federal Water Pollution Control Act, now known as the Clean Water Act. Once treated, the liquid portion, or effluent, can be discharged into a body of water, the receiving water. The solid portion, or sludge, is further treated in an anaerobic digester.

Primary Treatment Primary treatment is a physical process designed to remove materials that will settle out, removing approximately 50% of the solids and 25% of the BOD. Raw sewage is first passed through a series of screens to remove large objects such as sticks, rags, and trash (figure 31.1). Skimmers then remove scum and other floating materials. The sewage is allowed to settle in a sedimentation tank, facilitating removal of the solids. Once the settling period

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Primary Treatment physical removal of organic material Anaerobic Sludge Digestion anaerobic microbial degradation of organic material Sedimentation tank

Screens Raw sewage

Effluent

Sludge Anaerobic digester

Drying bed

Disposal, incineration, or use as a soil enhancer

Secondary Treatment microbial degradation of organic material Activated sludge process: Option 1

Aeration tank

Advanced Treatment additional purifying treatments (chemical, physical, or microbial)

Air or O2 Sedimentation tank

Option A To sludge digestion

Treatments vary, but may include precipitation of phosphates, removal of ammonia, and biological degradation of nitrates

Trickling filter system: Option 2

Trickling filter

Sedimentation tank To sludge digestion

Lagoons: Option 3

Option B

Disinfection destruction of pathogens and other microbes

Treatments such as chlorination, UV light, ozone

Artificial wetlands: Option 4 Discharge to receiving water

FIGURE 31.1 Municipal Wastewater Treatment The processes consist of primary treatment, secondary treatment, advanced treatment (optional), disinfection, and anaerobic sludge digestion.

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Trickling filter system. This method is frequently used for smaller wastewater treatment plants. A rotating arm sprays sewage over a bed of plastic or coarse gravel and rocks, the surfaces of which become coated with a biofilm of microbes that aerobically degrade the organic materials (figure 31.2). The film consists of a heterogeneous mix of bacteria, fungi, algae, protozoa, and nematodes. The rate of sewage flow can be adjusted so that waste materials are maximally degraded.

is complete, the sludge is removed and the primary treated wastewater that remains is sent for secondary treatment.

Secondary Treatment Secondary treatment is chiefly a biological process designed to convert most of the suspended solids in sewage to inorganic compounds and cell mass that can then be removed, eliminating as much as 95% of the BOD. Microbial growth is actively encouraged during secondary treatment, allowing aerobic organisms to oxidize the biologically degradable organic material to CO2 and H2O. Note that because secondary treatment relies on the metabolic activities of microorganisms, the processes could be devastated if too much toxic industrial wastes or hazardous household materials were dumped into sewage systems, killing the microbial population. Methods used for secondary treatment of wastewater include:

Lagoons. The wastewater is channeled into shallow ponds, or lagoons, where it remains for several days to a month or more, depending on the design of the lagoon. Algae and cyanobacteria that grow at the surface provide O2, enabling aerobic organisms in the ponds to degrade the sewage.

Activated sludge process. This common system employs mixed aerobic microbes that are adapted to utilize the nutrients available in sewage and grow as suspended biofilms, or flocs. Although the organisms are often naturally present in sewage, large numbers are inoculated into the wastes by introducing a small portion of leftover sludge from the previous load of treated wastes. An abundance of O2 is supplied by mixing the sewage in an aerator. As the microbes proliferate, the organic matter is converted into both biomass and waste products such as CO2. Following the aeration, the wastewater is again sent to a sedimentation tank. There, most of the flocs settle and the resulting sludge is removed; a portion of this sludge is introduced to a new load of wastewater to act as an inoculum. A complication of the activated sludge process occurs when filamentous bacteria such as Thiothrix species overgrow in the wastewater during treatment, creating a buoyant mass that does not settle. This problem, bulking, interferes with the separation of the solid sludge from the liquid effluent. ■ biofilm, p. 85 ■ Thiothrix, p. 259

Artificial wetlands. These employ the same principles as lagoons, but their more advanced designs not only offer a means to treat wastewater, but also provide a habitat for birds and other wildlife (figure 31.3). For example, the wastewater treatment processes in Arcata, California, use a series of marshes that now attract a variety of shorebirds and serve as a wildlife sanctuary.

Advanced Treatment As water supplies are becoming scarce, and in order to comply with discharge standards designed to protect surface groundwaters, many communities are finding advanced treatment necessary. This encompasses any purification process beyond secondary treatment; it may involve physical, chemical, or biological processes, or any combination of these. Advanced treatment is expensive, however, and has not been common in the past. Often, advanced treatment is designed to remove ammonia, nitrates, and phosphates—compounds that foster the growth of algae FIGURE 31.2 Trickling Filter Wastewater is

50–100 feet Arm rotates slowly as effluent sprays onto plastic or rocks covered with a variety of microorganisms.

channeled into the revolving arm, and then trickles through holes in the bottom of the arm onto plastic or a gravel and rock bed. The surfaces are coated with a biofilm of microbes that aerobically degrade the organic materials as they trickle through the bed. The effluent has a greatly reduced BOD.

~15 feet

Water trickles through.

Effluent—goes either to advanced treatment or directly to disinfection.

Effluent from primary treatment

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Nutrients from air and surface soil

Ponds with aerators

Nutrient Peat

Deep sediments

Marsh

Wastewater enters system. Meadow Anaerobic digestion of sludge

Wastewater is aerated to stimulate aerobic organisms that breakdown waste.

Pond

Effluent flows into the marsh where pollutants are further metabolized by bacteria and other microorganisms attached to the plant roots.

In this pond, algae feed on and transform harmful nutrients.

Meadow grasses trap remaining pollutants. Water flowing here is now cleared of pollutants.

FIGURE 31.3 Artificial Wetland

and cyanobacteria in the receiving waters. The concentrations of these nutrients, which are very low in unpolluted waters, normally limit the growth of the photosynthetic organisms. Consequently, if the nutrients are added, photosynthetic organisms proliferate, often leading to a surface scum composed of buoyant masses of cells (see figure 11.7). In addition, the photosynthetic organisms provide a source of carbon for other microbes, increasing the BOD and, consequently, threatening other forms of aquatic life. Ammonia is removed by a process called ammonia stripping, which liberates gaseous ammonia from the water. Nitrates can be removed by exploiting the activities of denitrifying bacteria. These organisms use nitrate as a terminal electron acceptor during anaerobic respiration, forming nitrogen gas. This gas is inert, nontoxic and easily removed. Phosphates are removed using chemi-

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cals that combine with phosphates, causing them to precipitate. ■ denitrification, p. 731

Disinfection Before discharge into the receiving water, the effluent is disinfected with chlorine, ozone, or UV light to decrease the numbers of microorganisms and viruses. If chlorine is used, the disinfected water can then be dechlorinated to avoid releasing excessive amounts of the toxic chemical into the environment. ■ chlorine, p. 119 ■ ozone, p. 120 ■ UV light, p. 116

Anaerobic Digestion Within the anaerobic digester, microorganisms act on the solids removed during the sedimentation steps of primary

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31.1 Microbiology of Wastewater Treatment

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PERSPECTIVE 31.1 Now They’re Cooking with Gas In rural areas of China, fuel for cooking and heating is often in short supply; as a consequence, the hay that should go for animal feed must be used for fuel. To alleviate this problem, many of the farmers build methane-producing tanks on their farms (figure 1). Near the farmhouse is an underground cement tank connected to the latrine and pigpen. Human and animal wastes along with water and some other organic materials such as straw are added to the tanks. As the natural process of fermentation occurs, methane gas (CH4) is produced. This gas rises to the top of the tank and is connected to the house with a hose. Enough gas is produced to provide lights and cooking fuel for the farm family. By producing its own gas, a family also saves money because it does not need to buy coal for cooking.

Organic material

anaerobic digestion (several steps)

CO2 + 4 H2

CH4 + 2 H2O methane

CH3COOH

CH4 + CO2

and secondary treatment. Various anaerobic populations act sequentially, ultimately converting much of the organic material to methane: Organic compoundsDorganic acids, CO2, H2 Organic acidsDacetate, CO2, H2 Acetate, CO2, H2Dmethane (CH4) Many wastewater treatment plants are equipped to use the methane generated, thereby avoiding the cost of other sources of energy to run their equipment.

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CH3COOH + H2 + CO2

After anaerobic digestion, water is removed from the remaining sludge, generating a nutrient-rich product called stabilized sludge. This can be incinerated or disposed of in landfills, but may also be used to improve soils and promote plant growth. The sludge generated by the city of Milwaukee, Wisconsin, is used to produce Milorganite®, a fertilizer for lawns, gardens, golf courses, and playfields. An increasing number of wastewater treatment facilities are finding similar ways to recycle their treated sludge. Concerns exist, however, about heavy metals and other pollutants that can sometimes be concentrated in the product.

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CHAPTER THIRTY ONE

Environmental Microbiology Venting

Venting

Wastewater from house Scum Outlet

Anaerobic digestion

Perforated pipes

Sludge

FIGURE 31.4 Septic Tank Wastewater enters the tank from the house.

Gravel

Within the tank, solid materials settle and undergo anaerobic degradation. Materials that do not settle exit through the outlet pipe, which permits seepage into the drainage field. Conditions in the drainage field must be aerobic so that the materials remaining can be degraded by the activities of aerobic microorganisms. If the drainage area is not properly designed, contaminated materials readily enter adjacent waters.

Individual Wastewater Treatment Systems Rural dwellings customarily rely on septic tanks for wastewater disposal. In theory, the septic tank makes sense; in practice, however, it often does not work correctly. Wastewater is collected in a large tank in which much of the solid material settles and is degraded by anaerobic microorganisms (figure 31.4). The fluid overflow from the tank has a high BOD and must be passed through a drainage field of sand and gravel designed to allow oxidation of the organic material in the same manner described for the trickling filter. The process, however, depends on adequate aeration and sufficient action by aerobic organisms in the drainage field. Unfortunately, certain conditions, such as a clay soil under a drainage field, can prevent adequate drainage, allowing anaerobic conditions to develop. Toxic materials can inhibit microbial activity in the drainage field. Drainage from a septic tank may contain pathogens; therefore, the tank must never be allowed to drain where it can contaminate water supplies.

MICROCHECK 31.1 Primary treatment is a physical process that removes material that will settle out. Secondary treatment is chiefly a biological process that converts most of the suspended material into inorganic compounds and microbial biomass. Advanced treatment is often designed to remove ammonia, phosphates, and nitrates. Anaerobic digestion converts much of the organic matter to methane. Septic tanks are individual wastewater treatment systems. ✓ What does the term BOD mean? What is its significance? ✓ What is the advantage of removing phosphates and nitrates from wastewater? ✓ Why would the processes of secondary treatment preclude denitrification?

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Drainage field

31.2 Drinking Water Treatment and Testing Focus Points Describe how water is typically treated to make it safe for drinking. Describe the importance of indicator organisms, and explain how total coliforms are detected.

Large cities generally obtain their drinking water from surface waters such as lakes or rivers. Because surface water may serve as the receiving water for another city’s wastewater effluent, drinking water treatment is intimately connected to wastewater treatment. The quality of the surface water is also affected by the characteristics of the watershed—the land over which water flows into the river or lake. Even pristine rivers are likely contaminated with feces of animals that inhabit the watershed. Smaller communities often use groundwater, pumped from a well, as a source of drinking water (figure 31.5). This water occurs in aquifers—water-containing layers of rock, sand, and gravel—that is replenished as water from rain and other sources seeps through the soil. Because aquifers are not directly exposed to rain, animals, and the atmosphere, they are somewhat protected from contamination. However, poorly located or maintained septic tanks and sewer lines, as well as sludge or other fertilizers, can lead to groundwater contamination. Public water systems in the United States are regulated under the Safe Drinking Water Act of 1974, amended in 1986 and 1996.

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31.2 Drinking Water Treatment and Testing

745

Rainfall

Refuse Irrigation Drinking water well Sludge Fertilizer Soil Septic tank Sewer line

Defective well casing

Groundwater

FIGURE 31.5 Groundwater The water in the aquifer is replenished as water from various sources seeps through the soil. Poorly located or maintained septic tanks and sewer lines, as well as sludge or other fertilizers, can lead to groundwater contamination.

This gives the Environmental Protection Agency (EPA) the authority to set drinking water standards in order to control the level of contaminants in drinking water. Standards are modified in response to new concerns; for example, regulations now govern the maximum levels of Cryptosporidium oocysts, Giardia cysts, and enteric viruses in drinking water. ■ Cryptosporidium, p. 610 ■ Giardia, p. 609

Water Treatment Processes The treatment of metropolitan water supplies is designed to eliminate pathogenic microbes as well as harmful chemicals (figure 31.6). First, water flows into a reservoir and is allowed to stand long enough for the particulate matter to settle. The water is then transferred to a tank where it is mixed with a flocculent chemical, such as aluminum potassium phosphate, or alum. This causes materials still suspended in the liquid to coagulate, forming aggregates that slowly sink to the bottom. As the clumps settle, they remove unwanted materials from the water, including some bacteria and viruses.

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Following the flocculation, the water is filtered, often through a thick bed of sand and gravel, to remove various microorganisms including bacteria and protozoan cysts and oocysts. Organic chemicals that may be harmful or impart undesirable tastes and odors can be removed by additional filtration through an activated charcoal filter, which adsorbs dissolved chemicals. Not only does filtration physically remove various particles, but microorganisms growing in biofilms on the filter materials use carbon from the water as it passes. This lowers the organic carbon content of the water, resulting in less microbial growth in pipes delivering the water. ■ filtration, p. 115 Finally, the water is treated with chlorine or other disinfectants to kill harmful bacteria, protozoa, and viruses that might remain. A concern with using chlorine, however, is that some of the disinfection by-products might be carcinogenic. In response to this concern, ultraviolet irradiation and ozone are increasingly being used as alternatives, but a small amount of chlorine must still be added to prevent problems associated with post-treatment contamination. Note that disinfection of waters with a high organic content requires more chlorine because organic compounds consume free

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Settle Step 1 Water is held in a series of reservoirs, where large materials sediment. Aluminum potassium sulfate (alum) may be added to cause flocculation of organic matter, which then settles out.

Alum Alum mixed with water

Coagulate

Settling basin Sand

Step 2 The water is then filtered through beds of sand, which removes almost all of the bacteria. Filtration through activated charcoal may be used to remove toxic or objectionable organic materials.

Filter

Chlorine Store Consumer use

Step 3 Finally, the water is disinfected to kill any pathogens that might remain. Chlorine, ultraviolet irradiation or ozone may be used for disinfection. Some cities also add fluoride to protect against dental cavities.

Reservoir

FIGURE 31.6 Steps in the Treatment of Municipal Water Supplies

chlorine. ■ chlorine, p. 119 ■ disinfection by-products, p. 110 ■ ultraviolet irradiation, p. 116 ■ ozone, p. 120

Water Testing A primary concern regarding the safety of drinking water is the possibility that it might be contaminated with any of a wide variety of intestinal pathogens, such as those discussed in chapter 25. It is not feasible to test for all of the pathogens, however, so indicator organisms function as surrogates. These microbes are routinely found in feces, survive longer than intestinal pathogens, and are relatively easy to detect and enumerate. The most common group of bacteria used as indicator organisms in the United States is total coliforms—lactose-fermenting members of the family Enterobacteriaceae, including E. coli. The group is functionally defined as facultatively anaerobic, Gram-negative, rod-shaped, non-spore-forming bacteria that ferment lactose, forming acid and gas within 48 hours at 35°C. Although total coliforms are routinely present in the intestinal contents of warm-blooded animals, certain species can also thrive in soils and on plant material. Thus, the presence of these organisms does not necessarily imply fecal pollution. To compensate for this shortcoming, fecal coliforms, a subset of total coliforms more likely to be of intestinal origin, are also used as indicator organisms. The most common fecal coliform is E. coli. Note that although

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some strains of E. coli can cause intestinal disease, the organism is used in water testing merely to indicate fecal pollution. Methods used to detect total coliforms in a water sample include: ONPG/MUG test. A water sample is added to a minimal medium containing ONPG (o-nitrophenyl-b-D-galactopyranoside) and MUG (4-methylumbelliferyl-b-D-glucuronide). Lactose-fermenting bacteria hydrolyze ONPG, yielding a yellow-colored compound; thus, all coliforms turn the medium yellow (figure 31.7). E. coli produces an enzyme that hydrolyzes MUG, generating a fluorescent compound. Because of ONPG and MUG, a sample can be assayed simultaneously for the presence of both total coliforms and E. coli. Presence/absence test. A 100-ml water sample is added to a lactose-containing broth that contains a vial to trap gas. If gas is produced, the broth is then tested to confirm the presence of coliforms.

The most probable number (MPN) method. This statistical assay of cell numbers employs successive dilution of a water sample in broth similar to that used in the presence/ absence test. Positive tubes from the MPN test (see figure 4.20) are further tested to confirm that the tubes actually contain coliforms. Membrane filtration. A water sample is passed through a filter that retains bacteria (see figure 4.19), concentrating the bacteria from a known volume of water. The filter is then placed on a lactose-containing selective and differential agar medium. ■ selective media, p. 96 ■ differential media, p. 97

The total coliform rule establishes a maximum number of positive samples (100 ml) permitted. That maximum relates to the number of samples routinely collected by the water system. The number collected ranges from 1 to 480 samples per month, depending on the size of the population served by the system. Systems that collect at least 40 samples per month are in violation if more than 5% are total coliform-positive in a month. Systems that collect fewer samples are in violation if more than one sample tests positive per month. If a sample tests positive, repeat samples within 24 hours are mandated. Total coliform-positive samples are also tested for either fecal coliforms or E. coli. If a water system exceeds the monthly total coliform limit, the system must notify the state and the public. Notification is also required if either of two sequential samples that test positive for total coliforms also test positive for fecal coliforms or E. coli. Because of limitations of total coliform and fecal coliform assays in predicting contamination with protozoan cysts and oocysts, alternatives are being explored. Other microbes that can be used as indicators of fecal pollution include enterococci, some Clostridium species, and certain types of bacteriophages.

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31.3 Microbiology of Solid Waste Treatment

FIGURE 31.7 ONPG/MUG Test Coliforms hydrolyze ONPG, yielding a yellow-colored compound. E. coli hydrolyzes MUG, generating a blue fluorescent compound.

MICROCHECK 31.2 Drinking water may be obtained from surface water or groundwater. Treatment of drinking water is designed to eliminate pathogens and harmful chemicals. In the United States, total and fecal coliforms are the most commonly used indicator organisms. ✓ What is an aquifer? ✓ Describe two methods of water testing. ✓ Which would be more likely to cause illness—a water sample that tested positive for coliforms or one that tested positive for E. coli O157:H7?

31.3 Microbiology of Solid Waste Treatment Focus Point Compare and contrast sanitary landfills and composting programs.

In addition to ridding our environment of wastes in water, we must dispose of the solid wastes (garbage) generated each day. Eliminating these has become an increasingly complex problem.

Sanitary Landfills for Solid Waste Disposal Sanitary landfills are widely used to dispose of non-hazardous solid wastes in a manner that minimizes damage to human health and the environment. Before sanitary landfills were developed,

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solid wastes were often piled up on the ground in open-burning dumps, attracting insects and rodents and causing aesthetic and public health problems. Federal standards dictate that sanitary landfills must be located away from wetlands, earthquake-prone faults, flood plains, or other sensitive areas. The excavated site is lined with plastic sheets or a special membrane atop a thick layer of clay, which minimizes leaching of contaminates from the wastes into the surrounding area. Next comes a layer of sand with drainage pipes; above this, the wastes are compacted and covered with a layer of soil every day. When a landfill is full, it is covered with soil and plants, and can be used for recreation and eventually as a site for construction. Methane and other gases are vented, and the methane is burned or recovered for use. There are several disadvantages to this type of waste management. First, only a limited number of sites are available for use near urban and suburban areas. Second, the organic content of landfills anaerobically decomposes very slowly, over a period of at least 50 years. During this time, the methane gas produced must be removed. If buildings are constructed before the methane is removed, disastrous gas explosions can occur. Pollutants such as heavy metals and pesticides can leak from landfill sites into the underground aquifers. It is very difficult to purify these aquifers once they have become contaminated. Sanitary landfills have traditionally been a low-cost method of handling large quantities of solid waste. Because of increased costs and decreased availability of land, however, many cities are looking for ways to decrease the amount of solid waste dumped in landfills. In some cities, the fees charged to people for garbage collection are based on the size of the container collected. The smaller the can, the lower the cost. This is intended to raise people’s awareness of how much solid waste they are generating as well as offer an incentive to recycle. Programs to recycle paper, plastics, glass, and metal are being implemented in many cities and counties with great success. Through these programs, landfill areas can be expected to be available for a longer period of time.

Municipal and Backyard Composting— Alternative to Landfills Composting is the natural decomposition of organic solid material. Municipal and home composting programs are becoming popular in many areas and are succeeding in reducing the amount of organic waste added to landfills. Backyard composting involves mixing garden debris with kitchen organic waste, excluding meats and fats (figure 31.8). If proper amounts of warmth, water, and air are provided to the mix, the bulk of the waste is reduced by two-thirds in a matter of months. The black organic material generated by composting can then be used to improve the soil in garden beds. A backyard compost pile usually starts with a supply of organic material such as leaves and grass clippings, as well as kitchen wastes. Often, some soil and water are added. Within a few days, microbial metabolism causes the inside of the pile to heat up. At 55°C to 66°C, pathogens are killed but thermophilic organisms are not affected. If the pile is frequently aerated, which

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Backyard Compost Municipal Compost

Pick up yard waste from private homes and city parks.

Yard waste (no heavy branches)

Yard waste

Hauled to transfer station

Kitchen waste (no meats or fats)

Compost bin

Addition of soil Hauled to compost station

Grind it.

Ground material is put in curing piles for approximately 18 months

Turning compost

Screened

Lid on Compost sold by the bulk or by the bag

(a)

Garden and yard use

Garden and yard use

FIGURE 31.8 Backyard Compost Heap

can be done by physically stirring and turning it, and it is kept moist, the composting can be completed in as little as 6 weeks. ■ thermophile, p. 91

Composting on a large scale offers cities a way to reduce the amount of garbage sent to their landfills. In some cities, yard wastes are collected separately from the main garbage. These wastes are then composted and used in various ways, including improving soils in city parks. Special machinery is used to compost on a large scale, and the composting can be accomplished in a very short time (figure 31.9).

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(b)

FIGURE 31.9 Municipal Composting (a) Process, (b) Composting station.

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31.4

Microbiology of Bioremediation

749

31.4 Microbiology of Bioremediation

Relative herbicide concentration

MICROCHECK 31.3 Composting makes use of the decomposing ability of natural organisms. It dramatically reduces the need for large landfills to dispose of solid waste. ✓ What are the advantages and disadvantages of landfills? ✓ List the steps in successful composting. ✓ Why would soil and water be added to a compost pile?

100 2,4,5-T 75

H

H

50

Bioremediation is the use of microorganisms to degrade or detoxify pollutants in a given environment. It may involve the use of specific organisms introduced into the polluted environment or, more commonly, it may take advantage of organisms already present, possibly adding nutrients to encourage their growth.

Pollutants Pollutants from domestic and industrial wastes have often been dumped into the environment as a matter of convenience. Fortunately, most organic compounds of natural origin can be degraded by one or more species of soil or aquatic organisms under appropriate conditions for microbial growth. As oil spills dramatically demonstrate, however, some natural materials can cause devastating effects before they are degraded. Synthetic compounds are more likely to be degradable if they have a chemical composition similar to that of naturally occurring substances. Xenobiotics, synthetic compounds totally different from any that occur in nature, often persist for long periods of time. This is because microorganisms are unlikely to have enzymes necessary for degrading foreign substances; such an enzyme would not give them a competitive advantage in a natural situation. Relatively slight molecular changes markedly alter the biodegradability of a compound. Perhaps the best-studied example involves the herbicides 2,4-dichlorophenoxyacetic acid (2,4-D) and 2,4,5-trichlorophenoxyacetic acid (2,4,5-T). The only difference between these two compounds is the additional chlorine atom on the latter. When 2,4-D is applied to the soil, it disappears within a period of several weeks, as a result of its degradation by microbes in the soil. When 2,4,5-T is applied, however, it is often still present more than a year later (figure 31.10). Its persistence is apparently due to the additional chlorine atom, which blocks the enzyme that makes the initial attack on 2,4-D. Most herbicides and insecticides not only are toxic to their target, but also have deleterious effects on fish, birds, and other animals. For example, the pesticide DDT accumulates in the fat of predatory birds through biological magnification (table 31.1). Small amounts of the pollutant that contaminate water are concentrated in minute plankton, which are eaten by minnows, accumulating even more in the fish. When large birds eat the fish,

nes95432_Ch31_738-752.indd 749

O

C

C

OH

2,4-D

6

2

5

3

C

OH

1 6

2

5

3

1

25

O

C O

O

Cl

4

Cl

Cl Cl

4

Cl

0 5

Focus Point Describe how two bioremediation strategies remove pollutants.

H

H

10

20

25

Time (days)

FIGURE 31.10 Comparison of the Rates of Disappearance of Two Structurally Related Herbicides, 2,4-D, and 2,4,5-T The addition of a third chlorine atom in the 2,4,5-T molecule blocks the enzyme that degrades the substance, so the compound remains in the environment.

the amount of chemical in tissues is tremendously magnified. The continuing ingestion of DDT, which accumulates in fat, results in an ever-greater concentration of the DDT as it passes upward through the food chain. DDT interferes with the reproductive process of birds, leading to the production of fragile eggs, which break before the young can hatch. Although banned in the United States, DDT is still used in other countries, particularly to control mosquitoes that transmit malaria.

Means of Bioremediation Many factors influence the degradation rate of pollutants. As a general rule, any practice that favors multiplication of microorganisms will increase the rate of degradation. Thus, providing adequate nutrients, maintaining the pH near neutrality, raising the temperature, and providing an optimal amount of moisture are all likely to promote pollutant degradation. ■ environmental factors that influence microbial growth, p. 90 ■ nutritional factors that influence microbial growth, p. 93

There are two general bioremediation strategies—biostimulation and bioaugmentation. Biostimulation enhances growth of indigenous microbes in a contaminated site by providing additional nutrients. Petroleum-degrading bacteria are naturally present in seawater, but they degrade oil at a very slow rate because the low levels of certain nutrients, including nitrogen

TABLE 31.1 Biological Magnification of DDT Parts per Million DDT

Source

0.00005

Water

0.04

Plankton

0.23

Minnow

3.57

Heron

22.8

Merganser (fish-eating duck)

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and phosphorus, limit their growth. To enhance bioremediation of oil spills, a fertilizer containing these nutrients, and which adheres to oil, was developed. When this fertilizer is applied to an oil spill, microbial growth is stimulated, leading to at least a threefold increase in the speed of degradation by the bacteria. (figure 31.11). Bioaugmentation relies on activities of microorganisms added to the contaminated material, complementing the resident population. The activated sludge process used during secondary treatment of wastewater is a form of bioaugmentation. A great deal of research is underway to develop microbial strains suited for bioaugmentation. One example, Burkholderia (Pseudomonas) cepacia, is capable of growth on 2,4,5-T and has been used successfully to remove this chemical from soil samples in the laboratory. However, microbes that thrive under laboratory conditions may not compete well in natural habitats. ■ activated sludge processes, p. 741

Successful bioremediation may also involve controlling metabolic processes by manipulating the availability of O2 and specific growth substrates. For example, anaerobic degradation of trichloroethylene (TCE), a solvent used to clean metal parts, results in the accumulation of vinyl chloride, a compound more toxic than TCE. Aerobic conditions are important to prevent this buildup. Some pollutants are degraded only when specific substrates are made available to the microbes. This phenomenon, called co-metabolism, occurs because the enzyme produced by the microbe to degrade the additional substrate degrades the pollutant as well. As an example, the enzymes produced by some microbes to degrade methane also degrade TCE. In this case, adding methane enhances the degradation of TCE. Bioremediation may be done either in situ (“in place”) or off-site. In situ bioremediation generally relies on biostimulation and is less disruptive. Oxygen (O2) can be added to contaminated groundwater and soil either by injecting hydrogen peroxide, which rapidly decomposes to liberate O2 and water, or pumping air into soil. Off-site processes may be performed using a bioreactor, a large tank designed to accelerate microbial processes.

FIGURE 31.11 Oil Spill Bioremediation Bioremediation was used to clean the shoreline contaminated by oil spilled from the Exxon Valdez. The growth of indigenous oil-degrading bacteria was stimulated by addition of nutrients. Comparing the uncleaned rocks on the left to the rocks cleaned by bioremediation on right shows the dramatic efficiency of bioremediation.

Both nutrients and oxygen may be added to facilitate microbial growth and metabolism, while the slurry is agitated to ensure that the microbes remain in contact with the contaminants. A slower process involves mounding the contaminated soil over a layer that traps seeping chemicals. To provide O2, the soil can be turned occasionally or air forced through.

MICROCHECK 31.4 Bioremediation uses microorganisms to degrade pollutants. Biostimulation and bioaugmentation are two methods employed. ✓ Give three reasons why pollutants can persist in the environment. ✓ What is meant by biological magnification? ✓ How would adding a third chlorine atom to 2,4-D (see figure 31.10) block the enzyme attack? (Hint: Explain in terms of enzyme and substrate structure.)

FUTURE CHALLENGES Better Identification of Pathogens in Water and Wastes One of the most important challenges in the field of water and waste treatment is the development of new and better methods to detect waterborne contaminants in both drinking water and environmental water samples. This would make it possible to follow the occurrence and persistence of pathogens in water supplies with greater accuracy, and aid in better reporting of waterborne illnesses. Methods being developed, but not yet perfected for use in this field, include the polymerase chain reaction (PCR) and a variety of fluorescence techniques and radioactivity labeling methods.

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Cysts of Giardia and oocysts of Cryptosporidium have been detected by amplifying specific regions of their DNA by PCR. In fact, using this method, it is possible to detect a single cyst of Giardia and to distinguish between species that are pathogenic for humans and those that are not. But problems arise in using these techniques with environmental samples that contain substances which inhibit the reaction. In addition, PCR detects DNA from dead organisms as well as living. Studies are needed to make these techniques feasible for use in water testing.

Viruses can also be detected by PCR. The viruses are concentrated by filtration onto membranes. Many different viruses can be detected simultaneously by combining gene probes from various groups of viruses. A problem is that viruses inactivated by disinfection procedures are still detected by PCR. To overcome this, viruses can be put into cell cultures to allow them to replicate, indicating that they are not inactivated, and the PCR is then performed on the infected cell cultures.

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Review Questions

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SUMMARY 31.1 Microbiology of Wastewater Treatment Biochemical Oxygen Demand (BOD) An important goal of wastewater treatment is the reduction of the biochemical oxygen demand (BOD).

Water Testing Total coliforms and fecal coliforms are used as indicator organisms; their presence suggests the possible presence of pathogens.

31.3 Microbiology of Solid Waste Treatment

Municipal Wastewater Treatment Methods (figures 31.1, 31.2, 31.3) Primary treatment is a physical process designed to remove materials that sediment out. Secondary treatment is chiefly a biological process designed to convert most of the suspended solids to inorganic compounds and microbial biomass, removing most of the BOD. Advanced treatment is often designed to remove ammonia, nitrates, and phosphates. Biosolids that result from anaerobic digestion of sludge can be used to improve soils and promote plant growth.

Sanitary Landfills for Solid Waste Disposal Landfills are used to dispose of solid wastes near towns and cities.

Individual Wastewater Treatment Systems (figure 31.4) Rural dwellings customarily rely on septic tanks for sewage disposal.

Pollutants Synthetic compounds are more likely to be biodegradable if they have a chemical composition similar to that of naturally occurring compounds

31.2 Drinking Water Treatment and Testing Water Treatment Processes (figure 31.6) Metropolitan water supplies are treated to remove particulate and suspended matter, various microorganisms, and organic chemicals. Chlorine or other disinfectants are then used to kill harmful microbes.

Municipal and Backyard Composting—Alternative to Landfills (figures 31.8, 31.9)

Composting reduces the amount of garbage sent to landfills.

31.4 Microbiology of Bioremediation

(figure 31.10).

Means of Bioremediation Biostimulation can be used to increase the effectiveness of oil degradation by naturally occurring bacteria (figure 31.11).

REVIEW QUESTIONS Short Answer 1. Describe how the BOD of a water sample is determined. 2. Which step of wastewater treatment removes most of the BOD? 3. Compare and contrast the activated sludge process and the trickling filter system used in secondary treatment of wastewater. 4. Why is it beneficial to remove nitrates and phosphates in wastewater? 5. How does a septic tank system work? 6. What is an aquifer? 7. Why do water-testing procedures look for coliforms rather than pathogens? 8. How does the ONPG/MUG test allow a sample to be assayed simultaneously for the presence of both coliforms and E. coli? 9. What aspect of 2,4,5-T makes it more likely to persist in the environment than 2,4-D? 10. Describe the use of bioremediation in the cleanup of oil spills.

Multiple Choice 1. A marked decrease in BOD during secondary treatment indicates a) lack of oxidation during treatment. b) effective aerobic decomposition during treatment. c) effective anaerobic decomposition during treatment. d) removal of all pathogenic bacteria. e) removal of all toxic chemicals. 2. Advanced treatment is often designed to remove a) BOD. b) nitrates and phosphates. c) bacteria. d) protozoa. e) methane.

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3. Which of the following pairs does not match? a) Potable water—presence of pathogens b) High BOD—high organic content c) Stabilized sludge—fertilizer d) Primary treatment—removal of material that settles e) Bulking—growth of filamentous bacteria 4. Which of the following is false? a) Bulking interferes with trickling filter systems. b) Artificial wetlands provide a habitat for wildlife. c) Removal of nitrates by microorganisms requires anaerobic conditions. d) Methane is a by-product of anaerobic digestion. 5. Which of the following pairs does not match? a) Surface water—watershed b) Groundwater—aquifer c) Sand and gravel filters—removes organic chemicals d) Alum—causes suspended material to coagulate e) Disinfection—chlorine, ozone, or ultraviolet light 6. Septic tanks should be placed a) as close to the well as possible. b) at least 500 feet from the house. c) under the house. d) in deep clay soil. e) where the overflow cannot contaminate any water supply.

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7. Which of the following statements about coliform testing methods is true? a) All determine the number of E. coli present in a sample. b) The MPN procedure precisely indicates the concentration of coliforms. c) The media employed test for the ability to ferment lactose. d) A positive test indicates that pathogens are definitely present in the sample. e) All coliforms hydrolyze ONPG and MUG. 8. Landfills are often used to dispose of a) household wastewater. b) commercial wastewater. c) solid wastes. d) petroleum wastes. e) wastewater effluent. 9. Backyard composting is an excellent way to dispose of a) cooking fats. b) garden debris. c) spoiled meats. d) insecticides. e) cleaning supplies. 10. Synthetic compounds are most likely to be biodegradable if they a) are totally different from anything found in nature. b) have three chlorine atoms per molecule. c) are plastics. d) are present in very large amounts. e) are chemically similar to naturally occurring substances.

Applications 1. A developer is interested in building vacation homes on 150 acres of oceanfront property. A priority is to retain as much natural beauty of the area as possible. Safe and effective sewage treatment must be part of the plan. What advantages and disadvantages of each of the following options proposed by an environmental consultant must the developer consider before selecting one? a. Individual septic tanks for each home

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b. Trickling filter central treatment system c. Artificial wetlands 2. A public health official is investigating waterborne diseases in Illinois. She notes that over half of the actual cases of waterborne diseases originating from drinking water were caused by Giardia lamblia. Other data showed that most cases of gastroenteritis attributed to exposure to recreational waters were caused by Cryptosporidium parvum. What does this suggest about controlling waterborne diseases?

Critical Thinking 1. Why is oil not degraded when in a natural habitat underground, yet susceptible to bioremediation in an oil spill? 2. The accompanying figure shows the effects of different treatments of drinking water on the incidence of typhoid fever in Philadelphia, 1890–1935. If filtration of drinking water caused such a dramatic decrease in the disease incidence, was it necessary to introduce chlorination a few years later? Why or why not?

Number of typhoid cases per 10,000 population

752

700

Filtration of drinking water

600 500 400

Chlorination of drinking water started

300 200 100 0

1890

1900

1910 Years

1920

1930

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32 Refrigeration is a method of food preservation.

Food Microbiology A Glimpse of History Pasteurization of milk and milk products is so common today it is hard to fathom that only during the twentieth century have federal, state, and local laws mandated it for all milk products. Although most large cities have required milk to be pasteurized since 1900, as late as 1930 most milk sold in rural areas was not routinely pasteurized. As a result, human diseases such as brucellosis and tuberculosis were fairly common. ■ brucellosis, p. 681 ■ tuberculosis, p. 514 Alice Catherine Evans, the first woman president of the Society of American Bacteriology (now the American Society for Microbiology), helped establish the connection between unpasteurized milk and brucellosis in humans. A graduate of both Cornell University and the University of Wisconsin, Evans worked for the U.S. Department of Agriculture, seeking out the sources of microbial contamination of dairy products. In 1917, Evans reported that cases of human brucellosis were related to the finding of Brucella abortus in cows’ milk. Her conclusion that B. abortus could be transmitted from cows to humans through milk conflicted with the prevailing view of a number of prominent scientists, including Robert Koch. In 1900, Koch had declared that bovine tuberculosis and brucellosis could not be transmitted to humans. As a result, at least 30 years elapsed before many scientists and dairy workers would accept the increasing evidence that diseases could be transmitted from cows to humans through the milk supply. In the 1920s, dairy herds were inspected and vaccinated for tuberculosis. Herds that passed inspection and were vaccinated were called certified herds, and their milk could be sold commercially without pasteurization. In the late 1930s, after a number of the children of dairy workers had died of brucellosis even though they had drunk only certified milk, the problem of milk-borne disease was finally acknowledged. Today, milk is routinely pasteurized, and only very small amounts of unpasteurized milk are sold in the United States.

W

hen you prepare a meal, you also invite a host of microorganisms to dinner. Practically all the food we purchase or grow—fruit, vegetable, meat, or dairy

product—harbors a variety of microorganisms. This is not surprising when one considers that bacteria and fungi are ubiquitous and are especially plentiful in soil and around animals. From the microbial perspective, food can be viewed as a fertile ecosystem in which these organisms vie for the nutrients. The successful microorganisms are able to multiply and predominate. Microorganisms on foods are not necessarily undesirable. Sometimes, their growth results in a more pleasant taste or texture. Foods that have been intentionally altered during production by carefully controlling the activity of bacteria, yeasts, or molds are called fermented (figure 32.1). For example, food manufacturers

Figure 32.1 Fermented Foods Fermented foods have been intentionally altered in their production by carefully controlling the growth and activity of microorganisms. 753

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KEY TERMS Fermented Foods Foods that have been intentionally altered during production by encouraging the activity of bacteria, yeasts, or molds.

Food Microbiology Food Spoilage Biochemical changes in foods that are perceived as undesirable. Foodborne Infection An illness that results from consuming microbes in a food product; ingested microbes colonize the host and cause disease.

Food Preservation Increasing the shelf life of foods by preventing the growth and concurrent metabolic activities of microorganisms.

purposely encourage some microorganisms to flourish in milk in order to produce foods such as sour cream and cheese. Alcoholic beverages, such as beer and wine, and many Asian food condiments, such as soy sauce and miso, also rely on microbial metabolism for their production. Strictly speaking, the term fermentation is used to describe only those metabolic activities that utilize pyruvate or another organic compound as an electron acceptor, with the result that alcohols and acids are produced. Food scientists, however, use the term more generally, to encompass any desirable change that a microorganism imparts to food. ■ fermentation, p. 147 Biochemical changes in foods, when perceived as undesirable, are called spoilage (figure 32.2). The processes that cause spoilage are often the same ones involved in fermentation of foods. In fact, a food product considered by one cultural population to be fermented may be considered spoiled by another. Sour milk and moldy bread are examples of foods considered spoiled as a result of microbial growth. The souring of milk, however, involves microbial processes analogous to those that cause the agreeable acidic flavor of sour cream, and the mold growing on bread may be related to the one that causes the blue veining in Gorgonzola cheese. Growth of pathogens such as Clostridium botulinum, Staphylococcus aureus, Salmonella species, and E. coli O157: H7 can result in foodborne illness but generally does not result in perceptible changes in quality of a food. Depending on the type of pathogen, the illness may result from consuming either the living organisms or the toxins they have produced during growth. Limiting microbial growth can preserve the quality of foods and prevent foodborne illnesses. Foods can be canned, pasteur-

(a)

(b)

Foodborne Intoxication An illness that results from the consumption of an exotoxin produced by a microorganism growing in a food product. Water Activity (aw) The relative amount of water available to microorganisms; pure water has an aw of 1.0.

ized, or irradiated to eliminate or decrease the numbers of microorganisms. Alternatively, the multiplication of microorganisms can be suppressed by storing food at cold temperatures, or by adding growth-inhibiting ingredients, called preservatives. The end products of some fermentation processes can preserve food by inhibiting the growth of many undesirable microorganisms.

32.1 Factors Influencing the Growth of Microorganisms in Foods Focus Point Describe four intrinsic factors and two extrinsic factors that influence the growth of microorganisms in foods.

Microorganisms have a competitive advantage in those foods with characteristics that enable them to multiply most rapidly. Understanding the factors that influence microbial growth is essential to maintaining food quality when producing fermented foods or prolonging the shelf life of perishable foods. The conditions naturally present in the food, such as moisture, acidity, and nutrients, are called intrinsic factors. Environmental conditions, such as the temperature and atmosphere of storage, are called extrinsic factors. All of these factors combine to determine which microorganisms can grow in a particular food product and

(c)

FIGURE 32.2 Examples of Spoiled Food (a) Apples infected by the fungus Venturia inaequalis, cause of apple scab. (b) Orange affected by a Penicillium mold. (c) Ear of corn and a lemon after several weeks in the refrigerator.

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32.1 Factors Influencing the Growth of Microorganisms in Foods

the rate of that growth. For example, bacteria are well suited for growth in the environment found in fresh meat and other moist, pH-neutral, nutrient-rich foods. Yeasts and molds can also grow under these conditions, but the more rapid increase of bacteria overwhelms these competitors. When conditions such as lack of moisture or high acidity restrict the growth of bacteria, fungi predominate despite their relatively slow growth.

Intrinsic Factors The growth of microorganisms in a food is influenced by the inherent characteristics of that food. In general, microbes multiply rapidly in moist, nutritionally rich, pH-neutral foods.

Water Availability Food products vary in terms of how much water is accessible to microorganisms. Fresh meats and milk, for example, have ample water and support growth of many microbes. Bread, nuts, and dried foods, on the other hand, provide a relatively arid environment. Some sugar-rich foods, such as jams and jellies, are seemingly moist, but most of that water is chemically interacting with the sugar, making it unavailable for use by microbes. Highly salted foods, for similar reasons, have little available moisture. The term water activity (aw) is used to designate the amount of water available in foods. By definition, pure water has an aw of 1.0. Most fresh foods have an aw above 0.98, whereas ham has an aw of 0.91, jam has an aw of 0.85, and some cakes have an aw of 0.70. Most bacteria require an aw above 0.90 for growth, which explains why fresh, moist foods spoil more quickly than dried, sugary, or salted foods. Fungi can grow at an aw as low as 0.80, which is why forgotten bread, cheese, jam, and dried foods often become moldy. Staphylococcus species, which are adapted to grow on the dry, salty surfaces of human skin, can grow at an aw of 0.86, lower than the minimum required by most common spoilage bacteria. Staphylococcus species normally do not compete well with other bacteria, but on salty products such as ham and other cured meats, they can multiply with little competition. Ham is a common vehicle for S. aureus food poisoning. ■ Staphylococcus aureus foodborne illness, p. 763

pH The pH of a food is important in determining which organisms can survive and thrive on it. Many species of bacteria, including most pathogens, are inhibited by acidic conditions and cannot grow at a pH below 4.5. An exception is the lactic acid bacteria, which can grow at a pH as low as 3.5 and are used in the production of fermented foods such as yogurt and sauerkraut. This group of bacteria produces lactic acid as a result of fermentative metabolism. Although they are useful in food production, their growth and accompanying acid production are also prime causes of spoilage of unpasteurized milk and other foods. Fungi can grow at a lower pH than most spoilage bacteria, leading to some acidic foods eventually becoming moldy. For example, the pH of lemons is approximately 2.2, which inhibits the growth of bacteria, including the lactic acid group, but some fungi can grow. ■ pH, p. 24 ■ lactic acid bacteria, p. 255 ■ pasteurization, p. 112

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The pH of a food product can also determine whether toxins can be produced. For instance, Clostridium botulinum, the causative agent of botulism, does not grow or produce toxin below pH 4.5, and so it is not considered a danger in highly acidic foods. This is why the canning process for acidic fruits and pickles is less stringent than that for foods with a higher pH. However, some newer varieties of tomatoes are less acidic than older types, and require the addition of acid if they are to be safely canned using these less stringent procedures.

Nutrients The nutrients present in a food determine the kinds of organisms that can grow in it. An organism requiring a particular vitamin cannot grow in a food lacking that vitamin. A microbe capable of synthesizing that vitamin, however, can grow if other conditions are favorable. Members of the genus Pseudomonas often spoil foods because they can synthesize essential nutrients and can multiply in various environments, including refrigeration.

Biological Barriers Rinds, shells, and other coverings help protect foods from invasion by microorganisms. Eggs, for example, retain their quality much longer with intact shells. Whole lemons keep longer than slices. Even so, microorganisms will eventually break down these coverings and cause spoilage.

Antimicrobial Chemicals Some foods contain natural antimicrobial chemicals that help prevent spoilage. Egg white, for instance, is rich in lysozyme. If lysozyme-susceptible bacteria breach the protective shell of an egg, they are destroyed by lysozyme before they can cause spoilage. Other examples of naturally occurring antimicrobial chemicals are benzoic acid in cranberries and allicin in garlic. ■ lysozyme, p. 62

Extrinsic Factors The extent of microbial growth varies greatly depending on the conditions under which a food is stored. Microorganisms multiply rapidly in warm, oxygen-rich environments such as the surface of meat stored at room temperature.

Storage Temperature The temperature of storage affects the rate of growth of microorganisms in food. Below its freezing point, water becomes crystalline and inaccessible, effectively halting microbial growth. At low temperatures above freezing, many enzymatic reactions are either very slow or non-existent, with the result that some microorganisms are unable to grow. Those that can do so at a reduced rate. Microorganisms that grow on refrigerated foods are most likely psychrophiles or psychrotrophs such as some members of the genus Pseudomonas. ■ psychrophiles, p. 91 ■ psychrotroph, p. 91

Atmosphere The presence or absence of O2 affects the type of microbial population able to grow in food. For example, members of the genus Pseudomonas are obligate aerobes, and consequently they

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cannot grow in foods stored under conditions that exclude all of their required oxygen. Excluding O2 from a food, however, may enable the growth of other bacteria, including the obligate anaerobe Clostridium botulinum. A case of botulism was traced to the consumption of a thick, homemade stew that had been slowly cooked and then left at room temperature overnight. The cooking process did not destroy the endospores of C. botulinum and had driven off the O2, thereby creating anaerobic conditions in which the organism thrived and produced toxin. ■ oxygen require-

Table 32.1 Foods Produced Using Lactic Acid Bacteria Food Milk Products Cheese (unripened)

Employs a starter culture usually containing Lactococcus cremoris and L. lactis

Cheese (ripened)

Employs rennin and a starter culture containing Lactococcus cremoris and L. lactis, ripened for weeks to years; other bacteria and/or fungi may be added to enhance flavor development

Yogurt

Employs a starter culture containing Streptococcus thermophilus and Lactobacillus delbrueckii subspecies bulgaricus

Sweet acidophilus milk

Lactobacillus acidophilus added for purported health benefits

ments, p. 92

MICROCHECK 32.1 Intrinsic factors (such as available moisture, pH, and the presence of antimicrobial chemicals) and extrinsic factors (including storage temperature and atmosphere) influence the type of microorganisms that grow and predominate in a food product. ✓ Why is Staphylococcus aureus more likely to be found in high numbers on ham than on fresh meat? ✓ Which is more important to refrigerate: homemade stew or bread? Why? ✓ Why would the cooking process create anaerobic conditions?

32.2 Microorganisms in Food and Beverage Production Focus Points Compare and contrast the production of cheese, yogurt, and acidophilus milk.

Characteristics

Vegetables Sauerkraut

Cabbage; succession of naturally occurring bacteria including Leuconostoc mesenteroides, Lactobacillus brevis, and Lactobacillus plantarum

Pickles

Cucumbers; naturally occurring bacteria

Poi

Taro root; naturally occurring bacteria; Hawaii

Olives

Green olives

Kimchee

Cabbage and other vegetables; Korea

Meats Dry and semidry sausages

Employs a starter culture containing species of Lactobacillus and Pediococcus, meat is stuffed into casings, incubated, heated, and then dried

Compare and contrast the production of pickled vegetables and fermented meat products. Compare and contrast the production of wine, beer, distilled spirits, and vinegar. Describe the production of soy sauce.

also produce flavorful and aromatic compounds that contribute to the overall quality of fermented foods. ■ lactic acid bacteria, p. 255 ■ obligate fermenters, p. 92

Yogurt, cheese, pickled vegetables, and other fermented foods are not only perceived as pleasant tasting, but the acids produced as a by-product of microbial metabolism inhibit the growth of many spoilage organisms as well as foodborne pathogens. Thus, fermentation historically has been, and continues to be today, an important method of food preservation, particularly when modern conveniences such as refrigeration are lacking.

Lactic Acid Fermentations by the Lactic Acid Bacteria The tart taste of yogurt, pickles, sharp cheeses, some sausages, and other foods is due to the production of lactic acid by one or more members of a group of bacteria known as the lactic acid bacteria (table 32.1). This group of organisms, including members of the genera Lactobacillus, Lactococcus, Streptococcus, Leuconostoc, and Pediococcus, are obligate fermenters that characteristically produce lactic acid as an end product of their metabolism. Some

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Cheese, Yogurt, and Other Fermented Milk Products In a cow’s udder, milk is sterile, but it rapidly becomes contaminated with a variety of microorganisms during milking and handling. Various species of lactic acid bacteria are inevitably introduced because they commonly reside on the udder. If the milk is not refrigerated, these bacteria readily ferment lactose, the predominant sugar in milk, producing lactic acid. The removal of the primary carbohydrate as a nutrient source, combined with the production of lactic acid, inhibits the growth of many other microorganisms in the milk. Aesthetic features of the milk change as well because lactic acid lowers the pH, which in turn causes the milk proteins to coagulate or curdle, and sours the flavor. ■ milk spoilage, p. 724

Today, with high quality control standards and the use of pasteurized milk, the commercial production of fermented milk products does not rely on naturally introduced lactic acid bacteria. Instead, starter cultures containing one or more strains

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of lactic acid bacteria are added to the milk. These strains are carefully selected to produce the most desirable flavors and textures. Precious starter cultures must be carefully maintained and protected against contamination, particularly by bacteriophages, which can damage or destroy them. ■ bacteriophage, p. 303 Cheese Cheese can be made from the milk of a wide variety of animals, but most common cheeses are made with cow’s milk. Sheep or goat’s milk can be used to give characteristic flavors. Cheeses are classified as very hard, hard, semisoft, and soft, according to their percentage of water. Cottage cheese is one of the simplest cheeses to make. Pasteurized milk is inoculated with a starter culture, usually containing Lactococcus cremoris and L. lactis, and then incubated until fermentation products cause the proteins in milk to coagulate. The coagulated proteins, or curd, are heated and cut into small pieces to facilitate drainage and removal of the liquid waste portion, or whey. Unlike most cheeses that undergo further microbial processes called ripening or curing, cottage cheese is unripened. The initial steps in the production of ripened cheese are the same as those of cottage cheese, except the enzyme rennin is added to the fermenting milk to hasten protein coagulation (figure 32.3). Rennin is an enzyme naturally found in the stomach of young calves, where it aids in digestion of the mother’s milk. Today, rennin is commercially produced using genetically engineered microorganisms. After the whey is removed, the curds are salted and pressed, and then they are shaped into the traditional forms of cheese, usually bricks or wheels. The cheese is then ripened to encourage characteristic changes in texture and flavor. Depending on the type of cheese, ripening can take from several weeks to several years. Changes imparted during this time are generally due to the metabolic activities of naturally occurring or starter lactic acid bacteria. Longer ripening gives rise to more acidic, sharper cheeses. Some cheeses are inoculated with other bacteria or fungi that impart characteristics particular to the kind of cheese. For example, the bacterium Propionibacterium shermanii ripens Swiss cheese and gives it the characteristic holes, or eyes, and a nutty flavor. This bacterium ferments organic compounds to produce propionic acid and CO2. The CO2 gas causes the holes in the cheese, while the propionic acid imparts the typical flavor. Propionic acid also inhibits spoilage organisms. Roquefort, Gorgonzola, and Stilton cheeses are ripened by the fungus Penicillium roquefortii. Growth of the fungus along cracks in the cheese gives these cheeses the distinctive bluish-green veins. Brie and Camembert are ripened by a white fungus such as P. candidum or P. camemberti inoculated on the surface of the cheese. The mycelia of the fungus produce enzymes that alter texture and flavor as they gradually work their way into the cheese. Limburger cheese is made in a similar manner, but with the bacterium Brevibacterium linens. ■ mycelium, p. 290 Yogurt To produce yogurt, pasteurized milk is concentrated slightly by evaporation and then inoculated with a starter culture containing Streptococcus thermophilus and Lactobacillus delbrueckii subspecies bulgaricus. The mixture is incubated at 40°C to 45°C for several hours, during which time these thermophilic bacteria grow

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Lactic acid production and rennin activity cause the milk proteins to coagulate. The coagulated mixture is cut to facilitate the separation of the solid curd and liquid whey.

The curd is heated and cut into small pieces. The liquid whey is removed by draining.

Curds are salted and pressed into blocks or wheels for aging.

Figure 32.3 Commercial Production of Cheese Why does a longer ripening process give rise to a sharper cheese?

rapidly and produce lactic acid and other end products, such as acetaldehyde, that contribute to the flavor. Carefully controlled incubation conditions favoring the balanced growth of the two species ensure the proper levels of acid and flavor compounds. Acidophilus Milk Traditional acidophilus milk is the product of fermentation by Lactobacillus acidophilus. The more readily available sweet acidophilus milk retains the flavor of fresh milk because it is not fermented. Instead, a culture of L. acidophilus is added immediately before packaging. The bacteria are simply included for their purported health benefits. Some evidence suggests they may aid in the digestion of lactose as well as prevent and reduce the severity of some diarrheal illnesses, but the role they play in the complex interactions of the human intestinal tract is not clear. Unlike most lactic acid bacteria used as starter cultures, L. acidophilus can potentially colonize the intestinal tract.

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Pickled Vegetables Another fermentation process known as pickling originated as a way to preserve vegetables such as cucumbers and cabbage. Today, pickled products such as sauerkraut (cabbage), pickles (cucumbers), and olives are valued for their flavor. Unlike the fermentation of milk products that rely on the use of starter cultures in the manufacturing process, fermentation of most vegetables utilizes naturally occurring lactic acid bacteria residing on the vegetables. One of the most well-studied natural fermentations is the production of sauerkraut. The cabbage is first shredded and layered with salt. The layers are firmly packed to provide an anaerobic environment. The salt draws water and nutrients from the cabbage, creating a brine that inhibits the growth of many microbes but permits the growth of the naturally occurring lactic acid bacteria. Under the correct conditions, natural successions of lactic acid bacteria grow. These bacteria—Leuconostoc mesenteroides, Lactobacillus brevis, and Lactobacillus plantarum—produce lactic acid, which lowers the pH, further inhibiting undesired microbes. The lactic acid and other end products of the fermentation give sauerkraut its characteristic tangy taste. When the desired flavor has been attained, usually after 2 to 4 weeks at room temperature, the sauerkraut is often canned. Similar processes are used to make some pickles, olives, and other vegetable products.

Table 32.2 Foods and Beverages Produced Using Alcoholic Fermentation by Yeast Product

Characteristics

Alcoholic Beverages Wine

Sugars in grape juice are fermented by Saccharomyces cerevisiae.

Sake

Amylase from mold (Aspergillus oryzae) converts the starch in rice to sugar, which is then fermented by S. cerevisiae.

Beer

Enzymes in germinated barley convert starches of barley and other grains to sugar, which is then fermented by S. cerevisiae.

Distilled spirits

Sugars, or starches that are converted to sugars, are fermented by S. cerevisiae; distillation purifies the alcohol.

Vinegar

Alcohol produced by fermentation is oxidized to acetic acid by species of Gluconobacter or Acetobacter.

Breads

S. cerevisiae ferments sugar; expansion of CO2 causes the bread to rise; alcohol is lost to evaporation during baking.

Fermented Meat Products

Wine

Traditionally, fermented meat products, such as salami, pepperoni, and summer sausage, were produced by enabling the small numbers of lactic acid bacteria naturally present to multiply to the point of dominance. Relying on the natural fermentation of meat is inherently risky, however, because the incubation conditions used to initiate fermentation can potentially support the growth and toxin production of pathogens such as Staphylococcus aureus and Clostridium botulinum. The development and use of reliable starter cultures assure rapid production of lactic acid, inhibiting the growth of pathogens and enhancing flavor development. Starter cultures used by U.S. sausage-makers typically contain species of Lactobacillus and/or Pediococcus, depending on the type of sausage. To make fermented sausages, meat is ground and combined with a starter culture and other ingredients including sugar, salt, and nitrite. The sugar serves as a substrate for fermentation, because meat does not naturally contain enough fermentable carbohydrate to produce sufficient amounts of lactic acid. Salt and nitrite contribute to the flavor of sausage; they also inhibit the growth of spoilage microorganisms and, most importantly, C. botulinum. After thorough blending, the mixture is stuffed into a casing and incubated from one to several days. The product can then be smoked or otherwise heated to kill bacteria. Finally, it is dried.

Wine is the product of the alcoholic fermentation of naturally occurring sugars in the juices of fruit, most commonly grapes. One of the most important variables in the quality of wine is the variety and quality of grapes used. The growing conditions and ripeness as well as other factors affect the grapes’ content of sugar, acids, and various organic compounds, which in turn critically influences the final product. Commercially, wine is made by crushing carefully selected grapes in a machine that removes the stems and collects the resulting solids and juices, or must (figure 32.4). For red wine, the entire must, including skins and pulp, of red grapes is put into the fermentation vat. The red color and complex flavors contributed by the tannins of red wines are derived from components of the grape skin and seeds. The solids are removed during fermentation by a wine press that separates them from the partially fermented juice once the desired amount of color and tannins have been extracted. For the production of white wines, the solids are removed immediately and only the clear juice of white, or occasionally red, grapes is fermented. Rose wines obtain their light pink color from the entire crushed red grape fermented for about 1 day, after which the juice is removed and fermented alone. The fermentation must be carefully controlled to ensure that desired reactions occur. Sulfur dioxide (SO2) is generally added to inhibit the growth of the natural microbial population of the grape, especially acetic acid bacteria. These bacteria can convert alcohol to acetic acid (vinegar) and are the most prevalent cause of wine spoilage. The fermentation process is initiated by the addition of specially selected strains of Saccharomyces cerevisiae. These strains are more resistant to the antimicrobial action of SO2 and produce a higher alcohol content than naturally occurring yeasts.

Alcoholic Fermentations by Yeast Some yeasts, such as members of the genus Saccharomyces, ferment simple sugars to produce ethanol and carbon dioxide. These yeasts are used to make a variety of alcoholic beverages as well as vinegar and bread (table 32.2).

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32.2 Microorganisms in Food and Beverage Production Stemmer-crusher

Fruit, most commonly grapes, is crushed to yield must, composed of solids and juices. Stems are removed. Red wines are made from the entire must of grapes. White wines are made from the clear juice of white or red grapes.

Stems Fermenting vat Sulfur dioxide is added to inhibit wild yeasts and spoilage bacteria. Specially selected strains of Saccharomyces are added. The fermentation process begins.

Settling vat The wine is siphoned several times to separate the fermented juice from the particulate debris.

759

In addition to the alcoholic fermentation of the grape sugars, a distinctly different type of fermentation, called malolactic fermentation, can occur during wine production. Lactic acid bacteria, primarily species of Leuconostoc, convert malic acid to the less acidic lactic acid. Red wines made from grapes grown in cool regions tend to have high levels of malic acid, and their flavor is mellowed by this fermentation. After fermentation, the wine is siphoned several times to remove the clear juice from the sediment of yeast and particulate debris. Most red wines and some white wines are then aged in oak barrels, contributing to the complexity of the flavor. Wine is clarified by filtration and bottled. The CO2 produced during fermentation is usually released before the wine is bottled, resulting in a “still” (noncarbonated) wine. Other processes are used to prepare carbonated wines such as champagne. The Japanese wine sake depends on several microbial fermentation reactions. First, cooked rice is inoculated with the fungus Aspergillus oryzae. The fungus produces the enzyme amylase, which degrades the rice starch to sugar. Then, a strain of Saccharomyces cerevisiae is added to convert the sugar to alcohol and CO2. Lactic acid bacteria add to the flavor by producing lactic acid and other fermentation end products.

Beer During the aging process, chemical and microbial changes occur that contribute to the complex flavors of wine.

Debris

Bottling

Wine is clarified by filtration and bottled.

Figure 32.4 Commercial Production of Wine

Fermentation is carried out at a carefully controlled temperature, which varies with the type of wine, for a period ranging from a few days to several weeks. During fermentation most of the sugar is converted to ethanol and CO2, generally resulting in a final alcohol content of less than 14%. Dry wines result from the complete fermentation of the sugar, whereas sweet wines contain residual sugar.

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Beer production is a multistep process designed to break down the starches of grains such as barley to produce simple sugars, which are then fermented by yeast. Yeasts alone cannot convert grain to alcohol because they lack the enzymes that degrade starch, the primary carbohydrate of grain. Sprouted or germinated barley, however, known as malted barley or malt, naturally contains these and other important enzymes. Dried, roasted malt is ground, mixed with adjuncts (starches, sugars, or whole grains such as rice, corn, or sorghum), and then soaked in warm water in a process called mashing (figure 32.5). During this process, enzymes of the malt act on the starches, converting them to fermentable sugars. The final characteristics of the beer, such as color, flavor, and foam, are derived entirely from compounds in the roasted malt. The adjuncts simply serve as readily available, less expensive sources of carbohydrates for alcohol production. After mashing, the residual solids, or spent grains, are removed to yield the sugary liquid called wort. Hops, the flowers of the vinelike hop plant, are added to the wort to impart a Aging in barrels

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Malt barley is cracked open before entering the mash tun.

Mill

The ingredients of mash—malt, water, and sometimes adjuvants— are mixed.

The mash is heated, allowing enzymes in the mash to convert starches into fermentable sugars. The liquid wort is then separated from the spent grains.

Mixing tank

Spent grains

Mash tun

Hops The wort is pumped into the brew kettle, where it is boiled while hops are slowly added. The wort is separated from the hops and cooled.

Brew kettle

Spent hops

Yeast A special strain of Saccharomyces, or brewer's yeast, is added to the wort. Fermentation begins. Excess yeast cells are removed after fermentation.

Fermenting tank Surplus yeast

a Saccharomyces cerevisiae strain referred to as S. carlsbergensis, tend to form clumps that sink to the bottom of the fermentation vat. These yeasts ferment best at temperatures between 6°C and 12°C and usually take 8 to 14 days to complete fermentation. In contrast, top-fermenting yeasts—certain strains of Saccharomyces cerevisiae—are distributed throughout the wort but are carried to the top of the vat by the rising CO2. They ferment at higher temperatures (14°C to 23°C) and over a shorter period (5 to 7 days). Most American beers are lagers produced by the bottom yeasts. Ales, porters, and stouts are made using top-fermenting yeasts. The fermentation process generates beer with an alcohol content ranging from 3.4% to 6%. Most of the yeasts settle out following fermentation and are removed. These yeasts can be sold as flavor and dietary supplements. The beer is then aged, during which time residual, unwanted flavor compounds are metabolized by remaining yeast cells or settle out. Cask-conditioned beer undergoes a second fermentation, which generates CO2 in the cask. Other beers must be carbonated to replace the CO2 that escapes during fermentation. After aging, beer is clarified by filtration, microorganisms are removed or killed using membrane filtration or pasteurization, and the product is packaged.

Distilled Spirits

The manufacturing of distilled spirits such as scotch, whiskey, and gin is initially similar to that of beer, except the wort is not boiled. Consequently, degradation of starch by the Lagering The beer is ripened in the lagering enzymes in the wort continues during the fertank tank. Yeast and unwanted flavor mentation. When the fermentation is complete, compounds settle out. the ethanol is collected by distillation. Different types of spirits are made in different ways. For example, rum is made by fermenting sugar cane or molasses. Malt scotch whiskey Beer is clarified by filtration, and Filtration and pasteurized or membrane filtered is the product of the fermentation of barley that bottling before bottling. is then aged for several years in oak sherry casks. The wood and the residual sherry contribute both flavor and color to the whiskey as Figure 32.5 Commercial Production of Beer What is the purpose of the membrane filtering it ages. Lactic acid bacteria are used to produce in the last step? lactic acid in grain mash for making sour-mash whiskey. The yeast S. cerevisiae subsequently ferments the sour mash to form alcohol. The distilled spirit tequila desirable bitter flavor to the beer and contribute antibacterial is traditionally made from the fermentation of juices from the substances. The mixture is boiled to extract the flavor compoagave plant using the bacterium Zymomonas mobilis. This bactenents of hops, concentrate the wort, inactivate enzymes, kill rium ferments sugars to ethanol and CO2 via a pathway similar to most microorganisms, and precipitate proteins, facilitating their the yeast alcoholic fermentation pathway. removal. The wort is then centrifuged to remove the solids, including hops and precipitated proteins, and cooled before being Vinegar transferred to the fermentation tank. Vinegar, an aqueous solution of at least 4% acetic acid, is the Special strains of brewer’s yeasts (as opposed to baker’s product of the oxidation of ethanol by the acetic acid bacteria— yeasts) are commonly used in beer-making. Bottom yeasts, such as

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32.2 Microorganisms in Food and Beverage Production

Acetobacter and Gluconobacter species. Acetic acid bacteria are strictly aerobic, Gram-negative rods, characterized by their ability to carry out a number of oxidations. They can tolerate high concentrations of acid as they oxidize alcohol to acetic acid. Alcohol is commercially converted to vinegar using processes that provide readily available oxygen to hasten the oxidation reaction. The vinegar generator sprays alcohol onto loosely packed wood shavings that harbor a biofilm of acetic acid bacteria. As the alcohol trickles through the bacteria-coated shavings, it is oxidized to acetic acid. In principle, the vinegar generator operates much like the trickling filter used in wastewater treatment by providing a large surface area for aerobic metabolism. The sub- Ingredients (mix) merged culture reactor is an enclosed system that continuously pumps small air bubbles into alcohol that has been inoculated with acetic acid bacteria. ■ trickling filter, p. 741 ■ biofilm, p. 85

and proteins in the soybeans are broken down, producing a yellow-green liquid containing fermentable sugars, peptides, and amino acids. After this initial step, the mixture is put into a large container with an 18% NaCl solution, or brine. Salttolerant microorganisms then grow and impart changes over an extended period. Microorganisms involved in this stage of fermentation include lactobacilli, pediococci, and yeasts. After the brine mixture is allowed to ferment for 8 to 12 months, the liquid soy sauce is removed. The residual solids are used as animal feed.

Ingredients of bread include yeast, milk or water, oil, flour, salt, and sugar.

Bread Yeast bread rises through the action of baker’s yeast—strains of Saccharomyces cerevisiae carefully selected for the commercial baking industry. The CO2 produced during fermentation causes the bread to rise, producing the spongy texture characteristic of yeast breads. The alcohol evaporates during baking. Yeast bread is made from a mixture of flour, sugar, salt, milk or water, yeast, and sometimes butter or oil (figure 32.6). Packaged baker’s yeast that can be reconstituted in warm water is readily available as pressed cakes or dried granules. An excess of yeast is added to enable adequate production of CO2 in a time period too short to permit multiplication of spoilage bacteria. Sourdough bread is made with a combination of yeast and lactic acid bacteria. Lactic acid is produced as well as alcohol and CO2, giving the bread its sour flavor.

761

Knead

The dough is thoroughly mixed and kneaded.

Rise (fermentation) The dough is put in a bowl and allowed to rise. During this time, the yeast produces ethanol and CO2. The dough rises to approximately double the original volume. The gas generated creates air pockets in the dough, producing the texture we see in the finished bread.

Changes Due to Mold Growth Molds contribute to the flavor and texture of some cheeses, as already discussed. In addition, many traditional dishes and condiments used throughout the world are produced by encouraging the growth of molds on food (table 32.3). Successions of naturally occurring microorganisms are often involved. The microbiological and chemical aspects of many of these traditional foods have not been extensively studied.

Following the period of rising, the dough is shaped into loaves and then goes through a second rising. The bread dough is then baked.

Baking

Soy Sauce Soy sauce is made by inoculating equal parts of cooked soybeans and roasted cracked wheat with a culture of either Aspergillus oryzae or A. sojae. The mixture, called koji, is allowed to stand for several days, during which time carbohydrates

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Note the holes caused by the production of CO2 and the evaporation of ethanol in the finished loaf of bread.

Figure 32.6 Bread Production

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Common Spoilage Bacteria Table 32.3 Foods Produced Using Molds Food

Characteristics

Soy sauce

Koji is produced by inoculating soybeans and cracked wheat with a starter culture of Aspergillus oryzae or A. sojae; the mixture is then added to a brine and incubated for many months.

Tempeh

Soybeans are fermented by lactic acid bacteria and then inoculated with a species of the mold Rhizopus; Indonesia.

Miso

Rice, soybeans, or barley are inoculated with Aspergillus oryzae; Asia.

Cheeses Roquefort, Gorgonzola, and Stilton

Curd is inoculated with Penicillium roquefortii.

Brie and Camembert

Wheels of cheese are inoculated with selected species of Penicillium.

MICROCHECK 32.2 Lactic acid bacteria are used to produce a variety of foods including cheese, yogurt, sauerkraut, and some sausages. Yeast is used to produce alcoholic beverages and breads. Some cheeses and many traditional foods owe their characteristics to changes caused by molds. ✓ Describe how the metabolism of lactic acid bacteria differs from that of most other microorganisms that can grow aerobically. ✓ How does the use of starter cultures improve the safety of fermented meat products? ✓ How could cottage cheese be produced without bacteria?

Numerous types of bacteria are important in food spoilage. Pseudomonas species can metabolize a wide variety of compounds, and grow on and spoil many different kinds of foods, including meats and vegetables. Psychrophilic species are notorious for spoiling refrigerated foods. Members of the genus Erwinia produce enzymes that degrade pectin, and so they commonly cause soft rot of fruits and vegetables. Acetobacter species transform ethanol to acetic acid, the principal acid of vinegar. Although this property is very beneficial to commercial producers of vinegar, it presents a great problem to wine producers. Milk products are sometimes spoiled by members of the genus Alcaligenes that form a glycocalyx, causing strings of slime, or “ropiness,” in raw milk. The lactic acid bacteria, including species of Streptococcus, Leuconostoc, and Lactobacillus, all produce lactic acid. Anyone who has unexpectedly consumed sour milk knows that this can be disagreeable. Members of the genera Bacillus and Clostridium are particularly troublesome causes of food spoilage because their heat-resistant endospores survive cooking and, in some cases, canning. Bacillus coagulans and B. stearothermophilus spoil some canned foods. ■ glycocalyx, p. 64

Common Spoilage Fungi A wide variety of fungi, including species of Rhizopus, Alternaria, Penicillium, Aspergillus, and Botrytis, spoil foods. Because fungi grow readily in acidic as well as low-moisture environments, fruits and breads are more likely to be spoiled by fungi than by bacteria. Aspergillus flavus grows on peanuts and other grains, producing aflatoxin, a potent carcinogen monitored by the Food and Drug Administration.

MICROCHECK 32.3

32.3 Food Spoilage

The metabolites of microbes can spoil foods by imparting undesirable flavors, odors, and textures. ✓ What characteristics of Pseudomonas species enable them to spoil such a wide variety of foods? ✓ Why do fungi most commonly spoil breads and fruits?

Focus Point Distinguish between fermented foods and spoiled foods.

Food spoilage encompasses any undesirable changes in food. Spoilage microorganisms produce metabolites that have repugnant tastes and odors. While these are aesthetically disagreeable, they are generally not harmful. This is not surprising when microbial growth requirements are considered. Most human pathogens grow best at temperatures near 37°C, whereas most foods are usually stored at temperatures well below the normal body temperature. Similarly, the nutrients available in fruits, vegetables, and other foods are generally not suitable for the optimum growth of human pathogens. As a result, the non-pathogens can easily outgrow the pathogens when competing for the same nutrients. Spoiled foods are considered unsafe to eat, however, because high numbers of spoilage organisms indicate that foodborne pathogens may be present as well.

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32.4 Foodborne Illness Focus Point Distinguish between foodborne intoxication and foodborne infection, and give two examples of each.

Foodborne illness, commonly referred to as food poisoning, occurs when a pathogen, or a toxin it produced, is consumed in a food product. Food production is carefully regulated in the United States to prevent foodborne illness. Federal, state, and local agencies cooperate in inspections to help enforce protective laws.In spite of strict controls, millions of cases of food poisoning are estimated to occur each year from foods prepared either commer-

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32.4

cially, at home, or in institutions such as hospitals and schools. The vast majority of these cases could have been prevented with proper storage, sanitation, and preparation. Table 32.4 lists some bacteria that cause foodborne illness in the United States. To more accurately determine the burden of foodborne illness in the United States, a government program called FoodNet (Foodborne Disease Active Surveillance Network) now collects data on laboratory-confirmed cases of diarrheal illness in 10 states, covering approximately 15% of the population (www. cdc.gov/foodnet). By gaining a better understanding of the epidemiology of foodborne diseases, these diseases can hopefully be prevented more easily.

Foodborne Intoxication Foodborne intoxication is an illness that results from the consumption of an exotoxin produced by a microorganism growing in a food product. When such a food product is ingested, it is the toxin that causes illness, not the living organisms (figure 32.7). Staphylococcus aureus and Clostridium botulinum are two examples of organisms that cause foodborne intoxication. ■ exotoxin, p. 403

Foodborne Illness

763

• Most bacteria that normally compete with Staphylococcus aureus are either killed by cooking or inhibited by high salt conditions.

• Clostridium botulinum endospores, common in soil and marine sediments, contaminate many different foods.

• Food handler inoculates S. aureus onto food.

• Endospores survive inadequate canning processes. Canned foods are anaerobic.

• S. aureus grows and produces toxin when food is allowed to slowly cool or is stored at room temperature.

• Surviving C. botulinum endospores germinate, grow, and produce toxin in low-acid canned foods.

• A person ingests the toxin-containing food. Symptoms of staph food poisoning, including nausea, abdominal cramping, and vomiting, begin after 4 to 6 hours.

• A person ingests the toxin-containing food. Symptoms of botulism, including weakness, double vision, and progressive inability to speak, swallow, and breathe, begin in 12 to 36 hours.

FIGURE 32.7 Typical Events Leading to Staphylococcus aureus and Clostridium botulinum Foodborne Intoxications

Staphylococcus aureus Many strains of Staphylococcus aureus produce a toxin that, when ingested, causes nausea and vomiting. Although S. aureus does not compete well with most spoilage organisms, it thrives in moist, rich foods in which other organisms have been killed or their growth inhibited. For example, S. aureus can grow with little competition on unrefrigerated salty products such as ham (aw of 0.91). Creamy pastries and starchy salads stored at room temperature also offer ideal conditions for the growth of this pathogen, because the cooking of the ingredients kills most other competing organisms. The source of S. aureus is usually a human carrier who has not followed adequate hygiene procedures, such as handwashing, before

preparing the food. If the organism is inoculated into a food that can support its growth, and the food is left at room temperature for several hours, S. aureus can grow and produce the toxin. Unlike most exotoxins, S. aureus toxin is heat-stable, so that cooking the food will not destroy it. ■ Staphylococcus aureus, p. 535

Botulism Botulism is a paralytic disease caused by ingestion of a neurotoxin produced by the anaerobic, spore-forming, Gram-positive

Table 32.4 Common Foodborne Illnesses Organism

Symptoms

Foods Commonly Implicated

Intoxication Clostridium botulinum

Weakness; double vision; progressive inability to speak, Low-acid canned foods such as vegetables and meats swallow, and breathe

Staphylococcus aureus

Nausea, vomiting, abdominal cramping

Cured meats, creamy salads, cream-filled pastries

Diarrhea, fever, abdominal pain, nausea, headache

Poultry, raw milk

Clostridium perfringens

Intense abdominal cramps, watery diarrhea

Meats, meat products

Escherichia coli O157:H7

Severe abdominal pain, bloody diarrhea; may progress to hemolytic uremic syndrome

Ground beef, raw vegetables, unpasteurized juices

Listeria monocytogenes

Influenza-like symptoms, fever, may progress to septicemia, meningitis

Raw milk, cheese, meats, raw vegetables

Salmonella species

Nausea, vomiting, abdominal cramps, diarrhea, fever

Poultry, eggs, milk, meat

Shigella species

Abdominal cramps; diarrhea with blood, pus, or mucus; fever; vomiting

Salads, raw vegetables

Vibrio parahaemolyticus

Diarrhea, abdominal cramps, nausea, vomiting, headache, fever, chills

Fish and shellfish

Infection Campylobacter species

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PERSPECTIVE 32.1 Botox for Beauty and Pain Relief The exotoxin produced by Clostridium botulinum is one of the most powerful poisons known. These anaerobic soil bacteria are sporeformers found naturally on many foods. They survive usual cooking methods and inadequate canning procedures. Should conditions become anaerobic in the food, toxin can be produced, and if ingested it causes botulism. A few milligrams of this exotoxin is sufficient to kill the entire population of a large city. The botulinum toxin blocks transmission of acetylcholine nerve signals to the muscles, resulting in paralysis and often in death. This is a very dangerous toxin. Yet surprisingly, in recent years the toxin, known

as botox, has become useful in treating various conditions. Botox is often used as a cosmetic treatment to remove facial lines, such as frown lines. Extremely dilute botox is injected directly into the area, paralyzing the muscles that are causing the frown or other lines. While the lines are erased, the effect is temporary and the treatment must be repeated after several months. Botox is also used to relieve a number of very painful and disabling conditions involving muscle contractions such as dystonia (severe muscle cramping). For example, cervical dystonia is a painful disease in

rod Clostridium botulinum. Unfortunately, growth of the organism and production of the deadly toxin may not result in any noticeable changes in the taste or appearance of the food. Canning processes for low-acid foods are specifically designed to destroy the endospores of this organism. If the endospores are not destroyed due to processing errors, or they are introduced post-processing, they can germinate in these foods. The resulting vegetative cells can then grow and produce toxin. Such errors are rare in commercially canned foods, and most cases of botulism are due to processing errors in home-canned foods. As an added safety measure, low-acid, home-canned foods should be boiled for at least 15 minutes immediately before consumption. The toxin is heat-labile (sensitive), and so the heat treatment will destroy any toxin that may have been produced. Cans that are damaged should be discarded, because they might have small holes through which C. botulinum could enter. Likewise, bulging cans indicate gas production, which could indicate microbial growth, and should be discarded. ■ botulism, p. 657 ■ neurotoxin, p. 405

Foodborne Infection Unlike foodborne intoxication, foodborne infection requires the consumption of living organisms. The symptoms of the illness, which usually do not appear for at least 1 day after eating the contaminated food, usually include diarrhea. Thorough cooking of food immediately before consumption will kill the organisms, thereby preventing infection. Escherichia coli O157:H7 and Salmonella and Campylobacter species are examples of organisms that cause foodborne infection (figure 32.8).

which muscles in the neck and shoulders contract involuntarily, causing jerky movements, muscle pain, and tremors. Injections of botox directly into the affected areas give relief for 3 to 4 months, after which the treatment can be repeated. Another example is Parkinson’s disease, a condition in which certain nerve cells are lost, resulting in tremor, impaired movement, and in some cases, dystonia. Botox injected into the affected muscles can give dramatic, although temporary, relief. So, in spite of its powerful and dangerous properties, botulinum toxin, when used with great care, can be a useful therapeutic agent.

Escherichia coli O157:H7 Escherichia coli O157:H7 causes bloody diarrhea that sometimes develops into hemolytic uremic syndrome (HUS), a life-threatening condition. The bacterium is commonly found in the intestinal tract of healthy cattle and other livestock, where it is subsequently shed in their feces. Because of this, meats can easily become contaminated. In 2007, a multistate, foodborne outbreak of E. coli O157:

• Incomplete cooking fails to kill all pathogens. Surviving Salmonella and/or Campylobacter can multiply as food is cooled slowly or stored at room temperature. • Live organisms are ingested. They multiply in the intestinal tract and cause disease. Symptoms include diarrhea, abdominal pain, and nausea.

Salmonella and Campylobacter Salmonella and Campylobacter are two genera commonly associated with poultry products such as chicken, turkey, and eggs. Inadequate cooking of these products can result in foodborne infection. Cross-contamination of other foods can result in the transfer of pathogens to those foods. For example, if a cutting board on which raw chicken was cut is then immediately used to cut up vegetables for a salad, the salad can become contaminated with Salmonella or Campylobacter species. ■ Salmonella, p. 601 ■ Campylobacter, p. 602

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• Incomplete cooking fails to kill all pathogens. Even low numbers of surviving E. coli O157:H7 can cause illness. • Live organisms are ingested. They multiply in the intestinal tract and cause disease. Symptoms include severe abdominal pain and bloody diarrhea.

FIGURE 32.8 Typical Events Leading to Salmonella, Campylobacter, and E. coli O157:H7 Foodborne Infection

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32.5

Food Preservation

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H7 was linked to frozen ground beef patties, resulting in a recall of 21.7 million pounds of the product. Ground meats such as these are a particularly troublesome source of infection. While the initial contamination by the bacterium normally occurs on the surface and is easily destroyed by searing the exterior of meats such as steaks, grinding the meat distributes the bacterial cells throughout the product. Prevention then involves more thorough cooking so that enough heat reaches the center to kill all E. coli cells. Outbreaks have also been linked to unpasteurized milk and produce that was contaminated with animal manure. ■ hemolytic uremic syndrome, p. 598

Pasteurization. Heating foods under controlled conditions at high temperatures for short periods of time destroys non-spore-forming pathogens and reduces the numbers of spoilage organisms without significantly altering the flavor.

MICROCHECK 32.4

Refrigeration. Refrigeration preserves food by slowing the growth rate of microbes. Many organisms, including most pathogens, are unable to multiply at low temperatures.

Foodborne intoxication results from the consumption of toxins produced by organisms growing in a food. Foodborne infection results from consumption of living organisms. ✓ How does cooking a home-canned food immediately prior to consumption prevent botulism? ✓ Which foodborne pathogen can cause hemolytic uremic syndrome? ✓ Why would a large number of competing microorganisms in a food sample result in lack of sensitivity of culture methods for detecting pathogens?

32.5 Food Preservation Focus Point Describe the methods used to preserve foods.

Preventing the growth and concurrent metabolic activities of microorganisms that cause spoilage and foodborne illness preserves the quality of food. Some methods of food preservation, such as drying and salting, have been known throughout the ages, whereas others have been discovered or developed more recently. The major methods of preserving foods—high-temperature treatment, low-temperature storage, addition of antimicrobial chemicals and irradiation—are briefly summarized here and described in more detail in chapter 5. Canning. The canning process destroys all spoilage and pathogenic organisms capable of growth at normal storage temperatures. Low-acid foods are processed using steam under pressure (autoclaving) in order to reach temperatures high enough to destroy the endospores of Clostridium botulinum. Acidic foods are not subjected to as stringent heating conditions because Clostridium botulinum cannot grow and produce toxin in those foods. ■ canning, p. 114

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■ pasteurization, p. 112

Cooking. Cooking, like pasteurization, can destroy nonspore-forming organisms. Cooking obviously alters the characteristics of food, however. Heat distribution may be uneven, resulting in survival of organisms in inadequately heated regions.

■ temperature requirements, p. 90

Freezing. Freezing stops microbial growth because water in the form of ice is unavailable for biological reactions. Some of the microbial cells will be killed by damage caused by ice crystals, but those remaining can grow and spoil food once it is thawed. Drying/reducing the aw. Drying foods or adding high concentrations of sugars or salts inhibits microbial growth by decreasing the available moisture. Eventually, however, molds may grow. ■ drying food, p. 122 Lowering the pH. Lowering the pH, either by adding acids or encouraging fermentation by lactic acid bacteria, inhibits a wide range of spoilage organisms and pathogens. Adding antimicrobial chemicals. Organic acids such as propionic acid, benzoic acid, and sorbic acid are naturally occurring antimicrobial chemicals that are added to a variety of foods to inhibit fungal growth. Nitrates are added to cured meats to inhibit growth of Clostridium botulinum and other organisms. Wine, fruit juices, and other products are preserved by the addition of sulfur dioxide. ■ chemical preservatives, p. 122

Irradiation. Gamma irradiation destroys microorganisms without significantly altering the flavor of foods such as spices and meats. ■ irradiation, p. 116

MICROCHECK 32.5 Food spoilage can be eliminated or delayed by destroying microorganisms or altering conditions to inhibit their growth. ✓ Why does the canning process for low-acid foods require higher temperatures than the temperature required in the canning process for acidic foods? ✓ Why are nitrates added to cured meats? ✓ Microorganisms are often grouped according to their optimum growth temperatures. Which of these groups is most likely to spoil refrigerated foods?

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CHAPTER THIRTY TWO

Food Microbiology

FUTURE CHALLENGES Using Microorganisms to Nourish the World The world’s steadily increasing population mandates the efficient use of finite natural resources and the development of new protein supplies to nourish that growing populace. One potential solution that addresses both of these needs is to cultivate microorganisms as a protein source, employing industrial by-products currently considered wastes as the growth medium. The term single-cell protein, or SCP, was coined in the 1960s to describe the use of unicellular organisms such as yeasts and bacteria as a protein source. Today, the term generally encompasses the use of multicellular microorganisms as well, and might more accurately be called microbial biomass. While whole cells can be consumed, a more palatable alternative is to extract proteins from those cells and use them to form textured protein products.

Yeasts are considered the most promising, largescale source of single-cell protein. They multiply rapidly, are larger than bacteria, and are more readily acceptable as a potential food. The most suitable type of yeast depends on the growth medium employed. The various genera of yeasts utilize differing carbohydrate sources and conditions for growth. For example Kluyveromyces marxianus can be grown on whey, a by-product of cheese-making; Saccharomyces cerevisiae can grow on molasses, a by-product of the sugar industry; and Candida utilis can multiply on cellulose-containing by-products of the pulp and paper industry. Most of these wastes must be supplemented with a nitrogen source, as well as various vitamins and minerals, in order to support the growth of yeasts or other microorganisms.

To a lesser extent, the use of bacteria as SCP is also being explored. The cyanobacterium Spirulina maxima can be cultivated in alkaline lakes and then harvested and dried. This requires adequate sunlight and warmth, making large-scale, year-round production practical in only some parts of the world. One of the chief concerns regarding the consumption of microorganisms as a protein source is their high concentration of nucleic acid, primarily RNA. Yeast and bacteria contain as much as eight times more RNA per gram as does meat. High levels of nucleic acid in the diet cause an increase in uric acid in the blood, which can lead to gout and kidney stones. Chemical and enzymatic methods are being developed to decrease the nucleic acid in SCP without altering the nutritional value of the protein.

SUMMARY 32.1 Factors Influencing the Growth of Microorganisms in Foods Intrinsic Factors Bacteria require a high aw. Fungi can grow in foods that have an aw too low to support the growth of bacteria. Many species of bacteria, including most pathogens, are inhibited by acidic conditions. The nutritional content of a food determines the kinds of organisms that can grow in it. Rinds, shells, and other coverings aid in protecting some foods from the invasion of microorganisms. Some foods contain natural antimicrobial chemicals that may help prevent spoilage. Extrinsic Factors Low temperatures halt or inhibit the growth of most foodborne microorganisms. Psychrophiles and psychrotrophs, however, grow at refrigeration temperatures. The presence or absence of O2 affects the type of microbial population able to grow in a food.

32.2 Microorganisms in Food and Beverage Production

myces cerevisiae (figure 32.4). Beer production is a multistep process designed to break down the starches of grains such as barley to produce simple sugars, which can then serve as a substrate for alcoholic fermentation by yeast (figure 32.5). Distilled spirits are produced using distillation to collect the alcohol generated during fermentation. Vinegar is the product of the oxidation of alcohol by the acetic acid bacteria. In breadmaking, the CO2 produced by yeast causes bread to rise, and the alcohol is lost to evaporation (figure 32.6). Changes Due to Mold Growth (table 32.3) Some cheeses and other foods are produced by encouraging the growth of molds on foods. Soy sauce is made by allowing species of Aspergillus to degrade a mixture of soybeans and wheat, which is then fermented in brine.

32.3 Food Spoilage Food spoilage is most often due to the metabolic activities of microorganisms as they grow and utilize the nutrients in the food.

Not only are fermented foods perceived as pleasant tasting, the acids produced inhibit the growth of many spoilage organisms as well as foodborne pathogens.

Common Spoilage Bacteria Pseudomonas, Erwinia, Acetobacter, Alcaligenes, lactic acid bacteria, and endosporeformers are important causes of food spoilage.

Lactic Acid Fermentations by the Lactic Acid Bacteria (table 32.1) The tart taste of yogurt, pickles, sharp cheese, and some sausages is due to the metabolic products of the lactic acid bacteria. Starter cultures, and sometimes rennin, are added to pasteurized milk to make cheese. Other bacteria or fungi are sometimes added to ripened cheese to impart characteristic flavors or textures (figure 32.3). Fermentation of vegetables, pickling, relies on naturally occurring lactic acid bacteria. Commercial sausage production utilizes starter cultures to rapidly decrease the pH and prevent the growth of pathogens.

Common Spoilage Fungi Fungi grow readily in acidic as well as low-moisture environments; therefore, fruits and breads are more likely to be spoiled by fungi than by bacteria.

Alcoholic Fermentations by Yeast (table 32.2) Wine is the product of the alcoholic fermentation of naturally occurring sugars in the juices of fruit by specially selected strains of Saccharo-

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32.4 Foodborne Illness (table 32.4) Foodborne Intoxication Foodborne intoxication results from consuming a toxin produced by a microorganism growing in a food product (figure 32.7). Many strains of Staphylococcus aureus produce a toxin that, when ingested, causes nausea and vomiting. Botulism is caused by ingestion of a neurotoxin produced by the anaerobic, spore-forming, Gram-positive rod Clostridium

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Review Questions botulinum. As an added safety measure, low-acid home-canned foods should be boiled at least 15 minutes immediately before consumption to ensure destruction of potential botulinum toxin. Foodborne Infection Foodborne infection requires the consumption of living organisms (figure 32.8). Thorough cooking of food immediately before consumption will kill bacteria, thereby preventing foodborne infection. Salmonella and Campylobacter species are commonly associated with poultry products. Some

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outbreaks of E. coli O157:H7 have been traced to undercooked contaminated hamburger patties and produce contaminated with manure.

32.5 Food Preservation Food spoilage can be eliminated or delayed by destroying microorganisms or altering conditions to inhibit their growth. Methods used to preserve foods include canning, pasteurization, cooking, freezing, refrigeration, reducing the aw, lowering the pH, adding antimicrobial chemicals, and irradiation.

REVIEW QUESTIONS Short Answer 1. 2. 3. 4. 5. 6. 7. 8. 9. 10.

What is the purpose of rennin in cheese-making? What causes the bluish-green veins to form in blue cheese? What causes the holes to form in Swiss cheese? What is the difference between traditional acidophilus milk and sweet acidophilus milk? What is the purpose of the mashing step in beer-making? Explain how Alcaligenes species cause “ropiness” in raw milk. Explain the significance of Aspergillus flavus growing in grain products. Explain the typical sequence of events that lead to botulism. Explain the typical sequence of events that lead to staphylococcal food poisoning. How does canning differ from pasteurization?

Multiple Choice 1. Benzoic acid is an antimicrobial chemical naturally found in which of the following foods? a) Apples b) Cranberries c) Eggs d) Milk e) Yogurt 2. The aw of a food product reflects which of the following? a) Acidity of the food b) Presence of antimicrobial constituents such as lysozyme c) Amount of water available d) Storage atmosphere e) Nutrient content 3. What is a generally minimum pH for growth and toxin production by Clostridium botulinum and other foodborne pathogens? a) 8.5 b) 7.0 c) 6.5 d) 4.5 e) 2.0 4. Which of the following organisms cause foodborne intoxication? a) E. coli O157:H7 b) Campylobacter species c) Lactobacillus species d) Salmonella species e) Staphylococcus aureus 5. Which group of organisms most commonly spoils breads, fruits, and dried foods? a) Acetobacter b) Fungi c) Lactic acid bacteria d) Pseudomonas e) Saccharomyces 6. Canned pickles require less stringent heat processing than canned beans, because pickles a) contain fewer nutrients. b) are more acidic.

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7.

8. 9.

10.

c) have a lower aw. d) contain antimicrobial chemicals. e) are less likely to be contaminated with endospores. Which of the following genera is used in bread, wine, and beer production? a) Lactobacillus b) Pseudomonas c) Saccharomyces d) Streptococcus e) Staphylococcus Most spoilage bacteria cannot grow below an aw of a) 0.3. b) 0.5. c) 0.7. d) 0.9. e) 1.0. Which of the following is often added to wine to inhibit growth of the natural microbial population of grapes? a) Benzoic acid b) Lactic acid c) Carbon dioxide d) Sulfur dioxide e) Oxygen In the brewing process, the sugar and nutrient extract obtained by soaking germinated grain in warm water is called a) baker’s yeast. b) hops. c) malt. d) must. e) wort.

Applications 1. A small cheese-manufacturing company in Wisconsin is looking for ways to reduce the costs of disposing of whey, a cheese byproduct. As a food microbiologist working at the company, what would you suggest that the company do with the thousands of liters of whey being produced per month so the company can actually profit from it? 2. A microbiologist is troubleshooting a batch of home-brewed ale that did not ferment properly. She noticed that the alcohol content was only 2%, well below the desired level. Microscopic examination showed numerous yeast cells. Chemical analysis showed low levels of sugar, high levels of CO2, and large amounts of protein in the liquid. What did the microbiologist conclude as the probable cause of the beer not coming out properly?

Critical Thinking 1. It has been argued that the nature of the growth of fungi in Roquefort cheese, indicated by the appearance of bluish-green veins, is evidence that these fungi require oxygen for growth. How does this evidence lead to the conclusion? 2. In the production of sauerkraut, a natural succession of lactic acid bacteria is observed growing in the product. What causes the succession? What does this tell you about the optimal growth conditions of the different species of lactic acid bacteria?

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Microbial Mathematics Because prokaryotes are very tiny and can multiply to very large numbers of cells in short time periods, convenient and simple ways are used to designate their numbers without resorting to many zeros before or after the number. In the study of microbiology, it is important to gain an understanding of the metric system, which is used in scientific measurements. The basic unit of measure is the meter, which is equal to about 39 inches. All other units are fractions of a meter: 1 decimeter is one tenth ⫽ 0.1 meter 1 centimeter is one hundredth ⫽ 0.01 meter 1 millimeter is one thousandth ⫽ 0.001 meter Because prokaryotes are much smaller than a millimeter, even smaller units of measure are used. A millionth of a meter is a micrometer ⫽ 0.000001 meter, and is abbreviated μm. This is the most frequently used size measurement in microbiology, since bacteria are in this size range. For comparison, a human hair is about 75 μm wide. Since it is inconvenient to write so many zeros in front of the 1, an easier way of denoting the same number is through the use of superscript, or exponential, numbers (exponents). One hundred dollars can be written 102 dollars. The 10 is called the base number and the 2 is the exponent. Conversely, one hundredth of a dollar is 10:2 dollars; thus the exponent is negative. The base most commonly used in biology is 10 (which is designated as log10). The above information can be summarized as follows: 1 millimeter ⫽ 1 mm ⫽ 0.001 meter ⫽ 10⫺3 meter 1 micrometer ⫽ 1 μm ⫽ 0.000001 meter ⫽ 10⫺6 meter 1 nanometer ⫽ 1 nm ⫽ 0.000000001 meter ⫽ 10⫺9 meter

1 milligram ⫽ 1 mg ⫽ 0.001 gram ⫽ 10⫺3 g 1 microgram ⫽ 1 μg ⫽ 0.000001 gram ⫽ 10⫺6 g 1 nanogram ⫽ 1 ng ⫽ 0.000000001 gram ⫽ 10⫺9 g 1 picogram ⫽ 1 pg ⫽ 0.000000000001 gram ⫽ 10⫺12 g Note that the number of zeros before the 1 is one less than the exponent. The value of the number is obtained by multiplying the base by itself the number of times indicated by the exponent. Thus, 101 ⫽ 10 ⫻ 1 ⫽ 10 102 ⫽ 10 ⫻ 10 ⫽ 100 103 ⫽ 10 ⫻ 10 ⫻ 10 ⫽ 1,000 When the exponent is negative, the base and exponent are divided into 1. For example, 10⫺2 ⫽ 1/10 ⫻ 1/10 ⫽ 1/100 ⫽ 0.01 When multiplying numbers having exponents to the same base, the exponents are added. For example, 103 ⫻ 102 ⫽ 105 (not 106) When dividing numbers having exponents to the same base, the exponents are subtracted. For example, 105 ⫼ 102 ⫽ 103 In both cases, only if the bases are the same can the exponents be added or subtracted.

The same prefix designations can be used for weights. The basic unit of weight is the gram, abbreviated g. Approximately 450 grams are in a pound.

A-1

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Microbial Teminology Singular and Plurals Singular

Plural

Singular

Plural

alga ameba bacillus bacterium cilium clostridium coccus conidium datum diagnosis fimbria flagellum focus

algae amebae bacilli bacteria cilia clostridia cocci conidia data diagnoses fimbriae flagella foci

fungus hydrolysis hypha inoculum medium mucosa mycelium mycosis phylum pilus nucleus septum synthesis

fungi hydrolyses hyphae inocula media mucosae mycelia mycoses phyla pili nuclei septa syntheses

Meanings of Prefixes and Suffixes Prefix or Suffix

Meaning

Example

a-, anaeranti-ase chlor-chrom-cide co-, com-, con-cyande-demendo-enterepierythroeuexoextraflav-gen

not, without air against enzyme green color causing death together blue down, from people, district within intestine upon red well, normal outside outside of yellow produce, originate

avirulent (lacking virulence), anaerobic (without air) aerobic antiseptic penicillinase chlorophyll metachromatic (staining differently with the same dye) germicide coenzyme pyocyanin (a blue bacterial pigment) dehydrate (remove water) epidemic endospore (spore within a cell) enteritis (inflammation of the intestine) epidermis erythocyte (red blood cell) eukaryotic (true nucleus) exoenzyme (enzyme that acts outside the cell that produced it) extracellular flavoprotein (a protein containing a yellow enzyme) antigen (a substance that induces a production of antibodies)

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Appendix II

Microbial Terminology

A-3

Prefix or Suffix

Meaning

Example

glycheterohomohydrhyperhypoiso-itis leukoly-, -lys, -lytmesometamicromillimitomonomultimycmyx-oid -ose -osis panparapathoperi-phag-phil -phot-phyll pleopolypost pyo-stasym-, synthermotrans-trich-troph toxzym-

sweet other common, same water excessive, above under same, equal inflammation white loosen; dissolve middle changed small; one-millionth part one-thousandth part thread single many fungus mucus resembling a sugar disease of all beside disease around eat like, having affinity for light leaf more many after pus stop together heat through, across hair nourishment poison ferment

glycemia (the presence of sugar in the blood) heterotroph (organism that obtains carbon from organic compounds) homologous (similar in structure or origin) dehydrate hypersensitive hypotonic (having low osmotic pressure) isotonic (having the same osmotic pressure) appendicitis, meningitis leukocyte (white blood cell) bacteriolysis (dissolution of bacteria) mesophilic (preferring moderate temperatures) metachromatic (staining differently with the same dye) microscopic millimeter (10 :3 meter) mitochondrion (small, rod-shaped or granular organelle) monotrichous (having a single flagellum) multinuclear (having many nuclei) mycotic (caused by fungus) myxomycete (slime mold) lymphoid (resembling lymphocytes) lactose (milk sugar) coccidioidomycosis (disease caused by Coccidioides) pandemic (widespread epidemic) parasite (an organism that feeds in and at expense of the host) pathogenic (producing disease) peritrichous (having flagella on all sides) phagocyte (a cell that ingests other cell substances) eosinophilic (staining with the dye eosin) photosynthesis chlorophyll (green leaf pigment) pleomorphic (occurring in more than one form) polymorphonuclear (having a many-shaped nucleus) postnatal (after birth) pyogenic (producing pus) bacteriostatic (inhibiting bacterial multiplication) symbiosis (life together) thermophilic (liking heat) transfusion monotrichous (having a single flagellum) autotroph (organism that obtains carbon from CO2) toxin enzyme

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Pronunciation Key for Bacterial, Fungal, Protozoan, and Viral Names A Acetobacter (a-see⬘-toe-back-ter) Achromobacter (a-krome⬘-oh-back-ter) Acinetobacter calcoaceticus (a-sin-et⬘-oh-back-ter kal-koh-ahsee⬘-ti-kus) Actinomyces israelii (ak-tin-oh-my⬘-seez iz-ray⬘-lee-ee) Actinomycetes (ak-tin-oh-my⬘-seats) Adenovirus (ad⬘-eh-no-vi-rus) Agrobacterium tumefaciens (ag-rho-bak-teer⬘-ee-um too-mehfaysh⬘-ee-enz) Alcaligenes (al-ka-li⬘-jen-ease) Amoeba (ah-mee⬘-bah) Arbovirus (are⬘-bow-vi-rus) Aspergillus niger (ass-per-jill⬘-us nye⬘-jer) Aspergillus oryzae (ass-per-jill⬘-us or-eye⬘-zee) Azolla (aye-zol⬘-lah) Azotobacter (ay-zoh⬘-toe-back-ter)

Clostridium botulinum (kloss-trid⬘-ee-um bot-you-line⬘-um) Clostridium difficile (kloss-trid⬘-ee-um dif⬘-fi-seal) Clostridium perfringens (kloss-trid⬘-ee-um per-frin⬘-gens) Clostridium tetani (kloss-trid⬘-ee-um tet⬘-an-ee) Coccidioides immitis (cock-sid-ee-oid⬘-eez im⬘-mi-tiss) Coronavirus (kor-oh⬘-nah-vi-rus) Corynebacterium diphtheriae (koh-ryne⬘-nee-bak-teer-ee-um diftheer⬘-ee-ee) Coxsackievirus (cock-sack-ee⬘-vi-rus) Cryptococcus neoformans (krip-toe-cock⬘-us knee-oh-for⬘-manz) Cytophaga (sigh-taw⬘-fa-ga)

D Desulfovibrio (dee-sul-foh-vib⬘-ree-oh)

E B Bacillus anthracis (bah-sill⬘-us an-thra⬘-siss) Bacillus cereus (bah-sill⬘-us seer⬘-ee-us) Bacillus coagulans (bah-sill⬘-us coh-ag⬘-you-lans) Bacillus fastidiosus (bah-sill⬘-us fas-tid-ee-oh⬘-sus) Bacillus stearothermophilus (bah-sill⬘-us steer-oh-ther-maw⬘-fill-us) Bacillus subtilis (bah-sill⬘-us sut⬘-ill-us) Bacillus thuringiensis (bah-sill⬘-us thur⬘-in-jee-en-sis) Bacteroides (back⬘-ter-oid⬘-eez) Baculovirus (back⬘-you-low-vi-rus) Beggiatoa (beg-gee-ah-toe⬘-ah) Beijerinckia (by-yer-ink⬘-ee-ah) Bordetella pertussis (bor-deh-tell⬘-ah per-tuss⬘-iss) Borrelia burgdorferi (bor-real⬘-ee-ah berg-dor⬘-fir-ee) Bradyrhizobium (bray-dee-rye-zoe⬘-bee-um) Branhamella (bran-ham-el⬘-lah) Brucella abortus (bru-sell⬘-ah ah-bore⬘-tus)

Eikenella corrodens (eye-keh-nell⬘-ah kor-roh⬘-denz) Entamoeba histolytica (en-ta-mee⬘-bah his-toh-lit⬘-ik-ah) Enterobacter (en⬘-ter-oh-back-ter) Enterococcus faecalis (en⬘-ter-oh-kock⬘-us fee-ka⬘-liss) Enterovirus (en⬘-ter-oh-vi-rus) Epidermophyton (eh-pee-der⬘-moh-fy-ton) Escherichia coli (esh-er-ee⬘-she-ah koh⬘-lee)

F Filobasidiella neoformans (fee-loh-bah-si-dee-ell⬘-ah knee-ohfor⬘-manz) Flavivirus (flay⬘-vih-vi-rus) Flavobacterium (flay-vo-back-teer⬘-ee-um) Francisella tularensis (fran-siss-sell⬘-ah tu-lah-ren⬘-siss) Frankia (frank⬘-ee-ah) Fusobacterium (fu⬘-zoh-back-teer-ee-um)

C

G

Campylobacter jejuni (kam⬘-peh-low-back-ter je-june⬘-ee) Candida albicans (kan⬘-did-ah al⬘-bi-kanz) Caulobacter (caw⬘-loh-back-ter) Ceratocystis ulmi (see⬘-rah-toe-sis-tis ul⬘-mee) Chlamydia trachomatis (klah-mid⬘-ee-ah trah-ko-ma⬘-tiss) Claviceps purpurea (kla⬘-vi-seps purr-purr⬘-ee-ah) Clostridium acetobutylicum (kloss-trid⬘-ee-um a-seat-tow-bu-till⬘-i-kum)

Gallionella (gal-ee-oh-nell⬘-ah) Gardnerella vaginalis (gard-nee-rel⬘-lah va-jin-al⬘-is) Giardia intestinalis (jee-are⬘-dee-ah in-test⬘-tin-al-is) Giardia lamblia (jee-are⬘-dee-ah lamb⬘-lee-ah) Gluconobacter (glue-kon-oh-back⬘-ter) Gonyaulax (gon-ee-ow⬘-lax) Gymnodinium breve (jim-no-din⬘-i-um brev-eh)

A-4

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Appendix III Pronunciation Key for Bacterial, Fungal, Protozoan, and Viral Names

A-5

H

P

Haemophilus influenzae (hee-moff⬘-ill-us in-flew-en⬘-zee) Helicobacter pylori (he⬘-lih-koh-back-ter pie-lore⬘-ee) Hepadnavirus (hep-ad⬘-nah-vi-rus) Hepatitis virus (hep-ah-ti⬘-tis vi-rus) Herpes simplex (her⬘-peas sim⬘-plex) Herpes zoster (her⬘-peas zoh⬘-ster) Histoplasma capsulatum (his-toh-plaz⬘-mah cap-su-lah⬘-tum) Hyphomicrobium (high-foh-my-krow⬘-bee-um)

Papillomavirus (pap-il-oh⬘-ma-vi-rus) Parainfluenza virus (par-ah-in-flew-en⬘-zah vi-rus) Paramecium (pair⬘-ah-mee-see-um) Paramyxovirus (par-ah-mix⬘-oh-vi-rus) Parvovirus (par⬘-vo-vi-rus) Pasteurella multocida (pass-ture-ell⬘-ah mul-toe-sid⬘-ah) Pediococcus soyae (ped-ih-oh-ko⬘-kus soy⬘-ee) Penicillium camemberti (pen-eh-sill⬘-ee-um cam-em-bare⬘-tee) Penicillium roqueforti (pen-eh-sill⬘-ee-um rok-e-for⬘-tee) Peptostreptococcus (pep⬘-to-strep-to-ko-kus) Phytophythora infestans (fy⬘-toe-fy-thor-ah in-fes⬘-tanz) Picornavirus (pi-kor⬘-na-vi-rus) Plasmodium falciparum (plaz-moh⬘-dee-um fall-sip⬘-air-um) Plasmodium malariae (plaz-moh⬘-dee-um ma-lair⬘-ee-ee) Plasmodium ovale (plaz-moh⬘-dee-um oh-vah⬘-lee) Plasmodium vivax (plaz-moh⬘-dee-um vye⬘-vax) Pneumocystis carinii (new-mo-sis⬘-tis car⬘-i⬘-nee-ee) Poliovirus (poe⬘-lee-oh-vi-rus) Polyoma virus (po-lee-oh⬘-mah vi-rus) Propionibacterium acnes (proh-pee-ah-nee-bak-teer⬘-ee-um ak⬘-neez) Propionibacterium shermanii (proh-pee-ah-nee-bak-teer⬘-ee-um sher-man⬘-ee-ee) Proteus mirabilis (proh⬘-tee-us mee-rab⬘-il-us) Pseudomonas aeruginosa (sue-dough-moan⬘-ass aye-rue-gin-o⬘-sa)

I Influenza virus (in-flew-en⬘-za vi-rus)

K Klebsiella pneumoniae (kleb-see-ell⬘-ah new-moan⬘-ee-ee)

L Lactobacillus brevis (lack-toe-ba-sil⬘-lus bre⬘-vis) Lactobacillus bulgaricus (lack-toe-ba-sil⬘-lus bull-gair⬘-i-kus) Lactobacillus casei (lack-toe-ba-sil⬘-us kay⬘-see-ee) Lactobacillus plantarum (lack-toe-ba-sil⬘-us plan-tar⬘-um) Lactobacillus thermophilus (lack-toe-ba-sil⬘-us ther-mo⬘-fil-us) Lactococcus lactis (lack-toe-kock⬘-us lak⬘-tiss) Legionella pneumophila (lee-jon-ell⬘-ah new-moh⬘-fill-ah) Leptospira interrogans (lep-toe-spire⬘-ah in-ter-roh⬘-ganz) Leuconostoc citrovorum (lew-kow-nos⬘-tok sit-ro-vor⬘-um) Listeria monocytogenes (lis-tear⬘-ee-ah mon⬘-oh-sigh-tojen⬘-eze)

M Malassezia (mal-as-seez⬘-e-ah) Methanobacterium (me-than⬘-oh-bak-teer-ee-um) Methanococcus (me-than-oh-ko⬘-kus) Microsporum (my-kroh-spore⬘-um) Mobiluncus (moh-bi-lun⬘-kus) Moraxella catarrhalis (more-ax-ell⬘-ah kah-tah-rah⬘-liss) Moraxella lacunata (more-ax-ell⬘-ah lak-u-nah⬘-tah) Mucor (mu⬘-kor) Mycobacterium leprae (my-koh-bak-teer⬘-ee-um lep-ree) Mycobacterium tuberculosis (my-koh-bak-teer⬘-ee-um too-berkew-loh⬘-siss) Mycoplasma pneumoniae (my-koh-plaz⬘-mah newmoan⬘-ee-ee)

N Neisseria gonorrhoeae (nye-seer⬘-ee-ah gahn-oh-ree⬘-ee) Neisseria meningitidis (nye-seer⬘-ee-ah men-in-jit⬘-id-iss) Neurospora sitophila (new-rah⬘-spor-ah sit-oh-phil⬘-ah)

O Orthomyxovirus (or-thoe-mix⬘-oh-vi-rus) Oscillatoria (os-sil-la-tor⬘-ee-ah)

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R Rabies virus (ray⬘-bees vi-rus) Retrovirus (re⬘-trow-vi-rus) Rhabdovirus (rab⬘-doh-vi-rus) Rhinovirus (rye⬘-no-vi-rus) Rhizobium (rye-zoh⬘-bee-um) Rhizopus nigricans (rise⬘-oh-pus nye⬘-gri-kanz) Rhizopus stolon (rise⬘-oh-pus stoh⬘-lon) Rhodococcus (roh-doh-koh⬘-kus) Rickettsia rickettsii (rik-kett⬘-see-ah rik-kett⬘-see-ee) Rotavirus (row⬘-tah-vi-rus) Rubella virus (rue-bell⬘-ah vi-rus) Rubeola virus (rue-bee-oh⬘-la vi-rus)

S Saccharomyces carlsbergensis (sack-ah-row-my⬘-sees karls-bergen⬘-siss) Saccharomyces cerevisiae (sack-ah-row-my⬘-sees sara-vis⬘-ee-ee) Saccharomyces rouxii (sack-ah-row-my⬘-sees roos⬘-ee-ee) Salmonella enteritidis (sall-moh-nell⬘-ah en-ter-it⬘-id-iss) Salmonella typhi (sall-moh-nell⬘-ah tye⬘-fee) Salmonella typhimurium (sall-moh-nell⬘-ah tye-fe-mur⬘-ee-um) Serratia marcescens (ser-ray⬘-sha mar-sess-sens) Shigella dysenteriae (shig-ell⬘-ah diss-en-tair⬘-ee-ee) Spirillum minus (spy-rill⬘-um my⬘-nus) Sporothrix schenckii (spore⬘-oh-thrix shenk-ee-ee) Staphylococcus aureus (staff-ill-oh-kok⬘-us aw⬘-ree-us) Staphylococcus epidermidis (staff-ill-oh-kok⬘-us epi-der⬘-mid-iss) Streptobacillus moniliformis (strep-tow-bah-sill⬘-us mon-ill-i-form⬘-is) Streptococcus agalactiae (strep-toe-kock⬘-us a-ga-lac⬘-tee-ee) Streptococcus cremoris (strep-toe-kock⬘-us kre-more⬘-iss) Streptococcus mutans (strep-toe-kock⬘-us mew⬘-tanz)

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A-6

Appendix III Pronunciation Key for Bacterial, Fungal, Protozoan, and Viral Names

Streptococcus pneumoniae (strep-toe-kock⬘-us new-moan⬘-ee-ee) Streptococcus pyogenes (strep-toe-kock⬘-us pie-ah-gen-ease) Streptococcus salivarius (strep-toe-kock⬘-us sal-ih-vair⬘-ee-us) Streptococcus sanguis (strep-toe-kock⬘-us san⬘-gwis) Streptococcus thermophilis (strep-toe-kock⬘-us ther-moh⬘-fill-us) Streptomyces griseus (strep-toe-my⬘-seez gree⬘-see-us)

V

T

Y

Thiobacillus (thigh-oh-bah-sill⬘-us) Torulopsis (tore-you-lop⬘-siss) Treponema pallidum (tre-poh-nee⬘-mah pal⬘-ih-dum) Trichomonas vaginalis (trick-oh-moan⬘-as vag-in-al⬘-iss) Trichophyton (trick-oh-phye⬘-ton) Trypanosoma brucei (tri-pan⬘-oh-soh-mah bru⬘-see-ee)

Yersinia enterocolitica (yer-sin⬘-ee-ah en-ter-oh-koh-lih⬘-tih-kah) Yersinia pestis (yer-sin⬘-ee-ah pess⬘-tiss)

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Varicella-zoster virus (var-ih-sell⬘-ah zoh⬘-ster vi-rus) Veillonella (veye-yon-ell⬘-ah) Vibrio anguillarum (vib⬘-ree-oh an-gwil-air⬘-um) Vibrio cholerae (vib⬘-ree-oh kahl⬘-er-ee)

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Metabolic Pathways FIGURE IV.1 The Entner-Doudoroff Pathway H

Glucose 6phosphate

HO

CH2O P O

H

H OH

H

H

OH

OH

NADP

+

Glucose 6phosphate dehydrogenase NADPH

6-phosphogluconod-lactone

H HO

CH2O P O H OH

H

H

OH

O

H2O

Lactonase

COO-

6-phosphogluconate

H

C

OH

HO

C

H

H

C

OH

H

C

OH

CH2O P 6-phosphogluconate dehydrase

H2O COOC

O

CH2 2-keto-3-deoxy-6phosphogluconate

H

C

OH

H

C

OH

CH2O P KDPG aldolase Glyceraldehyde H 3-phosphate

CHO

COO-

C

C

OH

CH2O P

O

CH3 Pyruvate

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A-8

Appendix IV

Metabolic Pathways

H HO

Prokaryotes

Eukaryotes

CH2OH O

CH2OH O

H

H OH

H

H

OH

H

OH

HO

H OH

H

H

OH

Glucose

H OH

Glucose PEP Pyruvate

ATP Hexokinase ADP

Group transport enzymes

H HO

CH2O P O OH

H

H

OH

H

Glucose 6phosphate

OH

Phosphohexose isomerase O

P OH2C H

H

CH2OH

HO

OH

OH

Fructose 6phosphate

H

ATP

Phosphofructokinase

ADP O

P OH2C H

CH2O P

H

OH

OH

H

Fructose 1,6bisphosphate

OH

Fructose bisphosphate aldolase

CH2O P

CHO Glyceraldehyde 3-phosphate

H

C

C

OH

O

Dihydroxyacetone phosphate

CH2OH

CH2O P

Pi NAD NADH + H

Glyceraldehyde3-phosphate dehydrogenase

+

+

COO P H

C

OH

CH2O P 1,3-bisphosphoglycerate

Phosphoglycerate kinase

COO-

COO-

ADP ATP H

C

OH

Phosphoglycerate mutase

CH2O P 3-phosphoglycerate

COOC

O

CH3

FIGURE IV.2 The Embden-Meyerhof-Parnas Pathway Commonly called glycolysis or the glycolytic pathway.

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ATP

ADP

Pyruvate kinase

H

C

O P

2-phosphoglycerate

CH2OH

Enolase H2O COOC

O P

CH2

Pyruvate Phosphoenolpyruvate

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Appendix IV COO-

H HO

CH2O P O H OH

H

H OH Glucose 6phosphate

CH2O P O

+

H OH

NADP NADPH

Glucose 6phosphate dehydrogenase

H

H OH

HO

H

H2O O

H OH 6-phosphogluconod-lactone 6-phosphogluconate dehydrogenase

H

C

OH

HO

C

H

H

C

OH

H

C

OH

Metabolic Pathways

A-9

FIGURE IV.3 The Pentose Phosphate Pathway

CH2O P 6-phosphogluconate + NADP NADPH CO2 CH2OH

Phosphopentose isomerase

C

O

H

C

OH

H

C

OH

Phosphopentose epimerase

Phosphopentose epimerase

CH2O P

Phosphoglucoisomerase

CHO H

C

OH

H

C

OH

H

C

OH

CH2OH

Ribulose 5phosphate

C

O

HO

C

H

H

C

OH

CH2O P Ribose 5phosphate

H

CH2O P Transketolase

Xylulose 5phosphate

CHO

CH2OH

C

C

O

HO

C

H

H

C

OH

H

C

OH

H

C

OH

OH

CH2O P Glyceraldehyde 3-phosphate

Transaldolase CH2OH C

O

HO

C

H

H

C

OH

H

C

OH

CH2O P Sedoheptulose 7-phosphate

CH2OH

CHO

O

H

C

OH

HO

C

H

H

C

OH

H

C

OH

CH2O P Fructose 6phosphate

C

CH2O P

CH2O P Erythrose 4phosphate CH2OH C

O

HO

C

H

H

C

OH

H

C

OH

Xylulose 5phosphate Transketolase CHO H

C

OH

CH2O P Glyceraldehyde 3-phosphate

CH2O P Fructose 6phosphate

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A-10

Appendix IV

Metabolic Pathways O CH3

C S Acetyl

CoA CoA

O Malate dehydrogenase

COO-

C CH2 +

HO

NADH + H

CH

COO-

CH2

COO-

NAD

+

Citrate synthase

COO-

Oxaloacetate

SH

CoA H2O

COO-

CH2

+

HO

COO-

C

CH2 COOCitrate

L-Malate

Aconitase 2+ Fe

Fumarase H2O

H2O

H

C

CH2

COO-

C

-OOC

C H Fumarate

COOCOO-

CH COOCis-aconitate

FADH2 Succinate dehydrogenase

H2O Aconitase

FAD

CH2

Fe

COO-

CH2 COOSuccinate GTP HO CoA

2+

SH SuccinylCoA synthase

CH2

COO-

CH

COO-

CH COOIsocitrate

GDP + Pi NAD CH2

+

COO-

CH2

NADH + H NADH + H

O C S CoA Succinyl-CoA

NAD

a-ketoglutarate dehydrogenase complex CoA

+

+

CO2

+

CH2

COO-

CH2

SH CO2

Isocitrate dehydrogenase

O C COOa-ketoglutarate

Mn

2+

FIGURE IV.4 The Tricarboxylic Acid Cycle (TCA Cycle) Also referred to as the Krebs cycle or the citric acid cycle.

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Answers to Multiple Choice Questions Chapter 1

Chapter 5

Chapter 9

Chapter 13

Chapter 17

1. 2. 3. 4. 5. 6. 7. 8. 9. 10.

1. 2. 3. 4. 5. 6. 7. 8. 9. 10.

1. 2. 3. 4. 5. 6. 7. 8. 9. 10.

1. 2. 3. 4. 5. 6. 7. 8. 9. 10.

1. 2. 3. 4. 5. 6. 7. 8. 9. 10.

D A B C B B C A E A

C D A B B C E D C A

C C E B B C B B B D

C B E A C E D C A A

C A D D A C C D D A

Chapter 2

Chapter 6

Chapter 10

Chapter 14

Chapter 18

1. 2. 3. 4. 5. 6. 7. 8. 9. 10.

1. 2. 3. 4. 5. 6. 7. 8. 9. 10.

1. 2. 3. 4. 5. 6. 7. 8. 9. 10.

1. 2. 3. 4. 5. 6. 7. 8. 9. 10.

1. 2. 3. 4. 5. 6. 7. 8. 9. 10.

C A E A B C B D E A

D C D E B A D D D E

E B E B D B C D B E

D A B B D B A D E A

A E A D E C A C A A

Chapter 3

Chapter 7

Chapter 11

Chapter 15

Chapter 19

1. 2. 3. 4. 5. 6. 7. 8. 9. 10.

1. 2. 3. 4. 5. 6. 7. 8. 9. 10.

1. 2. 3. 4. 5. 6. 7. 8. 9. 10.

1. 2. 3. 4. 5. 6. 7. 8. 9. 10.

1. 2. 3. 4. 5. 6. 7. 8. 9. 10.

A A E B B C E C D A

B A A A C B B C D D

E B E B D A D B C D

B E A B A E A C D C

D C E D A D C A C C

Chapter 4

Chapter 8

Chapter 12

Chapter 16

Chapter 20

1. 2. 3. 4. 5. 6. 7. 8. 9. 10.

1. 2. 3. 4. 5. 6. 7. 8. 9. 10.

1. 2. 3. 4. 5. 6. 7. 8. 9. 10.

1. 2. 3. 4. 5. 6. 7. 8. 9. 10.

1. 2. 3. 4. 5. 6. 7. 8. 9. 10.

B B C B D B E A D B

C A D A B D A B A B

C A B A, C A B A, B, E A C A, B

E E D D B D D A B D

A B A B E B B E C E

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A-12

Appendix V Answers to Multiple Choice Questions

Chapter 21

Chapter 24

Chapter 27

Chapter 30

1. 2. 3. 4. 5. 6. 7. 8. 9. 10.

1. 2. 3. 4. 5. 6. 7. 8. 9. 10.

1. 2. 3. 4. 5. 6. 7. 8. 9. 10.

1. 2. 3. 4. 5. 6. 7. 8. 9. 10.

D C A B A B D D A C

B E C A A C D C E B

B C C D C E A D A B

A A C D A D C C B A

Chapter 22

Chapter 25

Chapter 28

Chapter 31

1. 2. 3. 4. 5. 6. 7. 8. 9. 10.

1. 2. 3. 4. 5. 6. 7. 8. 9. 10.

1. 2. 3. 4. 5. 6. 7. 8. 9. 10.

1. 2. 3. 4. 5. 6. 7. 8. 9. 10.

E C E A B A A C D D

C A B D A D C D C E

E A C E C C C A A E

B B A A C E C C B E

Chapter 23

Chapter 26

Chapter 29

Chapter 32

1. 2. 3. 4. 5. 6. 7. 8. 9. 10.

1. 2. 3. 4. 5. 6. 7. 8. 9. 10.

1. 2. 3. 4. 5. 6. 7. 8. 9. 10.

1. 2. 3. 4. 5. 6. 7. 8. 9. 10.

E E A E B A C A D D

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D D C B C B A B C C

D D A B C A E A E E

B C D E B B C D D E

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ABC transport systems A type of active transport system that requires ATP as an energy source (ATP Binding-Cassette). abscess A localized collection of pus within a tissue. A-B toxin Exotoxin composed of an active subunit (A-subunit) and a binding subunit (B-subunit). acellular Not composed of cells, therefore not living. acid-fast staining A procedure used to stain certain microorganisms, particularly members of the genus Mycobacterium, that do not readily take up dyes. acidic amino acids Amino acids with more carboxyl (JCOOH) than amino (JNH2) groups. acidophiles Organisms that grow optimally at a pH below 5.5. acquired resistance Development of antimicrobial resistance in a previously sensitive organism; occurs through spontaneous mutation or acquisition of new genetic information. actin Protein that makes up actin filaments of eukaryotic cells; it can rapidly assemble and subsequently disassemble to cause motion. actin filaments Cytoskeletal structures of eukaryotic cells that enable the cell cytoplasm to move. actinomycetes Filamentous bacteria; many are valuable in the production of antibiotics. activated macrophages Macrophages stimulated by cytokines to enlarge and become metabolically active, with greatly increased capability to kill and degrade intracellular organisms and materials. activated sludge method A method of sewage treatment in which wastes are degraded by complex populations of aerobic microorganisms. activated T cell T cell activated by exposure to antigen in conjunction with required accessory signals. activation energy Initial energy required to break a chemical bond. activator-binding site Sequence of DNA that precedes an ineffective promoter; binding of an activator to this site enhances the ability of RNA polymerase to initiate transcription at that promoter. active immunity Protective immunity produced by an individual in response to an antigenic stimulus. active site Site on an enzyme molecule to which substrate binds; also known as the catalytic site. active transport Energy-consuming process by which molecules are carried across cell boundaries; can accumulate compounds against a concentration gradient. acute infections Infections in which the symptoms and signs have a rapid onset and are usually severe, often with fever, but short-lived. acute inflammation Short-term inflammatory response, marked by a prevalence of neutrophils. acylated homoserine lactone (AHL) Small signal molecules that can move freely in and out of cells; provides cells with a mechanism of assessing cell density (quorum sensing).

adaptive immunity Protection provided by host defenses that develop throughout life; involves B cells and T cells. ADCC (antibody-dependent cellular cytotoxicity) Killing of target cells by macrophages, granulocytes, or natural killer cells that contact the target via their Fc receptors binding to Fc of antibodies attached to the target. adenosine diphosphate (ADP) The acceptor of free energy in a cell; that energy is used to add an inorganic phosphate (Pi) to ADP, generating ATP. adenosine triphosphate (ATP) The energy currency of a cell, serving as the ready and immediate donor of free energy. adherence A necessary first step in colonization and infection, in which the pathogen attaches to host cells to avoid being removed from the body. adhesin Component of a microorganism that is used to bind to surfaces. adhesion molecule Molecule on the surface of a cell that allows that cell to adhere to other cells. adjuvant Substance that increases the immune response to antigen. ADP Abbreviation for adenosine diphosphate. adsorption Attachment of one substance to the surface of another. aerobic respiration Metabolic process in which electrons are transferred from the electron transport chain to molecular oxygen (O2). aerosol Material dispersed into the air as a fine mist. aerotaxis Movement toward or away from molecular oxygen. aerotolerant anaerobes Organisms that can grow in the presence of O2 but never use it as a terminal electron acceptor; also called obligate fermenters. affinity maturation The “fine-tuning’’ of the fit of an antibody molecule for an antigen; it is due to mutations that occur as activated B cells multiply. aflatoxin Potent toxin made by Aspergillus flavus. agar Polysaccharide extracted from marine algae; used to solidify microbiological media. agarose Highly purified form of agar used in gel electrophoresis. agar slant Microbiological medium that has been solidified with agar and stored in a tube that was held at a shallow angle as the medium solidified, creating a larger surface area. agglutination Clumping together of cells or particles. AIDS Acquired immunodeficiency syndrome. AIDS-related complex (ARC) A group of symptoms–fever, fatigue, diarrhea, and weight loss–that herald the onset of AIDS. alga (pl. algae) A primitive photosynthetic eukaryotic organism. alkalophiles Organisms that grow optimally at a pH above 8.5. alkylating agent Chemical that adds alkyl groups (short chains of carbon atoms) to purines and pyrimidines; promotes mutations.

alkyl group Short chain or single carbon atom such as a methyl group (JCH3). allele One form of a gene. allergen Antigen that causes an allergy. allergic rhinitis Hay fever; sneezing, runny nose, teary eyes resulting from exposure of a sensitized person to inhaled antigen; an IgE-mediated allergic reaction. allergy Hypersensitivity, especially of the IgEmediated type. allograft Organ or tissue graft transplanted between genetically nonidentical members of the same species. allosteric enzyme An enzyme that contains a site— the allosteric site—to which a small molecule can bind and change enzyme activity. alpha (a) hemolysis Type of hemolysis observed on blood agar, characterized by a zone of greenish clearing around the colonies. alternative pathway Pathway of complement activation initiated by the binding of a complement protein (C3b) to cell surfaces. amalgam Mixture of mercury with other metals to form a paste that hardens; used to fill cavities in teeth. amino acids Subunits of a protein molecule. aminoglycosides Group of antimicrobial medications; they interfere with protein synthesis. amino terminal (or N terminal) The end of the protein molecule that has an unbonded JNH2 group. ammonification The decomposition process that converts organic nitrogen into ammonia (NH3). amphibolic pathways Metabolic pathways that play roles in both catabolism and anabolism. amylases Enzymes that digest starches. anabolism Cellular processes that use the energy stored in ATP to synthesize and assemble subunits such as amino acids; synonymous with biosynthesis. anaerobic Without molecular oxygen (O2). anaerobic respiration Metabolic process in which electrons are transferred from the electron transport chain to a terminal electron acceptor other than O2. analytical study An epidemiological study done to identify specific risk factors associated with developing a certain disease. anamnestic response (See secondary response.) anaphylaxis Allergic reaction caused by IgE; generalized hypersensitive reaction to an allergen that can cause a profound drop in blood pressure. anaplerotic reactions Chemical reactions that bypass certain steps of the central metabolic pathways; they are used to replenish some of the intermediates drawn off for biosynthesis. anion Negatively charged ion. anneal Form a double-stranded duplex from two complementary strands of DNA.

G-1

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G-2

GLOSSARY

anoxic Devoid of O2. anoxygenic phototrophs Photosynthetic bacteria that use hydrogen sulfide or organic compounds rather than water as a source of electrons for reducing power; they do not generate O2. antagonistic In antimicrobial therapy, a combination of antimicrobial medications in which the action of one interferes with the action of the other. antenna complex Complex in photosynthetic organisms composed of hundreds of lightgathering pigments; acts as a funnel, capturing light energy and transferring it to reaction-center chlorophyll. antibacterial drug Chemical used to treat bacterial infections. antibiogram Antibiotic susceptibility pattern; used to distinguish between different bacterial strains. antibiotic Chemical produced by certain molds and bacteria that kills or inhibits the growth of other microorganisms. antibiotic-associated colitis Intestinal disease caused by overgrowth of toxin-producing strains of Clostridium difficile; typically, occurs when a person is taking antimicrobial medications. antibody Immunoglobulin protein produced by the body in response to a substance; it reacts specifically with that substance. anticodon Sequence of three nucleotides in a tRNA molecule that is complementary to a particular codon in mRNA. antigen Molecule that reacts specifically with an antibody or immune lymphocyte. antigen-antibody complex Linked group of antibodies bound to antigen. antigen-binding sites Regions at the ends of the two arms of an antibody molecule that recognize a specific antigen; two identical antigen-binding sites are on each monomer of antibody. antigen-presenting cells (APCs) Cells such as B cells, macrophages, and dendritic cells that can present exogenous antigen to helper T cells. antigenic determinant Part of an antigen molecule that binds the specific antibody; an epitope. antigenic drift Slight changes that occur in the antigens of a virus; specific antibodies made in response to the antigen before the change occurred are only partially protective. antigenic shift Major changes that can occur in the antigens of a virus. antigenic variation Routine alteration by a microorganism in the characteristics of certain of its surface proteins. antigen presentation Process in which cells display antigen in the groove of MHC molecules for inspection by T cells. antimicrobial drug Chemical used to treat microbial infections; also called an antimicrobial. antiparallel Term used to describe opposing orientations of the two strands of DNA in the double helix; one strand is oriented in the 5⬘ to 3⬘ direction and its complement is oriented in the 3⬘ to 5⬘ direction. antisense strand Complement to the sense (or plus) strand of RNA; also called the minus (:) strand. antiseptic A disinfectant that is non-toxic enough to be used on skin. antiserum A preparation of serum containing protective antibodies. antitoxin An antibody preparation that protects against a given toxin.

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aplastic anemia Potentially lethal condition in which the body is unable to make blood cells. apoptosis Programmed cell death. arbovirus Arthropod-borne virus. One of a large group of RNA viruses carried by insects and mites that act as biological vectors. Archaea One of the two domains of prokaryotes; many archaea grow in extreme environments. arteriosclerosis Condition characterized by thickening and loss of elasticity of the walls of arteries; “hardening of the arteries.” arthropod Classification grouping of invertebrate animals that includes insects, ticks, lice, and mites. Arthus reaction Hypersensitivity reaction caused by immune complexes and neutrophils. artificial wetland method Method of sewage treatment in which sewage is channeled into successive ponds where both aerobic and anaerobic degradation occurs. artificially acquired immunity Active or passive immunity acquired through artificial means such as vaccination or administration of immune serum globulin. aseptic Free of microorganisms and viruses; sterile. aseptic technique Use of specific methods and sterile materials to exclude contaminating microorganisms from an environment. asexual Reproduction not preceded by the union of cells or exchange of DNA. A-site (or aminoacyl site) Site on the ribosome to which tRNAs enter to donate their amino acid; acceptor site. asthma Immediate respiratory allergy resulting from mediator release from mast cells in the lower airways. astrobiology Study of life in the universe. atomic force microscope Type of scanning probe microscope that has a tip mounted so it can bend in response to the slightest force between the tip and the sample. ATP Abbreviation for adenosine triphosphate. ATP synthase Protein complex that harvests the energy of a proton motive force to synthesize ATP. attack rate Proportional number of cases developing in a population exposed to an infectious agent. attenuated vaccine Vaccine composed of a weakened form of a disease-causing microorganism or virus that is generally unable to cause disease; the vaccine strain is able to replicate inside its host. autoantibodies Antibodies that bind to “self” proteins. autoclave Device employing steam under pressure to sterilize materials that are stable to heat and moisture. autoimmune disease Disease produced as a result of an immune reaction against one’s own tissues. autolyze To spontaneously disintegrate as a result of enzymes within the cell. autoradiography The use of film to detect a radioactive molecule. autotroph Organism that uses CO2 as its main source of carbon. auxotroph A microorganism that requires an organic growth factor. avirulent Lacking disease-causing attributes. aw Abbreviation for water activity. axial filaments Characteristic structure of motility found in spirochetes.

axon The long thin extension of a nerve cell. azoles Large family of chemically synthesized medications, some of which have antifungal activity.

bacillus (pl. bacilli) Cylindrical-shaped bacterium; also referred to as a rod. bacitracin Antimicrobial medication that inhibits cell wall biosynthesis by interfering with the transport of peptidoglycan precursors across the cytoplasmic membrane. bacteremia Bacterial cells circulating in the bloodstream. Bacteria One of the two domains of prokaryotes; all medically important prokaryotes are in the domain Bacteria. bactericidal Able to kill bacteria. bacteriochlorophyll Type of chlorophyll used by purple and green bacteria; absorbs wavelengths of light that penetrate to greater depths and are not used by other photosynthetic organisms. bacteriocins Proteins made by bacteria that kill certain other bacteria. bacteriophage A virus that infects bacteria; often abbreviated to phage. bacteriorhodopsin Pigment of some prokaryotes that absorbs energy from sunlight and uses it to expel protons from the cell, generating a proton gradient. bacteriostatic Able to inhibit the growth of bacteria. balanced pathogenicity Host parasite relationship in which the parasite persists in the host while causing minimal harm. basal body Structure that anchors the flagellum to the cell wall and cytoplasmic membrane. base Refers to the purine or pyrimidine ring structure found in nucleic acids. base analog Compound that resembles a purine or pyrimidine base closely enough to be incorporated into a nucleotide in place of a natural base; the resulting molecule can be incorporated into DNA. base-pairing The hydrogen bonding of adenine (A) to thymine (T) and cytosine (C) to guanine (G); occurs between two complementary strands of DNA. basement membrane Thin layer of fibrous material that underlies epithelial cells. basic amino acids Amino acids with more basic (JNH3⫹) groups than acid (JCOO⫺) groups. basophil Leukocyte with large dark-staining granules that contain histamine and other mediators of inflammation; receptors on cell surfaces bind monomers of IgE. B-cell receptor Membrane-bound derivative of the antibody that a B cell is programmed to make; it enables the B cell to recognize a specific antigen. B cells Lymphocytes programmed to produce antibody molecules. beta- ( b ) hemolysis Type of hemolysis observed on blood agar that is characterized by a clear zone around a colony. beta- ( b ) lactam drugs Group of antimicrobial medications that inhibit peptidoglycan synthesis and have a shared chemical structure called a b -lactam ring. bilayer membrane (or unit membrane) Double layer of phospholipid molecules that forms the major structure of the cytoplasmic (plasma) membrane.

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GLOSSARY bile Yellow-colored fluid produced by the liver that aids in the absorption of nutrients from the intestine. binary fission Asexual process of reproduction in which one cell divides to form daughter cells. binding protein Protein that functions in the ABC transport system; resides immediately outside of the cytoplasmic membrane to deliver a given molecule to a specific transport complex within the membrane. binomial system System of naming each species of organism with two Latin words that indicate the genus and species. biochemical oxygen demand (BOD) Measure of the amount of biologically degradable organic material in water. biocide Compound such as a disinfectant that is toxic to many forms of life, including microorganisms. biodiversity Diversity in the number of species inhabiting an ecosystem and their evenness of distribution. biofilm Polysaccharide-encased community of microorganisms. bioinformatics Developing and using computer technology to store, retrieve, and analyze nucleotide sequence data. bioleaching Conversion of metals to a soluble form due to the metabolic oxidation of insoluble metal sulfides by microorganisms. biological vector Organism that acts as a host for a pathogen before it is transmitted to another organism; the pathogen can multiply to high numbers within it. bioluminescence Biological production of light. biomass Total weight of all organisms in any particular environment. bioremediation Process that uses microorganisms to degrade harmful chemicals. biosphere The sum of all the regions of the earth where life exists. biotechnology The use of microbiological and biochemical techniques to solve practical problems and produce more useful products. biotype A group of strains that have a characteristic biochemical pattern different from other strains; also called a biovar. blood agar Type of rich agar medium that contains red blood cells and can be used to detect hemolysis. blood-brain barrier Property of the central nervous system blood vessels that restricts passage of infectious agents and certain molecules (such as medications) into the brain and spinal cord. blunt end The type of DNA ends generated by a restriction enzyme that cuts directly in the middle of the recognition sequence. BOD Abbreviation for biochemical oxygen demand. boil Painful localized collection of pus within the skin and subcutaneous tissue; a furuncle. bonds Forces that hold atoms or molecules together. bone marrow Soft material that fills bone cavities and contains stem cells for all blood cells. botulinum toxin Toxin produced by Clostridium botulinum that can cause a fatal paralysis in people who consume it. bright-field microscope Type of light microscope that illuminates the field of view evenly. brine Salty water; used to cure fish and meats. broad host range plasmid A plasmid that can replicate in a wide variety of unrelated bacteria.

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broad-spectrum antimicrobials Antimicrobials that inhibit or kill a wide range of microorganisms, often including both Gram-positive and Gramnegative bacteria. Bt-toxin Protein crystal naturally produced by Bacillus thuringiensis as it forms endospores; toxic to insect larvae that consume it. bubo Enlarged, tender lymph node characteristic of plague and some venereal diseases. bubonic plague Form of plague that typically develops when Yersinia pestis is injected via the bite of an infected flea. budding Asexual reproductive technique that involves a pushing out of a part of the parent cell that eventually gives rise to a new daughter cell. Also, a process by which some viruses are released from host cells. buffer Substance in a solution that acts to prevent changes in pH. bulking Overgrowth of filamentous microorganisms in sewage at treatment facilities; interferes with the separation of the solid sludge from the liquid effluent. burst size Number of newly formed virus particles released from a single cell.

Calvin cycle Metabolic pathway used by many autotrophs to incorporate CO2 into an organic form; also called the Calvin-Benson cycle. cAMP Abbreviation for cyclic AMP. cancer Abnormally growing cells that can spread from their site of origin; malignant tumors. candidiasis Fungal diseases caused by Candida albicans. candle jar Closed jar in which a lit candle converts some of the O2 in air to CO2 and water vapor; used to cultivate capnophiles. CAP Abbreviation for cyclic AMP-activating protein. cap Methylated guanine derivative added to the 5⬘ end of eukaryotic mRNA before transcription is complete. capnophiles Organisms that require increased concentrations of CO2 (5% to 10%) and approximately 15% O2. capsid Protein coat that surrounds the nucleic acid of a virus. capsule A distinct thick gelatinous material that surrounds some types of microorganisms; sometimes correlated with an organism’s ability to cause disease. carbapenems Group of antimicrobial medications that interferes with peptidoglycan synthesis; very resistant to inactivation by b -lactamases. carbohydrate Compounds containing principally carbon, hydrogen, and oxygen atoms in a ratio of 1:2:1. carbon fixation Process of converting inorganic carbon (CO2) to an organic form. carboxyl terminal (or C terminal) The end of the protein molecule that has an unbonded JCOOH group. carbuncle Painful infection of the skin and subcutaneous tissues; manifests as a cluster of boils. carcinogen A chemical or radiation that causes cancer. cariogenic Causing dental caries, tooth decay. carotenoids Accessory pigment found in a wide variety of photosynthetic organisms that increases the efficiency of light capture by absorbing wavelengths of light not absorbed by chlorophylls; mammals can use one of the carotenoids (betacarotene) as a source of vitamin A.

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carrier (1) Type of protein found in cell membranes that transports certain compounds across the membrane; may also be called a permease or transporter protein. (2) A human or other animal that harbors a pathogen without noticeable ill effects. carrier cell A virus-infected cell that extrudes virions as it multiplies. carrier state State of infection in which the agent can be detected in body fluids without causing disease symptoms. cascade In biology, a series of reactions that, once started, continues to the final step by each step triggering the next in a special order; activation of the complement cascade is an example. caseous necrosis Type of localized tissue death resulting in a cheeselike consistency, characteristic of tuberculosis and certain other chronic infectious diseases. catabolism Cellular processes that harvest the energy released during the breakdown of compounds such as glucose and use that energy to synthesize ATP, the energy currency of all cells. catabolite Product of catabolism. catabolite repression The mechanism by which cells decrease the expression of genes that encode certain degradative enzymes in the presence of a compound such as glucose. catalase Enzyme that breaks down hydrogen peroxide (H2O2) to produce water (H2O) and oxygen gas (O2). catalyst Substance that speeds up the rate of a chemical reaction without being altered or depleted in the process. cations Positively charged ions. CD markers Abbreviation for cluster of differentiation markers. CD4 lymphocytes T lymphocytes bearing the CD4 markers; helper T cells are CD4 cells. CD8 lymphocytes T lymphocytes bearing the CD8 markers; cytotoxic T cells are CD8 cells. cDNA DNA obtained by using reverse transcriptase to synthesize DNA from an RNA template in vitro; lacks introns that characterize eukaryotic DNA. cell culture (or tissue culture) Cultivation of animal or plant cells in the laboratory. cell envelope The layers surrounding the contents of the cell; includes the cytoplasmic membrane, cell wall, and capsule (if present). cell wall Rigid barrier that surrounds a cell, keeping the contents from bursting out; in prokaryotes, peptidoglycan provides rigidity to the cell wall. cell-mediated immunity (CMI) (See cellular immunity.) cellular immunity (also called cell-mediated immunity or CMI) The immune response mediated by T lymphocytes (T cells). cellulose Polymer of glucose subunits; principal structural component of plant cell walls. central metabolic pathways Glycolysis, the TCA cycle, and the pentose phosphate pathway. cephalosporins Group of antimicrobial medications that interfere with peptidoglycan synthesis. cestode Tapeworm. chain terminator A dideoxynucleotide; when this molecule is incorporated into a growing strand of DNA, no additional nucleotides can be added, and elongation of the strand ceases. challenge In immunology, to give an antigen to provoke an immunologic response in a subject previously sensitized to the antigen.

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GLOSSARY

chancre Sore resulting from an ulcerating infection; the “hard chancre” of primary syphilis is typically firm and painless. chaperones Proteins that help other proteins fold properly. chemical bond Force that holds atoms together to form molecules. chemically defined media Bacteriological media composed of ingredients of fixed chemical composition; generally used for specific experiments when nutrients must be precisely controlled. chemiosmotic gradient Accumulation of protons on one side of a membrane due to expulsion of protons by the electron transport chain; used by prokaryotes to power the synthesis of ATP, fuel certain transport processes, and drive the rotation of flagella; also called the proton motive force. chemiosmotic theory The theory that a proton gradient is formed by the electron transport chain and is then used to power the synthesis of ATP. chemoautotrophs Organisms that use chemicals as a source of energy and CO2 as the major source of carbon. chemoheterotrophs Organisms that use chemicals as a source of energy, and organic compounds as a source of carbon. chemokine Cytokine important in chemotaxis of immune cells. chemolithoautotrophs Organisms that obtain energy by degrading reduced inorganic compounds such as hydrogen gas (H2), and use CO2 as a source of carbon. chemolithotrophs Organisms that obtain energy by degrading reduced inorganic chemicals such as hydrogen gas (H2); in general, chemolithotrophs are chemolithoautotrophs. chemoorganoheterotrophs Organisms that obtain both energy and carbon from organic compounds. chemoorganotrophs Organisms that obtain energy by degrading organic compounds such as glucose; in general, chemoorganotrophs are chemoorganoheterotrophs. chemostat Device used to grow bacteria in the laboratory that allows nutrients to be added and waste products to be removed continuously. chemotaxis Directed movement of an organism in response to a certain chemical in the environment. chemotherapeutic agent Chemical used as a therapeutic medication to treat a disease. chemotrophs Organisms that obtain energy by degrading chemical compounds. chickenpox Disease caused by the herpesvirus, varicella. chloramphenicol Antimicrobial medication that interferes with protein synthesis. chlorophylls The primary light-absorbing pigments used in photosynthesis. chloroplasts Organelles in photosynthetic eukaryotic cells that harvest the energy of sunlight and use it to synthesize ATP, which is then used to fuel the synthesis of organic compounds. chlorosomes Structures in which the accessory pigments in green bacteria are located. chocolate agar Type of agar medium that contains red blood cells heated under controlled conditions to lyse them, releasing their nutrients; used to culture fastidious bacteria. cholesterol Sterol found in animal cell membranes; provides rigidity to eukaryotic membranes.

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chromatin Complex of histones and DNA that make up the chromosomes of eukaryotic cells. chromosome Array of genes responsible for the determination and transmission of hereditary characteristics. chronic infections Infections that develop slowly and persist for months or years. chronic inflammation Long-term inflammatory response, marked by the prevalence of macrophages, giant cells, and granulomas. cilium (pl. cilia) Short, projecting hairlike organelle of locomotion, similar in function to a flagellum. circulative transmission Transmission of viruses to plants by insects within which the virus circulates but does not multiply. cirrhosis A chronic progressive condition affecting the liver characterized by formation of strands of scar tissue; various causes, but commonly due to alcoholism. citric acid cycle Metabolic pathway that incorporates acetyl-CoA, ultimately generating CO2 and reducing power, also known as the tricarboxylic acid (TCA) cycle and the Krebs cycle. clade Subtype of a virus such as human immunodeficiency virus (HIV), defined by similar amino acid sequences of their envelope proteins. class In classification, a collection of similar orders; a collection of several classes makes up a phylum. class switching The process that allows a B cell to change the antibody class it is programmed to make; through class switching plasma cells that descend from the B cell can make antibodies other than IgM. classical pathway Pathway of complement activation initiated by antigen-antibody complexes. classification Process of arranging organisms into similar or related groups, primarily to provide easy identification and study. clonal selection and expansion Selection and activation of a lymphocyte by interaction of antigen and specific antigen receptor on the lymphocyte surface, causing the lymphocyte to proliferate. clonal deletion Elimination of lymphocytes that have an antigen receptor that binds to normal host molecules. clone Group of cells derived from a single cell. closed system Batch system (such as a tube or flask of broth, or an agar plate) used for growing microorganisms; nutrients are not replenished and wastes are not removed. clusters of differentiation (CD) markers Molecules on the surface of T cells and other white blood cells that are used by scientists to distinguish subsets of cells. CMI Abbreviation for cell-mediated immunity. CO2 fixation Process of converting inorganic carbon (CO2) to an organic form. coagulase Non-enzymatic product synthesized by Staphylococcus aureus that clots plasma. coccus (pl. cocci) Spherical-shaped bacterial cell. codon Set of three nucleotides. coenzyme Non-protein organic compound that assists some enzymes, acting as a loosely bound carrier of small molecules or electrons. cofactor Non-protein component required for the activity of some enzymes. cohesive ends Single-stranded overhangs generated when DNA is digested with a restriction enzyme that cuts asymmetrically within the recognition sequence; sticky ends.

cohort group Population with a known exposure to a specific risk factor that is followed over time in a prospective study. coliforms (See total coliform.) colonization Establishment of a site of reproduction of microbes on a material, animal, or person without necessarily resulting in tissue invasion or damage. colony Population of bacterial cells arising from a single cell. colony blotting Technique that uses a probe to detect a given DNA sequence in colonies growing on an agar plate. colony-forming unit A unit that gives rise to a single colony; may be a single cell or multiple cells attached to one another. colony-stimulating factors A group of cytokines that direct the formation of the various types of blood cells from stem cells. combination therapy Administration of two or more antimicrobial medications simultaneously to prevent growth of mutants that might be resistant to one of the antimicrobials. commensalism Relationship between two organisms in which one partner benefits from the association and the other is unaffected. commercially sterile Free of all microorganisms capable of growing under normal storage conditions; the endospores of some thermophiles may remain. common-source epidemic Outbreak of disease due to contaminated food, water, or other single source of infectious agent. communicable diseases Diseases that are spread from an infected animal or person to another animal or person. community All of the living organisms in a given area. competent Physiological condition in which a bacterial cell is capable of taking up DNA. competitive inhibition Type of enzyme inhibition that occurs when the inhibitor competes with the normal substrate for binding to the active site. complement system Series of serum proteins involved with innate immunity; complement system proteins can be rapidly activated, contributing to protective outcomes including inflammation, lysis of foreign cells, and opsonization. complementary Describes bases in nucleic acid which hydrogen bond to one another; A (adenine) is complementary to T (thymine), and G (guanine) is complementary to C (cytosine). complex medium Medium for growing bacteria that has some ingredients of variable chemical composition. compound microscope Microscope that employs multiple magnifying lenses; the lenses in combination visually enlarge an object by a factor equal to the product of each lens’s magnification. condenser lens Lens used to focus the illumination of a microscope; positioned between the light source and the specimen and does not affect the magnification. confocal scanning laser microscope Type of microscope that focuses a laser beam to illuminate a given point on one vertical plane of a specimen; after successive regions and planes have been scanned, a computer can construct a threedimensional image of a thick structure. congenital A condition existing from the time of birth.

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GLOSSARY conidia Asexual spores borne on hyphae; produced by fungi and bacteria of the genus Streptomyces. conjugate vaccine A vaccine composed of a polysaccharide antigen covalently attached to a large protein molecule; this type of vaccine converts what would be a T-independent antigen into a T-dependent antigen. conjugation Mechanism of gene transfer in bacteria that involves cell-to-cell contact. conjugative plasmid Plasmid that carries the genes for sex pili and can transfer copies of itself to other bacteria during conjugation. constant region The part of an antibody molecule that does not vary in amino acid sequences among molecules of the same immunoglobulin class. co-stimulatory molecules Surface proteins expressed by antigen presenting cells (APCs) when the cell senses molecules that signify an invading microbe or tissue damage; they facilitate activation of naive T cells that recognize antigen presented by dendritic cells. constitutive enzyme An enzyme that is constantly synthesized by a cell. contact dermatitis A T-cell-mediated inflammation of the skin occurring in sensitized individuals as a result of contact with the particular antigen; a form of delayed hypersensitivity. contagious diseases Diseases that are spread from one host to another very readily. continuous culture Method used to maintain cells in a state of uninterrupted growth by continuously adding nutrients and removing waste products; a type of open system. convalescence Period of recuperation and recovery from an illness. convergent evolution Process of evolution when two genetically different organisms develop similar environmental adaptations. corepressor Molecule that binds to an inactive repressor and, as a consequence, enables it to function as a repressor. cortex Layer of the endospore that helps maintain the core in a dehydrated state, thereby protecting it from the effects of heat. counterstain In a differential staining procedure, the stain applied to impart a contrasting color to bacteria that do not retain the primary stain. covalent bond Strong chemical bond formed by the sharing of electrons between atoms. critical instruments Medical instruments such as needles and scalpels that come into direct contact with body tissue. cross-contamination Transfer of pathogens from one item to another. cross-sectional study Study that surveys a range of people to determine the prevalence of characteristics including disease, risk factors associated with disease, or previous exposure to a disease-causing agent. croup Acute obstruction of the larynx occurring mainly in infants and young children, often resulting from respiratory syncytial or other viral infections. crown gall tumor A tumor on a plant caused by Agrobacterium tumefaciens. CSF Abbreviation for colony-stimulating factor. curd Coagulated milk proteins, produced during cheese-making. cyanobacteria Group of Gram-negative oxygenic phototrophs genetically related to chloroplasts.

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cyclic AMP-activating protein (CAP) Protein that binds to cAMP to promote gene transcription. cyclic photophosphorylation Type of photophosphorylation in which electrons are returned directly to the chlorophyll; used to synthesize ATP without generating reducing power. cyst Dormant resting protozoan cell characterized by a thickened cell wall. cysticercus (pl. cysticerci) Cystlike larval form of tapeworms. cystitis Inflammation of the urinary bladder. cytochromes Proteins that carry electrons, usually as members of electron transport chains. cytokines Low molecular weight regulatory protein made by cells that affect the behavior of other cells; cytokines attach to specific cytokine receptors and are essential for communication between cells. cytokine receptor Type of surface receptor that binds a chemokine. cytopathic effect Observable change in a cell in vitro produced by viral action such as lysis of the cell. cytoplasm Viscous fluid within a cell. cytoplasmic membrane Thin, lipid bilayer that surrounds the cytoplasm and defines the boundary of a cell. cytoskeleton Dynamic filamentous network that provides structure and shape to eukaryotic cells. cytotoxic Kills cells. cytotoxic T cells Type of lymphocyte programmed to destroy corrupt “self” cells. cytotoxin Toxin that damages a variety of different cell types. dark-field microscope Type of microscope that directs light toward the specimen at an angle, so that only light scattered by the specimen enters the objective lens; materials in the specimen stand out as bright objects against a dark background. dark reactions Process of carbon fixation in photosynthetic organisms; the ATP used to drive the process is obtained in the light reactions; the dark reactions are called the light-independent reactions. dark repair Enzymes of DNA repair that do not depend on visible light. death phase Stage in which the number of viable bacterial cells in a population decreases at an exponential rate. decarboxylation Removal of carbon dioxide from a chemical. decimal reduction time Time required for 90% of the organisms to be killed under specific conditions; D value. decontamination Treatment to reduce the number of pathogens to a level considered safe. defensins Short antimicrobial peptides produced naturally by a variety of eukaryotic cells to fight infections. degerm Treatment used to decrease the number of microbes in an area, usually skin. degranulation Release of mediators from granules in the cell, as histamine is released from mast cells. dehydration synthesis Chemical reaction in which H2O is removed with the result that two molecules are joined together. dehydrogenation Oxidation reaction in which both an electron and an accompanying proton are removed. delayed hypersensitivity Hypersensitivity caused by cytokines released from sensitized T lymphocytes;

G-5

reactions occur within 48 to 72 hours after exposure of a sensitized individual to antigen. denaturation (1) Disruption of the three-dimensional structure of a protein molecule. (2) The separation of the complementary strands of DNA. denaturing gradient gel electrophoresis (DGGE) A procedure that gradually denatures doublestranded nucleic acid during gel electrophoresis and, as a consequence, separates similar-sized fragments according to their melting point, which is related to the nucelotide sequence. dendritic cells Antigen-presenting cells that play an essential role in activation of naive T cells. denitrification Bacterial conversion of nitrate to gaseous nitrogen by anaerobic respiration. dental plaque A biofilm on teeth. deoxyribonucleic acid (DNA) Macromolecule in the cell that carries the genetic information. deoxyribose A 5-carbon sugar molecule found in DNA. depth filter Type of filter with complex, tortuous passages that allow the suspending fluid to pass through while retaining microorganisms. dermatophytes Fungi that live on the skin and can be responsible for disease of the hair, nails, and skin. dermis The layer of skin that underlies the epidermis. descriptive study Type of study that seeks to characterize a disease outbreak by determining the characteristics of the persons involved and the place and time of the outbreak. dessication Dehydration. detritus Fresh or partially degraded organic matter used as a food source by decomposers. diapedesis Movement of leukocytes from blood vessels into tissues in response to a chemotactic stimulus during inflammation. diatomaceous earth Sedimentary soil composed largely of the skeletons of diatoms; contains large amounts of silicon. diauxic growth Two-step growth frequency observed when bacteria are growing in media containing two carbon sources. diazotroph Organism that can fix nitrogen. dichotomous key Flowchart of tests used for identifying an organism; each test gives either a positive or negative result. dideoxy chain termination method A technique used to determine the nucleotide sequence of a strand of DNA; in the procedure, a small amount of chain terminator (a dideoxynucleotide) is added to an in vitro synthesis reaction. dideoxynucleotide (ddNTP) Nucleotide that lacks the 3⬘ OH group, the portion required for the addition of subsequent nucleotides during DNA synthesis. differential media Culture media that contain certain ingredients such as sugars in combination with pH indicators; used to distinguish among organisms based on their metabolic traits. differential staining Type of staining procedure used to distinguish one group of bacteria from another by taking advantage of the fact that certain bacteria have distinctly different chemical structures in some of their components. differentiate In cell development, a change in a cell associated with the acquisition of distinct morphological and functional properties. diffusion Movement of substances from a region of high concentration to a region of low concentration. digesting Treating with an enzyme such as a restriction enzyme, thereby generating

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G-6

GLOSSARY

degradation products, such as restriction fragments. diluent Sterile solution used to make dilutions. dimorphic Able to assume two forms, as the yeast and mold forms of pathogenic fungi. diphtheroids Gram-positive cells that are clubshaped and arranged to form V-shapes and palisades; resembles the typical microscopic morphology of Corynebacterium diphtheriae. diplococci Cocci that typically occur in pairs. directly observed therapy Method used to ensure that patients comply with their antimicrobial therapy; health care workers routinely visit patients in the community and watch them take their medications. direct microscopic count Method of determining the number of microbial cells in a measured volume of liquid by counting them microscopically using special glass slides. direct selection Technique of selecting mutants by plating organisms on a medium on which the desired mutants but not the parent will grow. disaccharide Carbohydrate molecule consisting of two monosaccharide molecules. disease Process resulting in tissue damage or alteration of function, producing body changes noticeable by physical examination or laboratory tests. disinfectant A chemical used to destroy many microorganisms and viruses. disinfection Process of reducing or eliminating pathogenic microorganisms or viruses in or on a material so that they are no longer a hazard. disinfection by-product (DBPs) Compounds formed when chlorine or other disinfectants react with naturally-occurring chemicals in water. disseminate To spread. disseminated intravascular coagulation Devastating condition in which clots form in small blood vessels, leading to failure of vital organs. division Taxonomic rank that groups similar classes; also called a phylum. A collection of similar divisions makes up a kingdom. DNA Abbreviation for deoxyribonucleic acid. DNA-based vaccine Vaccine composed of segments of naked DNA from infectious organisms that can be introduced directly into muscle tissue; the host tissue expresses the DNA for a short time, producing the microbial antigens encoded by the DNA. Vaccines of this type are still in developmental stages. DNA cloning Procedure by which DNA is inserted into a replicon such as a plasmid or bacteriophage, which is then introduced into cells where the replicon can replicate. (See gene cloning.) DNA fingerprinting The use of characteristic patterns in the nucleotide sequence of DNA to match a specimen to a probable source. DNA gyrase Enzyme that helps relieve the tension in DNA caused by the unwinding of the two strands of the DNA helix. DNA library Collection of cloned molecules that together encompass the entire genome of an organism of interest; each clone can be viewed as one “book” of the total genetic information of the organism of interest. DNA ligase Enzyme that forms covalent bonds between adjacent fragments of DNA. DNA-mediated transformation Process of gene transfer in which DNA is transferred as a “naked” molecule.

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DNA microarray (See microarray.) DNA polymerases Enzymes that synthesize DNA; they use one strand as a template to generate the complementary strand. DNA probe A piece of DNA, labeled in some manner, that is used to identify the presence of a certain sequence DNA by hybridizing it to its complement. DNA replication Duplication of a DNA molecule. DNA sequencing Determining the sequence (order) of nucleotide bases in a strand of DNA. domain (1) Level of taxonomic classification above the kingdom level; there are three domains— Bacteria, Archaea, and Eucarya. (2) Distinct globular regions that characterize immunoglobulin molecules. donor Refers to the cell that donates DNA in DNA transfer. double-blind Type of study where neither the physicians nor the patients know who is receiving the actual treatment. doubling time Time it takes for the number of cells in a population to double; the generation time. downstream Direction toward the 3⬘ end of an RNA molecule or the analogous (⫹) strand of DNA. droplet transmission Transmission of infectious agents through inhalation of respiratory droplets. Durham tube Small inverted tube placed in a broth of sugar-containing media that is used to detect gas production by a microorganism. D value Abbreviation for the decimal reduction time. dysentery Condition characterized by crampy abdominal pain and bloody diarrhea. eclipse period Time during which viruses exist within the host cell separated into their protein and nucleic acid components. ecological niche The role that an organism plays in a particular ecosystem. ecosystem An environment and the organisms that inhabit it. eczema Condition characterized by a blistery skin rash, with weeping of fluid and formation of crusts, usually due to an allergy. edema Swelling of tissues caused by accumulation of fluid. edible vaccine Vaccine created by transferring genes encoding key antigens from infectious agents into plants. Vaccines of this type are still in developmental stages. effector Any molecule that causes an effect. effector T cell A descendent of an activated T cell that has become armed with the ability to produce specific cytokines and other substances, endowing the cell with specific protective attributes. electrochemical gradient A separation of charged ions across the membrane. electron Negatively charged component of an atom that orbits the nucleus of the atom. electron microscope Microscope that uses electrons instead of light and can magnify images in excess of 100,000⫻. electron transport chain Series of electron carriers that transfer electrons from donors such as NADH to acceptors such as oxygen, ejecting protons in the process. electrophoresis Technique that uses an electric current to separate either DNA fragments or proteins. electroporation Process of treating cells with an electric current to introduce DNA into them.

element A substance that is composed of a single type of atom. elementary body Small dense-appearing infectious form of Chlamydia species that is released upon death and rupture of the host cell. ELISA Abbreviation for enzyme-linked immunosorbent assay. Embden-Meyerhof pathway Metabolic pathway that oxidizes glucose to pyruvate, generating ATP and reducing power; also known as glycolysis and the glycolytic pathway. emerging diseases Diseases that have increased in incidence in the past two decades. encephalitis Inflammation of the brain. endemic Constantly present in a population. endergonic Chemical reaction that requires a net input of energy because the products have more free energy than the starting compounds. endocarditis Inflammation of the heart valves or lining of the heart chambers. endocytosis Process through which cells take up particles by enclosing them in a vesicle pinched off from the cell membrane. endogenous antigen An antigen produced within a given host cell. endogenous pyrogen Fever-inducing substance (such as cytokines) made by the body. endonuclease An enzyme that cleaves bonds internally in the backbone of DNA. endoplasmic reticulum (ER) Organelle of eukaryotes where macromolecules destined for the external environment of other organelles are synthesized. endosome Vesicle formed when a cell takes up material from the surrounding environment using the process of endocytosis. endospore A kind of resting cell, characteristic of a limited number of bacterial species; highly resistant to heat, radiation, and disinfectants. endosymbiont Microorganism that resides within another cell, providing a benefit to the host cell. endosymbiont theory Theory that the ancestors of mitochondria and chloroplasts were bacteria that had been residing within other cells in a mutually beneficial partnership. endothelial cell Cell type that lines the blood and lymph vessels. endotoxic shock Septic shock that occurs as a result of endotoxin (lipopolysaccharide) circulating in the bloodstream. endotoxin Lipopolysaccharide, a toxic component of the outer membrane of Gram-negative cells that can elicit symptoms such as fever and shock; lipid A is the molecule responsible for the toxic effects of endotoxin. end product inhibition Inhibition of gene activity by the end product of a biosynthetic pathway. energy The capacity to do work. energy source Compound a cell oxidizes to harvest energy; also called an electron donor. enrichment culture Culture method that provides conditions to enhance the growth of one particular organism in a mixed population. enterics A common name for members of the family Enterobacteriaceae. enterobacteria (See enterics.) enterotoxin Poisonous substance, usually of bacterial origin, that causes diarrhea and vomiting. Entner-Doudoroff pathway Pathway that converts glucose to pyruvate and glyceraldehyde-

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GLOSSARY 3-phosphate by producing 6-phosphogluconate and then dehydrating it. enveloped viruses Viruses that have a lipid bilayer surrounding their nucleocapsid. enzyme A protein that functions as a catalyst. enzyme-linked immunosorbent assay (ELISA) Technique used for detecting and quantifying specific antigens or antibodies by using an antibody labeled with an enzyme. enzyme-substrate complex Transient form that occurs in an enzyme-mediated reaction, as the enzyme converts a substrate into a product. eosinophil A type of white blood cell; thought to be primarily important in expelling parasitic worms from the body. EPA Abbreviation for Environmental Protection Agency, a federal agency. epidemic A disease or other occurrence whose incidence is higher than expected within a region or population. epidemiology The study of factors influencing the frequency and distribution of diseases. epidermis The outermost layer of skin. epithelial cell Cell type that lines the surfaces of the body. epitope Region of an antigen recognized by antibodies and antigen receptors on lymphocytes. ergosterol Sterol found in fungal cell membranes; the target of many antifungal drugs. ergot Poisonous substance produced by the fungus that causes rye smut. erythrocytes Red blood cells. E-site (or exit site) Site on the ribosome from which tRNAs exit after donating their amino acid to the adjacent tRNA. ester bond Covalent bond formed between a JCOOH group and an JOH group with the removal of H2O. ethambutol Antimycobacterial drug that inhibits enzymes required for synthesis of mycobacterial cell wall components. ethidium bromide Mutagenic dye that binds to nucleic acid by intercalating between the bases; ethidium bromide-stained DNA is fluorescent when viewed with UV light. Eucarya Name of the domain comprising eukaryotic organisms. eukaryote Organism composed of one or more eukaryotic cells. eukaryotic cell Complex cell type differing from a prokaryotic cell mainly in having a nuclear membrane surrounding its chromosomes. eutrophic A nutrient-rich environment supporting the excessive growth of algae and other autotrophs. evolutionary chronometer A molecule such as rRNA that can be used to measure the time elapsed since two organisms diverged from a common ancestor. exanthem A skin rash. excision repair Mechanism of DNA repair in which a fragment of single-stranded DNA containing mismatched bases is removed. exergonic Describes a chemical reaction that releases energy because the starting compounds have more free energy than the products. exfoliatin A bacterial toxin that causes sloughing of the outer epidermis. exocytosis Process by which eukaryotic cells expel material; membrane-bound vesicles inside the cell

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fuse with the plasma membrane, releasing their contents to the external medium. exoenzyme Enzyme that acts outside the cell that produces it. exoerythrocytic Occurring outside the red blood cells, as the developmental cycle in malaria that occurs in the liver. exogenous antigen An antigen that originated outside a given host cell. exogenous pyrogen Fever-inducing substance (such as bacterial endotoxin) made from an external source. exons Portions of eukaryotic genes that are expressed; interrupted by introns. exotoxin Soluble poisonous protein substance released by a microorganism. experimental study Type of study done to assess the effectiveness of measures to prevent or treat disease. exponential phase Stage of growth of a bacterial culture in which cells are multiplying exponentially; log phase. external node Point on a phylogenetic tree that represents a named species that still exists. external transmission (or temporary transmission) Refers to transmission of viruses to plants by insects in which the virus is associated with the external mouthparts of the insect. extrachromosomal DNA in a cell that is not part of the chromosome. extremophiles Organisms that live under extremes of temperature, pH, or other environmental conditions. extrinsic factors In food microbiology, environmental conditions, such as the temperature and atmosphere, that influence the rate of microbial growth. Fab (fragment antigen-binding) region Portion of an antibody molecule that binds to the antigen. facilitated diffusion Transport process that enables movement of impermeable compounds from one side of the membrane to the other by exploiting a concentration gradient; does not require expenditure of energy by the cell. facultative Flexible with respect to growth conditions; for example, able to live with or without O2. facultative anaerobe Organism that grows best in the presence of oxygen (O2), but can grow in its absence. FAD Abbreviation for flavin adenine dinucleotide, an electron carrier. fallopian tube The tubes that convey ova from the ovaries to the uterus. FAME Stands for fatty acid methyl ester; a component of a technique that identifies bacteria based on their cellular fatty acid composition. family Taxonomic group between order and genus. fasciitis Inflammation of the fascia, bands of fibrous tissue that underlie the skin and surround muscle and body organs. fastidious Exacting; refers to organisms that require growth factors. fatty acid A molecule consisting of long chains of carbon atoms bonded to hydrogen atoms with an acidic group (JCOOH) at one end. F⫺ cell Recipient bacterial cell in conjugation. F⫹ cell Donor bacterial cell in conjugation, transfers the F plasmid.

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F plasmid (See fertility plasmid.) Fc region Crystallizable end of the constant region of an immunoglobulin molecule; responsible for binding to Fc receptors on cells, for initiating the classical pathway of complement activation, and for other biological functions. fecal coliforms Thermotolerant coliform bacteria. fecal-oral transmission Transmitting organisms that colonize the intestine by ingesting fecally contaminated material. feedback inhibition Inhibition of the first enzyme of a biosynthetic pathway by the end product of that pathway; also called allosteric or end product inhibition. feeding tolerance Lack of immune response to a specific antigen resulting from introducing the antigen orally. fermentation Metabolic process in which the final electron acceptor is an organic compound such as pyruvate or a derivative. fertility plasmid (or F plasmid) Plasmid found in donor cells of E. coli that codes for the F or sex pilus and makes the cell F⫹. fever An increase in internal body temperature to 37.8°C or higher. fibronectin Glycoprotein occurring on the surface of cells and also in a circulating form that adheres tightly to medical devices; certain pathogens attach to it to initiate colonization. filterable viruses The old terminology for viruses. fimbria (pl. fimbriae) Type of pilus that enables cells to attach to a specific surface. first-line antimicrobials In antimycobacterial drug therapy, the antimicrobials that are preferred because they are most effective as well as least toxic. first-line defenses The barriers that separate and shield the interior of the body from the surrounding environment. flagellin Protein subunits that make up the filament of flagella. flagellum (pl. flagella) (1) In prokaryotic cells, a long protein appendage composed of subunits of flagellin that provides a mechanism of motility. (2) In eukaryotic cells, a long whiplike appendage composed of microtubules in a 9⫹2 arrangement that provides a mechanism of locomotion. flavin adenine dinucleotide (FAD) A derivative of the vitamin riboflavin that functions as an electron carrier. flavoprotein A flavin-containing electron carrier that functions in the electron transport chain. flow cytometer Instrument that counts cells in a suspension by measuring the scattering of light by individual cells as they pass by a laser. fluid mosaic model Model that describes the dynamic nature of the cytoplasmic membrane. fluke Short, non-segmented, bilaterally symmetrical flatworm. fluorescence-activated cell sorter (FACS) Machine that sorts fluorescent-labeled cells in a mixture by passing single cells in a stream past photodetectors. fluorescence in situ hybridization (FISH) A procedure that uses a fluorescently labeled probe to detect specific nucleotide sequences within intact cells affixed to a microscope slide. fluorescence microscope Special type of microscope used to observe cells that have been stained or tagged with fluorescent dyes. fluoroquinolones Group of antimicrobial drugs that interferes with nucleic acid synthesis.

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GLOSSARY

fomites Inanimate objects such as books, tools, or towels that can act as transmitters of pathogenic microorganisms or viruses. foodborne intoxication Disease resulting from ingestion of food that contains a toxin produced by a microorganism. foraminifera Protozoa that have silicon or calcium in their cell walls. forespore Portion of the endospore formed during the process of sporulation that will ultimately become the core of the endospore. fowl cholera Worldwide septicemic illness of wild and domestic fowl, caused by Pasteurella multocida; focus of the discovery by Pasteur that an attenuated organism could be used as a vaccine. fragmentation Form of asexual reproduction in which a filament composed of a string of cells breaks apart, forming multiple reproductive units. frameshift mutation Mutation resulting from the addition or deletion of a number of nucleotides not divisible by three. free energy Amount of energy that can be gained by breaking the bonds of a compound; does not include the energy that is always lost as heat. freeze-etching Process used to prepare specimens for transmission electron microscopy that allows viewing of the shape of underlying regions within structures of a cell. fruiting body With respect to myxobacteria, a complex aggregate of cells, visible to the naked eye, produced when nutrients or water are depleted. fungemia Fungi circulating in the bloodstream. fungicide Kills fungi; used to describe the effects of some antimicrobial chemicals. fungistatic Able to inhibit the growth of fungi. fungus (pl. fungi) A non-photosynthetic eukaryotic heterotroph. furuncle A boil; a localized skin infection that penetrates into the subcutaneous tissue, usually caused by Staphylococcus aureus. GALT Abbreviation for gut-associated lymphoid tissue. gametes Haploid cells that fuse with other gametes to form the diploid zygote in sexual reproduction. gamma globulin Portion of blood serum proteins that contains IgG. ganglion (pl. ganglia) Small body near the spinal column representing a bulge in a peripheral nerve at the site where the sensory nerve cells are located. gas chromatography Technique of separating and identifying gaseous components of a substance. gastroenteritis Acute inflammation of the stomach and intestines; often applied to the syndrome of nausea, vomiting, diarrhea, and abdominal pain. gas vesicles Small rigid compartments produced by some aquatic bacteria that provide buoyancy to the cell; gases, but not water, flow freely into the vesicles, thereby decreasing the density of the cell. G ⫹ C content Percentage of guanine plus cytosine in double-stranded DNA; also called the GC content. gel electrophoresis Technique that uses electric current to separate either DNA fragments or proteins according to size by drawing them through a slab of gel. gene The functional unit of a genome.

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gene cloning Procedure by which genes are inserted into a replicon such as a plasmid or bacteriophage, which is then introduced into cells where the replicon can replicate. gene fusion The joining of two genes. gene library Sum total of all of the genes of an organism that have been inserted into cloning vectors. generalized transducing phage Bacteriophage that is capable of transferring any part of the bacterial chromosome from one cell to another. (By contrast, a specialized transducing phage transfers only specific parts of the genome.) generalized transduction Transfer of any bacterial gene to another bacterium by a phage. general paresis Group of symptoms arising from nervous system damage, usually occurring 10 to 20 years after contracting syphilis; often manifest by emotional instability, memory loss, hallucinations, abnormalities of the eyes, and paralysis. general secretory pathway Primary mechanism bacterial cells use to secrete proteins; proteins destined for secretion are recognized by their characteristic sequence of amino acids that make up the amino terminal end. generation time Time it takes for the number of cells in a population to double; doubling time. genetic engineering Process of deliberately altering an organism’s genetic information by changing its nucleic acid sequences. genetic reassortment Exchange of genetic information following two different segmented viruses infecting the same cell. genetic recombination The joining together of genes from different organisms. genetics The study of the function and transfer of genes. genome Complete set of genetic information in a cell. genome mining Searching genomic databases; for example, companies might search genomic databases to locate ORFs that may encode proteins of medical value. genomic island Large segment of DNA that has been acquired from another species through horizontal gene transfer. Examples include pathogenicity islands and antibiotic resistant islands. genomics Study and analysis of the nucleotide sequence of DNA. genotype The sequence of nucleotides in the DNA of an organism. genus (pl. genera) Category of related organisms, usually containing several species. The first name of an organism in the Binomial System of Nomenclature. germicide Agent that kills microorganisms and inactivates viruses. germination Sum total of the biochemical and morphological changes that an endospore or other resting cell undergoes before becoming a vegetative cell. giant cell Very large cell with many nuclei, formed by the fusion of many macrophages during a chronic inflammatory response; found in granulomas. gingivitis Inflammation of the gums. global control The simultaneous regulation of numerous unrelated genes. glucans Polysaccharides composed of repeating subunits of glucose; involved in formation of dental plaque.

glucose-salts Type of chemically defined medium that contains only glucose and certain inorganic salts; supports the growth of E. coli. glycan chain High molecular weight linear polymer of alternating subunits of N-acetylglucosamine and N-acetylmuramic acid that serves as the backbone of the peptidoglycan molecule. glycocalyx Gel-like layer that surrounds some cells and generally functions as a mechanism of either protection or attachment. glycogen Polysaccharide composed of glucose molecules. glycolipids Lipids that have various sugars attached. glycolysis Metabolic pathway that oxidizes glucose to pyruvate, generating ATP and reducing power; also called the Embden-Meyerhoff pathway and the glycolytic pathway. glycolytic pathway Glycolysis. glycoproteins Proteins with covalently bonded sugar molecules. glycosylase An enzyme that removes oxidized guanine from DNA by breaking a bond between deoxyribose and the oxidized guanine. goblet cells Mucus-secreting epithelial cells. Golgi apparatus Series of membrane-bound flattened sacs within eukaryotic cells that serve as the site where macromolecules synthesized in the endoplasmic reticulum are modified before they are transported to other destinations. Gram-negative bacteria Bacteria that lose the crystal violet in the Gram stain procedure and therefore stain pink; the cell wall of these organisms is composed of a thin layer of peptidoglycan surrounded by an outer membrane. Gram-positive bacteria Bacteria that retain the crystal violet stain in the Gram stain procedure and therefore stain purple; the cell wall of these organisms is composed of a thick layer of peptidoglycan. Gram stain Staining technique that divides bacteria into one of two groups, Gram-positive or Gramnegative, on the basis of color; among bacteria, the staining reaction correlates well with cell wall structure. granulation tissue New tissue formed during healing of an injury, consisting of small, red, translucent nodules containing abundant blood vessels. granulocytes White blood cells characterized by the presence of prominent granules; basophil granules stain dark with basophilic dyes, eosinophils stain bright red with eosinophilic dyes, and neutrophils do not take up either stain. granuloma Found in a chronic inflammatory response, collections of lymphocytes and stages of macrophages; an attempt by the body to wall off and contain persistent organisms and antigens. griseofulvin Antifungal medication that appears to interfere with the action of tubulin, a necessary factor in nuclear division. group translocation Type of transport process that chemically alters a molecule during its passage through the cytoplasmic membrane. growth curve Growth pattern observed when cells are grown in a closed system; consists of five stages—lag phase, log phase (or exponential phase), stationary phase, death phase, and the phase of prolonged decline. growth factors Compounds that a particular bacterium cannot synthesize and therefore must be included in a medium which supports the growth of that organism.

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GLOSSARY gumma Localized area of chronic inflammation and necrosis in tertiary syphilis, often manifest as a swelling.

HAART Highly active antiretroviral therapy; a cocktail of medications that act at different sites during replication of human immunodeficiency virus. hairy leukoplakia Whitish patch, usually appearing on the tongue of individuals with severe immunodeficiency, thought to be caused by reactivation of latent Epstein-Barr virus (EBV) infection. half-life Time it takes for one-half of the original number of molecules of a compound to be eliminated or degraded. halophile Organism that prefers or requires a high salt (NaCl) medium to grow. haploid Containing only a single set of genes. hapten Substance that can combine with specific antibodies but which cannot incite the production of those antibodies unless it is attached to a large carrier molecule. haustoria Specialized hypha of parasitic fungi that can penetrate plant or animal cell walls. heavy chain The two higher molecular weight polypeptide chains that make up an antibody molecule; the type of heavy chain dictates the class of antibody molecule. helicase Enzyme that unwinds the DNA helix ahead of the replication fork. helminth A parasitic worm. helper T cells Type of lymphocyte programmed to activate B cells and macrophages, and assist other aspects of adaptive immunity. hemagglutination Clumping of red blood cells. hemagglutination inhibition Immunological test used to detect antibodies against certain viruses which naturally cause red blood cells to agglutinate; antibodies that bind the virus inhibit the usual agglutination. hemagglutinin A protein important in the virulence of the influenza virus. hematopoietic stem cells Bone marrow cells that give rise to all blood cells. hemolytic disease of the newborn (HDN) Disease of the fetus or newborn caused by transplacental passage of maternal antibodies against the baby’s red blood cells, resulting in red cell destruction; usually anti-Rhesus (Rh) antibodies are involved and the disease is called Rh disease; also called erythroblastosis fetalis. hemolytic uremic syndrome (HUS) Serious condition characterized by red cell breakdown and kidney failure; a sequel to infection by certain Shiga toxin-producing strains of Shigella dysenteriae and Escherichia coli. hepatitis Inflammation of the liver; various causes, but most commonly the result of viral infection, particularly by the hepatitis viruses. hepatitis B virus An enveloped DNA virus with an unusual mode of replication involving reverse transcriptase; cause of hepatitis B. herd immunity Phenomenon that occurs when a critical concentration of immune hosts prevents the spread of an infectious agent. hermaphroditic Having both male and female reproductive structures in the same organism. herpes zoster Another name for shingles; a disease that results from reactivation of the herpesvirus causing chickenpox.

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heterocyst Specialized non-photosynthetic cells of cyanobacteria within which nitrogen fixation occurs. heterophile antibody Antibody that reacts with the red blood cells of another animal. heterotroph Organism that obtains carbon from an organic compound such as glucose. Hfr cells (high frequency of recombination cells) Rare cells in the F⫹ population that can transfer their chromosome to an F⫺ cell. high-copy-number plasmid Plasmid whose numbers in the cell range from 50 to 500. high efficiency particulate air (HEPA) filters Special filters that remove from air nearly all particles, including microorganisms, that have a diameter greater than 0.3 μm. high-energy phosphate bond Bond that joins a phosphate group to a molecule and releases a relatively high amount of energy when hydrolyzed; denoted by the symbol ~. high-level disinfectant Chemical used to destroy all viruses and vegetative cells, but not endospores. high-temperature-short-time (HTST) method Most common pasteurization protocol; using this method, milk is pasteurized by holding it at 72°C for 15 seconds. histamine A substance found in basophil and mast cell granules that upon release can cause dilation and increased permeability of blood vessel walls and other effects; a mediator of inflammation. HIV disease The illness caused by human immunodeficiency virus, marked by gradual impairment of the immune system, ending in AIDS. HLA Abbreviation for human leukocyte antigen. homologous With respect to DNA, stretches that have similar or identical nucleotide sequences and probably encode similar characteristics. homologous recombination Genetic recombination between stretches of similar or identical nucleotide sequences. homoserine lactone (HSL) Freely diffusible molecule used by certain types of bacteria to sense the density of cells within their population. hook Curved flagellar structure that connects the filament of the flagellum to the cell surface. hops Flowers of the vinelike hop plant; they are added to wort to impart a desirable bitter flavor to beer and contribute antibacterial substances. horizontal gene transfer Transmission of DNA from one bacterium to another through conjugation, DNA-mediated transformation, or transduction; also called lateral gene transfer. horizontal transmission Transfer of a pathogen from one person to another through contact, ingestion of food or water, or via a living agent such as an insect. host Organism on or in which smaller organisms or viruses live, feed, and reproduce. host cell In immunology, one of the body’s own cells. host range The range of animals or cell types that a pathogen can infect. HSV-1 (herpes simplex virus-1) Member of the herpes family of viruses that causes cold sores and other types of infection. HSV-2 (herpes simplex virus-2) Member of the herpes family of viruses; principal cause of genital herpes. HTST Abbreviation for high-temperature-short-time pasteurization.

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human leukocyte antigen (HLA) Human MHC molecules. humoral immune response Antibody response. hybridization The annealing of two complementary strands of DNA from different sources to create a hybrid double-stranded molecule. hybridoma Cell made by fusing a lymphocyte, such as an antibody-producing B cell, with a cancer cell. hydrogenation Reduction reaction in which an electron and an accompanying proton is added to a molecule. hydrogen bond Weak attraction between a positively-charged hydrogen atom of one compound and a negatively charged atom of another compound; the charges of the two atoms are due to polar covalent bonds. hydrolysis Chemical reaction in which a molecule is broken down as H2O is added. hydrophilic Water loving; soluble in water. hydrophobic bonds Weak bonds formed between molecules as a result of their mutual repulsion of water molecules. hyperimmune globulin Immunoglobulin prepared from the sera of donors with large amounts of antibodies to certain diseases, such as tetanus; used to prevent or treat the disease. hypersensitivity Also termed allergy; heightened immune response to antigen. hyperthermophiles Organisms that have an optimum growth temperature between 70°C and 110°C. hypervariable regions Small areas in the Fab portion of the immunoglobulin light and heavy polypeptide chains that bind the antigenic epitope. hypha (pl. hyphae) Threadlike structure that characterizes the growth of most fungi and some bacteria such as members of the genus Streptomyces. hyposensitization (or desensitization) Form of therapy for immediate IgE-mediated allergies in which extremely small but increasing amounts of antigen are injected regularly over a period of months, directing the response from IgE to IgG. hypoxic Deficient in oxygen. ID50 The number of organisms that, when administered, will cause infection in approximately 50% of hosts. identification In taxonomy, the process of characterizing an isolate in order to determine the group (taxon) to which it belongs. IFN Abbreviation for interferons. IgA proteases Enzymes that degrade IgA; they may have other roles as well. illness Period of time during which symptoms and signs of disease occur. immune complex Complex of antigen and antibody bound together, often with some complement system components included. immune serum globulin Immunoglobulin G portion of pooled plasma from many donors, containing a wide variety of antibodies; used to provide passive protection. immunity Protection against infectious agents and other substances. immunoassay Tests using immunological reagents such as antigens and antibodies. immunocompromised A host with weaknesses or defects in the innate or adaptive defenses. immunodeficiency Inability to produce a normal immune response to antigen.

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G-10

GLOSSARY

immunodiffusion tests Precipitation reactions carried out in agarose or other gels. immunoelectrophoresis Technique for separating proteins by subjecting the mixture to an electric current followed by diffusion and precipitation in gels using antibodies against the separated proteins. immunofluorescence Technique used to identify particular antigens microscopically in cells by the binding of a fluorescent antibody to the antigen. immunogen Antigen that induces an immune response. immunoglobulin Glycoprotein molecules that react specifically with the substance that induced their formation; antibodies. immunological tolerance (See tolerance.) immunology The study of immunity, or protection against infectious and other agents, and conditions arising from the mechanisms involved in immunity, such as hypersensitivities. immunosuppression Non-specific suppression of adaptive immune responses. immunotherapy Techniques used to modify the immune system action for a favorable effect. inactivated vaccine Vaccine composed of killed bacteria, inactivated virus, or fractions of the agent; the agent in the vaccine is unable to replicate. inapparent (or subclinical) infections Infections in which symptoms do not occur or are mild enough to go unnoticed. incidence rate Number of new cases of a disease within a specific time period in a given population. inclusion body Microscopically visible structure within a cell representing the site at which an infecting virus replicates; can occur within the nucleus or the cytoplasm. incubation period Interval between entrance of a pathogen into a susceptible host and the onset of illness caused by that pathogen. index case First identified case of a disease in an epidemic. indirect contact Means of transmitting infectious disease via fomites. indirect selection In microbial genetics, a technique for isolating mutants and identifying organisms unable to grow on a medium on which the parents do grow; often involves replica plating. induced mutation Mutation that results from the organism being treated with an agent that alters its DNA. inducer Substance that activates transcription of certain genes. inducible enzyme Enzyme synthesized only under certain environmental conditions. induction Process by which a prophage is excised from the host cell DNA; activation of gene transcription. infection Growth and multiplication of a parasitic organism or virus in or on the body of the host with or without the production of disease. infectious disease Disease caused by a microbial or viral infection. infectious dose Number of microorganisms or viruses sufficient to establish an infection; often expressed as ID50 in which 50% of the hosts are infected. inflammation Innate response to injury characterized by swelling, heat, redness, and pain in the affected area.

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initiation complex Complex of a 30S ribosomal subunit, a tRNA that carries f-Met, and elongation factors that comes together at a start codon on mRNA and begins the process of translation. innate immunity Immunity that is not affected by prior contact with the infectious agent and is not mediated by lymphocytes. innate resistance Resistance of an organism to an antimicrobial medication due to the inherent characteristics of that type organism; also called intrinsic resistance. inner membrane (1) In prokaryotic cells, the cytoplasmic membrane of Gram-negative bacteria. (2) In eukaryotic cells, the membrane on the interior side of an organelle that has a double membrane. inorganic A compound that contains no CJH bonds. insert DNA that is (or will be) joined to a vector to create a recombinant DNA molecule. insertion mutation Mutation resulting from the integration of a transposon into a gene. insertion sequence (IS) Short piece of DNA that has the ability to move from one site on a DNA molecule to another; simplest type of transposable element. insulin-dependent diabetes mellitus (IDDM) Diabetes caused by autoimmune destruction of pancreatic cells by cytotoxic T cells. intercalating agents Agents that insert themselves between two nucleotides in opposite strands of a DNA double helix. interference microscope Type of light microscope that employs special optical devices to cause the specimen to appear as a three-dimensional image; an example is the Nomarski differential interference contrast microscope. interferons Cytokines that induce cells to resist viral replication. interleukins Cytokines produced by leukocytes. intermediate fibers Component of the eukaryotic cell cytoskeleton. intermediate-level disinfectant Type of chemical used to destroy all vegetative bacteria including mycobacteria, fungi, and most, but not all, viruses. internal node Branch point on a phylogenetic tree that represents an ancestor to modern organisms. intranuclear inclusion body Structure found within the nucleus of cells infected with certain viruses such as the cytomegalovirus. intrinsic resistance (See innate resistance.) intron Part of the eukaryotic chromosome that does not code for a protein; removed from the RNA transcript before the mRNA is translated. inverted repeat Sequence of nucleotides on one strand of DNA that is identical to DNA on another strand when both are read in the same direction, that is, 5⬘ to 3⬘; associated with transposable elements. in vitro In a test tube or other container as opposed to inside a living plant or animal. in vivo Inside a living plant or animal as opposed to a test tube or other container. ion Positively or negatively charged atom or molecule. ionic bond Bond formed by the attraction of positively charged atoms or molecules to negatively charged ones. IS Abbreviation for insertion sequence. isomer Molecule with the same number and types of atoms as another but differing in its structure. isotope Form of an element that differs in atomic weight from the form most common in nature.

Jarisch-Herxheimer reaction Abrupt but transitory worsening of symptoms after starting effective antibacterial treatment, thought to be caused by substances released by the death of the bacteria.

keratin A water-repelling protein found in hair, nails, and the outermost cells of the epidermis. kinetic energy Energy of motion. kingdom Taxonomic rank that groups several phyla or divisions; a collection of similar kingdoms makes up a domain. Kirby-Bauer disc diffusion test Procedure used to determine whether a bacterium is susceptible to concentrations of an antimicrobial compound usually present in the bloodstream of an individual receiving the antimicrobial. Koch’s Postulates The criteria used to determine the cause of an infectious disease by culturing the agent and reproducing the disease. Koplik spots Lesions of the oral cavity caused by measles virus that resemble a grain of salt on a red base. Krebs cycle Metabolic pathway that incorporates acetyl-CoA, and generates ATP (or GTP), CO2, and reducing power; also called the tricarboxylic acid (TCA) cycle and the citric acid cycle. labeled Tagged with a detectable marker such as a radioactive isotope, a fluorescent dye, or an enzyme. lac operon Operon that encodes the proteins required for the degradation of lactose; it has served as one of the most important models for studying gene regulation. lactic acid bacteria Group of Gram-positive bacteria that generate lactic acid as a major end product of their fermentative metabolism. lactoferrin Iron-binding protein found in leukocytes, saliva, mucus, milk, and other substances; helps defend the body by depriving microorganisms of iron. lactose Disaccharide consisting of one molecule of glucose and one of galactose. lacZⴕ gene Gene used to visually determine whether or not a vector contains a fragment inserted into a multiple cloning site. lagging strand In DNA replication, the strand that is synthesized as a series of fragments. lagooning Sewage treatment method in which sewage is channeled into shallow lagoons, during which time it is degraded by anaerobic and/or aerobic organisms. lag phase Stage in the growth of a bacterial culture characterized by extensive macromolecule and ATP synthesis but no increase in the number of viable cells. laminar flow hood Biological safety cabinet in which laboratory personnel work with potentially dangerous airborne pathogens; a continuous flow of incoming and outgoing air is filtered through HEPA filters to contain microorganisms within the cabinet. Lancefield grouping Classification of ␤-hemolytic streptococci based on serological identification. latent infection Infection in which the infectious agent is present but not active. latent state The state of a phage when its DNA is integrated into the genome of the host. lateral gene transfer (See horizontal gene transfer.)

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GLOSSARY leading strand In DNA replication, the DNA strand that is synthesized as a continuous fragment. leaky Refers to a mutation in which the mutant gene codes for a protein that is partially functional. lecithin Component of mammalian cell membranes; attacked by the a-toxin of Clostridium perfringens and other lecithinases. lectin pathway Pathway of complement system activation initiated by binding of mannan-binding lectins to microbial cell walls. leghemoglobin Protein synthesized by leguminous plants that carries O2 within a Rhizobiumharboring nodule. lethal dose (LD) Concentration of an infectious agent that causes death; often expressed as LD50, the concentration of substances in which 50% of the hosts are killed by the agent. leukemia Cancer of the leukocytes (white blood cells). leukocidins Substances that kill white blood cells. leukocytes White blood cells. leukotrienes Substances active in inflammation, leading to chemotaxis and increased vascular permeability; produced by mast cells, basophils, and macrophages. L-forms Bacterial variants that have lost the ability to synthesize the peptidoglycan portion of their cell wall. lichen Organism composed of a fungus in a symbiotic association with either a green alga or a cyanobacterium. ligand A specific molecule that binds to a given receptor. light chains In an antibody, the two lighter molecular weight polypeptide chains that make up the molecule. light-dependent reactions Processes used by phototrophs to harvest energy from sunlight; the energy-gathering component of photosynthesis. light-independent reactions Stage of photosynthesis in which the ATP generated in the light-dependent reactions is used to fix carbon; also called dark reactions. light microscope Microscope that uses visible light to observe objects. light reactions (See light-dependent reactions.) light repair Process by which bacteria repair UV damage to their DNA only in the presence of light. lincosamides Group of antimicrobials that interferes with protein synthesis. lipid One of a diverse group of organic substances all of which are relatively insoluble in water, but soluble in alcohol, ether, chloroform, or other fat solvents. lipid A Portion of lipopolysaccharide (LPS) that anchors the molecule in the lipid bilayer of the outer membrane of Gram-negative cells; it plays an important role in the body’s ability to recognize the presence of invading bacteria, but is also responsible for the toxic effects of LPS. lipopolysaccharide (LPS) Molecule formed by bonding of lipid to polysaccharide; a part of the outer membrane of Gram-negative bacteria. lipoprotein Macromolecule formed by the bonding of lipid to protein. lipoteichoic acids Component of the Gram-positive cell wall that is linked to the cytoplasmic membrane. localized infections Infections limited to one site in or on the body, as a furuncle. locus Designated location on a chromosome. log phase Stage of growth of a bacterial culture in which the cells are multiplying exponentially.

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low-copy-number plasmid Plasmid whose numbers in the cell are one or two copies. low-level disinfectants Type of chemical used to destroy fungi, enveloped viruses, and vegetative bacteria except mycobacteria. LPS Abbreviation for lipopolysaccharide. luciferase Enzyme that catalyzes the chemical reactions that produce bioluminescence. lymph Clear yellow liquid that flows within lymphatic vessels; generally contains lymphocytes and may contain globules of fat. lymphadenopathy syndrome (LAS) Marked generalized enlargement of lymph nodes that often occurs at the end of the period of clinical well-being in HIV disease. lymphangitis Inflammation of lymphatic vessels. lymphatic vessels Vessels that carry lymph, which is collected from the fluid that bathes the body’s tissues. lymphocyte Small, round, or oval white blood cell with a large nucleus and a small amount of cytoplasm; involved in adaptive immunity. lymphoid tissues and organs Collections of lymphocytes and related cells involved in immune responses. lymphokines Cytokines secreted by lymphocytes. lysate Remains of cells and virions that are released after lysis of cells. lyse To burst. lysogenic conversion Modification of the properties of a cell resulting from expression of phage DNA integrated into a bacterial chromosome. lysogens Bacteria that carry a prophage integrated into their chromosome. lysosome Membrane-bound structure in eukaryotic cells that contains powerful degradative enzymes. lysozyme Enzyme that degrades the peptidoglycan layer of the bacterial cell wall. MacConkey agar Type of selective and differential bacteriological medium used to isolate certain Gram-negative rods such as those that typically reside in the intestine. macroenvironment Overall environment in which an organism lives; opposed to microenvironment. macrolides Group of antimicrobial medications that interfere with protein synthesis. macromolecule Very large molecule usually composed of repeating subunits. macrophages Differentiated phagocytes of the mononuclear phagocyte system that can engulf and destroy microorganisms and other extraneous materials, function as antigen-presenting cells, and carry out ADCC (antibody-dependent cellular cytotoxicity). magnetotaxis Movement by bacterial cells containing magnetite crystals in response to a magnetic field. major histocompatibility complex (MHC) Cluster of genes coding for key cell surface proteins important in antigen presentation. malaise Vague feeling of uneasiness or discomfort. malignant tumor Abnormal growth of cells no longer under normal control that have the potential to spread to other parts of the body. MALT Abbreviation for mucosal-associated lymphoid tissue. mannan-binding lectins (MBLs) Pattern-recognition molecules the body uses to detect polymers of

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mannose, which are typically found on microbial but not mammalian cells. mast cells Granule-containing tissue cells similar in appearance and function to the basophils of the blood, with receptors for the Fc portion of IgE; important in the inflammatory response and immediate allergic reactions. maturation The stage in viral replication in which the various components of the virion assemble to form a whole virion; also called assembly. MBC Abbreviation for minimum bactericidal concentration. M cells Specialized epithelial cells lying over Peyer’s patches that collect material in the intestine and transfer it to the lymphoid tissues beneath. mechanical vector Organism such as a fly that physically moves contaminated material from one location to another. mechanisms of pathogenicity Methods that pathogens use to evade host defenses and cause damage to the host. medium (pl. media) Any material used for growing organisms. megakaryocyte The large blood cell from which platelets arise. meiosis Process in eukaryotic cells by which the chromosome number is reduced from diploid (2N) to haploid (1N). melting Denaturating of double-stranded DNA. membrane attack complex (MAC) Complex of certain components of the complement system that forms pores in the cell membrane, resulting in lysis of the cell. membrane-damaging toxin Toxin that disrupts plasma membranes of eukaryotic cells. membrane filtration A technique used to determine the number of bacterial cells in a liquid sample that has a relatively low number of organisms; concentrates bacteria by filtration before they are plated. membrane proteins Specialized proteins embedded in the membrane bilayer; some function as receptors and others function as transport proteins. memory cells Lymphocytes that persist in the body after an immune response to an antigen; upon subsequent exposure to the same antigen, they must differentiate and usually proliferate to become effector cells. memory response (See secondary response.) meninges Membranes covering the brain and spinal cord. meningitis Inflammation of the meninges. merozoite Stage in the life cycle of certain protozoa, such as the malaria-causing Plasmodium species. mesophiles Bacteria that grow most rapidly at temperatures between 20°C and 45°C. messenger RNA (mRNA) Single-stranded RNA that binds to ribosomes and directs the synthesis of protein. metabolism Sum total of all the enzymatic chemical reactions in a cell. metabolite Any product of metabolism. metachromatic granules Polyphosphate granules found in the cytoplasm of some bacteria that appear as different colors when stained with a basic dye. methanogens Group of Archaea that obtain energy by oxidizing hydrogen gas, using CO2 as a terminal electron acceptor, thereby generating methane (CH4). MHC Abbreviation for major histocompatibility complex.

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GLOSSARY

MHC molecules Molecules on the surface of cells used to present antigen to T cells; the MHC molecules, encoded by the major histocompatibility complex (MHC), are also involved in the immunological rejection of transplanted tissue and organs. MIC Abbreviation for minimum inhibitory concentration. microaerophiles Organisms that require small amounts of oxygen (2% to 10%) for growth, but are inhibited by higher concentrations. microarray A solid support that contains a fixed pattern of numerous different single-stranded nucleic acid fragments of known sequences. microenvironment Environment immediately surrounding an individual microorganism. microtiter plate A small tray containing numerous wells, usually 96. microtubules Cytoskeleton structures of a eukaryotic cell that form mitotic spindles, cilia, and flagella; long hollow cylinders composed of tubulin. microvillus (pl. microvilli) Tiny cylindrical process from luminal surfaces of cells such as those lining the intestine; increases surface area of the cell. mineralization Complete breakdown of organic molecules to inorganic molecules. minimum bactericidal concentration (MBC) Lowest concentration of a specific antimicrobial medication that kills 99.9% of cells in a culture of a given strain of bacteria. minimum inhibitory concentration (MIC) Lowest concentration of a specific antimicrobial medication that prevents the growth of a given strain of bacteria in vitro. minus (ⴚ) strand (1) The DNA strand used as a template for RNA synthesis. (2) The complement to the plus (or sense) strand of RNA. Also called the antisense strand. miracidium First larval form of a fluke, hatching from the ovum as a ciliated organism. mismatch repair Repair mechanism in which a repair enzyme recognizes improperly hydrogenbonded bases and excises a short stretch of nucleotides containing these bases. mitochondrion Organelle in eukaryotic cells in which the majority of ATP synthesis occurs. mitogen Substance that induces mitosis; causes proliferation of cells. mitosis Nuclear division process in eukaryotic cells that ensures the daughter cells receive the same number of chromosomes as the original parent. MMWR Abbreviation for Morbidity and Mortality Weekly Report, published by the Centers for Disease Control and Prevention (CDC). mobilize (plasmids) To prepare DNA for transfer by conjugation. mold A filamentous fungus. mole Amount of a chemical in grams that contains 6.023 ⫻ 1023 molecules; it is equal to the molecular weight of the chemical, or the sum of the atomic weights of all the atoms in a molecule of that chemical. molecular postulates The criteria used to study a microbe’s virulence factors by using genetic and other molecular techniques. molecular weight Relative weight of an atom or molecule based on a scale in which the H atom with one proton is assigned the weight of 1.0. molecule Chemical consisting of two or more atoms held together by chemical bonds.

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monobactams Group of antimicrobial medications that interferes with peptidoglycan synthesis; very resistant to b-lactamases. monocistronic RNA transcript that carries the gene. monoclonal antibodies Antibody molecules with a single specificity produced in vitro by lymphocytes that have been fused with a type of malignant myeloma cell. monocytes Mononuclear phagocytes of the blood; part of the mononuclear phagocyte system of professional phagocytes. monomer Subunit of a polymer. mononuclear phagocyte system (MPS) System of mononuclear cells (monocytes and macrophages) that are scattered throughout the body and highly efficient at phagocytosis. monosaccharide A sugar; a simple carbohydrate generally having the formula Cn H2n On, where n can vary in number from three to eight. morbidity Illness; most often expressed as the rate of illness in a given population at risk. mordant Substance that increases the affinity of cellular components for a dye. morphology Form or shape of a particular organism or structure. mortality Death; most often expressed as a rate of death in a given population at risk. most probable number (MPN) method Statistical estimate of cell numbers based on the theory of probability; a sample is successively diluted to determine the point at which subsequent dilutions receive no cells. M protein A protein found in the cell walls of Group A streptococci that is associated with virulence. mRNA Messenger RNA. mucociliary escalator Moving layer of mucus and cilia lining the respiratory tract that traps bacteria and other particles and moves them into the throat. mucosa (See mucous membrane.) mucosal-associated lymphoid tissue (MALT) Lymphoid tissue present in the mucosa of the respiratory, gastrointestinal, and genitourinary tracts. mucous membrane Epithelial barrier that is coated with mucus. multiple-cloning site Small sequence of DNA that contains several unique restriction enzyme recognition sites into which foreign DNA can be cloned. mushroom Filamentous multicelled fungus with macroscopic fruiting bodies. mutagen Any agent that increases the frequency at which DNA is altered (mutated). mutant Organism that has a changed nucleotide sequence or arrangement of nucleotides in its DNA. mutation A change in the nucleotide sequence of a cell’s DNA, which is then passed on to daughter cells. mutualism A symbiotic association in which both partners benefit. myasthenia gravis Autoimmune disease characterized by muscle weakness, caused by autoantibodies. mycelium (pl. mycelia) Tangled, matlike mass of fungal hyphae. mycology The study of fungi. mycorrhiza Symbiotic relationship between certain fungi and the roots of plants. mycosis (pl. mycoses) Disease caused by a fungus.

myxobacteria Group of Gram-negative bacteria that congegrate to form complex structures called fruiting bodies. N-acetylglucosamine (NAG) One of the two alternating subunits of the glycan chains that make up peptidoglycan. NADP/NADPH Abbreviations for the oxidized/ reduced forms of nicotinamide adenine dinucleotide phosphate, an electron carrier. NAD/NADH Abbreviations for the oxidized/reduced forms of nicotinamide adenine dinucleotide, an electron carrier. narrow host range plasmid Plasmid that only replicates in one or a few closely related species of bacteria. narrow-spectrum antimicrobials Antimicrobial medications that inhibit or kill a limited range of bacteria. National Molecular Subtyping Network for Foodborne Disease Surveillance (See PulseNet.) natural killer cell (See NK cell.) natural selection Selection by the environment of those cells best able to grow in that environment. naturally acquired immunity Active or passive immunity acquired through natural means such as exposure to a disease-causing agent, breastfeeding, or transfer of IgG to a fetus in utero. necrotic Dead; refers to dead cells or tissues in contact with living cells, as necrotic tissue in wounds. negative staining Staining technique that employs an acidic dye to stain the background against which colorless cells can be seen. negative (ⴚ) strand (See minus (⫺) strand.) Negri body Viral inclusion body characteristic of rabies. nematodes Roundworms. neurotoxin Toxin that damages the nervous system. neurotransmitter Any of a group of substances released from the terminations of nerve cells when they are stimulated; they cross to the adjacent cell and cause it to be excited or inhibited. neutron Uncharged component of an atom found in the nucleus. neutrophiles Organisms that can live and multiply within the range of pH 5 (acidic) to pH 8 (basic) and have a pH optimum near neutral (pH 7). neutrophils (See polymorphonuclear neutrophils.) nitrification Conversion of ammonia (NH3) to nitrate (NO3⫺). nitrifiers Group of Gram-negative bacteria that obtain energy by oxidizing inorganic nitrogen compounds such as ammonia or nitrate. nitrogen fixation Conversion of nitrogen gas to ammonia. NK cell Large granular, non-T, non-B lymphocyte that can kill cells to which antibody has bound and cells that do not bear MHC class I molecules on the surface. Nomarski differential interference contrast microscope Type of microscope that has a device for separating light into two beams that pass through the specimen and then recombine; light waves are out of phase when they recombine, resulting in the three-dimensional appearance of material in the specimen.

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GLOSSARY nomenclature System of assigning names to organisms; a component of taxonomy. non-communicable diseases Disease that cannot be transmitted from one individual to another. non-competitive inhibition Type of enzyme inhibition that results from a molecule binding to the enzyme at a site other than the active site. non-critical instruments Medical instruments and surfaces such as stethoscopes and countertops that only come into contact with unbroken skin. non-cyclic photophosphorylation Type of photophosphorylation in which high-energy electrons are drawn off to generate reducing power; electrons must still be returned to chlorophyll, but they must come from a source such as water. non-polar covalent bond Bond formed by sharing electrons between atoms that have equal attraction for the electrons. nonsense mutation A mutation which generates a stop codon, resulting in a shortened protein. normal microbiota (or normal flora) That group of microorganisms that colonizes the body surfaces but does not usually cause disease. nosocomial infection Infection acquired during hospitalization. notifiable diseases Group of diseases that are reported to the CDC by individual states; typically these diseases are of relatively high incidence or otherwise a potential danger to public health. nuclear envelope Double membrane that separates the nucleus from the cytoplasm in eukaryotic cells. nucleic acids hybridization (See hybridization.) nucleic acids Ribonucleic acid (RNA) and deoxyribonucleic acid (DNA). nucleocapsid Viral nucleic acid and its protein coat. nucleoid Region of a prokaryotic cell containing the DNA. nucleolus Region within the nucleus where ribosomal RNAs are synthesized. nucleosome Unit of the chromatin of eukaryotic cells that consists of a complex of histones around which the linear DNA wraps twice. nucleotides Basic subunits of ribonucleic or deoxyribonucleic acid consisting of a purine or pyrimidine covalently bonded to ribose or deoxyribose, which is covalently bound to a phosphate molecule. nucleus Membrane-bound organelle in a eukaryotic cell that contains chromosomes and the nucleolus. numerical taxonomy Method of classification based on the phenotypes of prokaryotes; determines the relatedness of different organisms based on the percentage of characteristics that two groups have in common. O antigen Antigenic polysaccharide portion of lipopolysaccharide, the molecule that makes up the outer leaflet of the outer membrane of Gramnegative bacteria. objective lens Lens of a compound microscope that is closest to the specimen. obligate aerobes Organisms that require oxygen for growth. obligate anaerobes Organisms that cannot multiply if O2 is present; they are often killed by traces of O2 because of its toxic derivatives. obligate fermenters Organisms that can grow in the presence of O2 but never use it as a terminal electron acceptor; also called aerotolerant anaerobes.

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obligate intracellular parasites Organisms that grow only inside living cells. occlusion bodies Masses of viruses inside or outside cells. ocular lens Lens of a compound microscope that is closest to the eye. oil A liquid fat. Okazaki fragment Nucleic acid fragment synthesized as a result of the discontinuous replication of the lagging strand of DNA. oligonucleotide Short chain of nucleotides. oligosaccharide Short chain of monosaccharide subunits joined together by covalent bonds; shorter than a polysaccharide. oligotrophic environment A nutrient-poor environment. oligotrophs Organisms that can grow in a nutrientpoor environment. oncogene Gene whose activity is involved in turning a normal cell into a cancer cell. open reading frame (ORF) Stretch of DNA, generally longer than 300 base pairs, that has a reading frame beginning with a start codon and ending with a stop codon; it suggests that the region encodes a protein. open system Method used to maintain cells in a state of continuous growth by continuously adding nutrients and removing waste products; also called a continuous culture. operator Region located immediately downstream of a promoter to which a repressor can bind; binding of the repressor to the operator effectively prevents RNA polymerase from progressing past that region and blocks transcription. operon Group of linked genes whose expression is controlled as a single unit. opine Unusual amino acid derivative; a portion of the Ti plasmid of Agrobacterium tumefaciens is transferred to plant cells and directs the plant cells to synthesize this compound. opportunistic pathogen Organism that causes disease only in hosts with impaired defense mechanisms or when introduced into an unusual location; also called an opportunist. opsonization Enhanced phagocytosis, usually caused by coating of the particle to be ingested with either antibody or complement system components. opthalmia neonatorum Eye infection of newborns usually caused by Neisseria gonorrhoeae or Chlamydia trachomatis, acquired from infected mothers during the birth process. optical isomer (or stereoisomer) Mirror image of a compound. optimal proportion Relative proportions of antigen and antibody at which both are fully incorporated in a precipitate. optimum growth temperature Temperature at which a microorganism multiplies most rapidly. oral tolerance Decreased reactivity of immune cells resulting from feeding an antigen. order Taxonomic classification between class and family. organ A structure composed of different tissues coordinated to perform a specific function. organelle A cell structure that performs a specific function. organic A compound in which a carbon atom is covalently bonded to a hydrogen atom. origin of replication Distinct region of a DNA molecule at which replication is initiated.

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origin of transfer Short stretch of nucleotides, a part of which is transferred first when a plasmid is transferred to a recipient cell; necessary for plasmid transfer. osmosis Movement of water across a membrane from a dilute solution to a more concentrated solution. osmotic pressure Pressure exerted by water on a membrane due to a difference in the concentration of molecules on each side of the membrane. O-specific polysaccharide side chain The portion of LPS that is directed away from the membrane, at the end opposite of lipid A; because its composition varies, it can sometimes be used to identify species or strains. outbreak Cluster of cases occurring during a brief time interval and affecting a specific population; may herald the onset of an epidemic. outer membrane (1) In prokaryotic cells, the unique lipid bilayer of Gram-negative cells that surrounds the peptidoglycan layer. (2) In eukaryotic cells, the membrane on the cytoplasmic side of organelles that have double membranes. oxazolidinones Group of antimicrobial drugs that interferes with protein synthesis. oxidase test Rapid biochemical test used to detect the activity of cytochrome c oxidase. oxidation Removal of an electron. oxidation-reduction reactions Chemical reactions in which one or more electrons is transferred from one molecule to another; the compound that loses electrons becomes oxidized and the chemical that gains electrons becomes reduced. oxidative phosphorylation Synthesis of ATP from ADP and inorganic phosphate using the energy of a proton motive force, which is generated by harvesting chemical energy. oxygenic photosynthesis Photosynthetic reaction that releases O2. oxygenic phototrophs Phototrophic organisms that produce O2. palindrome Two stretches of DNA on opposite strands that are identical when oriented in the same direction, that is, 5⬘ to 3⬘ or 3⬘ to 5⬘. pandemic A worldwide epidemic. para-aminobenzoic acid (PABA) Intermediate in the pathway for folic acid synthesis in bacteria; sulfa drugs have a similar structure to PABA. parasitism Association in which one organism, the parasite, benefits at the expense of the other organism, the host. parent strain Refers to the original strain of a bacterium used in an experiment; term is often used in place of wild-type strain. passive diffusion Process in which molecules flow freely into and out of a cell so that the concentration of any particular molecule is the same on the inside as it is on the outside of the cell. passive immunity Protective immunity resulting from the transfer of antibody-containing serum produced by other individuals or animals. pasteurization Process of heating food or other substances under controlled conditions of time and temperature to kill pathogens and reduce the total number of microorganisms without damaging the substance. pathogen Organism or virus causing a disease. pathogenesis Process by which disease develops.

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GLOSSARY

pathogenicity islands Stretches of DNA in bacteria that code for virulence factors and appear to have been acquired from other bacteria. pattern recognition Method by which the innate immune system recognizes invading microbes; the system uses receptors and other molecules that bind lipopolysaccharide, peptidoglycan, and other molecular patterns associated with microbes. peliosis hepatis Serious condition characterized by formation of blood-filled cysts in the liver, caused by Bartonella henselae; usually a complication of AIDS or other severe immunodeficiency. penicillin Antibiotic that interferes with the synthesis of the peptidoglycan portion of bacterial cell walls. penicillin-binding proteins (PBPs) Target of b-lactam antimicrobial drugs; their role in bacteria is peptidoglycan synthesis. penicillin enrichment Method for increasing the relative proportion of auxotrophic mutants in a population by killing off the growing prototrophic cells with penicillin. pentamer Polymer composed of five monomeric structural units. pentose phosphate pathway Metabolic pathway that initiates the degradation of glucose, generating reducing power in the form of NADPH, and two precursor metabolites. peptide bond Covalent bond formed between the JCOOH group of one amino acid and the JNH2 group of another amino acid; characteristic of proteins. peptide interbridge Component of the peptidoglycan layer of Gram-positive bacteria; the short chain of amino acids that links the peptide side chains of adjacent N-acetylmuramic acid molecules. peptide vaccine Vaccine composed of key antigenic peptides from disease-causing microbes. Vaccines of this type are still in developmental stages. peptidyl site (or P-site) Site on the ribosome to which the tRNA that temporarily carries the elongating amino acid chain resides. peptidoglycan Macromolecule found only in bacteria that provides rigidity to the bacterial cell wall. The basic structure of peptidoglycan is an alternating series of two major subunits N-acetylmuramic acid (NAM) and N-acetylglucosamine (NAG); chains of these alternating subunits, are cross-linked by peptide chains. peptone Common component of bacteriological media; consists of proteins originating from any of a variety of sources that have been hydrolyzed to amino acids and short peptides by treatment with enzymes, acids, or alkali. perforin Molecule produced by TC cells and NK cells to destroy target cells. periplasm (or periplasmic gel) Gel that fills the region between the outer membrane and the cytoplasmic membrane in Gram-negative bacteria. peristalsis The rhythmic contractions of the intestinal tract that propel food and liquid. peritrichous flagella Distribution of flagella over the entire surface of a cell. peroxidase enzymes Enzymes found in neutrophil granules, saliva, and milk that together with hydrogen peroxide and halide ions make up an effective antimicrobial system. persistent Refers to infection in which the causative agent remains in the body for long periods of time, often without causing symptoms of disease.

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petechia (pl. petechiae) Small purplish spot on the skin or mucous membrane caused by hemorrhage. Petri dish Two-part dish of glass or plastic often used to contain medium solidified with agar, on which bacteria are grown. Peyer’s patches Collections of lymphoid cells in the gastrointestinal tract; part of the mucosalassociated lymphoid tissue (MALT). pH Scale of 0 to 14 that expresses the acidity or alkalinity of a solution. phage Shortened term for bacteriophage. phage induction Process by which phage DNA is excised from bacterial chromosomal DNA. phagocytes Cells that specialize in engulfing and digesting microbes and cell debris. phagocytosis (v. phagocytize) The process by which certain cells ingest particulate matter by surrounding and enveloping those materials, bringing them into the cell in a membrane-bound vesicle. phagolysosome Membrane-bound vacuole generated when a phagosome fuses with a lysosome. phagosome Membrane-bound vacuole that contains the material engulfed by a phagocyte. phase-contrast microscope Type of light microscope that employs special optical devices to amplify the difference in the refractive index of a cell and the surrounding medium, increasing the contrast of the image. phase variation The reversible and random alteration of expression of certain bacterial structures such as fimbriae by switching on and off the genes that encode those structures. phenotype The properties of a cell determined by the expression of the genotype. phospholipase Membrane-damaging toxin that enzymatically removes the polar head group on phospholipids. phospholipid Lipid that has a phosphate molecule as part of its structure. phosphotransferase system Type of group translocation in which the transported molecule is phosphorylated as it passes through the cytoplasmic membrane. photoautotrophs Organisms that use light as the energy source and CO2 as the major carbon source. photoheterotrophs Organisms that use light as the energy source and organic compounds as the carbon source. photooxidation Chemical reaction occurring as a result of absorption of light energy in the presence of oxygen. photophosphorylation Synthesis of ATP from ADP and inorganic phosphate using the energy of a proton motive force, which is generated by harvesting radiant energy. photoreactivation (or light repair) Breakage of the covalent bonds joining thymine dimers in the light, thereby restoring the DNA to its original state. photosynthesis Reactions used to harvest the energy of light to synthesize ATP, which is then used to power carbon fixation. photosystems Protein complexes within which chlorophyll and other light-gathering pigments are organized; located in special photosynthetic membranes. phototaxis Directed movement in response to variations in light. phototrophs Organisms that use light as a source of energy.

phycobiliproteins Light-harvesting pigments of cyanobacteria; they absorb energy from wavelengths of light that are not well absorbed by chlorophyll. phylogenetic tree Type of diagram that depicts the evolutionary heritage of organisms. phylogeny Evolutionary relatedness of organisms. phylum (pl. phyla) Collection of similar classes; a collection of similar phyla makes up a kingdom; a phylum may also be called a division. phytoplankton Floating and swimming algae and photosynthetic prokaryotic organisms of lakes and oceans. pilus (pl. pili) Hairlike appendages on many Gramnegative bacteria that function in conjugation and for attachment. pinocytosis Process by which eukaryotic cells take in liquid and small particles from the surrounding environment by internalizing and pinching off small pieces of their own membrane, bringing along a small volume of liquid and any material attached to the membrane. plankton Primarily microscopic organisms floating freely in most waters. plaque (1) Clear area in a monolayer of cells. (2) In dentistry, a polysaccharide-encased community of bacteria (a biofilm) that adheres to a tooth surface. plasma Fluid portion of non-clotted blood. plasma cell End cell of the B-cell series, fully differentiated to produce and secrete large amounts of antibody. plasma membrane Semipermeable membrane that surrounds the cytoplasm in a cell; cytoplasmic membrane. plasmid Small extrachromosomal circular DNA molecule that replicates independently of the chromosome; often codes for antibiotic resistance. plasmolysis Process in which water diffuses out of a cell, causing the cytoplasm to dehydrate and shrink from the cell wall. plate count Method used to determine the number of viable cells in a specimen by determining the number of colonies that arise when the specimen is added to an agar medium. platelets (or thrombocytes) Small cell fragments in the blood that are essential for blood clotting; arise from large bone marrow cells called megakaryocytes. pleomorphic Bacteria that characteristically vary in shape. pleurisy Inflammation of the pleura, membranes that line the lung and chest cavity; often marked by a sharp pain associated with breathing. plus (ⴙ) strand (1) The DNA strand that is complementary to the strand used as a template for RNA synthesis. (2) Of the two RNA molecules that can theoretically be transcribed from doublestranded DNA, the one that can be translated to make a protein; also called the sense strand. PMN Abbreviation for polymorphonuclear neutrophil. pneumonia Inflammation of the lungs accompanied by filling of the air sacs with fluids such as pus and blood. pneumonic plague Disease that develops when Yersinia pestis infects the lungs. point mutation Mutation in which only a single base pair is involved. polar covalent bond Bond formed by sharing electrons between atoms that have unequal attraction for the electrons.

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GLOSSARY polarity (1) The degree of affinity that an atom has for electrons; this results in positive or negative charges on atoms in a molecule. (2) The 5⬘ to 3⬘ directionality of a nucleic acid fragment. (3) The transfer of DNA from one cell to another in an exclusive direction, for example from an F⫹ cell to an F⫺ cell. poly A tail Series of approximately 200 adenine derivatives that are added to the 3⬘ end of an mRNA transcript in eukaryotic cells; thought to stabilize the transcript and enhance translation. polycistronic An mRNA molecule that carries more than one gene. polygenic (1) A trait encoded by more than one location on the chromosome. (2) An mRNA molecule that carries more than one gene. polymer Large molecules formed by the joining together of repeating small molecules (subunits). polymerase chain reaction (PCR) Method used to create millions of copies of a given region of DNA in only a matter of hours. polymorphic Having different distinct forms. polymorphonuclear neutrophils (PMNs) Type of phagocytic cell; the nuclei of these cells are segmented and composed of several lobes. polymyxin B Type of antimicrobial medication that damages cytoplasmic membranes. polypeptide Chain of amino acids joined by peptide bonds; also called a protein. polyribosome Assembly of multiple ribosomes attached to a single mRNA molecule; also called a polysome. polysaccharide Long chains of monosaccharide subunits. polysaccharide vaccine Vaccine composed of polysaccharides, which make up the capsule of certain organisms. polyunsaturated fatty acid Fatty acid that contains numerous double bonds. porins Proteins in the outer membrane of Gramnegative bacteria that form channels through which small molecules can pass. portal of entry Place of entry of microorganisms into the host. portal of exit Place where infectious agents leave the host to find a new host. positive selection Process that permits only those T cells that recognize MHC molecules to some extent to develop further. positive (ⴙ) strand (See plus (⫹) strand.) potential energy Stored energy; it can exist in a variety of forms including chemical bonds, a rock on the top of a hill, and water behind a dam. pour-plate method Method of inoculating an agar medium with bacterial cells while the agar is liquid and then pouring it into a Petri dish, where the agar hardens; the colonies grow both on the surface and within the medium. precipitation reaction Reaction of antibody with soluble antigen to form an insoluble substance. precursor metabolites Metabolic intermediates of catabolic pathways that can be used in anabolic pathways. preservation The process of inhibiting the growth of microorganisms in products to delay spoilage. prevalence Total number cases, both old and new, in a given population at risk at a point in time. primary culture Cells taken and grown directly from the tissues of an animal. primary immune response Immune response that occurs upon first exposure to an antigen.

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primary infection Infection in a previously healthy individual, such as measles in a child who has not had measles before. primary lymphoid organs Organs in which lymphocytes mature; the thymus and bone marrow. primary metabolites Compounds synthesized by a cell during the log phase. primary pathogen Microbe able to cause disease in an otherwise healthy individual. primary producers Organisms that convert CO2 into organic compounds; by doing so, they sustain other life forms, including humans. primary response The response that marks the adaptive immune system’s first encounter with a particular antigen. primary stain First dye applied in a multistep differential staining procedures; generally stains all cells. primary structure Refers to the sequence of amino acids in a protein. primary treatment In treatment of wastewater, a physical process designed to remove materials that will settle out. primase Enzyme that synthesizes small fragments of RNA to serve as primers for DNA synthesis during DNA replication. primer RNA molecule that initiates the synthesis of DNA. prion Infectious protein that has no nucleic acid. probe In nucleic acid hybridization, a single-stranded piece of nucleic acid that has been tagged with a detectable marker; it is used to identify homologous nucleic acid by allowing it to hybridize to its complement. productive infection Virus infection in which more virions are produced. proglottid One of the segments that make up most of the body of a tapeworm. pro-inflammatory cytokines Any of a group of cytokines that contribute to the inflammatory response. prokaryote Single-celled organism that does not contain a membrane-bound nucleus. prokaryotic cell Cell characterized by lack of a nuclear membrane and thus no true nucleus. promoter Nucleotide sequence to which RNA polymerase binds to initiate transcription. propagated epidemic Outbreak of disease in which the infectious agent is transmitted to others, resulting in steadily increasing numbers of people becoming ill. prophage Latent form of a temperate phage whose DNA has been inserted into the host’s DNA. prophylaxis Prevention of disease. prospective study Study that looks ahead to see if the risk factors identified by a retrospective study predict a tendency to develop the disease. prosthecate bacteria Group of gram-negative bacteria that have extensions projecting from the cells, thereby increasing their surface area. protease Enzyme that degrades protein; the protease encoded by HIV is the target of several anti-HIV medications. protein Macromolecule consisting of amino acid subunits. protein A Protein produced by Staphylococcus aureus that inhibits phagocytosis of the organism by binding to the Fc portion of antibodies. protein subunit vaccine Vaccine composed of key protein antigens or antigenic fragments of an

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infectious agent, rather than whole cells or viruses. protist Designation for eukaryotic organisms other than plants, animals, and fungi; may be unicellular or multicellular. proton Positively charged component of an atom. proton motive force Form of energy generated by the electron transport chain, which expels protons to create a chemiosmotic gradient. proton pump Complex of electron carriers in the electron transport chain that ejects protons from the cell. proto-oncogene A type of gene involved in tumor formation; it codes for a protein that activates transcription. prototroph Organism that has no organic growth requirements other than a source of carbon and energy. protozoa Group of single-celled eukaryotic organisms. provirus Latent form of a virus in which the viral DNA is incorporated into the chromosome of the host. pseudomembranous colitis Disease of the colon caused by Clostridium difficile in which patches called pseudomembranes, composed of dead epithelium, inflammatory cells and clotted blood, form on the intestinal lining. pseudopods Transient armlike extensions formed by phagocytes and protozoa; they surround and enclose extracellular material, including bacteria, during the process of phagocytosis. P-site (or peptidyl site) Site on the ribosome where the tRNA that temporarily carries the elongating amino acid chain resides. psychrophile Microorganism that grows best between ⫺5°C and 15°C. psychrotroph Organism that has an optimum temperature between 20°C and 30°C. puerperal fever Childbed fever; infection of the uterus following childbirth, commonly caused by Streptococcus pyogenes. pulsed-field gel electrophoresis Type of gel electrophoresis that is used to separate very large fragments of DNA. PulseNet Surveillance network established by the Centers for Disease Control and Prevention to facilitate the tracking of foodborne disease outbreaks; catalogues the RFLPs of certain pathogenic organisms. Also called the National Molecular Subtyping Network for Foodborne Disease Surveillance. pure culture A population of organisms descended from a single cell. purine Component of RNA and DNA; the two major purines are adenine and guanine. pus Thick, opaque, often yellowish material that forms at the site of infection, made up of dead neutrophils and tissue debris. putrefaction Digestion of proteins by enzymes to yield foul-smelling products. pyelonephritis Infection of the kidneys. pyoderma Any skin disease characterized by production of pus. pyogenic Pus-producing. pyrimidine Component of RNA and DNA; the three major pyrimidines are thymine, cytosine, and uracil. pyrogens Fever-inducing substances. pyruvate End product of glycolysis; a precursor metabolite used in the synthesis of certain amino acids.

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G-16

GLOSSARY

quaternary ammonium compounds Cationic (positively charged) detergents that are non-toxic enough to be used to disinfect food preparation surfaces; also called quats. quaternary structure Level of structure of a protein molecule consisting of several polypeptide chains. quinone A lipid-soluble electron carrier that functions in the electron transport chain. quorum sensing Communication between bacterial cells by means of small molecules, permitting the cells to sense the density of cells. radial immunodiffusion test Quantitative antigenantibody precipitation in gel test in which one reactant is distributed throughout the gel and the other reactant diffuses into the gel, producing a ring of precipitation. rDNA DNA that encodes ribosomal RNA (rRNA). reactive oxygen A form of oxygen that is highly toxic to cells because it damages DNA. reading frames Grouping of a stretch of nucleotides into sequential triplets; an mRNA molecule has three reading frames, but only one is typically used in translation. receptor Type of membrane protein that binds to specific molecules in the environment, providing a mechanism for the cell to sense and adjust to its surroundings. receptor-mediated endocytosis Type of pinocytosis that allows cells to internalize extracellular ligands that bind to the cell’s receptors. recognition sequence The DNA sequence recognized by a particular restriction enzyme. recombinant DNA molecule DNA molecule created by joining DNA from two different sources in vitro; a vector-insert chimera is a recombinant DNA molecule. recombinant vaccines Subunit vaccines produced by genetic engineering. redox reactions Transfer of electrons from one compound to another; one compound becomes reduced and the other becomes oxidized. reducing agents Compounds that readily donate electrons to another compound, thereby reducing the other compound. reducing power Reduced electron carriers such as NADH, NADPH, and FADH2; their bonds contain a form of usable energy. reduction Process of adding electrons to a molecule. refraction Bending of light rays that occurs when light passes from one medium to another. regulatory protein Protein that binds to DNA, either blocking or enhancing the function of RNA polymerase. regulatory T cells Type of lymphocyte that helps control the immune response. regulon Set of related genes that are transcribed as separate units but are controlled by the same regulatory protein. replica plating Technique for the simultaneous transfer of organisms in separated colonies from one medium to another medium. replication fork In DNA synthesis, the site at which the double helix is being unwound to expose the single strands that can function as templates. replicon Piece of DNA that is capable of replicating; contains an origin of replication. reporter gene Gene that has a detectable phenotype and can be fused to a gene of interest, providing a

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mechanism by which to monitor the expression of the gene of interest. repressible enzyme Enzyme whose synthesis can be turned off by certain conditions. repressor Protein that binds to the operator site and prevents transcription. reservoir Source of a disease-causing organism. resident microbiota Normal microbiota that typically inhabit body sites for extended periods. resistance plasmid (or R plasmid) Plasmid that carries genetic information for resistance to one or more antimicrobial medications and heavy metals. resolve To clearly separate. respiration Process that involves transfer of electrons stripped from a chemical energy source to an electron transport chain, generating a proton motive force that is then used to synthesize ATP. respire To use the processes of respiration. response regulator In a two-component regulatory system, the protein that binds to DNA. restriction enzyme Type of enzyme that recognizes and cleaves a specific sequence of DNA. restriction fragment length polymorphism (RFLP) Pattern of fragment sizes obtained by digesting DNA with one or more restriction enzymes. restriction fragments Fragments generated when DNA is cut with restriction enzymes. reticulate body Fragile, replicating, non-infectious intracellular form of Chlamydia species. retrospective study Type of study done following a disease outbreak; compares the actions and events surrounding clinical cases with those of controls. retroviruses Group of viruses that carry their genetic information as single-stranded RNA; they have the enzyme reverse transcriptase, which forms a DNA copy that is then integrated into the host cell chromosome. reverse transcriptase Enzyme that synthesizes double-stranded DNA complementary to an RNA template. reversion Process by which a second mutation corrects a defect caused by an earlier mutation. Reye’s syndrome Often fatal condition characterized by vomiting, coma, and brain and liver damage, mostly occurring in children treated with aspirin for influenza or chickenpox. RFLP Abbreviation for restriction fragment length polymorphism. rheumatoid arthritis Severe crippling autoimmune disease of the joints, caused by cytokines from inflammatory TH1 cells and immune complexes. rhizosphere Zone around plant roots containing organic materials exuded by the roots. rhuMab (recombinant human monoclonal antibody) Monoclonal antibody derived from a laboratory animal in which part of the molecule has been replaced with the human equivalent. ribonucleic acid (RNA) Macromolecules in a cell that play a role in converting the information coded by the DNA into amino acid sequences in protein. ribose A 5-carbon sugar found in RNA. ribosomal RNA (rRNA) Type of RNA present in ribosomes; the nucleotide sequences of these are increasingly being used to classify and, in some cases, identify microorganisms. ribosome Structure that facilitates the joining of amino acids during the process of translation; composed of protein and ribosomal RNA. ribosome-binding site Sequence of nucleotides in bacterial mRNA to which a ribosome binds; the

first time the codon for methionine (AUG) appears after that site, translation generally starts. ribotyping Technique used to distinguish among related strains; detects RFLPs in ribosomal RNA genes. ribozymes RNA molecules that have a catalytic function. rifamycins Group of antimicrobial medications that block transcription. risk factors Specific conditions associated with high frequencies of disease. RNA Abbreviation for ribonucleic acid. RNA polymerase Enzyme that catalyzes the synthesis of RNA using a DNA template. RNases Enzymes that degrade RNA. rod Cylindrical-shaped bacterium; also called a bacillus. rolling circle replication Mechanism of DNA replication in which a single strand of DNA is synthesized. rough endoplasmic reticulum Organelle where proteins destined for locations other than the cytoplasm are synthesized. roundworm A helminth that has a cylindrical, tapered body; a nematode. R plasmids Plasmids that encode resistance to one or more antimicrobial medications and heavy metals. rRNA Ribosomal RNA. RTF Abbreviation for resistance transfer factor. rubisco Enzyme that initiates the Calvin cycle by joining CO2 to the 5-carbon compound ribulose1,5-bisphosphate.

salinity Amount of salt in a solution. SALT Skin-associated lymphoid tissues. sanitization Process of substantially reducing the microbial populations on objects to achieve acceptably safe public health levels. saprophyte Organism that takes in nutrients from dead and decaying matter. saturated Refers to a fatty acid that contains no double bonds. scanning electron microscope (SEM) Type of electron microscope that scans a beam of electrons back and forth over the surface of a specimen; used for observing surface details, but not internal structures of cells. scavenger receptor Receptor on phagocytes that facilitates the engulfment of various materials that have charged molecules on their surface. schizogony Process of multiple fission in which the nucleus divides a number of times before individual daughter cells are produced. schizont Multinucleate stage in the development of certain protozoa, such as the ones that cause malaria. scolex Attachment organ of a tapeworm, the head end. scrapie Common name for a neurological disease of sheep; it is caused by a prion. sebum Oily secretion of the sebaceous glands of the skin. secondary response (or memory response) Enhanced immune response that occurs upon second or subsequent exposure to specific antigen, caused by the rapid activation of long-lived memory cells; anamnestic response. secondary infection Infection that occurs along with or immediately following another infection, usually as a result of the first infection. secondary lymphoid organs Peripheral lymphoid organs where mature lymphocytes function in immune responses; they include the adenoids,

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GLOSSARY tonsils, spleen, appendix, and lymph nodes, among others. secondary metabolites Metabolic products synthesized during late-log and stationary phase. secondary structure Refers to the arrangement of amino acids in a protein; the two major arrangements are helices and sheets. secondary treatment In treatment of wastewater, a biological process designed to convert most of the suspended solids to microbial mass and inorganic compounds. segmented virus Virus that has a genome consisting of multiple different nucleic acid fragments. selectable marker Gene that encodes a selectable phenotype such as antibiotic resistance. selective enrichment Method of increasing the relative proportion of one particular species in a broth culture by including a selective agent that inhibits the growth of other species. selectively permeable Material that allows some but not other molecules to pass through freely. selective medium Culture medium that inhibits the growth of certain microorganisms and therefore favors the growth of desired microorganisms. selective toxicity Causing greater harm to a pathogen than to the host. self-assembly Spontaneous formation of a complex structure from its component molecules without the aid of enzymes. self-transmissible plasmid Plasmid that codes for all of the information necessary for its own transfer. semiconservative replication Nucleic acid replication that results in each of the two doublestranded molecules containing one of the original strands (the template strand) and one newly synthesized strand. semicritical instruments Medical instruments such as endoscopes that come into contact with mucous membranes, but do not penetrate body tissues. semipermeable Describes material that allows the passage of some but not other molecules. sense strand Of the two RNA molecules that can theoretically be transcribed from double-stranded DNA, the one that can be translated to make a protein; also called the plus (⫹) strand. sensitization Prior immunization; allergic reactions to an antigen occur only in sensitized individuals who have been exposed to that particular antigen. sepsis A bloodstream infection. septic shock An array of effects including fever, drop in blood pressure, and disseminated intravascular coagulation, that results from infection of the bloodstream or circulating endotoxin. septic tank A large tank used for individual sewage treatment systems; wastes are collected in the tank and degraded by anaerobic organisms, with the organic compounds in the resulting fluid degraded in a drainage field by aerobic organisms. septicemia Acute illness caused by infectious agents or their products circulating in the bloodstream; blood poisoning. serial dilutions Series of dilutions, usually twofold or tenfold, used to determine the titer or concentration of a substance in solution. seroconversion Change from serum without specific antibodies to serum positive for specific antibodies. serogroup Microorganisms within a species that are the same antigenically as determined by specific antisera.

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serology The study of in vitro antibody-antigen reactions. serotype A group of strains that have a characteristic antigenic structure that differs from other strains; also called a serovar. serum Fluid portion of blood that remains after blood clots. sex pilus Thin protein appendage required for attachment of two bacteria prior to DNA transfer by conjugation. Also called F pilus. shake tube Tube of agar medium that has been uniformly inoculated with a bacterial culture in order to determine the oxygen requirement of that organism. shingles (or herpes zoster) Condition resulting from the reactivation of the varicella-zoster virus. shock Condition with multiple causes characterized by low blood pressure and circulation of the blood inadequate to sustain normal function of vital organs; septic shock results from growth of microorganisms in the body; toxic shock results from a circulating exotoxin. siderophore Iron-binding substance produced by bacteria to scavenge iron. sigma (␴) factor Component of RNA polymerase that recognizes and binds to the promoter. signal sequence Characteristic series of hydrophobic amino acids at the amino terminal end of a protein destined for secretion; functions as a tag, directing transport of the protein through the membrane. signal transduction Process that transmits information from outside of a cell to the inside, allowing that cell to respond to changing environmental conditions. signature sequences Characteristic sequences in the genes encoding ribosomal RNA that can be used to classify or identify certain organisms. signs Effects of a disease observed by examining the patient. similarity coefficient Numerical value that can be used to classify prokaryotes based on their phenotypic characteristics. simple diffusion Movement of molecules or ions in solution from a region of high concentration to a region of low concentration; does not involve transport proteins. simple staining Staining technique that employs a basic dye to impart color to cells. single-cell protein (SCP) Use of microorganisms such as yeast and bacteria as a protein source. site-specific recombination Mechanism by which a piece of DNA becomes part of a larger piece of DNA; involves identical sequences on each piece of DNA. size standard In gel electrophoresis of DNA, a series of DNA fragments of known sizes added to a lane of the gel to be used as a basis for later size comparison. skin-associated lymphoid tissue (SALT) Secondary lymphoid tissue consisting of collections of lymphoid cells under the skin. slime layer Type of glycocalyx that is diffuse and irregular. slime mold Terrestrial organism that is similar to the fungi but not related genetically. slow infection An infection that takes a long period of time before symptoms appear. smear In a staining procedure, the film obtained by placing a drop of a liquid containing a microbe on a glass microscope slide and allowing it to air dry.

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smooth endoplasmic reticulum Organelle of eukaryotic cells that is the site of lipid synthesis and degradation and calcium ion storage. solute Dissolved molecule in a solution. SOS repair Complex, inducible repair process used to repair highly damaged DNA. specialized transduction Transfer of only specific bacterial genes by phage from one bacterium to another. species Group of related isolates or strains; the lowest basic unit of taxonomy. spikes (or attachment proteins) Structures on the outside of the virion that bind to host cell receptors. spirillum (pl. spirilla) Curved rod long enough to form spirals. spirochetes Long helical bacteria that have a flexible cell wall and an axial filament. splicing Process that removes introns from eukaryotic precursor RNA to generate mRNA. spoilage Biochemical changes in foods that are perceived as undesirable. spontaneous generation Discredited theory that organisms can arise from non-living matter. spontaneous mutation Mutation that occurs naturally without the addition of mutagenic agents. spore Type of differentiated, specialized cell formed by certain organisms; includes some types of dormant cells that are resistant to adverse conditions and the reproductive structures formed by fungi. sporozoite Elongated infectious form of certain protozoa; for example, in malaria, the form entering the body from a mosquito bite, infectious for liver cells. sporulation In bacteria, a complex, highly ordered sequence of morphological changes during which a bacterial vegetative cell produces a specialized cell greatly resistant to environmental adversity; eukaryotes can also undergo sporulation. spread plate Technique used to cultivate bacteria by uniformly spreading a suspension of cells onto the surface of an agar plate. sputum Material coughed from the lungs. start codon Codon at which translation is initiated; in prokaryotes, typically the first AUG after a ribosome-binding site. starter cultures Strains of microorganisms added to a food to initiate the fermentation process. stationary phase Stage of growth of a culture in which the number of viable cells remains constant. stereoisomer (or optical isomer) Mirror image of a compound. sterilant A chemical used to destroy all microorganisms and viruses in a product, rendering it sterile. sterile Completely free of all microorganisms and viruses; an absolute term. sterilization The process of destroying or removing all microorganisms and viruses through physical or chemical means. steroid Type of lipid with a specific four-membered ring structure. stock culture Culture stored for use as an inoculum in later procedures. stop codon Codon that does not code for an amino acid and is not recognized by a tRNA; signals the end of the polypeptide chain. strain Population of cells descended from a single cell.

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G-18

GLOSSARY

streak plate Simplest and most commonly used technique for isolating bacteria; a series of successive streak patterns is used to sequentially dilute an inoculum on the surface of an agar plate. streptococcal pyrogenic exotoxins (SPEs) Family of genetically related toxins produced by certain strains of Streptococcus pyogenes, responsible for scarlet fever, toxic shock, and “flesh-eating” necrotizing fasciitis. stromatolite Coral-like mat of filamentous microorganisms. structural isomers Molecules that contain the same elements but in different arrangements that are not mirror images; structural isomers have different names and properties. subclinical Infection or disease with no apparent symptoms. substrate (1) Substance on which an enzyme acts to form products. (2) Surface on which an organism will grow. substrate-level phosphorylation Transfer of the high-energy phosphate from a phosphorylated compound to ADP to form ATP. sucrose Disaccharide consisting of a molecule of glucose bonded to fructose; common table sugar. sugar-phosphate backbone Series of alternating sugar and phosphates moieties of a DNA molecule. sulfa drugs Group of antimicrobial drugs that inhibit folic acid synthesis. sulfanilamide Antimicrobial drug that inhibits folic acid synthesis; one of the sulfa drugs. sulfate-reducers Group of obligate anaerobes that use sulfate (SO42⫺) as a terminal electron acceptor, producing hydrogen sulfide as an end product. sulfur-oxidizing bacteria Group of Gram-negative bacteria that obtain energy by oxidizing elemental sulfur and reduced sulfur compounds, thereby generating sulfuric acid. S unit Unit of measurement that expresses the sedimentation rate of a compound; reflects the mass and density of the compound; “S” stands for Svedberg. superantigens Molecules that stimulate T lymphocytes by binding to MHC class II molecules and to part of the T-cell receptor distinct from the antigenbinding site, resulting in activation of many T cells, overproduction of cytokines, severe reactions, and sometimes fatal shock. superficial mycoses Fungal infections that affect the hair, skin, or nails. superoxide (O2⫺) Toxic derivative of O2. superoxide dismutase Enzyme that degrades superoxide to produce hydrogen peroxide. surface receptors Proteins in the membrane of a cell to which certain signal molecules bind; they enable the inner workings of the cell to sense and respond to signals outside of the cell. swarmer cells Motile cells of sheathed bacteria that disperse to new locations. symbiosis The living together of two dissimilar organisms or symbionts. symptoms Effects of a disease experienced by the patient. syncytium (pl. syncytia) Multinucleate body formed by the fusion of cells. synergistic Describes the acting together of agents to produce an effect greater than the sum of the effects of the individual agents. synergistic infection An infection in which two or more species of pathogens act together to produce

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an effect greater than the sum of effects if each pathogen were acting alone. synthetic medium Medium in which the chemical composition and quantity of every component is known. systemic infection Infection in which the infectious agent spreads throughout the body. systemic mycoses Fungal infections that affect the tissues deep in the body. tapeworm A helminth that has a segmented, ribbon-shaped body; a cestode. Taq polymerase Heat-stable DNA polymerase of the thermophilic bacterium Thermus aquaticus. target cell In immunology, cell that is the direct recipient of a T cell’s effector functions. target DNA In the PCR procedure, the region to be amplified. taxa Groups into which organisms are classified. taxonomy The science that studies organisms in order to arrange them into groups; those organisms with similar properties are grouped together and separated from those that are different. Taxonomy encompasses identification, classification, and nomenclature. TC cells Effector form of a cytotoxic T cell; it induces apoptosis in infected or cancerous “self” cells. T-cell receptor Molecule on a T cell that enables the T cell to recognize a specific antigen. T cells Lymphocytes that mature in the thymus; they are responsible for cellular immune responses and function as helper cells in the antibody response. T-dependent antigens Antigens that evoke an antibody response only with the participation of TH cells. T-DNA Portion of the Ti plasmid of Agrobacterium tumefaciens that is transferred into a plant cell. teichoic acids Component of the Gram-positive cell wall, composed of chains of a common subunit, either ribitol-phosphate or glycerol-phosphate, to which various sugars and D-alanine are usually attached. temperate phage Bacteriophage that can either become integrated into the host cell DNA as a prophage or replicate outside the host chromosome leading to cell lysis. template Strand of nucleic acid that a polymerase uses to synthesize a complementary strand. terminal electron acceptor Chemical that is ultimately reduced as a consequence of chemotrophic metabolism. tertiary structure Level of structure of a protein described by its three-dimensional nature; two major shapes exist, globular and fibrous. tertiary treatment In treatment of wastewater, any purification process beyond secondary treatment, generally designed to remove nitrates and phosphates. tetracyclines Group of antimicrobial medications that interfere with protein synthesis. TH cell Effector form of a helper T cell; it activates B cells and macrophages, and releases cytokines that stimulate other aspects of the immune system. therapeutic index Ratio of minimum toxic dose to minimum effective dose of a medication. thermophile Organism with an optimum growth temperature between 45°C and 70°C. thrush Infection of the mouth by Candida albicans. thylakoids Membrane-bound disclike structures within the stroma of chloroplasts; they contain chlorophyll.

thymine dimer Two adjacent thymine molecules on the same strand of DNA joined together through covalent bonds. thymus Primary lymphoid organ, located in the upper chest, in which T lymphocytes mature. T-independent antigens Antigens that can activate B cells without the assistance of a TH cell. Ti plasmid (See tumor-inducing plasmid.) tissue culture Culture of plant or animal cells that grows in an enriched medium outside the plant or animal. titer Measure of the concentration of a substance in solution; for example, the amount of a specific antibody in serum, usually measured as the highest dilution of serum that will test positive for antibody. tolerance Specific unresponsiveness of the adaptive immune system that reflects its ability to ignore any given molecule, such as a normal cellular protein. toll-like receptors (TLRs) A group of surface receptors that recognize specific compounds unique to microbes, enabling the cell to sense the presence of invading microbes and then alert other components of the host’s defenses. total coliforms Facultative, non-spore-forming, Gram-negative rods that ferment lactose, producing acid and gas within 48 hours at 35°C; because most typically reside in the intestine, they are used as indicators of fecal pollution. toxemia Circulation of toxins in the bloodstream. toxin Poisonous chemical substance. toxoid Modified form of a toxin that is no longer toxic but is able to stimulate the production of antibodies that will neutralize the toxin. trace elements Elements that are required in very minute amounts by all cells; they include cobalt, zinc, copper, molybdenum, and manganese. trachoma Potentially serious chronic eye disease caused by certain strains of Chlamydia trachomatis. transamination Transfer of an amino group from an amino acid to a recipient compound, converting the recipient compound to an amino acid. transcript Fragment of RNA, synthesized using one of the two strands of DNA as a template. transcription Process of transferring genetic information coded in DNA into messenger RNA (mRNA). transcytosis Transport of a substance across a border made up of cells; a cell takes up the substance from one side of the border and then releases it to the other side. transduction Mechanism of gene transfer between bacteria in which bacterial DNA is transferred inside a phage. transfer RNA (tRNA) Type of RNA that delivers the appropriate amino acid to the ribosome during translation. transferrin An iron-binding protein found in blood and tissue fluids. transformed cells Bacterial, animal, or plant cells containing inheritable changes. transfusion reaction Reaction characterized by fever, low blood pressure, pain, nausea, and vomiting, resulting from the transfusion of immunologically incompatible blood. transgenic Plants and animals into which new DNA has been introduced. transient expression Expression of a gene for a short period of time. Often refers to expression of genes introduced into cells and not integrated into the genome.

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GLOSSARY transient microbiota Microorganisms that are only temporary residents of body sites. transition step Step in metabolism that links glycolysis to the TCA cycle; converts pyruvate to acetyl-CoA. translation Process by which genetic information in the messenger RNA directs the order of amino acids in protein. translocation Advancement of a ribosome a distance of one codon during translation. transmissible spongiform encephalopathies Group of fatal neurodegenerative diseases of humans and animals in which brain tissue develops spongelike holes. transmission electron microscope (TEM) Type of microscope that directs a beam of electrons at a specimen; used to observe fine details of cell structure. transport protein Type of protein found in cell membranes that functions in the transport of certain compounds across the membrane; may be called a permease or a carrier. transport systems Mechanisms used to transport small molecules across the cytoplasmic membrane. transposable element (or transposon) Gene that moves from one DNA molecule to another within the same cell or from one site on a DNA molecule to another site on the same molecule. transposition Movement of a piece of DNA from one site in a molecule to another site in the same cell. trematodes Flatworms known as flukes. tricarboxylic acid (TCA) cycle Metabolic pathway that incorporates acetyl-CoA, ultimately generating ATP (or GTP), CO2, and reducing power, also called the Krebs cycle and the citric acid cycle. trichomes Filamentous multicellular associations of cyanobacteria that may or may not be enclosed within a sheath. trickling filter method Treatment method for small sewage plants in which a rotating arm sprays sewage onto a bed of rocks coated with a biofilm of organisms that aerobically degrades the wastes. triglyceride Molecule consisting of three molecules of the same or different fatty acids bonded to glycerol. trimethoprim Antimicrobial medication that interferes with folic acid synthesis. tRNA Transfer RNA. trophozoite Vegetative feeding form of some protozoa. tubercle Granuloma formed in tuberculosis. tumble Rolling motion of a motile cell that is caused by an abrupt change in the direction of rotation of flagella. tumor-inducing (Ti) plasmid Plasmid of Agrobacterium tumefaciens that enables the

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organism to cause tumors in plants; a derivative of the plasmid is used as a vector by scientists to introduce DNA into plants. tumor necrosis factors (TNFs) A group of cytokines that play an important role in the inflammatory response and other aspects of immunity. turbidity Cloudiness; the turbidity of a bacterial suspension is proportional to the number of cells in that suspension. tyndallization Repeated cycles of heating and incubation to kill spore-forming bacteria. type III secretions system Mechanism by which bacterial pathogens transfer gene products directly into host cells.

ubiquity Widespread prevalence. ultra-high-temperature (UHT) method A method that uses heat to render a product free of all microorganisms that can grow under normal storage conditions. ultraviolet (UV) light Electromagnetic radiation with wavelengths between 175 and 350 nm; invisible. uncoating In virology, the separation of the protein coat from the nucleic acid of the virion. unsaturated Refers to a fatty acid with one or more double bonds. upstream Direction toward the 5⬘ end of either an RNA molecule or the analogous (⫹) strand of DNA. urea A waste product of protein catabolism by the body’s cells; present in various body fluids, notably urine. urticaria Hives; an allergic skin reaction characterized by the formation of itchy red swellings. UV Abbreviation for ultraviolet light.

vaccine Preparation of attenuated or inactivated microorganisms or viruses or their components used to immunize a person or animal against a particular disease. vancomycin Antimicrobial medication that interferes with peptidoglycan synthesis. variable region The portion of an antibody molecule that contains the antigen-binding sites; tremendous variation exists between the amino acid sequences of variable regions in different antibody molecules. vector (1) In molecular biology, a piece of DNA that acts as a carrier of a cloned fragment of DNA. (2) In epidemiology, any living organism that can carry a disease-causing microbe; most commonly arthropods such as mosquitoes and ticks. vegetative cell Typical, actively multiplying cell. vehicle Inanimate carrier of an infectious agent from one host to another.

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vertical transmission Transfer of a pathogen from a pregnant woman to the fetus, or from a mother to her infant during childbirth. vibrio (pl. vibrios) Short, curved rod-shaped bacterial cell. villus (pl. villi) Narrow protrusion from a membrane such as the intestinal lining. viremia Viruses circulating in the bloodstream. virion Viral particle in its inert extracellular form. viroid Piece of RNA that does not have a protein coat but does replicate within living cells. virulence Relative ability of a pathogen to overcome body defenses and cause disease. virulence determinants Arsenal of mechanisms of pathogenicity of a given microbe. virus Acellular or non-living agent composed of nucleic acid surrounded by a protein coat. vitamin One of a group of organic compounds found in small quantities in natural foodstuffs that are necessary for the growth and reproduction of an organism; usually converted into coenzymes. volutin Storage form of phosphate found inside certain bacterial cells; because granules of volutin exhibit characteristic staining with the dye methylene blue, they are called metachromatic granules. water activity (aw) Quantitative measure of the water available. water molds Non-photosynthetic members of the heterokons; similar to the fungi but not related genetically. Western blotting Procedure that uses labeled antibody molecules to detect specific proteins. whey Liquid portion that remains after milk proteins coagulate during cheese-making. wide host range plasmid Plasmid that can replicate in unrelated bacteria. wild type Form of an organism that is isolated from nature. yeast Unicellular fungus. zone of inhibition Region around a chemical saturated disc where bacteria are unable to grow due to adverse effects of the compound in the disc. zoonosis (pl. zoonoses) Disease of animals that can be transmitted to humans. zooplankton Floating and swimming small animals and protozoa found in marine environments, usually in association with the phytoplankton. zygote Diploid cell formed by the sexual fusion of two haploid cells.

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Chapter 1 Opener: © Science VU/Visuals Unlimited; 1.3: © Bettmann/ Corbis; 1.5: © Kathy Talaro/Visuals Unlimited; 1.6: © Cabisco/Visuals Unlimited; 1.7a: © Dr. John D. Cunningham/Visuals Unlimited; 1.7b: © C. Shih & R. Kessel/Visuals Unlimited; 1.8: © Manfred Kage/Peter Arnold; 1.9a: © K.G. Murti/Visuals Unlimited; 1.9b: © Thomas Broker/ Phototake; 1.9c: © K.G. Murti/Visuals Unlimited; 1.10: © U.S. Department of Agriculture/Dr. Diemer; 1.11: © Stanley B. Prusiner/Visuals Unlimited; Perspective 1.1 (Figure 1): Courtesy of Milton P. Gordon and Syed Tanveer Haider; Perspective 1.1 (Figure 2): Courtesy of Dr. Heide N. Schulz/Max Planck Institute for Marine Microbiology; Perspective 1.1 (Figure 3): Courtesy of Reinhard Rachel and Harald Huber, University of Regensburg, Germany.

Progulske and S.C. Holt, Journal of Bacteriology, 143:1003-1018, 1980; 3.37a: © Fred Hossler/Visuals Unlimited; 3.37b: © Science VU/Visuals Unlimited; 3.40: © D. Blackwill and D. Maratea/Visuals Unlimited; 3.41a: Courtesy of Dr. Charles Brinton, Jr.; 3.41b: © U.S. Department of Agriculture/Harley W. Moon; 3.42a: © CNRI/SPL/Photo Researchers, Inc.; 3.42b: © Dr. Gopal Murti/SPL/Photo Researchers; 3.44: Courtesy of Dr. Edwin S. Boatman; 3.45: Courtesy of J.F.M. Hoeniger, J. Bacteriol. 96:1835, 1968. American Society for Microbiology; 3.47c: Courtesy of Thomas Fritsche; 3.52b: © Garry T. Cole/Biological Photo Service; 3.53b: © Keith Porter/Photo Researchers, Inc.; 3.54: © George Chapman/Visuals Unlimited/ Getty; 3.55: © R. Bolendar & D. Fawcett/Visuals Unlimited; 3.56: Courtesy of Charles J. Flickinger

Chapter 2 Opener: © Scott Camazine/Photo Researchers, Inc.; Perspective 2.1 (Figure 1a): © Mark Antman/The Image Works; Perspective (Figure 1b): © SIU/Peter Arnold

Chapter 4 Opener: © Michael Klein/VISUM/The Image Works; 4.2: © Dr. Dennis Kunkel/Visuals Unlimited; 4.3: Courtesy of the Center for Biofilm Engineering, Montana State University-Bozeman, Image by P. Stoodley; 4.4: © Michael Gabridge/Visuals Unlimited; 4.5: © Fred Hossler/Visuals Unlimited; 4.11a: © Christine Case/Visuals Unlimited; 4.11b: © L. M. Pope and D. R. Grote/Biological Photo Service; 4.12: © Dr. Elmer Koneman/ Visuals Unlimited; 4.13: © Becton, Dickson and Company; 4.14: Courtesy of Thermoforma, Forma Scientific Division; 4.19a: © Dennis Kunkel/ Phototake; 4.19b: © Kathy Talaro/Visuals Unlimited; 4.21: © Richard Megna/Fundamental Photographs

Chapter 3 Opener: © Terry Beveridge/Biological Photo Service; 3.1: Courtesy of Leica, Inc., Deerfield, FL; 3.2 (both): © W. A. Jensen; 3.3a: © Richard Megna/Fundamental Photographs; 3.4: © Wim van Egmond/Visuals Unlimited; 3.5: © P. Johnson/Photo Researchers, Inc.; 3.6: © T. E. Adams/Visuals Unlimited; Table 3.1 (Bright field): From S. T. Williams, M.E. Sharpe and J.G. Holt (Eds.), Bergey’s Manual of Systematic Bacteriology, Vol. 4. © 1989 Williams and Wilkins Co., Baltimore. Micrograph from T. Cross, University of Bradford, Bradford, U.K.; Table 3.1b (Phase -Contrast): © Wim van Egmond/Visuals Unlimited; Table 3.1 (Interference): © P. Johnson/Photo Researchers, Inc.; Table 3.1 (Darkfield): © T. E. Adams/Visuals Unlimited; Table 3.1 (Fluorescence): © Evans Roberts; Table 3.1 (Confocal): Courtesy of Michael W. Davidson/ National High Magnetic Field Lab; Table 3.1 (Transmission): © R. Kessel & C. Shih/Visuals Unlimited; Table 3.1 (Scanning): © David M. Phillips/ Visuals Unlimited; Table 3.1 (Atomic Force Microscope): © Torunn Berge/Photo Researchers, Inc.; 3.7: © Evans Roberts; 3.8 (both): Courtesy of Michael W. Davidson/National High Magnetic Field Lab; 3.10a: © R. Kessel & C. Shih/Visuals Unlimited; 3.10b: © H. Aldrich/Visuals Unlimited; 3.11: © David M. Phillips/Visuals Unlimited; 3.12: © Torunn Berge/Photo Researchers, Inc.; 3.14b: © Leon J. Le beau/Biological Photo Service; 3.15: Public Health Image Library/Centers for Disease Control, Photo by Dr. George P. Kubica; 3.16: © Dr Gladden Willis/Visuals Unlimited/Getty; 3.17: © Jack M. Bostrack/Visuals Unlimited; 3.18: © E. Chan/Visuals Unlimited; 3.19a: Courtesy of Molecular Probes, Eugene, OR; 3.19b: © Richard L. Moore/Biological Photo Service; 3.19c: © Evans Roberts; 3.20a, b: © David M. Phillips/Visuals Unlimited; 3.20c: © Dennis Kunkel/ Phototake; 3.20d: © Veronika Burmeister/Visuals Unlimited; 3.20e, f: © David M. Phillips/Visuals Unlimited; 3.21a: Courtesy of Walther Stoeckenius; 3.21b: Courtesy of James T. Staley; 3.22a (top): © George Musil/Visuals Unlimited; 3.22a (bottom): © David M. Phillips/Visuals Unlimited; 3.22b: © R. Kessel & C. Shih/Visuals Unlimited; 3.22c: © Oliver Mecks/Photo Researchers, Inc; 3.23b: Courtesy of L. Santo, H. Hohl, and H. Frank, Journal of Bacteriology 99:824, 1969. American Society for Microbiology; 3.31: Courtesy of Dale C. Birdsell; Table 3.5: © Leon J. Lebeau/Biological Photo Service; 3.33c, 3.34d: © Terry Beveridge, University of Guelph; 3.35: Courtesy of Dr. Edwin S. Boatman; 3.36a: Courtesy of K.J. Cheng and J. W. Costerton; 3.36b: Courtesy of A.

Chapter 5 Opener: © Southern Illinois University/Photo Researchers, Inc.; 5.1a: © Yoav Levy/Phototake; 5.1c, d: © Rosenfeld Images/LTD/SPL/Photo Researchers, Inc.; 5.1d: © Bob Daemmrich/The Image Works; 5.1e: © Nieto/Herrican/Photo Researchers, Inc.; 5.4 (both): © Evans Roberts; 5.6: © Pall/Visuals Unlimited; 5.8: © Dennis Kunkel/Phototake Chapter 6 Opener: © Brock May/Photo Researchers, Inc.; 6.2: © Farrell Grehan/Photo Researchers, Inc.; 6.3 (top): © Photodisc Vol. Series 74, photo by Robert Glusie; 6.3 (bottom): © Jane Burton/Bruce Coleman, Inc; 6.9b, c: From Voet: Biochemistry, 1/e, 0471617695, 1990, John Wiley & Sons; 6.21 (acetone), 6.21 (wine, beer): © Brian Moeskau/McGraw-Hill; 6.21 (acetic acid, lactic acid): © Dennis Strete/Fundamental Photographs; 6.21 (cheese): © Photodisc/McGraw-Hill; 6.21 (yogurt, dairy, pickle): © Brian Moeskau/ McGraw-Hill; 6.21 (Formic acid, Ethyl alcohol): © Dennis Strete/ Fundamental Photographs Chapter 7 Opener: © D. Struthers/Toney Stone Images/Getty; 7.4: From J. Cairns, “The Chromosome of E. coli” in Cold Spring Harbor Symposia on Quantitative Biology, 77. © 1963 by Cold Spring Harbor Laboratory Press Chapter 8 Opener: © Dr. Gopal Murti/SPL/Custom Medical Stock Photo; 8.6: © Matt Meadows/Peter Arnold, Inc; 8.22: Courtesy of C. Brinton, Jr. and J. Carnahan Chapter 9 Opener: © Jean Claude Revy/Phototake; 9.2b: © Richard T. Nowitz/Photo Researchers, Inc.; 9.5: Courtesy of Pamela Silver and Jason Karana, Harvard Medical School, Dana Farber Cancer Institute. Photo provided by Howell Martin; 9.9: Reprinted with permission from Edvotek, Inc.; 9.13: © Josh Westrich/zefa/Corbis; 9.20: Dr. R. Rachel, and Prof. Dr. K.O. Stetter, University of Regensburg, Lehrstuhl fuer Mikrobiologie,

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CREDITS Regensburg, Germany.; 9.21: Courtesy of Rosetta Inpharmatics © 2002 Rosetta Inpharmatics, Inc. All rights reserved. Chapter 10 Opener: © Meckes/Ottawa/Photo Researchers, Inc.; 10.2a: © George Wilder/Visuals Unlimited; 10.2b: Courtesy of Dr. Thomas R. Fritsche, M.D., Ph.D., Clinical Microbiology Division, University of Washington, Seattle; 10.3a: © E. Koneman/Visuals Unlimited; 10.3b: © Biophoto Associates/Photo Researchers, Inc.; 10.4a: © Denise Anderson; 10.4b,c: © Dennis Strete/Fundamental Photographs; 10.6a: Courtesy of bioMerieux, Inc.; 10.6b: Courtesy of Becton, Dickinson and Company; 10.9b: Courtesy of Patricia Exekiel Moor; 10.10c, 10.11: © Evans Roberts Chapter 11 Opener, 11.1a: © F. Widdel/Visuals Unlimited; 11.1b: © Ralph Robinson/Visuals Unlimited; 11.2a: © Thomas Tottleben/ Tottleben Scientific Company; 11.2b: © David M. Phillips/Visuals Unlimited; 11.3: © John Walsh/Photo Researchers, Inc.; 11.4a: Courtesy of Dr. Heinrich Kaltwasser. From ASM News 53(2): Cover, 187.; 11.4b: From M. P. Starr et al (Eds.), The Prokaryotes. Springer-Verlag.; 11.5: From J. G. Holt (Ed.), The Shorter Bergey’s Manual of Determinative Bacteriology, 8/e, 1977. Williams and Wilkins Co., Baltimore; 11.6a: Courtesy of Isao Inouye, University of Tsukuba, Mark A. Shneegurt, Wichita State University and Cyanosite (www.cyanosite.bio.purdue.edu/ index.html); 11.6b: © M. I. Walker/Photo Researchers, Inc.; 11.7: Courtesy of Wayne Carmichael, Wright State University, Mark A. Schneegurt, Wichita State University and Cyanosite (www.cyanosite.bio. purdue.edu/index.html); 11.8: Courtesy of Roger Burks, University of California Riverside, Mark A. Schneegurt, Wichita State University and Cyanosite (www.cyanosite.bio.purdue.edu/index.html); 11.9a: Courtesy of J. T. Staley and J. P. Dalmasso; 11.9b: Courtesy of Dr. James Staley; 11.10: © John D. Cunningham/Visuals Unlimited; 11.11: © Dennis Kunkel/Phototake; 11.12: © Evans Roberts; 11.13: © CNRI/Phototake; 11.15a: © Eric Grave/Photo Researchers, Inc.; 11.15b: © Soad Tabaqchali/ Visuals Unlimited; 11.16 (both): Courtesy of Harold L. Sadoff; 11.17a: Courtesy of Mary F. Lampe; 11.17b: © Patricia L. Grilione/Phototake; 11.18: From S. T. Williams, M.E. Sharpe and J.G. Holt (Eds.), Bergey’s Manual of Systematic Bacteriology, Vol. 4. © 1989 Williams and Wilkins Co., Baltimore. Micrograph from T. Cross, University of Bradford, Bradford, U.K.; 11.19, 11.20a: © John D. Cunningham/Visuals Unlimited; 11.20b: From N. R. Krieg and J. G. Holt (Eds.), Bergey’s Manual of Systematic Bacteriology, Vol. 1, 1984. Williams and Wilkins Co., Baltimore; 11.21, 11.22a: Courtesy of J. T. Staley and J. P. Dalmasso; 11.23a: From J.T. Staley, M.P. Bryant, N. Pfennig, and J.G. Holt (Eds.) Bergey’s Manual of Systematic Bacteriology, Vol. 3. © 1989 Williams and Wilkins Co., Baltimore; 11.24a: © Alfred Pasieka/Peter Arnold, Inc.; 11.25a: Courtesy of Amy Cheng Vollmer, Swarthmore College; 11.25b: © Kenneth Lucas/Biological Photo Service; 11.26: Courtesy of Betsy L. Williams; 11.27: © Michael Gabridge/Visuals Unlimited; 11.28: © Alfred Pasieka/Peter Arnold, Inc.; 11.29: Courtesy of R. R. Friis, J. Bacteriol. 110:706, 1972. American Society for Microbiology; 11.30: © Wayne P. Armstrong, Life Sciences Department, Palomar College; 11.31: Dr. R. Rachel, and Prof. Dr. K.O. Stetter, University of Regensburg, Lehrstuhl fuer Mikrobiologie, Regensburg, Germany.; 11.32: US Geological Survey, Photo by David E. Wieprecht Chapter 12 Opener: © John D. Cunningham/Visuals Unlimited; 12.2a: © Cabisco/Visuals Unlimited; 12.2b: © John D. Cunningham/Visuals Unlimited; 12.3: © Martha Nester; 12.5: © David M. Phillips/Visuals Unlimited; 12.6: © Arthur M. Siegelman/Visuals Unlimited; 12.7 (all): Courtesy of Fritz Schoenknecht; 12.9a: © E. Chan/Visuals Unlimited; 12.9b: © Inga Spence/Tom Stack & Associates; 12.9c: © Bob Pool/Tom Stack & Associates; 12.10: © A.B. Dowsette/SPL/Photo Researchers; 12.13a: © Martha Nester; 12.13b: © Bruce Iverson; 12.14b, 12.15 (all): © Martha Nester; 12.16b: © Carolina Biological Supply/Phototake; 12.18, 12.20, 12.21: Courtesy of Sam Eng and Fritz Schoenknecht; Future Chalanges, p. 299: Centers for Disease Control

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Chapter 13 Opener: © Oliver Mecks/Photo Researchers, Inc; 13.1a: Courtesy of Harold Fisher, University of Rhode Island and Robley Williams, University of California Berkeley; 13.1b: © Dennis Kunkel/Phototake; 13.1c: © Thomas Broker/Phototake; 13.8: Courtesy of Harold Fisher; 13.12a: © Prof. L. Caro/SPL/Photo Researchers; 13.12b: Courtesy of Dr. Rafael Martinez, University of California, Los Angeles; 13.12c: © Oliver Mecks/Photo Researchers, Inc. Chapter 14 Opener: © Scott Camazine/Photo Researchers, Inc.; 14.1a: © CDC/Science Source/Photo Researchers; 14.1b: © K. G. Murti/Visuals Unlimited; 14.1c: Courtesy of Dr. Frederick A. Murphy, Centers for Disease Control and Prevention; 14.6b: © Dr. Dennis Kunkel/Visuals Unlimited; 14.12: © Michael Gabridge/Custom Medical Stock; 14.13 (all): Courtesy of M. Cooney; 14.14: © Terry Hazen/Visuals Unlimited; DROP: © E. Chan/ Visuals Unlimited; 14.15: Courtesy of Fred Williams, National Exposure Research Laboratory/U.S. EPA; 14.16b: Courtesy of M. Cooney; 14.17a: © Dean Glawe/Biological Photo Service; 14.17b: © Bruce Iverson; 14.17c: © Dean Glawe/Biological Photo Service; 14.18: © Science VU/Visuals Unlimited; 14.19: © Barbara J. Miller/Biological Photo Service; 14.20: © BSIP/Photo Researchers Chapter 15 Opener: © David M. Phillips/Visuals Unlimited; 15.8b: Reprinted from Wendell F. Rosse et al., “Immune Lysis of Normal Human and Parozysmal Nocturnal Hemogloginuria (PNH) Red Blood Cells,” Journal of Experimental Medicine, 123:969, 1996. Rockefeller University Press; 15.10: © Meckes/Ottawa/SPL/Photo Researchers, Inc. Chapter 16 Opener: © Lennart Nilsson/Boehringer Ingelheim International GMBH; 16.11a: Courtesy of Dr. James W. Vardiman; 16.11b: © NIBSCS/ SPL/Photo Researchers; 16.11c: © D. Fawcett/Visuals Unlimited Chapter 17 Opener: © Kevin Noran/Tony Stone/Getty; 17.5: Courtesy of Chihiro Sasakawa, University of Tokyo; 17.6: Courtesy of Mark A. Jepson, from Trends in Microbiology (98)v6:359-365, “Studying M cells and their role in infection”; M.A. Jepson and M.A. Clark, Elsevier Press; 17.8: Courtesy of Pascale F. Cossart, From B. Finlay and P. F. Cossart, Science 276:720, April 4, 1997 Chapter 18 Opener: © Mario Tama/Getty Images; 18.2: © STU/Custom Medical Stock; 18.6: © Bart’s Medical Library/Phototake; 18.7e: © Public Health Image Library; 18.8: © Kenneth E. Greer/Visuals Unlimited; 18.9: © SIU/Visuals Unlimited Chapter 19 Opener, 19.1 (top left): © SPL/Photo Researchers; 19.1 (top right): © Dag Sundberg/Photographer’s Choice/Getty Images; 19.1 (bottom left): © BSIP/Phototake; 19.1 (bottom right): © SPL/Photo Researchers; 19.3: © Jean Claude Revy - ISM/Phototake; 19.5b: © Dr. Dan Schadler/ Oglethorpe University; 19.9: © Science VU/Wellcome/Visuals Unlimited; 19.10: © Centers for Disease Control; 19.12: © Bob Coyle/McGraw-Hill; 19.13: Courtesy of Genelabs Diagnostics Chapter 20 Opener: © Gianni Tortoli/Photo Researchers; 20.1a (top): © Photodisc/McGraw-Hill; 20.1a (bottom): © Corbis Digital Stock CD/ McGraw-Hill; 20.1b (hands): © Photodisc/McGraw-Hill; 20.1b (tick): Courtesy of University of Nebraska/Department of Entomology; 20.1b (phone): © Photodisc/McGraw-Hill; 20.1b (sneeze): © Kent Wood/Photo Researchers; 20.1b (foods): © Photodisc/McGraw-Hill; 20.3 (both): © Joan K. Mann; 20.9: © WHO, Geneva Switzerland; 20.11: © B. Seitz/ Photo Researchers Chapter 21 Opener: © SPL/Photo Researchers; 21.5 (both): Reprinted with permission of Robert L. Perkins from A. S. Klainer and R. L. Perkins, Journal of Infectious Diseases, 122:4, 1970 © University of Chicago Press; 21.10: © Fred Marsik/Visuals Unlimited; 21.11: Courtesy bioMerieux, St. Louis, MO; 21.12 (both): AB Biodisk

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CREDITS

Chapter 22 Opener: © Mediscan/Visuals Unlimited; 22.2, 22.3, 22.5: © Evans Roberts; 22.7: © SPL/Photo Researchers; 22.9: © A.B. Dowsette/ SPL/Photo Researchers; 22.10: © LeBeau/Custom Medical Stock Photo; 22.11 (both): © St. Francis Hospital/Joan K. Mann; 22.12a: © Evans Roberts; 22.12b: © Larry Jensen/Visuals Unlimited; 22.13: Courtesy of J.B. Baseman; from P.C. Hu, A.M. Collier, and J.B. Baseman “J. Exp. Med.” 145:1328, 1977. Rockefeller University Press.; 22.14: Courtesy of Dr. Kenneth Bromberg; 22.17: © Biophoto Associates/Photo Researchers, Inc.; 22.18a: © John D. Cunningham/Visuals Unlimited; 22.18b: © CNRI/ Phototake; 22.19: © SPL/Photo Researchers; 22.20: © Science VU/Visuals Unlimited; 22.24a: Centers for Disease Control; 22.24b: © E. Chan/Visuals Unlimited; 22.26 (both): © Evans Roberts Chapter 23 Opener: © SPL/Photo Researchers; 23.1: Courtesy of Karen A. Holbrook; 23.2a, b: © Carroll H. Weiss/Camera M.D. Studios; 23.2c: Courtesy of Glenn D. Roberts, Mayo Clinic; 23.3: © SPL/Photo Researchers; 23.4: Courtesy of National Institute Slide Bank/The Welcome Center for Medical Sciences; 23.5: © SPL/Photo Researchers; 23.6: © Evans Roberts; 23.7: © Ken Greer/Visuals Unlimited; 23.8: Courtesy of Rocky Mountain Laboratory, Hamilton, Montana, CDC; 23.10: © Ed Reschke/Peter Arnold, Inc.; 23.11: © SPL/Photo Researchers; 23.12: © Charles W. Stratton/Visuals Unlimited; 23.14: © C. C. Duncan/Medical Images, Inc.; 23.15a: © CDC/ Dr. Libero Ajello; 23.15b: © Dr. G. W. Willis/Visuals Unlimited; 23.16: © John D. Cunningham/Visuals Unlimited; 23.17: © Carroll H. Weiss/ Camera M.D. Studios; 23.18: © Oliver Mecks/Photo Researchers, Inc; 23.19: © Lowell Georgia/Photo Researchers, Inc; 23.20: © Dr. P. Marazzi/ SPL/Photo Researchers, Inc; 23.21: © Carroll H. Weiss/Camera M.D. Studios; 23.23 (both): © CDC; 23.24: © CNRI/SPL/Photo Researchers, Inc.; 23.25a: © Dr. P. Marazzi/SPL/Photo Researchers, Inc; 23.25b: © Evans Roberts; 23.26a: © Dr. P. Marazzi/SPL/Photo Researchers, Inc; 23.26b: © A.M. Siegelman/Visuals Unlimited

Morris D. Cooper, Ph.D., Professor of Medical Microbiology, Southern Illinois University School of Medicine, Springfield, IL; 26.12: Courtesy of National Institute Slide Bank/The Welcome Center for Medical Sciences; 26.13: Courtesy of S. Eng and F. Schoenknecht; 26.14: Courtesy of Thomas Diepgen, University Heidelberg; 26.15: © Carroll H. Weiss/Camera M.D. Studios; 26.16: © L. Winograd/Biological Photo Service; 26.17a: © Carroll H. Weiss/Camera M.D. Studios; 26.17b: © Harvey Blank, M.D./Camera M.D. Studios; 26.18: Courtesy of National Institute Slide Bank/The Welcome Center for Medical Sciences; 26.19: © Biophoto Associates/Photo Researchers, Inc.; 26.20: © Dr. F. C. Skvara/Peter Arnold, Inc; 26.21: © David M. Phillips/Visuals Unlimited Chapter 27 Opener: © Dr. Linda Stannard, UCT/Science Photo Library/ Photo Researchers; 27.4: © John Durham/SPL/Photo Researchers, Inc.; 27.5: © Kenneth Greer/Visuals Unlimited; 27.6: © Mary K. Stallone/The Medical File Inc.; 27.8: © Palo Koch/Photo Researchers, Inc; 27.9: © John D. Cunningham/Visuals Unlimited; 27.10: © Science VU/Dr. Soad Tabaqchali/ Visuals Unlimited; 27.13: Courtesy of National Institute Slide Bank/The Welcome Center for Medical Sciences; 27.14: © Evans Roberts; 27.15: © Bettmann/Corbis; 27.17a: © Tektoff-BM/CNRI/SPL/Photo Researchers, Inc.; 27.17b: © Tobey Sanford; 27.18: © Evans Roberts; 27.19: © Mary K. Stallone/The Medical File Inc.; 27.20: © Cabisco/Visuals Unlimited; 27.21: © Dr. Terry Kreeger/Visuals Unlimited Chapter 28 Opener: © Dr. Tony Brain/SPL/Photo Researchers, Inc; 28.2: © Kenneth Greer/Visuals Unlimited; 28.4: © Science Source/Photo Researchers, Inc; 28.6: © A.M. Siegelman/Visuals Unlimited; 28.7 (both): Courtesy of Joe Hinnebusch, From Hinnebusch, B.J., Perry, R.D., and Schwan, T.G., Science 273:367, 19 July 1996.; 28.9a: © Ed Reschke/Peter Arnold, Inc.; 28.9b: © Jacquin Carrillo-Farga/Science Source/Photo Researchers, Inc.

Chapter 24 Opener: © Moore/Custom Medical Stock Photo; 24.3: © Michael English/Medical Images, Inc.; 24.4: © Evans Roberts; 24.5: © Kenneth E. Greer/Visuals Unlimited; 24.6a: © Leonard Morse, M.D./ Medical Images, Inc.; 24.6b: © Carroll H. Weiss/Camera M.D. Studios; 24.6c: © A.M. Siegelman/Visuals Unlimited; 24.7: Centers for Disease Control; 24.8: © A.M. Siegelman/Visuals Unlimited; 24.10, 24.11: Courtesy of National Institute Slide Bank/The Welcome Center for Medical Sciences; 24.12: Courtesy of Dr. John Slack; 24.13: © Kenneth E. Greer/Visuals Unlimited; 24.14: © Leonard Morse, M.D./Medical Images, Inc.

Chapter 29 Opener: © Manfred Kage/Peter Arnold, Inc.; 29.2: Courtesy of Stuart Fischman, D.M.D; 29.12: © St. Mary’s Hospital Medical School/SPL/ Photo Researchers, Inc.; 29.13: © Cecil H. Fox/Photo Researchers; 29.14a: © E. Koneman/Visuals Unlimited; 29.14c: Courtesy of Dr. Thomas R. Fritsche, M.D., Ph.D., Clinical Microbiology Division, University of Washington, Seattle; 29.15: © Dr. F.C. Skvara/Peter Arnold, Inc.; 29.16 (top): © ISM/Phototake; 29.16 (bottom): © Paula Inhad/Custom Medical Stock Photo; 29.17: Courtesy of Dr. Edwin P. Ewuing, Jr./Centers for Disease Control

Chapter 25 Opener: © Garry Watson/Photo Researchers, Inc; 25.3: © Fred Hossler/Visuals Unlimited; 25.5 (both), 6a: From S. Schluger, R.A. Yaodels and R.C. Page, “Periodontal Disease,” 1977. © Lea & Febiger, Philadelphia; 25.6b: © Evans Roberts; 25.9a: © Dr P. Marazzi/Photo Researchers, Inc.; 25.9b: © Frederick C. Skvara, M.D.; 25.10: © Science VU/Visuals Unlimited; 25.12: © Veronika Burmeister/Visuals Unlimited; 25.14: Courtesy of Philippe J. Sansonette, M.D., Professeur Institut Pasteur; 25.15: © David M. Rollins/Visuals Unlimited; 25.16: © Moredun Animal Health Ltd./Photo Researchers, Inc.; 25.17: © Science Source/Photo Researchers, Inc.; 25.22: © P.M. Motta & F. M. Magliocca/SPL/Photo Researchers, Inc.; 25.23: © Michael Abbey/Photo Researchers, Inc.; 25.24a: © Oliver Meckers/Photo Researchers, Inc.

Chapter 30 Opener: © Grant Heilman Photography; 30.4: From Y. Cohen and E. Rosenberg, “Microbial Mats,” Fig. 1a, pg. 4, 1989, American Society for Microbiology; 30.5: © SPL/Photo Researchers; 30.8: © Nancy Pearsall; 30.11a: © WHOI-D. Foster/Visuals Unlimited; 30.12b: © Stephan Imhof/ Philipps-Universität; 30.12c: © R.L. Peterson/Biological Photo Service; 30.13b: © John D. Cunningham/Visuals Unlimited; p. 737: Courtesy of J.P. Dalmasso

Chapter 26 Opener: © Kwangshin Kim/Photo Researchers, Inc.; 26.3: © Science VU/Fred Marsik/Visuals Unlimited; 26.4: © Custom Medical Stock Photo; 26.5: Centers for Disease Control; 26.8: © Biological Photo Service/Terraphotographics; 26.9: © Biophoto Associates/Photo Researchers, Inc.; 26.10: Courtesy of Stanley Falkow; 26.11: Courtesy of

Chapter 32 Opener: © Michael Newman/PhotoEdit; 32.1: © Paul Webster/ Tony Stone/Getty; 32.2 (all): © Martha Nester; 32.3 (all): Courtesy of the Wisconsin Milk Marketing Board; 32.6 (all): © Martha Nester; 32.7 (left): © Rachael Epstein/PhotoEdit; 32.7 (right): © William J. Weber/Visuals Unlimited; p. 764 (both): © Felicia Martinez/PhotoEdit

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Chapter 31 Opener: © Myrleen Cate/PhotoEdit; 31.7: Courtesy of IDEXX Laboratories, Inc.; 31.8: © Alan L. Detrick/Photo Researchers, Inc.; 31.9: © Phil Degginger/Color-Pic, Inc.; 31.11 (both): © Science VU/Visuals Unlimited

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Page numbers followed by t and f indicate tables and figures, respectively.

A ABC transport systems, 58, 58f, 58t, 59f, 73 ABO blood group antigens and antibodies in, 418, 418t typing in, 443, 443f abomasum, 735 abscess, 360, 534, 560, 561f definition of, 532t peritonsillar, 501 A-B toxins, 404t, 405, 513–514. See also botulinum toxin; cholera toxin; diphtheria toxin; pertussis toxin action of, 405, 406f in vaccines and therapies, 405 Acanthamoeba, virus in, 305 Accutane (isotretinoin), 534 acellular organisms, 12 acetaldehyde, 148 in fermentation, 147f acetic acid, 758, 758t, 760–761 acetic acid bacteria, 760–761 Acetobacter, 758t, 761–762 acetoin, 148 acetone, 148, 255 acetyl-CoA, 132, 132t, 133f, 141f, 142, 150 acetyl group, 30 acid(s), 24, 24f mixed, as fermentation end product, 148, 148f organic, of metabolic pathways, 129 production, and detection of bacterial growth, 99t, 103 acid-fast rods, medically important, 272t acid-fast stain, 48t, 50, 50f, 238, 261 acidic amino acids, 26, 27f acidic dyes, 49 Acidithiobacillus, 253t acidophiles, 24, 90t, 93 thermophilic extreme, 276 acidophilus milk, 756t, 757 Acidothiobacillus, 260 Acidothiobacillus ferroxidans, 93, 150–151 Acinetobacter baumannii, infection, nosocomial, 463t acne, 534 acquired immune deficiency syndrome (AIDS), 7, 427t, 428, 629t, 640–642, 642t, 697–710. See also HIV disease atypical progression to, 704–705 causative agent of, 5f, 641, 642t defining diseases of, 698, 699t early clusters of, 460

epidemic, 7, 640, 698, 698f epidemiology of, 641, 642t lifestyle and, 705–706, 706t pathogenesis of, 331, 333f, 641, 642t poverty and, 718 prevention and treatment of, 641, 642t, 705–709, 706t protozoan disease in, 286 symptoms of, 640–641, 642t vaccine sought for, 437t, 709–710 acquired resistance, to antimicrobial drugs, 470t, 472 Acremonium cephalosporium, 476 actin, 74 filaments, in eukaryotic cells, 74, 75f tails, and infection, 400, 400f Actinobacteria, 252t, 263t Actinomyces israelii, 570, 571f, 572t actinomycosis, 570–571, 572t causative agent of, 570, 572t epidemiology of, 571, 572t incubation period of, 572t pathogenesis of, 570–571, 572t prevention and treatment of, 571, 572t symptoms of, 570, 571f, 572t activated sludge method, of sewage treatment, 741, 750 activation energy, 130, 130f activator(s), of transcription, 177 activator-binding site, 177 activators, of transcription, 178f active immunity, 432, 432f definition of, 432t active site, of enzyme, 134, 135f active transport, in prokaryotic cells, 58, 58t, 58f–59f ACTs, 693, 694t acute infection, 325f, 325–328, 395 definition of, 321t acute necrotizing ulcerative gingivitis. See trench mouth acute-phase proteins, 360, 676 acute retroviral syndrome (ARS), 699, 704–705 acyclovir, 487, 487t, 488, 547, 639 acylated homoserine lactone, 181 acyl carrier protein, 155 adaptive immune response, 346–347, 366–390 artificially acquired, 432, 432f B cells in, 367, 368f cellular, 367f, 368f, 368–369 clonal selection in, 375, 376f definition of, 367t humoral, 367, 368f versus innate immune response, 366 key terms for, 367t lymphoid system and, 369f, 369–370

memory/memory cells in, 366–367, 368f, 375, 378–379 natural killer cells in, 384 naturally acquired, 432, 432f normal microbiota and, 393 primary, 367, 377–379, 377f secondary or anamnestic, 367 strategy of, 367–369 T cells in, 368–369, 368f ADCC. See antibody-dependentcellular cytotoxicity additive antimicrobial drugs, 472 adefovir dipivoxil, 608 adenine, 33, 33f, 161–162 adenoids, 496 adenosine deaminase deficiency, 427 adenosine diphosphate (ADP), 25, 130, 130f enzyme stimulation by, 137 adenosine triphosphate (ATP), 32, 130, 130f in carbon fixation, 154, 155f definition of, 127t detection, in measurement of bacterial growth, 99t, 103 enzyme inhibition by, 137 in eukaryotic cells, 76–77, 77f generation/synthesis of, 127, 127f, 133f, 139–147, 140f ATP synthase and, 142, 145–146 electron transport and, 142–147, 144f in fermentation, 147, 254 in glycolysis, 139, 140f, 146 in oxidative phosphorylation, 134t, 142, 146–147 in photosynthesis, 153–154 in respiration, 132–133, 133f, 134t, 142, 146 in transition step, 141f, 146 in tricarboxylic acid cycle, 141f, 142, 146 maximum theoretical yield from aerobic respiration, 146–147, 146f metabolic role of, 25, 25f, 130, 130f in prokaryotic cells, 57 proton motive force and, 142–147 transport systems using, 58, 58f, 58t, 59f utilization of, 127, 127f Adenoviridae, 324t. See also adenoviruses adenoviruses, 304f, 324t lower respiratory tract infection, 519 pharyngitis, 508, 508t epidemiology of, 508, 508t pathogenesis of, 508, 508t prevention and treatment of, 508, 508t symptoms of, 508, 508t

adenylic acid, 33f, 158 adherence in antibody-antigen binding, 372f antibody-antigen binding and, 372–373 of bacteria, 64, 64f, 66, 397–398, 398f of pathogens, 397–398, 398f adhesin, 66, 398, 398f adhesion molecules, in innate immune response, 354 adjuncts, in beer production, 759 adjuvants, for vaccines, 435–436 definition of, 432t ADP. See adenosine diphosphate advanced treatment definition of, 739t of wastewater, 740f, 741–742 Aedes mosquito, 295t, 660, 688–689 aerobe(s), obligate, 90t, 92, 92t, 253t, 261–262 aerobic chemolithotrophs, 253t, 259–260 aerobic chemoorganotrophs, 253t, 261–263 characteristics of, 253t aerobic respiration, 133, 134t, 253, 739 by Escherichia coli, 144–145, 145f maximum theoretical ATP yield from, 146–147 aerobic sewage treatment, 739 aerotaxis, 66 aerotolerant anaerobe(s), 92, 92t, 147, 534 affinity, of enzyme, 137 affinity maturation, of B cells, 378, 378f aflatoxin, 292, 410, 762 African sleeping sickness, 667–668, 668t, 691 causative agent of, 286t, 288, 668, 668f, 668t epidemiology of, 668, 668t incubation period of, 668t pathogenesis of, 411, 668, 668t prevention and treatment of, 668, 668t symptoms of, 667–668, 668t African trypanosomiasis, 667–668 agammaglobulinemia, 426, 427t agar, 4f, 31t, 83, 87, 87f, 96, 96t algae as source of, 87, 283 blood, 96, 96t, 97f, 238 chocolate, 96, 96t MacConkey, 96t, 97, 97f, 238 nutrient, 96, 96t Thayer-Martin, 96, 96t Agaricus campestris, 289t, 291f agarose, 214–215 agar plate, 87 agar slant, 88

I-1

nes95432_ind_I1-I40.indd I-1

9/16/08 10:26:17 AM

I-2

INDEX

age, and disease, 456 agents, 12 agglutination, 338, 373 definition of, 432t agglutination reactions, 372f, 443, 443f agglutination tests direct, 443 latex, 443, 443f passive, 443 Agrobacterium, 263t, 265, 265f, 727 tumor-inducing plasmid of, 206, 206f, 217, 265 Agrobacterium tumefaciens, 217, 265f AIDS. See also acquired immune deficiency syndrome definition of, 699 AIDS-related complex (ARC), 699 airborne transmission, 455, 455f, 464 air filtration, 112t, 115, 455, 464 alanine, 27f albendazole, 491t albuterol, for asthma, 417 Alcaligenes, 762 alcohol(s), as germicides, 118–119, 118t alcoholic beverages, production of, 6, 753–754, 758–760, 758t alcoholic fermentation, by yeasts, in food production, 753–754, 758–761, 758t aldehyde group, 30, 31f aldehydes, 118t, 119 alder, nitrogen-fixing root nodules of, 735 Alexander the Great, 738 alga (pl., algae), 10–11, 11f, 281–285 as agar source, 87, 283 blue-green. See cyanobacteria brown, 283t cell walls of, 283, 283t characteristics of, 10–11, 11t classification of, 282, 283t colonial, dark-field microscopy of, 43f coralline, 283t definition of, 281t eukaryotic cell structures in, 283–284 filamentous, dark-field microscopy of, 43f golden brown, 283t green, 11f, 43f, 283t habitats of, 282, 283t major groups of, characteristics of, 283t motility of, 283t multicellular, 282–283 and paralytic shellfish poisoning, 282, 284–285 photosynthesis in, 152–153, 152t, 281–282 pigments of, 282, 283t red, 283t reproduction of, 283–284, 283t, 284f in soil, 728 storage products of, 283t structure of, 282–283, 282f toxic, 726 toxins of, 282, 284–285 unicellular, 282 algologists, 281

nes95432_ind_I1-I40.indd I-2

algology, 281 alimentary system infections. See digestive system infections alkalophiles, 24, 90t, 93 alkylating agents, 190, 191t alleles, in MHC molecules, 385 allergens, 414–415 definition of, 415 wheal and flare skin test for, 416f allergic encephalitis, 665 allergic rhinitis, 415, 417 allergy(ies), 414. See also hypersensitivities to antimicrobial drugs, 472 definition of, 415 to fungi, 292 hygiene hypothesis for, 393 to latex, 422 to penicillin, 383 allicin, 755 allografts, 423 definition of, 415 allosteric enzyme(s), 137, 157 regulation of, 137 allosteric inhibition, 176 allosteric site, 137 allylamines, 488f, 489, 489t alpha helix, 28 alpha hemolysis, 97, 97f alpha interferon. See interferon alpha α-ketogluterate, 132t, 141f, 142, 156, 157f α-toxin, 535–536, 537t, 569 Alternaria, 762 alternative sigma (σ) factors, 177 Altman, Sidney, 175 AluI, 214t alum in drinking water treatment, 745 as vaccine adjuvant, 436 Alzheimer’s disease, protein folding in, 37 amalgam, for dental fillings, 587 Amanita muscaria, 289f amantadine, 486, 487t, 521 amebiasis, 286t, 612–613, 614t causative agent of, 612–613, 613f, 614t epidemiology of, 613, 614t pathogenesis of, 613, 614t prevention and treatment of, 613, 614t symptoms of, 613, 614t amebic dysentery, 613 amebic meningoencephalitis, primary, 667 American Society for Microbiology, 753 Ames, Bruce, 197 Ames test, for mutagens, 197, 197f amides, 27f amikacin, 474t, 477 amino acid(s) acidic, 26, 27f alcoholic, 27f aromatic, 27f synthesis of, 156–157, 157f basic, 26, 27f D-form, 26, 27f–28f, 64 hydrophilic, 26, 28 hydrophobic, 26, 28 imino, 27f

L-form, 26, 27f–28f natural, 26 peptide bonding of, 28, 28f stereoisomeric forms of, 26, 27f–28f structure of, 26, 27f subunits, 26 sulfur-containing, 27f synthesis of, 156–157, 728 aminoglycosides, 474t, 477, 477f amino group, 26, 26f, 27f 2-amino purine, 190, 191f, 191t amino terminal, 28 ammonia oxidizers, 150, 260 ammonia stripping, 742 ammonification, 730 amoxicillin, 473t, 476, 476f, 572 amoxicillin-clavulanic acid (Augmentin), 476, 572 amphibolic pathways, 132 amphotericin B, 488, 489t, 577, 667 ampicillin, 470, 473t, 476, 476f, 599 amylase(s), 149, 149f, 158 salivary, 583 Anabaena, 252t, 253t nitrogen fixation by, 258, 258f Anabaena azollae, 258, 735 anabolic pathways, 155–158, 156f anabolism, 127, 127f definition of, 127t anaerobe(s) aerotolerant, 90t, 92, 92t, 147 facultative, 90t, 92, 92t, 134, 147, 253t, 262 obligate, 90t, 92, 92t, 147, 253, 756 characteristics of, 252t culture of, 98 anaerobe chamber, 98, 98f anaerobe container, 98, 98f anaerobic chemolithotrophs, characteristics of, 252t anaerobic chemoorganotrophs, 254 characteristics of, 252t and fermentation, 254–256 respiration in, 134t, 252t anaerobic chemotrophs, 253–256 anaerobic cultures, 98, 98f anaerobic digestion, in sewage treatment, 739, 742–743 definition of, 739t anaerobic environments, 91 anaerobic respiration, 133, 253, 731 by chemoorganotrophs, 134t, 252t by obligate anaerobes, 92 anaerobic sewage treatment, 739 anaerobic wounds, 561, 566–571 anal cancer, in immunodeficient patients, 711 analytical studies, in epidemiology, 458 anammox, 731 anamnestic response, 367 anaphylactic shock, 415, 417 anaphylaxis, 414 definition of, 415 generalized, 417 localized, 416–417 anatomical barriers breaching of, by pathogens, 399–400 as ecosystems, 392–393 immune function of, 348, 348f Ancalomicrobium adetum, 53f Ancylostoma duodenale, 298t

anemia aplastic, chloramphenicol and, 472, 478 autoimmune hemolytic, 424t malaria and, 692 aneurysm, 678 definition of, 675t animal(s), as habitats, 270–274 animal bite(s), 663–664 animal cells, 70f animal feed, antimicrobial drugs in, 486, 602 Animalia, 234 animal reservoirs, 453 animal viruses, 302–303, 321–343 acute infections by, 325–328, 325f assembly or maturation of, 328, 328f attachment of, 325–326, 329t carriers, 329 chronic infections by, 329–332, 330f, 332t classification of, 321–323 comparison with phages, 329t DNA, 324t DNA replication in, 326–328, 329t effects on cells they infect, 334f entry by, 326, 326f–327f, 329t genetic reassortment of, 335, 335f genome of, 322, 326–328 host range of, 335 interactions with hosts, 325–333 latent infections by, 329–332, 330f, 331t nomenclature for, 322 nucleic acid replication in, 326–328 persistent infections by, 325, 329–332 protein synthesis in, 326–328 release of, 328, 329f, 329t replication of, targeting to site of, 326, 329t RNA, 323t shapes of, 321, 322f shedding of, 328 slow infections by, 329–332, 330f structure of, 321–322, 322f study of, methods for, 336–338 transcription of, 326–328, 327f transmission of, 328 fecal-oral route for, 322, 324t groupings based on, 322–324, 324t uncoating of, 326, 329t anions, 20–21 annealing, of DNA, 213f, 214, 227–229 Anopheles mosquito, 286, 295t, 692f, 693–694, 694t anoxic atmosphere, 253 anoxygenic photosynthesis, 152, 152t, 154, 256 anoxygenic phototrophs, 251, 253t, 256–257 definition of, 252t filamentous, 252t antagonism, microbial, 723 antagonistic antimicrobial drugs, 472 antenna complex, of photosystem, 152 antennae pigments, 152 anthrax, 2, 4f, 26, 69, 264, 391, 396 for bioterrorism, 264, 466 use in 2001, 2, 5f, 466, 512

9/2/08 5:33:35 PM

Index cutaneous, 466, 512 gastrointestinal, 466 inhalation, 512 inhalational, 466 prophylaxis against, 466 vaccine, 434t, 466 “anthrax pneumonia,” 512 antibacterial drugs characteristics of, 473t–474t definition of, 470t inhibition by of cell wall synthesis, 473t–474t, 475–477, 475f–476f of folate synthesis, 474t of metabolic pathways, 474t, 478–479, 479f of nucleic acid synthesis, 474t, 478 of protein synthesis, 473t–474t, 477–478, 477f interference by with cell membrane integrity, 474t, 479 with processes essential to Mycobacterium tuberculosis, 474t, 479 mechanism of action of, 61–62, 473–479, 473f antibiograms, 244t, 245–246, 246f antibiotic(s) bacterial production of, 723 definition of, 470t design, genome mining and, 182 development of, 208 discovery of, 470 from fungi, 293 new, development of, 5f, 208, 470, 491 as secondary metabolites, 89 semisynthetic, 471 from Streptomyces, 265, 470–471 transport systems and, 79 antibiotic-associated colitis, 472, 478, 586 antibiotic-associated diarrhea, 350, 393 antibiotic susceptibility patterns, 244t, 245–246, 246f antibody(ies), 347, 366–367 anti-human IgG, 439, 444, 446 anti-Rh, 419 avoidance by eukaryotic parasites, 410–411 by pathogens, 403 combinatorial associations in, 387 constant region of, 372, 372f cross-reactive, 408 in cytotoxic hypersensitivities, 418 damage associated with, 408 definition of, 367t diversity of, 387, 387f generation of, 387, 387f fluorescent, 51f, 52 gene rearrangement in, 387, 387f heavy and light chains of, 371, 372f heterophile, 686 imprecise joining of, 387 maternal, transplacental transmission of, 374, 374f, 432 monoclonal, 5f, 417–418, 439, 440f natural, 418 nature of, 371–375 obtaining, 439

nes95432_ind_I1-I40.indd I-3

as opsonins, 372f, 373 polyclonal, 439 production by B cells, 367 reactions with antigens agglutination, 372f, 373, 443, 443f antibody-dependent cellular cytotoxicity, 372f, 373, 384 complement activation, 372f, 373 immobilization and prevention of adherence, 372–373, 372f neutralization, 372, 372f opsonization, 372f, 373 precipitation, 372f, 373, 441–443, 441f–443f protective outcomes of, 372–373, 372f quantifying, 439, 441f and serology, 240 structure and properties of, 371–372, 372f testing for, 438–448 titer, 378, 439 rise in, 439 variable region of, 372, 372f and viruses, 410 antibody-dependent-cellular cytotoxicity (ADCC), 372f, 373, 384, 418, 703 antibody response B cells and, 367, 368f primary, 367 characteristics of, 377–379, 377f secondary (memory), 367 T cells and, 368f anticodon, 171t, 172, 172f antifungal drugs cell division targeted by, 488f, 489, 489t characteristics of, 489t mechanisms of action, 73, 488–490, 488f, 489t nucleic acid synthesis targeted by, 488f, 489–490, 489t plasma membrane synthesis and function targeted by, 488f, 488–489, 489t antigen(s), 240, 243, 347, 366 adaptive immune response to, 366–390 primary, 367, 377–379, 377f secondary or anamnestic, 367 B-cell response to, 367 definition of, 367t, 370–371 endogenous, 380 exogenous, 380 nature of, 370–371 processing of, 380 recognition of, 367–369, 378–384 T-cell response to, 368–369, 378–384 T-dependent, 377 response to, 377f testing for, 438–448 T-independent, 377, 383 response to, 379, 379f antigen-antibody complexes, 408 antigen-antibody reactions agglutination, 372f, 373, 443, 443f antibody-dependent cellular cytotoxicity, 372f, 373, 384

complement activation, 372f, 373 immobilization and prevention of adherence, 372f, 372–373 neutralization, 372, 372f opsonization, 372f, 373 precipitation, 372f, 373, 441f, 441–443 protective outcomes of, 372f, 372–373 quantifying, 439, 441f and serology, 240 antigenic [term], use of, 371 antigenic determinants, 371, 371f antigenic drift, 335, 520, 520f definition of, 321t, 496t antigenic shift, 335, 520, 520f definition of, 321t, 496t antigenic variation, 335, 403, 519–520, 520f antigen presentation, 377, 377f, 380 by B cells, 377, 377f by major histocompatibility complex class I molecules, 380, 380f by major histocompatibility complex class II molecules, 380f MHC molecule diversity and, 385 superantigens and, 406, 406f and vaccines, 383 antigen-presenting cell(s) (APC), 380–381 definition of, 367t antigen-sampling processes, exploitation of, by pathogens, 399–400, 400f antihelminthic drugs, 490–491, 490t–491t antihistamines, for hypersensitivity reactions, 416 anti-human IgG antibodies, 439, 444, 446 antimicrobial chemicals, in food, 755 antimicrobial drugs, 469–494 action of, 471 spectrum of, 471 additive, 472 adverse effects of, 472 allergic reactions to, 472 antagonistic, 472 bacterial production of, 723 bacterial sensitivity to, determination of, 480–483, 480f–482f commercial modifications to testing, 482, 482f E test for, 482, 482f Kirby-Bauer disc diffusion test for, 481–482, 481f broad-spectrum, 470t, 471 combinations of, effects of, 472 concentrations in blood or other body fluids, measurement of, 481, 481f definition of, 470, 470t design, genome mining and, 182 development of, 208 discovery of, 469–470 excretion of, 472 features of, 471–472 history and development of, 469–470 key terms for, 470t magic bullet, 208

I-3

metabolism of, 472 minimum bactericidal concentration of, 481 minimum inhibitory concentration of, 480–481, 480f, 482, 482f narrow-spectrum, 470t, 472 new, development of, 5f, 208, 470, 491 resistance to. See antimicrobial resistance selective toxicity of, 471 suppression of normal microbiota, 393 suppression of normal microbiota by, 350, 472, 586 synergistic, 472 therapeutic index of, 471 tissue distribution of, 472 toxic effects of, 472 transport systems and, 79 use and misuse of, global impact of, 486 antimicrobial procedures. See also microbial control selection of, 110–111 antimicrobial resistance, 123, 472, 483–486, 578 acquired, 470t, 472 acquisition of, 483–484, 484f drug-inactivating enzymes in, 483, 484f emergence and spread of, prevention of, 485–486 gene transfer in, 484, 484f global impact of, 486 increased elimination of drugs in, 483–484, 484f innate or intrinsic, 470t, 472 mechanisms of, 483–484, 484f mutations and, 195 prevention of, 491 public education on, 485 responsibilities of patients in, 485 responsibilities of physicians and health care workers in, 485 R plasmids and, 205–207, 205f, 205t, 470t, 484 as selectable marker for cloning vectors, 219, 219f selective advantage of, 483, 483f spontaneous mutations in, 484, 484f target molecule alteration in, 483, 484f transposons and, 185, 207–208, 207f antimicrobial substances, in innate immune response, 348–349, 349f antiparallel DNA strands, 163f, 164 antiparasitic drugs, 490–491, 490t–491t antiprotozoan drugs, 490–491, 490t antiseptics, 117 definition of, 108, 108t antiserum, 433 definition of, 432t antitoxin, 366, 433 antiviral drugs assembly and release of viral particles targeted by, 487t, 488 characteristics of, 487t definition of, 470t entry inhibitors, 486, 486f for influenza, 486, 487t, 521

9/2/08 5:33:35 PM

I-4

INDEX

antiviral drugs—Continued integrase inhibitors, 488 mechanisms of action, 486–488, 486f nucleic acid synthesis targeted by, 486f, 487–488, 487t and viral uncoating, 486, 486f, 487t antiviral proteins activated, 357, 357f inactive, 357–358, 357f ANUG (acute necrotizing ulcerative gingivitis). See trench mouth Apicomplexa, 286, 286t, 610 APITM, 239, 241f aplastic anemia, chloramphenicol and, 472, 478 aplastic crisis, 552 apoptosis, 354, 357–358, 357f, 362, 375, 382, 382f, 704 definition of, 347t viruses and, 409 apple scab, 754f aquatic bacteria, 53, 53f, 263t, 266–270, 309 gas vesicles in, 68–69 sheathed, 263t, 266, 266f aquatic environments, specialized, 726 aquatic habitats, 725–727, 731 aquatic phages, 309 Aquifacae, 252t aquifers, 744 Aquifex, 253t, 260 arachnids, as vectors of disease, 295, 295t, 297 arachnoid, 648 arboviruses, 322–323, 660, 661t, 689 definition of, 648t ARC (AIDS-related complex), 699 Archaea, 232, 234, 235f cell walls of, 64 characteristics of, 10, 10t, 40, 56, 235t, 254 extreme conditions for, 94, 275–276 as extremophiles, 90 temperature requirements of, 91 Arenaviridae, 323t arginine, 27f aromatic amino acids, synthesis of, 156–157, 157f ARS. See acute retroviral syndrome arsenic, as preservative, 120 artemisinin, 693 arteries, 675f, 676 arteriosclerosis, 676 arthropods, 295–297, 295t, 322–323, 455, 660 definition of, 281t Arthus reaction, 420 artificial competence, in DNA-mediated transformation, 201, 201f artificial wetlands, in sewage treatment, 741, 742f ascariasis, 298t Ascaris, 298t wet mount of, 237f Ascaris lumbricoides, 298t Ascomycetes, 288–289, 289t ascorbic acid, as reducing agent, 98 aseptic meningitis, 659 aseptic techniques, 4f, 86, 107, 109 definition of, 108t A-site, in translation, 173, 174f

nes95432_ind_I1-I40.indd I-4

asparagine, 27f aspartame, 18 aspartic acid, 27f Aspergillus, 11f, 289t, 292, 762 Aspergillus flavus, 762 toxin of, 410 Aspergillus nidulans, 293 Aspergillus oryzae, 758t, 761, 762t Aspergillus sojae, 761, 762t Association for Professionals in Infection Control and Epidemiology, 466 asthma, 292, 415, 417 dust mites and, 297 fungi and, 292 astrobiology, 276 asymptomatic carriers, 453 asymptomatic infection, 453 Atabrine. See quinacrine ataxia-telangiectasia, 427t athlete’s foot, 410, 554 atom(s), 18–20 composition of, 18–19, 19f atomic force microscopes, 41, 45t, 48, 48f atomic number, 19–20, 19t atomic weight, 18t, 20 ATP, 19t. See also adenosine triphosphate ATP synthase, 142, 145–146 atrium, cardiac, 675f, 676 attachment proteins, 303, 321, 325 attachment spikes, 303, 321, 325 attack rate, 451, 451t attenuated vaccines, 433–435, 434t definition of, 432t versus inactivated vaccines, 435t attractant, of bacteria, 66 atypical pneumonia, 478 Augmentin, 476, 572 auramine, 51f, 52 autoantibodies, 387, 441 autoantibody-mediated disease, 425 autoclaves, 112t, 113–114 flash, 113 indicators used in, 113–114, 113f pressurized steam in, 113, 113f autograft, 423 definition of, 415 autoimmune disease, 366, 414–430 characteristics of, 424t definition of, 415 spectrum of, 425 superantigens and, 406 treatment of, 425–426 autoimmune hemolytic anemia, 424t autoimmune process, 424 autoimmunity, and HIV infection, 704 autolysis, 509 definition of, 496t autotrophs, 94 auxotrophs, 186t, 187 isolation of, 195–196 avermectins, 491t Avery, Oswald T., 5f, 199, 495 avian influenza, 5f, 461, 520, 524, 524f AVPs. See antiviral proteins axial filament, 269 axons, 648 definition of, 648t azelaic acid, 534 Azelex, 534 azidothymidine (AZT), 332

azithromycin, 474t, 478, 633 azoles, 488f, 489, 489t Azolla, 258, 735 Azorhizobium, 263t, 265 Azospirillum, 728 Azotobacter, 263t, 264, 264f, 721, 727, 730 AZT. See azidothymidine Aztec Empire, 7 aztreonam, 474t, 477

B bacillary angiomatosis, 573 Bacille Calmette-Guérin (BCG), 516 Bacillus, 264 antibiotics from, 471 characteristics of, 263t control/destruction of, 110 endospores, 51, 68 in food spoilage, 762 infection, ocular, 505 intestinal, in obese people, 394 in milk, 724 in soil, 727 bacillus (pl., bacilli), 53 bacillus (shape), 52f Bacillus alcalophilus, 93 Bacillus anthracis, 396, 512 for bioterrorism, 264, 466 use in 2001, 2, 5f, 466 endospores of, 69, 264 infection, 2, 391. See also anthrax medical importance of, 264, 272t structure of, 26 toxin of, 404t Bacillus coagulans, 762 Bacillus fastidiosus, 95 Bacillus megaterium, 14, 14f Bacillus stearothermophilus, 762 Bacillus subtilis, 62f natural competence in, 200 bacitracin, 474t, 477 backyard composting, 747, 748f BACs. See bacterial artificial chromosomes bacteremia, 395, 675 bacteria. See also specific organisms and types adherence of, 64, 64f, 66, 397–398, 398f animal habitats of, 270–274 antigenic variation in, 181 aquatic, 53, 68–69, 263t, 266–270, 309 associating with plants, 205–206, 217, 265, 721, 734–735, 734f bioluminescent, 263t, 268–269, 269f in bioremediation, 6, 86 breaching of anatomical barriers by, 399–400 carbon sources for, 95, 95t cell wall-less, 272t, 273 cell wall of, 30, 32, 59–64, 59f chemotactic, 66, 66f chromosomes of, 67–68 chronic diseases caused by, 9 classification of, 232 Bergey’s Manual of Systematic Bacteriology for, 234, 236t by DNA base ratio (GC content), 248, 248t

DNA hybridization for, 247–248, 248t genotype characteristics for, 248t numerical taxonomy for, 248 phenotype characteristics for, 248, 248t relatedness in, methods of determining, 246–248, 248t ribosomal RNA in, 232, 248t, 249 strategies for, 233–236 colonization by, 398 colony, 86, 87f, 238 growth of, 89–90 control/destruction of, 107–125. See also microbial control cylindrical or rod, 52–53, 52f cytoskeleton of, 68 damage to host caused by, 403–408 defense against. See immunity delivery of effector molecules by, 398 deriving nutrition from other organisms, 267–269 disinfectant-resistant, 123 DNA repair systems in, 195t drugs against. See antibacterial drugs ecophysiology of, 263–276, 263t energy sources for, 94–95, 95t exotoxins of, 403–407, 404t fastidious, 94, 155 flagellated, 65–66, 65f in food production, 756–762 as food source, 766 in food spoilage, 754, 754f, 762 genetically engineered, 215–217 for protein production, 216–217 uses of, 215–217 gene transfer in, 198–208 general experimental approach for detecting, 198, 198f gliding, 66 glycocalyx of, 64, 64f Gram-negative, 40, 49, 55t, 238 agents targeting peptidoglycan in, 61–62 antimicrobial resistance of, 476 cell wall of, 61, 63f endotoxin of, 407–408 flagella in, 65f inner membrane of, 61 medically important, 271t outer membrane of, 61, 63f periplasm of, 61, 63f protein secretion by, 61 serum-resistant, 400–401 type III secretion systems of, 398, 398f Gram-positive, 40, 49, 55t, 238 cell wall of, 61, 62–63, 62f medically important, 272t in soil, 727 Gram-positive versus Gram-negative, 60t groupings of, 53, 53f growth curve of, 88–89, 88f–89f growth of, 83–106. See also culture(s); culture media closed (batch) systems for, 88 detection and measurement of, 99–103, 99 environmental factors and, 90–93, 90t

9/16/08 10:26:39 AM

Index exponential, health consequences of, 84–85, 85t in food, 754–756 in laboratory conditions, 88–90 in nature, 104 nutritional factors and, 93–95 open system for, 88 oxygen requirements for, 90t, 91–92, 755–756 pH and, 90t, 92–93 temperature and, 90–91, 90t, 91f, 137 water availability and, 90t, 93, 755 haploid nature of, 190 heat-resistant, 2 hiding within host cell, 400 hydrogen, 150, 150t identification of biochemical tests for, 237t, 238–239, 239f, 240t fatty acid analysis for, 237t, 240, 241f genotypic characteristics used in, 237t, 241–243 Gram stain for, 238, 238f by metabolic differences, 237t, 238–240 methods for, 237t by microscopic morphology, 237–238, 237t nucleic acid probes for, 237t, 241–242, 242f phenotypic characteristics for, 237–241, 237t polymerase chain reaction for, 237t, 242 sequencing ribosomal RNA genes for, 237t, 242–243, 243f serology for, 237t, 240 interaction of mixed organisms in nature, 86 iron, 150, 150t lacking cell wall, 63–64, 63f lactic acid, 755 in low-nutrient environments, 723 magnetotactic, 66, 66f, 270 morphology of, 52–53 motility of, 65–66, 65f, 66f unusual mechanisms of, 269–270 multicellular associations of, 53–54, 264, 264f in nature, 104, 721 new species of discovery of, 16 search for, 16 nitrifying, 150, 150t nomenclature for, 12, 235 petroleum-degrading, 749–750, 750f phototactic, 66 plasmids of, 68 pleomorphic, 53 prosthecate, 263t, 266–267 definition of, 252t resting stage of, 264–265 sensitivity to antimicrobial drugs, determination of, 480–483, 480f–482f shape of, 52f, 52–53, 232, 237 sheathed, 263t, 266, 266f, 726 size of, 237 variations in, 14, 14f, 15, 15f spherical (coccus), 52–53, 52f

nes95432_ind_I1-I40.indd I-5

storage granules in, 68, 68f, 270 strains, characterizing differences of, 243–245, 244t structure of, 54–70 sulfate-reducing, 145 sulfur, 150, 150t sulfur-oxidizing, definition of, 252t taxonomy, 233–236 terrestrial, 263–266, 263t, 727–728 transport systems of, 57–59, 79 twitching, 66 useful products from, 6–7 viruses of, 302–319. See also phage(s) key terms for, 303t vital activities of, 6 Bacteria (domain), 232, 234, 235f characteristics of, 10, 10t, 40, 56, 235t phylogenetic tree of, 246, 247f bacterial culture. See culture(s) bacterial genetics, 185–211 key term for, 186t bacterial infections. See also specific infections biofilms and, 86 bladder (cystitis), 621–622, 622t blood and vascular system, 677–680 central nervous system, 650–658 foodborne, 243, 455, 754, 763–765, 763t, 764f lower digestive system, 595–603 lower respiratory, 509–518 lymph nodes and spleen, 680–685 pyogenic, 427, 562 sexually transmitted, 629–637 skin, 535–545 upper digestive system, 586–591 upper respiratory, 499–506 vaginal (vaginosis), 625–626, 626t waterborne, 455 wound anaerobic, diseases due to, 566–571 bite, 572–576 common, 562–565 bactericidal, definition of, 108, 108t bactericidal drugs, 470t, 471 bacteriochlorophyll, 152, 152t, 256 bacteriocins, 723 bacterioid, 734 bacteriophage(s), 12f, 302–319. See also phage(s) definition of, 303, 303t T4, 304f transduction by, 201, 202f bacterioplankton, 309 bacteriorhodopsin, 275 bacteriostatic, 117 definition of, 108t bacteriostatic drugs, 470t, 471 Bacterium radicola, 721 Bacteroides anaerobic conditions for, 92 animal habitats of, 272 infection blood (septicemia), 679 of human bite wounds, 575 intestinal, in lean people, 394 medical importance of, 271t in mucous membranes, 272

in normal microbiota, 272 genitourinary, 620 of respiratory system, 498t, 499 Bacteroides fragilis, 272, 478 Bacteroidetes, medical importance of, 271t baker’s yeast, 761. See also Saccharomyces cerevisiae balanced pathogenicity, 325, 397, 453 Balantidium, 286t Balantidium coli, 286 Baltimore, David, 332, 697 BamHI, 214t Bang, Frederik, 681 Bang’s disease. See brucellosis Bartonella henselae, 572–574, 574t Bartonella quintana, 296 basal body, of bacterial flagella, 65f, 66 base(s), 24, 24f base, DNA. See DNA base(s) base analogs, 190, 191f, 191t basement membrane, 348, 349f base-pairing, of DNA, 163–164, 163f and nucleic acid hybridization, 227–229 base substitution, 188, 188f basic amino acids, 26, 27f basic dyes, 49 Basidiomycetes, 288–289, 289t basidiomycetes, 666 basophils, 350, 351f, 352t batch systems, 88 B-cell receptors, 368, 377 B cells (B lymphocytes), 352, 367–368 activation of, 377 TH cells in, 383 affinity maturation of, 378, 378f antibody production by, 367 in antibody response, 367, 368f primary, 377–379 to T-dependent antigens, 379 to T-independent antigens, 379f antigen presentation by, 377, 377f antigen recognition by, 367 antigen-specific, clones of, 368, 375 class switching in, 378, 378f clonal deletion of, 387 definition of, 367t development of, 370, 385–388 gene rearrangement in, 387, 387f in humoral immunity, 367–368, 368f in immunodeficiencies, 426, 427t imprecise joining in, 387 lymphomas, in immunodeficient patients, 711 memory, 367, 368f, 375, 376f, 378–379 in mononucleosis, 686, 687f self-reactive, negative selection of, 387 BCG. See Bacille Calmette-Guérin Bdellovibrio, 228f, 263t, 267 Beadle, George, 161 beer commercial production of, 759–760, 760f fermentation of, 4f, 6, 754, 758t, 759–760, 760f filtration of, 115, 760f bee sting, and anaphylaxis, 417 Beggiatoa, 253t, 259–260, 259f, 731

I-5

Beijerinck, Martinus Willem, 251, 302, 721 Beijerinckia, 721 benzalkonium chloride, 118t, 121 benzimidazoles, 491t benzoic acid, 122, 755, 765 benzyl penicillin. See penicillin G Bergey’s Manual of Systematic Bacteriology, 234, 236t β-carotene, 217 β-galactosidase, 149, 176 β-lactamase, 476 extended-spectrum, 476 β-lactamase inhibitor, penicillin plus, 476 β-lactam drugs, 473t, 475, 475f β-lactam rings, 475, 475f β-oxidation, 149f, 150 beta hemolysis, 97, 97f beta interferon. See interferon beta beta phage, 307t beta sheet, 28 beverage production, microorganisms in, 756–762 bidirectionality, of DNA replication, 164, 165f Bifidobacterium, 272t, 273 biguanides, 118t, 119 bilayer membrane, 36, 36f, 56, 56f bile, 584 definition of, 582t bile pigment, 584 binary fission, 10, 53, 84, 84f, 164 of algae, 283–284, 284f protozoan, 288, 288f in yeast, 289 Binaviridae, 323t binding proteins, 58 Binomial System of Nomenclature, 12 bioaugmentation, 750 biochemical oxygen demand definition of, 739t reduction in sewage treatment, 739 biochemical tests for bacteria identification, 238–239, 239f, 240t for bacterial identification, 237t commercial modifications of, 239–240, 241f dichotomous key for, 239, 241f important, characteristics of, 240t biochemical typing, for characterizing bacterial strains, 243, 244t biocides, 108 biodiversity, 221 definition of, 6, 722 Golden Age of, 16 biofilms, 54, 64, 85–86, 85f–86f, 180, 398, 585, 722, 724 definition of, 84 and infection, 120 in sewage treatment, 741 biofuels, 126, 148 biogeochemical cycling, 728–733 bioinformatics, 181, 208, 221 bioleaching, 260, 260f biological barriers, of food, 755 biological magnification, of DDT, 749, 749t biological vector, 295, 455 bioluminescent bacteria, 263t, 268–269, 269f

9/16/08 10:26:40 AM

I-6

INDEX

biomass definition of, 6, 722 as food source, 766 measurement of, 99t, 102–103 biomass production, 728 biomining, 150–151 biopsies, 540–541 bioreactor, 750 bioremediation, 86, 262, 727, 749–750 applications of, 6 definition of, 6, 739t, 749 means of, 749–750 microbiology of, 749–750 off-site, 750 of oil spills, 6, 749–750, 750f in situ, 750 biosphere, definition of, 722 biostimulation, 749 biosynthesis, 127 precursor molecules in, 155–158, 156f biotechnology, 212–231, 293–294 applications of, 215–218 definition of, 212 in mining industry, 151 plant, 206 tools of, 213–215 bioterrorism, 431 anthrax for, 264, 466 2001 attacks, 2, 5f, 466, 512 category A agents, 466 category B agents, 466 DNA technologies and, 221 smallpox as potential agent for, 7, 431, 466, 554 biotype, 243 biovar, 243 Bishop, Michael, 5f 1,3-bisphosphoglycerate, 140f bite wound infections, 572–576 human bites, 574–576, 575t Pasteurella multocida, 572, 572t streptobacillary rat bite fever, 574, 575t black bread mold (Rhizopus stolonifer), 289, 289t, 291f black death. See plague bladder, 619, 619f of algae, 283 infections of, 621–622, 622t blades, of algae, 282 bleach. See sodium hypochlorite blood antimicrobial drugs in, measurement of, 481, 481f precautions with, 465 system, anatomy and physiology of, 675–676, 675f blood agar, 96, 96t, 97f, 238 blood-brain barrier, 649 definition of, 648t blood infections, 674–696 bacterial, 677–680 protozoan, 690–694 viral, 686–690 blood poisoning. See septicemia bloodstream, as pathway to CNS, 649–650 blood transfusion, hypersensitivity reactions to, 418 bloom, 258, 258f algal, phages and, 309

nes95432_ind_I1-I40.indd I-6

blue-green algae. See cyanobacteria B lymphocytes. See B cells (B lymphocytes) body fluids antimicrobial drugs in, measurement of, 481, 481f precautions with, 465 Body Substance Isolation, 465 body weight, and intestinal microbiota, 394 boil(s), 360, 395, 535, 536f boiling, for microbial control, 112, 112t bone, extensions from, as pathway to CNS, 650 bone marrow, 369f bone marrow transplantation, 424 booster vaccines, 435 Bordetella pertussis, 403, 513, 513f, 514t infection, reductions in, 461 toxin of, 404t Borrelia, 273 Borrelia burgdorferi, 543, 543f infection, 544f, 545t. See also Lyme disease medical importance of, 272t, 273 vectors for, 295t, 297 Borrelia hermsii, medical importance of, 272t, 273 Borrelia recurrentis, 272t, 273, 296 Botox, 658, 764 Botrytis, 762 bottom yeasts, 760 botulinum antitoxin, 405, 466 botulinum toxin, 69, 114, 122, 404t, 405, 657–658, 764 cosmetic and medicinal uses of, 658, 764 botulism, 397, 657–658, 658t, 763–764, 763f anaerobic conditions and, 92, 255, 756 bioterrorism potential of, 466 canning process and, 114, 764 causative agent of, 69, 92, 657, 657f, 658t definition of, 648t epidemiology of, 658, 658t foodborne, 657–658, 763–764 intestinal, 657–658 nitrate additives and, 122 pathogenesis of, 657–658, 658t prevention and treatment of, 658, 658t symptoms of, 657, 658t wound, 657–658 bovine spongiform encephalopathy, 7, 320 Boyer, Herbert, 5f bradykinin, 360 Bradyrhizobium, 263t, 265, 734 brain, 648, 648f pathways to, 649–650 branch, of phylogenetic tree, 246, 247f, 249 branched metabolic pathways, 129, 129f bread-making, 6, 758t, 761, 761f breakbone fever (dengue), 323, 688 breast cancer, susceptibility genes, 192

breast-feeding antibody transmission via, 374, 432 HIV infection transmission via, 705 breath test, for Helicobacter pylori, 239 brevetoxin, 284 Brevibacterium linens, 757 brewer’s yeast, 760, 760f bright-field microscopes, 41–43, 44f, 44t brine, 122 broad host range plasmids, 205 broad-spectrum antimicrobial, 470t, 471 broad-spectrum penicillins, 473t, 476, 476f 5-bromouracil, 190, 191f, 191t bronchiolitis, 496 bronchitis, 496 brown algae, 283t Brucella, 682 infection, 681–682, 683t. See also brucellosis bioterrorism potential of, 466 Brucella abortus, 682, 753 Brucella canis, 682 Brucella melitensis, 681–682 Brucella suis, 682 brucellosis, 681–682, 683t, 753 causative agent of, 682, 683t epidemiology of, 682, 683t incubation period of, 683t pathogenesis of, 682, 683t prevention and treatment of, 682, 683t symptoms of, 682, 683t vaccine, for domestic animals, 682 Brugia malayi, 298t Bt-toxin, 217 buboes, 674, 682 definition of, 675t bubonic plague, 7, 262, 682, 684 budding definition of, 321t of viruses, 328, 329f in yeast, 289, 290f buffer(s), 24 for culture media, 96 bulking, of filamentous organisms, 260 Bunyaviridae/bunyaviruses, 322, 323t, 519, 522, 660 Burgdorfer, Willy, 542 Burkholderia (Pseudomonas) cepacia, in bioremediation, 750 Burkholderia mallei, bioterrorism potential of, 466 Burkholderia pseudomallei, bioterrorism potential of, 466 Burkitt’s lymphoma, 331t, 334t, 686, 711 burns, 560 infection of, 564–565, 564f, 576 burst size definition of, 303t of phages, 308 2,3-butanediol, 148, 148f, 240t butanol, 148, 255 butyric acid, as fermentation end product, 148, 148f

C C3a complement protein, 356, 356f, 360

CagA, 590 calcium, as major element, 93–94, 94t calcofluor white, 52 Caliciviridae/caliciviruses, 323t calicivirus, electron micrograph of, 338f Calvin-Benson cycle. See Calvin cycle Calvin cycle, 152t, 154, 155f yield of, 154 Campylobacter animal habitats of, 273 infection, 763t, 764, 764f. See also campylobacteriosis oxidase test for, 144 reservoirs of, 453 campylobacteriosis, 454, 602–603, 603t causative agent of, 602–603, 603f, 603t epidemiology of, 603, 603t incubation period of, 603t pathogenesis of, 603, 603t prevention and treatment of, 603, 603t symptoms of, 602, 603t Campylobacter jejuni infection, 602–603, 603f, 603t medical importance of, 271t, 273 cancer, 5f. See also tumor(s) human, viruses associated with, 334t in immunodeficient patients, 710–711 vaccine sought for, 437t Candida, infection, nosocomial, 463t Candida albicans, 289f infection, 292, 292t, 350, 625–626, 626t. See also candidiasis in immunocompromised hosts, 410 in normal microbiota, 350, 585 vulvovaginitis, 350 wet mount of, 237f candidiasis, 292, 292t in burns, 576 cutaneous, 554, 555f secondary, 538 vulvovaginal, 625–626, 626f, 626t causative agent of, 626, 626f, 626t epidemiology of, 626, 626t incubation period of, 626t pathogenesis of, 626, 626t prevention and treatment of, 626, 626t symptoms of, 625, 626t candle jar, 97 canning process, commercial, 111, 111f, 114, 114f, 764 cap, RNA, 175 C5a peptidase, 401, 500, 500t capnophiles, 97 capsid, 303, 304f, 321 capsomers, 303, 321, 328, 328f capsule(s) and avoidance of phagocytosis, 401–402 definition of, 50 of prokaryotic cells, 55t, 64, 64f staphylococcal, 537t capsule stain, 48t, 50–51, 50f carbapenems, 473t, 477 carbohydrate(s), 19t, 30–32 carbol fuchsin, 50, 50f carbolic acid, 107, 120

9/2/08 5:33:37 PM

Index carbon, 19 atomic structure of, 19t covalent bonding of, 19t, 21, 21f as major element, 93–94, 94t in purine rings, sources of, 157–158, 158f sources of, classification of organisms by, 95, 95t carbon cycle, 94, 728–729, 729f pollution and, 728 carbon dioxide in carbon cycle, 729 fixation. See carbon fixation increased, for cultures, 97 as terminal electron acceptor, 728 use of, by phytoplankton, 285 carbon fixation, 94, 150, 152, 152t, 154, 729 Calvin cycle of, 152t, 154, 155f carbon monoxide, in carbon cycle, 729 carboxyl group, 26, 26f, 27f carboxyl terminal, 28 carbuncles, 535 definition of, 532t carcinogens, 191 fungal, 292 possible, testing for, 196–197, 197f carcinoma definition of, 698t in HIV-infected (AIDS) patients, 710 cariogenic plaque, 587, 587f definition of, 582t carotenes, 283t carotenoids, 152, 152t, 283 carrier(s), 395, 453 viral, 331 carrier cells, 311, 312f definition of, 303t carrier proteins, 58, 73 carrier state, of hepatitis B virus, 331 Carroll, James, 690 Carville, Lousiana, leprosarium, 647 case(s), definition of, 458 case-control studies, 458 caseous necrosis, 516, 525 caspofungin, 489, 489t cat(s), and Toxoplasma gondii, 286, 714, 714f, 715t catabolism, 127, 127f definition of, 127t of organic compounds other than glucose, 148–150, 149f catabolite activator protein, 179 catabolite repression, 179 catalase, 92, 349 bacteria lacking, 255 testing for, in identification of bacteria, 238, 239f, 240t catalytic site, of enzyme, 134, 135f category A agents, with bioterrorism potential, 466 category B agents, with bioterrorism potential, 466 category C agents, bioterrorism potential of, 466 catheter(s), urinary, 619t catheter-related infections, 464, 621–622 vascular, 678 cations, 20–21 cat scratch disease, 572–574, 573f, 574t causative agent of, 572, 574t

nes95432_ind_I1-I40.indd I-7

epidemiology of, 573, 574t incubation period of, 574t pathogenesis of, 573, 574t prevention and treatment of, 574, 574t symptoms of, 572–573, 573f, 574t Caulobacter, 263t, 266–267, 267f cavities, dental. See dental caries cavity, pulmonary, with tuberculosis, 516 C3b complement protein, 356, 373 inactivation of, 401–402, 401f C5 complement protein, 356, 356f–357f, 360 C6 complement protein, 356, 356f–357f C7 complement protein, 356, 356f–357f C8 complement protein, 356, 356f–357f C9 complement protein, 356, 356f–357f C content (G + C content), 248t CCR5, 353, 641, 702 CD. See clusters of differentiation CD46, 398 CDC. See Centers for Disease Control and Prevention CD4 cells, 381 functions of, 381f, 383 HIV and, 408, 641, 702–705, 702f, 708 CD8 cells, 381 functions of, 382–383, 382f in HIV infection, 704–705 cDNA, 218, 219f Cech, Thomas, 175 cecum, 735 cefaclor, 473t, 477 cefepime, 473t, 477 cefibuten, 473t, 477 cefixime, 473t, 477 cefprozil, 473t, 477 cell(s), 4f. See also eukaryotic cell(s); prokaryotic cell(s) chemical components of, 23–25 comparison with viruses, 306t immune system, 350–352, 351f, 352t, 353f differentiation of, 350 in innate immunity, communication among, 353–354 small molecules in, 25, 25f cell count(s) direct, 99–100, 99t direct microscopic, 99t, 100, 100f instruments for, 99t, 100, 100f of viable cells, 99t, 100–102, 101f cell culture, 336–337, 337f cell division, antifungal drugs targeting, 488f, 489t cell envelope, of prokaryotic cells, 54 cell line, established, 336 cell-mediated hypersensitivity, delayed, 415t, 421–422, 421f–423f in infectious disease, 422 cell membrane, lipids in, 35 cell membrane integrity, interference with, by antibacterial drugs, 474t, 479 cell products, detection in assessment of bacterial growth, 99t cellular immunity, 367, 368f overview of, 367f, 368–369, 368f cellular organisms, 11 cellulases, 149, 149f

cellulose, 32, 32f, 71, 735 degradation of, 149 by microbes, 6 hydrolysis of, 149 cell walls of algae, 283 antibacterial drugs targeting, 61–62, 473t–474t, 475–477, 475f–476f, bacteria lacking characteristics of, 63–64, 63f medically important, 272t, 273 of domain Archaea, 64 of Gram-negative bacteria, 61, 63f of Gram-positive bacteria, 61, 62–63, 62f of prokaryotic cells, 54, 54f, 55t, 59–64, 59f protozoan, 287, 287f Celsus, 360 Centers for Disease Control and Prevention, 459–460, 465 central dogma of molecular biology, 162, 162f central metabolic pathways, 132–134, 133f, 138–142 comparison of, 139t central nervous system, 648. See also transmissible spongiform encephalopathies anatomy and physiology of, 648–650, 648f–649f infections of, 647–673 bacterial, 650–658 fungal, 666–667 key terms for, 648t protozoan, 667–669 viral, 658–666 pathways to, 649–650 centriole, 70f cephalexin, 473t, 477 cephalosporins, 473t, 475–477 β-lactam ring of, 475, 475f inactivation of, 477 Cephalosporium, 471 cephradine, 473t, 477 Ceratocystis ulmi, 293 cercaria, 298t, 299, 299f cerebral malaria, 692 cerebrospinal fluid, 648, 649f cervical cancer in immunodeficient women, 711 papillomaviruses and, 553, 639–640 cervix, 620, 620f cestodes, 295, 297, 298t. See also tapeworm(s) cetylpyridinium chloride, 118t, 121 Chadwick, Edwin, 738 Chagas disease, 691 Chain, Ernst, 470 chain terminators, 222, 223f chancre definition of, 619t hard, 633, 634f soft, 636, 637f syphilitic, 633, 634f chancroid, 629t, 636–637, 637t causative agent of, 637, 637t epidemiology of, 637, 637t incubation period of, 637t pathogenesis of, 637, 637t

I-7

prevention and treatment of, 637, 637t symptoms of, 637f, 637t channel proteins, 73 chaperone proteins, 29, 37, 173 Chediak-Higashi disease, 427, 427t cheese-making, 126, 148, 255–256, 756t, 756–757, 757f, 762t genetically engineered bacteria and, 217 chemical(s) cancer-causing ability of. See also carcinogens testing for, 196–197, 197f for microbial control, 107–108, 116–121, 118t chemical additives, to food, 110, 122, 765 chemical bonds, 20–23 chemical constituents, in measurement of bacterial growth, 99t, 103 chemical energy conversion of radiant energy into, 153–154 sources, metabolic role of, 130–131 chemically defined media, 95–96, 96t definition of, 84 chemical mediators, released from mast cells, 416, 416f chemical mutagens, 190–192, 191t chemical preservatives, 122 chemical reactions activation energy of, 130, 130f endergonic, 128–129 energetics of, 130, 130f exergonic, 128 chemiosmotic theory, 142–143 chemoautotrophs, 95 chemoheterotrophs, 95. See also chemoorganotroph(s) chemokines, 353, 354t chemolithoautotrophs, 95, 95t, 154, 722, 732, 732f chemolithotrophs, 95, 253, 731 aerobic, 259–260 characteristics of, 253t anaerobic, characteristics of, 252t definition of, 252t metabolism in, 150, 150t thermophilic, 150 chemoorganoheterotrophs, 95, 95t, 727. See also chemoorganotroph(s) chemoorganotroph(s), 95, 128, 128f aerobic, 253t, 261–263 characteristics of, 253t metabolic pathways and processes in, 134t respiration in, 253t anaerobic, 254 characteristics of, 252t and fermentation, 254–256 respiration in, 134t, 252t definition of, 252t chemostat, 90 chemotaxis, 66, 66f, 353, 358 chemotherapeutic agent, 470, 470t chemotrophs, 253 anaerobic, 253–256 definition of, 252t chicken eggs, embryonated, 336 chickenpox (varicella), 324t, 545–547, 548t

9/2/08 5:33:37 PM

I-8

INDEX

chickenpox (varicella)—Continued alimentary effects of, 592 causative agent of, 546, 547f, 548t congenital syndrome, 546 epidemiology of, 547, 548t incubation period of, 548t latent infection by, 330 latent infection of, 330f, 331t, 546, 546f pathogenesis of, 546–547, 548t prevention and treatment of, 487, 547, 548t secondary infection with, 547 symptoms of, 545–546, 546f, 548t vaccine, 434t, 547 children, routine immunization for, 436–437 effectiveness of, 437t importance of, 436–437 schedule for, 436–437 chitin, 31t, 71, 610 Chlamydia, 274, 274f medical importance of, 271t chlamydial genital system infections, 629t, 631–633, 633t causative agent of, 631–632, 633t epidemiology of, 632–633, 633t incubation period of, 633t pathogenesis of, 632, 633f, 633t prevention and treatment of, 633, 633t symptoms of, 631, 633t Chlamydia trachomatis, 120 infection, 629t genital system, 629t, 631–633, 633t inflammatory response to, 408 neonatal, 120 medical importance of, 271t, 274f Chlamydophila (Chlamydia) pneumoniae infection, in arteriosclerosis, 676 medical importance of, 271t, 274f Chlamydophila (Chlamydia) psittaci bioterrorism potential of, 466 medical importance of, 271t, 274f chloramphenicol, 472, 474t, 477f, 478, 483, 542 chloramphenicol acetyltransferase, 483 chlorhexidine, 118t, 119, 123 chlorine, as disinfectant, 118t, 119–120 carcinogenic potential of, 745 for drinking water, 745–746 in drinking water, 119, 745 in sewage treatment, 742 chlorine dioxide, 119 Chlorobi, 252t Chlorobium, 252t, 257 Chloroflexi, 252t Chloroflexus, 252t, 257 chlorophyll(s), 10, 77, 152, 152f, 152t, 283 reaction-center, 152, 152f chlorophyll a, 152, 152t chlorophyll b, 283t Chlorophyta, 283t chloroplasts, 10, 70f, 71t, 77, 77f, 152, 153f, 283 cyanobacteria and, 152 of eukaryotic cells, 77 chloroquine, 490t, 693 resistance to, 693, 693f

nes95432_ind_I1-I40.indd I-8

chlorosomes, 153, 257 chocolate agar, 96, 96t cholera, 396, 457, 596–598, 598t causative agent of, 243, 397, 403, 581, 596, 596f, 598t climate changes and, 462, 597 definition of, 582t ecology of, 597 epidemiology of, 596–597, 598t incubation period of, 598t pandemics, 596 pathogenesis of, 596, 596f, 597f, 598t prevention and treatment of, 597–598, 598t reductions in, 461 in refugee camps, 462, 581 symptoms of, 596, 598t vaccine, 435, 598 water as source of infection, 4f, 581, 596–597, 738 cholera toxin, 404t, 596, 597f cholesterol, 35f, 36, 73 Chondromyces, 263t, 264f, 265 chromatin, 76 Chromatium, 252t, 256 chromatogram, of fatty acid profiles, 240 chromosome(s) of eukaryotic cells, 72t, 76 nucleotide sequences of, 5f of prokaryotic cells, 54f, 55t, 67–68, 67f, 72t transfer of, 203, 203f, 204f, 204t chronic infection(s), 9, 329–332, 330f, 332t, 395 definition of, 321t chronic wasting disease, 340t, 342, 669, 669f Chrysophyta, 283t chymosin, genetically engineered production of, 217 Chytridiomycetes, 289 cilia, 11f of eukaryotic cells, 71t, 74–75 protozoan, 286, 286t, 287 ciliated cells, 498 ciliates, 286, 286t Ciliophora, 286, 286t, 287, 610 ciprofloxacin, 167, 474t, 478, 681 circulative transmission, of plant viruses, 340 cirrhosis, definition of, 582t citrate, 141f, 142 citrate test, 240t citric acid cycle, 132. See also tricarboxylic acid cycle civil unrest, and disease, 462 CJD. See Creutzfeldt-Jakob disease (CJD) clade(s) definition of, 698t of HIV, 699 clarithromycin, 474t, 478 class, definition of, 234 classification of algae, 282, 283t Bergey’s Manual of Systematic Bacteriology for, 234, 236t definition of, 233, 233t of eukaryotes, ribosomal RNA in, 249, 280, 281f of fungi, 288–290, 289f

of prokaryotes, 232, 246–248 by DNA base ratio (GC content), 248, 248t DNA hybridization for, 247–248, 248t genotype characteristics for, 248t numerical taxonomy for, 248 phenotype characteristics for, 248, 248t relatedness in, methods of determining, 246–248, 248t ribosomal RNA in, 232, 248t, 249 strategies for, 233–236 of protozoa, 285–286, 286t systems of, 234 five-kingdom, 234 three-domain, 234, 235f class switching, of immunoglobulins, 378, 378f Clean Water Act, 739 climate changes, 614 and disease, 462 clindamycin, 474t, 478 clofazimine, 656 clonal expansion, of lymphocytes, 375, 376f clonal selection, of lymphocytes, 375, 376f definition of, 367t clonal selection theory, 375, 376f clones, of antigen-specific cells, 368, 375 cloning DNA, 215–217, 216f of eukaryotic genes into prokaryotic cells, vectors for, 218–220 generating recombinant molecule for, 218–220 into high-copy-number vector, 216, 216f ideal vector for, 218–219, 219f introduction of recombinant DNA into new host, 220 gene, 212 closed systems, for bacterial cultures, 88 clostridial myonecrosis. See gas gangrene Clostridium, 254–255, 257, 727 characteristics of, 252t, 263t control/destruction of, 110 endospore stain of, 51 and fermentation, 254 fermentation in, 148, 148f in food spoilage, 762 intestinal, in obese people, 394 in mucous membranes, 272 sporulation of, 69, 69f, 255, 264, 264f testing water for, 746 Clostridium acetobutylicum, 255 Clostridium botulinum, 754 anaerobic conditions for, 92, 255, 756 bioterrorism potential of, 466 control/destruction of, 114, 122, 764 endospores of, 69, 255 infection/intoxication, 397, 657–658, 657f, 658t, 756, 758, 763–764, 763f, 763t. See also botulism

medical importance of, 272t pH requirements of, 755 prophages and, 311, 311t reservoirs of, 453 toxin of, 404, 404t, 405, 657–658 cosmetic and medicinal uses of, 658, 764 Clostridium difficile, 350 infection in antibiotic-associated colitis, 393, 472, 478, 586 nosocomial, 463t Clostridium perfringens infection foodborne, 763t of wounds (gas gangrene), 69, 255, 568–570, 569f, 570t, 573 medical importance of, 272t sporulation of, 69, 255 toxin of, 404t, 405 Clostridium tetani infection, 559, 561, 566–568, 566f, 568t. See also tetanus reductions in, 461 medical importance of, 272t reservoirs of, 453 sporulation of, 69, 255, 264f toxin of, 404t clotrimazole, 489, 489t clumping factor, 535, 537t, 563 clusters of differentiation (CD), 381 CMV. See cytomegalovirus CNS. See central nervous system CoA, 33. See coenzyme A coagulase, 535, 537t, 563 cobalt, 94 Coccidioides immitis, 290, 292, 292t infection, 525–526, 525f–526f, 526t coccidioidomycosis, 292, 292t, 525–526, 526t causative agent of, 525, 525f, 526t epidemiology of, 525–526, 526f, 526t pathogenesis of, 525, 526t prevention and treatment of, 526, 526t symptoms of, 525, 526t coccobacillus, 52f, 53 coccus (pl., cocci), 52–53, 52f CODIS (Combined DNA Index System), 225 codon(s), 170, 171f definition of, 162t start, 171t, 172–173 stop, 171t, 173 coenzyme(s), 135–136, 136t coenzyme A, 133f, 136t, 141f, 142, 150 coenzyme Q, in electron transport chain of mitochondria, 143–145, 144f cofactors, for enzymes, 135–136, 135f CO2 fixation. See carbon fixation Cohen, Stanley, 5f cohesive ends, of DNA fragments, 213f, 214 Cohn, Ferdinand, 2, 232 cohort groups, 458 colds, 507–508 causative agents of, 507, 507f, 508t endemic, 451 epidemiology of, 507, 508t incubation period of, 394, 508t

9/2/08 5:33:38 PM

Index pathogenesis of, 507, 508t prevention and treatment of, 507–508, 508t symptoms of, 507, 508t cold sores, 592, 592f colicins, 349–350 coliforms, 102, 262 fecal, 746 testing water for, 262, 746, 747f total, 746 rule for, 746 colitis, antibiotic-associated, 350, 472, 478, 586 collagen, 560, 561f collagenase, 569, 575 colonization, 394, 397–398 definition of, 392t colony bacterial, 86, 87f growth of, 89–90 morphology of, 238 colony blotting, 228, 228f definition of, 213t colony-forming units, 101 colony-stimulating factors, 350, 351f, 353, 354t colostrum, 374 combinatorial associations, in antibodies, 387 co-metabolism, 750 commensalism, 392 commercially sterile, 114 common cold. See colds common-source epidemic, 457, 457f communicable disease, 394–395, 451, 451t community(ies), 722 environmental changes and, 723–724 microbial interaction in, 86 community-acquired infections, 564 competence artificial, in DNA-mediated transformation, 201, 201f definition of, 200 natural, in DNA-mediated transformation, 200 competition, microbial, 723, 723f competitive inhibition, of enzymes, 137–138, 137t, 138f, 475, 479 complementary bases (DNA), 34, 163–164, 163f complement regulatory proteins, 401 complement system, 347, 355–356, 356f, 357f, 441–442 abnormalities in, 426, 427t activation of, 355–356 alternative pathway of, 355, 356f in antigen-antibody binding, 372f, 373 classical pathway of, 355, 356f lectin pathway of, 355, 356f protective outcomes of, 356, 356f avoidance by pathogens, 400–401, 401f components of, 356 definition of, 347t and inflammation, 356, 356f, 360 and lysis of foreign cells, 356, 356f membrane attack complex of, 356, 357f nomenclature for, 356

nes95432_ind_I1-I40.indd I-9

and opsonization, 356, 356f resistance to, by Yersinia pestis, 683, 684t complex media, 96, 96t definition of, 84 composite transposons, 207–208, 207f, 208t composting, 747–748, 748f municipal, 748, 748f compound(s), definition of, 20–21 compound microscope, 41–42 condenser lens, of microscope, 42 confocal scanning laser microscopes, 45f, 45t, 46, 46f, 725 congenital cytomegalic inclusion disease, 715 congenital rubella syndrome, 550–551 congenital syphilis, 635–636, 636f congenital varicella syndrome, 546 conidia, 265, 727 conjugate vaccines, 383, 435, 650 conjugation, 66, 186t, 199, 202–204, 203f bacterial-plant, 206, 265 chromosome transfer by, 203, 203f, 204f, 204t plasmid transfer by, 204t, 206 conjunctivitis, 496 bacterial, 504–506, 505f causative agent of, 504–505 definition of, 496t epidemiology of, 506 inclusion, 633 pathogenesis of, 505–506 prevention and treatment of, 506 conserved (core) genome, 205 constant region, of antibodies, 372, 372f constitutive enzymes, 176 consumers, 722, 723f definition of, 722t primary, 722 secondary, 722 tertiary, 722 contact, and infection, 454 contact dermatitis, 421–422 contact hypersensitivities, 421–422, 422f–423f contact lens, infections with, 505 contagious disease, 394–395 continuous cultures, 88, 90 contrast, in microscopes, 42–43 control(s), definition of, 458 contused wounds, 560 convalescence, 395, 395f convergent evolution, 294 definition of, 281t cooking, 765 copper, 94 biomining of, 151 as enzyme cofactor, 136 as preservative, 120 Corallina gracilis, 282f corallines, 283t core enzyme, 169 core genome, 205 corepressors, of transcription, 177 Coronaviridae, 322, 323t Cortez, Hernando, 7 Corynebacterium, 262, 262f, 534 characteristics of, 253t in mucous membranes, 272

in normal microbiota, of respiratory system, 498t Corynebacterium diphtheriae, 503f infection, 262, 502–504, 505t, 559. See also diphtheria reductions in, 461 medical importance of, 262, 272t phage infection in, 307t prophage and, 311, 311t toxin of, 176, 397, 404t, 405, 502–504, 559 coryneforms, 262 cosmetics, preservation/protection of, 110 co-stimulatory molecules, dendritic cells expressing, 382, 436 cosystem(s), relationship among producers, consumers, and decomposers in, 722 cotrimoxazole, 599 coughing, paroxysmal, 513–514 Coulter counter, 99f, 100, 100f counterstain, 49f, 50 counting chambers, 100, 100f counts, cell. See cell count(s) covalent bonds, 19t, 20–22, 22f definition of, 21 non-polar and polar, 21–22, 21t, 22f of nucleotides, 33, 33f cowpox, 324t, 431 Coxiella, 274, 274f Coxiella burnetii, 274, 678 bioterrorism potential of, 466 evasion of host defenses by, 403 medical importance of, 271t, 274 small-cell variants, 274 Coxsackievirus, 324t nervous system infections, 659, 659t crabs (pubic lice), 296 cranberries, 755 Creutzfeldt-Jakob disease (CJD), 340t, 342, 668, 670t definition of, 648t Crick, Francis, 5f, 199 cristae, 76, 76f critical instruments, 111 Crohn’s disease (CD), 9 crop rotation, 721 cross-contamination, 455, 764 cross-reactive antibodies, 408 cross-sectional studies, 458 croup, 521 definition of, 496t crown gall, 206, 206f cryptococcal meningoencephalitis, 292t, 666–667, 667t causative agent of, 666, 666f, 667t epidemiology of, 667, 667t pathogenesis of, 666–667, 667t prevention and treatment of, 667, 667t symptoms of, 666, 667t Cryptococcus neoformans, 11f, 289t, 292t. See Filobasidiella (Cryptococcus) neoformans capsule stain of, 50f infection, 666–667, 666f, 667t cryptosporidiosis, 455, 610–611, 611t causative agent of, 286, 286t, 611t, 612, 612f epidemiology of, 611t, 612

I-9

incubation period of, 611t, 612 pathogenesis of, 611t, 612 prevention and treatment of, 611, 611t symptoms of, 611t, 612 Cryptosporidium, 286t in drinking water, 745, 750 Cryptosporidium parvum control/destruction of, 110 infection, 286, 286t, 455, 610–612, 611t, 612f crystal violet, 49, 49f CTC, 52 C terminal, 28 Cubicin, 537 Culex, 295t, 661 cultural practices, and susceptibility to disease, 456 culture(s), 86–88, 95–99 anaerobic, 98, 98f atmospheric conditions for, 97–98 cell, 336–337, 337f closed or batch systems, 88 continuous or open system, 88, 90 death phase of, 88f, 89 enrichment, 98, 99f exponential or log phase of, 88–89, 88f growth curve of, 88–89, 88f–89f identification of microorganisms by, 238 increased carbon dioxide for, 97 lag phase of, 88, 88f microaerophilic, 98 microbial control and, 109 primary, 336, 337f prolonged decline phase of, 88f, 89, 89f pure, 86–88 definition of, 84 obtaining, 86–88 stationary phase of, 88f, 89 stock, maintaining, 88 streak-plate method of, 87–88, 87f tissue, 336, 337f viral, 336–337, 337f weight of, 99t, 103 culture media, 86 characteristics of, 96t chemically defined, 95–96, 96t complex, 95–96, 96t development of, 4f, 83 differential, 96t, 97, 97f for Escherichia coli, 96, 96t general categories of, 95–96 selective, 96–97, 96t solid, cultivating bacteria on, 86–87 special types of, 96–97 curd, 757 curing, of cheese, 757 CXCR-4, 353, 702 cyanobacteria, 258–259, 724 bloom caused by, 258, 258f characteristics of, 95, 152, 253t, 258, 258f definition of, 252t filamentous, 258–259, 259f geosmin production by, 259 light-dependent reactions in, 153–154, 153f nitrogen-fixing, 95, 258, 259f, 730, 735 photosynthesis in, 152–154, 152t

9/2/08 5:33:39 PM

I-10

INDEX

Cyanobacteria, 252t cyclic adenosine monophosphate (cAMP), 33 A-B toxins and, 514, 596, 597f in catabolite repression, 179 cyclical metabolic pathways, 129, 129f cyclic photophosphorylation, 153 Cyclospora cayetanensis, 612, 612t cyclosporiasis, 612, 612t causative agent of, 462, 612, 612t epidemiology of, 462, 612, 612t pathogenesis of, 612, 612t prevention and treatment of, 612, 612t symptoms of, 612, 612t cyclosporin, for autoimmune disease, 425 cyclosporin A, 424 cyst bacterial, 264, 264f protozoan, 287, 610, 714, 714f cysteine, 27f as reducing agent, 98 cysticercosis, 298f, 298t cysticercus (pl., cysticerci), 298f, 298t cystic fibrosis, 564 cystitis bacterial, 621–622, 622t, 623 causative agents of, 621, 622t epidemiology of, 621–622, 622t incubation period of, 622t pathogenesis of, 621, 622t prevention and treatment of, 622, 622t symptoms of, 621, 622t definition of, 619t honeymoon, 621 cytidylic acid, 33f cytochrome(s), in electron transport chain, 143–145 cytochrome bc1 complex, 143 cytochrome c, 240t in electron transport chain, 143–144, 144f cytochrome c oxidase complex, 144 cytokine(s), 353–354, 679 in asthma, 417 definition of, 347t fever-inducing, 362 in hypersensitivity reactions, 416, 416f important, 354t in innate immune response, 347, 353–354, 354t pro-inflammatory, 354, 360, 362 superantigens and, 406 cytokine receptors, 353 cytolysins, 405 cytomegalovirus (CMV), 324t congenital inclusion disease, 715 infection, 715–717, 716f, 717t epidemiology of, 716, 717t latent, 331t pathogenesis of, 716, 716f, 717t prevention and treatment of, 487, 716–717, 717t symptoms of, 715, 717t interactions with immune cells, 409, 409f cytopathic effects, of viruses, 328, 337, 337f cytoplasm of eukaryotic cells, 70f of prokaryotic cells, 54

nes95432_ind_I1-I40.indd I-10

cytoplasmic membrane, of prokaryotic cells, 54, 54f, 55–57, 55t directed movement of molecules across, 57–59, 58t in energy transformation, 57, 57f permeability of, 56–57, 56f structure and chemistry of, 56, 56f cytosine, 33, 33f, 161–162 cytoskeleton bacterial, 68 of eukaryotic cells, 70f, 71t, 74, 75f cytotoxic (type II) hypersensitivities, 414, 415t, 418–420 cytotoxic T cell, definition of, 367t cytotoxins, 382, 404t, 405

D dacryocystitis, 496 daily life, microbial control in, 108, 109f dairy products fermentation of, 6, 126, 255–256, 255f, 753–754, 756–757, 756t pasteurization of, 682 dalfopristin, 474t, 478 dams, and schistosomiasis, 461–462 dandruff, 533 Danielson, Daniel C., 647 dapsone, 656 daptomycin, 474t, 479, 537 dark-field microscopes, 43, 44f, 44t dark-field microscopy of algae, 43f of spirochetes, 269, 269f of Treponema pallidum, 634, 634f dark reactions, 151 dark repair, of thymine dimers, 195t Dawson, M. H., 199 day care centers, 461, 599 ddI. See didanosine DDT, 6, 691, 693–694, 749 biological magnification of, 749, 749t dead zone, in marine environments, 726, 726f deamination, 149f, 150 death phase, of microbial growth, 88f, 89 decarboxylation, 142 decimal reduction time, 111, 111f decolorizing agents, 49f, 50 decomposers, 722, 723f, 729 in carbon cycle, 729 definition of, 722t decontamination, definition of, 108 defective phages, 313 defense mechanisms. See immunity defensins, 349, 491 degerm(ing), definition of, 108, 108t degranulation, of mast cells, 415, 415f dehydration synthesis, 19t, 25, 25f of disaccharides, 32 of peptide bonds, 28, 28f dehydrogenation, 131 Deinococcus, 252t, 253t, 262 Deinococcus radiodurans, 262 delaviridine, 487t, 488, 708 delayed cell-mediated hypersensitivities, 415t, 421–422, 421f–423f in infectious disease, 422 Delft School, 251

Demodex brevis, 297 Demodex folliculorum, 297 denaturation, 227 of DNA, 163, 248, 248f of proteins, 29f, 29–30 temperature and, 91 denaturing gradient gel electrophoresis (DGGE), 725 dendritic cells, 351f, 352, 352t, 436 definition of, 367t expressing co-stimulatory molecules, 382 subsets of, 383–384 and T cell activation, 381–382 dengue, 323, 323t–324t, 688 dengue hemorrhagic fever, pathogenesis of, 410 denitrification, 731, 741–742 definition of, 722t dental calculus, 588 dental caries, 586–587, 589t causative agent of, 587, 589t incubation period of, 589t pathogenesis of, 587, 587f, 589t prevention and treatment of, 587, 589t symptoms of, 586–587, 589t dental plaque, 64, 86, 398, 585, 585f, 588, 588f dentin, 582, 584f deoxyadenosine-5´-phosphate, 33f deoxyribonucleic acid. See DNA (deoxyribonucleic acid) deoxyribose, 30, 30f, 31t, 33, 33f depth filters, 115 Dermacentor, 295t Dermacentor andersoni, 297, 541, 541f Dermacentor variabilis, 541 dermatitis, contact, 421–422, 422f dermatophyte infections, 410, 554, 555f dermis, 532f, 533 as physical barrier to infection, 348 descriptive studies in epidemiology, 457–458 of person, 457 of place, 457 of time, 457–458 desensitization, 417 desiccation, 122 Desulfovibrio, 252t, 254 detergent(s), enzymes in, 158 detritus, 722, 729 deuterium, 26 Deuteromycetes, 288–289, 289t development, and emerging diseases, 461–462 dextran, 31t, 32, 32f DGGE (denaturing gradient gel electrophoresis), 725 d’Herelle, Felix, 302, 316 diabetes mellitus, type 1, 424t treatment of, 425–426 diaminopimelic acid, 61 diapedesis, 360, 361f diaper rash, 555f diarrhea, 595–596. See also specific causative agents and illnesses antibiotic-associated, 350, 393 Enterobacteriaceae causing, 262 Escherichia coli causing, 599–601, 600t foodborne causes of, 763t

prevention and treatment of, 614 protozoan, 286, 286t traveler’s, 599–601 viral causes, 323t diatomaceous earth, 283 diatoms, 280, 283, 283t, 285 diauxic growth curve, 179, 179f diazotrophs, 730 DIC. See disseminated intravascular coagulation dichlorodiphenyltrichloroethane. See DDT 2,4-dichlorophenoxyacetic acid (2,4-D), 749, 749f dichotomous key for biochemical tests, 239, 241f definition of, 233t dicloxacillin, 473t, 476, 476f didanosine (ddI), 487, 487t dideoxy chain termination method, of DNA sequencing, 222–223, 222f–223f dideoxynucleotide, 222–223, 223f Diener, Theodor, 5f diethylcarbamazine, 491t differential media, 96t, 97, 97f definition of, 84 differential stains, 48t, 49–50 differentiation, of immune system cells, 350 diffusion facilitated, 58, 58t simple, 56 diffusion bioassay, 481 DiGeorge syndrome, 426, 427t digestive system anatomy and physiology of, 582–585, 583f functions of, 582 lower, 583f normal microbiota of, 585–586 upper, 583f bacterial infections, 586–591 viral infections, 592–594 digestive system infections, 581–617 key terms for, 582t lower, 595–614 bacterial, 595–603 protozoan, 610–614 viral, 604–609 diglycerides, 35 dihydroxyacetone phosphate, 132t, 140f diluent, in cell counting, 100 dimorphic fungi, 290, 410, 525–526, 576, 577f dinoflagellates, 283t, 284–285, 284f diphtheria, 502–504, 505t causative agent of, 176, 262, 397, 502–504, 505t, 559 epidemiology of, 503, 505t immune response to, 366 incubation period of, 505t pathogenesis of, 502–504, 505t prevention and treatment of, 503–504, 505t symptoms of, 502, 505t vaccine, 366, 405, 434t, 435, 437t, 503–504 diphtheria toxin, 176, 366, 404t, 405, 502–504, 504f, 559 diphtheroids, 262, 533–534, 533t Diphyllobothrium latum, 298t

9/2/08 5:33:39 PM

Index diplococci, 53 diploid cell, 76 of algae, 284 Dipylidium caninum, 296 direct agglutination tests, 443, 443f direct cell counts, 99–100, 99t direct contact, and infection, 454 direct fluorescent antibody test, 444, 444f directly observed therapy, in tuberculosis, 485, 517 definition of, 496t direct microscopic count, 97t, 99t, 100, 100f direct selection, of mutants, 195, 195f disaccharidases, 149, 149f disaccharides, 30, 31t, 32 hydrolysis of, 149, 149f disease(s). See also specific causative agents and diseases chronic, caused by bacteria, 9 communicable, 394–395, 451, 451t contagious, 394–395 definition of, 392t, 394 emerging, 7–8, 8f, 461–462 endemic, 451, 451t germ theory of, 4f, 107, 391 infectious, 391–413, 392t. See also infectious disease microbes and, 392–413 non-communicable, 451 notifiable, 459–460, 459t old, resurgence of, 8–9 population characteristics and, 456–457 rate, in population, 451 reduction and eradication of, 460–461 surveillance of, 459–460 susceptibility to age and, 456 in elderly, 8–9 gender and, 456 general health and, 456 genetic factors in, 456–457 in HIV infection, 9 religious/cultural practices and, 456 temperature and, 91 zoonotic, 453. See also zoonoses disinfectant(s), 86, 118t definition of, 108, 108t for drinking water, 745–746 general-purpose, 117 high-level, 117 intermediate-level, 117 low-level, 117 overuse and misuse of, 123 disinfectant-resistant bacteria, 123 disinfection chemicals used in, 116–121, 118t definition of, 108 of wastewater, 740f, 742 disinfection by-products (DBPs), 110 D-isomers, 61 disseminated infection, 395 gonococcal, 631 disseminated intravascular coagulation, 420, 541, 679, 684 definition of, 675t distemper, 322 distilled spirits, fermentation/ production of, 758t, 760

nes95432_ind_I1-I40.indd I-11

disulfide bonds, of immunoglobulins, 371, 372f diversity of antibodies, 387, 387f key terms for, 252t metabolic, in prokaryotes, 252–262, 252t–253t division, definition of, 234 DNA (deoxyribonucleic acid), 5f, 32–34 antiparallel strands, 163f, 164 bacterial, 34, 67–68, 67f base substitution in, 189, 189f biological function of, 199 characteristics of, 162–164 cloning, 215–217, 216f of eukaryotic genes into prokaryotic cells, vectors for, 218–220 generating recombinant molecule for, 218–220 ideal vector for, 218–219, 219f obtaining DNA for, 218 techniques for, 218f composition of, 161 damaged, repair of, 192–194, 195t, 310 denaturation of, 163, 227, 242, 242f, 248, 248f double-stranded helix, 34, 34f, 163, 163f eukaryotic, 76 extrachromosomal, 186t foreign, 208 restriction of, 314–316 genetically engineered production of, 217 homologous, nucleic acid hybridization for localization of, 227–229 melting of, 163, 248, 248f methylation of, 314, 315f mitochondrial (mtDNA), 212 nucleotides of, 32–33, 33f open reading frames of, 182 phage excision of, 309f, 310 integration in bacterial chromosome, 309f, 310 repair of, 310 plasmid, 55t, 68 prokaryotic, 54f, 55t, 67–68, 67f and protein synthesis, 161–184 recombinant, 214. See also recombinant DNA technology of, 212–231 replication of, 164–167, 165f–166f in animal viruses, 326–328, 327f, 329t bidirectionality of, 164, 165f components of, 165t definition of, 162, 162t initiation of, 166 origin of, 165t, 166 overview of, 162f in phages, 307f, 308, 311, 312f, 329t replication fork in, 165f, 166–167, 167f in retroviruses, 332, 333f semiconservative, 164

sequence. See also genome(s); nucleotide sequences analysis of, 182 single-stranded, phage with, lytic infection by, 311 smallest amount in any organism, 15 structure of, 163, 163f for study, source of, 217 supercoiled, 67–68, 67f synthesis of, 33, 33f target, in polymerase chain reaction, 223–224, 224f transfer of, 198–208, 204t transferred (T-DNA), 206 tritiated thymidine labeling of, 26 DNA base(s), 161 complementary, 34, 163, 163f definition of, 33 incorporation, errors in, repair of, 192–193 modified, repair of, 193, 194f, 195t pairing of, 163–164, 163f DNA-based vaccines, 437, 709 DNA base ratio, 248, 248t DNA fingerprinting, 225 DNA fragments annealing, 213f, 214, 227 cohesive ends of, 213f, 214 discrete-sized, generation of, 225–226, 226f sticky ends of, 213f, 214 DNA gyrase, 165t, 167, 478 DNA hybridization, for prokaryote classification, 247–248, 248t DNA ligase, 165t, 167, 193, 193f, 194f, 213f, 214 DNA-mediated transformation, 186t, 199–201, 204t artificial competence in, 201, 201f in DNA cloning, 220 entry of DNA in, 200, 200f integration of donor DNA in, 200, 200f multiplication of transformed cells in, 200–201, 200f natural competence in, 200 DNA microarrays, 227–229, 229f, 229t definition of, 213t DNA polymerase, 165f, 165t, 166, 166f definition of, 162t in DNA sequencing, 222, 222f in polymerase chain reaction, 242, 262 proofreading by, 192, 195t, 332 DNA probes, 227–229, 227f, 229t, 241–242, 242f definition of, 213t DNAse, 199 DNA sequence(s) detection of nucleic acid hybridization for, 227–229 nucleic acid probes for, 227–229, 229t, 241–242, 242f polymerase chain reaction for, 223–226, 229t, 242 Southern blot for, 227 polymerase chain reaction for, 223–226, 224f DNA sequencing, 221–223 applications of, 221, 229t

I-11

automated, 222–223, 223f for characterizing bacterial strains, 243–244 dideoxy chain termination method of, 222–223, 222f–223f in identification of prokaryotes, 242 techniques used in, 221–223 DNA viruses animal, 322, 324t, 326–328 bacterial, 304 Dochez, A. R., 495 dodder, 340, 340f Domagk, Gerhard, 470 domains, 10, 232 definition of, 233t, 234 three-domain classification system, 234, 235f domoic acid, 285 donor electron, metabolic role of, 131 in gene transfer, 198 in plasmid transfer, 202–203 Doolittle, Ford, 5f dose infectious, 394–395, 455–456 infective, 338 lethal, 338 double-blind study, 458 double-stranded DNA helix, 34, 34f, 163, 163f doubling time, 84 downstream transcription, 168 doxycycline, 474t for Rocky Mountain spotted fever, 542 DPT vaccine, 503–504 dracunculiasis, 460 drinking water chlorination of, 119, 745 contamination of. See also waterborne disease; water pollution federal standards for, 744–745 fluoridation of, 587 ozone for disinfection of, 120, 745 sources of, 744 testing of, 262, 746, 747f, 750 treatment of, 738, 745–746 droplet transmission, 455 drotrecogin alpha, 680 drug(s). See also antibiotic(s); antimicrobial drugs; antiparasitic drugs; antiprotozoan drugs; antiviral drugs; specific drug design, genome mining and, 182 development of, 208 dry heat, 112t, 114 drying food, 122, 765 dry weight, 103 DTaP vaccine (acellular pertussis), 435–437, 514, 567 Duffy blood group antigens, 410 Duke’s disease, 552 Dulbecco, R., 697 dura, 648 Dutch elm disease, 289, 293 D value, 111, 111f dyes acidic, 49 basic, 49 fluorescent, 51f, 52, 100, 444, 725 for microscopy, 48–52, 48t

9/2/08 5:33:40 PM

I-12

INDEX

dysentery, 595 amebic, 613 bacterial, 598 definition of, 582t protozoan, 286, 286t in refugee camps, 462

E earache, 504–506. See also otitis media ear infections, biofilms in, 86 early proteins, 308 Eastern equine encephalitis, 660–661 Ebola virus, 322f, 323t, 461 echinocandins, 488f, 489, 489t echovirus, 324t nervous system infections, 659, 659t ecological niche, 722 ecology definition of, 722 microbial, 721–737 definition of, 722 principles of, 722–725 study of, 724–725 ecophysiology, 263–276, 263t definition of, 263 EcoRI, 214t ecosystem(s), 722 anatomical barriers as, 392–393 biogeochemical cycling and energy flow in, 728–733 definition of, 392 energy sources for, 732–733, 732f relationship among producers, consumers, and decomposers in, 723f skin as, 392–393, 533 ectomycorrhizae, 733f, 734 ectopic pregnancy, 631 Edelman, Gerald, 366 edible vaccines, 217, 437, 447 efavirenz, 487t, 488, 708 effector lymphocytes, 375 T cells, 368f, 369 effluent, 739 definition of, 739t efflux pumps, 58, 483 eflornithine, 490t Ehrlich, Paul, 5f, 469 Ehrlichia, 274 Ehrlichia chaffeenis, medical importance of, 271t, 274 ehrlichiosis, 274 Eikenella corrodens, 64f elderly, disease susceptibility in, 8–9 electrochemical gradient, 57, 57f electromagnetic radiation, 115 frequency of, 115, 115f wavelength, 115, 115f electromagnetic spectrum, 115, 115f electron(s), 18–19, 19f electron acceptor, terminal, 131, 148, 253–254, 724, 728, 730 electron carriers, 131t electron acceptance by, 143 in electron transport chain, 143 metabolic role of, 131, 131t electron donors, metabolic role of, 131 electron microscopes, 41, 45f, 45t, 46–47, 47f counting virions with, 338, 338f

nes95432_ind_I1-I40.indd I-12

versus light microscope, 42f, 47f resolving power of, 42f electron orbitals, 18–19, 19f electron photomicrograph, 46 electron shells, 19f, 20 electron transport chain, 57, 57f, 142–147, 143f definition of, 127t of Escherichia coli, 144–145, 145f metabolic role of, 142–147, 143f of mitochondria, 143–144, 144f in photosynthesis, 153–154, 153f of prokaryotes, 144–145, 145f electrophoresis, gel, 214–215, 214f denaturing gradient, 725 in polymerase chain reaction, 242 pulsed-field, 244, 244t, 245f size standard for, 214f, 215 electroporation, 201, 201f, 220 element(s), 19–20 biogeochemical cycling of, 728–733 common in living world, 19 atomic structure of, 19t definition of, 19 major, 93–94, 94t required, for microbial growth, 93–94, 94t trace, 94 as enzyme cofactors, 136 elementary body, 274, 632 elephantiasis, 274 ELISA. See enzyme-linked immunosorbent assay elongation in RNA synthesis, 169, 170f in translation, 173, 174f elongation factors, 173 Embden-Meyerhof-Parnas pathway, 132 Embden-Meyerhof pathway. See also glycolysis embolus (pl., emboli), 678 definition of, 675t embryonated chicken eggs, 336 emerging diseases, 7–8, 8f, 461–462 enamel, tooth, 582, 584f encephalitis allergic, 665 definition of, 648 herpes simplex, 592, 659 measles, 548, 659 mumps, 593, 659 viral, 323t, 659–661, 661t causative agents of, 660, 661t epidemic, 660, 661t epidemiology of, 660, 660f, 661t pathogenesis of, 660, 661t prevention and treatment of, 660–661, 661t symptoms of, 660, 661t encephalopathies, spongiform, 340t, 341, 669–670, 670t in humans, 669–670, 670t causative agents of, 669, 670t epidemiology of, 669–670, 670t pathogenesis of, 669, 670t prevention and treatment of, 670, 670t symptoms of, 669, 670t endemic disease, 451, 451t endergonic reactions, 128–129

endocarditis acute bacterial, 677 bacterial, 563 with brucellosis, 682 definition of, 675t, 677 pneumococcal, 510 subacute bacterial, 501, 586, 677–678, 678t causative agent of, 677–678, 678t definition of, 675t epidemiology of, 678, 678t incubation period of, 678t pathogenesis of, 678, 678t prevention and treatment of, 678, 678t symptoms of, 677, 678t endocytic vesicle, 73–74 endocytosis, 73–74, 73f definition of, 321t receptor-mediated, 74, 408 viral entry via, 74, 79, 326, 326f–327f endomycorrhizae, 733–734, 733f endonucleases, restriction, 314 endoplasmic reticulum, 70f, 71t, 74, 77–78, 78f rough, 71t, 78, 78f smooth, 71t, 78, 78f endosome, 74, 355 endospore(s), 2–3, 55t, 69–70, 69f, 255, 727 control/destruction of, 108, 110–111, 117 core of, 69, 69f core wall of, 69, 69f cortex of, 69, 69f germination of, 70 mother cell of, 69, 69f sporulation of, 69–70, 69f, 255, 264, 264f endospore-formers, 264, 264f, 727 characteristics of, 263t pathogenic, 69 endospore stain, 48t, 51, 51f endosymbiont, 77, 265 endosymbiont theory, 77 endotoxemia, 679–680 endotoxic shock, 407, 678–679 endotoxin(s), 61, 63f, 407–408 definition of, 392t versus exotoxins, 407, 407t of Gram-negative cell walls, 60t endpoint, of viral quantal assay, 338 end products, of metabolic pathways, 129, 129f energy. See also metabolism activation, 130, 130f adenosine triphosphate and, 25, 25f, 130, 130f definition of, 128 flow, in ecosystems, 728–733 free, 128 harvesting of, 128–129 kinetic, 128, 128f potential, 128, 128f radiant capture of, in photosynthesis, 152–153 in photosynthesis, conversion into chemical energy, 153–154 relative gains, in different types of metabolism, 150, 151f

sources, 94–95, 95t chemical, metabolic role of, 130–131 classification of organisms by, 95t definition of, 130 for ecosystems, 732–733, 732f enfuvirtide, 486, 487t, 708 England, foot-and-mouth disease in, 7 enrichment cultures, 98, 99f Entamoeba, 286t Entamoeba histolytica, 612–613 infection, 286, 612–613, 614t life cycle of, 613f enteric(s). See Enterobacteriaceae enteric fever, 595 enteric viruses, 322 enteroaggregative Escherichia coli, 600, 600t Enterobacter, 262 characteristics of, 253t fermentation pathway of, 148, 148f medical importance of, 271t methyl-red test for, 148 enterobacteria. See Enterobacteriaceae Enterobacteriaceae, 262, 262f characteristics of, 253t fermentation pathways of, 148 infection blood (septicemia), 679 nosocomial, 463t ocular, 504 treatment of, 477 medical importance of, 271t methyl-red test for, 148 in mucous membranes, 272 testing water for, 746 Voges-Proskauer test for, 148 enterobiasis (pinworm disease), 298t Enterobius vermicularis, 298t Enterococcus, 255 antimicrobial resistance of, 484 characteristics of, 252t infection, nosocomial, 463t medical importance of, 272t nomenclature, 249 Enterococcus faecalis, 455, 621 antimicrobial resistance of, 207–208, 207f portal of entry for, 455 enteroinvasive Escherichia coli, 600, 600t enteropathogenic Escherichia coli, 600, 600t enterotoxigenic Escherichia coli, 404t, 600, 600t enterotoxins, 404t, 405, 407, 537t EnterotubeTM, 239, 241f enterovirus, 322, 324t, 662 Entner-Doudoroff pathway, 132 enveloped virus(es), 117, 303, 305f, 321, 326, 326f environment(s) aquatic, 725–727, 731 bacteria in, study of, 104 extreme, 94, 275–276 healthcare, as reservoir of infection, 463 and microbial growth, 90–93, 90t terrestrial, 263–266, 263t, 727–728 environmental changes, microorganisms and, 723–724 Environmental Protection Agency, 117, 745

9/2/08 5:33:40 PM

Index environmental reservoirs, 453–454 enzyme(s), 21–22, 25, 126, 134–138. See also specific enzyme action, mechanisms and consequences of, 134–135, 135f activity, environmental factors and, 136–137, 136f allosteric, 137, 157 regulation of, 137 allosteric inhibition, 137, 137f cofactors for, 135–136, 135f constitutive, 176 core, 169 definition of, 127t, 134 in detergents, 158 drug-inactivating, 483, 484f genes encoding, 161, 176 hydrolytic, 148 inducible, 176 inhibition of, 137–138, 137t competitive, 137–138, 137t, 138f, 475, 479 noncompetitive, 137–138, 137f, 137t metabolic role of, 129–130, 130f modification, 314 nomenclature for, 134 novel, discovering and exploiting, 158 in pulp and paper industry, 158 repressible, 176 restriction, 5f, 213–214, 314 suicide, 357 enzyme-linked immunosorbent assay (ELISA), 445–446, 446f definition of, 432t direct, 445–446, 445f–446f indirect, 445f, 446 for pregnancy, 445–446, 446f enzyme-substrate complex, 134–135, 135f eosinophils, 350, 351f, 352t epidemics, 451 AIDS, 7, 640, 698, 698f cholera, 581 common-source, 457, 457f diphtheria, 366 influenza, 7, 7f, 335–336, 519–520 propagated, 457f, 457–458 epidemiological studies, 457–458 epidemiologists, 450 hospital, 464 epidemiology, 450–468 definition of, 450 factors affecting, 455–457 key terms for, 451t principles of, 451–457 epidermis, 532, 532f definition of, 532t as physical barrier to infection, 348 Epidermophyton, 554 epididymis, 620, 620f epifluorescence microscope, 46 epiglottitis, 496 epilimnion, 726 epinephrine, for generalized anaphylaxis, 417 epithelial cells direct uptake of pathogens by, 399 as physical barrier to infection, 348, 349f

nes95432_ind_I1-I40.indd I-13

epitopes, 371, 371f Epstein-Barr virus infection, 331t, 686–690, 687f, 688t, 711 tumors associated with, 334t, 686 Epulopisicium, 15, 15f, 263t, 269 equine encephalitis, 295t, 323, 660–661 ergosterol, 73, 488 ergot drug derivative of, 292 poisoning, 292 Erwinia, 762 erythema infectiosum (fifth disease), 552, 553f erythema migrans, 542, 542f erythrocyte(s), 350 hemagglutination of, 443 transfused, cytotoxic hypersensitivities and, 418 erythrogenic toxin, 501 erythromycin, 474t, 478 for pertussis, 514 for pneumococcal pneumonia, 510 for pneumonia, 512 erythrose 4-phosphate, 132t, 139–141, 157 Escherichia coli, 14f adherence of, 66, 67f, 398 aerobic respiration of, 144–145, 145f anaerobic respiration of, 144–145 biochemical test for, 241f biosynthesis of precursor metabolites in, 131–132, 132t, 139, 142, 156f characteristics of, 253t chromosome of, 67f replication, 166 colony, 238 conserved (core) genome of, 205 control/destruction of, 316 culture media for, 96, 96t diarrhea-causing, 599–601, 600t diauxic growth curve of, 179, 179f DNA, 67f doubling time of, 84 electron transport chain of, 144–145, 145f enteroaggregative, 600, 600t enteroinvasive, 600, 600t enteropathogenic, 600, 600t enterotoxigenic, 398, 404t, 600, 600t gene expression in, 176–178 generation time, 166 Gram stain of, 49f, 238 growth factors for, 94 as host for cloned DNA, 215–217, 220 infection, 262 alimentary. See Escherichia coli gastroenteritis blood (septicemia), 679 foodborne, 754, 763t, 764–765, 764f meningitis, 655t nervous system, in newborns, 650 nosocomial, 463t urinary tract, 398, 621 medical importance of, 271t membrane proteins in, 56

metabolism in, 127, 144–145 ATP-generating options in, 144–145, 147 coenzymes in, 136 fermentation pathway in, 148 precursor metabolites in, 131–132, 132t, 139, 142 motility of, 66 nomenclature for, 12 in normal microbiota, 58, 349–350 oxygen requirements of, 92 phage infection in, 306–307, 307f, 307t, 315f pili of, 67f plasmid transfer in, 202–203, 203f, 600 preferential use of glucose in, 179 serological typing of, 243 shape of, 53 Shiga toxin-producing, 600, 600t strains, characterizing differences of, 243–245 study of, as typical bacterium, 232 taxonomic ranks of, 234t temperature requirements of, 91 testing water for, 746, 747f toxins of, 404t, 407, 599 two-component regulatory system, 180 vectors for, 455 virulence factors of, 600 Voges-Proskauer test for, 148 Escherichia coli gastroenteritis, 599–601, 601t causative agent of, 600, 600t, 601t epidemiology of, 600, 601t incubation period of, 601t pathogenesis of, 600, 601t prevention and treatment of, 600–601, 601t symptoms of, 599, 601t Escherichia coli O157:H7, 61, 243, 397, 404t, 600 control/destruction of, 116 foodborne infection by, 455, 754, 763t, 764–765, 764f vectors for, 455 E-site, in translation, 173, 174f esophagus, 583–584, 583f established cell line, 336 E test, 482, 482f ethambutol, 474t, 479 ethanol, 126 in fermentation, 147f, 148, 148f ethidium bromide, 191, 191t, 215, 242 ethyl alcohol, 118, 118t ethylene oxide gas, 118t, 119, 123 Eucarya, 10, 232, 234, 235f, 280 characteristics of, 10, 10t, 235t comparison of, 11t definition of, 281t Euglena, 283t Euglenophyta, 283t eukaryote(s), 10, 11t, 232 characteristics of, 10 classification of, 280 ribosomal RNA in, 249, 280, 281f electron transport chain in, 143–144, 144f gene expression in, 175–176, 175f, 175t regulation of, 179–180

I-13

genetically engineered, 217 key terms for, 281t mutualism with microorganisms, 733–735 nomenclature for, 281 pathogenesis of, mechanisms of, 410–411 eukaryotic cell(s) in algae, 283 characteristics of, 10, 40 chloroplasts in, 70f, 71t, 77 chromosomes of, 76 cilia of, 71t, 74–75 cytoskeleton of, 70f, 71t, 74, 75f endoplasmic reticulum of, 71t, 77–78, 78f flagella of, 71t, 74–75, 75f Golgi apparatus of, 70f, 71t, 78–79, 78f internal protein structures, 71t microscopic studies of, 40 mitochondria of, 70f, 71t, 76–77, 76f nucleus of, 40, 70f, 71t, 75–76, 76f organelles of, 70–71, 71t, 75–79 peroxisomes of, 71t photosynthetic, light-dependent reactions in, 153–154, 153f plasma membrane of, 70f, 71t, 72–73 transfer of molecules across, 73–74 versus prokaryotic cells, 72t protein secretion by, 72t, 74 protein structures within, 74–75 ribosomes of, 71t, 72t, 74, 175–176 size of, 14, 40, 70 structure of, 70–81, 70f transport system in, 70–71, 71f, 72t, 73f variability of, 71 eukaryotic cell structure(s), in protozoa, 287 eukaryotic DNA, 76 eukaryotic genes cloning into prokaryotic cells, vectors for, 218–220 removal of introns from, 219f Euryarchaeota, 252t eutrophic, definition of, 722t eutrophication, 725, 725f Evans, Alice Catherine, 753 evolution, 5f convergent, 294 definition of, 281t microbial, and emerging diseases, 461 evolutionary chronometers, 246 evolutionary relatedness, 233, 246. See also relatedness determination of, 249 exanthems, 545 definition of, 532t exanthem subitum (roseola), 552 excisase, 310 excision repair, of thymine dimers, 193, 194f, 195t exergonic reactions, 128 exfoliatin, 407, 537t, 538 definition of, 532t exocytosis, 73–74, 73f in phagocytosis, 358 viral release by, 328 exoenzyme S, 565

9/2/08 5:33:41 PM

I-14

INDEX

exoerythrocytic stage, of malaria, 692 exons, 175 exotoxins, 403–407, 404t–405t definition of, 392t, 403 versus endotoxin, 407, 407t functional categories of, 405 streptococcal, 563 exponential growth, 84–85, 85t exponential phase (log phase), of bacterial growth, 88–89, 88f definition of, 84 extended-spectrum β-lactamases, 476 extended-spectrum penicillins, 473t, 476 extensively-drug-resistant Mycobacterium tuberculosis (XDR-TB), 485, 517 external otitis, 496 external transmission, of plant viruses, 340 extrachromosomal DNA, 186t extrachromosomal plasmids, 204 extracts, 96, 96t extreme conditions, 94, 275–276 extreme halophiles, 93, 275, 275f, 275t, 726 extreme thermophiles, 275–276, 275t extremophiles, 90, 247 enzymes produced by, 158 extrinsic factors, in microbial growth in food, 754–756 extrusion, of phages, 306 eye infections bacterial, conjunctivitis, 504–506 chlamydial, 633 conjunctivitis, 496 cytomegalovirus, 715–716, 716f Neisseria gonorrhoeae, 120, 504, 631 toxoplasmosis, 713 eye protection, 465

F Fab (fragment antigen binding) region, 371, 372f, 402f, 403 face shield, 465 facilitated diffusion, 58, 58t FACS (fluorescence-activated cell sorter), 447 facultative anaerobes, 92, 92t, 134, 147, 253t, 262 definition of, 84 FAD, 131, 131t as enzyme cofactor, 136, 136t in tricarboxylic acid cycle, 141f, 142 FADH2, 131, 131t in electron transport chains, 143–144, 144f–145f in oxidative phosphorylation, 142 in tricarboxylic acid cycle, 141f, 142, 146 fallopian tubes, 620, 620f definition of, 619t famciclovir, 547, 639 family, definition of, 234 fascia, 564 fasciitis, necrotizing, 501, 563 causative agent of, 563, 563f epidemiology of, 564 pathogenesis of, 564

nes95432_ind_I1-I40.indd I-14

prevention and treatment of, 564 symptoms of, 563 fastidious bacteria, 94, 155 fat(s), 35, 35f hydrolysis of, 149f, 150 fatty acid(s), 35, 35f analysis, for identification of bacteria, 237t, 240 monounsaturated, 35, 35f polyunsaturated, 35 profiles, chromatogram of, 240 in prokaryotic cytoplasmic membrane, 56 saturated, 35, 35f synthesis of, 155–156 unsaturated, 35, 35f fatty acid methyl ester (FAME), 240 Fc (fragment crystallizable) region, 371, 372f, 384, 402–403, 402f, 420 FDA. See Food and Drug Administration F′ donors, 204, 204f fd phage, 307t, 311, 311f, 313t fecal bacteria, 596–597 fecal coliforms, 746 fecal contamination, 102, 262, 596–597, 599, 605–606, 610, 739 testing water for, 746, 747f fecal-oral transmission, 322, 324t, 455, 599 Federal Water Pollution Control Act, 739 feedback inhibition, 137, 137f fermentation, 92, 126, 133–134, 133f, 134t, 252t, 253–256 alcoholic, by yeasts, 758–761, 758t of beer, 4f, 6, 754, 758t, 759–760, 760f biochemical tests for, in identification of bacteria, 239, 239f, 240t of bread, 758t, 761, 761f of dairy products, 6, 126, 255, 255f, 753–754, 756–757, 756t health benefits of bacteria used in, 6 definition of, 127t of distilled spirits, 758t, 760 end products of, 147–148, 148f lactic acid, 254 in food production, 255, 756–757, 756t lactose, differential culture media for, 97, 97f malolactic, 759 metabolic pathways and processes of, 147–148, 148f of vinegar, 758t, 760–761 of wine, 754, 758–759, 758t, 759f fermented foods, 753–754 fermenters, obligate, 90t, 92, 147, 756 fertility plasmids. See F plasmids fetus as allograft, 423 toxoplasmosis in, 713 fever, 348, 362–363 fever blisters, 592, 592f fibrin, 560, 561f fibrinogen, 560, 561f fibroblasts, 560, 561f fibronectin, 560 fibronectin-binding protein, 537t

fibrous proteins, 28, 29f fifth disease (erythema infectiosum), 552, 553f filament(s) actin, 74, 75f axial, 269 of bacterial flagella, 65, 65f intermediate, 74, 75f filamentous anoxygenic phototrophs, 252t, 257 filamentous cyanobacteria, 258–259, 259f filamentous hemagglutinin, 513 filamentous phages, 306, 311, 311f–312f replication of, 311, 312f single-stranded DNA of, replication of, 311, 312f filamentous protein appendages, of prokaryotic cells, 55t, 65–67 filamentous sulfur oxidizers, 259–260 Filaria, 298t filariasis, 298t Filobasidiella (Cryptococcus) neoformans. See Cryptococcus neoformans Filoviridae, 323t filter(s) depth, 115 high-efficiency particulate air, 115 membrane, 115, 115f filterable viruses, 302 filtration of air, 112t, 115, 455, 464 of beer, 115, 760f of drinking water, 745 of fluids, 112t, 115, 115f membrane, 99t, 101, 101f in water testing, 746 removal of microorganisms by, 112t, 115, 115f fimbriae, 66, 181, 398 Finlay, Carlos, 690 Fire, Andrew, 179 Firmicutes, 252t, 263t intestinal, in obese people, 394 first-line defenses, 348–350 definition of, 347 fitter cells, 89, 89f 5′ end, of DNA, 162–163 five-kingdom classification system, 234 fixed specimens, 49 flagella (sing., flagellum), 10–11, 25 of eukaryotic cells, 71t, 72t, 74–75, 75f peritrichous, 65f, 66, 262 polar, 65f, 66 of prokaryotic cells, 54f, 55t, 65–66, 65f, 72t structure and arrangement of, 65–66, 65f protozoan, 286, 286t, 287 of spirochetes, 269 stain, 48t, 51, 51f flagellin, 65, 65f, 360 Flagyl. See metronidazole flaming, 114 flash autoclaving, 113 flatworms. See flukes; tapeworm(s); trematodes flavin adenine dinucleotide. See FAD flavins, 143

Flaviviridae/flaviviruses, 295t, 323t, 660, 689 flavoproteins, 143 fleas, as vectors of disease, 295–296, 295t, 674, 682–685, 684f, 685t Fleming, Alexander, 5f, 470 flesh-eating infections, 394, 501, 563, 563f, 565t flocculation, 745 flocs, 741 Florey, Howard, 470 flow cytometer, 100 flow cytometry, 447 fluconazole, 489, 489t, 626 flucytosine, 488f, 489–490, 489t fluid filtration, 112t, 115, 115f fluid mosaic model, 56 flukes, 295, 298t, 299. See also flatworms; trematodes fluorescein, 444 fluorescence-activated cell sorter (FACS), 447 fluorescence in situ hybridization, 227–228, 229f, 242, 725 techniques for, 228, 229f fluorescence polarization immunoassay, 444–445 fluorescent antibody test definition of, 432t direct, 444, 444f indirect, 444, 444f fluorescent dyes, 51f, 52, 100, 444, 725 fluorescent microscopes, 43–46, 45f, 45t, 46f fluorescent tags, 51f, 52, 100 fluoride, and teeth, 587 fluoroquinolones, 167, 474t, 478 f-Met, 173, 174f folate antagonists, 490t folate inhibitors, 474t, 478–479, 479f folliculitis, 535 definition of, 532t food(s) antimicrobial chemicals in, 755 atmosphere of, 755–756 biological barriers of, 755 fermented, 753–754 genetically engineered, 5f genetically modified, 217, 221 microbial growth in, 754–756 extrinsic factors in, 754–756 intrinsic factors in, 754–755 microorganisms as potential, 766 nutrients in, 755 pH of, 755, 765 preparation, surfaces for, disinfection of, 121 preservation, 122, 754, 765 chemical additives and, 110, 122, 765 drying in, 122, 765 irradiation and, 110, 765 salt and, 93, 122 sugar and, 93, 122 temperature and, 91, 110, 122 water availability reduction and, 122, 765 production microbial control in, 109–110, 109f microbiology in, 6 microorganisms in, 126, 255–256, 293, 756–762

9/2/08 5:33:41 PM

Index spoilage, 91, 754, 754f, 762 common bacteria in, 762 common fungi in, 762 storage, 455 temperature for, 755 water availability in, 122, 755 food additives, 110, 122, 765 Food and Drug Administration (FDA), 116–117, 221 foodborne illness, 397, 455, 754, 763– 765. See also specific causative agents and illnesses botulism, 657–658 common, 763t food distribution/importation and, 462 tracing sources of, 243 foodborne infection, 763t, 764–765, 764f foodborne intoxication, 397, 405, 763–764, 763f, 763t food chain, 722 food microbiology, 753–767 principles of, 753–754 food web, 722 foot-and-mouth disease genetically engineered vaccine for, 216 outbreak in England, 2001, 7 Foraminifera, 287, 287f foreign DNA, 208 restriction of, 314–316 forespore, 69, 69f formaldehyde, 118t, 119 formalin, 119 foscarnet, 487t, 488, 716–717 fossil fuels, 728 F1 plasmid, 684t F plasmids integration in chromosome, 203, 203f–204f transfer of, 202–203, 203f Fracastorius, 391 Fracastoro, Girolamo, 4f fragmentation, algal reproduction by, 284, 284f frameshift mutation, 189, 189f, 190–191, 191f Francis, Edward, 680 Francisella tularensis, 680–681 bioterrorism potential of, 466 Frankia, 735 Franklin, Rosalind, 5f free energy, 128, 128f free-living spirochetes, characteristics of, 263t freeze-drying, 122 freeze etching, 47, 47f freeze fracturing, 47 freezing, in food preservation, 91, 122, 755, 765 freshwater, 726, 738 thermal stratification in, 726 Friedlander, Carl, 40 fructose, 30, 31f, 31t fructose 1,6-bisphosphate, 140f fructose-6-phosphate, 132t, 140f, 154, 155f fruiting body, 54, 264, 264f, 294, 294f fucoxanthin, 283t fumarate, 141f, 142 fungemia, 675

nes95432_ind_I1-I40.indd I-15

Fungi (kingdom), 234 Fungi Imperfectï, 289t fungus (pl., fungi), 10, 11f, 281, 288–294 allergic reactions to, 292 cell wall of, 71 characteristics of, 11, 11t classification of, 288–290, 289f control/destruction of, 117 decomposition by, 729, 730f definition of, 281t dimorphic, 290, 410, 525–526, 576, 577f disease/infections caused by in humans, 288, 292, 292t nervous system, 666–667 pathogenesis of, 410 in plants, 288–289, 293 pulmonary, 525–527 skin, 554–555, 555f in wounds, 576–577 drugs against. See antifungal drugs economic importance of, 293–294 in food, 754–756, 762 forms of, common groupings of, 289–290, 290f–291f growth requirements of, 292 habitats of, 289t, 290–292, 727–728 in normal microbiota, 410 of skin, 533, 533t, 534–535 parasitic, 290 pH requirements of, 292 reproduction of, 288–289, 289t saprophytic, 290 size of, 288, 289f in soil, 727–728 symbiotic relationships with insects, 293 with other organisms, 292–293, 294f, 733–734 toxins of, effect of, 292, 410 furuncles (boils), 535, 536f definition of, 532t fusion, cell, in immunodeficiency disorders, 704 fusion inhibitors, 708 fusion protein, 326 F1 virulence factor, of Yersinia pestis, 683–684, 684t

G Gajdusek, D. Carlton, 5f, 320 galactose, 30–31, 31f, 31t gallbladder, 584 Gallionella, 726 Gallo, Robert, 5f, 697 gametes, 691 of algae, 284 gametocytes, 691 gamma globulin, 433 gamma interferon. See interferon gamma gamma irradiation, 116, 765 gammopathy, monoclonal, 427t ganciclovir, 487t, 488, 716–717 ganglion (pl., ganglia), 648 definition of, 648t Gardnerella vaginalis, 625 garlic, 755 gas gangrene, 69, 255, 568–570, 570t, 573

causative agent of, 569, 570t epidemiology of, 569, 570t incubation period of, 570t pathogenesis of, 569, 570t prevention and treatment of, 569, 570t symptoms of, 569, 569f, 570t gas production detection, in assessment of bacterial growth, 99t, 103 gastritis definition of, 589 Helicobacter pylori, 589–591, 591t causative agent of, 9, 590, 590f epidemiology of, 590–591, 591t pathogenesis of, 590, 590f, 591t prevention and treatment of, 591, 591t symptoms of, 589, 591t gastroenteritis, 595 Campylobacter jejuni, 273, 602–603, 603t definition of, 582t Escherichia coli, 599–601, 601t foodborne microorganisms and, 763t Norovirus, 604–605, 605t rotaviral, 604, 604f, 605t Salmonella, 601–602, 602t Vibrio cholerae. See cholera viral, 322, 323t gastrointestinal disease, seasonal occurrence of, 458, 458f gastrointestinal tract. See digestive system; specific organ gas vesicles, of prokaryotic cells, 55t, 68–69, 256 Gates, Bill, 447 GC content (G + C content), 248 gelatinase test, 240t gel electrophoresis, 214–215, 214f definition of, 213t denaturing gradient, 725 in polymerase chain reaction, 242 pulsed-field, 244, 244t, 245f size standard for, 214f, 215 Genbank, 208 gender, and susceptibility to disease, 456 gene(s), 161 cloning, 212 definition of, 162, 162t global control of, 176 jumping. See transposons polygenic, in MHC molecules, 385 reporter, 217, 217f gene expression, 162. See also transcription; translation alterations in. See mutation(s) in bacteria, 168–173 environmental fluctuations and, 180–181 eukaryotic, regulation of, 179–180 eukaryotic versus prokaryotic, 175–176, 175t natural selection and, 181 quorum sensing and, 180–181, 181f, 269 regulation of, 89, 164, 176–179, 186 negative, 177, 177f positive, 177, 178f

I-15

principles of, 176 signal transduction and, 180–181 gene fusion, 217, 217f gene mutation, 187–192. See also mutation(s) gene pool, mobile, 205–208 gene product, definition of, 162 generalized transducing phages, 313 generalized transduction, 201, 202f, 313 general paresis, 635 general-purpose disinfectants, 117 general secretory pathway, 59 generation time, 84, 166 definition of, 84 gene rearrangement, and antibody diversity, 387, 387f gene therapy, 427 for immunologic disorders, 428 genetic(s) bacterial, 185–211 key term for, 186t definition of, 162 key terms for, 162t overview of, 162–164, 162f genetically engineered food, 5f genetically modified food, 217, 221 genetically modified organisms, 221 genetic code, 170, 171f degenerate, 170 reading frames of, 170, 171f, 171t, 172f genetic engineering, 5f, 212–213 applications of, 215–218, 215t of bacteria, 215–217, 229t concerns about, 221 definition of, 213t for DNA production, 217 of eukaryotes, 217 of IgG, in hypersensitivities, 417 of plants, 206, 217 for protein production, 216–217 techniques used in, 218–220 of vaccines, 216 of yeasts, 293–294 genetic reassortment, 520 of viruses, 335, 335f genetic recombination, 198 genetic transformation, 5f gene transfer, 186 and antimicrobial resistance, 484, 484f in bacteria, general experimental approach for detecting, 198, 198f bacteria to plant, 205–206, 206f, 265 in conjugation, 199, 202–204, 204t in DNA-mediated transformation, 199–201, 204t horizontal, 5f, 198, 246 definition of, 233t lateral, 198, 246 definition of, 233t mechanisms of, 198–208, 204t by phages, 201, 202f, 204t, 313, 314f in transduction, 199, 201, 202f, 204t, 313, 314f by transposons, 185, 207–208, 207f genital herpes simplex, 330, 592, 629t, 638–639, 638f, 639t causative agents of, 638, 639t

9/2/08 5:33:42 PM

I-16

INDEX

genital herpes simplex—Continued epidemiology of, 638, 639t pathogenesis of, 638, 639t prevention and treatment of, 638–639, 639t symptoms of, 638, 638f, 639t vaccine sought for, 437t genital system female, anatomy and physiology of, 620, 620f male, anatomy and physiology of, 620, 620f normal microbiota of, 620–621 genital system diseases, 625–628 chlamydial, 631–633, 633t sexually transmitted, 323, 324t, 454, 618, 628–643 bacterial, 629–637 common, 629t protozoal, 642–643 risk, in unprotected intercourse, 628f scope of problem, 628–629 symptoms of, 628, 629t viral, 323, 324t, 638–642 genital warts, 639–640, 639f, 641t genitourinary infections, 618–646. See also genital system diseases; urinary tract infections key terms for, 619t genitourinary system anatomy and physiology of, 619–620, 619f–620f definition of, 619 normal microbiota of, 620–621 genome(s) conserved (core), 205 definition of, 162, 162t of HIV, 700f, 701 Human Genome Project, 221 medical importance of, 182, 208 of Mycoplasma genitalium, 273 sequencing of, 181–182 representative microorganisms with, 181 viral, 304, 322, 326–328 exchange of, 335, 335f genome mining, 182 genomic island, 186t, 208, 208t genomics, 181–182, 208, 221, 725 definition of, 162 genomic typing, for characterizing bacterial strains, 243–244, 244t, 245f genotype(s), 186, 186t characteristics in classification of prokaryotes, 248t in identification of prokaryotes, 237t, 241–243 gentamicin, 474t, 477, 681 genus definition of, 233t, 234 nomenclature for, 12 Geobacillus (Bacillus) stearothermophilus, in autoclave indicators, 114 geosmin, 259, 265, 727 Geotrichum candidium, nucleus of, 76f German measles. See rubella germicide(s), 116–121 classes of, 118–121, 118t

nes95432_ind_I1-I40.indd I-16

compatibility with treated material, 117 cost and availability of, 117 definition of, 108, 108t environmental risk of, 117 less toxic alternatives to, 123 organic matter and, 117 overuse and misuse of, 123 potency of, 117 residue of, 117 selection of, 117 sites of action, 116–117, 117f storage and stability of, 117 toxicity of, 117 germination, of endospores, 70 germ theory of disease, 4f, 107, 391, 450 germ tube, 290, 291f giant cells, 359, 361, 383 Giardia, 286t control/destruction of, 110 in drinking water, 745, 750 Giardia lamblia, 286 infection, 610–611, 610t, 611f, 628 pathogenesis of, 410 giardiasis, 610–611, 610t, 628 causative agent of, 610, 610t, 611f epidemiology of, 610t, 611 pathogenesis of, 610t, 611 prevention and treatment of, 461, 610, 610t symptoms of, 610, 610t gingival crevices, 582, 584f, 585, 588 gingivitis, 588 acute necrotizing ulcerative. See trench mouth definition of, 582t gingko, nitrogen-fixing root nodules of, 735 gliding motility, 66 global control of genes, 176 global warming, 614 phytoplankton and, 285 globular proteins, 28, 29f glomerulonephritis, 420 acute, post-streptococcal, 408, 501, 539, 539f gloves, medical, 465 glucans, 71, 587 definition of, 582t Gluconobacter, 758t, 761 glucose, 30–31, 31f, 31t in catabolite repression, 179 and control of lac operon, 178f, 179 in disaccharide formation, 31t, 32 metabolism, 132, 133f, 138–142, 140f preferential use in E. coli, 179 glucose isomerase, 158 glucose-6-phosphate, 132t, 140f glucose-salts, 96, 96t glutamate, synthesis of, 156–157, 157f, 728 glutamic acid, 27f glutamine, 27f glutaraldehyde, 118t, 119, 123 glycan chain, 60, 60f, 62, 62f glyceraldehyde-3-phosphate, 139–141, 140f, 154, 155f glycerol, 35, 35f synthesis of, 155–156 glycine, 27f glycocalyx, of prokaryotic cells, 54f, 55t, 64, 64f

glycogen, 31t, 32, 32f glycogen storage, in prokaryotic cells, 68 glycolipids, adherence to, 398, 398f glycolysis, 132, 132t, 133f, 134t, 139, 139t, 140f ATP yield in, 139, 140f, 146 yield of, 139 glycolytic pathway. See glycolysis glycoproteins, 30, 73, 326 adherence to, 398, 398f glycosylase, 193, 194f, 195t glycylcyclines, 474t, 478 glyphosphate (RoundupTM), genetically engineered plants resistant to, 217 goblet cells, 498 golden brown algae, 283t Golgi apparatus, 70f, 71t, 78–79, 78f, 328 gonorrhea, 629–631, 629t, 632t. See also Neisseria gonorrhoeae asymptomatic, 453, 629 causative agent of, 273, 630, 630f, 632t disseminated infection, 401 epidemiology of, 455, 631, 632t incubation period of, 632t in men, 630 pathogenesis of, 630–631, 630f, 632t prevention and treatment of, 631, 632t symptoms of, 629, 632t in women, 621, 630 Gonyaulax, 285 gonyautoxins, 285 Gorgas, William C., 690 gown, medical, 465 graft-versus-host reaction, 424 Gram, Hans Christian Joachim, 4f, 40, 49 Gram-negative bacteria, 40, 49, 55t, 238 agents targeting peptidoglycan in, 61–62 antimicrobial resistance of, 476 cell wall of, 61, 63f distinguishing structures of, 60t endotoxin of, 407–408 flagella in, 65f general characteristics of, 60t inner membrane of, 61 medically important, 271t outer membrane of, 61, 63f periplasm of, 61, 63f protein secretion by, 61 representative genera of, 60t serum-resistant, 400–401 type III secretion systems of, 398, 398f Gram-negative cocci, medically important, 271t Gram-negative curved rods, 254 medically important, 271t Gram-negative rods, medically important, 271t Gram-negative septicemia, 678–680 causative agents of, 679 epidemiology of, 680 pathogenesis of, 679–680, 679f prevention and treatment of, 680 symptoms of, 678–679

Gram-positive bacteria, 40, 49, 55t, 238 agents targeting peptidoglycan in, 61–62 cell wall of, 61, 62–63, 62f distinguishing structures of, 60t general characteristics of, 60t versus Gram-negative bacteria, 60t medically important, 272t representative genera of, 60t in soil, 727 Gram-positive cocci, medically important, 272t Gram-positive rods, medically important, 272t Gram’s iodine, 49 Gram stain, 4f, 40, 48t, 49–50, 49f cell wall composition and, 62–63 for identification of bacteria, 238, 238f granulation tissue, 560, 561f granule(s), in neutrophils, 359 granulocyte(s), 350, 351f, 352t granuloma(s), 359, 361, 383, 515, 515f definition of, 496t pyogenic, 560 granulomatous disease, chronic, 427, 427t Graves’ disease, 424t, 425 Great Salt Lake, 726 green algae, 283t green bacteria, 257 light-dependent reactions in, 154 photosynthesis in, 152–154, 152t sulfur, 154, 252t, 257, 257f, 731 green fluorescent protein, 217, 217f Griffith, Frederick, 5f, 199 griseofulvin, 293, 488f, 489, 489t groundwater, 726, 744, 745f group A Streptococcus, 495 β-hemolytic, 495, 499, 539 infection, flesh-eating, 501, 563, 563f group B Streptococcus, 495, 650 group C Streptococcus, 495 group D Streptococcus, 495 group translocation, 58t, 59, 59f growth, microbial. See microbial growth growth curve, 88–89, 88f–89f death phase of, 88f, 89 exponential phase (log phase) of, 84, 88–89, 88f lag phase of, 88, 88f late log phase of, 89 phase of prolonged decline, 88f, 89, 89f stationary phase of, 88f, 89 growth factors, 94 guanine, 33, 33f, 161–162 guanosine triphosphate (GTP), 141f, 142 guanylic acid, 33f, 158 Guillain-Barré syndrome, 521, 603 Gulf of Mexico, dead zone in, 726 gum disease, 588, 588f, 589t gumma, 635, 635f Gymnodinium breve, 284–285, 284f

H HAART, 707–709 habitats of algae, 282, 283t

9/2/08 5:33:42 PM

Index animals as, 270–274 aquatic, 725–727, 731 terrestrial, 727–728 Hadlow, William, 320 Haemophilus, 273 culture medium for, with increased carbon dioxide, 97 in normal microbiota genitourinary, 620 of respiratory system, 498t, 499 Haemophilus ducreyi infection, 629t, 637, 637t medical importance of, 271t, 273 Haemophilus influenzae antigenic types of, 650 genome, 181 infection, 504 age and, 456 nervous system (meningitis), 456, 650, 650f, 651, 651f, 655t reductions in, 461 respiratory, 499, 505 secondary, 519, 548 medical importance of, 271t, 273 in normal microbiota, of respiratory system, 498t, 499 polysaccharide capsule of, 379, 383 type B, vaccine, 434t, 435, 437t, 650 vaccine, 383 hair follicles, 532f, 533 infections of, 535–537 causative agent of, 535–536 epidemiology of, 537 pathogenesis of, 536 prevention and treatment of, 537 symptoms of, 535 hairpin loop, 170, 170f hairy leukoplakia, 699, 699f half-life, 472 Halobacterium, 275, 275f, 275t halogens, 118t, 119–120 halophiles, 90t, 93, 726 extreme, 93, 275, 275f, 275t Halorubrum, 275, 275t halotolerance, 90t, 93 hand washing, 108, 450, 454, 464 Hansen, Gerhard Henrik Armauer, 647 Hansen’s disease (leprosy), 91, 384, 655–656, 656t causative agent of, 655, 656f, 656t delayed cell-mediated hypersensitivity in, 422 epidemiology of, 656, 656t historical perspective on, 647 incubation period of, 394, 656, 656t lepromatous, 656 pathogenesis of, 655–656, 656t prevention and treatment of, 656, 656t symptoms of, 655, 655f, 656t temperature and, 91 treatment of, 478 tuberculoid, 656 hantavirus, 7–8, 323t, 453–454, 522–523, 523t bioterrorism potential of, 466 hantavirus pulmonary syndrome, 7–8, 522–523, 523t causative agents of, 522, 523t epidemiology of, 522–523, 523f, 523t

nes95432_ind_I1-I40.indd I-17

incubation period of, 523t pathogenesis of, 522, 523t prevention and treatment of, 523, 523t symptoms of, 522, 523t H antigen, 243, 262f, 520, 520f, 549 haploid cell(s), 186, 190 of algae, 284 definition of, 186t haptens, 383, 417 hard chancre, 633, 634f haustoria, 290 Haverhill fever, 574 hay fever, 292. See allergic rhinitis health general, and susceptibility to disease, 456 microbes and, 392–413 healthcare-associated infections, 462–465. See also nosocomial infections healthcare setting(s) air filtration in, 464 reservoirs of infectious agents in, 462–464 transmission of infectious agents in, 464 airborne, 464 by healthcare personnel, 464 by medical devices, 464 healthcare workers protection of, 465 as reservoirs of infection, 463 in transmission of infectious agents, 464 heart, 675–676, 675f heart valve disease. See endocarditis heat. See also temperature in destruction of microorganisms and viruses, 111–114, 112t dry, 112t, 114 moist, 112–114, 112t heat-resistant bacteria, 2 heavy chains, of immunoglobulins, 371, 372f combinatorial associations of, 387 gene rearrangement and, 387, 387f heavy metals, as antiprotozoan and antihelminthic drugs, 490t helical viruses, 303, 304f helicases, 165t, 166 Helicobacter, 273 Helicobacter pylori, 590f breath test for, 239 and gastric ulcers, 273 medical importance of, 271t, 273 motility of, 65 oxygen requirements of, 92 pH requirements of, 92–93 virulent strains of, 590 Helicobacter pylori gastritis, 589–591, 591t causative agent of, 9, 590, 590f, 591t epidemiology of, 590–591, 591t pathogenesis of, 590, 590f, 591t prevention and treatment of, 591, 591t symptoms of, 589, 591t Heliobacterium, 252t, 257 helix double stranded DNA, 34, 34f, 163, 163f protein, 28, 29f

helminths, 10, 11t, 14f definition of, 281t disease caused by, 295, 297–299, 298t drugs against, 490–491, 490t–491t infection, pathogenesis of, 410–411 intestinal, drugs against, 491t tissue, drugs against, 491t helper T cell, definition of, 367t hemagglutination definition of, 443 of viruses, 337, 338f hemagglutinin, 335, 519 filamentous, 513 hematin, 637 hematopoiesis, 350 hematopoietic stem cells, 350, 351f, 424 heme, 143 hemolysin, 97, 405, 499 hemolysis alpha, 97, 97f beta, 97, 97f differential culture media for, 97, 97f hemolytic anemia, autoimmune, 424t hemolytic disease of newborn, 418–420, 419f definition of, 415 hemolytic Streptococcus, 495, 499, 539 hemolytic uremic syndrome, 7, 598–600, 764–765 definition of, 582t prevention of, 614 hemophilia definition of, 698t and HIV disease, 705 hemorrhagic fevers, bioterrorism potential of, 466 Henle, J., 4f HEPA. See high-efficiency particulate air filters Hepadnaviridae, 324t. See also hepatitis and specific hepatitis viruses hepatitis definition of, 582t infectious. See hepatitis A virus serum. See hepatitis B virus viral, 604, 628–629 hepatitis A virus, 323t–324t, 604 infection, 605–606, 609t epidemiology of, 605–606, 605f incidence of, 605f incubation period of, 394, 609t pathogenesis of, 605 prevention and treatment of, 606, 609t transmission of, 605–606, 609t vaccine, 434t in HIV-infected (AIDS) patients, 712t hepatitis B immune globulin, 433, 608 hepatitis B virus, 324t, 606, 606f antigens, 606 DNA replication in, 331 immunity, 606 infection, 604, 606–608, 609t carriers of, 331, 606 chronic, 330–331, 330f, 332t, 606 epidemiology of, 607, 607f incidence of, 607f

I-17

incubation period of, 609t pathogenesis of, 606–607, 607f prevention and treatment of, 465, 607–608, 609t symptoms of, 606 transmission of, 607, 609t, 628–629 replication of, 607, 607f tumors associated with, 334t vaccine, 216, 434t, 435, 607–608 in HIV-infected (AIDS) patients, 712t hepatitis C virus, 323t, 604, 608 infection, 608, 609t chronic, 332t epidemiology of, 608 incubation period of, 609t pathogenesis of, 608 prevention and treatment of, 608, 609t symptoms of, 608 transmission of, 608, 609t tumors associated with, 334t vaccine sought for, 437t hepatitis D virus infection, 609t hepatitis E virus infection, 609t hepatitis G virus infection, 609t hepatitis viruses, 323 hepatovirus, 324t herbicide(s), as pollutants, 749 herbicide-resistant plants, 217 herbivores, microorganisms and, 735 herd immunity, 433, 451t, 456 hereditary angioneurotic edema, 426 herpes simplex labialis, 592, 592f herpes simplex virus, 324t, 592 infection, 592–593, 593t delayed cell-mediated hypersensitivity in, 422 epidemiology of, 592, 593t genital, 330, 437t, 592, 629t, 638–639, 638f, 639t incubation period of, 593t nervous system (encephalitis), 592, 659 pathogenesis of, 592, 593t prevention and treatment of, 487–488, 593, 593t symptoms of, 592, 592f, 593t type 1 (HSV-1), 330, 331t, 592, 659 type 2 (HSV-2), 324t, 330, 331t, 592, 638, 639t, 659 Herpesviridae, 324t herpesviruses, 323. See also cytomegalovirus; Epstein-Barr virus; herpes simplex virus; varicellazoster virus antigen presentation inhibited by, 409 infection antiviral drugs for, 487–488 human type 8 (HHV-8), 334t, 711 latent, 330, 331t and tumor formation, 333 type 6, in roseola, 552 herpes zoster, 330, 330f, 331t, 395, 546, 546f herpetic whitlow, 592 Hess, Fannie, 83 Hesse, Fanny, 4f Hesse, Walter, 4f heterocyst, 258, 259f

9/2/08 5:33:43 PM

I-18

INDEX

heterophile antibody, 686 heterotrophs, 94, 722 fungi as, 292 hexachlorophene, 118t, 120, 123 hexose(s), 31, 31f Hfr cells, 203, 203f–204f HICPAC. See Hospital Infection Control Program Advisory Committee high-copy-number plasmid, 205 high-copy-number vector, cloning into, 216, 216f high-efficiency particulate air (HEPA) filters, 115, 455, 464 high-energy phosphate bonds, 130 high frequency of recombination (Hfr) cells, 203, 203f–204f high-fructose corn syrup, 158 high-level disinfectants, 117 highly active antiretroviral therapy, 707–709 high-temperature-short-time method (HTST), of pasteurization, 112–113 histamine, in hypersensitivity reactions, 415, 415f, 416 histidine, 27f histones, 76 Histoplasma capsulatum, infection, 292, 292t, 526–527, 527f, 527t histoplasmosis, 526–527, 527t causative agent of, 292, 292t, 526– 527, 526f, 527f, 527t epidemiology of, 527, 527t, 527f granulomatous response in, 359 incubation period of, 527t pathogenesis of, 527, 527t prevention and treatment of, 527, 527t symptoms of, 526, 527t HIV. See human immunodeficiency virus (HIV) HIV disease, 640–642, 642t, 697–710 causative agent of, 5f, 699–701, 700f, 709t complications/infections with, 710–718 cryptococcal, 666–667 cryptosporidiosis, 610 cytomegalovirus, 715–717, 717t fungal infections of lung, 525– 527 malignant tumors, 333, 710–711 Mycobacterium avium complex, 717–718, 718t periodontal disease, 588 Pneumocystis jirovecii, 292t, 698, 712–713, 712f susceptibility to, 9 toxoplasmosis, 713–715, 715t tuberculosis, 9, 461, 514, 717 deaths due to, 707, 707f definition of, 699 epidemiology of, 641, 642t, 705, 706f, 709t immunization in individuals with, 547, 551, 712, 712t incubation period of, 642t, 709t key terms for, 698t natural history of, 704, 704f origin of, 8 pandemic, 640

nes95432_ind_I1-I40.indd I-18

pathogenesis of, 331–332, 333f, 641, 642t, 701–705, 701f, 702f, 703f–704f, 709t persons at increased risk for, 706, 706t poverty and, 718 prevention and treatment of, 487–488, 641, 642t, 705–706, 709t entry inhibitors for, 486, 486f lifestyle and, 705–706, 706t symptoms of, 640–641, 642t, 699, 699f, 709t treatment of, 332, 641, 642t, 707–710, 709t costs of, 709, 718 side effects of, 709 vaccine sought for, 437t, 447, 709–710 in women, 705, 706f hives. See urticaria HLA. See human leukocyte antigens (HLA) holdfast, 266, 267f, 282 homologous recombination, 200 definition of, 186t homology, of proteins, 182 homoserine lactone, 181 honeymoon cystitis, 621 Hong Kong flu, 336 hook, of bacterial flagella, 65f, 66 Hooke, Robert, 4f first observation of microorganism, 1 hookworm disease, 298t hops, 759–760, 760f horizontal gene transfer, 5f, 186, 198, 246 definition of, 186t, 233t horizontal transmission, 454 hospital(s) air filtration in, 455 microbial control in, 108–109, 109f operating room contamination in, by bacterial pathogen, 121 reservoirs of infectious agents in, 462–464 hospital-acquired infection. See nosocomial infections hospital epidemiologist, 464 Hospital Infection Control Program Advisory Committee (HICPAC), 465 host(s) colonization of, 394 definition of, 392 immunocompromised, 392, 392t viral, definition of, 303t of viruses, 302 animal, interactions of viruses with, 325–333 phage interactions with, 306f, 306–313, 313t host cell(s) cultivation for viral study, 336–337, 337f and immune response, 347 host-microbe interactions, 391–413 symbiotic, 392 host-pathogen interactions, 9 host range(s) of animal viruses, 335 of phages, 314–316 of plasmids, 205

HPV. See human papillomavirus HTLV. See human T-lymphotropic virus HTST (high-temperature-short-time method), of pasteurization, 112–113 human behavior, changes in, and emerging diseases, 461 human bite infections, 574–576, 575t causative agents of, 575, 575t epidemiology of, 575, 575t incubation period of, 575t pathogenesis of, 575, 575t prevention and treatment of, 575, 575t symptoms of, 574, 575t Human Genome Project, 221 human herpesvirus-8 (HHV-8), 711 tumors associated with, 334t human immunodeficiency virus (HIV), 162, 323t–324t, 699–701, 709t accessory gene products of, 700f, 701 attachment and entry of, 325–326, 701–703, 702f cellular targets of, 701–703, 701f control/destruction of, 110 discovery of, 5f, 697 evasion of host defenses by, 410 genetic variability of, 703–704, 704f genome, 700f, 701 infection, 331–332, 408, 428, 629t, 640–642, 642t, 698–710. See also HIV disease acute, 699, 704–705, 709 CD4 T cells in, 381 chemokine receptors in, 353 definition of, 699 prevention of, 465 slow, 331, 333f trichomoniaisis and, 642 nucleotide sequence amplification, polymerase chain reaction for, 224 origin of, 8, 705 replication of, 332, 333f, 641, 703, 703f resistant strains of, 709 structure of, 699, 700f and syncytium formation, 410 testing for, 446, 697 T lymphocyte destruction by, 641, 702–705 transmission of, 323, 641, 642t, 705, 709t type 1 (HIV-1), 641, 699–701, 705 subtypes of, 699–700 type 2 (HIV-2), 641, 700, 705 human leukocyte antigens (HLA), 385, 424 Human Microbiome Project, 221, 394 human papillomavirus, 629t, 639–640. See also papillomaviruses tumors associated with, 334t vaccine, 434t, 435, 640 human reservoirs, 453 human T-cell lymphotropic virus (HTLV), 334t, 697 type 1, 334 tumors associated with, 334t

humoral immunity, 367–368, 368f overview of, 367–368, 368f humus, 727 Hutchinson’s teeth, 636f hyaluronic acid capsule, 500, 500t hyaluronidase, 536, 537t, 569, 575 hybridization DNA, for classifying prokaryotes, 247–248, 248t nucleic acid, 227–229, 237t applications of, 227–229 hybridomas, 440, 440f hydrogen, 19 atomic structure of, 19t atomic weight of, 20 isotopes of, 26 as major element, 93–94, 94t hydrogenation, 131 hydrogen bacteria, 150, 150t hydrogen bonds, 19t, 20, 22–23, 22f, 23f hydrogen carriers, 131 hydrogen gas, as electron source, for photosynthesis, 154 Hydrogenobacter, 253t, 260 hydrogen-oxidizing bacteria, 253t, 260 hydrogen peroxide, 92, 118t, 120, 123, 189, 358 hydrogen sulfide, 150, 251, 254, 256, 731 as electron source, for photosynthesis, 154 testing for, in identification of bacteria, 240t hydrolysis, 25, 25f, 148–149, 149f of disaccharides, 149, 149f of high-energy phosphate bonds, 130, 130f of lipids, 149f, 150 of polysaccharides, 149, 149f of proteins, 149f, 150 hydrolytic enzymes, 148, 149f hydrolytic reaction, 25, 25f hydrophilic amino acids, 26, 28 hydrophilic head, 56 hydrophobic amino acids, 26, 28 hydrophobic interactions, 28 hydrophobic tail, 56 hydrothermal vents, 91, 94–95, 151, 254, 726, 732, 732f definition of, 722t hygiene hypothesis, 393 hyperimmune globulin, 433 hypersensitivities, 414–423 contact, 421–422, 422f–423f cytotoxic (type II), 414, 415t, 418–420 delayed cell-mediated (type IV), 415t, 421–422, 421f–423f in infectious disease, 422 discovery of, 414 immediate IgE-mediated (type I), 375, 383, 414–418, 415t, 416f immunotherapy for, 417 immune complex-mediated (type III), 415, 415t, 420, 421f major types, characteristics of, 414t to penicillin, 383, 417 types of, 414–415 hyperthermophiles, 90t, 91, 91f, 275–276 methane-generating, 275, 275t sulfur- and sulfate-reducing, 254, 275–276, 275t

9/2/08 5:33:43 PM

Index hypha (pl., hyphae), 265, 265f, 290, 291f Hyphomicrobium, 263t, 267, 268f hypnozoites, 692 hypolimnion, 726 hyposensitization, 417 hypoxic, definition of, 722t hypoxic waters, 726

I icosahedral symmetry, 321 of viruses, 303 ID50, 338, 394 identification definition of, 233, 233t of prokaryotes/bacteria biochemical tests for, 237t, 238–239, 239f, 240t fatty acid analysis for, 237t, 240 genotypic characteristics used in, 237t, 241–243 by metabolic differences, 237t, 238–240 methods for, 237t by microscopic morphology, 237t, 237–238, 238f nucleic acid probes for, 237t, 241–242, 242f phenotypic characteristics for, 237–241, 237t polymerase chain reaction for, 237t, 242 sequencing ribosomal RNA genes for, 237t, 242–243, 243f serology for, 237t, 240 by size and shape, 237 Ignicoccus, 15, 15f, 276 illness, 395, 395f imidazoles, 489, 489t imipenem, 473t, 477 imiquimod, 640 immobilization, in antibody-antigen binding, 372–373, 372f immune complex(es), 420 immune complex disease, 420, 421f immune complex-mediated hypersensitivity, 415, 415t, 420, 421f immune globulin, 433 immune response adaptive, 366–390. See also adaptive immune response applications of, key terms for, 432t avoidance, by viruses, 409–410 cells of, 350–352, 351f, 352t, 353f differentiation of, 350 cellular, 367f, 368–369, 368f overview of, 368f damaging effects of, 408 humoral, 367–368, 368f overview of, 367–368, 368f innate, 346–365. See also innate immune response non-specific. See innate immune response immunity, 456 active, 432, 432f age and, 456 artificially acquired, 432, 432f herd, 433, 451t, 456 naturally acquired, 432, 432f passive, 432, 432f transplantation, 428

nes95432_ind_I1-I40.indd I-19

immunization, 431–438. See also specific immunizations current progress in, 437–438 global, 447 in immunodeficient patients, 516, 547, 551, 712, 712t important agents for, 434t neglect of, 8, 433, 436 principles of, 432–433 procedures for, 433–438 routine, for children effectiveness of, 436–437, 437t importance of, 436–437 recommended schedule for, 436–437 immunoassay, 438, 438f fluorescence polarization, 444–445 immunoblot, definition of, 432t immunocompromise, 392. See also acquired immune deficiency syndrome; human immunodeficiency virus; immunodeficiency disorders and activation of latent infection, 464 definition of, 392t immunodeficiency, 414 definition of, 415 key terms for, 698t immunodeficiency disorders, 426–428. See also specific disorders immunization and, 516, 547, 551, 712, 712t primary (congenital), 426–427, 427t genetic defects in, 427t secondary (acquired), 426–428, 427t infectious complications of, 712–718 malignant tumors with, 710–711 immunodiffusion tests, 441–442, 442f immunoelectrophoresis, 443, 443f immunofluorescence, 51f, 52 immunogen(s), 371 immunogenic [term], use of, 371 immunoglobulin(s), 326, 371–375 characteristics of, 373t classes of, 371, 373–375, 373t class switching of, 378, 378f combinatorial associations in, 387 constant region of, 372, 372f diversity of, 387, 387f gene rearrangement in, 387, 387f heavy and light chains of, 371, 372f immunoelectrophoresis of, 443, 443f imprecise joining in, 387 structure and properties of, 371–372, 372f variable region of, 372, 372f immunoglobulin A, 371, 374 in breast milk, 432 characteristics of, 373t, 374 secretory, 373t, 374, 398 selective deficiency of, 426, 427t immunoglobulin A proteases, 398, 403 immunoglobulin D, 371, 374 characteristics of, 373t, 374 immunoglobulin E, 371, 374–375 characteristics of, 374–375 hypersensitivities mediated by, 375, 383, 414–418, 415t, 416f

immunotherapy for, 417, 417f protective role of, 415 immunoglobulin G, 371, 374 in antibody-dependent cellular cytotoxicity, 373 characteristics of, 373t, 374 class-switching to, 378, 378f in colostrum, 374 diversity of, 387, 387f in gamma immunoglobulin, 433 gene rearrangement in, 387, 387f genetically engineered, 417 heavy and light chains of, 372f maternal, transplacental transmission of, 374, 374f, 432 in opsonization, 373 in Rh disease, 418–419 immunoglobulin M, 371, 374, 650 B-cell production of, 378, 378f characteristics of, 373t, 374 class-switching from, 378, 378f in hypersensitivity reactions, 419 immunologically privileged sites, 423 immunologic disorders, 414–430 treatment of, new approaches to, 428 immunologic tests, 438–448 principles of, 439–441 quantitation of, 439, 441f immunologic tolerance, 367, 377, 403, 414, 426 immunosuppression agents for, 424 and fetus, 423 and organ transplantation, 423 immunotherapy, for IgE-mediated hypersensitivities, 417, 417f definition of, 415 impetigo, 538–540, 540t causative agent of, 539, 540t definition of, 532t epidemiology of, 540, 540t incubation period of, 540t pathogenesis of, 539–540, 540t prevention and treatment of, 540, 540t symptoms of, 538–539, 540t imprecise joining, in antibodies, 387 inactivated vaccine(s), 435–436 versus attenuated vaccines, 435t definition of, 432t inactivated whole agent vaccines, 435 inapparent infection, 394 incidence, 451, 451t incineration, 112t, 114 incised wounds, 560 inclusion body, 337, 546–547, 664, 664f inclusion conjunctivitis, 633 incubation period, 394, 395f, 456 index case, 451t, 457–458 India ink, in capsule stain, 50, 50f indicator organisms definition of, 739t in water testing, 746 indinavir, 487t, 488 indirect contact, and infection, 455 indirect fluorescent antibody test, 444, 444f indirect selection, of mutants, 195–196, 195f indole, testing for, in identification of bacteria, 240t

I-19

induced fit, of enzyme, 134–135 induced mutations, 190–192 inducers, of transcription, 177 inducible enzymes, 176 induction, phage, 310 industry, microbial control in, 109f, 110 infantile paralysis. See polio infarcts, cerebral, 652 infection(s), 394. See also specific infection acute, 325–328, 325f, 392t, 395 definition of, 321t asymptomatic, 453 chronic, 9, 329–332, 330–331, 330f, 332t, 392t, 395 definition of, 321t community-acquired, 564 definition of, 392t, 394 disseminated, 395 establishment of, 397–398 healthcare-associated, 462–465 inapparent, 394 latent, 329–332, 330f, 331t, 392t, 395, 395f activation, in immunocompromised patients, 464 definition of, 321t nosocomial activation of, 464 localized, 395 nosocomial, 462–465 persistent, 325, 329–332 definition of, 321t phage latent, 306, 306f productive, 306, 306f primary, 394 reservoirs of, 451, 452f, 453–454 in healthcare settings, 462–464 secondary, 394, 538 slow, 329–332, 330f, 548 definition of, 321t subclinical, 394 symptomatic, 453 synergistic, 575 systemic or generalized, 395, 675 Infection Control Committee, 465 infection control practitioner, 464 infection thread, 734 infectious agents portal of entry for, 451, 452f, 455 portal of exit for, 451, 452f, 454 infectious disease characteristics of, 394–395 convalescence from, 395, 395f course of, 394–395, 395f definition of, 394 delayed cell-mediated hypersensitivity in, 422 duration of symptoms in, 395 establishing cause of, 395–396 Koch’s postulates for, 395–396, 396f molecular Koch’s postulates for, 396 incubation period for, 394, 395f principles of, 394–395 terms used in study of, 392t infectious mononucleosis. See mononucleosis infective dose, 338, 394–395, 455–456

9/2/08 5:33:44 PM

I-20

INDEX

inflammation, 347, 360–362 acute, 360–361 chronic, 361 circumvention of, apoptosis and, 362 complement system and, 356, 356f, 360 damage from, 361–362, 408 definition of, 347t four cardinal signs of, 360 initiation of, 360 in innate immune response, 361f outcomes of, 361–362 process of, 360–361, 361f vaccine adjuvants and, 435–436 inflammatory response, 359. See also inflammation influenza A, 519–521 antiviral drugs for, 487–488, 521 influenza B, 519 influenza C, 519 influenza vaccine, 434t, 435, 521 in HIV-infected (AIDS) patients, 712t improvements sought in, 437t influenza virus, 12f, 323t–324t, 325–326, 338 age and, 456 antigenic drift of, 335, 520, 520f antigenic shift of, 335, 520, 520f endemic, 451 endocytosis of, 74 epidemic/pandemic, 7, 7f, 335, 519–521 genetic reassortment of, 335 infection, 519–521, 521t antiviral drugs for, 487–488, 487t, 521 causative agents of, 519, 520f, 521t epidemiology of, 519–520, 520f, 521t historical perspective on, 336 incubation period of, 519, 521t pathogenesis of, 519, 521t prevention and treatment of, 487–488, 487t, 521, 521t symptoms of, 519, 521t infusions source of, importance of, 2 in spontaneous generation experiments, 2 inhibition allosteric, 176 competitive, 475, 479 enzyme allosteric, 137, 137f competitive, 137–138, 137t, 138f noncompetitive, 137–138, 137f, 137t feedback, 137, 137f zone of, 482 initiation complex, in translation, 173 initiation factors, in translation, 173 injectisome(s), 398, 398f innate immune response, 346–365 versus adaptive immunity, 366 adhesion molecules in, 354 antimicrobial substances in, 348–349, 349f cell communication in, 353–354 cells in, 350–352, 351f, 352t, 353f complement system in, 355–356, 356f, 357f

nes95432_ind_I1-I40.indd I-20

cytokines in, 353–354, 354t definition of, 347t fever and, 362–363 first-line defenses in, 347 inflammation in, 360–362, 361f key terms for, 347t overview of, 347–348 phagocytes in, 347 physical (anatomical) barriers in, 348, 348f sensor systems in, 354–358 surface receptors in, 353 toll-like receptors in, 347, 355, 355f inner membrane, of eukaryotic cells, 76 inorganic compounds, 19t, 21 insecticides, as pollutants, 749 insects. See also arthropods; specific insect plant virus transmission by, 340 circulative, 340 external or temporary, 340 symbiotic relationships with fungi, 293 as vectors of disease, 295–297, 295t insertional inactivation, 189 insertion sequence, 207, 207f, 208t insulin, 5f, 584 genetically engineered production of, 216 insulin-dependent diabetes mellitus. See diabetes mellitus, type 1 integrase, 701–702 definition of, 698t integrase inhibitors, 488, 708 intensive care units, transmission of infectious agents in, 464, 464f intercalating agents, 190–191, 191f, 191t interference microscopes, 43, 43f–44f, 44t interferon(s), 353, 354t antiviral activity of, 357–358, 357f viral avoidance of, 409 for hepatitis B infection, 608 interferon alpha, 354t interferon beta, 354t interferon gamma, 353–354, 354t interleukin(s), 353, 354t interleukin-1, 354, 354t, 514, 679 interleukin-2, 354, 354t, 382 interleukin-3, 354t interleukin-4, 354, 354t interleukin-5, 354, 354t interleukin-6, 354, 354t interleukin-10, 354, 354t interleukin-14, 354, 354t intermediate(s), in metabolic pathways, 129, 129f, 133f intermediate filaments, 74, 75f intermediate-level disinfectants, 117 intermediate mycoses, 292 International Code for the Nomenclature of Bacteria, 235 intestinal botulism, 657–658 intestinal infections bacterial, 595–603 viral, 604–609 intestines, 583f normal microbiota of, 585–586 intoxication, foodborne, 763–764, 763f, 763t intranuclear inclusion bodies, 546–547

intrinsic factors, in microbial growth in food, 754–755 intrinsic resistance, to antimicrobial drugs, 470t, 472 introns, 175, 175t removal of, from eukaryotic DNA, 218, 219f inverted repeat, 207, 207f iodine as disinfectant, 118t, 120 in Gram stain, 49 radioactive, 26, 26f iodophores, 120 iodoquinol, 490t ion(s), 20 ionic bonds, 20–21, 20f Iridoviridae, 324t iron acquisition, Yersinia pestis and, 684, 684t as limiting nutrient for bacteria, 398 as major element, 93–94, 94t iron bacteria, 150, 150t iron springs, 726 iron-sulfur proteins, 143 irradiation in drinking water treatment, 745 of food, 110, 765 gamma, 116 mutagenic action of, 191t, 192 in sewage treatment, 742 ultraviolet, 112t, 115f, 116 DNA damage from, repair of, 193, 194f, 195t, 310 mutagenic action of, 191t, 192 isocitrate, 141f, 142 isograft, 423 definition of, 415 isolation procedures, 465 isoleucine, 27f isometric viruses, 303, 304f, 321, 322f isoniazid, 474t, 479, 516–517 isopropyl alcohol, 118, 118t isotopes in biological research, 26, 26f definition of, 26 isotretinoin (Accutane), 534 itraconazole, 489, 489t, 577 ivermectin, 491t Iwanowski, Dmitri, 4f, 302 Ixodes, 295t Ixodes scapularis, 297, 543, 544f

J Jacob, Francois, 177 jaundice, 584, 608, 689 Jenner, Edward, 4f, 431 Jerne, Niels Kai, 5f jock itch, 554 juice, pasteurization of, 112 jumping genes. See transposons

K Kaposi’s sarcoma, 9, 333, 710–711, 710f Kaposi’s sarcoma associated herpesvirus, 710 keratin, 532 as physical barrier to infection, 348

ketoconazole, 489, 489t keto group, 30, 31f kidney(s), 619, 619f kidney infections, 621 kimchee, 756t kinetic energy, 128, 128f King, Mary-Claire, 212 kingdom(s) definition of, 234 five-kingdom classification system, 234 Kirby-Bauer disc diffusion test, 481–482, 481f kissing disease. See mononucleosis Kitasato, Shibasaburo, 559, 674 Klebsiella, 262 characteristics of, 253t infection, bladder, 621 methyl-red test for, 148 Voges-Proskauer test for, 148 Klebsiella pneumoniae infection, 510t, 511, 511f medical importance of, 271t Klein, Johann, 450 Kluyver, Albert, 232, 251 Kluyveromyces marxianus, 766 knockout mutation, 188 Koch, Robert, 366, 396, 559, 674 studies by anthrax/germ theory of disease, 2, 4f, 391 brucellosis, 753 culturing methods, 4f, 83 Vibrio cholerae, 581, 738 Koch’s postulates, 4f, 391, 395–396, 396f Kohler, Georges, 5f, 440 koji, 761 Koplik’s spots, 549, 549f, 592 Krebs cycle, 132. See also tricarboxylic acid cycle kuru, 5f, 320, 340t, 669

L lacerated wounds, 560 lac operon, 177–179, 178f glucose and, 178f, 179 lactose and, 177–178, 178f LaCrosse encephalitis virus, 660, 661f lactate, in fermentation, 147f lactic acid, 147–148, 148f lactic acid bacteria, 147–148, 155, 254–255, 755 characteristics of, 252t definition of, 252t in food production, 255, 756t, 756–757, 760 testing for, 238 Lactobacillus, 255, 255f characteristics of, 252t fermentation pathway of, 148f in food production/fermentation, 126, 255, 255f, 756, 756t, 758 in food spoilage, 762 in mucous membranes, 272 in normal microbiota, 350, 620 as probiotic, 411 protective role of, 393 Lactobacillus acidophilus, 411, 756t, 757 Lactobacillus brevis, 756t, 758

9/16/08 10:26:52 AM

Index Lactobacillus bulgaricus, 411 Lactobacillus delbruecki subsp. bulgaricus, 756t, 757 Lactobacillus plantarum, 756t, 758 Lactobacillus rhamnosus CG, 411 Lactococcus, 255 characteristics of, 252t in food production, 126, 255, 756–757, 756t nomenclature, 249 Lactococcus cremoris, 756t, 757 Lactococcus lactis, 235, 724, 756t, 757 lactoferrin, 349, 398, 583 lactose, 31t, 32 and control of lac operon, 177–178, 178f fermentation, differential culture media for, 97, 97f hydrolysis of, 149 lacZ′ gene, in vector, function of, 219–220, 220f lagging strand, in DNA replication, 167 lagoons, in sewage treatment, 741 lag phase, of bacterial growth, 88, 88f lakes, 726 LAL (Limulus amoebocyte lysate) assay, 408 lambda phage, 306, 307t, 308–311, 309f, 313t specialized transduction by, 313 lamivudine (3TC), 487, 487t, 608, 708 Lancefield, Rebecca, 495 Lancefield grouping, 650 of Streptococcus, 495 landfills, 747 large intestine, 585 normal microbiota of, 393f, 585–586 laryngitis, 496 Lassa fever virus, 323t late log phase, of bacterial growth, 89 latent infection, 395, 395f activation, in immunocompromised patients, 464 animal virus, 330, 330f, 331t definition of, 321t nosocomial activation of, 464 phage, 306, 306f viral, 329–332 latent state, viral, definition of, 303t lateral gene transfer, 186, 198, 246 definition of, 233t latex agglutination test, 443, 443f latex allergy, 422 LAV. See lymphadenopathy virus Lazear, Jesse, 690 LD50, 338 leading strand, in DNA replication, 167 leaky mutation, 188 lecithin, 565, 569 lectin pathway, of complement activation, 355, 356f Lederberg, Esther, 196 Lederberg, Joshua, 5f, 196 leghemoglobin, 265, 734 Legionella, 269 characteristics of, 263t Legionella pneumophila, 269 infection, 7, 517–518, 518f, 518t medical importance of, 269, 271t Legionnaires’ disease, 7, 269, 517–518, 518t causative agent of, 517–518, 518f, 518t

nes95432_ind_I1-I40.indd I-21

epidemiology of, 518, 518t incubation period of, 518t pathogenesis of, 518, 518t prevention and treatment of, 518, 518t symptoms of, 518, 518t legumes, 265, 721, 735 Leishmania infection (leishmaniasis), 286, 286t, 422, 531, 691 pathogenesis of, 410–411 prevention and treatment of, 490tl lentiviruses, 331–332, 699 Lepiota rachodes, 291f lepromatous leprosy, 656 leprosarium(s), 647 leprosy, 422, 647. See also Hansen’s disease (leprosy) Leptospira, 263t, 270 Leptospira interrogans infection, 270, 622f, 622–623, 624t. See also leptospirosis medical importance of, 270, 272t leptospirosis, 622–624, 624t causative agent of, 270, 622f, 622–623, 624t epidemiology of, 623, 624t incubation period of, 623, 624t pathogenesis of, 623, 624t prevention and treatment of, 623–624, 624t symptoms of, 622, 624t vaccine, for domestic animals, 624 Leptothrix, 263t, 266, 726 lethal dose, viral, 338 leucine, 27f Leuconostoc, 252t, 255 in food production, 756, 756t, 758 in food spoilage, 762 Leuconostoc mesenteroides, 756t, 758 leukemia, 428 leukocidins, 536–537, 537t, 575 leukocyte(s), 350–352, 351f, 352t and inflammation, 361f polymorphonuclear neutrophilic, 350, 352t leukocyte adhesion deficiency, 427, 427t leukotrienes in asthma, 417 in hypersensitivity reactions, 415 L-forms, 574 lice pubic, 296 as vectors of disease, 295–296, 295t, 296f lichen, 292, 293f, 294f, 727 ligands, 73, 353 light chains, of immunoglobulins, 371, 372f combinatorial associations of, 387 light-dependent reactions, 151 in cyanobacteria and photosynthetic eukaryotic cells, 153–154, 153f in purple and green bacteria, 154 light-independent reactions, 151 light microscopes, 41–42, 41f, 42f, 44t contrast in, 42–43 versus electron microscopes, 42f, 47f magnification in, 41–42 principles of, 41–42 resolving power of, 42, 42f

light reactions, 151 light repair, of thymine dimers, 193, 194f, 195t lignin, 729, 730f Limulus amoebocyte lysate (LAL) assay, 408 lincomycin, 474t lincosamides, 474t, 477f, 478 linear metabolic pathways, 129, 129f linen, hospital, handling of, 465 linezolid (Zyvox), 5f, 474t, 537 Linnaeus, Carl, 12 lipase(s), 149f, 150, 158, 536, 537t lipid(s), 19t, 25, 35–37, 36t biological importance of, 35 compound, 35–36, 36t hydrolysis of, 149f, 150 molecular weight of, 35 simple, 35–36, 149f, 150 solubility properties of, 36, 36f synthesis of, 155–156 lipid A, 61, 63f, 407–408 lipid rafts, 73, 328 lipopolysaccharide, 36, 61, 243, 379, 407–408 chemical structure of, 61, 63f of Gram-negative bacteria, 61, 63f and inflammatory response, 360 lipoproteins, 30, 36 lipoteichoic acids, 61 Lister, Joseph, 4f, 107 Listeria monocytogenes, 456 control/destruction of, 316 evasion of host defenses by, 400, 400f, 403 infection, 653–654, 654t, 763t actin tail in, 400, 400f meningitis, 655t listeriosis, 456, 653–654, 654t–655t causative agent of, 653, 654t epidemiology of, 654, 654t foodborne, 763t pathogenesis of, 654, 654t prevention and treatment of, 654, 654t symptoms of, 653, 654t liver, 583f, 584–585 lobster allergy, 416 localized infection, 395 lockjaw. See tetanus Loeffler, Frederick, 366 logarithms, for determining size of microorganisms, 14 log phase, of bacterial growth, 88–89, 88f–89f low-copy-number plasmid, 205 lower digestive system infections, 595–614 bacterial, 595–603 protozoan, 610–614 viral, 604–609 lower respiratory infections bacterial, 509–518 structures commonly involved in, 496–498, 497f viral, 519–524 low-level disinfectants, 117 low-temperature storage, 91, 122, 765 luciferase, 269 lumen of eukaryotic organelles, 70–71 intestinal, 584 lumpy jaw. See actinomycosis

I-21

lungs, fungal infections of, 525–527 lupus erythematosus. See systemic lupus erythematosus Lyme disease, 7–8, 542–544, 542f–544f, 545t causative agent of, 273, 543, 543f, 544f, 545t ecology of, 556 epidemiology of, 543–544, 543f, 545t incubation period of, 545t pathogenesis of, 543, 545t prevention and treatment of, 544, 545t symptoms of, 542–543, 542f, 545t ticks as vectors for, 295t, 297, 542– 544, 544f, 545t, 556 lymph, 370, 370f, 676–677 lymphadenopathy syndrome, 699 lymphadenopathy virus (LAV), 697 lymphangitis, 676, 677f definition of, 675t lymphatics/lymphatic system, 370, 370f, 676–677 anatomy and physiology of, 675f, 676–677 infections of, 674–699 protozoan diseases of, 690–694 lymphatic vessels, 369f, 370, 676–677 lymph nodes, 369–370, 369f, 675f, 676 bacterial diseases of, 680–685 lymphocyte(s), 351f, 352, 352t. See also B cells (B lymphocytes); T cells (T lymphocytes) activated, 375, 376f clonal selection and expansion of, 375, 376f definition of, 367t development of, 385–388 diversity of, generation of, 387, 387f effector, 375, 376f B cells, 378f T cells, 368f, 369 immature, 375, 376f in inflammation, 360 naive, 375, 376f lymphogranuloma venereum, 631 lymphoid organs primary, 369f, 370 secondary, 369f, 370 lymphoid system anatomy of, 369f, 369–370 tissues and organs of, 676–677 mucosal-associated, 598 skin-associated, 531–532 viral diseases of, 686–690 lymphoid tissue mucosal-associated, 369f, 370, 374 skin-associated, 369f, 370, 531–532 lymphoma, 331t, 334t, 686, 711 definition of, 698t in HIV-infected (AIDS) patients, 710 lyophilization, 88, 122 lysate, 337 lysine, 27f lysine decarboxylase, testing for, in identification of bacteria, 240t lysis cell, 57 of foreign cells, complement system and, 356, 356f

9/2/08 5:33:45 PM

I-22

INDEX

lysogen(s), 306, 309, 309f definition of, 303t immunity of, 310 lysogenic conversion, 306, 310–311, 333, 596 definition of, 303t LysolTM, 120 lysosomes, 70f, 71t, 72t, 79, 328, 358 lysozymes, 62, 308, 349, 583, 755 bacterial sensitivity to, 60t lytic phages, 306 assembly or maturation of, 308 attachment of, 307f, 308, 329t burst size of, 308 penetration by, 307f, 308, 329t proteins, synthesis of, 307f, 308 release of, 308, 329t replication of, RNA polymerase and, 308 with single-stranded DNA, 311 single-stranded RNA, replication by, 308 transcription of, 307f, 308

M Mab. See monoclonal antibodies MAC. See membrane attack complex; Mycobacterium avium complex MacConkey agar, 96t, 97, 97f, 238 MacLeod, Colin, 5f, 199 macroenvironment, definition of, 722 macroglobulinemia, 428 macrolides, 477f, 478 macromolecules, 19t, 25 classes of, 25 components of, 25 definition of, 25 localization of, using radioactive isotopes, 26, 26f structure and function of, 36t subunits of, 25 synthesis and breakdown of, 25, 25f macrophage(s), 350–352, 351f, 352t activated, 359 activation of, 358–359 TH cells in, 383, 384f alveolar, infection via, 399–400 avoidance, by pathogens, 401 definition of, 347t fusion into giant cells (granulomas), 359 in HIV infection, 702–705 in inflammation, 361 in septicemia, 679, 679f specialized attributes of, 358–359 toll-like receptors of, 358–359 macules, in chickenpox, 545, 546f mad cow disease, 7, 320, 340t, 342, 669–670, 670t Madura foot, 576 “magic bullet,” 208 magnesium as enzyme cofactor, 136 as major element, 93–94, 94t Magnetospirillum, 263t, 270 Magnetospirillum (Aquaspirillum) magnetotacticum, 66f, 270 magnetotaxis, 66, 66f, 270 magnification, in microscope, 41–42, 42f major elements, 93–94, 94t

nes95432_ind_I1-I40.indd I-22

major facilitator superfamily (MFS), 58, 58t major histocompatibility complex (MHC), 38, 380, 380f, 381f, 387f, 501 in autoimmune disease, 424–425 class I, 381f, 384 antigen presentation by, 381, 381f “counterfeit,” 409, 409f viral inhibition of, 409, 409f class II, 377, 377f, 381f antigen presentation by, 381f, 383 deficiency, 427t superantigens and, 406, 406f definition of, 367t diversity of, 38 loci of, 38 polymorphisms of, 38 in transplantation immunity, 424 malachite green, 49, 51, 51f malaise, 538 malaria, 288, 690–694, 694t antimicrobial resistance in, 693, 693f causative agent of, 286, 286t, 691, 692f, 694t cerebral, 692 climate changes and, 462 epidemiology of, 693, 693f, 694t eradication efforts, 299 exoerythrocytic stage of, 692 geographic distribution of, 299 incubation period of, 694t mortality rate for, 299, 692–693 mosquitoes as vectors for, 286, 295–296, 295t, 455, 691– 692, 692f, 694, 694t pathogenesis of, 410, 691–693, 694t prevention and treatment of, 461, 490t, 693–694, 694t reductions in, 461 resistance to, in persons of African descent, 457 symptoms of, 691, 694t vaccine sought for, 437t, 693 Malarone®, 490t Malassezia, 534 Malassezia furfur, 534–535, 534f malate, 141f, 142 malignancy, of lymphoid system, 427 malnutrition, and immune function, 427 malolactic fermentation, 759 MALT. See mucosal-associated lymphoid tissue malt, 759 malted barley, 759 maltose, 31t hydrolysis of, 149 manganese, 94 mannan, 71 mannan-binding lectin, 355, 356f mannose, 31, 31f, 31t, 355 M antigen, 549 Mantoux test, 438, 516 maraviroc, 487t Marburg virus, 323t marine environments, 726 Marshall, Barry, 5f Martin, Betty, 647 mashing, in beer production, 759, 760f masks, 465 mass, 19

mast cells, 350, 352t degranulation of, 415, 415f in hypersensitivity reactions, 374 Mastigophora, 286, 286t, 287, 610 mastoid(s), 650 mastoiditis, 496 streptococcal, 501 matrix, in mitochondria, 76f, 77 matrix protein, 304, 321 maturation, viral, definition of, 303t MBC. See minimum bactericidal concentration McCarty, Maclyn, 5f, 199 McClintock, Barbara, 5f, 185, 190 M cells, 370, 399, 399f, 400f, 408, 447, 598 ruffling, induced by pathogens, 399, 399f MDR-TB. See multiple-drug-resistant Mycobacterium tuberculosis measles, 323t–324t, 547–549, 550t alimentary effects of, 592 causative agent of, 549, 550t encephalitis, 548, 659 epidemiology of, 549, 550t German. See rubella immune response to, 366 incidence of, 549 incubation period of, 550t pathogenesis of, 325, 325f, 326, 549, 549f, 550t pneumonia, 548 prevention and treatment of, 549, 550t reductions in, 460 secondary infections with, 427, 548 symptoms of, 547–548, 548f, 550t vaccine, 434t, 435–436, 549 in immunodeficient patients, 551, 712t measles, mumps, rubella vaccine, 549 in HIV-infected (AIDS) patients, 712t meat products, fermented, 756t, 758 mebendazole, 491t mechanical vector, 295, 455 media, culture. See culture media medical devices/equipment classification by potential risk of infection, 111 transmission of infectious agents by, 464 medical microbiology, 7–9 Golden Age of, 7 past triumphs in, 7 present and future challenges in, 7–9 mefloquine, 490t, 693, 694t megakaryocytes, 350 meglumine antimonate, 490t meiosis, 76, 284 melarsoprol, 490t Mello, Craig, 179 melting, of DNA, 163, 248, 248f membrane attack complex (MAC), 356, 357f avoidance by pathogens, 400–401 definition of, 347t membrane-damaging toxins, 401, 404t membrane filters, 115, 115f

membrane filtration, 99t, 101, 101f in water testing, 746 membrane fusion, viral entry via, 326, 326f, 327f membrane proteins, in prokaryotic cells, 56 memory, immunologic, 366–367 memory cells, 367, 368f, 375, 376f, 378–379 memory lymphocyte(s), definition of, 367t menaquinone, 145 Mendel, Gregor, 161 meninges, 648, 648f definition of, 648t meningitis, 650 aseptic, 659 bacterial, 650–654 causative agent of, 273 definition of, 648 diagnosis of, 649, 649f Haemophilus influenzae, 456, 650–651, 651f, 655t incidence of, 650 Listeria monocytogenes, 653 meningococcal, 650–652, 653t, 655t causative agent of, 273, 652, 653t epidemiology of, 652, 653f, 653t incubation period of, 653t pathogenesis of, 652, 652f, 653t prevention and treatment of, 478, 652–653, 653t symptoms of, 651–652, 652f, 653t mumps, 593, 659, 659t pneumococcal, 510, 650, 651f, 655t streptococcal, 501 vaccine, 652–653 viral, 658–659, 659t causative agents of, 659, 659t epidemiology of, 659, 659t incubation period of, 659t pathogenesis of, 659, 659t prevention and treatment of, 659, 659t symptoms of, 659, 659t meningococcal conjugate vaccine, 434t meningococcal disease, vaccine, 434t meningococcal polysaccharide vaccine, 434t meningoencephalitis cryptococcal, 292t, 666–667, 667t causative agent of, 666, 666f, 667t epidemiology of, 667, 667t pathogenesis of, 666–667, 667t prevention and treatment of, 667, 667t symptoms of, 666, 667t definition of, 648t, 649 primary amebic, 667 mercury, 120 meropenem, 473t, 477 merozoites, 691 mesophiles, 90t, 91, 91f Mesorhizobium, 263t, 265 messenger RNA (mRNA), 164, 168–170 in animal viruses, 326–327, 327f definition of, 162t eukaryotic, 175–176, 175f, 175t in cloning, 218, 219f polycistronic, 168, 332

9/2/08 5:33:45 PM

Index precursor, 175 in translation, 170–171, 171t, 173f metabolic differences, identification of prokaryotes by, 237t, 238–240 metabolic pathways adenosine triphosphate in, 130, 130f anabolic, 155–158, 156f branched, 129, 129f central, 132–134, 133f, 138–142 comparison of, 139t components of, 129f, 129–131 cyclical, 129, 129f electron carriers in, 131, 131t enzymes in, 129–130, 130f inhibition of, by antibacterial drugs, 474t, 478–479, 479f linear, 129, 129f precursor metabolites in, 131–132 metabolism, 126–160. See also fermentation; respiration adenosine triphosphate and, 25, 25f, 130, 130f in aerobic growth of chemoorganotrophs, 128, 128f, 134t of antimicrobial drugs, 472 in chemolithotrophs, 150, 150t classification of microorganisms by, 95, 95t definition of, 126 diversity in prokaryotes, 252–262, 252t, 253t energy gains in different types of, 150, 151f overview of, 132–134, 133f principles of, 127–134 scheme of, 133f terminology used for, 127t metabolite(s) precursor, 131–132, 138–142 biosynthesis in E. coli, 131–132, 132t, 139, 142 definition of, 127t generation of, 138–142, 140f subunit synthesis from, 155–158 primary, 89, 89f secondary, 89, 89f metachromatic granules, 68, 270 metagenomics, 217, 221, 725 metal(s) heavy, as antiprotozoan and antihelminthic drugs, 490t pollution by, 120 in sterilization and disinfection, 118t, 120 metal sulfides, oxidation of, 260, 260f metastasis, definition of, 698t metastatic tumors, in HIV-infected (AIDS) patients, 710 Metchnikoff, Elie, 4f, 346 methane generation in carbon cycle, 729, 729f landfills producing, 747 as sewage treatment byproduct, 743 methane-generating hyperthermophiles, 275, 275t methanogens, 254, 254f, 275t, 729, 729f characteristics of, 252t definition of, 252t Methanosarcina, 252t, 254, 254f, 275t

nes95432_ind_I1-I40.indd I-23

Methanospirillum, 252t, 254, 254f, 275t Methanothermus, 275, 275t methicillin, 470, 473t, 476, 476f methicillin-resistant Staphylococcus aureus (MRSA), 485, 537, 563 methionine, 27f, 173 methylation, of DNA, 314, 315f methylene blue, 49–50, 68 methyl red test, 148, 240t metronidazole, 490t, 610, 643 MHC. See major histocompatibility complex MIC (minimum inhibitory concentration), of antimicrobial drugs, 480–481, 480f, 482f mice, as vectors of disease, 522 miconazole, 489, 489t Micrasterias, 11f microaerophiles, 90t, 92, 92t microaerophilic cultures, 98 microbes antagonism of, 86 competition among, 86 definition of, 6 underground, 732–733 The Microbe’s Contribution to Biology (Kluyver and van Niel), 251 microbial communities, mixed, 86 microbial control, 107–125 approaches to, 107–110 chemicals for, 107–108, 116–121, 118t in daily life, 108, 109f definitions related to, 108t environmental conditions and, 111 filtration for, 112t, 115, 115f in food and food production facilities, 109–110, 109f. See also food preservation heat for, 111–114, 112t in hospitals, 108–109, 109f in industry, 109f, 110 for medical equipment, potential risk of infection and, 111 in microbiology laboratories, 109 number of microorganisms initially present and, 110–111, 111f physical methods of, 107–108, 115–116 principles of, 108 procedure for, selection of, 110–111 radiation for, 112t, 115–116 situational considerations in, 108–110, 109f type of microorganism and, 110 microbial diversity, Golden Age of, 16 microbial ecology, 721–737 definition of, 722 key terms for, 722t principles of, 722–725 study of, 724–725 microbial evolution, and emerging diseases, 461 microbial growth control of. See microbial control definition of, 84 environmental factors and, 90–93, 90t in food, factors influencing, 754–756 in laboratory conditions, 88–90 nutritional factors and, 93–95

oxygen requirements for, 90t, 91–92, 92t, 755–756 pH and, 90t, 92–93 temperature and, 90–91, 90t, 91f, 137 water availability and, 90t, 93, 755 microbial mat, 724, 724f definition of, 722t microbial world, 13f features of, 6 members of, 9–12 new members of, search for, 16 size in, 12f–13f, 14, 14f, 15, 15f microbiology applications of, 6–7 food, 753–767 human perspective on, 6–9 major milestones of, 4f–5f medical, 7–9 microbiology laboratories, microbial control in, 109 microbiota colonization by, 394 normal, 9, 221, 272, 348–350, 392, 392t, 393–394, 393f and adaptive immune response, 393 anatomical barriers as ecosystem of, 392–393 definition of, 393 of digestive system, 585–586 dynamic nature of, 393–394 fungi in, 410 of genitourinary system, 620 of intestines, 585–586 of large intestine, 393f of mouth, 393f, 585 of nose, 393f protective role of, 393 of respiratory system, 498–499, 498t of skin, 393f, 533, 533t, 534–535 suppression by antimicrobial drugs, 393, 472, 586 of throat, 393f of urethra, 393f of vagina, 393f pathogenic, 9 patient’s, and nosocomial infections, 463–464 resident, 393 transient, 393 virulence of, 394 Micrococcus, 253t, 261, 272t oxygen requirements of, 92 Micrococcus luteus, 261, 261f microcyst, 265 Microcystis aeruginosa, 259 microenvironment, definition of, 722 microorganisms. See also specific microorganisms as model organisms, 9 mutualism with eukaryotes, 733–735 origin of, 1–5 as subjects for study, 9 vital activities of, 6 microRNA (miRNA), 179–180 microscope(s), 1, 41–48, 44t–45t atomic force, 41, 45t, 48, 48f bright-field, 41–43, 44f, 44t

I-23

compound, 41–42, 42f confocal scanning laser, 45f, 45t, 46, 46f, 725 contrast in, 42–43 dark-field, 43, 44f, 44t, 269, 269f, 634, 634f electron, 41, 42f, 45f, 45t, 46–47, 47f, 338, 338f counting virions with, 338, 338f epifluorescence, 46 fluorescent, 43–46, 45f, 45t, 46f interference, 43, 43f–44f, 44t light, 41–43, 41f, 42f, 44t, 47f magnification, 41–42, 42f phase-contrast, 43, 43f, 44f, 44t refraction in, 42, 42f resolving power of, 42, 42f scanning electron, 45t, 47, 47f transmission electron, 46–47, 47f van Leeuwenhoek’s, 9, 9f, 40 microscopic morphology, identification of prokaryotes by, 237–238, 237t, 238f microscopy dark-field, of Treponema pallidum, 634, 634f in microbial ecology, 725 staining techniques for, 48–52, 48t Microspora, 286, 286t Microsporidium, 286t Microsporum, 554, 555f microtiter plate, 439, 441f microtubules, 74, 75f 9 + 2 arrangement of, 74 microvilli, 70f, 584 definition of, 582t microwaves, 115f heat of, effect on microorganisms, 116 middle ear, 650 milk acidophilus, 756t, 757 fermentation of, 6, 753–754, 756–757, 756t health benefits of bacteria used in, 6 pasteurization of, 112–113, 753 spoilage of, 762 unpasteurized, microbial succession in, 724, 724f Milorganite, 743 Milstein, Cesar, 5f, 440 mimivirus, 305 mineralization, 722 minimum bactericidal concentration (MBC), 481 minimum inhibitory concentration (MIC), of antimicrobial drugs, 480–481, 480f, 482f mining industry bioleaching in, 260, 260f biotechnology in, 151 microbes in, 150–151 minus (–) strand, of DNA, 168, 168f, 168t mismatch repair, of damaged DNA, 192–193, 193f, 195t miso, 762t missense mutation, 188, 188f Mitchell, Peter, 142 mites, as vectors of disease, 295, 297, 297f

9/16/08 10:27:07 AM

I-24

INDEX

mitochondria algal, 283 electron transport chain of, 143– 144, 144f of eukaryotic cells, 70f, 71t, 76–77, 76f origin of, 77 protein complexes of, 143–144 mitochondrial DNA (mtDNA), 212 mitosis, 76, 284 mixed acids, as fermentation end product, 148, 148f MMR. See measles, mumps, rubella vaccine mobile genetic elements, 205–208, 303 mobilizable plasmids, 205 Mobiluncus, 625 modification enzymes, 314 moist heat, 112–114, 112t molarity, 22–23 mold(s), 11, 11f, 290 disease/infection caused by, 410 in food production, 761, 762t in food spoilage, 754, 754f slime, 288, 294–295, 294f water, 288, 294–295 mole(s) (unit), 22 molecular biology central dogma of, 162, 162f revolution in, 212 molecular Koch’s postulates, 396 molecular weight, 22–23 molecule(s) definition of, 20 formation of, 20–23 small, in cells, 25, 25f molybdenum, 94 monobactams, 474t, 477 monocistronic transcription, 168, 175 monoclonal antibodies, 5f, 417–418, 439–440, 440f therapy with, for septicemia, 680 in transplantation medicine, 424 monoclonal gammopathy, 427t monocytes, 350, 351f, 352t in inflammation, 360 Monod, Jacques, 9, 177 monoglycerides, 35 monolayer, 336 mononuclear phagocytes, 350–352, 351f, 352t, 353f mononuclear phagocyte system (MPS), 350, 353f mononucleosis, 324t, 686–688, 688t causative agent of, 331t, 686, 688t encephalitis in, 659 epidemiology of, 687–688, 688t hepatitis in, 608 incubation period of, 686, 688t pathogenesis of, 686, 687f, 688t prevention and treatment of, 688, 688t symptoms of, 592, 686, 688t monosaccharides, 30–31, 30f, 31t, 36t monounsaturated fatty acids, 35, 35f Montagnier, Luc, 5f, 697 Montagu, Lady Mary Wortley, 431, 495 Moraxella, in normal microbiota, of respiratory system, 498t, 499 Moraxella catarrhalis, in normal microbiota, of respiratory system, 499

nes95432_ind_I1-I40.indd I-24

Moraxella lacunata, 504 morbidity, 451t Morbidity and Mortality Weekly Report, 459–460, 459t morbidity rate, 451 mordants, 49, 49f mortality, 451t mortality rate, 451 mosquitoes anatomy of, 296, 296f control of, 690–691, 694 as vectors, 295t, 296, 455 for dengue, 688 for encephalitis, 660, 660f, 661t for equine encephalitis, 295t for malaria, 286, 295–296, 295t, 455, 691–692, 692f, 694, 694t for yellow fever, 295t, 688–690, 690t most probable number method, of cell counting, 99t, 101–102, 102f in water testing, 746 mother cell, of endospore, 69, 69f motor nerves, 648 mouth, 582, 583f infections of, 586–589, 588f, 589t normal microbiota of, 393f, 585 moxifloxacin, 474t, 478 M13 phage, 306, 307t, 311, 313t M protein, 402, 500, 500f, 500t mRNA. See messenger RNA MRSA. See methicillin-resistant Staphylococcus aureus MS2 phage, 307t, 313t mtDNA. See mitochondrial DNA mucociliary escalator, 348, 498 definition of, 496t mucosa, 374 mucosal-associated lymphoid tissue (MALT), 369f, 370, 374, 393, 598 mucous membranes, 348, 348f bacteria in, 272–273 as ecosystem, 392–393 penetration, by pathogens, 399–400 as physical barrier to infection, 348 mucus, 498 Mullis, Kary, 5f multicellular parasites, 295–299 multi-enzyme complexes, 28 multiple-drug-resistant Mycobacterium tuberculosis (MDR-TB), 485, 517 multiple fission, protozoan, 288, 288f multiprotein complexes, 28 mumps, 323t, 593–594, 594t causative agent of, 593, 594t epidemiology of, 594, 594f, 594t immune response to, 366 incidence of, 594, 594f, 594t incubation period of, 594t nervous system infections, 593, 659, 659t pathogenesis of, 325–326, 594, 594t prevention and treatment of, 594, 594t symptoms of, 593, 593f, 594t vaccine, 434t, 435, 594 mushrooms, 11, 289f, 290, 291f, 727–728 must, in wine production, 758

mutagens Ames test for, 197, 197f chemical, 190–192, 191t common, 191t radiation, 191t, 192 mutant(s), 161, 186 penicillin enrichment of, 196, 196f mutant selection, 195–199 direct, 195, 195f indirect, 195–196, 196f mutation(s), 186–192 definition of, 186t frameshift, 189, 189f, 190–191, 191f induced, 190–192 knockout, 188 leaky, 188 missense, 188, 188f nonsense, 188 null, 188 point, 188 rate of, definition of, 187–188 reversion of, 188 silent, 188 spontaneous, 187–190, 187f repair of, 195t viral, 410 mutualism definition of, 392 between microorganisms and eukaryotes, 733–735 myasthenia gravis, 424t, 425 mycelium, 11f, 265, 290, 291f Mycobacterium, 261 acid-fast staining of, 50, 50f, 238, 261 characteristics of, 253t control/destruction of, 110, 115, 117 fluorescent dye for, 52 fluorescent staining of, 51f, 52 infection, treatment of, 478 Mycobacterium avium, 717, 718f Mycobacterium avium complex, 717–718, 718t infection causative agent of, 717, 718f, 718t epidemiology of, 718, 718t pathogenesis of, 717, 718t prevention and treatment of, 718, 718t symptoms of, 717, 718t Mycobacterium celatum, 717 Mycobacterium ganavense, 717 Mycobacterium haemophilum, 717 Mycobacterium intracellulare, 717 Mycobacterium kansasii, 717 Mycobacterium leprae, 655, 656f growth of, 91 infection, 655, 656f, 656t. See also Hansen’s disease (leprosy) medical importance of, 261, 272t temperature requirements of, 91 Mycobacterium scrofulaceum, 717 Mycobacterium szulgai, 717 Mycobacterium tuberculosis, 391 acid-fast stain of, 238 antimicrobial resistance of, 485, 516–517 antimicrobials for, 474t control/destruction of, 110–111 doubling time of, 84 extensively-drug-resistant, 485, 517

infection, 397, 514–517, 515f–516f, 517t. See also tuberculosis latent, 395 via macrophages, 399–400 medical importance of, 261, 272t multiple-drug-resistant, 485, 517 portal of exit for, 454 tests for, 438 tuberculin skin test for, 421–422, 421f, 516, 516f Mycobacterium xenopi, 717 mycologist, 288 mycology, 288 mycoplasma, 14f Mycoplasma, 273 infection, vaginal, 625 Mycoplasma genitalium, genome, 273 Mycoplasma pneumoniae, 14, 273, 273f infection, 510t, 511–512, 512f lack of cell wall in, 63, 63f, 273 medical importance of, 272t, 273 mycorrhizae, 293, 727, 733–734 mycoses, 292, 292t intermediate, 292 pulmonary, 525–527 superficial, 292 superficial cutaneous, 554–555 causative agents of, 554, 555f epidemiology of, 555 pathogenesis of, 555 prevention and treatment of, 555 symptoms of, 555 systemic, 292 mycotoxins, 410 myonecrosis, clostridial. See gas gangrene myxameba, 294 myxobacteria, 264–265 characteristics of, 263t definition of, 252t multicellular associations of, 53–54 swarm of, 264 Myxococcus, 263t, 265 myxoma virus, 397 myxoviruses, 338

N N-acetylglucosamine (NAG), 60, 62f N-acetylmuramic acid (NAM), 60–61, 62f, 477 NaCl. See salt NAD+, 131, 131t as enzyme cofactor, 136, 136t in transition step, 142 in tricarboxylic acid cycle, 142 NADH, 131, 131t, 132, 149f, 150 in electron transport chains, 143–145, 144f–145f in fermentation, 148 in glycolysis, 140f, 146 in oxidative phosphorylation, 142 in transition step, 142, 146 in tricarboxylic acid cycle, 141f, 142, 146 NADH dehydrogenase, in aerobic respiration, 144, 145f NADP+, 131, 131t as enzyme cofactor, 136 NADPH, 131, 131t in carbon fixation, 154, 155f

9/2/08 5:33:46 PM

Index in pentose phosphate pathway, 139–141 in photosynthesis, 153–154 Naegleria, 287f Naegleria fowleri, 667 naftifine, 489, 489t naive lymphocyte, 375, 376f naked DNA, transfer of, 199–201, 200f naked viruses, 110, 117, 303, 305f, 321, 326 nanoarchaea, 276 Nanoarchaeota, 276 Nanoarchaeum, 275t Nanoarchaeum equitans, 15, 15f, 276 narrow host range plasmids, 205 narrow-spectrum antimicrobial, 470t, 472 nasal spray vaccines, 447 nasopharyngeal carcinoma, 686 nasopharynx, 499 National Aeronautics and Space Administration (NASA), Sea Wide Field Sensor, 285 National Disease Surveillance Network, 459–460 National Institutes of Health (NIH), 221 National Molecular Subtyping Network for Foodborne Disease Surveillance (PulseNet), 244 Natronobacterium, 275, 275t Natronococcus, 275, 275t natural amino acids, 26 natural antibodies, 418 natural competence, in DNA-mediated transformation, 200 natural killer (NK) cells, 352, 373, 384 in immunodeficiency disorders, 426, 427t, 703 interactions with viruses, 409, 409f in transplantation immunity, 423 naturally acquired immunity, 432 natural penicillins, 473t, 476 natural selection, 181, 186 nature bacterial growth in, 104, 721 interaction of mixed microbial communities in, 86 Necator americanus, 298t necrosis, 679 definition of, 675t necrotizing fasciitis, 394, 501, 563 causative agent of, 563, 563f epidemiology of, 564 pathogenesis of, 564 prevention and treatment of, 564 symptoms of, 563 Needham, John, 2 needle exchange programs, 707 Nef, 700f, 701 negative control, of transcription, 177, 177f negative selection of self-reactive B cells, 387 of self-reactive T cells, 387–388 negative staining, 49 Negri bodies, 664, 664f definition of, 648t Neisseria, 273 cultures increased carbon dioxide for, 97 media for, 96

nes95432_ind_I1-I40.indd I-25

growth factors for, 94 infection, complement abnormalities and, 426 Neisseria gonorrhoeae, 120. See also gonorrhea adherence of, 398 antigenic variation in, 181, 403 antimicrobial resistance of, 630–631 culture media for, 96 evasion of host defenses by, 401, 403 Gram stain of, 238, 238f groupings of, 53 infection, 621, 629–631, 629t, 630f, 632t. See also gonorrhea eye, 120, 631 inflammatory response to, 408 ocular, 504 medical importance of, 271t, 273 nucleotide sequence amplification, polymerase chain reaction for, 224 portal of exit for, 454 Neisseria meningitidis infection, 478, 650, 651f, 652f, 653t, 655t. See also meningitis, meningococcal medical importance of, 271t, 273 in normal microbiota, of respiratory system, 499 serogrouping of, 652 nelfinavir, 487t, 488 Nelmes, Sarah, 431 nematodes, 295, 297, 298t. See also roundworms definition of, 281t neomycin, 474t, 477 neoplasm. See also tumor(s) Nereocystis luetkeana, 284f nerve(s) motor, 648 as pathway to CNS, 649 sensory, 648 nervous system. See also central nervous system infections, 647–673 NETs. See neutrophil extracellular traps neuraminidase, 488, 519 neuranimidase inhibitors, 487t, 488 neurodegenerative disease prions causing, 12, 13f, 37, 340t protein folding and, 37 Neurospora, 289t Neurospora crassa, 161, 293 neurotoxins, 285, 404t, 405, 657–658 definition of, 281t, 648t neutralization, in antibody-antigen binding, 372, 372f neutron(s), 18–19, 19f neutrophil(s), 350, 351f, 352t avoidance, by pathogens, 401 definition of, 347t in inflammation, 359–360 specialized attributes of, 359–360 neutrophile(s), 24, 90t, 92 neutrophil extracellular traps, 359–360 neutrophilic granules, 359 nevirapine, 487t, 488, 708 niclosamide, 491t nicotinamide adenine dinucleotide. See NAD+

nicotinamide adenine dinucleotide phosphate. See NADP+ Nipah virus, bioterrorism potential of, 466 nitrate in anaerobic respiration, 145 in food preservation, 122, 765 formation, by nitrifying bacteria, 150 removal, in sewage treatment, 731 as terminal electron acceptor, 728, 730 nitric oxide, 359, 514 nitrification, 260, 730–731 definition of, 722t nitrifiers, 260, 730–731 definition of, 252t nitrifying bacteria, 150, 150t, 253t, 260 nitrite in anaerobic respiration, 145 in food preservation, 122 formation, by nitrifying bacteria, 150 oxidation, by nitrifying bacteria, 150 as terminal electron acceptor, 728, 730 nitrite oxidizers, 260 Nitrobacter, 253t, 260 Nitrococcus, 253t, 260 nitrofurtimox, 490t nitrogen, 19 atomic structure of, 19t as major element, 93–94, 94t in purine rings, sources of, 157–158, 158f nitrogenase, 258, 730 nitrogen cycle, 260, 728, 730–732, 730f pollution and, 728 nitrogen fixation, 6, 94, 721, 728, 730 by Azotobacter, 264, 721, 730 by cyanobacteria, 95, 258, 258f, 735 definition of, 722t by rhizobia, 265, 721, 734–735, 734f symbiotic, 265, 721, 734–735, 734f nitrogen gas, in anaerobic respiration, 145 nitroimidazoles, 490t nitrosamines, 122 Nitrosococcus, 253t, 260 nitrosoguanidine, 190 Nitrosomonas, 253t, 260 nitrous acid, mutagenic action of, 190, 191t nitrous oxide, in anaerobic respiration, 145 NK cells. See natural killer cells Nobel Prizes, won by microbiologists, 9, 126 nodes, of phylogenetic tree, 246, 247f nod factors, 734 NOD (nucleotide-binding oligomerization domain) proteins, 347 Nomarski differential interference contrast microscope, 43, 43f nomenclature, 12 for animal viruses, 322 for bacteria, 12, 235 changes in, 249

I-25

definition of, 233, 233t for eukaryotes, 281 non-communicable disease, 451 noncompetitive inhibition, of enzymes, 137–138, 137f, 137t non-critical equipment, medical, 111 noncyclic photophosphorylation, 153 non-homologous recombination, definition of, 186t non-nucleoside polymerase inhibitors, 487t, 488 non-nucleoside reverse transcriptase inhibitors, 487, 487t, 488, 708 non-polar covalent bonds, 21t, 21–22 nonsense mutation, 188 non-specific immune response. See also innate immune response normal microbial microbiota. See normal microbiota normal microbiota, 9, 221, 272, 348– 350, 392, 392t, 393–394, 393f and adaptive immune response, 393 anatomical barriers as ecosystem of, 392–393 definition of, 393 of digestive system, 585–586 dynamic nature of, 393–394 fungi in, 410 of genitourinary system, 620 intestinal, in obese and lean people, 394 of intestines, 585–586 of large intestine, 393f of mouth, 393f, 585 of nose, 393f protective role of, 393 of respiratory system, 498–499, 498t of skin, 270–272, 393f, 533–534, 533t suppression by antimicrobial drugs, 350, 472, 586 of throat, 393f of urethra, 393f of vagina, 393f Norovirus, 323t, 605f infection, nosocomial, 463t Norovirus gastroenteritis, 604–605, 605t causative agent of, 604, 605f epidemiology of, 605 incubation period of, 605t pathogenesis of, 605 prevention and treatment of, 605, 605t symptoms of, 604, 605t Norwalk virus. See Norovirus nose, normal microbiota of, 393f nosocomial infections, 108, 121, 462–465, 564, 678 causes of, 462, 463t genitourinary, 618, 621 prevention of, 464–465 relative frequency of, by type, 462, 462f reservoirs of, 462–464 septicemia, 678–680 transmission of, 464 notifiable disease, 459–460, 459t N terminal, 28 nuclear envelope, of eukaryotic cells, 70f, 75, 76f

9/16/08 10:27:20 AM

I-26

INDEX

nuclear pores, of eukaryotic cells, 76, 76f nucleic acid(s), 19t, 25, 32–34, 36t replication of, in animal viruses, 326–328 16S ribosomal, in classification of prokaryotes, 246–247, 248t synthesis antibacterial drugs targeting, 474t, 478 antifungal drugs targeting, 488f, 489t antiviral drugs targeting, 486f, 487–488, 487t nucleic acid hybridization, 227–229, 237t applications of, 227–229 nucleic acid probes, to detect specific DNA sequences, 227–229, 241–242, 242f nucleocapsid, 303, 304f, 321 nucleoid, 10, 54f, 67 of prokaryotic cells, 54–55 nucleolus, of eukaryotic cells, 70f, 76 nucleoside, 33f definition of, 698t nucleoside analogs, 487, 487t nucleoside reverse transcriptase inhibitors, 487t, 708 nucleosome, 76 nucleotide(s), 32, 36t, 161–163 chain of, 3´ and 5´ end, 33–34, 33f covalent bonding of, 33, 33f phosphodiester bonds between, 33, 33f removal or addition of, 189, 189f synthesis of, 157–158, 158f nucleotide analog, 487 nucleotide-binding oligomerization domain (NOD) proteins, 347 nucleotide sequences, 170, 171f. See also DNA sequencing changes in. See also mutation(s) first complete, of bacterial chromosome, 5f in identification of prokaryotes, 242 of mitochondria, 212 reading frames of, 170, 171f, 171t, 172f nucleus algal, 283 atomic, 19 eukaryotic, 40, 70f, 72t, 75–76, 76f of eukaryotic cells, 71t null mutation, 188 numerical taxonomy, 248 nutrient(s) acquisition of, 722–723, 723f cycling, in ecosystems, 728–733 in food, and microbial growth, 755 low, bacteria in environment with, 723 and microbial growth, 93–95 nutrient agar, 96, 96t nutrient broth, 96, 96t nutrition. See nutrient(s) nystatin, 488, 489t

O O antigens, 243, 262f obesity, normal intestinal microbiota in, 394

nes95432_ind_I1-I40.indd I-26

objective lens, of microscope, 41, 41f, 42f obligate aerobes, 90t, 92, 92t, 253t, 261–262 definition of, 84 obligate anaerobes, 90t, 92, 92t, 98, 147, 253 characteristics of, 252t definition of, 84 obligate fermenters, 90t, 92, 147, 756 obligate intracellular parasites, 12, 271t, 273–274, 304 oceans, 726 ocular lens, of microscope, 41–42, 41f oil(s), 35 oil spill bioremediation, 6, 749–750, 750f Okazaki fragment, 165t, 167 oleic acid, 35, 35f oligosaccharides, 30, 32 oligotrophic, definition of, 722t oligotrophic waters, 725–726 olives, 756t, 758 omalizumab, 417–418 omasum, 735 oncogenes, 5f, 333 ONPG/MUG test, 746, 747f oomycetes, 294. See also water molds Opa proteins, 630 open reading frames (ORFs), 182 open systems, for bacterial cultures, 88, 90 operating room, contamination of, by bacterial pathogen, 121 operator, DNA, 177 operators, viral, 310 operon, 177 lac, 177–179, 178f glucose and, 178f, 179 lactose and, 177–178, 178f ophthalmia neonatorum, 120, 631 definition of, 619t opine, 206, 206f, 265 opportunist(s), definition of, 394 opportunistic pathogens, 261, 586 definition of, 392t, 394 opsonins, 356, 500 opsonization, 356, 356f, 372f, 373 avoidance, by pathogens, 402–403, 402f definition of, 347t optical isomers, 18. See also stereoisomers optimal proportion, for precipitation reaction, 441, 441f optimum growth temperature, 90–91 oral rehydration solution (ORS), 596 oral tolerance, 426 definition of, 415 orbitals, of electron, 18–19, 19f orchitis gonococcal, 630 mumps, 593 order, definition of, 234 organ(s), 71 organelles, of eukaryotic cells, 70–71, 72t, 75–79 organic acids, of metabolic pathways, 129 organic compounds, 19t, 21 as electron source, for photosynthesis, 154

Orientia, 274 Orientia tsutsugamushi, medical importance of, 271t, 274 Orla-Jensen, Sigurd, 232 Orthomyxoviridae/orthomyxoviruses, 323t, 519 orthophosphate, 732 orthophthalaldehyde, 118t, 119 Oscillatoria, 258f oseltamivir, 487t, 488, 521 osmosis, 56–57, 56f osmotic pressure, 57 O specific polysaccharide side chain, 61, 63f osteomyelitis with brucellosis, 682 definition of, 675t otitis media, 496, 650 bacterial, 504–506 causative agent of, 504–505 definition of, 496t epidemiology of, 506 pathogenesis of, 505–506, 506f prevention and treatment of, 506 streptococcal, 501 Ouchterlony test, 441, 442f outbreak, 451, 451t outer membrane bacterial, 60t of eukaryotic cells, 76 of Gram-negative bacteria, 61, 63f ovaries, 620, 620f oxaloacetate, 132t, 141f, 142 oxantel, 491t oxazolidinones, 474t, 477f, 478 oxidase, testing for, in identification of bacteria, 240t oxidase test, 144 oxidation-reduction reaction, 130–131, 131f oxidative phosphorylation, 130, 142–147 ATP yield from, 133f, 134t, 142, 146–147 definition of, 127t ØX174 phage, 307t, 313t oxygen, 19 atomic structure of, 19t atomic weight of, 20 biochemical demand (BOD), reduction in sewage treatment, 739 as major element, 93–94, 94t reactive forms of, 189 requirements for, and microbial growth, 90t, 91–92, 92t, 755–756 supply, 6 and carbon cycle, 729 as terminal electron acceptor, 145 toxic derivatives of, 92l oxygenic photosynthesis, 152, 152t, 257 oxygenic phototrophs, 257–259 characteristics of, 253t definition of, 252t ozone, 118t, 120, 123, 742, 745

P palindromes, 213 pancreas, 583f

pandemics, 335, 451, 451t AIDS, 640, 698, 698f cholera, 596 influenza, 7, 335–336 papillomas (warts), 552–553, 553f definition of, 619t genital, 639–640, 639f, 641t Papillomaviridae, 324t papillomaviruses, 322f, 323, 324t, 552–553, 553f and p53 regulation, 409 sexually transmitted infection, 629t causative agent of, 639, 641t epidemiology of, 640, 641t incubation period of, 641t pathogenesis of, 639–640, 641t prevention and treatment of, 640, 641t symptoms of, 639, 639f, 641t and tumor formation, 333 Pap (Papanicolaou) smear, 640, 640f, 641t papules, in chickenpox, 545, 546f para-aminobenzoic (PABA), 138, 138f, 479 Paracineta, 43f parainfluenza virus, 323t paralytic shellfish poisoning, 282, 284–285 paramecium, 11f, 286–287 Paramecium bursaria, 43f Paramyxoviridae/paramyxoviruses, 323t, 519, 593–594 parasite(s), 10, 11t, 392 damage to host caused by, 411 drugs against, 490–491, 490t–491t multicellular, 295–299 obligate intracellular, 12, 271t, 273–274 parasitemia, definition of, 648t parasitic infection, pathogenesis of, 410–411 parasitism, 392 paratartaric acid, 18 parotids, 582 swelling, with mumps, 593, 593f paroxysmal coughing, 513–514 Parvoviridae, 324t. See also parvoviruses parvoviruses, 324t, 552 passive immunity, 432–433, 432f artificial, 432–433 definition of, 432t and immune complex-mediated (type III) hypersensitivity, 420 natural, 432–433 passive transport, 58, 58t Pasteur, Louis, 18, 674 studies by fermentation, 126 immunization, 665 Pasteurella multocida, 572 pasteurization, 4f, 112 refuting spontaneous generation, 2, 3f–4f stereochemistry, 18 Pasteurella multocida bite wound infections, 572, 572t epidemiology of, 572, 572t incubation period of, 572t pathogenesis of, 572, 572t prevention and treatment of, 572, 572t symptoms of, 572, 572t

9/2/08 5:33:46 PM

Index pasteurization, 4f, 112–113, 112t, 682, 765 definition of, 108, 108t high-temperature-short-time method of, 112–113 of milk, 112–113, 753 ultra-high-temperature method of, 113 patch test, for contact hypersensitivity, 422 pathogen(s), 8. See also specific pathogens adherence of, 397–398, 398f breaching of anatomical barriers by, 399–400 damage to host caused by, 403–408 defense against. See immunity definition of, 391, 394 directed uptake by cells, 399 distribution of, in infection, 395 epithelial cell uptake of, 399 exotoxins of, 403–407, 404t–405t exploitation of antigen-sampling processes by, 399–400 immunity to, 456–457 invasion of host tissue by, 397 mechanisms of, 397–413 mimicking host molecules, 403 opportunistic, 261, 392t, 394, 586 primary, 392t strategies of, 391 toxin production by, 397 pathogenesis mechanisms of, 397–413 viral, mechanisms of, 408–410 pathogenicity, 394 balanced, 325, 397, 453 mechanisms of, 397–413 pathogenicity islands, 208, 398, 595 patient-care equipment, precautions with, 465 patient placement, in hospitals, 465 pattern recognition, 346 PBPs. See penicillin-binding proteins PCBs. See polychlorinated biphenyls PCR. See polymerase chain reaction PCR product, 225–226, 226f peanut allergy, 417 Pediculus humanus, 295t, 296, 296f Pediococcus, in food production, 756, 756t, 758 peliosis hepatitus, 573 Pelodictyon, 252t, 257 pelvic inflammatory disease (PID), 630–631 definition of, 619t penicillin(s), 5f, 62, 293, 470, 473t, 475–476, 537 allergic reactions to, 383, 417, 472 bacterial sensitivity to, 60t for bite wound infections, 572 β-lactam ring of, 475, 475f broad-spectrum, 473t, 476, 476f discovery of, 470 extended-spectrum, 473t, 476 family of, 470, 471f, 476, 476f inactivation of, 476 inhibition of cell wall synthesis by, 475–476 natural, 473t, 476 penicillinase-resistant, 473t, 476, 476f

nes95432_ind_I1-I40.indd I-27

plus β-lactamase inhibitor, 476 for pneumococcal pneumonia, 510 resistance to, 470, 483–486 for syphilis, 636 penicillinase, 196, 476 penicillinase-resistant penicillins, 473t, 476, 476f penicillin-binding proteins (PBPs), 475 penicillin enrichment, of mutants, 196, 196f penicillin G, 470, 473t, 476, 476f penicillin V, 473t, 476, 476f Penicillium, 289t, 293, 470–471 in food, 754f, 757, 762, 762t Penicillium camemberti, 757 Penicillium candidum, 757 Penicillium chrysogenum, 476 Penicillium roquefortii, 757, 762t pentose phosphate pathway, 132, 132t, 133f, 139–141, 139t pepsin, 584 peptide(s), as immunizing agents, 710 peptide bonds, 19t, 28 peptide vaccines, 437 peptidoglycan, 10, 60–61, 60f, 60t, 62f antibacterial drugs targeting, 61–62, 473t, 475–477, 475f–476f of Gram-negative bacteria, 61, 63f of Gram-positive bacteria, 62f immune response to, 407–408 peptone, 96, 96t peracetic acid, 118t, 120 pericardium, 675, 675f periodontal disease, 588, 588f, 589t causative agent of, 588, 589t epidemiology of, 588, 589t in HIV-infected (AIDS) patients, 588 incubation period of, 589t pathogenesis of, 588, 588f, 589t prevention and treatment of, 588, 589t symptoms of, 588, 589t peripheral nervous system, 648 periplasm, 60t, 267, 269 of Gram-negative bacteria, 61, 63f perishable products, preservation of, 108, 108t, 110, 121–122. See also food preservation peristalsis, 348, 584 peritrichous flagella, 65f, 66, 262 permeases, 58 peroxidase enzymes, 349 peroxisomes, 79 of eukaryotic cells, 71t peroxygens, 118t, 120 persistent infection, definition of, 321t person, epidemiological studies of, 457 personal care products, preservation/ protection of, 110 pertussis, 513–514, 514t causative agent of, 513, 513f, 514t epidemiology of, 514, 514t incubation period of, 514t pathogenesis of, 513–514, 514t prevention and treatment of, 514, 514t symptoms of, 513, 514t vaccine, 434t, 436, 514 acellular, 435, 514 killed, 435 pertussis toxin, 513–514

petechia (pl., petechiae), 652, 652f definition of, 648t, 675t Petri dish, 87 petroleum-degrading bacteria, 749–750, 750f Peyer’s patches, 369f, 370, 399–400, 408, 447, 602 Pfiesteria piscida, 285 pH, 19t, 24 and dental caries, 587, 587f and enzyme activity, 136–137, 136f of food, 755, 765 and fungal growth, 292 indicator, in biochemical tests, 239, 239f and microbial growth, 90t, 92–93 Phaeophyta, 283t phage(s), 12f, 13f aquatic, 309 for characterizing bacterial strains, 244t, 244–245, 245f comparison with animal viruses, 329t defective, 313 definition of, 303 DNA excision of, 309f, 310 integration in bacterial chromosome, 309f integration into bacterial chromosome, 310 repair of, 310 replication of, 308, 311, 312f, 329t extrusion of, 306, 311, 312f filamentous, 306, 311, 312f replication of, 311, 312f single-stranded DNA in, replication of, 311, 312f host ranges of, 314–316 important, representative, 307t interactions with host cells, 306–313, 313t latent infection by, 306, 306f in latent state, replication of, 308–311, 309f lytic, 306 assembly or maturation of, 308 attachment of, 307f, 308, 329t burst size of, 308 penetration by, 307f, 308, 329t proteins, synthesis of, 308 release of, 308, 329t replication of, RNA polymerase and, 308 with single-stranded DNA, 311 transcription of, 307f, 308 productive infection by, 306, 306f receptors for, 314, 315f replicative form of, 311 restriction-modification system and, 314–316, 315f sheath or tail of, 303, 304f specialized transducing, 313, 314f temperate, 306, 308, 313, 314f therapeutic use of, 316 transduction by, 201, 202f, 204t, 313 virulent, 307, 313 phage-induced proteins, 307f, 308 phage induction, 310 phage typing, for characterizing bacterial strains, 244t, 244–245, 245f, 314

I-27

phagocyte(s), 4f, 347 avoiding recognition and attachment by, 401–403 defective, in immunodeficiency disorders, 426–427 definition of, 347t in inflammatory response, 360, 361f macrophages as, 358–359 mononuclear, 350–352, 351f, 352t, 353f neutrophils as, 359 pathogens avoiding destruction by, 401–403, 402f preventing encounters with, 401 phagocytosis, 74, 347, 358–360, 359f chemotaxis in, 358 definition of, 347t destruction and digestion in, 358 engulfment in, 358 exocytosis in, 358 pathogens avoiding destruction in, 401–403, 402f process of, 358, 359f recognition and attachment in, 358 phagolysosome, 74, 358 pathogen survival within, 403 phagosome, 74, 358, 383, 384f escape from, by pathogens, 403 fusion with lysosome, 358 prevention of, 403 pharmaceutical proteins, genetically engineered production of, 216 pharyngitis, 496 adenoviral, 508, 508t causative agent of, 508, 508t epidemiology of, 508, 508t pathogenesis of, 508, 508t prevention and treatment of, 508, 508t symptoms of, 508, 508t definition of, 496t streptococcal, 499–502, 499f. See also strep throat phase-contrast microscopes, 43, 43f, 44f, 44t phase variation, in gene expression, 181 pH buffers, 96 phenol (carbolic acid), 107, 120, 491t phenolics, 118t, 120 phenotype(s), 186, 233 characteristics in classification of prokaryotes, 248, 248t in identification of prokaryotes, 237–241, 237t definition of, 186t phenylalanine, 18, 27f synthesis of, 156–157, 157f phenylalanine deaminase, testing for, in identification of bacteria, 240t pH indicator, of bacterial growth, 103 Phipps, James, 431 phosphate(s), 33, 33f phosphate bonds, high-energy, 130, 130f phosphoenolpyruvate, 132t, 140f, 157 2-phosphoglycerate (2PG), 140f 3-phosphoglycerate (3PG), 132t, 140f, 154 phospholipase, 405 phospholipid(s), 36, 36f

9/2/08 5:33:47 PM

I-28

INDEX

phospholipid bilayer, 36, 36f, 56, 56f phosphorus, 19 atomic structure of, 19t as major element, 93–94, 94t phosphorus cycle, 732 phosphorylation oxidative, 130, 142–147 adenosine triphosphate generated by, 134t, 142, 146 ATP yield from, 133f, 134t, 142, 146–147 substrate-level, 130, 147 adenosine triphosphate generated by, 134t definition of, 127t phosphotransferase system, 59 photoautotrophs, 95, 95t, 154, 722 Photobacterium, 269 characteristics of, 263t photoheterotrophs, 95, 95t photophosphorylation, 130, 153–154 cyclic, 153 definition of, 127t noncyclic, 153 photoreactivation, 193, 194f, 195t photosynthesis, 10, 77, 128, 128f, 151–154, 732 in algae, 152–153, 152t, 281–282 anoxygenic, 152, 152t, 154, 256 in aquatic habitats, 725–726 comparison of mechanisms used by different organisms, 152t in cyanobacteria, 152–154, 153f in eukaryotic cells, 153–154, 153f oxygenic, 152, 152t, 257 in purple and green bacteria, 152–154, 152t radiant energy in capture of, 152–153 conversion into chemical energy, 153–154 photosynthetic pigments, 256–257, 724–725 accessory, 152, 152t of algae, 282, 283t reaction-center, 152 role of, 152–153 photosystems, 152–154, 152f, 152t in cyanobacteria and eukaryotic cells, 153–154, 153f in purple and green bacteria, 154 phototaxis, 66 phototrophs anoxygenic, 251, 256–257 characteristics of, 253t definition of, 252t filamentous, 252t oxygenic, 257–259 characteristics of, 253t definition of, 252t pH scale, 24, 24f phycobilins, 152, 152t, 283t phycobiliproteins, 258 phycocyanin, 283, 283t phycoerythrin, 283t phylogenetic tree, 246, 247f, 249 branch of, 246, 247f deeply branching, 246, 247f nodes, 246, 247f phylogeny, 233 definition of, 233t phylum, definition of, 234

nes95432_ind_I1-I40.indd I-28

physical barriers breaching of, by pathogens, 399–400 as ecosystems, 392–393 immune function of, 348, 348f physical methods, of microbial control, 107–108 Phytophthora infestans, 280, 294 phytoplankton, 282, 286–287 definition of, 281t effects on global warming, 285 pia, 648 pickled vegetables, 756t, 758 pickles, 756t, 758 pickling, 758 Picornaviridae/picornaviruses, 322, 323t, 408, 659 human, classification of, 324t Picrophilus, 275t, 276 Picrophilus oshimae, 93 PID (pelvic inflammatory disease), 630–631 pili, 181, 398, 398f of prokaryotic cells, 54f, 55t, 66, 67f sex (F), in plasmid transfer, 202–203, 203f pilin, 181 pilus adhesin, 684, 684t pinkeye, 504–506. See conjunctivitis pinocytosis, 73–74, 73f pinworm disease, 298t piperacillin, 473t, 476, 476f piperazines, 491t place, of disease acquisition, 457 placebo, 458 plague, 682–685, 685t bioterrorism potential of, 466 bubonic, 7, 262, 682, 684 causative agent of, 262, 399, 674, 684t, 685t epidemiology of, 684, 685t fleas as vector for, 295t, 296, 455, 674, 682–685, 684f, 685t incubation period of, 685t pathogenesis of, 453, 684, 684f, 685t pneumonic, 262, 466, 682, 684 prevention and treatment of, 685, 685t reductions in, 461 reservoirs for, 453, 684 septicemic, 684 symptoms of, 682, 685t vaccine, 685 plant(s) bacterial gene transfer to, 206, 206f, 265 cells, 70f chloroplast in, 70f cellulose in, microbial digestion of, 6 as edible vaccines, 217, 437, 447 fungal disease in, 288–289, 293 genetic engineering of, 217 herbicide-resistant, 217 with improved nutritional value, 217 metabolism of. See photosynthesis plasmid transfer to, 205–206 symbiotic relationships of with bacteria, 265, 265f–266f, 721, 734–735, 734f

with fungi, 292–293, 734–735, 734f with nitrogen-fixers, 721, 734–735, 734f transgenic, 217 Plantae, 234 plantar warts, 553 plant viruses, 302–303, 321, 339–340 insect transmission of, 340 circulative, 340 external or temporary, 340 purposely maintained, 339, 340f spread of, 339–340 vectors for, 340 symptoms of, 339, 339f Pla protease, 683, 684t plaque assay, of viruses, 337–338, 338f plasma, immunological testing of, 439 plasma cells, 367, 375, 376f, 378, 378f definition of, 367t plasmadesmata, 339 plasma membrane antifungal drugs targeting, 488–489, 488f, 489t of eukaryotic cells, 70f, 71t, 72–73 transfer of molecules across, 73–74 plasmid(s), 205–207, 208t broad host range, 205 cells cured of, 205 conjugation with plants, 206 conjugative, 205 definition of, 186t extrachromosomal, 204 fertility (F), 202–203 high-copy-number, 205 integration in chromosome, 203, 203f–204f low-copy-number, 205 mobilizable, 205 narrow host range, 205 of prokaryotic cells, 55t, 68 promiscuous, 205 resistance (R), 205–207, 205f, 470t, 484 self-transmissible, 205 traits coded by, 205, 205t transfer of, 68, 202–203, 203f, 204t, 205 in Escherichia coli, 202–203, 203f, 600 origin of, 202 transfer to plants, 205–206 tumor-inducing, of Agrobacterium, 206, 206f, 217, 265 plasmodium, 294 Plasmodium, 286, 286t, 288, 295, 295t antimicrobial resistance of, 693, 693f drugs against, 490t infection, 690–694, 694t. See also malaria life cycle of, 691, 692f Plasmodium falciparum, 691–693 Plasmodium malariae, 691–692 Plasmodium ovale, 691 Plasmodium vivax, 457, 691–693, 692f infection, pathogenesis of, 410 plasmolysis, 93, 93f, 122 plate counts, 99t, 100–101, 101f definition of, 84 platelet(s), 350 pleated structure, of proteins, 28

pleomorphic bacteria, 53 pleomorphic viruses, 321 pleura, 498 pleurisy, 498, 510 plus (+) strand, of DNA, 168, 168f, 168t PMNs, 350. See also polymorphonuclear neutrophilic leukocytes pneumococcal vaccine, 434t, 510 in HIV-infected (AIDS) patients, 712t pneumococcus. See Streptococcus pneumoniae Pneumocystis jirovecii, 292t, 426, 698, 712–713, 712f, 713t pneumocystosis, 292t, 698, 712–713, 713t causative agent of, 712–713, 712f, 713t epidemiology of, 712–713, 713t incubation period of, 713t pathogenesis of, 712, 713t prevention and treatment of, 713, 713t symptoms of, 712, 713t pneumolysin, 509 pneumonia, 238, 496, 509–512 “anthrax,” 512 atypical, 478 Chlamydia trachomatis, 633 definition of, 496t Klebsiella, 510t, 511 causative agent of, 510t, 511, 511f epidemiology of, 510t, 511 incubation period of, 510t pathogenesis of, 510t, 511 prevention and treatment of, 510t, 511 symptoms of, 510t, 511 Legionella, 7, 517–518, 518t causative agent of, 517–518, 518f, 518t epidemiology of, 518, 518t incubation period of, 518t pathogenesis of, 518, 518t prevention and treatment of, 518, 518t symptoms of, 517, 518t measles, 548 mycoplasmal, 510t, 511–512 causative agent of, 510t, 511, 512f epidemiology of, 510t, 512 incubation period of, 510t pathogenesis of, 510t, 511, 512f prevention and treatment of, 510t, 512 symptoms of, 510t, 511 pneumococcal, 509–510, 510t causative agent of, 509, 509f, 510t epidemiology of, 510, 510t incubation period of, 510t pathogenesis of, 509–510, 510f, 510t prevention and treatment of, 510, 510t symptoms of, 509, 510t vaccine, 434t, 510, 712t with respiratory syncytial infection, 521–522 streptococcal, 501 pneumonic, definition of, 675t pneumonic plague, 262, 466, 682, 684

9/2/08 5:33:47 PM

Index pneumonitis, 496 poi, 756t point mutation, 188 poison ivy, 422 poison oak, 422, 422f polar covalent bonds, 21–22, 21t, 22f polar flagella, 65f, 66 polar head group, 36, 36f polarity, in transcription, 168 polio, 396, 409, 661–663, 663t causative agent of, 661–662, 662f, 663t epidemiology of, 662, 663f, 663t pathogenesis of, 322, 325, 662, 663t prevention and treatment of, 662–663, 663t reduction/eradication of, 436, 662–663, 663f, 670 reductions in, 460 symptoms of, 661, 662f, 663t vaccines, 434t, 436, 662–663, 670, 712t campaign for, as example of vaccination strategy, 436 effective, characteristics of, 433 reversion to virulence, 662, 670 Sabin, 435–436, 662–663, 670 Salk, 435–436, 662–663 universal, effectiveness of, 437t poliomyelitis. See polio poliovirus, 323t–324t control/destruction of, 110 plaque formed by, 338f pollutant(s), 738, 749 biological cleanup of (bioremediation), 6, 749–750 pollution and eutrophication, 725, 725f, 732 metal compounds and, 120 and nitrogen cycle, 728 water, 738 sewage treatment and, 738–744 polyadenylation, 175 poly A tail, 175, 175t poly-β-hydroxybutyrate, 68, 68f polychlorinated biphenyls (PCBs), 6 polycistronic transcription, 168, 332 polyenes, 488, 488f, 489t polygenic genes, in MHC molecules, 387f polygenic mRNA, 332 polymerase chain reaction, 5f, 223–226, 224f, 262, 725 definition of, 213t discrete-sized fragments in, generation of, 225–226, 226f for DNA fingerprinting, 225 exponential amplification of target DNA in, 226, 227f for identification of prokaryotes/ bacteria, 237t, 242 primer pairs, selection, 226 three-step amplification cycle, 224–225, 224f in water testing, 750 polymers, 25 synthesis and breakdown of, 25, 25f polymorphic organisms, definition of, 281t polymorphic protozoa, 287, 287f polymorphonuclear neutrophilic leukocytes, 350, 352t, 360

nes95432_ind_I1-I40.indd I-29

polymyxin B, 474t, 479 Polyomaviridae, 324t polypeptide chain, 28 Polyporus sulphureus, 289f polyprotein, 328, 332 polyribosomes, 171t, 173 polys, 350. See also polymorphonuclear neutrophilic leukocytes polysaccharide(s), 25, 30, 31t, 32, 32f, 36t hydrolysis of, 149, 149f as T-independent antigens, 379, 435 polysaccharide vaccines, 379, 435 polysome, 173 polyunsaturated fatty acids, 35 population characteristics, in epidemiology, 456–457 population expansion, and emerging diseases, 461 porins, 61, 63f bacterial, 60t pork tapeworms (Taenia solium), 297, 298f, 298t Porphyromonas gingivalis, 588 portal of entry, 451, 452f, 455, 496 portal of exit, 451, 452f, 454 Porter, Rodney, 366 Portier, Paul, 414 positive control, of transcription, 177, 178f positive selection, of self-reactive T cells, 387–388 post-polio syndrome, 662 post-translational modification, 173 potable water, 738 potassium, as major element, 93–94, 94t potassium iodide, 577 potato, black wart disease of, 289 potato blight, 280, 294 potato spindle tuber viroids, 13f potential energy, 128, 128f potential hydrogen. See pH pour-plate method, of cell counting, 100–101, 101f poverty, and HIV disease, 718 Poxviridae/poxviruses, 324t P pili, 398 p53 protein, viral regulation of, 409 praziquantel, 491t precipitation reactions, 372f, 373, 441–443, 441f–443f definition of, 432t precursor metabolites (molecules), 131–132, 138–142 biosynthesis in E. coli, 131–132, 132t, 139, 142, 156f definition of, 127t generation of in glycolysis, 139, 140f in pentose phosphate pathway, 139–141 in transition step, 141f, 142 in tricarboxylic acid cycle, 141f, 142 subunit synthesis from, 155–158, 156f precursor mRNA, 175 pregnancy antibody transmission during, 374, 374f, 432 avoidance of attenuated vaccines in, 433–435

chickenpox during, 546 ectopic, 631 rubella during, 550–551 syphilis during, 635–636, 636f pregnancy tests enzyme-linked immunosorbent assay, 445–446, 446f monoclonal antibodies in, 440 presence/absence test, 746 preservation definition of, 108, 108t of food, 108, 108t, 110, 122, 754, 765 chemical additives and, 110, 122, 765 drying in, 122, 765 irradiation and, 110, 765 water availability reduction and, 122, 765 of perishable products, 108, 108t, 110, 121–122 preservatives, 754 pressure, high, 112t, 116 pressurized steam in commercial canning process, 114, 114f sterilization using, 112t, 113, 113f, 114f prevalence, 451, 451t Prevotella, 625 primaquine, 490t, 693 primary consumers, 722 primary cultures, 336, 337f primary metabolites, 89, 89f primary pathogen, 392t primary producers, 95, 257, 282, 722, 723f definition of, 722t primary treatment definition of, 739t of wastewater, 739–741, 740f primase, 165t, 166 primer definition of, 162t of DNA replication, 165t, 166, 222, 222f, 242 prion(s), 5f, 12, 13f, 320, 331–332, 341–342 between-species transmission of, 669 characteristics of, 12, 13t, 669 control/destruction of, 108, 669 definition of, 321t disease caused by, 12, 13f, 37, 331–332, 340t, 341–342, 669–670, 670t hospital precautions against, 109 replication of, 341–342, 342f probe technology, 227–229, 241–242, 242f probiotics, 6, 411 producers, primary, 722, 723f product of chemical reactions, 128f metabolic, 129, 129f productive infection, 306, 306f viral, definition of, 303t proglottids, of tapeworms, 297, 298f proguanil, 693 pro-inflammatory cytokines, 354, 360 Prokaryotae (kingdom), 234

I-29

prokaryote(s), 10. See also bacteria characteristics of, 10 classification of, 232, 246–248 by DNA base ratio (GC content), 248, 248t DNA hybridization for, 247–248, 248t genotype characteristics for, 248t numerical taxonomy for, 248 phenotype characteristics for, 248, 248t relatedness in, methods of determining, 246–248, 248t ribosomal RNA in, 232, 246–247, 248t, 249 strategies for, 233–236 cultivating, in laboratory, 95–99. See also culture(s) diversity of, 251–279 DNA sequence of, analysis of, 182 ecophysiological diversity of, 263t ecophysiology of, 263–276, 263t electron transport chain in, 144–145, 145f gene expression in, 175t, 175–176 growth of dynamics of, 83–106 environmental factors and, 90–93, 90t nutritional factors and, 93–95 oxygen requirements for, 90t, 91–92, 92t pH and, 90t, 92–93 water availability and, 90t, 93 identification of biochemical tests for, 237t, 238–239, 239f, 240t fatty acid analysis for, 237t, 240 genotypic characteristics for, 237t, 241–243 by metabolic differences, 237t, 238–240 methods for, 237t by microscopic morphology, 237t, 237–238, 238f nucleic acid probes for, 237t, 241–242, 242f phenotypic characteristics for, 237–241, 237t polymerase chain reaction for, 237t, 242 sequencing ribosomal RNA genes for, 237t, 242–243, 243f serology for, 237t, 240 metabolic diversity in, 252t–253t, 252–262 nitrogen-fixing, 730 shape of, 237 size of, 14, 14f, 15, 15f, 237 in soil, 727–728 taxonomy, 233–236 prokaryotic cell(s) capsule of, 55t, 64, 64f cell wall of, 59–64 characteristics of, 10, 40 chromosomes of, 55t, 67–68, 67f, 72t cloning eukaryotic genes into, vectors for, 218–220 cytoplasmic membrane of, 54, 55–57, 55t, 56f

9/2/08 5:33:48 PM

I-30

INDEX

prokaryotic cell(s)—Continued DNA, 55t energy transformation in, 57, 57f versus eukaryotic cells, 72t filamentous protein appendages of, 55t, 65–67 flagella of, 55t, 65–66, 65f, 72t gas vesicles of, 55t, 68–69 glycocalyx of, 55t, 64, 64f groupings of, 53, 53f internal structures of, 67–70 microscopic studies of, 40 morphology of, 52–53 multicellular associations of, 53–54, 264 permeability of, 56–57 pili of, 55t, 66, 67f plasmids of, 55t, 68 protein secretion by, 57, 59, 72t ribosomes of, 55t, 68, 68f, 72t, 171, 172f size of, 14, 14f, 40 slime layer of, 55t, 64, 64f storage granules of, 55t, 68, 68f structure of, 54–70, 54f, 55t transport mechanisms in, 57–59, 58t proline, 27f prolonged decline phase, in microbial growth, 88f, 89, 89f promiscuous plasmids, 205 promoter(s) definition of, 162t of transcription, 168, 168t, 169f Prontosil, 470 proofreading, by DNA polymerase, 192, 195t, 332 propagated epidemics, 457–458, 457f prophage(s), 309, 309f maintenance in integrated state, 310 properties conferred by, 311t prophylaxis, 414–430 Propionibacterium, 148, 148f, 252t, 255–256 in normal microbiota, 349 Propionibacterium acnes, 534 Propionibacterium shermanii, 757 propionic acid in cheese-making, 148, 255–256, 757 as fermentation end product, 148, 148f, 255–256 in food preservation, 122, 765 propionic acid bacteria, 270 prospective studies, 458 prostaglandin(s) in asthma, 417 in hypersensitivity reactions, 415 prostate gland, 620, 620f prosthecae, 263t, 266–267 prosthecate bacteria, 263t, 266–267 definition of, 252t protease(s), 37, 134, 149f, 150, 158, 536, 537t, 701 definition of, 698t IgA, 398, 403 protease inhibitors, 332, 487t, 488, 641, 708 protein(s), 19t, 25–30, 36t. See also specific protein acute-phase, 360, 676 attachment, 303, 321, 325

nes95432_ind_I1-I40.indd I-30

binding, 58 chaperone, 29, 37, 173 denaturation of, 29–30, 29f temperature and, 91 early, 308 in eukaryotic cells, 72t, 74–75 fibrous, 28, 29f folding, 29, 37, 173 incorrect, and disease, 37 functions of, 28–30, 36t, 161–162 genetically engineered production of, 216–217 globular, 28, 29f homology of, 182 hydrolysis of, 149f, 150 matrix, 304, 321 membrane, in prokaryotic cells, 56 nucleotide-binding oligomerization domain (NOD), 347 phage-induced, 307f, 308 post-translational modification of, 173 primary structure of, 28, 29f quaternary structure of, 28, 29f receptor, in prokaryotic cells, 56 ribosomal, 68 secondary structure of, 28, 29f secretion by eukaryotic cells, 72t, 74 by Gram-negative bacteria, 61 by prokaryotic cells, 57, 59, 72t single-cell, as food source, 766 structure of, 28–30 substituted, 30 subunits, 36t synthesis in animal viruses, 326–328 in eukaryotic cells, 72t, 74 inhibition of, by antibacterial drugs, 474t, 477–478, 477f in phages, 308 in prokaryotic cells, 68, 72t synthesis of, DNA and, 161–184 tertiary structure of, 28, 29f transport, 58–59, 58f, 72t, 73 truncated, 188 protein A, 536, 537t, 563 protein F, 500, 500f, 500t protein folding problem, 37 protein G, 500, 500f, 500t protein subunit vaccines, 435 Proteobacteria, 252t–253t, 263t medical importance of, 271t Proteus, 262 characteristics of, 253t infection, bladder, 621 medical importance of, 271t Protista, 234 protists, 10 proton(s), 18, 19f proton ejection, general mechanisms of, 143 proton motive force, 57, 57f, 58, 58f, 130 ATP synthase and, 142, 145–146 and ATP synthesis, 142–147 definition of, 127t generation of, 142–147, 143f in mitochondria, 143–144, 144f in prokaryotes, 144–145, 145f in photosynthesis, 153–154, 153f proton pumps, 143

prototrophs, 187 definition of, 186t protozoa (sing., protozoan), 10–11, 11f, 71, 281, 285–288 cell wall of, 287, 287f characteristics of, 10, 11t classification of, 285–286, 286t definition of, 281t drugs against, 490–491, 490t eukaryotic cell structures of, 287 feeding in, 287 habitats of, 286–287 and human disease, 286t, 288 of blood vascular and lymphatic systems, 690–694 of lower digestive system, 610–614 sexually transmitted, 642–643 infection, pathogenesis of, 410–411 interference microscopy of, 43f intestinal, drugs against, 490t motility of, 285–286, 286t phagocytosis by, 74 polymorphic, 287, 287f reproduction of, 286t, 287–288, 288f in soil, 728 structure of, 287 protozoology, 285–286 provirus, 332 Prowazek, Stanislaus, 531 PrP, 320–321, 341, 669 PrPc, 321, 341, 669 PrPSc, 321, 341 Prusiner, Stanley, 5f, 320–321 PsaA adhesin, 684, 684t pseudomembranous colitis, 586. See also antibiotic-associated colitis definition of, 582t Pseudomonas, 261–262 biochemical capabilities of, 261 biofilm of, 120 carbon/energy sources of, 95 characteristics of, 253t control/destruction of, 110, 116, 316 in food, 755, 762 infection nosocomial, 463t, 564 ocular, 505 secondary, 538 treatment of, 476 medical importance of, 261–262 oxidase test for, 144 pigment production by, 238, 261, 261f, 564f, 565 Pseudomonas aeruginosa Gram-negative cell wall of, 63f infection bladder, 621 blood (septicemia), 679 of burns and wounds, 564–565, 564f community-acquired, 564 nosocomial, 463 treatment of, 477 medical importance of, 261–262, 271t operating room contamination by, 121 pigment production by, 238, 261f, 564f, 565 toxin of, 565

pseudopeptidoglycan, 64 pseudopodia, 286, 286t, 287 pseudopods, 74, 358 P-site, in translation, 173, 174f psittacosis, 274 psychrophiles, 90t, 91, 91f, 755 psychrotrophs, 90t, 91, 91f, 755 pubic lice, 296 public health departments, 460 public health infrastructure, breakdown of, 461 public health network, 460 pUC18, 219–220 Puccinia graminis, 293 puerperal fever, 4f, 450, 618, 625 definition of, 619t puffballs, 290 pulsed-field gel electrophoresis, 244, 244t, 245f puncture wounds, 560–561 pure culture, 86–88 definition of, 84 obtaining, 86–88 purified protein derivative (PPD), 438 purines, 33, 33f chemical modification of, 190 synthesis of, 157–158, 158f purple bacteria, 251, 256–257, 724 light-dependent reactions in, 154 non-sulfur, 95, 257 characteristics of, 252t photosynthesis in, 152–154, 152t sulfur, 256, 256f, 731 characteristics of, 252t pus, 360, 361f pustules, in chickenpox, 546, 546f putrefaction, 724 pyelonephritis, 621, 680 definition of, 619t subclinical, 623 pylorus, 584 pyocyanin, 565 pyoderma, 538–540, 539f definition of, 532t pyogenic bacterial infections, 562 in Chediak-Higashi disease, 427 pyogenic granuloma, 560 pyoverdin, 565 pyrantel pamoate, 491t pyrazinamide, 474t, 479 pyrazinoisoquinolines, 491t pyridoxal phosphate, 136t pyrimethamine, 490t pyrimidine(s), 33, 33f chemical modification of, 190 synthesis of, 157–158 Pyrodictium, 275–276, 275t, 276f Pyrodictium occultum, 275–276 pyrogenic, definition of, 496t pyrogens, 362 endogenous, 362 exogenous, 362 Pyrolobus, 275–276, 275t Pyrolobus fumarimii, 275 Pyrrophyta, 283t, 284 pyruvate, 132t, 133f, 138–142, 140f, 141f in fermentation, 147, 147f, 148f

Q Qβ phage, 307t, 313t

9/2/08 5:33:48 PM

Index Q fever, 274, 403, 678 quantal assays, of viruses, 337–338 quantitation, of viruses, 337–338 quaternary ammonium compounds (quats), 121 quinacrine, 490t, 610 quinidine, 693 quinolones, 490t quinones in aerobic respiration, 144–145 in anaerobic respiration, 145 in electron transport chain, 143, 145 quinupristin, 474t, 478, 537 quorum sensing, 180–181, 181f, 200, 269

R rabbit fever. See tularemia rabies, 323t–324t, 572, 663–665, 665t causative agent of, 663, 664f, 665t endocytosis of, 74 epidemiology of, 664–665, 665t incubation period of, 394, 663, 665, 665t pathogenesis of, 322f, 453, 663–664, 664f, 665t prevention and treatment of, 665, 665t survivors of, 665 symptoms of, 663, 665t vaccine, 434t, 435, 665 rabies immune globulin, 433 radial immunodiffusion test, 441–442, 442f radiant energy capture of, 152–153 conversion into chemical energy, 153–154 radiation in destruction of microorganisms and viruses, 112t, 115–116 in drinking water treatment, 745 electromagnetic, 115 electron accelerators and, 116 of food, 110, 116, 765 gamma, 116 ionizing, 112t, 116 mutagenic action of, 191t, 192 ultraviolet, 112t, 115f, 116 DNA damage from, repair of, 193, 194f, 195t, 310 mutagenic action of, 191t, 192 X ray, 116 radicola. See also Rhizobium radioactive isotopes, 26 radioisotopes, 239, 242 raltegravir, 487t, 488, 708 rat bite fever, streptobacillary, 574, 575t causative agent of, 574, 575t epidemiology of, 574, 575t incubation period of, 575t pathogenesis of, 574, 575t prevention and treatment of, 574, 575t symptoms of, 574, 575t rate(s) attack, 451, 451t of disease, in population, 451 morbidity, 451 mortality, 451

nes95432_ind_I1-I40.indd I-31

rDNA, 242 reactants, 128 reaction-center photosynthetic pigments, 152, 152f reactive oxygen, definition of, 186t reading frames, of genetic code, 170, 171f, 171t, 172f receiving waters, in sewage treatment, 739 receptor(s). See also specific receptors for animal viruses, 325–326 in eukaryotic cells, 73 for phages, 314, 315f in prokaryotic cells, 56 receptor-ligand interactions, 73 receptor-mediated endocytosis, 74, 408 recipient, in gene transfer, 198 recognition sequence, of restriction enzymes, 213f, 218–219 recombinant(s), 198 recombinant DNA introduction into new host, 220 technology, 212–231 applications of, 215–218 concerns about, 221 recombinant DNA molecule, generation of, 218–220 recombinant vaccine, 435 recombination genetic, 198 homologous, 200 red algae, 283t red blood cells. See erythrocyte(s) Redi, Francesco, 1–2 redox reactions, 130–131, 131f red tides, 284–285 reducing agents, in culture media, 99 reducing power, 131, 133f, 256 in carbon fixation, 154, 155f in glycolysis, 139, 140f in pentose phosphate pathway, 139, 141 in photosynthesis, 152t, 153–154 in transition step, 141f, 142 in tricarboxylic acid cycle, 141f, 142 Reed, Walter, 690 refraction, in microscopes, 42, 42f refractive index, 42 refrigeration, 91, 122, 765 refugee camps, 462, 581 relapsing fever, 296 relatedness, 232–233, 248 conflicting data on, 249 DNA base ratio (GC content) and, 248 DNA hybridization and, 247–248 methods of determining, for classification of prokaryotes, 246–248, 248t phylogenetic tree of, 249 16S ribosomal nucleic acid and, 246–247, 248t release factors, 173 religious practices, and susceptibility to disease, 456 rennin, 757, 757f Reoviridae, 323t, 408 repellent, of bacteria, 66 replica plating, 196, 196f replication of DNA, 164–167, 165f–166f

in animal viruses, 326–328, 327f, 329t bidirectionality of, 164, 165f components of, 165t definition of, 162 initiation of, 166 origin of, 165t, 166 overview of, 162f in phages, 308, 311, 312f, 329t replication fork in, 165f, 166–167, 167f in retroviruses, 332, 333f semiconservative, 164 of prions, 341–342, 342f viral, 304–305 cycle of, 329t targeting to site of, 326, 329t replication fork, 165f, 166–167, 167f replicative form, of phages, 311 replicons, 198, 198f, 208t definition of, 186t reporter gene, 217, 217f repressible enzymes, 176 repressors of transcription, 177, 177f viral, 310 reservoir(s), of infection, 451, 452f, 453–454 definition of, 451t environmental, 453–454 in healthcare settings, 462–464 human, 453 non-human animal, 453 resident microbiota, 393 resistance, to antimicrobial drugs. See antimicrobial resistance resistance genes, 205, 205f resistance plasmids, 205–207, 205f, 470t, 484 resistance transfer factor (RTF), 205, 205f resolving power, of microscope, 42, 42f respiration, 132–133, 133f, 142–147 aerobic, 133, 134t, 253, 739 by Escherichia coli, 144–145, 145f maximum theoretical ATP yield from, 146–147, 146f anaerobic, 133, 134t, 253, 731 by chemoorganotrophs, 252t by Escherichia coli, 144–145 by obligate anaerobes, 92 ATP generation in, 134t definition of, 127t respiratory infections, 495–530, 497f fungal, 525–527 key terms for, 496t lower bacterial, 509–518 structures commonly involved in, 496–498, 497f viral, 519–524 respiratory syncytial virus, 521–522, 522t causative agent of, 521–522, 522t epidemiology of, 522, 522t incubation period of, 522t pathogenesis of, 522, 522t prevention and treatment of, 522, 522t symptoms of, 521, 522t seasonal occurrence of, 458, 458f transmission of, 455

I-31

upper bacterial, 499–506 structures commonly involved in, 496, 497f viral, 507–509 respiratory syncytial virus (RSV), infection, nosocomial, 463t respiratory system anatomy and physiology of, 495–498, 497f normal microbiota of, 498t, 498–499 respiratory viruses, 322, 324t response regulators, 180, 180f resting stage, of bacteria, 264–265 restriction enzyme(s), 5f, 213–214, 314 action of, 213, 213f in characterizing bacterial strains, 244 common, 214t definition of, 213t nomenclature for, 214 restriction fragment(s), 214 restriction fragment length polymorphisms (RFLPs) for characterizing bacterial strains, 244, 244t, 245f detection of, methods for, 244, 245f restriction-modification system, 314–316, 315f reticulate body, 274, 274f, 632 reticuloendothelial system. See mononuclear phagocyte system retinitis cytomegalovirus, 715–716, 716f toxoplasmosis, 713 retrospective studies, 458 Retroviridae, 323t. See also retroviruses retroviruses, 5f, 162, 218, 323t, 428 infection by, 331–332 replication of, 332, 333f slow infection by, 333f tumors caused by, 333–334 Rev, 700f, 701 reverse transcriptase, 218, 219f, 332, 333f, 606, 607f, 701 definition of, 582t, 698t discovery of, 697 inhibition of, 487–488, 487t, 641, 708 reversion, of mutation, 188 Reye’s syndrome, 546 RFLPs. See restriction fragment length polymorphisms R genes, 205, 205f Rhabdoviridae/rhabdoviruses, 322f, 323t, 663 Rh disease, 418–420, 419f rheumatic fever, 385, 408 acute, 501 and endocarditis, 677 rheumatoid arthritis, 424t, 425, 425f treatment of, 426 rhinitis, 496 Rhinovirus, 322 rhinoviruses, 323t, 324t, 507–508, 507f, 508t rhizobia, 263t, 265, 266f nitrogen fixation by, 265, 721, 734–735, 734f

9/16/08 10:27:34 AM

I-32

INDEX

Rhizobium, 265, 727 characteristics of, 263t nitrogen fixation by, 265, 721, 734–735, 734f symbiotic relationship with plants, 265, 265f–266f rhizoids, 290 Rhizopus, 293, 762 Rhizopus stolonifer, 289, 289t, 291f rhizosphere, 728 definition of, 722t rhodamine, 52, 444 Rhodobacter, 252t, 257 Rhodophyta, 283t Rhodopseudomonas, 252t, 257 rhodopsin, 725 Rhodospirillum rubrum, storage granules in, 68f rhuMab, 418, 439 RIA. See radioimmunoassay ribavirin, 487t, 608, 665 ribonucleic acid. See RNA ribose, 30, 30f, 31t, 34 α and β forms, 31f ribose-5-phosphate, 132t, 139–141, 158 ribosomal proteins, 68 ribosomal RNA (rRNA), 68, 164, 171t, 242, 243f in classification of eukaryotes, 280, 281f in classification of prokaryotes, 232, 246–247, 248t, 249 definition of, 162t gene sequencing, in identification prokaryotes, 237t, 242–243, 243f in identification of uncultivated organisms, 242–243 in microbial ecology studies, 725 small subunit (SS, SSU), 242 ribosome(s), 25 of chloroplasts, 77 definition of, 162t of eukaryotic cells, 70f, 71t, 72t, 74, 175–176 of mitochondria, 77 of prokaryotic cells, 55t, 68, 68f, 72t, 171, 172f prokaryotic 70S, 242, 243f in translation, 171–172, 171t, 172f ribosome-binding site, 171t, 172 ribozymes, 175 ribulose 1,5-biphosphate, 155, 155f ribulose biphosphate carboxylase, 155 rice, symbiotic nitrogen fixation and, 735 Richet, Charles, 414 Ricketts, Howard, 531 Rickettsia, 274 Rickettsia akari, 297 Rickettsial pox, 297 Rickettsia prowazekii, 531 medical importance of, 271t, 274 vectors for, 295t, 296 Rickettsia rickettsii, 531, 540–541, 540f medical importance of, 271t, 274 vectors for, 295t, 297 rifampin, 474t, 478, 516–517, 656 rifamycins, 474t, 478 rimantadine, 486, 487t, 521 ringworm, 410, 554, 555f ripening, of cheese, 756t, 757

nes95432_ind_I1-I40.indd I-32

ritonavir, 487t, 488 river blindness, 9, 274 rivers, 726 RNA (ribonucleic acid), 32, 34 catalytic properties of, 175 characteristics of, 164 double-stranded, long, sensors that detect, 357–358, 357f eukaryotic, 175–176, 175t capped, 175 processing of, 175 splicing of, 175, 175f, 175t messenger, 164, 168–170 in animal viruses, 326–327, 327f eukaryotic, 175–176, 175f, 175t in cloning, 218, 219f polycistronic, 168, 168t, 332 precursor, 175 in translation, 170, 171t, 173f and replication of animal viruses, 326–328 ribosomal, 68, 164, 171t in classification of eukaryotes, 280, 281f in classification of prokaryotes, 232, 246–247, 248t, 249 gene sequencing, in identification of prokaryotes, 237t, 242–243, 243f in microbial ecology studies, 725 synthesis of elongation in, 169, 170f initiation of, 169, 170f process of, 170f termination of, 170, 170f as template for phage replication, 308 in transcription, 168–170, 168f transfer, 164, 174f, 179f structure of, 172, 172f in translation, 171t, 172 tritiated urindine labeling of, 26 viroid, 342 RNA-induced silencing complex (RISC), 179, 179f RNA interference (RNAi), 179, 179f RNA phages, replication of, 308 RNA polymerase, 168–170, 168t definition of, 162t and phage replication, 308 RNases, 164 RNA viruses, 321, 519 animal, 323t bacterial, 304 Rocky Mountain spotted fever, 540–542, 542t causative agent of, 274, 531, 540–541, 540f, 542t epidemiology of, 541, 541f, 542t incubation period of, 542t pathogenesis of, 541, 542t prevention and treatment of, 542, 542t symptoms of, 540, 540f, 542t ticks as vectors for, 295t, 297, 531, 540–542, 542t rod-shaped bacteria, 52–53, 52f Roll Back Malaria, 693 root nodule bacteria, 721, 734–735, 734f. See also Rhizobium rose gardener’s disease. See sporotrichosis

roseola (exanthem subitum, roseola infantum), 552 Ross, Ronald, 691 rotaviral gastroenteritis, 604, 605t causative agents of, 604, 604f, 605f epidemiology of, 604 incubation period of, 605t pathogenesis of, 604 prevention and treatment of, 604, 605t symptoms of, 604, 605t vaccine, 434t rotaviruses, 324t, 604, 604f, 605t rough endoplasmic reticulum, 70f, 71t, 78, 78f RoundupTM (glyphosphate), genetically engineered plants resistant to, 217 roundworms, 10, 14f, 295, 297, 298t. See also nematodes clinical specimen, wet mount of, 237, 237f Rous, F. Peyton, 5f Roux, Emile, 366, 674 R plasmids, 205–207, 205f, 470t, 484 rRNA. See ribosomal RNA R side chain, 26, 26f rubella, 549–552, 552t causative agent of, 550, 552t chronic infection in, 332t congenital syndrome, 550–551 epidemiology of, 551, 551f, 552t incubation period of, 552t pathogenesis of, 550–551, 552t prevention and treatment of, 551–552, 552t reported cases of, 551, 551f symptoms of, 549–550, 550f, 552t vaccine, 434t, 435–436 rubeola, 547. See also measles rubisco, 154 ruffling, 399, 399f rum, 760 rumen, 149, 735 run, in chemotaxis, 66, 66f rye smut, 289, 292

S Sabin, Albert, 661 Sabin vaccine, 435–436, 662–663 problems with, 436, 662–663 Saccharomyces fermentation pathway of, 148, 148f in food production, 293, 758–761, 758t Saccharomyces carlsbergensis, 760 Saccharomyces cerevisiae characteristics of, 289t in food production, 758–760 as food source, 766 Safe Drinking Water Act of 1974, 744 safranin, 49, 49f, 50 St. Louis encephalitis virus, 660–661 sake, 758t, 759 salivary glands, 582–583, 583f Salk, Jonas, 661 Salk vaccine, 435–436, 662–663 Salmonella in Ames test, 197 characteristics of, 253t control/destruction of, 116, 122 directed uptake by cells, 399, 399f

evasion of host defenses by, 403 infection, 397, 601–602, 602t. See also salmonellosis medical importance of, 262, 271t prophage and, 311t reservoirs of, 453 serotypes of, 601 uptake by epithelial cells, 399, 399f Salmonella bongori, 601 Salmonella enterica, 243, 601 probiotic effective against, 411 Salmonella Enteritidis, 262, 271t, 601 infectious dose of, 394 Salmonella Typhi, 262, 271t, 456, 595, 601–602 Salmonella Typhimurium, 601 Salmonella typhimurium, ruffling induced by, 399f salmonellosis, 243, 595, 601–602, 602t causative agents of, 601, 602t epidemiology of, 602, 602t foodborne, 455, 602, 754, 763t, 764, 764f incubation period of, 602, 602t infectious dose for, 394 pathogenesis of, 602, 602t prevention and treatment of, 602, 602t symptoms of, 601, 602t SALT. See skin-associated lymphoid tissue salt and enzyme activity, 136–137 and food preservation, 93, 122 growth-inhibiting effects of, 93 halophiles in high concentrations of, 93, 275, 275f, 726 water solubility of, 24, 24f salt lakes, 726 Salvarsan, 5f, 469–470 sandfly fever, 324t sanitary landfills, 747 definition of, 739t sanitize, definition of, 108 saprophytes, 261, 410 saprophytic fungi, 290 saquinavir, 487t, 488 Sarcina, groupings of, 53 Sarcodina, 286, 286t, 287, 610 sarcoma. See also Kaposi’s sarcoma definition of, 698t in HIV-infected (AIDS) patients, 710–711 Sarcomastigophora, 286, 286t Sarcoptes scabiei, 297, 297f SARS. See severe acute respiratory syndrome (SARS) saturated fatty acids, 35, 35f sauerkraut, 755, 756t, 758 sausage, 756t, 758 saxitoxin, 285 SBE. See subacute bacterial endocarditis scabies, 297, 297f, 628 scalded skin syndrome, 407, 537–538, 538f, 538t causative agent of, 538, 538t epidemiology of, 538, 538t incubation period of, 538t pathogenesis of, 538, 538t prevention and treatment of, 538, 538t

9/2/08 5:33:49 PM

Index secondary infection with, 538 symptoms of, 538, 538f, 538t scanning electron microscopes, 45t, 47, 47f scarlet fever, 501 scavenger receptor, 358 Schaudinn, Fritz, 618 Schistosoma, infection, 362, 461–462. See also schistosomiasis pathogenesis of, 410–411 Schistosoma mansoni, 298t, 299, 299f schistosomiasis, 385 causative agent of, 298t, 299, 299f, 362 pathogenesis of, 362, 410, 461–462 schizogony, 288, 288f schizont, 691 Schleiden, Mathias, 4f Schwann, Theodor, 4f SCID. See severe combined immunodeficiency scintillation counters, 26f scolex, of tapeworms, 297, 298f scotch, 760 SCP. See single-cell protein scrapie, 13f, 320, 340t, 342, 669–670 scrotum, 620, 620f sealant, dental, 587 seasonal occurrence, of disease, 458, 458f seawater, 726 Sea Wide Field Sensor, 285 sebaceous glands, 533 definition of, 532t sebum, 532f, 533 secondary consumers, 722 secondary infection, 394, 538 secondary metabolites, 89, 89f secondary treatment definition of, 739t of wastewater, 740f, 741 secretion system definition of, 582t type III, 398, 398f, 399, 595 segmented viruses, 321 definition of, 321t genome exchange in, 335, 335f selectable marker, of vectors, 219, 219f selective enrichment, 98 selective IgA deficiency, 426, 427t selective media, 96–97, 96t definition of, 84 selective toxicity, of antimicrobial drugs, 471 self-assembly, of phages, 308 “self” cell(s), 347, 362, 366, 381–382, 382f, 387–388 self-reactive B cells, negative selection of, 387 self-reactive T cells, positive and negative selection of, 387–388 self-transmissible plasmids, 205 semen, 620 definition of, 619t semiconservative replication, 164 semicritical instruments, 111 semisynthetic antibiotics, 471 Semmelweis, Ignaz, 4f, 450, 464 sensitization, 415, 416f sensors, in signal transduction, 180, 180f sensor systems, in innate immune response, 354–358

nes95432_ind_I1-I40.indd I-33

sensory nerves, 648 septicemia, 395, 602, 675, 678 definition of, 675t Gram-negative, 678–680 causative agents of, 679 epidemiology of, 680 pathogenesis of, 679–680, 679f prevention and treatment of, 680 symptoms of, 678–679 nosocomial, 679–680 pneumococcal, 510 septicemic plague, 684 septic shock, 407–408, 675 definition of, 675t septic tanks, 744, 744f definition of, 739t serial dilutions, 439 serine, 27f seroconversion, 439 serogrouping, 652 serological typing, for characterizing bacterial strains, 243, 244t serology definition of, 432t, 439 identification of bacteria by, 237t, 240 in immunological testing, 439–441 seronegative, definition of, 439 seropositive, definition of, 439 Serratia marcescens, 186, 621 culture characteristics of, 238 pigment production by, 238 serum, immunological testing of, 438–439 serum hepatitis. See hepatitis B virus serum-resistant bacteria, 400–401 serum sickness, 420 definition of, 415 severe acute respiratory syndrome (SARS), 5f, 7, 323t, 528 severe combined immunodeficiency (SCID), 426–427, 427t sewage treatment, 6, 68, 254, 731 activated sludge method of, 741, 750 aerobic, 739 anaerobic, 739 anaerobic digestion in, 739, 742–743 artificial wetlands in, 741, 742f bulking of filamentous organisms in, 260 historical perspective on, 738 individual systems for, 744, 744f lagoons in, 741 methane as byproduct of, 743 primary, 739–741, 740f protozoa in, 287 reduction of biochemical oxygen demand in, 739 secondary, 740f, 741 trickling filter system of, 741, 741f sex pili, 66 in plasmid transfer, 202–203, 203f sexually transmitted disease, 323, 324t, 454, 618. See also specific diseases bacterial, 629–637 common, 629t prevention of, 643 protozoal, 642–643 risk, in unprotected intercourse, 628f

scope of problem, 628–629 symptoms of, 628, 629t viral, 323, 324t, 638–642 shake tube, 91 sheath, of phage, 303, 304f sheathed bacteria, 263t, 266, 266f, 726 shedding, of viruses, 328 sheets, in protein structure, 28 shellfish allergies, 416 shellfish poisoning, paralytic, 282, 284–285 shells, electron, 19f, 20 Shiga toxin, 598–599, 614 Shiga toxin-producing Escherichia coli, 600, 600t Shigella antimicrobial resistance of, 599 characteristics of, 253t directed uptake by cells, 399 evasion of host responses by, 403 exploitation of antigen-sampling processes by, 399, 400f hiding within host cell, 400 infection, 262, 598–599, 599f, 599t. See also shigellosis infectious dose of, 394 medical importance of, 271t portal of entry for, 455 prevention and treatment of, 461 vectors for, 455 Shigella boydii, 598 Shigella dysenteriae, 595, 598 infection, 397 toxin of, 404t Shigella flexneri, 598 Shigella sonnei, 598 shigellosis, 598–599, 599f, 599t, 628 causative agents of, 262, 598, 599t in day care centers, 461, 599 epidemiology of, 454, 599, 599t foodborne, 763t incubation period of, 599t infectious dose for, 394 pathogenesis of, 598–599, 599f, 599t prevention and treatment of, 599, 599t symptoms of, 598, 599t transmission of, 454, 599 shingles, 330, 330f, 331t, 395, 546–547, 546f shock anaphylactic, 415, 417, 472 definition of, 417 endotoxic, 407, 678–679 in meningitis, 652 septic, 407–408, 675 definition of, 675t superantigens and, 406 short interfering RNA (siRNA), 180 short tandem repeats, 225 “shrub” of life, 246, 247f sickle cell anemia, 693 siderophores, 398 sigma (σ) factors, 168t, 169, 170f alternative, 177 signaling, of eukaryotic cells, 73 signal sequence, 59, 173 signal transduction, 180–181 signature sequences, 242 definition of, 233t

I-33

signs, definition of, 394 silent mutation, 188 silver, in sterilization and disinfection, 118t, 120 silver nitrate, 120 silver sulfadiazine, 118t, 120 simple diffusion, 56 simple lipids, 35–36 hydrolysis of, 149f, 150 simple staining, 48t, 49 single-cell protein, 766 Sinorhizobium, 263t, 265, 734 sinuses, 650 sinusitis, 496 bacterial, 504–506 causative agent of, 504–505 epidemiology of, 506 pathogenesis of, 505–506 prevention and treatment of, 506 streptococcal, 501 symptoms of, 504 site specific recombination, 310 16S ribosomal nucleic acid in classification of prokaryotes, 246–247, 248t in microbial ecology studies, 725 skin anatomy and physiology of, 531–533, 532f as ecosystem, 392–393, 533 normal microbiota of, 270–272, 393f, 533, 533t, 534–535 penetration, by pathogens, 399 as physical barrier to infection, 348 skin-associated lymphoid tissue (SALT), 369f, 370, 531–532 skin infections, 531–558 bacterial, 535–545 key terms for, 532t viral, 545–554 skin tests tuberculin, 421–422, 421f, 516, 516f for tuberculosis, 438 sleeping sickness. See African sleeping sickness slim disease, 699t slime layers, 55t, 64, 64f, 85 slime molds, 294–295 acellular, 294, 294f cellular, 294, 294f classification of, 288 plasmodial, 294 slow infection, viral, 329–332, 330f definition of, 321t slow virus disease, 341, 341t sludge, 739 definition of, 739t stabilized, 743 slug, of slime mold, 294 small intestine, 583f, 584 normal microbiota of, 585–586 smallpox, 4f–5f, 7, 324t, 461f bioterrorism potential of, 7, 431, 466 factors discouraging use of, 554 factors encouraging use of, 554 simulated attack, 554 eradication of, 7, 431, 460 last case of, 431 vaccine, 7, 431, 437t

9/2/08 5:33:50 PM

I-34

INDEX

smear, 49 Smith, Hamilton, 5f Smith, S. B., 581 smooth endoplasmic reticulum, 70f, 71t, 78, 78f smuts, 289, 292 Snow, John, 4f, 457, 581 soap, for microbial control, 108 Society of American Bacteriology, 753 sodium chloride. See salt sodium hypochlorite, 111 sodium stibogluconate, 490t sodium thioglycollate, as reducing agent, 98 soft chancre, 636, 637f soil, 727–728 algae in, 728 bacteria in, 263–266, 263t characteristics of, 727 fungi in, 727–728 microorganisms in, 727–728 prokaryotes in, 727–728 protozoa in, 728 texture of, 727 solar energy, 732 solid waste composting for, 747–748, 748f sanitary landfills for, 747 treatment, microbiology of, 747–748 solute, 56 solute concentration, cellular effect of, 93, 93f sorbic acid, 122, 765 SOS mutagenesis, 193 SOS repair, 192–193, 195t, 310 sourdough bread, 761 sour-mash whiskey, 760 Southern blot, 227 soy sauce, 761, 762t Spallanzani, 2 “Spanish flu,” 336 specialized transducing phages, 313, 314f specialized transduction, 201, 313, 314f species definition of, 233t, 234 nomenclature for, 12 spectrophotometer, 102, 103f spelunkers’ disease. See histoplasmosis spent grains, in beer production, 759, 760f sperm, 620 SPEs. See streptococcal pyrogenic exotoxins Sphaerotilus, 263t, 266, 266f, 726 spinal cord, 648, 648f pathways to, 649–650 Spirillium, 263t, 270 Spirillium volutans, 270 spirillum (pl., spirilla), 52f, 53 Spirochaeta, 263t, 270 Spirochaeta pallida, 618. See also Treponema pallidum Spirochaetes, 263t spirochete(s), 52f, 53, 269–270, 618 dark-field microscopy of, 269, 269f definition of, 252t free-living, 263t, 270 medically important, 272t motility of, 269 Spirogyra, dark-field microscopy of, 43f

nes95432_ind_I1-I40.indd I-34

Spirulina, 258f Spirulina maxima, 766 spleen, 369f, 370, 677 bacterial diseases of, 680–685 rupture of, 686, 692 splicing, of eukaryotic RNA, 175, 175f, 175t spoilage, food, 754, 754f, 762 spongiform encephalopathies, 340t, 341, 341f, 669–670, 670t definition of, 648t in humans, 669–670, 670t causative agents of, 669, 670t epidemiology of, 669–670, 670t pathogenesis of, 669, 670t prevention and treatment of, 670, 670t symptoms of, 669, 670t Spongomorpha, interference microscopy of, 43f spontaneous generation, theory of, 1–5, 4f spontaneous mutations, 187–190, 187f repair of, 195t spore(s), 69. See also endospore(s) spore coat, 69, 69f spore stain, 51 Sporothrix schenkii, 292t, 576–577, 577f, 577t sporotrichosis, 292t, 576–577, 577t causative agent of, 576, 577f, 577t epidemiology of, 577, 577t incubation period of, 577, 577t pathogenesis of, 577, 577t prevention and treatment of, 577, 577t symptoms of, 576, 576f, 577t sporozoa (Apicomplexa), 286, 286t, 610 sporozoites, 691 sporulation, 69f, 69–70, 255, 264, 264f spread-plate method, of cell counting, 100–101, 101f sputum, 510 definition of, 496t stabilized sludge, 743 stain(s), 48t acid-fast, 48t, 50, 50f, 238, 261 capsule, 48t, 50–51, 50f differential, 48t, 49–50 endospore, 48t, 51, 51f flagella, 48t, 51, 51f Gram, 4f, 40, 48t, 49–50, 49f cell wall composition and, 62–63 for identification of bacteria, 238, 238f primary, 49 simple, 48t special to identify bacteria, 238 to observe cell structures, 48t, 50–51 staining for microscopy, 48–52, 48t negative, 49 process of, 48–49 simple, 48t, 49 stalk, 266, 267f standard(s), of drug concentration, 481, 481f standard curve, of drug concentrations, 481, 481f

Standard Precautions, 465 Stanier, Roger, 232 Stanley, Wendell, 302 staphylococcal infection, nosocomial, 463t Staphylococcus. See also specific types animal habitats of, 270–272 in food, 755 groupings of, 53 halotolerance of, 93 infection, wound, 562–563, 562f in normal microbiota genitourinary, 620 of respiratory system, 498, 498t of skin, 270–272, 533, 533t, 534 Staphylococcus aureus antibiotic resistance of, 185, 207–208, 207f antimicrobial resistance of, 476, 484–485, 563, 578 carriers of, 453 catalase-positive, 427 control/destruction of, 120, 122 evasion of host defenses by, 402–403 Fc receptors of, 402–403 Gram stain of, 49f infection, 395 diseases caused by, 535t of ear, 505 foodborne, 397, 406–407, 754–755, 758, 763, 763f, 763t heart valve (endocarditis), 677 nosocomial, 463, 463t prevention and treatment of, 578 in scalded skin syndrome, 537–538, 538f, 538t secondary, 519, 546, 548 skin, 535–537, 538t in toxic shock syndrome, 562, 626–627, 628t treatment of, 470 of wounds, 399, 562–564, 562f, 565t, 572, 575 medical importance of, 272, 272t methicillin-resistant, 537 multiply-resistant, 537 in normal microbiota, of respiratory system, 498, 498t phage typing of, 245f portal of exit for, 454 strains of, characterization of, 245f, 537 versus Streptococcus pyogenes, 539t superantigens of, 404t, 406–407 toxin of, 404t, 407 vaccine, 578 virulence factors of, 536, 537t, 563 Staphylococcus epidermidis, 270, 272t, 534 infection heart valve (endocarditis), 678t nosocomial, 463 of wounds, 562–563 Staphylococcus saprophyticus, 272, 272t, 621 starch, 31t hydrolysis of, 149 start codon, 171t, 172–173 starter cultures, 756–757

stationary phase, of bacterial growth, 88f, 89 stavudine, 708 STDs. See sexually transmitted disease steam, pressurized in commercial canning process, 114, 114f sterilization using, 112t, 113, 113f–114f stem cell research, 428 stem cells, 350, 351f, 385 and treatment of type 1 diabetes mellitus, 426 stereochemistry, 18 stereoisomers, 18 of amino acids, 26, 27f–28f sterilants, 117 definition of, 108t sterile commercially, 114 definition of, 108, 108t sterilization, 86, 108 chemicals for, 116–121, 118t definition of, 108, 108t dry heat for, 112t, 114 pressurized steam for, 112t, 113, 113f, 114f steroids, 35–36, 35f for asthma, 417 for autoimmune disorders, 425 sterols, 35f, 36, 64, 73 sticky end, of DNA fragments, 213f, 214 Stigmatella, 263t, 265 stipe, 282 stock cultures, 88 stomach, 583f, 584 stomach cancer, Helicobacter pylori and, 590 stop codon, 171t, 173 premature generation of, 189 storage granules, of prokaryotes/bacteria, 55t, 68, 68f, 270 Storrs, Eleanor E., 655 strain(s) antibiograms of, 245–246, 246f biochemical typing of, 243, 244t definition of, 233, 233t designations of, 12 differences, characterization of, 243–245, 244t genomic typing of, 243–244, 244t phage typing of, 244–245, 244t, 245f serological typing of, 243, 244t stramenophiles, 294 streak-plate method, for cultures, 87–88, 87f strep throat, 238, 394, 499–502, 499f, 502t causative agent of, 499, 499f, 502t epidemiology of, 501–502, 502t incubation period of, 502t pathogenesis of, 500–501, 500f, 502t prevention and treatment of, 502, 502t symptoms of, 499, 502t vaccine sought for, 437t streptobacillary rat bite fever, 574, 575t causative agent of, 574, 575t epidemiology of, 574, 575t incubation period of, 575t pathogenesis of, 574, 575t

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Index prevention and treatment of, 574, 575t symptoms of, 574, 575t streptococcal pyrogenic exotoxins (SPEs), 500t, 501, 563 Streptococcus, 255, 255f. See also specific types adherence of, 64, 398 beta-hemolytic, latex agglutination test for, 443, 443f characteristics of, 252t colony, 238 fermentation pathway of, 148f in food production, 756, 756t, 757 in food spoilage, 762 groupings of, 53 hemolysis in detection of, 97 infection, treatment of, 470 Lancefield grouping of, 495 in mucous membranes, 272 nomenclature, 249 in normal microbiota genitourinary, 620 of mouth, 585 of respiratory system, 498t, 499 serology, 240 Streptococcus agalactiae, 650 infection, meningitis, 655t Streptococcus mutans, 64, 587, 589t, 614 Streptococcus pneumoniae antimicrobial resistance of, 485 capsule, 64, 402 evasion of host defenses by, 402 Gram stain of, 238, 238f infection heart valve (endocarditis), 677 lower respiratory (pneumonia), 509–510, 509f, 510t nervous system (meningitis), 510, 650, 651f, 655t secondary, 548 upper respiratory, 505 medical importance of, 272t in normal microbiota, of respiratory system, 498t polysaccharide capsule of, 379 vaccine, 435 Streptococcus pyogenes, 92, 233, 394 biochemical tests for, 238 evasion of host defenses by, 401–403 Fc receptors of, 402–403 hemolysis in detection of, 97 immunofluorescence, 51f infection, 397 of ear, 505 invasive (flesh-eating), 501, 563, 563f, 565t nosocomial, 463 in puerperal fever, 450 secondary, 519, 546, 548 skin (impetigo), 538–540, 539f, 540t throat (strep throat), 394, 499f, 499–502, 502t vaccine sought for, 437t vaginal, 620–621 latex agglutination test for, 443, 443f medical importance of, 255, 272t mimicking host molecules, 403 M protein of, 402

nes95432_ind_I1-I40.indd I-35

prophages and, 311, 311t serology, 240 versus Staphylococcus aureus, 539t superantigens of, 404t, 406, 501 toxin of, 401, 404t, 405 virulence factors of, 500–501, 500f, 500t Streptococcus thermophilus, 756t, 757 streptogramins, 474t, 477f, 478 streptokinase, 501 and serum sickness, 420 streptolysin O, 401, 405, 500t, 501 streptolysin S, 500t, 501 Streptomyces, 265, 265f antibiotic production by, 265, 470, 723, 727 characteristics of, 263t conidia of, 727 Streptomyces somaliensis, 265 streptomycin, 470, 474t, 477 resistance to, 195, 195f, 484 Streptomycin griseus, 470 stroma, in chloroplasts, 77, 77f stromatolites, 246 Strongyloides stercoralis, 298t strongyloidiasis, causative agent of, 298t structural isomers, of monosaccharides (sugars), 3 subacute bacterial endocarditis, 501, 563, 586, 677–678, 678t causative agent of, 677–678, 678t definition of, 675t epidemiology of, 678, 678t incubation period of, 678t pathogenesis of, 678, 678t prevention and treatment of, 678, 678t symptoms of, 677, 678t subacute sclerosing panencephalitis, 548 submerged culture reactor, 761 substituted proteins, 30 substrate, 129 substrate-level phosphorylation, 130 ATP yield from, 134t, 147 definition of, 127t subunits, of macromolecules, 25 succession, microbial, 724, 724f succinate, 141f, 142 succinate dehydrogenase complex, 143–144 succinyl-CoA, 141f, 142 sucrose, 31t, 32 hydrolysis of, 149 sugar(s), 30–32 α and β links, 30, 31f fermentation, tests for, in identification of bacteria, 239, 239f, 240t and food preservation, 93, 122 growth-inhibiting effects of, 93 linear forms, 30–31, 31f metabolism of, 126, 132–134, 133f ring forms, 30–31, 31f structural isomers of, 31 sugar-phosphate backbone, 162 suicide enzymes, 357 sulfa drugs, 138, 138f, 470, 474t, 478–479, 479f, 490t sulfanilamide, 138, 470 sulfate, as terminal electron acceptor, 145, 724, 728, 731

sulfate-reducers, 145, 252t, 724 thermophiles, 254, 275–276 Sulfolobus, 275t, 276, 276f sulfonamides, 474t, 478–479, 479f, 490t sulfur, 19, 724 atomic structure of, 19t as major element, 93–94, 94t sulfur bacteria, 150, 150t characteristics of, 252t green, 154, 252t, 257, 257f, 731 purple, 252t, 256, 256f, 724, 731 sulfur cycle, 254, 259, 731–732, 731f sulfur dioxide, in preservation, 758, 766 sulfur granules, 571, 571f sulfuric acid, 259 sulfur oxidation, 731 sulfur oxidizers, 276, 276f, 731 bacteria, 259–260 characteristics of, 253t, 254 filamentous, 253t, 259–260 unicellular, 253t, 260 sulfur-oxidizing, nitrate-reducing bacteria, 263t, 270 sulfur-oxidizing bacteria, definition of, 252t sulfur reduction, 731–732 sulfur springs, 726 sulfur thermophiles, 254, 275–276 superantigens, 404t, 406–407, 501, 563, 627 superbugs, 221 drugs against, 491 supercoiled DNA, 67–68, 67f superficial mycoses, 292 cutaneous, 554–555 causative agents of, 554, 555f epidemiology of, 555 pathogenesis of, 555 prevention and treatment of, 555 symptoms of, 554 supernatant, 337 superoxide, 92, 189, 358 superoxide dismutase, 92 surface receptors, in innate immune response, 353 surface waters, 744 surgical wounds, 560 infection of, 560 surveillance, infectious disease, 459–460 SV 40, 324t S (Svedberg) value, of ribosomes, 68, 171 swarm, of cells, 264 swarmer cells, 266, 267f sweat glands, 532f, 533 sweet acidophilus milk, 756t, 757 swimmer’s itch, 298t swine influenza vaccine, 521 Swiss cheese production, 255–256 symbionts, definition of, 392 symbiosis, 722 definition of, 392 symbiotic nitrogen fixation, 265, 721, 734–735, 734f symbiotic relationships, 733–735 between microorganisms and hosts, 392 symptomatic infections, 453 symptoms, duration of, 395, 395f

I-35

synapse, of phages, 310, 310f syncytia (sing., syncytium), 410, 522 Synechococcus, 252t, 258 Synercid, 478, 537 synergistic antimicrobial drugs, 472 synergistic infection, 575 syphilis, 91, 396, 629t, 633–636, 636t, 676 causative agent of, 273, 618, 634, 634f, 636t congenital, 635–636, 636f epidemiology of, 636, 636t historical perspective on, 618 incubation period of, 636t pathogenesis of, 635, 635f, 636t prevention and treatment of, 5f, 469, 636, 636t primary, 633–636, 635t secondary, 633–636, 635f, 635t stages of, 633, 635t symptoms of, 633, 634f, 636t targeting for elimination, 634 temperature and, 91 tertiary, 633–636, 635f, 635t systemic infection, 395, 675 systemic lupus erythematosus, 424t, 425 systemic mycoses, 292 systemic viruses, 322

T tacrolimus, 424 Taenia solium, 298f, 298t tafenoquine, 490t, 693 tail, of phage, 303, 304f tannin, 758 tapeworm(s), 10, 295, 297, 298f, 298t Taq polymerase, 224–225, 262 target cell, 380 target DNA, in polymerase chain reaction, 223–224, 224f tartaric acid, 18 Tat, 700f, 701 Tatum, Edward, 5f taxonomy definition of, 233, 233t of Escherichia coli, 234t hierarchies in, 234, 235f key terms for, 233t principles of, 233–236 TCA. See tricarboxylic acid cycle Tc cell(s), 381 definition of, 367t functions of, 382–383, 382f T-cell receptors, 368–369, 377, 380, 380f superantigens and, 406–407, 406f T cells (T lymphocytes), 332, 352, 368–369 activation of, 381–382 dendritic cells and, 381–382 in antibody response, 368f antigen presentation to, 368–369, 380 by major histocompatibility complex class I, 381, 381f, 409f by major histocompatibility complex class II molecule, 381f antigen recognition by, 367–369, 378–384, 381f

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I-36

INDEX

T cells (T lymphocytes)—Continued antigen response by, 378–384 CD4, 381 functions of, 381f, 383 CD8, 381 functions of, 382–383, 382f in cellular immunity, 368f, 368–369 clonal selection and expansion of, 375 cytotoxic, 368f, 368–369, 381 in transplantation immunity, 423 development of, 370 effector, 368f, 369 helper, 368f, 368–369 in HIV infection, 641, 702–705 in mononucleosis, 686, 687f in immunodeficiency disorders, 426, 427t memory, 367 origin of, 370 regulatory, 369 self-reactive, positive and negative selection of, 387–388 subsets of, 383–384 superantigens and, 406f, 406–407 and vaccination, 379, 383, 435 Tdap vaccine, 514 T-dependent antigens, response to, 650 technological advances, and emerging diseases, 461 teeth decay of, 586–587, 589t plaque on, 64, 86 structure of, 582, 584f teichoic acids, 60t, 61, 62f Temin, Howard, 332, 697 tempeh, 762t temperate phages, 306, 308, 313, 314f definition of, 303t temperature and disease, 91 and enzyme activity, 136–137, 136f and food preservation, 91, 110, 122 for food storage, 91, 122, 755 and microbial control, 110–111, 112t and microbial growth, 90–91, 90t, 91f, 137 optimum growth, 90–91 in pasteurization, 112–113 template, DNA, 164, 222, 222f temporary transmission, of plant viruses, 340 tequila, 760 terbinafine, 489, 489t terminal cleaning, 121 terminal electron acceptor, 131, 148, 253–254, 724, 728, 730 definition of, 127t terminator, of transcription, 168t, 170, 170f terrestrial environment, 727–728 bacteria in, 263–266, 263t terrorism, biological, 431, 466 anthrax for, 264, 466 2001 attacks, 2, 5f, 466, 512 DNA technologies and, 221 smallpox as potential agent for, 7, 431, 466, 554 tertiary consumers, 722 testicles, 620, 620f tetanospasmin, 566, 567f

nes95432_ind_I1-I40.indd I-36

tetanus, 566–568, 568t causative agent of, 69, 255, 559, 561, 566, 566f, 568t epidemiology of, 456, 567, 568t incubation period of, 568t neonatal, 566f, 567–568 pathogenesis of, 566–567, 567f, 568t prevention and treatment of, 567–568, 568t symptoms of, 566, 566f, 568t vaccine, 405, 434t, 435, 567–568 and wound management, 568t tetanus immune globulin, 433, 568 tetanus toxin, 404t tetracycline(s), 474t, 477–478, 477f for leptospirosis, 624 for mycoplasmal pneumonia, 512 tetrahydrofolate, 136t tetrahydropyrimidines, 491t Tetrahymena, 175 tetrapeptide chain, 61 Thayer-Martin agar, 96, 96t TH cell(s) in B cell activation, 383 definition of, 367t functions of, 383 in macrophage activation, 383, 384f TH1 cells, 383–384 TH2 cells, 383–384 therapeutic index, 471 therapeutic vaccine, definition of, 698t thermal stratification, in freshwater environments, 726 thermocline, 726 thermophiles, 90t, 91, 91f enzymes produced by, 158 extreme, 275–276, 275t methane-generating, 275, 275t sulfur- and sulfate-reducing, 254, 275–276 thermophilic extreme acidophiles, 276 Thermophilus, 275t Thermophilus aquaticus, 225 Thermoplasma, 276 Thermoplasma acidophilum, 276 thermotaxis, 66 Thermotoga maritima, 246 Thermus, 252t, 253t, 262 Thermus aquaticus, 262 thiabendazole, 491t thiamin pyrophosphate, 136t thin sectioning, 47, 47f Thiobacillus, 253t, 731 Thiodictyon, 252t, 256 Thiomargarita, characteristics of, 263t Thiomargarita namibiensis, 15, 15f, 270, 731 Thioploca, 263t, 270, 731 Thiospirillum, 252t, 256 Thiothrix, 253t, 259–260, 259f, 731 threadworm, 298t three-domain classification system, 234, 235f 3′ end, of DNA, 162–163 3TC. See lamivudine threonine, 27f throat, normal microbiota of, 393f thrush, in immunocompromised hosts, 410 Thucydides, 391 thylakoids, 77, 77f, 152 thymidine, in biological research, 26

thymidylic acid, 33f thymine, 33, 33f, 161–162 thymine dimers, repair of, 192, 192f, 193, 195t excision (dark) repair, 193, 194f, 195t light repair, 193, 194f, 195t thymus gland, 369f, 370, 425 thyroid disease, autoimmune. See Graves’ disease thyroid scan, 26, 26f thyroid-stimulating hormone, 425 ticarcillin, 473t, 476, 476f ticks, as vectors of disease, 295, 295t, 297 in Lyme disease, 295t, 297, 542–544, 544f, 545t, 556 in Rocky Mountain spotted fever, 295t, 297, 531, 540–542 tigecycline, 478 timing, of disease, 457–458, 458f tin, as preservative, 120 T-independent antigens, 383, 407 polysaccharides as, 379, 383, 435 response to, 379, 379f tinea barbae, 554 tinea capitis, 554 tinea corporis, 554 tinea cruris, 554 tinea pedis, 554, 555f tinea versicolor, 534, 534f Ti plasmid, 265 tissue(s), 71 tissue cultures, 336, 337f tissue degrading enzymes, streptococcal, 500t, 501 titer antibody, 378, 439 rise in, 439 viral, 338, 338f T lymphocytes. See T cells (T lymphocytes) TNT (trinitrotoluene), bioremediation of, 6 tobacco mosaic virus, 12f, 302, 304f, 721 assembly or maturation of, 328, 328f maturation of, 328, 328f symptoms of, 339f tobramycin, 474t, 477 Togaviridae/togaviruses, 295t, 323t, 660 tolerance immunologic, 377, 403, 414, 426 oral, 426 definition of, 415 toll-like receptors, 347, 355, 355f, 358–359, 407, 679 definition of, 347t Tonegawa, Susumu, 387 tonsillitis, 496 tonsils, 496 tooth. See teeth top-fermenting yeasts, 760 topoisomerase(s), 478 topoisomerase II, 478 total coliform rule, 746 total coliforms, in water testing, 746 total weight, of culture, in measurement of bacterial growth, 99t, 103 toxemia, 395

toxicity of antimicrobial drugs, 472 selective, 471 of germicides, 117 toxic shock syndrome, 7 definition of, 619t staphylococcal, 562, 626–627, 628t causative agent of, 627, 628t epidemiology of, 626, 628t incubation period of, 628t pathogenesis of, 627, 628t prevention and treatment of, 627, 628t reported cases of, 626, 627f symptoms of, 626, 628t streptococcal, 501, 563 toxic shock syndrome toxin, 406, 537t, 627 toxin(s), 403–408. See also specific types A-B, 404t, 405 action of, 406f algal, 282, 284–285 definition of, 281t fungal, 292, 410 ingested, 397 in intestinal infections, 595 membrane-damaging, 401, 404t, 405–406 nervous system (neurotoxins), 285, 657–658 production of, by microbes, 397 toxin A, 565 toxoids, 405, 435 Toxoplasma gondii, 288 animal hosts of, 286, 714, 714f, 715t drugs against, 490t infection, 714–715, 714f, 715t. See also toxoplasmosis nosocomial, 464 risk in pregnant women, 374 life cycle of, 714, 714f toxoplasmosis, 713–715, 715t causative agent of, 286, 286t, 288, 713–714, 714f, 715t congenital, 713 epidemiology of, 714–715, 715t fetal, 374, 713 incubation period of, 715t latent infection, 464 pathogenesis of, 714, 715t prevention and treatment of, 490t, 715, 715t symptoms of, 713, 715t T4 phage, 304f, 307, 307f, 307t, 313t trace elements, 94 as enzyme cofactors, 136 trachoma, 632 definition of, 619t transamination, 156 transcript, of RNA, 164 transcription, 162, 168–170, 168f activators of, 177, 178f of animal viruses, 326–328, 327f components of, 168t control of mechanisms in, 176–177 negative, 177, 177f positive, 177, 178f definition of, 162t, 168 downstream, 168

9/2/08 5:33:51 PM

Index of lytic phages, 307f, 308 monocistronic, 168, 175 overview of, 162f polycistronic, 168, 332 promoters of, 168, 169f, 170f repressors of, 177, 177f RNA synthesis in elongation in, 169, 170f initiation of, 169 termination of, 170, 170f upstream, 168 transcription terminator, 168t, 170, 170f transcytosis, 399 transducing particle, 201 transduction, 199, 201, 204t definition of, 186t generalized, 201, 202f, 313 by phages, 201, 202f, 204t, 313, 314f specialized, 201, 313, 314f transferred DNA (T-DNA), 206 transferrin, 349, 398 transfer RNA (tRNA), 164 definition of, 162t structure of, 172, 172f in translation, 171t, 172, 179f transformation, DNA-mediated. See DNA-mediated transformation transfusion reactions, 418 transgenic organisms, 217 transgenic plants, 217 transient microbiota, 393 transition step, metabolic, 132, 132t, 133f, 139t, 141–142, 141f ATP yield in, 141f, 146 yield of, 142 translation, 162, 170–173 components of, 170, 171t definition of, 162t, 170 elongation in, 173, 179f initiation of, 172–173, 173f, 179f messenger RNA in, 170, 171t overview of, 162f process of, 179f ribosomes in, 171–172, 171t, 172f termination of, 173, 179f transfer RNA in, 171t, 172, 179f translocation, 173 transmissible mink encephalopathy, 341t transmissible spongiform encephalopathies, 340t, 341, 341f, 669–670, 670t in humans, 669–670, 670t causative agents of, 669, 670t epidemiology of, 669–670, 670t pathogenesis of, 669, 670t prevention and treatment of, 670, 670t symptoms of, 669, 670t transmission, 451, 452f, 454–455. See also vector(s) by air, 455, 455f, 464 of animal viruses, groupings based on, 322–323, 324t by contact, 454 droplet, 455 fecal-oral, 322, 324t, 455, 599 by food, 455 in healthcare settings, 464 horizontal, 454 of plant viruses, by insects, 340

nes95432_ind_I1-I40.indd I-37

circulative, 340 external or temporary, 340 portal of exit for, 451, 452f, 454 sexual, 323, 324t, 454 vertical, 454 by water, 455 Transmission-Based Precautions, 465 transmission electron microscopes, 45t, 46–47, 47f transplantation immunity, 423–424, 428 transplant patients, complications/infections in, 710–718 transport proteins, 58–59, 58f, 72t, 73 transport systems active, 58, 58t, 58f–59f ATP used by, 58, 59f in eukaryotic cells, 70–71, 71f, 72t passive, 58 in prokaryotic cells, 57–59, 58t, 72t proton motive force used by, 58, 58f understanding and exploiting, in drug development, 79 transposable element (transposon), 5f. See also transposons definition of, 186t transposase, 207, 208t transposition, 189–190, 189f, 191–192 transposons, 185, 189–190, 189f, 208t and antimicrobial resistance, 185, 207–208, 207f composite, 207–208, 207f, 208t detection of, 185, 190, 190f discovery of, 185 gene transfer by, 185, 207–208 to unrelated bacteria, 207–208, 207f mutation by, 191–192, 191t structure of, 207–208, 207f travel, and disease exposure/spread, 8, 295 traveler’s diarrhea, 599–601 trematodes, 295, 298t, 299. See also flatworms; flukes definition of, 281t trench fever, 296 trench mouth, 588–589, 588f, 589t causative agent of, 589, 589t epidemiology of, 589, 589t pathogenesis of, 589, 589t prevention and treatment of, 589t symptoms of, 589, 589t Treponema, 273 dark-field microscopy of, 43, 634, 634f infection, oral, 588–589, 589t Treponema pallidum, 396, 469 dark-field microscopy of, 43, 634, 634f immunoassay for, 438 infection, 455, 618, 629t, 633–636, 634f, 635f, 636t. See also syphilis medical importance of, 272t, 273 triazoles, 489, 489t tricarboxylic acid cycle, 132, 132t, 133f, 134t, 139t, 141–142, 141f ATP yield in, 141f, 142, 146 yield of, 142 Trichinella spiralis, 298t trichinellosis. See trichinosis trichinosis, 298t

trichloroethylene (TCE), bioremediation of, 750 2,4,5-trichlorophenoxyacetic acid (2,4,5-T), 749, 749f trichomes, 258, 258f Trichomonas, 286t Trichomonas vaginalis, 286, 288 infection, 629t, 642–643, 642f, 643t trichomoniasis, 286t, 629t, 642–643, 643t causative agent of, 642–643, 642f, 643t epidemiology of, 643, 643t incubation period of, 643t pathogenesis of, 643, 643t prevention and treatment of, 643, 643t symptoms of, 642, 643t Trichophyton, 554, 555f trichuriasis, 298t Trichuris trichiura, 298t trickling filter system, of sewage treatment, 741, 741f triclosan, 118t, 120 triglycerides, 35, 35f trimethoprim, 474t, 478–479, 479f trimethoprim-sulfamethoxazole, 623, 713, 715 trinitrotoluene (TNT), bioremediation of, 6 tritium, 26 tRNA. See transfer RNA Tropheryma whippelii, 243, 678 trophic levels, 722, 723f trophozoite, 287, 610, 611f, 691 Trypanosoma, infection, 286, 286t, 287–288, 690–691. See also African sleeping sickness prevention and treatment of, 490t Trypanosoma brucei, 667, 667f, 668t, 690–691 Trypanosoma brucei gambiense, 286, 667 Trypanosoma brucei rhodesiense, 286, 667 Trypanosoma cruzi, 691 trypanosomiasis, 667–668, 667f, 668t. See also African sleeping sickness African, 667–668 American (Chagas disease), 691 tryptophan, 27f synthesis of, 156–157, 157f tsetse fly, 288, 667–668 tubercle, 515, 515f definition of, 496t tuberculin skin test, 421–422, 421f, 516, 516f tuberculoid leprosy, 656 tuberculosis, 4f, 514–517, 517t, 753 antimicrobial resistance in, 485, 516–517 antimicrobials for, 474t causative agent of, 515, 515f, 517t delayed cell-mediated hypersensitivity in, 422 directly observed therapy for, 485, 517 epidemiology of, 516, 517t extensively drug-resistant (XDRTB), 485, 517 granulomatous response in, 359, 515

I-37

in HIV disease, 9, 461, 514, 717 incidence of, 514–515, 514f incubation period of, 517t latent infection, 395 microorganisms causing, control/ destruction of, 110–111, 120 multiple-drug-resistant (MDR-TB), 485, 517 pathogenesis of, 515–516, 517t prevention and treatment of, 479, 517, 517t first-line drugs for, 479 second-line drugs for, 479 resurgence in, 461, 514–515, 514f skin test for, 421–422, 421f, 516, 516f symptoms of, 515, 517t tests for, 438 vaccine, 434t, 517, 712t tubulin, 74 tularemia, 680–681, 682t causative agent of, 680, 682t epidemiology of, 681, 681f, 682t incubation period of, 682t pathogenesis of, 680–681, 681f, 682t prevention and treatment of, 681, 682t symptoms of, 680, 682t vaccine, 681 tulips, purposely maintained viruses in, 339, 340f tumble, in chemotaxis, 66, 66f tumor(s) in HIV disease, 333, 710–711 human, viruses and, 333–334 viruses causing, 333–334 Epstein-Barr, 686, 711 in humans, 334t tumor-inducing plasmid, of Agrobacterium, 206, 206f, 217, 265 tumor necrosis factors, 353–354, 354t alpha, 353–354, 354t, 360 beta, 354t in septicemia, 679, 679f turbidity, in measurement of bacterial growth, 99t, 102–103, 103f twitching motility, 66 two-component regulatory system, 180, 180f, 200 Twort, F. W., 302 Tyndall, John, 2–3 type III secretion systems, 398, 398f, 399, 595 typhoid fever, 262, 271t, 456, 595, 601–602 typhoid fever vaccine, 434t, 712t Typhoid Mary, 602 typhus, 295t epidemic, 274 scrub, 274, 297 tyrosine, 27f synthesis of, 156–157, 157f

U ubiquinone in aerobic respiration, 144–145 in electron transport chain, 143–145 ubiquinone oxidase, 145, 145f

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I-38

INDEX

UHT (ultra-high-temperature) method, of pasteurization, 113 ulcer(s), caused by Helicobacter pylori, 5f, 9, 273, 589–591, 590f, 591t gastric, 273 ultracentrifuge, ribosomes in, 68 ultra-high-temperature (UHT) method, of pasteurization, 113 ultraviolet irradiation, 112t, 115f, 116 DNA damage from, repair of, 193, 194f, 195t, 310 in drinking water treatment, 745 mutagenic action of, 191t, 192 in sewage treatment, 742 Ulva, 284 uncoating, of viruses, 326, 329t, 486, 486f, 487t underground microbes, 732–733 undulant fever. See brucellosis unicellular sulfur oxidizers, 253t, 260 United Nations Children’s Fund, 693 United Nations Development Program, 693 Universal (Blood and Body Fluid) Precautions, 465 unsaturated fatty acids, 35, 35f upper digestive system infections bacterial, 586–591 viral, 592–594 upper respiratory infections bacterial, 499–506 structures commonly involved in, 496, 497f viral, 507–509 upstream transcription, 168 uracil, 33f, 34, 168 urease, 93, 273, 590 biochemical tests for, in identification of bacteria, 239, 239f, 240t ureters, 619, 619f urethra, 619, 619f, 620, 620f definition of, 619t infections, 621 normal microbiota of, 393f, 620 uridine, in biological research, 26 urinary system anatomy and physiology of, 619, 619f normal microbiota of, 620 urinary tract infections, 272, 398, 619, 621–624 nosocomial, 618 urticaria, 415–416 definition of, 415 uterine infections, nosocomial, 618. See also puerperal fever

V VacA, 590 vaccination, 4f, 366 vaccine(s), 7, 431, 434t. See also specific vaccines A-B toxins and, 405 adjuvants for, 435–436 advances in (future directions for), 437–438, 437t, 447 antigen presentation and, 383 attenuated, 433–435 definition of, 432t attenuated versus inactivated, 435t

nes95432_ind_I1-I40.indd I-38

booster, 435 conjugate, 383, 435, 650 definition of, 433 DNA-based, 437, 709 edible, 217, 437, 447 effective, characteristics of, 433 genetically engineered production of, 216 inactivated, 435–436 definition of, 432t inactivated whole agent, 435 memory cells and, 379 new or improved being sought, 437t, 438, 447 novel types of, 447 peptide, 437 polysaccharide, 379, 383, 435 protein subunit, 435 recombinant, 435 strategy for, polio campaign as example of, 436 therapeutic, definition of, 698t T-independent antigens and, 379, 383, 435 toxoid, 405, 435 for universal immunization, 447 VLP (virus-like particle), 435 vaccinia virus, 324t, 431, 710 vacuole, central, 70f vagina, 620, 620f normal microbiota of, 393f, 620 vaginitis, 288 candidal, in immunocompromised hosts, 410 vaginosis, bacterial, 625–626, 625f, 626t causative agent of, 625, 626t epidemiology of, 625, 626t incubation period of, 626t pathogenesis of, 625, 625f, 626t prevention and treatment of, 625, 626t symptoms of, 625, 626t valence, 21 valine, 27f valley fever. See coccidioidomycosis vancomycin, 474t, 477 resistance to, 477, 484–485 vancomycin-intermediate Staphylococcus aureus (VISA), 485 vancomycin-resistant enterococci (VRE), 484 vancomycin-resistant Staphylococcus aureus (VRSA), 485 van Leeuwenhoek, Anton, 1, 4f, 9, 40, 391 van Niel, Cornelis B., 232, 251 V antigen, 683, 684t variable region, of antibodies, 372, 372f varicella-zoster immune globulin (VZIG), 547 varicella-zoster virus. See also chickenpox infection, 487, 545–547 latent, 330, 330f, 331t, 395, 546, 546f of lower respiratory tract, 519 vaccine, 434t, 547, 712t variolation, 431 Varmus, Harold, 5f vascular system bacterial infections of, 677–680

protozoan diseases of, 690–694 viral diseases of, 686–690 vas deferens, 620, 620f vector(s), 216, 218–219, 455 for cloning, 218–220 of eukaryotic genes into prokaryotic cells, 218–220 ideal, properties of, 218–219, 219f lacZ′ gene in, 219–220, 220f selectable marker for, 219, 219f definition of, 213t of disease arthropods as, 295–297, 295t, 322–323, 455, 660 biological, 295, 455 mechanical, 295, 455 high-copy-number, cloning into, 216, 216f for plant viruses, 340 vegetables, pickled, 756t, 758 vegetative bacteria, 255, 264f vegetative cell, 69, 69f veins, 675f, 676 venereal diseases. See sexually transmitted disease ventricles cardiac, 675f, 676 cerebral, 648 Venturia inaequilis, 754f vertical gene transfer, 186 vertical transmission, 454 vesicle(s) in chickenpox, 546, 546f of eukaryotic cells, 71, 71f fusion of, 71, 71f gas, in aquatic bacteria, 55t, 68–69 viable cells counting, 99t, 101, 101f–102f fluorescent dyes for, 52 vibrio (shape), 52f, 53 Vibrio, 268–269 Vibrio cholerae Eltor variant of, 243 infection, 403, 595, 596–598, 596f, 598t. See also cholera water as source of, 738 medical importance of, 269, 271t new serotype of, 461 new strain of, 597 portal of exit for, 454 prophage and, 311t toxin of, 397, 404t, 407, 596, 597f Vibrio fischeri, 263t, 268 Vibrio parahaemolyticus, 269, 271t, 763t Vif, 700f, 701 villi, intestinal, 584 Vincent’s disease. See trench mouth vinegar, production, 758t, 760–761 vinegar generator, 761 viral infections. See also specific infections acute, 325–328, 325f carriers, 329 central nervous system, 659–666 chronic, 329–332, 330f, 332t interferons and, 357–358, 357f latent, 306, 306f, 329–332, 330f, 331t lower digestive system, 604–609

lower respiratory tract, 519–524 lymphoid and blood vascular, 686–690 pathogenesis of, mechanisms of, 408–410 persistent, 325, 329–332 sexually transmitted, 323, 324t, 638–642 skin, 545–554 slow, 329–332, 330f, 548 upper digestive system, 592–594 upper respiratory, 507–509 viremia, 395, 659, 675 definition of, 648t viridans streptococci, infection, heart valve (endocarditis), 677–678, 678t virion(s), 303, 304f, 305, 305f counting, with electron microscope, 338, 338f definition of, 303t viroid(s), 5f, 12–13, 13f, 342 characteristics of, 12, 13t size of, 12, 13f virulence, definition of, 496t virulence factors (determinants), 394, 397 definition of, 392t of Escherichia coli, 600 of Staphylococcus aureus, 536, 537t, 563 of Streptococcus pyogenes, 500–501, 500f, 500t of Yersinia pestis, 682–683, 684t virulent phages, 307, 313 virus(es), 5f, 12–13, 12f, 13f animal, 302–303, 321–343. See also animal viruses effects on cells they infect, 334f antibodies and, 410 antigenic drift, 335, 520, 520f antigenic shift, 335, 520, 520f apoptosis regulation by, 409 architecture of, 303–304, 304f, 321–322, 322f assays, titer or endpoint of, 338, 338f avoiding antiviral effects of interferons, 409 avoiding immune response, 409–410 bacterial, 302–319. See also phage(s) key terms for, 303t binding to host cells, 408–409 bioterrorism potential of, 466 budding of, 328, 329f characteristics of, 12, 13t, 303–306 comparison with cells, 306t complex, 303, 304f control/destruction of chemicals for, 116–121, 118t heat for, 112–114, 112t cultures, 336–337, 337f cytopathic effects of, 328, 337, 337f defense against. See immunity drugs against. See antiviral drugs effects on cells they infect, 334f endocytosis for entry of, 326, 326f–327f endocytosis of, 74, 79 enteric, 322, 324t entry of, 326, 326f, 327f, 329t

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Index enveloped, 110, 117, 303, 305f, 321, 326, 326f exocytosis for release of, 328 filterable, 302 genetic reassortment of, 335, 335f genome of, 304, 322, 326–328 head of, 303 helical, 303, 304f hemagglutination of, 337, 338f host range of, 314–316, 335 hosts for, 302–303 icosahedral symmetry of, 303 infection by. See viral infections interactions with host cells, 306–313, 306f invasion by, 408–409 isometric, 303, 304f, 321, 322f key terms for, 321t microbe mimicking by, 305 mutations of, 410 naked, 110, 117, 303, 305f, 321, 326 plant, 302–303, 321, 339–340. See also plant viruses plaque assay of, 337–338, 338f pleomorphic, 321 quantal assays of, 337–338 quantitation of, 337–338 regulation of host cell death by, 409 release from cells, 328 replication, 304–305, 329t replication site of, targeting to, 326, 329t respiratory, 322, 324t segmented, 321 definition of, 321t genome exchange in, 335, 335f shapes of, 303, 304f, 321, 322f sheath of, 303 shedding of, 328 size of, 14, 14f, 304, 305f structure of, 321–322, 322f study of, methods for, 336–338 systemic, 322 tail of, 303 testing water for, 750 transcription of, 307f, 308, 326–328, 327f transmission of, 328 fecal-oral route for, 322, 324t groupings based on, 324t tumor, 333–334 in AIDS, 333, 711 Epstein-Barr, 686, 711 in humans, 334t uncoating of, 326, 329t antiviral drugs and, 486, 486f, 487t unusual, 305 zoonotic, 322, 324t virus particle, 305 VISA. See vancomycin-intermediate Staphylococcus aureus vital force, in spontaneous generation theory, 2 vitamin(s) coenzymes synthesized from, 136, 136t in food, assessment of, fastidious bacteria in, 94 synthesis of, by intestinal bacteria, 586 vitamin A, 217 vitamin K, bacterial synthesis of, 145

nes95432_ind_I1-I40.indd I-39

VitekTM, 240 VLP (virus-like particle) vaccine, 435 Voges-Proskauer test, 148, 240t volutin granules, 68, 270 Volvox, 282f dark-field microscopy of, 43f von Behring, Emil, 366, 559, 674 von Liebig, Justus, 126 Vpr, 700f, 701 Vpu, 700f, 701 VRE. See vancomycin-resistant enterococci vulva, 620, 620f vulvovaginal candidiasis, 350, 625–626, 626f, 626t causative agent of, 626, 626f, 626t epidemiology of, 626, 626t incubation period of, 626t pathogenesis of, 626, 626t prevention and treatment of, 626, 626t symptoms of, 625–626, 626t vulvovaginitis, candidal, 350

W Waksman, Selman, 470 wars, and disease, 462 warts (papillomas), 552–553, 553f genital, 639–640, 641t waste treatment, 738–752 key terms for, 739t wastewater, 739 definition of, 739t treatment of, 86, 731. See also sewage treatment wasting disease, chronic, 340t, 342, 669, 669f water availability of in food, 122, 755 and microbial growth, 90t, 93, 755 reduction in, and preservation, 122, 765 biological importance of, 23–24 bonding properties of, 23–24, 23f diffusion, in prokaryotic cells, 56 drinking chlorination of, 119, 745 contamination of. See also waterborne disease; water pollution federal standards for, 744–745 fluoridation of, 587 ozone for disinfection of, 120, 745 sources of, 744 testing of, 262, 746, 747f, 750 treatment of, 738, 745–746, 746f as electron source, for photosynthesis, 153–154 forms of, 23–24, 23f molecule, 23 polar covalent bonds in, 22, 22f polar nature of, 23–24 potable, 738 receiving, in sewage treatment, 739 surface, 744 as universal solvent of life, 24 water activity, in food, 755 waterborne disease, 455, 738. See also specific causative agents and diseases

water molds, 294–295 classification of, 288 water pollution, 738 sewage treatment and, 738–744 watershed, 744 water treatment facilities, industry, microbial control in, 110 Watson, James, 5f, 199 Weekly Epidemiological Record, 460 weight, of culture dry, 103 total, 99t, 103 wet, 103 Western blot, 446, 446f definition of, 432t Western equine encephalitis, 323, 660–661 West Nile fever, 7, 295, 323, 324t, 660, 660f wetlands, artificial, in sewage treatment, 741, 742f wet mount, 50, 237, 237f wet weight, 103 wheat mosaic virus, symptoms of, 339f wheat rust, 293 whey, 757 Whipple’s disease, 243, 678 whipworm disease, 298t white blood cells. See leukocyte(s) Whittaker, R. H., 234 WHO. See World Health Organization whooping cough. See pertussis wild-type organisms, 187 Wilkins, Maurice, 5f wine commercial production of, 758–759, 759f fermentation of, 754, 758–759, 758t, 759f pasteurization of, 112 spoilage of, 762 Winogradsky, Sergei, 721 Wiscott-Aldrich syndrome, 427t Woese, Carl, 5f, 232, 234 Wöhler, Friedrich, 126 Wolbachia, 274 Wolbachia pipientis, 274 World Bank, 693 World Health Organization (WHO), 431, 447, 460, 568, 691, 693 worldwide disease surveillance, 460 wort, 759, 760f wound(s) abscesses, 560, 561f anaerobic, 561 anatomy and physiology of, 560–561, 561f burn, 560 classification of, 560 contused, 560 incised, 560 lacerated, 560 management of, tetanus prevention in, 568t punctured, 560 wound botulism, 657–658 wound infections, 559–580 bacterial anaerobic, diseases due to, 566–571 bite, 572–576 common, 562–565

I-39

fungal, 576–577 group A streptococcal (flesheating), 563, 563f, 565t leading causes of, 565t Pseudomonas aeruginosa, 564–565, 565t epidemiology of, 565 pathogenesis of, 565 prevention and treatment of, 565 symptoms of, 564–565, 564f staphylococcal, 399, 562–563, 565t causative agents of, 562, 562f epidemiology of, 563 pathogenesis of, 562–563 prevention and treatment of, 563 symptoms of, 562 Wuchereria bancrofti, 298t

X xanthophylls, 283t XDR-TB. See tuberculosis, extensively drug-resistant (XDR-TB) xenobiotics, 749 xenografts, 423 Xenopsylla cheopis, 295t x-gal, 220 X-linked agammaglobulinemia, 427t X-linked hyper-IgM syndrome, 427t X-rays, mutagenic action of, 191t, 192

Y yeast(s), 11, 14f, 289–290, 290f alcoholic fermentation by, in food production, 758–761, 758t in baking, 6, 761. See also Saccharomyces cerevisiae bottom, 760 brewer’s, 760, 760f budding in, 289, 290f definition of, 281t disease/infection caused by, 410 economic importance of, 293–294 as food source, 766 genetically engineered, 293–294 in normal microbiota, of skin, 533t, 534–535 nucleus of, 76f in skin infections, 534–535, 534f structure of, 289, 290f in sugar breakdown, 126 top-fermenting, 760 vaginal, wet mount of, 237, 237f yellow fever, 323, 323t, 686, 688–690, 690t causative agent of, 689, 690t epidemiology of, 689, 689f, 690, 690t hepatitis in, 608 incubation period of, 690t mosquitoes as vectors for, 295t, 688–690, 690t pathogenesis of, 689, 690t prevention and treatment of, 690, 690t Reed, Walter and, 690 symptoms of, 689, 690t vaccine, 434t, 435, 689–690, 690t, 712t

9/16/08 10:28:00 AM

I-40

INDEX

Yersin, Alexandre Emile John, 366, 674 Yersinia, characteristics of, 253t Yersinia pestis bioterrorism potential of, 466 discovery of, 674 fleas as vector for, 295t, 296, 455, 674, 682–685, 684f, 685t infection, 397, 399, 682–685, 685t. See also plague medical importance of, 262, 271t reservoirs for, 453

nes95432_ind_I1-I40.indd I-40

virulence factors of, 682–683, 684t yogurt production, 255, 255f, 755, 756–757, 756t Yops (Yersinia outer-membrane proteins), 683, 684t

Z zanamivir, 487t, 488, 521 zidovudine (AZT), 487, 487t, 707–708, 708f

zinc, 94 as enzyme cofactor, 136 Zinsser, Hans, 495 zone of inhibition, 481f, 482 zone of optimal proportion, for precipitation reactions, 441, 441f zoonoses, 322, 324t, 453. See also specific zoonoses definition of, 321t zoonotic viruses, 322 zooplankton, 282, 286–287

zoospores, 294 zoster immune globulin, 547 Zygomycetes, 288–289, 289t zygote, 691 of algae, 284 definition of, 675t Zymomonas, 148 Zymomonas mobilis, 760 Zyvox. See linezolid

9/2/08 5:33:53 PM