Microbiology. A systems approach

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THIRD EDITION

Marjorie Kelly Cowan Miami University

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MICROBIOLOGY: A SYSTEMS APPROACH, THIRD EDITION Published by McGraw-Hill, a business unit of The McGraw-Hill Companies, Inc., 1221 Avenue of the Americas, New York, NY 10020. Copyright © 2012 by The McGraw-Hill Companies, Inc. All rights reserved. Previous editions © 2009 and 2006. 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 acid-free paper. 1 2 3 4 5 6 7 8 9 0 QDB/QDB 1 0 9 8 7 6 5 4 3 2 1 ISBN 978–0–07–352252–4 MHID 0–07–352252–X Vice President, Editor-in-Chief: Marty Lange Vice President, EDP: Kimberly Meriwether David Senior Director of Development: Kristine Tibbetts Sponsoring Editor: Lynn M. Breithaupt Senior Developmental Editor: Kathleen R. Loewenberg Marketing Manager: Amy L. Reed Lead Project Manager: Sheila M. Frank Senior Buyer: Laura Fuller Senior Media Project Manager: Jodi K. Banowetz Senior Designer: Laurie B. Janssen Cover Image: Dr. Volker Brinkmann/Visuals Unlimited, Inc. Senior Photo Research Coordinator: John C. Leland Photo Research: Emily Tietz/Editorial Image, LLC Compositor: Electronic Publishing Services Inc., NYC Typeface: 10/12 Palatino LT Std Printer: Quad/Graphics All credits appearing on page or at the end of the book are considered to be an extension of the copyright page. Library of Congress Cataloging-in-Publication Data Cowan, M. Kelly. Microbiology : a systems approach / Marjorie Kelly Cowan. — 3rd ed. p. cm. Includes index. ISBN 978–0–07–352252–4 — ISBN 0–07–352252–X (hard copy : alk. paper) 1. Microbiology. I. Title. QR41.2.C69 2012 616.9’041 — dc22 2010037851

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Brief Contents

CHAPTER

1

CHAPTER

The Main Themes of Microbiology CHAPTER

CHAPTER

Host Defenses I: Overview and Nonspecific Defenses 397

1

2

The Chemistry of Biology

CHAPTER

27

3

CHAPTER

4

CHAPTER

CHAPTER

CHAPTER

168

8

CHAPTER

CHAPTER

CHAPTER

268

11 12 13

Microbe-Human Interactions: Infection and Disease 362

512

19 20 21

Infectious Diseases Affecting the Respiratory System 622

10

Drugs, Microbes, Host—The Elements of Chemotherapy 327

CHAPTER

CHAPTER

232

Physical and Chemical Control of Microbes

18

Infectious Diseases Affecting the Cardiovascular and Lymphatic Systems 584

9

Genetic Engineering and Recombinant DNA CHAPTER

490

Infectious Diseases Affecting the Nervous System 550

7

Microbial Genetics

17

Diagnosing Infections

CHAPTER

Microbial Metabolism: The Chemical Crossroads of Life 198 CHAPTER

459

Infectious Diseases Affecting the Skin and Eyes

139

Microbial Nutrition, Ecology, and Growth

CHAPTER

CHAPTER

108

6

An Introduction to the Viruses CHAPTER

80

5

Eukaryotic Cells and Microorganisms

16

Disorders in Immunity

Prokaryotic Profiles: The Bacteria and Archaea CHAPTER

15

Host Defenses II: Specific Immunity and Immunization 424

Tools of the Laboratory: The Methods for Studying Microorganisms 55 CHAPTER

14

297

22

Infectious Diseases Affecting the Gastrointestinal Tract 660 CHAPTER

23

Infectious Diseases Affecting the Genitourinary System 708 CHAPTER

24

Environmental Microbiology CHAPTER

741

25

Applied Microbiology and Food and Water Safety 762

iii

About the Authors Kelly Cowan has been a microbiologist at Miami University since 1993. She received her Ph.D. at the University of Louisville, and later worked at the University of Maryland Center of Marine Biotechnology and the University of Groningen in The Netherlands. Kelly has published (with her students) twenty-four research articles stemming from her work on bacterial adhesion mechanisms and plant-derived antimicrobial compounds. But her first love is teaching—both doing it and studying how to do it better. She is chair of the Undergraduate Education Committee of the American Society for Microbiology (ASM). When she is not teaching or writing, Kelly hikes, reads, takes scuba lessons, and still tries to (s)mother her three grown kids.

The addition of a proven educator as a digital author makes a proven learning system even better. Writing a textbook takes an enormous amount of time and effort. No textbook author has the time to write a great textbook and also write an entire book’s worth of accompanying digital learning tools—at least not with any amount of success or accuracy. In the past this material has often been built after the text publishes, but hopefully in time for classes to start! With the new digital era upon us, it is time to begin thinking of digital tools differently. In classrooms across the country thousands of students who are visual learners and have been using computers, video games, smartphones, music players, and a variety of other gadgets since they could talk are begging for an interactive way to learn their course material. Enter the digital author. With this third edition, we are so excited to add professor Jennifer Herzog from Herkimer County Community College to the team. Jen has worked hand-in-hand with the textbook author, creating online tools that truly complement and enhance the book’s content. She ensured that all key topics in the book have interactive, engaging activities spanning levels of Bloom’s taxonomy, and tied to Learning Outcomes in the book. Instructors can now assign material based on what they cover in class, assess their students on the Learning Outcomes, and run reports indicating individual and/or class performance on a variety of data. Because of Jen, we can now offer you a robust digital learning program, tied to Learning Outcomes, to enhance your lecture and lab, whether you run a traditional, hybrid, or fully online course.

iv

Preface

tand g to unders n ti a in c s a f find it ing is Students: ink you will th I teresting th ! in ld r e o h T w l t. n ia e b onm the micro ith our envir gy. For one w lo d io n b Welcome to a o r , s ic u m h it ith ur es interact w experience w f o t lo much of yo a d d how microb n a a h , y w d o a n e right you has alr nd while you h microbes A it . w s e d b te o that each of r la ic u p er m ly po uses and oth re thorough ir a v u the form of o m y o in r , f g , s e in e b m th o a r c ic y ll m a ew material actu ith quite a f w s e c n ie r e own genetic p em as well. e bad ex th m o y s b d d a te h fi e ly n be rerequisite p y tl y a n e a r g e ir have probab n u e q re ly be e and doesn’t have certain ts u n e o d y , tu e health car s s e th s f a o g e in s r d dis te in n k e ll d in y suited for a are intereste u o y in the biolog f I d This book is n . u y o tr r g is k m c e a ch gb f biology or you a stron e iv g l ils. Don’t il ta w e k d knowledge o o y o r b a s is s e th c unne some way, portant for g you with in im lm is e h ic p w profession in r to e v this ut o A grasp of nisms, witho . a s g n r io o s o s r e f ic o m r of alth p ot in the he n e ’r u o y if ten thought this book. f o h it s worry a w w d th e y r in a tt centu nd can be a y. The 20 g lo io B ies and the f r o o everyone—a e e g th A m e tu th n qua n called sign of the elopment of v le e ib d This has bee is e v t th s o h it s, w the m es oject is just ge of Physic r A P e e ding of gen th m n o s n a ta e s f r G e o d n n a u m d Hu ente is lativity. The an unpreced e v a h e rganisms. Th o w o theory of re r y r ic tu m n f e c o wer ical ; in the 21st auty and po e b e th t new biolog e r r Biology Age o p f r t te c e in p s d e n out a nd a new r d to read ab e e n l and DNA, a ’l u o y ols e you the to iv g n a c k o o b elly Cowan . K d a — e h a s r a e the y discoveries in

I dedicate this book to all public health workers who devote their lives to bringing the advances and medicines enjoyed by the industrialized world to all humans.

v

Connecting Instructors to Students McGraw-Hill Higher Education and Blackboard® have teamed up! What does this mean for you? Your life, simplified. Now you and your students can access McGraw-Hill Connect™ and Create™ right from within your Blackboard course—all with one single sign on! Say goodbye to the days of logging in to multiple applications.

Deep integration of content and tools. Not only do you get single sign on with Connect and Create, you also get deep integration of McGraw-Hill content and content engines right in Blackboard. Whether you’re choosing a book for your course or building Connect assignments, all the tools you need are right where you want them—inside of Blackboard. Seamless gradebooks. Are you tired of keeping multiple gradebooks and manually synchronizing grades into Blackboard? We thought so. When a student completes an integrated Connect assignment, the grade for that assignment automatically (and instantly) feeds your Blackboard grade center.

A solution for everyone. Whether your institution is already using Blackboard or you just want to try Blackboard on your own, we have a solution for you. McGraw-Hill and Blackboard can now offer you easy access to industry leading technology and content, whether your campus hosts it, or we do. Be sure to ask your local McGraw-Hill representative for details.

Author Kelly Cowan is now on Twitter! She shares interesting facts, breaking news in microbiology, teaching hints and tips, and more. If you have a Twitter account, follow her: @CowanMicro. To set up a Twitter account, go to twitter.com.

vi

and Students to Course Concepts Introducing McGraw-Hill ConnectPlus™ Microbiology McGraw-Hill ConnectPlus™ Microbiology integrated learning platform provides auto-graded assessments; a customizable, assignable eBook; an adaptive diagnostic tool; and powerful reporting against Learning Outcomes and level of difficulty—all in an easy-to-use interface. Connect Microbiology is specific to your book and can be completely customized to your course and specific Learning Outcomes, so you help your students connect to just the material they need to know.

Save time with auto-graded assessments and tutorials. Fully editable, customizable, auto-graded interactive assignments using high-quality art from the textbook, animations, and videos from a variety of sources take you way beyond multiple choice. Assignable content is available for every Learning Outcome in the book. Extremely high-quality content, created by digital author Jennifer Herzog, includes case study modules, concept mapping activities, animated learning modules, and more!

“. . . I and my adjuncts have reduced the time we spend on grading by 90 percent and student test scores have risen, on average, 10 points since we began using Connect!” —William Hoover, Bunker Hill Community College

Gather assessment information Generate powerful data related to student performance against Learning Outcomes, specific topics, level of difficulty, and more.

vii

INSTRUCTORS Connect via Customization Presentation Tools allow you to customize your lectures. Enhanced Lecture Presentations contain lecture outlines, Flex Art, art, photos, tables, and animations embedded where appropriate. Fully customizable, but complete and ready to use, these presentations will enable you to spend less time preparing for lecture! Flex Art Fully editable (labels and leaders) line art from the text, with key figures that can be manipulated. Take the images apart and put them back together again during lecture so students can understand one step at a time. Animations Over 100 animations bringing key concepts to life, available for instructors and students. Animation PPTs Animations are truly embedded in PowerPoint® for ultimate ease of use! Just copy and paste into your custom slideshow and you’re done!

Take your course online—easily— with one-click Digital Lecture Capture. McGraw-Hill Tegrity Campus™ records and distributes your lectures with just a click of a button. Students can view them anytime/anywhere via computer, iPod, or mobile device. Tegrity Campus indexes as it records your slideshow presentations, and anything shown on your computer, so students can use keywords to find exactly what they want to study.

viii

STUDENTS Connect 24/7 with Personalized Learning Plans Access content anywhere, any time, with a customizable, interactive eBook. McGraw-Hill ConnectPlus eBook takes digital texts beyond a simple PDF. With the same content as the printed book, but optimized for the screen, ConnectPlus has embedded media, including animations and videos, which bring concepts to life and provide “just in time” learning for students. Additionally, fully integrated, self-study questions and in-line assessments allow students to interact with the questions in the text and determine if they’re gaining mastery of the content. These questions can also be assigned by the instructor.

“Use of technology, especially LEARNSMART, assisted greatly in keeping on track and keeping up with the material.” —student, Triton College

McGraw-Hill LearnSmart™ A Diagnostic, Adaptive Learning System McGraw-Hill LearnSmart is an adaptive diagnostic tool, powered by Connect Microbiology, which is based on artificial intelligence and constantly assesses a student’s knowledge of the course material. Sophisticated diagnostics adapt to each student’s individual knowledge base in order to match and improve what they know. Students actively learn the required concepts more easily and efficiently.

“I love LearnSmart. Without it, I would not be doing as well.”

Self-study resources are also available at www.mhhe.com/cowan3.

—student, Triton College

ix

Making Connections Connecting Students to Their Future Careers Many students taking this course will be entering the health care field in some way, and it is absolutely critical that they have a good background in the biology of microorganisms. Author Kelly Cowan has made it her goal to help all students make the connections between microbiology and the world they see around them. She does this through the features that this textbook has become known for: its engaging writing style, instructional art program, and focus on active learning. The “building blocks” approach establishes the big picture first and then gradually layers concepts onto this foundation. This logical structure helps students build knowledge and connect important concepts.

“Diagnosing Infections” Chapter Chapter 17 brings together in one place the current methods used to diagnose infectious diseases. The chapter starts with collecting samples from the patient and details the biochemical, serological, and molecular methods used to identify causative microbes. Diagnosing Infections 17 Case File Hepatitis C is a chronic liver infection that can be either silent (with no noticeable symptoms) or debilitating. Either way, 80% of infected persons experience continuing liver destruction. Chronic hepatitis C infection is the leading cause of liver transplants in the United States. The virus that causes it is bloodborne, and therefore patients who undergo frequent procedures involving transfer of blood are particularly susceptible to infection. Kidney dialysis patients belong to this group. In 2008, a for-profit hemodialysis facility in New York was shut down after nine of its patients were confirmed as having become infected with hepatitis C while undergoing hemodialysis treatments there between 2001 and 2008. When the investigation was conducted in 2008, investigators found that 20 of the facility’s 162 patients had been documented with hepatitis C infection at the time they began their association with the clinic. All the current patients were then offered hepatitis C testing, to determine how many had acquired hepatitis C during the time they were receiving treatment at the clinic. They were considered positive if enzyme-linked immunosorbent assay (ELISA) tests showed the presence of antibodies to the hepatitis C virus. ◾ Health officials did not test the workers at the hemodialysis facility for hepatitis C because they did not view them as likely sources of the nine new infections. Why not? ◾ Why do you think patients were tested for antibody to the virus instead of for the presence of the virus itself?

Unequaled Level of Organization in the Infectious Disease Material Microbiology: A Systems Approach takes a unique approach to diseases by consistently covering multiple causative agents of a particular disease in the same section and summarizing this information in tables. The causative agents are categorized in a logical manner based on the presenting symptoms in the patient. Through this approach, students study how diseases affect patients—the way future health care professionals will encounter them in their jobs. A summary table follows the textual discussion of each disease and summarizes the characteristics of agents that can cause that disease. This approach is refreshingly logical, systematic, and intuitive, as it encourages clinical and critical thinking in students—the type of thinking they will be using if their eventual careers are in health care. Students learn to examine multiple possibilities for a given condition and grow accustomed to looking for commonalities and differences among the various organisms that cause a given condition. x

Continuing the Case appears on page 504.

Outline and Learning Outcomes 17.1 Preparation for the Survey of Microbial Diseases 1. Name the three major categories of microbe identification techniques. 17.2 On the Track of the Infectious Agent: Specimen Collection 2. Identify some important considerations about collecting samples from patients for microbial identification. 3. Explain the ideas behind presumptive versus confirmatory data.

490

CHAPTER

21

Infectious Diseases Affecting the Respiratory System 622

21.1 The Respiratory Tract and Its Defenses 623 21.2 Normal Biota of the Respiratory Tract 624 21.3 Upper Respiratory Tract Diseases Cause by Microorganisms 624 Sinusitis 626 y y Infection) 627 y Acute OtitisggMedia (Ear bination of surgical removal of the fungus and intravenous pathogenesis of this condition is brought about by the conPharyngitis 628 antifungal al therapy (Disease Table 21.2). fluence of several factors: predisposition to infection because Diphtheria 632 21.4 Diseases Caused by Microorganisms Affecting Disease Table 21.2 Sinusitis Both the Upper and Lower Respiratory Tract 633 Respiratory Syncytial Virus Infection 635 Influenza 635 Various bacteria, often mixed infection Various fungi Causative Organism(s) Whooping Cough 633 Introduction by trauma or opportunistic Endogenous (opportunism) Most Common Modes 21.5 Lower Respiratory Tract Diseases overgrowth of Transmission Caused by Microorganisms 640 – – Virulence Factors Tuberculosis 640 Culture not usually performed; diagnosis based on Same Culture/Diagnosis Pneumonia 645 ing clinical presentation, occasionally X rays or other imaging technique used Prevention

–

–

Treatment

Broad-spectrum antibiotics

Physical removal of fungus; in severe cases antifungals used

Distinctive Features

Much more common than fungal

Suspect in immunocompromised patients

Chapter Opening Case Files! Each chapter opens with a Case File, which helps the students understand how microbiology impacts their lives and grasp the relevance of the material they’re about to learn. The questions that directly follow the Case File challenge students to begin to think critically about what they are about to read, expecting that they’ll be able to answer them once they’ve worked through the chapter. A new Continuing the Case feature now appears within the chapter to help students follow the real-world application of the case. The Case File Wrap-Up summarizes the case at the end of the chapter, pulling together the applicable content and the chapter’s topics. Nearly all case files are new in the third edition, including hot microbiological topics that are making news headlines today.

34

Chapter 2

The Chemistry of Biologyy

Other effects of bonding result in differences ferences in polarfe vity 2 form covav ity. When atoms of different electronegativity lent bonds, the electrons are not shared equally eq and may be pulled more toward one atom than another. nother. This pull n causes one end of a molecule to assume a partial negative charge and the other end to assume a partial p positive charge. A molecule with such an asymmetrical ccal distribution of charges is termed polar and has positivee and negative poles. Observe the water molecule shown in n figure gu ure 2.6 and note that, because the oxygen atom is largerr and d has more protons than the hydrogen atoms, it will tend nd to n t draw the shared electrons with greater force toward d its itts nucleus. This unequal force causes the oxygen part off the th he molecule to express a negative charge (due to the electrons eecttrons being attracted there) and the hydrogens to express sss a positive charge (due to the protons). The polar nature off w water plays an extensive role in a number of biological reactions, cctiions, which la enterica ella ne nel arecasdiscussed Polarity is a significant property p of es of Salmolater. llos 13 is ed not one C) m salm ms ofmolecules manypto large in living systems and greatly rreatly infl influflue Control (CD typical sym re than ers for Diseas mo more entters Cen any ofreactivity the C ing their ber 2008. The ences both of their structure. casesand scientists at lt from ingest during Novem

y y of Biolog try tr The Chemis C a se

File 2

ess off 27 tate may resu break o A group of people in a dozen sstat diarrhea, and a similar out m seen in the weeks later, omiting and vvom anism ction in sick

infe include erica. Two of the org died, salmonella) ciess,, of S. ent same strain ecie spe ubsp sub cted, nine had sed by the (infection with unique su become infe nd to be cau nt strains, or Canada had es was fou un. 1,500 differe 14 states, begAbout states and A Note Diatomic Elements oss had 46 acr ns from atio ead ple , spr fullllyy studying 82 peo 68 inal investig 9, 682 by carefu the disease crim l 200 ters ry era clus rua sev s, ase files, y, and e dise ak. By Feb ptccy, A profile upt kru ankr ba y food-born first outbre aining DN d for ban You will that hydrogen, oxygen, nitrogen, chlorine, hlorine, and h obtnotice ks to identif ation had file this means st ins of stra DC that see latedshown a large corpor the CD break. Usually s (iso iodine are often in notation with a 2 subscript—H rript—H2 orr a branch of were pare isolate rce of an out e sou com cas s to the this e PulseNet is in be tion Obre elements are diatomic iing that in ak strains 2. These ts (two atoms), meaning that informa s thought to g ntis ate out usin scie isol two C al and m um se—CDstate, they exist in pairs, ratherr than as a the bacteri pure elemental rints from the databa h bacteriu seNet Pultheir rints, of eac e the fingerp use aus Beca aks. Bec rint within the single atom. The reason for this phenomenon has to called fingerp bre erp o do with out fing nt any differe nnesota and erent from Min in diff difffere ter bacteria) from also but their valences. The electrons in the outer shell are configured ffigured so but another— g Nut peanut n.. ion e,, King Nut e atio stiigat similar to one tainers of Kin al investig aspat toien complete full outer shell th hey bind. ts. At thea tim soldfor both atoms when they 5-pound con demiologic the and epi ed ned a, i ia, from an pen d d ope org n uno un ate , Gefor yourself in figures 2.3 and 2.5. Most initiate kelythis You can see ost of the o in Bla bacteria isol identified in . A) in rs. ers was (PC me a and a sum , nsu eric o eric con co fa ory S. ent ectly toare dire ation of Am diatomicnelements gases.linked to nut butter fact nut Corpor e s rather tha t, in the pea d byy the Pea of them wer e institution Connecticu w ure few larg act a er y nuf oth onl and ins, but ter was ma ca terias, peanut but enterica stra aurants, cafe different S. hospitals, rest ed several to schools, teria reveal d n of the bac 2. Electronegativity—the ability to ld attract electrons. be use Examinatio e profiles cou s. think these the illnesse how do you DNA? erprinting, als make up of DNA fing ? ak? eak ails ◾ What chemic bre br det out cific t of an wing the spe in is nott par ◾ Without kno bacterial stra 34. (–) on page 34. t a particular e appearss to show tha ng the Cass (–) ing in Continu

27

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Figure 2.6 Polar molecule. (a) A simple model andd (b) a three-dimensional model of a water molecule indicate the polarity, or unequal distribution, of electrical charge, which is caused by the pull ecule. of the shared electrons toward the oxygen side of the molecule.

“The organization is well planned so that the topics are presented logically, allowing the student to understand basic information before more advanced material is introduced.”

When covalent bonds are formed between atoms that have the same or similar electronegativity, the electrons are shared equally between the two atoms. Because of this balanced distribution, no part of the molecule has a greater attraction for the electrons. This sort of electrically neutral molecule is termed nonpolar.

Ionic Bonds: Electron Transfer Among Atoms 52 electrons In reactions that form ionic bonds, are Chapte r 2transferred The Chemis try of Biolog completely from one atom to another and are not shared. gyy g These reactions invariably occurhyd between with valences rogen,atoms oxygen , nithas rogen, it followthat that complement each other, meaning one atom an and many s the basic oth her err atoms, and law s of muchelectrons unfilled shell that will readily is accept and the other che mistry and more. The nd ph n phys combinatio Case File 2 ysiics cs,, but it racreadily atom has an unfilled shell thatcha will electrons. A n of the teristics,lose see ato Wrap-U reactions, om ms produces Up p desthat and produ criboccurs striking example is the reaction between sodium In this case, ed as livi cts tha ng. t t ccan onl S. enterica (Na) and chlorine (Cl). Elemental sodium is a soft, lustrous y be Typhimurium identified as was the outbreak metal so reactive that it can burn fl esh, and molecular chlorine strain and fou nd in peanut Fundamen was pro tal duc Ch ts is a very poisonous yellow gas. But when the twoara arecte commanufactured the PCA plan ristics of C in t as well as The bod 3 Ce ies of ellls in ill person bined, they form sodium chloride (NaCl)—the familiar nonlss even in a tan s—and ker truck tha consist of onl living things such as thatt had bee toxic table salt—a compound with properties bacterrria to tran y quite different tra sport pea ia and n used a d protoz p nut pas plants contain a single cell, whereas oa te. from either parent element (figure 2.7). C Com tho tha tril se t plic e oth lions of cel li atin er companies i g matters an nim maals all cells hav ls and ls. Regardles of ani had used the was th How does this transformation occur? has 11 electhe e Sodium h ffactt a food items; s of o the peanut paste th he organism at last count, spherical, pol few common character t manufffact to , the paste had trons (2 in shell one, 8 in shell two, and only in, shell three), istics. Th a ure actu ygo1nal peanut-conta re T ey tend cubica been traced ining produc plasm (inter l, has to be or cylindrica to over 3,00 ts, including so it is 7 short of having a complete outer Chlorine nalshell. and dog bisc cell con l, and 0 a the th tents) is enc pea heiirr protouits mic memb nut but . Two other b ter cr ranand crac 17 electrons (2 in shell one, 8 in shell two, 7einIns shell three), ased in a cel rrack a ker Senftenberg, S. enterica e (se erss c l or o cytoplasstrains, Mb ight 2.3). Th were discove con M andaka ing shell. red ak ey DNAThese making it 1 short of a completetain outer two atoms ka k PCA in hav and crac and riboso processing e chrrom ks in the con om mo they are exc oso plant, and a som me cr cret meess s for protein e floo are very reactive with one another, because atom eedingalysodium r thir of the peanut butter d variant, Ten ssyntthe complex in th hessis, few in the factory. nesse is, and see e , was fou ee, function. As ilaritieand fo oun o Comparison will readily donate its single sim electron a st chlorine strains with nd s, mo d in ide i fro cell typatom of DNA from DNA from stra f om mentally dif m these es fall into frrom these ins isolated will avidly receive it. (The reaction is slightly more involved e three ferent line that none of one o of thr from ill individ s (di hreeee fundathe strains wer seemingly scussed in ivvidu v uals als reve revvvea simwith e linked to any than a single sodium atom’s combining a single chloride cha ple bac aled led pte On r January 28, 1): the terial and arc illness. th he small, structurally 2009, PCA ann mo atom (Insight 2.2), but this complexity does notpli detract fromhaeal cells and pea re com nuts and pea ounced a volu an nd the t e larger, cated nut-containin Eukaryotic n ry reca nta alllll of all a g products facility since cells are fou eukaryotic cells. processed January 1, 200 protists. Th nd in anima ed in its G 7. Records ind Geo ey contain e rgia knowingly ship ls, plants tts,, fu icated the a number fun fun called ped peanut ngi gi,, and e compan aneoflles butter contain 3. In general, neral, when a salt is formed, theorg ending the name of the th negativelyof complex nyy had n times in the tha int t nte n ing per ern pre rrn naal parts Salmone involving gro form useful vious 2 years, onelllla ch charged ion is changed to -ide. a at leas le eas e and functionss fo sam wth, nutriti t 12 a e crim mo inal inquiry was nth. PCA filed for orr the on, organelles are t cell w begu for bankrup un defined as cel or metabolism. By con that tcy on Februa nven nve functions and l component enttion ryy 13. ion, s that perfo are enclosed for orm m and par sp spe pec by titi gen cifi ific me on fic erally no oth mbranes. Org the Case C ase File 2 Continuing Continui Cont inuing inui ng geuk tthe he C Case ase ase aryCa otic er e organelles aanelles cell into sm iity is misle most visible ll also . This appare aller compar elle adi organelle is tment nt simplicDNA is a long moleculema made up of repeatthe nucleus, prokaryotes ng, however, becaus e s. s The ss sur rounded by e the fine a roughly bal is complex. structure of a double me b l-sh The ing units called nucleotides. engage in DNA l aped Ov of identity the cell.and mb nea ran rly every act erall, prokaryotic cel e that con Other organe onttain o nucleotides order in which the four end and many a ain ls can ivit lles oplasm(adenine, s y the inc tha lud t eukaryoti ic reticulum can functio e the Golgi c cells can , vacuoles, n occur are the guanine, thymine, and cytosine) a par app Chapters aratus, Bacter , and mitoch 4 and 5 del in ways that eukary ial and arc ondria. otes ve deeply iaa. by a haeal cells ma basis for the genetic information prokaryotic lar “have held into the pro cannot. nots” becaus y seem to and eukary be otic cells. perties of off for this particular stretch off DNA. h informaf the t celluareThe deseventual the cribed expression e, sak e of compar e ce 2.3 Learning atcal of wh physical features that tion by the cell results in the productionby physic c the feature es k. e isson iso n, the y lac t y They have Outcomes— no o nu can be used to distinguish one cell from another.. Also, because be ecause e Can You . . ucl cleus . 11. . DNA is used to transfer genetic information from one o generation gene eration e original to the next, all cells descended from a single origina a cell have havve simiChap teral Summ strains that lar or identical DNA sequences, while the DNA from frrom r strain nsary n that are not closely related is2 less alike. The DNA differences differrences re tha at exist a 2.1 1 At Ato ms, B Bond ds, and dled M Mo have to S. enterica between the various types of d en nterica n l lec ule l BloSalmonella s: F cks Fund damenttall B Buiildi on being subdivided into many•strains, or serotypes, based b n differldin ding di d Protons (p + andSalmonella In )fact, ences in the major surface components. neutrons (nstrains 0 atom. Electro ) make up the − nsd(eserotype, nucleu species, and such as are often identified by their•genus, se e) orbit the erotype, such uss of u o aan All elem nuc leu s. ents areTennessee. com S. enterica Typhimurium or S. enterica Ten nnessee. posed of ato numbersserotype ms but diff of protons, neutrons, and er in the • Isotopes electrons the are varieties y pos po of oss ses one eesss. number of element tha protons but different num t contain thee sam saame • The num bers of neu ber of electron tron onss.. o s in an elem (comp pareed ent nt’ss outerm d with the ost o t orbital t tal tota t l number the element i pos ’s ’ chemical properties and sible) determines • Covalen t bonds are reactivity. ity che ch mic are shared i al bonds between ato in which elec ms. Equally tron form nonpol s distributed ar covalent electrons bonds, where tributed elec trons form as unequally polar covalen • Ionic bon dist bonds. ds are che mical bonds site charge resulting from s. The outer oppoelectron she receives elec ll either don trons from ates or another ato shell of eac m so that h atom is com the outer pletely filled .

. . point out

three charac

teristics all

cells share?

• H Hyd drogen

b bond ds are we form betwe ak k che h mic i all attr en covalen tt acti tions th tly bonded that oxygens or hydrog nitrogens on well as van different mo ens and either der Waals forces are crit lecules. These as biological pro ically importa cesses. nt in • Chemical equations express the between ato chemical exc ms or molecu hanges les. • Solutions are mixture s of solutes be separated and solvent by filtration s that cannot or settling. • The pH, ranging from a highly acid basic solution ic solution , refers to to a hig the concen ions. It is exp tration of hyd hly ressed as a number from rogen • Biologists 0 to 14. define organi c molecules both carbon as those con and hydrog taining en. • Carbon is the backbo ne of biolog of its ability ical compou to form sing nds becaus bonds with le, double, e itself and ma or triple cov ny different alent elements.

—Terri J. Lindsey, Ph.D., Tarrant County College

xi

Making Connections Connecting Students to the Content with a Truly Instructional Art Program

“The figures and tables found in this book are detailed enough to provide valuable information without being too overwhelming. Another strength of this book are the animations that accompany it.”

High

ATP used to perform cellular work

6

H C4 HO Energy Level of Chemical Compound

An instructional art program not only looks pretty, but helps students visualize complex concepts and processes and paints a conceptual picture for them. The art combines vivid colors, multidimensionality, and self-contained narrative to help students study the challenging concepts of microbiology from a visual perspective. Art is often paired with photographs or micrographs to enhance comprehension.

CH2OH C5 O H

H OH C2 3C OH H Glucose

H C1 OH

3 The energy in electrons and hydrogens is captured and transferred to ATP. ATP is spent to drive the thousands of cell functions.

ATP Hydrogen ions with electrons

Hydrogen ions with electrons 1

Ox

ida

tio Glucose of n en of is oxidized zy glu m as it passes co eca se through sequential ta by lyz metabolic pathways, m ed ea resulting in the removal pa ns th of hydrogens and their wa ys accompanying electrons. During part of these pathways, the glucose carbon skeleton is also dismantled, giving rise to the end product CO2.

Hydrogen ions with electrons

2 These reactions lower the available energy in each successive reaction, but they effectively route that energy into useful cell activities.

Final electron acceptor 2H+ + 2 e– + 1–2 O2

4 In aerobic metabolism, the electrons and hydrogen ions generated by the respiratory pathways combine with oxygen to produce another end product, water.

H2 O OP C PO

End products

CO2

Low Progress of Energy Extraction over Time

Figure 8.11 A simplified model of energy production. The central events of cell energetics include the release of energy during the systematic dismantling of a fuel such as glucose. This is achieved by the shuttling of hydrogens and electrons to sites in the cell where their energy can be transferred to ATP. In aerobic metabolism, the final products are CO2 and H2O molecules.

—Jedidiah Lobos, Antelope Valley College

Clot Bacteria Bacteria in wound

Neutrophil Seepage of plasma and migration of WBC out of blood vessels Vasodilation

Mast cells release chemical mediators

Vasoconstriction

1 Injury/Immediate Reactions

2 Vascular Reactions

Scab Neutrophils

Scar

Pus

Lymphocytes

Fibrous exudate

3 Edema and Pus Formation Rubor (inflammation)

Macrophage

4 Resolution/Scar Formation Edema due to collected fluid

Newly healed tissue

Process Figure 14.14 The major events in inflammation. 1 Injury → Reflex narrowing of the blood vessels (vasoconstriction) lasting for a short time → Release of chemical mediators into area. 2 Increased diameter of blood vessels (vasodilation) → Increased blood flow → Increased vascular permeability → Leakage of fluid (plasma) from blood vessels into tissues (exudate formation). 3 Edema → Infiltration of site by neutrophils and accumulation of pus. 4 Macrophages and lymphocytes → Repair, either by complete resolution and return of tissue to normal state or by formation of scar tissue.

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Process Figures Many difficult microbiological concepts are best portrayed by breaking them down into stages that students will find easy to follow. These process figures show each step clearly marked with a yellow, numbered circle and correlated to accompanying narrative to benefit all types of learners. Process figures are clearly marked next to the figure number. The accompanying legend provides additional explanation.

Connecting Students to Microbiology with Relevant Examples Real Clinical Photos Help Students Visualize Diseases Clinical Photos Figure 5.17 Nutritional sources (substrates) for fungi. (a) A fungal mycelium growing on raspberries. The fine hyphal filaments and black sporangia are typical of Rhizopus. (b) The skin of the foot infected by a soil fungus, Fonsecaea pedrosoi.

Color photos of individuals affected by disease provide students with a real-life, clinical view of how microorganisms manifest themselves in the human body.

(a)

(b)

Figure 18.3 Impetigo lesions on the face.

Nucleus

Combination Figures

Ventral depression

Line drawings combined with photos give students two perspectives: the realism of photos and the explanatory clarity of illustrations. The authors chose this method of presentation often to help students comprehend difficult concepts.

Nuclei

Trophozoite Nuclei

Cyst

(a)

Giant cell

Paramyxovirus

Uncoating

Host cell 1

Host cell 2

(b)

Figure 22.21 Giardia lamblia trophozoite. (a) Schematic drawing. (b) Scanning electron micrograph of intestinal surface, revealing (on the left) the lesion left behind by adhesive disk of a Giardia that has detached. The trophozoite on the right is lying on its “back” and is revealing its adhesive disk. Host cell 3 (a)

(b)

Point of cell fusion

Figure 22.8 The effects of paramyxoviruses. (a) When they infect a host cell, paramyxoviruses induce the cell membranes of adjacent cells to fuse into large multinucleate giant cells, or syncytia. (b) This fusion allows direct passage of viruses from an infected cell to uninfected cells by communicating membranes. Through this means, the virus evades antibodies.

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Making Connections Connecting Students to Microbiology Through Student-Centered Pedagogy Pedagogy Created to Promote Active Learning New Learning Outcomes and “Can You?” Assessment Questions Every chapter in the book now opens with an Outline and a list of Learning ◾ Was this an instance of HA-MRSA or CA-MRSA? Outcomes. “Can You?” questions conclude each major section of the ◾ How is S. aureus commonly spread? text. The Learning Outcomes are tightly correlated to digital material. Inf In nfe fecttio ious Dis isea ease ses Affec ti Instructors can easily measure student learning in relation to the specific th he Sk ng kin in an and Outline and Learning Outcomes d Eye e s Learning Outcomes used in their course. You can also assign “Can 18.1 The Skin and Its Defenses Case File 18 Cas 1. Describe the important anatomical features You?” questions to students through the eBook with McGraw-Hill 2. List the natural defenses present in the skin. 18.2 Normal Biota of the Skin ConnectPlus Microbiology. 3. List the types of normal biota presently know 115

Over the pas tures t several year Internal Struc Cell: meth the cause of Eukaryotic s, m ethic icillin skin illin--resi of the infec resisstan ta t Staphylo tions among and Func tion coccus aure ffoot ootb 5.3 Form or engage in contact ball all players, us

New

(MRSA) has sports. MRS wrestlers, fenc w derivative com become infam A strains are ers, and othe o mon monly resista ous as ly used to treat tant to man r athletes who acquired) MRS y drugs, inclu taph phase sstap hylo yloco A and CA Inter cocc ccal ding methicillin share equipment al inf infections. (communit can lead to Clinicians now , a penicillin ity-a ty-accqui quire serious (ofte red) d) MRSA distinguish A. Spread of n fatal) invo between HA Humans are olvement of the bacterium (hospitalnott tthe the he only victim heart, lung he from the initia outbreak invo s, and bone ms of MRSA. l infection site lving a new s. On Janu Jan born Africcan ary 29, 2008 cutaneous an elephant a pustules that , the San Dieg and th three of its were labora o Zoo repo Prophase determine ratory conf human care rted a MRS the course irmed as MRS takers. The A and scope humans exhi A infection. ◾ Was this off the outb bited An investiga reak. an instance tion was initia of HA-MR ◾ How is RSA ted to SA or CA-M S. aureuss com RSA? monly spre sprread? ad?

18.3 Skin Diseases Caused by Microorganisms n rioles Cent Cen h matin Chro 4. List theCh possible causative agents, modes of t and prevention/treatment for each of the dise Cell membrane cellulitis, staphylococcal scalded skin syndrom lope Nuclear enve maculopapular rash diseases,lewartlike eruptio Nucleolus fibers

Animated Learning Modules

Certain topics in microbiology need help to come to life off the page. Animations, video, audio, and text all combine to help students understand complex processes. Many figures (a) in the text have a corresponding animation available Figure 5.7 Changes in the cell and online for students and instructors. Key topics now nucleus that accompany mitosis in a eukaryotic cell such as a yeast. (a) Before have an Animated Learning Module assignable mitosis (at interphase), chromosomes are visible only as chromatin. As mitosis proceeds through Connect. A new icon in the text indicates (early prophase), chromosomes take on a fine, threadlike appearance as they condense, and the when these learning modules are available. nuclear membrane and nucleolus are temporarily

g furrow vage Cleavag C

Telophase

hase Early telop

Spind

Daughter cells

Cytoplasm

512

Centromere

Outline and mosome ChroLea rnin

Continuing

the Case appe

ars on page g Out Ou ccom Early 521. omes 18.1 The Skin metaphase and Its Defe nses 1. Describe the importan t anatomical 2. List the features of natural defe o the skin. nses present 18.2 Normal in the skin. Biota of the Skin 3. List the types off norm al biota pres 18.3 Skin Diseases Cau ently know n to occupy the skin. 4. List the poss sed by Microorganis ms ible causative agents, mod and preventio es of transmiss n/treatment for each of cellulitis, stap eion, virulence facto the diseMeta hylococcal rs, diagnost asesphas of the skin. scalded skin ic techniqu maculopapul These are: syndrome, es, ar rash dise acne, impe gas gangrene ases, wartlike tigo, , vesicular/pust eruptions, large ular rash dise pustular skin ases, lesions, and cutaneous mycoses.

se has Late anaphase

hase

Early anap

(a)

Notes Notes appear, where appropriate, throughout the text. They give students helpful information about various terminologies, exceptions to the rule, or provide clarification and A Note About Clones further explanation Like so many words in biology, the word “clone” has two of the prior subject. different, although related, meanings. In this chapter we will

disrupted. (b) By metaphase, the chromosomesnges in the cell aand Cha Figure 5.7 mpany mitosis in a are fully visible as X-shaped structures. Theacco shapea yeast. (a) Before nucleus that such as s are aryotic cell at chromosome is due to duplicated chromosomeseuk attached e interphase), proceeds mitosis (at n. As mitosis as chromati on a fine, visible onlyfibers a central point, the centromere. Spindle mosomes take and the hase), chro condense, (early prop arance as they tem orarily appe attach to these and facilitate the separation of nucleolus are temp threadlike omes brane and mo mos mem chro ar the nucle metaphase, T shape (b) ByLater tures. The individual chromosomes during metaphase. struc disrupted. hed at le as X-shaped are fully visib mosomes attac icated chro dle fibers phases serve in the completion of chromosomal is due to dupl romere. Spin cent the t, ra n of ratio a central poin tate the sepa r e and facili separation and division of the cell proper into ph e. Late g metaphas attach to thes mosomes durin of chromosomal individual chro pletion daughter cells. in the com proper into phases serve of the cell and division separation . daughter cells

discuss genetic clones created within microorganisms. What we are cloning is genes. We use microorganisms to allow us to manipulate and replicate genes outside of the original host of that gene. You are much more likely to be familiar with the otherr type of cloning—which we will call whole-organism cloning. It Nutritional is also known as reproductive cloning. ing. Table This is 7.3 the process off Categories of Microbes by Energy and Carbon Source creating an identical organism using DNA from an original. g the Category/Carbon Source Energy Source Example Dolly the sheep was the first cloned whole organism, and many Nonliving Environment Autotroph/CO2 others followed in her wake. These processes are beyond the scope of this book.

Photoautotroph

Sunlight

Photosynthetic organisms, such as algae, plants, cyanobacteria

Chemoautotroph

Simple inorganic chemicals

Only certain bacteria, such as methanogens, deep-sea vent bacteria

Heterotroph/Organic

Other Organisms or Sunlight

Chemoheterotroph Saprobe Parasite Photoheterotroph

xiv

Metabolic conversion of the nutrients from other organisms

Protozoa, fungi, many bacteria, animals

Metabolizing the organic matter of dead organisms

Fungi, bacteria (decomposers)

Utilizing the tissues, fluids of a live host

Various parasites and pathogens; can be bacteria, fungi, protozoa, animals

Sunlight

Purple and green photosynthetic bacteria

Centromere

(b)

Tables This edition contains numerous illustrated tables. Horizontal contrasting lines set off each entry, making it easy to read.

INSIGHT 7.2

Cashing In on “Hot” Microbes

The smoldering thermal springs in Yellowstone National Park are more than just one of the geologic wonders of the world. They are also a hotbed of some of the most unusual microorganisms in the world. The thermophiles thriving at temperatures near the boiling point are the focus of serious interest from the scientific community. For many years, biologists have been intrigued that any living organism could function at such high temperatures. Such questions as these come to mind: Why don’t they melt and disintegrate, why don’t their proteins coagulate, and how can their DNA possibly remain intact? One of the earliest thermophiles to be isolated was Thermus aquaticus. It was discovered by Thomas Brock in Yellowstone’s Mushroom Pool in 1965 and was registered with the American Type Culture Collection. Interested researchers studied this species and discovered that it has extremely heat-stable proteins and nucleic acids, and its cell membrane does not break down readily at high temperatures. Later, an extremely heat-stable DNA- replicating enzyme was isolated from the species. What followed is a riveting example of how pure research for the sake of understanding and discovery also offered up a key ingredient in a multimillion-dollar process. Once an enzyme was em discovered that was capable of copying DNA at very high temp peratures (65°C to 72°C), researchers were able to improve upon hii a technique called the polymerase chain reaction (PCR), which n could amplify a single piece of DNA into hundreds of thousands of identical copies. The process had been invented already, b but d all the replication had to take place under high temperatures and en n of the DNA polymerases available at the time were quickly denay of tured. The process was slow and cumbersome. The discovery m the heat-stable enzyme, called Taq polymerase (from Thermus o aquaticus), revolutionized PCR, making it an indispensable to tool oss for forensic science, microbial ecology, and medical diagnosis. p (Kary Mullis, who recognized the utility of Taq and developed stt the PCR technique in 1983, won the Nobel Prize in Chemistry for it in 1993.)

Insight Readings Found throughout each chapter, current, real-world readings allow students to see an interesting application of the concepts they’re studying.

Biotechnology researchers harvesting samples in Yellowstone National Park.

Spurred by this remarkable success story, biotechnology companies have descended on Yellowstone, which contains over 10,000 hot springs, geysers, and hot habitats. These industries are looking to unusual bacteria and archaea as a source of “extremozymes,” enzymes that operate under high temperatures and acidity. Many other organisms with useful enzymes have been discovered.DISEASES Some INFECTIOUS AFFECTING provide applications in the dairy, brewing, and baking industries The Skin and Eyes for high-temperature processing and fermentations. Others are being considered for waste treatment and bioremediation. Trachoma Chlamydia trachomatis This quest has also brought attention to questions such as: Who owns these microbes, and can their enzymes be patented? In Conjunctivitis Keratitis the year 2000, the Park Service secured a legal ruling that allows Neisseria gonorrhoeae Herpes simplex virus it to share inAcanthamoeba the profits from companies and to add that money to Chlamydia trachomatis Various bacteria its operating budget. The U.S. Supreme Court has also ruled that Various viruses a microbe isolated from natural habitats cannot be patented. Only the technology that uses the microbe can be patented. River Blindness Onchocerca volvulus + Wolbachia Large Pustular Skin Lesions

Leishmania species Bacillus anthracis

Acne

Propionibacterium acnes

Major Desquamation Diseases

Staphylococcus aureus Vesicular or Pustular Rash Disease

Human herpesvirus 3 (Varicella) Variola virus

System Summary Figures “Glass body” figures at the end of each disease chapter highlight the affected organs and list the diseases that were presented in the chapter. In addition, the microbes that could cause the diseases are color coded by type of microorganism.

Maculopapular Rash Diseases

Measles virus Rubella virus Parvovirus B19 Human herpesvirus 6 or 7

Cellulitis

Staphylococcus aureus Streptococcus pyogenes

Gas Gangrene

Clostridium perfringens Impetigo

Staphylococcus aureus Streptococcus pyogenes

Wart and Wartlike Eruptions

Cutaneous and Superficial Mycoses

Human papillomaviruses Molluscum contagiosum viruses

Trichophyton Microsporum Epidermophyton Malassezia

▶ Summing Up

Helminths

Bacteria Taxonomic Organization Microorganisms Causing Diseases of the Skin and Eyes

Microorganism Gram-positive bacteria Propionibacterium acnes Staphylococcus aureus

Streptococcus pyogenes Clostridium perfringens Bacillus anthracis Gram-negative bacteria Neisseria gonorrhoeae Chlamydia trachomatis Wolbachia (in combination with Onchocerca) DNA viruses Human herpesvirus 3 (varicella) virus Variola virus Parvovirus B19 Human herpesvirus 6 and 7 Human papillomavirus Molluscum contagiosum virus Herpes simplex virus RNA viruses Measles virus Rubella virus Fungi Trichophyton Microsporum Epidermophyton Malassezia species Protozoa Leishmania spp. Acanthamoeba Helminths Onchocerca volvulus (in combination with Wolbachia)

Disease

Viruses Protozoa Fungi

Chapter Location

Acne Impetigo, cellulitis, scalded skin syndrome, folliculitis, abscesses (furuncles and carbuncles), necrotizing fasciitis Impetigo, cellulitis, erysipelas, necrotizing fasciitis, scarlet fever Gas gangrene Cutaneous anthrax

Acne, p. 515 Impetigo, p. 516 System S Syste y t m Summary S y Fi Figur Figure g e 18.25 18 25 Cellulitis, p. 521 Scalded skin syndrome, p. 522, Insight 18.1, p. 518, Note on p. 521 Impetigo, p. 520 Cellulitis, p. 521, Insight 18.1, p. 518 Gas gangrene, p. 523 Large pustular skin lesions, p. 543

Neonatal conjunctivitis Neonatal conjunctivitis, trachoma River blindness

Conjunctivitis, p. 540 Conjunctivitis, p. 540 Trachoma, p. 541 River blindness, p. 543

Chickenpox Smallpox Fifth disease Roseola Warts Molluscum contagiosum Keratitis

Vesicular or pustular rash diseases, p. 525 Vesicular or pustular rash diseases, p. 527 Maculopapular rash diseases, p. 532 Maculopapular rash diseases, p. 532 Warts and wartlike eruptions, p. 534 Warts and wartlike eruptions, p. 534 Keratitis, p. 542

Measles Rubella

Maculopapular rash diseases, p. 530 Maculopapular rash diseases, p. 531

Ringworm Ringworm Ringworm Superficial mycoses

Ringworm, p. 536 Ringworm, p. 536 Ringworm, p. 536 Superficial mycoses, p. 538

Leishmaniasis

Large pustular skin lesions, p. 535

River blindness

River blindness, p. 543

“The Systems Summary at the end of the chapters is terrific. I also really like the Checkpoints for the diseases chapters that list the causative agent, transmission, virulence factor, etc., for each disease. Really fantastic. I just love this book.” — Judy Kaufman, Monroe Community College

Taxonomic List of Organisms A taxonomic list of organisms is presented at the end of each disease chapter so students can see the diversity of microbes causing diseases in that body system.

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Making Connections Connecting to Different Learning Styles with Active Learning The end-of-chapter material for the third edition is now linked to Bloom’s taxonomy. It has been carefully planned to promote active learning and provide review for different learning styles and levels of difficulty. Multiple-Choice and True-False questions (Knowledge and Comprehension) precede the synthesis-level Visual Connections questions and Concept Mapping exercises. The consistent layout of each chapter allows students to develop a learning strategy and gain confidence in their ability to master the concepts, leading to success in the class!

Chapter Summary A brief outline of the main chapter concepts is provided for students with important terms highlighted. Key terms are also included in the glossary at the end of the book.

Multiple-Choice Questions Students can assess their knowledge of basic concepts by answering these questions. Other types of questions and activities that follow build on this foundational knowledge. The ConnectPlus eBook allows students to quiz themselves interactively using these questions!

Chapter Summary 4 4.1 1 P Prokaryotic k ti F Form and dF Function ti • Prokaryotes are the oldest form of cellular life. They are also the most widely dispersed, occupying every conceivable microclimate on the planet. 4.2 External Structures • The external structures of bacteria include appendages (flagella, fimbriae, and pili) and the glycocalyx. • Flagella vary in number and arrangement as well as in the type and rate of motion they produce.

4.3 The Cell Envelope: The Boundary Layer of Bacteria • The cell envelope is the complex boundary structure surrounding a bacterial cell. In gram-negative bacteria, the envelope consists of an outer membrane, the cell wall, and the cell membrane. Gram-positive bacteria have only the cell wall and cell membrane. • In a Gram stain, stain gram gram-positive positive bacteria retain the crystal violet and stain purple. Gram-negative bacteria lose the crystal violet and stain red from the safranin counterstain. 4.5and Prokaryotic Shapes, Arrangements, and Sizes Multiple-Choice andbacteria True-False Questions Knowledge Comprehension • Gram-positive have thick cell walls of peptido• Most prokaryotes have one of three general sshapes: glycan and acidic polysaccharides such as teichoic acid. coccus (round), bacillus (rod), or spiral, based on the The Select cell walls of gram-negative bacteria are thinner and Multiple-Choice Questions. the correct answer from the answers provided. configuration of the cell wall Two types of spiral cells c are 1. Which of the following is not found in all bacterial cells? a. cell membrane c. ribosomes b. a nucleoid d. actin cytoskeleton 2. Pili are tubular shafts in ______ bacteria that serve as a means of ______. a. gram-positive, genetic exchange b. gram-positive, attachment c. gram-negative, genetic exchange d. gram-negative, protection 3. An example of a glycocalyx is a. a capsule. c. an outer membrane. b. a pilus. d. a cell wall. 4. Which of the following is a primary bacterial cell wall function? a. transport c. support b. motility d. adhesion 5. Which of the following is present in both gram-positive and gram-negative cell walls? a. an outer membrane c. teichoic acid b. peptidoglycan d. lipopolysaccharides

Critical Thinking Questions Using the facts and concepts they just studied, students must reason and problem solve to answer these specially developed questions. Questions do not have just a single correct answer and thus open doors to discussion and application.

xvi

4.4 Bacterial Structure 4 4 B t i l IInternal t l St t • The cytoplasm of bacterial cells serves as a solvent for materials used in all cell functions. • The genetic material of bacteria is DNA. Genes are arranged on large, circular chromosomes. Additional genes are carried on plasmids. • Bacterial ribosomes are dispersed in the cytoplasm in chains (polysomes) and are also embedded in the cell membrane. • Bacteria may store nutrients in their cytoplasm in structures called inclusions. Inclusions vary in structure and the materials that are stored. • Some bacteria manufacture long actin filaments that help determine their cellular shape. • A few families of bacteria produce dormant bodies called endospores, which are the hardiest of all life forms, surviving for hundreds or thousands of years. • The genera Bacillus and Clostridium are sporeforme sporeformers, and both contain deadly pathogens.

6. Darkly stained granules are concentrated crystals of ______ that are found in ______. a. fat, Mycobacterium c. sulfur, Thiobacillus b. dipicolinic acid, Bacillus d. PO4, Corynebacterium 7. Bacterial endospores usually function in Critical Thinking a. reproduction. c. protein synthesis.Questions b. survival. d. storage.

8. A bacterial arrangement in packets of eight cells is described as a ______. a. micrococcus c. tetrad b. diplococcus d. sarcina 9. To which division of bacteria do cyanobacteria belong? a. Tenericutes c. Firmicutes b. Gracilicutes d. Mendosicutes 10. Which stain is used to distinguish differences between the cell walls of medically important bacteria? a. simple stain c. Gram stain b. acridine orange stain d. negative stain True-False Questions. If the statement is true, leave as is. If it is false, correct it by rewriting the sentence. 11. One major difference in the envelope structure between grampositive bacteria and gram-negative bacteria is the presence or absence of a cytoplasmic membrane. 12. A research microbiologist looking at evolutionary relatedness between two bacterial species is more likely to use Bergey’s Manual of Determinative Bacteriology than Bergey’s Manual of Systematic Bacteriology. 13. Nanobes may or may not actually be bacteria. 14. Both bacteria and archaea are prokaryotes. 15. A collection of bacteria that share an overall similar pattern of traits is called a species.

Application and Analysis

These questions are suggested as a writing-to-learn experience. For each question, compose a one- or two-paragraph answer that includes the factual information needed to completely address the question. 1. a. Name several general characteristics that could be used to define the prokaryotes. b. Do any other microbial groups besides bacteria have prokaryotic cells? c. What does it mean to say that prokaryotes are ubiquitous? In what habitats are they found? Give some general means by which bacteria derive nutrients.

2. a. Describe the structure of a flagellum and how it operates. What are the four main types of flagellar arrangement? b. How does the flagellum dictate the behavior of a motile bacterium? Differentiate between flagella and periplasmic flagella. 3. Differentiate between pili and fimbriae.

Concept Mapping Exercises Three different types of concept mapping activities are used throughout the text in the end-of-chapter material to help students learn and retain what they’ve read. Concept Mapping exercises are now made interactive on ConnectPlus Microbiology!

Visual Connections Visual Connections questions, renamed from the 2nd edition, take images and concepts learned in previous chapters and ask students to apply that knowledge to concepts newly learned in the current chapter.

Concept Mapping

Synthesis

Appendix D provides guidance for working with concept maps. 1. Construct your own concept map using the following words as the concepts. Supply the linking words between each pair of concepts.

Visual Connections

genus serotype

species domain

Borrelia spirochete

burgdorferi

Synthesis

These questions use visual images or previous content to make connections to this chapter’s concepts. 1. From chapter 3, figure 3.10. Do you believe that the bacteria spelling “Klebsiella” or the bacteria spelling “S. aureus” possess the larger capsule? Defend your answer.

2. From chapter 1, figure 1.14. Study this figure. How would it be drawn differently if the archaea were more closely related to bacteria than to eukaryotes? Plants Animals Fungi Protists

Domain Bacteria Cyanobacteria

Domain Archaea

Chlamydias Gram-positive Endospore Gram-negative Spirochetes bacteria producers bacteria

Methane producers

Prokaryotes that live in extreme salt

Domain Eukarya Prokaryotes that live in extreme heat

Eukaryotes

Ancestral Cell Line (first living cells)

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Making Connections New to Microbiology, A Systems Approach Global changes: Case Files The Case Files are now more integrated into the chapter, with the chapter-opening “Case File,” a “Continuing the Case” box, and a final “Case Wrap-Up.” All but two of these chapter case files are new to this edition. The Case Files are linked to the second edition of Laboratory Applications in Microbiology, A Case Study Approach, by Barry Chess. Learning Outcomes and “Can You. . .” Assessment Questions ● The chapter overviews now include Learning Outcomes, which help focus the student’s attention on key concepts in the chapter. All Connect online content is directly correlated to these same Learning Outcomes. ● Each section of a chapter ends with assessment questions that tie directly to the Learning Outcomes. Additional online Connect questions will also help analyze performance against the Learning Outcomes. Improved End-of-Chapter Material ● Each Chapter Summary is now bulleted and easier to read. ● All review questions are now linked to Bloom’s taxonomy. ● Answers for all multiple-choice, true-false, and matching questions are available in Appendix C for student self-practice. ● Corresponding interactive Concept Maps in Connect reinforce the key terms and concepts in the chapter mapping exercises.

Chapter changes: Chapter 1 ● A new discussion about the subject of evolution has been added. ● The tree of life was expanded to a “web of life” based on new findings. Chapter 2 ● A new Insight reading on the periodic table is now included. ● The chapter has been updated with a new emphasis on the regulatory RNAs. Chapter 3 ● The presentation on magnification, resolution, and contrast has been improved. ● The different types of microscopes are more clearly illustrated and compared side-by-side in a new table (table 3.5).

● Information about the cytoskeleton has been revised from two fiber types to three (actin filaments, microtubules, and intermediate filaments). ● The figure illustrating the eukaryotic cell now includes the prokaryotic cell for comparison. ● The discussion on the taxonomy of protists has been updated. Chapter 6 ● The ubiquity of viruses and their role in the biosphere and evolution receives significant attention. ● The discussion of different viral replication strategies has been greatly improved. ● The discussion of cancer and viruses has been expanded. ● The bacteriophage life cycle illustration now includes the lysogenic and lytic phases in one illustration. Chapter 7 ● The order of presenting diffusion versus osmosis has been switched for better presentation. ● The facilitated diffusion figure has been improved. ● A large section of text and accompanying figures about biofilms and quorum sensing has been added. ● The binary fission figure has been updated to reflect current research findings. Chapter 8 ● An illustration about activation energy has been added to this chapter. ● A new visual icon based on the first overview figure in the chapter has been included with several later figures to help students better understand where each of the later figures fits in “the big picture.” ● The Krebs Cycle illustration has been moved out of a boxed reading and into the main text. ● The illustrations of the electron transport system have been greatly improved, and prokaryotes are now emphasized over eukaryotes.

Chapter 4 ● Sixteen pieces of art in this chapter have been updated or improved. ● The use of the terms bacterium versus prokaryote has been clarified.

Chapter 9 ● The phrase horizontal gene transfer is now used to describe transformation, transduction, and conjugation, and the significance of this phenomenon for eukaryotic development is discussed. ● Content on phase variation and pathogenicity islands has been added. ● A new Insight reading about the virulence of Salmonella in space and how it relates to earth infections has been added.

Chapter 5 ● The concept of Last Common Ancestor is introduced, based on the newest research on the evolutionary history of prokaryotes and eukaryotes.

Chapter 10 ● More emphasis has been put on automated versus manual sequencing. ● A new section on synthetic biology has been added.

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● More information on siRNAs and gene silencing techniques as therapeutic interventions is now included. ● Information on single nucleotide polymorphisms (SNPs) in the human genome was added. ● The discussion on microarray analysis has been improved. ● The section on ethical issues has been expanded.

Chapter 17 ● The section on genotyping has been updated. For example, the PNA FISH technique is now included. ● The discussion of specificity and sensitivity has been improved. ● Information about imaging in microbial diagnosis has been added.

Chapter 11 ● Osmotic pressure as a control measure has been included in this chapter.

Chapter 18 ● New, paradigm-shifting data from the Human Microbiome Project about normal biota have been added to this chapter. ● A discussion regarding the current thought that antimicrobial peptides are a major skin defense has also been included.

Chapter 12 ● Information on the fifth generation of cephalosporins is now included. ● More information about the efficacy of antibiotics in biofilm infections has been added. ● A new table (Table 12.3) about the spectrum of activity of various antibacterials has been added. ● The possibility of phage therapy is now included in this chapter. ● The role of bystander microbes in harboring antibiotic resistance has been added. Chapter 13 ● This chapter was updated with a discussion of the Human Microbiome Project, which is revolutionizing the idea of normal biota. ● A new discussion of the role of stress hormones on the expression of pathogenicity genes in bacteria is now in this chapter. ● A new figure summarizing the path to disease (Figure 13.8) has been added. ● The section on epidemiology has been improved. Chapter 14 ● The chapter now addresses the difference between non-self antigens that are pathogenic and non-self antigens that are commensal, and how that trains the immune response. ● Content on pattern recognition receptors (PRRs) has been added to the discussion of pathogen-associated molecular patterns (PAMPs). ● The nonspecific immune system has been reorganized into four sections: inflammation, phagocytosis, fever, and antimicrobial proteins. Chapter 15 ● The content has been restructured so it is easier to follow (sections were renamed after the flowchart that appears at the beginning of the chapter). ● New information on TH17 cells and T regulatory cells has been included. ● New information on CD3 molecules as part of the T-cell receptor has been added. ● The “types of vaccines” have been reordered to a much more logical format. ● An Insight reading about the antivaccination movement has been added. Chapter 16 ● The first illustration in this chapter and the organization of disorders have been rearranged and improved for better clarity. ● It has been made more apparent that autoimmune diseases fit into multiple “Types of Hypersensitivities” sections by the reorganization of content in these sections.

Chapter 20 ● CMV has been removed as a cause of infectious mononucleosis, reflecting new data; similarly, HTLV-II has been removed as a cause of hairy cell leukemia. ● A section on Chikungunya virus hemorrhagic fever has been added. ● Important new data on vaccine failure and also success for HIV, including a new approach that some say could eliminate HIV, have been included. Chapter 21 ● More emphasis has been put on polymicrobial diseases in the respiratory tract. ● A section on an important new cause of pharyngitis has been added. ● A separate note about “emerging pneumonias” has been added; the information on SARS has been moved out of the main pneumonia table and included with this category, along with the new adenovirus pneumonias, reflecting the relative importance of these infections. ● A new Insight reading linking the timeline of influenza pandemics with historical events has been added. Chapter 22 ● New material on normal biota in the stomach has been added. ● A discussion regarding the link between oral biota and heart disease has been included. ● A new Insight reading on the possible microbial cause of Crohn’s disease appears. Chapter 23 ● New information about the different biota (and infection consequences) of circumcised versus uncircumcised men is now included. ● A “Note” box explaining the confusing world of STD statistics has been added. ● A discussion on parents’ fears about the HPV vaccine has been included. Chapter 24 ● This chapter was significantly rewritten to incorporate genomic findings of new microbes in the environment. ● New findings about viruses and genes in the ocean are also included. Chapter 25 ● The section on water contamination has been moved from chapter 24 to this chapter. ● Chapter headings were changed to be more logical to the reader. ● Information about algal biofuels has been added.

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Making Connections Customize your course materials to your learning outcomes! Create what you’ve only imagined. Introducing McGraw-Hill Create™—a new, self-service website that allows you to create custom course materials— print and eBooks—by drawing upon McGraw-Hill’s comprehensive, cross-disciplinary content. Add your own content quickly and easily. Tap into other rights-secured third-party sources as well. Then, arrange the content in a way that makes the most sense for your course. Even personalize your book with your course name and information! Choose the best format for your course: color print, black-and-white print, or eBook. The eBook is now even viewable on an iPad! And, when you are done, you will receive a free PDF review copy in just minutes!

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Need a lab manual for your microbiology course? Customize any of these manuals— add your text material—and Create your perfect solution! McGraw-Hill offers several lab manuals for the microbiology course. Contact your McGraw-Hill representative for packaging options with any of our lab manuals. Brown: Benson’s Microbiological Applications: Laboratory Manual in General Microbiology, 12th edition Short Version (978-0-07-337527-4) Complete Version (978-0-07-730213-9)

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Chess: Laboratory Applications in Microbiology: A Case Study Approach, 2nd edition (978-0-07340237-6)

Morello: Lab Manual and Workbook in Microbiology: Applications to Patient Care, 10th edition (978-0-07-352253-1)

Chess: Photographic Atlas for Laboratory Applications in Microbiology, 1st edition (978-0-07-737159-3)

Kleyn: Microbiology Experiments, 6th edition (978-0-07-299549-7)

Visit McGraw-Hill Create —www.mcgrawhillcreate.com— today and begin building your perfect book. xx

Acknowledgments I am most grateful to my patient students who have tried to teach me how to more effectively communicate a subject I love. The professors who reviewed manuscript for me were my close allies, especially when they were liberal in their criticism! Kathy Loewenberg at McGraw-Hill was polite enough not to point out how often she had to fix things for me and for that I thank her. Lynn Breithaupt, Amy Reed, Marty Lange, Michael Lange, and Sheila Frank were indispensable members of the team that helped this edition come together. In the end, it is not possible to write and rewrite an 800+ page book without impacting the way you live with people around you. So I thank my family: Ted, Taylor, Sam, Suzanne, and new son-in-law Aaron for their patience and understanding. I promise to learn how to use that stove this year! —Kelly Cowan

Reviewers Michelle L. Badon, University of Texas at Arlington Suzanne Butler, Miami Dade College Chantae M. Calhoun, Lawson State Community College Sujata Chiplunkar, Cypress College James K. Collins, University of Arizona Robin L. Cotter, Phoenix College Ana L. Dowey, Palomar College Melissa Elliott, Butler Community College Elizabeth Emmert, Salisbury University Luti Erbeznik, Oakland Community College Clifton Franklund, Ferris State University Susan Finazzo, Georgia Perimeter College Christina A. Gan, Highline Community College Elmer K. Godeny, Baton Rouge Community College Jenny Hardison, Saddleback College Julie Harless, Lone Star College–Montgomery Jennifer A. Herzog, Herkimer County Community College Dena Johnson, Tarrant County College NW Richard D. Karp, University of Cincinnati Judy Kaufman, Monroe Community College Janardan Kumar, Becker College Terri J. Lindsey,Tarrant County College District–South Campus Jedidiah Lobos, Antelope Valley College Melanie Lowder, University of North Carolina at Charlotte Elizabeth F. McPherson, The University of Tennessee Steven Obenauf, Broward College Gregory Paquette, University of Rhode Island Marcia M. Pierce, Eastern Kentucky University Teri Reiger, University of Wisconsin–Oshkosh

Brenden Rickards, Gloucester County College Seth Ririe, Brigham Young University–Idaho Benjamin Rowley, University of Central Arkansas Mark A. Schneegurt, Wichita State University Denise L. Signorelli,College Southern Nevada Heidi R. Smith, Front Range Community College Steven J. Thurlow, Jackson Community College Sanjay Tiwary, Hinds Community College Liana Tsenova, NYC College of Technology Winfred Watkins, McLennan Community College Valerie A. Watson, West Virginia University Suzi Welch, Howard College, San Angelo

Symposium Participants Linda Allen, Lon Morris College Michelle Badon, University of Texas–Arlington Carroll Bottoms, Collin College Nancy Boury, Iowa State University William Boyko, Sinclair Community College Chad Brooks, Austin Peay State University Terri Canaris, Brookhaven College Liz Carrington, Tarrant County College Erin Christensen, Middlesex Community College Deborah Crawford, Trinity Valley Community College Paula Curbo, Hill College John Dahl, Washington State University David Daniel, Weatherford College Alison Davis, East Los Angeles College Ana Dowey, Palomar College

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Acknowlegments

Susan Finazzo, Georgia Perimeter College Clifton Franklund, Ferris State University Edwin Gines-Candalaria, Miami–Dade College Amy Goode, Illinois Central College Todd Gordon, Kansas City Kansas Community College Gabriel Guzman, Triton College Judy Haber, California State University–Fresno Julie Harless, Lone Star College Jennifer Herzog, Herkimer County Community College Dena Johnson, Tarrant County College Eunice Kamunge, Essex County College Amine Kidane, Columbus State Community College Terri Lindsey, Tarrant County College Peggy Mason, Brookhaven College Caroline McNutt, Schoolcraft College Elizabeth McPherson, University of Tennessee–Knoxville Tracey Mills, Ivy Tech CC–Lawrence Campus Bethanye Morgan, Tarrant County College Steven Obenauf, Broward College Tammy Oliver, Eastfield College Janis Pace, Southwestern University

Marcia Pierce, Eastern Kentucky University Madhura Pradhan, The Ohio State University Todd Primm, Sam Houston State University Jackie Reynolds, Richland College Beverly Roe, Erie Community College Silvia Rossbach, Western Michigan University Benjamin Rowley, University of Central Arkansas Mark Schneegurt, Wichita State University Teri Shors, University of Wisconsin Margaret Silva, Mountain View College Heidi Smith, Front Range Community College Sherry Stewart, Navarro College Debby Sutton, Mountain View College Louise Thai, University of Missouri–Columbia Steven Thurlow, Jackson Community College Sanjay Tiwary, Hinds Community College Stephen Wagner, Stephen F Austin State University Delon Washo-Krupps, Arizona State University Winifred Watkins, McLennan Community College Samia Williams, Santa Fe Community College

Table of Contents Preface

xvi

CHAPTER

1

The Main Themes of Microbiology 1 1.1 The Scope of Microbiology 2 1.2 The Impact of Microbes on Earth: Small Organisms with a Giant Effect 2 Microbial Involvement in Shaping Our Planet 3 1.3 Humans Use of Microorganisms 6 1.4 Infectious Diseases and the Human Condition 8 1.5 The General Characteristics of Microorganisms 10 Cellular Organization 10 Lifestyles of Microorganisms 10 1.6 The Historical Foundations of Microbiology 11 The Development of the Microscope: “Seeing Is Believing” 11 The Establishment of the Scientific Method 15 Deductive and Inductive Reasoning 16 The Development of Medical Microbiology 17 1.7 Naming, Classifying, and Identifying Microorganisms 18 Assigning Specific Names 18 The Levels of Classification 20 The Origin and Evolution of Microorganisms 20 Systems of Presenting a Universal Tree of Life 22 INSIGHT 1.1 The More Things Change …

9

INSIGHT 1.2 The Fall of Superstition and the Rise of Microbiology 12 INSIGHT 1.3 Martian Microbes and Astrobiology Chapter Summary 24 Multiple-Choice and True-False Knowledge and Comprehension 25 Critical Thinking Questions Application and Analysis Concept Mapping Synthesis 26 Visual Connections Synthesis 26

CHAPTER

2

The Chemistry of Biology

19

25

The Major Elements of Life and Their Primary Characteristics 30 Bonds and Molecules 32 2.2 Macromolecules: Superstructures of Life 41 Carbohydrates: Sugars and Polysaccharides 42 Lipids: Fats, Phospholipids, and Waxes 45 Proteins: Shapers of Life 47 The Nucleic Acids: A Cell Computer and Its Programs 2.3 Cells: Where Chemicals Come to Life 51 Fundamental Characteristics of Cells 52 INSIGHT 2.1 The Periodic Table: Not as Concrete as You Think 31

INSIGHT 2.2 Redox: Electron Transfer and Oxidation-Reduction Reactions 35 INSIGHT 2.3 Membranes: Cellular Skins

46

Chapter Summary 52 Multiple-Choice and True-False Knowledge and Comprehension 53 Critical Thinking Questions Application and Analysis 53 Concept Mapping Synthesis 54 Visual Connections Synthesis 54

CHAPTER

3

Tools of the Laboratory: The Methods for Studying Microorganisms 55 3.1 Methods of Culturing Microorganisms—The Five I’s Inoculation: Producing a Culture 57 Isolation: Separating One Species from Another 57 Media: Providing Nutrients in the Laboratory 58 Back to the Five I’s: Incubation, Inspection, and Identification 65 3.2 The Microscope: Window on an Invisible Realm 66 Microbial Dimensions: How Small Is Small? 67 Magnification and Microscope Design 68 Variations on the Light Microscope 71 Preparing Specimens for Optical Microscopes 71 INSIGHT 3.1 Animal Inoculation: “Living Media”

27

2.1 Atoms, Bonds, and Molecules: Fundamental Building Blocks 28 Different Types of Atoms: Elements and Their Properties 29

49

59

INSIGHT 3.2 The Evolution in Resolution: Probing Microscopes 76 Chapter Summary 77 Multiple-Choice and True-False Knowledge and Comprehension 77 Critical Thinking Questions Application and Analysis 78 Concept Mapping Synthesis 79 Visual Connections Synthesis 79

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CHAPTER

4

Prokaryotic Profiles: The Bacteria and Archaea 80 4.1 Prokaryotic Form and Function 81 The Structure of a Generalized Bacterial Cell 83 4.2 External Structures 83 Appendages: Cell Extensions 83 4.3 The Cell Envelope: The Boundary Layer of Bacteria 89 Differences in Cell Envelope Structure 89 Structure of the Cell Wall 89 Mycoplasmas and Other Cell-Wall-Deficient Bacteria 92 The Gram-Negative Outer Membrane 93 Cell Membrane Structure 93 Functions of the Cell Membrane 94 4.4 Bacterial Internal Structure 94 Contents of the Cell Cytoplasm 94 Bacterial Endospores: An Extremely Resistant Stage 96 4.5 Prokaryotic Shapes, Arrangements, and Sizes 98 4.6 Classification Systems in the Prokaryotae 101 Taxonomic Scheme 102 Diagnostic Scheme 102 Species and Subspecies in Prokaryotes 102 4.7 The Archaea 102 Archaea: The Other Prokaryotes 102 INSIGHT 4.1 Biofilms—The Glue of Life

87

INSIGHT 4.2 The Gram Stain: A Grand Stain INSIGHT 4.3 Redefining Prokaryotic Size

90

INSIGHT 5.1 The Extraordinary Emergence of Eukaryotic Cells 110 INSIGHT 5.2 Two Faces of Fungi

CHAPTER 106

5

Eukaryotic Cells and Microorganisms 108 5.1 The History of Eukaryotes 109 5.2 Form and Function of the Eukaryotic Cell: External Structures 111 Locomotor Appendages: Cilia and Flagella 112 The Glycocalyx 113 Form and Function of the Eukaryotic Cell: Boundary Structures 113 5.3 Form and Function of the Eukaryotic Cell: Internal Structures 114 The Nucleus: The Control Center 114 Endoplasmic Reticulum: A Passageway in the Cell 116 Golgi Apparatus: A Packaging Machine 116 Mitrochondria: Energy Generators of the Cell 118

124

Chapter Summary 136 Multiple-Choice and True-False Knowledge and Comprehension 137 Critical Thinking Questions Application and Analysis Concept Mapping Synthesis 138 Visual Connections Synthesis 138

99

Chapter Summary 105 Multiple-Choice and True-False Knowledge and Comprehension 106 Critical Thinking Questions Application and Analysis Concept Mapping Synthesis 107 Visual Connections Synthesis 107

CHAPTER

Chloroplasts: Photosynthesis Machines 119 Ribosomes: Protein Synthesizers 119 The Cytoskeleton: A Support Network 119 Survey of Eukaryotic Microorganisms 120 5.4 The Kingdom of the Fungi 121 Fungal Nutrition 122 Organization of Microscopic Fungi 122 Reproductive Strategies and Spore Formation 125 Fungal Identification and Cultivation 126 The Roles of Fungi in Nature and Industry 126 5.5 The Protists 127 The Algae: Photosynthetic Protists 127 Biology of the Protozoa 128 5.6 The Parasitic Helminths 133 General Worm Morphology 134 Life Cycles and Reproduction 134 A Helminth Cycle: The Pinworm 134 Helminth Classification and Identification 135 Distribution and Importance of Parasitic Worms 135

137

6

An Introduction to the Viruses 139 6.1 The Search for the Elusive Viruses 140 0 6.2 The Position of Viruses in the Biological Spectrum 6.3 The General Structure of Viruses 143 Size Range 143 Viral Components: Capsids, Nucleic Acids, and Envelopes 143 6.4 How Viruses Are Classified and Named 149 6.5 Modes of Viral Multiplication 151 Multiplication Cycles in Animal Viruses 151 Viruses That Infect Bacteria 157 6.6 Techniques in Cultivating and Identifying Animal Viruses 160 Using Live Animal Inoculation 160 Using Bird Embryos 161 Using Cell (Tissue) Culture Techniques 161 6.7 Medical Importance of Viruses 163 6.8 Other Noncellular Infectious Agents 163 6.9 Treatment of Animal Viral Infections 165 INSIGHT 6.1 A Positive View of Viruses

141

INSIGHT 6.2 Artificial Viruses Created!

163

INSIGHT 6.3 A Vaccine for Obesity?

164

141

Table of Contents Chapter Summary 165 Multiple-Choice and True-False Knowledge and Comprehension 166 Critical Thinking Questions Application and Analysis Concept Mapping Synthesis 167 Visual Connections Synthesis 167

CHAPTER

166

7

Microbial Nutrition, Ecology, and Growth 168 7.1 Microbial Nutrition 169 Chemical Analysis of Microbial Cytoplasm 169 Sources of Essential Nutrients 170 Transport Mechanisms for Nutrient Absorption 174 The Movement of Molecules: Diffusion and Transport 175 The Movement of Water: Osmosis 176 Endocytosis: Eating and Drinking by Cells 180 7.2 Environmental Factors That Influence Microbes 180 Temperature Adaptations 180 Gas Requirements 183 Effects of pH 185 Osmotic Pressure 185 Miscellaneous Environmental Factors 185 Ecological Associations Among Microorganisms 185 Interrelationships Between Microbes and Humans 188 7.3 The Study of Microbial Growth 189 The Basis of Population Growth: Binary Fission 189 The Rate of Population Growth 189 The Population Growth Curve 191 Stages in the Normal Growth Curve 191 Other Methods of Analyzing Population Growth 193 INSIGHT 7.1 Life in the Extremes

INSIGHT 7.2 Cashing In on “Hot” Microbes

182

186

INSIGHT 7.4 Steps in a Viable Plate Count—Batch Culture Method 192 Chapter Summary 195 Multiple-Choice and True-False Knowledge and Comprehension 195 Critical Thinking Questions Application and Analysis Concept Mapping Synthesis 196 Visual Connections Synthesis 197

CHAPTER

196

8

Microbial Metabolism: The Chemical Crossroads of Life

Adenosine Triphosphate: Metabolic Money 210 8.3 The Pathways 211 Catabolism: Getting Materials and Energy 211 Aerobic Respiration 212 Pyruvic Acid—A Central Metabolite 214 The Krebs Cycle—A Carbon and Energy Wheel 214 Steps in the Krebs Cycle 214 The Respiratory Chain: Electron Transport and Oxidative Phosphorylation 217 Summary of Aerobic Respiration 219 Anaerobic Respiration 220 Fermentation 220 8.4 Biosynthesis and the Crossing Pathways of Metabolism 223 The Frugality of the Cell—Waste Not, Want Not 223 Anabolism: Formation of Macromolecules 224 Assembly of the Cell 225 8.5 It All Starts with Light 225 INSIGHT 8.1 Enzymes as Biochemical Levers INSIGHT 8.2 Unconventional Enzymes

202

INSIGHT 8.3 The Enzyme Name Game

203

201

INSIGHT 8.4 Pasteur and the Wine-to-Vinegar Connection Chapter Summary 228 Multiple-Choice and True-False Knowledge and Comprehension 229 Critical Thinking Questions Application and Analysis Concept Mapping Synthesis 230 Visual Connections Synthesis 231

CHAPTER

222

230

9

Microbial Genetics 232

173

INSIGHT 7.3 Life Together: Mutualism

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198

8.1 The Metabolism of Microbes 199 Enzymes: Catalyzing the Chemical Reactions of Life 199 Regulation of Enzymatic Activity and Metabolic Pathways 206 8.2 The Pursuit and Utilization of Energy 208 Energy in Cells 208 A Closer Look at Biological Oxidation and Reduction 209

9.1 Introduction to Genetics and Genes: Unlocking the Secrets of Heredity 233 The Nature of the Genetic Material 234 The DNA Code: A Simple Yet Profound Message 235 The Significance of DNA Structure 237 DNA Replication: Preserving the Code and Passing It On 238 9.2 Applications of the DNA Code: Transcription and Translation 240 The Gene-Protein Connection 241 The Major Participants in Transcription and Translation 242 Transcription: The First Stage of Gene Expression 244 Translation: The Second State of Gene Expression 244 Eukaryotic Transcription and Translation: Similar Yet Different 249 Alternative Splicing and RNA Editing 250 The Genetics of Animal Viruses 251 9.3 Genetic Regulation of Protein Synthesis 251 The Lactose Operon: A Model for Inducible Gene Regulation in Bacteria 251 A Repressible Operon 253 Phase Variation 254

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Antibiotics That Affect Transcription and Translation 254 9.4 Mutations: Changes in the Genetic Code 255 Causes of Mutations 256 Categories of Mutations 256 Repair of Mutations 257 The Ames Test 257 Positive and Negative Effects of Mutations 258 9.5 DNA Recombination Events 259 Horizontal Gene Transfer in Bacteria 259 Pathogenicity Island: Special “Gifts” of Horizontal Gene Transfer? 264 INSIGHT 9.1 Deciphering the Structure of DNA

236

INSIGHT 9.2 Small RNAs: An Old Dog Shows Off Some New(?) Tricks 242 INSIGHT 9.3 Salmonella in Space

254

Chapter Summary 265 Multiple-Choice and True-False Knowledge and Comprehension 265 Critical Thinking Questions Application and Analysis Concept Mapping Synthesis 267 Visual Connections Synthesis 267

CHAPTER

266

10

Genetic Engineering and Recombinant DNA 268 10.1 Basic Elements and Applications of Genetic Engineering 269 10.2 Tools and Techniques of Genetic Engineering 270 DNA: The Raw Material 270 Enzymes for Dicing, Splicing, and Reversing Nucleic Acids 270 Analysis of DNA 271 10.3 Methods in Recombinant DNA Technology: How to Imitate Nature 278 Technical Aspects of Recombinant DNA and Gene Cloning 278 Construction of a Recombinant, Insertion into a Cloning Host, and Genetic Expression 280 10.4 Biochemical Products of Recombinant DNA Technology 282 10.5 Genetically Modified Organisms 283 Recombinant Microbes: Modified Bacteria and Viruses 284 Transgenic Plants: Improving Crops and Foods 284 Transgenic Animals: Engineering Embryos 286 Synthetic Biology 286 10.6 Genetic Treatments: Introducing DNA into the Body 287 Gene Therapy 287 DNA Technology as Genetic Medicine 288 10.7 Genome Analysis: Maps and Profiles 289 Genome Mapping and Screening: An Atlas of the Genome 289 DNA Profiles: A Unique Picture of a Genome 290 INSIGHT 10.1 OK, the Genome’s Sequenced—What’s Next? 274

INSIGHT 10.2 A Moment to Think

284

INSIGHT 10.3 DIYBio: Citizen Scientists

285

Chapter Summary 293 Multiple-Choice and True-False Knowledge and Comprehension 294 Critical Thinking Questions Application and Analysis Concept Mapping Synthesis 295 Visual Connections Synthesis 296

CHAPTER

295

11

Physical and Chemical Control of Microbes 297 11.1 Controlling Microorganisms 298 General Considerations in Microbial Control 298 Relative Resistance of Microbial Forms 299 Terminology and Methods of Microbial Control 300 What is Microbial Death? 301 How Antimicrobial Agents Work: Their Modes of Action 304 11.2 Methods of Physical Control 305 Heat as an Agent of Microbial Control 305 The Effects of Cold and Desiccation 309 Radiation as a Microbial Control Agent 309 Decontamination by Filtration: Techniques for Removing Microbes 312 Osmotic Pressure 312 11.3 Chemical Agents in Microbial Control 313 Choosing a Microbial Chemical 314 Factors That Affect the Germicidal Activity of Chemicals 315 Germicidal Categories According to Chemical Group 315 INSIGHT 11.1 Microbial Control in Ancient Times INSIGHT 11.2 Decontaminating Congress

299

302

INSIGHT 11.3 Pathogen Paranoia: “The Only Good Microbe Is a Dead Microbe” 313 INSIGHT 11.4 The Quest for Sterile Skin

319

Chapter Summary 323 Multiple-Choice and True-False Knowledge and Comprehension 324 Critical Thinking Questions Application and Analysis Concept Mapping Synthesis 325 Visual Connections Synthesis 326

CHAPTER

325

12

Drugs, Microbes, Host—The Elements of Chemotherapy 327 12.1 Principles of Antimicrobial Therapy 328 The Origins of Antimicrobial Drugs 330 12.2 Interactions Between Drug and Microbe 330 Mechanisms of Drug Action 331 12.3 Survey of Major Antimicrobial Drug Groups 335

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Table of Contents

Antibacterial Drugs Targeting the Cell Wall 336 Antibacterial Drugs Targeting Protein Synthesis 339 Antibacterial Drugs Targeting Folic Acid Synthesis 341 Antibacterial Drugs Targeting DNA or RNA 341 Antibacterial Drugs Targeting Cell Membranes 341 Antibiotics and Biofilms 342 Agents to Treat Fungal Infections 342 Antiparasitic Chemotherapy 343 Antiviral Chemotherapeutic Agents 343 New Approaches to Antimicrobial Therapy 350 Helping Nature Along 351 12.4 Interaction Between Drug and Host 352 Toxicity to Organs 352 Allergic Responses to Drugs 353 Suppression and Alteration of the Microbiota by Antimicrobials 353 12.5 Consideration in Selecting an Antimicrobial Drug 354 Identifying the Agent 354 Testing for the Drug Susceptibility of Microorganisms 354 The MIC and Therapeutic Index 356 An Antimicrobial Drug Dilemma 357 INSIGHT 12.1 From Witchcraft to Wonder Drugs

Nosocomial Infections: The Hospital as a Source of Disease 384 Universal Blood and Body Fluid Precautions 385 Which Agent Is the Cause? Using Koch’s Postulates to Determine Etiology 386 13.3 Epidemiology: The Study of Disease in Populations 388 Who, When, and Where? Tracking Disease in the Population 388 INSIGHT 13.1 Life Without Microbiota

INSIGHT 13.3 The Classic Stages of Clinical Infections INSIGHT 13.4 Koch’s Postulates Still Critical

329 CHAPTER

INSIGHT 12.3 The Rise of Drug Resistance

348

Host Defenses I: Overview and Nonspecific Defenses 397

CHAPTER

13

Microbe-Human Interactions: Infection and Disease 362 13.1 The Human Host 363 Contact, Infection, Disease—A Continuum 363 Resident Biota: The Human as a Habitat 363 Indigenous Biota of Specific Regions 366 13.2 The Progress of an Infection 366 Becoming Established: Step One—Portals of Entry 369 The Size of the Inoculum 372 Becoming Established: Step Two—Attaching to the Host 372 Becoming Established: Step Three—Surviving Host Defenses 373 Causing Disease 373 The Process of Infection and Disease 375 Signs and Symptoms: Warning Signals of Disease 378 The Portal of Exit: Vacating the Host 378 The Persistence of Microbes and Pathologic Conditions 379 Reservoirs: Where Pathogens Persist 379 The Acquisition and Transmission of Infectious Agents 382

394

14

334

360

376

387

Chapter Summary 392 Multiple-Choice and True-False Knowledge and Comprehension 393 Critical Thinking Questions Application and Analysis Concept Mapping Synthesis 395 Visual Connections Synthesis 396

INSIGHT 12.2 A Quest for Designer Drugs

Chapter Summary 358 Multiple-Choice and True-False Knowledge and Comprehension 359 Critical Thinking Questions Application and Analysis Concept Mapping Synthesis 360 Visual Connections Synthesis 361

368

INSIGHT 13.2 Laboratory Biosafety Levels and Classes of Pathogens 370

14.1 Defense Mechanisms of the Host in Perspective 398 Barriers: A First Line of Defense 398 14.2 The Second and Third Lines of Defense: An Overview 401 14.3 Systems Involved in Immune Defenses 402 The Communicating Body Compartments 402 14.4 The Second Line of Defense 410 The Inflammatory Response: A Complex Concert of Reactions to Injury 410 The Stages of Inflammation 410 Phagocytosis: Cornerstone of Inflammation and Specific Immunity 414 Fever: An Adjunct to Inflammation 416 Antimicrobial Proteins: 1) Interferon 417 Antimicrobial Proteins: 2) Complement 418 Overall Stages in the Complement Cascade 418 Antimicrobial Proteins: 3) Iron-Binding Proteins and 4) Antimicrobial Peptides 419 INSIGHT 14.1 When Inflammation Gets Out of Hand

411

INSIGHT 14.2 The Dynamics of Inflammatory Mediators INSIGHT 14.3 Some Facts About Fever

417

Chapter Summary 421 Multiple-Choice and True-False Knowledge and Comprehension 422 Critical Thinking Questions Application and Analysis Concept Mapping Synthesis 423 Visual Connections Synthesis 423

422

412

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Table of Contents

CHAPTER

15

CHAPTER

Host Defenses II: Specific Immunity and Immunization 424

Disorders in Immunity

15.1 Specific Immunity: The Third and Final Line of Defense 425 Development of the Dual Lymphocyte System 426 Entrance and Presentation of Antigens and Clonal Selection 426 Activation of Lymphocytes and Clonal Expansion 426 Products of B Lymphocytes: Antibody Structure and Functions 426 15.2 Step I: Lymphocyte Development 428 Markers on Cell Surfaces Involved In Recognition of Self and Nonself 428 The Development of Lymphocyte Diversity 428 The Origin of Immunological Diversity 429 Clonal Selection 429 15.3 Step II: Presentation of Antigens 432 Entrance and Processing of Antigens 432 Cooperation in Immune Reactions to Antigens 433 The Role of Antigen Processing and Presentation 433 Presentation of Antigen to the Lymphocytes and Its Early Consequences 434 15.4 Steps III and IV: B-Cell Response 435 Activation of B Lymphocytes: Clonal Expansion and Antibody Production 435 Product of B Lymphocytes: Antibody Structure and Functions 436 15.5 Step III and IV: T-Cell Response 440 Cell-Mediated Immunity (CMI) 440 15.6 Specific Immunity and Vaccination 443 Natural Active Immunity: Getting the Infection 444 Natural Passive Immunity: Mother to Child 444 Artificial Active Immunization: Vaccination 445 Artificial Passive Immunization: Immunotherapy 445 Immunization: Methods of Manipulating Immunity for Therapeutic Purposes 446 Development of New Vaccines 450 Route of Administration and Side Effects of Vaccines 450 To Vaccinate: Why, Whom, and When? 451 INSIGHT 15.1 Monoclonal Antibodies: Variety Without Limit 444 INSIGHT 15.2 The Lively History of Active Immunization

Chapter Summary 455 Multiple-Choice and True-False Knowledge and Comprehension 456 Critical Thinking Questions Application and Analysis Concept Mapping Synthesis 457 Visual Connections Synthesis 458

452

459

16.1 The Immune Response: A Two-Sided Coin 460 16.2 Type I Allergic Reactions: Atopy and Anaphylaxis 461 Allergy/Hypersensitivity 461 Epidemiology and Modes of Contact with Allergens 461 The Nature of Allergens and Their Portals of Entry 462 Mechanisms of Type I Allergy: Sensitization and Provocation 463 Cytokines, Target Organs, and Allergic Symptoms 465 Specific Diseases Associated with IgE- and Mast-CellMediated Allergy 466 Anaphylaxis: An Overpowering Systemic Reaction 468 Diagnosis of Allergy 468 Treatment and Prevention of Allergy 469 16.3 Type II Hypersensitivities: Reactions That Lyse Foreign Cells 470 The Basis of Human ABO Antigens and Blood Types 470 Antibodies Against A and B Antigens 471 The Rh Factor and Its Clinical Importance 473 Other RBC Antigens 474 Mechanisms of Immune Complex Disease 474 16.4 Type III Hypersensitivities: Immune Complex Reactions 474 Types of Immune Complex Disease 475 16.5 Type IV Hypersensitivities: Cell-Mediated (Delayed) Reactions 476 Delayed-Type Hypersensitivity 476 Contact Dermatitis 476 T Cells and Their Role in Organ Transplantation 476 16.6 An Inappropriate Response Against Self: Autoimmunity 479 Genetic and Gender Correlation in Autoimmune Disease 480 The Origins of Autoimmune Disease 480 Examples of Autoimmune Disease 481 16.7 Immunodeficiency Diseases: Hyposensitivity of the Immune System 482 Primary Immunodeficiency Diseases 482 Secondary Immunodeficiency Diseases 485 INSIGHT 16.1 Of What Value Is Allergy?

446

INSIGHT 15.3 Manipulating the Immune System to Fight Lots of Things Besides Infections 447 INSIGHT 15.4 Where the Anti-Vaxxers Get It Wrong

16

466

INSIGHT 16.2 Why Doesn’t a Mother Reject Her Fetus? INSIGHT 16.3 Pretty, Pesky, Poisonous Plants

478

INSIGHT 16.4 The Mechanics of Bone Marrow Transplantation 479 INSIGHT 6.5 An Answer to the Bubble Boy Mystery

457

Chapter Summary 486 Multiple-Choice and True-False Knowledge and Comprehension 487 Critical Thinking Questions Application and Analysis Concept Mapping Synthesis 488 Visual Connections Synthesis 489

485

488

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CHAPTER

17

Diagnosing Infections

490

17.1 Preparation for the Survey of Microbial Diseases 491 Phenotypic Methods 491 Genotypic Methods 491 Immunologic Methods 491 17.2 On the Track of the infectious Agent: Specimen Collection 492 Overview of Laboratory Techniques 493 17.3 Phenotypic Methods 495 Immediate Direct Examination of Specimen 495 Cultivation of Specimen 495 17.4 Genotypic Methods 497 DNA Analysis Using Genetic Probes 497 Nucleic Acid Sequencing and rRNA Analysis 498 Polymerase Chain Reaction 498 17.5 Immunologic Methods 499 General Features of Immune Testing 499 Agglutination and Precipitation Reactions 500 The Western Blot for Detecting Proteins 502 Complement Fixation 503 Miscellaneous Serological Tests 504 Fluorescent Antibodies and Immunofluorescence Testing 504 Immunoassays 504 In Vivo Testing 507 A Viral Example 507 INSIGHT 17.1 The Uncultured

492

INSIGHT 17.2 When Positive Is Negative: How to Interpret Serological Test Results 500 Chapter Summary 509 Multiple-Choice and True-False Knowledge and Comprehension 509 Critical Thinking Questions Application and Analysis Concept Mapping Synthesis 511 Visual Connections Synthesis 511

CHAPTER

510

18

Infectious Disease Affecting the Skin and Eyes 512 18.1 The Skin and Its Defenses 513 18.2 Normal Biota of the Skin 514 18.3 Skin Diseases Caused by Microorganisms 515 Acne 515 Impetigo 516 Cellulitis 521 Staphylococcal Scalded Skin Syndrome (SSSS) 522 Gas Gangrene 523 Vesicular or Pustular Rash Diseases 524 Maculopapular Rash Diseases 530

xxix

Wartlike Eruptions 534 Large Pustular Skin Lesions 535 Ringworm (Cutaneous Mycoses) 536 Superficial Mycoses 538 18.4 The Surface of the Eye and Its Defenses 539 18.5 Normal Biota of the Eye 540 18.6 Eye Diseases Caused by Microorganisms 540 Conjunctivitis 540 Trachoma 541 Keratitis 542 River Blindness 543 INSIGHT 18.1 The Skin Predators: Staphylococcus and Streptococcus and Their Superantigens 518 INSIGHT 18.2 Smallpox: An Ancient Scourge Becomes a Modern Threat 527 INSIGHT 18.3 Naming Skin Lesions

528

Chapter Summary 546 Multiple-Choice and True-False Knowledge and Comprehension 547 Critical Thinking Questions Application and Analysis Concept Mapping Synthesis 548 Visual Connections Synthesis 549

CHAPTER

547

19

Infectious Diseases Affecting the Nervous System 550 19.1 The Nervous System and Its Defenses 551 19.2 Normal Biota of the Nervous System 552 19.3 Nervous System Diseases Caused by Microorganisms 552 Meningitis 552 Neonatal Meningitis 558 Meningoencephalitis 561 Acute Encephalitis 562 Subacute Encephalitis 564 Rabies 568 Poliomyelitis 570 Tetanus 573 Botulism 574 African Sleeping Sickness 577 INSIGHT 19.1 Baby Food and Meningitis

560

INSIGHT 19.2 A Long Way from Egypt: West Nile Virus in the United States 563 INSIGHT 19.3 Toxoplasmosis Leads to More Car Accidents? 566 INSIGHT 19.4 Polio 572 INSIGHT 19.5 Botox: Anti-Wrinkles, Anti-Cancer. Chapter Summary 581 Multiple-Choice and True-False Knowledge and Comprehension 582 Critical Thinking Questions Application and Analysis Concept Mapping Synthesis 583 Visual Connections Synthesis 583

576

582

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CHAPTER

20

21.5 Lower Respiratory Tract Diseases Caused by Microorganisms 640 Tuberculosis 640 Pneumonia 645

Infectious Diseases Affecting the Cardiovascular and Lymphatic Systems 584

INSIGHT 21.1 Flus Over the Years

20.1 The Cardiovascular and Lymphatic Systems and Their Defenses 585 The Cardiovascular System 585 The Lymphatic System 586 Defenses of the Cardiovascular of Lymphatic Systems 586 20.2 Normal Biota of the Cardiovascular and Lymphatic Systems 587 20.3 Cardiovascular and Lymphatic System Diseases Caused by Microorganisms 587 Endocarditis 588 Septicemias 589 Plague 590 Tularemia 592 Lyme Disease 593 Infectious Mononucleosis 596 Hemorrhagic Fever Diseases 597 Nonhemorrhagic Fever Diseases 599 Malaria 602 Anthrax 606 HIV Infection and AIDS 608 Adult T-Cell Leukemia 616 INSIGHT 20.1 Floss For Your Heart?

587

INSIGHT 20.2 The Arthropod Vectors of Infectious Disease INSIGHT 20.3 Fewer Mosquitoes—Not So Fast INSIGHT 20.4 AIDS-Defining Illnesses (ADIs)

605

609

Chapter Summary 619 Multiple-Choice and True-False Knowledge and Comprehension 620 Critical Thinking Questions Application and Analysis Concept Mapping Synthesis 621 Visual Connections Synthesis 621

CHAPTER

620

21

Infectious Diseases Affecting the Respiratory System 622 21.1 The Respiratory Tract and Its Defenses 623 21.2 Normal Biota of the Respiratory Tract 624 21.3 Upper Respiratory Tract Diseases Caused by Microorganisms 624 Sinusitis 626 Acute Otitis Media (Ear Infection) 627 Pharyngitis 628 Diphtheria 632 21.4 Diseases Caused by Microorganisms Affecting Both the Upper and Lower Respiratory Tracts 633 Whooping Cough 633 Respiratory Syncytial Virus Infection 635 Influenza 635

594

638

INSIGHT 21.2 Fungal Lung Diseases

649

INSIGHT 12.3 Bioterror in the Lungs

650

Chapter Summary 657 Multiple-Choice and True-False Knowledge and Comprehension 658 Critical Thinking Questions Application and Analysis Concept Mapping Synthesis 659 Visual Connections Synthesis 659

CHAPTER

658

22

Infectious Diseases Affecting the Gastrointestinal Tract 660 22.1 The Gastrointestinal Tract and Its Defenses 661 22.2 Normal Biota of the Gastrointestinal Tract 663 22.3 Gastrointestinal Tract Diseases Caused by Microorganisms (Nonhelminthic) 664 Tooth and Gum Infections 664 Dental Caries (Tooth Decay) 664 Periodontal Diseases 666 Mumps 668 Gastritis and Gastric Ulcers 670 Acute Diarrhea 671 Acute Diarrhea with Vomiting (Food Poisoning) 682 Chronic Diarrhea 684 Hepatitis 688 22.4 Gastrointestinal Tract Diseases Caused by Helminths 692 General Clinical Considerations 692 Disease: Intestinal Distress as the Primary Symptom 694 Disease: Intestinal Distress Accompanied by Migratory Symptoms 696 Liver and Intestinal Disease 698 Disease: Muscle and Neurological Symptoms 699 Liver Disease 700 INSIGHT 22.1 Crohn’s Is an Infection That We Get from Cows? 663 INSIGHT 22.2 A Little Water, Some Sugar, and Salt Save Millions of Lives 679 INSIGHT 22.3 Microbes Have Fingerprints, Too

683

INSIGHT 22.4 Treating Inflammatory Bowel Disease with Worms? 694 Chapter Summary 705 Multiple-Choice and True-False Knowledge and Comprehension 706 Critical Thinking Questions Application and Analysis Concept Mapping Synthesis 707 Visual Connections Synthesis 707

707

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CHAPTER

23

INSIGHT 24.3 It’s Raining Bacteria

Chapter Summary 759 Multiple-Choice and True-False Knowledge and Comprehension 759 Critical Thinking Questions Application and Analysis Concept Mapping Synthesis 760 Visual Connections Synthesis 761

Infectious Diseases Affecting the Genitourinary System 708 23.1 The Genitourinary Tract and Its Defenses 709 23.2 Normal Biota of the Urinary Tract 711 Normal Biota of the Male Genital Tract 712 Normal Biota of the Female Genital Tract 712 23.3 Urinary Tract Diseases Caused by Microorganisms Urinary Tract Infections (UTIs) 712 Leptospirosis 713 Urinary Schistosomiasis 714 23.4 Reproductive Tract Diseases Caused by Microorganisms 715 Vaginitis and Vaginosis 715 Prostatitis 718 Discharge Diseases with Major Manifestation in the Genitourinary Tract 718 Genital Ulcer Diseases 723 Wart Diseases 731 Group B Streptococcus “Colonization”—Neonatal Disease 733 INSIGHT 23.1 Pelvic Inflammatory Disease and Infertility INSIGHT 23.2 The Pap Smear

712

720

733

Chapter Summary 738 Multiple-Choice and True-False Knowledge and Comprehension 739 Critical Thinking Questions Application and Analysis Concept Mapping Synthesis 740 Visual Connections Synthesis 740

756

739

CHAPTER

760

25

Applied Microbiology and Food and Water Safety 762 25.1 Applied Microbiology and Biotechnology 763 25.2 Microorganisms in Water and Wastewater Treatment 763 Water Monitoring to Prevent Disease 766 25.3 Microorganisms Making Food and Spoiling Food 769 Microbial Fermentations in Food Products from Plants 769 Microbes in Milk and Dairy Products 772 Microorganisms as Food 774 Microbial Involvement in Food-Borne Diseases 774 Prevention Measures for Food Poisoning and Spoilage 774 25.4 Using Microbes to Make Things We Need 778 From Microbial Factories to industrial Factories 780 Substance Production 781 INSIGHT 25.1 Bioremediation: The Pollution Solution? INSIGHT 25.2 The Waning Days of a Classic Test?

CHAPTER

24

Environmental Microbiology 741

764

767

INSIGHT 25.3 Wood or Plastic: On the Cutting Edge of Cutting Boards 776 INSIGHT 25.4 Microbes Degrade—and Repair—Ancient Works of Art 782

24.1 Ecology: The Interconnecting Web of Life 742 The Organization of Ecosystems 743 Energy and Nutritional Flow in Ecosystems 744 24.2 The Natural Recycling of Bioelements 747 Atmospheric Cycles 747 The Sedimentary Cycles 749 24.3 Microbes on Land and in Water 753 Environmental Sampling in the Genomic Era 753 Soil Microbiology: The Composition of the Lithosphere 753 Deep Subsurface Microbiology 755 Aquatic Microbiology 755

Chapter Summary 784 Multiple-Choice and True-False Knowledge and Comprehension 784 Critical Thinking Questions Application and Analysis Concept Mapping Synthesis 785 Visual Connections Synthesis 785

INSIGHT 24.1 Greenhouse Gases, Fossil Fuels, Cows, Termites, and Global Warming 750

Glossary

INSIGHT 24.2 Cute Killer Whale—Or Swimming Waste Dump? 752

Index

785

APPENDIX A Exponents A1 APPENDIX B Significant Events in Microbiology A3 APPENDIX C Answers to Multiple-Choice and Selected True-False Matching Questions

A4

APPENDIX D An Introduction to Concept Mapping A6 Credits

G1 C1

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The Main Themes of Microbiology 1 Case File In 2000, genomic researcher J. Craig Venter stood with physician and geneticist Francis Collins and U.S. President Bill Clinton to announce that the Human Genome Project, a worldwide effort to identify all the genes in a human being, was essentially complete. Two years later, Venter was aboard his 95-foot sailboat, the Sorcerer II, “fishing” for new genomes to map—those of microorganisms living in the ocean. As the Sorcerer II sailed the Sargasso Sea, Venter and his assistants collected 200-liter samples of seawater and filtered them so that only organisms 1 to 3 μm in size were retained. They then froze these life forms onto filter paper and sent them to Venter’s facility in Rockville, Maryland, for analysis. Using molecular biology techniques first developed for the Human Genome Project, Venter hoped to classify the new life forms by identifying novel genes without having to coax organisms to grow in the lab. Venter’s efforts were so successful that many people compared his voyage to that of the British naturalist Charles Darwin, which had occurred over 170 years earlier and led to Darwin’s theory of evolution, a premise that underlies nearly every aspect of biology today. ◾ What are some possible benefits of discovering new microbial species? ◾ What does the theory of evolution state? Continuing the Case appears on page 15.

Outline and Learning Outcomes 1.1 The Scope of Microbiology 1. List the various types of microorganisms. 2. Identify multiple types of professions using microbiology. 1.2 The Impact of Microbes on Earth: Small Organisms with a Giant Effect 3. Describe the role and impact of microbes on earth. 4. Explain the theory of evolution and why it is called a theory.

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Chapter 1

The Main Themes of Microbiology

1.3 Human Use of Microorganisms 5. Explain the ways that humans manipulate organisms for their own uses. 1.4 Infectious Diseases and the Human Condition 6. Summarize the relative burden of human disease caused by microbes. 1.5 The General Characteristics of Microorganisms 7. Differentiate between prokaryotic and eukaryotic microorganisms. 8. Identify a third type of microorganism. 9. Compare and contrast the relative sizes of the different microbes. 1.6 The Historical Foundations of Microbiology 10. Make a time line of the development of microbiology from the 1600s to today. 11. List some recent microbiology discoveries of great impact. 12. Explain what is important about the scientific method. 1.7 Naming, Classifying, and Identifying Microorganisms 13. Differentiate between the terms nomenclature, taxonomy, and classification. 14. Create a mnemonic device for remembering the taxonomic categories. 15. Correctly write the binomial name for a microorganism. 16. Draw a diagram of the three major domains. 17. Explain the difference between traditional and molecular approaches to taxonomy.

1.1 The Scope of Microbiology Microbiology is a specialized area of biology that deals with living things ordinarily too small to be seen without magnification. Such microscopic organisms are collectively referred to as microorganisms (my″-kroh-or′-gun-izms), microbes, or several other terms depending on the kind of microbe or the purpose. In the context of infection and disease, some people call them germs, viruses, or agents; others even call them “bugs”; but none of these terms are clear. In addition, some of these terms place undue emphasis on the disagreeable reputation of microorganisms. But, as we will learn throughout the course of this book, only a small minority of microorganisms are implicated in causing harm to other living beings. There are several major groups of microorganisms that we’ll be studying. They are bacteria, algae, protozoa, helminths (parasitic invertebrate animals such as worms), and fungi. All of these microbes—just like plants and animals—can be infected by viruses, which are noncellular, parasitic, proteincoated genetic elements, dependent on their infected host. They can cause harm to the host they infect. Although viruses are not strictly speaking microorganisms—namely, cellular beings—their evolutionary history and impact are intimately connected with the evolution of microbes and their study is thus integrated in the science of microbiology. As we will see in subsequent chapters, each group of microbes exhibits a distinct collection of biological characteristics. The nature of microorganisms makes them both very easy and very difficult to study—easy because they reproduce so rapidly and we can quickly grow large populations in the laboratory and difficult because we can’t see them directly. We rely on a variety of indirect means of analyzing them in addition to using microscopes. Microbiology is one of the largest and most complex of the biological sciences because it includes many diverse

biological disciplines. Microbiologists study every aspect of microbes—their cell structure and function, their growth and physiology, their genetics, their taxonomy and evolutionary history, and their interactions with the living and nonliving environment. The latter includes their uses in industry and agriculture and the way they interact with mammalian hosts, in particular, their properties that may cause disease or lead to benefits. Some descriptions of different branches of study appear in table 1.1. Studies in microbiology have led to greater understanding of many general biological principles. For example, the study of microorganisms established universal concepts concerning the chemistry of life (see chapters 2 and 8); systems of inheritance (see chapter 9); and the global cycles of nutrients, minerals, and gases (see chapter 24).

1.1 Learning Outcomes—Can You . . . 1. . . . list the various types of microorganisms? 2. . . . identify multiple types of professions using microbiology?

1.2 The Impact of Microbes on Earth: Small Organisms with a Giant Effect The most important knowledge that should emerge from a microbiology course is the profound influence microorganisms have on all aspects of the earth and its residents. For billions of years, microbes have extensively shaped the development of the earth’s habitats and the evolution of other life forms. It is understandable that scientists searching for life on other planets first look for signs of microorganisms. Bacterial-type organisms have been on this planet for about 3.5 billion years, according to the fossil record. It appears that they were the only living inhabitants on earth

1.2 The Impact of Microbes on Earth: Small Organisms with a Giant Effect

for almost 2 billion years. At that time (about 1.8 billion years ago), a more complex type of single-celled organism arose, of a eukaryotic (yoo″-kar-ee-ah′-tik) cell type. Eu-kary means true nucleus, which gives you a hint that those first inhabitants, the bacteria, had no true nucleus. For that reason they are called prokaryotes (proh″-kar′-ee-otes) (prenucleus).

A Note About “-Karyote” Versus “-Caryote” You will see the terms prokaryote and eukaryote spelled with c (procaryote and eucaryote) as well as k. Both spellings are accurate. This book uses the k spelling.

The early eukaryotes were the precursors of the cell type that eventually formed multicellular animals, including humans. But you can see from figure 1.1 how long that took! On the scale pictured in the figure, humans seem to have just appeared. The prokaryotes preceded even the earliest animals by about 3 billion years. This is a good indication that humans are not likely to—nor should we try to— eliminate bacteria from our environment. They’ve survived and adapted to many catastrophic changes over the course of their geologic history. Another indication of the huge influence bacteria exert is how ubiquitous they are. Microbes can be found nearly everywhere, from deep in the earth’s crust, to the polar ice caps and oceans, to the bodies of plants and animals. Being mostly invisible, the actions of microorganisms are usually not as obvious or familiar as those of larger plants and animals. They make up for their small size by occurring in large numbers and living in places that many other organisms cannot survive. Above all, they play central roles in the earth’s landscape that are essential to life. When we point out that prokaryotes have adapted to a wide range of conditions over the 3.8 billion years of their

3

presence on this planet, we are talking about evolution. The presence of life in its present form would not be possible if the earliest life forms had not changed constantly, adapting to their environment and circumstances. Getting from the far left in figure 1.1 to the far right, where humans appeared, involved billions and billions of tiny changes, starting with the first cell that appeared about a billion years after the planet itself was formed. You have no doubt heard this concept described as the “theory of evolution.” Let’s clarify some terms. Evolution is the accumulation of changes that occur in organisms as they adapt to their environments. It is documented every day in all corners of the planet, an observable phenomenon testable by science. It is often referred to as the theory of evolution. This has led to great confusion among the public. As we will explain in section 1.6, scientists use the term “theory” in a different way than the general public does. By the time a principle has been labeled a theory in science, it has undergone years and years of testing and not been disproven. This is much different than the common usage, as in “My theory is that he overslept and that’s why he was late.” The theory of evolution, like the germ theory and many other scientific theories, are labels for well-studied and well-established natural phenomena.

Microbial Involvement in Shaping Our Planet Microbes are deeply involved in the flow of energy and food through the earth’s ecosystems.1 Most people are aware that plants carry out photosynthesis, which is the light-fueled conversion of carbon dioxide to organic material, accompanied by the formation of oxygen (called oxygenic photosynthesis). However, bacteria invented photosynthesis long before first plants appeared, first as a 1. Ecosystems are communities of living organisms and their surrounding environment.

Humans appeared. Mammals appeared. Cockroaches, termites appeared. Reptiles appeared. Eukaryotes appeared. Probable origin of earth

Prokaryotes appeared.

Figure 1.1 Evolutionary time

4 billion years ago

3 billion years ago

2 billion years ago

1 billion years ago

Present time

line. The first bacteria appeared approximately 3.5 billion years ago. They were the only form of life for half of the earth’s history.

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Chapter 1

The Main Themes of Microbiology

Table 1.1 Microbiology—A Sampler A. Medical Microbiology This branch deals with microbes that cause diseases in humans and animals. Researchers examine factors that make the microbes virulent and mechanisms for inhibiting them.

Figure A. A staff microbiologist at the Centers for Disease Control and Prevention (CDC) examines a culture of influenza virus identical to one that circulated in 1918. The lab is researching why this form of the virus was so deadly and how to develop vaccines and other treatments. Handling such deadly pathogens requires a high level of protection with special headgear and hoods. B. Public Health Microbiology and Epidemiology These branches monitor and control the spread of diseases in communities. Institutions involved in this concern are the U.S. Public Health Service (USPHS) with its main agency, the Centers for Disease Control and Prevention (CDC) located in Atlanta, Georgia, and the World Health Organization (WHO), the medical limb of the United Nations.

Figure B. Epidemiologists from the CDC employ an unusual method for microbial sampling. They are collecting grass clippings to find the source of an outbreak of tularemia in Massachusetts.

C. Immunology This branch studies the complex web of protective substances and cells produced in response to infection. It includes such diverse areas as vaccination, blood testing, and allergy (see chapters 15, 16, and 17).

Figure C. An immunologist harvests chicken antibodies from egg yolks.

1.2 The Impact of Microbes on Earth: Small Organisms with a Giant Effect

D. Industrial Microbiology This branch safeguards our food and water, and also includes biotechnology, the use of microbial metabolism to arrive at a desired product, ranging from bread making to gene therapy. Microbes can be used to create large quantities of substances such as amino acids, beer, drugs, enzymes, and vitamins.

Figure D. Food inspectors sample a beef carcass for potential infectious agents. The safety of the food supply has wide-ranging importance.

E. Agricultural Microbiology This branch is concerned with the relationships between microbes and domesticated plants and animals. Plant specialists focus on plant diseases, soil fertility, and nutritional interactions. Animal specialists work with infectious diseases and other associations animals have with microorganisms.

Figure E. Plant microbiologists examine images of alfalfa sprouts to see how microbial growth affects plant roots.

F. Environmental Microbiology These microbiologists study the effect of microbes on the earth’s diverse habitats. Whether the microbes are in freshwater or saltwater, topsoil or the earth’s crust, they have profound effects on our planet. Subdisciplines of environmental microbiology are Aquatic microbiology—the study of microbes in the earth’s surface water Soil microbiology—the study of microbes in terrestrial parts of the planet Geomicrobiology—the study of microbes in the earth’s crust and Astrobiology (also known as exobiology)—the search for/study of microbial and other life in places off of our planet (see Insight 1.3)

Figure F. Researchers collect samples and data in Lake Erie.

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Chapter 1

The Main Themes of Microbiology

(a)

(b)

Figure 1.2 Examples of microbial habitats. (a) Summer pond with a thick mat of algae—a rich photosynthetic community. (b) Microbes play a large role in decomposing dead animal and plant matter.

process that did not produce oxygen (anoxygenic photosynthesis). This anoxygenic photosynthesis later evolved into oxygenic photosynthesis, which not only produced oxygen but also was much more efficient in extracting energy from sunlight. Hence, bacteria were responsible for changing the atmosphere of the earth from one without oxygen to one with oxygen. The production of oxygen also led to the use of oxygen for aerobic respiration and the formation of ozone, both of which set off an explosion in species diversification. Today, photosynthetic microorganisms (bacteria and algae) account for more than 70% of the earth’s photosynthesis, contributing the majority of the oxygen to the atmosphere (figure 1.2a). Another process that helps keep the earth in balance is the process of biological decomposition and nutrient recycling. Decomposition involves the breakdown of dead matter and wastes into simple compounds that can be directed back into the natural cycles of living things (figure 1.2b). If it were not for multitudes of bacteria and fungi, many chemical elements would become locked up and unavailable to organisms; we humans would drown in our own industrial and personal wastes! In the long-term scheme of things, microorganisms are the main forces that drive the structure and content of the soil, water, and atmosphere. For example: • The very temperature of the earth is regulated by gases, such as carbon dioxide, nitrous oxide, and methane, which create an insulation layer in the atmosphere and help retain heat. Many of these gases are produced by microbes living in the environment and the digestive tracts of animals.

• Recent estimates propose that, based on weight and numbers, up to 50% of all organisms exist within and beneath the earth’s crust in sediments, rocks, and even volcanoes. It is increasingly evident that this enormous underground community of microbes is a significant influence on weathering, mineral extraction, and soil formation. • Bacteria and fungi live in complex associations with plants that assist the plants in obtaining nutrients and water and may protect them against disease. Microbes form similar interrelationships with animals, notably, in the stomach of cattle, where a rich assortment of bacteria digest the complex carbohydrates of the animals’ diets.

1.2 Learning Outcomes—Can You . . . 3. . . . describe the role and impact of microbes on the earth? 4. . . . explain the theory of evolution and why it is called a theory?

1.3 Human Use of Microorganisms Microorganisms clearly have monumental importance to the  earth’s operation. It is this very same diversity and versatility that also makes them excellent candidates for solving human problems. By accident or choice, humans have been using microorganisms for thousands of years to improve life and even to shape civilizations. Baker’s and brewer’s yeast, types of single-celled fungi, cause bread to rise and ferment sugar into alcohol to make wine and  beers. Other fungi are used to make special cheeses

1.3 Human Use of Microorganisms

such as Roquefort or Camembert. These and other “home” uses of microbes have been in use for thousands of years. For example, historical records show that households in ancient Egypt kept moldy loaves of bread to apply directly to wounds and lesions. When humans manipulate microorganisms to make products in an industrial setting, it is called biotechnology. For example, some specialized bacteria have unique capacities to mine precious metals or to clean up human-created contamination (figure 1.3). Genetic engineering is an area of biotechnology that manipulates the genetics of microbes, plants, and animals for the purpose of creating new products and genetically modified organisms (GMOs). One powerful technique for designing GMOs is termed recombinant DNA technology. This technology makes it possible to transfer genetic material from one organism to another and to deliberately alter DNA.2 Bacteria and fungi were some of the first organisms to be genetically engineered. This was possible because they are single-celled organisms and they are so adaptable to changes in their genetic makeup. Recombinant DNA technology has unlimited potential in terms of medical, industrial, and agricultural uses. Microbes can be engineered to synthesize desirable products such as drugs, hormones, and enzymes. Among the genetically unique organisms that have been designed by bioengineers are bacteria that mass produce antibiotic-like substances, yeasts that produce human insulin, pigs that produce human hemoglobin, and plants that contain natural pesticides or fruits that do not ripen too rapidly. The techniques also pave the way for characterizing human genetic material and diseases. Another way of tapping into the unlimited potential of microorganisms is the science of bioremediation (by′-oh-ree-mee-dee-ay″-shun). This process involves the introduction of microbes into the environment to restore stability or to clean up toxic pollutants. Microbes have a surprising capacity to break down chemicals that would be harmful to other organisms. This includes even manmade chemicals that scientists have developed and for which there are no natural counterparts. Agencies and companies have developed microbes to handle oil spills and detoxify sites contaminated with heavy metals, pesticides, and other chemical wastes (figure 1.3c). The solid waste disposal industry is interested in developing methods for degrading the tons of garbage in landfills, especially human-made plastics and paper products. One form of bioremediation that has been in use for some time is the treatment of water and sewage. Because clean freshwater supplies are dwindling worldwide, it will become even more important to find ways to reclaim polluted water.

1.3 Learning Outcomes—Can You . . . 5. . . . explain the ways that humans manipulate organisms for their own uses?

2. DNA, or deoxyribonucleic acid, is the chemical substance that comprises the genetic material of organisms.

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(a)

(b)

(c)

Figure 1.3 Microbes at work. (a) An aerial view of a copper mine looks like a giant quilt pattern. The colored patches are bacteria in various stages of extracting metals from the ore. (b) Microbes as synthesizers. Fermenting tanks at a winery. (c) Members of a biohazard team from the National Oceanic and Atmospheric Agency (NOAA) participate in the removal and detoxification of 63,000 tons of crude oil released by a wrecked oil tanker on the coast of Spain. The bioremediation of this massive spill made use of naturally occurring soil and water microbes as well as commercially prepared oil-eating species of bacteria and fungi.

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Chapter 1

The Main Themes of Microbiology

1.4 Infectious Diseases and the Human Condition

14,000

One of the most fascinating aspects of the microorganisms with which we share the earth is that, despite all of the benefits they provide, they also contribute significantly to human misery as pathogens (path′-oh-jenz). The vast majority of microorganisms that associate with humans cause no harm. In fact, they provide many benefits to their human hosts. There is little doubt that a diverse microbial biota living in and on humans is an important part of human well-being. However, humankind is also plagued by nearly 2,000 different microbes that can cause various types of disease. Infectious diseases still devastate human populations worldwide, despite significant strides in understanding and treating them. The World Health Organization (WHO) estimates there are a total of 10 billion new infections across the world every year. Infectious diseases are also among the most common causes of death in much of humankind, and they still kill a significant percentage of the U.S. population. Table 1.2 depicts the 10 top causes of death per year (by all causes, infectious and noninfectious) in the United States and worldwide. The worldwide death toll from infections is about 13 million people per year. For example, the CDC reports that every 30 seconds a child dies from malaria. In figure 1.4, you can see that high-income countries like ours see many more deaths caused by chronic, noninfectious, diseases (heart disease, cancer, stroke) than those caused by infections. Low-income countries (on the left on the graph) suffer high rates of death from these diseases but even higher rates of deaths from infections. Economics is closely tied to survival in these countries. Malaria, which kills more than a million people every year worldwide, is caused by a microorganism transmitted by mosquitoes (see chapter 20). Currently, the most effective way for citizens of developing countries to avoid infection with the causal agent of malaria is to sleep under a bed net, because the mosquitoes are most active in the evening. Yet even this inexpensive

Total deaths (000)

12,000 10,000 8,000 6,000 4,000 2,000 0

Low income countries

Lower middle Upper middle income countries income countries

Communicable diseases, maternal and perinatal conditions, and nutritional deficiencies

High income countries

Chronic diseases* Injuries

*Chronic diseases include cardiovascular diseases, cancers, chronic respiratory disorders, diabetes, neuropsychiatric and sense organ disorders, musculoskeletal and oral disorders, digestive diseases, genitourinary diseases, congenital abnormalities, and skin diseases.

Figure 1.4 The role of infectious diseases vs. other causes of death in countries of varying income. solution is beyond the reach of many. Mothers in Southeast Asia and elsewhere have to make nightly decisions about which of their children will sleep under the single family bed net, because a second one, priced at about $3 to $5, is too expensive for them. Adding to the overload of infectious diseases, we are also witnessing an increase in the number of new (emerging) and older (reemerging) diseases. AIDS, hepatitis C, and viral encephalitis are examples of diseases that cause severe mortality and morbidity. To somewhat balance this trend, there have also been some advances in eradication of diseases such as polio, measles, and leprosy and diseases caused by certain parasitic worms. One of the most eye-opening discoveries in recent years is that many diseases that used to be considered noninfectious probably do involve microbial infection. The most famous of these is gastric ulcers, now known to be caused by a bacterium called Helicobacter. But there are more. An association has been established between certain cancers and bacteria and

Table 1.2 Top Causes of Death—All Diseases United States

No. of Deaths

Worldwide

No. of Deaths

1. Heart disease

652,000

1. Heart disease

12.2 million

2. Cancer

559,000

2. Stroke

5.7 million

3. Stroke

144,000

3. Cancer

5.7 million

4. Chronic lower-respiratory disease

131,000

4. Respiratory infections*

3.9 million

5. Unintentional injury (accidents)

118,000

5. Chronic lower-respiratory disease

3.6 million

6. Diabetes

75,000

6. Accidents

3.5 million

7. Alzheimer’s disease

72,000

7. HIV/AIDS

2.9 million

8. Influenza and pneumonia

63,000

8. Perinatal conditions

2.5 million

9. Kidney problems

44,000

9. Diarrheal diseases

2.0 million

10. Septicemia (bloodstream infection)

34,000

*Diseases in red are those most clearly caused by microorganisms. Source: Data from the World Health Organization, 2008.

10. Tuberculosis

1.6 million

1.4

viruses, between diabetes and the Coxsackie virus, and between schizophrenia and a virus called the Borna agent. Diseases as different as multiple sclerosis, obsessive compulsive disorder, coronary artery disease, and even obesity have been linked to chronic infections with microbes or viruses. It seems that the golden age of microbiological discovery, during which all of the “obvious” diseases were characterized and cures or preventions were devised for them, should more accurately be referred to as the first golden age. We’re now discovering the subtler side of microorganisms. Their roles in quiet but slowly destructive diseases are now well known. These include female infertility caused by Chlamydia infection, and malignancies such as liver cancer (hepatitis viruses) and cervical cancer (human papillomavirus). Here again, lowincome countries differ from high-income countries. It seems that up to 26% of cancers in low-income countries are caused

INSIGHT 1.1

Infectious Diseases and the Human Condition

by viruses or bacteria, while less than 7% of malignancies in the developed world are microbially induced. As mentioned earlier, another important development in infectious disease trends is the increasing number of patients with weakened defenses that are kept alive for extended periods. They are subject to infections by common microbes that are not pathogenic to healthy people. There is also an increase in microbes that are resistant to drugs. It appears that even with the most modern technology available to us, microbes still have the “last word,” as the great French scientist Louis Pasteur observed (Insight 1.1).

1.4 Learning Outcomes—Can You . . . 6. . . . summarize the relative burden of human disease caused by microbes?

The More Things Change . . .

In 1964, the surgeon general of the United States delivered a speech to Congress: “It is time to close the book on infectious diseases,” he said. “The war against pestilence is over.” In 1998, Surgeon General David Satcher had a different message. The Miami Herald reported his speech with this headline: “Infectious Diseases a Rising Peril; Death Rates in U.S. Up 58% Since 1980.” The middle of the last century was a time of great confidence in science and medicine. With the introduction of antibiotics in the 1940s, and a lengthening list of vaccines that prevented the most frightening diseases, Americans felt that it was only a matter of time before diseases caused by microorganisms (i.e., infectious diseases) would be completely manageable. The nation’s attention turned to the so-called chronic diseases, such as heart disease, cancer, and stroke. So what happened to change the optimism of the 1960s to the warning expressed in the speech from 1998? Dr. Satcher explained it this way: “Organisms changed and people changed.” First, we are becoming more susceptible to infectious disease precisely because of advances in medicine. People are living longer. Sicker people are staying alive much longer than in the past. Older and sicker people have heightened susceptibility to what we might call garden-variety microbes. Second, the population has become more mobile. Travelers can crisscross the globe in a matter of hours, taking their microbes with them and

United States Surgeon General Luther Terry addressing a press conference in 1964.

9

United States Surgeon General David Satcher in 1998.

introducing them into new “naive” populations. Third, there are growing numbers of microbes that truly are new (or at least, new to us). The conditions they cause are called emerging diseases. Changes in agricultural practices and encroachment of humans on wild habitats are just two probable causes of emerging diseases. The mass production and packing of food increases the opportunity for large outbreaks, especially if foods are grown in fecally contaminated soils or are eaten raw or poorly cooked. In the past several years, dozens of food-borne outbreaks have been associated with the bacterium Escherichia coli O157:H7 in fresh vegetables, fruits, and meats. Fourth, microorganisms have demonstrated their formidable capacity to respond and adapt to our attempts to control them, most spectacularly by becoming resistant to the effects of our miracle drugs. And there’s one more thing: Evidence is mounting that many conditions formerly thought to be caused by genetics or lifestyle, such as heart disease and cancer, can often be at least partially caused by microorganisms. Microbes never stop surprising us—in their ability not only to harm but also to help us. The best way to keep up is to learn as much as you can about them. This book is a good place to start.

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The Main Themes of Microbiology

1.5 The General Characteristics of Microorganisms Cellular Organization As discussed earlier, two basic cell lines appeared during evolutionary history. These lines, termed prokaryotic cells and eukaryotic cells, differ not only in the complexity of their cell structure (figure 1.5a) but also in contents and function. In general, prokaryotic cells are about 10 times smaller than eukaryotic cells, and they lack many of the eukaryotic cell structures such as organelles. Organelles are small, doublemembrane-bound structures in the eukaryotic cell that perform specific functions and include the nucleus, mitochondria, and chloroplasts. The microorganisms that consist of these two different cell types (called prokaryotes and eukaryotes) are covered in more detail in chapters 4 and 5. All prokaryotes are microorganisms, but only some eukaryotes are microorganisms. The majority of microorganisms are single-celled (all prokaryotes and some eukaryotes), but some consist of a few cells (figure 1.6). Certain invertebrate animals—such as helminths (worms), many of which can be seen with the naked eye, are also included in the study of infectious diseases because of the way they are transmitted and the way the body responds to them, though they are not microorganisms.

Lifestyles of Microorganisms The majority of microorganisms live a free existence in habitats such as soil and water, where they are relatively harmless and often beneficial. A free-living organism can derive all required foods and other factors directly from the nonliving environment. Some microorganisms require interactions with other organisms. Sometimes these microbes are termed parasites. They are harbored and nourished by

other living organisms called hosts. A parasite’s actions cause damage to its host through infection and disease. Although parasites cause important diseases, they make up only a small proportion of microbes.

A Note on Viruses Viruses are subject to intense study by microbiologists. As mentioned before, they are not independently living cellular organisms. Instead, they are small particles that exist at the level of complexity somewhere between large molecules and cells (figure 1.5b). Viruses are much simpler than cells; outside their host, they are composed essentially of a small amount of hereditary material (either DNA or RNA but never both) wrapped up in a protein covering that is sometimes enveloped by a protein-containing lipid membrane. In this extracellular state, they are individually referred to as a virus particle or virion. When inside their host organism, in the intracellular state, viruses usually exist only in the form of genetic material that confers a partial genetic program on the host organisms. That is why many microbiologists refer to viruses as parasitic particles; however, a few consider them to be very primitive organisms. Nevertheless, all biologists agree that viruses are completely dependent on an infected host cell’s machinery for their multiplication and dispersal.

1.5 Learning Outcomes—Can You . . . 7. . . . differentiate between prokaryotic and eukaryotic microorganisms? 8. . . . identify a third type of microorganism? 9. . . . compare and contrast the relative sizes of the different microbes?

(b) Virus Types

(a) Cell Types Prokaryotic

Eukaryotic Nucleus Mitochondria Chromosome

Ribosomes

Envelope Capsid

Ribosomes

Nucleic acid AIDS virus

Cell wall Cell membrane Flagellum

Flagellum

Cell membrane

Bacterial virus

Figure 1.5 Cell structure. (a) Comparison of a prokaryotic cell and a eukaryotic cell (not to scale). (b) Two examples of viruses. These cell types and viruses are discussed in more detail in chapters 4, 5, and 6.

1.6

The Historical Foundations of Microbiology

11

Fungus Fungus Human hair

Protozoan

Red blood cell Helminth: Head (scolex) of Taenia solium

Helminth is visible to the naked eye 20 microns

Bacterium Virus 200 nm

Fungus: Syncephalastrum Bacteria A single virus particle

Protozoan: Vorticella

Bacterium: E. coli

Virus: Herpes simplex

Figure 1.6 Five types of microorganisms. The drawing at top right shows relative size differences. The photos of organisms around the drawing are pictured at different magnifications in order to show their details.

1.6 The Historical Foundations of Microbiology If not for the extensive interest, curiosity, and devotion of thousands of microbiologists over the last 300 years, we would know little about the microscopic realm that surrounds us. Many of the discoveries in this science have resulted from the prior work of men and women who toiled long hours in dimly lit laboratories with the crudest of tools. Each additional insight, whether large or small, has added to  our current knowledge of living things and processes. This  section summarizes the prominent discoveries made in the past 300 years: microscopy; the rise of the scientific method; and the development of medical microbiology, including the germ theory and the origins of modern microbiological techniques. Table B.1 in appendix B summarizes some of the pivotal events in microbiology, from its earliest beginnings to the present.

The Development of the Microscope: “Seeing Is Believing” From very earliest history, humans noticed that when certain foods spoiled they became inedible or caused illness, and yet other “spoiled” foods did no harm and even had enhanced flavor. Indeed, several centuries ago, there was already a sense that diseases such as the black plague and smallpox were caused by some sort of transmissible matter. But the causes of such phenomena were vague and obscure because the technology to study them was lacking. Consequently, they remained cloaked in mystery and regarded with superstition—a trend that led even well-educated scientists to believe in spontaneous generation (Insight 1.2). True awareness of the widespread distribution of microorganisms and some of their characteristics was finally made possible by the development of the first microscopes. These devices revealed microbes as discrete entities sharing many of the characteristics of larger, visible plants and

12

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INSIGHT 1.2

The Main Themes of Microbiology

The Fall of Superstition and the Rise of Microbiology

For thousands of years, people believed that certain living things arose from vital forces present in nonliving or decomposing matter. This ancient belief, known as spontaneous generation, was continually reinforced as people observed that meat left out in the open soon “produced” maggots, that mushrooms appeared on rotting wood, that rats and mice emerged from piles of litter, and other similar phenomena. Though some of these early ideas seem quaint and ridiculous in light of modern knowledge, we must remember that, at the time, mysteries in life were accepted, and the scientific method was not widely practiced. Even after single-celled organisms were discovered during the mid-1600s, the idea of spontaneous generation continued to exist. Some scientists assumed that microscopic beings were an early stage in the development of more complex ones. Over the subsequent 200 years, scientists waged an experimental battle over the two hypotheses that could explain the origin of simple life forms. Some tenaciously clung to the idea of abiogenesis (a = without, bio = life, genesis = beginning— beginning in absence of life), which embraced spontaneous generation. On the other side were advocates of biogenesis (beginning with life) saying that living things arise only from others of their same kind. There were serious proponents on both sides, and each side put forth what appeared on the surface to be plausible explanations of why their evidence was more correct. Gradually, the abiogenesis hypothesis was abandoned, as convincing evidence for biogenesis continued to mount. The following series of experiments were among the most important in finally tipping the balance. One of the first people to test the spontaneous generation theory was Francesco Redi of Italy. He conducted a simple experiment in which he placed meat in a jar and covered it with fine gauze. Flies gathering at the jar were blocked from entering and thus laid their eggs on the outside of the gauze. The maggots subsequently developed without access to the meat, indicating that

animals. Several early scientists fashioned magnifying lenses, but their microscopes lacked the optical clarity needed for examining bacteria and other small, single-celled organisms. The likely earliest record of microbes is in the works of Englishman Robert Hooke. In the 1660s, Hooke studied a great diversity of material from household objects, plants, and trees; described for the first time cellular structures in tree bark; and drew sketches of “little structures” that seemed to be alive. Using a single-lens microscope he made himself, Hooke described spots of mold he found on the sheepskin cover of a book: These spots appear'd, through a good Microscope, to be a very pretty shap'd vagetative body, which, from almost the same part of the Leather, shot out multitudes of small long cylindrical and transparent stalks, not exactly straight, but a little bended with the weight of a round and white knob that grew on the top of each of them. . . .

maggots were the offspring of flies and did not arise from some “vital force” in the meat. This and related experiments laid to rest the idea that more complex animals such as insects and mice developed through abiogenesis, but it did not convince many scientists of the day that simpler organisms could not arise in that way. Redi’s Experiment

Closed

Meat with no maggots

Maggots hatching into flies

Open

The Frenchman Louis Jablot reasoned that even microscopic organisms must have parents, and his experiments with hay infusions (dried hay steeped in water) supported that hypothesis. He divided into two containers an infusion that had been boiled to destroy any living things: a heated container that was closed to the air and a heated container that was freely open to Jablot’s Experiment Infusions

Covered Dust

Remains clear; no growth

Uncovered Dust

Heavy microbial growth

Figure 1.7a is a reproduction of the drawing he made to accompany his written observations. Hooke paved the way for even more exacting observations of microbes by Antonie van Leeuwenhoek, a Dutch linen merchant and self-made microbiologist. Imagine a dusty linen shop in Holland in the late 1600s. Ladies in traditional Dutch garb came in and out, choosing among the bolts of linens for their draperies and upholstery. Between customers, Leeuwenhoek retired to the workbench in the back of his shop, grinding glass lenses to ever-finer specifications so he could see with increasing clarity the threads in his fabrics. Eventually, he became interested in things other than thread counts. He took rainwater from a clay pot, smeared it on his specimen holder, and peered at it through his finest lens. He found “animals appearing to me ten thousand times less than those which may be perceived in the water with the naked eye.”

1.6

the air. Only the open vessel developed microorganisms, which he presumed had entered in air laden with dust. Additional experiments further defended biogenesis. Franz Shultze and Theodor Schwann of Germany felt sure that air was the source of microbes and sought to prove this by passing air through strong chemicals or hot glass tubes into heat-treated infusions in flasks. When the infusions again remained devoid of living things, the supporters of abiogenesis claimed that the treatment of the air had made it incapable of the spontaneous development of life.

The Historical Foundations of Microbiology

13

part of the necks. He heated the flasks to sterilize the broth and then incubated them. As long as the flask remained intact, the broth remained sterile; but if the neck was broken off so that dust fell directly down into the container, microbial growth immediately commenced. Pasteur summed up his findings, “For I have kept from them, and am still keeping from them, that one thing which is above the power of man to make; I have kept from them the germs that float in the air, I have kept from them life.” Pasteur’s Experiment

Shultze and Schwann’s Test Air inlet Flame heats air. Previously sterilized infusion remains sterile.

Microbes being destroyed Vigorous heat is applied.

Then, in the mid-1800s, the acclaimed chemist and microbiologist Louis Pasteur entered the arena. He had recently been studying the roles of microorganisms in the fermentation of beer and wine, and it was clear to him that these processes were brought about by the activities of microbes introduced into the beverage from air, fruits, and grains. The methods he used to discount abiogenesis were simple yet brilliant. To further clarify that air and dust were the source of microbes, Pasteur filled flasks with broth and fashioned their openings into long, swan-neck-shaped tubes. The flasks’ openings were freely open to the air but were curved so that gravity would cause any airborne dust particles to deposit in the lower

He didn’t stop there. He scraped the plaque from his teeth, and from the teeth of some volunteers who had never cleaned their teeth in their lives, and took a good close look at that. He recorded: “In the said matter there were many very little living animalcules, very prettily a-moving. . . . Moreover, the other animalcules were in such enormous numbers, that all the water . . . seemed to be alive.” Leeuwenhoek started sending his observations to the Royal Society of London, and eventually he was recognized as a scientist of great merit. Leeuwenhoek constructed more than 250 small, powerful microscopes that could magnify up to 300 times

Neck on second sterile flask is broken; growth occurs.

(a)

Figure 1.7 The first depiction of microorganisms. (a) Drawing of “hairy mould” colony made by Robert Hooke in 1665. (b) Photomicrograph of the fungus probably depicted by Hooke. It is a species of Mucor, a common indoor mold.

Broth free of live cells (sterile)

(b)

Neck intact; airborne microbes are trapped at base, and broth is sterile.

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The Main Themes of Microbiology

(figure 1.8). Considering that he had no formal training in science, his descriptions of bacteria and protozoa (which he called “animalcules”) were astute and precise. Because of Leeuwenhoek’s extraordinary contributions to microbiology, he is known as the father of bacteriology and protozoology. From the time of Hooke and Leeuwenhoek, microscopes became more complex and improved with the addi-

Lens Specimen holder

Focus screw

Handle

(a)

(b)

Figure 1.8 Leeuwenhoek’s microscope. (a) A brass replica of a Leeuwenhoek microscope and how it is held. (b) Examples of bacteria drawn by Leeuwenhoek.

tion of refined lenses, a condenser, finer focusing devices, and built-in light sources. The prototype of the modern compound microscope, in use from about the mid-1800s, was capable of magnifications of 1,000 times or more. Even our modern laboratory microscopes are not greatly different in basic structure and function from those early microscopes. The technical characteristics of microscopes and microscopy are a major focus of chapter 3. These events marked the beginning of our understanding of microbes and the diseases they can cause. Discoveries continue at a breakneck pace, however. In fact, the 2000s are being widely called the Century of Biology, fueled by our new abilities to study genomes and harness biological processes. Microbes have led the way in these discoveries and continue to play a large role in the new research. Of course, between the “Golden Age of Microbiology” and the “Century of Biology” there have been thousands of important discoveries. But to give you a feel for what has happened most recently, let’s take a glimpse of some very recent discoveries that have had huge impacts on our understanding of microbiology. Discovery of restriction enzymes—1970s. Three scientists, Daniel Nathans, Werner Arber, and Hamilton Smith, discovered these little molecular “scissors” inside prokaryotes. They chop up DNA in specific ways. Their job in the prokaryotes is to destroy invading (viral) DNA. The reason their discovery was such a major event in biology is that these enzymes can be harvested from the bacteria and then utilized in research labs to cut up DNA in a controlled way that then allows us to splice the DNA pieces into vehicles that can carry them into other cells. This opened the floodgates to genetic engineering—and all that has meant for the treatment of diseases, the investigation into biological processes, and the biological “revolution” of the 21st century. The invention of the PCR technique—1980s. The polymerase chain reaction (PCR) was a breakthrough in our ability to detect tiny amounts of DNA and then amplify them into quantities sufficient for studying. It has provided a new and powerful method for discovering new organisms and diagnosing infectious diseases and for forensic work such as crime scene investigation. Its inventor is Kary Mullis, a scientist working at a company in California at the time. He won the Nobel Prize for this invention in 1993. The importance of biofilms in infectious diseases— 1980s, 1990s, and 2000s. Biofilms are accumulations of bacteria and other microbes on surfaces. Often there are multiple species in a single biofilm and often they are several layers thick (figure 1.9). They have been recognized in environmental microbiology for a long time. Biofilms on rocks, biofilms on ship hulls, even biofilms on ancient paintings have been well studied. We now understand that biofilms are relatively common in the human body (dental plaque is a great example) and may be responsible for infections that are tough to conquer, such as some ear infections and recalcitrant infections of the prostate. Biofilms are also a big danger to the

1.6

Channel

The Historical Foundations of Microbiology

15

rent understandings of nature. Some of these observations have been confirmed so many times over such a long period of time that they are, if not “fact,” very close to fact. Many other observations will be altered over and over again as new findings emerge. And that is the beauty of science.

The Establishment of the Scientific Method Biofilm material

Figure 1.9 A biofilm made of three different bacterial species. This biofilm was artificially grown in the lab by adding three bacterial species to a flowing chamber. The film is several bacterial layers thick and mimics the kinds of biofilms found in industrial settings, such as in water lines, and also in human infections.

success of any foreign body implanted in the body. Artificial hips, hearts, and even IUDs (intrauterine devices) have all been seen to fail due to biofilm colonization. The importance of small RNAs—2000s. Once we were able to sequence entire genomes (another big move forward), scientists discovered something that turned a concept we literally used to call “dogma” on its head. You will learn in chapter 9 that DNA leads to the creation of proteins, the workhorses of all cells. The previously held “Central Dogma of Biology” was that RNA (a molecule related to DNA) was the go-between molecule. DNA was made into RNA, which dictated the creation of proteins. Genome sequencing has revealed that perhaps only 2% of DNA leads to a resulting protein. There is a lot of RNA that is being made that doesn’t end up with a protein counterpart. These pieces of RNA are usually small. It now appears that they have absolutely critical roles in regulating what happens in the cell. This is important not just to correct scientific assumptions but there are important practical uses as well. It has led to new approaches to how diseases are treated. For example, if the small RNAs are in bacteria infecting humans, they can be new targets for antimicrobial therapy. The preceding example highlights a feature of biology— and all of science—that is perhaps underappreciated. Because we have thick textbooks containing all kinds of assertions and “facts,” many people think science is an iron-clad collection of facts. Wrong! Science is an ever-evolving collection of new information, gleaned from observable phenomena and synthesized with old information to come up with the cur-

A serious impediment to the development of true scientific reasoning and testing was the tendency of early scientists to explain natural phenomena by a mixture of belief, superstition, and argument. The development of an experimental system that answered questions objectively and was not based on prejudice marked the beginning of true scientific thinking. These ideas gradually crept into the consciousness of the scientific community during the 1600s. The general approach taken by scientists to explain a certain natural phenomenon is called the scientific method. A primary aim of this method is to formulate a hypothesis, a tentative explanation to account for what has been observed or measured. A good hypothesis should be in the form of a statement. It must be capable of being either supported or discredited by careful observation or experimentation. For example, the statement that “microorganisms cause diseases” can be experimentally determined by the tools of science, but the statement “diseases are caused by evil spirits” cannot.

Case File 1

Continuing the Case

In 1831, Charles Darwin embarked on a 5-year voyage around the globe on a ship called the HMS Beagle. While on this journey, Darwin identified many never-beforeseen plant and animal species. Eventually his studies of these organisms led to the development off his d l h theory of evolution by natural selection, which states, in part, that as the genetic material of living beings changes over time, new life forms with unique structures and functions are produced. Traits that favor the survival of an organism, such as the ability to metabolize a new food source, are retained and passed on to the organism’s descendents. J. Craig Venter’s initial efforts led to the discovery of 1.2 million new genes and 1,800 new species. He heads an organization called the Institute for Biological Energy Alternatives. One of the institute’s goals is to create synthetic organisms tailor-made for a specific purpose, such as synthesizing chemicals, degrading waste products, or producing energy. It stands to reason that Venter’s discovery of new species will increase the potential for even more useful products, both naturally occurring and manmade.

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The Main Themes of Microbiology

Deductive and Inductive Reasoning Science is a process of investigation, using observation, experimentation, and reasoning. In some investigations, you make individual decisions by using accepted general principles as a guide. This is called deductive reasoning. Deductive reasoning, using general principles to explain specific observations, is the reasoning of mathematics, philosophy, politics, and ethics; deductive reasoning is also the way a computer works. All of us rely on deductive reasoning as a way to make everyday decisions—like whether you should open attachments in e-mails from unknown senders (figure 1.10). We use general principles as the basis for examining and evaluating these decisions.

Inductive Reasoning Where do general principles come from? Religious and ethical principles often have a religious foundation; political principles reflect social systems. Some general principles, however, such as those behind the deductive reasoning example above, are not derived from religion or politics but from observation of the physical world around us. If you drop an apple, it will fall whether or not you wish it to and despite any laws you may pass that forbid it to do so. Science is devoted to discovering the general principles that govern the operation of the physical world. How do scientists discover such general principles? Scientists are, above all, observers: They look at the world to understand how it works. It is from observations that scientists determine the principles that govern our physical world. The process of discovering general principles by careful examination of specific cases is termed inductive reasoning. This way of thought first became popular about 400 years ago, when Isaac Newton, Francis Bacon, and others began to conduct experiments and from the results infer general principles about how the world operates. Their experiments were sometimes quite simple. Newton’s consisted simply of releas-

Deductive reasoning

General principle

Knowing that opening attachments from unknown senders can introduce viruses or other bad things to your computer, you chose the specific action of not opening the attachment.

Inductive reasoning You have performed the specific action of clicking on unknown attachments three different times and each time your computer crashed This leads you to conclude that opening unknown attachments can be damaging to your computer.

Figure 1.10 Deductive and inductive reasoning.

ing an apple from his hand and watching it fall to the ground. From a host of particular observations, each no more complicated than the falling of an apple, Newton inferred a general principle—that all objects fall toward the center of the earth. This principle was a possible explanation, or hypothesis, about how the world works. You also make observations and formulate general principles based on your observations, like forming a general principle about the reliability of unknown e-mail attachments in figure 1.10. Like Newton, scientists work by forming and testing hypotheses, and observations are the materials on which they build them. As you can see, the deductive process is used when a general principle has already been established; induction is a discovery process, and leads to the creation of a general principle. A lengthy process of experimentation, analysis, and testing eventually leads to conclusions that either support or refute the hypothesis. If experiments do not uphold the hypothesis—that is, if it is found to be flawed—the hypothesis or some part of it is rejected; it is either discarded or modified to fit the results of the experiment. If the hypothesis is supported by the results from the experiment, it is not (or should not be) immediately accepted as fact. It then must be tested and retested. Indeed, this is an important guideline in the acceptance of a hypothesis. The results of the experiment must be published and then repeated by other investigators. In time, as each hypothesis is supported by a growing body of data and survives rigorous scrutiny, it moves to the next level of acceptance—the theory. A theory is a collection of statements, propositions, or concepts that explains or accounts for a natural event. A theory is not the result of a single experiment repeated over and over again but is an entire body of ideas that expresses or explains many aspects of a phenomenon. It is not a fuzzy or weak speculation, as is sometimes the popular notion, but a viable declaration that has stood the test of time and has yet to be disproved by serious scientific endeavors. Often, theories develop and progress through decades of research and are added to and modified by new findings. At some point, evidence of the accuracy and predictability of a theory is so compelling that the next level of confidence is reached and the theory becomes a law, or principle. For example, although we still refer to the germ theory of disease, so little question remains that microbes can cause disease that it has clearly passed into the realm of law. The theory of evolution falls in this category as well. Science and its hypotheses and theories must progress along with technology. As advances in instrumentation allow new, more detailed views of living phenomena, old theories may be reexamined and altered and new ones proposed. But scientists do not take the stance that theories or even “laws” are ever absolutely proved. The characteristics that make scientists most effective in their work are curiosity, open-mindedness, skepticism, creativity, cooperation, and readiness to revise their views of natural processes as new discoveries are made. The events described in Insight 1.2 provide important examples.

1.6

The Development of Medical Microbiology Early experiments on the sources of microorganisms led to the profound realization that microbes are everywhere: Not only are air and dust full of them, but the entire surface of the earth, its waters, and all objects are inhabited by them. This discovery led to immediate applications in medicine. Thus, the seeds of medical microbiology were sown in the mid to latter half of the 19th century with the introduction of the germ theory of disease and the resulting use of sterile, aseptic, and pure culture techniques.

The Discovery of Spores and Sterilization Following Pasteur’s inventive work with infusions (see Insight 1.2), it was not long before English physicist John Tyndall provided the initial evidence that some of the microbes in dust and air have very high heat resistance and that particularly vigorous treatment is required to destroy them. Later, the discovery and detailed description of heat-resistant bacterial endospores by Ferdinand Cohn, a German botanist, clarified the reason that heat would sometimes fail to completely eliminate all microorganisms. The modern sense of the word sterile, meaning completely free of all life forms (including spores) and virus particles, was established from that point on (see chapter 11). The capacity to sterilize objects and materials is an absolutely essential part of microbiology, medicine, dentistry, and some industries.

The Development of Aseptic Techniques From earliest history, humans experienced a vague sense that “unseen forces” or “poisonous vapors” emanating from decomposing matter could cause disease. As the study of microbiology became more scientific and the invisible was made visible, the fear of such mysterious vapors was replaced by the knowledge and sometimes even the fear of “germs.” About 125 years ago, the first studies by Robert Koch clearly linked a microscopic organism with a specific disease. Since that time, microbiologists have conducted a continuous search for disease-causing agents. At the same time that abiogenesis was being hotly debated, a few physicians began to suspect that microorganisms could cause not only spoilage and decay but also infectious diseases. It occurred to these rugged individualists that even the human body itself was a source of infection. Dr. Oliver Wendell Holmes, an American physician, observed that mothers who gave birth at home experienced fewer infections than did mothers who gave birth in the hospital; and the Hungarian Dr. Ignaz Semmelweis showed quite clearly that women became infected in the maternity ward after examinations by physicians coming directly from the autopsy room. The English surgeon Joseph Lister took notice of these observations and was the first to introduce aseptic (ay-sep′-tik) techniques aimed at reducing microbes in a medical setting and preventing wound infections. Lister’s concept of asep-

The Historical Foundations of Microbiology

17

sis was much more limited than our modern precautions. It mainly involved disinfecting the hands and the air with strong antiseptic chemicals, such as phenol, prior to surgery. It is hard for us to believe, but as recently as the late 1800s surgeons wore street clothes in the operating room and had little idea that hand washing was important. Lister’s techniques and the application of heat for sterilization became the foundations for microbial control by physical and chemical methods, which are still in use today.

The Discovery of Pathogens and the Germ Theory of Disease Louis Pasteur of France (figure 1.11) introduced techniques that are still used today. Pasteur made enormous contributions to our understanding of the microbial role in wine and beer formation. He invented pasteurization and completed some of the first studies showing that human diseases could arise from infection. These studies, supported by the work of other scientists, became known as the germ theory of disease. Pasteur’s contemporary, Robert Koch, established Koch’s postulates, a series of proofs that verified the germ theory and could establish whether an organism was pathogenic and which disease it caused (see chapter 13). About 1875, Koch used this experimental system to show that anthrax was caused by a bacterium called Bacillus anthracis. So useful were his postulates that the causative agents of 20 other diseases were discovered between 1875 and 1900, and even today, they are the standard for identifying pathogens of plants and animals. Numerous exciting technologies emerged from Koch’s prolific and probing laboratory work. During this golden age

Figure 1.11 Louis Pasteur (1822–1895), one of the founders of microbiology. Few microbiologists can match the scope and impact of his contributions to the science of microbiology.

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The Main Themes of Microbiology

of the 1880s, he realized that study of the microbial world would require separating microbes from each other and growing them in culture. It is not an overstatement to say that he and his colleagues invented most of the techniques that are described in chapter 3: inoculation, isolation, media, maintenance of pure cultures, and preparation of specimens for microscopic examination. Other highlights in this era of discovery are presented in later chapters on microbial control (see chapter 11) and vaccination (see chapter 15).

1.6 Learning Outcomes—Can You . . . 10. . . . make a time line of the development of microbiology from the 1600s to today? 11. . . . list some recent microbiology discoveries of great impact? 12. . . . explain what is important about the scientific method?

Identification is the process of discovering and recording the traits or organisms so that they may be recognized or named and placed in an overall taxonomic scheme. With the rapid increase in knowledge largely due to the mind-boggling pace of improvement in scientific instrumentation and analysis, taxonomy has never stood still. Instead, it has evolved from a science that artificially classified organisms from a viewpoint of the organism’s usefulness, danger, or esthetic appeal to humans to a science that devised a system of natural relationships between organisms. A survey of some general methods of identification appears in chapter 3. Discovery of present or extinct life forms in space would certainly provide an ultimate test for our existing taxonomy and shed light on the origins of life on our planet earth (Insight 1.3).

Assigning Specific Names

1.7 Naming, Classifying, and Identifying Microorganisms Students just beginning their microbiology studies are often dismayed by the seemingly endless array of new, unusual, and sometimes confusing names for microorganisms. Learning microbial nomenclature is very much like learning a new language, and occasionally its demands may be a bit overwhelming. But paying attention to proper microbial names is just like following a baseball game or a theater production: you cannot tell the players apart without a program! Your understanding and appreciation of microorganisms will be greatly improved by learning a few general rules about how they are named. The science of classifying living beings is taxonomy. It originated more than 250 years ago when Carl von Linné (also known as Linnaeus; 1701–1778), a Swedish botanist, laid down the basic rules for classification and established taxonomic categories, or taxa (singular: taxon). Von Linné realized early on that a system for recognizing and defining the properties of living beings would prevent chaos in scientific studies by providing each organism with a unique name and an exact “slot” in which to catalog it. This classification would then serve as a means for future identification of that same organism and permit workers in many biological fields to know if they were indeed discussing the same organism. The von Linné system has served well in categorizing the 2 million or more different kinds of organisms that have been discovered since that time, including organisms that have gone extinct. The primary concerns of modern taxonomy are still naming, classifying, and identifying. These three areas are interrelated and play a vital role in keeping a dynamic inventory of the extensive array of living and extinct beings. In general, Nomenclature is the assignment of scientific names to the various taxonomic categories and individual organisms. Classification attempts the orderly arrangement of organisms into a hierarchy of taxa.

Many macroorganisms are known by a common name suggested by certain dominant features. For example, a bird species might be called a red-headed blackbird or a flowering plant species a black-eyed Susan. Some species of microorganisms (especially those that directly or indirectly affect our well-being) are also called by informal names, including human pathogens such as “gonococcus” (Neisseria gonorrhoeae) or fermenters such as “brewer’s yeast” (Saccharomyces cerevisiae), or the recent “Iraqabacter” (Acinetobacter baumannii), but this is not the usual practice. If we were to adopt common names such as the “little yellow coccus” the terminology would become even more cumbersome and challenging than scientific names. Even worse, common names are notorious for varying from region to region, even within the same country. A decided advantage of standardized nomenclature is that it provides a universal language, thereby enabling scientists from all countries to accurately exchange information. The method of assigning a scientific or specific name is called the binomial (two-name) system of nomenclature. The scientific name is always a combination of the generic (genus) name followed by the species name. The generic part of the scientific name is capitalized, and the species part begins with a lowercase letter. Both should be italicized (or underlined if using handwriting), as follows: Staphylococcus aureus The two-part name of an organism is sometimes abbreviated to save space, as in S. aureus, but only if the genus name has already been stated. The source for nomenclature is usually Latin or Greek. If other languages such as English or French are used, the endings of these words are revised to have Latin endings. An international group oversees the naming of every new organism discovered, making sure that standard procedures have been followed and that there is not already an earlier name for the organism or another organism with that same name. The inspiration for names is extremely varied and often rather imaginative. Some species have been named in honor of a microbiologist who originally

1.7

INSIGHT 1.3

Naming, Classifying, and Identifying Microorganisms

Martian Microbes and Astrobiology

Professional and amateur scientists have long been intrigued by the possible existence of life on other planets and in the surrounding universe. This curiosity has given rise to a new discipline—astrobiology—that applies principles from biology, chemistry, geology, and physics to investigate extraterrestrial life. One of the few accessible places to begin this search is the planet Mars. It is relatively close to the earth and the only planet in the solar system besides earth that is not extremely hot, cold, or bathed in toxic gases. The possibility that it could support at least simple life forms has been an important focus of NASA space projects stretching over 30 years. Several Mars explorations have included experiments and collection devices to gather evidence for certain life signatures or characteristics. One of the first experiments launched with the Viking Explorer was an attempt to culture microbes from Martian soil. Another used a gas chromatograph to check for complex carbon-containing (organic) compounds in the soil samples. No signs of life or organic matter were detected. But in scientific research, a single experiment is not sufficient to completely rule out a hypothesis, especially one as attractive as this one. Many astrobiologists reason that the nature of the “life forms” may be so different that they require a different experimental design. In 1996, another finding brought considerable excitement and controversy to the astrobiology community. Scientists doing electron microscopic analyses of an ancient Martian meteorite from the Antarctic discovered tiny rodlike structures that resembled earth bacteria. Though the idea was appealing, many scientists argued that the rods did not contain the correct form of carbon and that geologic substances often contain crystals that mimic other objects. Another team of NASA researchers later discovered chains of magnetite crystals (tiny iron oxide magnets) in another Martian meteorite. These crystals bear a distinct resemblance to forms found in certain modern bacteria on earth and are generally thought to be formed only by living processes.

A fossil ossil cell cell?

Martian microbes b or mere molecules? l l ? Internall view off a section of a 4.5-billion-year-old Martian meteor shows an intriguing tiny cylinder (50,000×).

Growing blobs of water on leg of a Mars lander (2009).

Obviously, these findings have added much fodder for speculation and further research. There has been a great deal of evidence that the planet harbored water at one time, considered to be a prerequisite for life of any kind. Channels resembling rivers have been documented by the multiple Mars landers NASA has deployed. Some scientists believe that there is still liquid water on Mars, perhaps in subsurface aquifers that bubble to the surface from time to time. In 2009, a group of scientists reported on photographs that were taken of the legs of the Phoenix lander. The photographs appeared to show large droplets of water (see photo). The “droplets” grew larger over time, leading scientists to conclude that the (salty) water was absorbing more moisture from water vapor in the atmosphere. Whether this turns out to be true or not, the evidence for life-sustaining water on Mars seems to be accumulating. Astrobiologists long ago put aside the quaint idea of meeting “little green men” when they got to the red planet, but they have not yet given up the possibility of finding “little green microbes.” One hypothesis proposes that microbes hitchhiking on meteors and asteroids have seeded the solar system and perhaps universe with simple life forms. Certainly, of all organisms on earth, hardy prokaryotes are the ones most likely to survive the rigors of such travel. Recently scientists have tested this hypothesis and found that the bacteria in the experiment survived conditions that mimicked an asteroid hit. This raises the possibility that microbes could have traveled from a planet with life forms on it to other planets and possibly seeded a new beginning of life there. It also makes us wonder whether microbes could have blasted off of the surface of the earth only to return thousands of years later in asteroid hits, thereby confusing our sense of how organisms here evolved. As Benjamin Weiss of the Massachusetts Institute of Technology said in response to this study, “It’s becoming more apparent that the planets are unlikely to have been biologically isolated from one another.” For more information on this subject, use a search engine to access the NASA Astrobiology Institute, NASA Mission to Mars, or NASA Exploration Program websites.

19

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discovered the microbe or who has made outstanding contributions to the field. Other names may designate a characteristic of the microbe (shape, color), a location where it was found, or a disease it causes. Some examples of specific names, their pronunciations, and their origins are: • Staphylococcus aureus (staf′-i-lo-kok′-us ah′-ree-us) Gr. staphule, bunch of grapes, kokkus, berry, and Gr. aureus, golden. A common bacterial pathogen of humans. • Campylobacter jejuni (cam′-peh-loh-bak-ter jee-joo′-neye) Gr. kampylos, curved, bakterion, little rod, and jejunum, a section of intestine. One of the most important causes of intestinal infection worldwide. • Lactobacillus sanfrancisco (lak′-toh-bass-ill′-us san-fransiss′-koh) L. lacto, milk, and bacillus, little rod. A bacterial species used to make sourdough bread. • Vampirovibrio chlorellavorus (vam-py′-roh-vib-ree-oh klor-ell-ah′-vor-us) F. vampire; L. vibrio, curved cell; Chlorella, a genus of green algae; and vorus, to devour. A small, curved bacterium that sucks out the cell juices of Chlorella. • Giardia lamblia (jee-ar′-dee-uh lam′-blee-uh) for Alfred Giard, a French microbiologist, and Vilem Lambl, a Bohemian physician, both of whom worked on the organism, a protozoan that causes a severe intestinal infection. Here’s a helpful hint: These names may seem difficult to pronounce and the temptation is to simply “slur over them.” But when you encounter the names of microorganisms in the chapters ahead, it will be extremely useful to take the time to sound them out and repeat them until they seem familiar. You are much more likely to remember them that way—and they are less likely to end up in a tangled heap with all of the new language you will be learning.

The Levels of Classification The main units of a classification scheme are organized into several descending ranks, beginning with a most general allinclusive taxonomic category as a common denominator for organisms to exclude all others, and ending with the smallest and most specific category. This means that all members of the highest category share only one or a few general characteristics, whereas members of the lowest category are essentially the same kind of organism—that is, they share the majority of their characteristics. The taxonomic categories from top to bottom are: domain, kingdom, phylum or division,3 class, order, family, genus, and species. Thus, each kingdom can be subdivided into a series of phyla or divisions, each phylum is made up of several classes, each class contains several orders, and so on. Because taxonomic schemes are to some extent artificial, certain groups of organisms may not exactly fit into the main categories. In such a case, additional taxonomic levels can be 3. The term phylum is used for bacteria, protozoa, and animals; the term division is used for algae, plants, and fungi.

imposed above (super) or below (sub) a taxon, giving us such categories as “superphylum” and “subclass.” Let’s compare the taxonomic breakdowns of a human and a protozoan (proh′-tuh-zoh′-uhn) to illustrate the fine points of this system (figure 1.12). Humans and protozoa are both organisms with nucleated cells (eukaryotes); therefore, they are in the same domain but they are in different kingdoms. Humans are multicellular animals (Kingdom Animalia) whereas protozoa are single-cellular organisms that, together with algae, belong to the Kingdom Protista. To emphasize just how broad the category “kingdom” is, ponder the fact that we humans belong to the same kingdom as jellyfish. Of the several phyla within this kingdom, humans belong to the Phylum Chordata, but even a phylum is rather all-inclusive, considering that humans share it with other vertebrates as well as with creatures called sea squirts. The next level, Class Mammalia, narrows the field considerably by grouping only those vertebrates that have hair and suckle their young. Humans belong to the Order Primates, a group that also includes apes, monkeys, and lemurs. Next comes the Family Hominoidea, containing only humans and apes. The final levels are our genus, Homo (all races of modern and ancient humans), and our species, sapiens (meaning wise). Notice that for the human as well as the protozoan, the taxonomic categories in descending order become less inclusive and the individual members more closely related. We need to remember that all taxonomic hierarchies are based on the judgment of scientists with certain expertise in a particular group of organisms and that not all other experts may agree with the system being used. Consequently, no taxa are permanent to any degree; they are constantly being revised and refined as new information becomes available or new viewpoints become prevalent. In this text, we are usually concerned with only the most general (kingdom, phylum) and specific (genus, species) taxonomic levels.

The Origin and Evolution of Microorganisms As we indicated earlier, taxonomy, the science of classification of biological species, is used to organize all of the forms of modern and extinct life. In biology today, there are different methods for deciding on taxonomic categories, but they all rely on the degree of relatedness among organisms. The scheme that represents the natural relatedness (relation by descent) between groups of living beings is called their phylogeny (Gr. phylon, race or class; L. genesis, origin or beginning), and—when unraveled—biologists use phylogenetic relationships to refine the system of taxonomy. To understand the natural history of and the relatedness among organisms, we must understand some fundamentals of the process of evolution. Evolution is an important theme that underlies all of biology, including the biology of microorganisms. As we said earlier, evolution states that the hereditary information in living beings changes gradually through time (usually hundreds of millions of years) and that these changes result in various structural and functional

1.7

Naming, Classifying, and Identifying Microorganisms

Domain: Eukarya (All eukaryotic organisms)

Domain: Eukarya (All eukaryotic organisms)

Kingdom: Animalia

Kingdom: Protista Includes protozoa and algae

Lemur

Sea squirt

21

Sea star

Phylum: Chordata

Phylum: Ciliophora Only protozoa with cilia

Class: Mammalia

Class: Hymenostomea Single cells with regular rows of cilia; rapid swimmers

Order: Primates

Order: Hymenostomatida Elongated oval cells with cilia in the oral cavity

Family: Hominoidea

Family: Parameciidae Cells rotate while swimming and have oral grooves.

Genus: Homo

Genus: Paramecium Pointed, cigar-shaped cells with macronuclei and micronuclei

Species: sapiens (a)

Species: caudatum Cells cylindrical, long, and pointed at one end (b)

Figure 1.12 Sample taxonomy. Two organisms belonging to the Eukarya domain, traced through their taxonomic series. (a) Modern humans, Homo sapiens. (b) A common protozoan, Paramecium caudatum.

changes through many generations. The process of evolution is selective in that those changes that most favor the survival of a particular organism or group of organisms tend to be retained whereas those that are less beneficial to survival tend to be lost. Charles Darwin called this process natural selection. Evolution is founded on the two preconceptions that (1)  all new species originate from preexisting species and (2)  closely related organisms have similar features because they evolved from a common ancestor; hence, difference emerged by divergence. Usually, evolution progresses toward greater complexity but there are many examples of evolution toward lesser complexity (reductive evolution). This is

because individual organisms never evolve in isolation but as populations of organisms in their specific environments, which exert the functional pressures of selection. Because of the divergent nature of the evolutionary process, the phylogeny, or relatedness by descent, of organisms is often represented by a diagram of a tree. The trunk of the tree represents the origin of ancestral lines, and the branches show offshoots into specialized groups (clades) of organisms. This sort of arrangement places taxonomic groups with less divergence (less change in the heritable information) from the common ancestor closer to the root of the tree and taxa with lots of divergence closer to the top (figures 1.13 and 1.14).

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Systems of Presenting a Universal Tree of Life

units, or kingdoms: the monera, protists, plants, fungi, and animals, all of which consisted of one of the two cell types, the prokaryotic and eukaryotic. Whittaker’s five-kingdom system quickly became the standard (see figure 1.13). With the rise of genetics as a molecular science, newer methods for determining phylogeny have led to the development of a differently shaped tree—with important implications for our understanding of evolutionary relatedness. Molecular genetics allowed an in-depth study of the structure and function of the genetic material at the molecular level. These studies have revealed that two of the four macromolecules that contribute to cellular structure and function, the proteins and nucleic acids, are very well suited to study how organisms differ from one another because their sequences can be aligned and compared. In 1975, Carl Woese discovered that one particular macromolecule, the ribonucleic acid in the small subunit of the ribosome (ssu rRNA), was highly conserved—meaning that it was nearly identical in organisms within the smallest taxonomic category, the species. Based on a vast amount of experimental data and the knowledge that protein synthesis proceeds in

The first trees of life were constructed a long time ago on the basis of just two kingdoms, plants and animals, by Charles Darwin and Ernst Haeckel. These trees were chiefly based on visible morphological characteristics. It became clear that certain (micro)organisms such as algae and protozoa, which only existed as single cells, did not truly fit either of those categories, so a third kingdom was recognized by Haeckel for these simpler organisms. It was named Protista. Eventually, when significant differences became evident among even the unicellular organisms, a fourth kingdom was established in the 1870s by Haeckel and named Monera. Almost a century passed before Robert Whittaker extended this work and added a fifth kingdom for fungi during the period of 1959 to 1969. The relationships that were used in Whittaker’s tree were those based on structural similarities and differences, such as prokaryotic and eukaryotic cellular organization, and the way these organisms obtained their nutrition. These criteria indicated that there were five major taxonomic

Figure 1.13 Traditional Whittaker system of classification. In this system,

Angiosperms

kingdoms are based on cell structure and type, the nature of body organization, and nutritional type. Bacteria and Archaea (monerans) are made of prokaryotic cells and are unicellular. Protists are made of eukaryotic cells and are mostly unicellular. They can be photosynthetic (algae), or they can feed on other organisms (protozoa). Fungi are eukaryotic cells and are unicellular or multicellular; they have cell walls and are not photosynthetic. Plants have eukaryotic cells, are multicellular, have cell walls, and are photosynthetic. Animals have eukaryotic cells, are multicellular, do not have cell walls, and derive nutrients from other organisms.

Arthropods Echinoderms

Annelids Ferns

Mosses

nts

pla

PLANTS

Mollusks

Club fungi

ed

Se

Nematodes

Yeasts

(Plantae)

FUNGI

Molds

Flatworms

(Myceteae)

ANIMALS (Animalia) Sponges

Slime molds

Red algae

Ciliates

First multicellular organisms appeared 0.6 billion years ago.

Flagellates

Green algae Brown algae

Amoebas PROTISTS

EUKARYOTES

(Protista)

PROKARYOTES

Source: After Dolphin, Biology Lab Manual, 4th ed., Fig. 14.1, p. 177, McGraw-Hill.

Chordates

Gymnosperms

Diatoms

Apicomplexans

Dinoflagellates Early eukaryotes

MONERA Archaea

5 kingdoms 2 cell types

Bacteria

Earliest cell

First cells appeared 3–4 billion years ago.

First eukaryotic cells appeared ⫾2 billion years ago.

1.7

Naming, Classifying, and Identifying Microorganisms Plants

Domain Bacteria Cyanobacteria

Domain Archaea

Chlamydias Gram-positive Endospore Gram-negative Spirochetes bacteria producers bacteria

Methane producers

Prokaryotes that live in extreme salt

Animals

Fungi

23 Protists

Domain Eukarya Prokaryotes that live in extreme heat

Eukaryotes

Ancestral Cell Line (first living cells)

Figure 1.14 Woese-Fox system. A system for representing the origins of cell lines and major taxonomic groups as proposed by Carl Woese and colleagues. They propose three distinct cell lines placed in superkingdoms called domains. The first primitive cells, called progenotes, were ancestors of both lines of prokaryotes (Domain Bacteria and Archaea), and the Archaea emerged from the same cell line as eukaryotes (Domain Eukarya). Some of the traditional kingdoms are still present with this system (see figure 1.13).

all organisms facilitated by the ribosome, Woese hypothesized that ssu rRNA provides a “biological chronometer” or a “living record” of the evolutionary history of a given organism. Extended analysis of this molecule in prokaryotic and eukaryotic cells indicated that all members in a certain group of bacteria, then known as archaeobacteria, had ssu rRNA with a sequence that was significantly different from the ssu rRNA found in other bacteria and in eukaryotes. This discovery led Carl Woese and collaborator George Fox to propose a separate taxonomic unit for the archaeobacteria, which they named Archaea. Under the microscope, they resembled the prokaryotic structure of bacteria, but molecular biology has revealed that the archaea, though prokaryotic in nature, were actually more closely related to eukaryotic cells than to bacterial cells (see table 4.6). To reflect these relationships, Carl Woese and George Fox proposed an entirely new system that assigned all known organisms to one of the three major taxonomic units, the domains, each being a different type of cell (see figure 1.14). The domains are the highest level in hierarchy and can contain many kingdoms and superkingdoms. The prokaryotic cell types are represented by the domains Archaea and Bacteria, whereas eukaryotes are all placed in the domain Eukarya. Analysis of the ssu rRNAs from all organisms in these three domains suggests that all modern

and extinct organisms on earth arose from a common ancestor. Therefore, eukaryotes did not emerge from prokaryotes. Both types of cells emerged separately from a different, now extinct, cell type. To add another level of complexity, the most current data suggests that “trees” of life do not truly represent the relatedness—and evolution—of organisms at all. It has become obvious that genes travel horizontally—meaning from one species to another in nonreproductive ways—and that the neat generation-to-generation changes are combined with neighbor-to-neighbor exchanges of DNA. For example, it is estimated that 40% to 50% of human DNA has been carried to humans from other species (by viruses). Another example: The genome of the cow contains a piece of snake DNA. For these reasons, most scientists like to think of a web as the proper representation of life these days. The threedomain system somewhat complicates the presentation of organisms in the original Kingdom Protista, which is now a collection of protozoa and algae that exist in several separate kingdoms (discussed in chapter 5). Nevertheless, this new scheme does not greatly affect our presentation of most microbes, because we will discuss them at the genus or species level. But be aware that biological taxonomy and, more important, our view of how organisms evolved on earth are in a period of transition. Keep in mind that our methods of classification or evolutionary schemes reflect our current

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Case File 1

The Main Themes of Microbiology

Wrap-Up

Based on the extraordinary success of the first Sorcerer II voyage, a more extensive second voyage visited many different locations around the world, including the Galápagos Islands, where Darwin made many of his observations. J. Craig Venter’s second voyage lled discovery d to the h d of 20 million new genes and thousands of new protein families. Of particular interest to Venter were a group of genes called rhodopsins, which help bacteria capture energy from the sun. Venter hopes these bacteria may one day be used as an alternative energy source. He articulated this hope in a 2007 interview when he said, “We really need to find an alternative to taking carbon out of the ground, burning it, and putting it into the atmosphere. That is the single biggest contribution I could make.” On March 19, 2009, the Sorcerer II left her home port of San Diego for a third voyage. Further exciting discoveries seem likely. See: 2007. PLoS Biol. 2007 Mar 13; 5(3): 16.

understanding and will change as new information is uncovered. Please note that viruses are not included in any of the classification or evolutionary schemes, because they are not cells or organisms and their position in a “tree of life” cannot be determined. The special taxonomy of viruses is discussed in chapter 6.

1.7 Learning Outcomes—Can You . . . 13. . . . differentiate between the terms nomenclature, taxonomy, and classification? 14. . . . create a mnemonic device for remembering the taxonomic categories? 15. . . . correctly write the binomial name for a microorganism? 16. . . . draw a diagram of the three major domains? 17. . . . explain the difference between traditional and molecular approaches to taxonomy?

Chapter Summary 1.1 The Scope of Microbiology • Microorganisms are defined as “living organisms too small to be seen with the naked eye.” Among the members of this huge group of organisms are bacteria, algae, protozoa, fungi, parasitic worms (helminths), and viruses. • Microorganisms live nearly everywhere and influence many biological and physical activities on earth. • There are many kinds of relationships between microorganisms and humans; most are beneficial, but some are harmful. 1.2 The Impact of Microbes on Earth: Small Organisms with a Giant Effect • Groups of organisms are constantly evolving to produce new forms of life. • Microbes are crucial to the cycling of nutrients and energy that are necessary for all life on earth. 1.3 Human Use of Microorganisms • Humans have learned how to manipulate microbes to do important work for them in industry, medicine, and in caring for the environment. 1.4 Infectious Diseases and the Human Condition • In the last 120 years, microbiologists have identified the causative agents for many infectious diseases. In addition, they have discovered distinct connections between microorganisms and diseases whose causes were previously unknown. • While microbial diseases continue to cause disease worldwide, low-income countries are much harder hit by them directly and indirectly. 1.5 The General Characteristics of Microorganisms • Excluding the viruses, there are two types of microorganisms: prokaryotes, which are small and lack a nucleus and organelles, and eukaryotes, which are larger and have both a nucleus and organelles.

• Viruses are not cellular and are therefore sometimes

called particles rather than organisms. They are included in microbiology because of their small size and close relationship with cells. 1.6 The Historical Foundations of Microbiology • The microscope made it possible to see microorganisms and thus to identify their widespread presence, particularly as agents of disease. • The theory of spontaneous generation of living organisms from “vital forces” in the air was disproved once and for all by Louis Pasteur. • The scientific method is a process by which scientists seek to explain natural phenomena. It is characterized by specific procedures that either support or discredit an initial hypothesis. • Knowledge acquired through the scientific method is rigorously tested by repeated experiments by many scientists to verify its validity. A collection of valid hypotheses is called a theory. A theory supported by much data collected over time is called a law. • Scientific dogma or theory changes through time as new research brings new information. • Medical microbiologists developed the germ theory of disease and introduced the critically important concept of aseptic technique to control the spread of disease agents. 1.7 Naming, Classifying, and Identifying Microorganisms • The taxonomic system has three primary functions: naming, classifying, and identifying species. • The major groups in the most advanced taxonomic system are (in descending order): domain, kingdom, phylum or division, class, order, family, genus, and species. • Evolutionary patterns show a treelike or weblike branching thereby describing the diverging evolution of all life forms from the gene pool of a common ancestor. • The Woese-Fox classification system places all eukaryotes in the domain Eukarya and subdivides the prokaryotes into the two domains Archaea and Bacteria.

Multiple-Choice and True-False Questions

Multiple-Choice and True-False Questions

25

Knowledge and Comprehension

Multiple-Choice Questions. Select the correct answer from the answers provided. 1. Which of the following is not considered a microorganism? a. alga c. protozoan b. bacterium d. mushroom 2. Which process involves the deliberate alteration of an organism’s genetic material? a. bioremediation c. decomposition b. biotechnology d. recombinant DNA technology 3. Which of the following parts was absent from Leeuwenhoek’s microscopes? a. focusing screw b. lens c. specimen holder d. condenser 4. Abiogenesis refers to the a. spontaneous generation of organisms from nonliving matter. b. development of life forms from preexisting life forms. c. development of aseptic technique. d. germ theory of disease. 5. A hypothesis can be defined as a. a belief based on knowledge. b. knowledge based on belief. c. a scientific explanation that is subject to testing. d. a theory that has been thoroughly tested.

8. Which of the following are prokaryotic? a. bacteria c. protists b. archaea d. both a and b 9. Order the following items by size, using numbers: 1 = smallest through 8 = largest. AIDS virus worm amoeba coccus-shaped bacterium rickettsia white blood cell protein atom 10. How would you classify a virus? a. prokaryotic b. eukaryotic c. neither a nor b True-False Questions. If the statement is true, leave as is. If it is false, correct it by rewriting the sentence. 11. Organisms in the same order are more closely related than those in the same family.

6. When a hypothesis has been thoroughly supported by longterm study and data, it is considered a. a law. b. a speculation. c. a theory. d. proved.

Critical Thinking Questions

7. Which is the correct order of the taxonomic categories, going from most specific to most general? a. domain, kingdom, phylum, class, order, family, genus, species b. division, domain, kingdom, class, family, genus, species c. species, genus, family, order, class, phylum, kingdom, domain d. species, family, class, order, phylum, kingdom

12. Eukaryotes evolved from prokaryotes. 13. Prokaryotes have no nucleus. 14. In order to be called a theory, a scientific idea has to undergo a great deal of testing. 15. Microbes are ubiquitous.

Application and Analysis

These questions are suggested as a writing-to-learn experience. For each question, compose a one- or two-paragraph answer that includes the factual information needed to completely address the question. 1. Explain the important contributions microorganisms make in the earth’s ecosystems. 2. Why was the abandonment of the spontaneous generation theory so significant? Using the scientific method, describe the steps you would take to test the theory of spontaneous generation.

6. Evolution accounts for the millions of different species on the earth and their adaptation to its many and diverse habitats. Explain this. Cite examples in your answer. 7. Where do you suppose the “new” infectious diseases come from?

3. a. Differentiate between a hypothesis and a theory. b. Is the germ theory of disease really a law? Why or why not?

8. Can you develop a scientific hypothesis and means of testing the cause of stomach ulcers? (Is it caused by an infection? By too much acid? By a genetic disorder?)

4. What is a binomial system of nomenclature, and why is it used?

9. Where do you suppose viruses came from? Why do they require the host’s cellular machinery?

5. Compare the new domain system with the five-kingdom system. Does the newer system change the basic idea of prokaryotes and eukaryotes? What is the third cell type?

10. Archaea are often found in hot, sulfuric, acidic, salty habitats, much like the early earth’s conditions. Speculate on the origin of life, especially as it relates to the archaea.

26

Chapter 1

The Main Themes of Microbiology

Concept Mapping

Synthesis

Appendix D provides guidance for working with concept maps. 1. Supply your own linking words or phrases in this concept map, and provide the missing concepts in the empty boxes. Cellular microbes

Noncellular microbe

Nucleus No nucleus

Visual Connections

Synthesis

These questions use visual images or previous content to make connections to this chapter’s concepts. 1. Figure 1.1. Look at the blue bar (the time that prokaryotes have been on earth) and at the pink arrow (the time that humans appeared). Speculate on the probability that we will be able to completely disinfect our planet or prevent all microbial diseases. Humans appeared. Mammals appeared. Cockroaches, termites appeared. Reptiles appeared. Eukaryotes appeared. Probable origin of earth

Prokaryotes appeared.

4 billion years ago

3 billion years ago

2 billion years ago

1 billion years ago

Present time

www.connect.microbiology.com Enhance your study of this chapter with study tools and practice tests. Also ask your instructor about the resources available through ConnectPlus, including the media-rich eBook, interactive learning tools, and animations.

The Chemistry of Biology 2 Case File A group of scientists at the Centers for Disease Control (CDC) noted 13 cases of Salmonella enterica infection in sick people in a dozen states during November 2008. The typical symptoms of salmonellosis (infection with salmonella) include vomiting and diarrhea, and may result from ingesting any of more than 1,500 different strains, or unique subspecies, of S. enterica. Two weeks later, a similar outbreak of 27 cases of the disease, spread across 14 states, was found to be caused by the same strain of the organism seen in the first outbreak. By February 2009, 682 people from 46 states and Canada had become infected, nine had died, a large corporation had filed for bankruptcy, and several criminal investigations had begun. PulseNet is a branch of the CDC that seeks to identify food-borne disease clusters by carefully studying the bacterial isolates thought to be the source of an outbreak. Usually this means obtaining DNA profiles, called fingerprints, of each bacterium and using that information to compare isolates (isolated strains of bacteria) from different outbreaks. Because the fingerprints from the two outbreak strains in this case were similar to one another—but also different from any fingerprint within the PulseNet database—CDC scientists initiated an epidemiological investigation. S. enterica was identified in unopened 5-pound containers of King Nut peanut butter in Minnesota and Connecticut, in the peanut butter factory, and in bacteria isolated from the patients. At the time, King Nut peanut butter was manufactured by the Peanut Corporation of America (PCA) in Blakely, Georgia, and sold to schools, hospitals, restaurants, cafeterias, and other large institutions rather than directly to consumers. Examination of the bacteria revealed several different S. enterica strains, but only a few of them were linked to the illnesses. ◾ What chemicals make up DNA? ◾ Without knowing the specific details of DNA fingerprinting, how do you think these profiles could be used to show that a particular bacterial strain is not part of an outbreak? Continuing the Case appears on page 34.

27

28

Chapter 2

The Chemistry of Biology

Outline and Learning Outcomes 2.1 Atoms, Bonds, and Molecules: Fundamental Building Blocks 1. Explain the relationship between atoms and elements. 2. List and define four types of chemical bonds. 3. Differentiate between a solute and a solvent. 4. Give a brief definition of pH. 2.2 Macromolecules: Superstructures of Life 5. Name the four main families of biochemicals. 6. Provide examples of cell components made from each of the families of biochemicals. 7. Explain primary, secondary, tertiary, and quaternary structure as seen in proteins. 8. List the three components of nucleic acids. 9. Name the nucleotides of DNA and of RNA. 10. List the three components of ATP. 2.3 Cells: Where Chemicals Come to Life 11. Point out three characteristics all cells share.

2.1 Atoms, Bonds, and Molecules: Fundamental Building Blocks The universe is composed of an infinite variety of substances existing in the gaseous, liquid, and solid states. All such tangible materials that occupy space and have mass are called matter. The organization of matter—whether air, rocks, or bacteria—begins with individual building blocks called atoms. An atom is defined as a tiny particle that cannot be subdivided into smaller substances without losing its properties. Even in a science dealing with very small things, an

atom’s minute size is striking; for example, an oxygen atom is only 0.0000000013 mm (0.0013 nm) in diameter, and 1 million of them in a cluster would barely be visible to the naked eye. The exact composition of atoms has been well established by extensive physical analysis using sophisticated instruments. In general, an atom derives its properties from a combination of subatomic particles called protons (p+), which are positively charged; neutrons (n0), which have no charge (are neutral); and electrons (e−), which are negatively charged. The relatively larger protons and neutrons make up a central Nucleus

Hydrogen

Shell

1 proton 1 electron

Hydrogen Shells

Shell 2 Shell 1

Nucleus

proton Orbitals

Nucleus

Carbon (a)

6 protons 6 neutrons 6 electrons

Carbon

neutron electron

(b)

Figure 2.1 Models of atomic structure. (a) Three-dimensional models of hydrogen and carbon that approximate their actual structure. The nucleus is surrounded by electrons in orbitals that occur in levels called shells. Hydrogen has just one shell and one orbital. Carbon has two shells and four orbitals; the shape of the outermost orbitals is paired lobes rather than circles or spheres. (b) Simple models of the same atoms make it easier to show the numbers and arrangements of shells and electrons and the numbers of protons and neutrons in the nucleus. (Not to accurate scale.)

2.1

core, or nucleus,1 that is surrounded by one or more electrons (figure 2.1). The nucleus makes up the larger mass (weight) of the atom, whereas the electron region accounts for the greater volume. To get a perspective on proportions, consider this: If an atom were the size of a baseball stadium, the nucleus would be about the size of a marble! The stability of atomic structure is largely maintained by (1) the mutual attraction of the protons and electrons (opposite charges attract each other) and (2) the exact balance of proton number and electron number, which causes the opposing charges to cancel each other out. At least in theory, then, isolated intact atoms do not carry a charge. 1. Be careful not to confuse the nucleus of an atom with the nucleus of a cell (discussed later).

Atoms, Bonds, and Molecules: Fundamental Building Blocks

29

Different Types of Atoms: Elements and Their Properties All atoms share the same fundamental structure. All protons are identical, all neutrons are identical, and all electrons are identical. But when these subatomic particles come together in specific, varied combinations, unique types of atoms called elements result. Each element has a characteristic atomic structure and predictable chemical behavior. To date, about 118 elements, both naturally occurring and artificially produced by physicists, have been described. By convention, an element is assigned a distinctive name with an abbreviated shorthand symbol. The elements are often depicted in a periodic table. Table 2.1 lists some of the elements common

Table 2.1 The Major Elements of Life and Their Primary Characteristics Element

Atomic Symbol*

Atomic Mass**

Calcium

Ca

40.1

Ca

Carbon

C

12.0

CO3−2

C-14

14.0

Chlorine

Cl

35.5

Cl−

Component of disinfectants, used in water purification

Cobalt

Co

58.9

Co2+, Co3+

Trace element needed by some bacteria to synthesize vitamins

Co-60

60

Copper

Cu

63.5

Cu+, Cu2+

Necessary to the function of some enzymes; Cu salts are used to treat fungal and worm infections

Hydrogen

H

1

H+

Necessary component of water and many organic molecules; H2 gas released by bacterial metabolism

H3

3

Iodine Iodine•

I I-131, I-125

126.9 131, 125

I−

Iron

Fe

55.8

Fe2+, Fe3+

Necessary component of respiratory enzymes; required by some microbes to produce toxin

Magnesium

Mg

24.3

Mg2+

A trace element needed for some enzymes; component of chlorophyll pigment

Manganese

Mn

54.9

Mn2+, Mn3+

Trace element for certain respiratory enzymes

Nitrogen

N

14.0

NO3−

Component of all proteins and nucleic acids; the major atmospheric gas

Oxygen

O

16.0

Phosphorus Phosphorus•

P P-32

31 32

Potassium

K

39.1

K

Sodium

Na

23.0

Na+

Necessary for transport; maintains osmotic pressure; used in food preservation

Sulfur

S

32.1

SO4−2

Important component of proteins; makes disulfide bonds; storage element in many bacteria

Zinc

Zn

65.4

Zn++

An enzyme cofactor; required for protein synthesis and cell division; important in regulating DNA

Carbon•

Cobalt•

Hydrogen•

Examples of Ionized Forms 2+

Significance in Microbiology Part of outer covering of certain shelled amoebas; stored within bacterial spores Principal structural component of biological molecules Radioactive isotope used in dating fossils

An emitter of gamma rays; used in food sterilization; used to treat cancer

Has 2 neutrons; radioactive; used in clinical laboratory procedures A component of antiseptics and disinfectants; used in the Gram stain Radioactive isotopes for diagnosis and treatment of cancers

An essential component of many organic molecules; molecule used in metabolism by many organisms PO43−

A component of ATP, nucleic acids, cell membranes; stored in granules in cells Radioactive isotope used as a diagnostic and therapeutic agent

+

Required for normal ribosome function and protein synthesis; essential for cell membrane permeability

*Based on the Latin name of the element. The first letter is always capitalized; if there is a second letter, it is always lowercased. **The atomic mass or weight is equal to the average mass number for the isotopes of that element.

30

Chapter 2

The Chemistry of Biology

to biological systems, their atomic characteristics, and some of the natural and applied roles they play.

Electron Orbitals and Shells

The unique properties of each element result from the numbers of protons, neutrons, and electrons it contains, and each element can be identified by certain physical measurements. Isotopes are variant forms of the same element that differ in the number of neutrons. These multiple forms occur naturally in certain proportions. Carbon, for example, exists primarily as carbon 12 with 6 neutrons; but a small amount (about 1%) is carbon 13 with 7 neutrons and carbon 14 with 8 neutrons. Although isotopes have virtually the same chemical properties, some of them have unstable nuclei that spontaneously release energy in the form of radiation. Such radioactive isotopes play a role in a number of research and medical applications. Because they emit detectable signs, they can be used to trace the position of key atoms or molecules in chemical reactions, they are tools in diagnosis and treatment, and they are even applied in sterilization procedures (see ionizing radiation in chapter 11). Another application of isotopes is in dating fossils and other ancient materials.

The structure of an atom can be envisioned as a central nucleus surrounded by a “cloud” of electrons that constantly rotate about the nucleus in pathways (see figure  2.1). The pathways, called orbitals, are not actual objects or exact locations but represent volumes of space in which an electron is likely to be found. Electrons occupy energy shells, proceeding from the lower-level energy electrons nearest the nucleus to the higher-level energy electrons in the farthest orbitals. Electrons fill the orbitals and shells in pairs, starting with the shell nearest the nucleus. The first shell contains one orbital and a maximum of 2 electrons; the second shell has four orbitals and up to 8 electrons; the third shell with nine orbitals can hold up to 18 electrons; and the fourth shell with 16 orbitals contains up to 32 electrons. The number of orbitals and shells and how completely they are filled depend on the numbers of electrons, so that each element will have a unique pattern. For example, helium has only a filled first shell of 2 electrons; oxygen has a filled first shell and a partially filled second shell of 6 electrons; and magnesium has a filled first shell, a filled second one, and a third shell that fills only one orbital, so is nearly empty. As we will see, the chemical properties of an element are controlled mainly by the distribution of electrons in the outermost shell. Figure 2.1 and figure 2.2 present various

Atomic number Chemical symbol

H

C

Chemical name

HYDROGEN

The Major Elements of Life and Their Primary Characteristics

1

Mg

12

12p

11

SODIUM

7

NITROGEN

O OXYGEN

7p

C

8

8p

N

O

1

2•8•2

2•4

2•5

2•6

AT. MASS 1.00

AT. MASS 24.30

AT. MASS 12.01

AT. MASS 14.00

AT. MASS 16.00

K

19

POTASSIUM

Na

Ca

20

15

S

16

SULFUR

15p

20p

K

P PHOSPHORUS

CALCIUM

19p

11p

N

6p

Mg

H

Na

CARBON

MAGNESIUM

1p

Number of e in each energy level

6

17

CHLORINE

16p

P

Ca

Cl

17p

S

Cl

2•8•1

2•8•8•1

2•8•8•2

2•8•5

2•8•6

2•8•7

AT. MASS 22.99

AT. MASS 39.10

AT. MASS 40.08

AT. MASS 30.97

AT. MASS 32.06

AT. MASS 35.45

Figure 2.2 Examples of biologically important atoms. Simple models show how the shells are filled by electrons as the atomic numbers increase. Notice that these elements have incompletely filled outer shells since they have less than 8 electrons.

2.1

INSIGHT 2.1

Atoms, Bonds, and Molecules: Fundamental Building Blocks

31

The Periodic Table: Not as Concrete as You Think

Most of us have seen images of the periodic table like the one in figure 2.3 over and over again as we progressed through school. Like many things in science, it seems easy to view the periodic table as “set in stone,” with only an occasional addition to the end of it as new elements are found. But since the time it was proposed, there have been legitimate arguments about how it should be represented. These arguments continue today. The first periodic table, the work of Russian chemist Dimitri Mendeleev, was published in 1869. It is called the periodic table because it lays out the pattern of chemicals based on certain properties in them that repeat. Repeating patterns = periodicity. When you realize that the rows indicate increasing atomic number and each column represents a group in which

A Note About Mass, Weight, and Related Terms Mass refers to the quantity of matter that an atomic particle contains. The proton and neutron have almost exactly the same mass, which is about 1.66 × 10–24 grams, a unit of mass known as a Dalton (Da) or unified atomic mass unit (U). All elements can be measured in these units. The terms mass and weight are often used interchangeably in biology, even though they apply to two different but related aspects of matter. Weight is a measurement of the gravitational pull on the mass

the elements have related valences, which confers on them similar chemical properties, the current table seems elegant and, well, right. However, current scientists have been questioning whether the two-dimensional way of representing the elements is the best. The table leads to some minor inaccuracies that not all chemists are comfortable with. Two 3-D representations have been proposed and are pictured here. Also, you see here a unique walk-up version of the traditional periodic table. Another example of how science—even the most familiar “facts” and ideas—is an ever-evolving entity.

of a particle, atom, or object. Consequently, it is possible for something with the same mass to have different weights. For example, an astronaut on the earth (normal gravity) would weigh more than the same astronaut on the moon (weak gravity). Atomic weight has been the traditional usage for biologists, because most chemical reactions and biological activities occur within the normal gravitational conditions on earth. This permits use of the atomic weight as a standard of comparison. You will also see the terms formula weight and molecular weight used interchangeably, and they are indeed synonyms. They both mean the sum of atomic weights of all atoms in a molecule.

32

Chapter 2

The Chemistry of Biology

simplified models of atomic structure and electron maps. Figure 2.3 presents all the elements in the familiar periodic table. (Although 118 have been described, only 112 have been officially sanctioned to date.) To see how the periodic table might look different, see Insight 2.1.

Bonds and Molecules Most elements do not exist naturally in pure, uncombined form but are bound together as molecules and compounds. A molecule is a distinct chemical substance that results from the combination of two or more atoms. Some molecules such as oxygen (O2) and nitrogen gas (N2) consist of atoms of the same element. Molecules that are combinations of two or more different elements are termed compounds. Compounds such as water (H2O) and biological molecules (proteins, sugars, fats) are the predominant substances in living systems. When atoms bind together in molecules, they lose the properties of the atom and take on the properties of the combined substance. The chemical bonds of molecules and compounds result when two or more atoms share, donate (lose), or accept (gain) electrons (figure 2.4). The number of electrons in the outermost shell of an element is known as its valence. The valence determines the degree of reactivity and the types of bonds an element can make. Elements with a filled outer orbital are relatively stable because they have no extra electrons to share with or donate to other atoms. For example, helium has one filled shell, with no tendency either to give

up electrons or to take them from other elements, making it a stable, inert (nonreactive) gas. Elements with partially filled outer orbitals are less stable and are more apt to form some sort of bond. Many chemical reactions are based on the tendency of atoms with unfilled outer shells to gain greater stability by achieving, or at least approximating, a filled outer shell. For example, an atom such as oxygen that can accept 2 additional electrons will bond readily with atoms (such as hydrogen) that can share or donate electrons. We explore some additional examples of the basic types of bonding in the following section. In addition to reactivity, the number of electrons in the outer shell also dictates the number of chemical bonds an atom can make. For instance, hydrogen can bind with one other atom, oxygen can bind with up to two other atoms, and carbon can bind with four.

Covalent Bonds and Polarity: Molecules with Shared Electrons Covalent (cooperative valence) bonds form between atoms that share electrons rather than donating or receiving them. A simple example is hydrogen gas (H2), which consists of two hydrogen atoms. A hydrogen atom has only a single electron, but when two of them combine, each will bring its electron to orbit about both nuclei, thereby approaching a filled orbital (2  electrons) for both atoms and thus creating a single covalent bond (figure 2.5a). Covalent bonding also occurs in

1 1A

18 8A Atomic number

9

1

H 1.008

2 2A

3

4

Hydrogen

2

F Fluorine

Atomic mass

19.00

He

13 3A

14 4A

15 5A

16 6A

17 7A

5

6

7

8

9

10

Helium 4.003

Li

Be

B

C

N

O

F

Ne

Lithium

Beryllium

Boron

Carbon

Nitrogen

Oxygen

Fluorine

Neon

6.941

9.012

10.81

12.01

14.01

16.00

19.00

20.18

11

12

13

14

15

16

17

Na

Mg

Sodium

Magnesium

22.99

19

18

4 4B

5 5B

6 6B

7 7B

8

9 8B

10

11 1B

12 2B

Al

Si

P

S

Cl

Ar

Aluminum

Silicon

Phosphorus

Sulfur

Chlorine

Argon

24.31

3 3B

26.98

28.09

30.97

32.07

35.45

39.95

20

21

22

23

24

25

26

27

28

29

30

31

32

33

34

35

36

K

Ca

Sc

Ti

V

Cr

Mn

Fe

Co

Ni

Cu

Zn

Ga

Ge

As

Se

Br

Kr

Potassium

Calcium

Scandium

Titanium

Vanadium

Chromium

Manganese

Iron

Cobalt

Nickel

Copper

Zinc

Gallium

Germanium

Arsenic

Selenium

Bromine

Krypton

39.10

40.08

44.96

47.88

50.94

52.00

54.94

55.85

58.93

58.69

63.55

65.39

69.72

72.59

74.92

78.96

79.90

83.80

37

38

39

40

41

42

43

44

45

46

47

48

49

50

51

52

53

54

Rb

Sr

Y

Zr

Nb

Mo

Tc

Ru

Rh

Pd

Ag

Cd

In

Sn

Sb

Te

I

Xe

Rubidium

Strontium

Yttrium

Zirconium

Niobium

Molybdenum

Technetium

Ruthenium

Rhodium

Palladium

Silver

Cadmium

Indium

Tin

Antimony

Tellurium

Iodine

Xenon

85.47

87.62

88.91

91.22

92.91

95.94

(98)

101.1

102.9

106.4

107.9

112.4

114.8

118.7

121.8

127.6

126.9

131.3

55

56

57

72

73

74

75

76

77

78

79

80

81

82

83

84

85

86

Cs

Ba

La

Hf

Ta

W

Re

Os

Ir

Pt

Au

Hg

Tl

Pb

Bi

Po

At

Rn

Cesium

Barium

Lanthanum

Hafnium

Tantalum

Tungsten

Rhenium

Osmium

Iridium

Platinum

Gold

Mercury

Thallium

Lead

Bismuth

Polonium

Astatine

Radon

132.9

137.3

138.9

178.5

180.9

183.9

186.2

190.2

192.2

195.1

197.0

200.6

204.4

207.2

209.0

(210)

(210)

(222)

87

88

89

104

105

106

107

108

109

110

111

112

(113)

114

(115)

116

(117)

(118)

Ra

Ac

Rf

Db

Sg

Bh

Hs

Mt

Ds

Rg

Francium

Radium

Actinium

Rutherfordium

Dubnium

Seaborgium

Bohrium

Hassium

Meitnerium

Darmstadtium

Roentgenium

(223)

Fr

(226)

(227)

(257)

(260)

(263)

(262)

(265)

(266)

(269)

(272)

Metals 58

Metalloids

Nonmetals

Figure 2.3 The periodic table.

59

60

61

62

63

64

65

66

67

68

69

70

71

Ce

Pr

Nd

Pm

Sm

Eu

Gd

Tb

Dy

Ho

Er

Tm

Yb

Lu

Cerium

Praseodymium

Neodymium

Promethium

Samarium

Europium

Gadolinium

Terbium

Dysprosium

Holmium

Erbium

Thulium

Ytterbium

Lutetium

140.1

140.9

144.2

(147)

150.4

152.0

157.3

158.9

162.5

164.9

167.3

168.9

173.0

175.0

90

91

92

93

94

95

96

97

98

99

100

101

102

103

Th

Pa

U

Np

Pu

Am

Cm

Bk

Cf

Es

Fm

Md

No

Lr

Thorium

Protactinium

Uranium

Neptunium

Plutonium

Americium

Curium

Berkelium

Californium

Einsteinium

Fermium

Mendelevium

Nobelium

Lawrencium

232.0

(231)

238.0

(237)

(242)

(243)

(247)

(247)

(249)

(254)

(253)

(256)

(254)

(257)

The 1–18 group designation has been recommended by the International Union of Pure and Applied Chemistry (IUPAC) but is not yet in wide use.

2.1

33

Hydrogen Bond

Ionic Bond

Covalent Bonds

Atoms, Bonds, and Molecules: Fundamental Building Blocks

Molecule A

H (+)

Single

(–) (+)

O

(–)

or N

Molecule B (c)

(b)

Figure 2.4 General representation of three types of bonding. (a) Covalent bonds, both single and double. (b) Ionic bond. (c) Hydrogen bond. Note that hydrogen bonds are represented in models and formulas by dotted lines, as shown in (c).

Double

(a)

oxygen gas (O2) but with a difference. Because each atom has 2 electrons to share in this molecule, the combination creates two pairs of shared electrons, also known as a double covalent bond (figure 2.5b). The majority of the molecules associated with living things are composed of single and double covalent bonds between the most common biological ele+

H e–

ments (carbon, hydrogen, oxygen, nitrogen, sulfur, and phosphorus), which are discussed in more depth in chapter 7. Double bonds in molecules and compounds introduce more rigidity than single bonds. A slightly more complex pattern of covalent bonding is shown for methane gas (CH4) in figure 2.5c. H2

H e–

e– 1p+

1p+

+

Hydrogen atom

1p+

e–

1p+

H ⬊H

Single bond Hydrogen molecule

Hydrogen atom

(a)

H

Figure 2.5 Examples of molecules with covalent bonding. (a) A hydrogen

⬊

1p+

⬊

H⬊ C ⬊ H 8p+ 8n

H

8p+ 8n

H

⬊ ⬊

⬊

O⬊⬊O

Double bond (b)

C

6p+ 6n

H

H

⬊

Molecular oxygen (O2)

1p+

H Methane (CH4) (c)

1p+

1p+

molecule is formed when two hydrogen atoms share their electrons and form a single bond. (b) In a double bond, the outer orbitals of two oxygen atoms overlap and permit the sharing of 4 electrons (one pair from each) and the saturation of the outer orbital for both. (c) Simple, three-dimensional, and working models of methane. Note that carbon has 4 electrons to share and hydrogens each have one, thereby completing the shells for all atoms in the compound, and creating 4 single bonds.

34

Chapter 2

The Chemistry of Biology

Other effects of bonding result in differences in polarity. When atoms of different electronegativity 2 form covalent bonds, the electrons are not shared equally and may be pulled more toward one atom than another. This pull causes one end of a molecule to assume a partial negative charge and the other end to assume a partial positive charge. A molecule with such an asymmetrical distribution of charges is termed polar and has positive and negative poles. Observe the water molecule shown in figure 2.6 and note that, because the oxygen atom is larger and has more protons than the hydrogen atoms, it will tend to draw the shared electrons with greater force toward its nucleus. This unequal force causes the oxygen part of the molecule to express a negative charge (due to the electrons being attracted there) and the hydrogens to express a positive charge (due to the protons). The polar nature of water plays an extensive role in a number of biological reactions, which are discussed later. Polarity is a significant property of many large molecules in living systems and greatly influences both their reactivity and their structure.

A Note About Diatomic Elements You will notice that hydrogen, oxygen, nitrogen, chlorine, and iodine are often shown in notation with a 2 subscript—H2 or O2. These elements are diatomic (two atoms), meaning that in their pure elemental state, they exist in pairs, rather than as a single atom. The reason for this phenomenon has to do with their valences. The electrons in the outer shell are configured so as to complete a full outer shell for both atoms when they bind. You can see this for yourself in figures 2.3 and 2.5. Most of the diatomic elements are gases.

When covalent bonds are formed between atoms that have the same or similar electronegativity, the electrons are shared equally between the two atoms. Because of this balanced distribution, no part of the molecule has a greater attraction for the electrons. This sort of electrically neutral molecule is termed nonpolar.

Ionic Bonds: Electron Transfer Among Atoms In reactions that form ionic bonds, electrons are transferred completely from one atom to another and are not shared. These reactions invariably occur between atoms with valences that complement each other, meaning that one atom has an unfilled shell that will readily accept electrons and the other atom has an unfilled shell that will readily lose electrons. A striking example is the reaction that occurs between sodium (Na) and chlorine (Cl). Elemental sodium is a soft, lustrous metal so reactive that it can burn flesh, and molecular chlorine is a very poisonous yellow gas. But when the two are combined, they form sodium chloride 3 (NaCl)—the familiar nontoxic table salt—a compound with properties quite different from either parent element (figure 2.7). How does this transformation occur? Sodium has 11 electrons (2 in shell one, 8 in shell two, and only 1 in shell three), so it is 7 short of having a complete outer shell. Chlorine has 17 electrons (2 in shell one, 8 in shell two, and 7 in shell three), making it 1 short of a complete outer shell. These two atoms are very reactive with one another, because a sodium atom will readily donate its single electron and a chlorine atom will avidly receive it. (The reaction is slightly more involved than a single sodium atom’s combining with a single chloride atom (Insight 2.2), but this complexity does not detract from 3. In general, when a salt is formed, the ending of the name of the negatively charged ion is changed to -ide.

2. Electronegativity—the ability to attract electrons.

Case File 2 (–)





(–)

O

⬊

⬊

H

+

8p

H O

1p

+

(+) (a)

1p

+

H

H

(+)

(+)

(+) (b)

Figure 2.6 Polar molecule. (a) A simple model and (b) a three-dimensional model of a water molecule indicate the polarity, or unequal distribution, of electrical charge, which is caused by the pull of the shared electrons toward the oxygen side of the molecule.

Continuing the Case

DNA is a long molecule made up of repeating units called nucleotides. The identity and order in which the four nucleotides (adenine, guanine, thymine, and cytosine) occur are the basis for the genetic information held by a particular stretch of DNA. The eventual expression off this h informaf tion by the cell results in the production of physical features that can be used to distinguish one cell from another. Also, because DNA is used to transfer genetic information from one generation to the next, all cells descended from a single original cell have similar or identical DNA sequences, while the DNA from strains that are not closely related is less alike. The DNA differences that exist between the various types of Salmonella have led to S. enterica being subdivided into many strains, or serotypes, based on differences in the major surface components. In fact, Salmonella strains are often identified by their genus, species, and serotype, such as S. enterica Typhimurium or S. enterica serotype Tennessee.

2.1

(a)

+

+

11p 12n°

17p 18n°

Sodium atom (Na) ⬊ ⬊

(b) Na⬊ Cl Cl

⬊ ⬊

 Na

⬊ Cl

Chlorine atom (Cl)

[Na]+ [CI]− + Sodium

− Chloride

(c)

(d)

Figure 2.7 Ionic bonding between sodium and chlorine. (a) When the two elements are placed together, sodium loses its single outer orbital electron to chlorine, thereby filling chlorine’s outer shell. (b) Simple model of ionic bonding. (c) Sodium and chloride ions form large molecules, or crystals, in which the two atoms alternate in a definite, regular, geometric pattern. (d) Note the cubic nature of NaCl crystals at the macroscopic level.

Atoms, Bonds, and Molecules: Fundamental Building Blocks

INSIGHT 2.2

Redox: Electron Transfer and Oxidation-Reduction Reactions

The metabolic work of cells, such as synthesis, movement, and digestion, revolves around energy exchanges and transfers. The management of energy in cells is almost exclusively dependent on chemical rather than physical reactions because most cells are far too delicate to operate with heat, radiation, and other more potent forms of energy. The outershell electrons are readily portable and easily manipulated sources of energy. It is in fact the movement of electrons from molecule to molecule that accounts for most energy exchanges in cells. Fundamentally, then, a cell must have a supply of atoms that can gain or lose electrons if they are to carry out life processes. The phenomenon in which electrons are transferred from one atom or molecule to another is termed an oxidation and reduction (shortened to redox) reaction. The term oxidation was originally adopted for reactions involving the addition of oxygen. In current usage, the term oxidation can include any reaction causing electron loss, regardless of the involvement of oxygen. By comparison, reduction is any reaction that causes an atom to receive electrons, because all redox reactions occur in pairs. To analyze the phenomenon, let us again review the production of NaCl but from a different standpoint. When these two atoms react to form sodium chloride, a sodium atom gives up an electron to a chlorine atom. During this reaction, sodium is oxidized because it loses an electron, and chlorine is reduced because it gains an electron (figure 2.7). With this system, an atom such as sodium that can donate electrons and thereby reduce another atom is a reducing agent. An atom that can receive extra electrons and thereby oxidize another molecule is an oxidizing agent. You may find this concept easier to keep straight if you think of redox agents as partners: The reducing partner gives its electrons away and is oxidized; the oxidizing partner receives the electrons and is reduced. A mnemonic device to keep track of this is “LEO says GER” (Lose Electrons Oxidized; Gain Electrons Reduced). Redox reactions are essential to many of the biochemical processes discussed in chapter 8. In cellular metabolism, electrons are frequently transferred from one molecule to another as described here. In other reactions, oxidation and reduction occur with the transfer of a hydrogen atom (a proton and an electron) from one compound to another. e−

e−

the fundamental reaction as described here.) The outcome of this reaction is not many single, isolated molecules of NaCl but rather a solid crystal complex that interlinks millions of sodium and chloride ions (figure 2.7c,d).

Ionization: Formation of Charged Particles Molecules with intact ionic bonds are electrically neutral, but they can produce charged particles when dissolved in a liquid called a solvent. This phenomenon, called ionization, occurs when the ionic bond is broken and the atoms dissociate (separate)

Reducing agent

Oxidizing agent

Oxidized product

Reduced product

Simplified diagram of the exchange of electrons during an oxidation-reduction reaction.

35

36

Chapter 2

The Chemistry of Biology

into unattached, charged particles called ions (figure 2.8). To illustrate what gives a charge to ions, let us look again at the reaction between sodium and chlorine. When a sodium atom reacts with chlorine and loses 1 electron, the sodium is left with one more proton than electrons. This imbalance produces a positively charged sodium ion (Na+). Chlorine, on the other hand, has gained 1 electron and now has 1 more electron than protons, producing a negatively charged ion (Cl−). Positively charged ions are termed cations, and negatively charged ions are termed anions. (A good mnemonic device is to think of the “t” in cation as a plus (+) sign and the first “n” in anion as a negative (−) sign.) Substances such as salts, acids, and bases that release ions when dissolved in water are termed electrolytes because their charges enable them to conduct an electrical current. Owing to the general rule that particles of like charge repel each other and those of opposite charge attract each other, we can expect ions to interact electrostatically with other ions and polar molecules. Such interactions are important in many cellular chemical reactions, in the formation of solutions, and in the − + + −

NaCl crystals

Na

+

Na Cl

Na

−

Cl

+

Na

Cl

+

Na

Cl

−

−

Cl

H

Na +

Cl

−

−

Na

+

+

+

−

Cl

+

H

− +

reactions microorganisms have with dyes. The transfer of electrons from one molecule to another constitutes a significant mechanism by which biological systems store and release energy.

Hydrogen Bonding Some types of bonding do not involve sharing, losing, or gaining electrons but instead are due to attractive forces between nearby molecules or atoms. One such bond is a hydrogen bond, a weak type of bond that forms between a hydrogen covalently bonded to one molecule and an oxygen or nitrogen atom on the same molecule or on a different molecule. Because hydrogen in a covalent bond tends to be positively charged, it will attract a nearby negatively charged atom and form an easily disrupted bridge with it. This type of bonding is usually represented in molecular models with a dotted line. A simple example of hydrogen bonding occurs between water molecules (figure  2.9). More extensive hydrogen bonding is partly responsible for the structure and stability of proteins and nucleic acids, as you will see later on. Other similar noncovalent associations between molecules are the van der Waals forces. These weak attractions occur between molecules that demonstrate low levels of polarity. Neighboring groups with slight attractions will interact and remain associated. These forces are an essential factor in maintaining the cohesiveness of large molecules with many packed atoms. It is safe to say that though each of these two types of bonds, hydrogen bonds and van der Waals forces, are relatively weak on their own, they provide great stability to molecules because there are often many of them in one area. The weakness of each individual bond also provides flexibility, allowing molecules to change their shapes and also to bind and unbind to other objects relatively easily. The fundamental processes of life involve bonding and unbond-

O Cl

Cl

−

−

Na

+

H

−

H

+

Water molecule

+

O

–

–

Hydrogen bonds +

+

11p

+

17p

−

_

(cation)

(anion)

H

O

H

–

H

Chlorine atom (Cl − )

+

– +

–

Sodium ion (Na+)

H

O

–

+ +

–

H O

+

H

–

H

–

Figure 2.8 Ionization. When NaCl in the crystalline form is added to water, the ions are released from the crystal as separate charged particles (cations and anions) into solution. (See also figure 2.12.) In this solution, Cl− ions are attracted to the hydrogen component of water, and Na+ ions are attracted to the oxygen (box).

H

O –

+

+

Figure 2.9 Hydrogen bonding in water. Because of the polarity of water molecules, the negatively charged oxygen end of one water molecule is weakly attracted to the positively charged hydrogen end of an adjacent water molecule.

2.1

ing (for example, the DNA helix has to “unbond” or unwind in order for replication to occur, enzymatic reactions require proteins to bind to other molecules and then be released), and hydrogen bonds and van der Waals forces are custom made for doing just that.

Chemical Shorthand: Formulas, Models, and Equations The atomic content of molecules can be represented by a few convenient formulas. We have already been using the molecular formula, which concisely gives the atomic symbols and the number of the elements involved in subscript (CO2, H2O). More complex molecules such as glucose (C6H12O6) can also be symbolized this way, but this formula is not unique, because fructose and galactose also share it. Molecular formulas are useful, but they only summarize the atoms in a compound; they do not show the position of bonds between atoms. For this purpose, chemists use structural formulas illustrating the relationships of the atoms and the number and types of bonds (figure 2.10). Other structural models present the three-dimensional appearance of a molecule, illustrating the orientation of atoms (differentiated by color) and the molecule’s overall shape (figure 2.11). These are often called space-filling models, as you can get an idea of how the molecule actually occupies its space. The spheres surrounding each atom indicate how far the atom's influence can be felt, let's say. Sometimes it is also referred to as the atom's volume. The printed page tends to make molecules appear static, but this picture is far from correct, because molecules are capable of changing through chemical reactions. For ease in tracing chemical exchanges between atoms or molecules, and to provide some sense of the dynamic character of reactions, chemists use shorthand equations containing symbols, numbers, and arrows to simplify or summarize the major characteristics of a reaction. Molecules entering or starting a reaction are called reactants, and substances left by a reaction are called products. In most instances, summary chemical reactions do not give the details of the exchange, in order to keep the expression simple and to save space. In a synthesis reaction, the reactants bond together in a manner that produces an entirely new molecule (reactant A plus reactant B yields product AB). An example is the production of sulfur dioxide, a by-product of burning sulfur fuels and an important component of smog:

37

Atoms, Bonds, and Molecules: Fundamental Building Blocks

(a)

Molecular formulas

O2

H2

H2O

H Structural formulas

H

O

H

O

CO2

CH4 H

H O

O

C

O

C

H

H

H

(b) Cyclohexane (C6H12) H

H

H C

H C

H H

H

C H C

H H

C

C H

H H

H

C C

C H

H C (c)

Benzene (C6H6)

C C

H

H Also represented by

(d)

Figure 2.10 Comparison of molecular and structural formulas.

(a) Molecular formulas provide a brief summary of the elements in a compound. (b) Structural formulas clarify the exact relationships of the atoms in the molecule, depicting single bonds by a single line and double bonds by two lines. (c) In structural formulas of organic compounds, cyclic or ringed compounds may be completely labeled, or (d) they may be presented in a shorthand form in which carbons are assumed to be at the angles and attached to hydrogens. See figure 2.15 for structural formulas of three sugars with the same molecular formula, C6H12O6.

O H

(a)

O

C

O

H

(b)

S + O2 → SO2 Some synthesis reactions are not such simple combinations. When water is synthesized, for example, the reaction does not really involve one oxygen atom combining with two hydrogen atoms, because elemental oxygen exists as O2 and elemental hydrogen exists as H2. A more accurate equation for this reaction is: 2H2 + O2 → H2O The equation for reactions must be balanced—that is, the number of atoms on one side of the arrow must equal the

(c)

Figure 2.11 Three-dimensional, or space-filling, models of (a) water, (b) carbon dioxide, and (c) glucose. The red atoms are oxygen, the white ones hydrogen, and the black ones carbon.

38

Chapter 2

The Chemistry of Biology

number on the other side to reflect all of the participants in the reaction. To arrive at the total number of atoms in the reaction, multiply the prefix number by the subscript number; if no number is given, it is assumed to be 1. In decomposition reactions, the bonds on a single reactant molecule are permanently broken to release two or more product molecules. One example is the resulting molecules when large nutrient molecules are digested into smaller units; a simpler example can be shown for the common chemical hydrogen peroxide: 2H2O2 → 2H2O + O2 During exchange reactions, the reactants trade portions between each other and release products that are combinations of the two. This type of reaction occurs between acids and bases when they form water and a salt: AB + XY

AX + BY

The reactions in biological systems can be reversible, meaning that reactants and products can be converted back and forth. These reversible reactions are symbolized with a double arrow, each pointing in opposite directions, as in the preceding exchange reaction. Whether a reaction is reversible depends on the proportions of these compounds, the difference in energy state of the reactants and products, and the presence of catalysts (substances that increase the rate of a reaction). Additional reactants coming from another reaction can also be indicated by arrows that enter or leave at the main arrow: CD C X + XY ⎯→ XYD

Solutions: Homogeneous Mixtures of Molecules A solution is a mixture of one or more substances called solutes uniformly dispersed in a dissolving medium called a solvent. An important characteristic of a solution is that the solute cannot be separated by filtration or ordinary settling. The solute can be gaseous, liquid, or solid, and the solvent is usually a liquid. Examples of solutions are salt or sugar dissolved in water and iodine dissolved in alcohol. In general, a solvent will dissolve a solute only if it has similar electrical characteristics as indicated by the rule of solubility, expressed simply as “like dissolves like.” For example, water is a polar molecule and will readily dissolve an ionic solute such as NaCl, yet a nonpolar solvent such as benzene will not dissolve NaCl. Water is the most common solvent in natural systems, having several characteristics that suit it to this role. The polarity of the water molecule causes it to form hydrogen bonds with other water molecules, but it can also interact readily with charged or polar molecules. When an ionic solute such as NaCl crystals is added to water, it is dissolved, thereby releasing Na+ and Cl− into solution. Dissolution occurs because Na+ is attracted to the negative pole of the water molecule and Cl− is attracted to the positive pole; in this way, they are drawn away from the crystal separately into solution. As it leaves, each ion becomes hydrated, which means that it is surrounded by a sphere of water molecules (figure 2.12). Molecules such as salt or sugar that attract water to their surface are termed hydrophilic. Nonpolar molecules, such as benzene, that repel water are considered hydrophobic. A third class of molecules, such as the phospholipids in cell membranes, are considered amphipathic because they have both hydrophilic and hydrophobic properties.

Hydrogen

+ + +

+ +

+

−

+

+

+

+

−

−

−

Na+

+

− +

+ +

− +

−

−

+

+

+

−

+

+

+ +

−

+

−

+

−

−

+

+

− +

+

+

+ Cl −

+

+

−

+

−

+

+

+

+

+

+

+

+

−

+

−

+

+

+

+ +

+

−

−

+

+

−

−

−

Water molecules

+

−

+

−

Oxygen

+

− +

−

+ +

+

− +

+

−

+

−

Figure 2.12 Hydration spheres formed around ions in solution. In this example, a sodium cation attracts the negatively charged region of water molecules, and a chloride anion attracts the positively charged region of water molecules. In both cases, the ions become covered with spherical layers of specific numbers and arrangements of water molecules.

2.1

Because most biological activities take place in aqueous (water-based) solutions, the concentration of these solutions can be very important (see chapter 7). The concentration of a solution expresses the amount of solute dissolved in a certain amount of solvent. It can be calculated by weight, volume, or percentage. A common way to calculate percentage of concentration is to use the weight of the solute, measured in grams (g), dissolved in a specified volume of solvent, measured in milliliters (ml). For example, dissolving 3 g of NaCl in 100 ml of water produces a 3% solution; dissolving 30 g in 100 ml produces a 30% solution; and dissolving 3 g in 1,000 ml (1 liter) produces a 0.3% solution. A common way to express concentration of biological solutions is by its molar concentration, or molarity (M). A standard molar solution is obtained by dissolving one mole, defined as the molecular weight of the compound in grams, in 1 liter (1,000 ml) of solution. To make a 1 mole solution of sodium chloride, we would dissolve 58 grams of NaCl to give 1 liter of solution; a 0.1 mole solution would require 5.8 grams of NaCl in 1 liter of solution.

Acidity, Alkalinity, and the pH Scale

39

because it remains in possession of that electron. Ionization of water is constantly occurring, but in pure water containing no other ions, H+ and OH− are produced in equal amounts, and the solution remains neutral. By one definition, a solution is considered acidic when a component dissolved in water (acid) releases excess hydrogen ions4 (H+); a solution is basic when a component releases excess hydroxyl ions (OH–), so that there is no longer a balance between the two ions. To measure the acid and base concentrations of solutions, scientists use the pH scale, a graduated numerical scale that ranges from 0 (the most acidic) to 14 (the most basic). This scale is a useful standard for rating relative acidity and basicity; use figure 2.13 to familiarize yourself with the pH readings of some common substances. Because the pH scale is a logarithmic scale, each increment (from pH 2.0 to pH 3.0) represents a tenfold change in concentration of ions. (Take a moment to glance at Appendix A to review logarithms and exponents.) More precisely, the pH is based on the negative logarithm of the concentration of H+ ions (symbolized as [H+]) in a solution, represented as: pH = −log[H+] The quantity is expressed in moles per liter. Recall that a mole is simply a standard unit of measurement and refers to the amount of substance containing 6 × 1023 atoms. Acidic solutions have a greater concentration of H+ than OH−, starting with pH 0, which contains 1.0 mole H+/liter. 4. Actually, it forms a hydronium ion (H3O+), but for simplicity’s sake, we will use the notation of H+.

0. 1

M

hy dr oc 2. hl 0 or ic 2. aci 3 d ac id 2. lem spr 4 o in 3. vin n ju g w 0 eg ic a re a e te r 3. d w r 5 sa ine 4. ue 2 b rk 4. ee rau 6 r t a 5. cid 0 ch rain ee se 6. 0 yo 6. gur t 6 c 7. ow 0 's d 7. isti milk 4 lle h d 8. um wa an te 0 s r 8. eaw blo o 4 so ate d di r um 9. bi 2 ca bo rb ra on x, at al e ka lin 10 e .5 so m ils ilk of m 11 ag .5 ne ho si us a e 12 ho .4 ld lim am e m w 13 on a .2 te ia r ov en cl 1 ea M ne po r ta ss iu m hy dr ox id e

Another factor with far-reaching impact on living things is the concentration of acidic or basic solutions in their environment. To understand how solutions develop acidity or basicity, we must look again at the behavior of water molecules. Hydrogens and oxygen tend to remain bonded by covalent bonds, but in certain instances, a single hydrogen can break away as the ionic form (H+), leaving the remainder of the molecule in the form of an OH− ion. The H+ ion is positively charged because it is essentially a hydrogen ion that has lost its electron; the OH− is negatively charged

Atoms, Bonds, and Molecules: Fundamental Building Blocks

pH 0

1

2

3

Acidic

4

[H+]

5

6

7

Neutral

8

9

10

[OH–]

11

12

13

14

Basic (alkaline)

Figure 2.13 The pH scale. Shown are the relative degrees of acidity and basicity and the approximate pH readings for various substances.

40

Chapter 2

The Chemistry of Biology

Each of the subsequent whole-number readings in the scale changes in [H+] by a tenfold reduction, so that pH 1 contains [0.1 mole H+/liter], pH 2 contains [0.01 mole H+/liter], and so on, continuing in the same manner up to pH 14, which contains [0.00000000000001 mole H+/liter]. These same concentrations can be represented more manageably by exponents: pH 2 has an [H+] of 10−2 mole, and pH 14 has an [H+] of 10−14 mole (table 2.2). It is evident that the pH units are derived from the exponent itself. Even though the basis for the pH scale is [H+], it is important to note that, as the [H+] in a solution decreases, the [OH−] increases in direct proportion. At midpoint—pH 7, or neutrality—the concentrations are exactly equal and neither predominates, this being the pH of pure water previously mentioned. In summary, the pH scale can be used to rate or determine the degree of acidity or basicity (also called alkalinity) of a solution. On this scale, a pH below 7 is acidic, and the lower the pH, the greater the acidity. A pH above 7 is basic, and the higher the pH, the greater the basicity. Incidentally, although pHs are given here in even whole numbers, more often, a pH reading exists in decimal form, for example, pH 4.5 or 6.8 (acidic) and pH 7.4 or 10.2 (basic). Because of the damaging effects of very concentrated acids or bases, most cells operate best under neutral, weakly acidic, or weakly basic conditions (see chapter 7). Aqueous solutions containing both acids and bases may be involved in neutralization reactions, which give rise to water and other neutral by-products. For example, when equal molar solutions of hydrochloric acid (HCl) and sodium hydroxide (NaOH, a base) are mixed, the reaction proceeds as follows: HCl + NaOH → H2O + NaCl

Table 2.2 Hydrogen Ion and Hydroxide Ion Concentrations at a Given pH Moles/Liter of Hydrogen Ions

Logarithm

pH

Moles/Liter of OH−

1.0

10−0

0

10−14

0.1

−1

10

1

10−13

0.01

10−2

2

10−12

0.001

10−3

3

10−11

0.0001

10−4

4

10−10

0.00001

10−5

5

10−9

0.000001

−6

10

6

10−8

0.0000001

10−7

7

10−7

0.00000001

10−8

8

10−6

−9

10−5

0.000000001

10

9

0.0000000001

10−10

10

10−4

0.00000000001

−11

10

11

10−3

0.000000000001

10−12

12

10−2

0.0000000000001

−13

10

13

10−1

0.00000000000001

10−14

14

10−0

Here the acid and base ionize to H+ and OH− ions, which form water, and other ions, Na+ and Cl−, which form sodium chloride. Any product other than water that arises when acids and bases react is called a salt. Many of the organic acids (such as lactic and succinic acids) that function in metabolism are available as the acid and the salt form (such as lactate, succinate), depending on the conditions in the cell (see chapter 8).

The Chemistry of Carbon and Organic Compounds So far, our main focus has been on the characteristics of atoms, ions, and small, simple substances that play diverse roles in the structure and function of living things. These substances are often lumped together in a category called inorganic chemicals. A chemical is usually inorganic if it does not contain both carbon and hydrogen. Examples of inorganic chemicals include NaCl (sodium chloride), Mg3(PO4)2 (magnesium phosphate), CaCO3 (calcium carbonate), and CO2 (carbon dioxide). In reality, however, most of the chemical reactions and structures of living things involve more complex molecules, termed organic chemicals. These are carbon compounds with a basic framework of the element carbon bonded to other atoms. Organic molecules vary in complexity from the simplest, methane (CH4 ; see figure 2.5c), which has a molecular weight of 16, to certain antibody molecules (part of our immune systems) that have a molecular weight of nearly 1,000,000 and are among the most complex molecules on earth. The role of carbon as the fundamental element of life can best be understood if we look at its chemistry and bonding patterns. The valence of carbon makes it an ideal atomic building block to form the backbone of organic molecules; it has 4 electrons in its outer orbital to be shared with other atoms (including other carbons) through covalent bonding. As a result, it can form stable chains containing thousands of carbon atoms and still has bonding sites available for forming covalent bonds with numerous other atoms. The bonds that carbon forms are linear, branched, or ringed, and it can form four single bonds, two double bonds, or one triple bond (figure 2.14). The atoms with which carbon is most often associated in organic compounds are hydrogen, oxygen, nitrogen, sulfur, and phosphorus.

Functional Groups of Organic Compounds One important advantage of carbon’s serving as the molecular skeleton for living things is that it is free to bind with an unending array of other molecules. These special molecular groups or accessory molecules that bind to organic compounds are called functional groups. Functional groups help define the chemical class of certain groups of organic compounds and confer unique reactive properties on the whole molecule (table 2.3). Because each type of functional group behaves in a distinctive manner, reactions of an organic compound can be predicted by knowing the kind of functional group or groups it carries. Many reactions rely upon functional groups such as R—OH or R—NH2. The —R designation on a molecule is shorthand for residue, and its placement in a formula indicates that the residue (functional group) varies from one compound to another.

2.2

C

C 1

H

H

Macromolecules: Superstructures of Life

41

Table 2.3 Representative Functional Groups and

C H

Classes of Organic Compounds C

C 1

O

O

C

Formula of Functional Group

O

R* C

N

C 1

N

C N

C

C

C 1

C

C C

O

H O

R

Name

Class of Compounds

Hydroxyl

Alcohols, carbohydrates

Carboxyl

Fatty acids, proteins, organic acids

Amino

Proteins, nucleic acids

Ester

Lipids

Sulfhydryl

Cysteine (amino acid), proteins

Carbonyl, terminal end

Aldehydes, polysaccharides

Carbonyl, internal

Ketones, polysaccharides

Phosphate

DNA, RNA, ATP

C OH

C

C 1

C

H C

C

C R

C

C 1

O

C

NH2

H N

C

N O

(a) R

C

Linear

O

C

C

C

C

C

C

C

C

C

R

H

C R

C

SH

H

Branched

O C

C

C

C

C

C

C

C R

C

C

C

H C O Ringed

R

C C C

C C

C

C C

C

C C

C C

C

C

O R

C

(b)

C

O

P

OH

OH *The R designation on a molecule is shorthand for residue, and it indicates that what is attached at that site varies from one compound to another.

Figure 2.14 The versatility of bonding in carbon. In most compounds, each carbon makes a total of four bonds. (a) Both single and double bonds can be made with other carbons, oxygen, and nitrogen; single bonds are made with hydrogen. Simple electron models show how the electrons are shared in these bonds. (b) Multiple bonding of carbons can give rise to long chains, branched compounds, and ringed compounds, many of which are extraordinarily large and complex.

2.1 Learning Outcomes—Can You . . . 1. 2. 3. 4.

. . . explain the relationship between atoms and elements? . . . list and define four types of chemical bonds? . . . differentiate between a solute and a solvent? . . . give a brief defintion of pH?

2.2 Macromolecules: Superstructures of Life The compounds of life fall into the realm of biochemistry. Biochemicals are organic compounds produced by (or components of) living things, and they include four main families: carbohydrates, lipids, proteins, and nucleic acids (table  2.4). The compounds in these groups are assembled from smaller molecular subunits, or building blocks, and because they are often very large compounds, they are termed macromolecules. All macromolecules except lipids are formed by polymerization, a process in which repeating subunits termed monomers are bound into chains of various lengths termed polymers. For

42

Chapter 2

The Chemistry of Biology

Table 2.4 Macromolecules and Their Functions Macromolecule

Description/Basic Structure

Examples

Notes About the Examples

Monosaccharides

3- to 7-carbon sugars

Glucose, fructose

Disaccharides

Two monosaccharides

Maltose (malt sugar)

Chains of monosaccharides

Lactose (milk sugar) Sucrose (table sugar) Starch, cellulose, glycogen

Sugars involved in metabolic reactions; building block of disaccharides and polysaccharides Composed of two glucoses; an important breakdown product of starch Composed of glucose and galactose Composed of glucose and fructose Cell wall, food storage

Triglycerides

Fatty acids + glycerol

Fats, oils

Phospholipids

Fatty acids + glycerol + phosphate Fatty acids, alcohols

Membrane components

Waxes

Mycolic acid

Cell wall of mycobacteria

Steroids

Ringed structure

Cholesterol, ergosterol

In membranes of eukaryotes and some bacteria

Amino acids

Enzymes; part of cell membrane, cell wall, ribosomes, antibodies

Serve as structural components and perform metabolic reactions

Chromosomes; genetic material of viruses Ribosomes; mRNA, tRNA

Mediate inheritance

Carbohydrates

Polysaccharides

Lipids Major component of cell membranes; storage

Proteins

Nucleic acids Pentose sugar + phosphate + nitrogenous base Purines: adenine, guanine Pyrimidines: cytosine, thymine, uracil Deoxyribonucleic acid (DNA) Ribonucleic acid (RNA)

Contains deoxyribose sugar and thymine, not uracil Contains ribose sugar and uracil, not thymine

example, proteins (polymers) are composed of a chain of amino acids (monomers). The large size and complex, threedimensional shape of macromolecules enables them to function as structural components, molecular messengers, energy sources, enzymes (biochemical catalysts), nutrient stores, and sources of genetic information. In the following section and in later chapters, we consider numerous concepts relating to the roles of macromolecules in cells. Table 2.4 will also be a useful reference when you study metabolism in chapter 8.

Carbohydrates: Sugars and Polysaccharides The term carbohydrate originates from the composition of members of this class: they are combinations of carbon (carbo-) and water (-hydrate). Although carbohydrates can be generally represented by the formula (CH2O)n, in which n indicates the number of units of this combination of atoms (figure 2.15a), some carbohydrates contain additional atoms of sulfur or nitrogen. Carbohydrates exist in a great variety of configurations. The common term sugar (saccharide) refers to a simple carbohy-

Facilitate expression of genetic traits

drate such as a monosaccharide or a disaccharide. A monosaccharide is a simple sugar containing from 3 to 7 carbons; a disaccharide is a combination of two monosaccharides; and a polysaccharide is a polymer of five or more monosaccharides bound in linear or branched chain patterns (figure 2.15b). Monosaccharides and disaccharides are specified by combining a prefix that describes some characteristic of the sugar with the suffix -ose. For example, hexoses are composed of 6 carbons, and pentoses contain 5 carbons. Glucose (Gr. sweet) is the most common and universally important hexose; fructose is named for fruit (one place where it is found); and xylose, a pentose, derives its name from the Greek word for wood. Disaccharides are named similarly: lactose (L. milk) is an important component of milk; maltose means malt sugar; and sucrose (Fr. sugar) is common table sugar or cane sugar.

The Nature of Carbohydrate Bonds The subunits of disaccharides and polysaccharides are linked by means of glycosidic bonds, in which carbons (each is assigned a number) on adjacent sugar units are bonded to the

2.2

H

Aldehyde group

O

H

H

O

C1

C1

C2 OH

HO H

C

H

C

H

C

1

HO

C3 H

HO

C

H

2

H

OH

CH2OH O 5 HO H H

C2 OH

OH

H

3

OH

6

H

HO OH

OH

5

H

4

OH

4

H

O

5

H

Ketone group

6

CH2OH

C3 H

43

H

C1 O

H

6

H

Macromolecules: Superstructures of Life

C

H

C

H

4

H

4

3

OH

6

2

H

OH

C

H

C

H

C

H

4 5 6

O

6

C3 H

H

H OH

OH

OH

HO

1

H

5

C2 O HOCH2

OH

5

OH

2

H

OH HO CH 1 2

H

OH

3

4

OH

OH

H

H

Glucose

Galactose

Fructose

(a)

O

O

O O

Monosaccharide O

Disaccharide O

O O

O O

O

O CH2

O

O

O O

O

O O

O

O

O

O

O

O

O

O

O

CH2

O

O

O

O

O

O

O

O

O O

O

O O

O

O

O

O

O

O

O

O

O O

Polysaccharide (b)

Figure 2.15 Common classes of carbohydrates. (a) Three hexoses with the same molecular formula and different structural formulas. Both linear and ring models are given. The linear form emphasizes aldehyde and ketone groups, although in solution the sugars exist in the ring form. Note that the carbons are numbered so as to keep track of reactions within and between monosaccharides. (b) Major saccharide groups, named for the number of sugar units each contains.

same oxygen atom like links in a chain (figure 2.16). For example, maltose is formed when the number 1 carbon on a glucose bonds to the oxygen on the number 4 carbon on a second glucose; sucrose is formed when glucose and fructose bind oxygen between their number 1 and number 2 carbons; and

lactose is formed when glucose and galactose connect by their number 1 and number 4 carbons. In order to form this bond, 1 carbon gives up its OH group and the other (the one contributing the oxygen to the bond) loses the H from its OH group. Because a water molecule is produced, this reaction is

H2O O

C C

C

C

C

H OH C ⴙ C OH H C C

O

C O

O H C

C

C

C

C

O

C

C H C

C

C

(a) 6

CH2OH O C

5 HO H 4 C OH H 3 C

H

H 2 C

6

5 H H ⴙ C4 OH CH HO 3 C

CH2OH O C

H

H

1C

1C

H

OH

Galactose (b)

6

CH2OH O C

ⴙ

H 2 C OH

Glucose

OH

5 HO H 4 C OH H 3 C

H

6

CH2OH O C

5 H H O C4 OH H 3 C

1() C

H 2 C

H

OH Lactose

OH 1() C

H 2 C

OH

H

Figure 2.16 Glycosidic ⴙ

H2O

bond in a common disaccharide. (a) General scheme in the formation of a glycosidic bond by dehydration synthesis. (b) A 1,4 bond between a galactose and glucose produces lactose.

44

Chapter 2

The Chemistry of Biology

known as dehydration synthesis, a process common to most polymerization reactions (see proteins, page 47). Three polysaccharides (starch, cellulose, and glycogen) are structurally and biochemically distinct, even though all are polymers of the same monosaccharide—glucose. The basis for their differences lies primarily in the exact way the glucoses are bound together, which greatly affects the characteristics of the end product (figure 2.17). The synthesis and breakage of each type of bond requires a specialized catalyst called an enzyme (see chapter 8).

The Functions of Polysaccharides Polysaccharides typically contribute to structural support and protection and serve as nutrient and energy stores. The cell walls in plants and many microscopic algae derive their strength and rigidity from cellulose, a long, fibrous polymer (figure 2.17a). Because of this role, cellulose is probably one of the most common organic substances on the earth, yet it is digestible only by certain bacteria, fungi, and protozoa. These microbes, called decomposers, play an essential role in breaking down and recycling plant materials (see figure 7.2). Some bacteria secrete slime layers of a glucose polymer called dextran. This substance causes a sticky layer to develop on teeth that leads to plaque, described later in chapter 22. Other structural polysaccharides can be conjugated (chemically bonded) to amino acids, nitrogen bases, lipids, or proteins. Agar, an indispensable polysaccharide in preparing solid culture media, is a natural component of

certain seaweeds. It is a complex polymer of galactose and sulfur-containing carbohydrates. The exoskeletons of certain fungi contain chitin (ky-tun), a polymer of glucosamine (a sugar with an amino functional group). Peptidoglycan (pep-tih-doh-gly′-kan) is one special class of compounds in which polysaccharides (glycans) are linked to peptide fragments (a short chain of amino acids). This molecule provides the main source of structural support to the bacterial cell wall. The cell wall of gram-negative bacteria also contains lipopolysaccharide, a complex of lipid and polysaccharide responsible for symptoms such as fever and shock (see chapters 4 and 13). The outer surface of many cells has a “sugar coating” composed of polysaccharides bound in various ways to proteins (the combination is a glycoprotein). This structure, called the glycocalyx, functions in attachment to other cells or as a site for receptors—surface molecules that receive external stimuli or act as binding sites. Small sugar molecules account for the differences in human blood types, and carbohydrates are a component of large protein molecules called antibodies. Viruses also have glycoproteins on their surface with which they bind to and invade their host cells. Polysaccharides are usually stored by cells in the form of glucose polymers such as starch (figure 2.17b) or glycogen, but only organisms with the appropriate digestive enzymes can break them down and use them as a nutrient source. Because a water molecule is required for breaking the bond between two glucose molecules, digestion is also termed hydrolysis. Starch is the primary storage food of green plants, microscopic algae, and some fungi; glycogen (ani-

6

6

6

CH2OH CH2OH CH2OH 5 5 O O O H H H H H H H H H 4 1 α 4 1 α 4 1 α O O O O H H OH OH H OH 5

CH2OH O

H H 4 OH O H

H

H 1 β

OH

H

O

OH H H

4 OH 1 H H O CH2OH

β

H O

CH2OH O 4H 1 OH H H

H β

H OH

O

4 OH

H

OH H H

H

O CH2OH

1 β

3

O

H

2

OH

3

H

2

OH

3

H

2

OH

6

CH2OH O H H H 4 1 Branch O OH H Branch point 2 3 HO O H H 6 C OH 5 O H H H 4 1 O O OH H 5

H bonds

3

H

(a) Cellulose

2

OH

(b) Starch

Figure 2.17 Polysaccharides. (a) Cellulose is composed of β glucose bonded in 1,4 bonds that produce linear, lengthy chains of polysaccharides that are H-bonded along their length. This is the typical structure of wood and cotton fibers. (b) Starch is also composed of glucose polymers, in this case α glucose. The main structure is amylose bonded in a 1,4 pattern, with side branches of amylopectin bonded by 1,6 bonds. The entire molecule is compact and granular.

2.2

mal starch) is a stored carbohydrate for animals and certain groups of bacteria and protozoa.

45

of a single molecule of glycerol bound to three fatty acids (figure 2.18). Glycerol is a 3-carbon alcohol5 with three OH groups that serve as binding sites, and fatty acids are longchain hydrocarbon molecules with a carboxyl group (COOH) at one end that is free to bind to the glycerol. The hydrocarbon portion of a fatty acid can vary in length from 4 to 24 carbons; and, depending on the fat, it may be saturated or unsaturated. If all carbons in the chain are singlebonded to 2  other carbons and 2 hydrogens, the fat is saturated; if there is at least one CKC double bond in the chain, it is unsaturated. The structure of fatty acids is what gives fats and oils (liquid fats) their greasy, insoluble nature. In general, solid fats (such as butter) are more saturated, and liquid fats (such as oils) are more unsaturated. In recent

Lipids: Fats, Phospholipids, and Waxes The term lipid, derived from the Greek word lipos, meaning fat, is not a chemical designation but an operational term for a variety of substances that are not soluble in polar solvents such as water (recall that oil and water do not mix) but will dissolve in nonpolar solvents such as benzene and chloroform. This property occurs because the substances we call lipids contain relatively long or complex C—H (hydrocarbon) chains that are nonpolar and thus hydrophobic. The main groups of compounds classified as lipids are triglycerides, phospholipids, steroids, and waxes. Important storage lipids are the triglycerides, a category that includes fats and oils. Triglycerides are composed

5. Alcohols are carbon compounds containing OH groups.

3 H2O s

Fatty acid

Macromolecules: Superstructures of Life

Carboxylic R Hydrocarbon acid chain

Triglyceride

Ester Hydrocarbon Glycerol bond chain

Glycerol H H

H

H

C

OH

C

HO

+

OH

C

HO

OH

HO

O

H

H

H

H

H

H

C

C

C

C

C

C

C

H

H

H

H

H

H

O

H

H

H

H

H

H

C

C

C

C

C

C

C

H

H

H

H

H

H

O

H

H

H

H

H

H

C

C

C

C

C

C

C

H

H

H

H

H

H

H

O

H H

C

O

H

C

O

H

C

O

C

R

O C

R

O C

R

H

(a) Fatty acids 1

Triglycerides

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

C

C

C

C

C

C

C

C

C

C

C

C

C

C

C

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

O C HO

H

Palmitic acid, a saturated fatty acid 2 H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

C

C

C

C

C

C

C

C

C

C

C

C

C

C

C

C

C

H

H

H

H

H

H

H

H

H

O C

H

HO

(b)

H

H

Linolenic acid, an unsaturated fatty acid

Figure 2.18 Synthesis and structure of a triglyceride. (a) Because a water molecule is released at each ester bond, this is another form of dehydration synthesis. The jagged lines and R symbol represent the hydrocarbon chains of the fatty acids, which are commonly very long. (b) Structural and three-dimensional models of fatty acids and triglycerides. (1) A saturated fatty acid has long, straight chains that readily pack together and form solid fats. (2) An unsaturated fatty acid—here a polyunsaturated one with 3 double bonds—has bends in the chain that prevent packing and produce oils (right).

46

Chapter 2

INSIGHT 2.3

The Chemistry of Biology

Membranes: Cellular Skins

(a)

(b)

(a) Extreme magnification of a cross section of a cell membrane, which appears as double tracks. (b) A generalized version of the fluid mosaic model of a cell membrane indicates a bilayer of lipids with globular proteins embedded to some degree in the lipid matrix. This structure explains many characteristics of membranes, including flexibility, solubility, permeability, and transport.

Variable alcohol group

years there has been a realization that a type of triglyceride, called popularly “trans fat” is harmful to the health of those who consume it. A trans fat is an unsaturated triglyceride with one or more of its fatty acids in a position (trans) that is not often found in nature, but is a common occurrence in processed foods. In most cells, triglycerides are stored in long-term concentrated form as droplets or globules. When they are acted on by digestive enzymes called lipases, the fatty acids and glycerol are freed to be used in metabolism. Fatty acids are a superior source of energy, yielding twice as much per gram as other storage molecules (starch). Soaps are K+ or Na+ salts of fatty acids whose qualities make them excellent grease removers and cleaners (see chapter 11).

Phosphate

HC

CH

O

O

OC

OC

Charged head

Glycerol

Polar lipid molecule

HCH HCH

Polar head Nonpolar tails

HCH HCH HCH HCH HCH HCH

Tail

Phospholipids in single layer

HCH HCH HCH HCH HCH HCH

HC HC HC H HC H HC H HC H HC H HC H HC H HC H

Membrane Lipids A class of lipids that serves as a major structural component of cell membranes is the phospholipids. Although phospholipids also contain glycerol and fatty acids, they have some significant differences from triglycerides. Phospholipids contain only two fatty acids attached to the glycerol, and the third glycerol binding site holds a phosphate group. The phosphate is in turn bonded to an alcohol, which varies from one phospholipid to another (figure 2.19a). These lipids have a hydrophilic region from the charge on the phosphoric acid–alcohol “head” of the molecule and a hydrophobic region that corresponds to the long, uncharged “tail” (formed by the fatty acids). When exposed to an aqueous solution, the charged heads are attracted to the water phase, and the nonpolar tails are repelled from the water phase (figure 2.19b). This property causes lipids to naturally assume single and double layers (bilayers), which contribute to their biological significance

R O 2 O P O O HCH H

H

HCH HCH HCH

Water

HCH

(1)

HCH HCH

Phospholipid bilayer

HCH HCH HCH

Water

Water

HCH H

(a)

Fatty acids

(b)

(2)

Figure 2.19 Phospholipids—membrane molecules. (a) A model of a single molecule of a phospholipid. The phosphate-alcohol head lends a charge to one end of the molecule; its long, trailing hydrocarbon chain is uncharged. (b) The behavior of phospholipids in water-based solutions causes them to become arranged (1) in single layers called micelles, with the charged head oriented toward the water phase and the hydrophobic nonpolar tail buried away from the water phase, or (2) in double-layered phospholipid systems with the hydrophobic tails sandwiched between two hydrophilic layers.

2.2

The word membrane appears frequently in descriptions of cells in this chapter and in chapters 4 and 5. The word itself describes any lining or covering, including such multicellular structures as the mucous membranes of the body. From the perspective of a single cell, however, a membrane is a thin, double-layered sheet composed of lipids such as phospholipids and sterols (averaging about 40% of membrane content) and protein molecules (averaging about 60%). The primary role of membranes is as a cell membrane that completely encases the cytoplasm. Membranes are also components of eukaryotic organelles such as nuclei, mitochondria, and chloroplasts, and they appear in internal pockets of certain prokaryotic cells. Even some viruses, which are not cells at all, can have a membranous protective covering. Cell membranes are so thin—on the average, just 0.0070 μm (7 nm) thick—that they cannot actually be seen with an optical microscope. Even at magnifications made possible by electron microscopy (500,000×), very little of the precise architecture can be visualized, and a cross-sectional view has the appearance of railroad tracks. Following detailed microscopic and chemical analysis, S. J. Singer and C. K. Nicholson proposed a simple and elegant

in membranes. When two single layers of polar lipids come together to form a double layer, the outer hydrophilic face of each single layer will orient itself toward the solution, and the hydrophobic portions will become immersed in the core of the bilayer. The structure of lipid bilayers confers characteristics on membranes such as selective permeability and fluid nature (Insight 2.3).

47

Macromolecules: Superstructures of Life

theory for membrane structure called the fluid mosaic model. According to this theory, a membrane is a continuous bilayer formed by lipids that are oriented with the polar lipid heads toward the outside and the nonpolar tails toward the center of the membrane. Embedded at numerous sites in this bilayer are various-size globular proteins. Some proteins are situated only at the surface; others extend fully through the entire membrane. The configuration of the inner and outer sides of the membrane can be quite different because of the variations in protein shape and position. Membranes are dynamic and constantly changing because the lipid phase is in motion and many proteins can migrate freely about, somewhat as icebergs do in the ocean. This fluidity is essential to such activities as engulfment of food and discharge or secretion by cells. The structure of the lipid phase provides an impenetrable barrier to many substances. This property accounts for the selective permeability and capacity to regulate transport of molecules. It also serves to segregate activities within the cell’s cytoplasm. Membrane proteins function in receiving molecular signals (receptors), in binding and transporting nutrients, and in acting as enzymes, topics to be discussed in chapters 7 and 8.

Glycolipid

Phospholipids

Cell membrane

Steroids and Waxes Steroids are complex ringed compounds commonly found in cell membranes and animal hormones. The best known of these is the sterol (meaning a steroid with an OH group) called cholesterol (figure 2.20). Cholesterol reinforces the structure of the cell membrane in animal cells and in an unusual group of cell-wall-deficient bacteria called the mycoplasmas (see chapter 4). The cell membranes of fungi also contain a sterol, called ergosterol. Chemically, a wax is an ester formed between a longchain alcohol and a saturated fatty acid. The resulting material is typically pliable and soft when warmed but hard and water resistant when cold (paraffin, for example). Among living things, fur, feathers, fruits, leaves, human skin, and insect exoskeletons are naturally waterproofed with a coating of wax. Bacteria that cause tuberculosis and leprosy produce a wax that repels ordinary laboratory stains and contributes to their pathogenicity.

Proteins: Shapers of Life The predominant organic molecules in cells are proteins, a fitting term adopted from the Greek word proteios, meaning first or prime. To a large extent, the structure, behavior, and unique qualities of each living thing are a consequence of the

Protein

Site for ester bond with a fatty acid

C

Globular protein

CH2

CH2 H2C C CH

Cholesterol

Cholesterol

HO H

C HC

CH2 CH CH

CH3 H2 C H 2C CH3

C HC

CH2 C H2

CH CH3 CH2 CH2 CH2

CH CH3 CH3

Figure 2.20 Cutaway view of a membrane with its bilayer of lipids. The primary lipid is phospholipid—however, cholesterol is inserted in some membranes. Other structures are protein and glycolipid molecules. Cholesterol can become esterified with fatty acids at its OH– group, imparting a polar quality similar to that of phospholipids.

48

Chapter 2

The Chemistry of Biology

proteins they contain. To best explain the origin of the special properties and versatility of proteins, we must examine their general structure. The building blocks of proteins are amino acids, which exist in 20 different naturally occurring forms (table 2.5). Various combinations of these amino acids account for the nearly infinite variety of proteins. Amino acids have a basic skeleton consisting of a carbon (called the α carbon) linked to an amino group (NH2), a carboxyl group (COOH), a hydrogen atom (H), and a variable R group. The variations among the amino acids occur at the R group, which is different in each amino acid and imparts the unique characteristics to the molecule and to the proteins that contain it (figure 2.21). A covalent bond called a peptide bond forms between the amino group on one amino acid and the carboxyl group on another amino acid. As a result of peptide bond formation, it is possible to produce molecules varying in length from two amino acids to chains containing thousands of them. Various terms are used to denote the nature of proteins. Peptide usually refers to a molecule composed of short chains of amino acids, such as a dipeptide (two amino acids), a tripeptide (three), and a tetrapeptide (four). A polypeptide contains an unspecified number of amino acids but usually has more than 20 and is often a smaller subunit of a protein. A protein is the largest of this class of compounds and usually contains a minimum of 50 amino acids. It is common for the term protein to be used to describe all of these molecules; we

used it in its general sense in the first sentence of this paragraph. But not all polypeptides are large enough to be considered proteins. In chapter 9, we see that protein synthesis is not just a random connection of amino acids; it is directed by information provided in DNA.

Protein Structure and Diversity The reason that proteins are so varied and specific is that they do not function in the form of a simple straight chain of amino acids (called the primary structure). A protein has a natural

Structural Formula

Amino Acid

H

Alanine

␣ carbon O

H

H

N

C

C

H

C

H

H

H

H

H

N

C

O C OH

Valine

CH H

C

H

H

C

H

H

H

N

C

C

H

C

H

Acid

Abbreviation

Characteristic of R Groups

Alanine

Ala

nonpolar

Arginine

Arg

+

Asparagine

Asn

polar

H

H

H

N

C

C

H

C

H

Asp

–

Cys

polar

Glutamic acid

Glu

–

Glutamine

Gln

polar

C

Glycine

Gly

polar

H

Histidine

His

+

Isoleucine

Ile

nonpolar

Leucine

Leu

nonpolar

Lys

+

Methionine

Met

nonpolar

Phenylalanine

Phe

nonpolar

Proline

Pro

nonpolar

Serine

Ser

polar

Threonine

Thr

polar

Tryptophan

Trp

nonpolar

Tyrosine

Tyr

polar

Valine

Val

nonpolar

O OH

Aspartic acid

Lysine

OH

SH

Cysteine

+ = positively charged; − = negatively charged.

O

Cysteine

Their Abbreviations

H

H

H

Table 2.5 Twenty Amino Acids and

OH

Phenylalanine

C H

C

H

C

H

C

H

C

H

H

H

N

C

C

H

C

H

O OH

Tyrosine

C H

C

H

C

C

H

C

H

C OH

Figure 2.21 Structural formulas of selected amino

acids. The basic structure common to all amino acids is shown in blue type; and the variable group, or R group, is placed in a colored box. Note the variations in structure of this reactive component.

2.2

tendency to assume more complex levels of organization, called the secondary, tertiary, and quaternary structures (figure 2.22). The primary (1°) structure is the type, number, and order of amino acids in the chain, which varies extensively from protein to protein. The secondary (2°) structure arises when various functional groups exposed on the outer surface of the molecule interact by forming hydrogen bonds. This interaction causes the amino acid chain to twist into a coiled configuration called the α helix or to fold into an accordion pattern called a β -pleated sheet. Many proteins contain both types of secondary configurations. Proteins at the secondary level undergo a third degree of torsion called the tertiary (3°) structure created by additional bonds between functional groups (figure 2.22c). In proteins with the sulfur-containing amino acid cysteine, considerable tertiary stability is achieved through covalent disulfide bonds between sulfur atoms on two different parts of the molecule. Some complex proteins assume a quaternary (4°) structure, in which more than one polypeptide forms a large, multiunit protein. This is typical of antibodies (see chapter 15) and some enzymes that act in cell synthesis. The most important outcome of the various forms of bonding and folding is that each different type of protein develops a unique shape, and its surface displays a distinctive pattern of pockets and bulges. As a result, a protein can react only with molecules that complement or fit its particular surface features like a lock and key. Such a degree of specificity can provide the functional diversity required for many thousands of different cellular activities. Enzymes serve as the catalysts for all chemical reactions in cells, and nearly every reaction requires a different enzyme (see chapter 8). This specificity comes from the architecture of the binding site which determines which molecules fit it. The same is true of antibodies; antibodies are complex glycoproteins with specific regions of attachment for bacteria, viruses, and other microorganisms. Certain bacterial toxins (poisonous products) react with only one specific organ or tissue; and proteins embedded in the cell membrane have reactive sites restricted to a certain nutrient. The functional three-dimensional form of a protein is termed the native state, and if it is disrupted by some means, the protein is said to be denatured. Such agents as heat, acid, alcohol, and some disinfectants disrupt (and thus denature) the stabilizing intrachain bonds and cause the molecule to become nonfunctional, as described in chapter 11.

The Nucleic Acids: A Cell Computer and Its Programs The nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), were originally isolated from the cell nucleus. Shortly thereafter, they were also found in other parts of nucleated cells, in cells with no nuclei (bacteria), and in viruses. The universal occurrence of nucleic acids in all known cells and viruses emphasizes their important roles as informational molecules. DNA, the master computer of cells, contains a special coded genetic program with detailed and specific instructions for each organism’s heredity. It transfers

Macromolecules: Superstructures of Life

49

the details of its program to RNA, “helper” molecules responsible for carrying out DNA’s instructions and translating the DNA program into proteins that can perform life functions. For now, let us briefly consider the structure and some functions of DNA, RNA, and a close relative, adenosine triphosphate (ATP). Both DNA and RNA are polymers of repeating units called nucleotides, each of which is composed of three smaller units: a nitrogen base, a pentose (5-carbon) sugar, and a Gly (a)

Asp

Trp

Gln

Leu

His

Val

Phe

Amino acid sequence

Ala

Lys Glu

Beta-pleated sheet

Alpha helix

Random coil

(b)

Folded polypeptide chain

(c)

Two or more polypeptide chains

(d)

Figure 2.22 Stages in the formation of a functioning

protein. (a) Its primary structure is a series of amino acids bound in a chain. (b) Its secondary structure develops when the chain forms hydrogen bonds that fold it into one of several configurations such as an α helix or β-pleated sheet. Some proteins have several configurations in the same molecule. (c) A protein’s tertiary structure is due to further folding of the molecule into a three-dimensional mass that is stabilized by hydrogen, ionic, and disulfide bonds between functional groups. (d) The quaternary structure exists only in proteins that consist of more than one polypeptide chain. The chains in this protein each have a different color.

50

Chapter 2

The Chemistry of Biology HOCH2 O

N base Pentose sugar

H

H

Phosphate (a) A nucleotide, composed of a phosphate, a pentose sugar, and a nitrogen base (either A,T,C,G, or U) is the monomer of both DNA and RNA. Backbone

HOCH2 O

OH H

H

H

H

OH H

H

OH H

OH OH

Deoxyribose

Ribose

(a) Pentose sugars

Backbone P

DNA D

A

T

U

D

P C

G

P D

G

C

P T

A

P

R

P D

A

T

P C

G

D

P

H

Adenine (A)

Guanine (G)

H H

H3C

H N

O

H

H

H N

N

N

R

H bonds (c) In RNA, the polymer is composed of alternating ribose (R) and phosphate (P) attached to nitrogen bases (A,U,C,G), but it is usually a single strand.

Figure 2.23 The general structure of nucleic acids. phosphate (figure 2.23a).6 The nitrogen base is a cyclic compound that comes in two forms: purines (two rings) and pyrimidines (one ring). There are two types of purines—adenine (A) and guanine (G)—and three types of pyrimidines—thymine (T), cytosine (C), and uracil (U) (figure 2.24). A characteristic that differentiates DNA from RNA is that DNA contains all of the nitrogen bases except uracil, and RNA contains all of the nitrogen bases except thymine. The nitrogen base is covalently bonded to the sugar ribose in RNA and deoxyribose (because it has one less oxygen than ribose) in DNA. Phosphate provides the final covalent bridge that connects sugars in series. Thus, the backbone of a nucleic acid strand is a chain of alternating phosphate-sugar-phosphate-sugar molecules, and the nitrogen bases branch off the side of this backbone (figure 2.23b,c).

The Double Helix of DNA DNA is a huge molecule formed by two very long polynucleotide strands linked along their length by hydrogen bonds between complementary pairs of nitrogen bases. The pairing 6. The nitrogen base plus the pentose is called a nucleoside.

N

H

O

P

(b) In DNA, the polymer is composed of alternating deoxyribose (D) and phosphate (P) with nitrogen bases (A,T,C,G) attached to the deoxyribose. DNA almost always exists in pairs of strands, oriented so that the bases are paired across the central axis of the molecule.

N

(b) Purine bases

P A

H

N

H

H

R

P D

N

P C

D

N

P G

D

H

R

P D

H N

H

P C

D

N N

R

P

O

N P

A

D

H N

R

P D

H

P

RNA

H

N

O

H

N

O

H

N

H

H

H

Thymine (T)

Cytosine (C)

Uracil (U)

O

(c) Pyrimidine bases

Figure 2.24 The sugars and nitrogen bases that make up DNA and RNA. (a) DNA contains deoxyribose, and RNA contains ribose. (b) A and G purine bases are found in both DNA and RNA. (c) Pyrimidine bases are found in both DNA and RNA, but T is found only in DNA, and U is found only in RNA.

of the nitrogen bases occurs according to a predictable pattern: Adenine always pairs with thymine, and cytosine with guanine. The bases are attracted in this way because each pair shares oxygen, nitrogen, and hydrogen atoms exactly positioned to align perfectly for hydrogen bonds (figure 2.25). For ease in understanding the structure of DNA, it is sometimes compared to a ladder, with the sugar-phosphate backbone representing the rails and the paired nitrogen bases representing the steps. Owing to the manner of nucleotide pairing and stacking of the bases, the actual configuration of DNA is a double helix that looks somewhat like a spiral staircase. As is true of protein, the structure of DNA is intimately related to its function. DNA molecules are usually extremely long. The hydrogen bonds between pairs break apart when DNA is being copied, and the fixed complementary base pairing is essential to maintain the genetic code.

RNA: Organizers of Protein Synthesis Like DNA, RNA consists of a long chain of nucleotides. However, RNA is often a single strand, except in some viruses.

2.3

Cells: Where Chemicals Come to Life

51

NH2 N 7 8 O –O

P O–

O O

P O–

O O

P

9 N O

5 6 1N 4 3 2 N

CH2 O

O– OH

OH Adenosine

Adenosine diphosphate (ADP) Adenosine triphosphate (ATP) (a)

O

O

O

T D

Figure 2.25 A structural representation of the double helix of DNA. Shown are the details of hydrogen bonds between the nitrogen bases of the two strands.

A

D Hydrogen P O bonds

O O

P

C D

G O

P

O

D

D

O

T

A

P

O

O

(b)

Figure 2.26 An ATP molecule. (a) The structural formula. Wavy lines connecting the phosphates represent bonds that release large amounts of energy. (b) A ball and stick model.

D

O

P

It contains ribose sugar instead of deoxyribose and uracil instead of thymine (see figure 2.23). Several functional types of RNA are formed using the DNA template through a replicationlike process. Three major types of RNA are important for protein synthesis. Messenger RNA (mRNA) is a copy of a gene (a single functional part of the DNA) that provides the order and type of amino acids in a protein; transfer RNA (tRNA) is a carrier that delivers the correct amino acids for protein assembly; and ribosomal RNA (rRNA) is a major component of ribosomes (described in chapter 4). A fourth type of RNA is the RNA that acts to regulate the genes and gene expression. More information on these important processes is presented in chapter 9.

ates adenosine diphosphate (ADP). ADP can be converted back to ATP when the third phosphate is restored, thereby serving as an energy depot. Carriers for oxidation-reduction activities (nicotinamide adenine dinucleotide [NAD], for instance) are also derivatives of nucleotides (see chapter 8).

2.2 Learning Outcomes—Can You . . . 5. . . . name the four main families of biochemicals? 6. . . . provide examples of cell components made from each of the families of biochemicals? 7. . . . explain primary, secondary, tertiary, and quaternary structure as seen in proteins? 8. . . . list the three components of nucleic acids? 9. . . . name the nucleotides of DNA? RNA? 10. . . . list the three components of ATP?

ATP: The Energy Molecule of Cells A relative of RNA involved in an entirely different cell activity is adenosine triphosphate (ATP). ATP is a nucleotide containing adenine, ribose, and three phosphates rather than just one (figure 2.26). It belongs to a category of high-energy compounds (also including guanosine triphosphate [GTP]) that give off energy when the bond is broken between the second and third (outermost) phosphate. The presence of these high-energy bonds makes it possible for ATP to release and store energy for cellular chemical reactions. Breakage of the bond of the terminal phosphate releases energy to do cellular work and also gener-

2.3 Cells: Where Chemicals Come to Life As we proceed in this chemical survey from the level of simple molecules to increasingly complex levels of macromolecules, at some point we cross a line from the realm of lifeless molecules and arrive at the fundamental unit of life called a cell.7 A cell is indeed a huge aggregate of carbon, hydrogen, 7. The word cell was originally coined from an Old English term meaning “small room” because of the way plant cells looked to early microscopists.

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oxygen, nitrogen, and many other atoms, and it follows the basic laws of chemistry and physics, but it is much more. The combination of these atoms produces characteristics, reactions, and products that can only be described as living.

Fundamental Characteristics of Cells The bodies of living things such as bacteria and protozoa consist of only a single cell, whereas those of animals and plants contain trillions of cells. Regardless of the organism, all cells have a few common characteristics. They tend to be spherical, polygonal, cubical, or cylindrical, and their protoplasm (internal cell contents) is encased in a cell or cytoplasmic membrane (see Insight 2.3). They have chromosomes containing DNA and ribosomes for protein synthesis, and they are exceedingly complex in function. Aside from these few similarities, most cell types fall into one of three fundamentally different lines (discussed in chapter 1): the small, seemingly simple bacterial and archaeal cells and the larger, structurally more complicated eukaryotic cells. Eukaryotic cells are found in animals, plants, fungi, and protists. They contain a number of complex internal parts called organelles that perform useful functions for the cell involving growth, nutrition, or metabolism. By convention, organelles are defined as cell components that perform specific functions and are enclosed by membranes. Organelles also partition the eukaryotic cell into smaller compartments. The most visible organelle is the nucleus, a roughly ballshaped mass surrounded by a double membrane that contains the DNA of the cell. Other organelles include the Golgi apparatus, endoplasmic reticulum, vacuoles, and mitochondria. Bacterial and archaeal cells may seem to be the cellular “have nots” because, for the sake of comparison, they are described by what they lack. They have no nucleus and generally no other organelles. This apparent simplicity is misleading, however, because the fine structure of

Case File 2

Wrap-Up

In this case, S. enterica Typhimurium was identified as the outbreak strain and was found in peanut products manufactured in the PCA plant as well as in ill persons—and even in a tanker truck that had been used to transport peanut paste. Complicating matters was the h ffact that other companies had used the peanut paste to manufacture food items; at last count, the paste had been traced to over 3,000 peanut-containing products, including peanut butter crackers and dog biscuits. Two other S. enterica strains, Mbandaka and Senftenberg, were discovered in cracks in the concrete floor of the PCA processing plant, and a third variant, Tennessee, was found in peanut butter in the factory. Comparison of DNA from these three strains with DNA from strains isolated from ill individuals revealed that none of the strains were linked to any illness. On January 28, 2009, PCA announced a voluntary recall of all peanuts and peanut-containing products processed in its Georgia facility since January 1, 2007. Records indicated the company had knowingly shipped peanut butter containing Salmonella at least 12 times in the previous 2 years, and a criminal inquiry was begun that same month. PCA filed for bankruptcy on February 13. See: 2009. MMWR 58:85–90.

prokaryotes is complex. Overall, prokaryotic cells can engage in nearly every activity that eukaryotic cells can, and many can function in ways that eukaryotes cannot. Chapters 4 and 5 delve deeply into the properties of prokaryotic and eukaryotic cells.

2.3 Learning Outcome—Can You . . . 11. . . . point out three characteristics all cells share?

Chapter Summary 2.1 Atoms, Bonds, and Molecules: Fundamental Building Blocks • Protons (p+) and neutrons (n0) make up the nucleus of an atom. Electrons (e−) orbit the nucleus. • All elements are composed of atoms but differ in the numbers of protons, neutrons, and electrons they possess. • Isotopes are varieties of one element that contain the same number of protons but different numbers of neutrons. • The number of electrons in an element’s outermost orbital (compared with the total number possible) determines the element’s chemical properties and reactivity. • Covalent bonds are chemical bonds in which electrons are shared between atoms. Equally distributed electrons form nonpolar covalent bonds, whereas unequally distributed electrons form polar covalent bonds. • Ionic bonds are chemical bonds resulting from opposite charges. The outer electron shell either donates or receives electrons from another atom so that the outer shell of each atom is completely filled.

• Hydrogen bonds are weak chemical attractions that

• • •

• •

form between covalently bonded hydrogens and either oxygens or nitrogens on different molecules. These as well as van der Waals forces are critically important in biological processes. Chemical equations express the chemical exchanges between atoms or molecules. Solutions are mixtures of solutes and solvents that cannot be separated by filtration or settling. The pH, ranging from a highly acidic solution to a highly basic solution, refers to the concentration of hydrogen ions. It is expressed as a number from 0 to 14. Biologists define organic molecules as those containing both carbon and hydrogen. Carbon is the backbone of biological compounds because of its ability to form single, double, or triple covalent bonds with itself and many different elements.

Multiple-Choice and True-False Questions

53

• Functional (R) groups are specific arrangements of

• Proteins are called the “shapers of life” because of the

organic molecules that confer distinct properties, including chemical reactivity, to organic compounds.

many biological roles they play in cell structure and cell metabolism. • Protein structure determines protein function. Structure and shape are dictated by amino acid composition and by the pH and temperature of the protein’s immediate environment. • Nucleic acids are biological molecules whose polymers are chains of nucleotide monomers linked together by phosphate–pentose sugar covalent bonds. Doublestranded nucleic acids are linked together by hydrogen bonds. Nucleic acids are information molecules that direct cell metabolism and reproduction. Nucleotides such as ATP also serve as energy transfer molecules in cells.

2.2 Macromolecules: Superstructures of Life • Macromolecules are very large organic molecules (polymers) built up by polymerization of smaller molecular subunits (monomers). • Carbohydrates are biological molecules whose polymers are monomers linked together by glycosidic bonds. Their main functions are protection and support (in organisms with cell walls) and also nutrient and energy stores. • Lipids are biological molecules such as fats that are insoluble in water. Their main functions are as cell components, cell secretions, and nutrient and energy stores. • Proteins are biological molecules whose polymers are chains of amino acid monomers linked together by peptide bonds.

2.3 Cells: Where Chemicals Come to Life • As the atom is the fundamental unit of matter, so is the cell the fundamental unit of life.

Multiple-Choice and True-False Questions

Knowledge and Comprehension

Multiple-Choice Questions. Select the correct answer from the answers provided. 1. The smallest unit of matter with unique characteristics is a. an electron. c. an atom. b. a molecule. d. a proton. 2. The ____ charge of a proton is exactly balanced by the ____ charge of a (an) ____. a. negative, positive, electron b. positive, neutral, neutron c. positive, negative, electron d. neutral, negative, electron 3. Electrons move around the nucleus of an atom in pathways called a. shells. c. circles. b. orbitals. d. rings. 4. Bonds in which atoms share electrons are defined as ____ bonds. a. hydrogen c. double b. ionic d. covalent 5. Hydrogen bonds can form between ____ adjacent to each other. a. two hydrogen atoms b. two oxygen atoms c. a hydrogen atom and an oxygen atom d. negative charges 6. An atom that can donate electrons during a reaction is called a. an oxidizing agent. c. an ionic agent. b. a reducing agent. d. an electrolyte. 7. A solution with a pH of 2 ____ than a solution with a pH of 8. a. has less H+ c. has more OH– b. has more H+ d. is less concentrated

Critical Thinking Questions

8. Proteins are synthesized by linking amino acids with ____ bonds. a. disulfide c. peptide b. glycosidic d. ester 9. DNA is a hereditary molecule that is composed of a. deoxyribose, phosphate, and nitrogen bases. b. deoxyribose, a pentose, and nucleic acids. c. sugar, proteins, and thymine. d. adenine, phosphate, and ribose. 10. RNA plays an important role in what biological process? a. replication c. lipid metabolism b. protein synthesis d. water transport True-False Questions. If the statement is true, leave as is. If it is false, correct it by rewriting the sentence. 11. Elements have varying numbers of protons, neutrons, and electrons. 12. Covalent bonds are those that are made between two different elements. 13. A compound is called “organic” if it is made of all-natural elements. 14. Cysteine is the amino acid that participates in disulfide bonds in proteins. 15. Membranes are mainly composed of macromolecules called carbohydrates.

Application and Analysis

These questions are suggested as a writing-to-learn experience. For each question, compose a one- or two-paragraph answer that includes the factual information needed to completely address the question. 1. Which kinds of elements tend to make covalent bonds? 2. Distinguish between a single and a double bond.

3. Why are hydrogen bonds relatively weak? 4. What determines whether a substance is an acid or a base?

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5. What atoms must be present in a molecule for it to be considered organic? 6. What characteristics of carbon make it ideal for the formation of organic compounds? 7. The “octet rule” in chemistry helps predict the tendency of atoms to acquire or donate electrons from the outer shell. It says that those with fewer than 4 tend to donate electrons and those with more than 4 tend to accept additional electrons; those with exactly 4 can do both. Using this rule, determine what category each of the following elements falls

Concept Mapping

into: N, S, C, P, O, H, Ca, Fe, and Mg. (You will need to work out the valence of the atoms.) 8. Draw the following molecules and determine which are polar: Cl2, NH3, CH4. 9. Distinguish between polar and ionic compounds, using your own words. 10. Looking at figure 2.25, can you see why adenine forms hydrogen bonds with thymine and why cytosine forms them with guanine?

Synthesis

Appendix D provides guidance for working with concept maps.

Membranes

1. Supply your own linking words or phrases in this concept map, and provide the missing concepts in the empty boxes.

are made of

are made of

are made of Amino acids

C

Visual Connections

R

NH2

Synthesis

These questions use visual images or previous content to make connections to this chapter’s concepts. 1. Figure 2.19a and Figure 2.20. Speculate on why sterols like cholesterol can add “stiffness” to membranes that contain them.

Membrane phospholipid

Phosphate

R O ⴚ O P O O HCH H HC

CH

O

O

OC

OC

HCH HCH HCH HCH HCH HCH HCH HCH Tail

HCH HCH HCH HCH HCH HCH

HC HC HC H HC H HC H HC H HC H HC H HC H HC H H

Cholesterol Charged head

Glycerol

HO Site for ester bond H C CH2 with a fatty acid CH2 H2C C CH

C HC

CH2 CH CH

CH3 H2 C H2C CH3

C HC

CH2 C H2

CH CH3

HCH

CH2

HCH

CH2

HCH

CH2

HCH

CH CH3 CH3

HCH HCH HCH HCH HCH HCH H

Fatty acids

www.connect.microbiology.com Enhance your study of this chapter with study tools and practice tests. Also ask your instructor about the resources available through ConnectPlus, including the media-rich eBook, interactive learning tools, and animations.

Tools of the Laboratory The Methods for Studying Microorganisms 3 Case File One August morning in 2008, a large proportion of the inmates at a Wisconsin county jail awoke complaining of nausea, vomiting, and diarrhea. The local health department suspected an outbreak of foodborne illness, and along with the Wisconsin Division of Public Health, initiated an investigation. Because of the strict routine and controlled environment of prison life, it was relatively easy to find out what the inmates had eaten in the past 24 hours and how their food had been prepared. A written questionnaire distributed to the inmates revealed 194 probable cases of food intoxication. Four respondents commented on the unusual taste of the casserole they had eaten the night before, which contained macaroni, ground beef, ground turkey, frozen vegetables, and gravy. Stool samples were obtained from six symptomatic inmates and cultured for the presence of pathogenic bacteria. ◾ What five basic techniques are used to identify a microorganism in the laboratory? ◾ What types of media might a lab technician use to differentiate bacteria from one another? Continuing the Case appears on page 66.

Outline and Learning Outcomes 3.1 Methods of Culturing Microorganisms: The Five I’s 1. Explain what the five I’s mean and what each step entails. 2. Name and define the three ways to categorize media. 3. Provide examples for each of the three categories of media. 3.2 The Microscope: Window on an Invisible Realm 4. Convert among different lengths within the metric system. 5. Describe the earliest microscopes. 6. List and describe the three elements of good microscopy. 7. Differentiate between the principles of light and electron microscopy. 8. Name the two main categories of stains. 9. Give examples of a simple, differential, and special stain.

55

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Chapter 3

Tools of the Laboratory An Overview of Major Techniques Performed by Microbiologists to Locate, Grow, Observe, and Characterize Microorganisms

Specimen Collection: Nearly any object or material can serve as a source of microbes. Common ones are body fluids and tissues, foods, water, or soil. Specimens are removed by some form of sampling device: a swab, syringe, or a special transport system that holds, maintains, and preserves the microbes in the sample.

A GUIDE TO THE FIVE I’s: How the Sample Is Processed and Profiled 1

Syringe

2

Bird embryo

Streak plate

Incubator

Blood bottle 1. Inoculation: The sample is placed into a container of sterile medium containing appropriate nutrients to sustain growth. Inoculation involves spreading the sample on the surface of a solid medium or introducing the sample into a flask or tube. Selection of media with specialized functions can improve later steps of isolation and identification. Some microbes may require a live organism (animal, egg) as the growth medium.

2. Incubation: An incubator creates the proper growth temperature and other conditions. This promotes multiplication of the microbes over a period of hours, days, and even weeks. Incubation produces a culture—the visible growth of the microbe in or on the medium.

Microscopic morphology: shape, staining reactions

Subculture

Isolation

3. Isolation: One result of inoculation and incubation is isolation of the microbe. Isolated microbes may take the form of separate colonies (discrete mounds of cells) on solid media, or turbidity (free-floating cells) in broths. Further isolation by subculturing involves taking a bit of growth from an isolated colony and inoculating a separate medium. This is one way to make a pure culture that contains only a single species of microbe.

4. Inspection: The colonies or broth cultures are observed macroscopically for growth characteristics (color, texture, size) that could be useful in analyzing the specimen contents. Slides are made to assess microscopic details such as cell shape, size, and motility. Staining techniques may be used to gather specific information on microscopic morphology.

Biochemical tests

Immunologic tests

DNA analysis

5. Identification: A major purpose of the Five I’s is to determine the type of microbe, usually to the level of species. Information used in identification can include relevant data already taken during initial inspection and additional tests that further describe and differentiate the microbes. Specialized tests include biochemical tests to determine metabolic activities specific to the microbe, immunologic tests, and genetic analysis.

Figure 3.1 A summary of the general laboratory techniques carried out by microbiologists. It is not necessary to perform all the steps shown or to perform them exactly in this order, but all microbiologists participate in at least some of these activities. In some cases, one may proceed right from the sample to inspection, and in others, only inoculation and incubation on special media are required.

3.1

3.1 Methods of Culturing Microorganisms: The Five I’s Biologists studying large organisms such as animals and plants can, for the most part, immediately see and differentiate their experimental subjects from the surrounding environment and from one another. In fact, they can use their senses of sight, smell, hearing, and even touch to detect and evaluate identifying characteristics and to keep track of growth and developmental changes. Microbiologists, however, are confronted by some unique problems. First, most habitats (such as the soil and the human mouth) harbor microbes in complex associations, so it is often necessary to separate the species from one another. Second, to maintain and keep track of such small research subjects, microbiologists usually have to grow them under artificial (and thus distorting) conditions. A third difficulty in working with microbes is that they are invisible and widely distributed, and undesirable ones can be introduced into an experiment and cause misleading results. Microbiologists use five basic techniques to manipulate, grow, examine, and characterize microorganisms in the laboratory: inoculation, incubation, isolation, inspection, and identification (the Five I’s; figure 3.1). Some or all of these procedures are performed by microbiologists, whether beginning laboratory students, researchers attempting to isolate drug-producing bacteria from soil, or clinical microbiologists working with a specimen from a patient’s infection. These procedures make it possible to handle and maintain microorganisms as discrete entities whose detailed

Methods of Culturing Microorganisms: The Five I’s

57

biology can be studied and recorded. Keep in mind as we move through this chapter: It is not necessary to cultivate a microorganism to identify it anymore, though it still remains a very common method. You will read about noncultivation methods of identifying microbes in chapter 17.

Inoculation: Producing a Culture To cultivate, or culture, microorganisms, one introduces a tiny sample (the inoculum) into a container of nutrient medium (pl. media), which provides an environment in which they multiply. This process is called inoculation. Any instrument used for sampling and inoculation must initially be sterile. The observable growth that appears in or on the medium after incubation is known as a culture. The nature of the sample being cultured depends on the objectives of the analysis. Clinical specimens for determining the cause of an infectious disease are obtained from body fluids (blood, cerebrospinal fluid), discharges (sputum, urine, feces), or diseased tissue. Other samples subject to microbiological analysis are soil, water, sewage, foods, air, and inanimate objects. Procedures for proper specimen collection are discussed in chapter 17.

Isolation: Separating One Species from Another

Certain isolation techniques are based on the concept that if an individual bacterial cell is separated from other cells and provided adequate space on a nutrient surface, it will grow into a discrete mound of cells called a colony (figure 3.2). If it was formed from a single cell, a colony consists of just that one species and no other. Proper isolation requires that a small number of cells be inoculated into Mixture of cells in sample a relatively large volume or over an expansive area of medium. It generally requires the following materials: a medium that has a relatively firm surface (see agar in “PhysiSeparation of cal States of Media,” page 60), a Petri dish cells by spreading Microscopic view Parent (a clear, flat dish with a cover), and inoculator dilution on agar cells ing tools. In the streak plate method, a small medium droplet of culture or sample is spread over the Incubation surface of the medium with an inoculating loop according to a pattern that gradually Growth increases the number of cells. thins out the sample and separates the cells spatially over several sections of the plate (figure 3.3a,b). Because of its ease and effectiveness, the streak plate is the method of Microbes become choice for most applications. visible as isolated Macroscopic view In the loop dilution, or pour plate, techcolonies containing nique, the sample is inoculated serially into millions of cells. a series of cooled but still liquid agar tubes so as to dilute the number of cells in each successive tube in the series (figure 3.3c,d). Inoculated tubes are then plated out (poured) Figure 3.2 Isolation technique. Stages in the formation of an isolated colony, into sterile Petri dishes and are allowed to showing the microscopic events and the macroscopic result. Separation techniques solidify (harden). The end result (usually in such as streaking can be used to isolate single cells. After numerous cell divisions, a the second or third plate) is that the number macroscopic mound of cells, or a colony, will be formed. This is a relatively simple yet of cells per volume is so decreased that cells successful way to separate different types of bacteria in a mixed sample.

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have ample space to grow into separate colonies. One difference between this and the streak plate method is that in this technique some of the colonies will develop deep in the medium itself and not just on the surface. With the spread plate technique, a small volume of liquid, diluted sample is pipetted onto the surface of the medium and spread around evenly by a sterile spreading tool (sometimes called a “hockey stick”). Like the streak plate, cells are pushed onto separate areas on the surface so that they can form individual colonies (figure 3.3e,f ). Before we continue to cover information on the Five I’s, we will take a side trip to look at media in more detail.

Media: Providing Nutrients in the Laboratory A major stimulus to the rise of microbiology in the late 1800s was the development of techniques for growing microbes out of their natural habitats and in pure form in the laboratory. This milestone enabled the close examination of a microbe and its morphology, physiology, and genetics. It was evident from the very first that for successful cultivation, each microorganism had to be provided with all of its required nutrients in an artificial medium. Some microbes require only a very few simple inorganic compounds for growth; others need a complex list of specific

Figure 3.3 Methods for isolating bacteria. (a) Steps in a quadrant streak plate and (b) resulting isolated colonies of bacteria. (c) Steps in the loop dilution method and (d) the appearance of plate 3. (e) Spread plate and (f) its result. Note: This method only works if the spreading tool (usually an inoculating loop) is resterilized after each of steps 1– 4.

1

2

3

4

5

(a) Steps In a Streak Plate

(b)

1

2

3

1

2

3

(c) Steps In Loop Dilution

(d)

“Hockey stick” 1 (e) Steps In a Spread Plate

2 (f)

3.1

INSIGHT 3.1

Methods of Culturing Microorganisms: The Five I’s

59

Animal Inoculation: “Living Media”

A great deal of attention has been focused on the uses of animals in biology and medicine. Animal rights activists are vocal about practically any experimentation with animals and have expressed their outrage quite forcefully. Certain kinds of animal testing may seem trivial and unnecessary, but many times it is absolutely necessary to use animals bred for experimental purposes, such as guinea pigs, mice, chickens, and even armadillos. Such animals can be an indispensable aid for studying, growing, and identifying microorganisms. One special use of animals involves inoculation of the early life stages (embryos) of birds. Vaccines for influenza are currently produced in chicken embryos. The major rationales for live animal inoculation can be summarized as follows:

4. Animals are sometimes required to determine the pathogenicity or toxicity of certain bacteria. One such test is the mouse neutralization test for the presence of botulism toxin in food. This test can help identify even very tiny amounts of toxin and thereby can avert outbreaks of this disease. Occasionally, it is necessary to inoculate an animal to distinguish between pathogenic or nonpathogenic strains of Listeria or Candida (a yeast). 5. Some microbes will not grow on artificial media but will grow in a suitable animal and can be recovered in a more or less pure form. These include animal viruses, the spirochete of syphilis, and the leprosy bacillus (grown in armadillos).

1. Animal inoculation is an essential step in testing the effects of drugs and the effectiveness of vaccines before they are administered to humans. It makes progress toward prevention, treatment, and cure possible without risking the lives of humans. 2. Researchers develop animal models for evaluating new diseases or for studying the cause or process of a disease. Koch’s postulates are a series of proofs to determine the causative agent of a disease and require a controlled experiment with an animal that can develop a typical case of the disease. 3. Animals are an important source of antibodies, antisera, antitoxins, and other immune products that can be used in therapy or testing.

The nude or athymic mouse has genetic defects in hair formation and thymus development. It is widely used to study cancer, immune function, and infectious diseases.

inorganic and organic compounds. This tremendous diversity is evident in the types of media that can be prepared. More than 500 different types of media are used in culturing and identifying microorganisms. Culture media are contained in test tubes, flasks, or Petri dishes, and they are inoculated by such tools as loops, needles, pipettes, and swabs. Media are extremely varied in nutrient content and consistency and can be specially formulated for a particular purpose. Culturing microbes that cannot grow on artificial media (all viruses and certain bacteria) requires cell cultures or host animals (Insight 3.1). For an experiment to be properly controlled, sterile technique is necessary. This means that the inoculation must start with a sterile medium and inoculating tools with sterile tips

must be used. Measures must be taken to prevent introduction of nonsterile materials, such as room air and fingers, directly into the media.

Types of Media Media can be classified according to three properties (table 3.1): 1. physical state, 2. chemical composition, and 3. purpose, functional type. Most media discussed here are designed for bacteria and fungi, though algae and some protozoa can be propagated in media.

Table 3.1 Three Categories of Media Classification Physical State*

Chemical Composition

1. 2. 3. 4.

1. Synthetic (chemically defined) 2. Nonsynthetic (complex; not

Liquid Semisolid Solid (can be converted to liquid) Solid (cannot be liquefied)

chemically defined)

Functional Type 1. 2. 3. 4.

General purpose Enriched Selective Differential

5. 6. 7. 8.

Anaerobic growth Specimen transport Assay Enumeration

*Some media can serve more than one function. For example, a medium such as brain-heart infusion is general purpose and enriched; mannitol salt agar is both selective and differential; and blood agar is both enriched and differential.

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Physical States of Media Liquid media are water-based solutions that do not solidify at temperatures above freezing and that tend to flow freely when the container is tilted (figure 3.4). These media, termed broths, milks, or infusions, are made by dissolving various solutes in distilled water. Growth occurs throughout the container and can then present a dispersed, cloudy, or particulate appearance. A common laboratory medium, nutrient broth, contains beef extract and peptone dissolved in water. Methylene blue milk and litmus milk are opaque liquids containing whole milk and dyes. Fluid thioglycollate is a slightly viscous broth used for determining patterns of growth in oxygen. At ordinary room temperature, semisolid media exhibit a clotlike consistency (figure 3.5) because they contain an amount of solidifying agent (agar or gelatin) that thickens them but does not produce a firm substrate. Semisolid media are used to determine the motility of bacteria and to localize a reaction at a specific site. Solid media provide a firm surface on which cells can form discrete colonies (figure 3.6) and are advantageous for isolating and culturing bacteria and fungi. They come in two forms: liquefiable and nonliquefiable. Liquefiable solid media, sometimes called reversible solid media, contain a solidifying agent that changes their physical properties in response to temperature. By far the most widely used and effective of these agents is agar, a complex polysaccharide isolated from the red alga Gelidium. The benefits of agar are numerous. It is solid at room temperature, and it melts (liquefies) at the boiling temperature of water (100°C). Once liquefied, agar does not resolidify until it cools to 42°C, so it can be inoculated and poured in liquid form at temperatures (45° to 50°C) that will not harm the microbes or the handler. Agar is flexible and moldable, and it provides a basic framework to hold moisture and nutrients, though it is not itself a digestible nutrient for most microorganisms. Any medium containing 1% to 5% agar usually has the word agar in its name. Nutrient agar is a common one. Like nutrient broth, it contains beef extract and peptone, as well as 1.5% agar by weight. Many of the examples covered in the section on functional categories of media contain agar. Although gelatin is not nearly as satisfactory as agar, it will create a reasonably solid surface in concentrations of 10% to 15%. Agar medium is illustrated in figure 3.7 and figure 3.9. Nonliquefiable solid media have less versatile applications than agar media because they do not melt. They include materials such as rice grains (used to grow fungi), cooked meat media (good for anaerobes), and potato slices; all of these media start out solid and remain solid after heat sterilization. Other solid media containing egg and serum start out liquid and are permanently coagulated or hardened by moist heat.

Figure 3.4 Sample liquid media. (a) Liquid media tend to flow freely when the container is tilted. (b) Urea broth is used to show a biochemical reaction in which the enzyme urease digests urea and releases ammonium. This raises the pH of the solution and causes the dye to become increasingly pink. Left: uninoculated broth, pH 7; middle: weak positive, pH 7.5; right: strong positive, pH 8.0.

(a)

(0)

(⫹)

(⫹)

(b)

Figure 3.5 Sample semisolid media.

(a) Semisolid media have more body than liquid media but less body than solid media. They do not flow freely and have a soft, clotlike consistency. (b) Sulfur indole motility medium (SIM). The (1) medium is stabbed with an inoculum and incubated. Location of growth indicates nonmotility (2) or motility (3). If H2S gas is released, a black precipitate forms (4).

(a)

(b) 1

Figure 3.6 Solid

media that are reversible to liquids.

(a) Media containing 1%–5% agar are solid enough to remain in place when containers are tilted or inverted. They are reversibly solid and can be liquefied with heat, poured into a different container, and resolidified. (b) Nutrient gelatin contains enough gelatin (12%) to take on a solid consistency. The top tube shows it as a solid. The bottom tube indicates what happens when it is warmed or when microbial enzymes digest the gelatin and liquefy it.

(a)

(b)

2

3

4

3.1

Chemical Content of Media Media whose compositions are precisely chemically defined are termed synthetic (also known as defined). Such media contain pure organic and inorganic compounds that vary little from one source to another and have a molecular content specified by means of an exact formula. Synthetic media come in many forms. Some media, such as minimal media for fungi, contain nothing more than a few essential compounds such as salts and amino acids dissolved in water. Others contain a variety of defined organic and inorganic chemicals (table 3.2). Such standardized and reproducible media are most useful in research and cell culture when the exact nutritional needs of the test organisms are known. If even one component of a given medium is not chemically definable, the medium belongs in the complex category. Complex, or nonsynthetic, media contain at least one ingredient that is not chemically definable—not a simple, pure compound and not representable by an exact chemical formula. Most of these substances are extracts of animals, plants, or yeasts, including such materials as ground-up cells, tissues, and secretions. Examples are blood, serum, and meat extracts or infusions. Other nonsynthetic ingredients are milk, yeast extract, soybean digests, and peptone. Peptone is a partially degraded protein, rich in amino acids, that is often used as a carbon and nitrogen source. Nutrient broth, blood agar, and MacConkey agar, though different in function and appearance, are all complex nonsynthetic media. They present a rich mixture of nutrients for microbes that have complex nutritional needs. Table 3.2 provides a practical comparison of the two categories, using a Staphylococcus medium. Every substance in medium A is known to a very precise degree. The substances in medium B are mostly macromolecules that contain dozens of unknown (but required) nutrients. Both A and B will satisfactorily grow the bacterium.

Media for Different Purposes Microbiologists have many types of media at their disposal, with new ones being devised all the time. Depending on what is added, a microbiologist can fine-tune a medium for nearly any purpose. Until recently, microbiologists knew of only a few species of bacteria or fungi that could not be cultivated artificially. Newer DNA detection technologies have shown us just how wrong we were; it is now thought that there are many times more microbes that we don’t know how to cultivate in the lab than those that we do. Previous discovery and identification of microorganisms relied on our ability to grow them. Now we can detect a single bacterium in its natural habitat. General-purpose media are designed to grow as broad a spectrum of microbes as possible. As a rule, they are nonsynthetic and contain a mixture of nutrients that could

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Table 3.2A Chemically Defined Synthetic Medium for Growth and Maintenance of Pathogenic Staphylococcus aureus 0.25 Grams Each of These Amino Acids

0.5 Grams Each of These Amino Acids

0.12 Grams Each of These Amino Acids

Cystine Histidine Leucine Phenylalanine Proline Tryptophan Tyrosine

Arginine Glycine Isoleucine Lysine Methionine Serine Threonine Valine

Aspartic acid Glutamic acid

Additional ingredients 0.005 mole nicotinamide 0.005 mole thiamine Vitamins 0.005 mole pyridoxine 0.5 micrograms biotin 1.25 grams magnesium sulfate 1.25 grams dipotassium hydrogen phosphate 1.25 grams sodium chloride 0.125 grams iron chloride

Salts

Ingredients dissolved in 1,000 milliliters of distilled water and buffered to a final pH of 7.0.

Table 3.2B Brain-Heart Infusion Broth: A Complex, Nonsynthetic Medium for Growth and Maintenance of Pathogenic Staphylococcus aureus 27.5 2 5 2.5

grams brain, heart extract, peptone extract grams glucose grams sodium chloride grams di-sodium hydrogen phosphate

Ingredients dissolved in 1,000 milliliters of distilled water and buffered to a final pH of 7.0.

support the growth of a variety of microbial life. Examples include nutrient agar and broth, brain-heart infusion, and trypticase soy agar (TSA). An enriched medium contains complex organic substances such as blood, serum, hemoglobin, or special growth factors (specific vitamins, amino acids) that certain species must have in order to grow. Bacteria that require growth factors and complex nutrients are termed fastidious. Blood agar, which is made by adding sterile sheep, horse, or rabbit blood to a sterile agar base

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(figure 3.7a) is widely employed to grow fastidious streptococci and other pathogens. Pathogenic Neisseria (one species causes gonorrhea) are grown on Thayer-Martin medium or “chocolate” agar, which is made by heating blood agar (figure 3.7b).

Selective and Differential Media Some of the most inventive media recipes belong to the categories of selective and differential media (figure 3.8). These media are designed for special microbial groups, and they have extensive applications in isolation and identification. They can permit, in a single step, the preliminary identification of a genus or even a species. A selective medium (table 3.3) contains one or more agents that inhibit the growth of a certain microbe or

microbes (call them A, B, and C) but not others (D) and thereby encourages, or selects, microbe D and allows it to grow. Selective media are very important in primary isolation of a specific type of microorganism from samples containing dozens of different species—for example, feces, saliva, skin, water, and soil. They speed up isolation by suppressing the unwanted background organisms and favoring growth of the desired ones.

Mixed sample

(a)

(a)

General-purpose nonselective medium (All species grow.)

Mixed sample

General-purpose nondifferential medium (All species have a similar (b) appearance.) (b)

Figure 3.7 Examples of enriched media. (a) Blood agar plate growing bacteria from the human throat. Note that this medium also differentiates among colonies by the zones of hemolysis (clear areas) they may show. (b) Culture of Neisseria sp. on chocolate agar. Chocolate agar gets its brownish color from cooked blood (not chocolate) and does not produce hemolysis.

Selective medium (One species grows.)

Differential medium (All 3 species grow but may show different reactions.)

Figure 3.8 Comparison of selective and differential

media with general-purpose media. (a) A mixed sample containing three different species is streaked onto plates of generalpurpose nonselective medium and selective medium. Note the results. (b) Another mixed sample containing three different species is streaked onto plates of general-purpose nondifferential medium and differential medium. Note the results.

3.1

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63

Table 3.3 Selective Media, Agents, and Functions Medium

Selective Agent

Used For

Mueller tellurite

Potassium tellurite

Isolation of Corynebacterium diphtheriae

Enterococcus faecalis broth

Sodium azide, tetrazolium

Isolation of fecal enterococci

Phenylethanol agar

Phenylethanol chloride

Isolation of staphylococci and streptococci

Tomato juice agar

Tomato juice, acid

Isolation of lactobacilli from saliva

MacConkey agar

Bile, crystal violet

Isolation of gram-negative enterics

Salmonella/Shigella (SS) agar

Bile, citrate, brilliant green

Isolation of Salmonella and Shigella

Lowenstein-Jensen

Malachite green dye

Isolation and maintenance of Mycobacterium

Sabouraud’s agar

pH of 5.6 (acid)

Isolation of fungi—inhibits bacteria

Mannitol salt agar (MSA) (figure 3.9a) contains a high concentration of NaCl (7.5%) that is quite inhibitory to most human pathogens. One exception is the genus Staphylococcus, which grows well in this medium and consequently can be amplified in mixed samples. Bile salts, a component of feces, inhibit most gram-positive bacteria while permitting many gram-negative rods to grow. Media for isolating intestinal pathogens (MacConkey agar, Hektoen enteric [HE] agar) contain bile salts as a selective agent (figure 3.9b). Dyes such as methylene blue and crystal violet also inhibit certain gram-positive bacteria. Other agents that have selective properties are antimicrobial drugs and acid. Some selective media contain strongly inhibitory agents to favor the growth of a pathogen that would otherwise be overlooked because of its low numbers

Figure 3.9 Examples of media that are

in a specimen. Selenite and brilliant green dye are used in media to isolate Salmonella from feces, and sodium azide is used to isolate enterococci from water and food. Differential media allow multiple types of microorganisms to grow but are designed to display visible differences among those microorganisms. Differentiation shows up as variations in colony size or color, in media color changes, or in the formation of gas bubbles and precipitates (table 3.4). These variations come from the type of chemicals these media contain and the ways that microbes react to them. For example, when microbe  X metabolizes a certain substance not used by organism Y, then X will cause a visible change in the medium and Y will not. The simplest differential media show two reaction types such as the use or nonuse of a particular nutrient or a color change in some colonies but not in others. Some media are

(a)

both selective and differential.

(a) Mannitol salt agar is used to isolate members of the genus Staphylococcus. It is selective because Staphylococcus can grow in the presence of 7.5% sodium chloride, whereas many other species are inhibited by this high concentration. It contains a dye that also differentiates those species of Staphylococcus that produce acid from mannitol and turn the phenol red dye to a bright yellow. (b) MacConkey agar selects against gram-positive bacteria. It also differentiates between lactose-fermenting bacteria (indicated by a pink-red reaction in the center of the colony) and lactose-negative bacteria (indicated by an off-white colony with no dye reaction).

(b)

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Table 3.4 Differential Media

Medium

Substances That Facilitate Differentiation

Blood agar

Intact red blood cells

Types of hemolysis displayed by different species of Streptococcus

Mannitol salt agar

Mannitol, phenol red

Species of Staphylococcus

Hektoen enteric (HE) agar

Brom thymol blue, acid fuchsin, sucrose, salicin, thiosulfate, ferric ammonium citrate

Salmonella, Shigella, other lactose fermenters from nonfermenters

MacConkey agar

Lactose, neutral red

Bacteria that ferment lactose (lowering the pH) from those that do not

Urea broth

Urea, phenol red

Bacteria that hydrolyze urea to ammonia

Sulfur indole motility (SIM)

Thiosulfate, iron

H2S gas producers from nonproducers

Triple-sugar iron agar (TSIA)

Triple sugars, iron, and phenol red dye

Fermentation of sugars, H2S production

Birdseed agar

Seeds from thistle plant

Cryptococcus neoformans and other fungi

Differentiates Between

sufficiently complex to show three or four different reactions (figure 3.10). A single medium can be both selective and differential, owing to different ingredients in its composition. MacConkey agar, for example, appears in table 3.3 (selective media) and table 3.4 (differential media). Dyes can be used as differential agents because many of them are pH indicators that change color in response to the production of an acid or a base. For example, MacConkey agar contains neutral red, a dye that is yellow when neutral and pink or red when acidic. A common intestinal bacterium such as Escherichia coli that gives off acid when it metabolizes the lactose in the medium develops red to pink colonies, and one like Salmonella that does not give off acid remains its natural color (off-white).

Miscellaneous Media A reducing medium contains a substance (thioglycollic acid or cystine) that absorbs oxygen or slows the penetration of oxygen in a medium, thus reducing its availability. Reducing media are important for growing anaerobic bacteria or for determining oxygen requirements of isolates (described in chapter 7). Carbohydrate fermentation media contain sugars that can be fermented (converted to acids) and a pH indicator to show this reaction (see

(a)

(b)

Figure 3.10 Media that differentiate characteristics. (a) Triple-sugar iron agar (TSIA) in a slant tube. This medium contains three fermentable carbohydrates, phenol red to indicate pH changes, and a chemical (iron) that indicates H2S gas production. Reactions (from left to right) are: no growth; growth with no acid production; acid production in the bottom (butt) only; acid production all through the medium; and acid production in the butt with H2S gas formation (black). (b) A state-of-the-art medium developed for culturing and identifying the most common urinary pathogens. CHROMagar OrientationTM uses color-forming reactions to distinguish at least seven species and permits rapid identification and treatment. In the example, the bacteria were streaked so as to spell their own names.

figure 3.9a and figure 3.11). Media for other biochemical reactions that provide the basis for identifying bacteria and fungi are presented in chapter 17. Transport media are used to maintain and preserve specimens that have to be held for a period of time before clinical analysis or to sustain delicate species that die rapidly if not held under stable conditions. Transport media contain

3.1

Methods of Culturing Microorganisms: The Five I’s

65

ance of colonies, especially in bacteria and fungi. Colonies are actually large masses of piled-up cells (see chapter 7). In some ways, culturing microbes is analogous to gardening. Cultures are formed by “seeding” tiny plots (media) with microbial cells. Extreme care is taken to exclude weeds (contaminants). Once microbes have grown after incubation, the clinician must inspect the container (Petri dish, test tube, etc.). A pure culture is a container of medium that grows only a single known species or type of microorganism (figure 3.12a). Gas bubble

Outline of Durham tube

(a)

Figure 3.11 Carbohydrate fermentation in broths. This medium is designed to show fermentation (acid production) and gas formation by means of a small, inverted Durham tube for collecting gas bubbles. The tube on the left is an uninoculated negative control; the center tube is positive for acid (yellow) and gas (open space); the tube on the right shows growth but neither acid nor gas.

salts, buffers, and absorbants to prevent cell destruction by enzymes, pH changes, and toxic substances but will not support growth. Assay media are used by technologists to test the effectiveness of antimicrobial drugs (see chapter 12) and by drug manufacturers to assess the effect of disinfectants, antiseptics, cosmetics, and preservatives on the growth of microorganisms. Enumeration media are used by industrial and environmental microbiologists to count the numbers of organisms in milk, water, food, soil, and other samples.

(b)

Back to the Five I’s: Incubation, Inspection, and Identification Once a container of medium has been inoculated, it is incubated, which means it is placed in a temperature-controlled chamber (incubator) to encourage multiplication. Although microbes have adapted to growth at temperatures ranging from freezing to boiling, the usual temperatures used in laboratory propagation fall between 20°C and 40°C. Incubators can also control the content of atmospheric gases such as oxygen and carbon dioxide that may be required for the growth of certain microbes. During the incubation period (ranging from a day to several weeks), the microbe multiplies and produces growth that is observable macroscopically. Microbial growth in a liquid medium materializes as cloudiness, sediment, scum, or color. A common manifestation of growth on solid media is the appear-

(c)

Figure 3.12 Various conditions of cultures. (a) Three tubes containing pure cultures of Escherichia coli (white), Micrococcus luteus (yellow), and Serratia marcescens (red). (b) A mixed culture of M. luteus (bright yellow colonies) and E. coli (faint white colonies). (c) This plate of S. marcescens was overexposed to room air, and it has developed a large, white colony. Because this intruder is not desirable and not identified, the culture is now contaminated.

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This type of culture is most frequently used for laboratory study, because it allows the systematic examination and control of one microorganism by itself. Instead of the term pure culture, some microbiologists prefer the term axenic, meaning that the culture is free of other living things except for the one being studied. A standard method for preparing a pure culture is to subculture, or make a second-level culture from a well-isolated colony. A tiny bit of cells is transferred into a separate container of media and incubated (see figure 3.1, step 3). A mixed culture (figure 3.12b) is a container that holds two or more identified, easily differentiated species of microorganisms, not unlike a garden plot containing both carrots and onions. A contaminated culture (figure 3.12c) was once pure or mixed (and thus a known entity) but has since had contaminants (unwanted microbes of uncertain identity) introduced into it, like weeds into a garden. Because contaminants have the potential for causing disruption, constant vigilance is required to exclude them from microbiology laboratories, as you will no doubt witness from your own experience. Contaminants get into cultures when the lids of tubes or Petri dishes are left off for too long, allowing airborne microbes to settle into the medium. They can also enter on an incompletely sterilized inoculating loop or on an

Case File 3

Continuing the Case

The process of identifying a microbial pathogen in the laboratory follows a customary path of inoculation, incubation, isolation, inspection, and identification, often referred to as the Five I’s. These steps allow a laboratory technician to sample, grow, and a microbe d isolate l b in order to determine its physical, biochemical, and physiological properties. Once characterization is complete, it is generally a simple matter to identify the unknown microbe. Biochemical tests of the prisoners’ stool samples were negative for Salmonella, Shigella, Campylobacter, and Escherichia coli O157:H7. However, Clostridium perfringens enterotoxin was present in all six samples. C. perfringens is found in soil and also commonly inhabits the intestinal tracts of mammals, including humans. In addition, it is a frequent contaminant of meats and gravies and is usually associated with inadequate heating and cooling during the cooking process. When food products contaminated with C. perfringens are allowed to remain at temperatures between 40oC and 50oC (104oF and 122oF), enterotoxin-producing vegetative cells are rapidly produced; illness results from the enterotoxin’s action on the small intestine. C. perfringens is responsible for an estimated 250,000 cases of diarrhea annually in the United States.

instrument that you have inadvertently reused or touched to the table or your skin. How does one determine (i.e., identify) what sorts of microorganisms have been isolated in cultures? Certainly, microscopic appearance can be valuable in differentiating the smaller, simpler prokaryotic cells from the larger, more complex eukaryotic cells. Appearance can be especially useful in identifying eukaryotic microorganisms to the level of genus or species because of their distinctive morphological features; however, bacteria are generally not identifiable by these methods because very different species may appear quite similar. For them, we must include other techniques, some of which characterize their cellular metabolism. These methods, called biochemical tests, can determine fundamental chemical characteristics such as nutrient requirements, products given off during growth, presence of enzymes, and mechanisms for deriving energy. Several modern analytical and diagnostic tools that focus on genetic characteristics can detect microbes based on their DNA. Identification can also be accomplished by testing the isolate against known antibodies (immunologic testing). In the case of certain pathogens, further information on a microbe is obtained by inoculating a suitable laboratory animal. A profile is prepared by compiling physiological testing results with both macroscopic and microscopic traits. The profile then becomes the raw material used in final identification. In chapter 17, we present more detailed examples of identification methods.

Maintenance and Disposal of Cultures In most medical laboratories, the cultures and specimens constitute a potential hazard and require prompt and proper disposal. Both steam sterilizing (see autoclave, chapter 11) and incineration (burning) are used to destroy microorganisms. On the other hand, many teaching and research laboratories maintain a line of stock cultures that represent “living catalogs” for study and experimentation. The largest culture collection can be found at the American Type Culture Collection in Manassas, Virginia, which maintains a voluminous array of frozen and freeze-dried fungal, bacterial, viral, and algal cultures.

3.1 Learning Outcomes—Can You . . . 1. . . . explain what the Five I’s mean and what each step entails? 2. . . . name and define the three ways to categorize media? 3. . . . provide examples for each of the three categories of media?

3.2 The Microscope: Window on an Invisible Realm Imagine Leeuwenhoek’s excitement and wonder when he first viewed a drop of rainwater and glimpsed an amazing microscopic world teeming with unearthly creatures. Beginning

3.2

microbiology students still experience this sensation, and even experienced microbiologists remember their first view. Before we examine microscopes, let’s consider how small microbes actually are.

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67

and also with the atoms and molecules of the molecular world (figure 3.13). Whereas the dimensions of macroscopic organisms are usually given in centimeters (cm) and meters (m), those of microorganisms fall within the range of millimeters (mm) to micrometers (μm) to nanometers (nm). The size range of most microbes extends from the smallest bacteria, measuring around 200 nm, to protozoa and algae that measure 3 to 4 mm and are visible with the naked eye. Viruses, which can infect all organisms including microbes, measure between 20 nm and 800 nm, and some of them are thus not much bigger than large molecules, whereas others are just a tad larger than the smallest bacteria.

Microbial Dimensions: How Small Is Small? When we say that microbes are too small to be seen with the unaided eye, what sorts of dimensions are we talking about? The concept of thinking small is best visualized by comparing microbes with the larger organisms of the macroscopic world

1 mm Range of human eye

Reproductive structure of bread mold

Louse

Macroscopic Microscopic

100 mm

Nucleus Colonial alga (Pediastrum)

Range of light microscope

Amoeba

Red blood cell

White blood cell

10 mm Most bacteria fall between 1 and 10 mm in size 1 mm

Rickettsia bacteria

200 nm

Mycoplasma bacteria

100 nm

AIDS virus

Rod-shaped bacteria (Escherichia coli )

Coccus-shaped bacteria (Staphylococcus)

Poxvirus

Hepatitis B virus Range 10 nm of electron microscope

Poliovirus Flagellum Large protein

1 nm Require special microscopes 0.1 nm

Diameter of DNA

Amino acid (small molecule)

Hydrogen atom

(1 Angstrom)

Figure 3.13 The size of things. Common measurements encountered in microbiology and a scale of comparison from the macroscopic to the microscopic, molecular, and atomic. Most microbes encountered in our studies will fall between 100 μm and 10 nm in overall dimensions. The microbes shown are more or less to scale within size zone but not between size zones.

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Figure 3.14 Effects of magnification. Demonstration of the magnification and image-forming capacity of clear glass “lenses.” Given a proper source of illumination, this magnifying glass and crystal ball magnify a ruler two to three times. The microbial existence is indeed another world, but it would remain largely uncharted without an essential tool: the microscope. Your efforts in exploring microbes will be more meaningful if you understand some essentials of microscopy and specimen preparation.

Magnification and Microscope Design A discovery by early microscopists that spurred the advancement of microbiology was that a clear, glass sphere could act as a lens to magnify small objects. Magnification in most microscopes results from a complex interaction

between visible light waves and the curvature of the lens. When a beam or ray of light transmitted through air strikes and passes through the convex surface of glass, it experiences some degree of refraction, defined as the bending or change in the angle of the light ray as it passes through a medium such as a lens. The greater the difference in the composition of the two substances the light passes between, the more pronounced is the refraction. When an object is placed a certain distance from the spherical lens and illuminated with light, an optical replica, or image, of it is formed by the refracted light. Depending upon the size and curvature of the lens, the image appears enlarged to a particular degree, which is called its power of magnification and is usually identified with a number combined with × (read “times”). This behavior of light is evident if one looks through an everyday object such as a glass ball or a magnifying glass (figure 3.14). It is basic to the function of all optical, or light, microscopes, though many of them have additional features that define, refine, and increase the size of the image. The first microscopes were simple, meaning they contained just a single magnifying lens and a few working parts. Examples of this type of microscope are a magnifying glass, a hand lens, and Leeuwenhoek’s basic little tool shown earlier in figure 1.8a. Among the refinements that led to the development of today’s compound microscope were the addition of a second magnifying lens system, a lamp in the base to give off visible light and illuminate the specimen, and a special lens called the condenser that converges or focuses the rays of light to a single point on the object. The fundamental parts of a modern compound light microscope are illustrated in figure 3.15.

Ocular (eyepiece)

Body Nosepiece

Arm

Objective lens (4) Mechanical stage

Figure 3.15 The parts

of a student laboratory microscope. This microscope is a compound light microscope with two oculars (called binocular). It has four objective lenses, a mechanical stage to move the specimen, a condenser, an iris diaphragm, and a built-in lamp.

Substage condenser Aperture diaphragm control Base with light source Field diaphragm lever

Light intensity control

Coarse focus adjustment knob Fine focus adjustment knob Stage adjustment knobs

3.2

Principles of Light Microscopy To be most effective, a microscope should provide adequate magnification, resolution, and good contrast. Magnification of the object or specimen by a compound microscope occurs in two phases. The first lens in this system (the one closest to the specimen) is the objective lens, and the second (the one closest to the eye) is the ocular lens, or eyepiece (figure 3.16). The objective forms the initial image of the specimen, called the real image. When this image is projected up through the microscope body to the plane of the eyepiece, the ocular lens forms a second image, the virtual image. The virtual image is the one that will be received by the eye and converted to a retinal and visual image. The magnifying power of the objective alone usually ranges Brain

Retina

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69

from 4× to 100×, and the power of the ocular alone ranges from 10× to 20×. The total power of magnification of the final image formed by the combined lenses is a product of the separate powers of the two lenses:

Power of objective

×

Usual power × Total of ocular magnification

10× low power objective × 10× 40× high dry objective × 10× 100× oil immersion objective × 10×

= = =

100× 400× 1,000×

Microscopes are equipped with a nosepiece holding three or more objectives that can be rotated into position as needed. The power of the ocular usually remains constant for a given microscope. Depending on the power of the ocular, the total magnification of standard light microscopes can vary from 40× with the lowest power objective (called the scanning objective) to 2,000× with the highest power objective (the oil immersion objective).

Eye

Ocular lens

Virtual image

Objective lens

Light rays strike specimen.

Specimen Real image

Condenser lens

Light source

Figure 3.16 The pathway of light and the two stages in magnification of a compound microscope.

As light passes through the condenser, it forms a solid beam that is focused on the specimen. Light leaving the specimen that enters the objective lens is refracted so that an enlarged primary image, the real image, is formed. One does not see this image, but its degree of magnification is represented by the lower circle. The real image is projected through the ocular, and a second image, the virtual image, is formed by a similar process. The virtual image is the final magnified image that is received by the retina and perceived by the brain. Notice that the lens systems cause the image to be reversed.

Resolution: Distinguishing Magnified Objects Clearly As important as magnification is for visualizing tiny objects or cells, an additional optical property is essential for seeing clearly. That property is resolution, or resolving power. Resolution is the capacity of an optical system to distinguish or separate two adjacent objects or points from one another. For example, at a certain fixed distance, the lens in the human eye can resolve two small objects as separate points just as long as the two objects are no closer than 0.2 millimeters apart. The eye examination given by optometrists is in fact a test of the resolving power of the human eye for various-size letters read at a distance of 20 feet. Because microorganisms are extremely small and usually very close together, they will not be seen with clarity or any degree of detail unless the microscope’s lenses can resolve them. A simple equation in the form of a fraction expresses the main factors in resolution: Wavelength of light in nm Resolving power (RP) = _______________________ 2 × Numerical aperture of objective lens This equation demonstrates that the resolving power is a function of the wavelength of light that forms the image, along with certain characteristics of the objective. The light source for optical microscopes consists of a band of colored wavelengths in the visible spectrum. The shortest visible wavelengths are in the violet-blue portion of the spectrum (400 nanometers), and the longest are in the red portion (750 nanometers). Because the wavelength must pass between the objects that are being resolved, shorter wavelengths (in the 400–500 nanometer range) will provide better resolution (figure 3.17). Some microscopes have a special blue filter

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(a)

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(b)

Figure 3.17 Effect of wavelength on resolution. A simple model demonstrates how the wavelength influences the resolving power of a microscope. Here an outline of a hand represents the object being illuminated, and two different-size circles represent the wavelengths of light. In (a), the longer waves are too large to penetrate between the finer spaces and produce a fuzzy, undetailed image. In (b), shorter waves are small enough to enter small spaces and produce a much more detailed image that is recognizable as a hand.

placed over the lamp to limit the longer wavelengths of light from entering the specimen. The other factor influencing resolution is the numerical aperture, a mathematical constant that describes the relative efficiency of a lens in bending light rays. Without going into the mathematical derivation of this constant, it is sufficient to say that each objective has a fixed numerical aperture reading that is determined by the microscope design and ranges from 0.1 in the lowest power lens to approximately 1.25 in the highest power (oil immersion) lens. In practical terms, the oil immersion lens can resolve any cell or cell part as long as it is at least 0.2 micron in diameter, and it can resolve two adjacent objects as long as they are at least 0.2 micron apart (figure 3.19). In general, organisms that are 0.5 micron or more in diameter are readily seen. This includes fungi and protozoa, some of their internal structures, and most bacteria. However, a few bacteria and most viruses are far too small to be resolved by the optical microscope and require electron microscopy (discussed later in this chapter). In summary then, the factor that most limits the clarity of a microscope’s image is its resolving power. Even if a light microscope were designed to magnify several thousand times, its resolving power could not be increased, and the image it produced would simply be enlarged and fuzzy.

A Note About Oil Immersion Lenses The most important thing to remember is that a higher numerical aperture number will provide better resolution. In order for the oil immersion lens to arrive at its maximum resolving capacity, a drop of oil must be inserted between the tip of the lens and the specimen on the glass slide. Because oil has the same optical qualities as glass, it prevents refractive loss that normally occurs as peripheral light passes from the slide into the air; this property effectively increases the numerical aperture (figure 3.18).

Not resolvable

0.2 µm

Objective lens

Air

Oil

Slide

Figure 3.18 Workings of an oil immersion lens. Without oil, some of the peripheral light that passes through the specimen is scattered into the air or onto the glass slide; this scattering decreases resolution.

Resolvable

Figure 3.19 Effect of magnification. Comparison of cells that would not be resolvable versus those that would be resolvable under oil immersion at 1,000× magnification. Note that in addition to differentiating two adjacent things, good resolution also means being able to observe an object clearly.

3.2

Contrast The third quality of a well-magnified image is its degree of contrast from its surroundings. The contrast is measured by a quality called the refractive index. Refractive index refers to the degree of bending that light undergoes as it passes from one medium (such as water or glass) to another medium, such as some bacterial cells. The higher the difference in refractive indexes (the more bending of light), the sharper the contrast that is registered by the microscope and the eye. Because too much light can reduce contrast and burn out the image, an adjustable iris diaphragm on most microscopes controls the amount of light entering the condenser. The lack of contrast in cell components is compensated for by using special lenses (the phase-contrast microscope) and by adding dyes.

Variations on the Light Microscope Optical microscopes that use visible light can be described by the nature of their field, meaning the circular area viewed through the ocular lens. There are four types of visible-light microscopes: bright-field, dark-field, phasecontrast, and interference. A fifth type of optical microscope, the fluorescence microscope, uses ultraviolet radiation as the illuminating source; and another, the confocal microscope, uses a laser beam. Each of these microscopes is adapted for viewing specimens in a particular way, as described in table 3.5.

Preparing Specimens for Optical Microscopes A specimen for optical microscopy is generally prepared by mounting a sample on a suitable glass slide that sits on the stage between the condenser and the objective lens. The manner in which a slide specimen, or mount, is prepared depends upon: (1) the condition of the specimen, either in a living or preserved state; (2) the aims of the examiner, whether to observe overall structure, identify the microorganisms, or see movement; and (3) the type of microscopy available, whether it is bright-field, dark-field, phase-contrast, or fluorescence.

Fresh, Living Preparations Live samples of microorganisms are placed in wet mounts or in hanging drop mounts so that they can be observed as near to their natural state as possible. The cells are suspended in a suitable fluid (water, broth, saline) that temporarily maintains viability and provides space and a medium for locomotion. A wet mount consists of a drop or two of the culture placed on a slide and overlaid with a coverslip. Although this type of mount is quick and easy to prepare, it has certain disadvantages. The coverslip can damage larger cells, and the slide is very susceptible to drying and can contaminate the handler’s fingers. A more satisfactory alternative is the hanging drop preparation made with a special concave (depres-

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The Microscope: Window on an Invisible Realm

Coverslip

Hanging drop containing specimen Vaseline Depression slide

Figure 3.20 Hanging drop technique. Cross-section view of slide and coverslip. (Vaseline actually surrounds entire well of slide.)

sion) slide, a Vaseline adhesive or sealant, and a coverslip from which a tiny drop of sample is suspended (figure 3.20). These types of short-term mounts provide a true assessment of the size, shape, arrangement, color, and motility of cells. Greater cellular detail can be observed with phase-contrast or interference microscopy.

Fixed, Stained Smears A more permanent mount for long-term study can be obtained by preparing fixed, stained specimens. The smear technique, developed by Robert Koch more than 100 years ago, consists of spreading a thin film made from a liquid suspension of cells on a slide and air-drying it. Next, the air-dried smear is usually heated gently by a process called heat fixation that simultaneously kills the specimen and secures it to the slide. Another important action of fixation is to preserve various cellular components in a natural state with minimal distortion. Sometimes fixation of microbial cells is performed with chemicals such as alcohol and formalin. Like images on undeveloped photographic film, the unstained cells of a fixed smear are quite indistinct, no matter how great the magnification or how fine the resolving power of the microscope. The process of “developing” a smear to create contrast and make inconspicuous features stand out requires staining techniques. Staining is any procedure that applies colored chemicals called dyes to specimens. Dyes impart a color to cells or cell parts by becoming affixed to them through a chemical reaction. In general, they are classified as basic (cationic) dyes, which have a positive charge, or acidic (anionic) dyes, which have a negative charge. Because chemicals of opposite charge are attracted to each other, cell parts that are negatively charged will attract basic dyes and those that are positively charged will attract acidic dyes (table 3.6). Many cells, especially those of bacteria, have numerous negatively charged acidic substances and thus stain more readily with basic dyes. Acidic dyes, on the other hand, tend to be repelled by cells, so they are good for negative staining (discussed in the next section).

Negative Versus Positive Staining Two basic types of staining technique are used, depending upon how a dye reacts

Table 3.5 Comparison of Types of Microscopy Microscope

Maximum Practical Magnification

Resolution

Visible light as source of illumination Bright-field

2,000×

0.2 μm (200 nm) The bright-field microscope in the most widely used type of light microscope. Although we ordinarily view objects like the words on this page with light reflected off the surface, a brightfield microscope forms its image when light is transmitted through the specimen. The specimen, being denser and more opaque than its surroundings, absorbs some of this light, and the rest of the light is transmitted directly up through the ocular into the field. As a result, the specimen will produce an image that is darker than the surrounding brightly illuminated field. The bright-field microscope is a multipurpose instrument that can be used for both live, unstained material and preserved, stained material.

Paramecium (400×) Dark-field

2,000×

0.2 μm A bright-field microscope can be adapted as a dark-field microscope by adding a special disc called a stop to the condenser. The stop blocks all light from entering the objective lens—except peripheral light that is reflected off the sides of the specimen itself. The resulting image is a particularly striking one: brightly illuminated specimens surrounded by a dark (black) field. The most effective use of dark-field microscopy is to visualize living cells that would be distorted by drying or heat or that cannot be stained with the usual methods. Dark-field microscopy can outline the organism’s shape and permit rapid recognition of swimming cells that might appear in dental and other infections, but it does not reveal fine internal details.

Paramecium (400×) Phase-contrast

2,000×

0.2 μm

Paramecium (400×) Differential interference

2,000×

If similar objects made of clear glass, ice, cellophane, or plastic are immersed in the same container of water, an observer would have difficulty telling them apart because they have similar optical properties. Internal components of a live, unstained cell also lack contrast and can be difficult to distinguish. But cell structures do differ slightly in density, enough that they can alter the light that passes through them in subtle ways. The phase-contrast microscope has been constructed to take advantage of this characteristic. This microscope contains devices that transform the subtle changes in light waves passing through the specimen into differences in light intensity. For example, denser cell parts such as organelles alter the pathway of light more than less dense regions (the cytoplasm). Light patterns coming from these regions will vary in contrast. The amount of internal detail visible by this method is greater than by either bright-field or dark-field methods. The phase-contrast microscope is most useful for observing intracellular structures such as bacterial spores, granules, and organelles, as well as the locomotor structures of eukaryotic cells such as cilia.

0.2 μm

Like the phase-contrast microscope, the differential interference contrast (DIC) microscope provides a detailed view of unstained, live specimens by manipulating the light. But this microscope has additional refinements, including two prisms that add contrasting colors to the image and two beams of light rather than a single one. DIC microscopes produce extremely welldefined images that are vividly colored and appear three-dimensional.

Amoeba proteus (160×) Ultraviolet rays as source of illumination Fluorescent

2,000×

0.2 μm

Cheek epithelial cells (the larger unfocused green or red cells). Bacteria are the filamentous green and red rods and the green diplococci (400×).

The fluorescent microscope is a specially modified compound microscope furnished with an ultraviolet (UV) radiation source and a filter that protects the viewer’s eye from injury by these dangerous rays. The name of this type of microscopy originates from the use of certain dyes (acridine, fluorescein) and minerals that show fluorescence. The dyes emit visible light when bombarded by short ultraviolet rays. For an image to be formed, the specimen must first be coated or placed in contact with a source of fluorescence. Subsequent illumination by ultraviolet radiation causes the specimen to give off light that will form its own image, usually an intense yellow, orange, or red against a black field. Fluorescence microscopy has its most useful applications in diagnosing infections caused by specific bacteria, protozoans, and viruses.

Microscope

Maximum Practical Magnification

Resolution

Confocal

2,000×

0.2 μm

The scanning confocal microscope overcomes the problem of cells or structures being too thick, a problem resulting in other microscopes being unable to focus on all their levels. This microscope uses a laser beam of light to scan various depths in the specimen and deliver a sharp image focusing on just a single plane. It is thus able to capture a highly focused view at any level, ranging from the surface to the middle of the cell. It is most often used on fluorescently stained specimens but it can also be used to visualize live unstained cells and tissues.

Myofibroblasts, cells involved in tissue repair (400×) Electron beam forms image of specimen Transmission electron microscope (TEM)

100,000,000×

0.5 nm Transmission electron microscopes are the method of choice for viewing the detailed structure of cells and viruses. This microscope produces its image by transmitting electrons through the specimen. Because electrons cannot readily penetrate thick preparations, the specimen must be sectioned into extremely thin slices (20–100 nm thick) and stained or coated with metals that will increase image contrast. The darkest areas of TEM micrographs represent the thicker (denser) parts, and the lighter areas indicate the more transparent and less dense parts.

Coronavirus, causative agent of many respiratory infections (100,000×) Scanning electron microscope (SEM)

100,000,000×

10 nm The scanning electon microscope provides some of the most dramatic and realistic images in existence. This instrument is designed to create an extremely detailed three-dimensional view of all kinds of objects—from plaque on teeth to tapeworm heads. To produce its images, the SEM does not transmit electrons, it bombards the surface of a whole metal-coated specimen with electrons while scanning back and forth over it. A shower of electrons deflected from the surface is picked up with great fidelity by a sophisticated detector, and the electron pattern is displayed as an image on a television screen. The contours of the specimen resolved with scanning electron microscopy are very revealing and often surprising. Areas that look smooth and flat with the light microscope display intriguing surface features with the SEM.

2 microns An alga showing a cell wall made of calcium disks (10,000×) Atomically sharp tip probes surface of specimen Atomic force microscope (AFM)

100,000,000×

0.01 Angstroms

In atomic force microscopy, a diamond or metal tip with a radius of 1–50 nanometers scans a specimen and moves up and down with contour of surface at the atomic level. The movement of the tip is measured with a laser and translated into an image.

Prion fibrils, which may only be 5 mm in diameter Scanning tunneling microscope (STM)

100,000,000×

0.01 Angstroms

In scanning tunneling microscopy, a tungsten tip hovers over specimen while electrical voltage is applied, generating a current that is dependent on the distance between the tip and surface. Image is produced from the electrical signal of the tip’s pathway. See Insight 3.2 for more information about probing microscopes.

Strands of DNA (inset is a magnified view of the bare gold surface, verifying that it is clean).

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with the specimen (summarized in table 3.6). Most procedures involve a positive stain, in which the dye actually sticks to the specimen and gives it color. A negative stain, on the other hand, is just the reverse (like a photographic negative). The dye does not stick to the specimen but settles around its outer boundary, forming a silhouette. In a sense, negative staining “stains” the glass slide to produce a dark background around the cells. Nigrosin (blue-black) and India ink (a black suspension of carbon particles) are the dyes most commonly used for negative staining. The cells themselves do not stain because these dyes are negatively charged and are repelled by the negatively charged surface of the cells. The value of negative staining is its relative simplicity and the reduced shrinkage or distortion of cells, as the smear is not heat fixed. A quick assessment can thus be made regarding cellular size, shape, and arrangement. Negative staining is also used to accentuate the capsule that surrounds certain bacteria and yeasts (figure 3.21).

Simple Versus Differential Staining Positive staining methods are classified as simple, differential, or special (figure 3.21). Whereas simple stains require only a single dye and an uncomplicated procedure, differential stains use two differently colored dyes, called the primary dye and the counterstain, to distinguish between cell types or parts. These staining techniques tend to be more complex and sometimes require additional chemical reagents to produce the desired reaction.

Table 3.6 Comparison of Positive and Negative Stains Medium

Positive Staining

Negative Staining

Appearance of cell

Colored by dye

Clear and colorless

Most simple staining techniques take advantage of the ready binding of bacterial cells to dyes like malachite green, crystal violet, basic fuchsin, and safranin. Simple stains cause all cells in a smear to appear more or less the same color, regardless of type, but they can still reveal bacterial characteristics such as shape, size, and arrangement.

Types of Differential Stains A satisfactory differential stain uses differently colored dyes to clearly contrast two cell types or cell parts. Common combinations are red and purple, red and green, or pink and blue. Differential stains can also pinpoint other characteristics, such as the size, shape, and arrangement of cells. Typical examples include Gram, acidfast, and endospore stains. Some staining techniques (spore, capsule) fall into more than one category. Gram staining, a century-old method named for its developer, Hans Christian Gram, remains the most universal diagnostic staining technique for bacteria. It permits ready differentiation of major categories based upon the color reaction of the cells: gram-positive, which stain purple, and gram-negative, which stain pink (red). The Gram stain is the basis of several important bacteriological topics, including bacterial taxonomy, cell wall structure, and identification and diagnosis of infection; in some cases, it even guides the selection of the correct drug for an infection. Gram staining is discussed in greater detail in Insight 4.2. The acid-fast stain, like the Gram stain, is an important diagnostic stain that differentiates acid-fast bacteria (pink) from non-acid-fast bacteria (blue). This stain originated as a specific method to detect Mycobacterium tuberculosis in specimens. It was determined that these bacterial cells have a particularly impervi-

Case File 3

Background

Not stained (generally white)

Stained (dark gray or black)

Dyes employed

Basic dyes: Crystal violet Methylene blue Safranin Malachite green

Acidic dyes: Nigrosin India ink

Subtypes of stains

Several types: Simple stain Differential stains Gram stain Acid-fast stain Spore stain Special stains Capsule Flagella Spore Granules Nucleic acid

Few types: Capsule Spore

Wrap-Up

In instances where the number of bacteria in a sample is expected to be especially large, as would be the case with a fecal sample, many types of specialized media may be used to narrow the possibilities. Selective media contain inhibitory substances that allow only a single type of microbe to grow, while differential media allow most organisms to grow but produce visible differences among the various microbes. In this case, samples of the casserole the prisoners had eaten were analyzed using both selective and differential media and found to contain 43,000 colony-forming units (CFU) of C. perfringens per gram of casserole. Investigators learned that the company distributing meals to the jail routinely froze food that was not served and held it for up to 72 hours before using it to prepare dishes for later consumption. In this case, the ground beef and macaroni had been cooked the previous day, and several other food items were near their expiration dates. Also, proper documentation of cooling temperatures for both the ground beef and the macaroni was unavailable. Investigators concluded that improper handling of food in the kitchen was responsible for the prisoners’ illness. See: CDC. 2009. MMWR 58:138–41.

3.2

The Microscope: Window on an Invisible Realm

(a) Simple Stains

(b) Differential Stains

(c) Special Stains

Crystal violet stain of Escherichia coli

Gram stain Purple cells are gram-positive. Red cells are gram-negative.

India ink capsule stain of Cryptococcus neoformans

Methylene blue stain of Corynebacterium

Acid-fast stain Red cells are acid-fast. Blue cells are non-acid-fast.

Flagellar stain of Proteus vulgaris A basic stain was used to build up the flagella.

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Spore stain, showing spores (red) and vegetative cells (blue)

Figure 3.21 Types of microbiological stains. (a) Simple stains. (b) Differential stains: Gram, acid-fast, and spore. (c) Special stains: capsule and flagellar.

ous outer wall that holds fast (tightly or tenaciously) to the dye (carbol fuchsin) even when washed with a solution containing acid or acid alcohol. This stain is used for other medically important mycobacteria such as the Hansen’s disease (leprosy) bacillus and for Nocardia, an agent of lung or skin infections. The endospore stain (spore stain) is similar to the acidfast method in that a dye is forced by heat into resistant bodies called spores or endospores (their formation and significance are discussed in chapter 4). This stain is designed to distinguish between spores and the cells that they come from (so-called vegetative cells). Of significance in medical

microbiology are the gram-positive, spore-forming members of the genus Bacillus (the cause of anthrax) and Clostridium (the cause of botulism and tetanus)—dramatic diseases that we consider in later chapters. Special stains are used to emphasize certain cell parts that are not revealed by conventional staining methods. Capsule staining is a method of observing the microbial capsule, an unstructured protective layer surrounding the cells of some bacteria and fungi. Because the capsule does not react with most stains, it is often negatively stained with India ink, or it may be demonstrated by special positive stains. The fact that

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INSIGHT 3.2

Tools of the Laboratory

The Evolution in Resolution: Probing Microscopes

In the past, chemists, physicists, and biologists had to rely on indirect methods to provide information on the structures of the smallest molecules. But technological advances have created a new generation of microscopes that “see” atomic structure by actually feeling it. Scanning probe microscopes operate with a minute needle tapered to a tip that can be as narrow as a single atom! This probe scans over the exposed surface of a material on the end of an arm and records an image of its outer texture. (Think of an old-fashioned record player. . . .) These revolutionary microscopes have such profound resolution that they have the potential to image single atoms (but not subatomic structure yet) and to magnify 100 million times. There are two types of scanning probe microscopes, the atomic force microscope (AFM) and the scanning tunneling microscope (STM). The STM uses a tungsten probe that hovers near the surface of an object and follows its topography while simultaneously giving off an electrical signal of its pathway, which is then imaged on a screen. The STM was used initially for detecting defects on the surfaces of electrical

conductors and computer chips composed of silicon, but it has also provided the first incredible close-up views of DNA. The atomic force microscope (AFM) gently forces a diamond and metal probe down onto the surface of a specimen like a needle on a record. As it moves along the surface, any deflection of the metal probe is detected by a sensitive device that relays the information to an imager. The AFM is very useful in viewing the detailed structures of biological molecules such as antibodies and enzymes. These powerful new microscopes can also move and position atoms, spawning a field called nanotechnology—the science of the “small.” When this ability to move atoms was first discovered, scientists had some fun (see illustration on the left). But it has opened up an entirely new way to manipulate atoms in chemical reactions (illustration on the right) and to create nanoscale devices for computers and other electronics. In the future, it may be possible to use microstructures to deliver drugs and treat disease.

Scanning tunneling microscopy. The figure on the left was created when scientists dragged iron atoms over a copper matrix to spell (in kanji, a Japanese written alphabet) “atom” (literally: “original child”). On the right you see a chemical reaction performed by an STM microscope. At the top (a), two iodobenzene molecules appear as two bumps on a copper surface. The STM tip emits a burst of electrons and causes the iodine groups to dissociate from each of the benzene groups (b). The tip then drags away the iodine groups (c), and the two carbon groups bind to one another (d and e). Source: http://www.almaden.ibm.com/vis/stm/ atomo.html, page 80.

not all microbes exhibit capsules is a useful feature for identifying pathogens. One example is Cryptococcus, which causes a serious fungal meningitis in AIDS patients (see chapter 19). Flagellar staining is a method of revealing flagella, the tiny, slender filaments used by bacteria for locomotion. Because the width of bacterial flagella lies beyond the resolving power of the light microscope, in order to be seen, they must be enlarged by depositing a coating on the outside of the filament and then staining it. Their presence, number, and arrangement on a cell are taxonomically useful.

3.2 Learning Outcomes—Can You . . . 4. 5. 6. 7.

. . . convert among different lengths within the metric system? . . . describe the earliest microscopes? . . . list and describe the three elements of good microscopy? . . . differentiate between the principles of light and electron microscopy? 8. . . . name the two main categories of stains? 9. . . . give examples of a simple, differential, and special stain?

Chapter Summary

77

Chapter Summary 3.1 Methods of Culturing Microorganisms: The Five I’s • Many microorganisms can be cultured on artificial media, but some can be cultured only in living tissue or in cells. • Artificial media are classified by their physical state as either liquid, semisolid, liquefiable solid, or nonliquefiable solid. • Artificial media are classified by their chemical composition as either synthetic or nonsynthetic, depending on whether the exact chemical composition is known. • Artificial media are classified by their function as either general-purpose media or media with one or more specific purposes. Enriched, selective, differential, transport, assay, and enumerating media are all examples of media designed for specific purposes. • The Five I’s—inoculation, incubation, isolation, inspection, and identification—summarize the kinds of laboratory procedures used in microbiology. • Following inoculation, cultures are incubated at a specified temperature to encourage growth. • Isolated colonies that originate from single cells are composed of large numbers of cells piled up together. • A culture may exist in one of the following forms: A pure culture contains only one species or type of microorganism. A mixed culture contains two or more known species. A contaminated culture contains both known and unknown (unwanted) microorganisms. • During inspection, the cultures are examined and evaluated macroscopically and microscopically. • Microorganisms are identified in terms of their macroscopic or immunologic morphology; their microscopic morphology; their biochemical reactions; and their genetic characteristics. • Microbial cultures are usually disposed of in two ways: steam sterilization or incineration.

Multiple-Choice and True-False Questions

3.2 The Microscope: Window on an Invisible Realm • Magnification, resolving power, and contrast all influence the clarity of specimens viewed through the optical microscope. • The maximum resolving power of the optical microscope is 200 nm, or 0.2 μm. This is sufficient to see the internal structures of eukaryotes and the morphology of most bacteria. • There are six types of optical microscopes. Four types use visible light for illumination: bright-field, dark-field, phase-contrast, and interference microscopes. The fluorescence microscope uses UV light for illumination, but it has the same resolving power as the other optical microscopes. The confocal microscope can use UV light or visible light reflected from specimens. • Electron microscopes (EM) use electrons, not light waves, as an illumination source to provide high magnification (5,000× to 1,000,000×) and high resolution (0.5 nm). Electron microscopes can visualize cell ultrastructure (transmission EM) and three-dimensional images of cell and virus surface features (scanning EM). • The newest generation of microscope is called the scanning probe microscope and uses precision tips to image structures at the atomic level. • Specimens viewed through optical microscopes can be either alive or dead, depending on the type of specimen preparation, but all EM specimens are dead because they must be viewed in a vacuum. • Stains increase the contrast of specimens and they can be designed to differentiate cell shape, structure, and biochemical composition of the specimens being viewed.

Knowledge and Comprehension

Multiple-Choice Questions. Select the correct answer from the answers provided. 1. The term culture refers to the ____ growth of microorganisms in ____. a. rapid, an incubator c. microscopic, the body b. macroscopic, media d. artificial, colonies 2. A mixed culture is a. the same as a contaminated culture. b. one that has been adequately stirred. c. one that contains two or more known species. d. a pond sample containing algae and protozoa. 3. Resolution is ____ with a longer wavelength of light. a. improved c. not changed b. worsened d. not possible 4. A real image is produced by the a. ocular. c. condenser. b. objective. d. eye.

5. A microscope that has a total magnification of 1,500× when using the oil immersion objective has an ocular of what power? a. 150× c. 15× b. 1.5× d. 30× 6. The specimen for an electron microscope is always a. stained with dyes. c. killed. b. sliced into thin sections. d. viewed directly. 7. Motility is best observed with a a. hanging drop preparation. b. negative stain. c. streak plate. d. flagellar stain.

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8. Bacteria tend to stain more readily with cationic (positively charged) dyes because bacteria a. contain large amounts of alkaline substances. b. contain large amounts of acidic substances. c. are neutral. d. have thick cell walls.

10. A fastidious organism must be grown on what type of medium? a. general-purpose medium b. differential medium c. synthetic medium d. enriched medium

9. Multiple Matching. For each type of medium, select all descriptions that fit. For media that fit more than one description, briefly explain why this is the case. ____ mannitol salt agar a. selective medium ____ chocolate agar b. differential medium ____ MacConkey agar c. chemically defined ____ nutrient broth (synthetic) medium ____ Sabouraud’s agar d. enriched medium ____ triple-sugar iron agar e. general-purpose medium ____ Euglena agar f. complex medium ____ SIM medium g. transport medium

True-False Questions. If the statement is true, leave as is. If it is false, correct it by rewriting the sentence.

Critical Thinking Questions

11. Agar has the disadvantage of being easily decomposed by microorganisms. 12. A subculture is a culture made from an isolated colony. 13. The factor that most limits the clarity of an image in a microscope is the magnification. 14. Living specimens can be examined either by light microscopy or electron microscopy. 15. The best stain to use to visualize a microorganism with a large capsule is a simple stain.

Application and Analysis

These questions are suggested as a writing-to-learn experience. For each question, compose a one- or two-paragraph answer that includes the factual information needed to completely address the question. 1. a. Describe briefly what is involved in the Five I’s. b. Name three basic differences between inoculation and contamination. 2. a. Explain what is involved in isolating microorganisms and why it is necessary to do this. b. Compare and contrast three common laboratory techniques for separating bacteria in a mixed sample. c. Describe how an isolated colony forms. d. Explain why an isolated colony and a pure culture are not the same thing. 3. Differentiate between microscopic and macroscopic methods of observing microorganisms, citing a specific example of each method. 4. Trace the pathway of light from its source to the eye, explaining what happens as it passes through the major parts of the microscope. 5. Compare bright-field, dark-field, phase-contrast, and fluorescence microscopy as to field appearance, specimen appearance, light source, and uses. 6. a. Compare and contrast the optical compound microscope with the electron microscope. b. Why is the resolution so superior in the electron microscope?

c. What will you never see in an unretouched electron micrograph? 7. a. Why are some bacteria difficult to grow in the laboratory? Relate this to what you know so far about metabolism. b. Why are viruses hard to cultivate in the laboratory? 8. Biotechnology companies have engineered hundreds of different types of mice, rats, pigs, goats, cattle, and rabbits to have genetic diseases similar to diseases of humans or to synthesize drugs and other biochemical products. They have patented these animals, and they sell them to researchers for study and experimentation. a. What do you think of creating new life forms just for experimentation? b. Comment on the benefits, safety, and ethics of this trend. 9. Some human pathogenic bacteria are resistant to most antibiotics. How would you prove a bacterium is resistant to antibiotics using laboratory culture techniques? 10. Some scientists speculate that the reason we can’t grow some bacteria on artificial medium at this time is that they are found in polymicrobial communities in their natural settings. If that were true, how would you go about trying to cultivate them?

Concept Mapping

Concept Mapping

79

Synthesis

Appendix D provides guidance for working with concept maps. 1. Supply your own linking words or phrases in this concept map, and provide the missing concepts in the empty boxes. Good magnified image

Contrast

Magnification

2. Construct your own concept map using the following words as the concepts. Supply the linking words between each pair of concepts. inoculation

staining

isolation

biochemical tests

incubation

subculturing

inspection

source of microbes

identification

transport medium

medium

streak plate

multiplication

Wavelength

Visual Connections

Synthesis

These questions encourage active learning by connecting previously seen material to this chapter’s concepts. 1. Figure 3.3a and b. If you were using the quadrant streak plate method to plate a very dilute broth culture (with many fewer bacteria than the broth used for 3b) would you expect to see single, isolated colonies in quadrant 4 or quadrant 3? Explain your answer.

1

2

3

4

(a) Steps in a Streak Plate

2. From chapter 1, figure 1.6. Which of these photos from chapter 1 is an SEM image? Which is a TEM image? Bacter Bact Bac Bacteria teria teri ia

5 (b)

Bacterium: E. E coli

Fungus: Thamnidium

A single sin i g gle le virus vviru rus us u s particle pa parrt rtiticle

Virus: Herpes simplex

Protozoan: Vorticella

www.connect.microbiology.com Enhance your study of this chapter with study tools and practice tests. Also ask your instructor about the resources available through ConnectPlus, including the media-rich eBook, interactive learning tools, and animations.

Prokaryotic Profiles The Bacteria and Archaea 4 Case File A 15-year-old girl was admitted to the hospital after presenting at the emergency room (ER) in a semiconscious state. Feeling ill was nothing new for this patient—she had a 9-year history of systemic lupus erythematosus (SLE), a condition the ER physicians took into account as they examined her. SLE, sometimes called “lupus,” is an autoimmune disease in which the body produces antibodies against many of its own tissues; some organs eventually become damaged or fail to function. The specific symptoms of SLE differ, depending on which organs are affected, but kidney failure, heart problems, lung inflammation, and blood abnormalities are common. The cause of SLE is unknown. The patient’s initial workup revealed abnormally rapid breathing, fever, and low blood pressure. Additionally, her fingers and toes were cold, and she was producing no urine. The ER staff took samples of her blood and cerebrospinal fluid (CSF) and found bacteria in both. Because of the patient’s history of SLE, magnetic resonance imaging (MRI) of the abdomen was performed to assess the condition of her organs. The MRI revealed that the lupus had led to the complete destruction of the patient’s spleen, a complication called “autosplenectomy” that occurs in approximately 5% of SLE cases. ◾ The presence of bacteria in the blood and the cerebrospinal fluid is considered a serious sign. Why? Continuing the Case appears on page 88.

Outline and Learning Outcomes 4.1 Prokaryotic Form and Function 1. Name the structures all bacteria possess. 2. Name at least four structures that some, but not all, bacteria possess. 4.2 External Structures 3. Describe the structure and function of four different types of bacterial appendages. 4. Explain how a flagellum works in the presence of an attractant.

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4.1

Prokaryotic Form and Function

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4.3 The Cell Envelope: The Boundary Layer of Bacteria 5. Differentiate between the two main types of bacterial envelope structure. 6. Discuss why gram-positive cell walls are stronger than gram-negative cell walls. 7. Name a substance in the envelope structure of some bacteria that can cause severe symptoms in humans. 4.4 Bacterial Internal Structure 8. Identify five things that might be contained in bacterial cytoplasm. 9. Detail the causes and mechanisms of sporogenesis and germination. 4.5 Prokaryotic Shapes, Arrangements, and Sizes 10. Describe the three major shapes of prokaryotes. 11. Describe other more unusual shapes of prokaryotes. 4.6 Classification Systems in the Prokaryotae 12. Differentiate between Bergey’s Manual of Systematic Bacteriology and Bergey’s Manual of Determinative Bacteriology. 13. Name four divisions ending in –cutes and describe their characteristics. 14. Explain what a species is. 4.7 The Archaea 15. List some differences between archaea and bacteria.

In chapter 1, we described prokaryotes as being cells with no true nucleus. (Eukaryotes have a membrane around their DNA, and this structure is called the nucleus.) Some microbiologists have recently been suggesting that we are not defining what a prokaryote is, only what it is not—and therefore we are not really defining it at all. This is one way scientists work. A previously accepted notion (i.e., what a prokaryote is) is questioned publicly, causing a variety of reactions ranging from surprise to dismissal. Usually other scientists begin discussing the question and the truth that might be behind the assertion is examined in a new way. But this whole chapter is about the type of cell we call a prokaryote. So how do we know whether a cell is prokaryotic or eukaryotic? A prokaryote can be distinguished from the other type of cell (a eukaryote) because of certain characteristics it possesses: • The way its DNA is packaged: Prokaryotes have nuclear material that is not encased in a membrane (i.e., they do not have a nucleus). Eukaryotes have a membrane around their DNA (making up a nucleus). Prokaryotes don’t wind their DNA around proteins called histones; eukaryotes do. • The makeup of its cell wall: Prokaryotes (bacteria and archaea) generally have a wall structure that is unique compared to eukaryotes. Bacteria have sturdy walls made of a chemical called peptidoglycan. Archaeal walls are also tough and made of other chemicals, distinct from bacteria and distinct from eukaryotic cells. • Its internal structures: Prokaryotes don’t have complex, membrane-bounded organelles in their cytoplasm (eukaryotes do). A few prokaryotes have internal membranes, but they don’t surround organelles. Both prokaryotic and eukaryotic microbes are found throughout nature. Both can cause infectious diseases.

Examples of bacterial diseases include “strep” throat, Lyme disease, and ear infections. The medical response to them is informed by their “prokaryoteness.” Eukaryotic infections (examples: histoplasmosis, malaria) often require a different approach. In this chapter and coming chapters, you’ll discover why that is.

4.1 Prokaryotic Form and Function The evolutionary history of prokaryotic cells extends back at least 3.8 billion years. It is now generally thought that the very first cells to appear on the earth were a type of prokaryote, possibly related to modern forms that live on sulfur compounds in geothermal ocean vents. The fact that these organisms have endured for so long in such a variety of habitats indicates a cellular structure and function that are amazingly versatile and adaptable. The general cellular organization of a prokaryotic cell can be represented with this flowchart: External

Cell envelope

Internal

Appendages Flagella Pili Fimbriae Glycocalyx Capsule, slime layer (Outer membrane) Cell wall Cell membrane Cytoplasm Ribosomes Inclusions Nucleoid/chromosome Actin cytoskeleton Endospore

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Fimbriae—Fine, hairlike bristles extending from the cell surface that help in adhesion to other cells and surfaces.

Glycocalyx (pink coating)— A coating or layer of molecules external to the cell wall. It serves protective, adhesive, and receptor functions. It may fit tightly or be very loose and diffuse.

Bacterial chromosome or nucleoid—Composed of condensed DNA molecules. DNA directs all genetics and heredity of the cell and codes for all proteins.

Inclusion/Granule—Stored nutrients such as fat, phosphate, or glycogen deposited in dense crystals or particles that can be tapped into when needed.

Cell wall—A semirigid casing that provides structural support and shape for the cell.

Pilus—An elongate, hollow appendage used in transfers of DNA to other cells.

Plasmid—Double-stranded DNA circle containing extra genes.

Cell (cytoplasmic) membrane— A thin sheet of lipid and protein that surrounds the cytoplasm and controls the flow of materials into and out of the cell pool. Outer membrane—Extra membrane similar to cell membrane but also containing lipopolysaccharide. Controls flow of materials, and portions of it are toxic to mammals when released.

Ribosomes—Tiny particles composed of protein and RNA that are the sites of protein synthesis.

Actin cytoskeleton—Long fibers of proteins that encircle the cell just inside the cell membrane and contribute to the shape of the cell.

Flagellum—Specialized appendage attached to the cell by a basal body that holds a long, rotating filament. The movement pushes the cell forward and provides motility.

Endospore (not shown)— Dormant body formed within some bacteria that allows for their survival in adverse conditions.

Cytoplasm—Water-based solution filling the entire cell.

Figure 4.1 Structure of a bacterial cell. Cutaway view of a typical rod-shaped bacterium, showing major structural features. Note that not all components are found in all cells; dark-blue boxes indicate structures that all bacteria possess.

4.2

External Structures

All bacterial cells invariably have a cell membrane, cytoplasm, ribosomes, and one (or a few) chromosome(s); the majority have a cell wall, a cytoskeleton, and some form of surface coating or glycocalyx. Specific structures that are found in some but not all prokaryotes are flagella, pili, fimbriae, inclusions, endospores, and intracellular membranes.

4.2 External Structures

The Structure of a Generalized Bacterial Cell

Appendages: Cell Extensions

Bacterial cells appear featureless and two-dimensional when viewed with an ordinary microscope. Not until they are subjected to the scrutiny of the electron microscope and biochemical studies does their intricate and functionally complex nature become evident. Note that in this chapter, the descriptions of prokaryotic structure, except where otherwise noted, refer to the bacteria. Later in the chapter we will describe the ways in which archaea differ from bacteria. Otherwise, we will be focusing on bacteria. Figure 4.1 presents a three-dimensional anatomical view of a generalized, rodshaped, bacterial cell. As we survey the principal anatomical features of this cell, we will perform a microscopic dissection of sorts, following a course that begins with the outer cell structures and proceeds to the internal contents.

4.1 Learning Outcomes—Can You . . . 1. . . . name the structures all bacteria possess? 2. . . . name at least four structures that some, but not all, bacteria possess?

External

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Appendages Flagella Pili Fimbriae Glycocalyx Capsule, slime layer

Several discrete types of accessory structures sprout from the surface of bacteria. These long appendages are common but are not present on all species. Appendages can be divided into two major groups: those that provide motility (flagella and axial filaments) and those that provide attachment points or channels (fimbriae and pili).

Flagella—Prokaryotic Propellers The prokaryotic flagellum (flah-jel′-em), an appendage of truly amazing construction, is certainly unique in the biological world. The primary function of flagella is to confer motility, or self-propulsion—that is, the capacity of a cell to swim freely through an aqueous habitat. The extreme thinness of a bacterial flagellum necessitates high magnification to reveal its special architecture, which has three distinct parts: the filament, the hook (sheath), and the basal body (figure 4.2). The filament, a helical structure composed of proteins, is approximately 20 nanometers in diameter and varies from 1 to 70 microns in length. It is inserted into a curved, tubular hook. The hook is anchored to the cell by the basal body, a stack of rings firmly anchored

Filament Hook

Outer membrane Basal body

Cell wall Rod

Rings Cell membrane

(a)

(b)

Figure 4.2 Details of the basal body of a flagellum in a gram-negative cell. (a) The hook, rings, and rod function together as a tiny device that rotates the filament 360°. (b) An electron micrograph of the basal body of a bacterial flagellum.

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through the cell wall, to the cell membrane and the outer membrane. This arrangement permits the hook with its filament to rotate 360°, rather than undulating back and forth like a whip as was once thought. One can generalize that all spirilla, about half of the bacilli, and a small number of cocci are flagellated (these bacterial shapes are shown in figure 4.23). Flagella vary both in number and arrangement according to two general patterns: 1. In a polar arrangement, the flagella are attached at one or both ends of the cell. Three subtypes of this pattern are: monotrichous (mah″-noh-trik′-us), with a single flagellum; lophotrichous (lo″-foh-), with small bunches or tufts of flagella emerging from the same site; and amphitrichous (am″-fee-), with flagella at both poles of the cell. 2. In a peritrichous (per″-ee-) arrangement, flagella are dispersed randomly over the surface of the cell (figure 4.3). The presence of motility is one piece of information used in the laboratory identification or diagnosis of pathogens. Flagella are hard to visualize in the laboratory, but often it is sufficient to know simply whether a bacterial species is motile. One way to detect motility is to stab a tiny mass of cells into a soft (semisolid) medium in a test tube. Growth spreading rapidly through the entire medium is indicative of motility. Alternatively, cells can be observed microscopically with a hanging drop slide. A truly motile cell will flit, dart, or wobble around the field, making some progress, whereas

(a)

(b)

one that is nonmotile jiggles about in one place but makes no progress.

Fine Points of Flagellar Function Flagellated bacteria can perform some rather sophisticated feats. They can detect and move in response to chemical signals—a type of behavior called chemotaxis (ke″-moh-tak′ -sis). Positive chemotaxis is movement of a cell in the direction of a favorable chemical stimulus (usually a nutrient); negative chemotaxis is movement away from a repellent (potentially harmful) compound. The flagellum is effective in guiding bacteria through the environment primarily because the system for detecting chemicals is linked to the mechanisms that drive the flagellum. Located in the cell membrane are clusters of receptors1 that bind specific molecules coming from the immediate environment. The attachment of sufficient numbers of these molecules transmits signals to the flagellum and sets it into rotary motion. The actual “fuel” for the flagellum to turn is a gradient of protons (hydrogen ions) that are generated by the metabolism of the bacterium and that bind to and detach from parts of the flagellar motor within the cell membrane, causing the filament to rotate. If several flagella are present, they become aligned and rotate as a group (figure 4.4). As a flagellum rotates counterclockwise, the cell itself swims in a smooth linear direction toward the stimulus; this action is called a run. Runs are interrupted at various intervals by tumbles, during which the flagellum 1. Cell surface molecules that bind specifically with other molecules.

(c)

Figure 4.3 Electron micrographs depicting types of flagellar arrangements. (a) Monotrichous flagellum on the bacterium Bdellovibrio. (b) Lophotrichous flagella on Vibrio fischeri, a common marine bacterium (23,000×). (c) Unusual flagella on Aquaspirillum are amphitrichous (and lophotrichous) in arrangement and coil up into tight loops. (d) An unidentified bacterium discovered inside Paramecium cells exhibits peritrichous flagella. (d)

Source: (b) From Reichelt and Baumann, Arch. Microbiol. 94:283–330. © Springer-Verlag, 1973.

4.2

reverses direction and causes the cell to stop and change its course. It is believed that attractant molecules inhibit tumbles and permit progress toward the stimulus. Repellents cause numerous tumbles, allowing the bacterium to redirect itself away from the stimulus (figure 4.5). Some photosynthetic bacteria exhibit phototaxis, movement in response to light rather than chemicals.

External Structures

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by two or more long, coiled threads, the periplasmic flagella or axial filaments. A periplasmic flagellum is a type of internal flagellum that is enclosed in the space between the cell wall and the cell membrane (figure 4.6). The filaments curl closely around the spirochete coils yet are free to contract and impart a twisting or flexing motion to the cell. This form of locomotion must be seen in live cells such as the spirochete of syphilis to be truly appreciated.

Periplasmic Flagella Corkscrew-shaped bacteria called spirochetes (spy′-rohkeets) show an unusual, wriggly mode of locomotion caused

Appendages for Attachment and Mating The structures termed pilus (pil-us) and fimbria (fim′-bree-ah) are both bacterial surface appendages that provide some type of adhesion, but not locomotion. PF

PC

OS

(a)

(a)

Outer sheath (OS)

(b) Protoplasmic cylinder (PC)

Figure 4.4 The operation of flagella and the mode

of locomotion in bacteria with polar and peritrichous flagella. (a) In general, when a polar flagellum rotates in a counterclockwise direction, the cell swims forward. When the flagellum reverses direction and rotates clockwise, the cell stops and tumbles. (b) In peritrichous forms, all flagella sweep toward one end of the cell and rotate as a single group. During tumbles, the flagella lose coordination.

Periplasmic flagella (PF)

Peptidoglycan

Cell membrane Key

(b)

Tumble (T)

Run (R)

Tumble (T)

T T T T R R

(c)

Figure 4.6 The orientation of periplasmic flagella on (a) No attractant or repellent

(b) Gradient of attractant concentration

Figure 4.5 Chemotaxis in bacteria. (a) A bacterium moves via a random series of short runs and tumbles when there is no attractant or repellent. (b) The cell spends more time on runs as it gets closer to the attractant.

the spirochete cell. (a) Longitudinal section. (b) Cross section (end-on view). Contraction of the filaments imparts a spinning and undulating pattern of locomotion. (c) Electron micrograph captures the details of periplasmic flagella and their insertion points (arrows) in Borrelia burgdorferi, the cause of Lyme disease. One flagellum has escaped the outer sheath, probably during preparation for EM. (Bar = 0.2 microns)

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Pili

Fimbriae are small, bristlelike fibers sprouting off the surface of many bacterial cells (figure 4.7). Their exact composition varies, but most of them contain protein. Fimbriae have an inherent tendency to stick to each other and to surfaces. They may be responsible for the mutual clinging of cells that leads to biofilms and other thick aggregates of cells on the surface of liquids and for the microbial colonization of inanimate solids such as rocks and glass (Insight 4.1). Some pathogens can colonize and infect host tissues because of a tight adhesion between their fimbriae and epithelial cells (figure 4.7b). For example, the gonococcus (agent of gonorrhea) colonizes the genitourinary tract, and Escherichia coli colonizes the intestine by this means. Mutant forms of these pathogens that lack fimbriae are unable to cause infections. A pilus (also called a “sex” pilus) is an elongate, rigid tubular structure made of a special protein, pilin. So far, true pili have been found only on gram-negative bacteria, where they are utilized in a “mating” process between cells called conjugation,2 which involves partial transfer of DNA from 2. Although the term mating is sometimes used for this process, it is not a form of sexual reproduction.

Fimbriae

Figure 4.8 Three bacteria in the process of conjugating. Clearly evident are the sex pili forming mutual conjugation bridges between a donor (upper cell) and two recipients (two lower cells). (Fimbriae can also be seen on the donor cell.)

one cell to another (figure 4.8). A pilus from the donor cell unites with a recipient cell thereby providing a cytoplasmic connection for making the transfer. Production of pili is controlled genetically, and conjugation takes place only between compatible gram-negative cells. Conjugation in gram-positive bacteria does occur but involves aggregation proteins rather than “sex” pili. The roles of pili and conjugation are further explored in chapter 9.

The Bacterial Surface Coating, or Glycocalyx The bacterial cell surface is frequently exposed to severe environmental conditions. The glycocalyx develops as a coating of repeating polysaccharide units, protein, or both. This protects the cell and, in some cases, helps it adhere to its environment. Glycocalyces differ among bacteria in thickness, organization, and chemical composition. Some bacteria are covered with a loose shield called a slime layer that evidently protects them from loss of water and nutrients (figure 4.9a). A glycocalyx is called a capsule when it is bound more tightly to the cell than

(a) E. coli cells

G

Slime Layer

Capsule

(a)

(b)

Intestinal microvilli

(b)

Figure 4.7 Form and function of bacterial fimbriae. (a) Several cells of pathogenic Escherichia coli covered with numerous stiff fibers called fimbriae (30,000×). Note also the dark-blue granules, which are the chromosomes. (b) A row of E. coli cells tightly adheres by their fimbriae to the surface of intestinal cells (12,000×). This is how the bacterium clings to the body during an infection. (G = glycocalyx)

Figure 4.9 Drawing of sectioned bacterial cells to show

the types of glycocalyces. (a) The slime layer is a loose structure that is easily washed off. (b) The capsule is a thick, structured layer that is not readily removed.

4.2

INSIGHT 4.1

External Structures

Biofilms—The Glue of Life

Being aware of the widespread existence of microorganisms on earth, we should not be surprised that, when left undisturbed, they gather in masses, cling to various surfaces, and capture available moisture and nutrients. The formation of these living layers, called biofilms, is actually a universal phenomenon that all of us have observed. Consider the scum that builds up in toilet bowls and shower stalls in a short time if they are not cleaned; or the algae that collect on the walls of swimming pools; and, more intimately, the constant deposition of plaque on teeth. Microbes making biofilms is a primeval tendency that has been occurring for billions of years as a way to create stable habitats with adequate access to food, water, atmosphere, and other essential factors. Biofilms are often cooperative associations among several microbial groups (bacteria—and archaea—fungi, algae, and protozoa) as well as plants and animals. Substrates are most likely to accept a biofilm if they are moist and have developed a thin layer of organic material such as polysaccharides or glycoproteins on their exposed surface

First colonists

Organic surface coating Surface

Cells stick to coating.

Glycocalyx As cells divide, they form a dense mat bound together by sticky extracellular deposits.

Additional microbes are attracted to developing film and create a mature community with complex function.

(see figure below). This depositing process occurs within a few minutes to hours, making a slightly sticky texture that attracts primary colonists, usually bacteria. These early cells attach and begin to multiply on the surface. As they grow, various substances (receptors, fimbriae, slime layers, capsules, and even DNA molecules) increase the binding of cells to the surface and thicken the biofilm. The extracellular matrix (the green material in our drawing is clearly visible. As the biofilm evolves, it undergoes specific adaptations to the habitat in which it forms. In many cases, the earliest colonists contribute nutrients and create microhabitats that serve as a matrix for other microbes to attach and grow into the film, forming complex communities. The biofilm varies in thickness and complexity, depending upon where it occurs and how long it keeps developing. Complexity ranges from single cell layers to thick microbial mats with dozens of dynamic interactive layers. Biofilms are a profoundly important force in the development of terrestrial and aquatic environments. They dwell permanently in bedrock and the earth’s sediments, where they play an essential role in recycling elements, leaching minerals, and forming soil. Biofilms associated with plant roots promote the mutual exchange of nutrients between the microbes and roots. Invasive biofilms can wreak havoc with human-made structures such as cooling towers, storage tanks, air conditioners, and even stone buildings. Biofilms also have serious medical implications. Biofilms accumulate most easily on damaged tissues (such as rheumatic heart valves), hard tissues (teeth), and foreign materials (catheters, intrauterine devices [IUDs], artificial hip joints). But they also seem to grow on otherwise healthy tissues under certain conditions. Persistent ear infections and lung infections in patients with cystic fibrosis are due to biofilms. Microbes in a biofilm are extremely difficult to eradicate with antimicrobials. Previously it was assumed that the drugs had difficulty penetrating the viscous biofilm matrix. Now scientists have discovered that bacteria in biofilms turn on different genes when they are in a biofilm than when they are “freefloating.” This altered gene expression gives the bacteria a different set of characteristics, often making them impervious to antibiotics. It is estimated that treating biofilm-related infections costs more than 1 billion dollars in the United States alone.

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a slime layer is and it is denser and thicker (figure 4.9b). Capsules can be viewed after a special staining technique (figure 4.10a). They are also often visible due to a prominently sticky (mucoid) character to colonies on agar (figure 4.10b).

Specialized Functions of the Glycocalyx Capsules are formed by many pathogenic bacteria, such as Streptococcus pneumoniae (a cause of pneumonia, an infection of the lung), Haemophilus influenzae (one cause of meningitis), and Bacillus anthracis (the cause of anthrax). Encapsulated bacterial cells generally have greater pathogenicity because capsules protect the bacteria against white blood cells called phagocytes. Phagocytes are a natural body defense that can engulf and destroy foreign cells through phagocytosis, thus preventing infection. A capsular coating blocks the mechanisms that phagocytes use to attach to and engulf bacteria. By escaping phagocytosis, the bacteria are free to multiply and infect body tissues. Encapsulated bacteria that mutate to nonencapsulated forms usually lose their ability to cause disease. Other types of glycocalyces can be important in formation of biofilms. The thick, white plaque that forms on teeth

Case File 4

Continuing the Case

An MRI indicated that the SLE patient’s spleen was no longer functioning—in other words, she was “asplenic.” Asplenic individuals have low levels of both immunoglobulin M (a type of antibody) and memory B cells (a type of immune system cell that produces antibodies). Therefore, these patients are at much greater risk of infection by encapsulated bacteria. In this case, ER physicians ordered capsule staining of the bacteria isolated from the patient’s blood and CSF. Based in part on the results of the capsule staining, the bacterium isolated from both types of fluid was identified as Streptococcus pneumoniae, a heavily encapsulated bacterium commonly encountered in asplenic patients. ◾ There are clues here that a specific part of a patient’s defenses usually acts against encapsulated bacteria. Which part?

comes in part from the surface slimes produced by certain streptococci in the oral cavity. This slime protects them from being dislodged from the teeth and provides a niche for other oral bacteria that, in time, can lead to dental disease. The glycocalyx of some bacteria is so highly adherent that it is responsible for persistent colonization of nonliving materials such as plastic catheters, intrauterine devices, and metal pacemakers that are in common medical use (figure 4.11).

Capsule

Cell body Glycocalyx slime

(a)

Catheter surface

Cell cluster

(b)

Figure 4.10 Encapsulated bacteria. (a) Negative staining reveals the microscopic appearance of a large, well-developed capsule. (b) Colony appearance of a nonencapsulated (left) and encapsulated (right) version of a soil bacterium called Sinorhizobium.

Figure 4.11 Biofilm. Scanning electron micrograph of Staphylococcus aureus cells attached to a catheter by a slime secretion.

4.3 The Cell Envelope: The Boundary Layer of Bacteria

4.2 Learning Outcomes—Can You . . . 3. . . . describe the structure and function of four different types of bacterial appendages? 4. . . . explain how a flagellum works in the presence of an attractant?

4.3 The Cell Envelope: The Boundary Layer of Bacteria Cell envelope

(Outer membrane) Cell wall Cell membrane

The majority of bacteria have a chemically complex external covering, termed the cell envelope, that lies outside of the cytoplasm. It is composed of two or three basic layers: the cell wall, the cell membrane, and in some bacteria, the outer membrane. The layers of the envelope are stacked one upon another and are often tightly bonded together like the outer husk and casings of a coconut. Although each envelope layer performs a distinct function, together they act as a single protective unit.

Differences in Cell Envelope Structure More than a hundred years ago, long before the detailed anatomy of bacteria was even remotely known, a Danish physician named Hans Christian Gram developed a staining technique, the Gram stain, that delineates two generally different groups of bacteria (Insight 4.2). The two major groups

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shown by this technique are the gram-positive bacteria and the gram-negative bacteria. The structural difference denoted by the designations gram-positive and gram-negative lie in the cell envelope (figure 4.12). In gram-positive cells, a microscopic section resembles an open-faced sandwich with two layers: the thick cell wall, composed primarily of peptidoglycan (defined in the next section), and the cytoplasmic membrane. A similar section of a gram-negative cell envelope shows a complete sandwich with three layers: an outer membrane, a thin cell wall, and the cytoplasmic membrane. Moving from outside to in, the outer membrane (if present) lies just under the glycocalyx. Next comes the cell wall. Finally, the innermost layer is always the cytoplasmic membrane. Because only some bacteria have an outer membrane, we discuss the cell wall first.

Structure of the Cell Wall The cell wall accounts for a number of important bacterial characteristics. In general, it helps determine the shape of a bacterium, and it also provides the kind of strong structural support necessary to keep a bacterium from bursting or collapsing because of changes in osmotic pressure. In this way, the cell wall functions like a bicycle tire that maintains the necessary shape and prevents the more delicate inner tube (the cytoplasmic membrane) from bursting when it is expanded. The cell walls of most bacteria gain their relatively rigid quality from a unique macromolecule called peptidoglycan (PG). This compound is composed of a repeating framework of long glycan (sugar) chains cross-linked by short peptide (protein) fragments to provide a strong but flexible

Peptidoglycan Cell membrane Cell membrane

Peptidoglycan

Outer membrane Gram (+) Gram (–)

Figure 4.12 A comparison of the envelopes of gram-positive and gramnegative cells. (a) A photomicrograph of a Cell membrane Peptidoglycan (a)

(b)

Cell membrane Periplasmic space Peptidoglycan Outer membrane

gram-positive cell wall/membrane and an artist’s interpretation of its open-faced-sandwich-style layering with two layers. (b) A photomicrograph of a gram-negative cell wall/membrane and an artist’s interpretation of its complete-sandwichstyle layering with three distinct layers.

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Prokaryotic Profiles

The Gram Stain: A Grand Stain

In 1884, Hans Christian Gram discovered a staining technique gram-negative bacteria are colorless after decolorization, their presthat could be used to make bacteria in infectious specimens more ence is demonstrated by applying the counterstain safranin in the visible. His technique consisted of timed, sequential applications final step. of crystal violet (the primary dye), Gram’s iodine ( the mordant), This century-old staining method remains the universal basis an alcohol rinse (decolorizer), and a contrasting counterstain. for bacterial classification and identification. It permits differenThe initial counterstain used was yellow or brown and was later tiation of four major categories based upon color reaction and replaced by the red dye safranin. Bacteria that stain purple are shape: gram-positive rods, gram-positive cocci, gram-negative called gram-positive, and those that stain red are called gramrods, and gram-negative cocci (see table 4.1). The Gram stain can negative. also be a practical aid in diagnosing infection and in guiding drug Although these staining reactions involve an attraction of treatment. For example, Gram staining a fresh urine or throat the cell to a charged dye (see chapter 3), it is important to note specimen can help pinpoint the possible cause of infection, and that the terms gram-positive and gram-negative are not used to in some cases it is possible to begin drug therapy on the basis of indicate the electrical charge of cells or dyes but whether or not this stain. Even in this day of elaborate and expensive medical a cell retains the primary dye-iodine complex after decolorizatechnology, the Gram stain remains an important and unbeatable tion. There is nothing specific in the reaction of gram-positive first tool in diagnosis. cells to the primary dye or in the reaction of gram-negative cells to the counterstain. Microscopic Appearance of Cell Chemical Reaction in Cell Wall The different results in the Gram stain are (very magnified view) due to differences in the structure of the cell wall and how it reacts to the series of Gram (+) Gram (–) Gram (+) Gram (–) Step reagents applied to the cells. In the first step, crystal violet is added to 1. Crystal violet the cells in a smear. It stains them all the same Both cell walls affix the dye purple color. The second and key differentiating step is the addition of the mordant— 2. Gram's Gram’s iodine. The mordant is a stabilizer iodine that causes the dye to form large complexes Dye complex No effect in the peptidoglycan meshwork of the cell trapped in wall of iodine wall. Because the peptidoglycan layer in gram-positive cells is thicker, the entrapment 3. Alcohol of the dye is far more extensive in them than in gram-negative cells. Application of Crystals remain Outer membrane alcohol in the third step dissolves lipids in in cell wall weakened; wall the outer membrane and removes the dye loses dye from the peptidoglycan layer and the gram4. Safranin negative cells. By contrast, the crystals of (red dye) dye tightly embedded in the peptidoglycan Red dye masked Red dye stains of gram-positive bacteria are relatively inacby violet the colorless cell cessible and resistant to removal. Because

support framework (figure 4.13). The amount and exact composition of peptidoglycan vary among the major bacterial groups. Because many bacteria live in aqueous habitats with a low concentration of dissolved substances, they are constantly absorbing excess water by osmosis. Were it not for the strength and relative rigidity of the peptidoglycan in the cell wall, they would rupture from internal pressure. This function of the cell wall has been a tremendous boon to the drug industry. Several types of drugs used to treat

infection (penicillin, cephalosporins) are effective because they target the peptide cross-links in the peptidoglycan, thereby disrupting its integrity. With their cell walls incomplete or missing, such cells have very little protection from lysis (ly′-sis), which is the disintegration or rupture of the cell. Lysozyme, an enzyme contained in tears and saliva, provides a natural defense against certain bacteria by hydrolyzing the bonds in the glycan chains and causing the wall to break down. (Chapter 11 discusses the actions of antimicrobial chemical agents.)

4.3 The Cell Envelope: The Boundary Layer of Bacteria

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(a) The peptidoglycan can be seen as a crisscross network pattern similar to a chainlink fence.

(b) An idealized view of the molecular pattern of peptidoglycan. It contains alternating glycans (G and M) bound together in long strands. The G stands for N-acetyl glucosamine, and the M stands for N-acetyl muramic acid. A muramic acid molecule binds to an adjoining muramic acid on a parallel chain by means of a cross-linkage of peptides.

Glycan chains M

O

O

G M

M

G

M

G

M O

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(c) A detailed view of the links between the muramic acids. Tetrapeptide chains branching off the muramic acids connect by interbridges also composed of amino acids. The types of amino acids in the interbridge can vary and it may be lacking entirely (gram-negative cells). It is this linkage that provides rigid yet flexible support to the cell and that may be targeted by drugs like penicillin.

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Figure 4.13 Structure of peptidoglycan in the cell wall.

The Gram-Positive Cell Wall The bulk of the gram-positive cell wall is a thick, homogeneous sheath of peptidoglycan ranging from 20 to 80 nm in thickness. It also contains tightly bound acidic polysaccharides, including teichoic acid and lipoteichoic acid (figure  4.14).

Teichoic acid is a polymer of ribitol or glycerol (alcohols) and phosphate that is embedded in the peptidoglycan sheath. Lipoteichoic acid is similar in structure but is attached to the lipids in the plasma membrane. These molecules appear to function in cell wall maintenance and enlargement during

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Gram-Positive

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Figure 4.14 A comparison of the detailed structure of gram-positive and gram-negative cell envelopes.

cell division, and they also contribute to the acidic charge on the cell surface.

The Gram-Negative Cell Wall The gram-negative wall is a single, thin (1–3 nm) sheet of peptidoglycan. Although it acts as a somewhat rigid protective structure as previously described, its thinness gives gram-negative bacteria a relatively greater flexibility and sensitivity to lysis.

Nontypical Cell Walls Several bacterial groups lack the cell wall structure of gram-positive or gram-negative bacteria, and some bacteria have no cell wall at all. Although these exceptional forms can stain positive or negative in the Gram stain, examination of their fine structure and chemistry shows that they do not really fit the descriptions for typical gramnegative or -positive cells. For example, the cells of Mycobacterium and Nocardia contain peptidoglycan and stain gram-positive, but the bulk of their cell wall is composed of unique types of lipids. One of these is a very-long-chain fatty acid called mycolic acid, or cord factor, that contributes to the pathogenicity of this group (see chapter 21). The thick, waxy nature imparted to the cell wall by these lipids is also responsible for a high degree of resistance to certain chemicals and dyes. Such resistance is the basis for the

acid-fast stain used to diagnose tuberculosis and leprosy. In this stain, hot carbol fuchsin dye becomes tenaciously attached (is held fast) to these cells so that an acid-alcohol solution will not remove the dye (see chapter 3). Because they are from a more ancient and primitive line of prokaryotes, the archaea exhibit unusual and chemically distinct cell walls. In some, the walls are composed almost entirely of polysaccharides, and in others, the walls are pure protein; but as a group, they all lack the true peptidoglycan structure described previously. Because a few archaea and all mycoplasmas (next section) lack a cell wall entirely, their cell membrane must serve the dual functions of support and transport.

Mycoplasmas and Other Cell-Wall-Deficient Bacteria Mycoplasmas are bacteria that naturally lack a cell wall. Although other bacteria require an intact cell wall to prevent the bursting of the cell, the mycoplasma cell membrane is stabilized by sterols and is resistant to lysis. These extremely tiny, pleomorphic cells are very small bacteria, ranging from 0.1 to 0.5 μm in size. They range in shape from filamentous to coccus or doughnut-shaped. They are not obligate parasites and can be grown on artificial media, although added sterols are required for the cell membranes of some species. Mycoplasmas are found in many habitats, including plants,

4.3 The Cell Envelope: The Boundary Layer of Bacteria

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spheroplast (figure 4.16b). Evidence points to a role for L forms in certain infections.

The Gram-Negative Outer Membrane

Figure 4.15 Scanning electron micrograph of Mycoplasma pneumoniae (magnified 62,000×). Cells like these that naturally lack a cell wall exhibit extreme variation in shape.

soil, and animals. The most important medical species is Mycoplasma pneumoniae (figure 4.15), which adheres to the epithelial cells in the lung and causes an atypical form of pneumonia in humans (described in chapter 21). Some bacteria that ordinarily have a cell wall can lose it during part of their life cycle. These wall-deficient forms are referred to as L forms or L-phase variants (for the Lister Institute, where they were discovered). L forms arise naturally from a mutation in the wall-forming genes, or they can be induced artificially by treatment with a chemical such as lysozyme or penicillin that disrupts the cell wall. When a gram-positive cell is exposed to either of these two chemicals, it will lose the cell wall completely and become a protoplast, a fragile cell bounded only by a membrane that is highly susceptible to lysis (figure 4.16a). A gramnegative cell exposed to these same substances loses its peptidoglycan but retains at least part of its outer membrane, leaving a less fragile but nevertheless weakened

The outer membrane (OM) is somewhat similar in construction to the cell membrane, except that it contains specialized types of polysaccharides and proteins. The uppermost layer of the OM contains lipopolysaccharide (LPS). The polysaccharide chains extending off the surface function as antigens and receptors. The lipid portion of LPS has been referred to as endotoxin because it stimulates fever and shock reactions in gram-negative infections such as meningitis and typhoid fever. The innermost layer of the OM is a phospholipid layer anchored by means of lipoproteins to the peptidoglycan layer below. The outer membrane serves as a partial chemical sieve by allowing only relatively small molecules to penetrate. Access is provided by special membrane channels formed by porin proteins that completely span the outer membrane. The size of these porins can be altered so as to block the entrance of harmful chemicals, making them one defense of gram-negative bacteria against certain antibiotics (see figure 4.14).

Cell Membrane Structure Appearing just beneath the cell wall is the cell, or cytoplasmic, membrane, a very thin (5–10 nm), flexible sheet molded completely around the cytoplasm. Its general composition was described in chapter 2 as a lipid bilayer with proteins embedded to varying degrees (see Insight 2.3). Bacterial cell membranes have this typical structure, containing primarily phospholipids (making up about 30%–40% of the membrane mass) and proteins (contributing 60%–70%). Major exceptions to this description are the membranes of mycoplasmas, which contain high amounts of sterols—rigid lipids that stabilize and reinforce the membrane—and the membranes of archaea, which contain unique branched hydrocarbons rather than fatty acids.

Mutation or chemical treatment Cell wall (peptidoglycan) GramPositive

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Figure 4.16 The conversion of walled bacterial cells to L forms. (a) Gram-positive bacteria. (b) Gram-negative bacteria.

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Some environmental bacteria, including photosynthesizers and ammonia oxidizers, contain dense stacks of internal membranes that are studded with enzymes or photosynthetic pigments. The inner membranes allow a higher concentration of these enzymes and pigments and also accomplish a compartmentalization that allows for higher energy production.

4.3 Learning Outcomes—Can You . . . 5. . . . differentiate between the two main types of bacterial envelope structure? 6. . . . discuss why gram-positive cell walls are stronger than gramnegative cell walls? 7. . . . name a substance in the envelope structure of some bacteria that can cause severe symptoms in humans?

Functions of the Cell Membrane Because prokaryotes have none of the eukaryotic organelles, the cell membrane provides a site for functions such as energy reactions, nutrient processing, and synthesis. A major action of the cell membrane is to regulate transport, that is, the passage of nutrients into the cell and the discharge of wastes. Although water and small uncharged molecules can diffuse across the membrane unaided, the membrane is a selectively permeable structure with special carrier mechanisms for passage of most molecules (see chapter 7). The glycocalyx and cell wall can bar the passage of large molecules, but they are not the primary transport apparatus. The cell membrane is also involved in secretion, or the discharge of a metabolic product into the extracellular environment. The membranes of prokaryotes are an important site for a number of metabolic activities. Most enzymes of respiration and ATP synthesis reside in the cell membrane since prokaryotes lack mitochondria (see chapter 8). Enzyme structures located in the cell membrane also help synthesize structural macromolecules to be incorporated into the cell envelope and appendages. Other products (enzymes and toxins) are secreted by the membrane into the extracellular environment.

Practical Considerations of Differences in Cell Envelope Structure Variations in cell envelope anatomy contribute to several other differences between the two cell types. The outer membrane contributes an extra barrier in gram-negative bacteria that makes them impervious to some antimicrobial chemicals such as dyes and disinfectants, so they are generally more difficult to inhibit or kill than are gram-positive bacteria. One exception is alcohol-based compounds, which can dissolve the lipids in the outer membrane and disturb its integrity. Treating infections caused by gram-negative bacteria often requires different drugs from gram-positive infections, especially drugs that can cross the outer membrane. The cell envelope or its parts can interact with human tissues and contribute to disease. Proteins attached to the outer portion of the cell wall of several gram-positive species, including Corynebacterium diphtheriae (the agent of diphtheria) and Streptococcus pyogenes (the cause of strep throat), also have toxic properties. The lipids in the cell walls of certain Mycobacterium species are harmful to human cells as well. Because most macromolecules in the cell walls are foreign to humans, they stimulate antibody production by the immune system (see chapter 15).

4.4 Bacterial Internal Structure Internal

Cytoplasm Ribosomes Inclusions Nucleoid/chromosome Actin cytoskeleton Endospore

Contents of the Cell Cytoplasm Encased by the cell membrane is a gelatinous solution referred to as cytoplasm, which is another prominent site for many of the cell’s biochemical and synthetic activities. Its major component is water (70%–80%), which serves as a solvent for the cell pool, a complex mixture of nutrients including sugars, amino acids, and salts. The components of this pool serve as building blocks for cell synthesis or as sources of energy. The cytoplasm also contains larger, discrete cell masses such as the chromatin body, ribosomes, granules, and actin/tubulin strands that act as a cytoskeleton in bacteria that have them.

Bacterial Chromosomes and Plasmids: The Sources of Genetic Information The hereditary material of most bacteria exists in the form of a single circular strand of DNA designated as the bacterial chromosome. Some bacteria have multiple chromosomes. By definition, bacteria do not have a nucleus; that is, their DNA is not enclosed by a nuclear membrane but instead is aggregated in a dense area of the cell called the nucleoid (figure  4.17). The chromosome is actually an extremely long molecule of

Figure 4.17 Chromosome structure. Fluorescent staining highlights the chromosomes of the bacterial pathogen Salmonella enteritidis. The cytoplasm is orange, and the chromosome fluoresces bright yellow.

4.4

double-stranded DNA that is tightly coiled around special basic protein molecules so as to fit inside the cell compartment. Arranged along its length are genetic units (genes) that carry information required for bacterial maintenance and growth. Although the chromosome is the minimal genetic requirement for bacterial survival, many bacteria contain other, nonessential pieces of DNA called plasmids (refer to figure 4.1 for a representation of the nuclear material). These tiny strands exist as separate double-stranded circles of DNA, although at times they can become integrated into the chromosome. During conjugation, they may be duplicated and passed on to related nearby bacteria. During bacterial reproduction, they are duplicated and passed on to offspring. They are not essential to bacterial growth and metabolism, but they often confer protective traits such as resisting drugs and producing toxins and enzymes (see chapter 9). Because they can be readily manipulated in the laboratory and transferred from one bacterial cell to another, plasmids are an important agent in genetic engineering techniques.

Ribosomes: Sites of Protein Synthesis A prokaryotic cell contains thousands of tiny ribosomes, which are made of RNA and protein. When viewed even by very high magnification, ribosomes show up as fine, spherical specks dispersed throughout the cytoplasm that often occur in chains called polysomes. Many are also attached to the cell membrane. Chemically, a ribosome is a combination of a special type of RNA called ribosomal RNA, or rRNA (about 60%), and protein (40%). One method of characterizing ribosomes is by S, or Svedberg,3 units, which rate the molecular sizes of various cell parts that have been spun down and separated by

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molecular weight and shape in a centrifuge. Heavier, more compact structures sediment faster and are assigned a higher S rating. Combining this method of analysis with high-resolution electron micrography has revealed that the prokaryotic ribosome, which has an overall rating of 70S, is actually composed of two smaller subunits (figure 4.18). They fit together to form a miniature platform upon which protein synthesis is performed. Note: eukaryotic ribosomes are 80S— and this will be very important in future chapters. We examine the more detailed functions of ribosomes in chapter 9.

Inclusions, or Granules: Storage Bodies Most bacteria are exposed to severe shifts in the availability of food. During periods of nutrient abundance, some can compensate by laying down nutrients intracellularly in inclusion bodies, or inclusions, of varying size, number, and content. As the environmental source of these nutrients becomes depleted, the bacterial cell can mobilize its own storehouse as required. Some inclusion bodies carry condensed, energy-rich organic substances, such as glycogen and poly β-hydroxybutyrate (PHB), within special single-layered membranes (figure 4.19). A unique type of

3. Named in honor of T. Svedberg, the Swedish chemist who developed the ultracentrifuge in 1926.

(a)

MP

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Figure 4.18 A model of a prokaryotic ribosome, showing

the small (30S) and large (50S) subunits, both separate and joined.

Figure 4.19 Bacterial inclusion bodies. (a) Large particles (pink) of polyhydroxybutyrate are deposited in a concentrated form that provides an ample long-term supply of that nutrient (32,500×). (b) A section through Aquaspirillum reveals a chain of tiny iron magnets (magnetosomes = MP). These unusual bacteria use these inclusions to orient themselves within their habitat (123,000×).

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inclusion found in some aquatic bacteria is gas vesicles that provide buoyancy and flotation. Other inclusions, also called granules, are crystals of inorganic compounds and are not enclosed by membranes. Sulfur granules of photosynthetic bacteria and polyphosphate granules of Corynebacterium and Mycobacterium, described later, are of this type. The latter represent an important source of building blocks for nucleic acid and ATP synthesis. They have been termed metachromatic granules because they stain a contrasting color (red, purple) in the presence of methylene blue dye. Perhaps the most unique cell granule is not involved in cell nutrition but rather in cell orientation. Magnetotactic bacteria contain crystalline particles of iron oxide (magnetosomes) that have magnetic properties. The bacteria use these granules to be pulled by the polar and gravitational fields into deeper habitats with a lower oxygen content.

The Cytoskeleton Until very recently, scientists thought that the shape of all bacteria was completely determined by the peptidoglycan layer (cell wall). Although this is true of many bacteria, particularly the cocci, other bacteria produce long polymers of a protein called actin and tubulin, arranged in helical ribbons around the cell just under the cell membrane (figure 4.20). These fibers contribute to cell shape, perhaps by influencing the way peptidoglycan is manufactured, and also function in cell division. The fibers have been found in rod-shaped and spiral bacteria.

A Note on Terminology The word spore can have more than one usage in microbiology. It is a generic term that refers to any tiny compact cells that are produced by vegetative or reproductive structures of microorganisms. Spores can be quite variable in origin, form, and function. The bacterial type discussed here is called an endospore, because it is produced inside a cell. With the exception of the endospores of the bacterium Metabacterium polyspora mentioned in the text, they function in survival, not in reproduction, because no increase in cell numbers is involved in their formation. In contrast, the fungi produce many different types of spores for both survival and reproduction (see chapter 5).

Bacterial Endospores: An Extremely Resistant Stage Ample evidence indicates that the anatomy of bacteria helps them adjust rather well to adverse habitats. But of all microbial structures, nothing can compare to the bacterial endospore (or simply spore) for withstanding hostile conditions and facilitating survival. Endospores are dormant bodies produced by the bacteria Bacillus, Clostridium, and Sporosarcina. These bacteria have a two-phase life cycle—a vegetative cell and an endospore (figure 4.21). The vegetative cell is a metabolically active and growing entity that can be induced by environmental conditions to undergo spore formation, or sporulation. Once formed, the spore exists in an inert, resting condition that shows up prominently in a spore or Gram stain (figure 4.22). Features of spores, including size, shape, and position in the vegetative cell, are somewhat useful in identifying some species. Both gram-positive and gram-negative bacteria can form endospores, but the medically relevant ones are all grampositive. Most bacteria form only one endospore and therefore this is not a reproductive function for them. One bacterium called Metabacterium polyspora, an inhabitant of the guinea pig intestine, produces as many as nine endospores.

Endospore Formation and Resistance

Figure 4.20 Bacterial cytoskeleton. The actin fibers in these rod-shaped bacteria are fluorescently stained.

The depletion of nutrients, especially an adequate carbon or nitrogen source, is the stimulus for a vegetative cell to begin endospore formation. Once this stimulus has been received by the vegetative cell, it undergoes a conversion to become a sporulating cell called a sporangium. Complete transformation of a vegetative cell into a sporangium and then into an endospore requires 6 to 8 hours in most spore-forming species. Figure 4.21 illustrates some major physical and chemical events in this process. Bacterial endospores are the hardiest of all life forms, capable of withstanding extremes in heat, drying, freezing, radiation, and chemicals that would readily kill vegetative cells. Their survival under such harsh conditions is due to several factors. The heat resistance of spores has been

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Figure 4.21 A typical sporulation cycle in Bacillus species from the active vegetative cell to release and germination. This process takes, on average, about 10 hours. Inset is a high-magnification (10,000×) cross section of a single spore showing the dense protective layers that surround the core with its chromosome.

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Figure 4.22

Endospore inside Bacillus thuringiensis. The genus Bacillus forms endospores. B. thuringiensis additionally forms crystalline bodies (pink) that are used as insecticides.

linked to their high content of calcium and dipicolinic acid, although the exact role of these chemicals is not yet clear. We know, for instance, that heat destroys cells by inactivating proteins and DNA and that this process requires a certain amount of water in the protoplasm. Because the deposition of calcium dipicolinate in the endospore removes water and leaves the endospore very dehydrated, it is less vulnerable to the effects of heat. It is also metabolically inactive and highly resistant to damage from further drying. The thick, impervious cortex and spore coats also protect against radiation and chemicals. The longevity of bacterial spores verges

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on immortality. One record describes the isolation of viable endospores from a fossilized bee that was 25 million years old. More recently, microbiologists unearthed a viable endospore from a 250-million-year-old salt crystal. Initial analysis of this ancient microbe indicates it is a species of Bacillus that is genetically different from known species.

The Germination of Endospores After lying in a state of inactivity for an indefinite time, endospores can be revitalized when favorable conditions arise. The breaking of dormancy, or germination, happens in the presence of water and a specific chemical or environmental stimulus (germination agent). Once initiated, it proceeds 1 to completion quite rapidly (1— 2 hours). Although the specific germination agent varies among species, it is generally a small organic molecule such as an amino acid or an inorganic salt. This agent stimulates the formation of hydrolytic (digestive) enzymes by the endospore membranes. These enzymes digest the cortex and expose the core to water. As the core rehydrates and takes up nutrients, it begins to grow out of the endospore coats. In time, it reverts to a fully active vegetative cell, resuming the vegetative cycle.

Medical Significance of Bacterial Spores Although the majority of spore-forming bacteria are relatively harmless, several bacterial pathogens are sporeformers. In fact, some aspects of the diseases they cause are related to the persistence and resistance of their spores. Bacillus anthracis is the agent of anthrax; its persistence in endospore form makes it an ideal candidate for bioterrorism. The genus Clostridium includes even more pathogens, such as C. tetani, the cause of tetanus (lockjaw), and C. perfringens, the cause of gas gangrene. When the spores of these species are embedded in a wound that contains dead tissue, they can germinate, grow, and release potent toxins. Another toxin-forming species, C. botulinum, is the agent of botulism, a deadly form of food poisoning. (Each of these disease conditions is discussed in the infectious disease chapters, according to the organ systems it affects.) Because they inhabit the soil and dust, endospores are constant intruders where sterility and cleanliness are important. They resist ordinary cleaning methods that use boiling water, soaps, and disinfectants, and they frequently contaminate cultures and media. Hospitals and clinics must take precautions to guard against the potential harmful effects of endospores in wounds. Endospore destruction is a particular concern of the food-canning industry. Several endosporeforming species cause food spoilage or poisoning. Ordinary boiling (100°C) will usually not destroy such spores, so canning is carried out in pressurized steam at 120°C for 20 to 30 minutes. Such rigorous conditions ensure that the food is sterile and free from viable bacteria.

4.4 Learning Outcomes—Can You . . . 8. . . . identify five things that might be contained in bacterial cytoplasm? 9. . . . detail the causes and mechanisms of sporogenesis and germination?

4.5 Prokaryotic Shapes, Arrangements, and Sizes For the most part, prokaryotes function as independent singlecelled, or unicellular, organisms. Each individual prokaryotic cell is fully capable of carrying out all necessary life activities, such as reproduction, metabolism, and nutrient processing, unlike the more specialized cells of a multicellular organism. It should be noted that sometimes prokaryotes can act as a group. When bacteria are close to one another in colonies or in biofilms, they communicate with each other through chemicals that cause them to behave differently than if they were living singly. More surprisingly, many bacteria seem to communicate with each other using structures called nanowires, which are appendages that can be many microns long that attach bacterium to bacterium, transferring electrons or other substances. This is not the same as being a multicellular organism but it represents new findings about microbial cooperation. Prokaryotes exhibit considerable variety in shape, size, and colonial arrangement. See Insight 4.3 for a discussion on size. It is convenient to describe most prokaryotes by one of three general shapes as dictated by the configuration of the cell wall (figure 4.23). If the cell is spherical or ball-shaped, the prokaryote is described as a coccus (kok′-us). Cocci can be perfect spheres, but they also can exist as oval, bean-shaped, or even pointed variants. A cell that is cylindrical (longer than wide) is termed a rod, or bacillus (bah-sil′-lus). There is also a genus named Bacillus. As might be expected, rods are also quite varied in their actual form. Depending on the species, they can be blocky, spindle-shaped, round-ended, long and threadlike (filamentous), or even club-shaped or drumstickshaped. When a rod is short and plump, it is called a coccobacillus; if it is gently curved, it is a vibrio (vib′-ree-oh). A bacterium having a slightly curled or spiral-shaped cylinder is called a spirillum (spy-ril′-em), a rigid helix, twisted twice or more along its axis (like a corkscrew). Another spiral cell mentioned earlier in conjunction with periplasmic flagella is the spirochete, a more flexible form that resembles a spring. Because prokaryotic cells look two-dimensional and flat with traditional staining and microscope techniques, they are seen to best advantage with a scanning electron microscope, which emphasizes their striking three-dimensional forms (figure 4.23). It is common for cells of a single species to vary to some extent in shape and size. This phenomenon, called

4.5 Prokaryotic Shapes, Arrangements, and Sizes

INSIGHT 4.3

Redefining Prokaryotic Size

Most microbiologists believe we are still far from having a complete assessment of the prokaryotic world, mostly because the world is so large and prokaryotes are so small. This fact becomes evident in the periodic discoveries of exceptional bacteria that are reported in newspaper headlines. Among the most remarkable are giant and dwarf bacteria.

Big Bacteria Break Records In 1985, biologists discovered a new bacterium living in the intestine of surgeonfish that at the time was a candidate for the Guinness Book of World Records. The large cells, named Epulopiscium fishelsoni (“guest at a banquet of fish”), measure around 100 μm in length, although some specimens were as large as 300 μm. This record was recently broken when marine microbiologist Heide Schultz discovered an even larger species of bacteria living in ocean sediments near the African country of Namibia. These gigantic cocci are arranged in strands that look like pearls and contain hundreds of golden sulfur granules, inspiring their name, Thiomargarita namibia (“sulfur pearl of Namibia”) (see photo). The size of the individual cells ranges 3 mm), and many are large enough to from 100 up to 750 μm (— 4 see with the naked eye. By way of comparison, if the average bacterium were the size of a mouse, Thiomargarita would be as large as a blue whale! Closer study revealed that they are indeed prokaryotic and have bacterial ribosomes and DNA, but that they also have some unusual adaptations to their life cycle. They live an attached existence embedded in sulfide sediments (H2S) that are free of gaseous oxygen. They obtain energy through oxidizing these sulfides using dissolved nitrates (NO3). Because the quantities of these substances can vary with the seasons, they must be stored in cellular depots. The sulfides are carried as granules in the cytoplasm, and the nitrates occupy a giant, liquid-filled vesicle that takes up a major proportion of cell volume. Due to their morphology and physiology, the cells can survive for up to 3 months without an external source of nutrients by tapping into their “storage tanks.” These bacteria are found in such large numbers in the sediments that it is thought that they are essential to the ecological cycling of H2S gas in this region, converting it to less toxic substances.

Miniature Microbes—The Smallest of the Small At the other extreme, microbiologists are being asked to reevaluate the lower limits of bacterial size. Up until now it has been generally accepted that the smallest cells on the planet are some form of mycoplasma with dimensions of 0.2 to 0.3 μm, which is right at the limit of resolution with light microscopes. A new controversy is brewing over the discovery of tiny cells that look like dwarf bacteria but are 10 times smaller than mycoplasmas and a hundred times smaller

1 millimeter

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than the average bacterial cell. These minute cells have been given the name nanobacteria or nanobes (Gr. nanos, one-billionth). Nanobacteria-like forms were first isolated from blood and serum samples. The tiny cells appear to grow in culture, have cell walls, and contain protein and nucleic acids, but their size range is only from 0.05 to 0.2 μm. Similar nanobes have been extracted by mineralogists studying sandstone rock deposits in the ocean at temperatures of 100°C to 170°C and deeply embedded in billion-year-old minerals. The minute filaments were able to grow and are capable of depositing minerals in a test tube. Many geologists are convinced that these nanobes are real, that they are probably similar to the first microbes on earth, and that they play a strategic role in the evolution of the earth’s crust. Microbiologists tend to be more skeptical. It has been postulated that the minimum cell size to contain a functioning genome and reproductive and synthetic machinery is approximately 0.14 μm. They believe that the nanobes are really just artifacts or bits of larger cells that have broken free. Nanobe “believers” have recently been bolstered by a series of findings indicating that nanobes can infect humans and have been linked to diseases such as kidney stones and ovarian cancer. These diseases are influenced in some way by calcification that is catalyzed by nanobes. It seems the real question is not whether nanobes exist but whether we should classify them as bacteria. One of the early nanobe discoverers, Olavi Kajander, blames himself for getting scientists distracted by that question by first coining the name “nanobacteria.” “Calcifying self-propagating nanoparticles would have been much better,” he says now.* Additional studies are needed to test this curious question of nanobes, and possibly to answer some questions about the origins of life on earth and even other planets. *Wired.com news story, March 14, 2005.

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(a) Coccus

(b) Rod/Bacillus

(c) Vibrio

(d) Spirillum

(e) Spirochete

(f) Branching filaments

Key to Micrographs (a) Deinococcus (2,000⫻) (b) Lactobacillus bulgaricus (5,000⫻) (c) Vibrio cholerae (13,000⫻) (d) Aquaspirillum (7,500⫻) (e) Spirochetes on a filter (14,000⫻) (f) Streptomyces (1,500⫻)

Figure 4.23 Bacterial shapes and arrangements. Drawings show examples of shape variations for cocci, rods, vibrios, spirilla, spirochetes, and branching filaments. Below each shape is a micrograph of a representative example.

pleomorphism (figure 4.24), is due to individual variations in cell wall structure caused by nutritional or slight genetic differences. For example, although the cells of Corynebacterium diphtheriae are generally considered rod-shaped, in culture they display variations such as club-shaped, swollen, curved, filamentous, and coccoid. Pleomorphism reaches an extreme in the mycoplasmas, which entirely lack cell walls and thus display extreme variations in shape (see figure 4.15). The cells of prokaryotes can also be categorized according to arrangement, or style of grouping (see figure 4.23). The main factors influencing the arrangement of a particular

cell type are its pattern of division and how the cells remain attached afterward. The greatest variety in arrangement occurs in cocci, which can be single, in pairs (diplococci), in tetrads (groups of four), in irregular clusters (both staphylococci and micrococci), or in chains of a few to hundreds of cells (streptococci). An even more complex grouping is a cubical packet of eight, sixteen, or more cells called a sarcina (sar′-sih-nah). These different coccal groupings are the result of the division of a coccus in a single plane, in two perpendicular planes, or in several intersecting planes; after division, the resultant daughter cells remain attached.

4.6

Figure 4.24 Pleomorphic bacteria. If you look closely at this micrograph of stained Dermatophilus bacteria, you will see some coccoid cells, some long filamentous cells, and some rod-shaped cells.

Bacilli are less varied in arrangement because they divide only in the transverse plane (perpendicular to the axis). They occur either as single cells, as a pair of cells with their ends attached (diplobacilli), or as a chain of several cells (streptobacilli). Spirilla are occasionally found in short chains, but spirochetes rarely remain attached after division.

4.5 Learning Outcomes—Can You . . . 10. . . . describe the three major shapes of prokaryotes? 11. . . . describe other more unusual shapes of prokaryotes?

4.6 Classification Systems in the Prokaryotae Classification systems serve both practical and academic purposes. They aid in differentiating and identifying unknown species in medical and applied microbiology. They are also useful in organizing prokaryotes and as a means of studying their relationships and origins. Since classification was started around 200 years ago, several thousand species of bacteria and archaea have been identified, named, and cataloged. For years scientists have had intense interest in tracing the origins of and evolutionary relationships among prokaryotes, but doing so has not been an easy task. One of the questions that has plagued taxonomists is, “What characteristics are the most indicative of closeness in ancestry?” Early bacteriologists found it convenient to classify bacteria according to shape, variations in arrangement, growth

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characteristics, and habitat. However, as more species were discovered and as techniques for studying their biochemistry were developed, it soon became clear that similarities in cell shape, arrangement, and staining reactions do not automatically indicate relatedness. Even though the gram-negative rods look alike, there are hundreds of different species, with highly significant differences in biochemistry and genetics. If we attempted to classify them on the basis of Gram stain and shape alone, we could not assign them to a more specific level than class. Increasingly, classification schemes are turning to genetic and molecular traits that cannot be visualized under a microscope or in culture. One of the most viable indicators of evolutionary relatedness and affiliation is comparison of the sequence of nitrogen bases in ribosomal RNA, a major component of ribosomes. Ribosomes have the same function (protein synthesis) in all cells, and they tend to remain more or less stable in their nucleic acid content over long periods. Thus, any major differences in the sequence, or “signature,” of the rRNA is likely to indicate some distance in ancestry. This technique is powerful at two levels: It is effective for differentiating general group differences (it was used to separate the three superkingdoms of life discussed in chapter 1), and it can be fine-tuned to identify at the species level (for example in Mycobacterium and Legionella). Elements of these and other identification methods are presented in more detail in chapter 17. The definitive published source for prokaryotic classification, called Bergey’s Manual, has been in print continuously since 1923. The basis for the early classification in Bergey’s was the phenotypic traits of bacteria, such as their shape, cultural behavior, and biochemical reactions. These traits are still used extensively by clinical microbiologists or researchers who need to quickly identify unknown bacteria. As methods for RNA and DNA analysis became available, this information was used to supplement the phenotypic information. The current version of the publication, called Bergey’s Manual of Systematic Bacteriology, presents a comprehensive view of prokaryotic relatedness, combining phenotypic information with rRNA sequencing information to classify prokaryotes; it is a huge, five-volume set. (We need to remember that all prokaryotic classification systems are in a state of constant flux; no system is ever finished.) With the explosion of information about evolutionary relatedness among bacteria, the need for a Bergey’s Manual that contained easily accessible information for identifying unknown bacteria became apparent. Now there is a separate book, called Bergey’s Manual of Determinative Bacteriology, based entirely on phenotypic characteristics. It is utilitarian in focus, categorizing bacteria by traits commonly assayed in clinical, teaching, and research labs. It is widely used by microbiologists who need to identify bacteria but need not know their evolutionary backgrounds. This phenotypic classification is more useful for students of medical microbiology, as well.

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Taxonomic Scheme Bergey’s Manual of Determinative Bacteriology organizes the prokaryotes into four major divisions. These somewhat natural divisions are based on the nature of the cell wall. The Gracilicutes (gras″-ih-lik′-yoo-teez) have gram-negative cell walls and thus are thin-skinned; the Firmicutes have grampositive cell walls that are thick and strong; the Tenericutes (ten″-er-ik′-yoo-teez) lack a cell wall and thus are soft; and the Mendosicutes (men-doh-sik′-yoo-teez) are the archaea (also called archaebacteria), primitive prokaryotes with unusual cell walls and nutritional habits. The first two divisions contain the greatest number of species. The 200 or so species that are so-far known to cause human and animal diseases can be found in four classes: the Scotobacteria, Firmibacteria, Thallobacteria, and Mollicutes. The system used in Bergey’s Manual further organizes prokaryotes into subcategories such as classes, orders, and families, but these are not available for all groups.

Diagnostic Scheme As mentioned earlier, many medical microbiologists prefer an informal working system that outlines the major families and genera. Table 4.1 is an example of an adaptation of the phenotypic method of classification that might be used in clinical microbiology. This system is more applicable for diagnosis because it is restricted to bacterial disease agents, depends less on nomenclature, and is based on readily accessible morphological and physiological tests rather than on phylogenetic relationships. It also divides the bacteria into gram-positive, gram-negative, and those without cell walls and then subgroups them according to cell shape, arrangement, and certain physiological traits such as oxygen usage: Aerobic bacteria use oxygen in metabolism; anaerobic bacteria do not use oxygen in metabolism; and facultative bacteria may or may not use oxygen. Further tests not listed in the table would be required to separate closely related genera and species. Many of these are included in later chapters on specific bacterial groups.

Species and Subspecies in Prokaryotes Among most organisms, the species level is a distinct, readily defined, and natural taxonomic category. In animals, for instance, a species is a distinct type of organism that can produce viable offspring only when it mates with others of its own kind. This definition does not work for prokaryotes primarily because they do not exhibit a typical mode of sexual reproduction. They can accept genetic information from unrelated forms, and they can also alter their genetic makeup by a variety of mechanisms. Thus, it is necessary to hedge a bit when we define a bacterial species. Theoretically, it is a collection of bacterial cells, all of which share an overall similar pattern of traits, in contrast to other groups whose patterns differ significantly. Although

the boundaries that separate two closely related species in a genus are in some cases arbitrary, this definition still serves as a method to separate the bacteria into various kinds that can be cultured and studied. As additional information on prokaryotic genomes is discovered, it may be possible to define species according to specific combinations of genetic codes found only in a particular isolated culture. Individual members of given species can show variations, as well. Therefore more categories within species exist, but they are not well defined. Microbiologists use terms like subspecies, strain, or type to designate bacteria of the same species that have differing characteristics. Serotype refers to representatives of a species that stimulate a distinct pattern of antibody (serum) responses in their hosts, because of distinct surface molecules.

4.6 Learning Outcomes—Can You . . . 12. . . . differentiate between Bergey’s Manual of Systematic Bacteriology and Bergey’s Manual of Determinative Bacteriology? 13. . . . name four divisions ending in –cutes and describe their characteristics? 14. . . . explain what a species is?

4.7 The Archaea Archaea: The Other Prokaryotes The discovery and characterization of novel prokaryotic cells that have unusual anatomy, physiology, and genetics changed our views of microbial taxonomy and classification (see chapter 1). These single-celled, simple organisms, called archaea, are now considered a third cell type in a separate superkingdom (the Domain Archaea). We include them in this chapter because they are prokaryotic in general structure and they do share many bacterial characteristics. But it has become clear that they are actually more closely related to Domain Eukarya than to bacteria. For example, archaea and eukaryotes share a number of ribosomal RNA sequences that are not found in bacteria, and their protein synthesis and ribosomal subunit structures are similar. Table 4.2 outlines selected points of comparison of the three domains. Among the ways that the archaea differ significantly from other cell types are that certain genetic sequences are found only in their rRNA, and that they have unique membrane lipids and cell wall construction. It is clear that the archaea are the most primitive of all life forms and are most closely related to the first cells that originated on the earth 4 billion years ago. The early earth is thought to have contained a hot, anaerobic “soup” with sulfuric gases and salts in abundance. The modern archaea still live in the remaining habitats on the earth that have these same ancient conditions—the most extreme habitats in nature. It is for this reason that they are

4.7

Table 4.1 Medically Important Families and Genera of Bacteria, with Notes on Some Diseases* I. Bacteria with gram-positive cell wall structure Cocci in clusters or packets Family Micrococcaceae: Staphylococcus (members cause boils, skin infections) Cocci in pairs and chains Family Streptococcaceae: Streptococcus (species cause strep throat, dental caries) Anaerobic cocci in pairs, tetrads, irregular clusters Family Peptococcaceae: Peptococcus, Peptostreptococcus (involved in wound infections) Spore-forming rods Family Bacillaceae: Bacillus (anthrax), Clostridium (tetanus, gas gangrene, botulism) Non-spore-forming rods Family Lactobacillaceae: Lactobacillus, Listeria, Erysipelothrix (erysipeloid) Family Propionibacteriaceae: Propionibacterium (involved in acne) Family Corynebacteriaceae: Corynebacterium (diphtheria) Family Mycobacteriaceae: Mycobacterium (tuberculosis, leprosy) Family Nocardiaceae: Nocardia (lung abscesses) Family Actinomycetaceae: Actinomyces (lumpy jaw), Bifidobacterium Family Streptomycetaceae: Streptomyces (important source of antibiotics) II. Bacteria with gram-negative cell wall structure Aerobic cocci Neisseria (gonorrhea, meningitis), Branhamella Aerobic coccobacilli Moraxella, Acinetobacter Anaerobic cocci Family Veillonellaceae Veillonella (dental disease) Miscellaneous rods Brucella (undulant fever), Bordetella (whooping cough), Francisella (tularemia) Aerobic rods Family Pseudomonadaceae: Pseudomonas (pneumonia, burn infections) Miscellaneous: Legionella (Legionnaires’ disease) Facultative or anaerobic rods and vibrios Family Enterobacteriaceae: Escherichia, Edwardsiella, Citrobacter, Salmonella (typhoid fever), Shigella (dysentery), Klebsiella, Enterobacter, Serratia, Proteus, Yersinia (one species causes plague) Family Vibronaceae: Vibrio (cholera, food infection), Campylobacter, Aeromonas Miscellaneous genera: Chromobacterium, Flavobacterium, Haemophilus (meningitis), Pasteurella, Cardiobacterium, Streptobacillus Anaerobic rods Family Bacteroidaceae: Bacteroides, Fusobacterium (anaerobic wound and dental infections) Helical and curviform bacteria Family Spirochaetaceae: Treponema (syphilis), Borrelia (Lyme disease), Leptospira (kidney infection) Obligate intracellular bacteria Family Rickettsiaceae: Rickettsia (Rocky Mountain spotted fever), Coxiella (Q fever) Family Bartonellaceae: Bartonella (trench fever, cat scratch disease) Family Chlamydiaceae: Chlamydia (sexually transmitted infection) III. Bacteria with no cell walls Family Mycoplasmataceae: Mycoplasma (pneumonia), Ureaplasma (urinary infection) *Details of pathogens and diseases appear in chapters 18 through 23.

The Archaea

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Table 4.2 Comparison of Three Cellular Domains Characteristic

Bacteria

Archaea

Eukarya

Cell type

Prokaryotic

Prokaryotic

Eukaryotic

Chromosomes

Single, or few, circular

Single, circular

Several, linear

Types of ribosomes

70S

70S but structure is similar to 80S

80S

Contains unique ribosomal RNA signature sequences

+

+

+

Number of sequences shared with Eukarya

1

3

(all)

Protein synthesis similar to Eukarya

−

+

Presence of peptidoglycan in cell wall

+

−

−

Cell membrane lipids

Fatty acids with ester linkages

Long-chain, branched hydrocarbons with ether linkages

Fatty acids with ester linkages

Sterols in membrane

− (some exceptions)

−

+

often called extremophiles, meaning that they “love” extreme conditions in the environment. Metabolically, the archaea exhibit incredible adaptations to what would be deadly conditions for other organisms. These hardy microbes have adapted to multiple combinations of heat, salt, acid, pH, pressure, and atmosphere. Included in this group are methane producers, hyperthermophiles, extreme halophiles, and sulfur reducers. Members of the group called methanogens can convert CO2 and H2 into methane gas (CH4) through unusual and complex pathways. These archaea are common inhabitants of anaerobic swamp mud, the bottom sediments of lakes and oceans, and even the digestive systems of animals. The gas they produce collects in swamps and may become a source of

fuel. Methane may also contribute to the “greenhouse effect,” which maintains the earth’s temperature and can contribute to global warming (see chapter 24). Other types of archaea—the extreme halophiles— require salt to grow, and some have such a high salt tolerance that they can multiply in sodium chloride solutions (36% NaCl) that would destroy most cells. They exist in the saltiest places on the earth—inland seas, salt lakes, salt mines, and salted fish. They are not particularly common in the ocean because the salt content is not high enough. Many of the “halobacteria” use a red pigment to synthesize ATP in the presence of light. These pigments are responsible for the color of the Red Sea, and the red color of salt ponds (figure 4.25).

5 mm (a)

(b)

Figure 4.25 Halophiles around the world. (a) A solar evaporation pond in Owens Lake, California, is extremely high in salt and mineral content. The archaea that dominate in this hot, saline habitat produce brilliant red pigments with which they absorb light to drive cell synthesis. (b) A sample taken from a saltern in Australia viewed by fluorescent microscopy (1,000×). Note the range of cell shapes (cocci, rods, and squares) found in this community.

4.7

Archaea adapted to growth at very low temperatures are called psychrophilic (loving cold temperatures); those growing at very high temperatures are hyperthermophilic (loving high temperatures). Hyperthermophiles flourish at temperatures between 80°C and 113°C and cannot grow at 50°C. They live in volcanic waters and soils and submarine vents and are also often salt- and acid-tolerant as well. One member, Thermoplasma, lives in hot, acidic habitats in the waste piles around coal mines that regularly sustain a pH of 1 and a temperature of nearly 60°C. Archaea are not just environmental microbes. They have been isolated from human tissues such as the colon, the mouth, and the vagina. Recently, an association was found between the degree of severity of periodontal disease and the presence of archaeal RNA sequences in the gingiva, suggesting—but not proving—that archaea may be capable of causing human disease.

4.7 Learning Outcomes—Can You . . . 15. . . . List some differences between archaea and bacteria?

Case File 4

The Archaea

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Wrap-Up

The opening of the case asked why the discovery of bacteria in cerebrospinal fluid and the blood is a serious sign. You will learn in later chapters that these two body compartments are generally off limits to bacteria and have little or no normal microbial inhabitants, unlike the digestive tract or the respiratory tract. It is more difficult for microbes to enter both of these compartments for several reasons, one being that antibodies can attach to bacteria and prevent them from crossing the boundaries into these areas. Apparently this patient was missing the antibodies that would have acted against the encapsulated bacteria. The patient was treated for septic shock and respiratory failure for 9 days. Physicians administered dopamine and epinephrine to stabilize her blood pressure, as well as antibiotics to treat the underlying bacterial infection. Artificial ventilation was necessary for the first 4 days of treatment. Prior to being discharged, the patient was injected with pneumococcal vaccine and placed on prophylactic (preventive) penicillin therapy. She recovered fully. See: 2005. Rheumatology 44(12):1586−88.

Chapter Summary 4.1 Prokaryotic Form and Function • Prokaryotes are the oldest form of cellular life. They are also the most widely dispersed, occupying every conceivable microclimate on the planet. 4.2 External Structures • The external structures of bacteria include appendages (flagella, fimbriae, and pili) and the glycocalyx. • Flagella vary in number and arrangement as well as in the type and rate of motion they produce. 4.3 The Cell Envelope: The Boundary Layer of Bacteria • The cell envelope is the complex boundary structure surrounding a bacterial cell. In gram-negative bacteria, the envelope consists of an outer membrane, the cell wall, and the cell membrane. Gram-positive bacteria have only the cell wall and cell membrane. • In a Gram stain, gram-positive bacteria retain the crystal violet and stain purple. Gram-negative bacteria lose the crystal violet and stain red from the safranin counterstain. • Gram-positive bacteria have thick cell walls of peptidoglycan and acidic polysaccharides such as teichoic acid. The cell walls of gram-negative bacteria are thinner and have a wide periplasmic space. • The outer membrane of gram-negative cells contains lipopolysaccharide (LPS). LPS is toxic to mammalian hosts. • The bacterial cell membrane is typically composed of phospholipids and proteins, and it performs many metabolic functions as well as transport activities.

4.4 Bacterial Internal Structure • The cytoplasm of bacterial cells serves as a solvent for materials used in all cell functions. • The genetic material of bacteria is DNA. Genes are arranged on large, circular chromosomes. Additional genes are carried on plasmids. • Bacterial ribosomes are dispersed in the cytoplasm in chains (polysomes) and are also embedded in the cell membrane. • Bacteria may store nutrients in their cytoplasm in structures called inclusions. Inclusions vary in structure and the materials that are stored. • Some bacteria manufacture long actin filaments that help determine their cellular shape. • A few families of bacteria produce dormant bodies called endospores, which are the hardiest of all life forms, surviving for hundreds or thousands of years. • The genera Bacillus and Clostridium are sporeformers, and both contain deadly pathogens. 4.5 Prokaryotic Shapes, Arrangements, and Sizes • Most prokaryotes have one of three general shapes: coccus (round), bacillus (rod), or spiral, based on the configuration of the cell wall. Two types of spiral cells are spirochetes and spirilla. • Shape and arrangement of cells are key means of describing prokaryotes. Arrangements of cells are based on the number of planes in which a given species divides. • Cocci can divide in many planes to form pairs, chains, packets, or clusters. Bacilli divide only in the transverse plane. If they remain attached, they form chains or palisades.

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Prokaryotic Profiles • Variant forms within a species (subspecies) include

4.6 Classification Systems in the Prokaryotae • Prokaryotes are formally classified by phylogenetic relationships and phenotypic characteristics. • Medical identification of pathogens uses an informal system of classification based on Gram stain, morphology, biochemical reactions, and metabolic requirements. • A bacterial species is loosely defined as a collection of bacterial cells that shares an overall similar pattern of traits different from other groups of bacteria.

strains and types. 4.7 The Archaea • Archaea are another type of prokaryotic cell that constitute the third domain of life. They exhibit unusual biochemistry and genetics that make them different from bacteria. Many members are adapted to extreme habitats with low or high temperature, salt, pressure, or acid.

Multiple-Choice and True-False Questions

Knowledge and Comprehension

Multiple-Choice Questions. Select the correct answer from the answers provided. 1. Which of the following is not found in all bacterial cells? a. cell membrane c. ribosomes b. a nucleoid d. actin cytoskeleton 2. Pili are tubular shafts in ______ bacteria that serve as a means of ______. a. gram-positive, genetic exchange b. gram-positive, attachment c. gram-negative, genetic exchange d. gram-negative, protection 3. An example of a glycocalyx is a. a capsule. c. an outer membrane. b. a pilus. d. a cell wall. 4. Which of the following is a primary bacterial cell wall function? a. transport c. support b. motility d. adhesion 5. Which of the following is present in both gram-positive and gram-negative cell walls? a. an outer membrane c. teichoic acid b. peptidoglycan d. lipopolysaccharides 6. Darkly stained granules are concentrated crystals of ______ that are found in ______. a. fat, Mycobacterium c. sulfur, Thiobacillus b. dipicolinic acid, Bacillus d. PO4, Corynebacterium 7. Bacterial endospores usually function in a. reproduction. c. protein synthesis. b. survival. d. storage.

Critical Thinking Questions

8. A bacterial arrangement in packets of eight cells is described as a ______. a. micrococcus c. tetrad b. diplococcus d. sarcina 9. To which division of bacteria do cyanobacteria belong? a. Tenericutes c. Firmicutes b. Gracilicutes d. Mendosicutes 10. Which stain is used to distinguish differences between the cell walls of medically important bacteria? a. simple stain c. Gram stain b. acridine orange stain d. negative stain True-False Questions. If the statement is true, leave as is. If it is false, correct it by rewriting the sentence. 11. One major difference in the envelope structure between grampositive bacteria and gram-negative bacteria is the presence or absence of a cytoplasmic membrane. 12. A research microbiologist looking at evolutionary relatedness between two bacterial species is more likely to use Bergey’s Manual of Determinative Bacteriology than Bergey’s Manual of Systematic Bacteriology. 13. Nanobes may or may not actually be bacteria. 14. Both bacteria and archaea are prokaryotes. 15. A collection of bacteria that share an overall similar pattern of traits is called a species.

Application and Analysis

These questions are suggested as a writing-to-learn experience. For each question, compose a one- or two-paragraph answer that includes the factual information needed to completely address the question. 1. a. Name several general characteristics that could be used to define the prokaryotes. b. Do any other microbial groups besides bacteria have prokaryotic cells? c. What does it mean to say that prokaryotes are ubiquitous? In what habitats are they found? Give some general means by which bacteria derive nutrients.

2. a. Describe the structure of a flagellum and how it operates. What are the four main types of flagellar arrangement? b. How does the flagellum dictate the behavior of a motile bacterium? Differentiate between flagella and periplasmic flagella. 3. Differentiate between pili and fimbriae.

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4. a. Compare the cell envelopes of gram-positive and gramnegative bacteria. b. What function does peptidoglycan serve? c. Give a simple description of its structure. d. What happens to a cell that has its peptidoglycan disrupted or removed? e. What functions does the LPS layer serve?

7. a. Explain the characteristics of archaea that indicate that they constitute a unique domain of living things that is neither bacterial nor eukaryotic. b. What leads microbiologists to believe the archaea are more closely related to eukaryotes than to bacteria? c. What is meant by the term extremophile? Describe some archaeal adaptations to extreme habitats.

5. List five functions that the cell membrane performs in bacteria.

8. a. Name a bacterium that has no cell walls. b. How is it protected from osmotic destruction?

6. a. Describe the vegetative stage of a bacterial cell. b. Describe the structure of an endospore, and explain its function. c. Describe the endospore-forming cycle. d. Explain why an endospore is not considered a reproductive body. e. Why are endospores so difficult to destroy?

Concept Mapping

9. a. What are some possible adaptations that the giant bacterium Thiomargarita has had to make because of its large size? b. If a regular bacterium were the size of an elephant, estimate the size of a nanobe at that scale. 10. Propose a hypothesis to explain how bacteria and archaea could have, together, given rise to eukaryotes.

Synthesis

Appendix D provides guidance for working with concept maps. 1. Construct your own concept map using the following words as the concepts. Supply the linking words between each pair of concepts.

Visual Connections

genus serotype Borrelia spirochete

species domain burgdorferi

Synthesis

These questions use visual images or previous content to make connections to this chapter’s concepts. 1. From chapter 3, figure 3.10. Do you believe that the bacteria spelling “Klebsiella” or the bacteria spelling “S. aureus” possess the larger capsule? Defend your answer.

2. From chapter 1, figure 1.14. Study this figure. How would it be drawn differently if the archaea were more closely related to bacteria than to eukaryotes? Plants Animals Fungi Protists

Domain Bacteria Cyanobacteria

Domain Archaea

Chlamydias Gram-positive Endospore Gram-negative Spirochetes bacteria producers bacteria

Methane producers

Prokaryotes that live in extreme salt

Domain Eukarya Prokaryotes that live in extreme heat

Eukaryotes

Ancestral Cell Line (first living cells)

www.connect.microbiology.com Enhance your study of this chapter with study tools and practice tests. Also ask your instructor about the resources available through ConnectPlus, including the media-rich eBook, interactive learning tools, and animations.

Eukaryotic Cells and Microorganisms 5 Case File In June 2005, a ban on clamming was instituted along much of the Oregon coast after razor clams in that area were found to contain high levels of domoic acid, a naturally occurring toxin produced by algae in the genus Pseudo-nitzschia. Filter-feeding mollusks, such as clams and mussels, accumulate high levels of domoic acid during periods of robust algal growth known as blooms. Ingestion of domoic acid by humans causes amnesiac shellfish poisoning, which is marked by headache, dizziness, nausea, confusion, and potentially permanent loss of short-term memory. In severe cases, respiratory paralysis and death may occur within a day. A different kind of shellfish illness, paralytic shellfish poisoning, results from ingesting saxitoxins, which are, like domoic acid, produced by certain species of algae. In this case, algae in the genus Alexandrium produce the toxin, which then accumulates in mussels, clams, scallops, oysters, crabs, and lobsters during periods of greater than usual algal growth. Ingestion of saxitoxin by humans can lead to numbness, paralysis, disorientation, and death due to respiratory failure. Neither domoic acid nor saxitoxin is affected by temperature, so cooking or freezing has no effect on the toxin. ◾ The number of cases of seafood poisoning is far greater in the summer months. Besides the fact that people are more likely to harvest seafood when the weather is warm, why else would illnesses due to ingestion of harmful algae be more prevalent in the summer? ◾ The number and size of harmful algal blooms seem correlated to an increased use of fertilizers. Speculate on a possible connection between these two events. Continuing the Case appears on page 128.

Outline and Learning Outcomes 5.1 The History of Eukaryotes 1. Relate both prokaryotic and eukaryotic cells to the Last Common Ancestor. 2. List the types of eukaryotic microorganisms and denote which are unicellular and which are multicellular.

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5.1 The History of Eukaryotes

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5.2 Form and Function of the Eukaryotic Cell: External Structures 3. Differentiate between cilia and flagella in eukaryotes, and between flagella in prokaryotes and eukaryotes. 4. Describe the important characteristics of a glycocalyx in eukaryotes. 5. List which eukaryotic microorganisms have a cell wall. 6. List similarities and differences between eukaryotic and prokaryotic cytoplasmic membranes. 5.3 Form and Function of the Eukaryotic Cell: Internal Structures 7. Describe the important component parts of a nucleus. 8. Diagram how the nucleus, endoplasmic reticulum, and Golgi apparatus, together with vesicles, act together. 9. Explain the function of the mitochondria. 10. Discuss the function of chloroplasts and explain which cells contain them and why. 11. Explain the importance of ribosomes and differentiate between eukaryotic and prokaryotic types. 12. List and describe the three main fibers of the cytoskeleton. 5.4 The Kingdom of the Fungi 13. List some general features of fungal anatomy. 14. Differentiate among the terms heterotroph, saprobe, and parasite. 15. Connect the concepts of fungal hyphae and a mycelium. 16. Describe two ways in which fungal spores arise. 17. List two detrimental and two beneficial activities of fungi (from the viewpoint of humans). 5.5 The Protists 18. Use protozoan characteristics to explain why they are informally placed into a single group. 19. List three means of locomotion by protozoa. 20. Explain why a cyst stage might be useful. 21. Give an example of a disease caused by each of the four types of protozoa. 5.6 The Parasitic Helminths 22. List the two major groups of helminths and then the two subgroups of one of these groups. 23. Describe a typical helminth lifestyle.

5.1 The History of Eukaryotes Evidence from paleontology indicates that the first eukaryotic cells appeared on the earth approximately 2 billion years ago. Some fossilized cells that look remarkably like modern-day algae or protozoa appear in shale sediments from China, Russia, and Australia that date from 850 million to 950 million years ago (figure 5.1). While it used to be thought that eukaryotic cells evolved directly from prokaryotic cells, we now believe that both prokaryotes and eukaryotes evolved from a different kind of cell, a precursor to both prokaryotes and eukaryotes that biologists call the Last Common Ancestor. This ancestor was neither prokaryo-

tic nor eukaryotic, but gave rise to both in different ways. It now seems clear that some of the organelles that distinguish eukaryotic cells originated from more primitive cells that became trapped inside them (Insight 5.1). The structure of these first eukaryotic cells was so versatile that eukaryotic microorganisms soon spread out into available habitats and adopted greatly diverse styles of living. The first primitive eukaryotes were probably singlecelled and independent, but, over time, some forms began to aggregate, forming colonies. With further evolution, some of the cells within colonies became specialized, or adapted to perform a particular function advantageous to the whole colony, such as locomotion, feeding, or reproduction. Complex

Figure 5.1 Ancient eukaryotic protists caught up in fossilized rocks. (a) An alga-like cell found in Siberian shale deposits and dated from 850 million to 950 million years ago. (b) A large, disclike cell bearing a crown of spines is from Chinese rock dated 590 million to 610 million years ago. (a)

(b)

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INSIGHT 5.1

Eukaryotic Cells and Microorganisms

The Extraordinary Emergence of Eukaryotic Cells

For years, biologists have grappled with the problem of how a cell as complex as the modern eukaryotic cell originated. The explanation seems to be endosymbiosis, which suggests that eukaryotic cells arose when a very large prokaryote engulfed smaller prokaryotic cells that began to live and Larger Prokaryotic Cell reproduce inside the large cell rather than being destroyed. As the smaller cells took up permanent residence, they came to perform specialized functions for the larger cell, from (perhaps) serving Cell would have flexible membrane. as a nucleus, to performing functions such as food synthesis and oxygen utilization. Many of these endosymbionts enhanced the cell’s versatility and survival. Over time, the engulfed bacteria gave up their ability to live independently and transferred some of their genes to the host cell. The biologist responsible for early consideration of the theory of endosymbiosis is Dr. Lynn Margulis. Using molecular Early techniques, she accumulated convincing evidence of the relanucleus tionships between the organelles of modern eukaryotic cells and the structure of prokaryotes. In many ways, the mitochondrion of eukaryotic cells is something like a tiny cell within a cell. It is capable of independent division, contains a circular chromosome that has bacterial DNA sequences, and has ribosomes that are clearly prokaryotic. Mitochondria also have bacterial membranes and can be inhibited by drugs that affect only bacteria. Chloroplasts likely arose when endosymbiotic cyanobacteria provided their host cells with a built-in feeding mechanism. Margulis also found convincing evidence that eukaryotic cilia Early are the consequence of endosymbiosis between spiral bacteria endoplasmic and the cell membrane of early eukaryotic cells. reticulum As molecular techniques improve, more evidence accumulates for the endosymbiont “theory,” which is now widely Nuclear accepted among evolutionary scientists.

Smaller Prokaryotic Cell

Cells are aerobic bacteria, similar to purple bacteria.

Larger cell engulfs smaller one; smaller one survives and begins an endosymbiotic association.

Smaller bacterium becomes established in its host’s cytoplasm and multiplies; it can utilize aerobic metabolism and increase energy availability for the host. Early mitochondria Ancestral eukaryotic cell develops extensive membrane pouches that become the endoplasmic reticulum and nuclear envelope.

envelope

Photosynthetic bacteria (cyanobacteria) are also engulfed; they develop into chloroplasts. Ancestral cell

Chloroplast

(a) Dr Dr. Lynn Margulis

(b) Protozoa, fungi, animals

Algae, higher plants

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5.2 Form and Function of the Eukaryotic Cell: External Structures

multicellular organisms evolved as individual cells in the organism lost the ability to survive apart from the intact colony. Although a multicellular organism is composed of many cells, it is more than just a disorganized assemblage of  cells like a colony. Rather, it is composed of distinct groups of cells that cannot exist independently of the rest of the body. The cell groupings of multicellular organisms that have a specific function are termed tissues, and groups of tissues make up organs. Looking at modern eukaryotic organisms, we find examples of many levels of cellular complexity (table 5.1). All protozoa, as well as numerous algae and fungi, are unicellular. Truly multicellular organisms are found only among plants and animals and some of the fungi (mushrooms) and algae (seaweeds). Only certain eukaryotes are traditionally studied by microbiologists—primarily the protozoa, the microscopic algae and fungi, and animal parasites, or helminths.

5.1 Learning Outcomes—Can You . . . 1. . . . relate both prokaryotic and eukaryotic cells to the Last Common Ancestor? 2. . . . list the types of eukaryotic microorganisms and denote which are unicellular and which are multicellular?

Intermediate filaments Cell membrane

Cell wall*

Golgi apparatus

Table 5.1 Eukaryotic Organisms Studied in Microbiology Always Unicellular

May Be Unicellular or Multicellular

Always Multicellular

Protozoa

Fungi Algae

Helminths (have unicellular egg or larval forms)

5.2 Form and Function of the Eukaryotic Cell: External Structures The cells of eukaryotic organisms are so varied that no one member can serve as a typical example. Figure 5.2 presents the generalized structure of typical algal, fungal, and protozoan cells. The flowchart on the next page shows the organization of a eukaryotic cell, and compares it to the organization for prokaryotic cells that you already saw in chapter 4. In general, eukaryotic microbial cells have a cytoplasmic membrane, nucleus, mitochondria, endoplasmic reticulum, Golgi apparatus, vacuoles, cytoskeleton, and glycocalyx. A  cell wall, locomotor appendages, and chloroplasts are

Mitochondrion

Rough endoplasmic reticulum with ribosomes

Actin filaments Flagellum* Nuclear membrane with pores Nucleus Lysosome

Nucleolus Glycocalyx*

Fim mbriae Fimbriae

Smooth endoplasmic reticulum G Glycocalyx B acterial Bacterial ch hromosom me chromosome orr nucleoid

Microtubules

Incclusion/ Inclusion/ Gra anule Granule Ce ell wall Cell

Pilus P ilus Chloroplast*

Centrioles*

P lasmid Plasmid Ribosomes Ribosomes

*Structure not present in all cell types

Figure 5.2 Structure of a eukaryotic cell. The figure of a prokaryotic cell from chapter 4 is included here for comparison.

Ou uter Outer me embrane e membrane

Cell Cell (cytoplasmicc) (cytoplasmic) membrane Actin n cytoskeleton

Flagellum

Cyt Cytoplasm Endospore (not shown)

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Structure Flowchart

Eukaryotic cell

External

Appendages Flagella Cilia Glycocalyx Capsules Slimes

Boundary of cell

Cell wall Cytoplasmic membrane Cytoplasm Nucleus

Nuclear envelope Nucleolus Chromosomes

Organelles

Endoplasmic reticulum Golgi apparatus Mitochondria Chloroplasts

Internal

Ribosomes Lysosomes

Ribosomes Cytoskeleton

found only in some groups. In the following sections, we cover the microscopic structure and functions of the eukaryotic cell. As with the prokaryotes, we begin on the outside and proceed inward through the cell.

External

Appendages Flagella Cilia Glycocalyx Capsules Slimes

Locomotor Appendages: Cilia and Flagella Motility allows a microorganism to locate nutrients and to migrate toward positive stimuli such as sunlight; it also permits them to avoid harmful substances and stimuli. Locomotion by means of flagella or cilia is common in protozoa, many algae, and a few fungal and animal cells. Although they share the same name, eukaryotic flagella are much different from those of prokaryotes. The eukaryotic

Microtubules Microfilaments

flagellum is thicker (by a factor of 10), structurally more complex, and covered by an extension of the cell membrane. A single flagellum is a long, sheathed cylinder containing regularly spaced hollow tubules—microtubules—that extend along its entire length (figure 5.3a). A cross section reveals nine pairs of closely attached microtubules surrounding a single central pair. This scheme, called the 9 + 2 arrangement, is pattern of eukaryotic flagella and cilia (figure 5.3b). During locomotion, the adjacent microtubules slide past each other, whipping the flagellum back and forth. Although details of this process are too complex to discuss here, it involves expenditure of energy and a coordinating mechanism in the cell membrane. The placement and number of flagella can be useful in identifying flagellated protozoa and certain algae. Cilia are very similar in overall architecture to flagella, but they are shorter and more numerous (some cells have several thousand). They are found only on a single group of protozoa and certain animal cells. In the ciliated protozoa,

Microtubules

(a)

(b)

Figure 5.3 Microtubules in flagella. (a) Longitudinal section through a flagellum, showing microtubules. (b) A cross section that reveals the typical 9 + 2 arrangement found in both flagella and cilia.

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the cilia occur in rows over the cell surface, where they beat back and forth in regular oarlike strokes (figure 5.4). Such protozoa are among the fastest of all motile cells. On some cells, cilia also function as feeding and filtering structures.

The Glycocalyx Most eukaryotic cells have a glycocalyx, an outermost boundary that comes into direct contact with the environment (see figure 5.2). This structure, which is sometimes called an extracellular matrix, is usually composed of polysaccharides and appears as a network of fibers, a slime layer, or a capsule much like the glycocalyx of prokaryotes. Because of its positioning, the glycocalyx contributes to protection, adherence of cells to surfaces, and reception of signals from other cells and from the environment. The nature of the layer beneath the glycocalyx varies among the several eukaryotic groups. Fungi and most algae have a thick, rigid cell wall surrounding a cell membrane, whereas protozoa, a few algae, and all animal cells lack a cell wall and have only a cell membrane.

(a)

Form and Function of the Eukaryotic Cell: Boundary Structures Boundary of cell

Cell membrane

Cell wall Cytoplasmic membrane

Chitin Cell wall

The Cell Wall The cell walls of fungi and algae are rigid and provide structural support and shape, but they are different in chemical (b)

Oral groove with gullet

Glycoprotein

Mixed glycans

Glycocalyx

Figure 5.5 Cross-sectional views of fungal cell walls.

Macronucleus

Micronucleus

Contractile vacuole

(a)

(b)

composition from prokaryotic cell walls. Fungal cell walls have a thick, inner layer of polysaccharide fibers composed of chitin or cellulose and a thin outer layer of mixed glycans (figure 5.5). The cell walls of algae are quite varied in chemical composition. Substances commonly found among various algal groups are cellulose, pectin,1 mannans,2 and minerals such as silicon dioxide and calcium carbonate.

The Cytoplasmic Membrane

Power stroke

Recovery stroke

Figure 5.4 Structure and locomotion in ciliates. (a) The structure of a simple representative, Holophrya, with a regular pattern of cilia in rows. (b) Cilia beat in coordinated waves, driving the cell forward and backward. View of a single cilium shows that it has a pattern of movement like a swimmer, with a power forward stroke and a repositioning stroke.

The cytoplasmic (cell) membrane of eukaryotic cells is a typical bilayer of phospholipids in which protein molecules are embedded. In addition to phospholipids, eukaryotic membranes also contain sterols of various kinds. Sterols are different from phospholipids in both structure and behavior, as you may recall from chapter 2. Their relative rigidity makes eukaryotic membranes more stable. This strengthening feature is extremely important in those cells that lack a cell wall. Cytoplasmic membranes of eukaryotes are functionally similar to those of prokaryotes, serving as 1. A polysaccharide composed of galacturonic acid subunits. 2. A polymer of the sugar known as mannose.

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selectively permeable barriers. Membranes have extremely sophisticated mechanisms for transporting nutrients in and waste and other products out. You’ll read about these transport systems in prokaryotic membranes in chapter 7, but the systems in prokaryotes and eukaryotes are very similar.

5.2 Learning Outcomes—Can You . . . 3. . . . differentiate between cilia and flagella in eukaryotes, and between flagella in prokaryotes and eukaryotes? 4. . . . describe the important characteristics of a glycocalyx in eukaryotes? 5. . . . list which eukaryotic microorganisms have a cell wall? 6. . . . list similarities and differences between eukaryotic and prokaryotic cytoplasmic membranes?

5.3 Form and Function of the Eukaryotic Cell: Internal Structures Cytoplasm Nucleus

Nuclear envelope Nucleolus Chromosomes

Organelles

Endoplasmic reticulum Golgi apparatus Mitochondria Chloroplasts

Internal

Ribosomes Lysosomes

Ribosomes Cytoskeleton

Microtubules Microfilaments

Unlike prokaryotes, eukaryotic cells contain a number of individual membrane-bound organelles that are extensive enough to account for 60% to 80% of their volume. Endoplasmic reticulum

The Nucleus: The Control Center The nucleus is a compact sphere that is the most prominent organelle of eukaryotic cells. It is separated from the cell cytoplasm by an external boundary called a nuclear envelope. The envelope has a unique architecture. It is composed of two parallel membranes separated by a narrow space, and it is perforated with small, regularly spaced openings, or pores, formed at sites where the two membranes unite (figure 5.6). The nuclear pores are passageways through which macromolecules migrate from the nucleus to the cytoplasm and vice versa. The nucleus contains a matrix called the nucleoplasm and a granular mass, the nucleolus, that stains more intensely than the immediate surroundings because of its RNA content. The nucleolus is the site for ribosomal RNA synthesis and a collection area for ribosomal subunits. The subunits are transported through the nuclear pores into the cytoplasm for final assembly into ribosomes. A prominent feature of the nucleoplasm in stained preparations is a network of dark fibers known as chromatin. Analysis has shown that chromatin actually comprises the eukaryotic chromosomes, large units of genetic information in the cell. The chromosomes in the nucleus of most cells are not readily visible because they are long, linear DNA molecules bound in varying degrees to histone proteins, and they are far too fine to be resolved as distinct structures without extremely high magnification. During mitosis, however, when the duplicated chromosomes are separated equally into daughter cells, the chromosomes themselves become readily visible as discrete bodies (figure 5.7). This happens when the DNA becomes highly condensed by forming coils and supercoils around the histones to prevent the chromosomes from tangling as they are separated into new cells. This process is described in more detail in chapter 9.

Chromatin Nuclear pore

Nuclear pore (a)

Nuclear envelope

Nucleolus

Nucleolus (b)

Nuclear envelope

Figure 5.6 The nucleus. (a) Electron micrograph section of an interphase nucleus, showing its most prominent features. (b) Cutaway threedimensional view of the relationships of the nuclear envelope and pores.

5.3 Form and Function of the Eukaryotic Cell: Internal Structures

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Centrioles Interphase

Chromatin

Cell membrane Nuclear envelope

Prophase

Nucleolus Cytoplasm Daughter cells Cleavage furrow

Spindle fibers Centromere

Telophase

Chromosome Early metaphase

Early telophase

Metaphase

Late anaphase

Early anaphase

(a)

Figure 5.7 Changes in the cell and nucleus that accompany mitosis in a eukaryotic cell such as a yeast. (a) Before mitosis (at interphase), chromosomes are visible only as chromatin. As mitosis proceeds (early prophase), chromosomes take on a fine, threadlike appearance as they condense, and the nuclear membrane and nucleolus are temporarily disrupted. (b) By metaphase, the chromosomes are fully visible as X-shaped structures. The shape is due to duplicated chromosomes attached at a central point, the centromere. Spindle fibers attach to these and facilitate the separation of individual chromosomes during metaphase. Later phases serve in the completion of chromosomal separation and division of the cell proper into daughter cells.

Centromere

(b)

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The nucleus, as you’ve just seen, contains instructions in the form of DNA. Elaborate processes have evolved for transcription and duplication of this genetic material. In addition to mitosis, some cells also undergo meiosis, the process by which sex cells are created. Much of the protein synthesis and other work of the cell takes place outside the nucleus in the cell’s other organelles.

because of large numbers of ribosomes partly attached to its membrane surface. Proteins synthesized on the ribosomes are shunted into the inside space (the lumen) of the RER and held there for later packaging and transport. In contrast to the RER, the SER is a closed tubular network without ribosomes that functions in nutrient processing and in synthesis and storage of nonprotein macromolecules such as lipids.

Endoplasmic Reticulum: A Passageway in the Cell

Golgi Apparatus: A Packaging Machine

The endoplasmic reticulum (ER) is a microscopic series of tunnels used in transport and storage. Two kinds of endoplasmic reticulum are the rough endoplasmic reticulum (RER) (figure 5.8) and the smooth endoplasmic reticulum (SER). Electron micrographs show that the RER originates from the outer membrane of the nuclear envelope and extends in a continuous network through the cytoplasm, even all the way out to the cell membrane. This architecture permits the spaces in the RER, called cisternae (singular = cistern), to transport materials from the nucleus to the cytoplasm and ultimately to the cell’s exterior. The RER appears rough

The Golgi3 apparatus, also called the Golgi complex or body, is the site in the cell in which proteins are modified and then sent to their final destinations. It is a discrete organelle consisting of a stack of several flattened, disc-shaped sacs called cisternae. These sacs have outer limiting membranes and cavities like those of the endoplasmic reticulum, but they do not form a continuous network (figure 5.9). This organelle is always closely associated with the endoplasmic reticulum both in its location and function. At a site where it meets 3. Named for C. Golgi, an Italian histologist who first described the apparatus in 1898.

Nuclear envelope Nuclear pore

Polyribosomes Cistern

(b) Small subunit mRNA (a)

Ribosome

Large subunit

RER membrane Cistern

Protein being synthesized (c)

Figure 5.8 The origin and detailed structure of the rough endoplasmic reticulum (RER). (a) Schematic view of the origin of the RER from the outer membrane of the nuclear envelope. (b) Three-dimensional projection of the RER. (c) Detail of the orientation of a ribosome on the RER membrane.

5.3 Form and Function of the Eukaryotic Cell: Internal Structures

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Nucleolus Ribosome parts

Endoplasmic reticulum

Rough endoplasmic reticulum

Nucleus

Transitional vesicles Transitional vesicles

Golgi apparatus Condensing vesicles

Condensing vesicles Cisternae

Figure 5.9 Detail of the Golgi apparatus. The flattened layers are cisternae. Vesicles enter the upper surface and leave the lower surface.

the Golgi apparatus, the endoplasmic reticulum buds off tiny membrane-bound packets of protein called transitional vesicles that are picked up by the forming face of the Golgi apparatus. Once in the complex itself, the proteins are often modified by the addition of polysaccharides and lipids. The final action of this apparatus is to pinch off finished condensing vesicles that will be conveyed to organelles such as lysosomes or transported outside the cell as secretory vesicles (figure 5.10).

Nucleus, Endoplasmic Reticulum, and Golgi Apparatus: Nature’s Assembly Line As the keeper of the eukaryotic genetic code, the nucleus ultimately governs and regulates all cell activities. But, because the nucleus remains fixed in a specific cellular site, it must direct these activities through a structural and chemical network (figure 5.10). This network includes ribosomes, which originate in the nucleus, and the rough endoplasmic reticulum, which is continuously connected with the nuclear envelope, as well as the smooth endoplasmic reticulum and the Golgi apparatus. Initially, a segment of the genetic code of DNA containing the instructions for producing a protein is copied into RNA and passed out through the nuclear pores directly to the ribosomes on the endoplasmic reticulum. Here, specific proteins are synthesized from the RNA

Secretion by exocytosis

Cell membrane Secretory vesicle

Figure 5.10 The transport process. The cooperation of

organelles in protein synthesis and transport: nucleus → RER → Golgi apparatus → vesicles → secretion.

code and deposited in the lumen (space) of the endoplasmic reticulum. After being transported to the Golgi apparatus, the protein products are chemically modified and packaged into vesicles that can be used by the cell in a variety of ways. Some of the vesicles contain enzymes to digest food inside the cell; other vesicles are secreted to digest materials outside the cell, and yet others are important in the enlargement and repair of the cell wall and membrane. A lysosome is one type of vesicle originating from the Golgi apparatus that contains a variety of enzymes. Lysosomes are involved in intracellular digestion of food particles and in protection against invading microorganisms. They also participate in digestion and removal of cell debris in damaged tissue. Other types of vesicles include vacuoles (vak′-yoo-ohlz), which are membrane-bound sacs containing fluids or solid particles to be digested, excreted, or stored. They are formed in phagocytic cells (certain white blood cells and protozoa) in response to food and other substances that have been engulfed. The contents of a food vacuole are digested through the merger of the vacuole with a lysosome. This merged structure is called a phagosome (figure 5.11). Other types of vacuoles are used in storing reserve food such as fats and glycogen. Protozoa living in freshwater habitats regulate osmotic pressure by means of

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Food particle Lysosomes

Cell membrane Nucleus Golgi apparatus

Engulfment of food

Food vacuole

Formation of food vacuole

chondria appear as round or elongated particles scattered throughout the cytoplasm. The internal ultrastructure reveals that a single mitochondrion consists of a smooth, continuous outer membrane that forms the external contour, and an inner, folded membrane nestled neatly within the outer membrane (figure 5.12). The folds on the inner membrane, called cristae (kris′-te), may be tubular, like fingers, or folded into shelflike bands. The cristae membranes hold the enzymes and electron carriers of aerobic respiration. This is an oxygen-using process that extracts chemical energy contained in nutrient molecules and stores it in the form of high-energy molecules, or ATP. More detailed functions of mitochondria are covered in chapter 8. The spaces around the cristae are filled with a chemically complex fluid called the matrix, which holds ribosomes, DNA, and the pool of enzymes and other compounds involved in the metabolic cycle. Mitochondria (along with chloroplasts) are unique among organelles in that they divide independently of the cell, contain circular strands of DNA, and have prokaryotic-sized 70S ribosomes. These findings have prompted some intriguing speculations on their evolutionary origins (see Insight 5.1). DNA strand 70S ribosomes

Lysosome

Matrix Cristae Merger of lysosome and vacuole Phagosome

Inner membrane (a)

Outer membrane

Digestion Digestive vacuole Cristae (darker lines)

Figure 5.11 The origin and action of lysosomes in

Matrix (lighter spaces)

phagocytosis.

contractile vacuoles, which regularly expel excess water that has diffused into the cell (described later).

Mitochondria: Energy Generators of the Cell Although the nucleus is the cell’s control center, none of the cellular activities it commands could proceed without a constant supply of energy, the bulk of which is generated in most eukaryotes by mitochondria (my″-tohkon′-dree-uh). When viewed with light microscopy, mito-

(b)

Figure 5.12 General structure of a mitochondrion. (a) A three-dimensional projection. (b) An electron micrograph. In most cells, mitochondria are elliptical or spherical, although in certain fungi, algae, and protozoa, they are long and filament-like.

5.3 Form and Function of the Eukaryotic Cell: Internal Structures

Chloroplasts: Photosynthesis Machines Chloroplasts are remarkable organelles found in algae and plant cells that are capable of converting the energy of sunlight into chemical energy through photosynthesis. The photosynthetic role of chloroplasts makes them the primary producers of organic nutrients upon which all other organisms (except certain bacteria) ultimately depend. Another important photosynthetic product of chloroplasts is oxygen gas. Although chloroplasts resemble mitochondria, chloroplasts are larger, contain special pigments, and are much more varied in shape. There are differences among various algal chloroplasts, but most are generally composed of two membranes, one enclosing the other. There is a smooth, outer membrane in addition to an inner membrane. Inside the chloroplast is a third membrane folded into small, disclike sacs called thylakoids that are stacked upon one another into grana. These structures carry the green pigment chlorophyll and sometimes additional pigments as well. Surrounding the thylakoids is a ground substance called the stroma (figure 5.13). The role of the photosynthetic pigments is to absorb and transform solar energy into chemical energy, which is then used during reactions in the stroma to synthesize carbohydrates. We further explore some important aspects of photosynthesis in chapters 8 and 24.

119

to that of prokaryotic ribosomes, described in chapter 4. Both are composed of large and small subunits of ribonucleoprotein (see figure 5.8). By contrast, however, the eukaryotic ribosome (except in the mitochondrion) is the larger 80S variety that is a combination of 60S and 40S subunits. As in the prokaryotes, eukaryotic ribosomes are the staging areas for protein synthesis.

The Cytoskeleton: A Support Network The cytoplasm of a eukaryotic cell is crisscrossed by a flexible framework of molecules called the cytoskeleton (figure 5.14). This framework appears to have several functions, such as Cell membrane Actin filaments Mitochondrion Intermediate filaments Endoplasmic reticulum Microtubule

Ribosomes: Protein Synthesizers In an electron micrograph of a eukaryotic cell, ribosomes are numerous, tiny particles that give a “dotted” appearance to the cytoplasm. Ribosomes are distributed throughout the cell: Some are scattered freely in the cytoplasm and cytoskeleton; others are intimately associated with the rough endoplasmic reticulum as previously described. Still others appear inside the mitochondria and in chloroplasts. Multiple ribosomes are often found arranged in short chains called polyribosomes (polysomes). The basic structure of eukaryotic ribosomes is similar Chloroplast envelope (double membrane)

(a) 70S ribosomes

Stroma matrix

(b)

DNA strand Granum

Thylakoids

Figure 5.13 Detail of an algal chloroplast.

Figure 5.14 The cytoskeleton. (a) Drawing of microtubules, actin filaments, and intermediate filaments. (b) Microtubules are dyed fluorescent green in this micrograph.

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anchoring organelles, moving RNA and vesicles, and permitting shape changes and movement in some cells. The three main types of cytoskeletal elements are actin filaments, intermediate filaments, and microtubules. Actin filaments are long thin protein strands about 7 nanometers in diameter. They are found throughout the cell but are most highly concentrated just inside the cell membrane. Actin filaments are responsible for cellular movements such as contraction, crawling, pinching during cell division, and formation of cellular extensions. Microtubules are long, hollow tubes that maintain the shape of eukaryotic cells without walls and transport substances from one part of a cell to another. The spindle fibers that play an essential role in mitosis are actually microtubules that attach to chromosomes and separate them into daughter cells. As indicated earlier, microtubules are also responsible for the movement of cilia and flagella. Intermediate filaments are ropelike structures that are about 10 nanometers in diameter. (Their name comes from their intermediate size, between actin filaments and microtubules.) Their main role is in structural reinforcement of the cell and of organelles. For example, they support the structure of the nuclear envelope. Table 5.2 summarizes the differences between eukaryotic and prokaryotic cells. Viruses (discussed in chapter 6) are included as well.

Survey of Eukaryotic Microorganisms With the general structure of the eukaryotic cell in mind, let us next examine the amazingly wide range of adaptations that this cell type has undergone. The following sections contain a general survey of the principal eukaryotic microorganisms— fungi, algae, protozoa, and parasitic worms—while also introducing elements of their structure, life history, classification, identification, and importance.

5.3 Learning Outcomes—Can You . . . 7. . . . describe the important component parts of a nucleus? 8. . . . diagram how the nucleus, endoplasmic reticulum, and Golgi apparatus, together with vesicles, act together? 9. . . . explain the function of the mitochondria? 10. . . . discuss the function of chloroplasts and explain which cells contain them and why? 11. . . . explain the importance of ribosomes and differentiate between eukaryotic and prokaryotic types? 12. . . . list and describe the three main fibers of the cytoskeleton?

Table 5.2 The Major Elements of Life and Their Primary Characteristics Function or Structure

Characteristic*

Prokaryotic Cells

Eukaryotic Cells

Viruses**

Genetics

Nucleic acids Chromosomes True nucleus Nuclear envelope

+ + − −

+ + + +

+ − − −

Reproduction

Mitosis Production of sex cells Binary fission

− +/− +

+ + +

− − −

Biosynthesis

Independent Golgi apparatus Endoplasmic reticulum Ribosomes

+ − − +***

+ + + +

− − − −

Respiration

Mitochondria

−

+

−

Photosynthesis

Pigments Chloroplasts

+/− −

+/− +/−

− −

Motility/locomotor structures

Flagella Cilia

+/−*** −

+/− +/−

− −

Shape/protection

Membrane Cell wall Capsule

+ +*** +/−

+ +/− +/−

+/− − (have capsids instead) −

Complexity of function

+

+

+/−

Size (in general)

0.5−3 μm*****

2−100 μm

< 0.2 μm

*+ means most members of the group exhibit this characteristic; − means most lack it; +/− means some members have it and some do not. **Viruses cannot participate in metabolic or genetic activity outside their host cells. ***The prokaryotic type is functionally similar to the eukaryotic, but structurally unique. ****Much smaller and much larger bacteria exist; see Insight 4.3.

5.4 The Kingdom of the Fungi

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A Note About the Taxonomy of Eukaryotic Cells Exploring the origins of eukaryotic cells with molecular techniques has significantly clarified our understanding of relationships among the organisms in Domain Eukarya. The characteristics traditionally used for placing plants, animals, and fungi into separate kingdoms are general cell type, level of organization (body plan), and nutritional type. While it now appears that these criteria often do reflect accurate differences among these organisms and give rise to the same classifications as molecular techniques, in many cases the molecular data point to new and different classifications. Because our understanding of the phylogenetic relationships is still in development, there is not yet a single official system of taxonomy for presenting all of the eukaryotes. This is especially true of the protists (which contain algae and protozoa). Genetic analysis has determined that this group, generally classified at the kingdom level, is far more diverse than previously appreciated and probably should instead be divided into several different kingdoms. Some organisms we call protists are more related to fungi than they are to other protists, for instance. For that reason, most scientists believe that the label “protist” is meaningless, taxonomically. For the purposes of this book and your class, the term is still used as it refers to eukaryotes that are not plants, animals, or fungi. But be aware that the science is still developing.

5.4 The Kingdom of the Fungi Although fungi were originally classified with the green plants (along with algae and bacteria), they were later separated from plants and placed in a group with algae and protozoa (the Protista). Even at that time, however, many microbiologists were struck by several unique qualities of fungi that warranted their being placed into their own separate kingdom, and eventually they were. The Kingdom Fungi, or Myceteae, is large and filled with forms of great variety and complexity. For practical purposes, the approximately 100,000 species of fungi can be divided into two groups: the macroscopic fungi (mushrooms, puffballs, gill fungi) and the microscopic fungi (molds, yeasts). Although the majority of fungi are either unicellular or colonial, a few complex forms such as mushrooms and puffballs are considered multicellular. Cells of the microscopic fungi exist in two basic morphological types: yeasts and hyphae. A yeast cell is distinguished by its round to oval shape and by its mode of asexual reproduction. It grows swellings on its surface called buds, which then become separate cells. Hyphae (hy′-fee) are long, threadlike cells found in the bodies of filamentous fungi, or molds (figure 5.15). Some species form a pseudohypha, a chain of yeasts formed when buds remain attached in a row (figure 5.16). Because of its manner

(a)

Septum

(b)

Septa

Septate hyphae as in Penicillium

Nonseptate hyphae as in Rhizopus

(c)

Figure 5.15 Diplodia maydis, a pathogenic fungus of

corn plants. (a) Scanning electron micrograph of a single colony showing its filamentous texture (24×). (b) Close-up of hyphal structure (1,200×). (c) Basic structural types of hyphae.

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of formation, it is not a true hypha like that of molds. While some fungal cells exist only in a yeast form and others occur primarily as hyphae, a few, called dimorphic, can take either form, depending on growth conditions, such as changing temperature. This variability in growth form is particularly characteristic of some pathogenic molds.

Bud scar

Ribosomes Mitochondrion Endoplasmic reticulum

Fungal Nutrition

Nucleus

All fungi are heterotrophic. They acquire nutrients from a wide variety of organic materials called substrates (figure 5.17). Most fungi are saprobes, meaning that they obtain these substrates from the remnants of dead plants and animals in soil or aquatic habitats. Fungi can also be parasites on the bodies of living animals or plants, although very few fungi absolutely require a living host. In general, the fungus penetrates the substrate and secretes enzymes that reduce it to small molecules that can be absorbed by the cells. Fungi have enzymes for digesting an incredible array of substances, including feathers, hair, cellulose, petroleum products, wood, and rubber. It has been said that every naturally occurring organic material on the earth can be attacked by some type of fungus. Fungi are often found in nutritionally poor or adverse environments. Various fungi thrive in substrates with high salt or sugar content, at relatively high temperatures, and even in snow and glaciers. Their medical and agricultural impact is extensive. A number of species cause mycoses (fungal infections) in animals, and thousands of species are important plant pathogens. Fungal toxins may cause disease in humans, and airborne fungi are a frequent cause of allergies and other medical conditions (Insight 5.2).

Nucleolus Cell wall Cell membrane Golgi apparatus Storage vacuole Fungal (Yeast) Cell (a)

Organization of Microscopic Fungi

(b) Bud

Nucleus

Bud scars

The cells of most microscopic fungi grow in loose associations or colonies. The colonies of yeasts are much like those of bacteria in that they have a soft, uniform texture and appearance. The colonies of filamentous fungi are noted for the striking cottony, hairy, or velvety textures that arise from their microscopic organization and morphology. The woven, intertwining mass of hyphae that makes up the body or colony of a mold is called a mycelium. Although hyphae contain the usual eukaryotic organelles, they also have some unique organizational features. In most fungi, the hyphae are divided into segments by cross walls, or septa, a condition called septate (see figure 5.15c). The nature of the septa varies from solid partitions with no communication between the compartments to partial walls with small pores that allow the flow of organelles and nutrients

Figure 5.16 Microscopic morphology of yeasts. (a) General structure of

(c)

Pseudohypha

a yeast cell, representing major organelles. Note the presence of a cell wall and lack of locomotor organelles. (b) Scanning electron micrograph of the brewer’s, or baker’s, yeast Saccharomyces cerevisiae (21,000×). (c) Formation and release of yeast buds and pseudohypha (a chain of budding yeast cells).

5.4 The Kingdom of the Fungi

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Figure 5.17 Nutritional sources (substrates) for fungi. (a) A fungal mycelium growing on raspberries. The fine hyphal filaments and black sporangia are typical of Rhizopus. (b) The skin of the foot infected by a soil fungus, Fonsecaea pedrosoi.

(a)

(b)

between adjacent compartments. Nonseptate hyphae consist of one long, continuous cell not divided into individual compartments by cross walls. With this construction, the cytoplasm and organelles move freely from one region to another, and each hyphal element can have several nuclei. Hyphae can also be classified according to their particular function. Vegetative hyphae (mycelia) are responsible for the

(a) Vegetative Hyphae

visible mass of growth that appears on the surface of a substrate and penetrates it to digest and absorb nutrients. During the development of a fungal colony, the vegetative hyphae give rise to structures called reproductive, or fertile, hyphae, which branch off a vegetative mycelium. These hyphae are responsible for the production of fungal reproductive bodies called spores. Other specializations of hyphae are illustrated in figure 5.18.

(b) Reproductive Hyphae

Surface hyphae

Spores

Submerged hyphae

Rhizoids Spore Germ tube Substrate Hypha

(c) Germination

(d)

Figure 5.18 Functional types of hyphae using the mold Rhizopus as an example. (a) Vegetative hyphae are those surface and submerged filaments that digest, absorb, and distribute nutrients from the substrate. This species also has special anchoring structures called rhizoids. (b) Later, as the mold matures, it sprouts reproductive hyphae that produce asexual spores. (c) During the asexual life cycle, the free mold spores settle on a substrate and send out germ tubes that elongate into hyphae. Through continued growth and branching, an extensive mycelium is produced. So prolific are the fungi that a single colony of mold can easily contain 5,000 spore-bearing structures. If each of these released 2,000 single spores and if every spore were able to germinate, we would soon find ourselves in a sea of mycelia. Most spores do not germinate, but enough are successful to keep the numbers of fungi and their spores very high in most habitats. (d) Syncephalastrum demonstrates all major stages in the life cycle of a zygomycota.

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INSIGHT 5.2

Eukaryotic Cells and Microorganisms

Two Faces of Fungi

The importance of fungi in the ecological structure of the earth is well recognized. They are essential contributors to complex environments such as soil, and they play numerous beneficial roles as decomposers of organic debris and as partners to plants. Fungi also have great practical importance due to their metabolic versatility. They are productive sources of drugs (penicillin) to treat human infections and other diseases, and they are used in industry to ferment foods and synthesize organic chemicals. The fact that fungi are so widespread also means that they frequently share human living quarters, especially in locations that provide ample moisture and nutrients. Often their presence is harmless and limited to a film of mildew on shower stalls or other moist environments. In some cases, depending on the amount of contamination and the type of mold, these indoor fungi can also give rise to various medical problems. Such common air contaminants as Penicillium, Aspergillus, Cladosporium, and Stachybotrys all have the capacity to give off airborne spores and toxins that, when inhaled, cause a whole spectrum of symptoms sometimes referred to as “sick building syndrome.” (Sick building syndrome can also be caused by nonbiological factors, such as the formaldehyde in carpets and furniture.) The usual source of harmful fungi is the presence of chronically waterdamaged walls, ceilings, and other building materials that have come to harbor these fungi. People exposed to these houses or buildings report symptoms that range from skin rash, flulike reactions, sore throat, and headaches to fatigue, diarrhea, allergies, and immune suppression. Recent reports of sick buildings have been on the rise, affecting thousands of people, and some deaths have been reported in small children. The control of indoor fungi requires correcting the moisture problem, removing the contaminated materials, and decontaminating the living spaces. Mycologists are currently studying the mechanisms of toxic effects with an aim to develop better diagnosis and treatment.

(a)

Fungal Law Enforcement? Biologists are developing some rather imaginative uses for fungi as a way of controlling both the life and death of plants. Government biologists working for narcotic control agencies have unveiled a recent plan to use fungi to kill unwanted plants. The main targets would be plants grown to produce illegal drugs like cocaine and heroin in the hopes of cutting down on these drugs right at the source. A fungus infection (Fusarium) that wiped out 30% of the coca crop in Peru dramatically demonstrated how effective this might be. Since then, at least two other fungi that could destroy opium poppies and marijuana plants have been isolated. Purposefully releasing plant pathogens such as Fusarium into the environment has stirred a great deal of controversy. Critics in South America emphasize that even if the fungus appears specific to a particular plant, there is too much potential for it to switch hosts to food and ornamental plants and wreak havoc with the ecosystem. United States biologists who support the plan of using fungal control agents say that it is not as dangerous as massive spraying with pesticides, and that extensive laboratory tests have

(b)

(a) Stachybotrys chartarum hyphae and spores. (b) Drywall and wallpaper that have been colonized by mold.

proved that the species of fungi being used will be very specific to the illegal drug plants and will not affect close relatives. Some call it biological warfare; others call it an innovative combination of science and law enforcement. What do you think?

5.4 The Kingdom of the Fungi

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Reproductive Strategies and Spore Formation

Asexual Spore Formation

Fungi have many complex and successful reproductive strategies. Most can propagate by the simple outward growth of existing hyphae or by fragmentation, in which a separated piece of mycelium can generate a whole new colony. But the primary reproductive mode of fungi involves the production of various types of spores. (Do not confuse fungal spores with the more resistant, nonreproductive bacterial spores.) Fungal spores are responsible not only for multiplication but also for survival, producing genetic variation, and dissemination. Because of their compactness and relatively light weight, spores are dispersed widely through the environment by air, water, and living things. Upon encountering a favorable substrate, a spore will germinate and produce a new fungus colony in a very short time (see figure 5.18). The fungi exhibit such a marked diversity in spores that they are largely classified and identified by their spores and spore-forming structures. There are elaborate systems for naming and classifying spores, but we won’t cover them. The most general subdivision is based on the way the spores arise. Asexual spores are the products of mitotic division of a single parent cell, and sexual spores are formed through a process involving the fusing of two parental nuclei followed by meiosis.

There are two subtypes of asexual spore, sporangiospores and conidiospores, also called conidia (figure 5.19):

(a) Sporangiospores

(b)

1. Sporangiospores (figure 5.19a) are formed by successive cleavages within a saclike head called a sporangium, which is attached to a stalk, the sporangiophore. These spores are initially enclosed but are released when the sporangium ruptures. 2. Conidiospores, or conidia, are free spores not enclosed by a spore-bearing sac. They develop either by the pinching off of the tip of a special fertile hypha or by the segmentation of a preexisting vegetative hypha. There are many different forms of conidia, illustrated in figure 5.19b.

Sexual Spore Formation Fungi can propagate themselves successfully with their millions of asexual spores. That being the case, what is the function of their sexual spores? The answer lies in important variations that occur when fungi of different genetic makeup combine their genetic material. Just as in plants and animals, this linking of genes from two parents creates offspring with

Conidiospores Arthrospores

Phialospores

Chlamydospores

Sporangium

Blastospores Sporangiophore

(1)

(1)

(2)

(3)

Macroconidia Porospore

Microconidia (2)

(4)

(5)

Figure 5.19 Types of asexual mold spores. (a) Sporangiospores: (1) Absidia, (2) Syncephalastrum. (b) Conidial variations: (1) arthrospores (e.g., Coccidioides), (2) chlamydospores and blastospores (e.g., Candida albicans), (3) phialospores (e.g., Aspergillus), (4) macroconidia and microconidia (e.g., Microsporum), and (5) porospores (e.g., Alternaria).

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combinations of genes different from that of either parent. The offspring from such a union can have slight variations in form and function that are potentially advantageous in the adaptation and survival of their species. The majority of fungi produce sexual spores at some point. The nature of this process varies from the simple fusion of fertile hyphae of two different strains to a complex union of differentiated male and female structures and the development of special fruiting structures. It may be a surprise to discover that the fleshy part of a mushroom is actually a fruiting body designed to protect and help disseminate its sexual spores.

Fungal Identification and Cultivation Fungi are identified in medical specimens by first being isolated on special types of media and then being observed macroscopically and microscopically. Because the fungi are classified into general groups by the presence and type of sexual spores, it would seem logical to identify them in the same way, but sexual spores are rarely if ever detected in the laboratory setting. As a result, the asexual spore-forming structures and spores are usually used to identify organisms to the level of genus and species. Other characteristics that contribute to identification are hyphal type, colony texture and pigmentation, physiological characteristics, and genetic makeup. Even as bacterial and viral identification relies increasingly on molecular techniques, fungi are some of the most strikingly beautiful life forms, and their appearance under the microscope is still heavily relied on to identify them (figure 5.20a,b).

The Roles of Fungi in Nature and Industry Nearly all fungi are free-living and do not require a host to complete their life cycles. Even among those fungi that are pathogenic, most human infection occurs through accidental contact with an environmental source such as soil, water, or dust. Humans are generally quite resistant to fungal infection, except for two main types of fungal pathogens: the

(a)

primary pathogens, which can sicken even healthy persons, and the opportunistic pathogens, which attack persons who are already weakened in some way. So far, about 270 species of fungi have been found to be able to cause human disease. Mycoses (fungal infections) vary in the way the agent enters the body and the degree of tissue involvement (table 5.3). The list of opportunistic fungal pathogens has been increasing in the past few years because of newer medical techniques that keep immunocompromised patients alive. Even socalled harmless species found in the air and dust around us may be able to cause opportunistic infections in patients who already have AIDS, cancer, or diabetes (see Insight 21.2 in chapter 21). Fungi are involved in other medical conditions besides infections (see Insight 5.2). Fungal cell walls give off chemical substances that can cause allergies. The toxins produced by poisonous mushrooms can induce neurological disturbances and even death. The mold Aspergillus flavus synthesizes a potentially lethal poison called aflatoxin, which is the cause of a disease in domestic animals that have eaten grain contaminated with the mold and is also a cause of liver cancer in humans. Fungi pose an ever-present economic hindrance to the agricultural industry. A number of species are pathogenic to field plants such as corn and grain, and fungi also rot fresh produce during shipping and storage. It has been estimated that as much as 40% of the yearly fruit crop is consumed not by humans but by fungi. On the beneficial side, however, fungi play an essential role in decomposing organic matter and returning essential minerals to the soil. They form stable associations with plant roots (mycorrhizae) that increase the ability of the roots to absorb water and nutrients. Industry has tapped the biochemical potential of fungi to produce large quantities of antibiotics, alcohol, organic acids, and vitamins. Some fungi are eaten or used to impart flavorings to food. The yeast Saccharomyces produces the alcohol in beer and wine and the gas that causes bread to rise. Blue cheese, soy sauce, and cured meats derive their unique flavors from the actions of fungi (see chapter 25).

(b)

Figure 5.20 Representative fungi. (a) Circinella, a fungus associated with soil and decaying nuts. (b) Aspergillus, a ubiquitous environmental fungus that can be associated with human disease.

5.5 The Protists

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Table 5.3 Major Fungal Infections of Humans Degree of Tissue Involvement and Area Affected

Name of Infection

Name of Causative Fungus

Outer epidermis

Tinea versicolor

Malassezia furfur

Epidermis, hair, and dermis can be attacked.

Dermatophytosis, also called tinea or ringworm of the scalp, body, feet (athlete’s foot), toenails

Microsporum, Trichophyton, and Epidermophyton

Mucous membranes, skin, nails

Candidiasis, or yeast infection

Candida albicans

Superficial (not deeply invasive)

Systemic (deep; organism enters lungs; can invade other organs) Lung

Lung, skin

Coccidioidomycosis (San Joaquin Valley fever)

Coccidioides immitis dermatitidis

North American blastomycosis (Chicago disease)

Blastomyces

Histoplasmosis (Ohio Valley fever)

Histoplasma capsulatum

Cryptococcosis (torulosis)

Cryptococcus neoformans

Paracoccidioidomycosis (South American

Paracoccidioides brasiliensis

blastomycosis)

5.4 Learning Outcomes—Can You . . . 13. . . . list some general features of fungal anatomy? 14. . . . differentiate among the terms heterotroph, saprobe, and parasite? 15. . . . connect the concepts of fungal hyphae and a mycelium? 16. . . . describe two ways in which fungal spores arise? 17. . . . list two detrimental and two beneficial activities of fungi (from the viewpoint of humans)?

5.5 The Protists The algae and protozoa have been traditionally combined into the Kingdom Protista. The two major taxonomic categories of this kingdom are Subkingdom Algae and Subkingdom

(a)

(b)

Protozoa. Although these general types of microbes are now known to occupy several kingdoms, it is still useful to retain the concept of a protist as any unicellular or colonial organism that lacks true tissues. We will only briefly mention algae, as they do not cause human infections for the most part.

The Algae: Photosynthetic Protists The algae are a group of photosynthetic organisms usually recognized by their larger members, such as seaweeds and kelps. In addition to being beautifully colored and diverse in appearance, they vary in length from a few micrometers to 100 meters. Algae occur in unicellular, colonial, and filamentous forms, and the larger forms can possess tissues and simple organs. Figure 5.21 depicts various types of algae. Algal cells as a group exhibit all of the eukaryotic organelles. The most noticeable of these are the chloroplasts, which contain, in addition to the

(c)

Figure 5.21 Representative microscopic algae. (a) Spirogyra, a colonial filamentous form with spiral chloroplasts. (b) A collection of beautiful algae called diatoms shows the intricate and varied structure of their silica cell walls. (c) Pfiesteria piscicida. Although it is free-living, it is known to parasitize fish and release potent toxins that kill fish and sicken humans.

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green pigment chlorophyll, a number of other pigments that create the yellow, red, and brown coloration of some groups. Algae are widespread inhabitants of fresh and marine waters. They are one of the main components of the large floating community of microscopic organisms called plankton. In this capacity, they play an essential role in the aquatic food web and produce most of the earth’s oxygen. Other algal habitats include the surface of soil, rocks, and plants, and several species are even hardy enough to live in hot springs or snowbanks. Animal tissues would be rather inhospitable to algae, so algae are rarely infectious. One exception is Prototheca, an unusual nonphotosynthetic alga, which has been associated with skin and subcutaneous infections in humans and animals. The primary medical threat from algae is due to a type of food poisoning caused by the toxins of certain marine algae. During particular seasons of the year, the overgrowth of these motile algae imparts a brilliant red color to the water, which is referred to as a “red tide.” When intertidal animals feed, their bodies accumulate toxins given off by the algae that can persist for several months. Paralytic shellfish poisoning is caused by eating exposed clams or other invertebrates. It is marked by severe neurological symptoms and can be fatal. Ciguatera is another serious intoxication caused by algal toxins that have accumulated in fish such as bass and mackerel. Cooking does not destroy the toxin, and there is no antidote. Several episodes of a severe infection caused by Pfiesteria piscicida, a toxic algal form, have been reported over the past several years in the United States. The disease was first reported in fish and was later transmitted to humans. This newly identified species occurs in at least 20 forms, including spores, cysts, and amoebas (see figure 5.21c), that can release potent toxins. Both fish and humans develop neurological symptoms and bloody skin lesions. The cause of the epidemic has been traced to nutrient-rich agricultural runoff water that promoted the sudden “bloom” of Pfiesteria. These microbes first attacked and killed millions of fish and later people whose occupations exposed them to fish and contaminated water.

Biology of the Protozoa If a poll were taken to choose the most engrossing and vivid group of microorganisms, many biologists would choose the protozoa. Although their name comes from the Greek for “first animals,” they are far from being simple, primitive organisms. The protozoa constitute a very large group (about 65,000 species) of creatures that although single-celled, have startling properties when it comes to movement, feeding, and behavior. Although most members of this group are harmless, free-living inhabitants of water and soil, a few species are parasites collectively responsible for hundreds of millions of infections of humans each year. Before we consider a few examples of important pathogens, let us examine some general aspects of protozoan biology, remembering that the term “protozoan” is more of a convenience than an accurate taxonomic designation. As we describe them in the next paragraph, you will see why they are categorized together. It is because of their similar physical characteristics rather than their genetic relatedness, as it turns out.

Case File 5

Continuing the Case

Shortly after the 2005 shellfish harvesting closure, the Oregon Harmful Algal Bloom Monitoring Project was initiated. The project monitors water at five locations along the Oregon coast, retrieving samples every week or two (depending on the site) and examining each sample for the presence of algal species that produce domoic acid or saxitoxin. When sudden blooms lead to high levels of harmful algae, specific harvesting controls can be instituted. In Oregon, beaches are closed to clamming when domoic acid levels reach 20 parts per million (ppm) in randomly selected clams. Projects like this operate throughout the United States to ensure the safety of harvested seafood. Officials try to keep harvest control measures as geographically limited and short-lived as possible. On June 21, 2006, due in part to ongoing water sampling by the Oregon Harmful Bloom Monitoring Project, the entire Oregon coast was opened to razor clamming for the first time in 4 years (although short stretches of beach were temporarily closed later in the summer). ◾ Several months after beaches are closed to clamming, the same beaches can be declared safe and reopened. Why are unsafe clams later deemed safe?

Protozoan Form and Function Most protozoan cells are single cells containing the major eukaryotic organelles except chloroplasts. Their organelles can be highly specialized for feeding, reproduction, and locomotion. The cytoplasm is usually divided into a clear outer layer called the ectoplasm and a granular inner region called the endoplasm. Ectoplasm is involved in locomotion, feeding, and protection. Endoplasm houses the nucleus, mitochondria, and food and contractile vacuoles. Some ciliates and flagellates4 even have organelles that work somewhat like a primitive nervous system to coordinate movement. Because protozoa lack a cell wall, they have a certain amount of flexibility. Their outer boundary is a cell membrane that regulates the movement of food, wastes, and secretions. Cell shape can remain constant (as in most ciliates) or can change constantly (as in amoebas). Certain amoebas (foraminiferans) encase themselves in hard shells made of calcium carbonate. The size of most protozoan cells falls within the range of 3 to 300 μm. Some notable exceptions are giant amoebas and ciliates that are large enough (3 to 4 mm in length) to be seen swimming in pond water.

Nutritional and Habitat Range Protozoa are heterotrophic and usually require their food in a complex organic form. Free-living species scavenge dead plant or animal debris and even graze on live cells of bacteria and algae. Some species have special feeding structures such as oral grooves, which carry food particles into a passageway or gullet that packages 4. The terms ciliate and flagellate are common names of protozoan groups that move by means of cilia and flagella.

5.5 The Protists

the captured food into vacuoles for digestion. Some protozoa absorb food directly through the cell membrane. Parasitic species live on the fluids of their host, such as plasma and digestive juices, or they can actively feed on tissues. Although protozoa have adapted to a wide range of habitats, their main limiting factor is the availability of moisture. Their predominant habitats are fresh and marine water, soil, plants, and animals. Even extremes in temperature and pH are not a barrier to their existence; hardy species are found in hot springs, ice, and habitats with low or high pH. Many protozoa can convert to a resistant, dormant stage called a cyst.

Styles of Locomotion Except for one group (the Apicomplexa), protozoa can move through fluids by means of pseudopods (“false feet”), flagella, or cilia. A few species have both pseudopods (also called pseudopodia) and flagella. Some unusual protozoa move by a gliding or twisting movement Undulating membrane

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that does not appear to involve any of these locomotor structures. Pseudopods are blunt, branched, or long and pointed, depending on the particular species. The flowing action of the pseudopods results in amoeboid motion, and pseudopods also serve as feeding structures in many amoebas. (The structure and behavior of flagella and cilia were discussed in the first section of this chapter.) Flagella vary in number from one to several, and in certain species they are attached along the length of the cell by an extension of the cytoplasmic membrane called the undulating membrane (figure 5.22a). In most ciliates, the cilia are distributed over the entire surface of the cell in characteristic patterns. Because of the tremendous variety in ciliary arrangements and functions, ciliates are among the most diverse and awesome cells in the biological world. In certain protozoa, cilia line the oral groove and function in feeding; in others, they fuse together to form stiff props that serve as primitive rows of walking legs.

Flagellum

Nucleus

Pseudopod

Food vacuole

Waterexpelling vacuole

(a)

(b) Cytostome

Food vacuoles

Nucleus

Cilia

(c)

(d)

Figure 5.22 Examples of the four types of locomotion in protozoa. (a) Mastigophora: Trichomonas vaginalis, displaying flagella. (b) Sarcodina: Amoeba, with pseudopods. (c) Ciliophora: Stentor, displaying cilia. (d) Sporozoan: Cryptosporidium. Sporozoa have no specialized locomotion organelles.

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Life Cycles and Reproduction Most protozoa can be recognized in their motile feeding stage called the trophozoite. This is a stage that requires ample food and moisture to remain active. A large number of species are also capable of entering into a dormant, resting stage called a cyst when conditions in the environment become unfavorable for growth and feeding. During encystment, the trophozoite cell rounds up into a sphere, and its ectoplasm secretes a tough, thick cuticle around the cell membrane (figure 5.23). Because cysts are more resistant than ordinary cells to heat, drying, and chemicals, they can survive adverse periods. They can be dispersed by air currents and may even be an important factor in the spread of diseases such as amoebic dysentery. If provided with moisture and nutrients, a cyst breaks open and releases the active trophozoite. The life cycles of protozoans vary from simple to complex. Several protozoan groups exist only in the trophozoite state. Many alternate between a trophozoite and a cyst stage, depending on the conditions of the habitat. The life cycle of a parasitic protozoan dictates its mode of transmission to other hosts. For example, the flagellate Trichomonas vaginalis causes a common sexually transmitted disease. Because it does not form cysts, it is more delicate and must be transmitted by intimate contact between sexual partners. In contrast, intestinal pathogens such as Entamoeba histolytica and Giardia lamblia form cysts and are readily transmitted in contaminated water and foods.

All protozoa reproduce by relatively simple, asexual methods, usually mitotic cell division. Several parasitic species, including the agents of malaria and toxoplasmosis, reproduce asexually by multiple fission inside a host cell. Sexual reproduction also occurs during the life cycle of most protozoa. Ciliates participate in conjugation, a form of genetic exchange in which two cells fuse temporarily and exchange micronuclei. This process of sexual recombination yields new and different genetic combinations that can be advantageous in evolution.

Classification of Selected Important Protozoa As has been stated, taxonomists have problems classifying protozoa. They are very diverse and frequently frustrate attempts to generalize or place them in neat groupings. We will use a common and simple system of four groups, based on method of motility, mode of reproduction, and stages in the life cycle, summarized here and in figure 5.22. The Mastigophora (Also Called Zoomastigophora) Motility is primarily by flagella alone or by both flagellar and amoeboid motion. Single nucleus. Sexual reproduction, when present, by syngamy; division by longitudinal fission. Several parasitic forms lack mitochondria and Golgi apparatus. Most species form cysts and are free-living; the group also includes several parasites. Some species

Figure 5.23 The general life cycle exhibited by many protozoa. All

Trophozoite (active, feeding stage)

protozoa have a trophozoite form, but not all produce cysts.

Trophozoite is reactivated

Dr y

Cell rounds up, loses motility

k lac g, in nts rie ut

of n

Cyst wall breaks open

Mo

nu

Early cyst wall formation

is t

tr i e

nt

u

re

s

re

st

or

,

ed

Mature cyst (dormant, resting stage)

5.5 The Protists

are found in loose aggregates or colonies, but most are solitary. Members include: Trypanosoma and Leishmania, important blood pathogens spread by insect vectors; Giardia, an intestinal parasite spread in water contaminated with feces; Trichomonas, a parasite of the reproductive tract of humans spread by sexual contact (figure 5.22a). The Sarcodina (Amoebas) Cell form is primarily an amoeba (figure 5.22b). Major locomotor organelles are pseudopods, although some species have flagellated reproductive states. Asexual reproduction by fission. Two groups have an external shell; mostly uninucleate; usually encyst. Most amoebas are free-living and not infectious; Entamoeba is a pathogen or parasite of humans; shelled amoebas called foraminifera and radiolarians are responsible for chalk deposits in the ocean. The Ciliophora (Ciliated) Trophozoites are motile by cilia; some have cilia in tufts for feeding and attachment; most develop cysts; have both macronuclei and micronuclei; division by transverse fission; most have a definite mouth and feeding organelle; show relatively advanced behavior (figure 5.22c). The majority of ciliates are freeliving and harmless. The Apicomplexa (Sporozoa) Motility is absent in most cells except male gametes. Life cycles are complex, with welldeveloped asexual and sexual stages. Sporozoa produce special sporelike cells called sporozoites (figure 5.22d) following sexual reproduction, which are important in transmission of infections; most form thick-walled zygotes called oocysts; entire group is parasitic. Plasmodium, the

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most prevalent protozoan parasite, causes 100 million to 300 million cases of malaria each year worldwide. It is an intracellular parasite with a complex cycle alternating between humans and mosquitoes. Toxoplasma gondii causes an acute infection (toxoplasmosis) in humans, which is acquired from cats and other animals. Just as with the prokaryotes and other eukaryotes, protozoans that cause disease produce symptoms in different organ systems. These diseases are covered in chapters 18 through 23.

Protozoan Identification and Cultivation The unique appearance of most protozoa makes it possible for a knowledgeable person to identify them to the level of genus and often species by microscopic morphology alone. Characteristics to consider in identification include the shape and size of the cell; the type, number, and distribution of locomotor structures; the presence of special organelles or cysts; and the number of nuclei. Medical specimens taken from blood, sputum, cerebrospinal fluid, feces, or the vagina are smeared directly onto a slide and observed with or without special stains. Occasionally, protozoa are cultivated on artificial media or in laboratory animals for further identification or study.

Important Protozoan Pathogens Although protozoan infections are very common, they are actually caused by only a small number of species often restricted geographically to the tropics and subtropics (table 5.4). In this section, we look at an example of a very

Table 5.4 Major Pathogenic Protozoa Protozoan

Disease

Reservoir/Source

Entamoeba histolytica

Amoebiasis (intestinal and other symptoms)

Humans, water and food

Naegleria, Acanthamoeba

Brain infection

Free-living in water

Balantidiosis (intestinal and other symptoms)

Pigs, cattle

Giardia lamblia

Giardiasis (intestinal distress)

Animals, water and food

Trichomonas vaginalis

Trichomoniasis (vaginal symptoms)

Human

Trypanosoma brucei, T. cruzi

Trypanosomiasis (intestinal distress and widespread organ damage)

Animals, vector-borne

Leishmania donovani, L. tropica, L. brasiliensis

Leishmaniasis (either skin lesions or widespread involvement of internal organs)

Animals, vector-borne

Plasmodium vivax, P. falciparum, P. malariae

Malaria (cardiovascular and other symptoms)

Human, vector-borne

Toxoplasma gondii

Toxoplasmosis (flulike illness)

Animals, vector-borne

Cryptosporidium

Cryptosporidiosis (intestinal and other symptoms)

Free-living, water, food

Cyclospora cayetanensis

Cyclosporiasis (intestinal and other symptoms)

Water, fresh produce

Amoeboid Protozoa

Ciliated Protozoa Balantidium coli

Flagellated Protozoa

Apicomplexan Protozoa

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common protozoan disease that illustrates some of the main features of protozoan diseases. The study of protozoa and helminths is sometimes called parasitology. Although a parasite can technically be any organism that obtains food and other requirements at the expense of a host, the term parasite is most often used to denote protozoan and helminth pathogens.

Pathogenic Flagellate: Trypanosomes Trypanosomes are protozoa belonging to the genus Trypanosoma (try-pan″oh-soh′-mah). The two most important representatives are T. brucei and T. cruzi, species that are closely related but geographically restricted. Trypanosoma brucei occurs in Africa, where it causes approximately 35,000 new cases of sleeping sickness each year (see chapter 19). Trypanosoma cruzi, the cause of Chagas disease,5 is endemic to South and Central America, where it infects several million people a year. Both species have long, crescent-shaped cells with a single flagellum that is sometimes attached to the cell body by an undulating membrane. Both are found in the blood during infection and are transmitted by blood-sucking vectors. We use T. cruzi to illustrate the phases of a trypanosomal life cycle and to demonstrate the complexity of parasitic relationships. The trypanosome of Chagas disease relies on the close relationship of a warm-blooded mammal and an insect that feeds on mammalian blood. The mammalian hosts are numerous, including dogs, cats, opossums, armadillos, and foxes. The vector is the reduviid (ree-doo′-vee-id) bug, an insect that is sometimes called the “kissing bug” because of its habit of biting its host at the corner of the mouth. Transmission occurs from bug to mammal and from mammal to bug, but usually not from mammal to mammal, except across the placenta during pregnancy. The general phases of this cycle are presented in figure 5.24. The trypanosome trophozoite multiplies in the intestinal tract of the reduviid bug and is harbored in the feces. The bug seeks a host and bites the mucous membranes, usually of the eye, nose, or lips. As it fills with blood, the bug defecates on the bite site and contaminates it with feces containing the trypanosome. Ironically, the victims themselves inadvertently contribute to the entry of the microbe by scratching the bite wound. The trypanosomes ultimately become established and multiply in muscle and white blood cells. Periodically, these parasitized cells rupture, releasing large numbers of new trophozoites into the blood. Eventually, the trypanosome can spread to many systems, including the lymphoid organs, heart, liver, and brain. Manifestations of the resultant disease range from mild to very severe and include fever, inflammation, and heart and brain damage. In many cases, the disease has an extended course and can cause death. 5. Named for Carlos Chagas, the discoverer of T. cruzi.

Reduviid bug

(a) Infective Trypanosome

Cycle in Human Dwellings

(b) Mode of infection Cycle in the Wild

Figure 5.24 Cycle of transmission in Chagas disease. Trypanosomes (inset a) are transmitted among mammalian hosts and human hosts by means of a bite from the kissing bug (inset b).

Infective Amoebas: Entamoeba Several species of amoebas cause disease in humans, but probably the most common disease is amoebiasis, or amoebic dysentery, caused by Entamoeba histolytica (see chapter 22). This microbe is widely distributed in the world, from northern zones to the tropics, and is nearly always associated with humans. Amoebic dysentery is the fourth most common protozoan infection in the world. This microbe has a life cycle quite different from the trypanosomes in that it does not involve multiple hosts and a blood-sucking vector. It lives part of its cycle as a trophozoite and part as a cyst. Because the cyst is the more resistant form and can survive in water and soil for several weeks, it is the more important stage for transmission. The primary way that people become infected is by ingesting food or water contaminated with human feces.

5.6 The Parasitic Helminths

5.5 Learning Outcomes—Can You . . . 18. . . . use protozoan characteristics to explain why they are informally placed into a single group? 19. . . . list three means of locomotion by protozoa? 20. . . . explain why a cyst stage might be useful? 21. . . . give an example of a disease caused by each of the four types of protozoa?

5.6 The Parasitic Helminths Tapeworms, flukes, and roundworms are collectively called helminths, from the Greek word meaning worm. Adult animals are usually large enough to be seen with the naked eye, and they range from the longest tapeworms, measuring up to about 25 m in length, to roundworms

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less than 1 mm in length. Nevertheless, they are included among microorganisms because of their infective abilities and because the microscope is necessary to identify their eggs and larvae. On the basis of body type, the two major groups of parasitic helminths are the flatworms (Phylum Platyhelminthes) and the roundworms (Phylum Aschelminthes, also called nematodes). Flatworms have a very thin, often segmented body plan (figure 5.25), and roundworms have an elongate, cylindrical, unsegmented body (figure 5.26). The flatworm group is subdivided into the cestodes, or tapeworms, named for their long, ribbonlike arrangement, and the trematodes, or flukes, characterized by flat, ovoid bodies. Not all flatworms and roundworms are parasites by nature; many live free in soil and water. Because most disease-causing helminths spend part of their lives in the gastrointestinal tract, they are discussed in chapter 22.

Cuticle

Scolex

Proglottid

(a)

Suckers

Immature eggs

Fertile eggs

(b) 1 cm

Oral sucker Esophagus

Pharynx

Figure 5.25 Parasitic flatworms. (a) A cestode (tapeworm), showing the scolex;

Intestine

long, tapelike body; and magnified views of immature and mature proglottids (body segments). (b) Actual tapeworm. (c) The structure of a trematode (liver fluke). Note the suckers that attach to host tissue and the dominance of reproductive and digestive organs. (d) Actual liver fluke.

Ventral sucker Cuticle Vas deferens Uterus Ovary Testes Seminal receptacle

1 mm (c)

Excretory bladder

(d)

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Eukaryotic Cells and Microorganisms Copulatory spicule Anus Mouth

Female

Eggs

Male

Selfinfection

Cuticle Mouth Fertile egg

Autoinoculation Crossinfection

Figure 5.26 The life cycle of the pinworm, a roundworm. Eggs are the infective stage and are transmitted by unclean hands. Children frequently reinfect themselves and also pass the parasite on to others.

General Worm Morphology All helminths are multicellular animals equipped to some degree with organs and organ systems. In parasitic helminths, the most developed organs are those of the reproductive tract, with some degree of reduction in the digestive, excretory, nervous, and muscular systems. In particular groups, such as the cestodes, reproduction is so dominant that the worms are reduced to little more than a series of flattened sacs filled with ovaries, testes, and eggs (see figure 5.25a,b). Not all worms have such extreme adaptations as cestodes, but most have a highly developed reproductive potential, thick cuticles for protection, and mouth glands for breaking down the host’s tissue (figure 5.25c).

Life Cycles and Reproduction The complete life cycle of helminths includes the fertilized egg (embryo), larval, and adult stages. In the majority of helminths, adults derive nutrients and reproduce sexually in a host’s body. In nematodes, the sexes are separate and usually different in appearance; in trematodes, the sexes can be either separate or hermaphroditic, meaning that male and female sex organs are in the same worm; cestodes are generally hermaphroditic. For

a parasite’s continued survival as a species, it must complete the life cycle by transmitting an infective form, usually an egg or larva, to the body of another host, either of the same or a different species. The host in which larval development occurs is the intermediate (secondary) host, and adulthood and mating occur in the definitive (final) host. A transport host is an intermediate host that experiences no parasitic development but is an essential link in the completion of the cycle. In general, sources for human infection are contaminated food, soil, and water or infected animals, and routes of infection are by oral intake or penetration of unbroken skin. Humans are the definitive hosts for many of the parasites listed in table 5.5, and in about half the diseases, they are also the sole biological reservoir. In other cases, animals or insect vectors serve as reservoirs or are required to complete worm development. In the majority of helminth infections, the worms must leave their host to complete the entire life cycle. Fertilized eggs are usually released to the environment and are provided with a protective shell and extra food to aid their development into larvae. Even so, most eggs and larvae are vulnerable to heat, cold, drying, and predators and are destroyed or unable to reach a new host. To counteract this formidable mortality rate, certain worms have adapted a reproductive capacity that borders on the incredible: A single female Ascaris6 can lay 200,000 eggs a day, and a large female can contain over 25 million eggs at varying stages of development! If only a tiny number of these eggs makes it to another host, the parasite will have been successful in completing its life cycle.

A Helminth Cycle: The Pinworm To illustrate a helminth cycle in humans, we use the example of a roundworm, Enterobius vermicularis, the pinworm or seatworm. This worm causes a very common infestation of the large intestine. Worms range from 2 to 12 mm long and have a tapered, curved cylinder shape (see figure 5.26). The condition they cause, enterobiasis, is usually a simple, uncomplicated infection that does not spread beyond the intestine. A cycle starts when a person swallows microscopic eggs picked up from another infected person by direct contact or by touching articles that person has touched. The eggs hatch in the intestine and then release larvae that mature into adult worms within about 1 month. Male and female worms mate, and the female migrates out to the anus to deposit eggs, which cause intense itchiness that is relieved by scratching. Herein lies a significant means of dispersal: Scratching contaminates the fingers, which, in turn, transfer eggs to bedclothes and other inanimate objects. This person becomes a host and a source of eggs and can spread them to others in addition to reinfesting himself. Enterobiasis occurs most often among families and in other close living situations. Its distribution is worldwide among all socioeconomic groups, but it seems to attack younger people more frequently than older ones. 6. Ascaris is a genus of parasitic intestinal roundworms.

5.6 The Parasitic Helminths

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Table 5.5 Examples of Helminths and Their Modes of Transmission Classification

Common Name of Disease or Worm

Life Cycle Requirement

Spread to Humans By

Roundworms Nematodes Intestinal Nematodes Infective in egg (embryo) stage Ascaris lumbricoides Enterobius vermicularis Infective in larval stage Trichinella spiralis Tissue Nematodes Onchocerca volvulus Dracunculus medinensis

Ingestion

Ascariasis Pinworm

Humans Humans

Fecal pollution of soil with eggs Close contact

Trichina worm

Pigs, wild mammals

River blindness Guinea worm

Humans, black flies Humans and Cyclops (an aquatic invertebrate)

Consumption of meat containing larvae Burrowing of larva into tissue Fly bite Ingestion of water containing Cyclops

Blood fluke

Humans and snails

Ingestion of fresh water containing larval stage

Taenia solium

Pork tapeworm

Humans, swine

Diphyllobothrium latum

Fish tapeworm

Humans, fish

Consumption of undercooked or raw pork Consumption of undercooked or raw fish

Flatworms Trematodes Schistosoma japonicum

Cestodes

Helminth Classification and Identification The helminths are classified according to their shape; their size; the degree of development of various organs; the presence of hooks, suckers, or other special structures; the mode of reproduction; the kinds of hosts; and the appearance of eggs and larvae. They are identified in the laboratory by microscopic detection of the adult worm or its larvae and eggs, which often have distinctive shapes or external and internal structures. Occasionally, they are cultured in order to verify all of the life stages.

Distribution and Importance of Parasitic Worms About 50 species of helminths parasitize humans. They are distributed in all areas of the world that support human life. Some worms are restricted to a given geographic region, and many have a higher incidence in tropical areas. This knowledge must be tempered with the realization that jet-age travel, along with human migration, is gradually changing the patterns of worm infections, especially of those species that do not require alternate hosts or special climatic conditions for development. The yearly estimate of worldwide cases numbers in the billions, and these are not confined to developing countries. A conservative estimate places 50 million helminth infections in North America alone. The primary targets are malnourished children.

You have now learned about the variety of organisms that microbiologists study and classify. And as you’ve seen, many such organisms are capable of causing disease. In chapter 6, you’ll learn about the “not-quite-organisms” that can cause disease, namely, viruses.

5.6 Learning Outcomes—Can You . . . 22. . . . list the two major groups of helminths and then the two subgroups of one of these groups? 23. . . . describe a typical helminth lifestyle?

Case File 5

Wrap-Up

A primary reason for the increased number of cases of shellfish illness in the summer months is that algal growth is always greater when supported by warmer water temperatures. In addition, algal blooms often occur when phosphorus and nitrogen, which are common ingredients d in fertilizers, accumulate in the water. Fertilizers used on land leach into the groundwater and eventually find their way to open bodies of water, where they induce abnormally robust growth of algal populations. When algal levels decrease, the toxins eventually leach out of the shellfish, but it can take weeks to months before a beach may be safely reopened. See: Oregon Department of Fish and Wildlife. http://www.dfw.state.or.us/ MRP/shellfish/razorclams/plankton.asp.

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Chapter Summary 5.1 The History of Eukaryotes • Eukaryotes are cells with a nucleus and organelles compartmentalized by membranes. They, like prokaryotes, originated from a primitive cell referred to as the Last Common Ancestor. Eukaryotic cell structure enabled eukaryotes to diversify from single cells into a huge variety of complex multicellular forms. • The cell structures common to most eukaryotes are the cell membrane, nucleus, vacuoles, mitochondria, endoplasmic reticulum, Golgi apparatus, and a cytoskeleton. Cell walls, chloroplasts, and locomotor organs are present in some eukaryote groups. 5.2 Form and Function of the Eukaryotic Cell: External Structures • Microscopic eukaryotes use locomotor organs such as flagella or cilia for moving themselves or their food. • The glycocalyx is the outermost boundary of most eukaryotic cells. Its functions are protection, adherence, and reception of chemical signals from the environment or from other organisms. The glycocalyx is supported by either a cell wall or a cell membrane. • The cytoplasmic (cell) membrane of eukaryotes is similar in function to that of prokaryotes, but it differs in composition, possessing sterols as additional stabilizing agents. 5.3 Form and Function of the Eukaryotic Cell: Internal Structures • The genome of eukaryotes is located in the nucleus, a spherical structure surrounded by a double membrane. The nucleus contains the nucleolus, the site of ribosome synthesis. DNA is organized into chromosomes in the nucleus. • The endoplasmic reticulum (ER) is an internal network of membranous passageways extending throughout the cell. • The Golgi apparatus is a packaging center that receives materials from the ER and then forms vesicles around them for storage or for transport to the cell membrane for secretion. • The mitochondria generate energy in the form of ATP to be used in numerous cellular activities. • Chloroplasts, membranous packets found in plants and algae, are used in photosynthesis.

• Ribosomes are the sites for protein synthesis present in

both eukaryotes and prokaryotes. • The cytoskeleton maintains the shape of cells and pro-

duces movement of cytoplasm within the cell, movement of chromosomes at cell division, and, in some groups, movement of the cell as a unit. 5.4 The Kingdom of the Fungi • The fungi are nonphotosynthetic haploid species with cell walls. They are either saprobes or parasites and may be unicellular, colonial, or multicellular. • All fungi are heterotrophic. • Fungi have many reproductive strategies, including both asexual and sexual. • Fungi have asexual spores called sporangiospores and conidiospores. • Fungal sexual spores enable the organisms to incorporate variations in form and function. • Fungi are often identified on the basis of their microscopic appearance. • There are two categories of fungi that cause human disease: the primary pathogens, which infect healthy persons, and the opportunistic pathogens, which cause disease only in compromised hosts. 5.5 The Protists • The protists are mostly unicellular or colonial eukaryotes that lack specialized tissues. There are two major organism types: the algae and the protozoa. • Algae are photosynthetic organisms that contain chloroplasts with chlorophyll and other pigments. • Protozoa are heterotrophs that usually display some form of locomotion. Most are single-celled trophozoites, and many produce a resistant stage, or cyst. 5.6 The Parasitic Helminths • The Kingdom Animalia has only one group that contains members that are (sometimes) microscopic. These are the helminths or worms. Parasitic members include flatworms and roundworms that are able to invade and reproduce in human tissues.

Multiple-Choice and True-False Questions

Multiple-Choice and True-False Questions

137

Knowledge and Comprehension

Multiple-Choice Questions. Select the correct answer from the answers provided. 1. Both flagella and cilia are found primarily in a. algae. c. fungi. b. protozoa. d. both b and c 2. Features of the nuclear envelope include a. ribosomes. b. a double membrane structure. c. pores that allow communication with the cytoplasm. d. b and c e. all of these 3. The cell wall is found in which eukaryotes? a. fungi c. protozoa b. algae d. a and b

9. Mitochondria likely originated from a. archaea. b. invaginations of the cell membrane. c. bacteria. d. chloroplasts. 10. Most helminth infections a. are localized to one site in the body. b. spread through major systems of the body. c. develop within the spleen. d. develop within the liver.

4. Yeasts are _____ fungi, and molds are _____ fungi. a. macroscopic, microscopic b. unicellular, filamentous c. motile, nonmotile d. water, terrestrial

True-False Questions. If the statement is true, leave as is. If it is false, correct it by rewriting the sentence.

5. Algae generally contain some type of a. spore. c. locomotor organelle. b. chlorophyll. d. toxin. 6. Almost all protozoa have a a. locomotor organelle. c. pellicle. b. cyst stage. d. trophozoite stage. 7. All mature sporozoa are a. parasitic. b. nonmotile.

8. Parasitic helminths reproduce with a. spores. c. mitosis. b. eggs and sperm. d. cysts. e. all of these

11. Prokaryotes and eukaryotes arose from the same kind of primordial cell. 12. Hyphae that are divided into compartments by cross walls are called septate hyphae. 13. The infective stage of a protozoan is the trophozoite. 14. In humans, fungi can only infect the skin. 15. Fungi generally derive nutrients through photosynthesis.

c. carried by vectors. d. both a and b

Critical Thinking Questions

Application and Analysis

These questions are suggested as a writing-to-learn experience. For each question, compose a one- or two-paragraph answer that includes the factual information needed to completely address the question. 1. Construct a chart that reviews the major similarities and differences between prokaryotic and eukaryotic cells. 2. a. Describe the anatomy and functions of each of the major eukaryotic organelles. b. How are flagella and cilia similar? How are they different? c. Compare and contrast the smooth ER, the rough ER, and the Golgi apparatus in structure and function. 3. For what reasons would a cell need a “skeleton”? 4. a. Differentiate between the yeast and hypha types of fungal cell. b. What is a mold? c. What does it mean if a fungus is dimorphic?

5. What is a working definition of a “protist”? 6. a. Briefly outline the characteristics of the four protozoan groups. b. What is an important pathogen in each group? 7. Suggest some ways that one would go about determining if mitochondria and chloroplasts are modified prokaryotic cells. 8. Explain the general characteristics of the protozoan life cycle. 9. What general type of multicellular parasite is composed primarily of thin sacs of reproductive organs? 10. Can you think of a way to determine if a child is suffering from pinworms? Hint: Scotch tape is involved.

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Concept Mapping

Synthesis

Appendix D provides guidance for working with concept maps. 1. Construct your own concept map using the following words as the concepts. Supply the linking words between each pair of concepts.

Golgi apparatus

ribosomes

chloroplasts

flagella

cytoplasm

nucleolus

endospore

Visual Connections

Synthesis

These questions use visual images or previous content to make connections to this chapter’s concepts. 1. From chapter 4, figure 4.25a. You may have seen similar sites to this one. Can you think of two locations you encountered that have shown colorful evidence of microbial growth?

2. From chapter 1, figure 1.13. Which of the groups of organisms from this figure will contain a nucleus? Why?

Angiosperms

Chordates

Gymnosperms

Arthropods Echinoderms

Annelids Mosses

pla

Nematodes

Yeasts

nts

PLANTS

Mollusks

Club fungi

ed

Se

Ferns

(Plantae)

FUNGI

Molds

Flatworms

(Myceteae)

ANIMALS (Animalia) Sponges

Slime molds

Red algae Green algae

Ciliates

First multicellular organisms appeared 0.6 billion years ago.

Flagellates

Brown algae

Amoebas

PROTISTS

PROKARYOTES

EUKARYOTES

(Protista) Diatoms

Apicomplexans

Dinoflagellates Early eukaryotes

First eukaryotic cells appeared ⫾2 billion years ago.

MONERA Archaea

5 kingdoms 2 cell types

Bacteria

Earliest cell

First cells appeared 3–4 billion years ago.

www.connect.microbiology.com Enhance your study of this chapter with study tools and practice tests. Also ask your instructor about the resources available through ConnectPlus, including the media-rich eBook, interactive learning tools, and animations.

An Introduction to the Viruses 6 Case File Did you know that poultry farmers routinely use vaccines to keep their chickens from developing infectious diseases? This is especially true of larger farming operations. Here we describe an incident at a facility that produces vaccines for poultry. On November 25, 2006, a case of salmonellosis in an employee of such a facility was reported to the Maine Department of Health and Human Services (MDHHS). Because a similar case of salmonellosis had been reported 10 days earlier, the MDHHS began an outbreak investigation. Approximately one week prior to the first salmonellosis case, a spill had occurred in a fermentation room at the vaccine production facility, releasing 1 to 1.5 L of a highly concentrated culture of Salmonella enterica serotype Enteritidis (this bacterium is referred to as SE), that was being used in vaccine production. The room was unoccupied at the time of the spill, and afterward it was cleaned by a worker wearing a biohazard suit, hat, booties, mask, and gloves using 5% bleach and a commercial disinfectant effective against SE. That worker later reported the first case of salmonellosis. Following the first two reported cases, the workers in the production area filled out a questionnaire asking about their work routines and whether they had experienced symptoms of salmonellosis (defined as three or more loose, watery stools in a 24-hour period) since November 1, 2006. Of a total of 26 employees who had been working in the room where the spill occurred, 18 reported illness. No illness was seen in the seven workers who had never entered the room. In addition to the cases from the vaccine facility, seven SE isolates from persons presumably unconnected to the plant were submitted to the MDHHS during that same time period. ◾ The employee who originally cleaned the culture spill reported having diarrhea for 1 day but taking no time off work. What is the importance of this fact? ◾ The CDC estimates that the 42,000 cases of salmonellosis reported yearly may be only 10% of the actual number of cases. Why do you think this may be true? Continuing the Case appears on page 157.

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An Introduction to the Viruses

Outline and Learning Outcomes 6.1 The Search for the Elusive Viruses 1. Describe the significance of viruses being recognized as “filterable.” 6.2 The Position of Viruses in the Biological Spectrum 2. Construct arguments on both sides of the “Are viruses living?” debate. 3. Identify better terms for viruses than “alive” or “dead.” 6.3 The General Structure of Viruses 4. Discuss the size of viruses relative to other microorganisms. 5. Describe the function and structure(s) of viral capsids. 6. Distinguish between enveloped and naked viruses. 7. Explain the importance of viral surface proteins, or spikes. 8. Diagram the possible configurations of nucleic acid viruses may possess. 6.4 How Viruses Are Classified and Named 9. Explain why some find it difficult to assign species names to viruses. 10. Demonstrate how family and genus names in viruses are written. 6.5 Modes of Viral Multiplication 11. Diagram the five-step life cycle of animal viruses. 12. Explain what cytopathic effects are. 13. Discuss both persistent and transforming infections. 14. Provide a thorough description of lysogenic and lytic bacteriophage infections. 6.6 Techniques in Cultivating and Identifying Animal Viruses 15. List the three principal purposes of cultivating viruses. 16. Describe three ways in which viruses are cultivated. 6.7 Medical Importance of Viruses 17. Analyze the relative importance of viruses in human infection and disease. 6.8 Other Noncellular Infectious Agents 18. Name at least three noncellular infectious agents besides viruses. 6.9 Treatment of Animal Viral Infections 19. Discuss the primary reason that antiviral drugs are more difficult to design than antibacterial drugs.

6.1 The Search for the Elusive Viruses The discovery of the light microscope made it possible to see firsthand the agents of many bacterial, fungal, and protozoan diseases. But the techniques for observing and cultivating these relatively large microorganisms were useless for viruses. For many years, the cause of viral infections such as smallpox and polio was unknown, even though it was clear that the diseases were transmitted from person to person. The French scientist Louis Pasteur was certainly on the right track when he postulated that rabies was caused by a “living thing” smaller than bacteria, and in 1884 he was able to develop the first vaccine for rabies. Pasteur also proposed the term virus (L. poison) to denote this special group of infectious agents. The first substantial revelations about the unique characteristics of viruses occurred in the 1890s. First, D.  Ivanovski and M. Beijerinck showed that a disease in tobacco was caused by a virus (tobacco mosaic virus). Then, Friedrich Loeffler and Paul Frosch discovered an animal virus that causes foot-and-mouth disease in cattle. These

early researchers found that when infectious fluids from host organisms were passed through porcelain filters designed to trap bacteria, the filtrate remained infectious. This result proved that an infection could be caused by a cell-free fluid containing agents smaller than bacteria and thus first introduced the concept of a filterable virus. Over the succeeding decades, a remarkable picture of the physical, chemical, and biological nature of viruses began to take form. Years of experimentation were required to show that viruses were noncellular particles with a definite size, shape, and chemical composition. Using special techniques, they could be cultured in the laboratory. By the 1950s, virology had grown into a multifaceted discipline that promised to provide much information on disease, genetics, and even life itself (Insight 6.1).

6.1 Learning Outcomes—Can You . . . 1. . . . describe the significance of viruses being recognized as “filterable”?

6.2

INSIGHT 6.1

141

A Positive View of Viruses

Looking at this beautiful tulip, one would never guess that it derives its pleasing appearance from a viral infection. It contains tulip mosaic virus, which alters the development of the plant cells and causes complex patterns of colors in the petals. Aside from this, the virus does not cause severe harm to the plants. Despite the reputation of viruses as cell killers, there is another side of viruses— that of being harmless, and in some cases, even beneficial. Although there is no agreement on the origins of viruses, it is very likely that they have been in existence for billions of years. Virologists are convinced that viruses have been an important force in the evolution of living things. This is based on the fact that they interact with the genetic material of their host cells and that they carry genes from one host to another (transduction). It is convincing to imagine that viruses arose early in the history of cells as loose pieces of genetic material that became dependent nomads, moving from cell to cell. Viruses are also a significant factor in the functioning of many ecosystems. For example, it is documented that seawater can contain 10 million viruses per milliliter. Because viruses are made of the same elements as living cells, it is estimated that the sum of viruses in the ocean represents 270 million metric tons of organic matter. Over the past several years, biomedical experts have been looking at viruses as vehicles to treat infections and disease. Viruses are already essential for production of vaccines to treat

6.2 The Position of Viruses in the Biological Spectrum Viruses are a unique group of biological entities known to infect every type of cell, including bacteria, algae, fungi, protozoa, plants, and animals. Viruses are extremely abundant on our planet. Norwegian ocean waters have been found to contain 60,000 viruses in a single milliliter (less than a thimbleful) of water. Lake water contains many more— as many as 250 million viruses per milliliter. We are just beginning to understand the impact of these huge numbers of viruses in our environment. The exceptional and curious nature of viruses prompts numerous questions, including: Are they organisms; that is, are they alive? What role did viruses play in the evolution of life? What are their distinctive biological characteristics? How can particles so small, simple, and seemingly insignificant be capable of causing disease and death? 5. What is the connection between viruses and cancer?

1. 2. 3. 4.

The Position of Viruses in the Biological Spectrum

viral infections such as influenza, polio, and measles. Vaccine experts have also engineered new types of viruses by combining a less harmful virus such as vaccinia or adenovirus with some genetic material from a pathogen such as herpes simplex. This technique creates a vaccine that provides immunity but does not expose the person to the intact pathogen. Several of these types of vaccines are currently in development. Scientists have recently had important successes using a virus called vesicular stomatitis virus (VSV) to cure cancer. They alter a gene in VSV to make it completely safe for normal cells, and then inject it intravenously. VSV targets and kills tumor cells (in many different kinds of cancers, including brain, prostate, and ovarian cancers) and has even been shown to track down metastatic tumor cells in distant parts of the body. An older therapy getting a second chance involves use of bacteriophages to treat bacterial infections. This technique was tried in the past with mixed success but was abandoned for more efficient antimicrobial drugs. The basis behind the therapy is that bacterial viruses would seek out only their specific host bacteria and would cause complete destruction of the bacterial cell. Newer experiments with animals have demonstrated that this method can control infections as well as traditional drugs can. Some potential applications being considered are adding phage suspension to grafts to control skin infections and to intravenous fluids for blood infections.

In this chapter, we address these questions and many others. The unusual structure and behavior of viruses have led to debates about their connection to the rest of the microbial world. One viewpoint holds that since viruses are unable to multiply independently from the host cell, they are not living things but are more akin to infectious molecules. Another viewpoint proposes that even though viruses do not exhibit most of the life processes of cells, they can direct them and thus are certainly more than inert and lifeless molecules. This view is the predominant one among scientists today. This debate has greater philosophical than practical importance when discussing disease because viruses are agents of disease and must be dealt with through control, therapy, and prevention, whether we regard them as living or not. In keeping with their special position in the biological spectrum, it is best to describe viruses as infectious particles (rather than organisms) and as either active or inactive (rather than alive or dead).

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An Introduction to the Viruses

Viruses are not just agents of disease. They have many positive uses (Insight 6.1). More importantly than that, recent discoveries suggest that viruses have been absolutely vital in forming cells and other life forms as they are today. By infecting other cells, and sometimes influencing their genetic makeup, they have shaped the way cells, tissues, bacteria, plants, and animals have evolved to their present forms. For example, scientists think that anywhere from 35% to 90% of the human genome consists of sequences that come from viruses that have incorporated their genetic material permanently into human DNA. Bacterial DNA contains 10% to 20% viral sequences. As you learn more about how viruses work, you will see how this could happen. Viruses are different from their host cells in size, structure, behavior, and physiology. They are a type of obligate intracellular parasites that cannot multiply unless they invade a specific host cell and instruct its genetic and metabolic machinery to make and release quantities of new viruses. Other unique properties of viruses are summarized in table 6.1.

Table 6.1 Properties of Viruses • Are obligate intracellular parasites of bacteria, protozoa, fungi, algae, plants, and animals. • Are ubiquitous in nature and have had major impact on development of biological life. • Are ultramicroscopic in size, ranging from 20 nm up to 450 nm (diameter). • Are not cells; structure is very compact and economical. • Do not independently fulfill the characteristics of life. • Are inactive macromolecules outside the host cell and active only inside host cells. • Basic structure consists of protein shell (capsid) surrounding nucleic acid core. • Nucleic acid can be either DNA or RNA but not both. • Nucleic acid can be double-stranded DNA, single-stranded DNA, single-stranded RNA, or double-stranded RNA. • Molecules on virus surface impart high specificity for attachment to host cell.

6.2 Learning Outcomes—Can You . . .

• Multiply by taking control of host cell’s genetic material and regulating the synthesis and assembly of new viruses.

2. . . . construct arguments on both sides of the “Are viruses living?” debate? 3. . . . identify better terms for viruses than “alive” or “dead”?

• Lack enzymes for most metabolic processes. • Lack machinery for synthesizing proteins.

BACTERIA CELLS

Rickettsia 0.3 µm Viruses 1. Mimivirus 2. Herpes simplex 3. Rabies 4. HIV 5. Influenza 6. Adenovirus 7. T2 bacteriophage 8. Poliomyelitis 9. Yellow fever

Streptococcus 1 µm

(1)

(2)

450 nm 150 nm 125 nm 110 nm 100 nm 75 nm 65 nm 30 nm 22 nm

Protein Molecule 10. Hemoglobin molecule

E. coli 2 µm long (10) (9)

(8)

15 nm (7)

(3) (6) (4)

(5)

YEAST CELL – 7 µm

Figure 6.1 Size comparison of viruses with a eukaryotic cell (yeast) and bacteria. Viruses range from largest (1) to smallest (9). A molecule of protein (10) is included to indicate proportion of macromolecules.

6.3

(a)

(b)

The General Structure of Viruses

143

(c)

Figure 6.2 Methods of viewing viruses. (a) Negative staining of an orf virus (a type of poxvirus), revealing details of its outer coat. (b) Positive stain of the Ebola virus, a type of filovirus, so named because of its tendency to form long strands. Note the textured capsid. (c) Shadowcasting image of a vaccinia virus.

6.3 The General Structure of Viruses Size Range As a group, viruses represent the smallest infectious agents (with some unusual exceptions to be discussed later in this chapter). Their size relegates them to the realm of the ultramicroscopic. This term means that most of them are so minute (1 month duration) or esophagitis Isosporiasis, intestinal Cryptosporidiosis, chronic intestinal (>1 month duration)

Genitourinary and/or Reproductive Tract

Invasive cervical carcinoma (HPV) Herpes simplex chronic ulcers (>1 month duration)

610

Chapter 20 Infectious Diseases Affecting the Cardiovascular and Lymphatic Systems

Some of the most virulent complications are neurological. Lesions occur in the brain, meninges, spinal column, and peripheral nerves. Patients with nervous system involvement show some degree of withdrawal, persistent memory loss, spasticity, sensory loss, and progressive AIDS dementia. ▶

Causative Agent

HIV is a retrovirus, in the genus lentivirus. Many retroviruses have the potential to cause cancer and produce dire, often fatal diseases and are capable of altering the host’s DNA in profound ways. They are named “retroviruses” because they reverse the usual order of transcription. They contain an unusual enzyme called reverse transcriptase (RT) that catalyzes the replication of double-stranded DNA from singlestranded RNA. The association of retroviruses with their hosts can be so intimate that viral genes are permanently integrated into the host genome. In fact, as you have read in earlier chapters, it has become increasingly evident that retroviral sequences are integral parts of host chromosomes. Not only can this retroviral DNA be incorporated into the host genome as a provirus that can be passed on to progeny cells, but some retroviruses also transform cells and regulate certain host genes. The most prominent human retroviruses are the T-cell lymphotropic viruses I and II (HTLV-I and HTLV-II) and HTLV-III. Type I is associated with leukemia (discussed in a later section) and lymphoma; type III is now called HIV. There are two major types of HIV, namely HIV-1, which is the dominant form in most of the world, and HIV-2. HIV and other retroviruses display structural features typical of enveloped RNA viruses (figure 20.22a). The outermost component is a lipid envelope with transmembrane glycoprotein spikes and knobs that mediate viral adsorption to the host cell. HIV can only infect host cells that present the required receptors, which is a combination receptor consisting of the CD4 marker plus a coreceptor. The virus uses these receptors to gain entrance to several types of leukocytes and tissue cells (figure 20.22b). ▶

the nucleus of the host cell and integrates its DNA into host DNA (see figure 20.23). This latency accounts for the lengthy course of the disease. Despite being described as a “latent” stage, research suggests that new viruses are constantly being produced and new T cells are constantly being manufactured, in an ongoing race that ultimately the host cells lose (in the absence of treatment). The primary effects of HIV infection—those directly due to viral action—are harm to T cells and the central nervous system. The death of T cells and other white blood cells results

GP-120 GP-41 Protease molecule RNA strands Capsid Integrase molecules Reverse transcriptase molecules

(a)

Antireceptor spikes HIV

GP-41

Pathogenesis and Virulence Factors

As summarized in figure 20.23, HIV enters a mucous membrane or the skin and travels to dendritic cells, a type of phagocyte living beneath the epithelium. In the dendritic cell, the virus grows and is shed from the cell without killing it. The virus is amplified by macrophages in the skin, lymph organs, bone marrow, and blood. One of the great ironies of HIV is that it infects and destroys many of the very cells needed to combat it, including the helper (T4 or CD4) class of lymphocytes, monocytes, macrophages, and even B lymphocytes. The virus is adapted to docking onto its host cell’s surface receptors (see figure 20.22). It then induces viral fusion with the cell membrane and creates syncytia. Once the virus is inside the cell, its reverse transcriptase makes its RNA into DNA. Although initially it can produce a lytic infection, in many cells it enters a latent period in

GP-120

(b)

CD4 receptor on white blood cell

Co-receptor on white blood cell

Figure 20.22 The general structure of HIV. (a) The envelope contains two types of glycoprotein (GP) spikes, two identical RNA strands, and several molecules of reverse transcriptase, protease, and integrase encased in a protein capsid. (b) The snug attachment of HIV glycoprotein molecules (GP-41 and GP-120) to their specific receptors on a human cell membrane. These receptors are CD4 and a co-receptor called CCR-5 (fusin) that permit docking with the host cell and fusion with the cell membrane.

20.3 Cardiovascular and Lymphatic System Diseases Caused by Microorganisms

611

Docking and fusion Immune stimulus Steps show activity of one strand of viral DNA.

Reverse transcriptase ssRNA molecules Early ssDNA

Early dsDNA Complete dsDNA

Latent period

Complete ssDNA

mRNA

Translation of viral genes

of viral DNA tion crip s an Tr Provirus integrated into site on host Host DNA chromosome

Capsid assembly

Nucleus 1

2

The virus is adsorbed and endocytosed, and the twin RNAs are uncoated. Reverse transcriptase catalyzes the synthesis of a single complementary strand of DNA (ssDNA). This single strand serves as a template for synthesis of a double strand (ds) of DNA. In latency, dsDNA is inserted into the host chromosome as a provirus.

3

After a latent period, various immune activators stimulate the infected cell, causing reactivation of the provirus genes and production of viral mRNA.

HIV mRNA is translated by the cell’s synthetic machinery into virus components (capsid, reverse transcriptase, spikes), and the viruses are assembled. Budding of mature viruses lyses the infected cell.

Process Figure 20.23 The general multiplication cycle of HIV.

in extreme leukopenia and loss of essential T4 memory clones and stem cells. The viruses also cause formation of giant T cells and other syncytia, which allow the spread of viruses directly from cell to cell, followed by mass destruction of the syncytia. The destruction of T4 lymphocytes paves the way for invasion by opportunistic agents and malignant cells. The central nervous system is affected when infected macrophages cross the blood-brain barrier and release viruses, which then invade nervous tissue. Studies have indicated that some of the viral envelope proteins can have a direct toxic effect on the brain’s glial cells and other cells. The secondary effects of HIV infection are the opportunistic infections and malignancies that occur as the immune

system becomes progressively crippled by viral attack. These are summarized in Insight 20.4. ▶

Transmission

HIV transmission occurs mainly through two forms of contact: sexual intercourse and transfer of blood or blood products (figure 20.24). Babies can also be infected before or during birth, as well as through breast feeding. The mode of transmission is similar to that of hepatitis B virus, except that the AIDS virus does not survive for as long outside the host and it is far more sensitive to heat and disinfectants. And HIV is not transmitted through saliva, as hepatitis B can be.

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Chapter 20 Infectious Diseases Affecting the Cardiovascular and Lymphatic Systems

Infected blood Infected sexual secretions

Blood exposure through needles

HIV Infected white blood cells Direct blood exposure during sexual intercourse or other intimate contact

Semen, vaginal fluid exposure during sexual intercourse

Infected macrophage Epithelial cell

Lacerations

Membrane or skin portal of entry

Microscopic view of process

Dendritic cells underlying skin shelter and amplify virus.

Spread of virus to lymphatic organs, bone marrow, circulation

Figure 20.24 Primary sources and suggested routes of infection by HIV. In general, HIV is spread only by direct and rather specific routes. Because the blood of HIV-infected people harbors high levels of free virus in both very early and very late stages of infection and high levels of infected leukocytes throughout infection, any form of intimate contact involving transfer of blood (trauma, needle sharing) can be a potential source of infection. Semen and vaginal secretions also harbor free virus and infected white blood cells, and thus they are significant factors in sexual transmission. The virus can be isolated from urine, tears, sweat, and saliva but in such small numbers that these fluids are not considered sources of infection. Because breast milk contains significant numbers of leukocytes, neonates who have escaped infection prior to and during birth can still become infected through nursing.

▶

Epidemiology

Since the beginning of the AIDS epidemic in the early 1980s, 25 million people have died worldwide. The best global estimate of the number of individuals currently infected with HIV (in 2007) is 33 million, with approximately 733,000 in the United States. A large number of these people have not yet begun to show symptoms. Due to efforts of many global AIDS initiatives, many more people in the developing world are receiving lifesaving treatments. But the number of new infections is still growing faster than access to drugs: For every two people receiving treatment, five new people are diagnosed. AIDS first became a notifiable disease at the national level in 1984, and it has continued in an epidemic pattern, although the number of new AIDS cases occurring each year

20.3 Cardiovascular and Lymphatic System Diseases Caused by Microorganisms

in the United States has decreased since 1994. Even in the United States, despite treatment advances, HIV infection/ AIDS is the sixth most common cause of death among people ages 25 to 44, although it has fallen out of the top 150 list for causes of death overall. Table 20.1 spells out some shifts in the behaviors that result in HIV infection in the United States. Throughout the course of the epidemic, close to half (47%) of all cases can be traced to male-to-male sexual contact. The big changes are in the percentage of cases being transmitted by heterosexual contact (31% in 2007 vs. 11% culumlatively through 2000). In large metropolitan areas especially, as many as 60% of intravenous drug users (IDUs) can be HIV carriers. Infection from contaminated needles is growing more rapidly than any other mode of transmission, and it is another significant factor in the spread of HIV to the heterosexual population. In most parts of the world, heterosexual intercourse is the primary mode of transmission. In the industrialized world, the overall rate of heterosexual infection has increased dramatically in the past several years, especially in adolescent and young adult women. In the United States, about 31% of HIV infections arise from unprotected sexual intercourse with an infected partner of the opposite sex. Now that donated blood is routinely tested for antibodies to the AIDS virus, transfusions are no longer considered a serious risk. Because there can be a lag period of a few weeks to several months before antibodies appear in an infected person, it is remotely possible to be infected through donated blood. Rarely, organ transplants can carry HIV, so they too should be tested. Other blood products (serum, coagulation factors) were once implicated in AIDS. Thousands of hemophiliacs died from the disease in the 1980s and 1990s. It is now standard practice to heat-treat any therapeutic blood products to destroy all viruses.

Table 20.1 AIDS Cases in the United States by Exposure Category**

Exposure Category

Cumulative Percentage of New AIDS Cases Through 2000

Percentage of New AIDS Cases in 2007

Male-to-male sexual contact

46

47

Injection drug use

25

17

6

5

Heterosexual contact

11

31

Other*

11

11

Male-to-male sexual contact and injection drug use

*Includes hemophilia, blood transfusion, perinatal, and risk not reported or identified. **Data from the Centers for Disease Control and Prevention.

613

A small percentage of AIDS cases occur in people without apparent risk factors. This does not mean that some other unknown route of spread exists. Factors such as patient denial, unavailability of history, death, or uncooperativeness make it impossible to explain every case. We should note that not everyone who becomes infected or is antibody-positive develops AIDS. About 1% of people who are antibody-positive remain free of disease, indicating that functioning immunity to the virus can develop. Any person who remains healthy despite HIV infection is termed a nonprogressor. These people are the object of intense scientific study. Some have been found to lack the cytokine receptors that HIV requires. Others are infected by a weakened virus mutant. Treatment of HIV-infected mothers with a simple antiHIV drug has dramatically decreased the rate of maternalto-infant transmission of HIV during pregnancy. Current treatment regimens result in a transmission rate of approximately 11%, with some studies of multidrug regimens claiming rates as low as 5%. Evidence suggests that giving mothers protease inhibitors can reduce the transmission rate to around 1%. (Untreated mothers pass the virus to their babies at the rate of 33%.) The cost of perinatal prevention strategies (approximately $1,000 per pregnancy) and the scarcity of medical counseling in underserved areas has led to an increase in maternal transmission of HIV in developing parts of the world, at the same time that the developed world has seen a marked decrease. Medical and dental personnel are not considered a high-risk group, although several hundred medical and dental workers are known to have acquired HIV or become antibody-positive as a result of clinical accidents. A health care worker involved in an accident in which gross inoculation with contaminated blood occurs (as in the case of a needlestick) has a less than 1 in 1,000 chance of becoming infected. We should emphasize that transmission of HIV will not occur through casual contact or routine patient care procedures and that universal precautions for infection control (see chapter 13) were designed to give full protection for both worker and patient. ▶

Culture and Diagnosis

First, let’s define some terms. A person is diagnosed as having HIV infection if he or she has tested positive for the human immunodeficiency virus. This diagnosis is not the same as having AIDS. In late 2006, the CDC issued new recommendations that HIV testing become much more routine. The guidelines call for testing all patients accessing health care facilities and for HIV testing to be included in the routine panel of prenatal screening for pregnant women. In both cases, patients can opt out of the test, although no separate consent will be solicited besides the general consent for medical care. Most viral testing is based on detection of antibodies specific to the virus in serum or other fluids, which allows for the rapid, inexpensive screening of large numbers of samples.

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Chapter 20 Infectious Diseases Affecting the Cardiovascular and Lymphatic Systems

Testing usually proceeds at two levels. The initial screening tests include the older ELISA and newer latex agglutination and rapid antibody tests. Although these tests are largely accurate, around 1% of results are false positives, and they always require followup with a more specific test called Western blot analysis (see p. 502). This test detects several different anti-HIV antibodies and can usually rule out false positive results. Another inaccuracy can be false negative results that occur when testing is performed before the onset of detectable antibody production. To rule out this possibility, persons who test negative but feel they may have been exposed should be tested a second time 3 to 6 months later. Blood and blood products are sometimes tested for HIV antigens (rather than for HIV antibodies) to close the window of time between infection and detectable levels of antibodies during which contamination could be missed by antibody tests. In the United States, people are diagnosed with AIDS if they meet the following criteria: (1) they are positive for the virus, and (2) they fulfill one of these additional criteria: • They have a CD4 (helper T cell) count of fewer than 200 cells per microliter of blood. • Their CD4 cells account for fewer than 14% of all lymphocytes. • They experience one or more of a CDC-provided list of AIDS-defining illnesses (ADIs). The list of ADIs is long and includes opportunistic infections such as Pneumocystis jiroveci pneumonia and Cryptosporidium diarrhea; neoplasms such as Kaposi’s sarcoma and invasive cervical cancer; and other conditions such as wasting syndrome (see Insight 20.4). ▶

Prevention

Avoidance of sexual contact with infected persons is a cornerstone of HIV prevention. Abstaining from sex is an obvious prevention method, although those who are sexually active can also take steps to decrease their risk. Epidemiologists cannot overemphasize the need to screen prospective sex partners and to follow a monogamous sexual lifestyle. And monogamous or not, a sexually active person should consider every partner to be infected unless proven otherwise. This may sound harsh, but it is the only sure way to avoid infection during sexual encounters. Barrier protection (condoms) should be used when having sex with anyone whose HIV status is not known with certainty to be negative. Although avoiding intravenous drugs is an obvious deterrent, many drug addicts do not, or cannot, choose this option. In such cases, risk can be decreased by not sharing syringes or needles or by cleaning needles with bleach and then rinsing before another use. From the very first years of the AIDS epidemic, the potential for creating a vaccine has been regarded as slim, because the virus presents many seemingly insurmountable problems. Among them, HIV becomes latent in cells; its cell surface antigens mutate rapidly; and although it does elicit

immune responses, it is apparently not completely controlled by them. In view of the great need for a vaccine, however, none of those facts has stopped the medical community from moving ahead. Currently, multiple potential HIV vaccines are in clinical trials. Two very promising vaccines have failed to protect humans in clinical trials—the latest one tested in 2007 actually increased the chance of getting HIV in certain people. One of the problems seems to be that these vaccines are developed and then tested in primates, which is a problem since primates have not been successfully infected with HIV, but only with simian immunodeficiency virus, or SIV. It is closely related to HIV but apparently different enough that it gives misleading results with medicines meant for humans. That obstacle may have been overcome, as in late 2009 scientists announced that they had found a hybrid virus that can infect some types of primates and act like HIV. The next time a vaccine goes to human trials it may be that those results will more closely mirror the positive results in the animal model. A growing group of scientists is arguing for a completely different, and deceptively simple, preventive approach. The news of their strategy often has headlines like “We Can Wipe Out HIV Completely.” It sounds outrageous, but it is theoretically true. Their approach is to test everyone possible in all populations, and when you find all the people who are HIV-positive, treat them aggressively. We know that if we treat people with the drugs described in the next section, we can make them noninfectious. HIV would no longer be transmitted. It would be a massive effort—and cost a lot of money—but once we did it in a comprehensive way and everyone who was HIV-positive eventually died, HIV would be eliminated from the human population. Stay tuned to see how the world authorities who would have to come together for such an effort will respond to such an idea. ▶

Treatment

It must be clearly stated: There is no cure for HIV. None of the therapies do more than prolong life or diminish symptoms. Clear-cut guidelines exist for treating people who test HIV-positive. These guidelines are updated regularly. The most recent update involves beginning treatment much earlier than previously. Until now, recommendations called for beginning aggressive antiviral chemotherapy after AIDS manifested itself. The newer recommendations call for treatment to begin soon after HIV diagnosis. In addition to antiviral chemotherapy, HIV-positive persons should receive a wide array of drugs to prevent or treat a variety of opportunistic infections and other ADIs such as wasting disease. These treatment regimens vary according to each patient’s profile and needs. The first effective drugs developed were the synthetic nucleoside analogs (reverse transcriptase inhibitors) azidothymidine (AZT), didanosine (ddI), lamivudine (Epivir) (3TC), and stavudine (d4T). They interrupt the HIV multiplication cycle by mimicking the structure of actual nucleosides and being added to viral DNA by reverse transcriptase. Because these drugs lack all of the correct binding sites for

20.3 Cardiovascular and Lymphatic System Diseases Caused by Microorganisms

of its cycle. This therapy has been successful in reducing viral load to undetectable levels and facilitating the improvement of immune function. It has also reduced the incidence of viral drug resistance, because the virus would have to undergo three separate mutations simultaneously, at nearly impossible odds. Patients who are HIV-positive but asymptomatic can remain healthy with this therapy as well. The primary drawbacks are high cost, toxic side effects, drug failure due to patient noncompliance, and an inability to completely eradicate the virus. Although we opened this section by stating “There is no cure for HIV,” there have been some promising advances. In 2007, an HIV-positive man received a bone marrow transplant from a person who was known to possess two copies of a gene that prevents HIV from invading lymphocytes. The gene from the donor continued a mutation that eliminated the T-cell co-receptor for HIV on T cells. As late as 2009 the recipient was still free of virus. That strategy is not likely to be an answer for worldwide HIV treatment, as bone marrow transplants would be too drastic to treat the millions of HIV-positive people in

further DNA synthesis, viral replication and the viral cycle are terminated (figure 20.25a). Other reverse transcriptase inhibitors that are not nucleosides are nevirapine and efavirenz (Sustiva), both of which bind to the enzyme and restructure it. Another important class of drugs is the protease inhibitors (figure 20.25c), which block the action of the HIV enzyme (protease) involved in the final assembly and maturation of the virus. Examples of these drugs include indinavir (Crixivan), ritonavir (Norvir), and amprenavir (Agenerase). Another class of drugs called integrase inhibitors provide a means to stop virus multiplication (figure 20.25d). One of the latest additions to the arsenal is enfuvirtide (Fuzeon), a drug classified as a fusion inhibitor. It prevents the virus from fusing with the membrane of target cells, thereby stopping infection altogether (figure 20.25b). A regimen that has proved to be extremely effective in controlling AIDS and inevitable drug resistance is HAART, short for highly active antiretroviral therapy. By combining two reverse transcriptase inhibitors and one protease inhibitor in a “cocktail,” the virus is interrupted in two different phases

Location of reaction

Fusion inhibitor

External to cell Cytoplasm Nucleus

Reverse transcriptase ssRNA molecules

Receptors

Viral RNA

Viral DNA No complete viral DNA

Reverse AZT transcriptase

(a) and (b) Fusion inhibitors prevent docking of the virus to host cells. A prominent group of drugs (AZT, ddI, 3TC) are nucleoside analogs that inhibit reverse transcriptase. They are inserted in place of the natural nucleotide by reverse transcriptase but block further action of the enzyme and synthesis of viral DNA. Non-nucleoside RT inhibitors are also in use.

Virus cannot produce new infections.

HIV integrase

dsDNA of HIV

Defective virus

Nuclear membrane Integrase inhibitor

Uncut viral proteins

Nuc

leu

s

Host DNA

Protease inhibitor

HIV protease

(c) Protease inhibitors plug into the active sites on HIV protease.This enzyme is necessary to cut elongate HIV protein strands and produce functioning smaller protein units. Because the enzyme is blocked, the proteins remain uncut, and abnormal defective viruses are formed.

(d) Integrase inhibitors are a class of experimental drugs that attach to the enzyme required to splice the dsDNA from HIV into the host genome. This will prevent formation of the provirus and block future virus multiplication in that cell.

Figure 20.25 Mechanisms of action of anti-HIV drugs.

615

Integration site for viral DNA

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Chapter 20 Infectious Diseases Affecting the Cardiovascular and Lymphatic Systems

the world, and the donor genotype (two copies of the relevant gene) is very rare. But research continues into ways to exploit the knowledge gained in this hallmark experiment. One researcher is pursuing a gene therapy approach to redesign the T cells of infected patients so that they no longer have this receptor, hoping to eliminate the infection.

Disease Table 20.11 HIV Infection and AIDS

Causative Organism(s)

Human immunodeficiency virus 1 or 2

Most Common Modes of Transmission

Direct contact (sexual), parenteral (blood-borne), vertical (perinatal and via breast milk)

Virulence Factors

Attachment, syncytia formation, reverse transcriptase, high mutation rate

Culture/Diagnosis

Initial screening for antibody followed by Western blot confirmation of antibody

Prevention

Avoidance of contact with infected sex partner, contaminated blood, breast milk

Treatment

HAART (reverse transcriptase inhibitors plus protease inhibitors), Fuzeon, nonnucleoside RT inhibitors

Adult T-Cell Leukemia Leukemia is the general name for at least four different malignant diseases of the white blood cell–forming elements originating in the bone marrow. Some forms of leukemia are acute and others are chronic. Leukemias have many causes, only two of which are thought to be viral. The retrovirus HTLV-I is associated with a form of leukemia called adult T-cell leukemia. The signs and symptoms of all leukemias are similar and include easy bruising or bleeding, paleness, fatigue, and recurring minor infections. These symptoms are associated with the underlying pathologies of anemia, platelet deficiency, and immune dysfunction brought about by the disturbed lymphocyte ratio and function. In some cases of adult T-cell leukemia, cutaneous T-cell lymphoma is the prime clinical manifestation, accompanied by dermatitis, with thickened, scaly, ulcerative, or tumorous skin lesions. Other complications are lymphadenopathy and dissemination of the tumors to the lung, spleen, and liver. The possible mechanisms by which retroviruses stimulate cancer are not entirely clear. One hypothesis is that the virus carries an oncogene that, when spliced into a host’s chromosome and triggered by various carcinogens, can

Case File 20

Wrap-Up

Despite treatment with rifampin, ciprofloxacin, and clindamycin, as well as with anthrax immunoglobulin, the drum maker died about 2 weeks later. Postexposure prophylaxis was given to eight persons, including the patient’s immediate family, the main supplier of the skins, a person who assisted with the drum making, and a hospital worker. This incident was very similar to two 2006 cases in which drum makers in New York City and Scotland contracted anthrax while scraping animal hides for drumheads. In all three cases, the hides were imported from Africa, where anthrax is endemic. See: Health Protection Agency. 2008. Investigations following a death from anthrax.

immortalize the cell and deregulate the cell division cycle. One of HTLV’s genetic targets seems to be the gene and receptor for interleukin-2, a potent stimulator of T cells. Adult T-cell leukemia was first described by physicians working with a cluster of patients in southern Japan. Later, a similar clinical disease was described in Caribbean immigrants. In time, it was shown that these two diseases were the same. Although more common in Japan, Europe, and the Caribbean, a small number of cases occur in the United States. The disease is not highly transmissible; studies among families show that repeated close or intimate contact is required. Because the virus is thought to be transferred in infected blood cells, blood transfusions and blood products are potential agents of transmission. Intravenous drug users could spread it through needle sharing. Treatment may include a number of antineoplastic drugs, radiation therapy, and transplants. Alpha-interferon has been used with some effectiveness.

Disease Table 20.12 Adult T-Cell Leukemia

Disease

Adult T-cell leukemia

Causative Organism(s)

HTLV-I

Most Common Modes of Transmission

Unclear—blood-borne transmission implicated

Virulence Factors

Induction of malignant state

Culture/ Diagnosis

Differential blood count followed by histological examination of excised lymph node tissue

Prevention

–

Treatment

Antineoplastic drugs, interferon alpha

20.3 Cardiovascular and Lymphatic System Diseases Caused by Microorganisms

20.3 Learning Outcomes—Can You . . . 4. . . . list the possible causative agents, modes of transmission, virulence factors, diagnostic techniques, and prevention/treatment for the two forms of endocarditis? 5. . . . discuss what series of events may lead to septicemia and how it should be prevented and treated? 6. . . . list the possible causative agents, modes of transmission, virulence factors, diagnostic techniques, and prevention/treatment for cardiovascular system infections that have only one infectious cause? These are: plague, tularemia, Lyme disease, and infectious mononucleosis. 7. . . . discuss factors that distinguish hemorrhagic and nonhemorrhagic fever diseases?

617

8. . . . list the possible causative agents, modes of transmission, virulence factors, diagnostic techniques, and prevention/treatment for hemorrhagic fever diseases? 9. . . . list the possible causative agents, modes of transmission, virulence factors, diagnostic techniques, and prevention/treatment for nonhemorrhagic fever diseases? 10. . . . discuss all aspects of malaria, with special emphasis on epidemiology? 11. . . . describe what makes anthrax a good agent for bioterrorism and list the important presenting signs to look for in patients? 12. . . . discuss how the epidemiology of HIV infection in the United States has changed over time and why? 13. . . . discuss the epidemiology of HIV infection in the developing world?

▶ Summing Up

Taxonomic Organization Summing up Microorganisms Causing Disease in the Cardiovascular and Lymphatic System Microorganism Gram-positive endospore-forming bacteria Bacillus anthracis Gram-positive bacteria Staphylococcus aureus Streptococcus pyogenes Streptococcus pneumoniae Gram-negative bacteria Yersinia pestis Francisella tularensis Borrelia burgdorferi Brucella abortus, B. suis Coxiella burnetii Bartonella henselae Bartonella quintana Ehrlichia chaffeensis, E. phagocytophila, E. ewingii Neisseria gonorrhoeae Rickettsia rickettsii DNA viruses Epstein-Barr virus RNA viruses Yellow fever virus Dengue fever virus Ebola and Marburg viruses Lassa fever virus Chikungunya virus Retroviruses Human immunodeficiency virus 1 and 2 Human T-cell lymphotropic virus I Protozoa Plasmodium falciparum, P. vivax, P. ovale, P. malariae

Disease

Chapter Location

Anthrax

Anthrax, p. 606

Acute endocarditis Acute endocarditis Acute endocarditis

Endocarditis, p. 588 Endocarditis, p. 588 Endocarditis, p. 588

Plague Tularemia Lyme disease Brucellosis Q fever Cat-scratch disease Trench fever Ehrlichiosis Acute endocarditis Rocky Mountain spotted fever

Plague, p. 590 Tularemia, p. 592 Lyme disease, p. 593 Nonhemorrhagic fever diseases, p. 599 Nonhemorrhagic fever diseases, p. 600 Nonhemorrhagic fever diseases, p. 600 Nonhemorrhagic fever diseases, p. 601 Nonhemorrhagic fever diseases, p. 601 Endocarditis, p. 588 Nonhemorrhagic fever diseases, p. 601

Infectious mononucleosis

Infectious mononucleosis, p. 596

Yellow fever Dengue fever Ebola and Marburg hemorrhagic fevers Lassa fever Hemorrhagic fever

Hemorrhagic fevers, p. 597 Hemorrhagic fevers, p. 597 Hemorrhagic fevers, p. 598 Hemorrhagic fevers, p. 599 Hemorrhagic fevers, p. 598

HIV infection and AIDS Adult T-cell leukemia

HIV infection and AIDS, p. 608 Leukemias, p. 616

Malaria

Malaria, p. 602

INFECTIOUS DISEASES AFFECTING The Cardiovascular and Lymphatic Systems

Nonhemorrhagic Fever Diseases

Endocarditis

Brucella abortus Brucella suis Coxiella burnetii Bartonella henselae Bartonella quintana Ehrlichia chaffeensis Ehrlichia phagocytophila Ehrlichia ewingii

Various bacteria

Plague

Yersinia pestis

Septicemia

Various bacteria Various fungi

Infectious Mononucleosis

Epstein-Barr virus

Malaria

Plasmodium species Tularemia

Francisella tularensis Anthrax

Bacillus anthracis Lyme Disease

Borrelia burgdorferi HIV Infection and AIDS

Human immunodeficiency virus 1 or 2 Hemorrhagic Fever Diseases

Yellow fever virus Dengue fever virus Ebola virus Marburg virus Lassa fever virus Chikungunya virus

Leukemia

Human T-cell lymphotropic virus I

Helminths Bacteria Viruses Protozoa Fungi

System Summary Figure 20.26 618

Chapter Summary

619

Chapter Summary 20.1 The Cardiovascular and Lymphatic Systems and Their Defenses • The cardiovascular system is composed of the blood vessels and the heart. It provides tissues with oxygen and nutrients and carries away carbon dioxide and waste products. • The lymphatic system is a one-way passage, returning fluid from the tissues to the cardiovascular system. The cardiovascular system is highly protected from microbial infection, as it is not an open body system and it contains many components of the host’s immune system. 20.2 Normal Biota of the Cardiovascular and Lymphatic Systems • At the present time we believe that the cardiovascular and lymphatic systems contain no normal biota. 20.3 Cardiovascular and Lymphatic System Diseases Caused by Microorganisms • Endocarditis: An inflammation of the endocardium, usually due to an infection of the valves of the heart. • Acute Endocarditis: Most often caused by Staphylococcus aureus, group A streptococci, Streptococcus pneumoniae, and Neisseria gonorrhoeae. • Subacute Forms of Endocarditis: Almost always preceded by some form of damage to the heart valves or by congenital malformation. Alpha-hemolytic streptococci, such as Streptococcus sanguis, S. oralis, and S. mutans, are most often responsible; normal biota can also colonize abnormal valves. • Septicemias: Occur when organisms are actively multiplying in the blood. Most caused by bacteria, to a lesser extent by fungi. • Plague: Can manifest in three different ways: Pneumonic plague is a respiratory disease; bubonic plague causes inflammation and necrosis of the lymph nodes; septicemic plague is the result of multiplication of bacteria in the blood. Yersinia pestis is the causative organism. Fleas are principal agents in transmission of the bacterium. • Tularemia: Causative agent is a facultative intracellular gram-negative bacterium called Francisella tularensis. Disease is often called rabbit fever. • Lyme Disease: Caused by Borrelia burgdorferi. Syndrome mimics neuromuscular and rheumatoid conditions. B. burgdorferi is a unique spirochete transmitted primarily by lxodes ticks. • Infectious Mononucleosis: Vast majority of cases are caused by the herpesvirus Epstein-Barr virus (EBV). Cellmediated immunity can control the infection, but people usually remain chronically infected. • Hemorrhagic Fever Diseases: Extreme fevers often accompanied by internal hemorrhaging. Hemorrhagic fever diseases described here are caused by RNA enveloped viruses in one of three families: Arenaviridae, Filoviridae, and Flaviviridae. • Yellow Fever: Caused by an arbovirus, a singlestranded RNA flavivirus transmitted by the mosquito Aedes aegypti.

• Dengue Fever: Caused by a single-stranded RNA flavi-

•

• •

•

•

•

virus, also carried by Aedes mosquitoes. Mild infection is most common; a form called dengue hemorrhagic shock syndrome can be lethal. • Ebola and Marburg viruses are filoviruses (Family Filoviridae) endemic to Central Africa. Virus in the bloodstream leads to extensive capillary fragility and disruption of clotting. • The Lassa Fever virus is an arenavirus found in West Africa. Reservoir of the virus is a rodent found in Africa called the multimammate rat. Nonhemorrhagic Fever Diseases: Characterized by high fever without the capillary fragility that leads to hemorrhagic symptoms. • Brucellosis: Also called Malta fever, undulant fever, Bang’s disease. Genus Brucella contains tiny, aerobic gram-negative coccobacilli. Two species cause this disease in humans: B. abortus (in cattle) and B. suis (in pigs). • Q Fever: Caused by Coxiella burnetii, a very small pleomorphic gram-negative bacterium and intracellular parasite. C. burnetii harbored by wide assortment of vertebrates and arthropods, especially ticks. However, humans acquire infection mainly by environmental contamination and airborne transmission. • Cat-Scratch Disease: Bartonella henselae is causative agent. Infection connected with being clawed or bitten by a cat. • Trench Fever: Causative agent, Bartonella quintana, is carried by lice. Highly variable symptoms can include a 5- to 6-day fever, leg pains, headache, chills, and muscle aches. Ehrlichioses: There are four tick-borne, fever-producing diseases caused by members of the genus Ehrlichia. Rocky Mountain Spotted Fever: Another tick-borne disease; causes a distinctive rash. Caused by Rickettsia rickettsii. Malaria: Symptoms are malaise, fatigue, vague aches, and nausea, followed by bouts of chills, fever, and sweating. Symptoms occur at 48- or 72-hour intervals, as a result of synchronous rupturing of red blood cells. Causative organisms are Plasmodium species: P. malariae, P. vivax, P. falciparum, and P. ovale. Carried by Anopheles mosquito. Anthrax: Exhibits primary symptoms in various locations: skin (cutaneous anthrax), lungs (pulmonary anthrax), gastrointestinal tract, central nervous system (anthrax meningitis). Caused by Bacillus anthracis, grampositive endospore-forming rod found in soil. HIV Infection and AIDS: Symptoms directly tied to the level of virus in the blood vs. the level of T cells in the blood. • HIV is a retrovirus (genus lentivirus). Contains reverse transcriptase, which catalyzes the replication of double-stranded DNA from single-stranded RNA. Retroviral DNA incorporated into the host genome as provirus that can be passed on to progeny cells in latent state.

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Chapter 20 Infectious Diseases Affecting the Cardiovascular and Lymphatic Systems • Destruction of T4 lymphocytes paves way for invasion

• Adult T-Cell Leukemia: Leukemia is general name for at

by opportunistic agents and malignant cells. • HIV transmission occurs mainly through sexual intercourse and transfer of blood or blood products.

least four different malignant diseases of the white blood cell-forming elements of the bone marrow. Retrovirus HTLV-I is associated with one form of leukemia called adult T-cell leukemia.

Multiple-Choice and True-False

Knowledge and Comprehension

Multiple-Choice Questions. Select the correct answer from the answers provided. 1. When bacteria flourish and grow in the bloodstream, this is referred to as a. viremia. c. septicemia. b. bacteremia. d. fungemia. 2. Which of the following diseases is caused by a retrovirus? a. Lassa fever c. anthrax b. cat-scratch disease d. adult T-cell leukemia 3. The plague bacterium, Yersinia pestis, is transmitted mainly by a. mosquitoes. c. dogs. b. fleas. d. birds. 4. Rabbit fever is caused by a. Yersinia pestis. c. Borrelia burgdorferi. b. Francisella tularensis. d. Chlamydia bunnyensis. 5. A distinctive bull’s-eye rash results from a tick bite transmitting a. Lyme disease. c. Q fever. b. tularemia. d. Rocky Mountain spotted fever.

9. Wool-sorter’s disease is caused by a. Brucella abortus. c. Coxiella burnetii. b. Bacillus anthracis. d. rabies virus. 10. Which of the following is not a hemorrhagic fever? a. Lassa fever c. Ebola fever b. Marburg fever d. trench fever True-False Questions. If the statement is true, leave as is. If it is false, correct it by rewriting the sentence. 11. Brucellosis can be transmitted to humans by drinking contaminated milk. 12. Respiratory tract infection with Bartonella henselae is considered an AIDS-defining condition. 13. Lyme disease is caused by Rickettsia rickettsii.

6. Cat-scratch disease is caused by a. Coxiella burnetii. c. Bartonella quintana. b. Bartonella henselae. d. Brucella abortus.

14. Yellow fever is caused by a protozoan transmitted by fleas.

7. The bite of the Lone Star tick, Ixodes scapularis, can cause a. ehrlichioses. d. both a and b. b. Lyme disease. e. both b and c. c. trench fever.

Critical Thinking Questions

8. Cat-scratch disease is effectively treated with a. rifampin. c. amoxicillin. b. penicillin. d. acyclovir.

15. HIV in the United States is mainly transmitted via male homosexual sex.

Application and Analysis

These questions are suggested as a writing-to-learn experience. For each question, compose a one- or two-paragraph answer that includes the factual information needed to completely address the question. 1. What is endotoxic shock? 2. Explain how eradicating mosquitoes could make dengue fever worse. 3. Describe the infectious cycle of HIV. 4. Describe the life cycle of the malarial parasite, including the significant events of sexual and asexual reproduction. 5. What criteria are used in the United States to diagnose a person with AIDS? 6. a. What are retroviruses? Where does the name come from? b. Name some retroviruses implicated in human diseases.

7. a. What are the different locations in the human body that anthrax infection can be exhibited? b. Which of these are the most common forms of the disease? c. What organism(s) cause this disease? 8. Use the terms prevalence and incidence (chapter 13) to explain how better treatment options have led to a higher prevalence of AIDS in the world. 9. Provide some possible scientific explanations about why there are people who are HIV-positive but remain healthy and never develop AIDS—so-called nonprogressors? 10. What characteristics make tularemia a potential bioweapon?

Concept Mapping

Concept Mapping

621

Synthesis

Appendix D provides guidance for working with concept maps. 1. Provide the missing concepts in this map.

Protozoa

RNA viruses

cause

cause

Gram-negative bacteria cause Lyme disease

which may be trasmitted via tularemia

Visual Connections

Synthesis

These questions use visual images or previous content to make connections to this chapter’s concepts. 1. a. From chapter 14, figure 14.15. Imagine that the WBCs shown in this illustration are unable to control the microorganisms. Could the change that has occurred in the vessel wall help the organism spread to other locations? If so, how? b. If the organisms are able to survive phagocytosis, how could that impact the progress of this disease? Explain your answer. Endothelial cell Blood vessel

Margination

Diapedesis

Neutrophils

Tissue space

Chemotaxis

Chemotactic factors

(a)

(b)

www.connect.microbiology.com Enhance your study of this chapter with study tools and practice tests. Also ask your instructor about the resources available through ConnectPlus, including the media-rich eBook, interactive learning tools, and animations.

Infectious Diseases Affecting the Respiratory System 21 Case File Have you even been on a mission trip with your church or youth group? Each year, thousands of Americans travel to other countries, or to disaster areas within their own country (such as New Orleans after Hurricane Katrina), where they pitch in to perform all kinds of ordinary, but important, manual tasks, such as simple construction, renovation, or flood cleanup. For one such mission trip, a group of church volunteers from Pennsylvania and Virginia traveled to a church in Nueva San Salvador. A total of 35 volunteers went to El Salvador, traveling in three groups between January 3 and February 20, 2008. El Salvador didn’t turn out very well. Twenty of the volunteers came down with a serious respiratory disease resembling acute influenza within 3 to 25 days of arriving in El Salvador. To try to diagnose the disease and figure out how the patients had acquired it, public health officials began investigating the activities of all the volunteers, those affected by the illness as well as those unaffected. The volunteers had helped clean indoor and outdoor renovation sites, install electrical and plumbing components, build additional rooms onto the church, replace the roof, and excavate the septic tank. In addition, each of the mission groups had taken one day off during their stay to visit a local beach or lake. ◾ What diseases might be included in the differential diagnosis for this condition? ◾ When considering possible diseases, would the geographical location have any influence on your choices? Continuing the Case appears on page 648.

Outline and Learning Outcomes 21.1 The Respiratory Tract and Its Defenses 1. Draw or describe the anatomical features of the respiratory tract. 2. List the natural defenses present in the respiratory tract. 21.2 Normal Biota of the Respiratory Tract 3. List the types of normal biota presently known to occupy the respiratory tract. 21.3 Upper Respiratory Tract Diseases Caused by Microorganisms

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The Respiratory Tract and Its Defenses

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4. List the possible causative agents, modes of transmission, virulence factors, diagnostic techniques, and prevention/ treatment for each of the diseases of the upper respiratory tract. These are: rhinitis, sinusitis, otitis media, pharyngitis, and diphtheria. 5. Identify which disease is often caused by a mixture of microorganisms. 6. Identify two bacteria that can cause dangerous pharyngitis cases. 21.4 Diseases Caused by Microorganisms Affecting Both the Upper and Lower Respiratory Tracts 7. List the possible causative agents, modes of transmission, virulence factors, diagnostic techniques, and prevention/ treatment for each of the diseases infecting both the upper and lower respiratory tracts. These are: pertussis, RSV disease, and influenza. 8. Compare and contrast antigenic drift and antigenic shift in influenza viruses. 21.5 Lower Respiratory Tract Diseases Caused by Microorganisms 9. List the possible causative agents, modes of transmission, virulence factors, diagnostic techniques, and prevention/ treatment for each of the diseases infecting the lower respiratory tract. These are: tuberculosis, community-acquired pneumonia, and nosocomial pneumonia. 10. Discuss the problems associated with MDR-TB and XDR-TB. 11. Demonstrate an in-depth understanding of the epidemiology of tuberculosis infection. 12. Describe the importance of the recent phenomenon of cold viruses causing pneumonia. 13. List the distinguishing characteristics of nosocomial versus community-acquired pneumonia.

21.1 The Respiratory Tract and Its Defenses The respiratory tract is the most common place for infectious agents to gain access to the body. We breathe 24 hours a day, and anything in the air we breathe passes at least temporarily into this organ system. The structure of the system is illustrated in figure 21.1a. Most clinicians divide the system into two parts, the upper and

Nasal cavity

Nostril Oral cavity

Cilia

Pharynx

Microvilli

(b) Ciliary defense of the tracheal mucosa (5,000×)

Epiglottis Larynx Trachea Frontal sinus Bronchus

Ethmoid sinus Maxillary sinus

Bronchioles

Sphenoid sinus

(c)

Figure 21.1 The respiratory tract. (a) Important structures in the upper (a)

Right lung

Left lung

and lower respiratory tracts. (b) Ciliary defense of the respiratory tract. (c) The four pairs of sinuses in the face and skull.

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lower respiratory tracts. The upper respiratory tract includes the mouth, the nose, the nasal cavity and sinuses above it, the throat or pharynx, and the epiglottis and larynx. The lower respiratory tract begins with the trachea, which feeds into the bronchi and bronchioles in the lungs. Attached to the bronchioles are small balloonlike structures called alveoli, which inflate and deflate with inhalation and exhalation. These are the site of oxygen exchange in the lungs. Several anatomical features of the respiratory system protect it from infection. As described in chapter 14, nasal hair serves to trap particles. Cilia (figure 21.1b) on the epithelium of the trachea and bronchi (the ciliary escalator) propel particles upward and out of the respiratory tract. Mucus on the surface of the mucous membranes lining the respiratory tract is a natural trap for invading microorganisms. Once the microorganisms are trapped, involuntary responses such as coughing, sneezing, and swallowing can move them out of sensitive areas. These are first-line defenses. The second and third lines of defense also help protect the respiratory tract. Macrophages inhabit the alveoli of the lungs and the clusters of lymphoid tissue (tonsils) in the throat. Secretory IgA against specific pathogens can be found in the mucus secretions as well.

21.1 Learning Outcomes—Can You . . . 1. . . . draw or describe the anatomical features of the respiratory tract? 2. . . . list the natural defenses present in the respiratory tract?

21.2 Normal Biota of the Respiratory Tract Because of its constant contact with the external environment, the respiratory system harbors a large number of commensal microorganisms. The normal biota is generally limited to the upper respiratory tract, and gram-positive bacteria such as streptococci and staphylococci are very common. Note that some bacteria that can cause serious disease are frequently present in the upper respiratory tract as “normal” biota; these include Streptococcus pyogenes, Haemophilus influenzae, Streptococcus pneumoniae, Neisseria meningitidis, and Staphylococcus aureus. These bacteria can potentially cause disease if

their host becomes immunocompromised for some reason, and they can cause disease in other hosts when they are innocently transferred to them. Other normal biota bacteria include nonhemolytic and alpha-hemolytic streptococci, Moraxella species, and Corynebacterium species (often called diphtheroids). Yeasts, especially Candida albicans, also colonize the mucosal surfaces of the mouth. In the respiratory system, as in some other organ systems, the normal biota performs the important function of microbial antagonism (see chapter 13). This reduces the chances of pathogens establishing themselves in the same area by competing with them for resources and space. As is the case with the other body sites harboring normal biota, the microbes reported here are those we have been able to culture in the laboratory. More microbes will come to light as scientists catalog the genetic sequences in the Human Microbiome Project.

21.2 Learning Outcome —Can You . . . 3. . . . list the types of normal biota presently known to occupy the respiratory tract?

21.3 Upper Respiratory Tract Diseases Caused by Microorganisms Rhinitis, or the Common Cold In the course of a year, people in the United States suffer from about 1 billion colds, called rhinitis because rhin- means nose and -itis means inflammation. Many people have several episodes a year. Economists estimate that this fairly innocuous infection costs the United States $40 billion a year in trips to the doctors, medications, and lost work time. ▶

Signs and Symptoms

Everyone is familiar with the symptoms of rhinitis: sneezing, scratchy throat, and runny nose (rhinorrhea), which usually begin 2 or 3 days after infection. An uncomplicated cold generally is not accompanied by fever, although children can experience low fevers (less than 102°F). The incubation period is usually 2 to 5 days. Note that people with asthma and other underlying respiratory conditions, such as chronic

Respiratory Tract Defenses and Normal Biota Defenses

Normal Biota

Upper Respiratory Tract

Nasal hair, ciliary escalator, mucus, involuntary responses such as coughing and sneezing, secretory IgA

Moraxella, nonhemolytic and alpha-hemolytic streptococci, Corynebacterium and other diphtheroids, Candida albicans Note: Streptococcus pyogenes, Streptococcus pneumoniae, Haemophilus influenzae, Neisseria meningitidis, and Staphylococcus aureus often present as “normal” biota.

Lower Respiratory Tract

Mucus, alveolar macrophages, secretory IgA

None

21.3

obstructive pulmonary disease (COPD) often suffer severe symptoms triggered by the common cold. ▶

Causative Agents

The common cold is caused by one of over 200 different kinds of viruses. The particular virus is almost never identified, and the symptoms and handling of the infection are the same no matter which of the viruses is responsible. The most common type of virus leading to rhinitis is the group called rhinoviruses, of which there are 99 serotypes. Coronaviruses and adenoviruses are also major causes. Most viruses causing the common cold never lead to any serious consequences, but some of them can be serious for some patients. Starting in 2007, an apparently mutated strain of adenovirus started making the news: It had become highly virulent, and more common. We will cover it in the section about pneumonias, since that is what this adenovirus often results in. Also, the respiratory syncytial virus (RSV) causes colds in most people, but in some, especially children, they can lead to more serious respiratory tract symptoms. (RSV is discussed later in the chapter.) In this section, we consider all cold-causing viruses together as a group because they are treated similarly. Viral infection of the upper respiratory tract can predispose a patient to secondary infections by other microorganisms, such as bacteria. Secondary infections may explain why some people report that their colds improved when they were given antibiotics. The cold was caused by viruses; bacterial infection may have followed. ▶

Pathogenesis and Virulence Factors

Viruses that induce rhinitis do not have many virulence mechanisms. They must penetrate the mucus that coats the respiratory tract and then find firm attachment points. Once they are attached, they use host cells to produce more copies of themselves (see chapter 6). The symptoms we experience as the common cold are mainly the result of our body fighting back against the viral invaders. Virus-infected cells in the upper respiratory tract release chemicals that attract certain types of white blood cells to the site, and these cells release cytokines and other inflammatory mediators, as described earlier in chapters 14 and 16. These mediators generate a localized inflammatory reaction, characterized by swelling and inflammation of the nasal mucosa, leakage of fluid from capillaries and lymph vessels, and increased production of mucus. The similarity of these symptoms to those of inhalant allergies illustrates that the same immune reactions are involved in both conditions. ▶

Transmission and Epidemiology

Cold viruses are transmitted by droplet contact, but indirect transmission may be more common, such as when a healthy person touches a fomite and then touches one of his or her own vulnerable surfaces, such as the mouth, nose, or an eye. In some cases, the viruses can remain air-

Upper Respiratory Tract Diseases Caused by Microorganisms

625

borne in droplet nuclei and aerosols and can be transmitted in that way. The epidemiology of the common cold is fairly simple: Practically everybody gets them, and fairly frequently. Children have more frequent infections than adults, probably because nearly every virus they encounter is a new one and they have no secondary immunity to it. People can acquire some degree of immunity to a cold virus that they have encountered before, but because there are more than 200 viruses, this immunity doesn’t provide much overall protection. ▶

Prevention

There is no vaccine for rhinitis. A traditional vaccine would need to contain antigens from about 200 viruses to provide complete protection. Researchers are studying novel types of immunization strategies, however. Because most of the viruses causing rhinitis use only a few different chemicals on host epithelium for their attachment site, some scientists have proposed developing a vaccine that would stimulate antibody to the docking site on the host. Other approaches include inducing antibody to the sites of action for the inflammatory mediators. But for now, the best prevention is to stop the transmission between hosts. The best way to prevent transmission is frequent hand washing, followed closely by stopping droplets from traveling away from the mouth and nose by covering them when sneezing or coughing. It is better to do this by covering the face with the crook of the arm rather than the hand, because subsequent contact with surfaces is less likely. ▶

Treatment

No chemotherapeutic agents cure the common cold. A wide variety of over-the-counter agents, such as antihistamines and decongestants, improve symptoms by blocking inflammatory mediators and their action. The use of these agents may also cut down on transmission to new hosts, because fewer virus-loaded secretions are produced.

Disease Table 21.1 Rhinitis Causative Organism(s)

Approximately 200 viruses

Most Common Modes of Transmission

Indirect contact, droplet contact

Virulence Factors

Attachment proteins; most symptoms induced by host response

Culture/Diagnosis

Not necessary

Prevention

Hygiene practices

Treatment

For symptoms only

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Sinusitis Commonly called a sinus infection, this inflammatory condition of any of the four pairs of sinuses in the skull (figure 21.1c) can actually be caused by allergy (most common), infections, or simply by structural problems such as narrow passageways or a deviated nasal septum. The infectious agents that may be responsible for the condition commonly include a variety of viruses or bacteria and, less commonly, fungi. Infections of the sinuses often follow a bout with the common cold. The inflammatory symptoms of a cold produce a large amount of fluid and mucus and when trapped in the sinuses, these secretions provide an excellent growth medium for bacteria or fungi. So viral rhinitis is frequently followed by sinusitis caused by bacteria or fungi. ▶

Signs and Symptoms

A person suffering from any form of sinusitis experiences nasal congestion, pressure above the nose or in the forehead, and sometimes the feeling of a headache or a toothache. Facial swelling and tenderness are common. Discharge from the nose and mouth appears opaque and has a green or yellow color in the case of bacterial infections. Discharge caused by an allergy is usually clear, and the symptoms may be accompanied by itchy, watery eyes. ▶

Causative Agents Bacteria Any number of bacteria that are normal biota in the upper respiratory tract may cause sinus infections. Many cases are caused by Streptococcus pneumoniae, Streptococcus pyogenes, Staphylococcus aureus, and Haemophilus influenzae. The causative organism is usually not identified, but treatment is begun empirically, based on the symptoms. The bacteria that cause these infections are most often normal biota in the host and don’t have an arsenal of virulence factors that lead to their ability to cause disease. The pathogenesis of this condition is brought about by the confluence of several factors: predisposition to infection because

of underlying (often viral) infection; buildup of fluids, providing a rich environment for bacterial multiplication; and sometimes the anatomy of the sinuses, which can contribute to entrapment of mucus and bacterial growth. Bacterial sinusitis is not a communicable disease. Of course, the virus originally causing rhinitis is transmissible, but the host takes it from there by creating the conditions favorable for respiratory tract microorganisms to multiply in the sinus spaces, which normally do not harbor microorganisms to any significant extent. Sinusitis is extremely common, resulting in approximately 11.5 million office visits a year in the United States. A large proportion of these cases are allergic sinusitis episodes, but approximately 30% of them are caused by bacterial overgrowth in the sinuses. Women and residents of the southern United States have slightly higher rates. As with many upper respiratory tract infections, smokers have higher rates of infection than nonsmokers. Children who are exposed to large amounts of secondhand smoke are also more susceptible. Broad-spectrum antibiotics may be prescribed when the physician feels that the sinusitis is bacterial in origin (that is, when allergic sinusitis and fungal sinusitis are ruled out).

Fungi Fungal sinusitis is rare, but it is often recognized when antibacterial drugs fail to alleviate symptoms. Simple fungal infections may normally be found in the maxillary sinuses and are noninvasive in nature. These colonies are generally not treated with antifungal agents but instead are simply mechanically removed by a physician. Aspergillus fumigatus is a common fungus involved in this type of infection. The growth of fungi in this type of sinusitis may be encouraged by trauma to the area. More serious invasive fungal infections of the sinuses may be found in severely immunocompromised patients. Fungi such as Aspergillus and Mucor species may invade the bony structures in the sinuses and even travel to the brain or eye. These infections are treated aggressively with a combination of surgical removal of the fungus and intravenous antifungal therapy (Disease Table 21.2).

Disease Table 21.2 Sinusitis Causative Organism(s)

Various bacteria, often mixed infection

Various fungi

Most Common Modes of Transmission

Endogenous (opportunism)

Introduction by trauma or opportunistic overgrowth

Virulence Factors

–

–

Culture/Diagnosis

Culture not usually performed; diagnosis based on clinical presentation, occasionally X rays or other imaging technique used

Same

Prevention

–

–

Treatment

Broad-spectrum antibiotics

Physical removal of fungus; in severe cases antifungals used

Distinctive Features

Much more common than fungal

Suspect in immunocompromised patients

21.3

Acute Otitis Media (Ear Infection) This condition is another common sequela of rhinitis, or the common cold, and for reasons similar to the ones described for sinusitis. Viral infections of the upper respiratory tract lead to inflammation of the eustachian tubes and the buildup of fluid in the middle ear, which can lead to bacterial multiplication in those fluids. Although the middle ear normally has no biota, bacteria can migrate along the eustachian tube from the upper respiratory tract (figure 21.2). When bacteria encounter mucus and fluid buildup in the middle ear, they multiply rapidly. Their presence increases the inflammatory response, leading to pus production and continued fluid secretion. This fluid is referred to as effusion. Another condition, known as chronic otitis media, occurs when fluid remains in the middle ear for indefinite periods of time. Until recently, physicians considered it to be the result of a noninfectious immune reaction because they could not culture bacteria from the site and because antibiotics were not effective. New data suggest that this form of otitis media is caused by a mixed biofilm of bacteria that are attached to the membrane of the inner ear. Biofilm bacteria generally are less susceptible to antibiotics (as discussed in chapter 4), and their presence in biofilm form would explain the inability to culture them from ear fluids. ▶

Signs and Symptoms

Otitis media may be accompanied by a sensation of fullness or pain in the ear and loss of hearing. Younger children may exhibit irritability, fussiness, and difficulty in sleeping, eating, or hearing. Severe or untreated infections can lead to

External ear canal Eardrum (bulging)

Upper Respiratory Tract Diseases Caused by Microorganisms

rupture of the eardrum because of pressure of pus buildup, or to internal breakthrough of these infected fluids, which can lead to more serious conditions such as mastoiditis, meningitis, or intracranial abscess. ▶

Eustachian tube (inflamed)

Figure 21.2 An infected middle ear.

Causative Agents

Many different viruses and bacteria can cause acute otitis media, but the most common cause is Streptococcus pneumoniae (also discussed in the section on pneumonia later in this chapter). Haemophilus influenzae is another common cause of this condition; however, the incidence of all types of infections with this bacterium was significantly reduced with the introduction of a childhood vaccine against it in the 1980s. Scientists have now found that the majority of otitis media cases are mixed infections with viruses and bacteria acting together. Streptococcus pneumoniae appears as pairs of elongated, gram-positive cocci joined end to end. It is often called by the familiar name pneumococcus, and diseases caused by it are termed pneumococcal. ▶

Transmission and Epidemiology

Otitis media is a sequela of upper respiratory tract infection and is not communicable, although the upper respiratory infection preceding it is. Children are particularly susceptible, and boys have a slightly higher incidence than do girls. ▶

Prevention

A vaccine against S. pneumoniae has been a part of the recommended childhood vaccination schedule since 2000. The vaccine (Prevnar) is a seven-valent conjugated vaccine (see chapter 15). It contains polysaccharide capsular material from seven different strains of the bacterium complexed with a chemical that makes it more antigenic. It is distinct from another vaccine for the same bacterium (Pneumovax), which is primarily targeted to the older population to prevent pneumococcal pneumonia. ▶

Inflammatory exudate

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Treatment

Until the late 1990s, broad-spectrum antibiotics were routinely prescribed for otitis media. When it became clear that frequently treating children with these drugs was producing a bacterial biota with high rates of antibiotic resistance, the treatment regimen was reexamined. The current recommendation for uncomplicated acute otitis media with a fever below 104°F is “watchful waiting” for 72 hours to allow the body to clear the infection, avoiding the use of antibiotics. When antibiotics are used, antibiotic resistance must be considered. Children who experience frequent recurrences of ear infections sometimes have small tubes placed through the tympanic membranes into their middle ears to provide a means of keeping fluid out of the site when inflammation occurs (Disease Table 21.3).

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Disease Table 21.3 Otitis Media Causative Organism(s)*

Streptococcus pneumoniae

Haemophilus influenzae

Other bacteria

Most Common Modes of Transmission

Endogenous (may follow upper respiratory tract infection by S. pneumoniae or other microorganisms)

Endogenous (follows upper respiratory tract infection)

Endogenous

Virulence Factors

Capsule, hemolysin

Capsule, fimbriae

–

Culture/Diagnosis

Usually relies on clinical symptoms and failure to resolve within 72 hours

Same

Same

Prevention

Pneumococcal conjugate vaccine (heptavalent)

Hib vaccine

None

Treatment

Wait for resolution; if needed, amoxicillin (are high rates of resistance) or amoxicillin + clavulanate or cefuroxime

Same as for S. pneumoniae

Wait for resolution; if needed, a broad-spectrum antibiotic (azithromycin) might be used in absence of etiologic diagnosis

Distinctive Features

–

–

Suspect if fully vaccinated against other two

*Keep in mind that many bacterial cases of otitis media are complicated with viral coinfections.

Pharyngitis

Fusobacterium necrophorum

▶

Recently cases of severe sore throats caused by a bacterium called Fusobacterium necrophorum have cropped up in adolescents and young adults around the country. Some studies suggest it is as common as S. pyogenes in this age group. It can cause serious infections of the bloodstream and other organs, a condition called Lemierre’s syndrome. Doctors speculate that this disease was previously rarely seen since most sore throats were empirically treated with

Signs and Symptoms

The name says it all—this is an inflammation of the throat, which the host experiences as pain and swelling. The severity of pain can range from moderate to severe, depending on the causative agent. Viral sore throats are generally mild and sometimes lead to hoarseness. Sore throats caused by group A streptococci are generally more painful than those caused by viruses, and they are more likely to be accompanied by fever, headache, and nausea. Clinical signs of a sore throat are reddened mucosa, swollen tonsils, and sometimes white packets of inflammatory products visible on the walls of the throat, especially in streptococcal disease (figure 21.3). The mucous membranes may be swollen, affecting speech and swallowing. Often pharyngitis results in foul-smelling breath. The incubation period for most sore throats is generally 2 to 5 days. ▶

Causative Agents

A sore throat is most commonly caused by the same viruses causing the common cold. It can also accompany other diseases, such as infectious mononucleosis (described in chapter 20). Pharyngitis may simply be the result of mechanical irritation from prolonged shouting or from drainage of an infected sinus cavity. The most serious cause of pharyngitis is Streptococcus pyogenes. We will address this infection in depth, after a brief digression about an emerging cause of pharyngitis.

Figure 21.3 The appearance of the throat in pharyngitis and tonsillitis. The pharynx and tonsils become bright red and suppurative. Whitish pus nodules may also appear on the tonsils.

21.3

Upper Respiratory Tract Diseases Caused by Microorganisms

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broad-spectrum antibiotics, a treatment that generally kills F. necrophorum. Now that physicians are being much more judicious with antibiotic treatment, and generally not treating at all if strep tests are negative, this bacterium has a doorway to cause disease. This bacterium is sensitive to penicillin and related drugs, which are the first-line drugs for S. pyogenes as well. It does make the use of second-line drugs for strep throats less desirable as some of them, such as azithromycin, have no effect on this bacterium. There are currently no rapid diagnostic tests for F. necrophorum.

Streptococcus pyogenes

(a)

S. pyogenes is a gram-positive coccus that grows in chains. It does not form spores, is nonmotile, and forms capsules and slime layers. S. pyogenes is a facultative anaerobe that ferments a variety of sugars. It does not form catalase, but it does have a peroxidase system for inactivating hydrogen peroxide, which allows its survival in the presence of oxygen. ▶

Pathogenesis

Untreated streptococcal throat infections occasionally can result in serious complications, either right away or days to weeks after the throat symptoms subside. These complications include scarlet fever, rheumatic fever, and glomerulonephritis. More rarely, invasive and deadly conditions such as necrotizing fasciitis can result from infection by S. pyogenes. These invasive conditions are described in chapter 18.

Scarlet Fever Scarlet fever is the result of infection with an S. pyogenes strain that is itself infected with a bacteriophage. This lysogenic virus confers on the streptococcus the ability to produce erythrogenic toxin, described in the section on virulence. Scarlet fever is characterized by a sandpaper-like rash, most often on the neck, chest, elbows, and inner surfaces of the thighs. High fever accompanies the rash. It most often affects school-age children, and was a source of great suffering in the United States in the early part of the 20th century. In epidemic form, the disease can have a fatality rate of up to 95%. Most cases seen today are mild. They are easily recognizable and amenable to antibiotic therapy. Because of the fear elicited by the name “scarlet fever,” the disease is often called scarlatina in North America. Rheumatic Fever Rheumatic fever is thought to be due to an immunologic cross-reaction between the streptococcal M protein and heart muscle. It tends to occur approximately 3 weeks after pharyngitis has subsided. It can result in permanent damage to heart valves (figure 21.4). Other symptoms include arthritis in multiple joints and the appearance of nodules over bony surfaces just under the skin. Rheumatic fever is completely preventable if the original streptococcal infection is treated with antibiotics. Nevertheless, it is still a serious problem today in many parts of the world.

(b)

Mitral valve

Figure 21.4 The cardiac complications of rheumatic fever. Pathologic processes of group A streptococcal infection can extend to the heart. In this example, it is believed that cross-reactions between streptococcal-induced antibodies and heart proteins have a gradual destructive effect on the atrioventricular valves (especially the mitral valve) or semilunar valves. Scarring and deformation change the capacity of the valves to close and shunt the blood properly. (a) A normal valve, viewed from above. (b) A scarred mitral valve. The color difference in the two views is artificial.

Glomerulonephritis Glomerulonephritis is thought to be the result of streptococcal proteins participating in the formation of antigen-antibody complexes, which then are deposited in the basement membrane of the glomeruli of the kidney. It is characterized by nephritis (appearing as swelling in the hands and feet and low urine output), blood in the urine, increased blood pressure, and occasionally heart failure. It can result in permanent kidney damage. The incidence of poststreptococcal glomerulonephritis has been declining in the United States, but it is still common in Africa, the Caribbean, and South America. Toxic shock syndrome and necrotizing fasciitis are other, less frequent consequences of streptococcal infections, and are discussed in chapter 18.

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Virulence Factors

The virulence of S. pyogenes is partly due to the substantial array of surface antigens, toxins, and enzymes it can generate. Streptococci display numerous surface antigens (figure 21.5). Specialized polysaccharides on the surface of the cell wall help to protect the bacterium from being dissolved by the lysozyme of the host. Lipoteichoic acid (LTA) contributes to the adherence of S. pyogenes to epithelial cells in the pharynx. A spiky surface projection called M protein contributes to virulence by resisting phagocytosis and possibly by contributing to adherence. A capsule made of hyaluronic acid (HA) is formed by most S. pyogenes strains. It probably contributes to the bacterium’s adhesiveness. Because this HA is chemically indistinguishable from HA found in human tissues, it does not provoke an immune response from the host.

Extracellular Toxins Group A streptococci owe some of their virulence to the effects of hemolysins called streptolysins. The two types are streptolysin O (SLO) and streptolysin S (SLS).1 Both types cause beta-hemolysis of sheep blood agar (see “Culture and Diagnosis”). Both hemolysins rapidly injure many cells and tissues, including leukocytes and liver and heart muscle (in other forms of streptococcal disease). A key toxin in the development of scarlet fever is erythrogenic (eh-rith″-roh-jen′-ik) toxin. This toxin is responsible for the bright red rash typical of this disease, and it also induces fever by acting upon the temperature regulatory center in the brain. Only lysogenic strains of S. pyogenes that contain genes from a temperate bacteriophage can synthesize this toxin. (For a review of the concept of lysogeny, see chapter 6.) Some of the streptococcal toxins (erythrogenic toxin and streptolysin O) contribute to increased tissue injury 1. In SLO, O stands for oxygen because the substance is inactivated by oxygen. In SLS, S stands for serum because the substance has an affinity for serum proteins. SLS is oxygen-stable.

M-protein fimbriae Protein antigen Peptidoglycan Cytoplasm Hyaluronic acid capsule Lipoteichoic acid

Figure 21.5 Cutaway view of group A streptococcus.

by acting as superantigens. These toxins elicit excessively strong reactions from monocytes and T lymphocytes. When activated, these cells proliferate and produce tumor necrosis factor (TNF), which leads to a cascade of immune responses resulting in vascular injury. This is the likely mechanism for the severe pathology of toxic shock syndrome and necrotizing fasciitis. ▶

Transmission and Epidemiology

Physicians estimate that 30% of sore throats may be caused by S. pyogenes, adding up to several million cases each year. Most transmission of S. pyogenes is via respiratory droplets or direct contact with mucus secretions. This bacterium is carried as “normal” biota by 15% of the population, but transmission from this reservoir is less likely than from a person who is experiencing active disease from the infection because of the higher number of bacteria present in the disease condition. It is less common but possible to transmit this infection via fomites. Humans are the only significant reservoir of S. pyogenes. More than 80 serotypes of S. pyogenes exist, and thus people can experience multiple infections throughout their lives because immunity is serotype-specific. Even so, only a minority of encounters with the bacterium result in disease. An immunocompromised host is more likely to suffer from strep pharyngitis as well as serious sequelae of the throat infection. Although most sore throats caused by S. pyogenes can resolve on their own, they should be treated with antibiotics because serious sequelae are a possibility. ▶

Culture and Diagnosis

The failure to recognize group A streptococcal infections can have devastating effects. Rapid cultivation and diagnostic techniques to ensure proper treatment and prevention measures are essential. Several different rapid diagnostic test kits are used in clinics and doctors’ offices to detect group A streptococci from pharyngeal swab samples. These tests are based on antibodies that react with the outer carbohydrates of group A streptococci (figure 21.6a). Because the rapid tests have a significant possibility of returning a false-negative result, guidelines call for confirming the negative finding with a culture, which can be read the following day. A culture is generally taken at the same time as the rapid swab and is plated on sheep blood agar. S. pyogenes displays a beta-hemolytic pattern due to its streptolysins (and hemolysins) (figure 21.6b). If the pharyngitis is caused by a virus, the blood agar dish will show a variety of colony types, representing the normal bacterial biota. Active infection with S. pyogenes will yield a plate with a majority of beta-hemolytic colonies. Group A streptococci are by far the most common beta-hemolytic isolates in human diseases, but lately an increased number of infections by group B streptococci (also beta-hemolytic), as well as the existence of beta-hemolytic enterococci, have made it important to use differentiation tests. A positive bacitracin disc test (figure 21.6b) provides additional evidence for group A.

21.3

Upper Respiratory Tract Diseases Caused by Microorganisms

Figure 21.6 Streptococcal tests. (a) A rapid, direct test kit for diagnosis

Bacitracin disc

SXT disc

of group A infections. With this method, a patient’s throat swab is introduced into a system composed of latex beads and monoclonal antibodies. (Left) In a positive reaction, the C-carbohydrate on group A streptococci produces visible clumps. (Right) A smooth, milky reaction is negative. (b) Bacitracin disc test. With very few exceptions, only Streptococcus pyogenes is sensitive to a minute concentration (0.02 μg) of bacitracin. Any zone of inhibition around the B disc is interpreted as a presumptive indication of this species. (Note: Group A streptococci are negative for sulfamethoxazole-trimethoprim [SXT] sensitivity and the CAMP test.)

(a)

▶

Positive reaction

Negative reaction

No vaccine exists for group A streptococci, although many researchers are working on the problem. A vaccine against this bacterium would also be a vaccine against rheumatic fever, and thus it is in great demand. In the meantime, infection can be prevented by good hand washing, especially after coughing and sneezing and before preparing foods or eating.

(–) CAMP test

(b)

▶

Prevention

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Treatment

The antibiotic of choice for S. pyogenes is penicillin; many group A streptococci have become resistant to erythromycin, a macrolide antibiotic. In patients with penicillin allergies, a first-generation cephalosporin, such as cephalexin, is prescribed (Disease Table 21.4).

Disease Table 21.4 Pharyngitis Causative Organism(s)

Fusobacterium necrophorum

Streptococcus pyogenes

Viruses

Most Common Modes of Transmission

Opportunistic

Droplet or direct contact

All forms of contact

Virulence Factors

Endotoxin, leukotoxin

LTA, M protein, hyaluronic acid capsule, SLS and SLO, superantigens

–

Culture/Diagnosis

Growth on anaerobic agar

Beta-hemolytic on blood agar, sensitive to bacitracin, rapid antigen tests

Goal is to rule out S. pyogenes, further diagnosis usually not performed

Prevention

Hygiene practices

Hygiene practices

Hygiene practices

Treatment

Penicillin, cefuroxime

Penicillin, cephalexin in penicillinallergic

Symptom relief only

Distinctive Features

Common in adolescents and young adults, infections spread to cardiovascular system or deeper tissues

Generally more severe than viral pharyngitis

Hoarseness frequently accompanies viral pharyngitis

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Diphtheria

▶

For hundreds of years, diphtheria was a significant cause of morbidity and mortality, but in the last 50 years, both the number of cases and the fatality rate have steadily declined throughout the world. In the United States in recent years, only one or two cases have been reported each year. But when healthy people are screened for the presence of the bacterium, it is found in a significant percentage of them, indicating that the lack of cases is due to the protection afforded by immunization with the diphtheria toxoid, which is part of the childhood immunization series. Indeed, during the 1990s, a diphtheria epidemic occurred in the former Soviet Union in which 157,000 people became ill with diphtheria and 5,000 people died. This upsurge of cases was attributed to a breakdown in immunization practices and production of vaccine, which followed the breakup of the Soviet Union. These examples emphasize the importance of maintaining vaccination, even for diseases that have long been kept under control.

The exotoxin is encoded by a bacteriophage of C. diphtheriae. Strains of the bacterium that are not lysogenized by this phage do not cause serious disease. The exotoxin is of a type called A-B toxin. It is illustrated in figure 21.9 and explained briefly here. A-B toxins are so named because they consist of two parts, an A (active) component and a B (binding) component. The B component binds to a receptor molecule on the surface of the host cell. The next step is for the A component to be moved across the host cell membrane. The A components of most A-B toxins then catalyze a reaction by which they remove a sugar derivative called the ADP-ribosyl group from the coenzyme NAD and attach it to one host cell protein or another. This process is called ADP-ribosylation. This process disrupts the normal function of that host protein, resulting in some type of symptom for the patient. The release of diphtheria toxin in the blood leads to complications in distant organs, especially myocarditis and neuritis. Myocarditis can cause abnormal cardiac rhythms and in the worst cases can lead to heart failure. Neuritis affects motor nerves and may result in temporary paralysis of limbs, the soft palate, and even the diaphragm, a condition that can predispose a patient to other lower respiratory tract infections.

▶

Signs, Symptoms, and Causative Organism

The disease is caused by Corynebacterium diphtheriae, a non-spore-forming, gram-positive club-shaped bacterium (figure 21.7). The symptoms of diphtheria are experienced initially in the upper respiratory tract. At first the patient experiences a sore throat, lack of appetite, and low-grade fever. A characteristic membrane, usually referred to as a pseudomembrane, forms on the tonsils or pharynx (figure 21.8). The membrane is formed by the bacteria and consists of bacterial cells, fibrin, lymphocytes, and dead tissue cells; and it may be quite extensive. It adheres to tissues and cannot easily be removed. It may eventually completely block respiration. The patient may recover after this crisis. Alternatively, exotoxin manufactured by the bacterium may penetrate the bloodstream and travel throughout the body.

Figure 21.7 Corynebacterium diphtheriae.

▶

Pathogenesis and Virulence Factors

Prevention and Treatment

Diphtheria can easily be prevented by a series of vaccinations with toxoid, usually given as part of a mixed vaccine against tetanus and pertussis as well, called the DTaP (for diphtheria, tetanus, and acellular pertussis). If a patient has diphtheria, and it has progressed to the bloodstream, the adverse effects

Figure 21.8 Diagnosing diphtheria. The clinical appearance in diphtheria infection includes gross inflammation of the pharynx and tonsils marked by grayish patches (a pseudomembrane) and swelling over the entire area.

21.4

Diseases Caused by Microorganisms Affecting Both the Upper and Lower Respiratory Tracts

and tracheostomy or bronchoscopy to remove the membrane (sometimes called a pseudomembrane) may be indicated. Adults and adolescents should receive a DTaP booster.

Toxin precursor (inactive) A

B chain

B

B chain attaches to receptor.

A

Disulfide bond

Disease Table 21.5 Diphtheria B

A

A chain

B chain cannot attach. Resistant cell membrane

B

Binding site

633

Cell membrane (susceptible cell)

Causative Organism(s)

Corynebacterium diphtheriae

Most Common Modes of Transmission

Droplet contact, direct contact or indirect contact with contaminated fomites

Virulence Factors

Exotoxin: diphtheria toxin

Culture/Diagnosis

Tellurite medium—gray/black colonies, club-shaped morphology on Gram stain; treatment begun before definitive identification

Prevention

Diphtheria toxoid vaccine (part of DTaP)

Treatment

Antitoxin plus penicillin or erythromycin

Endocytosis begins.

A B

21.3 Learning Outcomes—Can You . . . Endocytic vacuole

4. . . . list the possible causative agents, modes of transmission, virulence factors, diagnostic techniques, and prevention/ treatment for each of the diseases of the upper respiratory tract? These are: rhinitis, sinusitis, otitis media, pharyngitis, and diphtheria. 5. . . . identify which disease is often caused by a mixture of microorganisms? 6. . . . identify two bacteria that can cause dangerous pharyngitis cases?

A B

A

Active enzyme leaves vacuole.

B Acidification of vacuole

A NAD + EF-2

ADP ribose–EF-2 + nicotinamide (inactivated)

Figure 21.9 A-B toxin of Corynebacterium diphtheriae.

The B chain attaches to host cell membrane, then the toxin enters the cell. The two chains separate and the A chain enters the cytoplasm as an active enzyme that ADP-ribosylates a protein (EF-2) needed for protein synthesis. Cell death follows.

21.4 Diseases Caused by Microorganisms Affecting Both the Upper and Lower Respiratory Tracts A number of infectious agents affect both the upper and lower respiratory tract regions. We discuss the more well-known diseases in this section; specifically, they are whooping cough, respiratory syncytial virus (RSV), and influenza.

Whooping Cough of toxemia are treated with diphtheria antitoxin derived from horses. Prior to injection, the patient must be tested for allergy to horse serum and be desensitized if necessary. The infection itself may be treated with antibiotics from the penicillin or erythromycin family. Bed rest, heart medication,

Whooping cough is also known as pertussis (the suffix -tussis is Latin for cough). A vaccine for this potentially serious infection has been available since 1926. The disease is still troubling to the public health community because its incidence has increased every year since the 1980s in the United

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States, despite improvements in the vaccine. In addition, in the recent past there has been concern over the vaccine among the general public. For these reasons, it is an important disease for health care professionals to understand. ▶

Signs and Symptoms

The disease has two distinct symptom phases called the catarrhal and paroxysmal stages, which are followed by a long recovery (or convalescent) phase, during which a patient is particularly susceptible to other respiratory infections. After an incubation period of from 3 to 21 days, the catarrhal stage begins when bacteria present in the respiratory tract cause what appear to be cold symptoms, most notably a runny nose. This stage lasts 1 to 2 weeks. The disease worsens in the second (paroxysmal) stage, which is characterized by severe and uncontrollable coughing (a paroxysm can be thought of as a convulsive attack). The common name for the disease comes from the whooping sound a patient makes as he or she tries to grab a breath between uncontrollable bouts of coughing. The violent coughing spasms can result in burst blood vessels in the eyes or even vomiting. In the worst cases, seizures result from small hemorrhages in the brain. As in any disease, the convalescent phase is the time when numbers of bacteria are decreasing and no longer cause ongoing symptoms. But the active stages of the disease damage the cilia on respiratory tract epithelial cells, and complete recovery of these surfaces requires weeks or even months. During this time, other microorganisms can more easily colonize and cause secondary infection. ▶

Causative Agent

Bordetella pertussis is a very small gram-negative rod. Sometimes it looks like a coccobacillus. It is strictly aerobic and fastidious, having specific nutritional requirements for successful culture. ▶

Pathogenesis and Virulence Factors

The progress of this disease can be clearly traced to the virulence mechanisms of the bacterium. It is absolutely essential for the bacterium to attach firmly to the epithelial cells of the mouth and throat, and it does so using specific adhesive molecular structures on its surface. One of these structures is called filamentous hemagglutinin (FHA). It is a fibrous structure that surrounds the bacterium like a capsule and is also secreted in soluble form. In that form, it can act as a bridge between the bacterium and the epithelial cell. Once the bacteria are attached in large numbers, production of mucus increases and localized inflammation ensues, resulting in the early stages of the disease. Then the real damage begins: The bacteria release multiple exotoxins that damage ciliated respiratory epithelial cells and cripple other components of the host defense, including phagocytic cells. The two most important exotoxins are pertussis toxin and tracheal cytotoxin. Pertussis toxin is a classic A-B toxin, like the

diphtheria toxin illustrated in figure 21.9. In the case of pertussis toxin, the host protein affected by the process of ADPribosylation is one that normally limits the production of cyclic AMP. Cyclic AMP is a critical molecule that regulates numerous functions inside host cells. The excessive amounts of cyclic AMP result in copious production of mucus and a variety of other effects in the respiratory tract and the immune system. Tracheal cytotoxin results in more direct destruction of ciliated cells. The cells are no longer capable of clearing mucus and secretions, leading to the extraordinary coughing required to get relief. Another important contributor to the pathology of the disease is B. pertussis endotoxin. As always with endotoxins, its release leads to the production of a host of cytokines that have direct and indirect effects on physiological processes and on the host response. ▶

Transmission and Epidemiology

B. pertussis is transmitted via respiratory droplets. It is highly contagious during both the catarrhal and paroxysmal stages. The disease manifestations are most serious in infants. Twenty-five percent of infections occur in older children and adults, who generally have milder symptoms. The disease results in 300,000 to 500,000 deaths annually worldwide. Pertussis outbreaks continue to occur in the United States and elsewhere. Even though it is estimated that approximately 85% of U.S. children are vaccinated against pertussis, it continues to be spread, perhaps by adults whose own immunity has dwindled. These adults may experience mild, unrecognized disease and unwittingly pass it to others. It has also been found that fully vaccinated children can experience the disease, possibly due to antigenic changes in the bacterium. ▶

Culture and Diagnosis

This disease is often diagnosed based solely on its symptoms because they are so distinctive. When culture confirmation is desired, nasopharyngeal swabs can be inoculated on specific media—Bordet-Gengou (B-G) medium, charcoal agar, or potato-glycerol agar. ▶

Prevention

The current vaccine for pertussis is an acellular formulation of important B. pertussis antigens. It results in far fewer side effects than the previous whole-cell vaccine, which was used until the mid-1990s. It is generally given in the form of the DTaP vaccine. Booster shots after the age of 11 are especially important for this disease. A second prevention strategy is the administration of antibiotics to contacts of people who have been diagnosed with the disease. Erythromycin or trimethoprim-sulfamethoxazole is given for 14 days to prevent disease in those who may have been infected. ▶

Treatment

Treating someone who is already ill with pertussis is focused on supportive care; antibiotics may or may not shorten the

21.4

Diseases Caused by Microorganisms Affecting Both the Upper and Lower Respiratory Tracts

course of the disease, which is often the case when major symptoms of a condition are the result of exotoxin secretion. Antibiotics (erythromycin) are sometimes administered because they do decrease the contagiousness of the patient.

Disease Table 21.6 Pertussis (Whooping Cough)

Causative Organism(s)

Bordetella pertussis

Most Common Modes of Transmission

Droplet contact

Virulence Factors

FHA (adhesion), pertussis toxin and tracheal cytotoxin, endotoxin

Culture/Diagnosis

Grown on B-G, charcoal, or potatoglycerol agar; diagnosis can be made on symptoms

Prevention

Acellular vaccine (DTaP), erythromycin or trimethoprimsulfamethoxazole for contacts

Treatment

Mainly supportive; erythromycin to decrease communicability

Respiratory Syncytial Virus Infection As its name indicates, respiratory syncytial virus (RSV) infects the respiratory tract and produces giant multinucleated cells (syncytia). It is a member of the paramyxovirus family and contains single-stranded negative-sense RNA. It is an enveloped virus. Outbreaks of droplet-spread RSV disease occur regularly throughout the world, with peak incidence in the winter and early spring. Children 6 months of age or younger, as well as premature babies, are especially susceptible to serious disease caused by this virus. RSV is the most prevalent cause of respiratory infection in the newborn age group, and nearly all children have experienced it by age 2. An estimated 100,000 children are hospitalized with RSV infection each year in the United States. The mortality rate is highest for children with complications such as prematurity, congenital disease, and immunodeficiency. Infection in older children and adults usually manifests as a cold. The first symptoms are fever that lasts for approximately 3 days, rhinitis, pharyngitis, and otitis. More serious infections progress to the bronchial tree and lung parenchyma, giving rise to symptoms of croup, which include acute bouts of coughing, wheezing, difficulty in breathing (called dyspnea), and abnormal breathing sounds (called rales). (Note: This condition is often called croup, and also bronchiolitis; be aware that both of these terms are clinical descriptions of diseases caused by a variety of viruses [in addition to RSV] and sometimes by bacteria.)

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The virus is highly contagious and is transmitted through droplet contact but also through fomite contamination. Diagnosis of RSV infection is more critical in babies than in older children or adults. The afflicted child is conspicuously ill, with signs typical of pneumonia and bronchitis. The best diagnostic procedures are those that demonstrate the viral antigen directly from specimens (direct and indirect fluorescent staining, ELISA, and DNA probes). There is no RSV vaccine available yet, but an effective passive antibody preparation is used as prevention in high-risk children and babies born prematurely. It is very expensive (about $6,000 for a five-dose treatment) and therefore insurance companies will only reimburse for it when children meet stringent criteria. But doctors say they’re not sure it has much a benefit, anyway. Of course, when parents of high-risk children learn of it, they want it. Ribavirin, an antiviral drug, can be administered as an inhaled aerosol to very sick children, although the clinical benefit is uncertain.

Disease Table 21.7 RSV Disease Causative Organism(s)

Respiratory syncytial virus (RSV)

Most Common Modes of Transmission

Droplet and indirect contact

Virulence Factors

Syncytia formation

Culture/Diagnosis

Direct antigen testing

Prevention

Passive antibody (humanized monoclonal) in high-risk children

Treatment

Ribavirin in severe cases

Influenza The “flu” is a very important disease to study for several reasons. First of all, everyone is familiar with the cyclical increase of influenza infections occurring during the winter months in the United States. Second, many conditions are erroneously termed the “flu,” while in fact only diseases caused by influenza viruses are actually the flu. Third, the way that influenza viruses behave provides an excellent illustration of the way other viruses can, and do, change to cause more serious diseases than they did previously. Influenzas that occur every year are called “seasonal” flus. Often these are the only flus that circulate each year. Occasionally another flu strain appears, one that is new and may cause worldwide pandemics. In some years, such as in 2009, both of these flus were issues. They had different symptoms, affected different age groups, and had separate vaccine protocols.

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Signs and Symptoms

Seasonal influenza begins in the upper respiratory tract but in serious cases may also affect the lower respiratory tract. There is a 1- to 4-day incubation period, after which symptoms begin very quickly. These include headache, chills, dry cough, body aches, fever, stuffy nose, and sore throat. Even the sum of all these symptoms can’t describe how a person actually feels: lousy. The flu is known to “knock you off your feet.” Extreme fatigue can last for a few days or even a few weeks. An infection with influenza can leave patients vulnerable to secondary infections, often bacterial. Influenza infection alone occasionally leads to a pneumonia that can cause rapid death, even in young healthy adults. Patients with emphysema or cardiopulmonary disease, along with very young, elderly, or pregnant patients, are more susceptible to serious complications. The pandemic virus, H1N1, or the swine flu of 2009, had similar symptoms but with a couple of differences. Not all patients had a fever (very unusual for influenza), and many patients had gastrointestinal distress. ▶

Causative Agent

All influenza is caused by one of three influenza viruses: A, B, or C. They belong to the Family Orthomyxoviridae. They are spherical particles with an average diameter of 80 to 120 nanometers. Each virion is covered with a lipoprotein envelope that is studded with glycoprotein spikes acquired during viral maturation (figure 21.10). Also note that the envelope contains proteins that form a channel for ions into the virus. The two glycoproteins that make up the spikes of the envelope and contribute to virulence are called hemagglutinin (H) and neuraminidase (N). The name hemagglutinin is derived from this glycoprotein’s agglutinating action on red blood cells, which is the basis for viral assays used to identify the viruses. Hemagglutinin contributes to infectivity by binding to host cell receptors of the respiratory mucosa, a process that facilitates viral penetration. Neuraminidase breaks down the protective mucous coating of the respiratory tract, assists in viral budding and release, keeps viruses from sticking together, and participates in host cell fusion.

The ssRNA genome of the influenza virus is known for its extreme variability. It is subject to constant genetic changes that alter the structure of its envelope glycoproteins. Research has shown that genetic changes are very frequent in the area of the glycoproteins recognized by the host immune response but very rare in the areas of the glycoproteins used for attachment to the host cell (figure 21.11). In this way, the virus can continue to attach to host cells while managing to decrease the effectiveness of the host response to its presence. This constant mutation of the glycoproteins is called antigenic drift—the antigens gradually change their amino acid composition, resulting in decreased ability of host memory cells to recognize them. An even more serious phenomenon is known as antigenic shift. The genome of the virus consists of just 10 genes, encoded on eight separate RNA strands. Antigenic shift is the swapping out of one of those genes or strands with a gene or strand from a different influenza virus. Some explanation is in order. First, we know that certain influenza viruses infect both humans and swine. Other influenza viruses infect birds (or ducks) and swine. All of these viruses have 10 genes coding for the same important influenza proteins (including H and N)—but the actual sequence of the genes is different in the different types of viruses. Second, when the two viruses just described infect a single swine host, with both virus types infecting the same host cell, the viral packaging step can accidentally produce a human influenza virus that contains seven human influenza virus RNA strands plus a single duck influenza virus RNA strand (figure 21.12). When that virus infects a human, no immunologic recognition of the protein that came from the duck virus occurs. Experts have traced the flu pandemics of 1918, 1957, 1968, 1977, and 2009 to strains of a virus that came from pigs (swine flu). Influenza A viruses are named according to the different types of H and N spikes they

Binding sites used to anchor virus to host cell receptors (low rate of mutation)

Matrix protein Negative-sense RNA, nucleoprotein Lipid envelope from host membrane

Site for antibody binding (high rate of mutation) Viral envelope Ion channel

Hemagglutinin (H) Neuraminidase (N) Ion channel

Figure 21.10 Schematic drawing of influenza virus.

Figure 21.11 Schematic drawing of hemagglutinin (HA) of influenza virus. Blue boxes depict site used to attach virus to host cells; green circles depict sites for anti-influenza antibody binding.

21.4 Duck influenza virus

Diseases Caused by Microorganisms Affecting Both the Upper and Lower Respiratory Tracts Human influenza virus

HA RNA NA RNA

HA RNA NA RNA

used to manufacture new viruses in the host cell, can make the difference between a somewhat pathogenic influenza virus and a lethal one. It is still not clear exactly how many of these minor changes can lead to pandemic levels of infection and a catastrophe for the public health. Insight 21.1 gives a breakdown of some of the important developments in the history of influenza. ▶

HA NA Human influenza virus with duck HA spike

and humans live close together, the swine can serve as a melting pot for creating “hybrid” influenza viruses that are not recognized by the human immune system.

display on their surfaces. For instance, in 2004 the most common circulating subtypes of influenza A viruses were H1N1 and H3N2. Influenza B viruses are not divided into subtypes because they are thought only to undergo antigenic drift and not antigenic shift. Influenza C viruses are thought to cause only minor respiratory disease and are probably not involved in epidemics. Scientists have also recently found that antigenic drift and shift are not even required to make an influenza virus deadly. It appears that a minor genetic alteration in another influenza virus gene, one that seems to produce an enzyme

Pathogenesis and Virulence Factors

The influenza virus binds primarily to ciliated cells of the respiratory mucosa. Infection causes the rapid shedding of these cells along with a load of viruses. Stripping the respiratory epithelium to the basal layer eliminates protective ciliary clearance. Combine that with what is often called a “cytokine storm” caused by the viral stimulus and the lungs experience severe inflammation and irritation. The illness is further aggravated by fever, headache, and the other symptoms just described. The viruses tend to remain in the respiratory tract rather than spread to the bloodstream. As the normal ciliated epithelium is restored in a week or two, the symptoms subside. As just noted, the glycoproteins and their structure are important virulence determinants. First of all, they mediate the adhesion of the virus to host cells. Second, they change gradually and sometimes suddenly, evading immune recognition. One feature of the 2009 H1N1 virus is that it bound to cells lower in the respiratory tract, and at a much higher rate, leading to massive damage, and often death, in the worstaffected patients. There were a total of around 12,000 deaths worldwide in the 2009 pandemic. ▶

Figure 21.12 Antigenic shift event. Where ducks and swine

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Transmission and Epidemiology

Inhalation of virus-laden aerosols and droplets constitutes the major route of influenza infection, although fomites can play a secondary role. Transmission is greatly facilitated by crowding and poor ventilation in classrooms, barracks, nursing homes, dormitories, and military installations in the late fall and winter. The drier air of winter facilitates the spread of the virus, as the moist particles expelled by sneezes and coughs become dry very quickly, helping the virus remain airborne for longer periods of time. In addition, the dry cold air makes respiratory tract mucous membranes more brittle, with microscopic cracks that facilitate invasion by viruses. Influenza is highly contagious and affects people of all ages. Annually, there are approximately 36,000 U.S. deaths from seasonal influenza and its complications, mainly among the very young and the very old. The 2009 H1N1 virus took a particularly heavy toll on young people. Previously healthy children and teenagers formed a small but important risk group, with quite a few becoming ill within hours and dying within days. ▶

Culture and Diagnosis

Very often, physicians will diagnose influenza based on symptoms alone. But there is a wide variety of culturebased and nonculture-based methods to diagnose the

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INSIGHT 21.1

Flu Over the Years

Every year seasonal flu causes fairly predictable illness and death in the United States and in the world. As noted in this chapter, approximately 36,000 people die of seasonal flu every year. But when antigenic shifts occur in circulating flu viruses, pandemic

flu can occur. The process by which this happens can be hard to follow. Here is an abbreviated summary of antigenic shift and pandemic events during the last 120 years.

Influenza Event 1889

Historical Event

H2 strain replaces H1 for first time. One million die. People born before 1889 retain some immunity to H1, which will be helpful in 1918. Johnstown flood

1918

An H1N1 virus evolved from a bird virus into a human virus. 50 million worldwide die. Those born before 1889 (approximately 30 years old and above) have some immunity.

1918 pandemic; WWI

Seasonal flu outbreaks from 1919 to 1957 are caused by H1 viruses.

1931

Swine flu (H1N1) first isolated from U.S. pig.

1957

H1 human virus replaced by H2N2 causes Asian flu pandemic, which kills 1.5 million. People born after this date will have less immunity to the 2009 H1N1.

Al Capone indicted

American Bandstand’s first show

Martin Luther King Jr. assassinated

1968

H3N2 virus causes Hong Kong flu; kills 1 million.

1976

H1N1 pig virus kills 1 human. Forty-eight million people are vaccinated against this new virus, leading to 532 people suffering from Guillain-Barré syndrome.

1998

H1N1 swine flu emerges in livestock; it is human/bird/swine and dominates U.S. pigs.

War rages in Kosovo

2004–6

H5N1 bird flu hits. It is deadly to humans but does not spread between humans. It is also found in pigs.

Indian Ocean tsunami

2007–8

Panic increases about H5N1 bird flu, but it does not mutate to be transmissible between humans.

Major worldwide recession

The WHO declares a pandemic with H1N1 swine flu. The pandemic began in Mexico, spread worldwide. There were fewer than 100,000 deaths.

Swine flu pandemic

2009

Jimmy Carter elected president

21.4

Diseases Caused by Microorganisms Affecting Both the Upper and Lower Respiratory Tracts

infection. Rapid influenza tests (such as PCR, ELISA-type assays, or immunofluorescence) provide results within 24 hours; viral culture provides results in 3 to 10 days. Cultures are not typically performed at the point of care; they must be sent to diagnostic laboratories, and they require up to 10 days for results. Despite these disadvantages, culture can be useful to identify which subtype of influenza is causing infections, which is important for public health authorities to know. In 2009, officials did not often test for H1N1 but tested for influenza A or B; assuming if it was A that it was H1N1, since the circulating seasonal virus was influenza B. When specimens were tested, 100% of the influenza A isolates were in fact the H1N1. As the epidemic progressed, all flu cases that were identified were influenza A, indicating that it had replaced the seasonal virus. ▶

Prevention

Preventing influenza infections and epidemics is one of the top priorities for public health officials. The standard vaccine for seasonal flu contains inactivated dead viruses that were grown in embryonated eggs. It has an overall effectiveness of 70% to 90%. The vaccine consists of three different influenza viruses (usually two influenza A and one influenza B) that have been judged to most resemble the virus variants likely to cause infections in the coming flu season. Because of the changing nature of the antigens on the viral surface, annual vaccination is considered the best way to avoid infection. Anyone over the age of 6 months can take the vaccine, and it is recommended for anyone in a high-risk group or for people who have a high degree of contact with the public. Because research in monkeys shows that fetuses exposed to influenza in utero have a much higher risk of developing brain disorders resembling schizophrenia, vaccination of would-be mothers is also advised. A vaccine called FluMist is a nasal mist vaccine consisting of the three strains of influenza virus in live attenuated form. It is designed to stimulate secretory immunity in the upper respiratory tract. Its safety and efficacy have so far been demonstrated only for persons between the ages of 5 and 49. It is not advised for immunocompromised individuals, and it is significantly more expensive than the injected vaccine. During the 2009 H1N1 pandemic, new vaccine containing the pandemic strain was quickly prepared. Officials noted that if the strain had been noticed just a few weeks earlier it could have been included in the normal, seasonal vaccine. As it was, the existence of two vaccines added to the complexity of preventing the flu that year. One of the most promising new vaccine prospects is a vaccine that would protect against all flu viruses and not need to be given every year. This vaccine, in testing stages, would target the ion-channel proteins that are present on the envelope of influenza viruses. Apparently these proteins are the same on all flu viruses, and they do not mutate readily.

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This discovery has the possibility of revolutionizing influenza prevention. ▶

Treatment

Influenza is one of the first viral diseases for which effective antiviral drugs became available. The drugs must be taken early in the infection, preferably by the second day. This requirement is an inherent difficulty because most people do not realize until later that they may have the flu. Amantadine and rimantadine can be used to treat and prevent some influenza type A infections, but they do not work against influenza type B viruses. Relenza (zanamivir) is an inhaled drug that works against influenza A and B. Tamiflu (oseltamivir) is available in capsules or as a powdered mix to be made into a drink. It can also be used for prevention of influenza A and B. Over the period of 2007– 2009 different influenza viruses began to show resistance to one or more of these drugs, which called into question the practice of using the drugs preventively in epidemics. As we know with all antimicrobials, the more we use them, the more quickly we lose them (the more quickly they lose their effectiveness).

Disease Table 21.8 Influenza Causative Organism(s)

Influenza A, B, and C viruses

Most Common Modes of Transmission

Droplet contact, direct contact or indirect contact

Virulence Factors

Glycoprotein spikes, overall ability to change genetically

Culture/Diagnosis

Viral culture (3–10 days) or rapid antigen-based or PCR tests

Prevention

Killed injected vaccine or inhaled live attenuated vaccine—taken annually

Treatment

Amantadine, rimantadine, zanamivir, or oseltamivir

21.4 Learning Outcomes—Can You . . . 7. . . . list the possible causative agents, modes of transmission, virulence factors, diagnostic techniques, and prevention/treatment for each of the diseases infecting both the upper and lower respiratory tracts? These are: pertussis, RSV disease, and influenza. 8. . . . compare and contrast antigenic drift and antigenic shift in influenza viruses?

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21.5 Lower Respiratory Tract Diseases Caused by Microorganisms In this section, we consider microbial diseases that affect the lower respiratory tract primarily—namely, the bronchi, bronchioles, and lungs, with minimal involvement of the upper respiratory tract. Our discussion focuses on tuberculosis and pneumonia.

Tuberculosis Mummies from the Stone Age, ancient Egypt, and Peru provide unmistakable evidence that tuberculosis (TB) is an ancient human disease. In fact, historically it has been such a prevalent cause of death that it was called “Captain of the Men of Death” and “White Plague.” After the discovery of streptomycin in 1943, the rates of tuberculosis in the developed world declined rapidly. But since the mid-1980s, it has reemerged as a serious threat. Worldwide, 2 billion people are currently infected. Two billion—that is one-third of the world’s population! The cause of tuberculosis is primarily the bacterial species Mycobacterium tuberculosis, informally called the tubercle bacillus. ▶

E Epithelioid ccells

Signs and Symptoms

A clear-cut distinction can be made between infection with the TB bacterium and the disease it causes. In general, humans are rather easily infected with the bacterium but are resistant to the disease. Estimates project that only about 5% of infected people actually develop a clinical case of tuberculosis. Untreated tuberculosis progresses slowly, and people with the disease may have a normal life span, with periods of health alternating with episodes of morbidity. The majority (85%) of TB cases are contained in the lungs, even though disseminated TB bacteria can give rise to tuberculosis in any organ of the body. Clinical tuberculosis is divided into primary tuberculosis, secondary (reactivation or reinfection) tuberculosis, and disseminated or extrapulmonary tuberculosis.

Primary Tuberculosis The minimum infectious dose for lung infection is around 10 bacterial cells. Alveolar macrophages phagocytose these cells, but they are not killed and continue to multiply inside the macrophages. This period of hidden infection is asymptomatic or is accompanied by mild fever. Some bacteria escape from the lungs into the blood and lymphatics. After 3 to 4 weeks, the immune system mounts a complex, cell-mediated assault against the bacteria. The large influx of mononuclear cells into the lungs plays a part in the formation of specific infection sites called tubercles. Tubercles are granulomas that consist of a central core containing TB bacteria in enlarged macrophages and an outer wall made of fibroblasts, lymphocytes, and macrophages (figure 21.13). Although this response further checks spread of infection and helps prevent the disease, it also carries a potential for damage. Frequently, as neutrophils come on the scene and release their enzymes, the centers of tubercles break down into necrotic caseous

Figure 21.13 Tubercle formation. Photomicrograph of a tubercle (16×). The massive granuloma infiltrate has obliterated the alveoli and set up a dense collar of fibroblasts, lymphocytes (granuloma cells), and epithelioid cells. The core of this tubercle is a caseous (cheesy) material containing the bacilli.

(kay′-see-us) lesions that gradually heal by calcification— normal lung tissue is replaced by calcium deposits. The response of T cells to M. tuberculosis proteins also causes a cell-mediated immune response evident in the skin test called the tuberculin reaction, a valuable diagnostic and epidemiological tool (figure 21.14).

Secondary (Reactivation) Tuberculosis Although the majority of adequately treated TB patients recover more or less completely from the primary episode of infection, live bacteria can remain dormant and become reactivated weeks, months, or years later, especially in people with weakened immunity. In chronic tuberculosis, tubercles filled with masses of bacteria expand, cause cavities in the lungs, and drain into the bronchial tubes and upper respiratory tract. The patient gradually experiences more severe symptoms, including violent coughing, greenish or bloody sputum, low-grade fever, anorexia, weight loss, extreme fatigue, night sweats, and chest pain. It is the gradual wasting of the body that

21.5

Lower Respiratory Tract Diseases Caused by Microorganisms

▶ Epidermis

Dermis

Injection of PPD

Small bleb develops

(a)

5–9 mm Positive if person is in category 1 (b)

10–14 mm Positive if person is in category 2

15 mm Positive if person is in category 3

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Causative Agents

M. tuberculosis is the cause of tuberculosis in most patients. It is an acid-fast rod, long and thin. It is a strict aerobe, and technically speaking, there is still debate about whether it is a gram-positive or a gram-negative organism. It is rarely called gram anything, however, because its acid-fast nature is much more relevant in a clinical setting (figure 21.15). It grows very slowly. With a generation time of 15 to 20 hours, a period of up to 6 weeks is required for colonies to appear in culture. (Note: The prefix Myco- might make you think of fungi, but this is a bacterium. The prefix in the name came from the mistaken impression that colonies growing on agar [figure 21.16] resembled fungal colonies. And be sure to differentiate this bacterium from Mycoplasma—they are unrelated.)

Figure 21.14 Skin testing for tuberculosis. (a, b) The Mantoux test. Tuberculin is injected into the dermis. A small bleb from the injected fluid develops but will be absorbed in a short time. After 48 to 72 hours, the skin reaction is rated by the degree (or size) of the raised area. The surrounding red area is not counted in the measurement. A reaction of less than 5 mm is negative in all cases. See also figure 16.14.

accounts for an older name for tuberculosis—consumption. Untreated secondary disease has nearly a 60% mortality rate.

Extrapulmonary Tuberculosis TB infection outside of the lungs is more common in immunosuppressed patients and young children. Organs most commonly involved in extrapulmonary TB are the regional lymph nodes, kidneys, long bones, genital tract, brain, and meninges. Because of the debilitation of the patient and the high load of TB bacteria, these complications are usually grave. Renal tuberculosis results in necrosis and scarring of the kidney and the pelvis, ureters, and bladder. This damage is accompanied by painful urination, fever, and the presence of blood and the TB bacterium in urine. Genital tuberculosis in males damages the prostate gland, epididymis, seminal vesicle, and testes; and in females, the fallopian tubes, ovaries, and uterus. Tuberculosis of the bones and joints is a common complication. The spine is a frequent site of infection, although the hip, knee, wrist, and elbow can also be involved. Advanced infiltration of the vertebral column produces degenerative changes that collapse the vertebrae, resulting in abnormal curvature of the thoracic region (humpback) or of the lumbar region (swayback). Neurological damage stemming from compression on nerves can cause extensive paralysis and sensory loss. Tubercular meningitis is the result of an active brain lesion seeding bacteria into the meninges. Over a period of several weeks, the infection of the cranial compartments can create mental deterioration, permanent retardation, blindness, and deafness. Untreated tubercular meningitis is invariably fatal, and even treated cases can have a 30% to 50% mortality rate.

Figure 21.15 A fluorescent acid-fast stain of Mycobacterium tuberculosis from sputum. Smears are evaluated in terms of the number of AFB (acid-fast bacteria) seen per field. This quantity is then applied to a scale ranging from 0 to 4+, 0 being no AFB observed and 4+ being more than 9 AFB per field.

Figure 21.16 Cultural appearance of Mycobacterium tuberculosis. growth.

Colonies with a typical granular, waxy pattern of

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Robert Koch identified that M. tuberculosis often forms serpentine cords while growing, and he called the unknown substance causing this style of growth cord factor. Cord factor appears to be associated with virulent strains, and it is a lipid component of the mycobacterial cell wall. All mycobacterial species have walls that have a very high content of complex lipids, including mycolic acid and waxes. This chemical characteristic makes them relatively impermeable to stains and difficult to decolorize (acid-fast) once they are stained. The lipid wall of the bacterium also influences its virulence and makes it resistant to drying and disinfectants. In recent decades, tuberculosis-like conditions caused by Mycobacterium avium and related mycobacterial species (sometimes referred to as the M. avium complex, or MAC) have been found in AIDS patients and other immunocompromised people. In this section, we consider only M. tuberculosis, although M. avium is discussed briefly near the conclusion. Before routine pasteurization of milk, humans acquired bovine TB, caused by a species called Mycobacterium bovis, from the milk they drank. It is very rare today, but in 2004, six people in a nightclub acquired bovine TB from a fellow reveler. One person died from her infection. ▶

Pathogenesis and Virulence Factors

The course of the infection—and all of its possible variations— was previously described under “Signs and Symptoms.” Important characteristics of the bacterium that contribute to its virulence are its waxy surface (contributing both to its survival in the environment and its survival within macrophages) and its ability to stimulate a strong cell-mediated immune response that contributes to the pathology of the disease. ▶

Transmission and Epidemiology

The agent of tuberculosis is transmitted almost exclusively by fine droplets of respiratory mucus suspended in the air. The TB bacterium is highly resistant and can survive for 8 months in fine aerosol particles. Although larger particles become trapped in mucus and are expelled, tinier ones can be inhaled into the bronchioles and alveoli. This effect is especially pronounced among people sharing small closed rooms with limited access to sunlight and fresh air. The epidemiological patterns of M. tuberculosis infection vary with the living conditions in a community or an area of the world. Factors that significantly affect people’s susceptibility to tuberculosis are inadequate nutrition, debilitation of the immune system, poor access to medical care, lung damage, and their own genetics. Put simply, TB is an infection of poverty. People in developing countries are often infected as infants and harbor the microbe for many years until the disease is reactivated in young adulthood. 1.8 million people died from TB in 2008, the equivalent of 4,500 a day. Case rates have begun to drop in the United States, from a high in 2004. About 60% of cases in the United States are in foreign-born persons. This is important to know as a health care provider so you can be alert for TB in certain populations. The

top five countries of origin of people in the United States with TB in 2009 were Mexico, Philippines, Vietnam, India, and China. ▶

Culture and Diagnosis

You are probably familiar with several methods of detecting tuberculosis in humans. Clinical diagnosis of tuberculosis relies on four techniques: (1) tuberculin testing, (2) chest X rays, (3) direct identification of acid-fast bacilli (AFB) in sputum or other specimens, and (4) cultural isolation and antimicrobial susceptibility testing.

Tuberculin Sensitivity and Testing Because infection with the TB bacillus can lead to delayed hypersensitivity to tuberculoproteins, testing for hypersensitivity has been an important way to screen populations for tuberculosis infection and disease. Although there are newer methods available, the most widely used test is still the tuberculin skin test, called the Mantoux test. It involves local injection of purified protein derivative (PPD), a standardized solution taken from culture fluids of M. tuberculosis. The injection is done intradermally into the forearm to produce an immediate small bleb. After 48 and 72 hours, the site is observed for a red wheal called an induration, which is measured and interpreted as positive or negative according to size (see figure 21.14). The accepted practices for tuberculin testing are currently limited to selected groups known to have higher risk for tuberculosis infection. It is no longer used as a routine screening method among populations of children or adults who are not within the target groups. The reasoning behind this change is to allow more focused screening and to reduce expensive and unnecessary follow-up tests and treatments. Guidelines for test groups and methods of interpreting tests are listed in the following summary.2 Category 1. Induration (skin reaction) that is equal to or greater than 5 millimeters is classified as positive in persons: • Who have had contact with actively infected TB patients • Who are HIV-positive or have risk factors for HIV infection • With past history of tuberculosis as determined through chest X rays Category 2. Induration that is equal to or greater than 10 millimeters is classified as positive in persons who are not in category 1 but who fit the following high-risk groups: • HIV-negative intravenous drug users • Persons with medical conditions that put them at risk for progressing from latent TB infection to active TB • Persons who live or work in high-risk residences such as nursing homes, jails, or homeless shelters • New immigrants from countries with high rates of TB • Low-income populations lacking access to adequate medical care 2. See the entire guidelines at www.thoracic.org

21.5

• High-risk adults from ethnic minority populations as determined by local public health departments • Children who have contact with members of high-risk adult populations

Lower Respiratory Tract Diseases Caused by Microorganisms

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Area of infection

Category 3. Induration that is equal to or greater than 15 millimeters is classified as positive in persons who do not meet criteria in categories 1 or 2. A positive reaction in a person from one of the risk groups is fairly reliable evidence of recent infection or reactivation of a prior latent infection. Because the test is not 100% specific, false positive reactions will occasionally occur in patients who have recently been vaccinated with the BCG vaccine. Because BCG vaccination can also stimulate delayed hypersensitivity, clinicians must weigh a patient’s vaccine history, especially among individuals who have immigrated from countries where the vaccine is routinely given. Another cause of a false positive reaction is the presence of an infection with a closely related species of Mycobacterium. A negative skin test usually indicates that ongoing TB infection is not present. In some cases, it may be a false negative, meaning that the person is infected but is not yet reactive. One cause of a false negative test may be that it is administered too early in the infection, requiring retesting at a later time. Subgroups with severely compromised immune systems, such as those with AIDS, advanced age, and chronic disease, may be unable to mount a reaction even though they are infected. Skin testing may not be a reliable diagnostic indicator in these populations.

Figure 21.17 Primary tuberculosis.

X Rays Chest X rays can help verify TB when other tests have given indeterminate results, and they are generally used after a positive test for further verification. X-ray films reveal abnormal radiopaque patches, the appearance and location of which can be very indicative. Primary tubercular infection presents the appearance of fine areas of infiltration and enlarged lymph nodes in the lower and central areas of the lungs (figure 21.17). Secondary tuberculosis films show more extensive infiltration in the upper lungs and bronchi and marked tubercles. Scars from older infections often show up on X rays and can furnish a basis for comparison when trying to identify newly active disease.

Figure 21.18 Ziehl-Neelsen staining of Mycobacterium tuberculosis in sputum.

Acid-Fast Staining The diagnosis of tuberculosis in people with positive skin tests or X rays can be backed up by acidfast staining of sputum or other specimens. Several variations on the acid-fast stain are currently in use. The Ziehl-Neelsen stain produces bright red acid-fast bacilli (AFB) against a blue background (figure 21.18). Fluorescence staining shows luminescent yellow-green bacteria against a dark background (see figure 21.15). Diagnosis that differentiates between M. tuberculosis and other mycobacteria must be accomplished as rapidly as possible so that appropriate treatment and isolation precautions can be instituted. The newer fast-identification techniques such as fluorescent staining (see figure 21.15), high-performance

liquid chromatography (HPLC) analysis of mycolic acids, and PCR diagnosis can and should be used to identify isolates as Mycobacterium. Even though newer cultivation schemes exist that shorten the incubation period from 6 weeks to several days, this delay is unacceptable for beginning treatment or isolation precautions. But culture still must be performed because growing colonies are required to determine antibiotic sensitivities. Because the specimens are often contaminated with rapid-growing bacteria that will interfere with the isolation of M. tuberculosis, they are pretreated with chemicals to remove contaminants and are plated onto selective medium

M. tuberculosis

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(such as Lowenstein-Jensen medium). M. tuberculosis colonies are depicted in figure 21.16. ▶

Prevention

Preventing TB in the United States is accomplished by limiting exposure to infectious airborne particles. Extensive precautions, such as isolation in negative-pressure rooms, are used in health care settings when a person with active TB is identified. Vaccine is generally not used in the United States, although an attenuated vaccine, called BCG, is used in many countries. BCG stands for Bacille Calmette-Guerin, named for two French scientists who created the vaccine in the early 1900s. It is a live strain of a bovine tuberculosis bacterium that has been made avirulent by long passage through artificial media. In 2007 scientists made the observation that the BCG vaccine currently used is fairly ineffective and that original BCG strains from a much earlier time induce stronger immunity in patients. There is talk of reviving the older BCG strains and perhaps using this new-old BCG vaccine more widely, in the face of treatment failures and the huge infection rates. Remember that persons vaccinated with BCG may respond positively to a tuberculin skin test. In the past, prevention in the context of tuberculosis referred to preventing a person with latent TB from experiencing reactivation. This strategy is more accurately referred to as treatment of latent infection and is considered in the next section. ▶

Treatment

Treatment of latent TB infection is effective in preventing fullblown disease in persons who have positive tuberculin skin tests and who are at risk for reactivated TB. Treatment with isoniazid for 9 months or with a combination of rifampin plus an additional antibiotic called pyrazinamide for 2 months is recommended. Treatment of active TB infection when the microorganism has been found to have no antibiotic resistance consists of 9 months of treatment with isoniazid plus rifampin, with pyrazinamide also taken for the first 2 months. If there is evidence of extrapulmonary tubercular disease, the treatment should be extended to 12 months. When the bacterium is resistant to one or more of the preceding agents, at least three additional antibiotics must be added to the treatment regimen and the duration of treatment should be extended. One of the biggest problems with TB therapy is noncompliance on the part of the patient. It is very difficult, even under the best of circumstances, to keep to a regimen of multiple antibiotics daily for months. And most TB patients are not living under the best of circumstances. But failure to adhere to the antibiotic regimen leads to antibiotic resistance in the slow-growing microorganism, and in fact many M. tuberculosis isolates are now found to be MDR-TB, or multidrug-resistant TB. For

A Note About Directly Observed Therapy Although it is highly labor intensive, directly observed therapy (DOT) seems to be the most effective means of curbing infections and preventing further development of antibiotic resistance. The WHO estimates that 8 million deaths have been prevented by DOT over the last 15 years. Patients are referred for DOT if a physician suspects they will have trouble adhering to the very rigorous and lengthy antibiotic schedule. At that point a public health worker is assigned to visit them at their home and/or workplace to watch them take their medicines. One innovative program to alleviate the laborintensiveness of such an approach has been developed at the Massachusetts Institute of Technology. Patients receive a container of filter paper that dispenses a filter paper at timed intervals. They dip the paper in their urine and if the antibiotic is present in their urine the filter paper reveals a code that the patient texts to a central database. If they miss fewer than five pills a month they receive free minutes for their cell phones.

this reason, it is recommended that all patients with TB be treated by directly observed therapy (DOT), in which ingestion of medications is observed by a responsible person (see Note). The threat to public health is so great when patients do not adhere to treatment regimens that the United States and other countries have occasionally incarcerated people—and isolated them—when they don’t follow their treatment schedules. In 2006, a new strain of M. tuberculosis was identified in Africa. It is particularly lethal for HIV-infected people and has been named XDR-TB (extensively drug-resistant TB). XDRTB is defined as resistance to isoniazid and rifampin plus resistance to any fluoroquinolone and at least one of three injectable second-line anti-TB drugs. Since 2006 XDR-TB has spread around the world, and the CDC estimates that 500,000 new cases are seen every year. In the United States, a handful of cases of XDR-TB occur each year.

Mycobacterium avium Complex (MAC) Before the introduction of effective HIV treatments, described in chapter 20, disseminated tuberculosis infection with MAC was one of the biggest killers of AIDS patients. It mainly affects patients with CD4 counts below 50 cells per milliliter of blood. Antibiotics to prevent this condition should be given to all patients with AIDS. In 2009 scientists discovered that M. avium is a frequent inhabitant of showerheads that are served by city water systems, and can be an important source of infection for people with a variety of underlying respiratory conditions (Disease Table 21.9).

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Disease Table 21.9 Tuberculosis Causative Organism(s)

Mycobacterium tuberculosis

Mycobacterium avium complex

Most Common Modes of Transmission

Vehicle (airborne)

Vehicle (airborne)

Virulence Factors

Lipids in wall, ability to stimulate strong cell-mediated immunity (CMI)

–

Culture/Diagnosis

Rapid methods plus culture; initial tests are skin testing

Positive blood culture and chest X ray

Prevention

Avoiding airborne M. tuberculosis, BCG vaccine in other countries

Rifabutin or azithromycin given to AIDS patients at risk

Treatment

Isoniazid, rifampin, and pyrazinamide + ethambutol or streptomycin for varying lengths of time (always lengthy); if resistant, two other drugs added to regimen

Azithromycin or clarithromycin plus one additional antibiotic

Distinctive Features

Responsible for nearly all TB except for some HIV-positive patients

Suspect this in HIV-positive patients

Pneumonia Pneumonia is a classic example of an anatomical diagnosis. It is defined as an inflammatory condition of the lung in which fluid fills the alveoli. The set of symptoms that we call pneumonia can be caused by a wide variety of different microorganisms. In a sense, the microorganisms need only to have appropriate characteristics to allow them to circumvent the host’s defenses and to penetrate and survive in the lower respiratory tract. In particular, the microorganisms must avoid being phagocytosed by alveolar macrophages, or at least avoid being killed once inside the macrophage. Bacteria and a wide variety of viruses can cause pneumonias. Viral pneumonias are usually, but not always, milder than those caused by bacteria. At the same time, some bacterial pneumonias are very serious and others are not. In addition, fungi such as Histoplasma can also cause pneumonia. Overall, U.S. residents experience 2 to 3 million cases of pneumonia and more than 45,000 deaths due to this condition every year. It is much more common in the winter. Physicians distinguish between community-acquired pneumonias and nosocomial pneumonias, because different bacteria are more likely to be causing the two types. Community-acquired pneumonias are those experienced by persons in the general population. Nosocomial pneumonias are those acquired by patients in hospitals and other health care residential facilities. All pneumonias have similar symptoms, which we describe next, followed by separate sections for each type of pneumonia. ▶

Signs and Symptoms

Pneumonias of all types usually begin with upper respiratory tract symptoms, including runny nose and congestion. Headache is common. Fever is often present, and the onset of lung symptoms follows. These symptoms are chest pain, fever,

cough, and the production of discolored sputum. Because of the pain and difficulty of breathing, the patient appears pale and presents an overall sickly appearance. The severity and speed of onset of the symptoms varies according to the etiologic agent. ▶

Causative Agents of Community-Acquired Pneumonia

Streptococcus pneumoniae (often called pneumococcus) accounts for about two-thirds of community-acquired bacterial pneumonia cases. It causes more lethal pneumonia cases than any other microorganism. Legionella is a less common but serious cause of the disease. Haemophilus influenzae had been a major cause of community-acquired pneumonia, but the introduction of the Hib vaccine in 1988 has reduced its incidence. A number of bacteria cause a milder form of pneumonia that is often referred to as “walking pneumonia.” Two of these are Mycoplasma pneumoniae and Chlamydophila pneumoniae (formerly known as Chlamydia pneumoniae).3 Histoplasma capsulatum is a fungus that infects many people but causes a pneumonia-like disease in relatively few. One virus causes a type of pneumonia that can be very serious: hantavirus, which emerged in 1993 in the United States. Pneumonia may be a secondary effect of influenza disease. Some physicians treat pneumonia empirically, meaning they do not determine the etiologic agent. The rest of this section covers pneumonias caused by S. pneumoniae, Legionella, Mycoplasma, the hantavirus, and the fungi Histoplasma and Pneumocystis in more detail.

3. The genus formerly known as Chlamydia contains two important human pathogens, Chlamydia pneumoniae and Chlamydia trachomatis. The latter remains “Chlamydia,” but the respiratory pathogen is now Chlamydophila pneumoniae.

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Pneumococci

(a)

Polymorphonuclear neutrophils

10 μm

(b)

Figure 21.19 Streptococcus pneumoniae. (a) Gram stain of sputum. (b) Alpha-hemolysis of S. pneumoniae on blood agar.

Streptococcus pneumoniae This bacterium, which is often simply called the pneumococcus, is a small, gram-positive flattened coccus that often appears in pairs, lined up end to end (figure 21.19a). It is alpha-hemolytic on blood agar (figure 21.19b). S. pneumoniae is normal biota in the upper respiratory tract of from 5% to 50% of healthy people. Infection can occur when the bacterium is inhaled into deep areas of the lung or by transfer of the bacterium between two people via respiratory droplets. S. pneumoniae is very delicate and does not survive long out of its habitat. Factors that favor the ability of the pneumococcus to cause disease are old age, the season (rate of infection is highest in the winter), underlying viral respiratory disease, diabetes, and chronic abuse of alcohol or narcotics. Healthy people commonly inhale this and other microorganisms into the respiratory tract without serious consequences because of the host defenses present there. Pneumonia is likely to occur when mucus containing a load of bacterial cells passes into the bronchi and alveoli. The pneumococci multiply and induce an overwhelming inflammatory response. The polysaccharide capsule of the bacterium prevents efficient phagocytosis, with the result that edematous fluids are continuously released into the lungs. In one form of pneumococcal pneumonia, termed lobar pneumonia, in which the infection is focused in and eventually totally fills an entire lobe of the lung, this fluid accumulates in the alveoli along with red and white blood cells. As the infection and inflammation spread rapidly through the lung, the patient can actually “drown” in his or her own secretions. If this mixture of exudates, cells, and bacteria solidifies in the air spaces, a condition known as consolidation (figure 21.20) occurs. In infants and the elderly, the areas of infection are usually spottier and centered more in the bronchi than in the

alveoli (bronchial pneumonia). Systemic complications of pneumonia are pleuritis and endocarditis, but pneumococcal bacteremia and meningitis are the greatest danger to the patient. Because the pneumococcus is such a frequent cause of pneumonia in older adults, this population is encouraged to seek immunization with the older pneumococcal polysaccharide vaccine, which stimulates immunity to the capsular polysaccharides of 23 different strains of the bacterium. Active disease is treated with antibiotics, but the choice of antibiotic is often difficult. Many isolates of S. pneumoniae are resistant to penicillin and its derivatives, as well as to the macrolides, so often cephalosporins are now prescribed. Treatment also varies based on whether the patient is outpatient or inpatient, and whether they are in ICU or not. This bacterium is clearly capable of rapid development of resistance, and effective treatment requires that the practitioner be familiar with local resistance trends.

Legionella pneumophila Legionella is a weakly gram-negative bacterium that has a range of shapes, from coccus to filaments. Several species or subtypes have been characterized, but L. pneumophila (lungloving) is the one most frequently isolated from infections. Although the organisms were originally described in the late 1940s, they were not clearly associated with human disease until 1976. The incident that brought them to the attention of medical microbiologists was a sudden and mysterious epidemic of pneumonia that afflicted 200 American Legion members attending a convention in Philadelphia and killed 29 of them. After 6 months of painstaking analysis, epidemiologists isolated the pathogen and traced its source to contaminated air-conditioning vents in the Legionnaires’ hotel.

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Capsule

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Cell Pneumococci

Exudate

Alveoli

Bronchus Bronchiole

Figure 21.20 The course of bacterial pneumonia. As the pneumococcus traces a pathway down the respiratory tree, it provokes intense inflammation and exudate formation. The blocking of the bronchioles and alveoli by consolidation of inflammatory cells and products is evident.

Legionella’s ability to survive and persist in natural habitats has been something of a mystery, yet it appears to be widely distributed in aqueous habitats as diverse as tap water, cooling towers, spas, ponds, and other fresh waters. It is resistant to chlorine. The bacteria can live in close association with free-living amoebas (figure 21.21). It is released during aerosol formation and can be carried for long distances. Cases have been traced to supermarket vegetable sprayers, Legionella bacteria

Amoeba cell

Figure 21.21 Legionella living intracellularly in the amoeba Hartmannella. Amoebas inhabiting natural waters appear to be the reservoir for this pathogen and a means for it to survive in rather hostile environments. The pathogenesis of Legionella in humans is likewise dependent on its uptake by and survival in phagocytes.

hotel fountains, and even the fallout from the Mount St. Helens volcano eruption in 1980. Although this bacterium can cause another disease called Pontiac fever, pneumonia is the more serious disease, with a fatality rate of 3% to 30%. Legionella pneumonia is thought of as an opportunistic disease, usually affecting elderly people and rarely being seen in children and healthy adults. It is difficult to diagnose, even with specific antibody tests. It is not transmitted person to person.

Mycoplasma pneumoniae Mycoplasmas, as you learned in chapter 4, are among the smallest known self-replicating microorganisms. They naturally lack a cell wall and are therefore irregularly shaped. They may resemble cocci, filaments, doughnuts, clubs, or helices. They are free-living but fastidious, requiring complex medium to grow in the lab. (This genus should not be confused with Mycobacterium.) Pneumonias caused by Mycoplasma (as well as those caused by Chlamydia and some other microorganisms) are often called atypical pneumonia—atypical in the sense that the symptoms do not resemble those of pneumococcal or other severe pneumonias. Mycoplasma pneumonia is transmitted by aerosol droplets among people confined in close living quarters, especially families, students, and the military. Lack of acute illness in most patients has given rise to the name “walking pneumonia.” For some reason, there is an increase in Mycoplasma pneumonias every 3 to 6 years in the United States. Diagnosis of Mycoplasma may begin with ruling out other bacteria or viral agents. Serological or PCR tests confirm the diagnosis. These bacteria do not stain with Gram’s stain and are not visible in direct smears of sputum.

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Hantavirus

Case File 21

In 1993, hantavirus suddenly burst into the American consciousness. A cluster of unusual cases of severe lung edema among healthy young adults arose in the Four Corners area of New Mexico. Most of the patients died within a few days. They were later found to have been infected with hantavirus, an agent that had previously only been known to cause severe kidney disease and hemorrhagic fevers in other parts of the world. The new condition was named hantavirus pulmonary syndrome (HPS). Since 1993, the disease has occurred sporadically, but it has a mortality rate of at least 33%. It is considered an emerging disease. ▶

▶

The church volunteers in El Salvador were doing heavy cleaning both indoors and outdoors, as well as working with soil (cleaning renovation sites, excavating the septic tank). Those activities point to the possible presence of two less common respiratory microorganisms: hantavirus and Histoplasma. Hantavirus is commonly found in places contaminated by mouse droppings, and the fungus Histoplasma often grows with the aid of bat and bird excrement in the places where it is endemic. Both microbes can become airborne when sweeping, digging, or vacuuming stirs up dust or dirt. ◾ Can you do some quick research to see whether hantavirus or Histoplasma is endemic to El Salvador?

Symptoms, Pathogenesis, and Virulence Factors

Common features of the prodromal phase of this infection include fever, chills, myalgias (muscle aches), headache, nausea, vomiting, and diarrhea or a combination of these symptoms. A cough is common but is not a prominent early feature. Initial symptoms resemble those of other common viral infections. Soon a severe pulmonary edema occurs and causes acute respiratory distress (ARDS, or acute respiratory distress syndrome, has many microbial and nonmicrobial causes; this is but one of them). The acute lung symptoms appear to be due to the presence of large amounts of hantavirus antigen, which becomes disseminated throughout the bloodstream (including the capillaries surrounding the alveoli of the lung). Massive amounts of fluid leave the blood vessels and flood the alveolar spaces in response to the inflammatory stimulus, causing severe breathing difficulties and a drop in blood pressure. The propensity to cause a massive inflammatory response could be considered a virulence factor for this organism.

Transmission and Epidemiology

Very soon after the initial cases in 1993, it became clear that the virus was associated with the presence of mice in close proximity to the victims. Investigators eventually determined that the virus, an enveloped virus of the bunyavirus family, is transmitted via airborne dust contaminated with the urine, feces, or saliva of infected rodents. Deer mice (figure 21.22) and other rodents can carry the virus with

few apparent symptoms. Small outbreaks of the disease are usually correlated with increases in the local rodent population. Epidemiologists suspect that rodents have been infected with this pathogen for centuries. It has no doubt been the cause of sporadic cases of unexplained pneumonia in humans for decades, but the incidence seems to be increasing, especially in areas of the United States west of the Mississippi River. ▶

Figure 21.22 The deer mouse, a major carrier of

Treatment and Prevention

The diagnosis is established by detection of IgM to hantavirus in the patient’s blood or by using PCR techniques to find hantavirus genetic material in clinical specimens. Treatment consists mainly of supportive care. Mechanical ventilation is often required. There is no specific treatment other than supportive care.

Histoplasma capsulatum Pulmonary infections with this dimorphic fungus have probably afflicted humans since antiquity, but it was not described until 1905 by Dr. Samuel Darling. Through the years, it has been known by various names: Darling’s disease, Ohio Valley fever, and spelunker’s disease. Certain aspects of its current distribution and epidemiology suggest that it has been an important disease for as long as humans have practiced agriculture. (See Insight 21.2 for other important fungal lung pathogens.) ▶

hantavirus.

Continuing the Case

Pathogenesis and Virulence Factors

Histoplasmosis presents a formidable array of manifestations. It can be benign or severe, acute or chronic, and it can show pulmonary, systemic, or cutaneous lesions. Inhaling a small dose of microconidia into the deep recesses of the lung establishes a primary pulmonary infection that is usually asymptomatic. Its primary location of growth is in the cytoplasm of phagocytes such as macrophages. It flourishes within these cells and is carried to other sites. Some people

21.5

INSIGHT 21.2

Lower Respiratory Tract Diseases Caused by Microorganisms

649

Fungal Lung Diseases

Increasingly, the microorganisms that cause pulmonary infections are fungi. Although still much rarer than bacterial lung infections, fungal pneumonias have shown a remarkable rise in incidence. One hospital in the Midwest reported an overall 20-fold increase in fungal infections (of all types) in the 10 years between the late 1970s and the late 1980s. And a great many of those infections occur in the lungs. As you read in chapter 5, two broad categories of fungi cause human infections: those considered to be primary pathogens, which readily cause disease even in healthy hosts, and opportunists, which cause disease primarily in hosts that are weakened due to underlying illness, advanced age, immune deficiency, or chemotherapy of some sort. The primary pathogens usually have restricted geographic distributions. Table 21.A describes major characteristics of these fungi. As you can imagine, when primary pathogens invade people with weakened immune systems, the results can be disastrous. In contrast to the primary pathogens, the opportunists are more likely to be ubiquitous and can affect weakened patients indiscriminately. Table 21.B lists some of the most common opportunistic fungal infections of the lungs. These opportunistic

fungal infections are the ones increasing at a steady rate in the modern era, for several reasons: • Fungi and their spores are everywhere. They constantly enter our respiratory tracts. They live in our GI tracts and on our skin. • Antibiotic use decreases the bacterial count in our bodies, leaving fungi unhindered and able to flourish. • More invasive procedures are being employed in hospitals and for outpatient procedures, opening pathways for fungi to access “sterile” areas of the body. • The number of patients who are immunosuppressed (or otherwise “weakened”) is constantly increasing. For these reasons, health care professionals should be particularly vigilant for symptoms of fungal diseases in patients who are hospitalized, are HIV-positive, or have other underlying health problems. Invasive fungal infections are extremely difficult to treat effectively; there is a significant mortality rate for patients suffering from opportunistic fungal infections in the lungs.

Table 21.A Primary Fungal Pathogens of the Lungs Pathogen

Geographic Distribution

Disease and Symptoms

Histoplasma capsulatum

All continents except Australia; highest rates in U.S. Ohio Valley

Histoplasmosis; aches, pains, and coughing; more severe symptoms include fever, night sweats, and weight loss

Blastomyces dermatitidis

Forest soils, areas of decaying wood and organic matter; worldwide distribution, in United States most common on East Coast and in Midwest

Blastomycosis—cough, chest pain, hoarseness, fever; severe cases involve skin and other organs; lung abscesses resemble malignant tumors; skin nodules, bone infections, involvement of central nervous system possible

Coccidioides immitis

Semiarid, hot climates; Mexico, Central and South America; southwest U.S., especially California and southern Arizona

Coccidioidomycosis—fever, chest pain, headaches, malaise, chronic infection can lead to pulmonary nodular growths and cavity formation in lungs

Paracoccidioides brasiliensis

Tropical and semitropical regions of South and Central America

Paracoccidioidomycosis—infections of lung and skin; in severe cases, fungus can invade lungs, skin, and lymphatic organs

Table 21.B Opportunistic Fungi in the Lungs Pathogen

Geographic Distribution

Pneumocystis (carinii) jiroveci

“PCP” pneumonia (see p. 651); cough, fever, shallow respiration, and cyanosis

Aspergillus spp.

Aspergillosis; fungus balls form in the lungs and other tissues, necrotic pneumonia, dissemination to the brain, heart, skin

Geotrichum candidum

Geotrichosis; secondary infections in tuberculosis or very ill patients

Cryptococcus neoformans*

Cryptococcosis; lung infections followed often by brain and meninges involvement

Candida albicans

Candidal lung infections; in HIV-positive and lung transplant patients

*Cryptococcus could fit in either category—primary or opportunistic pathogen—but its array of virulence factors are (individually) less potent than most of those expressed by primary pathogens. However, it often causes disease in otherwise healthy patients.

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INSIGHT 21.3

Infectious Diseases Affecting the Respiratory System

Bioterror in the Lungs

After the terrorist attacks of September 11, 2001, and the anthrax attacks via the U.S. Postal Service that occurred later that fall, the U.S. government renewed its interest in preparing for bioterror or biowarfare attacks of all kinds. The U.S. Public Health Service designated six infectious diseases as “Category A,” meaning that they have the highest priority in research and funding. Category A agents have the following characteristics:

Pulmonary Anthrax (or Inhalation Anthrax)

This disease is the result of lung infection with Bacillus anthracis (see chapter 20). It should be considered when there is lung congestion accompanied by fever, malaise, and headache. Chest X rays are very useful because a widened mediastinum (the interpleural space that appears as the dark divider in the center of most chest X rays) is pathognomic (path-oh1. They can be easily disseminated or no¯m-ik) for this disease. Typical brontransmitted from person to person. chopneumonia does not occur. In about 2. They result in high mortality rates and half of patients, a hemorrhagic meningitis have the potential for major public accompanies the pneumonitis. It is not health impact. transmitted from person to person, but 3. They have the ability to cause public because the bacterium forms endospores, panic and social disruption. these are easily disseminated through a X ray showing the widened mediastinum in 4. They require special action for public variety of methods. inhalation anthrax. health preparedness. The most useful test for this disease is Of the six diseases, three of them can have blood culture, because the organism is abuntheir primary effects in the respiratory tract: pulmonary anthrax, dant in blood. Treatment is with penicillin, doxycycline, or cipropneumonic plague, and tularemia. The other three diseases on the floxacin. People presumed to have been exposed to the agent are A list are botulism, smallpox, and viral hemorrhagic fevers. also treated with one of these antibiotics for 30 to 60 days, because One of the most important components of a successful bioterror the endospores may persist in the respiratory tract for several prevention strategy is early detection of infected persons. Because weeks before germinating and becoming susceptible to antibiotics. most of the conditions on the A list are rarely seen in the United A vaccine for anthrax is currently administered only to States, clinicians’ index of suspicion may be low. Here are the sympmilitary personnel and to some with occupational exposure to toms of the three agents that cause overt respiratory symptoms. livestock.

experience mild symptoms such as aches, pains, and coughing; but a few develop more severe symptoms, including fever, night sweats, and weight loss. The most serious systemic forms of histoplasmosis occur in patients with defective cell-mediated immunity such as AIDS patients. In these cases, the infection can lead to lesions in the brain, intestines, heart, liver, spleen, bone marrow, and skin. Persistent colonization of patients with emphysema and bronchitis causes chronic pulmonary histoplasmosis, a complication that has signs and symptoms similar to those of tuberculosis. ▶

Transmission and Epidemiology

The organism is endemically distributed on all continents except Australia. Its highest rates of incidence occur in the eastern and central regions of the United States, especially in the Ohio Valley. This fungus appears to grow most abundantly in moist soils high in nitrogen content, especially those supplemented by bird and bat droppings (figure 21.23). A useful tool for determining the distribution of H. capsulatum is to inject a fungal extract into the skin and monitor for

Figure 21.23 Sign in wooded area in Kentucky. The sign is covered in bird droppings. Up to 90% of the population in the Ohio Valley show evidence of past infection with Histoplasma.

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651

ease. As a bioterror weapon, it would most probably be disseminated via the aerosol This pneumonia illness is caused by Yerroute and most of the infections would no sinia pestis, the same agent responsible doubt be of the respiratory variety. The for bubonic plague (chapter 20). The first abrupt appearance of large numbers of signs of the pneumonic form are fever, people with acute pneumonitis that proheadache, weakness, and rapidly develgresses rapidly to sepsis would be the first oping pneumonia. Sometimes sputum is sign that a tularemia bioterror incident has bloody or watery. Within 2 to 4 days, reoccurred. Because F. tularensis does not spiratory failure and shock can ensue. The seem to be transmitted person to person, incidence of plague in the United States it would be unusual to find large numbers is low and generally of the bubonic type, of infected people over a short period of which is transmitted by fleas from a small time, which would raise the possibility mammal host. Y. pestis used as a bioterror Wright-Giemsa stain of Yersinia pestis from that there was an intentional release. agent would likely be disseminated as an peripheral blood. Tularemia is difficult to diagnose, aerosol, leading to large numbers of pneumonic cases. Gram stainand the first steps in a suspected bioterror incident would be to ing of sputum, blood, or lymph node aspirates would reveal gramrule out plague or anthrax pneumonic disease. The bacterium is negative rods, and additional staining with Wright or Giemsa stain extremely dangerous to laboratory workers, so caution must be would result in rods with characteristic bipolar staining. used if Francisella is suspected. Antibiotics such as tetracycline Without treatment, patients die within 2 to 6 days; but swift and gentamicin can prevent death in most cases. An investigaantibiotic therapy with streptomycin, gentamicin, tetracyclines, tional vaccine has been developed, but its use is not approved. or sulfonamides can save lives. A vaccine exists, but it does not As you can see, one of the greatest difficulties associated with protect against the pneumonic form of the disease and is no longer managing a bioterror incident is that initial symptoms in patients available in the United States. are nonspecific. The time it takes for public health officials to begin to suspect one of these unusual etiologic agents (as opposed to Tularemia common community-acquired respiratory infections) may make This infection, caused by Francisella tularensis, is not widely known in the difference between life and death for large numbers of people. the United States (see chapter 20). It can cause skin and bloodstream We already have one advantage, however. Since the fall of 2001, infections, lung disease, and severe ocular infections. The infectious U.S. health practitioners are much more alert to the possibility of dose is extremely low; as few as 10 bacteria can initiate serious disintentional dissemination of infectious agents.

Pneumonic Plague

allergic reactions (much like the TB skin test). Application of this test has verified the extremely widespread distribution of the fungus. In high-prevalence areas such as southern Ohio, Illinois, Missouri, Kentucky, Tennessee, Michigan, Georgia, and Arkansas, 80% to 90% of the population shows signs of prior infection. Histoplasmosis prevalence in the United States is estimated at about 500,000 cases per year, with several thousand of them requiring hospitalization and a small number resulting in death. People of both sexes and all ages incur infection, but adult males experience the majority of symptomatic cases. The oldest and youngest members of a population are most likely to develop serious disease.

a new infection, this test is not useful in diagnosis.) Fluorescent antibody to the fungus is also a useful diagnostic tool.

▶

Pneumocystis (carinii) jiroveci

Culture and Diagnosis

Discovering Histoplasma in clinical specimens is a substantial diagnostic indicator. Usually it appears as spherical, “fisheye” yeasts intracellularly in macrophages and occasionally as free yeasts in samples of sputum and cerebrospinal fluid. Complement fixation and immunodiffusion serological tests can support a diagnosis by showing a rising antibody titer. (Because a positive histoplasmin [skin] test does not indicate

▶

Prevention and Treatment

Avoiding the fungus is the only way to prevent this infection, and in many parts of the country this is impossible. Luckily, undetected or mild cases of histoplasmosis resolve without medical management. Chronic or disseminated disease calls for systemic antifungal chemotherapy. Amphotericin B and itraconazole are considered the drugs of choice and are usually administered in daily intravenous doses for up to several weeks. Surgery to remove affected masses in the lungs or other organs is sometimes also useful.

Although Pneumocystis jiroveci (formerly called P. carinii) was discovered in 1909, it remained relatively obscure until it was suddenly propelled into clinical prominence as the agent of Pneumocystis pneumonia (called PCP because of the old name of the fungus). PCP is the most frequent opportunistic infection in AIDS patients, most of whom will develop one or more episodes during their lifetimes.

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Symptoms, Pathogenesis, and Virulence Factors

In people with intact immune defenses, P. jiroveci is usually held in check by lung phagocytes and lymphocytes; but in those with deficient immune systems, it multiplies intracellularly and extracellularly. The massive numbers of fungi adhere tenaciously to the lung pneumocytes and cause an inflammatory condition. The lung epithelial cells slough off, and a foamy exudate builds up. Symptoms are nonspecific and include cough, fever, shallow respiration, and cyanosis (sı¯- h-no¯ -sis).

tion should be administered even if disease appears mild or is only suspected. It is sometimes given to patients with low T-cell counts to prevent the disease. The airways of patients in the active stage of infection often must be suctioned to reduce the symptoms (Disease Table 21.10).

Causative Agents of Nosocomial Pneumonia

Although conventional microscopy performed on sputum or lavage fluids is often used, immunofluorescence using monoclonal antibodies against the organism has a higher sensitivity.

About 1% of hospitalized or institutionalized people experience the complication of pneumonia. It is the second most common nosocomial infection, behind urinary tract infections. The mortality rate is quite high, between 30% and 50%. Although Streptococcus pneumoniae is frequently responsible, in addition it is very common to find a gram-negative bacterium called Klebsiella pneumoniae as well as anaerobic bacteria or even coliform bacteria in nosocomial pneumonia. Further complicating matters, many nosocomial pneumonias appear to be polymicrobial in origin—meaning that there are multiple microorganisms multiplying in the alveolar spaces. In nosocomial infections, bacteria gain access to the lower respiratory tract through abnormal breathing and aspiration of the normal upper respiratory tract biota (and occasionally the stomach) into the lungs. Stroke victims have high rates of nosocomial pneumonia. Mechanical ventilation is another route of entry for microbes. Once there, the organisms take advantage of the usual lowered immune response in a hospitalized patient and cause pneumonia symptoms.

▶

▶

e

▶

Transmission and Epidemiology

Unlike most of the human fungal pathogens, little is known about the life cycle or epidemiology of Pneumocystis. It is probably spread in droplet form between humans. Contact with the agent is so widespread that in some populations a majority of people show serological evidence of infection by the age of 3 or 4. Until the AIDS epidemic, symptomatic infections by this organism were very rare, occurring only among elderly people, premature infants, or patients that were severely debilitated or malnourished. ▶

Culture and Diagnosis

Prevention and Treatment

Traditional antifungal drugs are ineffective against Pneumocystis pneumonia because the chemical makeup of the organism’s cell wall differs from that of most fungi. The primary treatment is trimethoprim-sulfamethoxazole. This combina-

Culture and Diagnosis

Culture of sputum or of tracheal swabs is not very useful in diagnosing nosocomial pneumonia, because the condition is usually caused by normal biota. Obtaining cultures of fluids obtained through endotracheal tubes or from bronchoalveolar

Disease Table 21.10 Pneumonia Causative Organism(s)

Streptococcus pneumoniae

Legionella species

Mycoplasma pneumoniae

Most Common Modes of Transmission

Droplet contact or endogenous transfer

Vehicle (water droplets)

Droplet contact

Virulence Factors

Capsule

–

Adhesins

Culture/Diagnosis

Gram stain often diagnostic, alpha-hemolytic on blood agar

Requires selective charcoal yeast extract agar; serology unreliable

Rule out other etiologic agents

Prevention

Pneumococcal polysaccharide vaccine (23-valent)

–

No vaccine, no permanent immunity

Treatment

Cefotaxime, ceftriaxone, much resistance

Fluoroquinolone, azithromycin, clarithromycin

Recommended not to treat in most cases, doxycycline or macrolides may be used if necessary

Distinctive Features

Patient usually severely ill

Mild pneumonias in healthy people; can be severe in elderly or immunocompromised

Usually mild; “walking pneumonia”

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Lower Respiratory Tract Diseases Caused by Microorganisms

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A Note About Emerging Pneumonias In 2003 a virus from a family previously known only to cause cold-like symptoms burst onto the world stage as it started to cause pneumonias and death in Hong Kong. The SARS epidemic ended nearly as quickly as it started and since 2004 new cases of SARS have not been detected anywhere on the planet. Similarly, in 2007, a rare serotype of an adenovirus, which had previously only been known to cause mild respiratory disease, caused two U.S. outbreaks of severe pneumonia. We will highlight these two viruses briefly here. We do not include them in the main community-acquired pneumonia section and table since they are not well-established (in the case of the adenovirus) or currently active (in the case of SARS). But they are important illustrations of how changeable viruses can be, and how they can suddenly cause important outbreaks and epidemics.

eral dozen countries, from Australia and Canada to the United States, have reported cases. Most of the cases seem to have originated in people who had traveled to Asia or who had close contact with people from that region. Close contact (direct or droplet) seems to be required for its transmission. The virus is a previously unknown strain of coronavirus (family Coronaviridae). Symptoms begin with a fever of above 38°C (100.4°F) and progress to body aches and an overall feeling of malaise. Early in the infection, there seems to be little virus in the patient and a low probability of transmission. Within a week, viral numbers surge and transmissibility is very high. After 3 weeks, if the patient survives, viral levels decrease significantly and symptoms subside. Patients may or may not experience classic respiratory symptoms. They may develop breathing problems. Severe cases of the illness can result in respiratory distress and death.

Severe Acute Respiratory Syndrome–Associated Coronavirus In the winter of 2002, reports of an acute respiratory illness, originally termed an atypical pneumonia, began to filter in from Asia. In March of 2003, the World Health Organization issued a global health alert about the new illness. By mid-April, scientists had sequenced the entire genome of the causative virus, making the creation of diagnostic tests possible and paving the way for intensive research on the virus. The epidemic was contained by the end of July 2003, but in less than a year it had sickened more than 8,000 people. About 9% of those died. The disease was given the name SARS, for severe acute respiratory syndrome. It was concentrated in China and Southeast Asia, although sev-

Adenovirus 14 Adenoviruses generally cause mild disease. But in 2007 two separate outbreaks of severe pneumonia were caused by one serotype, adenovirus 14. The two outbreaks occurred simultaneously but showed no apparent link—one was on an Air Force base in Texas and the other was a community outbreak in Oregon. The infections were severe; in Oregon more than 75% of those infected were hospitalized and 33% required intubation. Eighteen percent of the patients in Oregon died. Retrospective examination of samples stored from 1993 to 2007 in Oregon found that this virus only started showing up after 2005. Cases continued to occur through mid-2008, but the epidemic had subsided.

Hantavirus

Histoplasma capsulatum

Pneumocystis jiroveci

Vehicle—airborne virus emitted from rodents

Vehicle—inhalation of contaminated soil

Droplet contact

Ability to induce inflammatory response

Survival in phagocytes

–

Serology (IgM), PCR identification of antigen in tissue

Usually serological (rising Ab titers)

Immunofluorescence

Avoid mouse habitats and droppings

Avoid contaminated soil/ bat, bird droppings

Antibiotics given to AIDS patients to prevent this

Supportive

Amphotericin B and/or itraconazole

Trimethoprim-sulfamethoxazole

Rapid onset; high mortality rate

Many infections asymptomatic

Vast majority occur in AIDS patients

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lavage provide better information but are fairly intrusive. It is also important to remember that if the patient has already received antibiotics, culture results will be affected. ▶

Prevention and Treatment

Because most nosocomial pneumonias are caused by microorganisms aspirated from the upper respiratory tract, measures that discourage the transfer of microbes into the lungs are very useful for preventing the condition. Elevating patients’ heads to a 45-degree angle helps reduce aspiration of secretions. Good preoperative education of patients about the importance of deep breathing and frequent coughing can reduce postoperative infection rates. Proper care of mechanical ventilation and respiratory therapy equipment is essential as well. Studies have shown that delaying antibiotic treatment of suspected nosocomial pneumonia leads to a greater likelihood of death. Even in this era of conservative antibiotic use, empiric therapy should be started as soon as nosocomial pneumonia is suspected, using multiple antibiotics that cover both gram-negative and gram-positive organisms.

Case File 21

Wrap-Up

The first time one of the church volunteers in El Salvador reported respiratory problems, a physician performed a chest X-ray. Although there are no specific radiographic signs that point definitively to histoplasmosis, this patient exhibited clear signs of inflammation, and i d the h physician suspected Histoplasma because it is endemic to Central and South America as well as to eastern Asia, Australia, and the midwestern United States. The diagnosis was confirmed in all 20 patients by conducting ELISA tests of urine or serum. ◾ Interestingly, histoplasmosis is highly prevalent in the Ohio River Valley of the United States. The majority of people living in this area are thought to have antibodies to the fungus, even though they may never have shown symptoms of the disease. Such persons may have been protected from the infection if they had taken a similar mission trip! See: 2009. JAMA 301(5):478−80.

Disease Table 21.11 Nosocomial Pneumonia

Causative Organism(s)

Gram-negative and gram-positive bacteria from upper respiratory tract or stomach

Most Common Modes of Transmission

Endogenous (aspiration)

Virulence Factors

–

Culture/Diagnosis

Culture of lung fluids

Prevention

Elevating patient’s head, preoperative education, care of respiratory equipment

Treatment

Broad-spectrum antibiotics

21.5 Learning Outcomes—Can You . . . 9. . . . list the possible causative agents, modes of transmission, virulence factors, diagnostic techniques, and prevention/treatment for each of the diseases infecting the lower respiratory tract? These are: tuberculosis, community-acquired pneumonia, and nosocomial pneumonia. 10. . . . discuss the problems associated with MDR-TB and XDR-TB? 11. . . . demonstrate an in-depth understanding of the epidemiology of tuberculosis infection? 12. . . . describe the importance of the recent phenomenon of cold viruses causing pneumonia? 13. . . . list the distinguishing characteristics of nosocomial versus community-acquired pneumonia?

21.5

Lower Respiratory Tract Diseases Caused by Microorganisms

▶ Summing Up

Taxonomic Organization Microorganisms Causing Disease in the Respiratory Tract Microorganism

Disease

Chapter Location

Gram-positive bacteria Streptococcus pneumoniae

Otitis media, pneumonia

S. pyogenes Corynebacterium diphtheriae

Pharyngitis Diphtheria

Otitis media, p. 627 Pneumonia, p. 645 Pharyngitis, p. 628 Diphtheria, p. 632

Otitis media Pharyngitis Whooping cough Tuberculosis Pneumonia

Otitis media, p. 627 Pharyngitis, p. 628 Whooping cough, p. 633 Tuberculosis, p. 640 Pneumonia, p. 646

Pneumonia

Pneumonia, p. 647

RSV disease Influenza Hantavirus pulmonary syndrome

RSV disease, p. 635 Influenza, p. 635 Pneumonia, p. 648

Pneumocystis pneumonia Histoplasmosis

Pneumonia, p. 651 Pneumonia, p. 648

Gram-negative bacteria Haemophilus influenzae Fusobacterium necrophorum Bordetella pertussis Mycobacterium tuberculosis,* M. avium complex Legionella spp. Other bacteria Mycoplasma pneumoniae RNA viruses Respiratory syncytial virus Influenza virus A, B, and C Hantavirus Fungi Pneumocystis jiroveci Histoplasma capsulatum

*There is some debate about the gram status of the genus Mycobacterium; it is generally not considered gram-positive or gram-negative.

655

INFECTIOUS DISEASES AFFECTING The Respiratory System

Otitis Media

Sinusitis

Streptococcus pneumoniae Haemophilus influenzae Other bacteria

Various bacteria Various fungi

Diphtheria

Rhinitis

Corynebacterium diphtheriae

200+ viruses

Pharyngitis

Streptococcus pyogenes Fusobacterium necrophorum Viruses

Whooping Cough

Bordetella pertussis

Influenza

Influenza virus A, B, or C

Respiratory Syncytial Virus Infection

RSV Pneumonia

Streptococcus pneumoniae Legionella Mycoplasma pneumoniae Hantavirus Histoplasma capsulatum Pneumocystis jiroveci

Tuberculosis

Mycobacterium tuberculosis Mycobacterium avium complex (MAC)

Bacteria Viruses Fungi

System Summary Figure 21.24 656

656

Chapter Summary

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Chapter Summary 21.1 The Respiratory Tract and Its Defenses • The upper respiratory tract includes the mouth, nose, nasal cavity and sinuses, throat (pharynx), and epiglottis and larynx. • The lower respiratory tract begins with the trachea, which feeds into the bronchi and bronchioles in the lungs. Alveoli, the site of oxygen exchange in the lungs, are attached to the bronchioles. • The ciliary escalator propels particles upward and out of the respiratory tract. Mucus on the surface of the mucous membranes traps microorganisms, and involuntary responses such as coughing, sneezing, and swallowing move them out of sensitive areas. Macrophages inhabit the alveoli of the lungs and the clusters of lymphoid tissue (tonsils) in the throat. Secretory IgA against specific pathogens can be found in the mucus secretions as well. 21.2 Normal Biota of the Respiratory Tract • Normal biota include Streptococccus pyogenes, Haemophilus influenzae, Streptococcus pneumoniae, Neisseria meningitidis, Staphylococcus aureus, Moraxella and Corynebacterium species, and Candida albicans. 21.3 Upper Respiratory Tract Diseases Caused by Microorganisms • Rhinitis, or the Common Cold: Caused by one of over 200 different kinds of viruses, most commonly the rhinoviruses, followed by the coronaviruses. Respiratory syncytial virus (RSV) causes colds in many people, but in some, especially children, can lead to more serious respiratory tract symptoms. • Sinusitis: Inflammatory condition most commonly caused by allergy or by a variety of viruses or bacteria and, less commonly, fungi. • Acute Otitis Media (Ear Infection): Viral infections of upper respiratory tract lead to inflammation of eustachian tubes and buildup of fluid in the middle ear, leading to bacterial multiplication in those fluids. Most common cause is Streptococcus pneumoniae. • Pharyngitis: The same viruses causing the common cold commonly cause inflammation of the throat. However, two potentially serious causes of pharyngitis are Streptococcus pyogenes and Fusobacterium necrophorum. Untreated streptococcal throat infections can result in scarlet fever, rheumatic fever, glomerulonephritis, and necrotizing fasciitis. Untreated F. necrophorum infections can lead to Lemierre’s syndrome. • Diphtheria: Caused by Corynebacterium diphtheriae, a non-spore-forming, gram-positive club-shaped bacterium. Employs exotoxin encoded by a bacteriophage of C. diphtheriae.

21.4 Diseases Caused by Microorganisms Affecting Both the Upper and Lower Respiratory Tracts • Whooping Cough: Caused by Bordetella pertussis. Releases exotoxins—pertussis toxin and tracheal cytotoxin—that damage ciliated respiratory epithelial cells and cripple other components of host defense, including phagocytic cells. • Respiratory Syncytial Virus (RSV): Produces giant multinucleated cells (syncytia). RSV is most prevalent cause of respiratory infection in newborn age group. • Influenza: Caused by one of three influenza viruses: A, B, or C. The ssRNA genome is subject to constant genetic changes that alter the structure of its envelope glycoprotein. This is called antigenic drift—resulting in decreased ability of host memory cells to recognize the virus. Antigenic shift, where one or more of eight RNA strands are swapped with gene or strand from a different influenza virus, is even more serious. 21.5 Lower Respiratory Tract Diseases Caused by Microorganisms • Tuberculosis: The cause is primarily the bacterium Mycobacterium tuberculosis. Vaccine generally not used in the United States, although an attenuated vaccine, called BCG, is used in many countries. • Mycobacterium avium complex: Before introduction of effective HIV treatments, disseminated tuberculosis infection with MAC was one of biggest killers of AIDS patients. • Pneumonia: An inflammatory condition of the lung in which fluid fills the alveoli; caused by wide variety of microorganisms. • Streptococcus pneumoniae: Main agent for communityacquired bacterial pneumonia cases. Legionella is a less common but serious cause of the disease. Haemophilus influenzae used to be a major cause, but use of the Hib vaccine has reduced its incidence. • Other bacterial causes are Mycoplasma pneumoniae and Chlamydophila pneumoniae. Histoplasma capsulatum, a fungus, causes a pneumonia-like disease. Hantavirus causes a pneumonia-like condition named hantavirus pulmonary syndrome (HPS). • Pneumonia may be a secondary effect of influenza disease. Physicians may treat pneumonia empirically, meaning they do not determine the etiologic agent. • Streptococcus pneumoniae and gram-negative Klebsiella pneumoniae are commonly responsible for nosocomial pneumonias. Furthermore, many nosocomial pneumonias appear to be polymicrobial in origin.

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Multiple-Choice and True-False Questions

Knowledge and Comprehension

Multiple-Choice Questions. Select the correct answer from the answers provided. 1. The two most common groups of virus associated with the common cold are a. rhinoviruses. d. both a and b. b. coronaviruses. e. both a and c. c. influenza viruses. 2. Which of the following conditions are associated with Streptococcus pyogenes? a. pharyngitis c. rheumatic fever b. scarlet fever d. all of the above 3. Which is not a characteristic of Streptococcus pyogenes? a. group A streptococcus c. sensitive to bacitracin b. alpha-hemolytic d. gram-positive 4. The common stain used to identify Mycobacterium species is a. Gram stain. c. negative stain. b. acid-fast stain. d. spore stain. 5. Which of the following techniques is used to diagnose tuberculosis? a. tuberculin testing b. chest X rays c. cultural isolation and antimicrobial testing d. all of the above 6. The DTaP vaccine provides protection against the following diseases, except a. diphtheria. c. pneumonia. b. pertussis. d. tetanus.

8. The vast majority of pneumonias caused by this organism occur in AIDS patients. a. hantavirus c. Pneumocystis jiroveci b. Histoplasma capsulatum d. Mycoplasma pneumoniae 9. The beta-hemolysis of blood agar observed with Streptococcus pyogenes is due to the presence of a. streptolysin. c. hyaluronic acid. b. M protein. d. catalase. 10. An estimated ____ of the world population is infected with Mycobacterium tuberculosis. a. 1/2 c. 1/3 b. 1/4 d. 3/4 True-False Questions. If the statement is true, leave as is. If it is false, correct it by rewriting the sentence. 11. Bordetella pertussis is the causative agent for whooping cough. 12. Mycoplasma pneumoniae causes “atypical” pneumonia and is diagnosed by sputum culture. 13. BCG vaccine is used in other countries to prevent Legionnaires’ disease. 14. Respiratory syncytial virus (RSV) is a respiratory infection associated with elderly people. 15. The “flu shot” can cause the flu in immunocompromised people.

7. Which of the following infections often has a polymicrobial cause? a. otitis media c. sinusitis b. nosocomial pneumonia d. all of the above

Critical Thinking Questions

Application and Analysis

These questions are suggested as a writing-to-learn experience. For each question, compose a one- or two-paragraph answer that includes the factual information needed to completely address the question. 1. What two vaccines are available for treating Streptococcus pneumoniae, and what are their target populations? 2. What parts of the body are affected by extrapulmonary tuberculosis? 3. a. What type of vaccine is used against Corynebacterium diphtheriae? b. What is the characteristic toxin produced by this microorganism? c. What treatment is suggested for a diphtheria infection? 4. a. Name the organisms responsible for the flu. b. To what family do these viruses belong? c. Describe the genome of this virus. 5. What are some of the likely explanations if you are not responding to antibiotic treatment for sinusitis? 6. Describe how you might design a vaccine against the common cold.

7. A 5-year-old boy is diagnosed with otitis media. He has severe pain in his left ear and a fever of 101°F. Inspection of the eardrum reveals that both membranes are red but intact. His history reveals that he seldom has ear infections. How would you treat this patient? 8. A graduate student from Namibia tests positive in the tuberculin skin test. Upon reading the patient history, the doctor determines that the test is a false positive and does not pursue further treatment. What is the possible explanation for the false positive skin test? 9. Why is noncompliance during TB therapy such a big concern? 10. Why do we need to take the flu vaccine every year? Why does it not confer long-term immunity to the flu like other vaccines?

Concept Mapping

Concept Mapping

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Synthesis

Appendix D provides guidance for working with concept maps. 1. Construct your own concept map using the following words as the concepts. Supply the linking words between each pair of concepts. FHA

tracheal cytotoxin

coughing

endotoxin

multiplication

cilia

pertussis toxin

mucus Bordetella pertussis

Visual Connections

Synthesis

These questions use visual images or previous content to make connections to this chapter’s concepts. 1. Figure 21.2. Some doctors suggest that gently forcing one’s ears to “pop” is an effective way to treat or even prevent ear infection. Use the following illustration to explain how this could work. External ear canal

2. From chapter 3, figure 3.21. Although there are many different organisms present in the respiratory tract, an acid-fast stain of sputum like the one shown here along with patient symptoms can establish a presumptive diagnosis of tuberculosis. Explain why.

Eardrum (bulging)

Acid-fast stain Red cells are acid-fast. Blue cells are non-acid-fast.

Inflammatory exudate Eustachian tube (inflamed)

www.connect.microbiology.com Enhance your study of this chapter with study tools and practice tests. Also ask your instructor about the resources available through ConnectPlus, including the media-rich eBook, interactive learning tools, and animations.

Infectious Diseases Affecting the Gastrointestinal Tract 22 Case File Following Hurricane Katrina in August 2005, relief agencies provided food and shelter to an estimated 240,000 of the region’s residents in a variety of locations. Approximately 24,000 evacuees were temporarily housed in the Reliant Park Sports and Convention Center in Houston, Texas, which was renamed Reliant City for the time being. A medical clinic was set up to serve the immediate needs of the residents. Over the next several weeks, 1,169 individuals visited the clinic exhibiting symptoms of acute gastroenteritis, specifically diarrhea, vomiting, or both. ◾ What are the organisms most commonly associated with acute gastroenteritis? ◾ How did this outbreak likely begin? How did it probably spread? Continuing the Case appears on page 682.

Outline and Learning Outcomes 22.1 The Gastrointestinal Tract and Its Defenses 1. Draw or describe the anatomical features of the gastrointestinal tract. 2. List the natural defenses present in the gastrointestinal tract. 22.2 Normal Biota of the Gastrointestinal Tract 3. List the types of normal biota presently known to occupy the gastrointestinal tract. 4. Describe how our view has changed of normal biota present in the stomach. 22.3 Gastrointestinal Tract Diseases Caused by Microorganisms (Nonhelminthic) 5. List the possible causative agents, modes of transmission, virulence factors, diagnostic techniques, and prevention/treatment for each of the kinds of oral diseases. 6. Discuss current theories about the connection between oral bacteria and cardiovascular disease.

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7. List the possible causative agents, modes of transmission, virulence factors, diagnostic techniques, and prevention/ treatment for mumps, gastritis, and gastric ulcers. 8. List the possible causative agents, modes of transmission, virulence factors, diagnostic techniques, and prevention/ treatment for acute and chronic diarrhea, and also for acute diarrhea with vomiting. 9. Differentiate among the main types of hepatitis and discuss each causative agent, mode of transmission, diagnostic techniques, prevention, and treatment of each. 22.4 Gastrointestinal Tract Diseases Caused by Helminths 10. Describe some distinguishing characteristics and commonalities seen in helminthic infections. 11. List four helminths that cause primarily intestinal symptoms, and identify which life cycle they follow and one unique fact about each one. 12. List four helminths that cause intestinal symptoms that may be accompanied by migratory symptoms, and identify which life cycle they follow and one unique fact about each one. 13. List the modes of transmission, virulence factors, diagnostic techniques, and prevention/treatment for each of the helminth infections resulting in liver and intestinal symptoms. These are infections caused by Opisthorchis sinensis, Clonorchis sinensis, and Fasciola hepatica. 14. Describe the type of disease caused by Trichinella species. 15. Diagram the life cycle of Schistosoma mansoni and S. japonicum, discuss how it differs from the life cycle of the Schistosoma involved in urinary disease, and describe the importance of all three organisms in world health.

22.1 The Gastrointestinal Tract and Its Defenses The gastrointestinal (GI) tract can be thought of as a long tube, extending from mouth to anus. It is a very sophisticated delivery system for nutrients, composed of eight main sections and augmented by four accessory organs. The eight sections are the mouth, pharynx, esophagus, stomach, small intestine, large intestine, rectum, and anus. Along the way, the salivary glands, liver, gallbladder, and pancreas add digestive fluids and enzymes to assist in digesting and processing the food we take in (figure 22.1). The GI tract is often called the digestive tract or the alimentary tract. Anything inside the GI tract is in some ways not “inside” the body; it is passing through an internal tube, called a lumen, and only those chemicals that are absorbed through the walls of the GI tract actually gain entrance to the internal portions of the body. Food begins to be broken down into absorbable subunits as soon as it enters the mouth, where the teeth begin to mechanically break down solid particles and where enzymes in saliva break the food down chemically. The swallowed food travels through the pharynx and into the esophagus, emptying into the stomach. Here the food is mixed with gastric juice, which has a very low pH and contains the important gastric enzyme pepsin, which breaks down proteins (peptides). From here the food travels to the small intestine, a long, tightly coiled portion of the lumen where most nutrient absorption takes place. The small intestine is divided into the duodenum (leading directly out of the stomach), the jejunum (most of the coiled part), and the ileum (connecting the coils to the large intestine). The pan-

creas secretes a variety of digestive enzymes into the small intestine, and the liver and the gallbladder work together to add bile. Once food leaves the small intestine, it enters the large intestine, which is divided into the cecum, the colon, the rectum, and the anus. In the large intestine, water and electrolytes are absorbed from any undigested food. What is left combines with mucus and bacteria from the large intestine, becoming fecal material. Forty to sixty percent of the mass of fecal material is composed of bacteria. The GI tract has a very heavy load of microorganisms, and it encounters millions of new ones every day. Because of this, defenses against infection are extremely important. All intestinal surfaces are coated with a layer of mucus, which confers mechanical protection. Secretory IgA can also be found on most intestinal surfaces. The muscular walls of the GI tract keep food (and microorganisms) moving through the system through the action of peristalsis. Various fluids in the GI tract have antimicrobial properties. Saliva contains the antimicrobial proteins lysozyme and lactoferrin. The stomach fluid is antimicrobial by virtue of its extremely high acidity. Bile is also antimicrobial. The entire system is outfitted with cells of the immune system, collectively called gut-associated lymphoid tissue (GALT). The tonsils and adenoids in the oral cavity and pharynx, small areas of lymphoid tissue in the esophagus, Peyer’s patches in the small intestine, and the appendix are all packets of lymphoid tissue consisting of T and B cells as well as cells of nonspecific immunity. One of their jobs is to produce IgA, but they perform a variety of other immune functions. Perhaps because of the great density of immune players

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Accessory Organs

Gastrointestinal Tract

Salivary glands Mouth

Pharynx

Esophagus

Stomach Liver

Gallbladder Small intestine

Pancreas

Large intestine

Rectum

Anus

Figure 22.1 Major organs of the digestive system.

in the intestines, they experience disease that is caused, or aggravated, by inflammatory processes (Insight 22.1). A huge population of commensal organisms lives in this system, especially in the large intestine. They provide the protection of microbial antagonism and avoid immune destruction through various mechanisms, including cloaking themselves with host sugars they find on the intestinal walls.

22.1 Learning Outcomes—Can You . . . 1. . . . draw or describe the anatomical features of the gastrointestinal tract? 2. . . . list the natural defenses present in the gastrointestinal tract?

22.2

INSIGHT 22.1

Normal Biota of the Gastrointestinal Tract

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Is Crohn’s an Infection That We Get from Cows?

There are two gastrointestinal conditions that cause massive suffering, yet are not covered in this chapter. Ulcerative colitis and Crohn’s disease are both considered inflammatory bowel diseases (IBDs), and as the name indicates, have long been thought to be the result of overactive and inappropriate immune reactions in the small and large intestines. Now it looks like one of those conditions may, in fact, have a microbial cause. Or, better said, a microbe might be one of the factors that contributes to the damage in the disease. Crohn’s disease has been the subject of intense scrutiny since it was noticed that cattle have a similar condition, characterized by chronic diarrhea, weight loss, neuropathy, and periods of remission. In cattle this is called Johne’s disease and is unambiguously caused by Mycobacterium avium subspecies paratuberculosis, known as MAP. A whopping 68% of U.S. dairy cows are infected with this bacterium, and it can easily be transmitted to humans through the food chain (beef and milk). As it happens, seven of eight Crohn’s patients have MAP bacteria in their tissues. And when they are treated with antimycobacterial drugs, many of them experience relief. Of course, this is biology and nothing is neat. For one thing, not every patient with Crohn’s is helped with antibiotic treatment. This could be explained by the difficulty of treating Mycobacterium, which we studied in the case of tuberculosis. Another puzzler is that one out of eight patients has no MAP. Some scientists

22.2 Normal Biota of the Gastrointestinal Tract As just mentioned, the GI tract is home to a large variety of normal biota. The oral cavity alone is populated by more than 550 known species of microorganisms, including Streptococcus, Neisseria, Veillonella, Staphylococcus, Fusobacterium, Lactobacillus, Corynebacterium, Actinomyces, and Treponema species. Fungi such as Candida albicans are also numerous. A few protozoa (Trichomonas tenax, Entamoeba gingivalis) also call the mouth “home.” Bacteria live on the teeth as well as the soft structures in the mouth. Numerous species of normal biota bacteria live on the teeth in large accretions called dental plaque, which is a kind of biofilm (see chapter 4). Bacteria are held in the biofilm by specific recognition molecules. Alphahemolytic streptococci are generally the first colonizers of the tooth surface after it has been cleaned. The streptococci attach specifically to proteins in the pellicle, a mucinous glycoprotein covering on the tooth. Then other species attach specifically to proteins or sugars on the surface of the streptococci, and so on. The pharynx contains a variety of microorganisms, which were described in chapter 21. Although the stomach was previously thought to be sterile, researchers in 2008 found the molecular signatures of 128 different species of microorganisms in the stomach. These must have mechanisms for overcoming the extreme acidity of the stomach fluid and can survive there. The large intestine has always

suspect a particular type of E. coli can also induce the inflammatory symptoms characteristic of Crohn’s. Supporting evidence for the role of MAP includes the fact that some patients treated with the traditional therapy, steroids to decrease the inflammation, actually do worse. It is tempting to speculate that this is because dampening the immune system would allow bacteria to flourish. Maybe it’s time for the gold standard of infectious disease causation to be employed: Koch’s postulates. Can you articulate a hypothesis and an experiment to prove that MAP causes Crohn’s?

been known to be a haven for billions of microorganisms (1011 per gram of contents), including the bacteria Bacteroides, Fusobacterium, Bifidobacterium, Clostridium, Streptococcus, Peptostreptococcus, Lactobacillus, Escherichia, and Enterobacter; the fungus Candida; and several protozoa as well. Researchers have also found archaea species there. The normal biota in the gut provide a protective function, but they also perform other jobs as well. Some of them help with digestion. Some provide nutrients that we can’t produce ourselves. E. coli, for instance, synthesizes vitamin K. Its mere presence in the large intestine seems to be important for the proper formation of epithelial cell structure. And the normal biota in the gut plays an important role in “teaching” our immune system to react to microbial antigens. Some scientists believe that the mix of microbiota in the healthy gut can influence a host’s chances for obesity or autoimmune diseases. The accessory organs (salivary glands, gallbladder, liver, and pancreas) are free of microorganisms, just as all internal organs are.

22.2 Learning Outcomes—Can You . . . 3. . . . list the types of normal biota presently known to occupy the gastrointestinal tract? 4. . . . describe how our view has changed of normal biota present in the stomach?

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22.3 Gastrointestinal Tract Diseases Caused by Microorganisms (Nonhelminthic)

the pulp, which contains blood vessels and nerves. These deeper infections lead to pain, referred to as a “toothache.”

Tooth and Gum Infections

Two representatives of oral alpha-hemolytic streptococci, Streptococcus mutans and Streptococcus sobrinus, seem to be the main causes of dental caries, although a mixed species consortium, consisting of other Streptococcus species and some lactobacilli, is probably the best route to caries. Note that in the absence of dietary carbohydrates bacteria do not cause decay.

It is difficult to pinpoint exactly when the “normal biota biofilm” just described becomes a “pathogenic biofilm.” If left undisturbed, the biofilm structure eventually contains anaerobic bacteria that can damage the soft tissues and bones (referred to as the periodontium) surrounding the teeth. Also, the introduction of carbohydrates to the oral cavity can result in breakdown of hard tooth structure (the dentition) due to the production of acid by certain oral streptococci in the biofilm. These two separate circumstances are discussed here.

Dental Caries (Tooth Decay) Dental caries is the most common infectious disease of human beings. The process involves the dissolution of solid tooth surface due to the metabolic action of bacteria. (Figure 22.2 depicts the structure of a tooth.) The symptoms are often not noticeable but range from minor disruption in the outer (enamel) surface of the tooth to complete destruction of the enamel and then destruction of deeper layers (figure 22.3). Deeper lesions can result in infection to the soft tissue inside the tooth, called

Crown

Cusp with occlusal surface Enamel Dentin Pulp cavity Gingival crevice Gingiva (gum)

Blood vessels and nerves in pulp

Root

Bone/socket Cementum Periodontal ligament Periodontal membrane Root canal

Figure 22.2 The anatomy of a tooth.

▶

▶

Causative Agent

Pathogenesis and Virulence Factors

In the presence of sucrose and, to a lesser extent, other carbohydrates, S. sobrinus and S. mutans produce sticky polymers of glucose called fructans and glucans. These adhesives help bind them to the smooth enamel surfaces and contribute to the sticky bulk of the plaque biofilm (figure 22.4). If mature plaque is not removed from sites that readily trap food, it can result in a carious lesion. This is due to the action of the streptococci and other bacteria that produce acid as they ferment the carbohydrates. If the acid is immediately flushed from the plaque and diluted in the mouth, it has little effect. However, in the denser regions of plaque, the acid can accumulate in direct contact with the enamel surface and lower the pH to below 5, which is acidic enough to begin to dissolve (decalcify) the calcium phosphate of the enamel in that spot. This initial lesion can remain localized in the enamel and can be repaired with various inert materials (fillings). Once the deterioration has reached the level of the dentin, tooth destruction speeds up and the tooth can be rapidly destroyed. Exposure of the pulp leads to severe tenderness and toothache, and the chance of saving the tooth is diminished. Teeth become vulnerable to caries as soon as they appear in the mouth at around 6 months of age. Early childhood caries, defined as caries in a child between birth and 6 years of age, can extensively damage a child’s primary teeth and affect the proper eruption of the permanent teeth. The practice of putting a baby down to nap with a bottle of fruit juice or formula can lead to rampant dental caries in the vulnerable primary dentition. This condition is called nursing bottle caries. ▶

Transmission and Epidemiology

The bacteria that cause dental caries are transmitted to babies and children by their close contacts, especially the mother or closest caregiver. There is evidence for transfer of oral bacteria between children in day care centers, as well. Although it was previously believed that humans don’t acquire S. mutans or S. sobrinus until the eruption of teeth in the mouth, it now seems likely that both of these species may survive in the infant’s oral cavity prior to appearance of the first teeth. Dental caries has a worldwide distribution. Its incidence varies according to many factors, including amount of carbohydrate consumption, hygiene practices, and host genetic factors. Susceptibility to caries generally decreases with age, possibly due to the fact that grooves and fissures—common sites of dental caries—tend to become more shallow as teeth

22.3

Gastrointestinal Tract Diseases Caused by Microorganisms (Nonhelminthic)

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(a) Acquired pellicle

(1) Pellicle formation

Enamel

Streptococci

Fusobacterium Spirochetes Lactobacilli

Actinomyces

Acid

(2) Initial colonization by bacteria and (3) plaque formation

(4) Acid formation and caries development

(b) Enamel affected

First-degree caries

Dentin penetrated

Second-degree caries

Exposure of pulp

Third-degree caries

Figure 22.3 Stages in plaque development and cariogenesis. (a) A microscopic view of pellicle and plaque formation, acidification, and destruction of tooth enamel. (b) Progress and degrees of cariogenesis.

(a)

(b)

Figure 22.4 The macroscopic and microscopic appearance of plaque.

(a) Disclosing tablets containing vegetable dye stain heavy plaque accumulations at the junction of the tooth and gingiva. (b) Scanning electron micrograph of the plaque biofilm with long filamentous forms and “corn cobs” that are mixed bacterial aggregates.

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are worn down. As the population ages, and natural teeth are retained for longer periods, the caries rate may well increase in the elderly, because receding gums expose the more susceptible root surfaces. ▶

Culture and Diagnosis

Dental professionals diagnose caries based on the tooth condition. Culture of the lesion is not routinely performed. ▶

Prevention and Treatment

The best way to prevent dental caries is through dietary restriction of sucrose and other refined carbohydrates. Regular brushing and flossing to remove plaque are also important. Most municipal communities in the United States add trace amounts of fluoride to their drinking water, because fluoride, when incorporated into the tooth structure, can increase tooth (as well as bone) hardness. Fluoride can also encourage the remineralization of teeth that have begun the demineralization process. These and other proposed actions of fluoride could make teeth less susceptible to decay. Fluoride is also added to toothpastes and mouth rinses and can be applied in gel form. Many European countries do not fluoridate their water due to concerns over additives in drinking water. There are several vaccines being tested to prevent dental caries. Some utilize the proteins that bacteria use for initial attachment; others consist of the enzyme streptococci use to produce glucans. One of the more promising experimental approaches is the oral application of IgA antibody directed to bacterial attachment proteins (that is, passive immunization). Treatment of a carious lesion involves removal of the affected part of the tooth (or the whole tooth in the case of advanced caries), followed by restoration of the tooth structure with an artificial material. An experimental treatment with great promise is the use of an antimicrobial peptide linked to a protein that attaches only to S. mutans, killing it and leaving the important normal biota intact.

Disease Table 22.1 Dental Caries Causative Organism(s)

Streptococcus mutans, Streptococcus sobrinus, others

Most Common Modes of Transmission

Direct contact

Virulence Factors

Adhesion, acid production

Culture/Diagnosis

–

Prevention

Oral hygiene, fluoride supplementation

Treatment

Removal of diseased tooth material

Periodontal Diseases Periodontal disease is so common that 97% to 100% of the population has some manifestation of it by age 45. Most kinds are due to bacterial colonization and varying degrees of inflammation that occur in response to gingival damage.

Periodontitis ▶ Signs and Symptoms The initial stage of periodontal disease is gingivitis, the signs of which are swelling, loss of normal contour, patches of redness, and increased bleeding of the gingiva. Spaces or pockets of varying depth also develop between the tooth and the gingiva. If this condition persists, a more serious disease called periodontitis results. This is the natural extension of the disease into the periodontal membrane and cementum. The deeper involvement increases the size of the pockets and can cause bone resorption severe enough to loosen the tooth in its socket. If the condition is allowed to progress, the tooth can be lost (figure 22.5). ▶

Causative Agent

Dental scientists stop short of stating that particular bacteria cause periodontal disease, because not all of the criteria for establishing causation have been satisfied. In fact, dental diseases (in particular, periodontal disease) provide an excellent model of disease mediated by communities of microorganisms rather than single organisms. When the polymicrobial biofilms consist of the right combination of bacteria, such as the anaerobes Tannerella forsythia (formerly Bacteroides forsythus), Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, and perhaps Fusobacterium and spirochete species, the periodontal destruction process begins. Evidence indicates that the presence of archaeal species in the gingival crevice is an important contributor to disease. If this is true, it will be the first link found between archaea and human disease. Scientists even suspect that aggressive versus chronic forms of periodontitis are mediated by communities that have different members or even different orders of succession. (Succession refers to the order in which microbes become part of the biofilm.) Other factors are also important in the development of periodontal disease, such as behavioral and genetic influences, as well as tooth position. The most common predisposing condition occurs when the plaque becomes mineralized (calcified) with calcium and phosphate crystals. This process produces a hard, porous substance called calculus above and below the gingival margin (edge) that can induce varying degrees of periodontal damage (figure 22.6). The presence of calculus leads to a series of inflammatory events that probably allow the bacteria to cause disease. ▶

Pathogenesis and Virulence Factors

Calculus and plaque accumulating in the gingival sulcus cause abrasions in the delicate gingival membrane, and the

22.3

Gastrointestinal Tract Diseases Caused by Microorganisms (Nonhelminthic)

Inflammation Tooth

Gingiva

Bone (a) Normal, nondiseased state of tooth, gingiva, and bone

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Bleeding gingiva Pocket

Calculus

(b) Calculus buildup and early gingivitis

Figure 22.5 Stages in soft-tissue infection, gingivitis, and periodontitis.

Calculus Caries

Areas of bone destruction

Bone resorption

(c) Late-stage periodontitis, with tissue destruction, deep pocket formation, loosening of teeth, and bone loss

which cause further inflammation and tissue damage. There is now a great deal of evidence that people with high numbers of the bacteria associated with periodontitis also have thicker carotid arteries, and increased rates of cardiovascular disease. ▶

Transmission and Epidemiology

As with caries, the resident oral bacteria, acquired from close oral contact, are responsible for periodontal disease. Dentists refer to a wide range of risk factors associated with periodontal disease, especially deficient oral hygiene. But because it is so common in the population, it is evident that most of us could use some improvement in our oral hygiene. ▶

Figure 22.6 The nature of calculus. Radiograph of

Culture and Diagnosis

Like caries, periodontitis is generally diagnosed by the appearance of the oral tissues.

mandibular premolar and molar, showing calculus on the top and a caries lesion on the right. Bony defects caused by periodontitis affect both teeth.

▶

chronic trauma causes a pronounced inflammatory reaction. The damaged tissues become a portal of entry for a variety of bacterial residents. The bacteria have an arsenal of enzymes, such as proteases, that destroy soft oral tissues. In response to the mixed infection, the damaged area becomes infiltrated by neutrophils and macrophages and, later, by lymphocytes,

Regular brushing and flossing to remove plaque automatically reduce both caries and calculus production. Mouthwashes are relatively ineffective in controlling plaque formation because of the high bacterial content of saliva and the relatively short-acting time of the mouthwash. Once calculus has formed on teeth, it cannot be removed by brushing but can be dislodged only by special mechanical procedures (scaling) in the dental office.

Prevention and Treatment

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Chapter 22 Infectious Diseases Affecting the Gastrointestinal Tract

Most periodontal disease is treated by removal of calculus and plaque and maintenance of good oral hygiene. Often, surgery to reduce the depth of periodontal pockets is required. Antibiotic therapy, either systemic or applied in periodontal packings, may also be utilized. There is some evidence that exposing the periodontium to blue light (similar to that used to whiten teeth) can selectively kill disease-causing anaerobes while leaving normal biota intact. It is also becoming clear that controlling the inflammation (through topical or systemic steroids) can have benefit, both for the periodontitis but also for focal disease such as in the cardiovascular system.

Necrotizing Ulcerative Gingivitis and Periodontitis The most destructive periodontal diseases are necrotizing ulcerative gingivitis (NUG) and necrotizing ulcerative periodontitis (NUP). The two diseases were formerly lumped under one name, acute necrotizing ulcerative gingivitis, or ANUG. These diseases are synergistic infections involving Treponema vincentii, Prevotella intermedia, and Fusobacterium species. These pathogens together produce several invasive factors that cause rapid advancement into the periodontal tissues. The condition is associated with severe pain, bleeding, pseudomembrane formation, and necrosis. Scientists believe that NUP may be an extension of NUG, but the conditions can be distinguished by the advanced bone destruction that results from NUP. Both diseases seem to result from poor oral hygiene, altered host defenses, or prior gum disease rather than being communicable. The diseases are common in AIDS patients and other immunocompromised populations. Diabetes and cigarette smoking can predispose people to these conditions. NUG and NUP usually respond well to broad-spectrum antibiotics, after debridement of damaged periodontal tissue (Disease Table 22.2).

Mumps The word mumps is Old English for lump or bump. The symptoms of this viral disease are so distinctive that Hippocrates clearly characterized it in the fifth century BC as a self-limited, mildly epidemic illness associated with painful swelling at the angle of the jaw (figure 22.7). ▶

Signs and Symptoms

After an average incubation period of 2 to 3 weeks, symptoms of fever, nasal discharge, muscle pain, and malaise develop. These may be followed by inflammation of the salivary glands (especially the parotids), producing the classic gopherlike swelling of the cheeks on one or both sides

Figure 22.7 The external appearance of swollen parotid glands in mumps (parotitis).

Disease Table 22.2 Periodontal Diseases Disease

Periodontitis

Necrotizing Ulcerative Gingivitis and Periodontitis

Causative Organism(s)

Polymicrobial community including some or all of: Tannerella forsythia, Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, others?

Polymicrobial community (Treponema vincentii, Prevotella intermedia, Fusobacterium species)

Most Common Modes of Transmission

–

–

Virulence Factors

Induction of inflammation, enzymatic destruction of tissues

Inflammation, invasiveness

Culture/Diagnosis

–

–

Prevention

Oral hygiene

Oral hygiene

Treatment

Removal of plaque and calculus, gum reconstruction, tetracycline, possibly anti-inflammatory treatments

Debridement of damaged tissue, metronidazole, clindamycin

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Gastrointestinal Tract Diseases Caused by Microorganisms (Nonhelminthic)

(see figure 22.7). Swelling of the gland is called parotitis, and it can cause considerable discomfort. Viral multiplication in salivary glands is followed by invasion of other organs, especially the testes, ovaries, thyroid gland, pancreas, meninges, heart, and kidney. Despite the invasion of multiple organs, the prognosis of most infections is complete, uncomplicated recovery with permanent immunity.

Complications in Mumps In 20% to 30% of young adult males, mumps infection localizes in the epididymis and testis, usually on one side only. The resultant syndrome of orchitis and epididymitis may be rather painful, but no permanent damage usually occurs. The popular belief that mumps readily causes sterilization of adult males is still held, despite medical evidence to the contrary. Perhaps this notion has been reinforced by the tenderness that continues long after infection and by the partial atrophy of one testis that occurs in about half the cases. Permanent sterility due to mumps is very rare. In mumps pancreatitis, the virus replicates in beta cells and pancreatic epithelial cells. Viral meningitis, characterized by fever, headache, and stiff neck, appears 2 to 10 days after the onset of parotitis, lasts for 3 to 5 days, and then dissipates, leaving few or no adverse side effects. Another rare event is infection of the inner ear that can lead to deafness.

Nuclei

▶

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Causative Agent

Mumps is caused by an enveloped single-stranded RNA virus (mumps virus) from the genus Paramyxovirus, which is part of the family Paramyxoviridae. Other members of this family that infect humans are Morbillivirus (measles virus) and the respiratory syncytial virus. The envelopes of paramyxoviruses possess spikes that have specific functions. ▶

Pathogenesis and Virulence Factors

A virus-infected cell is modified by the insertion of proteins called HN spikes into its cell membrane. The HN spikes immediately bind an uninfected neighboring cell, and in the presence of another type of spike called F spikes, the two cells permanently fuse. A chain reaction of multiple cell fusions then produces a syncytium (sin-sish′-yum) with cytoplasmic inclusion bodies, which is a diagnostically useful cytopathic effect (figure 22.8). The ability to induce the formation of syncytia is characteristic of the family Paramyxoviridae. ▶

Transmission and Epidemiology of Mumps Virus

Humans are the exclusive natural hosts for the mumps virus. It is communicated primarily through salivary and respiratory secretions. Infection occurs worldwide, with increases in the late winter and early spring in temperate climates.

Giant cell

Paramyxovirus

Uncoating

Host cell 1

Host cell 2

Host cell 3 (a)

(b)

Point of cell fusion

Figure 22.8 The effects of paramyxoviruses. (a) When they infect a host cell, paramyxoviruses induce the cell membranes of adjacent cells to fuse into large multinucleate giant cells, or syncytia. (b) This fusion allows direct passage of viruses from an infected cell to uninfected cells by communicating membranes. Through this means, the virus evades antibodies.

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Chapter 22 Infectious Diseases Affecting the Gastrointestinal Tract

High rates of infection arise among crowded populations or communities with poor herd immunity. Most cases occur in children under the age of 15, and as many as 40% are subclinical. Because lasting immunity follows any form of mumps infection, no long-term carrier reservoir exists in the population. The incidence of mumps had been reduced in the United States to around 300 cases per year. The incidence has become more unpredictable since 2006, though. In that year there were about 2,600 cases. The next 3 years saw cases in the low hundreds again, but then in 2010 there were more than 1,500 cases. The recommendation is to be sure to get two doses of MMR vaccine. ▶

Culture and Diagnosis

Diagnosis is usually based on the clinical sign of swollen parotid glands and known exposure 2 or 3 weeks previously. Because parotitis is not always present, and the incubation period can range from 7 to 23 days, a practical diagnostic alternative is to perform a direct fluorescent test for viral antigen or an ELISA test on a patient’s serum. ▶

Prevention and Treatment

The general pathology of mumps is mild enough that symptomatic treatment to relieve fever, dehydration, and pain is usually adequate. The new vaccine recommendations call for a dose of MMR at 12 to 15 months and a second dose at 4 to 6 years. Health care workers and college students who haven’t already had both doses are advised to do so.

Disease Table 22.3 Mumps Causative Organism(s)

Mumps virus (genus Paramyxovirus)

Most Common Modes of Transmission

Droplet contact

Virulence Factors

Spike-induced syncytium formation

Culture/Diagnosis

Clinical, fluorescent Ag tests, ELISA for Ab

Prevention

MMR live attenuated vaccine

Treatment

Supportive

Gastritis and Gastric Ulcers The curved cells of Helicobacter were first detected by J. Robin Warren in 1979 in stomach biopsies from ulcer patients. He and an assistant, Barry J. Marshall, isolated the microbe in culture and even served as guinea pigs by swallowing a large inoculum to test its effects. Both developed transient gastritis.

▶

Signs and Symptoms

Gastritis is experienced as sharp or burning pain emanating from the abdomen. Gastric ulcers are actual lesions in the mucosa of the stomach (gastric ulcers) or in the uppermost portion of the small intestine (duodenal ulcers). Both of these conditions are also called peptic ulcers. Severe ulcers can be accompanied by bloody stools, vomiting, or both. The symptoms are often worse at night, after eating, or under conditions of psychological stress. The second most common cancer in the world is stomach cancer (although it has been declining in the United States), and ample evidence suggests that long-term infection with H. pylori is a major contributing factor. ▶

Causative Agent

Helicobacter pylori is a curved gram-negative rod, closely related to Campylobacter, which we study later in this chapter. ▶

Pathogenesis and Virulence Factors

Once the bacterium passes into the gastrointestinal tract, it bores through the outermost mucous layer that lines the stomach epithelial tissue. Then it attaches to specific binding sites on the cells and entrenches itself. One receptor specific for Helicobacter is the same molecule on human cells that confers the O blood type. This finding accounts for the higher rate of ulcers in people with this blood type. Another protective adaptation of the bacterium is the formation of urease, an enzyme that converts urea into ammonium and bicarbonate, both alkaline compounds that can neutralize stomach acid. As the immune system recognizes and attacks the pathogen, infiltrating white blood cells damage the epithelium to some degree, leading to chronic active gastritis. In some people, these lesions lead to deeper erosions and ulcers that can lay the groundwork for cancer to develop. Before the bacterium was discovered, spicy foods, highsugar diets (which increase acid levels in the stomach), and psychological stress were considered to be the cause of gastritis and ulcers. Now it appears that these factors merely aggravate the underlying infection. ▶

Transmission and Epidemiology

The mode of transmission of this bacterium remains a mystery. Studies have revealed that the pathogen is present in a large proportion of the human population. It occurs in the stomachs of 25% of healthy middle-age adults and in more than 60% of adults over 60 years of age. H. pylori is probably transmitted from person to person by the oral-oral or fecal-oral route. It seems to be acquired early in life and carried asymptomatically until its activities begin to damage the digestive mucosa. Because other animals are also susceptible to H. pylori and even develop chronic gastritis, it has been proposed that the disease is a zoonosis transmitted from an animal reservoir. The bacterium has also been found in water sources. Approximately two-thirds of the world’s population are infected with H. pylori. It is not known what causes some

22.3

Gastrointestinal Tract Diseases Caused by Microorganisms (Nonhelminthic)

people to experience symptoms, although it is most likely that those with the right combination of aggravating factors are those who experience disease. ▶

Culture and Diagnosis

Diagnosis has typically been accomplished with endoscopy, a procedure in which a long flexible tube (figure 22.9) is inserted through the throat into the stomach to visualize any lesions there. The urea breath test is sometimes used. In this test, patients ingest urea that has a radioactive tag on its carbon molecule. If Helicobacter is present in a patient’s stomach, the bacterium’s urease breaks down the urea and the patient exhales radioactively labeled carbon dioxide. In the absence of urease, the intact urea molecule passes through the digestive system. Patients whose breath is positive for the radioactive carbon are considered positive for Helicobacter.

Light source

Eyepiece and controls

A stool test is also available. The HpSA (H. pylori stool antigen test) is an ELISA format test. ▶

Prevention and Treatment

The only preventive approaches available currently are those that diminish some of the aggravating factors just mentioned. Many over-the-counter remedies offer symptom relief; most of them act to neutralize stomach acid. The best treatment is a course of antibiotics augmented by acid suppressors. The antibiotics most prescribed are clarithromycin or metronidazole. Bismuth subsalicylate (Pepto-Bismol) or the prescription medication omeprazole is the most frequently administered acid suppressor.

Disease Table 22.4 Gastritis and Gastric Ulcers

Causative Organism(s)

Helicobacter pylori

Most Common Modes of Transmission

?

Virulence Factors

Adhesins, urease

Culture/Diagnosis

Endoscopy, urea breath test, stool antigen test

Prevention

None

Treatment

Antibiotics plus acid suppressors (clarithromycin or metronidazole plus omeprazole or bismuth subsalicylate)

Viewing end

(a)

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Acute Diarrhea

Pylorus region

Stomach

Endoscope Duodenum (b)

Figure 22.9 Endoscopy. (a) A flexible tube is inserted through the mouth into the stomach, (b) acting as a camera to visualize the stomach surface.

Diarrhea needs little explanation. In recent years, on average, citizens of the United States experienced 1.2 to 1.9 cases of diarrhea per person per year, and among children that number is twice as high. The incidence of diarrhea is even higher among children attending day care centers. In tropical countries, children may experience more than 10 episodes of diarrhea a year. In fact, more than 3 million children a year, mostly in developing countries, die from a diarrheal disease (see Insight 22.2). In developing countries, the high mortality rate is not the only issue. Children who survive dozens of bouts with diarrhea during their developmental years are likely to have permanent physical and cognitive effects. The effect on the overall well-being of these children is hard to estimate, but it is very significant. In the United States, up to a third of all acute diarrhea is transmitted by contaminated food (a case of diarrhea is usually defined as three or more loose stools in a 24-hour period). In recent years, consumers have become much more aware of the possibility of E. coli–contaminated hamburgers or Salmonellacontaminated ice cream. New food safety measures are being

Chapter 22 Infectious Diseases Affecting the Gastrointestinal Tract

implemented all the time, but it is still necessary for the consumer to be aware and to practice good food handling. Although most diarrhea episodes are self-limiting and therefore do not require treatment, others (such as E. coli O157:H7) can have devastating effects. In most diarrheal illnesses, antimicrobial treatment is contraindicated (inadvisable), but some, such as shigellosis, call for quick treatment with antibiotics. For public health reasons, it is important to know which agents are causing diarrhea in the community, but in most cases identification of the agent is not performed. In this section, we describe acute diarrhea having infectious agents as the cause. In the sections following this one, we discuss acute diarrhea and vomiting caused by toxins, commonly known as food poisoning, and chronic diarrhea and its causes.

Salmonella A decade ago, one of every three chickens destined for human consumption was contaminated with Salmonella, but the rate is now about 10%. Other poultry, such as ducks and turkeys, is also affected. Eggs are infected as well because the bacteria may actually enter the egg while the shell is being formed in the chicken. In 2007, peanut butter was found to be the source of a Salmonella outbreak in the United States. Salmonella is a very large genus of bacteria, but only one species is of interest to us: S. enterica is divided into many variants, based on variation in the major surface antigens. As mentioned in chapter 4, serotype or variant analysis aids in bacterial identification. Many gram-negative enteric bacteria are named and designated according to the following antigens: H, the flagellar antigen; K, the capsular antigen; and O, the cell wall antigen. Not all enteric bacteria carry the H and K antigens, but all have O, the polysaccharide portion of the lipopolysaccharide implicated in endotoxic shock (see chapter 20). Most species of gram-negative enterics exhibit a variety of subspecies, variant, or serotypes caused by slight variations in the chemical structure of the HKO antigens. Some bacteria in this chapter (for example, E. coli O157:H7) are named according to their surface antigens; however, we will use Latin variant names for Salmonella. Salmonellae are motile; they ferment glucose with acid and sometimes gas; and most of them produce hydrogen sulfide (H2S) but not urease. They grow readily on most laboratory media and can survive outside the host in inhospitable environments such as fresh water and freezing temperatures. These pathogens are resistant to chemicals such as bile and dyes, which are the basis for isolation on selective media. ▶

Signs and Symptoms

The genus Salmonella causes a variety of illnesses in the GI tract and beyond. Until fairly recently, its most severe manifestation was typhoid fever, which is discussed shortly. Since the mid-1900s, a milder disease usually called salmonellosis has been much more common (figure 22.10). Sometimes the condition is also called enteric fever or gastroenteritis. Whereas typhoid fever is caused by the typhi variant, gastro-

28 24

Cases per 100,000

672

A 1985 epidemic due to contaminated milk infected 14,000 people in the Midwest.

20 16

Cases of typhoid fever Cases of other salmonelloses

12 8 4 0 1940 1945 1950 1955 1960 1965 1970 1975 1980 1985 1990 19952000 2007 Year

Figure 22.10 Data on the prevalence of typhoid fever and other salmonelloses from 1940 to 2007. Nontyphoidal salmonelloses did occur before 1940, but the statistics are not available.

enteritises are generally caused by the variant known as paratyphi, hirschfeldii, and typhimurium. Another variant, which is sometimes called Arizona hinshawii (even though it is still a Salmonella), is a pathogen found in the intestines of reptiles. Most of these strains come from animals, unlike the typhi strain, which infects humans exclusively. Salmonella bacteria are normal intestinal biota in cattle, poultry, rodents, and reptiles. Salmonellosis can be relatively severe, with an elevated body temperature and septicemia as more prominent features than GI tract disturbance. But it can also be fairly mild, with gastroenteritis—vomiting, diarrhea, and mucosal irritation—as its major feature. Blood can appear in the stool. In otherwise healthy adults, symptoms spontaneously subside after 2 to 5 days; death is infrequent except in debilitated persons. Typhoid fever is so named because it bears a superficial resemblance to typhus, a rickettsial disease, even though the two diseases are otherwise very different. In the United States, the incidence of typhoid fever has remained at a steady rate for the last 30 years, appearing sporadically (see figure 22.10). Of the 50 to 100 cases reported annually, roughly half are imported from endemic regions. In other parts of the world, typhoid fever is still a serious health problem, responsible for 25,000 deaths each year and probably millions of cases. Typhoid fever, caused by the typhi variant of S. enterica, is characterized by a progressive, invasive infection that leads eventually to septicemia. Symptoms are fever, diarrhea, and abdominal pain. The bacterium infiltrates the mesenteric lymph nodes and the phagocytes of the liver and spleen. In some people, the small intestine develops areas of ulceration that are vulnerable to hemorrhage, perforation, and peritonitis. Its presence in the circulatory system may lead to nodules or abscesses in the liver or urinary tract. Because it is so rare compared with the less severe salmonellosis, the rest of this section refers mainly to salmonellosis and not to typhoid fever.

22.3

▶

Gastrointestinal Tract Diseases Caused by Microorganisms (Nonhelminthic)

Pathogenesis and Virulence Factors

The ability of Salmonella to cause disease seems to be highly dependent on its ability to adhere effectively to the gut mucosa. Recent research has uncovered an “island” of genes in Salmonella that seems to confer virulence on the bacterium. There are other pathogenicity islands, but this one is directly related to attachment. It is also believed that endotoxin is an important virulence factor for Salmonella. ▶

Transmission and Epidemiology

Animal products such as meat and milk can be readily contaminated with Salmonella during slaughter, collection, and processing. Inherent risks are involved in eating poorly cooked beef or unpasteurized fresh or dried milk, ice cream, and cheese. A 2001 U.S. outbreak was traced to green grapes. A particular concern is the contamination of foods by rodent feces. Several outbreaks of infection have been traced to unclean food storage or to food-processing plants infested with rats and mice. Most cases are traceable to a common food source such as milk or eggs. Some cases may be due to poor sanitation. In one outbreak, about 60 people became infected after visiting the Komodo dragon exhibit at the Denver zoo. They picked up the infection by handling the rails and fence of the dragon’s cage. In 2002, two people apparently acquired salmonellosis from a blood transfusion, and one of them died. The blood donor, who had an asymptomatic infection with Salmonella, had contracted the infection from his pet snake. ▶

Prevention and Treatment

The only prevention for salmonellosis is avoiding contact with the bacterium. In 1998, a vaccine was approved for use in poultry, making it the first “food safety” vaccine. A vaccine for humans is undergoing testing as well. Uncomplicated cases of salmonellosis are treated with fluid and electrolyte replacement; if the patient has underlying immunocompromise or if the disease is severe, trimethoprim-sulfamethoxazole is recommended. Typhoid fever, by contrast, is always treated with antibiotics, in part to clear the patient of the typhi strain, which has a tendency to be shed for weeks after recovery. A small number of people chronically carry the bacterium for longer periods in the gallbladder; from this site, the bacteria are constantly released into the intestine and feces. In some people, gallbladder removal is necessary to stop the shedding. Two vaccines are available for the typhi strain and are recommended for people traveling to endemic areas.

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native candidates can cause bloody diarrhea, such as E. coli and others. Isolation and identification follow the usual protocols for enterics. Stool culture is still the gold standard for identification in the case of Shigella infections. Although Shigella dysenteriae causes the most severe form of dysentery, it is uncommon in the United States and occurs primarily in the Eastern Hemisphere. In the past decade, the prevalent agents in the United States have been Shigella sonnei and Shigella flexneri, which cause approximately 20,000 to 25,000 cases each year, half of them in children. ▶

Signs and Symptoms

The symptoms of shigellosis include frequent, watery stools, as well as fever, and often intense abdominal pain. Nausea and vomiting are common. Stools often contain obvious blood and even more often are found to have occult (not visible to the naked eye) blood. Diarrhea containing blood is also called dysentery. Mucus from the GI tract will also be present in the stools. ▶

Pathogenesis and Virulence Factors

Shigellosis is different from many GI tract infections in that Shigella invades the villus cells of the large intestine rather than the small intestine. In addition, it is not as invasive as Salmonella and does not perforate the intestine or invade the blood. It enters the intestinal mucosa by means of lymphoid cells in Peyer’s patches. Once in the mucosa, Shigella instigates an inflammatory response that causes extensive tissue destruction. The release of endotoxin causes fever. Enterotoxin, an exotoxin that affects the enteric (or GI) tract, damages the mucosa and villi. Local areas of erosion give rise to bleeding and heavy secretion of mucus (figure 22.11). Shigella dysenteriae (and perhaps some of the other species) produces a heat-labile exotoxin called shiga toxin, which seems to be responsible for the more serious damage to the intestine as well as any systemic effects, including injury to nerve cells. It is an A-B toxin (see figure 21.9). To review, the B portion of the toxin attaches to host cells, and the whole toxin is internalized. Once inside, the A portion of the toxin exerts its effect. In the case of the shiga toxin, the A portion of the toxin binds to ribosomes, interrupting protein synthesis and leading to the damage just described. You’ll encounter shiga toxin again when we discuss E. coli O157:H7.

Shigella The Shigella bacteria are gram-negative straight rods, nonmotile and non-spore-forming. They do not produce urease or hydrogen sulfide, traits that help in their identification. They are primarily human parasites, though they can infect apes. All produce a similar disease that can vary in intensity. These bacteria resemble some types of pathogenic E. coli very closely. Diagnosis is complicated by the fact that several alter-

Figure 22.11 The appearance of the large intestinal mucosa in Shigella dysentery. Note the patches of blood and mucus, the erosion of the lining, and the absence of perforation.

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Transmission and Epidemiology

In addition to the usual oral route, shigellosis is also acquired through direct person-to-person contact, largely because of the small infectious dose required (from 10 to 200 bacteria). The disease is mostly associated with lax sanitation, malnutrition, and crowding; and it is spread epidemically in day care centers, prisons, mental institutions, nursing homes, and military camps. As in other enteric infections, Shigella can establish a chronic carrier condition in some people that lasts several months. ▶

Prevention and Treatment

The only prevention of this and most other diarrheal diseases is good hygiene and avoiding contact with infected persons. Although some experts say that bloody diarrhea in this country should not be treated with antibiotics (which is generally accepted for E. coli O157:H7 infections), most physicians recommend prompt treatment of shigellosis with trimethoprim-sulfamethoxazole (TMP-SMZ).

E. coli O157:H7 (EHEC) In January of 1993, this awkwardly named bacterium burst into the public’s consciousness when three children died after eating undercooked hamburgers at a fast-food restaurant in Washington State. The cause of their illness was determined to be this particular strain of E. coli, which had actually been recognized since the 1980s. Since then, it has led to approximately 73,000 illnesses and about 50 deaths each year in the United States. It is considered an emerging pathogen. Dozens of different strains of E. coli exist, many of which cause no disease at all. A handful of them cause various degrees of intestinal symptoms as described in this and the following section. Some of them cause urinary tract infections (see chapter 23). E. coli O157:H7 and its close relatives are the most virulent of them all. The group of E. coli of which this strain is the most famous representative is generally referred to as enterohemorrhagic E. coli, or EHEC. ▶

▶

Transmission and Epidemiology

The most common mode of transmission for EHEC is the ingestion of contaminated and undercooked beef, although other foods and beverages can be contaminated as well (figure 22.12). Ground beef is more dangerous than steaks or other cuts of meat, for several reasons. Consider the way that the beef becomes contaminated in the first place. The bacterium is a natural inhabitant of the GI tracts of cattle. Contamination occurs when intestinal contents contact the animal carcass, so bacteria are confined to the surface of meats. Because high heat destroys this bacterium, even a brief trip under the broiler is usually sufficient to kill E. coli on the surface of steaks or roasts. But in ground beef, the “surface” of meat is mixed and ground up throughout a batch, meaning any bacteria are mixed in also. This mixing explains why hamburgers should be cooked all the way through. Hamburger is also a common vehicle because meat processing plants tend to grind meats from several cattle sources together, thereby contaminating large amounts of hamburger with meat from one animal carrier. Other farm products may also become contaminated by cattle feces. Products that are eaten raw, such as lettuce, vegetables, and apples used in unpasteurized cider, are particularly problematic. In 2006, a major nationwide outbreak stemming from contaminated spinach held the headlines

Signs and Symptoms

E. coli O157:H7 is the agent of a spectrum of conditions, ranging from mild gastroenteritis with fever to bloody diarrhea. About 10% of patients develop hemolytic uremic syndrome (HUS), a severe hemolytic anemia that can cause kidney damage and failure. Neurological symptoms such as blindness, seizure, and stroke (and long-term debilitation) are also possible. These serious manifestations are most likely to occur in children younger than 5 and in elderly people. ▶

on bacteriophage in E. coli but are on the chromosome of Shigella dysenteriae, suggesting that the E. coli acquired the virulence factor through phage-mediated transfer. As described earlier for Shigella, the shiga toxin interrupts protein synthesis in its target cells. It seems to be responsible especially for the systemic effects of this infection. Another important virulence determinant for EHEC is the ability to efface (rub out or destroy) enterocytes, which are gut epithelial cells. The net effect is a lesion in the gut (effacement), usually in the large intestine. The microvilli are lost from the gut epithelium, and the lesions produce bloody diarrhea.

Pathogenesis and Virulence Factors

This bacterium owes much of its virulence to shiga toxins (so named because they are identical to the shiga exotoxin secreted by virulent Shigella species). Sometimes this E. coli is referred to as STEC (shiga-toxin-producing E. coli). For simplicity, EHEC is used here. The shiga toxin genes are present

25

Number of outbreaks (n=183)

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Chapter 22 Infectious Diseases Affecting the Gastrointestinal Tract

20

ground beef

other

unknown

produce

other beef

dairy

15 10 5 0 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000 2002

Figure 22.12 The emergence of E. coli O157:H7 Note how ground beef is much more often a source than other (muscle) meats.

22.3

Gastrointestinal Tract Diseases Caused by Microorganisms (Nonhelminthic)

for weeks. The disease can also be spread via the fecal-oral route of transmission, especially among young children in group situations. Even touching surfaces contaminated with cattle feces can cause disease, since ingesting as few as 10 organisms has been found to be sufficient to initiate this disease. ▶

Culture and Diagnosis

Infection with this type of E. coli should be confirmed with stool culture or with ELISA or PCR. ▶

Prevention and Treatment

The best prevention for this disease is never to eat raw or even rare hamburger. The shiga toxin is heat-labile and the E. coli is killed by heat as well. If you are thinking “I used to be able to eat rare hamburgers,” you are correct, but things have changed (see figure 22.12). The emergence of this pathogen in the early 1980s, probably resulting from a regular E. coli picking up the shiga toxin from Shigella, has changed the rules. No vaccine exists for E. coli O157:H7. A great deal of research is directed at vaccinating livestock to break the chain of transmission to humans. Antibiotics are contraindicated for this infection. Even with severe disease manifestations, antibiotics have been found to be of no help, and they may increase the pathology. Supportive therapy is the only option.

Other E. coli At least four other categories of E. coli can cause diarrheal diseases. Scientists call these enterotoxigenic E. coli, enteroinvasive E. coli, enteropathogenic E. coli, and enteroaggregative E. coli. In clinical practice, most physicians are interested in differentiating shiga-toxin-producing E. coli (EHEC) from all the others. Each of these is considered separately and briefly here; in Disease Table 22.5, the non-shiga-toxin-producing E. coli are grouped together in one column.

Enterotoxigenic E. coli (ETEC) The presentation varies depending on which type of E. coli is causing the disease. Traveler’s diarrhea, characterized by watery diarrhea, lowgrade fever, nausea, and vomiting, is usually caused by enterotoxigenic E. coli (ETEC). These strains also cause a great deal of illness in infants in developing countries. The bacterium is transmitted through the fecal-oral route or via contaminated vehicles or even fomites (such as a dirty glass). Travelers are susceptible to these strains because they are likely to be new to their immune systems. People living in endemic areas probably encounter the bacteria as infants. As the name suggests, the virulence of the bacterium derives from its ability to secrete two types of exotoxins that act on the enteric tract (enterotoxin). One toxin is a heatlabile A-B toxin, and it acts like the cholera toxin, described later. Another toxin, actually a group of toxins, is heat-stable. These toxins are very small proteins that alter host cell func-

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tion in order to cause large amounts of fluid secretion into the intestinal tract. The bacterium mainly affects the small intestine. Most infections with ETEC are self-limiting, however miserable they make you feel. They are treated only with fluid replacement. In infants, ETEC can be life-threatening, and fluid replacement is vital to survival.

Enteroinvasive E. coli (EIEC) These strains cause a disease that is very similar to Shigella dysentery. The bacteria invade gut mucosa and cause widespread destruction. Blood and pus will be found in the stool. Significant fever is often present. EIEC does not produce the heat-labile or heat-stable exotoxins just described and does not have a shiga toxin, despite the clinical similarity to Shigella disease. EIEC does seem to have a protein that is expressed inside host cells, which leads to its destruction. Disease caused by this bacterium is more common in developing countries. It is transmitted primarily through contaminated food and water. Treatment is supportive (including rehydration). Enteropathogenic E. coli (EPEC) These strains result in a profuse, watery diarrhea. Fever and vomiting are also common. The EPEC bacteria are very similar to the EHEC E. coli described earlier—they produce effacement of gut surfaces. The important difference between EPEC and EHEC is that EPEC does not produce a shiga toxin and, therefore, does not produce the systemic symptoms characteristic of those bacteria. EPEC has been known to cause outbreaks in hospital nurseries in this country but is more notorious for causing diarrhea in infants in developing countries. Most disease is self-limiting. As with any other diarrhea, however, it can be life-threatening in young babies. Rehydration is the main treatment. Enteroaggregative E. coli (EAEC) These bacteria are most notable for their ability to cause chronic diarrhea in young children and in AIDS patients. EAEC is considered in the section on chronic diarrhea.

Campylobacter Although you may never have heard of Campylobacter, it is considered to be the most common bacterial cause of diarrhea in the United States. It probably causes more diarrhea than Salmonella and Shigella combined, with 2 million cases of diarrhea credited to it per year. The symptoms of campylobacteriosis are frequent watery stools, fever, vomiting, headaches, and severe abdominal pain. The symptoms may last longer than most acute diarrheal episodes, sometimes extending beyond 2 weeks. They may subside and then recur over a period of weeks. Campylobacter jejuni is the most common cause, although there are other Campylobacter species. Campylobacters are slender, curved or spiral gram-negative bacteria propelled

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by polar flagella at one or both poles, often appearing in S-shaped or gull-winged pairs (figure 22.13). These bacteria tend to be microaerophilic inhabitants of the intestinal tract, genitourinary tract, and oral cavity of humans and animals. A close relative, Helicobacter pylori, is the causative agent of most stomach ulcers (described earlier). Transmission of this pathogen takes place via the ingestion of contaminated beverages and food, especially water, milk, meat, and chicken. Once ingested, C. jejuni cells reach the mucosa at the last segment of the small intestine (ileum) near its junction with the colon; they adhere, burrow through the mucus, and multiply. Symptoms commence after an incubation period of 1 to 7 days. The mechanisms of pathology appear to involve a heat-labile enterotoxin that stimulates a secretory diarrhea like that of cholera. In a small number of cases, infection with this bacterium can lead to a serious neuromuscular paralysis called Guillain-Barré syndrome. Guillain-Barré syndrome (GBS) is the leading cause of acute paralysis in the United States since the eradication of polio there. The good news is that many patients recover completely from this paralysis. The condition is still mysterious in many ways, but it seems to be an autoimmune reaction that can be brought on by infection with viruses and bacteria, by vaccination in rare cases, and even by surgery. The single most common precipitating event for the onset of GBS is Campylobacter infection. Twenty to forty percent of GBS cases are preceded by infection with Campylobacter. The reasons for this are not clear. (Note that even though 20% to 40% of GBS cases are preceded by Campylobacter infection, only about 1 in 1,000 cases of Campylobacter infection results in GBS.) Diagnosis of C. jejuni enteritis requires isolation of the bacterium from stool samples and occasionally from blood samples. More rapid presumptive diagnosis can be obtained from direct examination of feces with a dark-field microscope, which accentuates the characteristic curved rods and darting motility. This procedure is difficult to perform S

Comma

and not often used except in specialized labs. Resolution of infection occurs in most instances with simple, nonspecific rehydration and electrolyte balance therapy. In more severely affected patients, it may be necessary to administer erythromycin. Antibiotic resistance is growing in these bacteria. Because vaccines are yet to be developed, prevention depends on rigid sanitary control of water and milk supplies and care in food preparation.

Yersinia Species Yersinia is a genus of gram-negative bacteria that includes the infamous plague bacterium, Yersinia pestis (discussed in chapter 20). There are two species that cause GI tract disease: Y. enterocolitica and Y. pseudotuberculosis. The infections are most notable for the high degree of abdominal pain they cause. This symptom is accompanied by fever. Often the symptoms are mistaken for appendicitis. The disease is uncommon in the United States, but outbreaks do occasionally occur. Food and beverages can become contaminated with these bacteria, which inhabit the intestines of farm animals, pets, and wild animals. Transmission also occurs when people handle raw food and then touch fomites such as toys or baby bottles without washing their hands. The bacteria invade the small intestinal mucosa, and some enter the lymphatics and are harbored intracellularly in phagocytes. Inflammation of the ileum and mesenteric lymph nodes gives rise to severe abdominal pain. The infection occasionally spreads to the bloodstream, but systemic effects are rare. Two to three percent of patients experience joint pain a month following the diarrhea episode. This symptom resolves spontaneously within a few months. Infections with Y. pseudotuberculosis tend to be milder than those with Y. enterocolitica and center on lymph node inflammation rather than mucosal involvement. Simple rules of food hygiene are usually sufficient to prevent the spread of this infection. Antibiotics are not usually prescribed for this disease, unless bacteremia is documented. In that case, doxycycline, gentamicin, or TMP-SMZ is used.

Clostridium difficile Spiral

Figure 22.13 Scanning micrograph of Campylobacter jejuni, showing comma, S, and spiral forms.

Clostridium difficile is a gram-positive endospore-forming rod found as normal biota in the intestine. It was once considered relatively harmless but now is known to cause a condition called pseudomembranous colitis. It is also sometimes called antibiotic-associated colitis. In most cases, this infection seems to be precipitated by therapy with broad-spectrum antibiotics such as ampicillin, clindamycin, or cephalosporins. It is a major cause of diarrhea in hospitals, although community-acquired infections have been on the rise in the last few years. Also, new studies suggest that the use of gastric acid inhibitors for the treatment of heartburn can predispose patients to this infection. Although C. difficile is relatively noninvasive, it is able to superinfect the large intestine when drugs have disrupted the normal biota. It produces two enterotoxins, toxins A and B, that cause areas of necrosis in the wall of the intestine. The predomi-

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677

nant symptom is diarrhea commencing late in therapy or even after therapy has stopped. More severe cases exhibit abdominal cramps, fever, and leukocytosis. The colon is inflamed and gradually sloughs off loose, membranelike patches called pseudomembranes consisting of fibrin and cells (figure 22.14). If the condition is not stopped, perforation of the cecum and death can result. Mild, uncomplicated cases respond to withdrawal of antibiotics and replacement therapy for lost fluids and electrolytes. More severe infections are treated with oral vancomycin or metronidazole for several weeks until the intestinal biota returns to normal. Because infected persons often shed large numbers of spores in their stools, increased precautions are necessary to prevent spread of the agent to other patients who may be on antimicrobial therapy. Some new techniques on the horizon are vaccination with C. difficile toxoid and restoration of normal biota by ingestion of a mixed culture of lactobacilli and yeasts.

Vibrio cholerae

Figure 22.15 Vibrio cholerae. Note the characteristic curved

Cholera has been a devastating disease for centuries. It is not an exaggeration to say that the disease has shaped a good deal of human history in Asia and Latin America, where it has been endemic. These days we have come to expect outbreaks of cholera to occur after natural disasters, war, or large refugee movements, especially in underdeveloped parts of the world. Vibrios are comma-shaped rods with a single polar flagellum. They belong to the family Vibrionaceae. A freshly isolated specimen of Vibrio cholerae reveals quick, darting cells that slightly resemble a cooked hot dog or a comma (figure 22.15). Vibrio shares many cultural and physiological characteristics with members of the Enterobacteriaceae, a closely related family. Vibrios are fermentative and grow on ordinary or selective media containing bile at 37°C. They possess unique O and H antigens and membrane receptor antigens that provide some basis for classifying members of the family. There are two major biotypes, called classic and El Tor.

shape and single polar flagellum.

(a)

(b)

▶

Signs and Symptoms

After an incubation period of a few hours to a few days, symptoms begin abruptly with vomiting, followed by copious watery feces called secretory diarrhea. The intestinal contents are lost very quickly, leaving only secreted fluids. This voided fluid contains flecks of mucus, hence the description “rice-water stool.” Fluid losses of nearly 1 liter per hour have been reported in severe cases, and an untreated patient can lose up to 50% of body weight during the course of this disease. The diarrhea causes loss of blood volume, acidosis from bicarbonate loss, and potassium depletion, which manifest in muscle cramps, severe thirst, flaccid skin, sunken eyes, and in young children, coma and convulsions. Secondary circulatory consequences can include hypotension, tachycardia, cyanosis, and collapse from shock within 18 to

(c)

Figure 22.14 Antibiotic-associated colitis. (a) Normal colon. (b) A mild form of colitis with diffuse, inflammatory patches. (c) Heavy yellow plaques, or pseudomembranes, typical of more severe cases. Photographs were made by a sigmoidoscope, an instrument capable of photographing the interior of the colon.

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Chapter 22 Infectious Diseases Affecting the Gastrointestinal Tract

24 hours. If cholera is left untreated, death can occur in less than 48 hours, and the mortality rate approaches 55%. ▶

Pathogenesis and Virulence Factors

After being ingested with food or water, V. cholerae encounters the potentially destructive acidity of the stomach. This hostile environment influences the size of the infectious dose (108 cells), although certain types of food shelter the pathogen more readily than others. At the junction of the duodenum and jejunum, the vibrios penetrate the mucus barrier using their flagella, adhere to the microvilli of the epithelial cells, and multiply there. The bacteria never enter the host cells or invade the mucosa. The virulence of V. cholerae is due entirely to an enterotoxin called cholera toxin (CT), which disrupts the normal physiology of intestinal cells. It is a typical A-B type toxin as previously described for Shigella. When this toxin binds to specific intestinal receptors, a secondary signaling system is activated. Under the influence of this system, the cells shed large amounts of electrolytes into the intestine, an event accompanied by profuse water loss. ▶

Transmission and Epidemiology

Although the human intestinal tract was once thought to be the primary reservoir, it is now known that the parasite lives in certain endemic regions. The pattern of cholera transmission and the onset of epidemics are greatly influenced by the season of the year and the climate. Cold, acidic, dry environments inhibit the migration and survival of Vibrio, whereas warm, monsoon, alkaline, and saline conditions favor them. The bacteria survive in water sources for long periods of time. Recent outbreaks in several parts of the world have been traced to giant cargo ships that pick up ballast water in one port and empty it in another elsewhere in the world. Cholera ranks among the top seven causes of morbidity and mortality, affecting several million people in endemic regions of Asia and Africa. In nonendemic areas such as the United States, the microbe is spread by water and food contaminated by asymptomatic carriers, but it is relatively uncommon. Sporadic outbreaks occur along the Gulf of Mexico, and V. cholerae is sometimes isolated from shellfish in that region. ▶

ers with mild or asymptomatic cholera are serious goals, but they are difficult to accomplish because of inadequate medical provisions in those countries where cholera is endemic. Vaccines are available for travelers and people living in endemic regions. One vaccine contains killed V. cholerae but protects for only 6 months or less. An oral vaccine containing live, attenuated bacteria was developed to be a more effective alternative, but evidence suggests it also confers only short-term immunity. It is not available in the United States. The key to cholera therapy is prompt replacement of water and electrolytes, because their loss accounts for the severe morbidity and mortality. This therapy can be accomplished by various rehydration techniques that replace the lost fluid and electrolytes. One of these, oral rehydration therapy (ORT), is described in Insight 22.2. Cases in which the patient is unconscious or has complications from severe dehydration require intravenous replenishment as well. Oral antibiotics such as tetracycline and drugs such as trimethoprim-sulfamethoxazole can terminate the diarrhea in 48 hours. They also diminish the period of vibrio excretion.

Cryptosporidium Cryptosporidium is an intestinal protozoan of the apicomplexan type (see chapter 5) that infects a variety of mammals, birds, and reptiles. For many years, cryptosporidiosis was considered an intestinal ailment exclusive to calves, pigs, chickens, and other poultry, but it is clearly a zoonosis as well. The organism’s life cycle includes a hardy intestinal oocyst as well as a tissue phase. Humans accidentally ingest the oocysts with water or food that has been contaminated by feces from infected animals. The oocyst “excysts” once it reaches the intestines and releases sporozoites that attach to the epithelium of the small intestine (figure 22.16).

Culture and Diagnosis

During epidemics of this disease, clinical evidence is usually sufficient to diagnose cholera. But confirmation of the disease is often required for epidemiological studies and detection of sporadic cases. V. cholerae can be readily isolated and identified in the laboratory from stool samples. Direct dark-field microscopic observation reveals characteristic curved cells with brisk, darting motility as confirmatory evidence. Immobilization or fluorescent staining of feces with group-specific antisera is supportive as well. Difficult cases can be traced by detecting a rising antitoxin titer in the serum. ▶

Prevention and Treatment

Effective prevention is contingent on proper sewage treatment and water purification. Detecting and treating carri-

Figure 22.16 Scanning electron micrograph of Cryptosporidium attached to the intestinal epithelium.

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INSIGHT 22.2

Gastrointestinal Tract Diseases Caused by Microorganisms (Nonhelminthic)

679

A Little Water, Some Sugar, and Salt Save Millions of Lives

In 1970, a clinical trial was conducted on a very lowtech solution to the devastating problem of death from diarrhea, especially among children in the developing world. Until that time, the treatment, if a child could access it, was rehydration through an IV drip. This treatment usually required traveling to the nearest clinic, often miles or days away. Most children received no treatment at all, and 3 million of them died every year. Then scientists tested a simple sugar-salt solution that patients could drink. They tested it first in India, where cholera was rampant, and found that mortality rates were greatly decreased. After more testing in Bangladesh, Turkey, the Philippines, and the United States, oral-rehydration therapy (ORT) became the treatment of choice for diarrhea from all causes. The World Health Organization (WHO) and UNICEF began providing packages of the sugar and salt mixture and instructions for mixing it with boiled water to dozens of countries. They also oversaw training of individuals who could Volunteers in front of an Oral Rehydration Clinic in the Philippines. ORT clinics are commonplace in developing countries. in turn teach townspeople and villagers about ORT. The relatively simple solution, developed by few resources. It does not require medical facilities, highthe WHO, consists of a mixture of the electrolytes sodium technology equipment, or complex medication protocols. It chloride, sodium bicarbonate, potassium chloride, and glualso eliminates the need for clean needles, which is a pressing cose or sucrose dissolved in water. When administered early issue in many parts of the world. in amounts ranging from 100 to 400 milliliters per hour, the In 1978, the British Medical journal The Lancet called solution can restore patients in 4 hours, often bringing them ORT “potentially the most important medical advance this literally back from the brink of death. Infants and small chilcentury.” With estimates of at least a million lives saved every dren who once would have died now survive so often that the year since its introduction, this statement seems to have been mortality rate for treated cases of cholera is near zero. This proven correct. therapy has several advantages, especially for countries with

The organism penetrates the intestinal cells and lives intracellularly in them. It undergoes asexual and sexual reproduction in the gut and produces more oocysts, which are excreted from the host and after a short time become infective again. The oocysts are highly infectious and extremely resistant to treatment with chlorine and other disinfectants.

The prominent symptoms mimic other types of gastroenteritis, with headache, sweating, vomiting, severe abdominal cramps, and diarrhea. AIDS patients may experience chronic persistent cryptosporidial diarrhea that can be used as a criterion to help diagnose AIDS. The agent can be detected in fecal samples or in biopsies (figure 22.17) using ELISA or acid-fast

Human intestinal cell

Cryptosporidium merozoites (b)

Figure 22.17 (a) An electron micrograph of a (a)

Cryptosporidium merozoite that has penetrated the intestinal mucosa. (b) Isospora belli, showing oocysts in two stages of maturation.

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Chapter 22 Infectious Diseases Affecting the Gastrointestinal Tract

staining. Stool cultures should be performed to rule out other (bacterial) causes of infection. Cryptosporidiosis has a cosmopolitan distribution. Its highest prevalence is in areas with unreliable water and food sanitation. The carrier state occurs in 3% to 30% of the population in developing countries. The susceptibility of the general public to this pathogen has been amply demonstrated by several large-scale epidemics. In 1993, 370,000 people developed Cryptosporidium gastroenteritis from the municipal water supply in Milwaukee, Wisconsin. Other mass outbreaks of this sort have been traced to contamination of the local water reservoir by livestock wastes. Half of the outbreaks of diarrhea associated with swimming pools are caused by Cryptosporidium. Because chlorination is not entirely successful in eradicating the cysts, most treatment plants use filtration to remove them, but even this method can fail. Treatment is not usually required for otherwise healthy patients. Antidiarrheal agents (antimotility drugs) may be

used. Although no curative antimicrobial agent exists for Cryptosporidium, physicians will often try paromomycin, an aminoglycoside that can be effective against protozoa.

Rotavirus Rotavirus is a member of the Reovirus group, which consists of an unusual double-stranded RNA genome with both an inner and an outer capsid. Globally, rotavirus is the primary viral cause of morbidity and mortality resulting from diarrhea, accounting for nearly 50% of all cases. It is estimated that there are 1 million cases of rotavirus infection in the United States every year, leading to 70,000 hospitalizations. Peak occurrences of this infection are seasonal; in the U.S. Southwest, the peak is often in the late fall, and in the Northeast the peak comes in the spring. Diagnosis of rotavirus infections is usually not performed, as it is treated symptomatically. Nevertheless,

Disease Table 22.5 Acute Diarrhea Bacterial Causes Causative Organism(s)

Salmonella

Shigella

Shiga-toxinproducing E. coli O157:H7 (EHEC)

Other E. coli (non-shiga-toxin producing)

Campylobacter

Most Common Modes of Transmission

Vehicle (food, beverage), fecal-oral

Fecal-oral, direct contact

Vehicle (food, beverage), fecal-oral

Vehicle, fecal-oral

Vehicle (food, water), fecal-oral

Virulence Factors

Adhesins, endotoxin

Endotoxin, enterotoxin, shiga toxins in some strains

Shiga toxins; proteins for attachment, secretion, effacement

Various: proteins for attachment, secretion, effacement; heatlabile and/or heatstable exotoxins; invasiveness

Adhesins, exotoxin, induction of autoimmunity

Culture/Diagnosis

Stool culture, not usually necessary

Stool culture; antigen testing for shiga toxin

Stool culture, antigen testing for shiga toxin

Stool culture not usually necessary; in absence of blood, fever

Stool culture not usually necessary; dark-field microscopy

Prevention

Food hygiene and personal hygiene

Food hygiene and personal hygiene

Avoid live E. coli (cook meat and clean vegetables)

Food and personal hygiene

Food and personal hygiene

Treatment

Rehydration; no antibiotic for uncomplicated disease

TMP-SMZ, rehydration

Antibiotics contraindicated, supportive measures

Rehydration, antimotility agent

Rehydration, erythromycin in severe cases (antibiotic resistance rising)

Fever Present

Usually

Often

Often

Sometimes

Usually

Blood in Stool

Sometimes

Often

Usually

Sometimes

No

Distinctive Features

Often associated with chickens, reptiles

Very low ID50

Hemolytic uremic syndrome

EIEC, ETEC, EPEC

Guillain-Barré syndrome

22.3

Gastrointestinal Tract Diseases Caused by Microorganisms (Nonhelminthic)

studies are often conducted so that public health officials can maintain surveillance of how prevalent the infection is. Stool samples from infected persons contain large amounts of virus, which is readily visible using an electron microscope (figure 22.18). The virus gets its name from its physical appearance, which is said to resemble a “spoked wheel.” An ELISA test is also available. The virus is transmitted by the fecal-oral route, including through contaminated food, water, and fomites. For this reason, disease is most prevalent in areas of the world with poor sanitation. In the United States, rotavirus infection is relatively common, but its course is generally mild. The effects of infection vary with the age, nutritional state, general health, and living conditions of the patient. Babies from 6 to 24 months of age lacking maternal antibodies have the greatest risk for fatal disease. These children present symptoms of watery diarrhea, fever, vomiting, dehydration, and shock. The intestinal mucosa can be damaged in

681

Figure 22.18 Rotavirus visible in a sample of feces from a child with gastroenteritis.

Note the unique “spoked-wheel”

morphology of the virus.

Nonbacterial Causes Yersinia

Clostridium difficile

Vibrio cholerae

Cryptosporidium

Rotavirus

Other viruses

Vehicle (food, water), fecal-oral, indirect contact

Endogenous (normal biota)

Vehicle (water and some foods), fecaloral

Vehicle (water, food), fecal-oral

Fecal-oral, vehicle, fomite

Fecal-oral, vehicle

Intracellular growth

Enterotoxins A and B

Cholera toxin (CT)

Intracellular growth

–

–

Cold-enrichment stool culture

Stool culture, PCR, ELISA demonstration of toxins in stool

Clinical diagnosis, microscopic techniques, serological detection of antitoxin

Acid-fast staining, ruling out bacteria

Usually not performed

Usually not performed

Food and personal hygiene

–

Water hygiene

Water treatment, proper food handling

Oral live virus vaccine

Hygiene

None in most cases, doxycycline, gentamicin or TMPSMZ for bacteremia

Withdrawal of antibiotic, in severe cases metronidazole or vancomycin

Rehydration, in severe cases tetracycline, TMPSMZ

None, paromomycin used sometimes

Rehydration

Rehydration

Usually

Sometimes

No

Often

Often

Sometimes

Occasionally

Not usually; mucus prominent

No

Not usually

No

No

Severe abdominal pain

Antibiotic-associated diarrhea

Rice-water stools

Resistant to chlorine disinfection

Severe in babies

–

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Chapter 22 Infectious Diseases Affecting the Gastrointestinal Tract

a way that chronically compromises nutrition, and long-term or repeated infections can retard growth. Newborns seem to be protected by maternal antibodies. Adults can also acquire this infection, but it is generally mild and self-limiting. Children are treated with oral replacement fluid and electrolytes. A vaccine was introduced in 1998 but was withdrawn 9 months later because of a side effect called intussusception, a form of intestinal blockage that seemed to be associated with immunization. A new oral live virus vaccine has been available since 2006.

Other Viruses A bewildering array of viruses can cause gastroenteritis, including adenoviruses, noroviruses (sometimes known as Norwalk viruses), and astroviruses. They are extremely common in the United States and around the world. They are usually “diagnosed” when no other agent (such as those just described) is identified. Transmission is fecal-oral or via contamination of food and water. Viruses generally cause a profuse, watery diarrhea of 3 to 5 days duration. Vomiting may accompany the disease, especially in the early phases. Mild fever is often seen. In 2002, a series of gastroenteritis outbreaks occurred on cruise ships, most of which were ascribed to viruses other than rotavirus. Treatment of these infections always focuses on rehydration (Disease Table 22.5).

Case File 22

Continuing the Case

Besides providing shelter to the evacuees displaced by Hurricane Katrina, Reliant City housed numerous staff members and volunteers who also required cots, bedding, food, water, toilets, and shower facilities. Soon these workers, along with police officers and others having direct contact with the shelter residents, were reporting gastrointestinal symptoms similar to those of the patients who had presented at the clinic. This secondary spread, presumably by person-to-person contact or fomite transmission, indicated a causative agent with a very low infectious dose (ID). Initial laboratory testing for bacterial species most commonly suspected in cases of acute gastroenteritis—Salmonella, Shigella, E. coli, and Campylobacter—was negative. Similarly, none of the most common parasitic enteropathogens—Cryptosporidium, rotavirus, and adenovirus—were found. However, testing of stool samples or rectal swabs from 44 of the symptomatic patients identified norovirus in 22 of these samples. ◾ Norovirus often strikes passengers on luxurious cruise ships, an environment seemingly far removed from that of Reliant City. What similarities might these two environments share that would increase the risk of a norovirus outbreak?

Acute Diarrhea with Vomiting (Food Poisoning) If a patient presents with severe nausea and frequent vomiting accompanied by diarrhea, and reports that companions with whom he or she shared a recent meal (within the last 1 to 6 hours) are suffering the same fate, food poisoning should be suspected. Food poisoning refers to symptoms in the gut that are caused by a preformed toxin of some sort. In many cases, the toxin comes from Staphylococcus aureus. In others, the source of the toxin is Bacillus cereus or Clostridium perfringens. The toxin occasionally comes from nonmicrobial sources such as fish, shellfish, or mushrooms. In any case, if the symptoms are violent and the incubation period is very short, intoxication (the effects of a toxin) rather than infection should be considered. (Insight 22.3 has information about outbreak investigations in general.)

Staphylococcus aureus Exotoxin This illness is associated with eating foods such as custards, sauces, cream pastries, processed meats, chicken salad, or ham that have been contaminated by handling and then left unrefrigerated for a few hours. Because of the high salt tolerance of S. aureus, even foods containing salt as a preservative are not exempt. The toxins produced by the multiplying bacteria do not noticeably alter the food’s taste or smell. The exotoxin (which is an enterotoxin) is heat-stable; inactivation requires 100°C for at least 30 minutes. Thus, heating the food after toxin production may not prevent disease. The ingested toxin acts upon the gastrointestinal epithelium and stimulates nerves, with acute symptoms of cramping, nausea, vomiting, and diarrhea. Recovery is also rapid, usually within 24 hours. The disease is not transmissible person to person. Often, a single source will contaminate several people, leading to a mini-outbreak. The illness is caused by the toxin and does not require S. aureus to be present or alive in the contaminated food. If the bacterium is allowed to multiply in the food, it produces its exotoxin. Even if the bacteria are subsequently destroyed by heating, the preformed toxin will act quickly once it is ingested. As you learned earlier, many diarrheal diseases have symptoms caused by bacterial exotoxins. In most cases, the bacteria take up temporary residence in the gut and then start producing exotoxin, so the incubation period is longer than the 1 to 6 hours seen with S. aureus food poisoning. Because this toxin is heat-stable, mishandling of food, such as allowing bacteria to multiply and then heating or reheating, can provide the perfect conditions for food poisoning to occur. This condition is almost always self-limiting, and antibiotics are definitely not warranted.

Bacillus cereus Exotoxin Bacillus cereus is a sporulating gram-positive bacterium that is naturally present in soil. As a result, it is a common resident on vegetables and other products in close contact with soil. It produces two exotoxins, one of which causes a diarrheal-type disease, the other of which causes an emetic (ee-met′-ik) or

22.3

INSIGHT 22.3

Gastrointestinal Tract Diseases Caused by Microorganisms (Nonhelminthic)

683

Microbes Have Fingerprints, Too

Until recently, epidemiological investigations of outbreaks of disease relied primarily on careful examination of oral case histories and reports from the patients themselves, which might provide clues about the source of exposure. If organisms could be isolated and identified in the laboratory, they could provide evidence to support or negate a hypothetical exposure, but usually they could not provide definitive proof. When more sophisticated molecular methods for identifying microbial strains became available, the situation changed. A wide variety of techniques, including PCR, Southern blot analysis, and ribotyping, enabled the identification of bacteria below the species level and allowed the movement of a particular microbe to be traced through various hosts and environments. The most useful of these techniques for public health purposes seems to be the process called pulsed-field gel electrophoresis, or PFGE. PFGE is a technique for macrorestriction analysis. Pathogens are isolated from a patient, and their DNA is harvested. The DNA is then cut up with restriction enzymes specifically chosen so that they find only a few places to cut into the organism’s genome. The result is just a few very large pieces of DNA rather than the many small ones obtained with older methods of restriction analysis. The DNA fragments are then separated using the pulsed-field method of gel electrophoresis. This method involves constantly changing the direction of (pulsing) the electrical field during electrophoresis. You can think of it as teasing out the DNA pieces from one another

in the gel matrix. This method allows effective separation of the large pieces. Once the electrophoresis is finished, the fragments of different lengths can be seen as dark bands after the gel is immersed in a special stain. The lengths of the fragments and, thus, the pattern revealed by each microbe will be different—even for different strains of the same microbial species—because the enzymes are cut in different places on the genome where small DNA changes exist, corresponding to different strain types. This pattern is also called a DNA fingerprint, much like that used in forensic studies. In 1993, the CDC used PFGE for the first time to trace an outbreak of food-borne illness in the United States. They determined that the strain of E. coli O157:H7 found in patients had the same PFGE pattern as the strain found in the suspected hamburger patties that had been served at a fast-food restaurant. The use of the technique led to the creation of a national database called PulseNet, which contains the PFGE patterns of common foodborne pathogens that have been implicated in outbreaks. Participating PulseNet laboratories all around the country can compare PFGE patterns they obtain from patients or suspected foods to patterns in the centralized database. In this way, outbreaks that are geographically dispersed (for instance, those caused by contaminated meat that may have been distributed nationally) can be identified quickly. When new patterns come in, they are also archived so that other laboratories submitting the same patterns will quickly realize that the cases are related.

A pulsed-field gel electrophoresis “fingerprint.” The identity of the microbe is revealed in this pattern.

vomiting disease. The type of disease that takes place is influenced by the type of food that is contaminated by the bacterium. The emetic form is most frequently linked to fried rice, especially when it has been cooked and kept warm for long periods of time. These conditions are apparently ideal for the expression of the low-molecular-weight, heat-stable exotoxin having an emetic effect. The diarrheal form of the disease is usually associated with cooked meats or vegetables that are held at a warm temperature for long periods of time. These conditions apparently favor the production of the high-molecular-weight, heat-labile exotoxin. The symptom in these cases is a watery, profuse diarrhea that lasts only for about 24 hours. Diagnosis of the emetic form of the disease is accomplished by finding the bacterium in the implicated food source. Microscopic examination of stool samples is used to diagnose the diarrheal form of the disease. Of course, in everyday practice, neither diagnosis nor treatment is performed because of the short duration of the disease. In both cases, the only prevention is the proper handling of food.

Clostridium perfringens Exotoxin Another sporulating gram-positive bacterium that causes intestinal symptoms is Clostridium perfringens. You first read about this bacterium as the causative agent of gas gangrene in chapter 18. Endospores from C. perfringens can also contaminate many kinds of foods. Those most frequently implicated in disease are animal flesh (meat, fish) and vegetables such as beans that have not been cooked thoroughly enough to destroy endospores. When these foods are cooled, spores germinate, and the germinated cells multiply, especially if the food is left unrefrigerated. If the food is eaten without adequate reheating, live C. perfringens cells enter the small intestine and release exotoxin. The toxin, acting upon epithelial cells, initiates acute abdominal pain, diarrhea, and nausea in 8 to 16 hours. Recovery is rapid, and deaths are extremely rare. C. perfringens also causes an enterocolitis infection similar to that caused by C. difficile. This infectious type of diarrhea is acquired from contaminated food, or it may be transmissible by inanimate objects (Disease Table 22.6).

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Chapter 22 Infectious Diseases Affecting the Gastrointestinal Tract

Disease Table 22.6 Acute Diarrhea with Vomiting (Food Poisoning) Causative Organism(s)

Staphylococcus aureus exotoxin

Bacillus cereus

Clostridium perfringens

Most Common Modes of Transmission

Vehicle (food)

Vehicle (food)

Vehicle (food)

Virulence Factors

Heat-stable exotoxin

Heat-stable toxin, heat-labile toxin

Heat-labile toxin

Culture/Diagnosis

Usually based on epidemiological evidence

Microscopic analysis of food or stool

Detection of toxin in stool

Prevention

Proper food handling

Proper food handling

Proper food handling

Treatment

Supportive

Supportive

Supportive

Fever Present

Not usually

Not usually

Not usually

Blood in Stool

No

No

No

Distinctive Features

Suspect in foods with high salt or sugar content

Two forms: emetic and diarrheal

Acute abdominal pain

Chronic Diarrhea

Enteroaggregative E. coli (EAEC)

Chronic diarrhea is defined as lasting longer than 14 days. It can have infectious causes or can reflect noninfectious conditions. Most of us are familiar with diseases that present a constellation of bowel syndromes, such as irritable bowel syndrome and ulcerative colitis, neither of which is directly caused by a microorganism as far as we know. (Crohn’s disease may well have a microbial cause, Insight 22.1.) The other two conditions may indeed represent an overreaction to the presence of an infectious agent or another irritant, but the host response seems to be responsible for the pathology. When the presence of an infectious agent is ruled out by a negative stool culture or other tests, these conditions are suspected. People suffering from AIDS almost universally suffer from chronic diarrhea. Most of the patients who are not taking antiretroviral drugs have diarrhea caused by a variety of opportunistic microorganisms, including Cryptosporidium, Mycobacterium avium, and so forth. Recently, investigators have found that patients who are aggressively treating their HIV infection with the cocktail of drugs known as HAART (see chapter 20) still suffer from chronic diarrhea at a high rate. The causes for this diarrhea are not completely understood. A patient’s HIV status should be considered if he or she presents with chronic diarrhea. Next we examine a few of the microbes that can be responsible for chronic diarrhea in otherwise healthy people. Keep in mind that practically any disease of the intestinal tract has a sexual mode of transmission in addition to the ones that are commonly stated. For example, any kind of oral-anal sexual contact efficiently transfers pathogens to the “oral” partner. This mode is more commonly seen in cases of chronic illness than it is in patients experiencing acute diarrhea, for obvious reasons.

In the section on acute diarrhea, you read about the various categories of E. coli that can cause disease in the gut. One type, the enteroaggregative E. coli (EAEC), is particularly associated with chronic disease, especially in children. This bacterium was first recognized in 1987. It secretes neither the heat-stable nor heat-labile exotoxins previously described for enterotoxigenic E. coli (ETEC). It is distinguished by its ability to adhere to human cells in aggregates rather than as single cells (figure 22.19). Its presence appears to stimulate secretion of large amounts of mucus in the gut, which may be part of its role in causing chronic diarrhea. The bacterium also seems capable of exerting toxic effects on the gut epithelium, although the mechanisms are not well understood. Transmission of the bacterium is through contaminated food and water. It is difficult to diagnose in a clinical lab because EAEC is not easy to distinguish from other E. coli, including normal biota. And the designation EAEC is not

Nucleus of epithelial cell

Figure 22.19 Enteroaggregative E. coli adhering to epithelial cells.

22.3

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Gastrointestinal Tract Diseases Caused by Microorganisms (Nonhelminthic)

actually a serotype but is functionally defined as an E. coli that adheres in an aggregative pattern. This bacterium seems to be associated with chronic diarrhea in people who are malnourished. It is not exactly clear whether the malnutrition predisposes patients to this infection or whether this infection contributes to malnutrition. Probably both possibilities are operating in patients, who are usually children in developing countries. More recently, the bacterium has been associated with acute diarrhea in industrialized countries, perhaps providing a clue to this question. It may be that in well-nourished hosts the bacterium produces acute, self-limiting disease.

Cyclospora Cyclospora cayetanensis is an emerging protozoan pathogen. Since the first occurrence in 1979, hundreds of outbreaks have been reported in the United States and Canada. Its mode of transmission is fecal-oral, and most cases have been associated with consumption of fresh produce and water presumably contaminated with feces. This disease occurs worldwide, and although primarily of human origin, it is not spread directly from person to person. Outbreaks have been traced to imported raspberries, salad made with fresh greens, and drinking water. A major outbreak of this organism occurred on a cruise ship in April of 2009, where 135 of 1,318 passengers, and 25 crew members, became ill with Cyclospora. The organism is 8 to 10 micrometers in diameter and stains variably in an acid-fast stain. Diagnosis can be complicated by the lack of recognizable oocysts in the feces. Techniques that improve identification of the parasite are examination of fresh preparations under a fluorescent microscope and an acid-fast stain of a processed stool specimen (figure 22.20). A PCR-based test can also be used to identify Cyclospora and differentiate it from other parasites. This form of analysis is more sensitive and can detect protozoan genetic material even in the absence of actual cysts.

20 ␮m

The disease begins when oocysts enter the small intestine and release invasive sporozoites that invade the mucosa. After an incubation period of about 1 week, symptoms of watery diarrhea, stomach cramps, bloating, fever, and muscle aches appear. Patients with prolonged diarrheal illness experience anorexia and weight loss. Most cases of infection have been effectively controlled with trimethoprim-sulfamethoxazole lasting 1 week. Traditional antiprotozoan drugs are not effective. Some cases of disease may be prevented by cooking or freezing food to kill the oocysts.

Giardia Giardia lamblia is a pathogenic flagellated protozoan first observed by Antonie van Leeuwenhoek in his own feces. For 200 years, it was considered a harmless or weak intestinal pathogen; and only since the 1950s has its prominence as a cause of diarrhea been recognized. In fact, it is the most common flagellate isolated in clinical specimens. Observed straight on, the trophozoite has a unique symmetrical heart shape with organelles positioned in such a way that it resembles a face (figure 22.21). Four pairs of flagella emerge from Nucleus

Ventral depression

Nuclei

Trophozoite

Cyst

(a)

(b) Oocysts

Bacteria

Figure 22.20 An acid-fast stain of Cyclospora in a human fecal sample. The large (8–10 μm) cysts stain pink to red and have a wrinkled outer wall. Bacteria stain blue.

Figure 22.21 Giardia lamblia trophozoite. (a) Schematic drawing. (b) Scanning electron micrograph of intestinal surface, revealing (on the left) the lesion left behind by adhesive disk of a Giardia that has detached. The trophozoite on the right is lying on its “back” and is revealing its adhesive disk.

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Chapter 22 Infectious Diseases Affecting the Gastrointestinal Tract

the ventral surface, which is concave and acts like a suction cup for attachment to a substrate. Giardia cysts are small, compact, and contain four nuclei. ▶

Signs and Symptoms

Typical symptoms include diarrhea of long duration, abdominal pain, and flatulence. Stools have a greasy, malodorous quality to them. Fever is usually not present. ▶

Pathogenesis and Virulence Factors

Ingested Giardia cysts enter the duodenum, germinate, and travel to the jejunum to feed and multiply. Some trophozoites remain on the surface, while others invade the deeper crypts to varying degrees. Superficial invasion by trophozoites causes damage to the epithelial cells, edema, and infiltration by white blood cells, but these effects are reversible. The presence of the protozoan leads to maladsorption (especially of fat) in the digestive tract and can cause significant weight loss. ▶

Transmission and Epidemiology of Giardiasis

Giardiasis has a complex epidemiological pattern. The protozoan has been isolated from the intestines of beavers, cattle, coyotes, cats, and human carriers, but the precise reservoir is unclear at this time. Although both trophozoites and cysts escape in the stool, the cysts play a greater role in transmission. Unlike other pathogenic flagellates, Giardia cysts can survive for 2 months in the environment. Cysts are usually ingested with water and food or swallowed after close contact with infected people or contaminated objects. Infection can occur with a dose of only 10 to 100 cysts. Outbreaks of giardiasis point to a spectrum of possible modes of transmission. Community water supplies in areas throughout the United States have been implicated as common vehicles of infection. Giardia epidemics have been traced to water from fresh mountain streams as well as chlorinated municipal water supplies in several states. Infections are not uncommon in hikers and campers who used what they thought was clean water from ponds, lakes, and streams in remote mountain areas. Because wild mammals such as muskrats and beavers are intestinal carriers, they could account for cases associated with drinking water from these sources. Checking water for purity by its appearance obviously is unreliable, because the cysts are too small to be detected. Cases of fecal-oral transmission have been documented in day care centers; food contaminated by infected persons has also transmitted the disease. ▶

Culture and Diagnosis

Diagnosis of giardiasis can be difficult because the organism is shed in feces only intermittently. Sometimes ELISA tests are used to screen fecal samples for Giardia antigens, and PCR tests are available, although they are mainly used for detection of the protozoan in environmental samples.

▶

Prevention and Treatment

There is a vaccine against Giardia that can be given to animals, including dogs. No human vaccine is available. Avoiding drinking from freshwater sources is the major preventive measure that can be taken. Even municipal water is at some risk; water agencies have had to rethink their policies on water maintenance and testing. The agent is killed by boiling, ozone, and iodine; but unfortunately, the amount of chlorine used in municipal water supplies does not destroy the cysts. Treatment is with tinidazole or metronidazole.

Entamoeba Amoebas are widely distributed in aqueous habitats and are frequent parasites of animals, but only a small number of them have the necessary virulence to invade tissues and cause serious pathology. One of the most significant pathogenic amoebas is Entamoeba histolytica (en″-tah-mee′bah his″-toh-lit′-ih-kuh). The relatively simple life cycle of this parasite alternates between a large trophozoite that is motile by means of pseudopods and a smaller, compact, nonmotile cyst (figure 22.22a-c). The trophozoite lacks most of the organelles of other eukaryotes, and it has a large single nucleus that contains a prominent nucleolus called a karyosome. Amoebas from fresh specimens are often packed with food vacuoles containing host cells and bacteria. The mature cyst is encased in a thin yet tough wall and contains four nuclei as well as distinctive cigar-shaped bodies called chromatoidal bodies, which are actually dense clusters of ribosomes. ▶

Signs and Symptoms

As hinted by its species name, tissue damage is one of the formidable characteristics of untreated E. histolytica infection. Clinical amoebiasis exists in intestinal and extraintestinal forms. The initial targets of intestinal amoebiasis are the cecum, appendix, colon, and rectum. The amoeba secretes enzymes that dissolve tissues, and it actively penetrates deeper layers of the mucosa, leaving erosive ulcerations (figure 22.22d). This phase is marked by dysentery (bloody, mucus-filled stools), abdominal pain, fever, diarrhea, and weight loss. The most life-threatening manifestations of intestinal infection are hemorrhage, perforation, appendicitis, and tumorlike growths called amoebomas. Lesions in the mucosa of the colon have a characteristic flask-like shape. Extraintestinal infection occurs when amoebas invade the viscera of the peritoneal cavity. The most common site of invasion is the liver. Here, abscesses containing necrotic tissue and trophozoites develop and cause amoebic hepatitis. Another rarer complication is pulmonary amoebiasis. Other infrequent targets of infection are the spleen, adrenals, kidney, skin, and brain. Severe forms of the disease result in about a 10% fatality rate.

22.3 (a) Trophozoite

Gastrointestinal Tract Diseases Caused by Microorganisms (Nonhelminthic)

687

(b) Mature Cyst

Nucleus Chromatoidals Karyosome Nuclei

Red blood cells

(d)

(c) Excystment

Erosion of intestine

Figure 22.22 Entamoeba histolytica. (a) A trophozoite containing a single nucleus, a karyosome, and red blood cells. (b) A mature cyst with four nuclei and two blocky chromatoidals. (c) Stages in excystment. Divisions in the cyst create four separate cells, or metacysts, that differentiate into trophozoites and are released. (d) Intestinal amoebiasis and dysentery of the cecum. Red patches are sites of amoebic damage to the intestinal mucosa. (e) Trophozoite of Entamoeba histolytica. Note the fringe of very fine pseudopods it uses to invade and feed on tissue.

▶

Pathogenesis and Virulence Factors

(e)

Amoebiasis begins when viable cysts are swallowed and arrive in the small intestine, where the alkaline pH and digestive juices of this environment stimulate excystment. Each cyst releases four trophozoites, which are swept into the cecum and large intestine. There, the trophozoites attach by fine pseudopods (figure 22.22e), multiply, actively move about, and feed. In about 90% of patients, infection is asymptomatic or very mild, and the trophozoites do not invade beyond the most superficial layer. The severity of the infection can vary with the strain of the parasite, inoculum size, diet, and host resistance. The secretion of lytic enzymes by the amoeba seems to induce apoptosis of host cells. This means that the host is contributing to the process by destroying its own tissues on cue from the protozoan. The invasiveness of the amoeba is also a clear contributor to its pathogenicity.

Humans are the primary hosts of E. histolytica. Infection is usually acquired by ingesting food or drink contaminated with cysts released by an asymptomatic carrier. The amoeba is thought to be carried in the intestines of one-tenth of the world’s population, and it kills up to 100,000 people a year. Its geographic distribution is partly due to local sewage disposal and fertilization practices. Occurrence is highest in tropical regions (Africa, Asia, and Latin America), where night soil (human excrement) or untreated sewage is used to fertilize crops, and sanitation of water and food can be substandard. Although the prevalence of the disease is lower in the United States, as many as 10 million people could harbor the agent. Epidemics of amoebiasis are infrequent but have been documented in prisons, hospitals, juvenile care institutions, and communities where water supplies are polluted. Amoebic infections can also be transmitted by anal-oral sexual contact.

▶

▶

Transmission and Epidemiology of Amoebiasis

Entamoeba is harbored by chronic carriers whose intestines favor the encystment stage of the life cycle. Cyst formation cannot occur in active dysentery because the feces are so rapidly flushed from the body; but after recuperation, cysts are continuously shed in feces.

Culture and Diagnosis

Diagnosis of this protozoal infection relies on a combination of tests, including microscopic examination of stool for the characteristic cysts or trophozoites, ELISA tests of stool for E. histolytica antigens, and serological testing for the presence of antibodies to the pathogen. PCR testing is currently being

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Chapter 22 Infectious Diseases Affecting the Gastrointestinal Tract

Disease Table 22.7 Chronic Diarrhea Causative Organism(s)

Enteroaggregative E. coli (EAEC)

Cyclospora cayetanensis

Giardia lamblia

Entamoeba histolytica

Most Common Modes of Transmission

Vehicle (food, water), fecal-oral

Fecal-oral, vehicle

Vehicle, fecal-oral, direct and indirect contact

Vehicle, fecal-oral

Virulence Factors

?

Invasiveness

Attachment to intestines alters mucosa

Lytic enzymes, induction of apoptosis, invasiveness

Culture/Diagnosis

Difficult to distinguish from other E. coli

Stool examination, PCR

Stool examination, ELISA

Stool examination, ELISA, serology

Prevention

?

Washing, cooking food, personal hygiene

Water hygiene, personal hygiene

Water hygiene, personal hygiene

Treatment

None, or ciprofloxacin

TMP-SMZ

Tinidazole, metronidazole

Metronidazole or tinidazole, followed by iodoquinol or paromomycin

Fever Present

No

Usually

Not usually

Yes

Blood in Stool

Sometimes, mucus also

No

No, mucus present (greasy and malodorous)

Yes

Distinctive Features

Chronic in the malnourished

–

Frequently occurs in backpackers, campers

–

refined. It is important to differentiate E. histolytica from the similar Entamoeba coli and Entamoeba dispar, which occur as normal biota. ▶

Prevention and Treatment

No vaccine yet exists for E. histolytica, although several are in development. Prevention of the disease therefore relies on purification of water. Because regular chlorination of water supplies does not kill cysts, more rigorous methods such as boiling or iodine are required. Effective treatment usually involves the use of drugs such as iodoquinol, which acts in the feces, and metronidazole (Flagyl) or chloroquine, which work in the tissues. Dehydroemetine is used to control symptoms, but it will not cure the disease. Other drugs are given to relieve diarrhea and cramps, while lost fluid and electrolytes are replaced by oral or intravenous therapy. Infection with E. histolytica provokes antibody formation against several antigens, but permanent immunity is unlikely and reinfection can occur (Disease Table 22.7).

Hepatitis When certain viruses in fect the liver, they cause hepatitis, an inflammatory disease marked by necrosis of hepatocytes and a mononuclear response that swells and disrupts the liver architecture. This pathologic change interferes with the

liver’s excretion of bile pigments such as bilirubin into the intestine. When bilirubin, a greenish-yellow pigment, accumulates in the blood and tissues, it causes jaundice, a yellow tinge in the skin and eyes. The condition can be caused by a variety of different viruses. They are all named hepatitis viruses but only because they all can cause this inflammatory condition in the liver. Note that noninfectious conditions can also cause inflammation and disease in the liver, including some autoimmune conditions, drugs, and alcohol overuse.

Hepatitis A Virus Hepatitis A virus (HAV) is a nonenveloped, single-stranded RNA enterovirus. It belongs to the family Picornaviridae. In general, HAV disease is far milder and shorter term than the other forms. ▶

Signs and Symptoms

Most infections by this virus are either subclinical or accompanied by vague, flulike symptoms. In more overt cases, the presenting symptoms may include jaundice and swollen liver. Darkened urine is often seen in this and other hepatitises. Jaundice is present in only about 10% of the cases. Hepatitis A occasionally occurs as a fulminating disease and causes liver damage, but this manifestation is quite rare.

22.3

Gastrointestinal Tract Diseases Caused by Microorganisms (Nonhelminthic)

The virus is not oncogenic (cancer causing), and complete uncomplicated recovery results. ▶

A Note About Hepatitis E

Pathogenesis and Virulence Factors

Another RNA virus, called hepatitis E, causes a type of hepatitis very similar to that caused by hepatitis A. It is transmitted by the fecal-oral route, although it does not seem to be transmitted person to person. It is usually self-limiting, except in the case of pregnant women for whom the fatality rate is 15% to 25%. It is more common in developing countries, and almost all of the cases reported in the United States occur in people who have traveled to these regions. There is currently no vaccine.

The hepatitis A virus is generally of low virulence. Most of the pathogenic effects are thought to be the result of host response to the presence of virus in the liver. ▶

Transmission and Epidemiology

There is an important distinction between this virus and hepatitis B and C viruses: Hepatitis A virus is spread through the fecal-oral route (and is sometimes known as infectious hepatitis). In general, the disease is associated with deficient personal hygiene and lack of public health measures. In countries with inadequate sewage control, most outbreaks are associated with fecally contaminated water and food. Rates of infection in the United States have fallen from 12 per 100,000 persons/yr in 1995 to 1 per 100,000 in 2007. Most of these result from close institutional contact, unhygienic food handling, eating shellfish, sexual transmission, or travel to other countries. In 2003, the largest single hepatitis A outbreak to date in the United States was traced to contaminated green onions used in salsa dips at a Mexican restaurant. At least 600 people who had eaten at the restaurant fell ill with hepatitis A. Hepatitis A occasionally can be spread by blood or blood products, but this is the exception rather than the rule. In developing countries, children are the most common victims, because exposure to the virus tends to occur early in life, whereas in North America and Europe, more cases appear in adults. Because the virus is not carried chronically, the principal reservoirs are asymptomatic, short-term carriers (often children) or people with clinical disease. ▶

Culture and Diagnosis

Diagnosis of the disease is aided by detection of anti-HAV IgM antibodies produced early in the infection and by tests to identify HA antigen or virus directly in stool samples. ▶

Prevention and Treatment

Prevention of hepatitis A is based primarily on immunization. An inactivated viral vaccine (Havrix) has been in use since the mid-1990s. Short-term protection can be conferred by passive immune globulin. This treatment is useful for people who have come in contact with HAV-infected individuals, or who have eaten at a restaurant that was the source of a recent outbreak. It has also recently been discovered that administering Havrix after exposure can prevent symptoms. In the 2003 green onion outbreak, 9,000 patrons of the Mexican restaurant received passive immunization as a precaution. A combined hepatitis A/hepatitis B vaccine, called Twinrix, is recommended for people who may be at risk for both diseases, such as people with chronic liver dysfunction, intravenous drug users, and men who have sex with men. Travelers to areas with high rates of both diseases should obtain vaccine coverage as well.

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No specific medicine is available for hepatitis A once the symptoms begin. Drinking lots of fluids and avoiding liver irritants such as aspirin or alcohol will speed recovery. Patients who receive immune globulin early in the disease usually experience milder symptoms than patients who do not receive it.

Hepatitis B Virus Hepatitis B virus (HBV) is an enveloped DNA virus in the family Hepadnaviridae. Intact viruses are often called Dane particles. An antigen of clinical and immunologic significance is the surface (or S) antigen. The genome is partly doublestranded and partly single-stranded. ▶

Signs and Symptoms

In addition to the direct damage to liver cells just outlined, the spectrum of hepatitis disease may include fever, chills, malaise, anorexia, abdominal discomfort, diarrhea, and nausea. Rashes may appear and arthritis may occur. Hepatitis B infection can be very serious, even life-threatening. A small number of patients develop glomerulonephritis and arterial inflammation. Complete liver regeneration and restored function occur in most patients; however, a small number of patients develop chronic liver disease in the form of necrosis or cirrhosis (permanent liver scarring and loss of tissue). In some cases, chronic HBV infection can lead to a malignant condition. Patients who become infected as children have significantly higher risks of long-term infection and disease. In fact, 90% of neonates infected at birth develop chronic infection, as do 30% of children infected between the ages of 1 and 5, but only 6% of persons infected after the age of 5. This finding is one of the major justifications for the routine vaccination of children. Also, infection becomes chronic more often in men than in women. The mortality rate is 15% to 25% for people with chronic infection. HBV is known to be a cause of hepatocellular carcinoma. Investigators have found that mass vaccination against HBV in Taiwan, begun 18 years ago, has resulted in a significant decrease in liver cancer in that country. (Taiwan previously had one of the highest rates of this cancer.) It is speculated that cancer is probably a result of infection early in life and the longterm carrier state.

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Some patients infected with hepatitis B are coinfected with a particle called the delta agent, sometimes also called a hepatitis D virus. This agent seems to be a defective RNA virus that cannot produce infection unless a cell is also infected with HBV. Hepatitis D virus invades host cells by “borrowing” the outer receptors of HBV. When HBV infection is accompanied by the delta agent, the disease becomes more severe and is more likely to progress to permanent liver damage. ▶

Pathogenesis and Virulence Factors

The hepatitis B virus enters the body through a break in the skin or mucous membrane or by injection into the bloodstream. Eventually, it reaches the liver cells (hepatocytes) where it multiplies and releases viruses into the blood during an incubation period of 4 to 24 weeks (7 weeks average). Surprisingly, the majority of those infected exhibit few overt symptoms and eventually develop an immunity to HBV, but some people experience the symptoms described earlier. The precise mechanisms of virulence are not clear. The ability of HBV to remain latent in some patients contributes to its pathogenesis. Strangely, hepatitis B infection seems to be able to influence the gender of offspring. If one parent is a carrier, the child is more likely to be male than female. ▶

Transmission and Epidemiology

An important factor in the transmission pattern of hepatitis B virus is that it multiplies exclusively in the liver, which continuously seeds the blood with viruses. Electron microscopic studies have revealed up to 107 virions per milliliter of infected blood. Even a minute amount of blood (a millionth of a milliliter) can transmit infection. The abundance of circulating virions is so high and the minimal dose so low that such simple practices as sharing a toothbrush or a razor can transmit the infection. Over the past 10 years, HBV has also been detected in semen and vaginal secretions, and it can be transmitted by these fluids. Spread of the virus by means of close contact in families or institutions is also well documented. Vertical transmission is possible, and it predisposes the child to development of the carrier state and increased risk of liver cancer. It is sometimes known as serum hepatitis. Hepatitis B is an ancient disease that has been found in all populations, although the incidence and risk are highest among people living under crowded conditions, drug addicts, the sexually promiscuous, and those in certain occupations, including people who conduct medical procedures involving blood or blood products. This virus is one of the major infectious concerns for health care workers. Needle sticks can easily transmit the virus, and therefore most workers are required to have the full series of HBV vaccinations. Unlike the more notorious HIV, HBV remains infective for days in dried blood, for months when stored in serum at room temperature, and for decades if frozen. Although it is not inactivated after 4 hours of exposure to 60°C, boiling for the same period can destroy

it. Disinfectants containing chlorine, iodine, and glutaraldehyde show potent anti–hepatitis B activity. Cosmetic manipulation such as tattooing and ear or body piercing can expose a person to infection if the instruments are not properly sterilized. The only reliable method for destroying HBV on reusable instruments is autoclaving. ▶

Culture and Diagnosis

Serological tests can detect either virus antigen or antibodies. Radioimmunoassay and ELISA testing permit detection of the important surface antigen of HBV very early in infection. These same tests are essential for screening blood destined for transfusions, semen in sperm banks, and organs intended for transplant. Antibody tests are most valuable in patients who are negative for the antigen. ▶

Prevention and Treatment

Since 1981, the primary prevention for HBV infection is vaccination. The most widely used vaccines are recombinant, containing the pure surface antigen cloned in yeast cells. Vaccines are given in three doses over 18 months, with occasional boosters. Vaccination is a must for medical and dental workers and students, patients receiving multiple transfusions, immunodeficient persons, and cancer patients. The vaccine is also now strongly recommended for all newborns as part of a routine immunization schedule. As just mentioned, a combined vaccine for HAV/HBV may be appropriate for certain people. Passive immunization with hepatitis B immune globulin (HBIG) gives significant immediate protection to people who have been exposed to the virus through needle puncture, broken blood containers, or skin and mucosal contact with blood. Another group for whom passive immunization is highly recommended is neonates born to infected mothers. Mild cases of hepatitis B are managed by symptomatic treatment and supportive care. Chronic infection can be controlled with recombinant human interferon, adefovir dipivoxil, lamivudine (another nucleotide analog best known for its use in HIV patients), or a newly approved drug called entecavir (Baraclude). All of these can help to stop virus multiplication and prevent liver damage in many but not all patients. None of the drugs are considered curative.

Hepatitis C Virus Hepatitis C is sometimes referred to as the “silent epidemic” because more than 4 million Americans are infected with the virus, but it takes many years to cause noticeable symptoms. In the United States, its incidence fell between 1992 and 2003, but no further decreases have been seen since then. Liver failure from hepatitis C is one of the most common reasons for liver transplants in this country. Hepatitis C is an RNA virus in the Flaviviridae family. It used to be known as “non-A non-B” virus. It is usually diagnosed with a blood test for antibodies to the virus.

22.3

▶

Gastrointestinal Tract Diseases Caused by Microorganisms (Nonhelminthic)

Signs and Symptoms

People have widely varying experiences with this infection. It shares many characteristics of hepatitis B disease, but it is much more likely to become chronic. Of those infected, 75% to 85% will remain infected indefinitely. (In contrast, only about 6% of persons who acquire hepatitis B after the age of 5 will be chronically infected.) With HCV infection, it is possible to have severe symptoms without permanent liver damage, but it is more common to have chronic liver disease even if there are no overt symptoms. Cancer may also result from chronic HCV infection. Worldwide, HBV infection is the most common cause of liver cancer, but in the United States it is more likely to be caused by HCV. ▶

Pathogenesis and Virulence Factors

The virus is so adept at establishing chronic infections that researchers are studying the ways that it evades immunologic detection and destruction. The virus’s core protein seems to play a role in the suppression of cell-mediated immunity as well as in the production of various cytokines. ▶

691

rent risk for transfusion-associated HCV is thought to be 1 in 100,000 units transfused. Because HCV was not recognized sooner, a relatively large percentage of the population is infected. Eighty percent of the 4 million affected in this country are suspected to have no symptoms. It has a very high prevalence in parts of South America, Central Africa, and in China. ▶

Prevention and Treatment

There is currently no vaccine for hepatitis C. Various treatment regimens have been attempted; most include the use of therapeutic interferon and a more effective derivative of interferon called pegylated interferon. Some clinicians also prescribe ribavirin to try to suppress viral multiplication. The treatments are not curative, but they may prevent or lessen damage to the liver (Disease Table 22.8).

22.3 Learning Outcomes—Can You . . .

Transmission and Epidemiology

This virus is acquired in similar ways to HBV. It is more commonly transmitted through blood contact (both “sanctioned,” such as in blood transfusions, and “unsanctioned,” such as needle sharing by injecting drug users) than through transfer of other body fluids. Vertical transmission is also possible. Before a test was available to test blood products for this virus, it seems to have been frequently transmitted through blood transfusions. Hemophiliacs who were treated with clotting factor prior to 1985 were infected with HCV at a high rate. Once blood began to be tested for HIV (in 1985) and screened for so-called “non-A non-B” hepatitis, the risk of contracting HCV from blood was greatly reduced. The cur-

5. . . . list the possible causative agents, modes of transmission, virulence factors, diagnostic techniques, and prevention/treatment for each of the kinds of oral diseases? 6. . . . discuss current theories about the connection between oral bacteria and cardiovascular disease? 7. . . . list the possible causative agents, modes of transmission, virulence factors, diagnostic techniques, and prevention/treatment for mumps, gastritis, and gastric ulcers? 8. . . . list the possible causative agents, modes of transmission, virulence factors, diagnostic techniques, and prevention/treatment for acute and chronic diarrhea, and also for acute diarrhea with vomiting? 9. . . . differentiate among the main types of hepatitis and discuss the causative agent, mode of transmission, diagnostic techniques, prevention, and treatment of each?

Disease Table 22.8 Hepatitis Causative Organism(s)

Hepatitis A or E virus

Hepatitis B virus

Hepatitis C virus

Most Common Modes of Transmission

Fecal-oral, vehicle

Parenteral (blood contact), direct contact (especially sexual), vertical

Parenteral (blood contact), vertical

Virulence Factors

–

Latency

Core protein suppresses immune function?

Culture/Diagnosis

IgM serology

Serology (ELISA, radioimmunoassay)

Serology

Prevention

Hepatitis A vaccine or combined HAV/HBV vaccine

HBV recombinant vaccine

–

Treatment

Hep A: hepatitis A vaccine or immune globulin; Hep E: immune globulin

Interferon, nucleoside analogs

(Pegylated) interferon, with or without ribavirin

Distinctive Features

2–7 weeks

1–6 months

2–8 weeks

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Chapter 22 Infectious Diseases Affecting the Gastrointestinal Tract

22.4 Gastrointestinal Tract Diseases Caused by Helminths Helminths that parasitize humans are amazingly diverse, ranging from barely visible roundworms (0.3 mm) to huge tapeworms (25 m long). In the introduction to these organisms in chapter 5, we grouped them into three categories: nematodes (roundworms), trematodes (flukes), and cestodes (tapeworms), and we discussed basic characteristics of each group. You may wish to review those sections before continuing. In this section, we examine the intestinal diseases caused by helminths. Although they can cause symptoms that might be mistaken for some of the diseases discussed elsewhere in this chapter, helminthic diseases are usually accompanied by an additional set of symptoms that arise from the host response to helminths. Worm infection usually provokes an increase in granular leukocytes called eosinophils, which have a specialized capacity to destroy worms. This increase, termed eosinophilia, is a hallmark of helminthic infection and is detectable in blood counts. If the following symptoms occur coupled with eosinophilia, helminthic infection should be suspected. Helminthic infections may be acquired through the fecaloral route or through penetration of the skin, but most of them spend part of their lives in the intestinal tract. (Figure 22.23 depicts the four different types of life cycles of the helminths.) While the worms are in the intestines, they can produce a gamut of intestinal symptoms. Some of them also produce symptoms outside of the intestines; they are considered in separate categories.

General Clinical Considerations Because the diseases in this book are always arranged in the same way, based on how the disease appears in terms of signs and symptoms (how the patient appears upon presentation to the health care provider), this section on helminthic diseases adopts a bit of a different approach. We talk about diagnosis, pathogenesis and prevention, and treatment of the helminths as a group in the next subsections. Each type of infection is then described in the sections that follow. ▶

Pathogenesis and Virulence Factors in General

In most cases, helminths that infect humans do not have sophisticated virulence factors. They do have numerous adaptations that allow them to survive in their hosts. They have specialized mouthparts for attaching to tissues and for feeding, enzymes with which they liquefy and penetrate tissues, and a cuticle or other covering to protect them from host defenses. In addition, their organ systems are usually reduced to the essentials: getting food and processing it, moving, and reproducing. The damage they cause in the host is very often the result of the host’s response to the presence of the invader. Many helminths have more than one host during their lifetimes. If this is the case, the host in which the adult worm is found is called the definitive host (usually a vertebrate).

Sometimes the actual definitive host is not the host usually used by the parasite but an accidental bystander. Humans often become the accidental definitive hosts for helminths whose normal definitive host is a cow, pig, or fish. Larval stages of helminths are found in intermediate hosts. Humans can serve as intermediate hosts, too. Helminths may require no intermediate host at all or may need one or more intermediate hosts for their entire life cycle. ▶

Diagnosis in General

Diagnosis of almost all helminthic infections follows a similar series of steps. A differential blood count showing eosinophilia and serological tests indicating sensitivity to helminthic antigens all provide indirect evidence of worm infection. A history of travel to the tropics or immigration from those regions is also helpful, even if it occurred years ago, because some flukes and nematodes persist for decades. The most definitive evidence, however, is the discovery of eggs, larvae, or adult worms in stools or other tissues. The worms are sufficiently distinct in morphology that positive identification can be based on any stage, including eggs. That said, not all of these diseases result in eggs or larval stages that can easily be found in stool. ▶

Prevention and Treatment in General

Preventive measures are aimed at minimizing human contact with the parasite or interrupting its life cycle. In areas where the worm is transmitted by fecally contaminated soil and water, disease rates are significantly reduced through proper sewage disposal, using sanitary latrines, avoiding human feces as fertilizer, and disinfection of the water supply. In cases where the larvae invade through the skin, people should avoid direct contact with infested water and soil. Food-borne disease can be avoided by thoroughly washing and cooking vegetables and meats. Also, because adult worms, larvae, and eggs are sensitive to cold, freezing foods is a highly satisfactory preventive measure. These methods work best if humans are the sole host of the parasite; if they are not, control of reservoirs or vector populations may be necessary. Although several useful antihelminthic medications exist, the cellular physiology of the eukaryotic parasites resembles that of humans, and drugs toxic to them can also

Table 22.1 Antihelminthic Therapeutic Agents and Their Effects Drug

Effect

Piperazine Pyrantel Mebendazole Thiabendazole Praziquantel

Paralyzes worm so it can be expelled in feces Paralyzes worm so it can be expelled in feces Blocks key step in worm metabolism Blocks key step in worm metabolism Interferes with worm metabolism

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Gastrointestinal Tract Diseases Caused by Helminths

Cycle A

693

Cycle B Larvae enter tissue, migrate

Larvae hatch in intestine, enter tissue Food, water

Human

Human

Infective larva

Mature egg Environment

Environment

Early larva

Embryonic egg

Egg

In cycle A, the worm develops in intestine; egg is released with feces into environment; eggs are ingested by new host and hatch in intestine (examples: Ascaris, Trichuris).

In cycle B, the worms mature in intestine; eggs are released with feces; larvae hatch and develop in environment; infection occurs through skin penetration by larvae (example: hookworms).

Cycle C

Cycle D

Animal flesh

Cyst releases larvae Meat

Human

Encystment in muscle

Human Second larval stage

Food animal

Intermediate host(s)

Environment

Organ such as intestine, bladder

Environment First larval stage Eggs

Eggs In cycle D, eggs are released from human; humans are infected through ingestion or direct penetration by larval phase (examples: Opisthorchis and Schistosoma).

In cycle C, the adult matures in human intestine; eggs are released into environment; eggs are eaten by grazing animals; larval forms encyst in tissue; humans eating animal flesh are infected (example: Taenia).

Figure 22.23 Four basic helminth life and transmission cycles.

be toxic to us. Some antihelminthic drugs suppress a metabolic process that is more important to the worm than to the human. Others inhibit the worm’s movement and prevent it from maintaining its position in a certain organ. Therapy is also based on a drug’s greater toxicity to the more vulnerable helminths or on the local effects of oral drugs in the intestine.

Antihelminthic drugs of choice and their effects are given in table 22.1. Note that some helminths have developed resistance to the drugs used to treat them. In some cases, surgery may be necessary to remove worms or larvae, although this procedure can be difficult if the parasite load is high or is not confined to one area.

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INSIGHT 22.4

Treating Inflammatory Bowel Disease with Worms?

Probably every one of us knows someone who suffers from an inflammatory bowel condition such as Crohn’s disease or ulcerative colitis. Even though it seems that Mycobacterium species are responsible for Crohn’s, no such microbial cause has been found for ulcerative colitis (see Insight 22.1). The work described here suggests that the inflammation that accompanies the infection (in Crohn’s) and the entire syndrome (in ulcerative colitis) can be because the immune system is, well, bored. Many recent epidemiological investigations have revealed that inflammatory bowel disease (IBD) is most common in Western industrialized countries and is very rare in developing countries. More specifically, the prevalence of IBD in any given country is inversely proportional to the prevalence of helminthic infections in that country. Looking at the picture in this country, the incidence of helminthic infections decreased dramatically between the 1930s and the 1950s; the incidence of IBD began its continuous rise in the 1950s. Scientists suspect a connection here: that the absence of exposure to helminthic infection predisposes a person to IBD. These researchers have developed a hypothesis that the parts of the immune system that are activated during helminthic infection begin to “malfunction” when left idle, eventually resulting in damage to host tissue. Researchers wondered whether they could “treat” IBD by exposing patients to an intestinal helminthic infection. The first studies were conducted in mice, and the results looked promising. Then researchers at the University of Iowa conducted studies in human volunteers. They selected eight patients with either Crohn’s disease or ulcerative colitis and administered to them Gatorade containing 2,500 eggs of the pig whipworm Trichuris suis. They chose this worm because it colonizes the intestines for a few weeks and then is completely eliminated without treatment. It does not invade tissues, and the eggs that are shed in the stools are not infective.

Disease: Intestinal Distress as the Primary Symptom Both tapeworms and roundworms can infect the intestinal tract in such a way as to cause primary symptoms there. The pork tapeworm (Taenia solium) and the fish tapeworm (Diphyllobothrium latum) are highlighted, as well as two nematodes (roundworms): the whipworm Trichuris trichiura and the pinworm Enterobius vermicularis. Both of the roundworms are deposited in the small intestine and migrate to the large intestine. We start with these.

Trichuris trichiura The common name for this nematode—whipworm—refers to its likeness to a miniature buggy whip. Its life cycle and transmission is of the cycle A type (see figure 22.23). Humans are the sole host. Trichuriasis has its highest incidence in

The researchers found marked improvement in the inflammatory bowel conditions in all of the patients. They determined that the effects were of short duration and asked several of the patients to continue in the study, receiving fresh doses of T. suis every 3 weeks. All of these patients experienced significant and long-lasting remission of their IBD symptoms. What’s more, they indicated that they would be willing to continue the treatments indefinitely. There is also evidence that this approach could work for other autoimmune disorders, such as multiple sclerosis. And scientists in England have now determined that controlled infections with hookworms can ease the respiratory allergy symptoms of allergy sufferers. It seems that occasional contact with helminths keeps the complicated network of immunoregulatory mechanisms in good working order. This story serves to remind us about the intimate association between humans and their parasites.

areas of the tropics and subtropics that have poor sanitation. Embryonic eggs deposited in the soil are not immediately infective and continue development for 3 to 6 weeks in this habitat. Ingested eggs hatch in the small intestine, where the larvae attach, penetrate the outer wall, and go through several molts. The mature adults move to the large intestine and gain a hold with their long, thin heads, while the thicker tail dangles free in the intestinal lumen. Following sexual maturation and fertilization, the females eventually lay 3,000 to 5,000 eggs daily into the bowel. The entire cycle requires about 90 days, and untreated infection can last up to 2 years. Symptoms of this infection may include localized hemorrhage of the bowel caused by worms burrowing and piercing intestinal mucosa. This can also provide a portal of entry for secondary bacterial infection. Heavier infections can cause dysentery, loss of muscle tone, and rectal prolapse, which can prove fatal in children.

22.4

Gastrointestinal Tract Diseases Caused by Helminths

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Enterobius vermicularis This nematode is often called the pinworm, or seatworm. It is the most common worm disease of children in temperate zones. Some estimates put the prevalence of this infection in the United States at 5% to 15%, although most experts feel that this has declined in recent years. The transmission of this roundworm is of the cycle A type. Freshly deposited eggs have a sticky coating that causes them to lodge beneath the fingernails and to adhere to fomites. Upon drying, the eggs become airborne and settle in house dust. Worms are ingested from contaminated food or drink and from self-inoculation from one’s own fingers. Eggs hatch in the small intestine and release larvae that migrate to the large intestine. There the larvae mature into adult worms and mate. The symptoms of this condition are pronounced anal itching when the mature female emerges from the anus and lays eggs. Although infection is not fatal and most cases are asymptomatic, the afflicted child can suffer from disrupted sleep and sometimes nausea, abdominal discomfort, and diarrhea. A simple rapid test can be performed by pressing a piece of transparent adhesive tape against the anal skin and then applying it to a slide for microscopic examination. When one member of the family is diagnosed, the entire family should be tested and/or treated because it is likely that multiple members are infected.

Sucker Hooklets

(a) Tapeworm scolex showing sucker and hooklets.

Taenia solium In contrast to the last two helminths, this one is a tapeworm. Adult worms are usually around 5 meters long and have a scolex with hooklets and suckers to attach to the intestine (figure 22.24). Disease caused by T. solium (the pig tapeworm) is distributed worldwide but is mainly concentrated in areas where humans live in close proximity with pigs or eat undercooked pork. In pigs, the eggs hatch in the small intestine and the released larvae migrate throughout the organs. Ultimately, they encyst in the muscles, becoming cysticerci, young tapeworms that are the infective stage for humans. When humans ingest a live cysticercus in pork, the coat is digested and the organism is flushed into the intestine, where it firmly attaches by the scolex and develops into an adult tapeworm. Infection with T. solium can take another form when humans ingest the tapeworm eggs rather than cysticerci. Although humans are not the usual intermediate hosts, the eggs can still hatch in the intestine, releasing tapeworm larvae that migrate to all tissues. They form bladderlike sacs throughout the body that can cause serious damage. This transmission and life cycle are shown in cycle C in figure 22.23. The pork tapeworm is not the same as the more commonly known pork helminthic infection, trichinosis. It is discussed in a later section. For such a large organism, it is remarkable how few symptoms a tapeworm causes. Occasionally, a patient dis-

(b) Adult Taenia saginata. The arrow points to the scolex; the remainder of the tape, called the strobila, has a total length of 5 meters.

Figure 22.24 Tapeworm characteristics.

covers proglottids in his or her stool, and some patients complain of vague abdominal pain and nausea. Other tapeworms of the genus Taenia infect humans. One of them is the beef tapeworm, Taenia saginata. It usually causes similar general symptoms of helminthic infection. But humans are not known to acquire T. saginata infection by ingesting the eggs.

Diphyllobothrium latum This tapeworm has an intermediate host in fish. It is common in the Great Lakes, Alaska, and Canada. Humans are its definitive host. It develops in the intestine and can cause long-term symptoms. It can be transmitted in raw food such as sushi and sashimi made from salmon. (Reputable sushi restaurants employ authentic sushi chefs who are trained to carefully examine fish for larvae and other signs of infection.)

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As is the case with most tapeworms, symptoms are minor and usually vague and include possible abdominal discomfort or nausea. The tapeworm seems to have the ability to absorb and use the vitamin B12, making it unavailable to its human host. Anemia is therefore sometimes reported with this infection. You should be aware that certain people of Scandinavian descent have a genetic predisposition for not adsorbing B12. In these patients, Diphyllobothrium latum infection can be quite dangerous.

Hymenolepis species These relatively small tapeworms are the most common tapeworm infections in the world. There are two species: Hymenolepis nana, known as the dwarf tapeworm because it is only 15 to 40 mm in length, and H. diminuta, the rat tapeworm, which is usually 20 to 60 cm in length as an adult. The life cycle of these tapeworms often involves insects as well as the definitive host, which may be a rodent or a human. When eggs are passed in the feces of a rodent or human, they can be ingested by various insects, which are in turn accidentally ingested by humans (in cereals or other foods). Alternatively, eggs in the environment can be directly ingested by humans. Tapeworms become established in the small intestine, and eggs can be released after proglottids break off from the attached worms. Symptoms are mild, and the treatment of choice is praziquantel (Disease Table 22.9).

Disease: Intestinal Distress Accompanied by Migratory Symptoms A diverse group of helminths enter the body as larvae or eggs, mature to the worm stage in the intestine, and then migrate into the circulatory and lymphatic systems, after which they travel to the heart and lungs, migrate up the respiratory tree to the throat, and are swallowed. This journey returns the mature worms to the intestinal tract where they then take up residence. All of these conditions, in addition to causing symptoms in the digestive tract, may induce inflammatory reactions along their migratory routes, resulting in eosinophilia and, during their lung stage, pneumonia. Three different examples of this type of infection follow.

Ascaris lumbricoides Ascaris lumbricoides is a giant intestinal roundworm (up to 300 mm—a foot or more—long) that probably accounts for the greatest number of worm infections (estimated at 1 billion cases worldwide). Most reported cases in the United States occur in the southeastern states. Ascaris spends its larval and adult stages in humans and releases embryonic eggs in feces, which are then spread to other humans through food, drink, or contaminated objects placed in the mouth. The eggs thrive in warm, moist soils and resist cold and chemical disinfectants, but they are sensitive to sunlight, high temperatures, and drying. After ingested eggs hatch in

Disease Table 22.9 Intestinal Distress Causative Organism(s)

Trichuris trichiura (whipworm)

Enterobius vermicularis (pinworm)

Taenia solium (pork tapeworm)

Diphyllobothrium latum (fish tapeworm)

Hymenolepis nana and H. diminuta

Most Common Modes of Transmission

Cycle A: vehicle (soil) —also fecal-oral

Cycle A: vehicle (food, water), fomites, selfinoculation

Cycle C: vehicle (pork)—also fecaloral

Cycle C: vehicle (seafood)

Cycle C: vehicle (ingesting insects)–– also fecal-oral

Virulence Factors

Burrowing and invasiveness

–

–

Vitamin B12 usage

–

Culture/Diagnosis

Blood count, serology, egg or worm detection

Adhesive tape

Blood count, serology, egg or worm detection

Blood count, serology, egg or worm detection

Blood count, serology, egg or worm detection

Prevention

Hygiene, sanitation

Hygiene

Cook meat, avoid pig feces

Cook meat

Hygienic environment

Treatment

Mebendazole

Mebendazole, piperazine

Praziquantel

Praziquantel

Praziquantel

Distinctive Features

Humans sole host

Common in United States

Tapeworm; intermediate host is pigs

Large tapeworm; anemia

Most common tapeworm infection

22.4

Figure 22.25 A mass of Ascaris lumbricoides worms.

These worms had been passed by a child in Kenya in 2007.

the human intestine, the larvae embark upon an odyssey in the tissues. First, they penetrate the intestinal wall and enter the lymphatic and circulatory systems. They are swept into the heart and eventually arrive at the capillaries of the lungs. From this point, the larvae migrate up the respiratory tree to the glottis. Worms entering the throat are swallowed and returned to the small intestine, where they reach adulthood and reproduce, producing up to 200,000 fertilized eggs a day. Even as adults, male and female worms are not attached to the intestine and retain some of their exploratory ways. They are known to invade the biliary channels of the liver and gallbladder, and on occasion the worms emerge from the nose and mouth. Severe inflammatory reactions mark the migratory route; and allergic reactions such as bronchospasm, asthma, or skin rash can occur. Heavy worm loads can retard the physical and mental development of children (figure 22.25). One possibility with intestinal worm infections is self-reinoculation due to poor personal hygiene.

Gastrointestinal Tract Diseases Caused by Helminths

Ordinarily, the parasite is present in soil contaminated with human feces. It enters sites on bare feet such as hair follicles, abrasions, or the soft skin between the toes, but cases have occurred via mud that was splattered on the ankles of people wearing shoes. Infection has even been reported in people handling soiled laundry. On contact, the hookworm larvae actively burrow into the skin. After several hours, they reach the lymphatic or blood circulation and are immediately carried into the heart and lungs. The larvae proceed up the bronchi and trachea to the throat. Most of the larvae are swallowed with sputum and arrive in the small intestine, where they anchor, feed on blood, and mature. Eggs first appear in the stool about 6 weeks after the time of entry, and the untreated infection can last about 5 years. Symptoms from these infections follow the progress of the worm in the body. A localized dermatitis called ground itch may be caused by the initial penetration of larvae. The transit of the larvae to the lungs is ordinarily brief, but it can cause symptoms of pneumonia and eosinophilia. The potential for injury is greatest during the intestinal phase, when heavy worm burdens can cause nausea, vomiting, cramps, and bloody diarrhea. Because blood loss is significant, iron-deficient anemia develops, and infants are especially susceptible to hemorrhagic shock. Chronic fatigue, listlessness, apathy, and anemia worsen with chronic and repeated infections. Hookworm infections are treated with antihelminthic drugs, but frequent reinfection is a problem. In 2000, the Bill and Melinda Gates Foundation, recognizing the impact of worldwide hookworm infections, contributed $18 million to the development of a hookworm vaccine, and in 2006 they increased that contribution.

Necator americanus and Ancylostoma duodenale These two different nematodes are called by the common name hookworm. Necator americanus (nee-kay′-tor ah-mer″ih-cah′-nus) is endemic to the New World, and Ancylostoma duodenale (an′-kih-los′-toh-mah doo-oh-den-ah′-lee) is endemic to the Old World, although the two species overlap in parts of Latin America. Otherwise, with respect to transmission, life cycle, and pathology, they are usually lumped together. The hook refers to the adult’s oral cutting plates on its curved anterior end, by which it anchors to the intestinal villi (figure 22.26). Unlike other intestinal worms, hookworm larvae hatch outside the body and infect by penetrating the skin. Hookworm transmission is described by cycle B (see figure 22.23).

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(a)

(b)

Figure 22.26 Cutting teeth on the mouths of (a) Necator americanus and (b) Ancylostoma duodenale.

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Strongyloides stercoralis The agent of strongyloidiasis, or threadworm infection, is Strongyloides stercoralis (stron′-jih-loy-deez ster″-kor-ah′lis). This nematode is exceptional because of its minute size and its capacity to complete its life cycle either within the human body or outside in moist soil. It shares a similar distribution and life cycle to hookworms and afflicts an estimated 100 to 200 million people worldwide. Infection occurs when soil larvae penetrate the skin (cycle B in figure 22.23). The worm then enters the circulation, is carried to the respiratory tract and swallowed, and then enters the small intestine to complete development. Although an adult S. stercoralis lays eggs in the gut just as hookworms do, the eggs hatch into larvae in the colon and can remain entirely in the host’s body to complete the cycle. The larval form of the organism can likewise exit with feces and go through an environmental cycle. These numerous alternative life cycles greatly increase the chance of transmission and the likelihood for chronic infection. The first symptom of threadworm infection is usually a red, intensely itchy skin rash at the site of entry. Mild migratory activity in an otherwise normal person can escape notice, but heavy worm loads can cause symptoms of pneumonitis and eosinophilia. The nematode activities in the intestine produce bloody diarrhea, liver enlargement, and malabsorption. In immunocompromised patients, there is a risk of disseminated infection involving numerous organs (figure 22.27). Hardest hit are AIDS patients, transplant patients on immunosuppressant drugs, and cancer patients receiving irradiation therapy, who can die if not treated promptly (Disease Table 22.10).

Figure 22.27 A patient with disseminated Strongyloides infection. Trails under the skin indicate the migration tracks of the worms.

Liver and Intestinal Disease One group of worms that lands in the intestines has a particular affinity for the liver. Two of these worms are trematodes (flatworms), and they are categorized as liver flukes.

Opisthorchis sinensis and Clonorchis sinensis Opisthorchis sinensis and Clonorchis sinensis are two worms known as Chinese liver flukes. They complete their sexual development in mammals such as humans, cats, dogs, and swine. Their intermediate development occurs in snail and fish hosts. Humans ingest metacercariae in inadequately

Disease Table 22.10 Intestinal Distress plus Migratory Symptoms Causative Organism(s)

Ascaris lumbricoides (intestinal roundworm)

Necator americanus and Ancylostoma duodenale (hookworms)

Strongyloides stercoralis (threadworm)

Most Common Modes of Transmission

Cycle A: vehicle (soil/fecal-oral), fomites, self-inoculation

Cycle B: vehicle (soil), fomite

Cycle B: vehicle (soil), fomite

Virulence Factors

Induction of hypersensitivity, adult worm migration, and abdominal obstruction

Induction of hypersensitivity, adult worm migration, and abdominal obstruction

Induction of hypersensitivity, adult worm migration, and abdominal obstruction

Culture/Diagnosis

Blood count, serology, egg or worm detection

Blood count, serology, egg or worm detection

Blood count, serology, egg or worm detection

Prevention

Hygiene

Sanitation

Sanitation

Treatment

Albendazole

Albendazole

Ivermectin or thiabendazole

Distinctive Features

Roundworm; 1 billion persons infected

Penetrates skin, serious intestinal symptoms

Penetrates skin, severe for immunocompromised

22.4

cooked or raw freshwater fish (see cycle D in figure 22.23). Larvae hatch and crawl into the bile duct, where they mature and shed eggs into the intestinal tract. Feces containing eggs are passed into standing water that harbors the intermediate snail host. The cycle is complete when infected snails release cercariae that invade fish living in the same water. Symptoms of Opisthorchis and Clonorchis infection are slow to develop but include thickening of the lining of the bile duct and possible granuloma formation in areas of the liver if eggs enter the stroma of the liver. If the infection is heavy, the bile duct could be blocked.

Fasciola hepatica This liver fluke is a common parasite in sheep, cattle, goats, and other mammals and is occasionally transmitted to humans (figure 22.28). Periodic outbreaks in temperate regions of Europe and South America are associated with eating wild watercress. The life cycle is very complex, involving the mammal as the definitive host, the release of eggs in the feces, the hatching of eggs in the water into miracidia, invasion of freshwater snails, development and release of cercariae, encystment of metacercariae on a water plant, and ingestion of the cyst by a mammalian host eating the plant. The cysts release young flukes into the intestine that wander to the liver, lodge in the gallbladder, and develop into adults. Humans develop symptoms of vomiting, diarrhea, hepatomegaly, and bile obstruction only if they are chronically infected by a large number of flukes.

Oral sucker

Ovary

Testis

Digestive gland

Figure 22.28 Fasciola hepatica, the sheep liver fluke (2×).

Gastrointestinal Tract Diseases Caused by Helminths

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Disease Table 22.11 Liver and Intestinal Disease

Causative Organism(s)

Opisthorchis sinensis, Clonorchis sinensis

Fasciola hepatica

Most Common Modes of Transmission

Cycle D: vehicle (fish or crustaceans)

Cycle D: vehicle (water and water plants)

Virulence Factors

–

–

Culture/ Diagnosis

Blood count, serology, egg or worm detection

Blood count, serology, egg or worm detection

Prevention

Cook food, sanitation of water

Sanitation of water

Treatment

Praziquantel

Triclabendazole

Distinctive Features

Live in liver

Live in liver and gallbladder

Disease: Muscle and Neurological Symptoms Trichinosis is an infection transmitted by eating pork (and sometimes other wildlife) that have the cysts of Trichinella species embedded in the meat. The life cycle of this nematode is spent entirely within the body of a mammalian host such as a pig, bear, cat, dog, or rat. In nature, the parasite is maintained in an encapsulated (encysted) larval form in the muscles of these animal reservoirs and is transmitted when other animals prey upon them. The disease cannot be transmitted from one human to another except in the case of cannibalism. Because all wild and domesticated mammals appear to be susceptible to Trichinella species, one might expect human trichinosis to be common worldwide. But in reality, it is more common in the United States and in Europe than in the rest of the world. This distribution appears to be related to regional or ethnic customs of eating raw or rare pork dishes or wild animal meats. Bear meat is the source of up to one-third of the cases in the United States. Home or small-scale butchering enterprises that do not carefully inspect pork can spread the parasite, although commercial pork can also be a source. Practices such as tasting raw homemade pork sausage or serving rare pork or pork-beef mixtures have been responsible for sporadic outbreaks. The cyst envelope is digested in the stomach and small intestine, which liberates the larvae. After burrowing into the intestinal mucosa, the larvae reach adulthood and mate. The larvae that result from this union penetrate the intestine and enter the lymphatic channels and blood. All tissues are at risk for invasion, but final development occurs when the coiled larvae are encysted in the skeletal muscle. At maturity,

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the cyst is about 1 mm long and can be observed by careful inspection of meat. Although larvae can deteriorate over time, they have also been known to survive for years. Symptoms may be unnoticeable or they could be lifethreatening, depending on how many larvae were ingested in the tainted meat. The first symptoms, when present, mimic influenza or viral fevers, with diarrhea, nausea, abdominal pains, fever, and sweating. The second phase, brought on by the mass migration of larvae and their entrance into muscle, produces puffiness around the eyes, intense muscle and joint pain, shortness of breath, and pronounced eosinophilia. The most serious life-threatening manifestations are heart and brain involvement. Although the symptoms eventually subside, a cure is not available once the larvae have encysted in muscles. The most effective preventive measures for trichinosis are to adequately store and cook pork and wild meats.

Disease Table 22.12 Muscle and Neurological Symptoms

▶

Causative Agent

Schistosomes are trematodes, or flukes (see chapter 5), but they are more cylindrical than flat (figure 22.29). They are often called blood flukes. Flukes have digestive, excretory, neuromuscular, and reproductive systems, but they lack circulatory and respiratory systems. Humans are the definitive hosts for the blood fluke, and snails are the intermediate host. ▶

Pathogenesis and Virulence Factors

This parasite is clever indeed. Once inside the host, it coats its outer surface with proteins from the host’s bloodstream, basically “cloaking” itself from the host defense system. This coat reduces its surface antigenicity and allows it to remain in the host indefinitely. Other virulence attributes are the organism’s ability to invade intact skin and attach to vascular endothelium, to sequester iron from the bloodstream, and to induce a granulomatous response.

Causative Organism(s)

Trichinella species

Most Common Modes of Transmission

Vehicle (food)

Virulence Factors

–

▶

Culture/Diagnosis

Serology combined with clinical picture; muscle biopsy

Prevention

Cook meat

Treatment

Mebendazole, steroids

Distinctive Features

Brain and heart involvement can be fatal

The life cycle of the schistosome is of the “D” type, and is very complex (see figure 22.29). The cycle begins when infected humans release eggs into irrigated fields or ponds, either by deliberate fertilization with excreta or by defecating or urinating directly into the water. The egg hatches in the water and gives off an actively swimming ciliated larva called a miracidium (figure 22.29a), which instinctively swims to a snail and burrows into a vulnerable site, shedding its ciliated covering in the process. In the body of the snail, the miracidium multiplies into a larger, fork-tailed swimming larva called a cercaria (figure 22.29b). Cercariae are given off by the thousands into the water by infected snails. Upon contact with a human wading or bathing in water, cercariae attach themselves to the skin by ventral suckers and penetrate into hair follicles. They pass into small blood and lymphatic vessels and are carried to the liver. Here, the schistosomes achieve sexual maturity, and the male and female worms remain permanently entwined to facilitate mating (figure 22.29c). In time, the pair migrates to and lodges in small blood vessels at specific sites. Schistosoma mansoni and S. japonicum end up in the mesenteric venules of the small intestine. While attached to these intravascular sites, the worms feed upon blood, and the female lays eggs that are eventually voided in feces or urine. The disease is endemic to 74 countries located in Africa, South America, the Middle East, and the Far East. S. mansoni is found throughout these regions, but not in the Far East.

Liver Disease When liver swelling or malfunction is accompanied by eosinophilia, schistosomiasis should be suspected. Schistosomiasis has afflicted humans for thousands of years. The disease is caused by the blood flukes Schistosoma mansoni or S. japonicum, species that are morphologically and geographically distinct but share similar life cycles, transmission methods, and general disease manifestations. It is one of the few infectious agents that can invade intact skin. ▶

and blood in the urine. This condition is discussed in chapter 23 (genitourinary tract diseases). Occasionally, eggs from the worms are carried into the central nervous system and heart and create a severe granulomatous response. Adult flukes can live for many years and, by eluding the immune defenses, cause a chronic affliction.

Signs and Symptoms

The first symptoms of infection are itchiness in the area where the worm enters the body, followed by fever, chills, diarrhea, and cough. The most severe consequences, associated with chronic infection, are hepatomegaly and liver disease and splenomegaly. Other serious conditions caused by a different schistosome occur in the urinary tract—bladder obstruction

Transmission and Epidemiology

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S. japonicum has a much smaller geographical distribution than S. mansoni, only being found in the Far East. Schistosomiasis (including the urinary tract form) is the second most prominent parasitic disease after malaria, probably affecting 200 million people at any one time worldwide. Recent increases in its occurrence in Africa have been attributed to new dams on the Nile River, which have provided additional habitat for snail hosts. ▶

Culture and Diagnosis

Diagnosis depends on identifying the eggs in urine or feces. The clinical pictures of hepatomegaly, splenomegaly, or both also contribute to the diagnosis. ▶ (a) The miracidium phase, which infects the snail (300⫻).

Prevention and Treatment

The cycle of infection cannot be broken as long as people are exposed to untreated sewage in their environment. It is quite common for people to be cured and then to be reinfected because their village has no sewage treatment. A vaccine would provide widespread control of the disease, but so far none is licensed. More than one vaccine is in development, however. Praziquantel is the drug treatment of choice. It works by crippling the worms, making them more antigenic and thereby allowing the host immune response to eliminate them. Clinicians use an “egg hatching test” to determine whether an infection is current and whether treatment is actually killing the eggs. Urine or feces containing eggs is placed in room temperature water, and if miracidia emerge, the infection is still “active.”

Case File 22 (b) The cercaria phase, which is released by snails and burrows into the human host (5,000⫻).

(c) An electron micrograph of normal mating position of adult worms. The larger male worm holds the female in a groove on his ventral surface (2,000⫻).

Figure 22.29 Stages in the life cycle of Schistosoma.

Wrap-Up

Norovirus, the agent identified in many of the Reliant City patients, is a frequent cause of gastroenteritis outbreaks in the United States. Norovirus is highly contagious (ID less than 100 organisms) and is easily spread from person to person and by contact with contaminated materials. The typical incubation period is 24 to 48 hours, and the resulting symptoms persist for 12 to 60 hours. Such outbreaks are frequently caused by contaminated food or water and can also be associated with crowded living conditions, such as those at Reliant City. It is likely that one or more individuals were infected with the norovirus when they arrived at the shelter. Although the source of the initial infection is unknown, contact with contaminated floodwaters is a definite possibility. The infection spread quickly due to the crowded living conditions and shared facilities. Infection control measures, including isolating symptomatic individuals, distributing gel hand sanitizer, and educating staff and evacuees, quickly brought the outbreak under control. See: CDC. 2005. MMWR 54(40):1016−18

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Chapter 22 Infectious Diseases Affecting the Gastrointestinal Tract

Disease Table 22.13 Liver Disease Causative Organism(s)

Schistosoma mansoni, S. japonicum

Most Common Modes of Transmission

Cycle D: vehicle (contaminated water)

Virulence Factors

Antigenic “cloaking”

Culture/Diagnosis

Identification of eggs in feces, scarring of intestines detected by endoscopy

Prevention

Avoiding contaminated vehicles

Treatment

Praziquantel

Distinctive Features

Penetrates skin, lodges in blood vessels of intestine, damages liver

22.4 Learning Outcomes—Can You . . . 10. . . . describe some distinguishing characteristics and commonalities seen in helminthic infections? 11. . . . list four helminths that cause primarily intestinal symptoms, and identify which life cycle they follow and one unique fact about each one? 12. . . . list four helminths that cause intestinal symptoms that may be accompanied by migratory symptoms, and identify which life cycle they follow and one unique fact about each one? 13. . . . list the modes of transmission, virulence factors, diagnostic techniques, and prevention/treatment for each of the helminth infections resulting in liver and intestinal symptoms? These are infections caused by Opisthorchis sinensis, Clonorchis sinensis, and Fasciola hepatica. 14. . . . describe the type of disease caused by Trichinella species? 15. . . . diagram the life cycle of Schistosoma mansoni and S. japonicum, discuss how it differs from the life cycle of the Schistosoma involved in urinary disease, and describe the importance of all three organisms in world health.

Summing Up

703

▶ Summing Up

Taxonomic Organization Microorganisms Causing Disease in the GI Tract Microorganism Gram-positive endospore-forming bacteria Clostridium difficile Clostridium perfringens Bacillus cereus Gram-positive bacteria Streptococcus mutans Streptococcus sobrinus Staphylococcus aureus Gram-negative bacteria Campylobacter jejuni Helicobacter pylori Escherichia coli O157:H7 Other E. coli

Disease

Chapter Location

Antibiotic-associated diarrhea Food poisoning Food poisoning

Acute diarrhea, p. 676 Acute diarrhea and/or vomiting, p. 683 Acute diarrhea and/or vomiting, p. 682

Dental caries Dental caries Food poisoning

Dental caries, p. 664 Dental caries, p. 664 Acute diarrhea and/or vomiting, p. 682

Acute diarrhea Gastritis/gastric ulcers Acute diarrhea plus hemolytic syndrome Acute or chronic diarrhea Acute diarrhea or typhoid fever Acute diarrhea and dysentery Cholera Acute diarrhea Periodontal disease

Acute diarrhea, p. 675 Gastritis/gastric ulcers, p. 670 Acute diarrhea, p. 674 Acute diarrhea, p. 675 Chronic diarrhea, p. 684 Acute diarrhea, p. 672 Acute diarrhea, p. 673 Acute diarrhea, p. 677 Acute diarrhea, p. 676 Periodontal disease, p. 666

“Serum” hepatitis

Hepatitis, p. 689

“Infectious” hepatitis “Serum” hepatitis “Infectious” hepatitis Mumps Acute diarrhea

Hepatitis, p. 688 Hepatitis, p. 690 Hepatitis, p. 689 Mumps, p. 668 Acute diarrhea, p. 680

Salmonella Shigella Vibrio cholerae Yersinia enterocolitica and Y. pseudotuberculosis Tannerella forsythia, Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Treponema vincentii, Prevotella intermedia, Fusobacterium DNA viruses Hepatitis B virus RNA viruses Hepatitis A virus Hepatitis C virus Hepatitis E virus Mumps virus Rotavirus Protozoa Entamoeba histolytica Cryptosporidium Cyclospora Giardia lamblia Helminths—nematodes Ascaris lumbricoides

Chronic diarrhea Acute diarrhea Chronic diarrhea Chronic diarrhea

Chronic diarrhea, p. 686 Acute diarrhea, p. 678 Chronic diarrhea, p. 685 Chronic diarrhea, p. 685

Intestinal distress plus migratory symptoms

Enterobius vermicularis Trichuris trichiura Necator americanus and Ancylostoma duodenale

Intestinal distress Intestinal distress Intestinal distress plus migratory symptoms

Strongyloides stercoralis

Intestinal distress plus migratory symptoms

Trichinella spp. Helminths—cestodes Hymenolepis Taenia solium Diphyllobothrium latum Opisthorchis sinensis and Clonorchis sinensis Fasciola hepatica Helminths—trematodes Schistosoma mansoni, S. japonicum

Muscle and neurological symptoms

Intestinal distress plus migratory symptoms, p. 696 Intestinal distress, p. 695 Intestinal distress, p. 694 Intestinal distress plus migratory symptoms, p. 697 Intestinal distress plus migratory symptoms, p. 698 Muscle and neurological symptoms, p. 699

Intestinal distress Intestinal distress Intestinal distress Liver and intestinal disease Liver and intestinal disease

Intestinal distress, p. 696 Intestinal distress, p. 695 Intestinal distress, p. 695 Liver and intestinal disease, p. 698 Liver and intestinal disease, p. 699

Schistosomiasis

Helminthic liver disease, p. 700

INFECTIOUS DISEASES AFFECTING The Gastrointestinal Tract Helminthic Infections with Neurological and Muscular Symptoms

Trichinella spiralis

Mumps

Dental Caries

Mumps virus

Streptococcus mutans Streptococcus sobrinus Other bacteria

Gastritis and Gastric Ulcer

Helicobacter pylori

Periodontitis and Necrotizing Ulcerative Diseases

Schistosomiasis

Tannerella forsythia Aggregatibacter actinomycetemcomitans Porphyromonas gingivalis Treponema vincentii Prevotella intermedia Fusobacterium

Schistosoma mansoni Schistosoma japonicum Acute Diarrhea

Salmonella Shigella E. coli 0157:H7 Other E. coli Campylobacter Yersinia enterocolitica Yersinia pseudotuberculosis Clostridium difficile Vibrio cholerae Cryptosporidium Rotavirus Other viruses

Helminthic Infections with Intestinal and Migratory Symptoms

Ascaris lumbricoides Necator americanus Ancylostoma duodenale Strongyloides stercoralis Helminthic Infections with Liver and Intestinal Symptoms

Chronic Diarrhea

Tract Infections Causing Intestinal Distress

EAEC Cyclospora cayetanensis Giardia lamblia Entamoeba histolytica

Trichuris trichiura Enterobius vermicularis Taenia solium Diphyllobothrium latum

Acute Diarrhea and/or Vomiting (Food Poisoning)

Staphylococcus aureus Bacillus cereus Clostridium perfringens

Hepatitis

Hepatitis A or E Hepatitis B or C

Helminths Bacteria Viruses Protozoa

System Summary Figure 22.30 704

Chapter Summary

705

Chapter Summary 22.1 The Gastrointestinal Tract and Its Defenses • The gastrointestinal (GI) tract is composed of eight main sections—the mouth, pharynx, esophagus, stomach, small intestine, large intestine, rectum, and anus, and four accessory organs—the salivary glands, liver, gallbladder, and pancreas. • The GI tract has a very heavy load of microorganisms, and it encounters millions of new ones every day. There are significant mechanical, chemical, and antimicrobial defenses to combat microbial invasion. 22.2 Normal Biota of the Gastrointestinal Tract • Bacteria abound in all of the eight main sections of the gastrointestinal tract. Even the highly acidic stomach is heavily colonized. 22.3 Gastrointestinal Tract Diseases Caused by Microorganisms (Nonhelminthic) • Tooth and Gum Infections: Alpha-hemolytic Streptococcus mutans and Streptococcus sobrinus are main causes of dental caries. Periodontitis: The anaerobic bacteria Tannerella forsythia (formerly Bacteroides forsythus), Aggregatibacter actinomycetemcomitans, Porphyromonas, Fusobacterium, and spirochete species are causative agents. • Necrotizing Ulcerative Gingivitis and Periodontitis: Necrotizing ulcerative gingivitis (NUG) and necrotizing ulcerative periodontitis (NUP) are synergistic infections involving Treponema vincentii, Prevotella intermedia, and Fusobacterium species. • Mumps: Swelling of the salivary gland—a condition called parotitis. Mumps is caused by an enveloped, singlestranded RNA virus (mumps virus) from the genus Paramyxovirus. • Gastritis and Gastric Ulcers: Gastritis: sharp or burning pain emanating from the abdomen. Gastric ulcers: actual lesions in the mucosa of the stomach (gastric ulcers) or in the uppermost portion of the small intestine (duodenal ulcer). Helicobacter pylori, a curved gram-negative rod, is causative agent. • Acute Infectious Diarrhea: In United States, a third of all acute diarrhea is transmitted by contaminated food. • Salmonella: Salmonella enteritidis is divided into many serotypes, based on major surface antigens. Animal and dairy products are often contaminated with the bacterium. Typhoid fever, caused by S. enteritidis variant typhi, is a progressive, invasive infection that can lead to septicemia. • Shigella species give symptoms of frequent, watery, bloody stools, fever, and often intense abdominal pain. Diarrhea containing blood and mucus is also called dysentery. The bacterium Shigella dysenteriae produces a heat-labile exotoxin called shiga toxin. • Dozens of different strains of E. coli exist: E. coli O157:H7 and its close relatives are most virulent. This group of E. coli is referred to as enterohemorrhagic E. coli, or EHEC. E. coli O157:H7 is the agent of a spectrum of conditions, ranging from mild gastroenteritis with fever to bloody diarrhea. About 10% of patients develop hemolytic uremic syndrome (HUS), a severe hemolytic anemia that can

cause kidney damage and failure. Virulence is due to shiga toxins (often called STEC—shiga-toxin-producing E. coli). • Other E. coli: At least four other categories of E. coli cause diarrheal diseases. These are enterotoxigenic E. coli (traveler’s diarrhea), enteroinvasive E. coli, enteropathogenic E. coli, and enteroaggregative E. coli. • Campylobacter: Symptoms are frequent watery stools, fever, vomiting, headaches, and severe abdominal pain. Infrequently, infection can lead to serious neuromuscular paralysis called Guillain-Barré syndrome. • Yersinia enterocolitica and Y. pseudotuberculosis are both agents of GI disease via food and beverage contamination. • Clostridium difficile causes a condition called pseudomembranous colitis (antibiotic-associated colitis), precipitated by therapy with broad-spectrum antibiotics. • Vibrio cholerae: Symptoms of secretory diarrhea and severe fluid loss can lead to death in less than 48 hours. Produces enterotoxin called cholera toxin (CT), which disrupts the normal physiology of intestinal cells. • Cryptosporidium: Intestinal waterborne protozoan that infects mammals, birds, and reptiles. • Rotavirus: Primary viral cause of morbidity and mortality resulting from diarrhea, accounting for 50% of all cases. • Acute Diarrhea with Vomiting: Food poisoning refers to symptoms in the gut that are caused by a preformed toxin. • Staphylococcus aureus exotoxin: Heat-stable enterotoxin requires 100°C for 30 minutes for inactivation. Ingested toxin acts on gastrointestinal epithelium and stimulates nerves; acute symptoms of cramping, nausea, vomiting, and diarrhea. • Bacillus cereus exotoxin: B. cereus is common resident on vegetables and soil. Produces two exotoxins; one causes a diarrheal-type disease, the other causes an emetic disease. • Clostridium perfringens exotoxin: The toxin initiates acute abdominal pain, diarrhea, and nausea in 8 to 16 hours. • Chronic Diarrhea • Enteroaggregative E. coli (EAEC) is particularly associated with chronic disease, especially in children. Transmission is through contaminated food and water. • Cyclospora cayetanensis: Protozoan transmitted via the fecal-oral route; associated with fresh produce and water. • Giardia lamblia: Protozoan that can cause diarrhea of long duration, abdominal pain, and flatulence. Freshwater is common vehicle of infection. • Entamoeba histolytica: Freshwater protozoan that causes intestinal amoebiasis, targeting the cecum, appendix, colon, and rectum, leading to dysentery, abdominal pain, fever, diarrhea, and weight loss. • Hepatitis: Inflammatory disease marked by necrosis of hepatocytes and a mononuclear response that swells and disrupts the liver, causing jaundice. Can be caused by a variety of different viruses. • Hepatitis A virus (HAV): A nonenveloped, singlestranded RNA enterovirus of low virulence. Spread through fecal-oral route. Inactivated vaccine available.

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Chapter 22 Infectious Diseases Affecting the Gastrointestinal Tract • Hepatitis B virus (HBV): Enveloped DNA virus in

• Diphyllobothrium latum: The intermediate host is fish;

the family Hepadnaviridae. Can be very serious, even life-threatening; some patients develop chronic liver disease in the form of necrosis or cirrhosis. Also associated with hepatocellular carcinoma. Some patients infected with hepatitis B are coinfected with the delta agent, sometimes also called hepatitis D virus. HBV transmitted by blood and other bodily fluids. Virus is major infectious concern for health care workers. • Hepatitis C virus: RNA virus in Flaviviridae family. Shares characteristics of hepatitis B disease, but is much more likely to become chronic. More commonly transmitted through blood contact than through other body fluids.

can be transmitted in raw food such as sushi and sashimi made from salmon. • Helminthic Intestinal Infections: Intestinal distress accompanied by migratory symptoms. • Ascaris lumbricoides: Intestinal roundworm that releases eggs in feces; eggs then spread to other humans through fecal-oral routes. • Necator americanus and Ancylostoma duodenale: Both called by the common name “hookworm.” Hookworm larvae hatch outside the body in soil contaminated with feces and infect by penetrating skin. • Strongyloides stercoralis: Infection occurs when soil larvae penetrate skin, similar to hookworm infestations. Most susceptible are AIDS patients and immunocompromised patients. • Liver and Intestinal Disease: One group of worms has a particular affinity for the liver—liver flukes. • Opisthorchis sinensis and Clonorchis sinensis: Humans infected by eating inadequately cooked or raw freshwater fish and crustaceans. • Fasciola hepatica: Common parasite in sheep, cattle, goats, and other mammals. Humans develop symptoms only if chronically infected by a large number of flukes. • Muscle and Neurological Symptoms • Trichinosis: Transmitted by eating undercooked pork that has cysts of Trichinella embedded in the meat. • Schistosomiasis in intestines is caused by blood flukes Schistosoma mansoni and S. japonicum. Symptoms include fever, chills, diarrhea, liver and spleen disease.

22.4 Gastrointestinal Tract Diseases Caused by Helminths • Helminthic Intestinal Infections: Intestinal distress as the primary symptom. Both tapeworms and roundworms can infect intestinal tract in such a way as to cause primary symptoms there. • Trichuris trichiura: Symptoms may include localized hemorrhage of the bowel, caused by worms burrowing and piercing intestinal mucosa. • Enterobius vermicularis: “Pinworm”; most common worm disease of children in temperate zones. Not fatal, and most cases are asymptomatic. • Taenia solium: This tapeworm transmitted to humans by raw or undercooked pork. Other tapeworms of the genus Taenia, such as the beef tapeworm Taenia saginata, infect humans.

Multiple-Choice and True-False Questions

Knowledge and Comprehension

Multiple-Choice Questions. Select the correct answer from the answers provided. 1. Food moves down the GI tract through the action of a. cilia. c. gravity. b. peristalsis. d. microorganisms. 2. The microorganism(s) most associated with acute necrotizing ulcerative periodontitis (ANUP) is (are) a. Treponema vincentii. c. Fusobacterium. b. Prevotella intermedia. d. all of the above. 3. Gastric ulcers are caused by a. Treponema vincentii. c. Helicobacter pylori. b. Prevotella intermedia. d. all of the above. 4. Virus family Paramyxoviridae contains viruses that cause which of the following diseases? a. measles d. both a and b b. mumps e. both b and c c. influenza 5. Which of these microorganisms is considered the most common cause of diarrhea in the United States? a. E. coli c. Campylobacter b. Salmonella d. Shigella 6. Which of these microorganisms is associated with GuillainBarré syndrome? a. E. coli c. Campylobacter b. Salmonella d. Shigella

7. This microorganism is commonly associated with fried rice and produces an emetic (vomiting) toxin. a. Bacillus cereus c. Shigella b. Clostridium perfringens d. Staphylococcus aureus 8. This sporeformer contaminates meats as well as vegetables and is also the causative agent of gas gangrene. a. Bacillus cereus c. Shigella b. Clostridium perfringens d. Staphylococcus aureus 9. This hepatitis virus is an enveloped DNA virus. a. hepatitis A virus c. hepatitis C virus b. hepatitis B virus d. hepatitis E virus 10. In which helminth life cycle is a grazing animal involved? a. A b. B c. C d. D True-False Questions. If the statement is true, leave as is. If it is false, correct it by rewriting the sentence. 11. Mumps is a disease that affects humans and several other species. 12. Giardia lamblia is a water-borne, flagellated protozoan often associated with chronic diarrhea. 13. Pseudomembranous colitis (or antibiotic-associated colitis) is caused by Clostridium difficile. 14. Poor oral health has been associated with heart disease. 15. Enterobius vermicularis, commonly known as the pinworm, is a common cause of anal itching in young children in the United States.

Critical Thinking Questions

Critical Thinking Questions

707

Application and Analysis

These questions are suggested as a writing-to-learn experience. For each question, compose a one- or two-paragraph answer that includes the factual information needed to completely address the question. 1. a. Which microorganism(s) is (are) the major culprit(s) associated with tooth decay? b. How do these microorganisms facilitate tooth decay? 2. a. What is food poisoning? b. What are some likely microbial culprits associated with food poisoning? c. List some nonmicrobial sources of toxins involved in food poisoning. 3. Entamoeba histolytica can cause three different forms of amoebiasis. Discuss them. 4. How can hepatitis A infections be prevented?

6. Describe how to definitively diagnose most helminthic infections. 7. Compare the methods of transmission of hepatitis A and hepatitis B. 8. Why is a hamburger a greater risk for E. coli contamination than a steak? 9. Describe your strategy for treating a cholera patient. 10. Why is heating food contaminated with Staphylococcus aureus no guarantee that the associated food poisoning will be prevented?

5. a. What are the most common means of transmission of the hepatitis C virus? b. What is the current treatment for hepatitis C?

Concept Mapping

Synthesis

Appendix D provides guidance for working with concept maps. 1. Use 6 to 10 words from the Chapter Summary to create a concept map. Finish it by providing linking words.

Visual Connections

Synthesis

These questions use visual images or previous content to make connections to this chapter’s concepts. 1. From chapter 13, figure 13.6b. Imagine for a minute that the organism in this illustration is E. coli O157:H7. What would be one reason not to treat a patient having this infection with powerful antibiotics? Cell wall

Not drug resistant Drug-resistant mutant

E a rl

y

Exposure to drug

Endotoxin

(b)

2. From chapter 12, figure 12.14. Assume the growth on the first plate represents normal intestinal microbiota. How could you use these illustrations to explain the development of C. difficile– associated colitis?

La

te

Remaining population grows over time.

General physiological effects— fever, malaise, aches, shock

www.connect.microbiology.com Enhance your study of this chapter with study tools and practice tests. Also ask your instructor about the resources available through ConnectPlus, including the media-rich eBook, interactive learning tools, and animations.

Infectious Diseases Affecting the Genitourinary System 23 Case File Sometimes dedication to your job can get you in trouble. In 2004, a 56-year-old genetics professor at the University of Hawaii in Oahu was determined to continue working in his lab even though a local stream had overflowed and the campus was flooded. For 4 days, he slogged through standing water in his lab to keep his research going. Some time afterward, the professor developed blisters on his feet. A few days later, he started having flulike symptoms: fever and chills, followed by nausea and vomiting. He began to feel better, but then developed another phase of illness that featured tremors, impaired balance, and illusions of color before his eyes. ◾ Do you know of any diseases that a person can acquire simply by walking through standing water? Continuing the Case appears on page 714.

Outline and Learning Outcomes 23.1 The Genitourinary Tract and Its Defenses 1. Draw or describe the anatomical features of the genitourinary tracts of both genders. 2. List the natural defenses present in the genitourinary tracts. 23.2 Normal Biota of the Genitourinary Tract 3. List the types of normal biota presently known to occupy the genitourinary tracts of both genders. 23.3 Urinary Tract Diseases Caused by Microorganisms 4. List the possible causative agents, modes of transmission, virulence factors, diagnostic techniques, and prevention/treatment for each type of urinary tract infection (including leptospirosis and schistosomiasis).

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23.1 The Genitourinary Tract and Its Defenses

709

23.4 Reproductive Tract Diseases Caused by Microorganisms 5. Distinguish between vaginitis and vaginosis. 6. Discuss prostatitis. 7. List the possible causative agents, modes of transmission, virulence factors, and prevention/treatment for gonorrhea and Chlamydia infection. 8. Name three diseases that result in genital ulcers and discuss their important features. 9. Differentiate between the two diseases causing warts in the reproductive tract. 10. Provide some detail about the first “cancer vaccine” and how it works. 11. Identify the most important risk group for group B Streptococcus infection and why.

23.1 The Genitourinary Tract and Its Defenses As suggested by the name, the structures considered in this chapter are really two distinct organ systems. The urinary tract has the job of removing substances from the blood, regulating certain body processes, and forming urine and transporting it out of the body. The genital system has reproduction as its major function. It is also called the reproductive system. The urinary tract includes the kidneys, ureters, bladder, and the urethra (figure 23.1). The kidneys remove metabolic wastes from the blood, acting as a sophisticated filtration system. Ureters are tubular organs extending from each kidney to the bladder. The bladder is a collapsible organ that stores urine and empties it into the urethra, which is the conduit of urine to the exterior of the body. In males, the urethra is also the terminal organ of the reproductive tract, but in females the urethra is separate from the vagina, which is the outermost organ of the reproductive tract. Several defenses are present in the urinary system that help to prevent infection when microorganisms are introduced. The most obvious defensive mechanism is the flushing action of the urine flowing out of the system. The flow of urine also encourages the desquamation (shedding) of the epithelial cells lining the urinary tract. For example, each time a person urinates, he or she loses hundreds of thousands of epithelial cells! Any microorganisms attached to them are also shed, of course. Probably the most common microbial threat to the urinary tract is the group of microorganisms that comprise the normal biota in the gastrointestinal tract, because the two organ systems are in close proximity. But the cells of the epithelial lining of the urinary tract have different chemicals on their surfaces than do those lining the GI tract. For that reason, most bacteria that are adapted to adhere to the chemical structures in the GI tract cannot gain a foothold in the urinary tract. Urine, in addition to being acidic, also contains two antibacterial proteins, lysozyme and lactoferrin. You may recall that lysozyme is an enzyme that breaks down peptidoglycan. Lactoferrin is an iron-binding protein that inhibits bacterial

growth. Finally, secretory IgA specific for previously encountered microorganisms can be found in the urine. The male reproductive system produces, maintains, and transports sperm cells and is the source of male sex hormones. It consists of the testes, which produce sperm cells and hormones, and the epididymides, which are coiled tubes leading out of the testes. Each epididymis terminates in a vas deferens, which combines with the seminal vesicle and Right kidney

Ureters

Bladder

Urethra

Figure 23.1 The urinary system.

Left kidney

Pelvis

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Chapter 23 Infectious Diseases Affecting the Genitourinary System

Ureter

Seminal vesicle Urinary bladder Ejaculatory duct Rectum Prostate gland Bulbourethral gland

Anus

Urethra Penis

Ductus deferens Epididymis

Glans penis Foreskin Prepuce Coronal sulcus

Testis Scrotum

Medial view

Figure 23.2 The male reproductive system. terminates in the ejaculatory duct (figure 23.2). The contents of the ejaculatory duct empty into the urethra during ejaculation. The prostate gland is a walnut-shaped structure at the base of the urethra. It also contributes to the released fluid (semen). The external organs are the scrotum, containing the testes, and the penis, a cylindrical organ that houses the urethra. As for its innate defenses, the male reproductive system also benefits from the flushing action of the urine, which helps move microorganisms out of the system. The female reproductive system consists of the uterus, the fallopian tubes (also called uterine tubes), ovaries, and vagina (figure 23.3). During childbearing years, an egg is released from one of the ovaries approximately every 28 days. It enters the fallopian tubes, where fertilization by sperm may take place if sperm are present. The fertilized egg moves through the fallopian tubes to the uterus, where it is implanted in the uterine lining. If fertilization does not occur, the lining of the uterus degenerates and sloughs off; this is the process of menstruation. The terminal portion of the female reproductive tract is the vagina, which is a tube about 9 cm long. The vagina is the exit tube for fluids from the uterus, the channel for childbirth, and the receptive chamber for the penis during sexual intercourse. One very important tissue of the female reproductive tract is the cervix, which is the lower one-third of the uterus and the part that connects to the vagina. The opening of the uterus is part of the cervix.

The cervix is a common site of infection in the female reproductive tract. The natural defenses of the female reproductive tract vary over the lifetime of the woman. The vagina is lined with mucous membranes and, thus, has the protective covering of secreted mucus. During childhood and after menopause, this mucus is the major nonspecific defense of this system. Secretory IgA antibodies specific for any previously encountered infections would be present on these surfaces. During a woman’s reproductive years, a major portion of the defense is provided by changes in the pH of the vagina brought about by the release of estrogen. This hormone stimulates the vaginal mucosa to secrete glycogen, which certain bacteria can ferment into acid, lowering the pH of the vagina to about 4.5. Before puberty, a girl produces little estrogen and little glycogen and has a vaginal pH of about 7. The change in pH beginning in adolescence results in a vastly different normal biota in the vagina, described later. The biota of women in their childbearing years is thought to prevent the establishment and invasion of microbes that might have the potential to harm a developing fetus.

23.1 Learning Outcomes—Can You . . . 1. . . . draw or describe the anatomical features of the genitourinary tracts of both genders? 2. . . . list the natural defenses present in the genitourinary tracts?

23.2 Normal Biota of the Genitourinary Tract

711

Vertebral column

Uterine tube Ovary

Uterus Urinary bladder Symphysis pubis

Cervix of uterus

Mons pubis

Rectum

Urethra Vagina

Clitoris Urethral orifice Vaginal orifice Labia minora Labia majora

Medial view

Figure 23.3 The female reproductive system.

23.2 Normal Biota of the Genitourinary Tract In both genders, the outer region of the urethra harbors some normal biota. The kidney, ureters, bladder, and upper urethra are presumably kept sterile by urine flow and regular bladder emptying (urinating). The principal known residents of the urethra are the nonhemolytic streptococci, staphylococci,

corynebacteria, and some lactobacilli. Because the urethra in women is so short (about 3.5 cm long) and is in such close proximity to the anus, it can act as a pipeline for bacteria from the GI tract to the bladder, resulting in urinary tract infections. It should be noted that the outer surface of the penis is colonized by Pseudomonas and Staphylococcus species—aerobic bacteria. In an uncircumcised penis, the area under the foreskin is colonized by anaerobic gram-negatives. These

Genitourinary Tract Defenses and Normal Biota Defenses

Normal Biota

Urinary Tract (both genders)

Flushing action of urine; specific attachment sites not recognized by most nonnormal biota; shedding of urinary tract epithelial cells, secretory IgA, lysozyme, and lactoferrin in urine

Nonhemolytic Streptococcus, Staphylococcus, Corynebacterium, Lactobacillus

Female Genital Tract (childhood and postmenopause)

Mucus secretions, secretory IgA

Same as for urinary tract

Female Genital Tract (childbearing years)

Acidic pH, mucus secretions, secretory IgA

Predominantly Lactobacillus but also Candida

Male Genital Tract

Same as for urinary tract

Urethra: Same as for urinary tract; outer surface of penis: Pseudomonas and Staphylococcus; sulcus of uncircumcised penis: anaerobic gram-negatives

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Chapter 23 Infectious Diseases Affecting the Genitourinary System

bacteria tend to draw elements of the immune system closer to the skin surface and may make these men more susceptible to infections, especially by HIV, which infects immune cells.

Normal Biota of the Male Genital Tract Because the terminal “tube” of the male genital tract is the urethra, the normal biota of the male genital tract (that is, in the urethra) is comprised of the same residents just described.

Normal Biota of the Female Genital Tract In the female genital tract, only the vagina harbors a normal population of microbes. Starting at the cervix and for all organs above it, there is no normal biota. As just mentioned, before puberty and after menopause, the pH of the vagina is close to neutral and the vagina harbors a biota that is similar to that found in the urethra. After the onset of puberty, estrogen production leads to glycogen release in the vagina, resulting in an acidic pH. Lactobacillus species thrive in the acidic environment and contribute to it, converting sugars to acid. Their predominance in the vagina, combined with the acidic environment, discourages the growth of many microorganisms. The estrogen-glycogen effect continues, with minor disruptions, throughout the childbearing years until menopause, when the biota gradually returns to a mixed population similar to that of prepuberty. Note that the very common fungus Candida albicans is also present at low levels in the healthy female reproductive tract.

23.2 Learning Outcomes—Can You . . . 3. . . . list the types of normal biota presently known to occupy the genitourinary tracts of both genders?

23.3 Urinary Tract Diseases Caused by Microorganisms We consider two types of diseases in this section. Urinary tract infections (UTIs) result from invasion of the urinary system by bacteria or other microorganisms. Leptospirosis, by contrast, is a spirochete-caused disease transmitted by contact of broken skin or mucous membranes with contaminated animal urine.

Urinary Tract Infections (UTIs) Even though the flushing action of urine helps to keep infections to a minimum in the urinary tract, urine itself is a good growth medium for many microorganisms. When urine flow is reduced or bacteria are accidentally introduced into the bladder, an infection of that organ (known as cystitis) can occur. Occasionally, the infection can also affect the kidneys, in which case it is called pyelonephritis. If an infection is limited to the urethra, it is called urethritis. In practice,

urethritis is not a very useful term when referring to urinary tract infections; females often don’t notice urinary tract infections if they are limited to the urethra. And a male experiencing urethritis could be suffering from a sexually transmitted infection (covered later in the chapter). ▶

Signs and Symptoms

Cystitis is a disease of sudden onset. Symptoms include pain in the pubic area, frequent urges to urinate even when the bladder is empty, and burning pain accompanying urination (called dysuria). The urine can be cloudy due to the presence of bacteria and white blood cells. It may have an orange tinge from the presence of red blood cells (hematuria). Fever and nausea are frequently present. If back pain is present, it is an indication that the kidneys may also be involved (pyelonephritis). Inadequately treated pyelonephritis may result in septicemia, especially in the immunocompromised. If only the bladder is involved, the condition is sometimes called acute uncomplicated UTI. ▶

Causative Agents

In 95% of cystitis and pyelonephritis cases, the cause is bacteria that are normal biota in the gastrointestinal tract. Escherichia coli is by far the most common of these. Staphylococcus saprophyticus and Proteus mirabilis are also common culprits. These last two are only referenced in Disease Table 23.1 following the discussion of E. coli. The E. coli species that cause UTIs are ones that exist as normal biota in the gastrointestinal tract. They are not the ones that cause diarrhea and other digestive tract diseases. ▶

Pathogenesis and Virulence Factors

E. coli secure themselves in the gastrointestinal tract using specific adhesins on the ends of long fimbriae. They can also use these adhesins to attach to slightly different chemicals present on the epithelial lining of the urinary tract. Many E. coli that cause disease in the urinary tract also have different fimbriae with adhesins that recognize chemicals only present on cells lining the ureters and kidney. These E. coli exhibit a motility that allows them to travel along mucosal surfaces, so they seem to be specially adapted to ascending the urinary system. Their presence in these normally sterile areas induces an inflammatory response that we experience as symptoms and that may lead to scarring in the ureters and kidneys. ▶

Transmission and Epidemiology

Community-acquired UTIs are nearly always “transmitted” not from one person to another but from one organ system to another, namely from the GI tract to the urinary system. They are much more common in women than in men because of the shorter length of the female urethra and because of the nearness of the female urethral opening to the anus (see figure 23.3). Many women experience what have been referred to as “recurrent urinary tract infections,” although it is now known that some E. coli can

23.3 Urinary Tract Diseases Caused by Microorganisms

invade the deeper tissue of the urinary tract and therefore avoid being destroyed by antibiotics. They can emerge later to cause symptoms again. It is not clear how many “recurrent” infections are actually infections that reactivate in this way. Note that urinary tract infections are also the most common of nosocomial infections. Patients of both sexes who have urinary catheters are susceptible to infections with a variety of microorganisms, not just the three mentioned here. ▶

Prevention

There are currently two vaccines in clinical trials for this infection. But for now, prevention of all UTIs relies on more basic practices, such as emptying the bladder frequently and (for females) wiping from front to back after a bowel movement. People who are predisposed to UTIs often drink cranberry juice to prevent the disease. Scientists have found that there are multiple compounds in the juice that help to discourage the attachment of E. coli to urinary epithelium. ▶

Treatment

Ampicillin, amoxicillin, or sulfa drugs such as trimethoprim-sulfamethoxazole are most often used for UTIs of various etiologies. Often another nonantibiotic drug called phenazopyridine (Pyridium) is administered simultaneously. This drug relieves the very uncomfortable symptoms of burning and urgency. A large percentage of E. coli strains is resistant to penicillin derivatives, so these should

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be avoided. Also, a new strain of E. coli (ST131) has arisen which is highly virulent, and more troubling, resistant to multiple antibiotics. Medical professionals are ringing alarm bells about this strain saying that if it acquires resistance to one more class of antibiotics it will become virtually untreatable (Disease Table 23.1).

Leptospirosis This infection is a zoonosis associated with wild animals and domesticated animals. It can affect the kidneys, liver, brain, and eyes. It is considered in this section because it can have its major effects on the kidneys and because its presence in animal urinary tracts causes it to be shed into the environment through animal urine. ▶

Signs and Symptoms

Leptospirosis has two phases. During the early, or leptospiremic, phase, the pathogen appears in the blood and cerebrospinal fluid. Symptoms are sudden high fever, chills, headache, muscle aches, conjunctivitis, and vomiting. During the second phase (called the immune phase), the blood infection is cleared by natural defenses. This period is marked by milder fever; headache due to leptospiral meningitis; and Weil’s syndrome, a cluster of symptoms characterized by kidney invasion, hepatic disease, jaundice, anemia, and neurological disturbances. Long-term disability and even death can result from damage to the kidneys and liver, but they occur primarily with the most virulent strains and in elderly persons.

Disease Table 23.1 Urinary Tract Infections (Cystitis, Pyelonephritis) Causative Organism(s)

Escherichia coli

Staphylococcus saprophyticus

Proteus mirabilis

Most Common Modes of Transmission

Endogenous transfer from GI tract (opportunism)

Opportunism

Opportunism

Virulence Factors

Adhesins, motility

–

Urease enzyme, leads to kidney stone formation

Culture/Diagnosis

Often “bacterial infection” diagnosed on basis of increased white cells in urinalysis; if culture performed, bacteria may or may not be identified to species level

Often “bacterial infection” diagnosed on basis of increased white cells in urinalysis; if culture performed, bacteria may or may not be identified to species level

Often “bacterial infection” diagnosed on basis of increased white cells in urinalysis; if culture performed, bacteria may or may not be identified to species level

Prevention

Vaccine may be available soon; hygiene practices

Hygiene practices

Hygiene practices

Treatment

Cephalosporins: check for resistance

Ampicillin, amoxicillin, trimethoprim-sulfamethoxazole

Ampicillin or cephalosporins

Distinctive Features

–

–

Kidney stones and severe pain may ensue

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Case File 23

Continuing the Case

The dedicated genetics professor was diagnosed with leptospirosis, which, as you know, is usually transmitted by direct or indirect contact with animal urine. It is considered the most common zoonosis in the United States. Animals most commonly infected f d are cows, sheep, deer, and pigs. The bacterium is a spirochete that probably enters the bloodstream through minute breaks in the skin. ◾ People in certain occupations are more likely than others to come in contact with Leptospira. What occupations might these be? ◾ The diagnostic test considered definitive for leptospirosis is the IgM ELISA. Why IgM and not IgG?

▶

Pathogenesis and Virulence Factors

In 2003, Chinese scientists sequenced the entire genome of this bacterium and found a series of genes that code for virulence factors such as adhesins and invasion proteins. Because it appears that the bacterium evolved from its close relatives, which are free-living and cause no disease, finding out how the bacterium acquired these genes will be useful in understanding its pathogenesis. Hook

Transmission and Epidemiology

Leptospirosis is a zoonosis, affecting wild animals such as rodents, skunks, raccoons, and foxes and some domesticated animals, particularly horses, dogs, cattle, and pigs. It is found throughout the world, although it is more common in the tropics. It is an occupational hazard of people who work with animals or in the outdoors. Leptospires shed in the urine of an infected animal can survive for several months in neutral or alkaline soil or water. Infection occurs almost entirely through contact of skin abrasions or mucous membranes with animal urine or some environmental source containing urine. In 1998, dozens of athletes competing in the swimming phase of a triathlon in Illinois contracted leptospirosis from the water. In late 2009, the Philippines experienced a major outbreak after a series of typhoons flooded the country. At one point, 350 new cases a day were diagnosed. The disease is not transmissible person to person. ▶

Causative Agent

Leptospires are typical spirochete bacteria marked by tight, regular, individual coils with a bend or hook at one or both ends (figure 23.4). Leptospira interrogans (lep″-toh-spy′-rah in-terr′-oh-ganz) is the species that causes leptospirosis in humans and animals. There are nearly 200 different serotypes of this species distributed among various animal groups, which accounts for extreme variations in the disease manifestations in humans. ▶

▶

Prevention

The new DNA sequence data should reveal new targets for vaccines that will be more broadly useful. For now, the best prevention is to wear protective footwear and clothing and to avoid swimming and wading in natural water sources that are frequented by livestock. ▶

Treatment

Early treatment with amoxicillin or doxycycline rapidly reduces symptoms and shortens the course of disease, but delayed therapy is less effective. Other spirochete diseases, such as syphilis (described later), exhibit this same pattern of being susceptible to antibiotics early in the infection but less so later.

Disease Table 23.2 Leptospirosis Causative Organism(s)

Leptospira interrogans

Most Common Modes of Transmission

Vehicle—contaminated soil or water

Virulence Factors

Adhesins? Invasion proteins?

Culture/Diagnosis

Slide agglutination test of patient’s blood for antibodies

Prevention

Avoiding contaminated vehicles

Treatment

Doxycycline, amoxicillin

Urinary Schistosomiasis Figure 23.4 Leptospira interrogans, the agent of

leptospirosis.

Note the curved hook at the ends of the spirochete.

In chapter 22, we talked about schistosomiasis, because one of its two distinct disease manifestations occurs in the liver and spleen, both parts of the digestive system. One particular species of the trematode (helminth) lodges in the blood

23.4

Reproductive Tract Diseases Caused by Microorganisms

Disease Table 23.3 Urinary

vessels of the bladder. This may or may not result in symptoms. Alternatively, blood in the urine and, eventually, bladder obstruction can occur. ▶

Schistosomiasis

Signs and Symptoms

As with the other forms of schistosomiasis, the first symptoms of infestation are itchiness in the area where the worm enters the body, followed by fever, chills, diarrhea, and cough. Urinary tract symptoms occur at a later date. Remember that adult flukes can live for many years and, by eluding the immune defenses, cause chronic infection. ▶

Causative Agent

The urinary manifestations occur if a host is infected with a particular species of schistosome, Schistosoma haematobium. It is found throughout Africa, the Caribbean, and the Middle East. (S. mansoni and S. japonicum are the species responsible for liver manifestations.) Schistosomes are trematodes, or flukes (illustrated in figure 22.29). Humans are the definitive hosts for schistosomes, and snails are the intermediate hosts. ▶

Transmission and Epidemiology

The life cycle of the schistosome is described completely in chapter 22. After the worms pass into small blood and lymphatic vessels, they are carried to the liver. Eventually S. haematobium enters the venous plexus of the bladder. While attached to these intravascular sites, the worms feed upon blood, and the female lays eggs that are eventually voided in urine. The appropriate snail vector does not exist in the United States, so cases found there are virtually all imported. ▶

Culture and Diagnosis

Diagnosis depends on identifying the eggs in urine. ▶

Causative Organism(s)

Schistosoma haematobium

Most Common Modes of Transmission

Vehicle (contaminated water)

Virulence Factors

Antigenic “cloaking,” induction of granulomatous response

Culture/Diagnosis

Identification of eggs in urine

Prevention

Avoiding contaminated vehicles

Treatment

Praziquantel

23.3 Learning Outcomes—Can You . . . 4. . . . list the possible causative agents, modes of transmission, virulence factors, diagnostic techniques, and prevention/treatment for each type of urinary tract infection (including leptospirosis and schistosomiasis)?

Pathogenesis and Virulence Factors

Like the other species, S. haematobium is able to invade intact skin and attach to vascular endothelium. It engages in the same antigenic cloaking behavior as the other two species. The disease manifestations occur when the eggs in the bladder induce a massive granulomatous response that leads to leakage in the blood vessels and blood in the urine. Significant portions of the bladder eventually can be filled with granulomatous tissue and scar tissue. Function of the bladder is decreased or halted altogether. Chronic infection with S. haematobium can also lead to bladder cancer. ▶

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Prevention and Treatment

The cycle of infection cannot be broken as long as people are exposed to untreated sewage in their environment. It is quite common for people to be cured and then to be reinfected because their village has no sewage treatment. A vaccine would provide widespread control of the disease, but so far none is licensed. More than one vaccine is in development, however. Praziquantel is the drug treatment of choice and is quite effective at eliminating the worms.

23.4 Reproductive Tract Diseases Caused by Microorganisms We saw earlier that reproductive tract diseases in men almost always involve the urinary tract as well, and this is sometimes but not always the case with women. Note that although many of the infectious diseases of the reproductive tract are transmitted through sexual contact, not all of them are. We begin this section with a discussion of infections that are symptomatic primarily in women: vaginitis and vaginosis. Men may also harbor these infections with or without symptoms. We next consider three broad categories of sexually transmitted diseases (STDs): discharge diseases in which increased fluid is released in male and female reproductive tracts; ulcer diseases in which microbes cause distinct open lesions; and the wart diseases. The section concludes with a neonatal disease caused by group B Streptococcus colonization.

Vaginitis and Vaginosis ▶

Signs and Symptoms

Vaginitis, an inflammation of the vagina, is a condition characterized by some degree of vaginal itching, depending on the etiologic agent. Symptoms may also include burning, and sometimes a discharge, which may take different forms as well. From the name, it is obvious that vaginitis only affects women, but most of the agents can also colonize the male reproductive tract. ▶

Causative Agents

The most common cause of vaginitis is Candida albicans. The vaginal condition caused by this fungus is known as a yeast infection. Most women experience this condition one or

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Chapter 23 Infectious Diseases Affecting the Genitourinary System

multiple times during their lives. Other causes can be bacterial, as in the case of Gardnerella, or even protozoal, as in the case of Trichomonas. We describe each of these agents here.

Candida albicans C. albicans is a dimorphic fungus that is normal biota in from 50% to 100% of humans, living in low numbers on many mucosal surfaces such as the mouth, gastrointestinal tract, vagina, and so on. The vaginal condition it causes is often called vulvovaginal candidiasis. The yeast is easily detectable on a wet prep or a Gram stain of material obtained during a pelvic exam (figure 23.5). The presence of pseudohyphae in the smear is a clear indication that the yeast is growing rapidly and causing a yeast infection. ▶

Pathogenesis and Virulence Factors

The fungus grows in thick curdlike colonies on the walls of the vagina. The colony debris contributes to a white vaginal discharge. In otherwise healthy people, the fungus is not invasive and limits itself to this surface infection. Please note, however, that Candida infections of the bloodstream do occur and they have high mortality rates. They do not normally stem from vaginal infections with the fungus, however, but are seen most frequently in hospitalized patients. ▶

It is possible to transmit this yeast through sexual contact, especially if a woman is experiencing an overgrowth of it. The recipient’s immune system may well subdue the yeast so that it acts as normal biota in them. But the yeast may be passed back to the original partner during further sexual contact after treatment. By that time, the circumstances that led to it becoming dominant in the vagina may have returned to normal and its growth would be limited by the normal bacterial biota. So the sexual route of transmission is difficult to assess. Nevertheless, it is recommended that a patient’s sexual partner also be treated to short-circuit the possibility of retransmission. The important thing to remember is that Candida is an opportunistic fungus. Women with HIV infection experience frequently recurring yeast infections. Also, a small percentage of women with no underlying immune disease experience chronic or recurrent vaginal infection with Candida for reasons that are not clear. ▶

Prevention and Treatment

No vaccine is available for C. albicans. Topical and oral azole drugs are used to treat vaginal candidiasis, and some of them are now available over the counter. If infections recur frequently or fail to resolve, it is important to see a physician for evaluation.

Transmission and Epidemiology

Vaginal infections with this organism are nearly always opportunistic. Disruptions of the normal bacterial biota or even minor damage to the mucosal epithelium in the vagina can lead to overgrowth by this fungus. Disruptions may be mechanical, such as wearing very tight pants, or they may be chemical, as when broad-spectrum antibiotics taken for some other purpose temporarily diminish the vaginal bacterial population. Diabetics and pregnant women are also predisposed to vaginal yeast overgrowths. Some women are prone to this condition during menstruation. Epithelial cell

Bud Gram negative bacilli

Pseudohypha Yeast Hypha

Gardnerella Species The bacterium Gardnerella is associated with a particularly common condition in women in their childbearing years. This condition is usually called vaginosis rather than vaginitis because it doesn’t appear to induce inflammation in the vagina. It is also known as BV, or bacterial vaginosis. Despite the absence of an inflammatory response, a vaginal discharge is associated with the condition, which is said to have a very fishy odor, especially after sex. Itching is common. But it is also true that many women have this condition with no noticeable symptoms. Vaginosis is most likely a result of a shift from a predominance of “good bacteria” (lactobacilli) in the vagina to a predominance of “bad bacteria,” and one of those is Gardnerella vaginalis. This genus of bacteria is aerotolerant and gram-positive, although in a Gram stain it usually appears gram-negative. Probably a mixed infection leads to the condition, however. Anaerobic streptococci and other bacteria, particularly a genus known as Mobiluncus, that are normally found in low numbers in a healthy vagina can also often be found in high numbers in this condition. The often-mentioned fishy odor comes from the metabolic by-products of anaerobic metabolism by these bacteria. ▶

Figure 23.5 Gram stain of Candida albicans in a vaginal

smear.

Pathogenesis and Virulence Factors

The mechanism of damage in this disease is not well understood. But some of the outcomes are. Besides the symptoms just mentioned, vaginosis can lead to complications such as pelvic inflammatory disease (PID; to be discussed later in the chapter), infertility, and more rarely, ectopic

23.4

pregnancies. Babies born to some mothers with vaginosis have low birth weights. ▶

Transmission and Epidemiology

This mixed infection is not considered to be sexually transmitted, although women who have never had sex rarely develop the condition. It is very common in sexually active women. It may be that the condition is associated with sex but not transmitted by it. This situation could occur if the act of penetration or the presence of semen (or saliva) causes changes in the vaginal epithelium, or in the vaginal biota. We do not know exactly what causes the increased numbers of Gardnerella and other normally rare biota. The low pH typical of the vagina is usually higher in vaginosis. It is not clear whether this causes or is caused by the change in bacterial biota. ▶

Culture and Diagnosis

The condition can be diagnosed by a variety of methods. Sometimes a simple stain of vaginal secretions is used to examine sloughed vaginal epithelial cells. In vaginosis, some cells will appear to be nearly covered with adherent bacteria. In normal times, vaginal epithelial cells are sparsely covered with bacteria. These cells are called clue cells and are a helpful diagnostic indicator (figure 23.6). They can also be found on Pap smears. ▶

Prevention and Treatment

No known prevention exists. Asymptomatic cases are generally not treated. Women who find the condition uncomfortable or who are planning on becoming pregnant should be treated. Women who use intrauterine devices (IUDs) for contraception should also be treated because IUDs can provide a passageway for the bacteria to gain access to the upper reproductive tract. The usual treatment is oral or topical metronidazole or clindamycin.

Reproductive Tract Diseases Caused by Microorganisms

Trichomonas vaginalis Trichomonads are small, pear-shaped protozoa with four anterior flagella and an undulating membrane (figure 23.7). Trichomonas vaginalis seems to cause asymptomatic infections in approximately 50% of females and males, despite its species name. Trichomonads are considered asymptomatic infectious agents rather than normal biota because of evidence that some people experience long-term negative effects. Even though Trichomonas is a protozoan, it has no cyst form and it does not survive long out of the host. ▶

Pathogenesis and Virulence Factors

Many cases are asymptomatic, and men seldom have symptoms. Women often have vaginitis symptoms, which can include a white to green frothy discharge. Chronic infection can make a person more susceptible to other infections, including HIV. Also, women who become infected during pregnancy are predisposed to premature labor and low-birth-weight infants. Chronic infection may also lead to infertility. ▶

Transmission and Epidemiology

Because Trichomonas is common biota in so many people, it is easily transmitted through sexual contact. It has been called the most common nonviral sexually transmitted infection. It does not appear to undergo opportunistic shifts within its host (that is, to become symptomatic under certain conditions), but rather, the protozoan causes symptoms when transmitted to a noncarrier. Some debate exists over whether the protozoan can be transmitted through communal bathing, public facilities, and from mother to child, but if this type of transmission happens, it is only rarely.

Figure 23.6 Clue cell in bacterial vaginosis. These epithelial cells came from a pelvic exam. The cell in the middle has a large number of bacteria attached to it.

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Figure 23.7 Trichomonas vaginalis.

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Chapter 23 Infectious Diseases Affecting the Genitourinary System

Disease Table 23.4 Vaginitis/Vaginosis

▶

Causative Organism(s)

Candida albicans

Mixed infection, usually including Gardnerella

Trichomonas vaginalis

Most Common Modes of Transmission

Opportunism

Opportunism?

Direct contact (STD)

Virulence Factors

–

–

–

Culture/Diagnosis

Wet prep or Gram stain

Visual exam of vagina, or clue cells seen in Pap smear or other smear

Protozoa seen on Pap smear or Gram stain

Prevention

–

–

Barrier use during intercourse

Treatment

Topical or oral azole drugs, some over-the-counter drugs

Metronidazole or clindamycin

Metronidazole, tinidazole

Distinctive Features

White curdlike discharge

Discharge may have fishy smell

Discharge may be greenish

Disease Table 23.5 Prostatitis

Prevention and Treatment

There is no vaccine for Trichomonas. The antiprotozoal drug metronidazole is the drug of choice, although some isolates are resistant to it (Disease Table 23.4).

Prostatitis Prostatitis is an inflammation of the prostate gland (see figure 23.2). It can be acute or chronic. Acute prostatitis is virtually always caused by bacterial infection. The bacteria are usually normal biota from the intestinal tract or may have caused a previous urinary tract infection. Chronic prostatitis is also often caused by bacteria. Researchers have found that chronic prostatitis, often unresponsive to antibiotic treatment, can be caused by mixed biofilms of bacteria in the prostate. Some forms of chronic prostatitis have no known microbial cause, though many infectious disease specialists feel that one or more bacteria are involved, but they are simply not culturable with current techniques. The symptoms of prostatitis are pain in the pelvic area, lower back, or genital area; frequent urge to urinate; blood in the urine; and/or painful ejaculation. Acute prostatitis is accompanied by fever and chills and flulike symptoms. Patients appear to be quite ill with the acute form of the disease. Treatment involves antibiotics when bacteria are indicated. Also, muscle relaxers or drugs called alpha blockers, which relax the neck of the bladder, may be prescribed. Prostatitis is distinct from prostate cancer, a condition that may be associated with viral infection, according to recent research.

Causative Organism(s)

GI tract biota

Most Common Modes of Transmission

Endogenous transfer from GI tract; otherwise unknown

Virulence Factors

Various

Culture/Diagnosis

Digital rectal exam to examine prostate; culture of urine or semen

Prevention

None

Treatment

Antibiotics, muscle relaxers, alpha blockers

Distinctive Features

Pain in genital area and/or back, difficulty urinating

Discharge Diseases with Major Manifestation in the Genitourinary Tract Discharge diseases are those in which the infectious agent causes an increase in fluid discharge in the male and female reproductive tracts. Examples are trichomoniasis, gonorrhea, and Chlamydia infection. The causative agents are transferred to new hosts when the fluids in which they live contact the mucosal surfaces of the receiving partner. Trichomoniasis has been described in the preceding section because its disease manifestations are considered to be a vaginitis. In this section, we cover the other two major discharge diseases: gonorrhea and Chlamydia infection.

23.4

Normal

A Note About HIV and Hepatitis B and C This chapter is about diseases whose major (presenting) symptoms occur in the genitourinary tract. But some sexually transmitted diseases do not have their major symptoms in this system. HIV and hepatitis B and C can all be transmitted in several ways, one of them being through sexual contact. HIV is considered in chapter 20 because its major symptoms occur in the cardiovascular and lymphatic systems. Because the major disease manifestations of hepatitis B and C occur in the gastrointestinal tract, these diseases are discussed in chapter 22. Anyone diagnosed with any sexually transmitted disease should also be tested for HIV.

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Reproductive Tract Diseases Caused by Microorganisms Gonorrhea

Anaerobic infection

Ectopic (tubal) pregnancy Fallopian tube

Fimbriae

Scar tissue

Uterus

Peritoneum

Ovary

Cervix

Figure 23.8 Invasive gonorrhea in women. (Left) Normal

Gonorrhea Gonorrhea has been known as a sexually transmitted disease since ancient times. Its name originated with the Greek physician Claudius Galen, who thought that it was caused by an excess flow of semen. For a fairly long period in history, gonorrhea was confused with syphilis. Later, microbiologists went on to cultivate N. gonorrhoeae, also known as the gonococcus, and to prove conclusively that it alone was the etiologic agent of gonorrhea. ▶

Signs and Symptoms

In the male, infection of the urethra elicits urethritis, painful urination and a yellowish discharge, although a relatively large number of cases are asymptomatic. In most cases, infection is limited to the distal urogenital tract, but it can occasionally spread from the urethra to the prostate gland and epididymis (refer to figure 23.2). Scar tissue formed in the spermatic ducts during healing of an invasive infection can render a man infertile. This outcome is becoming increasingly rare with improved diagnosis and treatment regimens. In the female, it is likely that both the urinary and genital tracts will be infected during sexual intercourse. A mucopurulent (containing mucus and pus) or bloody vaginal discharge occurs in about half of the cases, along with painful urination if the urethra is affected. Major complications occur when the infection ascends from the vagina and cervix to higher reproductive structures such as the uterus and fallopian tubes (figure 23.8). One disease resulting from this progression is salpingitis (sal″-pin-jy′-tis). This inflammation of the fallopian tubes may be isolated, or it may also include inflammation of other parts of the upper reproductive tract, termed pelvic inflammatory disease (PID). It is not unusual for the microbe that initiates PID to become involved in mixed infections with anaerobic bacteria. The buildup of scar tissue from PID can block the fallopian tubes, causing sterility or ectopic pregnancies (Insight 23.1).

state. (Right) In ascending gonorrhea, the gonococcus is carried from the cervical opening up through the uterus and into the fallopian tubes. Pelvic inflammatory disease (PID) is a serious complication that can lead to scarring in the fallopian tubes, ectopic pregnancies, and mixed anaerobic infections.

Serious consequences of gonorrhea can occur outside of the reproductive tract. In a small number of cases, the gonococcus enters the bloodstream and is disseminated to the joints and skin. Involvement of the wrist and ankle can lead to chronic arthritis and a painful, sporadic, papular rash on the limbs. Rare complications of gonococcal bacteremia are meningitis and endocarditis. Children born to gonococcus carriers are also in danger of being infected as they pass through the birth canal. Because of the potential harm to the fetus, physicians usually screen pregnant mothers for its presence. Gonococcal eye infections are very serious and often result in keratitis, ophthalmia neonatorum, and even blindness (figure 23.9). A universal precaution to prevent such complications is the

Figure 23.9 Gonococcal ophthalmia neonatorum in a week-old infant.

The infection is marked by intense inflammation and edema; if allowed to progress, it causes damage that can lead to blindness. Fortunately, this infection is completely preventable and treatable.

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Chapter 23 Infectious Diseases Affecting the Genitourinary System

INSIGHT 23.1

Pelvic Inflammatory Disease and Infertility

The National Center for Health Statistics estimates that more than 6 million women in the United States have impaired fertility. There are many different reasons for infertility, but the leading cause is pelvic inflammatory disease, or PID. PID is caused by infection of the upper reproductive structures in women, namely the uterus, fallopian tubes, and ovaries. These organs have no normal biota, and when bacteria from the vagina are transported higher in the tract, they start a chain of inflammatory events that may or may not be noticeable to the patient. The inflammation can be acute, resulting in pain, abnormal vaginal discharge, fever, and nausea, or it can be chronic, with less noticeable symptoms. In acute cases, women usually seek care; in some ways, these can be considered the lucky ones. If the inflammation is curbed at an early stage by using antibiotics to kill the bacteria, chances are better that the long-term sequelae of PID can be avoided. The most notable long-term consequence is tubal infertility, caused by the repair step of inflammation. Inflammatory repair processes, especially in the fallopian tubes, can lead to the deposition of scar tissue that narrows the lumen in the tubes, in some cases closing them off completely. But if the lumen is only narrowed, fertilization may occur. A fertilized egg could then be unable to travel through the tube and implant in the uterine wall. In some cases, fertilized eggs implant in the tube walls or even leave the fallopian tubes and implant elsewhere in the

use of antibiotic eyedrops for newborn babies. The pathogen may also infect the pharynx and respiratory tract of neonates. Finding gonorrhea in children other than neonates is strong evidence of sexual abuse by infected adults, and it calls for child welfare consultation along with thorough bacteriologic analysis. ▶

Causative Agent

N. gonorrhoeae is a pyogenic gram-negative diplococcus. It appears as pairs of kidney bean–shaped bacteria, with their flat sides touching (figure 23.10). ▶

abdominal cavity. Both of these situations are known as ectopic pregnancies. Women with a history of PID have a seven- to tenfold greater chance of experiencing an ectopic pregnancy than other women. Ectopic pregnancy is a life-threatening situation. An embryo growing in the tube usually causes the tube to rupture in about 12 weeks, and an embryo in the abdominal cavity can cause the same complication as a tumor. Surgical intervention is usually required in either case to eliminate the embryo and save the woman’s life. Chlamydia infection is the leading cause of PID, followed closely by N. gonorrhoeae infection. But other bacteria, perhaps also including normal biota of the reproductive tract, can also cause PID if they are traumatically introduced into the uterus. Intercourse, tampon usage, the use of an intrauterine contraceptive device, and even douching can encourage the transmission of bacteria into the upper genital tract. (In addition to being a risk factor for PID, douching can also temporarily ease the symptoms of a reproductive tract infection, which could result in dangerous delays in seeking treatment.) With the relatively high rates of infertility in the developed world, the message needs to be loud and clear: PID is a preventable condition. Women who suspect for any reason that they may have a reproductive tract infection should always seek diagnosis and treatment from health care professionals.

The gonococcus also possesses an enzyme called IgA protease, which can cleave IgA molecules stationed on mucosal surfaces. In addition, it pinches off pieces of its outer membrane. These “blebs,” containing endotoxin, probably play a role in pathogenesis because they can stimulate portions of the nonspecific defense response, resulting in localized damage. Gonococci

Neutrophils

Pathogenesis and Virulence Factors

Successful attachment is key to the organism’s ability to cause disease. Gonococci use specific chemicals on the tips of fimbriae to anchor themselves to mucosal epithelial cells. They only attach to nonciliated cells of the urethra and the cervix, for example. Once the bacterium attaches, it invades the cells and multiplies on the basement membrane. The fimbriae may also play a role in slowing down effective immunity. The fimbrial proteins are controlled by genes that can be turned on or off, depending on the bacterium’s situation. This phenotypic change is called phase variation. In addition, the genes can rearrange themselves to put together fimbriae of different configurations. This antigenic variation confuses the body’s immune system. Antibodies that previously recognized fimbrial proteins may not recognize them once they are rearranged.

Figure 23.10 Gram stain of urethral pus from a male

patient with gonorrhea (1,000×). Note the intracellular (phagocytosed) gram-negative diplococci (arranged side-to-side) in polymorphonuclear leukocytes (neutrophils).

23.4

▶

Transmission and Epidemiology

N. gonorrhoeae does not survive more than 1 or 2 hours on fomites and is most infectious when transferred to a suitable mucous membrane. Except for neonatal infections, the gonococcus spreads through some form of sexual contact. The pathogen requires an appropriate portal of entry that is genital or extragenital (rectum, eye, or throat). Gonorrhea is a strictly human infection that occurs worldwide and ranks among the most common sexually transmitted diseases. Although about 350,000 cases are reported in the United States each year, it is estimated that the actual incidence is much higher—in the millions if one counts asymptomatic infections. Please refer to figure 23.11 and also the Note About STD Statistics on this page. It is important to consider the reservoir of asymptomatic males and females when discussing the transmission of the infection. Because approximately 10% of infected males and 50% of infected females experience no symptoms, it is often spread unknowingly. ▶

Culture and Diagnosis

In males, it is easy to diagnose this disease; a Gram stain of urethral discharge is diagnostic. The normal biota of the male urethra is so sparse that it is easy to see the diplococcus inside of neutrophils (see figure 23.10). In females, other methods, such as ELISA or PCR tests, are called for. Alternatively, the bacterium can be cultured on Thayer-Martin agar, a rich chocolate agar base with added antibiotics that inhibit competing bacteria. N. gonorrhoeae grows best in an atmosphere containing increased CO2. Because Neisseria is so fragile, it is best to inoculate it onto media directly from the patient rather than using a transport tube. Gonococci produce catalase, enzymes for fermenting various carbohydrates, and the enzyme cytochrome oxidase that can be used for identification as well. Gonorrhea is a reportable disease. ▶

Prevention

Currently, no vaccine is available for gonorrhea, although finding one is a priority for government health agencies. The

900,000

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development of a vaccine is hampered by the fact that no good animal model exists for the disease. Using condoms is an effective way to avoid transmission of this and other discharge diseases. ▶

Treatment

The CDC runs a program called the Gonococcal Isolate Surveillance Project (GISP) to monitor the occurrence of antibiotic resistance in N. gonorrhoeae. Penicillin was traditionally the drug of choice, but a large percentage of isolates now are able to produce penicillinase. Others are tetracycline resistant. As alternatives, practitioners have been using quinolones (like ciprofloxacin) or cephalosporins. But there is constantly rising resistance to quinolones, as well. This development highlights the need for practitioners to be aware of local resistance patterns before prescribing antibiotics for gonorrhea. The GISP provides this local data. Every month in 28 local STD clinics around the country, N. gonorrhoeae isolates from the first 25 males diagnosed with the infection are sent to regional testing labs and their antibiotic sensitivities are determined and the data are provided to the GISP program at the CDC.

Chlamydia Genital chlamydial infection is the most common reportable infectious disease in the United States. Annually, more than 1 million cases are reported but the actual infection rate may be 5 to 7 times that number. The overall prevalence among young adults in the United States is 4%. It is at least two to three times as common as gonorrhea. The vast majority of cases are asymptomatic. When we consider the serious consequences that may follow Chlamydia infection, those facts are very disturbing. ▶

Signs and Symptoms

In males who experience Chlamydia symptoms, the bacterium causes an inflammation of the urethra (a condition formerly called nongonococcal urethritis). The symptoms

A Note About STD Statistics

1,500,000 1,200,000

Reproductive Tract Diseases Caused by Microorganisms

Chlamydia Gonorrhea Syphilis all stages Syphilis primary and secondary

600,000 300,000 0 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008

Figure 23.11 Cases of STDs reported by state health departments: United States, 1997–2008.

It is difficult to compare the incidence of different STDs to one another, for several reasons. The first is that many, many infections are “silent,” and therefore infected people don’t access the health care system, and don’t get counted. Of course, we know that many silent infections are actually causing damage that won’t be noticed for years, and when it is, the original causative organism is almost never sought out. The second reason is that only some STDs are officially reportable to health authorities. Chlamydia infection and gonorrhea are, for example, but herpes and HPV are not (see table 13.10). In each section we will try to present accurate estimates of the prevalence and/or incidence of the diseases as we know them.

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mimic gonorrhea, namely discharge and painful urination. ▶ Pathogenesis and Virulence Factors Untreated infections may lead to epididymitis. Females who Chlamydia’s ability to grow intracellularly contributes to experience symptoms have cervicitis, a discharge, and often its virulence because it escapes certain aspects of the host’s salpingitis. Pelvic inflammatory disease is a frequent sequela immune response. Also, the bacterium has a unique cell wall of female chlamydial infection. A woman is even more likely that apparently prevents the phagosome from fusing with to experience PID as a result of a Chlamydia infection than as a the lysosome inside phagocytes. The presence of the bacteresult of gonorrhea. (The photo in figure 23.12 depicts Chlamyria inside cells causes the release of cytokines that provoke dia bacteria adhering inside a fallopian tube.) Up to 75% of Chlamydia infections are asymptomatic, which puts women at risk for developing PID because they don’t seek treatment for initial infections. The PID itself may be acute and painful, Microvilli or it may be relatively asymptomatic, allowing damage to the upper reproductive tract to continue unchecked. Certain strains of C. trachomatis can invade the lymphatic tissues, resulting in another condition called lymphogranuChlamydias loma venereum. This condition is accompanied by headache, fever, and muscle aches. The lymph nodes near the lesion begin to fill with granuloma cells and become enlarged and tender. These “nodes” can cause long-term lymphatic obstruction that leads to chronic, deforming edema of the genitalia or anus. The disease is endemic to South AmerNew host cell ica, Africa, and Asia but occasionally occurs in other parts of the world. Its incidence in the United States is about 500 cases per year. Babies born to mothers with Chlamydia EB 2 ␮m EB infections can develop eye infections and also pneumonia if they become infected during Host cell passage through the birth canal. Infant con6 junctivitis caused by contact with maternal Nucleus Chlamydia infection is the most prevalent form of conjunctivitis in the United States (100,000 1 cases per year). Antibiotic drops or ointment applied to newborns’ eyes are chosen to eliminate both Chlamydia and N. gonorrhoeae. ▶

Causative Agent

C. trachomatis is a very small gram-negative bacterium. It lives inside host cells as an obligate intracellular parasite. All Chlamydia species alternate between two distinct stages: (1)  a small, metabolically inactive infectious form called the elementary body, which is released by the infected host cell; and (2) a larger, noninfectious, actively dividing form called the reticulate body, which grows within the host cell vacuoles (figure 23.12). Elementary bodies are tiny, dense spheres shielded by a rigid, impervious envelope that ensures survival outside the eukaryotic host cell. Studies of reticulate bodies indicate that they are “energy parasites,” entirely lacking enzyme systems for synthesizing ATP, although they do possess ribosomes and mechanisms for synthesizing proteins, DNA, and RNA. Reticulate bodies ultimately become elementary bodies during their life cycle.

4

RB

5 Phagosomes with EB

EB

3 Binary fission

EB RB

2

Enlarged view of cycle in phagosome

Process Figure 23.12 The life cycle of Chlamydia.

1  The infectious stage, or elementary body (EB), is taken into phagocytic vesicles by the host cell. 2  In the phagosome, each elementary body develops into a reticulate body (RB). 3  Reticulate bodies multiply by regular binary fission. 4 and 5  Mature RBs become reorganized into EBs. 6  Completed EBs are released from the host cell. Inset features a micrograph of C. trachomatis adhering to a fallopian tube (1,750×).

23.4

intense inflammation. This defensive response leads to most of the actual tissue damage in Chlamydia infection. Of course, the last step of inflammation is repair, which often results in scarring, as described in Insight 23.1. This can have disastrous effects on a narrow tube like the fallopian tube. ▶

Transmission and Epidemiology

The reservoir of pathogenic strains of C. trachomatis is the human body. The microbe shows an astoundingly broad distribution within the population. Adolescent women are more likely than older women to harbor the bacterium because it prefers to infect cells that are particularly prevalent on the adolescent cervix. It is transmitted through sexual contact and also vertically. Fifty percent of babies born to infected mothers will acquire conjunctivitis (more common) or pneumonia (less common). ▶

Culture and Diagnosis

Infection with this microorganism is usually detected initially using a rapid technique such as PCR or ELISA. Direct fluorescent antibody detection is also used. Serology is not always reliable. In addition, antibody to Chlamydia is very common in adults and often indicates past, not present, infection. Isolating the bacterium and growing it in cell culture is the best method for detecting this bacterium, but because it is time-consuming and expensive, it is performed only in cases where 100% accuracy is required—such as in rape or child abuse cases. A urine test is available, which has definite advantages for widespread screening, but it is slightly less accurate for females than males.

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Prevention

As yet, no vaccine exists for Chlamydia. Researchers have developed several types of experimental vaccines, including a DNA vaccine, but none has been approved for use to date. Avoiding contact with infected tissues and secretions through abstinence or barrier protection (condoms) is the only means of prevention. ▶

Treatment

Treatment for this infection relies on being aware of it, so part of the guidelines issued by the CDC is a recommendation for annual screening of young women for presence of the bacterium. It is also recommended that older women with some risk factor (new sexual partner, for instance) also be screened. If infection is found, treatment is usually with azithromycin, a macrolide antibiotic. Note that according to public health officials, many patients become reinfected soon after treatment; therefore, the recommendation is that patients be rechecked for Chlamydia infection 3 to 4 months after treatment. Repeated infections with Chlamydia increase the likelihood of PID and other serious sequelae (Disease Table 23.6).

Genital Ulcer Diseases Three common infectious conditions can result in lesions on a person’s genitals: syphilis, chancroid, and genital herpes. In this section, we consider each of these. One very important fact to remember about the ulcer diseases is that having one of them increases the chances of infection with HIV because of the open lesions.

Disease Table 23.6 Genital “Discharge” Diseases (in Addition to Vaginitis/Vaginosis) Gonorrhea

Chlamydia

Causative Organism(s)

Neisseria gonorrhoeae

Chlamydia trachomatis

Most Common Modes of Transmission

Direct contact (STD), also vertical

Direct contact (STD), vertical

Virulence Factors

Fimbrial adhesins, antigenic variation, IgA protease, membrane blebs/endotoxin

Intracellular growth resulting in avoiding immune system and cytokine release, unusual cell wall preventing phagolysosome fusion

Culture/Diagnosis

Gram stain in males, rapid tests (PCR, ELISA) for females, culture on Thayer-Martin agar

PCR or ELISA, can be followed by cell culture

Prevention

Avoid contact; condom use

Avoid contact; condom use

Treatment

Many strains resistant to various antibiotics; local and current guidelines must be consulted

Azithromycin, doxycycline, and follow-up to check for reinfection

Distinctive Features

Rare complications include arthritis, meningitis, endocarditis

More commonly asymptomatic than gonorrhea

Effects on Fetus

Eye infections, blindness

Eye infections, pneumonia

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Syphilis The origin of syphilis1 is an obscure yet intriguing topic of speculation. The disease was first recognized at the close of the 15th century in Europe, a period coinciding with the return of Columbus from the West Indies. From this, some medical scholars have concluded that syphilis was introduced to Europe from the New World. However, a more probable explanation contends that the spirochete that causes the disease evolved from a related subspecies, perhaps an endemic bacterium already present in the Mediterranean basin. The combination of the immunologically naive population of Europe, the European wars, and sexual promiscuity set the stage for worldwide transmission of syphilis that continues to this day. A disturbing chapter of syphilis history in the United States is worth noting here. Beginning in 1932, the U.S. government conducted a study called the Tuskegee Study of Untreated Syphilis in the Negro Male, which eventually involved 399 indigent African-American men living in the South. Infected men were recruited into the study, which sought to document the natural progression of the disease. These men were never told that they had syphilis and were never treated for it, even after penicillin was shown to be an effective cure. The study ended in 1972 after it became public. In 1997, President Bill Clinton issued a public apology on behalf of the U.S. government, and the government has paid millions of dollars in compensation to the victims and their heirs. ▶

▶

Secondary Syphilis

About 3 weeks to 6 months after the chancre heals, the secondary stage appears. By then, many systems of the body have been invaded and the signs and symptoms are more profuse and intense. Initial symptoms are fever, headache, and sore throat, followed by lymphadenopathy and a peculiar red or brown rash that breaks out on all skin surfaces, including the palms of the hands and the soles of the feet (figure 23.13). A person’s hair often falls out. Like the

Signs and Symptoms

Untreated syphilis is marked by distinct clinical stages designated as primary, secondary, and tertiary syphilis. The disease also has latent periods of varying duration during which it is quiescent. The spirochete appears in the lesions and blood during the primary and secondary stages and, thus, is transmissible at these times. During the early latency period between secondary and tertiary syphilis, it is also transmissible. Syphilis is largely nontransmissible during the “late latent” and tertiary stages. Symptoms of each of these stages and congenital syphilis are briefly described here. ▶

enlarged and firm, but systemic symptoms are absent at this point. The chancre heals spontaneously without scarring in 3 to 6 weeks, but the healing is deceptive because the spirochete has escaped into the circulation and is entering a period of tremendous activity.

(a)

Primary Syphilis

The earliest indication of syphilis infection is the appearance of a hard chancre (shang’-ker) at the site of entry of the pathogen (see Disease Table 23.7 for photos of all three types of genital lesions). A chancre appears after an incubation period that varies from 9 days to 3 months. The chancre begins as a small, red, hard bump that enlarges and breaks down, leaving a shallow crater with firm margins. The base of the chancre beneath the encrusted surface swarms with spirochetes. Most chancres appear on the internal and external genitalia, but about 20% occur on the lips, oral cavity, nipples, fingers, or around the anus. Because these ulcers tend to be painless, they may escape notice, especially when they are on internal surfaces. Lymph nodes draining the affected region become 1. The term syphilis first appeared in a poem entitled “Syphilis sive Morbus Gallicus” by Fracastorius (1530), about a mythical shepherd whose name eventually became synonymous with the disease from which he suffered.

(b)

Figure 23.13 Symptom of secondary syphilis. The skin rash in secondary syphilis can form on the trunk, arms, and even palms and soles (this latter location is particularly diagnostic). The rash does not hurt or itch and can persist for months.

23.4

chancre, the lesions contain viable spirochetes and disappear spontaneously in a few weeks. The major complications of this stage, occurring in the bones, hair follicles, joints, liver, eyes, and brain, can linger for months and years. ▶

Latency and Tertiary Syphilis

After resolution of secondary syphilis, about 30% of infections enter a highly varied latent period that can last for 20 years or longer. During latency, although antibodies to the bacterium are readily detected, the bacterium itself is not. The final stage of the disease, tertiary syphilis, is relatively rare today because of widespread use of antibiotics. But it is so damaging that it is important to recognize. By the time a patient reaches this phase, numerous pathologic complications occur in susceptible tissues and organs. Cardiovascular syphilis results from damage to the small arteries in the aortic wall. As the fibers in the wall weaken, the aorta is subject to distension and fatal rupture. The same pathologic process can damage the aortic valves, resulting in insufficiency and heart failure. In one form of tertiary syphilis, painful swollen syphilitic tumors called gummas (goo-mahz′) develop in tissues such as the liver, skin, bone, and cartilage (figure 23.14). Gummas are usually benign and only occasionally lead to death, but they can impair function. Neurosyphilis can involve any part of the nervous system, but it shows particular affinity for the blood vessels in the brain, cranial nerves, and dorsal roots of the spinal cord. The diverse results include severe headaches, convulsions, atrophy of the optic nerve, blindness, dementia, and a sign called the Argyll-Robertson pupil—a condition caused by adhesions along the inner edge of the iris that fix the pupil’s position into a small irregular circle. ▶

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the fetal tissues. An infection leading to congenital syphilis can occur in any of the three trimesters, but it is most common in the second and third. The pathogen inhibits fetal growth and disrupts critical periods of development with varied consequences, ranging from mild to the extremes of spontaneous miscarriage or stillbirth. Early congenital syphilis encompasses the period from birth to 2 years of age and is usually first detected 3 to 8 weeks after birth. Infants often demonstrate such signs as profuse nasal discharge (figure 23.15a), skin eruptions, bone deformation, and nervous system abnormalities. The late form gives rise to an unusual assortment of problems in the bones, eyes, inner ear, and joints and causes the formation of Hutchinson’s teeth (figure  23.15b). The number of congenital syphilis cases is closely tied to the incidence in adults. ▶

Causative Agent

Treponema pallidum, a spirochete, is a thin, regularly coiled cell with a gram-negative cell wall. It is a strict parasite with complex growth requirements that necessitate cultivating it in living host cells. Most spirochete bacteria are nonpathogenic; Treponema and Leptospira, described earlier, are among the pathogens of this group. Syphilis is a complicated disease to diagnose. Not only do the stages each mimic other diseases, but their appearance can

Congenital Syphilis

The syphilis bacterium can pass from a pregnant woman’s circulation into the placenta and can be carried throughout

(a)

(b)

Figure 23.14 The pathology of late, or tertiary,

syphilis. An ulcerating syphilis tumor, or gumma, appears on the nose of this patient. Other gummas can be internal.

Figure 23.15 Congenital syphilis. (a) An early sign is snuffles, a profuse nasal discharge that obstructs breathing. (b) A common characteristic of late congenital syphilis is notched, barrel-shaped incisors (Hutchinson’s teeth).

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also be so separated in time as to seem unrelated. The chancre and secondary lesions must be differentiated from bacterial, fungal, and parasitic infections; tumors; and even allergic reactions. Overlapping symptoms of sexually transmitted infections that the patient is concurrently experiencing, such as gonorrhea or Chlamydia, can further complicate diagnosis. The disease can be diagnosed using two different strategies: either by detecting the bacterium in patient lesions or by looking for antibodies in the patient’s blood. ▶

Pathogenesis and Virulence Factors

Brought into direct contact with mucous membranes or abraded skin, T. pallidum binds avidly by its hooked tip to the epithelium (figure 23.16). At the binding site, the spirochete multiplies and penetrates the capillaries nearby. Within a short time, it moves into the circulation, and the body is literally transformed into a large receptacle for incubating the pathogen. Virtually any tissue is a potential target. The specific factor that accounts for the virulence of the syphilis spirochete appears to be outer membrane lipoproteins. These molecules appear to stimulate a strong inflammatory response, which is helpful in clearing the organism but can produce damage as well. T. pallidum produces no toxins and does not appear to kill cells directly. Studies have shown that, although phagocytes seem to act against it and several types of antitreponemal antibodies are formed, immune responses are unable to contain it. The primary lesion occurs when the spirochetes invade the spaces around arteries and stimulate an inflammatory response. Organs are damaged when granulomas form at these sites and block circulation. ▶

Transmission and Epidemiology

oxygen tension, and pH changes. It survives a few minutes to hours when protected by body secretions and about 36 hours in stored blood. Research with human subjects has demonstrated that the risk of infection from an infected sexual partner is 12% to 30% per encounter. The bacterium can also be transmitted to the fetus in utero. Syphilis infection through blood transfusion or exposure to fomites is rare. For centuries, syphilis was a common and devastating disease in the United States, so much so that major medical centers had “Departments of Syphilology.” Its effect on social life was enormous. This effect diminished quickly when antibiotics were discovered. In the 20th and 21st centuries, syphilis, like other STDs, has experienced periodic increases during times of social disruption. Most cases tend to be concentrated in larger metropolitan areas among prostitutes, their contacts, and crack cocaine users. If you examine figure 23.11, you won’t see much change in syphilis incidence. But since 2003, the rates have been increasing again in the United States. And syphilis continues to be a serious problem worldwide, especially in Africa and Asia. As mentioned previously, persons with syphilis often suffer concurrent infections with other STDs. Coinfection with the AIDS virus can be an especially deadly combination with a rapidly fatal course. ▶

Culture and Diagnosis

Syphilis can be detected in patients most rapidly by using dark-field microscopy of a suspected lesion. The lesions are gently squeezed or scraped to extract clear fluid. A wet mount is then observed for the characteristic size, shape, and motility of T. pallidum (figure 23.17). A single negative test is Spirochete

Red blood cell

Tissue cells

Humans are evidently the sole natural hosts and source of T.  pallidum. The bacterium is extremely fastidious and sensitive and cannot survive for long outside the host, being rapidly destroyed by heat, drying, disinfectants, soap, high Tip of spirochete

Host cell

Figure 23.16 Electron micrograph of the syphilis

spirochete attached to cells.

Figure 23.17 Treponema pallidum from a syphilitic chancre, viewed with dark-field illumination.

are highlighted next to human cells and tissue debris.

Its tight spirals

23.4

not enough to exclude syphilis because the patient may have removed the organisms by washing, so follow-up tests are recommended. Another microscopic test for discerning the spirochete directly in samples is direct immunofluorescence staining with monoclonal antibodies. Very commonly, blood tests are used for this diagnosis. These tests are based on detection of antibody formed in response to T. pallidum infection. Two kinds of antibodies are formed: those that specifically react with treponemal antigens and, perhaps surprisingly, those that are formed against nontreponemal antigens. After infection with T. pallidum, the body abnormally produces antibodies to a natural constituent of human cells called cardiolipin, and the presence of these cardiolipin antibodies is also indicative of T. pallidum infection. Several different tests detect these antibodies, such as rapid plasma reagin (RPR), VDRL, Kolmer, and the Wasserman test. More specific tests are available when considered necessary. One of these is the indirect immunofluorescent method called the FTA-ABS (fluorescent treponemal antibody absorbance) test. The test serum is first allowed to react with treponemal cells and then reacted with antihuman globulin antibody labeled with fluorescent dyes. If antibodies to the treponeme are present, the fluorescently labeled antibody will bind to the human antibody bound to the treponemal cells. The result is highly visible with a fluorescence microscope. A PCR test is available for syphilis, but its accuracy is dependent on the type of tissue being tested. ▶

Prevention

The core of an effective prevention program depends on detection and treatment of the sexual contacts of syphilitic patients. Public health departments and physicians are charged with the task of questioning patients and tracing their contacts. All individuals identified as being at risk, even if they show no signs of infection, are given immediate prophylactic penicillin in a single long-acting dose. The barrier effect of a condom provides excellent protection during the primary phase. Protective immunity apparently does arise in humans, allowing the prospect of an effective immunization program in the future, although no vaccine exists currently. ▶

Treatment

Throughout most of history, the treatment for syphilis was a dose of mercury or even a “mercurial rub” applied to external lesions. In 1906, Paul Ehrlich discovered that a derivative of arsenic called salvarsan could be very effective. The fact that toxic compounds like mercury and arsenic were used to treat syphilis gives some indication of how dreaded the disease was and to what lengths people would go to rid themselves of it. In 1918, Paul A. O’Leary formalized the practice of infecting syphilis patients with malaria as a therapeutic approach. The patients were allowed to have a dozen or so episodes of high fever and then were cured of the malaria with quinine. This procedure proved to be effective in curing syphilis. (“Malaria therapy” has also been

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investigated in recent years as an alternative treatment for HIV infection.) Once penicillin became available, it replaced all other treatments, and penicillin G retains its status as a wonder drug in the treatment of all stages and forms of syphilis. It is given parenterally in large doses with benzathine or procaine. The goal is to maintain a blood level lethal to the spirochete for at least 7 days. Alternative drugs (tetracycline and erythromycin) are less effective, and they are indicated only if penicillin allergy has been documented. It is important that patients be monitored for successful clearance of the spirochete.

Chancroid This ulcerative disease usually begins as a soft papule, or bump, at the point of contact. It develops into a “soft chancre” (in contrast to the hard syphilis chancre), which is very painful in men, but may be unnoticed in women (see Disease Table 23.7). Inguinal lymph nodes can become very swollen and tender. Chancroid is caused by a pleomorphic gram-negative rod called Haemophilus ducreyi. Recent research indicates that a hemolysin (exotoxin) is important in the pathogenesis of chancroid disease. It is very common in the tropics and subtropics and is becoming more common in the United States. Chancroid is transmitted exclusively through direct contact, especially sexually. This disease is associated with prostitutes and poor hygiene; uncircumcised men seem to be more commonly infected than those who have been circumcised. People may carry this bacterium asymptomatically. No vaccine exists. Prevention of chancroid is the same as for other sexually transmitted diseases: Avoid contact with infected tissues, either by abstaining from sexual contact or by proper use of barrier protection. Antibiotics such as azithromycin and ceftriaxone are effective, but patients should be reexamined after a course of treatment to ensure that the bacterium has been eliminated.

Genital Herpes Virtually everyone becomes infected with a herpesvirus at some time, because this large family of viruses can infect a wide range of host tissues. (We studied three herpesviruses in chapter 21 alone.) Genital herpes is caused by herpes simplex viruses (HSVs). Two types of HSV have been identified, HSV-1 and HSV-2. Other members of the herpes family are herpes zoster (causing chickenpox and shingles), cytomegalovirus (associated with congenital disease and also with HIV-associated disease), Epstein-Barr virus (causing infection of the lymphoid tissue as in infectious mononucleosis), and more recently identified viruses (herpesvirus-6, -7, and -8). Genital herpes is much more common than most people think. ▶

Signs and Symptoms

Genital herpes infection has multiple presentations. After initial infection, a person may notice no symptoms.

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Alternatively, herpes could cause the appearance of single or multiple vesicles on the genitalia, perineum, thigh, and buttocks. The vesicles are small and are filled with a clear fluid (see Disease  Table  23.7). They are intensely painful to the touch. The appearance of lesions the first time you get them can be accompanied by malaise, anorexia, fever, and bilateral swelling and tenderness in the groin. Occasionally central nervous system symptoms such as meningitis or encephalitis can develop. Thus, we see that initial infection can either be completely asymptomatic or be serious enough to require hospitalization. After recovery from initial infection, a person may have recurrent episodes of lesions. They are generally less severe than the original symptoms, although the whole gamut of possible severity is seen here as well. Some people never have recurrent lesions. Others have nearly constant outbreaks with little recovery time between them. On average, the number of recurrences is four or five a year. Their frequency tends to decrease over the course of years. In most cases, patients remain asymptomatic or experience recurrent “surface” infections indefinitely. Very rarely, complications can occur. Every year, one or two persons per million with chronic herpes infections develop encephalitis. The virus disseminates along nerve pathways to the brain (although it can also infect the spinal cord). The effects on the central nervous system begin with headache and stiff neck and can progress to mental disturbances and coma. The fatality rate in untreated encephalitis cases is 70%, although treatment with acyclovir is effective. Patients with underlying immunodeficiency are more prone to severe, disseminated herpes infection than are immunocompetent patients. Of greatest concern are patients receiving organ grafts, cancer patients on immunosuppressive therapy, those with congenital immunodeficiencies, and AIDS patients. Recent data suggest that people with HSV-1 are more prone to Alzheimer’s disease, particularly if they carry a particular variant of a particular gene. This is quite sobering when you think that approximately 80% of elderly people are HSV-1-positive, and up to 30% of them carry the gene variant. However, there is hope: Anti-herpes drugs may make a difference in Alzheimer’s in these people. ▶

Figure 23.18 Neonatal herpes simplex. This premature infant was born with the classic “cigarette burn” pattern of HSV infection. Babies can be born with the lesions or develop them 1 to 2 weeks after birth. nant women for the herpesvirus early in their prenatal care. (Don’t forget that most women who are infected do not even know it.) Pregnant women with a history of recurrent infections must be constantly monitored for any signs of viral shedding, especially in the last 4 weeks of pregnancy. If no evidence of recurrence is seen, vaginal birth is indicated, but any evidence of an outbreak at the time of delivery necessitates a cesarean section. ▶

Causative Agent

Both HSV-1 and HSV-2 can cause genital herpes if the virus contacts the genital epithelium, although HSV-1 is thought of as a virus that infects the oral mucosa, resulting in “cold sores” or “fever blisters” (figure 23.19), and HSV-2 is thought of as the genital virus. In reality, either virus can infect either region, depending on the type of contact. HSV-1 and HSV-2 are DNA viruses with icosahedral capsids and envelopes containing glycoprotein spikes. Like other enveloped viruses, herpesviruses are prone to deactivation by organic solvents or detergents and are unstable outside the host’s body.

Herpes of the Newborn

Although HSV infections in healthy adults are annoying and unpleasant, only rarely are they life-threatening. However, in the neonate and the fetus (figure 23.18), HSV infections are very destructive and can be fatal. Most cases occur when infants are contaminated by the mother’s reproductive tract immediately before or during birth, but they have also been traced to hand transmission from the mother’s lesions to the baby. Because HSV-2 is more often associated with genital infections, it is more frequently involved; however, HSV-1 infection has similar complications. In infants whose disease is confined to the mouth, skin, or eyes, the mortality rate is 30%, but disease affecting the central nervous system has a 50% to 80% mortality rate. Because of the danger of herpes to fetuses and newborns and also because of the increase in the number of cases of genital herpes, it is now standard procedure to screen preg-

Figure 23.19 Oral herpes infection. Tender itchy papules erupt around the mouth and progress to vesicles that burst, drain, and scab over. These sores and fluid are highly infectious and should not be touched.

23.4

▶

Pathogenesis and Virulence Factors

Herpesviruses have a tendency to become latent. The molecular basis of latency is not entirely clear. During latency, some type of signal causes most of the HSV genome not to be transcribed. This allows the virus to be maintained within cells of the nervous system between episodes. Recent research has found that microRNAs are responsible for the latency of HSV-1. It is further suggested that in some peripheral cells, viral replication takes place at a constant, slow rate, resulting in constant low-level shedding of the virus without lesion production. HSV-2 (or HSV-1, if it has infected the genital region) usually becomes latent in the ganglion of the lumbosacral spinal nerve trunk (figure 23.20). Reactivation of the virus can be triggered by a variety of stimuli, including stress, UV radiation (sunlight), injury, menstruation, or another microbial infection. At that point, the virus begins manufacturing large numbers of entire virions, which cause new lesions on the surface of the body served by the neuron, usually in the same site as previous lesions. HSV-1 (or HSV-2 if it is in the oral region) behaves in a similar way, but it becomes latent in the trigeminal nerve, which has extensive innervations in the oral region. ▶

Transmission and Epidemiology

Herpes simplex infection occurs globally in all seasons and among all age groups. Because these viruses are relatively sensitive to the environment, transmission is primarily through direct exposure to secretions containing the virus. People with active lesions are the most significant source of infection, but studies indicate that genital herpes can be transmitted even when no lesions are present (due to the constant shedding just referred to). As with all sexually transmitted diseases, many different figures are cited as to its prevalence in society. As you saw in the Note About STD Statistics in this chapter, the terminology

Reproductive Tract Diseases Caused by Microorganisms

729

associated with STDs can be confusing. Earlier in this chapter, you read that Chlamydia infection is the most common reported infectious disease in the United States. Elsewhere you might hear that gonorrhea is one of the most common reportable STDs in the United States. Both statements are true. It is also true that genital herpes is much more common than either of these diseases. Herpes, however, is not an officially reportable disease. It is estimated that about 20% of American adults have genital herpes. That estimate would put the number of infected people in this country at more than 42 million. Two-thirds of people who are infected don’t even know it, either because they have rare symptoms that they fail to recognize or because they have no symptoms at all. ▶

Culture and Diagnosis

These two viruses are sometimes diagnosed based on the characteristic lesions alone. PCR tests are available to test for these viruses directly from lesions. Alternatively, antibody to either of the viruses can be detected from blood samples. Detecting antibody to either HSV-1 or HSV-2 in blood does not necessarily indicate whether the infection is oral or genital or whether the infection is new or preexisting. Herpes-infected mucosal cells display notable characteristics in a Pap smear (figure 23.21). Laboratory culture and specific tests are essential for diagnosing severe or complicated herpes infections. They are also used when screening pregnant women for the presence of virus on the vaginal mucosa. A specimen of tissue or fluid is inoculated into a primary cell culture line and is then observed for cytopathic effects, which are characteristic for specific viruses. ▶

Prevention

No vaccine is currently licensed for HSV, but more than one is being tested in clinical trials, meaning that vaccines may Giant cell with multiple nuclei

Sacral ganglia

Normal cells

Sacral ganglion

Skin Inclusion

Lesions caused by HSV

Figure 23.20 HSV latent in lumbosacral ganglion. The ganglion is the nerve root near the base of the spine. When the virus is reactivated, it travels down the neuron to the body’s surface.

Figure 23.21 The appearance of herpesvirus infection in a Pap smear. A Pap smear of a cervical scraping shows enlarged (multinucleate giant) cells and intranuclear inclusions typical of herpes simplex, type 2. This appearance is not specific for HSV, but most other herpesviruses do not infect the reproductive mucosa.

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Chapter 23 Infectious Diseases Affecting the Genitourinary System

1

3

2

4

Figure 23.22 The female condom. The condom has a closed ring that fits over the cervix and an open ring that rests on the external genitalia.

Disease Table 23.7 Genital Ulcer Diseases

Syphilis

Chancroid

Herpes

Causative Organism(s)

Treponema pallidum

Haemophilus ducreyi

Herpes simplex 1 and 2

Most Common Modes of Transmission

Direct contact and vertical

Direct contact (vertical transmission not documented)

Direct contact, vertical

Virulence Factors

Lipoproteins

Hemolysin (exotoxin)

Latency

Culture/Diagnosis

Direct tests (immunofluorescence, dark-field microscopy), blood tests for treponemal and nontreponemal antibodies, PCR

Culture from lesion

Clinical presentation, PCR, Ab tests, growth of virus in cell culture

Prevention

Antibiotic treatment of all possible contacts, avoiding contact

Avoiding contact

Avoiding contact, antivirals can reduce recurrences

Treatment

Penicillin G

Azithromycin, ceftriaxone, ciprofloxacin

Acyclovir and derivatives

Distinctive Features

Three stages of disease plus latent period, possibly fatal

No systemic effects

Ranges from asymptomatic to frequent recurrences

Effects on Fetus

Congenital syphilis

None

Blindness, disseminated herpes infection

Appearance of Lesions

Vesicles

23.4

Reproductive Tract Diseases Caused by Microorganisms

731

become available very soon. In the meantime, avoiding contact with infected body surfaces is the only way to avoid HSV. Condoms provide good protection when they actually cover the site where the lesion is, but lesions can occur outside of the area covered by a condom. Women with herpes are sometimes counseled to use the female condom (figure 23.22) because these cover a substantial portion of the female external genitalia. In general, people experiencing active lesions should avoid sex. Because the virus can be shed when no lesions are present, barrier protection should be practiced at all times by persons infected with HSV. Mothers with cold sores should be careful in handling their newborns; they should never kiss their infants on the mouth. Hospital attendants with active oral herpes infection should be barred from the newborn nursery. Some of the drugs used to “treat” genital herpes really function to prevent recurrences of lesions. In this way, they serve as prevention for potential partners of people with herpes.

cal formulations can be applied directly to lesions, and pills are available as well. Sometimes medicines are prescribed on an ongoing basis to decrease the frequency of recurrences, and sometimes they are prescribed to be taken at the beginning of a recurrence to shorten it (Disease Table 23.7).

▶

▶

Treatment

Several agents are available for treatment. These agents often result in reduced viral shedding and a decrease in the frequency of lesion occurrence. They are not curative. Acyclovir and its derivatives (Zovirax, Valtrex) are very effective. Topi-

Wart Diseases In this section, we describe two viral STDs that cause wartlike growths. The more serious disease is caused by the human papillomavirus (HPV); the other condition, called molluscum contagiosum, apparently has no serious effects outside of the growths themselves.

Human Papillomaviruses These viruses are the causative agents of genital warts. But an individual can be infected with these viruses without having any warts, while still risking serious consequences.

Signs and Symptoms

Symptoms, if present, may manifest as warts—outgrowths of tissue on the genitals (Disease Table 23.8). In females, these growths can occur on the vulva and in and around the vagina. In males, the warts can occur in or on the penis and

Disease Table 23.8 Wart Diseases

HPV

Molluscum Contagiosum

Causative Organism(s)

Human papillomaviruses

Poxvirus, sometimes called the molluscum contagiosum virus (MCV)

Most Common Modes of Transmission

Direct contact (STD)—also autoinoculation, indirect contact

Direct contact (STD), also indirect and autoinoculation

Virulence Factors

Oncogenes (in the case of malignant types of HPV)

–

Culture/Diagnosis

PCR tests for certain HPV types, clinical diagnosis

Clinical diagnosis, also histology, PCR

Prevention

Vaccine available; avoid direct contact; prevent cancer by screening cervix

Avoid direct contact

Treatment

Warts or precancerous tissue can be removed; virus not treatable

Warts can be removed; virus not treatable

Distinguishing Features

Infection may or may not result in warts; infection may result in malignancy

Wartlike growths are only known consequence of infection

Effects on Fetus

May cause laryngeal warts

–

Appearance of Lesions

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Chapter 23 Infectious Diseases Affecting the Genitourinary System

the scrotum. In both sexes, the warts can appear in or on the anus and even on the skin around the groin, such as the area between the thigh and the pelvis. The warts themselves range from tiny, flat, inconspicuous bumps to extensively branching, cauliflower-like masses called condyloma acuminata. The warts are unsightly and can be obstructive, but they don’t generally lead to more serious symptoms. Other types of HPV can lead to more subtle symptoms. Certain types of the virus infect cells on the female cervix. This infection may be “silent,” or it may lead to abnormal cell changes in the cervix. Some of these cell changes can eventually result in malignancies of the cervix. The vast majority of cervical cancers are caused by HPV infection. (It is possible that chronic infections with other microorganisms cause a very small percentage of cervical malignancies.) Approximately 4,000 women die each year in the United States from cervical cancer. Also, data released in 2007 indicate a link between having had more than five oral sex partners and a greatly increased risk of throat cancer, presumably due to HPV. Males can also get cancer from infection with these viruses. The sites most often affected are the penis and the anus. These cases are much less common than cervical cancer. ▶

Causative Agent

The human papillomaviruses are a group of nonenveloped DNA viruses belonging to the Papovaviridae family. There are more than 100 different types of HPV. Some types are specific for the mucous membranes; others invade the skin. Some of these viruses are the cause of plantar warts, which often occur on the soles of the feet. Other HPVs cause the common or “seed” warts and flat warts. In this chapter, we are concerned only with the HPVs that colonize the genital tract. Among the HPVs that infect the genital tract, some are more likely to cause the appearance of warts. Others that have a preference for growing on the cervix can lead to cancerous changes. Five types in particular, HPV-16, -18, -31, -33, and -35, are closely associated with development of cervical cancer. ▶

Pathogenesis and Virulence Factors

Scientists are working hard to understand how viruses cause the growths we know as warts and also how some of them can cause cancer. The major virulence factors for cancercausing HPVs are oncogenes, which code for proteins that interfere with normal host cell function, resulting in uncontrolled growth. ▶

Transmission and Epidemiology

Young women have the highest rate of HPV infections; 25–46% of women under the age of 25 are infected with genital HPV. It is estimated that 14% of female college students become infected with this incurable condition each year. Overall, about 15% of people between 15 and 49 are HPV-

positive. It is difficult to know whether genital herpes or HPV is more common, but it is probably safe to assume that any unprotected sex carries a good chance of encountering either HSV or HPV. The mode of transmission is direct contact. Autoinoculation is also possible—meaning that the virus can be spread to other parts of the body by touching warts. Indirect transmission occurs but is more common for nongenital warts caused by HPV. ▶

Culture and Diagnosis

PCR-based screening tests can be used to test samples from a pelvic exam for the presence of dangerous HPV types. These tests are now recommended for women over the age of 30. ▶

Prevention

When discussing HPV prevention, we must consider two possibilities. One of these is infection with the viruses, which is prevented the same way other sexually transmitted infections are prevented—by avoiding direct, unprotected contact, but also by a vaccine approved in 2006 called Gardasil. The vaccine prevents infection by four types of HPV and is recommended in girls as young as age 9. Despite the fears of some parents, being vaccinated against the virus does not encourage girls to become sexually active, but instead causes them to realize the dangers of sex, according to a study conducted in 2009 among 553 teenage girls in Britain. The second issue is the prevention of cervical cancer. Even though women now have access to the vaccine, cancer can still result from HPV types not included in the vaccine. The good news is that cervical cancer is slow in developing, so that even if a woman is infected with a malignant HPV type, regular screening of the cervix can detect abnormal changes early. The standardized screen for cervical cell changes is the Pap smear (Insight 23.2). Precancerous changes show up very early, and the development process can be stopped by removal of the affected tissue. Women should have their first Pap smear by age 21 or within 3 years of their first sexual activity, whichever comes first. New Pap smear technologies have been developed; and depending on which one your physician uses, it is now possible that you need to be screened only once every 2 or 3 years. But you should base your screening practices on the sound advice of a physician. ▶

Treatment

Infection with any HPV is incurable. Genital warts can be removed through a variety of methods, some of which can be used at home. But the virus causing them will most likely remain with you. It is possible for the viral infection to resolve itself, but this is very unpredictable. Treatment of cancerous cell changes is an important part of HPV therapy, and it can only be instituted if the changes are detected through Pap smears. Again, the results of the infection are treated (cancerous cells removed), but the viral infection is not amenable to treatment.

23.4

INSIGHT 23.2

Reproductive Tract Diseases Caused by Microorganisms

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The Pap Smear

In the early part of the 20th century, a Greek-born physician named George Papanicolaou, who taught at Cornell University and collaborated with hospital physicians there, became interested in the cytological changes that take place in precancerous and cancerous tissue of the female reproductive tract. He developed a technique for evaluating “vaginal smears” for precancerous changes and in 1943 published a paper that would change women’s lives forever. The title was ”Diagnosis of Uterine Cancer by the Vaginal Smear.” The test came to be known as the Pap smear. The Pap smear is still the single best screening procedure available for cervical cancer, a disease that claims the lives of over 4,000 women every year in the United States. This incidence has decreased 74% since 1955, almost entirely due to the increased use of the Pap smear. The procedure is simple and painless: During a pelvic exam, a sample of cells is taken from the cervix using a wooden spatula or a small cervical brush. Then the sample is “smeared” onto a glass microscope slide and preserved with a fixative. In a newer method, the brush or spatula is rinsed with preservative fluid, the fluid is saved, and later it is automatically applied in a thin layer to a microscope slide. Whether the slide was made as a “smear” or as a “thin prep,” it is then viewed microscopically by a technician or, in newer methods, by a computer so that abnormal cells can be detected. A variety of “abnormal” results can be found and reported to the patient after a Pap smear. Here are some words that may appear on the Pap report: • Dysplasia—abnormal cells found, not cancer but with a slight potential for developing into very early cancer of the cervix, depending on the degree of dysplasia (mild, moderate, severe, or the most severe form called carcinoma in situ). • Squamous intraepithelial lesion (SIL)—a term that refers to the type of cells (squamous) that form the outer surface of the cervix. The “intraepithelial” designation refers to the observation that abnormal cells are only present on the surface of the cervix and not in the deeper tissue. • Cervical intraepithelial neoplasia (CIN)—another term referring to abnormal cells. “Neoplasia” means an abnor-

Molluscum Contagiosum An unclassified virus in the pox family can cause a condition called molluscum contagiosum. This disease can take the form of skin lesions, and it can also be transmitted sexually. The wartlike growths that result from this infection can be found on the mucous membranes or the skin of the genital area (see Disease Table 23.8). Few problems are associated with these growths beyond the warts themselves. In severely immunocompromised people, the disease can be more serious.

Normal cells are the small ones with small nuclei. The ones grouped together with large nuclei in them are abnormal.

mal growth of cells. There will often be a number after the CIN (that is, CIN-1 or CIN-3). The photo in this insight represents a smear diagnosed to be CIN-2. The number corresponds with how far the abnormal cells extend into the cervix. • Atypical squamous cells—cells appear abnormal, but the nature and degree of abnormality are unclear. Cervical cancer is nearly always caused by infection with human papillomavirus, as detailed in the section on HPV in this chapter. Because some types of HPV are shown to be more strongly associated with cervical cancer, a physician may perform a PCR test on cervical material to look for the presence of these HPV types. A negative HPV test can provide reassurance that the abnormalities detected on a Pap smear do not point to a cancerous or precancerous condition. Nearly all cervical cancer can be prevented if women get Pap smears on the recommended schedule. Thanks to the relatively simple Pap smear, countless women have avoided not only early deaths from cancer but also hysterectomies, which later stages of cervical cancer require.

The virus causing these growths can also be transmitted through fomites such as clothing or towels and through autoinoculation. For a more detailed description of this condition, see chapter 18 (Disease Table 23.8).

Group B Streptococcus “Colonization”— Neonatal Disease Ten to forty percent of women in the United States are colonized, asymptomatically, by a beta-hemolytic Streptococcus

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Chapter 23 Infectious Diseases Affecting the Genitourinary System

Case File 23

Wrap-Up

Once the professor had been definitively diagnosed with leptospirosis, health officials issued an Internet survey on campus to try to determine if any of the hundreds of students and staff who had helped with flood cleanup had been affected. In the end, they diagnosed only one other case, although 90 people did report experiencing a febrile illness within 30 days of the flood. One problem with leptospirosis is that the early signs are no different from those of other flulike illnesses, so affected people do not necessarily present to the health care system. Certain occupations predispose people to this disease, namely ones that put people in touch with animal urine. This includes veterinarians, meat packers, and farmers. IgM is considered a more useful diagnostic tool than IgG since if it is elevated, it indicates a recent infection. In this case, 48 of the 90 suspected cases were eventually tested, but other than the one additional case, no other ELISA test results were positive.

In 2002, the CDC recommended that all pregnant women be screened for group B Streptococcus colonization at 35 to 37 weeks of pregnancy. Women positive for the bacterium should be treated with penicillin or ampicillin unless the bacterium is found to be resistant to these and unless allergy to penicillin is present.

Disease Table 23.9 Group B Streptococcus Colonization

Causative Organism(s)

Group B Streptococcus

Most Common Modes of Transmission

Vertical

Virulence Factors

–

Culture/Diagnosis

Culture of mother’s genital tract

Prevention/Treatment

Treat mother with penicillin/ ampicillin

See: 2007. Am. J. Trop. Med. Hyg. 76(5):882–85.

23.4 Learning Outcomes—Can You . . . in Lancefield group B. Nonpregnant women experience no ill effects from this colonization. But when these women become pregnant and give birth, about half of their infants become colonized by the bacterium during passage through the birth canal or by ascension of the bacteria through ruptured membranes; thus, this colonization is considered a reproductive tract disease. A small percentage of infected infants experience lifethreatening bloodstream infections, meningitis, or pneumonia. If they recover from these acute conditions, they may have permanent disabilities such as developmental disabilities, hearing loss, or impaired vision. In some cases, the mothers also experience disease, such as amniotic infection or subsequent stillbirths.

5. . . . distinguish between vaginitis and vaginosis? 6. . . . discuss prostatitis? 7. . . . list the possible causative agents, modes of transmission, virulence factors, and prevention/treatment for gonorrhea and Chlamydia infection? 8. . . . name three diseases that result in genital ulcers and discuss their important features? 9. . . . differentiate between the two diseases causing warts in the reproductive tract? 10. . . . provide some detail about the first “cancer vaccine” and how it works? 11. . . . identify the most important risk group for group B Streptococcus infection and why?

Summing Up

▶ Summing Up

Taxonomic Organization Microorganisms Causing Disease in the Genitourinary Tract Microorganism Gram-positive bacteria Staphylococcus saprophyticus Gardnerella (note: stains gram-negative) Group B Streptococcus Gram-negative bacteria Escherichia coli Leptospira interrogans (spirochete) Proteus mirabilis Neisseria gonorrhoeae Chlamydia trachomatis Treponema pallidum (spirochete) Haemophilus ducreyi DNA viruses Herpes simplex viruses 1 and 2 Human papillomaviruses Poxviruses Fungi Candida albicans Protozoa Trichomonas vaginalis Helminth—trematode Schistosoma haematobium

Disease

Chapter Location

Urinary tract infection Vaginosis Neonatal disease

UTI, p. 712 Vaginitis or vaginosis, p. 716 Group B strep neonatal disease, p. 733

Urinary tract infection Leptospirosis Urinary tract infection plus kidney stones Gonorrhea “Chlamydia” Syphilis Chancroid

UTI, p. 712 Leptospirosis, p. 713 UTI, p. 712 Discharge diseases, p. 719 Discharge diseases, p. 721 Genital ulcer diseases, p. 724 Genital ulcer diseases, p. 727

Genital herpes Genital warts, cervical carcinoma Molluscum contagiosum

Genital ulcer diseases, p. 727 Wart diseases, p. 731 Wart diseases, p. 733

Vaginitis

Vaginitis or vaginosis, p. 715

Trichomoniasis (vaginitis)

Vaginitis or vaginosis, p. 717

Urinary schistosomiasis

Urinary schistosomiasis, p. 714

735

INFECTIOUS DISEASES AFFECTING The Genitourinary System

Leptospirosis

Leptospira interrogans Urinary Tract Infections

E. coli Staphylococcus saprophyticus Proteus mirabilis Genital Ulcer Diseases

Treponema pallidum Haemophilus ducreyi Herpes simplex virus 1 or 2

Urinary Schistosomiasis

Schistosoma haematobium

Discharge Diseases

Group B Streptococcus Neonatal Disease

Neisseria gonorrhoeae Chlamydia trachomatis

Group B Streptococcus

Wart Diseases

Vaginitis/Vaginosis

Human papilloma viruses Pox viruses (Molluscum contagiosum viruses)

Candida albicans Gardnerella species Trichomonas vaginalis

Helminth Bacteria Viruses Protozoa Fungi

System Summary Figure 23.23 736

INFECTIOUS DISEASES AFFECTING The Genitourinary System

Leptospirosis

Leptospira interrogans Urinary Schistosomiasis

Schistosoma haematobium Urinary Tract Infections (Uncommon)

E. coli Staphylococcus saprophyticus Proteus mirabilis Wart Diseases

Prostatitis

Human papilloma viruses Pox viruses (Molluscum contagiosum viruses)

Various

Genital Ulcer Diseases

Treponema pallidum Haemophilus ducreyi Herpes simplex virus 1 or 2 Discharge Diseases

Neisseria gonorrhoeae Chlamydia trachomatis

Helminth Bacteria Viruses

System Summary Figure 23.23 737

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Chapter Summary 23.1 The Genitourinary Tract and Its Defenses • The reproductive tract in males and females is composed of structures and substances that allow for sexual intercourse and the creation of a new fetus; protected by normal mucosal defenses and specialized features (such as low pH of the adult female reproductive tract). • The urinary system allows the excretion of fluid and wastes from the body. It has mechanical, chemical defense mechanisms. 23.2 Normal Biota of the Genitourinary Tract • Current knowledge is that the genital and the urinary systems have normal biota only in most distal regions. Normal biota in the male reproductive and urinary systems are in the distal part of the urethra and resemble skin biota. Same is generally true for the female urinary system. The normal biota in the female reproductive tract changes over the course of her lifetime. 23.3 Urinary Tract Diseases Caused by Microorganisms • Urinary Tract Infections (UTIs): Can occur at a number of sites; the bladder (cystitis), the kidneys (pyelonephritis), and the urethra (urethritis). Most common causes are Escherichia coli, Staphylococcus saprophyticus, and Proteus mirabilis. Community-acquired UTIs are most often transmitted from GI tract to urinary system. UTIs are most common of nosocomial infections. • Leptospirosis: Zoonosis associated with wild animals that affects kidneys, liver, brain, and eyes. Causative agent is Leptospira interrogans, a spirochete. • Urinary Schistosomiasis: This form of schistosomiasis is caused by S. haematobium. Bladder is damaged by trematode eggs and the granulomatous response they induce. 23.4 Reproductive Tract Diseases Caused by Microorganisms • Vaginitis and Vaginosis • Vaginitis most commonly caused by Candida albicans. Nearly always an opportunistic infection. • Gardnerella is associated with vaginosis that has a discharge but no inflammation in the vagina. Vaginosis could lead to complications such as pelvic inflammatory disease (PID). • Trichomonas vaginalis causes mostly asymptomatic infections in females and males. Trichomonas, a flagellated protozoan, is easily transmitted through sexual contact. • Prostatitis: Inflammation of the prostate; can be acute or chronic. Not all cases established to have microbial cause, but most are. • Discharge Diseases with Major Manifestation in the Genitourinary Tract: Diseases in which there is increase in fluid discharge in the male and female reproductive tracts. • Gonorrhea can elicit urethritis in males, but many cases are asymptomatic. In females, both the urinary and genital tracts may be infected during sexual intercourse. Major complications occur when infection reaches uterus and fallopian tubes.

One disease resulting from this is salpingitis, which can lead to pelvic inflammatory disease (PID). Causative agent, Neisseria gonorrhoeae, is a gram-negative diplococcus. • Chlamydia: Genital chlamydia is most common reportable infectious disease in the United States. In males: an inflammation of the urethra (NGU). Females: cervicitis, discharge, salpingitis, and frequently PID. Certain strains of Chlamydia trachomatis can invade lymphatic tissues, resulting in condition called lymphogranuloma venereum. • Genital Ulcer Diseases • Syphilis: Caused by spirochete Treponema pallidum, a thin, regularly coiled cell with a gram-negative cell wall. Three distinct clinical stages: primary, secondary, and tertiary syphilis, with a latent period between secondary and tertiary. Spirochete appears in lesions and blood during primary and secondary stages; is transmissible at these times. Also transmissible during early latency period. Largely nontransmissible during “late latent” and tertiary stages. The syphilis bacterium can lead to congenital syphilis, inhibiting fetal growth and disrupting critical periods of development. This can lead to spontaneous miscarriage or stillbirth. • Chancroid: Caused by Haemophilus ducreyi, a pleomorphic gram-negative rod. Transmitted exclusively through direct—mainly sexual— contact. • Genital herpes is caused by herpes simplex viruses (HSVs). Two types: HSV-1 and HSV-2. May be no symptoms, or may be fluid-filled, painful vesicles on genitalia, perineum, thigh, and buttocks. In severe cases, meningitis or encephalitis can develop. Patients remain asymptomatic or experience recurrent “surface” infections indefinitely. Infections in neonate and fetus can be fatal. HSV-1 and HSV-2 are DNA viruses with icosahedral capsids and envelopes containing glycoprotein spikes. Herpesviruses can become latent, via the incorporation of viral nucleic acid into the host genome in nerve cells. • Wart Diseases • Human papillomaviruses: Causative agents of genital warts. Certain types infect cells on female cervix that eventually result in malignancies of the cervix. Males can also get cancer from these viral types. • Human papillomaviruses are a group of nonenveloped DNA viruses belonging to the Papovaviridae family. At least five types are associated with cervical cancer. • Infection with any HPV is incurable. Genital warts can be removed, but virus will remain. Treatment of cancerous cell changes is an

Multiple-Choice and True-False Questions

739

• Group B Streptococcus “Colonization”—Neonatal

important part of HPV therapy, and it can only be instituted if the changes are detected through Pap smears. Vaccine for several types of HPV is now available. • A pox family virus causes a condition called molluscum contagiosum. Can take the form of wartlike growths in the membranes of the genitalia, and it can also be transmitted sexually.

Disease: Asymptomatic colonization of women by a beta-hemolytic Streptococcus in Lancefield group B is very common. When these women give birth, about half of their infants become colonized by the bacterium during passage through the birth canal or by ascension of the bacteria through ruptured membranes; some infected infants experience life-threatening bloodstream infections, meningitis, or pneumonia.

Multiple-Choice and True-False Questions

Knowledge and Comprehension

Multiple-Choice Questions. Select the correct answer from the answers provided. 8. Genital herpes transmission can be reduced or prevented by all of the following except a. a condom. c. the contraceptive pill. b. abstinence. d. a female condom.

1. Cystitis is an infection of the a. bladder. c. kidney. b. urethra. d. vagina. 2. Nongonococcal urethritis (NGU) is caused by a. Neisseria gonorrhoeae. c. Treponema pallidum. b. Chlamydia trachomatis. d. Trichomonas vaginalis. 3. Leptospirosis is transmitted to humans by a. person to person. c. mosquitoes. b. fomites. d. contaminated soil or water. 4. Syphilis is caused by a. Treponema pallidum. b. Neisseria gonorrhoeae.

c. Trichomonas vaginalis. d. Haemophilus ducreyi.

5. Bacterial vaginosis is commonly associated with the following organism: a. Candida albicans d. all of the above b. Gardnerella e. none of the above c. Trichomonas 6. This dimorphic fungus is a common cause of vaginitis. a. Candida albicans c. Trichomonas b. Gardnerella d. all of the above 7. There are estimates that approximately _______ % of adult Americans have genital herpes. a. 2 c. 20 b. 10 d. 50

Critical Thinking Questions

9. This protozoan can be treated with the drug Flagyl. a. Neisseria gonorrhoeae c. Treponema pallidum b. Chlamydia trachomatis d. Trichomonas vaginalis 10. Which group has the highest rate of HPV infection? a. female college students b. male college students c. college professors of either gender d. baby-boomers True-False Questions. If the statement is true, leave as is. If it is false, correct it by rewriting the sentence. 11. Genital herpes can be treated with acyclovir. 12. Chancroid is caused by a fungus. 13. The majority of cervical cancers are caused by human papillomavirus. 14. Chlamydia infection is the most common STD in the United States. 15. Group B Streptococcus infection is generally silent in adult females.

Application and Analysis

These questions are suggested as a writing-to-learn experience. For each question, compose a one- or two-paragraph answer that includes the factual information needed to completely address the question. 1. Describe the symptoms of Weil’s syndrome. 2. Describe the common treatments for gonorrhea. 3. a. What is PID? b. What are the two most common microorganisms associated with this disease? c. Describe the long-term consequences of untreated PID. 4. Describe the life cycle of Chlamydia. 5. What are some of the stimuli that can trigger reactivation of a latent herpesvirus infection? Speculate on why. 6. What are the clinical stages of syphilis?

7. In the photo in Insight 23.2, the abnormal cells have extraordinarily large nuclei. Speculate on why this is the case. 8. Why do you suppose a urine screening test for Chlamydia is more accurate for males than for females? 9. It has been stated that the actual number of people in the United States who have genital herpes may be a lot higher than official statistics depict. What are some possible reasons for this discrepancy? 10. Why are urinary tract infections such common nosocomial infections?

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Chapter 23 Infectious Diseases Affecting the Genitourinary System

Concept Mapping

Application and Analysis

Appendix D provides guidance for working with concept maps. 1. Construct your own concept map using the following words as the concepts. Supply the linking words between each pair of concepts. genital warts

curable

discharge

ulcers

herpes

warts

chancroid

syphilis

bacterium

incurable

molluscum contagiosum

cancer

virus

Visual Connections

Synthesis

These questions use visual images or previous content to make connections to this chapter’s concepts. 1. a. From chapters 20 and 23, figures 20.15 and 23.13a. Compare these two rashes. What kind of information would help you determine the diagnosis in both cases?

b. Now compare both of these to the rashes summarized in Disease Table 18.7 (p. 533). Which of the diseases in Disease Table 18.7 most resembles the rashes in the preceding question, and how would you distinguish among the three?

www.connect.microbiology.com Enhance your study of this chapter with study tools and practice tests. Also ask your instructor about the resources available through ConnectPlus, including the media-rich eBook, interactive learning tools, and animations.

Environmental Microbiology 24 Case File On March 24, 1989, the oil tanker Exxon Valdez ran aground on Bligh Reef in Prince William Sound, Alaska. Almost 41 million liters of crude oil spilled into the beautiful, pristine wilderness of the Sound. At this time (before the 2010 spill in the Gulf of Mexico), this was the largest oil spill in U.S. history. Americans watched in horror as about 2,000 kilometers of some of the most spectacular shores in the country were reduced to oil-covered graves for indigenous flora and fauna. As anyone who has washed clothes knows, oil stains can be difficult to remove. Extracting spilled oil from the natural environment is far more arduous and complex than removing oil stains from laundry. But just as in cleaning heavily stained clothes, the cleanup response team used hot water—specifically, steam under high pressure—to remove oil from the shores. At first this technique seemed to work. The shores superficially appeared as they had been before the oil spill; however, closer examination revealed that oil remained. The high-pressure steam cleaning had forced much of the oil deeper into the rocky shores of the Sound. Clearly, an additional solution was needed. ◾ Do you think steam cleaning was beneficial to the cleanup process? ◾ Can you think of some approaches environmental microbiologists might have used to speed up bioremediation in Prince William Sound? Continuing the Case appears on page 744.

Outline and Learning Outcomes 24.1 Ecology: The Interconnecting Web of Life 1. Define microbial ecology. 2. Summarize why our view of the abundance of microbes on earth has changed in recent years. 3. Discuss the terms ecosystem and community in relation to one another. 4. Differentiate between habitat and niche. 5. Draw an example of an energy pyramid, labeling producers and consumers. 6. Define bioremediation.

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24.2 The Natural Recycling of Bioelements 7. List five important elements of biogeochemical cycles. 8. Diagram a carbon cycle. 9. Point out where methanogens influence the carbon cycle. 10. List the four reactions involved in the nitrogen cycle. 11. Describe the process of nitrogen fixation, and provide some examples of organisms that perform it. 12. Give brief summaries of the sulfur and phosphorus cycles. 24.3 Microbes on Land and in Water 13. Outline the basic process used to perform metagenomic analysis of the environment. 14. List two important partnerships that occur in the soil. 15. Diagram the hydrologic cycle. 16. Discuss what metagenomic sampling of oceans has revealed. 17. Name the regions, top to bottom, of large bodies of standing water. 18. Define eutrophication and discuss its consequences.

This chapter emphasizes microbial activities that help maintain, sustain, and control the life support systems on the earth. This subject is explored from the standpoint of the natural roles of microorganisms in the environment and their contributions to the ecological balance, including soil, water, and mineral cycles.

24.1 Ecology: The Interconnecting Web of Life The study of microbes in their natural habitats is known as microbial ecology; the study of the practical uses of microbes in food processing, industrial production, and biotechnology is known as industrial or applied microbiology (see chapter 25). The two areas actually overlap to a considerable degree—largely because most natural habitats have been altered by human activities. Human intervention in natural settings has changed the earth’s warming and cooling cycles, increased wastes in soil, polluted water, and altered some of the basic relationships between microbial, plant, and animal life. We know one thing for certain: Microbes—the most vast and powerful resource of all—will be silently working in nature. In chapter 7, we first touched upon the widespread distribution of microorganisms and their adaptations to most habitats of the world, from extreme to temperate. Although we have known for a long time that geological features on the earth, including coal and limestone, are formed in small or large part by microbes, it is only recently that we have come to understand the sheer mass of microbial life present on our planet. Remember that the vast majority of microbial life has not yet been cultured. With the development of genomic techniques that do not rely on cultivating bacteria, we have discovered abundant microbial life all over—and within and around—our planet (figure 24.1). We are learning about the planet-shaping effects of bacteria deep in the earth’s core

Figure 24.1 A sample of water from a deep cavern as imaged by scanning electron microscopy. This view shows a bacterial biofilm that actively forms mineral deposits of zinc and sulfate (light green and yellow). This single image brings focus to several themes of this chapter: (1) Microbes work together in mixed communities, (2) microbes can alter the chemistry of the nonliving environment, and (3) microbes can be used to control undesirable wastes created by humans.

24.1

and deep in glaciers. The sheer abundance of viral life in the oceans has been a huge surprise. In fact, half of the earth’s biomass is probably made up of microbes. Regardless of their exact location or type of adaptation, microorganisms necessarily are exposed to and interact with their environment in complex and extraordinary ways. Microbial ecology studies interactions between microbes and their environment and the effects of those interactions on the earth. Unlike studies that deal with the activities of a single organism or its individual characteristics in the laboratory, ecological studies are aimed at the interactions taking place between organisms and their environment at many levels at any given moment. Therefore, ecology is a broad-based science that merges many subsciences of biology as well as geology, physics, and chemistry. Ecological studies deal with both the biotic and the abiotic components of an organism’s environment. Biotic factors are defined as any living or dead organisms1 that occupy an organism’s habitat. Abiotic factors include nonliving components such as atmospheric gases, minerals, water, temperature, and light. You may recall these from chapters 7 and 11 as factors that affect microbial growth. A collection of organisms together with its surrounding physical and chemical factors is defined as an ecosystem.

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Ecology: The Interconnecting Web of Life

Lithosphere Biosphere

Hydrosphere Atmosphere

Tropical forests

Biomes Temperate deciduous forests Taiga

South

Gradient in latitude

Tundra

North

Ecosystem

The Organization of Ecosystems The earth initially may seem like a random, chaotic place, but it is actually an incredibly organized, fine-tuned machine. Ecological relationships exist at several levels, ranging from the entire earth all the way down to a single organism (figure 24.2). The most all-encompassing of these levels, the biosphere, contains all physical locations on earth that support life, including the thin envelope of life that surrounds the earth’s surface and extending several miles below. This global ecosystem comprises the hydrosphere (water), the lithosphere (a few miles into the soil), and the atmosphere (a few miles into the air). The biosphere maintains or creates the conditions of temperature, light, gases, moisture, and minerals required for life processes. The biosphere can be naturally subdivided into terrestrial and aquatic realms. The terrestrial realm is usually distributed into particular climatic regions called biomes (by′-ohmz), each of which is characterized by a dominant plant form, altitude, and latitude. Particular biomes include grassland, desert, mountain, and tropical rain forest. The aquatic biosphere is generally divisible into freshwater and marine realms. We have also recently learned that the earth’s crust also supports a vast and diverse number of life forms, estimated to be equal to or even greater than life as we know it in aquatic and terrestrial realms. Biomes and aquatic ecosystems are generally composed of mixed assemblages of organisms that live together at the same place and time and that usually exhibit well-defined nutritional 1. Biologists make a distinction between nonliving and dead. A nonliving thing has never been alive, whereas a dead thing was once alive but no longer is.

Community

Population

Chlamydomonas

Individual Organism

Figure 24.2 Levels of organization in an ecosystem, ranging from the biosphere to the individual organism.

Chapter 24 Environmental Microbiology

All living things must obtain nutrients and a usable form of energy from their abiotic and biotic environments. The energy and nutritional relationships in ecosystems can be described in a number of convenient ways. A food chain, or energy pyramid, provides a simple summary of the general trophic (feeding) levels, designated as producers, consumers, and decomposers, and traces the flow and quantity of available energy from one level to another (figure 24.3). It is worth noting that microorganisms are the only living beings that exist at all three major trophic levels. The nutritional roles of microorganisms in ecosystems are summarized in table 24.1.

Continuing the Case

Decomposers

Steam cleaning the shores of Prince William Sound was beneficial in that it quickly removed large quantities of oil and improved the shoreline’s aesthetic appearance. But that cleaning method may have killed many of the bacteria that could have facilitated more rapid cleanup of the oil. Soon the cleanup crews had to employ an additional approach, one that relied on microorganisms to remove the oil. Many microorganisms—even those inhabiting the rocks on the shores of the Sound—have the capacity to utilize oil as a source of carbon and energy, simultaneously transforming it into harmless water and carbon dioxide. This process is called bioremediation. Crude oil is composed of hydrocarbons, which are rich sources of carbon for microorganisms; however, microorganisms require nutrients in addition to carbon. In fact, without additional nutrients, bacterial metabolism and bioremediation often do not proceed very quickly. Rapid cleanup of the Sound was imperative to minimize further negative impacts of the spill on this once-pristine environment. ◾ What needed to happen to rapidly increase the numbers of oil-degrading microbes on the shore?

Decomposers

Consumers

Quaternary consumers Tertiary consumers Secondary consumers Primary consumers Producers

Energy and Nutritional Flow in Ecosystems

Case File 24

Heterotrophs

or behavioral interrelationships. These clustered associations are called communities. Although most communities are identified by their easily visualized dominant plants and animals, they also contain a complex assortment of bacteria, fungi, algae, protozoa, and even viruses. The basic units of community structure are populations, groups of organisms of the same kind. For organisms with sexual reproduction, this level is the species. In contrast, prokaryotes are classified using taxonomic units such as “strain.” The organizational unit of a population is the individual organism, and each multicellular organism, in turn, has its own levels of organization (organs, tissues, cells). Ecosystems are generally balanced, with each organism existing in its particular habitat and niche. The habitat is the physical location in the environment to which an organism has adapted. In the case of microorganisms, the habitat is frequently a microenvironment, where particular qualities of oxygen, light, or nutrient content are somewhat stable. The niche is the overall role that a species (or population) serves in a community. This includes such activities as nutritional intake (what it eats), position in the community structure (what is eating it), and rate of population growth. A niche can be broad (such as scavengers that feed on nearly any organic food source) or narrow (microbes that decompose cellulose in forest litter or that fix nitrogen). Note that microbes exist as communities in and on plants and animals as well, including humans. Pure cultures are seldom found anywhere in nature. One exception to this rule is particularly noteworthy. In 2008, researchers found a bacterium living completely alone, with no other life forms in its ecosystem. It was found in a South African gold mine, in fluid collected in cracks in the rock 2 miles below the surface. Obviously, there is no light there, and there are also no photosynthetic organisms (such as plants) to offer the indirect benefits of photosynthesis for the bacterium to use. The bacterium, named Desulforudis audaxviator, has to extract everything it needs from an abiotic environment. Apparently it garners energy from the radioactive decay of uranium in the rocks, and it possesses genes that enable it to leach carbon and nitrogen from the environment. The interesting spin on this discovery is that it now makes the possibility of finding microbial life on other—mostly abiotic—planets suddenly more plausible. As one researcher said of Desulforudis: “This is just the kind of organism that could survive on Mars.”

Autotrophs

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Primary producers

Amount of available energy

Energy Source ⫹ CO2

Figure 24.3 A trophic and energy pyramid. The relative size of the blocks indicates the number of individuals that exist at a given trophic level. The orange arrow on the right indicates the amount of usable energy from producers to top consumers. Both the number of organisms and the amount of usable energy decrease with each trophic level. Decomposers are an exception to this pattern but only because they can feed from all trophic levels (gray arrows). Blocks shown on the left indicate the general nutritional types and levels that correspond with the pyramid.

24.1

Ecology: The Interconnecting Web of Life

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Food Chain

Table 24.1 The Major Roles of Microorganisms in Ecosystems Description of Activity

Examples of Microorganisms Involved

Photosynthesis

Algae, bacteria, sulfur bacteria

Chemosynthesis

Chemolithotrophic bacteria in thermal vents

Consumers

Predation

Free-living protozoa that feed on algae and bacteria; some fungi that prey upon nematodes

Decomposers

Degradation of plant and animal matter and wastes

Soil saprobes (primarily bacteria and fungi) that degrade cellulose, lignin, and other complex macromolecules

Role Primary producers

Mineralization of organic nutrients

Soil bacteria that reduce organic compounds to inorganic compounds such as CO2 and minerals

Cycling agents for biogeochemical cycles

Recycling compounds containing carbon, nitrogen, phosphorus, sulfur

Specialized bacteria that transform elements into different chemical compounds to keep them cycling from the biotic to the abiotic and back to the biotic phases of the biosphere

Parasites

Living and feeding on hosts

Viruses, bacteria, protozoa, fungi, and worms that play a role in population control

Life would not be possible without producers, because they provide the fundamental energy source that drives the trophic pyramid. Producers are the only organisms in an ecosystem that can produce organic carbon compounds such as glucose by assimilating (fixing) inorganic carbon (CO2) from the atmosphere. If CO2 is the sole source from which they can obtain carbon for growth, these organisms are called autotrophs. Most producers are photosynthetic organisms, such as plants and bacteria, that convert the sun’s energy into chemical bond energy. Photosynthesis was covered in chapter 8. A smaller but not less important amount of CO2 assimilation is brought about by bacteria called lithotrophs. These organisms derive energy from simple inorganic compounds such as ammonia, sulfides, and hydrogen by using redox reactions. In certain ecosystems (see thermal vents, Insight 7.3), lithotrophs are the sole supporters of the energy pyramid as primary producers. Consumers feed on other living organisms and obtain energy from bonds present in the organic substrates they contain. The category includes animals, protozoa, and a few bacteria and fungi. A pyramid usually has several levels of consumers, ranging from primary consumers (grazers or herbivores), which consume producers; to secondary consumers

Minnow

Top carnivore

Insect larva

Quaternary consumer

Cyclops

Tertiary consumer

Didinium

Secondary consumer

Paramecium

Primary consumer

Diatoms

Figure 24.4 Food chain. A food chain is the simplest way to present specific feeding relationships among organisms, but it may not reflect the total nutritional interactions in a community (figure not to scale).

(carnivores), which feed on primary consumers; to tertiary consumers, which feed on secondary consumers; and up to quaternary consumers (usually the last level), which feed on tertiary consumers. Figures 24.4 and 24.5 show specific organisms at these levels. Decomposers, primarily microbes inhabiting soil and water, break down and absorb the organic matter of dead organisms, including plants, animals, and other microorganisms. Because of their biological function, decomposers are active at all levels of the food pyramid. Without this

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Food Web

Figure 24.5 Food web. More complex trophic patterns are accurately depicted by a food web, which traces the multiple feeding options that exist for most organisms. Note: Arrows point toward the consumers. Compare this pattern of feeding with the chain in figure 24.4 (organisms not to scale).

Insect larva Minnow

Daphnia

Hydra

Rotifer

Didinium Coleps

Amoeba

Bacteria

Paramecium

Algae Sun

important nutritional class of saprobes, the biosphere would stagnate and die. The work of decomposers is to reduce organic matter into inorganic minerals and gases that can be cycled back into the ecosystem, especially for the use of primary producers. This process, also termed mineralization, is so efficient that almost all biological compounds can be reduced by some type of decomposer. Numerous microorganisms decompose cellulose and lignin, polysaccharides from plant cell walls that account for the vast bulk of detritus in soil and water. Surprisingly, decomposers can also break down most man-made compounds that are not naturally found on earth. This process is referred to as bioremediation. Often, bioremediation involves more than one kind of microbe, and the collection of participating microbes in this process is known as a consortium. The pyramid in figure 24.3 illustrates several limitations of ecosystems with regard to energy. Unlike nutrients, which can be passed among trophic levels, recycled, and reused, energy does not cycle. Maintenance of complex interdependent trophic relationships such as those shown in figures 24.4 and

24.5 requires a constant input of energy at the producer level. As energy is transferred to the next level, a large proportion (as high as 90%) of the energy will be lost in a form (primarily heat) that cannot be fed back into the system. Thus, the amount of energy available decreases at each successive trophic level. This energy loss also decreases the actual number of individuals that can be supported at each successive level.

24.1 Learning Outcomes—Can You . . . 1. . . . define microbial ecology? 2. . . . summarize why our view of the abundance of microbes on earth has changed in recent years? 3. . . . discuss the terms ecosystem and community in relation to one another? 4. . . . differentiate between habitat and niche? 5. . . . draw an example of an energy pyramid, labeling producers and consumers? 6. . . . define bioremediation?

24.2

n tio pira

Respiration

R es

For billions of years, microbes have played prominent roles in the formation and maintenance of the earth’s crust, the development of rocks and minerals, and the formation of fossil fuels. This revolution in understanding the biological involvement in geologic processes has given rise to a new field called geomicrobiology. A logical extension of this discipline is astromicrobiology, also known as exobiology—which is the study of life on planets and bodies other than earth. In the next several sections, we examine how, jointly and over a period of time, the varied microbial activities affect and are themselves affected by the abiotic environment.

Free CO2 in atmosphere

Combus tion

• All elements ultimately originate from a nonliving, longterm reservoir in the atmosphere, the lithosphere, or the hydrosphere. They cycle in pure form (N2) or as compounds (PO4). Their cycling is facilitated by redox reactions. • Elements make the rounds between the abiotic environment and the biotic environment. • Recycling maintains a necessary balance of nutrients in the biosphere so that they do not build up or become unavailable. • Cycles are complex systems that rely on the interplay of producers, consumers, and decomposers. Often the waste products of one organism become a source of energy or building material for another. • All organisms participate directly in recycling, but only certain categories of microorganisms have the metabolic pathways for converting inorganic compounds from one nutritional form to another.

Res pira ti o n

Because of the finite supply of life’s building blocks, the long-term sustenance of the biosphere requires continuous recycling of elements and nutrients. Essential elements such as carbon, nitrogen, sulfur, phosphorus, oxygen, and iron are cycled through biological, geologic, and chemical mechanisms called biogeochemical cycles. Although these cycles vary in certain specific characteristics, they share several general qualities, as summarized in the following list:

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and methane production. A convenient starting point from which to trace the movement of carbon is with carbon dioxide, which occupies a central position in the cycle and represents a large common pool that diffuses into all parts of the ecosystem (figure 24.6). As a general rule, the cycles of oxygen and hydrogen are closely allied to the carbon cycle. The principal users of the atmospheric carbon dioxide pool are photosynthetic autotrophs (photoautotrophs) such as plants, algae, and bacteria. An estimated 165 billion tons of organic material per year are produced by terrestrial and aquatic photosynthesis. Although we don’t yet know exactly how many autotrophs exist in the earth’s crust, a small amount of CO2 is used by these bacteria (chemolithoautotrophs) that derive their energy from bonds in inorganic chemicals. A review of the general equation for photosynthesis in figure 8.26 reveals that phototrophs use energy from the sun to fix CO2 into organic compounds such as glucose that can be used in synthesis. Photosynthesis is also the primary means by which the atmospheric supply of O2 is regenerated. Just as photosynthesis removes CO2 from the atmosphere, other modes of generating energy, such as respiration and fermentation, can be used to return it. As you may recall from the discussion of aerobic respiration in chapter 8, in the presence of O2, organic compounds such as glucose are degraded completely to CO2, with the release of energy

Volca nos

24.2 The Natural Recycling of Bioelements

The Natural Recycling of Bioelements

Photosynthesis (plants, algae)

CO32– (carbonate in sediments)

Atmospheric Cycles The Carbon Cycle Because carbon is the fundamental atom in all biomolecules and accounts for at least one-half of the dry weight of biomass, the carbon cycle is more intimately associated with the energy transfers and trophic patterns in the biosphere than are other elements. Carbon exists predominantly in the mineral state and as an organic reservoir in the bodies of organisms. A much smaller amount of carbon also exists in the gaseous state as carbon dioxide (CO2), carbon monoxide (CO), and methane (CH4). In general, carbon is recycled through ecosystems via carbon fixation, respiration, or fermentation of organic molecules, limestone decomposition,

Organic carbon decomposed by microorganisms (fungi, bacteria)

Organic carbon taken in by consumers (animals, protozoa)

Figure 24.6 The carbon cycle. This cycle traces carbon from the CO2 pool in the atmosphere to the primary producers (green) where it is fixed into protoplasm. Organic carbon compounds are taken in by consumers (blue) and decomposers (yellow) that produce CO2 through respiration and return it to the atmosphere (pink). Combustion of fossil fuels and volcanic eruptions also add to the CO2 pool. Some of the CO2 is carried into inorganic sediments by organisms that synthesize carbonate (CO3) skeletons. In time, natural processes acting on exposed carbonate skeletons can liberate CO2.

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and the formation of H2O. Carbon dioxide is also released by anaerobic respiration and by certain types of fermentation reactions. A small but important phase of the carbon cycle involves certain limestone deposits composed primarily of calcium carbonate (CaCO3). Limestone is produced when marine organisms such as mollusks, corals, protozoa, and algae form hardened shells by combining carbon dioxide and calcium ions from the surrounding water. When these organisms die, the durable skeletal components accumulate in marine deposits. As these immense deposits are gradually exposed by geologic upheavals or receding ocean levels, various decomposing agents liberate CO2 and return it to the CO2 pool of the water and atmosphere. The complementary actions of photosynthesis and respiration, along with other natural CO2-releasing processes such as limestone erosion and volcanic activity, have maintained a relatively stable atmospheric pool of carbon dioxide. Recent figures show that this balance is being disturbed as humans burn fossil fuels and other organic carbon sources. Fossil fuels, including coal, oil, and natural gas, were formed through millions of years of natural biological and geologic activities. Humans are so dependent upon this energy source that, within the past 25 years, the proportion of CO2 in the atmosphere has steadily increased from 32 to 36 ppm. Although this increase may seem slight and insignificant, most scientists now feel it has begun to disrupt the delicate temperature balance of the biosphere (Insight 24.1). Compared with carbon dioxide, methane gas (CH4) plays a secondary part in the carbon cycle, though it can be a significant product in anaerobic ecosystems dominated by meth an o gens (methane producers). In general, when methanogens reduce CO2 by means of various oxidizable substrates, they give off CH4. The practical applications of methanogens are covered in chapter 25 in a section on sewage treatment, and their contribution to the greenhouse effect is also discussed in Insight 24.1.

Atmospheric N2 gas

1

6

Soil

Root nodules Denitrification

Nitrogen fixation NH4+

2

Nitrification

Ammonification 5

NO2– Nitrifying bacteria

NO3–

Organic nitrogen

Plants, algae, other bacteria 3

Organic nitrogen

Animals, protozoa 4

The Nitrogen Cycle

Process Figure 24.7 A simplified view of events in the

Nitrogen (N2) gas is the most abundant component of the atmosphere, accounting for nearly 79% of air volume. As we will see, this extensive reservoir in the air is largely unavailable to most organisms. Only about 0.03% of the earth’s nitrogen is combined (or fixed) in some other form such as nitrates (NO3), nitrites (NO2), ammonium ion (NH4+), and organic nitrogen compounds (proteins, nucleic acids). The nitrogen cycle is relatively more intricate than other cycles because it involves such a diversity of specialized microbes to maintain the flow of the cycle. In many ways, it is actually more of a nitrogen “web” because of the array of adaptations that occur. Higher plants can utilize NO3− and NH4+; animals must receive nitrogen in organic form from plants or other animals; however, microorganisms can use all forms of nitrogen: NO2−, NO3−, NH4+, N2, and organic nitrogen. The cycle includes four basic types of reactions: nitrogen fixation, ammonification, nitrification, and denitrification (figure 24.7).

nitrogen cycle. 1  In nitrogen fixation, gaseous nitrogen (N2) is acted on by nitrogen-fixing bacteria, which give off ammonia (NH3). 2  Ammonia is converted to nitrite (NO2−) and nitrate (NO3−) by nitrifying bacteria in nitrification. 3  Plants, algae, and bacteria use nitrates to synthesize nitrogenous organic compounds (proteins, amino acids, nucleic acids). 4  Organic nitrogen compounds are used by animals and other consumers. 5  In ammonification, nitrogenous macromolecules from wastes and dead organisms are converted to NH4+ by ammonifying bacteria. NH4+ can be either directly recycled into nitrates or 6  returned to the atmospheric N2 form by denitrifying bacteria (denitrification).

Root Nodules: Natural Fertilizer Factories A significant symbiotic association occurs between rhizobia (ry-zoh′bee-uh) (bacteria in genera such as Rhizobium, Bradyrhizobium, and Azorhizobium) and legumes (plants such as soybeans, peas, alfalfa, and clover that characteristically produce seeds in pods). The infection of legume roots by these gram-negative, motile, rod-shaped bacteria causes

24.2

the formation of special nitrogen-fixing organs called root nodules (fi gure 24.8). Nodulation begins when rhizobia colonize specific sites on root hairs. From there, the bacteria invade deeper root cells and induce the cells to form tumorlike masses. The bacterium’s enzyme system supplies a constant source of reduced nitrogen to the plant, and the plant furnishes nutrients and energy for the activities of the bacterium. The legume uses the NH4+ to aminate (add an amino group to) various carbohydrate intermediates and thereby synthesize amino acids and other nitrogenous compounds that are used in plant and animal synthesis. Plant–bacteria associations have great practical importance in agriculture, because an available source of nitrogen is often a limiting factor in the growth of crops. The selffertilizing nature of legumes makes them valuable food plants in areas with poor soils and in countries with limited resources. It has been shown that crop health and yields can be improved by inoculating legume seeds with pure cultures of rhizobia, because the soil is often deficient in the proper strain of bacteria for forming nodules (figure 24.9).

Ammonification, Nitrification, and Denitrification In another part of the nitrogen cycle, nitrogen-containing organic matter is decomposed by various bacteria (Clostridium, Proteus, for example) that live in the soil and water. Organic detritus consists of large amounts of protein and nucleic acids from dead organisms and nitrogenous animal wastes such as urea and uric acid. The decomposition of Legume root

(b)

Bacteria

Nodules Infection thread

Early nodule

(a)

The Natural Recycling of Bioelements

(a)

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(b)

Figure 24.9 Inoculating legume seeds with Rhizobium bacteria increases the plant’s access to nitrogen. The legumes in (a) were inoculated and are healthy. The poor growth and yellowish color of the uninoculated legumes in (b) indicate a lack of nitrogen.

these substances splits off amino groups and produces NH4+. This process is thus known as ammonification. The ammonium released can be reused by certain plants or converted to other nitrogen compounds, as discussed next. The oxidation of NH4+ to NO2− and NO3− is a process called nitrification. It is an essential conversion process for generating the most oxidized form of nitrogen (NO3). This reaction occurs in two phases and involves two different kinds of lithotrophic bacteria in soil and water. In the first phase, certain gram-negative genera such as Nitrosomonas, Nitrosospira, and Nitrosococcus oxidize NH3 to NO2− as a means of generating energy. Nitrite is rapidly acted upon by a second group of nitrifiers, including Nitrobacter, Nitrosospira, and Nitrococcus, which perform the final oxidation of NO2− to NO3−. Nitrates can be assimilated through several routes by a variety of organisms (plants, fungi, and bacteria). Nitrate and nitrite are also important in anaerobic respiration where they serve as terminal electron acceptors; some bacteria use them as a source of oxygen as well. The nitrogen cycle is complete when nitrogen compounds are returned to the reservoir in the air by a reaction series that converts NO3− through intermediate steps to atmospheric nitrogen. The first step, which involves the reduction of nitrate to nitrite, is so common that hundreds of different bacterial species can do it. Several genera such as Bacillus, Pseudomonas, Spirillum, and Thiobacillus can carry out this denitrification process to completion as follows: NO3− → NO2− → NO → N2O → N2 (gas) This process illustrates that incomplete denitrification is the main source of the greenhouse gas nitrous oxide (N2O).

Figure 24.8 Nitrogen fixation through symbiosis. (a) Events leading to formation of root nodules. Cells of the bacterium Rhizobium attach to a legume root hair and cause it to curl. Invasion of the legume root proper by Rhizobium initiates the formation of an infection thread that spreads into numerous adjacent cells. The presence of bacteria in cells causes nodule formation. (b) Mature nodules that have developed in a sweet clover plant.

Sedimentary Cycles The Sulfur Cycle The sulfur cycle resembles the carbon cycle more than the nitrogen cycle in that sulfur is mostly in solid form and originates from natural sedimentary deposits in rocks, oceans, lakes, and swamps rather than from the atmosphere. Sulfur

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INSIGHT 24.1

Greenhouse Gases, Fossil Fuels, Cows, Termites, and Global Warming

Departure from Long-Term Mean (⬚C)

The sun’s radiant energy does more than drive photosynthesis; it also helps maintain the stability of the earth’s temperature and climatic conditions. As radiation impinges on the earth’s surface, much of it is absorbed, but a large amount of the infrared (heat) radiation bounces back into the upper levels of the atmosphere. For billions of years, the atmosphere has been insulated by a layer of gases (primarily CO2 ; CH4 ; water vapor; and nitrous oxide, N2O) formed by natural processes such as respiration and decomposition, which are part of biogeochemical cycles. This layer traps a certain amount of the reflected heat, yet also allows some of it to escape into space. As long as the amounts of heat entering and leaving are balanced, the mean temperature of the earth will not rise or fall in an erratic or life-threatening way. Although this phenomenon, called the greenhouse effect, is popularly viewed in a negative light, it must be emphasized that its function for eons has been primarily to foster life. The greenhouse effect has become a matter of concern because greenhouse gases appear to be increasing at a rate that could disrupt the temperature balance. In effect, a denser insulation layer will trap more heat energy and gradually heat the earth. The amount of CO2 released collectively by respiration, anaerobic microbial activity, fuel combustion, and volcanic activity has increased more than 30% since the beginning of the industrial era. By far the greatest increase in CO2 production results from human activities such as combustion of fossil fuels, burning forests to clear agricultural land, and manufacturing.

Deforestation has the added impact of removing large areas of photosynthesizing plants that would otherwise consume some of the CO2. Originally, experts on the greenhouse effect were concerned primarily about increasing CO2 levels, but it now appears that the other greenhouse gases combined may have a greater contribution than CO2, and they, too, are increasing. One of these gases, methane (CH4) released from the gastrointestinal tract of ruminant animals such as cattle, goats, and sheep, has doubled over the past century. A single cow is estimated to release 200–400 pounds of methane a year through its belching and flatulence. The gut of termites also harbors wood-digesting bacteria and methanogenic archaea. Even the human intestinal tract can support methanogens. Methane traps 21 times more heat than does carbon dioxide. Other greenhouse gases such as nitrous oxide and sulfur dioxide (SO2) are also increasing through automobile and industrial pollution. There is not yet complete agreement as to the extent and effects of global warming. It has been documented that the mean temperature of the earth has increased by ±1.0°C since 1860. If the rate of increase continues, by 2050 a rise in the average temperature of 4°C to 5°C will begin to melt the polar ice caps and raise the levels of the ocean 2 to 3 feet. Some experts predict more serious effects, including massive flooding of coastal regions, changes in rainfall patterns, expansion of deserts, and long-term climatic disruptions.

Global Mean Temperature over Land & Ocean 0.6 0.4 0.2 0.0 -0.2 -0.4 -0.6 1880

1900

1920

exists in the elemental form (S) and as hydrogen sulfide gas (H2S), sulfate (SO4), and thiosulfate (S2O3). Most of the oxidations and reductions that convert one form of inorganic sulfur to another are accomplished by bacteria. Plants and many microorganisms can assimilate only SO4 , and animals must have an organic source. Organic sulfur occurs in the amino acids cystine, cysteine, and methionine, which contain sulfhydryl (—SH) groups and form disulfide (S —S) bonds that contribute to the stability and configuration of proteins.

1940

1960

1980

2000

One of the most remarkable contributors to the cycling of sulfur in the biosphere are the thiobacilli. These gramnegative, motile rods flourish in mud, sewage, bogs, mining drainage, and brackish springs that can be inhospitable to organisms that require complex organic nutrients. But the metabolism of these specialized lithotrophic bacteria is adapted to extracting energy by oxidizing elemental sulfur, sulfides, and thiosulfate. One species, T. thiooxidans, is so efficient at this process that it secretes large amounts of sul-

24.2

furic acid into its environment, as shown by the following equation:

The Natural Recycling of Bioelements

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Insoluble Phosphate Rocks

Na2S2O3 + H2O + O2 → Na2SO4 + H2SO4 (sulfuric acid) + 4S

The Phosphorus Cycle Phosphorus is an integral component of DNA, RNA, and ATP, and all life depends upon a constant supply of it. It cycles between the abiotic and biotic environments almost exclusively as inorganic phosphate (PO4) rather than its elemental form (figure 24.10). The chief inorganic reservoir is phosphate rock, which contains the insoluble compound fluo rapatite, Ca 5(PO 4) 3F. Before it can enter biological systems, this mineral must be phosphatized—converted into more soluble PO43− by the action of acid. Phosphate is released naturally when the sulfuric acid produced by Thiobacillus dissolves phosphate rock. Soluble phosphate in the soil and water is the principal source for autotrophs, which fix it onto organic molecules and pass it on to heterotrophs in this form. Organic phosphate is returned to the pool of soluble phosphate by decomposers, and it is finally cycled back to the mineral reservoir by slow geologic processes such as sedimentation. Because the low phosphate content of many soils can limit productivity, phosphate is added to soil to increase agricultural yields. The excess runoff of fertilizer into the hydrosphere is often responsible for overgrowth of aquatic pests (see eutrophication in a subsequent section on aquatic habitats).

Other Forms of Cycling The involvement of microbes in cycling elements and compounds can be escalated by the introduction of toxic substances into the environment. Such toxic elements as arsenic, chromium, lead, and mercury as well as hundreds of thousands of synthetic chemicals introduced into the environment over the past hundred years are readily caught up in cycles by microbial actions. Some of these chemicals

Ca5(PO4)3F

Phosphatizing bacteria

Mining

PO4–3 Pool of soluble, inorganic phosphate Mineralization by microbes

Sedimentation

The marvel of this bacterium is its ability to create and survive in the most acidic habitats on the earth. It also plays an essential part in the phosphorus cycle, and its relative, T. ferrooxidans, participates in the cycling of iron. Other bacteria that can oxidize sulfur to sulfates are the photosynthetic sulfur bacteria mentioned in the section on photosynthesis. The sulfates formed from oxidation of sulfurous compounds are assimilated into biomass by a wide variety of organisms. The sulfur cycle reaches completion when inorganic and organic sulfur compounds are reduced. Bacteria in the genera Desulfovibrio and Desulfuromonas anaerobically reduce sulfates to hydrogen sulfide or metal sulfide as the final step in electron transport. Sites in ocean sediments and mud where these bacteria live usually emanate a strong, rotten-egg stench from H2S and may be blackened by the iron they contain.

Producers of organic phosphate (proteins, nucleic acids)

Consumers of organic phosphate

Figure 24.10 The phosphorus cycle. The pool of phosphate existing in sedimentary rocks is released into the ecosystem either naturally by erosion and microbial action or artificially by mining and the use of phosphate fertilizers. Soluble phosphate (PO43−) is cycled through producers, consumers, and decomposers back into the soluble pool of phosphate, or it is returned to sediment in the aquatic biosphere. will be converted into less harmful substances, but others, such as PCB and heavy metals, persist and flow along with nutrients into all levels of the biosphere. If such a pollutant accumulates in living tissue and is not excreted, it can be accumulated by living things through the natural trophic flow of the ecosystem. This process is known as bioaccumulation. Microscopic producers such as bacteria and algae begin the accumulation process. With each new level of the food chain, the consumers gather an increasing amount

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INSIGHT 24.2

Cute Killer Whale—Or Swimming Waste Dump?

In the early 1990s, Keiko the killer whale stole hearts as the star of the movie Free Willy. Eleven years later, Keiko died of pneumonia in a fjord in Norway, never having fully adjusted to being back in the wild. Even though whales that die close to shore are usually towed out to sea, Keiko was buried on the beach where he was found, probably because of the close connection humans felt with him. That was not the end of the story, however. Environmental groups in Norway raised concerns about burying the animal onshore due to the high probability that his tissues contained high amounts of PCBs. It was nothing personal against Keiko; whales all over the world have been found to have bioaccumulated this toxic chemical. PCBs (polychlorinated biphenyls) are very stable manufactured compounds that were heavily used in industrial settings from the 1930s to the 1970s. They found widespread use as insulating fluids in electrical applications. They are highly soluble in lipid compounds, and for that reason they bioaccumulate in the fat tissues of animals. The bioaccumulation seems to be worst near the poles of the earth, where many higher animals (including humans) use contaminated fish as a major part of their diets. Complicating this fact is the concentration of volatile PCBs in the atmosphere. Atmospheric circulation carries PCBs to the poles, and the cold temperatures cause the pollutants to condense and fall to the surface, where they further contaminate the food chain. In 1998, a group of polar bears in Norway was found to have bizarre developmental deformities. Seven bears of a group of 450 surveyed (approximately 2%) possessed both male and female reproductive organs—a bizarre mutation that was attributed to PCB accumulation in the bears’ bodies. PCB contamination of wildlife is not limited to the poles, however. In Belgium in 1994, four sperm whales were stranded and died in coastal waters. All were found to have 30 parts per million (ppm) PCBs in their kidneys and blubber. Beluga whales in the Gulf of St. Lawrence in eastern Canada have been found to have 3,200 ppm PCBs in their tissues—a level 1,600 times higher than the level of contamination that triggers EPA regulations requiring the incineration of any materials found to have that concentration of PCB. A bottlenose dolphin in Cape Cod was recently found to have 6,800 ppm PCBs. “This animal was, by definition, a swimming toxic waste dump,” says Roger Payne, author of Among Whales.

of the chemical, until the top consumers can contain toxic levels (Insight 24.2). One example of this is mercury compounds used in household antiseptics and disinfectants, agriculture, and industry. Elemental mercury precipitates proteins by attaching to functional groups and is most toxic in the ethyl or methyl mercury form. Recent studies have disclosed increased mercury content in fish taken from oceans and freshwater lakes in North America and even in canned tuna, adding to the risk in consumption of these products.

And that brings us back to Keiko. For weeks after he was buried in a quiet ceremony, local schoolchildren came to place rocks on his grave in a Viking tradition of respect. The stark contrast between that loving act and the fact that many people feel he should have been dug up and incinerated highlights the conflicted relationship we have with nature. We love it, but are we ignoring the damage we inflict upon it?

Keiko was buried on the shore of the Taknes Bay in Norway, December 15, 2003.

24.2 Learning Outcomes—Can You . . . 7. 8. 9. 10. 11.

. . . list five important elements of biogeochemical cycles? . . . diagram a carbon cycle? . . . point out where methanogens influence the carbon cycle? . . . list the four reactions involved in the nitrogen cycle? . . . describe the process of nitrogen fixation, and provide some examples of organisms that perform it? 12. . . . give brief summaries of the sulfur and phosphorus cycles?

24.3

24.3 Microbes on Land and in Water

Microbes on Land and in Water

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are sought (and known in advance) PCR can be used directly on the environmental sample to fish the “needle out of the haystack.” This is commonly performed when seeking 16s rRNA molecules. Novel sequences are still found in this way as the “fishing” is done with conserved sequences found on the different molecules. Once the DNA pieces are retrieved using either method, they can be sequenced, and it can be determined whether they match known sequences or are new to us. The DNA sequences can also be cloned into expression vectors, which can then be screened for their functions, or their products. These processes are summarized in figure 24.11.

As you have heard several times already in this book, until fairly recently, our understanding of which microbes inhabited a place, whether it was the human gut or your backyard pond, relied on culturing them. Just as there is a Human Microbiome Project, scientists have been busy using these techniques to identify the microbes living in the environment, which includes land, water, and air. The field of environmental genomics has revealed many surprising things, such as bacteria living in glaciers and deep under the seafloor.

Environmental Sampling in the Genomic Era

Soil Microbiology: The Composition of the Lithosphere

The methods for identifying bacteria and genes in the environment are evolving rapidly. As you know, when the genes of all microbes in a habitat are sampled, it is called metagenomics. We’ll discuss the basic principles here. The process always begins with an environmental sample, such as a gallon of seawater or a gram of soil. Techniques are available to extract the DNA from such samples. Fragments can then be cloned into plasmid vectors in the same way that we described in chapter 10. A library of DNA fragments can then be preserved and amplified. If specific gene sequences

At the microscopic level, soil is a dynamic ecosystem that supports complex interactions between numerous geologic, chemical, and biological factors. This rich region, called the lithosphere, teems with microbes, serves a dynamic role in biogeochemical cycles, and is an important repository for organic detritus and dead terrestrial organisms. Rock decomposition releases various-size particles, ranging from rocks, pebbles, and sand grains to microscopic Sequence-driven analysis Cloned DNA preparation

(a)

atgacgac...gatttaca tgggctcccatcgctag

(b)

Genomic sequence analysis

Restriction-digested vector ⫹

(c)

E.coli

Metagenomic library

⫹ Ligation

Transformation

Genomic DNA extraction

Function-driven analysis Heterologous gene expression

(d)

Transcription Heterologous genomic DNA

Recombinant DNA

mRNA Translation Protein

Figure 24.11 Construction and screening of genomic libraries directly from the environment. DNA has been extracted directly from (a) bacterial mats at Yellowstone National Park, (b) soil samples from Alaska, (c) cabbage white butterfly larvae, and (d) tube worms from hydrothermal vents. The DNA is cloned into suitable vectors and transformed into a bacterial host. Sequences or gene products can then be analyzed.

Secretion

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morsels that lie in a loose aggregate (figure 24.12). The porous structure of soil creates various-size pockets or spaces that provide numerous microhabitats. Some spaces trap moisture and form a liquid phase in which mineral ions and other nutrients are dissolved. Other spaces trap air that will provide gases to soil microbes, plants, and animals. Because both water and air compete for these pockets, the water content of soil is directly related to its oxygen content. Watersaturated soils contain less oxygen, and dry soils have more. Gas tensions in soil can also vary vertically. In general, the concentration of O2 decreases and that of CO2 increases with the depth of soil. Aerobic and facultative organisms tend to occupy looser, drier soils, whereas anaerobes are adapted to waterlogged, poorly aerated soils. Within the superstructure of the soil are varying amounts of humus, the slowly decaying organic litter from plant and animal tissues. This soft, crumbly mixture holds water like a sponge. It is also an important habitat for microbes that decompose the complex litter and gradually recycle nutrients. The humus content varies with climate, temperature, moisture and mineral content, and microbial action. Warm, tropical soils have a high rate of humus production and microbial decomposition. Because nutrients in these soils are swiftly released and used up, they do not accumulate. Fertilized agricultural soils in temperate climates build up humus at a high rate and are rich in nutrients. Humans can artificially increase the amount of humus by mixing plant refuse and animal wastes with soil and allowing natural decomposition to occur, a process called composting. Composting is a very active metabolic process that generates a great deal of heat. The temperature inside a well-maintained compost can reach 80°C to 100°C.

Living Activities in Soil The rich culture medium of the soil supports a fantastic array of microorganisms (bacteria, fungi, algae, protozoa, and viruses). A gram of moist loam soil with high humus content can have a microbe count as high as 10 billion, each competing for its own niche and microhabitat. Some of the most distinctive biological interactions occur in the rhizosphere, the zone of soil surrounding the roots of plants, which contains associated bacteria, fungi, and protozoa (see figure 24.12). Plants interact with soil microbes in a truly synergistic fashion. Studies have shown that a rich microbial community grows in a biofilm around the root hairs and other exposed surfaces. Their presence stimulates the plant to exude growth factors such as carbon dioxide, sugars, amino acids, and vitamins. These nutrients are released into fluid spaces, where they can be readily captured by microbes. Bacteria and fungi likewise contribute to plant survival by releasing hormonelike growth factors and protective substances. They are also important in converting minerals into forms usable by plants. We saw numerous examples in the nitrogen, sulfur, and phosphorus cycles. We previously observed that plants can form close symbiotic associations with microbes to fix nitrogen. Other mutualistic partnerships between plant roots and microbes

Saprophytic fungal hyphae Mycorrhizae hyphae Root

Sand

Mite

Mycorrhizae spores

Ciliated protist

Water Clay

Silt Flagellated protist Bacteria Organic materials Clay

Nematode

Actinomycete hyphae

Figure 24.12 The soil habitat. A typical soil habitat contains a mixture of clay, silt, and sand along with soil organic matter. Roots and animals (e.g., nematodes and mites), as well as protozoa and bacteria, consume oxygen, which rapidly diffuses into the soil pores where the microbes live. Note that two types of fungi are present: mycorrhizal fungi, which derive their organic carbon from plant roots; and saprophytic fungi, which help degrade organic material.

are mycorrhizae (my″-koh-ry′-zee). These associations occur when various species of basidiomycetes, ascomycetes, or zygomycetes attach themselves to the roots of vascular plants (figure 24.13). The plant feeds the fungus through photosynthesis, and the fungus sustains the relationship in several ways. By extending its mycelium into the rhizosphere, it helps anchor the plant and increases the surface area for capturing water from dry soils and minerals from poor soils. Plants with mycorrhizae can inhabit severe habitats more successfully than plants without them. The topsoil, which extends a few inches to a few feet from the surface, supports a host of burrowing animals such as nematodes, termites, and earthworms. Many of these animals are decomposer-reducer organisms that break down organic nutrients through digestion and also mechanically reduce or fragment the size of particles so that they are more readily mineralized by microbes. Aerobic bacteria initiate the digestion of organic matter into carbon dioxide and

24.3

Microbes on Land and in Water

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Transpiration Precipitation

Precipitation

Evaporation

Evaporation

Runoff Seepage

Figure 24.13 Mycorrhizae. These symbiotic associations between fungi and plant roots favor the absorption of water and minerals from the soil.

water and generate minerals such as sulfate, phosphate, and nitrate, which can be further degraded by anaerobic bacteria. Fungal enzymes increase the efficiency of soil decomposition by hydrolyzing complex natural substances such as cellulose, keratin, lignin, chitin, and paraffin. The soil is also a repository for agricultural, industrial, and domestic wastes such as insecticides, herbicides, fungicides, manufacturing wastes, and household chemicals. Applied microbiologists, using expertise from engineering, biotechnology, and ecology, work to explore the feasibility of harnessing indigenous soil microbes to break down undesirable hydrocarbons and pesticides (see chapter 25).

Deep Subsurface Microbiology For the past 30 years, scientists have been sampling the deep subsurface—2 miles and more below the surface. From the very beginning of these studies, the results have been astounding. With the advent of genomic sampling, the discoveries are piling up. For instance, bacteria deep beneath the surface metabolize petroleum to CO2 at a rate a million times slower than that of surface microbes, suggesting that the microbes may be anywhere from 100 years old to 100,000 years old. Many of these bacteria exist solely in biofilms on rock surfaces. Scientists are pondering how bacteria survive in very nearly abiotic environments, and are discovering new metabolic capabilities that may turn out to provide clues to the very origin of life.

Aquatic Microbiology Water occupies nearly three-fourths of the earth’s surface. The hydrologic cycle (figure 24.14) begins when surface water (lakes, oceans, rivers) exposed to the sun and wind evaporates and enters the vapor phase of the atmosphere. Living beings contribute to this reservoir by various activities. Plants lose moisture through transpiration (evapora-

Groundwater

Sedimentary rock Deep aquifers

Figure 24.14 The hydrologic cycle. The largest proportion of water cycles through evaporation, transpiration, and precipitation between the hydrosphere and the atmosphere. Other reservoirs of water exist in the groundwater or deep storage aquifers in sedimentary rocks. Plants add to this cycle by releasing water through transpiration, and heterotrophs release it through respiration.

tion through leaves), and all aerobic organisms give off water during respiration. Airborne moisture accumulates in the atmosphere, most conspicuously as clouds. Water is returned to the earth through condensation or precipitation (rain, snow), a process influenced by bacteria (Insight 24.3). The largest proportion of precipitation falls back into surface waters, where it circulates rapidly between running water and standing water. Only about 2% of water seeps into the earth or is bound in ice, but these are very important reservoirs. Table 24.2 shows how water

Table 24.2 Distribution of Water on Earth’s Surface Water Source

Water Volume, in Cubic Miles

Oceans Icecaps, glaciers Groundwater Freshwater lakes Inland seas Soil moisture Atmosphere Rivers

317,000,000 7,000,000 2,000,000 30,000 25,000 16,000 3,100 300

Percentage of Total Water 97.2269 2.14 0.61 0.009 0.008 0.005 0.001 0.0001 100.0000

Source: U.S. Geological Survey.

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INSIGHT 24.3

It’s Raining Bacteria

Is precipitation just a clever mechanism bacteria use to disperse themselves in the environment? It seems that’s at least one reason it rains. Meteorologists have known for a long time that clouds release rain and snow when particles of water become too large for the fine mist of a cloud to support. Tiny particles that cause the water to coalesce, termed nucleators, encourage the formation of raindrops or snowflakes. Traditionally, dust particles are thought to be the most important nucleators, though researchers have known since the 1970s that bacteria can serve this role as well. They just didn’t appreciate how frequently they do it. In 2008, a scientist from Louisiana State University analyzed snows around the world and found that bacteria served as nucleators in almost all of them. In other words: Bacteria were causing the precipitation. The news that bacteria were causing it to rain reverberated through the climate change community. The process of nucleation, and therefore, precipitation, seemed unpredictable when it only involved dust particles. The discovery that bacteria are largely responsible opens brand new avenues for predicting, and possibly controlling, the global climate. As just one thought experiment: Imagine the implications for drought-stricken areas of the world.

is distributed in the various surface compartments. Surface water collects in extensive subterranean pockets produced by the underlying layers of rock, gravel, and sand. This process forms a deep groundwater source called an aquifer. The water in aquifers circulates very slowly and is an important replenishing source for surface water. It can resurface through springs, geysers, and hot vents, and it is also tapped as the primary supply for one-fourth of all water used by humans. Although the total amount of water in the hydrologic cycle has not changed over millions of years, its distribution and quality have been greatly altered by human activities. Two serious problems have arisen with aquifers. First, as a result of increased well drilling, land development, and persistent local droughts, the aquifers in many areas have not been replenished as rapidly as they have been depleted. As these reserves are used up, humans will have to rely on other delivery sys-

tems such as pipelines, dams, and reservoirs, which can further disrupt the cycling of water. Second, because water picks up materials when falling through air or percolating through the ground, aquifers are also important collection points for pollutants. As we will see, the proper management of water resources is one of the greatest challenges of this century.

Marine Environments The ocean exhibits extreme variations in salinity, depth, temperature, hydrostatic pressure, and mixing. Even so, it supports a great abundance of bacteria and viruses, the extent of which has only been appreciated in very recent years. In the opening to chapter 1, you read that in 2004, J.  Craig Venter (the same Venter from the Human Genome Project, chapter 10) set sail on a 100-ft yacht to the Sargasso Sea to get the DNA profile of an entire ecosystem. The Sargasso Sea was thought to be relatively sparsely populated by life forms, as it was nutrient-poor. His team found a rich variety of life and discovered 1,800 new species and more than 1.2 million new genes. His group widened the search over the next 2 years and sailed around the world, collecting ocean samples all along the way. They eventually discovered 6 million new genes and thousands of new proteins—essentially doubling the number of known proteins. Proteins, of course, are responsible for nearly all of the activities of cells. The capabilities of microbes have been greatly underappreciated, in other words, because we have not been able to cultivate the vast majority of them in the laboratory. In another startling study, green sulfur photosynthetic bacteria were found growing in deep-sea vents, a place where the sun’s light cannot penetrate. These bacteria cannot live without light. It appears that the light they use to photosynthesize comes from chemical reactions, the breaking of mineral crystals, or from bubble formation. If these results hold up over time, this will be the first organism found to photosynthesize with anything other than sunlight. Oceans contain several million viruses per milliliter. Most of these viruses are bacteriophages and therefore pose no danger to humans, but as parasites of bacteria, they appear to be a natural control mechanism for these populations. Plus, their lysis of bacteria plays an important role in the turnover of nutrients in the ocean. An important discovery is that bacteriophages of cyanobacteria contain genes responsible for photosynthesis. It has been estimated that bacteriophages may be responsible for 5% of the planet’s photosynthesis (with marine cyanobacteria responsible for 40% or more).

Aquatic Communities The freshwater environment is a site of tremendous microbiological activity. Microbial distribution is associated with sunlight, temperature, oxygen levels, and nutrient availability. The uppermost portion is the most productive self-sustaining region because it contains large numbers of plankton, a floating microbial community that drifts with wave action and currents. A major member of this assemblage is the phytoplankton,

24.3

containing a variety of photosynthetic algae and cyanobacteria. The phytoplankton provide nutrition for zooplankton, microscopic consumers such as protozoa and invertebrates that filter, feed, prey, or scavenge. The plankton supports numerous other trophic levels such as larger invertebrates and fish. With its high nutrient content, the deeper regions also support an extensive variety and concentration of organisms, including aquatic plants, aerobic bacteria, and anaerobic bacteria actively involved in recycling organic detritus. Larger bodies of standing water develop gradients in temperature or thermal stratification, especially during the summer (figure 24.15). The upper region, called the epilimnion, is warmest, and the deeper hypolimnion is cooler. Between these is a buffer zone, the thermocline, that ordinarily prevents the mixing of the two. Twice a year, during the warming cycle of spring and the cooling cycle of fall, temperature changes in the water column break down the thermocline and cause the water from the two strata to mix. Mixing disrupts the stratification and creates currents that bring nutrients up from the sediments. This process, called upwelling, is associated with increased activity by certain groups of microbes and is one explanation for the periodic emergence of red tides in oceans (figure 24.16) caused

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(a)

Thermal Stratification (summer)

Prevailing wind

(b)

Epilimnion 25°C–22°C Thermocline 20°C–10°C Hypolimnion 9°C–4°C (a)

Seasonal Upwelling (fall and spring) Nutrients

(c) (b)

Figure 24.15 Profiles of a lake. (a) During summer, a lake becomes stabilized into three major temperature strata. (b) During fall and spring, cooling or heating of the water disrupts the temperature strata and causes upwelling of nutrients from the bottom sediments.

Figure 24.16 Red tides. (a) Single-celled red algae called dinoflagellates (Gymnodinium shown here) bloom in high-nutrient, warm seawater and impart a noticeable red color to it, as shown in (b). (b) An aerial view of California coastline in the midst of a massive red tide. (c) Fish washed ashore during a red tide bloom.

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Case File 24

Wrap-Up

Bioremediation, as discussed at the beginning of this chapter and also in the next chapter, relies on microorganisms to mineralize pollutants, such as oil spilled from an oil tanker. As with all microorganisms, those involved in bioremediation require nutrients. Oil is rich in carbon that microorganisms can utilize, but it lacks other essential nutrients, such as nitrogen and phosphorus. For this reason, environmental microbiologists attempted to accelerate bioremediation of the Exxon Valdez oil spill by applying fertilizers containing nitrogen and phosphorus. Approximately 50,000 kg of nitrogen and 5,000 kg of phosphorus were applied between 1989 and 1992. Overall, these enormous applications appeared to have the desired effect: Bacteria from fertilized beaches mineralized the components of oil up to 18 times faster than bacteria from beaches that did not receive fertilizer. While today the shoreline has still not completely recovered, the actions of the bacteria—with a little push from humans—set Prince William Sound’s shore on the right path. The cleanup in the Gulf of Mexico is a different story. The oil is dispersed across hundreds of miles of ocean water, and is much less concentrated than in the Alaska spill. Still, some believe that newly identified bacteria are sopping up the oil there as well. See: 1994. Nature. 368:413–418.

by toxin-producing dinoflagellates. A recent outbreak of fish and human disease on the eastern seaboard has been attributed to the overgrowth of certain species of these algae in polluted water. These algae produce a potent muscle toxin that can be concentrated by shellfish through filtration feeding. When humans eat clams, mussels, or oysters that contain the toxin, they develop paralytic shellfish poisoning. People living in coastal areas are cautioned not to eat shellfish during those months of the year associated with red tides (varies from one area to another). Because oxygen is not very soluble in water and is rapidly used up by the plankton, its concentration forms a gradient, from highest in the epilimnion to lowest at the bottom. In general, the amount of oxygen that can be dissolved is dependent on temperature. Warmer strata on the surface tend to carry lower levels of this gas. But of all the characteristics of water, the greatest range occurs in nutrient levels. Nutrientdeficient aquatic ecosystems are called oligotrophic (ahl″-ihgoh-trof′-ik). Species that can make a living on such starvation rations are Hyphomicrobium and Caulobacter. These bacteria have special stalks that capture even minuscule amounts of hydrocarbons present in oligotrophic habitats. At one time, it

Figure 24.17 Heavy surface growth of algae and cyanobacteria in a eutrophic pond.

was thought that viruses were present only in very low levels in aquatic habitats, but researchers have now discovered that there are anywhere from 2 to 10 times as many viruses as bacteria in marine and freshwater communities. The addition of excess quantities of nutrients to aquatic ecosystems, termed eutrophication, often wreaks havoc on the communities involved. The sudden influx of abundant nutrients along with warm temperatures encourages a heavy surface growth of cyanobacteria and algae called a bloom (figure 24.17). This heavy mat of biomass effectively shuts off the oxygen supply to the lake below. The oxygen content below the surface is further depleted by aerobic heterotrophs that actively decompose the organic matter. The lack of oxygen greatly disturbs the ecological balance of the community. It causes massive die-offs of strict aerobes (fish, invertebrates), and only anaerobic or facultative microbes will survive.

24.3 Learning Outcomes—Can You . . . 13. . . . outline the basic process used to perform metagenomic analysis of the environment? 14. . . . list two important partnerships that occur in the soil? 15. . . . diagram the hydrologic cycle? 16. . . . discuss what metagenomic sampling of oceans has revealed? 17. . . . name the regions, top to bottom, of large bodies of standing water? 18. . . . define eutrophication and discuss its consequences?

Chapter Summary

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Chapter Summary 24.1 Ecology: The Interconnecting Web of Life • The study of ecology includes both living (biotic) and nonliving (abiotic) components of the earth. • Ecosystems are organizations of living populations in specific habitats. Environmental ecosystems require a continuous outside source of energy for survival and a nonliving habitat consisting of soil, water, and air. • A living community is composed of populations that show a pattern of energy and nutritional relationships called a food web. Microorganisms are essential producers and decomposers in any ecosystem. 24.2 The Natural Recycling of Bioelements • Nutrients and minerals necessary to communities and ecosystems must be continuously recycled. These biogeochemical cycles involve transformation of elements from inorganic to organic forms and back again. Specific types of microorganisms are needed to convert many nutrients from one form to another. • Elements of critical importance to all ecosystems that cycle through various forms are carbon, nitrogen, sulfur, phosphorus, and water. Carbon and nitrogen are part of the atmospheric cycle. Sulfur and phosphorus are part of the sedimentary cycling of nutrients.

24.3 Microbes on Land and in Water • The earth’s land, water, and air are colonized by more microbes than we ever imagined. We have discovered the magnitude of their numbers through metagenomics, the sampling of the environment for DNA sequences. • The lithosphere, or soil, is an ecosystem in which mineralrich rocks are decomposed to organic humus, the base for the soil community. Soil ecosystems vary according to the kinds of rocks and amount of water, air, and nutrients present. • The deep subsurface, below land and sea, is colonized by a rich array of microbes that have a wide variety of metabolic capabilities. • The food web of the aquatic community is built on phytoplankton and zooplankton. The nature of the aquatic community varies with the temperature, depth, minerals, and amount of light present in each zone. • The ocean is populated by millions of microorganisms per milliliter. Photosynthetic bacteriophages are abundant. • Eutrophication of freshwater and marine systems is caused by the addition of excess nutrients. It causes major disruptions in the ecology of these systems.

Multiple-Choice and True-False Questions

Knowledge and Comprehension

Multiple-Choice Questions. Select the correct answer from the answers provided. 1. Which of the following is not a major subdivision of the biosphere? a. hydrosphere c. stratosphere b. lithosphere d. atmosphere 2. A/an ____ is defined as a collection of populations sharing a given habitat. a. biosphere c. biome b. community d. ecosystem 3. The quantity of available nutrients ____ from the lower levels of the energy pyramid to the higher ones. a. increases c. remains stable b. decreases d. cycles 4. Which of the following is considered a greenhouse gas? a. CO2 c. N2O b. CH4 d. all of these 5. Root nodules contain ____, which can ____. a. Azotobacter, fix N2 b. Nitrosomonas, nitrify NH3− c. rhizobia, fix N2 d. Bacillus, denitrify NO3− 6. Which element(s) has/have an inorganic reservoir that exists primarily in sedimentary deposits? a. nitrogen c. sulfur b. phosphorus d. both b and c 7. What percentage of the earth’s biomass is made of microbes? a. a small fraction c. all of it b. at least half of it d. all of the above

8. Genomic analysis of the land, sea, and air has shown us that a. there are many more animals than we expected. b. there were much fewer microbes than we expected. c. seawater is much more sterile than we expected. d. microbes colonize places we never imagined. 9. Microbes in the environment are likely to be a. living in biofilms on surfaces. b. living solitary and planktonic lives. c. nonculturable in the lab. d. two of the above. 10. Recent studies reveal that a. 100% of photosynthesis is accomplished by plants. b. viruses may well be responsible for some photosynthesis. c. the sun is the only source of energy for photosynthesis. d. none of the above True-False Questions. If the statement is true, leave as is. If it is false, correct it by rewriting the sentence. 11. Pure cultures are very common in the biosphere. 12. Bioremediation usually involves more than one type of microorganism. 13. The production of all nitrogenous compounds begins with the process called nitrogen fixation. 14. The high mercury content found in some fish is the result of a process called bioaccumulation. 15. As far as we know, all microorganisms exist in multiplespecies communities.

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Critical Thinking Questions

Application and Analysis

These questions are suggested as a writing-to-learn experience. For each question, compose a one- or two-paragraph answer that includes the factual information needed to completely address the question. 1. Compare the concepts of habitat and niche using Chlamydomonas (figure 24.2) as an example. 2. a. Outline the general characteristics of a biogeochemical cycle. b. What are the major sources of carbon, nitrogen, phosphorus, and sulfur? 3. a. In what major forms is carbon found? Name three ways carbon is returned to the atmosphere. b. Name a way it is fixed into organic compounds. c. What form is the least available for the majority of living things? 4. a. Describe nitrogen fixation, ammonification, nitrification, and denitrification. b. What form of nitrogen is required by plants? By animals? 5. a. Describe the structure of the soil and the rhizosphere. b. What is humus? c. Compare and contrast root nodules with mycorrhizae.

7. a. What causes the formation of the epilimnion, hypolimnion, and thermocline? b. What is upwelling? c. In what ways are red tides and eutrophic algal blooms similar and different? 8. What makes the bacterium found living alone in the South African gold mine the type of microbe that could survive on Mars? 9. a. What factors cause energy to decrease with each trophic level? b. How is it possible for energy to be lost and the ecosystem to still run efficiently? c. Are the nutrients on the earth a renewable resource? Why, or why not? 10. What eventually happens to the nutrients that run off into the ocean with sewage and other effluents?

6. a. Outline the modes of cycling water through the lithosphere, hydrosphere, and atmosphere. b. What are the roles of precipitation, condensation, respiration, transpiration, surface water, and aquifers?

Concept Mapping

Synthesis

Appendix D provides guidance for working with concept maps. 1. Supply your own linking words or phrases in this concept map, and provide the missing concepts in the empty boxes.

Oceans Rivers

Lakes

Sun

Plants

Aerobic organisms

Soil moisture Groundwater

Lakes Oceans Seas Rivers

Ice caps Glaciers

Visual Connections

Visual Connections

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Synthesis

These questions use visual images or previous content to make connections to this chapter’s concepts. 1. From chapter 6, figure 6.19. We suggested that bacteriophages in the ocean have two important functions, photosynthesis and the turnover of nutrients. Which of these two activities is more likely to be accomplished when the bacteriophage is in the lysogenic state?

2. From chapter 8, figure 8.26. What process does this represent? How does it link to the biogeochemical cycles from this chapter?

Lysogenic State

Viral DNA becomes latent as prophage.

H 2O

dent epen ht-D ions Lig React

Light-In de React pende Glucose ion s nt

ATP 2H + e NADPH

DNA splits

Viral DNA

Spliced viral genome

O2 Chloroplast

CO2

Bacterial DNA molecule

www.connect.microbiology.com Enhance your study of this chapter with study tools and practice tests. Also ask your instructor about the resources available through ConnectPlus, including the media-rich eBook, interactive learning tools, and animations.

Applied Microbiology and Food and Water Safety 25 Case File There are bacteria adapted to survive in every kind of habitat. There are marine bacteria and freshwater bacteria—and even some that thrive only in brackish waters, which are part marine and part fresh. Lately, bacteria that live in brackish waters have been causing serious wound infections, and even some deaths, in humans. In 2006, a mortgage broker in his 30s fell into a harbor in Hawaii 6 days after a sewage pipe failure had allowed 48 million gallons of sewage to flow into the harbor water. The man was admitted to the hospital, and within days he died from massive organ failure caused by septicemia with Vibrio vulnificus. You may be familiar with Vibrio cholerae, the diarrhea agent. Its relative, V. vulnificus, tends to invade breaks in the skin and then proliferate in the bloodstream, often causing massive infections necessitating amputation, and sometimes even leading to death. ◾ Once the man was admitted to the hospital, what steps would you take to determine what was making him ill? ◾ If you were a public official in charge of Hawaii’s recreational waters, how would you determine when the waters were safe again? Continuing the Case appears on page 769.

Outline and Learning Outcomes 25.1 Applied Microbiology and Biotechnology 1. Define biotechnology. 2. Compose a sentence about the history of applied microbiology.

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25.2 Microorganisms in Water and Wastewater Treatment 3. Outline the steps in water purification. 4. Differentiate water purification from sewage treatment. 5. Describe the primary and secondary phases of sewage treatment. 6. List five important pathogens of drinking water. 7. Explain why indicator bacteria are used as surrogates for pathogenic bacteria in examination of water safety. 8. Discuss the relevance of fecal coliforms. 25.3 Microorganisms Making Food and Spoiling Food 9. Name five foods and/or beverages that benefit from microbial fermentation. 10. Explain what microbial actions lead to leavening in bread. 11. Write the equation for turning yeast and sugar into alcoholic beverages. 12. Discuss why microorganisms themselves might be useful as food products. 13. Provide some background about HACCP procedures. 14. Report 10-year trends in food-borne illness. 15. Outline basic principles of using temperature to preserve food. 16. List mechanisms other than temperature that are used to preserve food. 25.4 Using Microorganisms to Make Things We Need 17. State the general aim(s) of industrial microbiology. 18. Distinguish between primary and secondary metabolites. 19. List the four steps of industrial product production from microbes. 20. List five different types of substances produced from industrial microbiology, and their applications.

25.1 Applied Microbiology and Biotechnology This chapter emphasizes the artificial applications of microbes in communal waste remediation, water treatment, and the manufacture of food, medical, biochemical, drug, and agricultural products. Key to the application of microbes is understanding their ecology (see chapters 7, 8, and 24) and the structure of their natural environments. Microbes have evolved by responding to functional pressures, as when nutrients are limited or unevenly available, or when other organisms are competing for the nutrients. Applied and industrial microbiologists have learned from microbes’ own survival mechanisms and have devised ways to manipulate them for use by people. The profound and sweeping involvement of microbes in the natural world is inescapable. Although our daily encounters with them usually go unnoticed, human and microbial life are clearly intertwined on many levels. It is no wonder that long ago humans realized the power of microbes and harnessed them for specific metabolic tasks. The practical applications of microorganisms in manufacturing products or carrying out a particular decomposition process belong to the large and diverse area of biotechnology. Biotechnology has an ancient history, dating back nearly 6,000 years to those first observant humans who discovered that grape juice left to sit resulted in wine or that bread dough properly infused with a starter would rise. Today, biotechnology has become a fertile ground for hundreds of applications in industry, medicine, agriculture, food sciences, and environmental protec-

tion, and it has even come to include the genetic alterations of microbes and other organisms. Most biotechnological systems involve the actions of bacteria, yeasts, molds, and algae that have been selected or altered to synthesize a certain food, drug, organic acid, alcohol, or vitamin. Many such food and industrial end products are obtained through fermentation, a general term used here to refer to the mass, controlled culture of microbes to produce desired organic compounds. It also includes the use of microbes in sewage control, pollution control, metal mining, and bioremediation, which was introduced in chapter 24 (Insight 25.1).

25.1 Learning Outcomes —Can You . . . 1. . . . define biotechnology? 2. . . . compose a sentence about the history of applied microbiology?

25.2 Microorganisms in Water and Wastewater Treatment Most drinking water comes from rivers, aquifers, and springs. Only in remote, undeveloped, or high mountain areas is this water used in its natural form. In most cities, it must be treated before it is supplied to consumers. Water supplies such as deep wells that are relatively clean and free of contaminants require less treatment than those from surface sources laden with wastes. The stepwise process in water purification as carried

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INSIGHT 25.1

Bioremediation: The Pollution Solution?

The soil and water of the earth have long been considered convenient repositories for solid and liquid wastes. Humans have been burying solid wastes for thousands of years, but the process has escalated in the past 50 years. Every year, about 300 metric tons of pollutants, industrial wastes, and garbage are deposited into the natural environment. Often, this dumping is done with the mistaken idea that naturally occurring microbes will eventually biodegrade (break down) waste material. Landfills currently serve as a final resting place for hundreds of castoffs from an affluent society, including yard wastes, paper, glass, plastics, wood, textiles, rubber, metal, paints, and solvents. This conglomeration is dumped into holes and is covered with soil. Although it is true that many substances are readily biodegradable, materials such as plastics and glass are not. Successful biodegradation also requires a compost containing specific types of microorganisms, adequate moisture, and oxygen. The environment surrounding buried trash provides none of these conditions. Large, dry, anaerobic masses of plant materials, paper, and other organic materials will not be successfully attacked by the aerobic microorganisms that dominate in biodegradation. As we continue to fill up hillsides with waste, the future of these landfills is a prime concern. One of the most serious of these concerns is that they will be a source of toxic compounds that seep into the ground and water.

In a search for solutions, waste management has turned to bioremediation—using microbes to break down or remove toxic wastes in water and soil. Some of these waste-eating microbes are natural soil and water residents with a surprising capacity to decompose even artificial substances. Because the natural, unaided process occurs too slowly, most cleanups are accomplished by commercial bioremediation services that treat the contaminated soil with oxygen, nutrients, and water to increase the rate of microbial action. Through these actions, levels of pesticides such as 2,4-D can be reduced to 96% of their original levels, and solvents can be reduced from 1 million parts per billion (ppb) to 10 ppb or less. Bacteria are also being used to help break up and digest oil from spills and refineries. Among the most important bioremedial microbes are species of Pseudomonas, Geobacter, and Bacillus and various toxin-eating fungi. So far, about 35 recombinant microbes have been created for bioremediation. Species of Rhodococcus and Burkholderia have been engineered to decompose PCBs, and certain forms of Pseudomonas now contain genes for detoxifying heavy metals, carbon tetrachloride, and naphthalene. With over 3,000 toxic waste sites in the United States alone, the need for effective bioremediation is a top priority.

This marsh had been used to dump oil refinery waste. The level of certain pollutants was over 130,000 ppm.

After bioremediation with nutrients and microbes, the levels were reduced to less than 300 ppm in 4 months. This area has been bioremediated to the point that the land may be used for growing plants.

out by most cities is shown in figure 25.1. Treatment begins with the impoundment of water in a large reservoir such as a dam or catch basin that serves the dual purpose of storage and sedimentation. The access to reservoirs is controlled to avoid contamination by animals, wastes, and runoff water. In addition, overgrowth of cyanobacteria and algae that add undesirable qualities to the water is prevented by pretreatment with copper sulfate (0.3 ppm). Sedimentation to remove large particulate matter is also encouraged during this storage period. Next, the water is pumped to holding ponds or tanks, where it undergoes further settling, aeration, and filtration.

Source: 2006. Proceedings of the National Academy of Science 103:15280–15287.

The water is filtered first through sand beds or pulverized diatomaceous earth to remove residual bacteria, viruses, and protozoa and then through activated charcoal to remove undesirable organic contaminants. Pipes coming from the filtration beds collect the water in storage tanks. The final step in treatment is chemical disinfection by bubbling chlorine gas through the tank until it reaches a concentration of 1 to 2 ppm (some municipal plants use chloramines for this purpose) (see chapter 11). A few pilot plants in the United States are using ozone or peroxide for final disinfection, but these methods are expensive and cannot sustain an antimicrobial

25.2

Sedimentation, addition of inhibitors

Catch basin of untreated water

Pumping station

Aeration, settling

Filtration

Holding tank

Sand Charcoal

Chlorination

Storage

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Tank of treated water

To consumer through domestic water pipes

Figure 25.2 Water: one source, many uses. but a large quantity is still being emptied raw (untreated) into the aquatic environment primarily because heavily contaminated waters require far more stringent and costly methods of treatment than are currently available to most cities. Sewage contains large amounts of solid wastes, dissolved organic matter, and toxic chemicals that pose a health risk. To remove all potential health hazards, treatment typically requires three phases: The primary stage separates out large matter; the secondary stage reduces remaining matter and can remove some toxic substances; and the tertiary stage completes the purification of the water (figure 25.3). Microbial activity is an integral part of the overall process. The systems for sewage treatment are massive engineering marvels. In the primary phase of treatment, floating bulkier materials such as paper, plastic waste, and bottles are skimmed Primary Stage

Secondary Stage

Sludge

Raw sewage

Figure 25.1 The major steps in water purification as

carried out by a modern municipal treatment plant.

effect over long storage times. The final quality varies, but most tap water has a slight odor or taste from disinfection. In many parts of the world, the same water that serves as a source of drinking water is also used as a dump for solid and liquid wastes (figure 25.2). Continued pressure on the finite water resources may require reclaiming and recycling of contaminated water such as sewage. Sewage is the used wastewater draining out of homes and industries that contains a wide variety of chemicals, debris, and microorganisms. The dangers of typhoid, cholera, and dysentery linked to the unsanitary mixing of household water and sewage have been a threat for centuries. In current practice, some sewage is treated to reduce its microbial load before release,

digester

Tertiary Stage

Supernatant H2O digester Solids

Liquid residue

Mixed

Aerated

Filtered

Filtered Skimming, settling

Settled solids

Chlorination

Solid wastes Disposal

Treated sewage released into Disposed or reclaimed body of water for anaerobic digester

Figure 25.3 The primary, secondary, and tertiary stages in sewage treatment.

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off. The remaining smaller, suspended particulates are allowed to settle. Sedimentation in settling tanks usually takes 2 to 10 hours and leaves a mixture rich in organic matter. This aqueous residue is carried into a secondary phase of active microbial decomposition, or biodegradation. In this phase, a diverse community of natural bioremediators (bacteria, algae, and protozoa) aerobically decomposes the remaining particles of wood, paper, fabrics, petroleum, and organic molecules inside a large digester tank (figure 25.4). This forms a suspension of material called sludge that tends to settle out and slow the process. To hasten aerobic decomposition of the sludge, most processing plants have systems to activate it by injecting air, mechanically stirring it, and recirculating it. A large amount of organic matter is mineralized into sulfates, nitrates, phosphates, carbon dioxide, and water. Certain volatile gases such as hydrogen sulfide, ammonia, nitrogen, and methane may also be released. Water from this process is siphoned off and carried to the tertiary

phase, which involves further filtering and chlorinating prior to discharge. Such reclaimed sewage water is usually used to water golf courses and parks rather than for drinking, or it is gradually released into large bodies of water. In some cases, the solid waste that remains after aerobic decomposition is harvested and reused. Its rich content of nitrogen, potassium, and phosphorus makes it a useful fertilizer. It is estimated that 63 percent of the 5.6 million tons of sludge made in the United States annually is recycled and applied to land. This has been viewed as a “green” alternative to burying or burning the sludge. But scientists are now raising concerns that hundreds of thousands of pounds of potent antimicrobial substances such as triclosan are also being spread on the ground, since these chemicals accumulate in the sludge and are not degraded by the typical process of wastewater treatment. Surprisingly, the levels of these substances in reused sludge are not regulated by the Environmental Protection Agency. The EPA does set acceptable levels for metals and for certain pathogenic bacteria. Recently, scientists found a way to harness the bacteria found in sewage to construct a microbial fuel cell to produce usable energy. In these experiments, wastewater bacteria form biofilms on special rods inserted in the sewage that is being treated. These biofilms generate electrons that are transferred via copper wires to cathodes, producing electricity. Considering the mounting waste disposal and energy shortage problems, these technologies should gain momentum.

Water Monitoring to Prevent Disease Microbiology of Drinking Water Supplies (a)

(b)

Figure 25.4 Treatment of sewage and wastewater. (a) Digester tanks used in the primary phase of treatment; each tank can process several million gallons of raw sewage a day. (b) View inside the secondary reactor shows the large stirring paddle that mixes the sludge to aerate it to encourage microbial decomposition.

We do not have to look far for overwhelming reminders of the importance of safe water. Worldwide epidemics of cholera have killed thousands of people, and an outbreak of Cryptosporidium in Wisconsin in the 1990s affecting 370,000 people was traced to a contaminated municipal water supply. In a large segment of the world’s population, the lack of sanitary water is responsible for billions of cases of diarrheal illness that kill 3 million children each year (see chapter 22). In the United States, nearly 1 million people develop water-borne illness every year. Good health is dependent on a clean, potable (drinkable) water supply. This means the water must be free of pathogens; dissolved toxins; and disagreeable turbidity, odor, color, and taste. As we shall see, water of high quality does not come easily, and we must look to microbes as part of the problem and part of the solution. Through ordinary exposure to air, soil, and effluents, surface waters usually acquire harmless, saprobic microorganisms. But along its course, water can also pick up pathogenic contaminants. Among the most prominent water-borne pathogens of recent times are the protozoa Giardia and Cryptosporidium; the bacteria Campylobacter, Salmonella, Shigella, Vibrio, and Mycobacterium; and hepatitis A and Norwalk viruses. Some of these agents (especially encysted protozoa) can survive in natural waters for long periods without a human host, whereas others are present only transiently and are rapidly lost. The microbial content of drinking water must be continuously monitored to ensure that the water is free of infectious agents.

25.2

Attempting to survey water for specific pathogens can be very difficult and time-consuming, so most assays of water purity are more focused on detecting fecal contamination. High fecal levels can mean the water contains pathogens and is consequently unsafe to drink. Thus, wells, reservoirs, and other water sources can be analyzed for the presence of various indicator bacteria. These species are intestinal residents of birds and mammals, and they are readily identified using routine lab procedures. Enteric bacteria most useful in the routine monitoring of microbial pollution are gram-negative rods called coliforms and enteric streptococci, which survive in natural waters but do not multiply there. Finding them in high numbers thus implicates recent or high levels of fecal contamination. Environmental Protection Agency standards for water sanitation are based primarily on the levels of coliforms, which are described as gram-negative, lactose-fermenting, gas-producing bacteria such as Escherichia coli, Enterobacter, and Citrobacter. Fecal contamination of marine waters that poses a risk for gastrointestinal disease is more readily correlated with gram-positive cocci, primarily in the genus Enterococcus. Occasionally, coliform bacteriophages and reoviruses (the Norwalk virus) are good indicators of fecal pollution, but their detection is more difficult and more technically demanding.

Water Quality Assays A rapid method for testing the total bacterial levels in water is the standard plate count. In this technique, a small sample of water is spread over the surface

INSIGHT 25.2

Microorganisms in Water and Wastewater Treatment

767

of a solid medium. The numbers of colonies that develop provide an estimate of the total viable population without differentiating coliforms from other species. This information is particularly helpful in evaluating the effectiveness of various water purification stages. Another general indicator of water quality is the level of dissolved oxygen it contains. It is established that water containing high levels of organic matter and bacteria will have a lower oxygen content because of consumption by aerobic respiration.

Coliform Enumeration Water quality departments employ some standard assays for routine detection and quantification of coliforms. The techniques available are: • simple tests, such as presence-absence broth, that detect coliform activity but do not quantify it; • rapid tests that isolate coliform colonies and provide quantities of coliforms present; and • rapid tests that identify specific coliforms and determine numbers. In many circumstances (drinking water, for example), it is important to differentiate between facultative coliforms (Enterobacter) that are often found in other habitats (soil, water) and true fecal coliforms that live mainly in human and animal intestines. Microbiologists are calling for the discontinuation of the use of coliforms as an indicator of fecal contamination (Insight 25.2). But this method is still widespread, so we cover its principles here.

The Waning Days of a Classic Test?

Keeping water and the seafood we harvest from it free from fecal contamination is absolutely imperative in making it safe to ingest. In the late 1800s, it was suggested that a good way to determine if water or its products had been exposed to feces was to test for E. coli. Although most E. coli strains are not pathogenic, they almost always come from a mammal’s intestinal tract so their presence in a sample is a clear indicator of fecal contamination. Because at the time it was too difficult to differentiate E. coli from the closely related species of Citrobacter, Klebsiella, and Enterobacter, laboratories instead simply reported whether a sample contained one of these isolates. (All of these bacteria ferment lactose and are phenotypically similar.) The terminology adopted was “coliform-” (E. coli– like) positive or negative. In other words, one of these bacteria was present in the sample but it was not necessarily E. coli. The use of this coliform assay has been the standard procedure since 1914, and it is still in widespread use. Pick up a newspaper in the summer, and you will likely find a report about a swimming pool or a river with a high coliform count. Coliform counts are also used to regulate food production and to trace the causes of food-borne outbreaks. Recently, microbiologists have noted serious problems with the use of coliforms to indicate fecal contamination. The main issue is that the three other bacterial species already mentioned, among others, are commonly found

growing in nonfecal environments such as fresh water and plants that eventually become food. In other words, if you’re not looking specifically for E. coli, you can’t be sure you’re looking for feces. In 1995, there was a minor panic when media outlets reported that iced tea from restaurants contained significant numbers of “fecal coliforms.” The public was outraged. One headline read, “Iced Tea Worse Than River Water.” Restaurants were named, and their reputations were damaged. When scientists did more detailed testing, they found that the predominant species found were Klebsiella and Enterobacter, both of which are normal colonizers of plants, such as tea leaves. Furthermore, despite the reports of widespread contamination with large numbers of “fecal coliforms,” no one ever became sick from drinking iced tea. Microbiologists are now advocating that E. coli alone—not the outdated grouping of coliforms—be used as an indicator of fecal contamination. Newer identification techniques make this as simple, if not simpler, than the standard coliform tests. But old habits die hard, and regulatory and public laboratories are proving slow to convert to the E. coli standard. An additional wrinkle has been added by the discovery by a research group in 2008 that E. coli can be present in biofilms on surfaces that the water is exposed to, without being detected by methods that only sample the water phase.

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The membrane filter method is a widely used rapid method that can be used in the field or lab to process and test larger quantities of water. This method is more suitable for dilute fluids, such as drinking water, that are relatively free of particulate matter, and it is less suitable for water containing heavy microbial growth or debris. This technique is related to the method described in chapter 11 for sterilizing fluids by filtering out microbial contaminants, except that in this system, the filter containing the trapped microbes is the desired end product. The steps in membrane filtration are diagrammed in figure 25.5a,b. After filtration, the membrane filter is placed in a Petri dish containing selective broth. After incubation, both nonfecal and fecal coliform colonies can be counted and often presumptively identified by their distinctive characteristics on these media (figure 25.5c,d). Another more time-consuming but useful technique is the most probable number (MPN) procedure, which detects coliforms by a series of presumptive, confirmatory, and completed tests. The presumptive test involves three subsets of fermentation tubes, each containing different amounts

of lactose or lauryl tryptose broth. The three subsets are inoculated with various-size water samples. After 24 hours of incubation, the tubes are evaluated for gas production. A positive test for gas formation is presumptive evidence of coliforms; negative for gas means no coliforms. The number of positive tubes in each subset is tallied, and this set of numbers is applied to a statistical table to estimate the most likely or probable concentration of coliforms. It does not specifically detect fecal coliforms. When a test is negative for coliforms, the water is considered generally fit for human consumption. But even slight coliform levels are allowable under some circumstances. For example, municipal waters can have a maximum of 4 coliforms per 100 ml; private wells can have an even higher count. There is no acceptable level for fecal coliforms, enterococci, viruses, or pathogenic protozoa in drinking water. Waters that will not be consumed but are used for fishing or swimming are permitted to have counts of 70 to 200 coliforms per 100 ml. If the coliform level of recreational water reaches 1,000 coliforms per 100 ml, health departments usually bar its usage.

(a) Membrane filter technique. The water sample is filtered through a sterile membrane filter assembly and collected in a flask.

(b) The filter is removed and placed in a small Petri dish containing a differential selective medium such as M-FD endo agar and incubated. (c) On M-FD endo medium, colonies of Escherichia coli often yield a noticeable metallic sheen. The medium permits easy differentiation of various genera of coliforms, and the grid pattern can be used as a guide for rapidly counting the colonies.

(d) Some tests for water-borne coliforms are based on formation of specialized enzymes to metabolize lactose. The MI tests shown here utilize synthetic substrates that release a colored substance when the appropriate enzymes are present. The total coliform count is indicated by the plate on the left; fecal coliforms (E. coli ) are seen in the plate on the right. This test is especially accurate with surface or groundwater samples. Total coliforms fluoresce under a black light.

E. coli colonies are blue under natural light.

Figure 25.5 Rapid methods of water analysis for coliform contamination.

25.3

Case File 25

Continuing the Case

The man sickened by the sewage spill had cuts on his feet, providing an obvious portal of entry for water-borne bacteria into his bloodstream. The infection seemed systemic, since he had a high fever and symptoms in many areas of his body. For these reasons, the most logical diagnostic procedure was to take a blood sample and perform blood cultures. When this was done, his blood grew V. vulnificus. As for the water and its potential threat to others, a microbiology team from the University of Hawaii was sent to investigate bacteria levels in the harbor water. The team counted the number of V. vulnificus in the water and concluded that neither more nor less were present than in other brackish waters around the area. However, the count was conducted 11 days after the end of the sewage spill (and, coincidentally, 11 days after the man had been in the water and become ill). So it is hard to say how high the levels of bacteria were at the time the man was in the water. Nevertheless, the team declared the waters “safe,” based on their observation that the bacteria levels were similar to those in other waters in the area. ◾ The incidence of V. vulnificus infections is increasing, especially in northern parts of the United States, compared to 10 years ago. Can you think of any reason why this might be happening?

25.2 Learning Outcomes—Can You . . . 3. . . . outline the steps in water purification? 4. . . . differentiate water purification from sewage treatment? 5. . . . describe the primary and secondary phases of sewage treatment? 6. . . . list five important pathogens of drinking water? 7. . . . explain why indicator bacteria are used as surrogates for pathogenic bacteria in examination of water safety? 8. . . . discuss the relevance of fecal coliforms?

25.3 Microorganisms Making Food and Spoiling Food All human food—from vegetables to caviar to cheese—comes from some other organism, and rarely is it obtained in a sterile, uncontaminated state. Food is but a brief stopover in the overall scheme of biogeochemical cycling. This means that microbes and humans are in direct competition for the nutrients in food, and we must be constantly aware that microbes’ fast growth rates give them the winning edge. Somewhere along the route of procurement, processing, or preparation,

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food becomes contaminated with microbes from the soil, the bodies of plants and animals, water, air, food handlers, or utensils. The final effects depend on the types and numbers of microbes and whether the food is cooked or preserved. In some cases, specific microbes can even be added to food to obtain a desired effect. The effects of microorganisms on food can be classified as beneficial, detrimental, or neutral to humans, as summarized by the following outline: Beneficial Effects Food is fermented or otherwise chemically changed by the addition of microbes or microbial products to alter or improve flavor, taste, or texture. Microbes can serve as food. Detrimental Effects Microbes cause food poisoning or food-borne illness. Microbes spoil food. Growth of microbes makes food unfit for consumption; adds undesirable flavors, appearance, and smell; destroys food value. Neutral Effects The presence or growth of certain microbes does not cause disease or change the nature of the food. As long as food contains no harmful substances or organisms, its suitability for consumption is largely a matter of taste. But what tastes like rich flavor to some may seem like decay to others. The test of whether certain foods are edible is guided by culture, experience, and preference. The flavors, colors, textures, and aromas of many cultural delicacies are supplied by bacteria and fungi. Poi, pickled cabbage, Norwegian fermented fish, and Limburger cheese are notable examples. If you examine the foods of most cultures, you will find some foods that derive their delicious flavor from microbes.

Microbial Fermentations in Food Products from Plants In contrast to methods that destroy or keep out unwanted microbes, many culinary procedures deliberately add microorganisms and encourage them to grow. Common substances such as bread, cheese, beer, wine, yogurt, and pickles are the result of food fermentations. These reactions actively encourage biochemical activities that impart a particular taste, smell, or appearance to food. The microbe or microbes can occur naturally on the food substrate, as in sauerkraut, or they can be added as pure or mixed samples of known bacteria, molds, or yeasts called starter cultures. Many food fermentations are synergistic, with a series of microbes acting in concert to convert a starting substrate to the desired end product. Because large-scale production of fermented milk, cheese, bread, alcoholic brews, and vinegar depends upon inoculation with starter cultures, considerable effort is spent selecting, maintaining, and preparing these cultures and excluding contaminants that can spoil the fermentation. Most starting raw materials are of plant origin (grains, vegetables, beans) and, to a lesser extent, of animal origin (milk, meat).

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Bread Microorganisms accomplish three functions in bread making: 1. leavening the flour-based dough, 2. imparting flavor and odor, and 3. conditioning the dough to make it workable. Leavening is achieved primarily through the release of gas to produce a porous and spongy product. Without leavening, bread dough remains dense, flat, and hard. Although various microbes and leavening agents can be used, the most common ones are various strains of the baker’s yeast Saccharomyces cerevisiae. Other gas-forming microbes such as coliform bacteria, certain Clostridium species, heterofermentative lactic acid bacteria, and wild yeasts can be employed, depending on the type of bread desired. Yeast metabolism requires a source of fermentable sugar such as maltose or glucose. Because the yeast respires aerobically in bread dough, the chief products of maltose fermentation are carbon dioxide and water rather than alcohol (the main product in beer and wine). Other contributions to bread texture come from kneading, which incorporates air into the dough, and from microbial enzymes, which break down flour proteins (gluten) and give the dough elasticity. Besides carbon dioxide production, bread fermentation generates other volatile organic acids and alcohols that impart delicate flavors and aromas. These are especially well developed in handmade bread, which is leavened more slowly than commercial bread. Yeasts and bacteria can also impart unique flavors, depending upon the culture mixture and baking techniques used. The pungent flavor of rye bread, for example, comes in part from starter cultures of lactic acid bacteria such as Lactobacillus plantarum, L. brevis, L. bulgaricus, Leuconostoc mesenteroides, and Streptococcus thermophilus. Sourdough bread gets its unique tang from Lactobacillus sanfrancisco.

Beer The production of alcoholic beverages takes advantage of another useful property of yeasts. By fermenting carbohydrates in fruits or grains anaerobically, they produce ethyl alcohol, as shown by this equation:

process, called malting, releases amylases that convert starch to dextrins and maltose, and proteases that digest proteins. Other sugar and starch supplements added in some forms of beer are corn, rice, wheat, soybeans, potatoes, and sorghum. After the sprouts have been separated, the remaining malt grain is dried and stored in preparation for mashing. The malt grain is soaked in warm water and ground up to prepare a mash. Sugar and starch supplements are then introduced to the mash mixture, which is heated to a temperature of about 65°C to 70°C. During this step, the starch is hydrolyzed by amylase and simple sugars are released. Heating this mixture to 75°C stops the activity of the enzymes. Solid particles are next removed by settling and filtering. Wort, the clear fluid that comes off, is rich in dissolved carbohydrates. It is boiled for about 2.5 hours with hops, the dried scales of the female flower of Humulus lupulus (figure 25.6), to extract the bitter acids and resins that give aroma and flavor to the finished product. Boiling also caramelizes the sugar and imparts a golden or brown color, destroys any bacterial contaminants that can destroy flavor, and concentrates the mixture. The filtered and cooled supernatant is then ready for the addition of yeasts and fermentation. Fermentation begins when wort is inoculated with a species of Saccharomyces that has been specially developed for beer making. Top yeasts such as Saccharomyces cerevisiae function at the surface and are used to produce the higher alcohol content of ales. Bottom yeasts such as S. uvarum (carlsbergensis) function deep in the fermentation vat and are used to make other beers. In both cases, the initial inoculum of yeast starter is aerated briefly to promote rapid growth and increase the load of yeast cells. Shortly thereafter, an insulating blanket of foam and carbon dioxide develops on the surface of the vat and promotes anaerobic conditions (figure 25.7). During 8 to 14 days of fermentation, the wort sugar is converted chiefly to ethanol and carbon dioxide. The diversity of flavors in the finished product is partly due to the release of small amounts of glycerol, acetic acid, and esters. Fermentation is self-limited, and it essentially ceases when a concentration of 3% to 6% ethyl alcohol is reached. Freshly fermented, or “green,” beer is lagered, meaning it is held for several weeks to months in vats near 0°C. Dur-

C6H12O6 → 2C2H5OH + 2CO2 (Yeast + Sugar = Ethanol + Carbon dioxide) Depending on the starting materials and the processing method, alcoholic beverages vary in alcohol content and flavor. The principal types of fermented beverages are beers, wines, and spirit liquors. The earliest evidence of beer brewing appears in ancient tablets by the Sumerians and Babylonians around 6000 BC. The starting ingredients for both ancient and present-day versions of beer, ale, stout, porter, and other variations are water, malt (barley grain), hops, and special strains of yeasts. The steps in brewing include malting, mashing, adding hops, fermenting, aging, and finishing. For brewer’s yeast to convert the carbohydrates in grain into ethyl alcohol, the barley must first be sprouted and softened to make its complex nutrients available to yeasts. This

Figure 25.6 Hops. Female flowers of hops, the herb that gives beer some of its flavor and aroma.

25.3

Figure 25.7

Anaerobic conditions in homemade beer production. A layer of carbon dioxide foam keeps oxygen out.

Microorganisms Making Food and Spoiling Food

any fruit can be rendered into wine. The essential starting point is the preparation of must, the juice given off by crushed fruit that is used as a substrate for fermentation. In general, grape wines are either white or red. The color comes from the skins of the grapes, so white wine is prepared either from white-skinned grapes or from red-skinned grapes that have had the skin removed. Red wine comes from the redor purple-skinned varieties. Major steps in making wine include must preparation (crushing), fermentation, storage, and aging (figure 25.8).

Processing Step

Outcome Formation of must with fruit sugars

Grape pressing

ing this maturation period, yeast, proteins, resin, and other materials settle, leaving behind a clear, mellow fluid. Lager beer is subjected to a final filtration step to remove any residual yeasts that could spoil it. Finally, it is carbonated with carbon dioxide collected during fermentation and packaged in kegs, bottles, or cans.

Heat sterilization

Elimination of contaminants

Yeast inoculation

Addition of desired organisms

Wine and Liquors Wine is traditionally considered any alcoholic beverage arising from the fermentation of grape juice, but practically

Fermentation of must

Alcohol production from sugars

Tank

Storage in barrels to age

Development of final wine bouquet

Barrel

Filtration and collection

Removal of yeast and particles

Bottling

(a)

771

(b)

Figure 25.8 Wine making. (a) Wine fermentation vats in a large commercial winery. (b) General steps in wine making.

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For proper fermentation, must should contain 12% to 25% glucose or fructose, so the art of wine making begins in the vineyard. Grapes are harvested when their sugar content reaches 15% to 25%, depending on the type of wine to be made. Grapes from the field carry a mixed biofilm on their surface called the bloom that can serve as a source of wild yeasts. Some wine makers allow these natural yeasts to dominate, but many wineries inoculate the must with a special strain of Saccharomyces cerevisiae, variety ellipsoideus. To discourage yeast and bacterial spoilage agents, wine makers sometimes treat grapes with sulfur dioxide or potassium metabisulfite. The inoculated must is thoroughly aerated and mixed to promote rapid aerobic growth of yeasts, but when the desired level of yeast growth is achieved, anaerobic alcoholic fermentation is begun. The temperature of the vat during fermentation must be carefully controlled to facilitate alcohol production. The length of fermentation varies from 3 to 5 days in red wines and from 7 to 14 days in white wines. The initial fermentation yields ethanol concentrations reaching 7% to 15% by volume, depending on the type of yeast, the source of the juice, and ambient conditions. The fermented juice (raw wine) is decanted and transferred to large vats to settle and clarify. Before the final aging process, it is flash-pasteurized to kill microorganisms and filtered to remove any remaining yeasts and sediments. Wine is aged in wooden casks for varying time periods (months to years), after which it is bottled and stored for further aging. During aging, nonmicrobial changes produce aromas and flavors (the bouquet) characteristic of a particular wine. The fermentation processes discussed thus far can only achieve a maximum alcoholic content of 17%, because concentrations above this level inhibit the metabolism of the yeast. The fermentation product must be distilled to obtain higher concentrations such as those found in liquors. During distillation, heating the liquor separates the more volatile alcohol from the less volatile aqueous phase. The alcohol is then condensed and collected. The alcohol content of distilled liquors is rated by proof, a measurement that is usually two times the alcohol content. Thus, 80 proof vodka contains 40% ethyl alcohol. Distilled liquors originate through a process similar to wine making, although the starting substrates can be extremely diverse. In addition to distillation, liquors can be subjected to special treatments such as aging to provide unique flavor or color. Vodka, a colorless liquor, is usually prepared from fermented potatoes, and rum is distilled from fermented sugarcane. Assorted whiskeys are derived from fermented grain mashes; rye whiskey is produced from rye mash, and bourbon from corn mash. Brandy is distilled grape, peach, or apricot wine.

in an anaerobic salty solution (brine) to extract sugar and nutrient-laden juices. The salt also disperses bacterial clumps, and its high osmotic pressure inhibits proteolytic bacteria and sporeformers that can spoil the product. Sauerkraut is the fermentation product of cabbage. Cabbage is washed, wilted, shredded, salted, and packed tightly into a fermentation vat. Weights cover the cabbage mass and squeeze out its juices. The fermentation is achieved by natural cabbage microbiota or by an added culture. The initial agent of fermentation is Leuconostoc mesenteroides, which grows rapidly in the brine and produces lactic acid. It is followed by Lactobacillus plantarum, which continues to raise the acid content to as high as 2% (pH 3.5) by the end of fermentation. The high acid content restricts the growth of spoilage microbes. Fermented cucumber pickles come chiefly in salt and dill varieties. Salt pickles are prepared by washing immature cucumbers, placing them in barrels of brine, and allowing them to ferment for 6 to 9 weeks. The brine can be inoculated with Pediococcus cerevisiae and Lactobacillus plantarum to avoid unfavorable qualities caused by natural microbiota and to achieve a more consistent product. Fermented dill pickles are prepared in a somewhat more elaborate fashion, with the addition of dill herb, spices, garlic, onion, and vinegar. Natural vinegar is produced when the alcohol in fermented plant juice is oxidized to acetic acid, which is responsible for the pungent odor and sour taste. Although a reasonable facsimile of vinegar could be made by mixing about 4% acetic acid and a dash of sugar in water, this preparation would lack the traces of various esters, alcohol, glycerin, and volatile oils that give natural vinegar its pleasant character. Vinegar is actually produced in two stages. The first stage is similar to wine or beer making, in which a plant juice is fermented to alcohol by Saccharomyces. The second stage involves an aerobic fermentation carried out by acetic acid bacteria in the genera Acetobacter and Gluconobacter. These bacteria oxidize the ethanol in a two-step process, as shown here:

Other Fermented Plant Products

Microbes in Milk and Dairy Products

Fermentation provides an effective way of preserving vegetables, as well as enhancing flavor with lactic acid and salt. During pickling fermentations, vegetables are immersed

Milk has a highly nutritious composition. It contains an abundance of water and is rich in minerals, protein (chiefly casein), butterfat, sugar (especially lactose), and vitamins. It starts its

2C2H5OH + 1/2 O2 → CH3CHO + H2O Ethanol Acetaldehyde CH3CHO + 1/2 O2 → CH3COOH Acetaldehyde Acetic acid The abundance of oxygen necessary in commercial vinegar making is furnished by exposing inoculated raw material to air by arranging it in thin layers in open trays, allowing it to trickle over loosely packed beechwood twigs and shavings, or aerating it in a large vat. Different types of vinegar are derived from substrates such as apple cider (cider vinegar), malted grains (malt vinegar), and grape juice (wine vinegar).

25.3

journey in the udder of a mammal as a sterile substance, but as it passes out of the teat, it is inoculated by the animal’s normal biota. Other microbes can be introduced by milking utensils. Because milk is a nearly perfect culture medium, it is highly susceptible to microbial growth. When raw milk is left at room temperature, a series of bacteria ferment the lactose, produce acid, and alter the milk’s content and texture (figure 25.9). This progression can occur naturally, or it can be induced, as in the production of cheese and yogurt. In the initial stages of milk fermentation, lactose is rapidly attacked by Streptococcus lactis and Lactobacillus species. The resultant lactic acid accumulation and lowered pH cause the milk proteins to coagulate into a solid mass called the curd. Curdling also causes the separation of a watery liquid called whey on the surface. Curd can be produced by microbial action or by an enzyme, rennin (casein coagulase), which is isolated from the stomach of unweaned calves.

Cheese Since 5000 BC, various forms of cheese have been produced by spontaneous fermentation of cow, goat, or sheep milk. Present-day, large-scale cheese production is carefully controlled and uses only freeze-dried samples of pure cultures. These are first inoculated into a small quantity of pasteurized milk to form an active starter culture. This amplified culture is subsequently inoculated into a large vat of milk, where rapid curd development takes place. Such rapid growth is desired because it promotes the overgrowth of the desired inoculum and prevents the activities of undesirable contaminants. Rennin is usually added to increase the rate of curd formation.

Figure 25.9 Microbes at work in milk products. Litmus milk is a medium used to indicate pH and consistency changes in milk resulting from microbial action. The first tube is an uninoculated, unchanged control. The second tube has a white, decolorized zone indicative of litmus reduction. The third tube has become acidified (pink), and its proteins have formed a loose curd. In the fourth tube, digestion of milk proteins has caused complete clarification or peptonization of the milk. The fifth tube shows a well-developed solid curd overlaid by a clear fluid, the whey.

Microorganisms Making Food and Spoiling Food

773

After its separation from whey, the curd is rendered to produce one of the 20 major types of soft, semisoft, or hard cheese (figure 25.10). The composition of cheese is varied by adjusting water, fat, acid, and salt content. Cottage and cream cheese are examples of the soft, more perishable variety. After light salting and the optional addition of cream, they are ready for consumption without further processing. Other cheeses acquire their character from “ripening,” a complex curing process involving bacterial, mold, and enzyme reactions that develop the final flavor, aroma, and other features characteristic of particular cheeses. The distinctive traits of soft cheeses such as Limburger, Camembert, and Liederkranz are acquired by ripening with a reddish-brown mucoid coating of yeasts, micrococci, and molds. The microbial enzymes permeate the curd and ferment lipids, proteins, carbohydrates, and other substrates. This process leaves assorted acids and other by-products that give the finished cheese powerful aromas and delicate flavors. Semisoft varieties of cheese such as Roquefort, bleu, or Gorgonzola are infused and aged with a strain of Penicillium roqueforti mold. Hard cheeses such as Swiss, cheddar, and Parmesan develop a sharper flavor by aging with selected bacteria. The pockets in Swiss cheese come from entrapped carbon dioxide formed by Propionibacterium, which is also responsible for its bittersweet taste.

Other Fermented Milk Products Yogurt is formed by the fermentation of milk by Lactobacillus bulgaricus and Streptococcus thermophilus. These organisms produce organic acids and other flavor components and can grow in such numbers that a gram of yogurt regularly contains 100 million bacteria. Live cultures of Lactobacillus acidophilus are an important additive to acidophilus milk, which is said to benefit digestion and to help maintain the normal biota of the intestine. Fermented milks such as kefir, koumiss, and buttermilk are a basic food source in many cultures.

Figure 25.10 Cheese making. The curd-cutting stage in the making of cheddar cheese.

Chapter 25 Applied Microbiology and Food and Water Safety

Prevention Measures for Food Poisoning and Spoilage It will never be possible to avoid all types of food-borne illness because of the ubiquity of microbes in air, water, food, and the human body. But most types of food poisoning require the growth of microbes in the food. In the case of food infections, an infectious dose (sufficient cells to initiate infection) must be present, and in food intoxication, enough cells to produce the toxin must be present. Thus, food poisoning or spoilage can be prevented by proper food handling, preparation, and storage. The methods shown in figure 25.12 1. One-third of all reported cases result from eating restaurant food.

100

Microbial Involvement in Food-Borne Diseases

Increase

60 40

Percent change

20 No change

0 –20 –40

Decrease

–60

Cryptosporidium

Yersinia

Vibrio

–100

STEC* 0157

–80 Campylobacter

The CDC estimates that several million people suffer each year from some form of food infection (see chapter 22). Until very recently, reports of food poisoning were escalating rapidly in the United States and worldwide. Outbreaks attributed to common pathogens (Salmonella, E. coli, Vibrio, hepatitis A, Listeria, Campylobacter, and various protozoa) had doubled in the past 20 years. A major factor in the escalation was the mass production and distribution of processed food such as raw vegetables, fruits, and meats. Improper handling can lead to gross contamination of these products with soil or animal wastes. Growing concerns about food safety led to a new approach to regulating the food industry. The system is called Hazard Analysis and Critical Control Point, or HACCP, and it is adapted from procedures crafted for the space program in the 1970s. It involves principles that are more systematic and scientific than previous random-sampling quality procedures. The program focuses on the identification, evaluation, control, and prevention of hazards at all stages of the food production process. Since 1998, HACCP has been phased in by the U.S. Department of Agriculture for meat and poultry processing plants and by the Food and Drug Administration for seafood

Percent change estimate 95% confidence interval

80

Shigella

At first, the thought of eating bacteria, molds, algae, and yeasts may seem odd or even unappetizing. We do eat their macroscopic relatives, such as mushrooms, truffles, and seaweed, but we are used to thinking of the microscopic forms as agents of decay and disease or, at most, as food flavorings. The consumption of microorganisms is not a new concept. In Germany during World War II, it became necessary to supplement the diets of undernourished citizens by adding yeasts and molds to foods. Several countries now commercially mass-produce food yeasts, bacteria, and in a few cases, algae. Although eating microbes has yet to win total public acceptance, their use as feed supplements for livestock is increasing. A technology that shows some promise in increasing world food productivity is single-cell protein (SCP). This material is produced from waste materials such as molasses from sugar refining, petroleum by-products, and agricultural wastes. In England, an animal feed called Pruteen is produced by mass culture of the bacterium Methylophilus methylotrophus. Mycoprotein, a product made from the fungus Fusarium graminearum, is also sold there. The filamentous texture of this product makes it a likely candidate for producing meat substitutes for human consumption. Health food stores carry bottles of dark green pellets or powder that are a culture of a spiral-shaped cyanobacterium called Spirulina. This microbe is harvested from the surface of lakes and ponds, where it grows in great mats. In some parts of Africa and Mexico, Spirulina has become a viable alternative to green plants as a primary nutrient source. It can be eaten in its natural form or added to other foods and beverages.

and juice plants. HACCP projects are taking place in facilities that process cheese, breakfast cereals, salad dressings, and bread. Figure 25.11 shows the changes that have taken place in the last decade in the incidences of specific confirmed foodborne diseases. You see that illness caused by most of the foodborne organisms has significantly decreased (this is the case when both the data point and the bars representing the confidence intervals are below the “no change” bar). Salmonella and Campylobacter show no significant change over the decade. The only food-borne illness showing a significant increase is that caused by Vibrio species. Keep in mind that many reported food poisoning outbreaks occur where contaminated food has been served to large groups of people,1 but most cases probably occur in the home and are not reported.

Salmonella

Microorganisms as Food

Listeria

774

*Shiga-toxin-producing Escherichia coli

Figure 25.11 Percentage change in incidence of foodborne illnesses in 2008 in United States compared with 1996–1998. Data are from the Foodborne Diseases Active Surveillance Network, and include only laboratory-confirmed cases of bacterial and parasitic illness.

25.3

Microorganisms Making Food and Spoiling Food

775

are aimed at preventing the incorporation of microbes into food, removing or destroying microbes in food, and keeping microbes from multiplying.

Care in Harvesting, Preparation

Preventing the Incorporation of Microbes into Food

Destruction of Microbes Heat Canning Pasteurization

Cooking

Radiation

Most agricultural products such as fruits, vegetables, grains, meats, eggs, and milk are naturally exposed to microbes. Vigorous washing reduces the levels of contaminants in fruits and vegetables, whereas meat, eggs, and milk must be taken from their animal source as aseptically as possible. Aseptic techniques are also essential in the kitchen. Contamination of foods by fingers can be easily remedied by hand washing and proper hygiene, and contamination by flies or other insects can be stopped by covering foods or eliminating pests from the kitchen. Care and common sense also apply in managing utensils. It is important to avoid cross-contaminating food by, for example, using the same cutting board for meat and vegetables without disinfecting it between uses. The subject of cutting board safety is discussed in Insight 25.3.

Preventing the Survival or Multiplication of Microbes in Food Because it is not possible to eliminate all microbes from certain types of food by clean techniques alone, a more efficient approach is to preserve the food by physical or chemical methods. Hygienically preserving foods is especially important for large commercial companies that process and sell bulk foods and must ensure that products are free from harmful contaminants. Regulations and standards for food processing are administered by two federal agencies: the Food and Drug Administration (FDA) and the U.S. Department of Agriculture (USDA).

Filtration

Prevention of Growth

Temperature and Food Preservation

Maintenance temperature Hot

Cold freezing

Preservative additives

Gas

Nitrogen salts

Figure 25.12 The primary methods of preventing food poisoning and food spoilage.

Heat is a common way to destroy microbial contaminants or to reduce the load of microorganisms. Commercial canneries preserve food in hermetically sealed containers that have been exposed to high temperatures over a specified time period. The temperature used depends on the type of food, and it can range from 60°C to 121°C, with exposure times ranging from 20 minutes to 115 minutes. The food is usually processed at a thermal death time (TDT; see chapter 11) that will destroy the main spoilage organisms and pathogens but will not alter the nutrient value or flavor of the food. For example, tomato juice must be heated to between 121°C and 132°C for 20 minutes to ensure destruction of the spoilage agent Bacillus coagulans. Most canning methods are rigorous enough to sterilize the food completely, but some only render the food “commercially sterile,” which means it contains live bacteria that are unable to grow under normal conditions of storage. Another use of heat is pasteurization, usually defined as the application of heat below 100°C to destroy nonresistant

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Chapter 25 Applied Microbiology and Food and Water Safety

INSIGHT 25.3

Wood or Plastic: On the Cutting Edge of Cutting Boards

Inquiring cooks have long been curious for the final word on which type of cutting board is the better choice for food safety. When the USDA recommended plastic cutting boards, it seemed the logical, reasonable choice. After all, plastic is nonabsorbent and easy to clean, presumably making it less likely to harbor bacteria and other microorganisms on its surface than wood is. But this recommendation was never based on evidence from scientific tests. Recently, two separate research groups turned their attention to this important kitchen question. What emerged from these studies came as rather a surprise—the two groups reached exactly opposite conclusions. First came the study by a team of microbiologists from the University of Wisconsin. They experimented with hardwood chopping blocks and acrylic plastic boards inoculated with pathogens such as Salmonella, Escherichia coli, and Listeria monocytogenes. One of the most unexpected results was that the wooden boards actually killed 99.9% of the bacteria within a few minutes. The team concluded from the lack of viable cells that wood must contain some antibacterial substances, although they were unable to isolate them. The plastic boards did not similarly reduce the numbers of pathogens and they failed to live up to expectations in other ways. For instance, they continued to harbor bacteria if left unwashed for a given time period. If they were scored by knives from extensive use, even after scrubbing with soap and water, they still held live bacteria. In contrast, even heavily used wooden boards did not grow microorganisms and had a far lower bacterial count. The Wisconsin researchers concluded that the grounds for advocating plastic are questionable and that wood is as safe as plastic, if not superior to it. In the other study, researchers from the Food and Drug Administration performed an electron microscope study of wood. They found that pathogens such as E. coli O157:H7 and Campylobacter became trapped in the porous spaces of wooden boards and were able to survive for 2 hours to several days, depending on the moisture content of the wood. They continue to recommend the use of plastic because bacteria trapped in wood would be difficult to remove and could be released during use. What is a chef to do? Although these contradictory studies seem not to provide a definitive answer, they can serve to emphasize an important point. The solution still exists in simple, commonsense guidelines that are the crux of good kitchen practices. It is apparent that both boards can be safe if properly

bacteria and yeasts in liquids such as milk, wine, and fruit juices. The heat is applied in the form of steam, hot water, or even electrical current. The most prevalent technology is the high-temperature short-time (HTST), or flash method, using extensive networks of tubes that expose the liquid to 72°C for 15 seconds (figure 25.13). An alternative method, ultrahigh-temperature (UHT) pasteurization, steams the product until it reaches a temperature of 134°C for at least 1 second. Although milk processed this way is not actually sterile, it is

(a)

(b) Double-sided plates of blood agar (top) and MacConkey agar (bottom) after swabbing with samples from cutting boards. The boards were equally contaminated with a fresh chicken carcass, and the samples were taken 10 minutes later. Results appear in (a) for the wooden board and in (b) for the plastic board. Note that, in this case, the wooden board yielded significantly fewer colonies on both types of media.

handled and their limitations are taken into account. All boards should be scrubbed with soap and hot water and disinfected between uses, especially if meats, poultry, or fish have been cut on them. Boards should be replaced if their surface has become too roughened with use, and wooden boards must not be left moist for any period of time.

often marketed as sterile, with a shelf life of up to 3 months. Older methods involve large bulk tanks that hold the fluid at a lower temperature for a longer time, usually 62.3°C for 30 minutes. Cooking temperatures used to boil, roast, or fry foods can render them free or relatively free of living microbes if carried out for sufficient time to destroy any potential pathogens. A quick warming of chicken or an egg is inadequate to kill microbes such as Salmonella. In fact, any meat is a potential

25.3

Microorganisms Making Food and Spoiling Food °C

Body temperature

100°

212° Boiling point

145°

40°

104°

37.7°

100°

Bacterial destruction occurs if high temperatures are maintained long enough.

*Bacteria multiply rapidly

98.6°

36.1°

97°

15°

59°

7.2° 0°

45° 32° Freezing point

Bacteria multiply

Bacteria multiply at a reduced rate

Bacterial growth inhibited

0°

Figure 25.13 A modern flash pasteurizer, a system

used in dairies for high-temperature short-time (HTST) pasteurization.

*Under ideal conditions, bacteria can divide every 20 minutes. At this rate, bacterial numbers could increase from 1 to 2,097,152 within 7 hours.

Source: Photo taken at Alta Dena Dairy, City of Industry, California.

source of infectious agents and should be adequately cooked. Because most meat-associated food poisoning is caused by nonsporulating bacteria, heating the center of meat to at least 80°C and holding it there for 30 minutes is usually sufficient to kill pathogens. Roasting or frying food at temperatures of at least 200°C or boiling it will achieve a satisfactory degree of disinfection. Any perishable raw or cooked food that could serve as a growth medium must be stored to prevent the multiplication of bacteria that have survived during processing or handling. Because most food-borne bacteria and molds that are agents of spoilage or infection can multiply at room temperature, manipulation of the holding temperature is a useful preservation method (figure 25.14). A good general directive is to store foods at temperatures below 4°C or above 60°C. Regular refrigeration reduces the growth rate of most mesophilic bacteria by 10 times, although some psychrotrophic microbes can continue to grow at a rate that causes spoilage. This factor limits the shelf life of milk, because even at 7°C, a population could go from a few cells to a billion in 10 days. Pathogens such as Listeria monocytogenes and Salmonella can also continue to grow in refrigerated foods. Freezing is a longer-term method for cold preservation. Foods can be either slow-frozen for 3 to 72 hours at −15°C to −23°C or rapidly frozen for 30 minutes at −17°C to −34°C. Because freezing cannot be counted upon to kill microbes, rancid, spoiled, or infectious foods will still be unfit to eat after freezing and defrosting. Salmonella is known to survive several months in frozen chicken and ice cream, and Vibrio parahaemolyticus

°F

62.8°

37°

777

Figure 25.14 Temperatures favoring and inhibiting

the growth of microbes in food. Most microbial agents of disease or spoilage grow in the temperature range of 15°C to 40°C. Preventing unwanted growth in foods in long-term storage is best achieved by refrigeration or freezing (4°C or lower). Preventing microbial growth in foods intended to be consumed warm in a few minutes or hours requires maintaining the foods above 60°C. Source: From Ronald Atlas, Microbiology: Fundamentals and Applications, 2nd ed., © 1998, p. 475. Reprinted by permission of Prentice Hall, Upper Saddle River, New Jersey.

can survive in frozen shellfish. For this reason, frozen foods should be defrosted rapidly and immediately cooked or reheated. However, even this practice will not prevent staphylococcal intoxication if the toxin is already present in the food before it is heated. Foods such as soups, stews, gravies, meats, and vegetables that are generally eaten hot should not be maintained at warm or room temperatures, especially in settings such as cafeterias, banquets, and picnics. The use of a hot plate, chafing dish, or hot water bath will maintain foods above 60°C, well above the incubation temperature of food-poisoning agents. As a final note about methods to prevent food poisoning, remember the simple axiom: “When in doubt, throw it out.”

Radiation Ultraviolet (nonionizing) lamps are commonly used to destroy microbes on the surfaces of foods or utensils, but they do not penetrate far enough to sterilize bulky foods or food

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Chapter 25 Applied Microbiology and Food and Water Safety

in packages. Food preparation areas are often equipped with UV radiation devices that are used to destroy spores on the surfaces of cheese, breads, and cakes and to disinfect packaging machines and storage areas. Food itself is usually sterilized by gamma or cathode radiation because these ionizing rays can penetrate denser materials. It must also be emphasized that this method does not cause the targets of irradiation to become radioactive. Concerns have been raised about the possible secondary effects of radiation that could alter the safety and edibility of foods. Experiments over the past 30 years have demonstrated some side reactions that affect flavor, odor, and vitamin content, but it is currently thought that irradiated foods are relatively free of toxic by-products. The government has currently approved the use of radiation in sterilizing beef, pork, poultry, fish, spices, grain, and some fruits and vegetables. Radiation also increases the shelf life of perishable foods, thus lowering their cost.

Other Forms of Preservation The addition of chemical preservatives to many foods can prevent the growth of microorganisms that could cause spoilage or disease. Preservatives include natural chemicals such as salt (NaCl) or table sugar and artificial substances such as ethylene oxide. The main classes of preservatives are organic acids, nitrogen salts, sulfur compounds, oxides, salt, and sugar. Organic acids, including lactic, benzoic, and propionic acids, are among the most widely used preservatives. They are added to baked goods, cheeses, pickles, carbonated beverages, jams, jellies, and dried fruits to reduce spoilage from molds and some bacteria. Nitrites and nitrates are used primarily to maintain the red color of cured meats (hams, bacon, and sausage). By inhibiting the germination of Clostridium botulinum spores, they also prevent botulism intoxication, but their effects against other microorganisms are limited. Sulfite prevents the growth of undesirable molds in dried fruits, juices, and wines and retards discoloration in various foodstuffs. Ethylene and propylene oxide gases disinfect various dried foodstuffs. Their use is restricted to fruit, cereals, spices, nuts, and cocoa. The high osmotic pressure contributed by hypertonic levels of salt plasmolyzes bacteria and fungi and removes moisture from food, thereby inhibiting microbial growth. Salt is commonly added to brines, pickled foods, meats, and fish. However, it does not retard the growth of pathogenic halophiles such as Staphylococcus aureus, which grows readily even in 7.5% salt solutions. The high sugar concentrations of candies, jellies, and canned fruits also exert an osmotic preservative effect. Other chemical additives that function in preservation are alcohols and antibiotics. Alcohol is added to flavoring extracts, and antibiotics are approved for treating the carcasses of chickens, fish, and shrimp. Food can also be preserved by desiccation, a process that removes moisture needed by microbes for growth by expos-

ing the food to dry, warm air. Solar drying was traditionally used for fruits and vegetables, but modern commercial dehydration is carried out in rapid-evaporation mechanical devices. Drying is not a reliable microbicidal method, however. Numerous resistant microbes such as micrococci, coliforms, staphylococci, salmonellae, and fungi survive in dried milk and eggs, which can subsequently serve as agents of spoilage and infections. In 2006, the Food and Drug Administration approved the spraying of bacteriophages onto ready-to-eat meat products. The bacteriophages are specific for Listeria and will act to kill the bacteria that would not otherwise be killed because the cold cuts and poultry are usually not cooked before consumption.

25.3 Learning Outcomes—Can You . . . 9. . . . name five foods and/or beverages that benefit from microbial fermentation? 10. . . . explain what microbial actions lead to leavening in bread? 11. . . . write the equation for turning yeast and sugar into alcoholic beverages? 12. . . . discuss why microorganisms themselves might be useful as food products? 13. . . . provide some background about HACCP procedures? 14. . . . report 10-year trends in food-borne illness? 15. . . . outline basic principles of using temperature to preserve food? 16. . . . list mechanisms other than temperature that are used to preserve food?

25.4 Using Microorganisms to Make Things We Need Virtually any large-scale commercial enterprise that enlists microorganisms to manufacture consumable materials is part of the realm of industrial microbiology. Here the term pertains primarily to bulk production of organic compounds such as antibiotics, hormones, vitamins, acids, solvents (table 25.1), and enzymes (table 25.2). Many of the processing steps involve fermentations similar to those described in food technology, but industrial processes usually occur on a much larger scale, produce a specific compound, and involve numerous complex stages. The aim of industrial microbiology is to produce chemicals that can be purified and packaged for sale or for use in other commercial processes. Thousands of tons of organic chemicals worth several billion dollars are produced by this industry every year. To create just one of these products, an industry must determine which microbes, starting compounds, and growth conditions work best. The research and development involved usually require an investment of 10 to 15 years and billions of dollars.

25.4 Using Microorganisms to Make Things We Need

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Table 25.1 Industrial Products of Microorganisms Chemical

Microbial Source

Substrate

Applications

Cephalosporins

Cephalosporium

Glucose

Antibacterial antibiotics, broad spectrum

Penicillins

Penicillium chrysogenum

Lactose

Antibacterial antibiotics, broad and narrow spectrum

Vitamin B12

Pseudomonas

Molasses

Dietary supplement

Steroids (hydrocortisone)

Rhizopus, Cunninghamella

Deoxycholic acid, stigmasterol

Treatment of inflammation, allergy; hormone replacement therapy

Pharmaceuticals

Food additives and amino acids Citric acid

Aspergillus, Candida

Molasses

Acidifier in soft drinks; used to set jam; candy additive; fish preservative; retards discoloration of crabmeat; delays browning of sliced peaches

Xanthan

Xanthomonas

Glucose medium

Food stabilizer; not digested by humans

Acetic acid

Acetobacter

Any ethylene source, ethanol

Food acidifier; used in industrial processes

Ethanol

Saccharomyces

Beet, cane, grains, wood, wastes

Additive to gasoline (gasohol)

Acetone

Clostridium

Molasses, starch

Solvent for lacquers, resins, rubber, fat, oil

Glycerol

Yeast

By-product of alcohol fermentation

Explosive (nitroglycerine)

Dextran

Klebsiella, Acetobacter, Leuconostoc

Glucose, molasses, sucrose

Polymer of glucose used as adsorbents, blood expanders, and in burn treatment; a plasma extender; used to stabilize ice cream, sugary syrup, candies

Miscellaneous

Table 25.2 Industrial Enzymes and Their Uses Enzyme

Source

Application

Amylase

Aspergillus, Bacillus, Rhizopus

Flour supplement, desizing textiles, mash preparation, syrup manufacture, digestive aid, precooked foods, spot remover in dry cleaning

Cellulase

Aspergillus, Trichoderma

Denim finishing (“stone-washing”), digestive aid, increase digestibility of animal feed, degradation of wood or wood by-products

Hyaluronidase

Various bacteria

Medical use in wound cleansing, preventing surgical adhesions

Keratinase

Streptomyces

Hair removal from hides in leather preparation

Pectinase

Aspergillus, Sclerotina

Clarifies wine, vinegar, syrups, and fruit juices by degrading pectin, a gelatinous substance; used in concentrating coffee

Proteases

Aspergillus, Bacillus, Streptomyces

To clear and flavor rice wines, process animal feed, remove gelatin from photographic film, recover silver, tenderize meat, unravel silkworm cocoon, remove spots

Rennet

Mucor

To curdle milk in cheese making

Streptokinase

Streptococcus

Medical use in clot digestion, as a blood thinner

One of the most active areas of research in industrial microbiology is the use of algal species to produce biofuels. The fuels would replace gasoline and jet fuel. You may recall that original attempts to produce biofuels involved plants such as corn and soybeans. This proved to be unpopular since the plants and

acreage used to grow it could have—and should have—been used for food. Quickly scientists realized that algae could be grown more easily and could produce vast quantities of oil in a controlled manner. The oil produced would also be easily biodegradable. The algae produce oil when exposed to sunlight

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Chapter 25 Applied Microbiology and Food and Water Safety

(figure 25.15). They use photosynthesis to manufacture O2 and biomass—namely, lipids or oils. Many government and private industries around the world are investing in massive research projects to bring this technology to a scale that will replace significant amounts of fossil fuels. Very often the microbes used by biotechnology and fermentation industries are mutant strains of fungi or bacteria that selectively synthesize large amounts of various metabolic intermediates, or metabolites. Two basic kinds of metabolic products are harvested by industrial processes: (1) Primary metabolites are produced during the major metabolic pathways and are essential to the microbe’s function. (2) Secondary metabolites are by-products of metabolism that may not be critical to the microbe’s function (figure 25.16).

In general, primary products are compounds such as amino acids and organic acids synthesized during the logarithmic phase of microbial growth, and secondary products are compounds such as vitamins, antibiotics, and steroids synthesized during the stationary phase (see chapter 7). Most strains of industrial microorganisms have been chosen for their high production of a particular primary or secondary metabolite. Certain mutated strains of yeasts and bacteria can produce 20,000 times more metabolite than a wild strain of that same microbe. Industrial microbiologists have several tricks to increase the amount of the chosen end product. First, they can manipulate the growth environment to increase the synthesis of a metabolite. For instance, adding lactose instead of glucose as the fermentation substrate increases the production of penicillin by Penicillium. Another strategy is to select microbial strains that genetically lack a feedback system to regulate the formation of end products, thus encouraging mass accumulation of this product. Many syntheses occur in sequential fashion, wherein the waste products of one organism become the building blocks of the next. During these biotransformations, the substrate undergoes a series of slight modifications, each of which gives off a different by-product. The production of an antibiotic such as tetracycline requires several microorganisms and 72 separate metabolic steps.

From Microbial Factories to Industrial Factories Figure 25.15. Algal bioreactor. The photobioreactor contains

Substrate

algae, water, and trace elements.

Synthesis of only primary Synthesis of primary and secondary metabolites (Synthesis of bymetabolites (Production of essential biochemicals) products nonessential to growth)

Industrial fermentations begin with microbial cells acting as living factories. When exposed to optimum conditions, they multiply in massive numbers and synthesize large volumes of a desired product. Producing appropriate levels of growth and fermentation requires cultivation of the microbes in a carefully controlled environment (figure 25.17). This process is basically similar to culturing bacteria in a test tube of nutri-

Log Number of Viable Cells

Stationary phase

Death phase

Exponential phase

Lag phase

Time

Figure 25.16 The origins of primary and secondary

microbial metabolites harvested by industrial processes.

Figure 25.17 A cell culture vessel used to mass-produce pharmaceuticals. Such elaborate systems require the highest levels of sterility and clean techniques.

25.4 Using Microorganisms to Make Things We Need

aerobic metabolism, and the large volumes make it difficult to provide adequate oxygen. Fermentors have a built-in device called a sparger that aerates the medium to promote aerobic growth. Paddles (impellers) located in the central part of the fermentor increase the contact between the microbe and the nutrients by vigorously stirring the fermentation mixture. Their action also maintains its uniformity.

Substance Production The general steps in mass production of organic substances in a fermentor are illustrated in figure 25.19. These can be summarized as: 1. introduction of microbes and sterile media into the reaction chamber; 2. fermentation; 3. downstream processing (recovery, purification, and packaging of product); and 4. removal of waste. Introduction of Reactants

ent broth. It requires a sterile medium containing appropriate nutrients, protection from contamination, provisions for introduction of sterile air or total exclusion of air, and a suitable temperature and pH. Many commercial fermentation processes have been worked out on a small scale in a lab and then scaled up to a large commercial venture. An essential component for scaling up is a fermentor, a device in which mass cultures are grown, reactions take place, and product develops. Some fermentors are large tubes, flasks, or vats, but most industrial types are metal cylinders with built-in mechanisms for stirring, cooling, monitoring, and harvesting product (figure 25.18). Fermentors are made of materials that can withstand pressure and are rust-proof, nontoxic, and leakproof. They range in holding capacity from small, 5-gallon systems used in research labs to larger, 5,000- to 100,000-gallon vessels and, in some industries, to tanks of 250 million to 500 million gallons. For optimum yield, a fermentor must duplicate the actions occurring in a tiny volume (a test tube) on a massive scale. Most microbes performing fermentations have an

Motor

781

Raw materials

Pretreatment with enzymes

Growth of stock culture for inoculum

Nutrients added Medium sterilized

Addition of nutrient and microbes

Valve

Fermentor chamber

Fermentation

Cooling water out

Sample line

pH buffer

O2

Impellers Temperature sensor and control unit

Cooling jacket

Cooling water in Valve Sparger Air in Valve Harvest line

Air filter

Downstream Processing and Waste Removal

Medium collected

Recovery of raw product

Microbes recovered

Filtration, extraction

Purification, drying

Solids collector

Downstream processing

Figure 25.18 A schematic diagram of an industrial fermentor for mass culture of microorganisms. Such instruments are equipped to add nutrients and cultures; to remove product under sterile or aseptic conditions; and to aerate, stir, and cool the mixture automatically.

Packaging

Figure 25.19 The general layout of a fermentation plant. These general steps are followed for industrial production of drugs, enzymes, fuels, vitamins, and amino acids.

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Chapter 25 Applied Microbiology and Food and Water Safety

INSIGHT 25.4

Microbes Degrade—and Repair—Ancient Works of Art

It has long been understood that microorganisms cause the deterioration of old books, statues, and paintings. The process of biodegradation, deterioration by living organisms (microbes or insects), is responsible for the crumbling of stone monuments and buildings all over the world, such as the Mayan temple depicted in the photo. Both bacteria and fungi are notorious for colonizing old books, paintings, stone, mortar, and concrete. This happens because microbes release chemicals that damage stone, and they can use cellulose (paper), glues (book binding), and other organic chemicals (paints, pigments) as nutrients. Watercolor and oil paintings are particularly vulnerable to microbial attack. A newer and more encouraging finding is that microbes can actually be used to restore works of art. In 2004, a group of Italian scientists managed to uncover a painting that had been obscured by a technique that earlier curators had used to “preserve” the fresco when it was no longer prudent for it to hang in its building in Pisa, Italy. When the 14th-century painting The Conversion of Saint Efisio and Battle by Spinello Aretino was damaged in a bomb that fell during World War II, technicians used an animal-based glue to apply gauze to the front of it and lifted it off of the wall onto the gauze matrix. They then applied a canvas to the back of the painting, attached it to a supporting sheet, and stored it. Illustration (a) depicts the painting covered by gauze. The idea behind that strategy in the 1940s was that the gauze on the front of the painting could later be removed by using solvents that would dissolve the glue. But over time, the glue formed complexes with other chemicals in the painting and became resistant to all known solvents. After these failed attempts, the scientists determined the chemical structure of the glue. Luckily, the glue was purely organic, and the paints used by the artist were purely inorganic. The scientists decided to apply a paste of whole bacteria that contained a mix of enzymes that they predicted would dissolve the glue but not the paint. Cultures of Pseudomonas stutzeri (b) were applied to the painting on saturated cotton wool. The scientists also added an extra protease, which served to “clean up” the organic residues that were left after the cleanup process. It was successful! The glue dissolved and the gauze was removed, revealing the painting underneath (c). Finally, after centuries of only damaging precious artworks, microbes, with a little help from humans, are repairing them.

(a)

(b)

(c)

25.4 Using Microorganisms to Make Things We Need

All phases of production must be carried out aseptically and monitored (usually by computer) for rate of flow and quality of product. The starting raw substrates include crude plant residues, molasses, sugars, fish and meat meals, and whey. Additional chemicals can be added to control pH or to increase the yield. In batch fermentation, the substrate is added to the system all at once and taken through a limited run until product is harvested. In continuous feed systems, nutrients are continuously fed into the reactor and the product is siphoned off throughout the run. Table 25.1 itemizes some of the major pharmaceutical substances, food additives, and solvents produced by microorganisms. Some newer technologies employ extremophiles and their enzymes to run the processes at high or low temperatures or in high-salt conditions. Hyperthermophiles have been adapted for high-temperature detergent and enzyme production. Psychrophiles are used for cold processing of reagents for molecular biology and medical tests. Halophiles are effective for processing of salted foods and dietary supplements.

Pharmaceutical Products Health care products derived from microbial biosynthesis are antibiotics, hormones, vitamins, and vaccines. The first mass-produced antimicrobic was penicillin, which came from Penicillium chrysogenum, a mold first isolated from a cantaloupe in Wisconsin. The current strain of this species has gone through decades of selective mutation and screening to increase its yield. (The original wild P. chrysogenum synthesized 60 mg/ml of medium, and the latest isolate yields 85,000 mg/ml.) The semisynthetic penicillin derivatives are produced by introducing the assorted side-chain precursors to the fermentation vessel during the most appropriate phase of growth. These experiences with penicillin have provided an important model for the manufacture of other antibiotics. Several steroid hormones used in therapy are produced industrially. Corticosteroids of the adrenal cortex, cortisone and cortisol (hydrocortisone), are invaluable for treating inflammatory and allergic disorders, and female hormones such as progesterone or estrogens are the active ingredients in birth control pills. For years, the production of these hormones was tedious and expensive because it involved purifying them from slaughterhouse animal glands or chemical syntheses. In time, it was shown that, through biotransformation, various molds could convert a precursor compound called diogenin into cortisone. By the same means, stigmasterol from soybean oil could be transformed into progesterone.

Miscellaneous Products An exciting innovation has been the development and industrial production of natural biopesticides using Bacillus

783

thuringiensis. During sporulation, these bacteria produce intracellular crystals that can be toxic to certain insects. When the insect ingests this endotoxin, its digestive tract breaks down and it dies, but the material is relatively nontoxic to other organisms. Commercial dusts are now on the market to suppress caterpillars, moths, and worms on various agricultural crops and trees. A strain of this bacterium is also being considered to control the mosquito vector of malaria (chapter 20) and the black fly vector of onchocerciasis (river blindness; chapter 18). Enzymes are critical to chemical manufacturing, the agriculture and food industries, textile and paper processing, and even laundry and dry cleaning. The advantage of enzymes is that they are very specific in their activity and are readily produced and released by microbes. Microbes and their enzymes are even proving to be useful in preserving our cultural heritage (Insight 25.4). Mass quantities of proteases, amylases, lipases, oxidases, and cellulases are produced by fermentation technology (see table 25.2). The wave of the future appears to be custom designing enzymes to perform a specific task by altering their amino acid content. Other compounds of interest that can be massproduced by microorganisms are amino acids, organic acids, solvents, and natural flavor compounds to be used in air fresheners and foods.

25.4 Learning Outcomes—Can You . . . 17. . . . state the general aim(s) of industrial microbiology? 18. . . . distinguish between primary and secondary metabolites? 19. . . . list the four steps of industrial product production from microbes? 20. . . . list five different types of substances produced from industrial microbiology, and their applications?

Case File 25

Wrap-Up

Climate change seems to be causing the overgrowth of V. vulnificus, as well as other bacteria, in waters that previously were less supportive of their growth. (We saw this also in the case file for chapter 7.) At the same time, the bacteria also continue to grow in southern waters. The result has been a 51% increase in Vibrio-caused wound infections in a recent 6-year period. In fact, more people die annually from Vibrio wound infections than from shark attacks. It seems that a new definition for microbiologically “safe” water may need to be devised. See: 2006. The Honolulu Advertiser, online version, June 10.

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Chapter 25 Applied Microbiology and Food and Water Safety

Chapter Summary 25.1 Applied Microbiology and Biotechnology • The use of microorganisms for practical purposes to benefit humans is called biotechnology.

organic acids in foods and beverages. Beer, wine, yogurt, and cheeses are examples of such processes. • Some microorganisms are used as a source of protein. Examples are single-cell protein, mycoprotein, and Spirulina. Microbial protein could replace meat as a major protein source. • Food-borne disease can be an intoxication caused by microbial toxins produced as by-products of microbial decomposition of food. Or it can be a food infection when pathogenic microorganisms in the food attack the human host after being consumed. • Heat, radiation, chemicals, and drying are methods used to limit numbers of microorganisms in food. The type of method used depends on the nature of the food and the type of pathogens or spoilage agents it contains.

25.2 Microorganisms in Water and Wastewater Treatment • Wastewater or sewage is treated in three stages to remove organic material, microorganisms, and chemical pollutants. The primary phase removes physical objects from the wastewater. The secondary phase removes the organic matter by biodegradation. The tertiary phase disinfects the water and removes chemical pollutants. • Significant water-borne pathogens include protozoa, bacteria, and viruses. • Water quality assays screen for coliforms as indicator organisms, or may assess the most probable number of microorganisms. As these results may be misleading, more emphasis is being placed on identifying the actual pathogens.

25.4 Using Microorganisms to Make Things We Need • Industrial microbiology refers to the bulk production of any organic compound derived from microorganisms. • It is likely that algal biofuels will soon replace large portions of fossil fuels currently being produced. • Industrial processes now produce antibiotics, hormones, vitamins, acids, solvents, vaccines, and enzymes from microbes.

25.3 Microorganisms Making Food and Spoiling Food • Microorganisms can compete with humans for the nutrients in food. Their presence in food can be beneficial, detrimental, or of neutral consequence to human consumers. • Food fermentation processes utilize bacteria or yeast to produce desired components such as alcohols and

Multiple-Choice and True-False Questions

Knowledge and Comprehension

Multiple-Choice Questions. Select the correct answer from the answers provided. 1. Drinking water utilities monitor their production system for the occurrence of a. methanogens. c. nematodes. b. coliform bacteria. d. yeasts.

6. When algae produce biofuels, what is the other significant byproduct of photosynthesis? a. CO2 c. waste b. energy d. O2

2. Milk is usually pasteurized by a. the high-temperature short-time method. b. ultrapasteurization. c. the batch method. d. electrical currents.

7. Secondary metabolites of microbes are formed during the ____ phase of growth. a. exponential c. trophophase b. stationary d. idiophase

3. During sewage treatment, microbial action on a large scale first takes place in the a. primary phase. b. secondary phase. c. Microbial action is not a part of sewage treatment. d. Microbial action takes place after the secondary phase. 4. Which of the following is unlikely to be a waterborne pathogen? a. Giardia lamblia c. Vibrio b. Salmonella d. Staphylococcus 5. The “bloom” in wine making refers to a. the flowering of the grape plant. b. the biofilm on the skin of the grapes. c. the fermentation taking place in vats. d. none of the above.

8. In industrial fermentation, which step precedes downstream processing? a. removal of waste b. introduction of microbes into chamber c. packaging of product d. fermentation 9. Which of the following are currently being produced through biotechnology? a. glycerol b. vitamins c. steroids d. all of the above 10. In biotechnology, fermentation refers to a. the anaerobic metabolism of microorganisms. b. the creation of alcoholic beverages. c. the mass culturing of microorganisms to yield large quantities of products. d. all of the above.

Critical Thinking Questions

True-False Questions. If the statement is true, leave as is. If it is false, correct it by rewriting the sentence. 11. Raw sewage is still being dumped into the aquatic environment in many places around the world. 12. Food products should always be kept completely free of microorganisms.

Critical Thinking Questions

785

13. Alcoholic beverages are produced by the fermentation of sugar to ethanol and carbon dioxide. 14. The incidence of many food-borne illnesses has been declining for some years now. 15. Refrigerating food prevents the growth of all bacteria.

Application and Analysis

These questions are suggested as a writing-to-learn experience. For each question, compose a one- or two-paragraph answer that includes the factual information needed to completely address the question. c. Why is there less tolerance for a fecal coliform in drinking 1. a. Draw a diagram of the flow of water in a water utility plant. or recreational water than other bacteria? b. Describe the three phases of sewage treatment. c. What is activated sludge? 7. If fermentation of sugars to produce alcohol in wine is anaerobic, why do winemakers make sure that the early phase 2. Describe five types of fermentations. of yeast growth is aerobic? 3. When are microbes on food harmless? 8. Predict the differences in the outcome if raw milk is incubated 4. Which microbes are used as starter cultures in bread, beer, for 48 hours versus pasteurized milk being incubated for the wine, cheeses, and sauerkraut? same length of time. 5. What are curds and whey, and what causes them? 9. Explain the ways that co-metabolism and biotransformations 6. Every year, supposedly safe municipal water supplies cause of microorganisms are harnessed in industrial microbiology. outbreaks of enteric illness. 10. Review chapter 10 and describe several ways that recombinant a. How in the course of water analysis and treatment might DNA technology can be used in biotechnology processes. these pathogens be missed? b. What kinds of microbes are they most likely to be?

Concept Mapping

Synthesis

Appendix D provides guidance for working with concept maps. 1. Construct your own concept map using the following words as the concepts. Supply the linking words between each pair of concepts. You may add additional concepts if desired. primary metabolites secondary metabolites fermentation

Visual Connections

microbes downstream processing substrate

pH biotransformations

Synthesis

These questions use visual images or previous content to make connections to this chapter’s concepts. 1. From chapter 3, figure 3.9b. If this MacConkey agar plate was inoculated with well water, would you report that coliforms were present in the water?

2. From Insight 25.3, illustration (a). This is a plate with blood agar on the top and MacConkey agar on the bottom. It has been inoculated with samples from a wooden cutting board that had been exposed to a raw chicken carcass. Knowing what you know about the properties of these two agars, say as much as you can about the bacteria growing on them.

www.connect.microbiology.com Enhance your study of this chapter with study tools and practice tests. Also ask your instructor about the resources available through ConnectPlus, including the media-rich eBook, interactive learning tools, and animations.

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APPENDIX

A

Exponents Dealing with concepts such as microbial growth often requires working with numbers in the billions, trillions, and even greater. A mathematical shorthand for expressing such numbers is with exponents. The exponent of a number

indicates how many times (designated by a superscript) that number is multiplied by itself. These exponents are also called common logarithms, or logs. The following chart, based on multiples of 10, summarizes this system.

Exponential Notation for Base 10 Number

Quantity

Exponential Notation* 0

Number Arrived at By:

One Followed By:

1

One

10

Numbers raised to zero power are equal to one

No zeros

10

Ten

101**

10 × 1

One zero

10 × 10

Two zeros

10 × 10 × 10

Three zeros

10 × 10 × 10 × 10

Four zeros

2

100

Hundred

10

1,000

Thousand

103 4

10,000

Ten thousand

10

100,000

Hundred thousand

105

1,000,000 1,000,000,000

Million Billion

10 × 10 × 10 × 10 × 10

Five zeros

6

10 times itself 6 times

Six zeros

9

10 times itself 9 times

Nine zeros

12

10 10

1,000,000,000,000

Trillion

10

10 times itself 12 times

Twelve zeros

1,000,000,000,000,000

Quadrillion

1015

10 times itself 15 times

Fifteen zeros

1,000,000,000,000,000,000

Quintillion

1018

10 times itself 18 times

Eighteen zeros

Other large numbers are sextillion (1021), septillion (1024), and octillion (1027). *The proper way to say the numbers in this column is 10 raised to the nth power, where n is the exponent. The numbers in this column can also be represented as 1 × 10n, but for brevity, the 1 × can be omitted. **The exponent 1 is usually omitted.

Converting Numbers to Exponent Form

number is multiplied by 10 with its appropriate exponent: 3568 is now 3.568 × 103.

As the chart shows, using exponents to express numbers can be very economical. When simple multiples of 10 are used, the exponent is always equal to the number of zeros that follow the 1, but this rule will not work with numbers that are more varied. Other large whole numbers can be converted to exponent form by the following operation: First, move the decimal (which we assume to be at the end of the number) to the left until it sits just behind the first number in the series (example: 3568. = 3.568). Then count the number of spaces (digits) the decimal has moved; that number will be the exponent. (The decimal has moved from 8. to 3., or 3 spaces.) In final notation, the converted

Rounding Off Numbers The notation in the previous example has not actually been shortened, but it can be reduced further by rounding off the decimal fraction to the nearest thousandth (three digits), hundredth (two digits), or tenth (one digit). To round off a number, drop its last digit and either increase the one next to it or leave it as it is. If the number dropped is 5, 6, 7, 8, or 9, the subsequent digit is increased by one (rounded up); if it is 0, 1, 2, 3, or 4, the subsequent digit remains as is. Using the example of 3.528, removing the 8 rounds off the 2 to a 3 and produces 3.53 (two digits). If further rounding is desired, A-1

A-2

Appendix A

the same rule of thumb applies, and the number becomes 3.5 (one digit). Other examples of exponential conversions follow. Rounded Off, Placed in Exponent Form

Number

Is the Same As

16,825. 957,654. 2,855,000.

1.6825 ×10 × 10 × 10 × 10 1.7 × 104 9.57654 × 10 × 10 × 10 × 10 × 10 9.58 × 105 2.855000 × 10 × 10 × 10 × 10 2.86 × 106 × 10 × 10

concepts such as pH that are based on very small numbers otherwise needing to be represented by large decimal fractions—for example, 0.003528. Converting this and other such numbers to exponential notation is basically similar to converting positive numbers, except that you work from left to right and the exponent is negative. Using the example of 0.003528, first convert the number to a whole integer followed by a decimal fraction and keep track of the number of spaces the decimal point moves (example: 0.003528 = 3.528). The decimal has moved three spaces from its t o original position, so the finished product is 3.528 × 10−3. Other examples follow.

Negative Exponents The numbers we have been using so far are greater than 1 and are represented by positive exponents. But the correct notation for numbers less than 1 involves negative exponents (10 raised to a negative power, or 10−n). A negative exponent says that the number has been divided by a certain power of 10 (10, 100, 1,000). This usage is handy when working with

Rounded Off, Expressed with Exponents

Number

Is the Same As

0.0005923

5.923 _________________

5.92 × 10−4

0.00007295

7.295 _____________________

7.3 × 10−5

10 × 10 × 10 × 10 10 × 10 × 10 × 10 × 10

APPENDIX

B

Significant Events in Microbiology Date

Discovery/People Involved

Date

Discovery/People Involved

1546

Italian physician Girolamo Fracastoro suggests that invisible organisms may be involved in disease.

1908

The German Paul Ehrlich* becomes the pioneer of modern chemotherapy by developing salvarsan to treat syphilis.

1660

Englishman Robert Hooke explores various living and nonliving matter with a compound microscope that uses reflected light.

1910

An American pathologist, Francis Rous,* discovers viruses that can induce cancer.

1668

Francesco Redi, an Italian naturalist, conducts experiments that demonstrate the fallacies in the spontaneous generation theory.

1928

Frederick Griffith lays the foundation for modern molecular genetics by his discovery of transformation in bacteria.

1676

Antonie van Leeuwenhoek, a Dutch linen merchant, uses a simple microscope of his own design to observe bacteria and protozoa.

1929

A Scottish bacteriologist, Alexander Fleming,* discovers and describes the properties of the first antibiotic, penicillin.

1796

English surgeon Edward Jenner introduces a vaccination for smallpox.

1933–1938

Germans Ernst Ruska* and B. von Borries develop the first electron microscope.

1838

Phillipe Ricord, a French physician, inoculates 2,500 human subjects to demonstrate that syphilis and gonorrhea are two separate diseases.

1935

Gerhard Domagk,* a German physician, discovers the first sulfa drug and paves the way for the era of antimicrobic chemotherapy.

1941

1847–1850

The Hungarian physician Ignaz Semmelweis substantiates his theory that childbed fever is a contagious disease transmitted to women by their physicians during childbirth.

Australian Howard Florey* and Englishman Ernst Chain*develop commercial methods for producing penicillin; this first antibiotic is tested and put into widespread use.

1944

1853–1854

John Snow, a London physician, demonstrates the epidemic spread of cholera through a water supply contaminated with human sewage.

Oswald Avery, Colin MacLeod, and Maclyn McCarty show that DNA is the genetic material.

1857

French bacteriologist Louis Pasteur shows that fermentations are due to microorganisms and originates the process now known as pasteurization.

1861

Louis Pasteur completes the definitive experiments that finally lay to rest the theory of spontaneous generation.

1867

The English surgeon Joseph Lister publishes the first work on antiseptic surgery, beginning the trend toward modern aseptic techniques in medicine.

1876–1877

German bacteriologist Robert Koch* studies anthrax in cattle and implicates the bacterium Bacillus anthracis as its causative agent.

1881

1882 1884

Joshua Lederberg* and E. L. Tatum* discover conjugation in bacteria. The Russian Selman Waksman* and his colleagues discover the antibiotic streptomycin. 1953

James Watson,* Francis Crick,* Rosalind Franklin, and Maurice Wilkins* determine the structure of DNA.

1954

Jonas Salk develops the first polio vaccine.

1959–1960

Gerald Edelman* and Rodney Porter* determine the structure of antibodies.

1972

Paul Berg* develops the first recombinant DNA in a test tube.

1973

Herb Boyer and Stanley Cohen clone the first DNA using plasmids.

Pasteur develops a vaccine for anthrax in animals.

1982

Koch introduces the use of pure culture techniques for handling bacteria in the laboratory.

Development of first hepatitis B vaccine using virus isolated from human blood.

1983

Isolation and characterization of human immunodeficiency virus (HIV) by Luc Montagnier* and Francoise Barre’-Sinoussi* of France and Robert Gallo of the United States.

Koch identifies the causative agent of tuberculosis. Koch outlines his postulates.

The polymerase chain reaction is invented by Kary Mullis.*

Elie Metchnikoff,* a Russian zoologist, lays groundwork for the science of immunology by discovering phagocytic cells. The Danish physician Hans Christian Gram devises the Gram stain technique for differentiating bacteria. 1885

Pasteur develops a special vaccine for rabies.

1892

A Russian, D. Ivanovski, is the first to isolate a virus (the tobacco mosaic virus) and show that it could be transmitted in a cell-free filtrate.

1898 1899

R. Ross* and G. Grassi demonstrate that malaria is transmitted by the bite of female mosquitoes. Dutch microbiologist Martinus Beijerinck further elucidates the viral agent of tobacco mosaic disease and postulates that viruses have many of the properties of living cells and that they reproduce within cells.

1903

American pathologist James Wright and others demonstrate the presence of antibodies in the blood of immunized animals.

1905

Syphilis is shown to be caused by Treponema pallidum, through the work of German bacteriologists Fritz Schaudinn and E. Hoffman.

First release of recombinant strain of Pseudomonas to prevent frost formation on strawberry plants. 1989

1990

Cancer-causing genes called oncogenes are characterized by J. Michael Bishop, Robert Huber, Hartmut Michel, and Harold Varmus. First clinical trials in gene therapy testing. Vaccine for Haemophilus influenzae, a cause of meningitis, is introduced.

1994

Human breast cancer gene isolated.

1995

First bacterial genome fully sequenced, for Haemophilus influenzae.

2000

A rough version of the human genome is mapped.

2001

Mailed anthrax spores cause major bioterrorism event.

2003

New roles for small nuclear RNAs discovered.

2006

New vaccine for a persistent microbe, human papillomavirus (HPV), is introduced. In 2008 Harald zur Hausen* was awarded the Nobel Prize for his discovery that human papilloma viruses cause cervical cancer.

*These scientists were awarded Nobel prizes for their contributions to the field.

A-3

APPENDIX

C

Answers to Multiple-Choice and True-False and Matching Questions Chapter 1 1. 2. 3. 4. 5. 6. 7. 8. 9.

10. 11.

12.

13. 14. 15.

d d d a c c c d 1st col: 3, 7, 4, 2 2nd col: 8, 5, 6, 1 c F: Organisms in the same family are more closely related than those in the same order. F: Eukaryotes and prokaryotes emerged independently. T T T

together in various combinations. 14. T 15. F: Membranes are mainly composed of macromolecules called phospholipids.

Chapter 3 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11.

Chapter 2 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12.

c c b d c a b c a b T F: Covalent bonds are those formed when two elements share electrons. 13. F: A compound is called “organic” if it contains both carbon and hydrogen bonded

A-4

12. 13.

14.

15.

b c b b c c a b abf, df, abf, ef, af, bef, ac, bef c or d F: Agar is not easily decomposed by microorganisms (gelatin can be). T F: The factor that most limits the clarity of an image in a microscope is the resolution. F: Living specimens can be examined with phasecontrast or differential interference microscopy. F: The best stain to use to visualize a microorganism with a large capsule is a negative stain.

Chapter 4 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11.

12.

13. 14. 15.

d c a c b d b d b c F: One major difference in the envelope structure between gram-positive bacteria and gram-negative bacteria is the presence or absence of an outer membrane. F: A research microbiologist looking at evolutionary relatedness between two bacterial species is more likely to use Bergey’s Manual of Systematic Bacteriology. T T T

and the cyst stages of protozoans can be infective. 14. F: In humans, fungi can infect skin, mucous membranes, lungs, and other areas. 15. F: Fungi generally derive nutrients by digesting organic substrates.

Chapter 6 1. 2. 3. 4. 5. 6. 7. 8. 9. 10.

11. 12.

13.

Chapter 5 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13.

b d or e d b b d d b c a T T F: Both the trophozoite

14.

15.

c d d a a b d a Herpesvirus rabies, cold sores, genital warts, mumps, rubella T F: A viral capsid is composed of subunits called capsomeres. F: The envelope of an animal virus is derived from the cell membrane of its host’s cell. F: The nucleic acid of animal viruses enters the cell through a process called penetration. T

Chapter 7 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11.

12. 13.

14.

15.

a a c b a a b c c b F: Active transport of a substance across a membrane requires energy. T F: Some biofilms consist of multiple species of bacteria. F: An obligate halophile is an organism that requires high salt concentration. F: A facultative anaerobe can grow with or without oxygen.

Chapter 8 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13.

a d d b b b a b c c T T F: One cycle of fermentation yields much less energy than one cycle

of aerobic respiration. 14. T 15. F: Exoenzymes are produced inside a cell then released to the outside.

Chapter 9 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11.

12. 13. 14.

15.

b b b c b a b d b c F: The DNA base pairs are held together primarily by hydrogen bonds. T T F: Messenger RNA is formed by transcription of a gene on the DNA template strand. T

Chapter 10 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11.

c d a b c c c d a d F: The synthetic unit of the polymerase chain reaction is the amplicon.

12. T 13. F: A DNA fragment with 450 bp will migrate farther toward the positive pole (away from the origin) than one with 2,500 bp. 14. T 15. F: Plasmids and bacteriophages are commonly used as cloning vectors.

Chapter 11 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12.

c a c b d b d d a b T F: The acceptable temperaturepressure combination for an autoclave is 121°C and 15 psi. 13. F: Ionizing radiation dislodges electrons from atoms. 14. T 15. F: Prions are highly resistant to denaturation by heat.

Appendix Chapter 12 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11.

12.

13. 14. 15.

b c b d b d a or b c c b F: Most antiviral agents work by blocking an essential viral activity. F: Sulfonamide drugs work by disrupting folic acid synthesis. T T F: Drug resistance can occur when a bacterium stops being susceptible to an antibiotic.

Chapter 14 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11.

12.

13. 14. 15.

Chapter 13 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11.

a b d c d b c d a a F: The presence of a few bacteria in the blood is called bacteremia. 12. T 13. F: A nosocomial infection is one that is acquired in a hospital or medical facility. 14. F: The general term that describes a decrease in the number of white

of microbes so they can be used in vaccines is called attenuation.

blood cells is leukopenia. 15. T

b b d b b c d a d c F: The liquid component of unclotted blood is called plasma. F: Pyrogenic bacteria are commonly associated with fever. T T F: The immune system uses markers on the surface of cells to distinguish self from nonself.

Chapter 16 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12.

d d c c b a d d d d T F: A positive tuberculin skin test is an example of delayed hypersensitivity. 13. F: Contact dermatitis can be caused by chemicals absorbed through the skin. 14. T 15. T

Chapter 15

Chapter 17

1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12.

1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11.

a c a c c a e c d d T F: Antibodies are secreted by plasma cells. 13. F: Vaccination is artificial active immunity. 14. F: IgA antibodies are found in body secretions. 15. F: The process of reducing the virulence

12. 13. 14. 15.

b a b c c b c a a d F: The tuberculin skin test is an example of an in vivo serological test. T T T F: Microorganisms that are grown from clinical samples

should be evaluated to determine their clinical significance.

Chapter 18 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11.

12.

13. 14.

15.

b a d e c b d d b c F: The enzyme coagulase is associated with pathogenic strains of Staphylococcus aureus. F: Fifth disease has no vaccine and no treatment. T F: The blistering and peeling of the skin in SSS are due to the ability of S. aureus to produce exfoliative toxins. F: Pseudomonas and Janthinobacterium dominate the normal skin biota.

Chapter 19 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11.

d a c d b d b a b a F: Toxoplasma gondii is a protozoan.

12. F: Amphotericin or itraconazole are the first-line treatments for coccidioidomycosis. 13. T 14. F: In the United States, wild animals are a common reservoir for rabies. 15. T

13. F: BCG vaccine is used in other countries to prevent TB. 14. F: RSV is a respiratory infection associated with infants. 15. F: The “flu shot” is an inactivated virus and cannot cause influenza.

Chapter 20

Chapter 22

1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12.

1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11.

c d b b a b d a b d T F: Respiratory tract infection with Pneumocystis jiroveci is an ADI. 13. F: Lyme disease is caused by Borrelia burgdorferi. 14. F: Yellow fever is caused by a virus transmitted by mosquitoes. 15. T

Chapter 21 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12.

d d b b d c d c a c T T

12. 13. 14. 15.

b d c d c c a b b c F: Humans are the only natural host for the mumps virus. T T T T

Chapter 23 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12.

a b d a b a c c d a T F: Chancroid is caused by a bacterium. 13. T 14. Chamydia is the most common reportable STD in the U.S. 15. T

A-5

Chapter 24 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11.

12. 13. 14. 15.

c b b d c d b d d b F: Pure cultures are very rare in the biosphere. T T T F: One microbe has been found to live in a singleorganism community.

Chapter 25 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12.

b a b d b d b d d c T F: Food products will usually be colonized by harmless microorganisms. 13. T 14. T 15. F: Refrigerating food prevents the growth of many bacteria, but some pathogens, such as Listeria and Salmonella, can continue to grow at low temperatures.

D

APPENDIX

An Introduction to Concept Mapping Concept maps are visual tools for presenting and organizing what you have learned. They can take the place of an outline, though for most people they contain much more meaning and can illustrate connections and interconnections in ways that ordinary outlines cannot. They are also very flexible. If you are creating a concept map, there is a nearly infinite number

of ways that they can be put together and still be “correct.” Concept maps are also a way to incorporate and exploit your own creative impulses, so that you are not stuck inside a rigid framework but can express your understanding of concepts and their connections in ways that make sense to you. This is an example of a relatively large concept map:

Prokaryotic cell structures

var vary aryy among bacteria bacteria and can be divided into

extensions

ffor or movement movement are mov

make up the make

that coat the cell ffor or mating are make up the make for attachment for are

flagella

cell wall

are for fformed ormed med by by cer tain bacteria certain bacteria and can be either e xternal xter nal or external

include but but are not limited to

cell membrane

glycocalyx

pili

internal structures

envelope

chromosomes ribosomes

fimbriae

may if present may be either

increase pathogenicity and are one for fform orm m of a

gramnegative

grampositive

contain nonessential DNA different diff erent than the are done on the DNA in the

form for m biofilms can form and is another type of capsules

are made of RNA and protein and are reponsible for for reponsible

plasmids acid-fast

slime layer stains can be helpful in

identification

A-6

endospores

energy reactions and transport

protein synthesis

may may be helpful in

Appendix D

There is a wide variety of different ways to work with concept maps, such as using them as an introductory overview of material or using them as an evaluation tool. There are even software programs that enable concept mappers to create elaborate maps, complete with sound bytes and photos. Some of these will even convert an outline into a concept map for you. In the end-of-chapter materials in this book, we use only three different methods, all of them fairly simple. These three are explained and illustrated here. All concept maps are made of two basic components: 1. Boxes or circles, each containing a single concept, which is most often a noun. The boxes are arranged on the page in vertical, horizontal, or diagonal rows or arrangements. They may also be arranged in a more free-form manner. 2. Connecting lines that join each concept box to at least one other box. Each connecting line has a word or a phrase associated with it—a linking word. These words/phrases are almost never nouns—but are verbs (like “requires”) or adjectives or adverbs (like “underneath”). In the end, a picture is created that maps what you know about a subject. It illustrates which concepts are bigger and which are details. It illustrates that multiple concepts may

be connected. Experts say that concept maps almost always lead us to conclude that all concepts in a subject can be connected in some way. This is true! And nowhere is it truer than in biology. The trick is to get used to finding the right connecting word to show how two concepts are, indeed, related. When you succeed, you will know the material in a deeper way than is possible by simply answering a single question or even a series of questions. The first kind of concept map used in this book is the “fill-in-the-blank” version. In these concept maps, you are provided with all the boxes and most of the concepts in the boxes. Some boxes may be blank for you to fill in with the appropriate concept. You will do this by looking at the concepts close to the box and examining the connecting word. In these maps, you will also encounter blanks for linking words/phrases. Sometimes all the blanks will be filled in, but there will be no connecting lines or phrases and you will have to supply these. In a few of these maps, you may be asked to draw the linking lines themselves. This is an exercise most like answering a simple question. In the example below, for instance, say to yourself, “Enzymes are __________ by pH and temperature.” You might ask yourself, “What relation do pH and temperature have with

Products

Substrates Protein or Enzymes

A-7

are made of

Catalysts that change the pH

Temperature

and the Activation energy

Acknowledgment: Pat Johnson, Palm Beach Community College, supplied information and a concept map for this Appendix.

A-8

Appendix D

enzymes?” Either way, you would probably end up with a linking phrase like are affected by or can be regulated by. There is some variation in what is a correct answer, but not wide variation. The second kind of concept map you will see is one in which you will be provided a list of words to be used as concepts. You will be asked to draw the boxes and put the words in them in some way that makes sense. Here, there will be a lot of variability based on your view of how the concepts might relate to each other. After you put the concepts in your own boxes, you will need to add linking words/phrases. By the time you have drawn your boxes and added the concepts, you will have many ideas about what kind of linkers you want.

The last type of concept map in this book is the “freestyle” version. You will simply be asked to choose 6 to 10 key words from the chapter and create a map—complete with linking words. Many students report that their first experiences with concept mapping can be frustrating. But when they have invested some time in their first few concept maps, many of them find they can never “go back” to organizing information in linear ways. Maps can make the time fly when you’re studying. And creating concept maps with a partner or a group is also a great way to review material in a meaningful way. Give concept maps a try. Let your creative side show!

A A-B toxin A class of bacterial exotoxin consisting of two components: a binding (B) component and an active (A) or enzymatic component. abiogenesis The belief in spontaneous generation as a source of life. abiotic Nonliving factors such as soil, water, temperature, and light that are studied when looking at an ecosystem. ABO blood group system Developed by Karl Landsteiner in 1904; the identification of different blood groups based on differing isoantigen markers characteristic of each blood type. abscess An inflamed, fibrous lesion enclosing a core of pus. abyssal zone The deepest region of the ocean; a sunless, high-pressure, cold, anaerobic habitat. acellular vaccine A vaccine preparation that contains specific antigens such as the capsule or toxin from a pathogen and not the whole microbe. Acellular (without a cell). acid-fast A term referring to the property of mycobacteria to retain carbol fuchsin even in the presence of acid alcohol. The staining procedure is used to diagnose tuberculosis. acid-fast stain a solution containing carbolfuchsin which, when bound to lipids in the envelopes of Mycobacterium species, cannot be removed with an acid wash. acidic A solution with a pH value below 7 on the pH scale. acidic fermentation An anaerobic degradation of pyruvic acid that results in organic acid production. acquired immunodeficiency syndrome See AIDS. actin protein component of long filaments of protein arranged under the cell membrane of bacteria; contribute to cell shape and division. actin cytoskeleton A scaffoldlike structure made of protein that lies under the cytoplasmic membrane of some bacteria. actinomycetes A group of filamentous, funguslike bacteria. active immunity Immunity acquired through direct stimulation of the immune system by antigen. active site The specific region on an apoenzyme that binds substrate. The site for reaction catalysis.

active transport Nutrient transport method that requires carrier proteins in the membranes of the living cells and the expenditure of energy. acute Characterized by rapid onset and short duration. acyclovir A synthetic purine analog that blocks DNA synthesis in certain viruses, particularly the herpes simplex viruses. adenine (A) One of the nitrogen bases found in DNA and RNA, with a purine form. adenosine deaminase (ADA) deficiency An immunodeficiency disorder and one type of SCIDS that is caused by an inborn error in the metabolism of adenine. The accumulation of adenine destroys both B and T lymphocytes. adenosine triphosphate (ATP) A nucleotide that is the primary source of energy to cells. adhesion The process by which microbes gain a more stable foothold at the portal of entry; often involves a specific interaction between the molecules on the microbial surface and the receptors on the host cell. adjuvant In immunology, a chemical vehicle that enhances antigenicity, presumably by prolonging antigen retention at the injection site. adsorption A process of adhering one molecule onto the surface of another molecule. aerobe A microorganism that lives and grows in the presence of free gaseous oxygen (O2). aerobic respiration Respiration in which the final electron acceptor in the electron transport chain is oxygen (O2). aerosols Suspensions of fine dust or moisture particles in the air that contain live pathogens. aerotolerant The state of not utilizing oxygen but not being harmed by it. aflatoxin From Aspergillus flavus toxin, a mycotoxin that typically poisons moldy animal feed and can cause liver cancer in humans and other animals. agammaglobulinemia Also called hypogammaglobulinemia. The absence of or severely reduced levels of antibodies in serum. agar A polysaccharide found in seaweed and commonly used to prepare solid culture media. agglutination The aggregation by antibodies of suspended cells or similar-size particles (agglutinogens) into clumps that settle.

agranulocyte One form of leukocyte (white blood cell) having globular, nonlobed nuclei and lacking prominent cytoplasmic granules. AIDS Acquired immunodeficiency syndrome. The complex of signs and symptoms characteristic of the late phase of human immunodeficiency virus (HIV) infection. alcoholic fermentation An anaerobic degradation of pyruvic acid that results in alcohol production. algae Photosynthetic, plantlike organisms that generally lack the complex structure of plants; they may be single-celled or multicellular and inhabit diverse habitats such as marine and freshwater environments, glaciers, and hot springs. allele A gene that occupies the same location as other alternative (allelic) genes on paired chromosomes. allergen A substance that provokes an allergic response. allergy The altered, usually exaggerated, immune response to an allergen. Also called hypersensitivity. alloantigen An antigen that is present in some but not all members of the same species. allograft Relatively compatible tissue exchange between nonidentical members of the same species. Also called homograft. allosteric Pertaining to the altered activity of an enzyme due to the binding of a molecule to a region other than the enzyme’s active site. alternative splicing The ability of eukaryotic organisms to create variant mRNAs from a single genetic sequence by cutting it in different places. amantadine Antiviral agent used to treat influenza; prevents fusion and uncoating of virus. Ames test A method for detecting mutagenic and potentially carcinogenic agents based upon the genetic alteration of nutritionally defective bacteria. amination The addition of an amine (—NH2) group to a molecule. amino acids The building blocks of protein. Amino acids exist in 20 naturally occurring forms that impart different characteristics to the various proteins they compose. aminoglycoside A complex group of drugs derived from soil actinomycetes that impairs ribosome function and has antibiotic potential. Example: streptomycin.

G-1

G-2

Glossary

ammonification Phase of the nitrogen cycle in which ammonia is released from decomposing organic material. amphibolism Pertaining to the metabolic pathways that serve multiple functions in the breakdown, synthesis, and conversion of metabolites. amphipathic Relating to a compound that has contrasting characteristics, such as hydrophilic-hydrophobic or acid-base. amphitrichous Having a single flagellum or a tuft of flagella at opposite poles of a microbial cell. amplicon DNA strand that has been primed for replication during polymerase chain reaction. anabolism The energy-consuming process of incorporating nutrients into protoplasm through biosynthesis. anaerobe A microorganism that grows best, or exclusively, in the absence of oxygen. anaerobic digesters Closed chambers used in a microbial process that converts organic sludge from waste treatment plants into useful fuels such as methane and hydrogen gases. Also called bioreactors. anaerobic respiration Respiration in which the final electron acceptor in the electron transport chain is an inorganic molecule containing sulfate, nitrate, nitrite, carbonate, and so on. analog In chemistry, a compound that closely resembles another in structure. anamnestic response In immunology, an augmented response or memory related to a prior stimulation of the immune system by antigen. It boosts the levels of immune substances. anaphylaxis The unusual or exaggerated allergic reaction to antigen that leads to severe respiratory and cardiac complications. anion A negatively charged ion. anoxygenic Non-oxygen-producing. annotating In the context of genome sequencing, it is the process of assigning biological function to genetic sequence. antagonism Relationship in which microorganisms compete for survival in a common environment by taking actions that inhibit or destroy another organism. antibiotic A chemical substance from one microorganism that can inhibit or kill another microbe even in minute amounts. antibody A large protein molecule evoked in response to an antigen that interacts specifically with that antigen. antibody-mediated immunity specific protection from disease provided by the products of B cells. anticodon The trinucleotide sequence of transfer RNA that is complementary to the trinucleotide sequence of messenger RNA (the codon). antigen Any cell, particle, or chemical that induces a specific immune response by B cells or T cells and can stimulate resistance to an infection or a toxin. See immunogen.

antigen binding site Specific region at the ends of the antibody molecule that recognize specific antigens. These sites have numerous shapes to fit a wide variety of antigens. antigenic drift Minor antigenic changes in the influenza A virus due to mutations in the spikes’ genes. antigenic shift Major changes in the influenza A virus due to recombination of viral strains from two different host species. antigenicity The property of a substance to stimulate a specific immune response such as antibody formation. antigen-presenting cell (APC) A macrophage or dendritic cell that ingests and degrades an antigen and subsequently places the antigenic determinant molecules on its surface for recognition by CD4 T lymphocytes. antigen-presenting cells Cells of the immune system that digest foreign cells and particles and place pieces of them on their own surfaces in such a way that other cells of the immune system recognize them. antihistamine A drug that counters the action of histamine and is useful in allergy treatment. antimetabolite A substance such as a drug that competes with, substitutes for, or interferes with a normal metabolite. antimicrobial A special class of compounds capable of destroying or inhibiting microorganisms. antimicrobial peptides Short protein molecules found in epithelial cells; have the ability to kill bacteria. antisense DNA A DNA oligonucleotide that binds to a specific piece of RNA, thereby inhibiting translation; used in gene therapy. antisense RNA An RNA oligonucleotide that binds to a specific piece of RNA, thereby inhibiting translation; used in gene therapy. antisepsis Chemical treatments to kill or inhibit the growth of all vegetative microorganisms on body surfaces. antiseptic A growth-inhibiting agent used on tissues to prevent infection. antiserum Antibody-rich serum derived from the blood of animals (deliberately immunized against infectious or toxic antigen) or from people who have recovered from specific infections. antitoxin Globulin fraction of serum that neutralizes a specific toxin. Also refers to the specific antitoxin antibody itself. apicomplexans A group of protozoans that lack locomotion in the mature state. apoenzyme The protein part of an enzyme, as opposed to the nonprotein or inorganic cofactors. apoptosis The genetically programmed death of cells that is both a natural process of development and the body’s means of destroying abnormal or infected cells. appendages Accessory structures that sprout from the surface of bacteria. They can be divided into two major groups: those that

provide motility and those that enable adhesion. applied microbiology The study of the practical uses of microorganisms. aquifer A subterranean water-bearing stratum of permeable rock, sand, or gravel. archaea Prokaryotic single-celled organisms of primitive origin that have unusual anatomy, physiology, and genetics and live in harsh habitats; when capitalized (Archaea), the term refers to one of the three domains of living organisms as proposed by Woese. arthroconidia Reproductive body of Coccidioides immitis, also arthrospore. Arthus reaction An immune complex phenomenon that develops after repeat injection. This localized inflammation results from aggregates of antigen and antibody that bind, complement, and attract neutrophils. artificial immunity Immunity that is induced as a medical intervention, either by exposing an individual to an antigen or administering immune substances to him or her. ascospore A spore formed within a saclike cell (ascus) of Ascomycota following nuclear fusion and meiosis. ascus Special fungal sac in which haploid spores are created. asepsis A condition free of viable pathogenic microorganisms. aseptic technique Methods of handling microbial cultures, patient specimens, and other sources of microbes in a way that prevents infection of the handler and others who may be exposed. assay medium Microbiological medium used to test the effects of specific treatments to bacteria, such as antibiotic or disinfectant treatment. assembly (viral) The step in viral multiplication in which capsids and genetic material are packaged into virions. astromicrobiology A branch of microbiology that studies the potential for and the possible role of microorganisms in space and on other planets. asymptomatic An infection that produces no noticeable symptoms even though the microbe is active in the host tissue. asymptomatic carrier A person with an inapparent infection who shows no symptoms of being infected yet is able to pass the disease agent on to others. atmosphere That part of the biosphere that includes the gaseous envelope up to 14 miles above the earth’s surface. It contains gases such as carbon dioxide, nitrogen, and oxygen. atom The smallest particle of an element to retain all the properties of that element. atomic number (AN) A measurement that reflects the number of protons in an atom of a particular element. atomic weight The average of the mass numbers of all the isotopic forms for a particular element.

Glossary atopy Allergic reaction classified as type I, with a strong familial relationship; caused by allergens such as pollen, insect venom, food, and dander; involves IgE antibody; includes symptoms of hay fever, asthma, and skin rash. ATP synthase A unique enzyme located in the mitochondrial cristae and chloroplast grana that harnesses the flux of hydrogen ions to the synthesis of ATP. attenuate To reduce the virulence of a pathogenic bacterium or virus by passing it through a non-native host or by long-term subculture. AUG (start codon) The codon that signals the point at which translation of a messenger RNA molecule is to begin. autoantibody An “anti-self” antibody having an affinity for tissue antigens of the subject in which it is formed. autoclave A sterilization chamber that allows the use of steam under pressure to sterilize materials. The most common temperature/ pressure combination for an autoclave is 121°C and 15 psi. autograft Tissue or organ surgically transplanted to another site on the same subject. autoimmune disease The pathologic condition arising from the production of antibodies against autoantigens. Example: rheumatoid arthritis. Also called autoimmunity. autoimmune regulator (AIRE) A protein that regulates the transcription of self antigens in the thymus; defects in AIRE can lead to inappropriate responses to self antigens. autotroph A microorganism that requires only inorganic nutrients and whose sole source of carbon is carbon dioxide. axenic A sterile state such as a pure culture. An axenic animal is born and raised in a germ-free environment. See gnotobiotic. axial filament A type of flagellum (called an endoflagellum) that lies in the periplasmic space of spirochetes and is responsible for locomotion. Also called periplasmic flagellum. azole Five-membered heterocyclic compounds typical of histidine, which are used in antifungal therapy.

B B lymphocyte (B cell) A white blood cell that gives rise to plasma cells and antibodies. bacillus Bacterial cell shape that is cylindrical (longer than it is wide). bacitracin Antibiotic that targets the bacterial cell wall; component of over-the-counter topical antimicrobial ointments. back-mutation A mutation that counteracts an earlier mutation, resulting in the restoration of the original DNA sequence. bacteremia The presence of viable bacteria in circulating blood. bacteremic Bacteria present in the bloodstream.

Bacteria When capitalized can refer to one of the three domains of living organisms proposed by Woese, containing all nonarchaea prokaryotes. bacteria (plural of bacterium) Category of prokaryotes with peptidoglycan in their cell walls and circular chromosome(s). This group of small cells is widely distributed in the earth’s habitats. bacterial chromosome A circular body in bacteria that contains the primary genetic material. Also called nucleoid. bactericide An agent that kills bacteria. bacteriocin Proteins produced by certain bacteria that are lethal against closely related bacteria and are narrow spectrum compared with antibiotics; these proteins are coded and transferred in plasmids. bacteriophage A virus that specifically infects bacteria. bacteristatic Any process or agent that inhibits bacterial growth. bacterium A tiny unicellular prokaryotic organism that usually reproduces by binary fission and usually has a peptidoglycan cell wall, has various shapes, and can be found in virtually any environment. barophile A microorganism that thrives under high (usually hydrostatic) pressure. basement membrane A thin layer (1–6 μm) of protein and polysaccharide found at the base of epithelial tissues. basic A solution with a pH value above 7 on the pH scale. basidiospore A sexual spore that arises from a basidium. Found in basidiomycota fungi. basidium A reproductive cell created when the swollen terminal cell of a hypha develops filaments (sterigmata) that form spores. basophil A motile polymorphonuclear leukocyte that binds IgE. The basophilic cytoplasmic granules contain mediators of anaphylaxis and atopy. beta oxidation The degradation of longchain fatty acids. Two-carbon fragments are formed as a result of enzymatic attack directed against the second or beta carbon of the hydrocarbon chain. Aided by coenzyme A, the fragments enter the Krebs cycle and are processed for ATP synthesis. beta-lactamase An enzyme secreted by certain bacteria that cleaves the beta-lactam ring of penicillin and cephalosporin and thus provides for resistance against the antibiotic. See penicillinase. binary fission The formation of two new cells of approximately equal size as the result of parent cell division. binomial system Scientific method of assigning names to organisms that employs two names to identify every organism— genus name plus species name. biochemistry The study of organic compounds produced by (or components of) living things. The four main categories of biochemicals are carbohydrates, lipids, proteins, and nucleic acids.

G-3

biodegradation The breaking down of materials through the action of microbes or insects. bioenergetics The study of the production and use of energy by cells. bioethics The study of biological issues and how they relate to human conduct and moral judgment. biofilm A complex association that arises from a mixture of microorganisms growing together on the surface of a habitat. biogenesis Belief that living things can only arise from others of the same kind. biogeochemical cycle A process by which matter is converted from organic to inorganic form and returned to various nonliving reservoirs on earth (air, rocks, and water) where it becomes available for reuse by living things. Elements such as carbon, nitrogen, and phosphorus are constantly cycled in this manner. biological vector An animal that not only transports an infectious agent but plays a role in the life cycle of the pathogen, serving as a site in which it can multiply or complete its life cycle. It is usually an alternate host to the pathogen. biomes Particular climate regions in a terrestrial realm. bioremediation Decomposition of harmful chemicals by microbes or consortia of microbes. biosensor A device used to detect microbes or trace amounts of compounds through PCR, genome techniques, or electrochemical signaling. biosphere Habitable regions comprising the aquatic (hydrospheric), soil-rock (lithospheric), and air (atmospheric) environments. biota Beneficial or harmless resident bacteria commonly found on and/or in the human body. biotechnology The use of microbes or their products in the commercial or industrial realm. biotic Living factors such as parasites, food substrates, or other living or once-living organisms that are studied when looking at an ecosystem. blast cell An immature precursor cell of B and T lymphocytes. Also called a lymphoblast. blocking antibody The IgG class of immunoglobulins that competes with IgE antibody for allergens, thus blocking the degranulation of basophils and mast cells. blood cells Cellular components of the blood consisting of red blood cells, primarily responsible for the transport of oxygen and carbon dioxide, and white blood cells, primarily responsible for host defense and immune reactions. blood-brain barrier Decreased permeability of the walls of blood vessels in the brain, restricting access to that compartment. botulinum Clostridium botulinum toxin. Ingestion of this potent exotoxin leads to flaccid paralysis.

G-4

Glossary

bradykinin An active polypeptide that is a potent vasodilator released from IgE-coated mast cells during anaphylaxis. broad spectrum Denotes drugs that have an effect on a wide variety of microorganisms. Brownian movement The passive, erratic, nondirectional motion exhibited by microscopic particles. The jostling comes from being randomly bumped by submicroscopic particles, usually water molecules, in which the visible particles are suspended. brucellosis A zoonosis transmitted to humans from infected animals or animal products; causes a fluctuating pattern of severe fever in humans as well as muscle pain, weakness, headache, weight loss, and profuse sweating. Also called undulant fever. bubo The swelling of one or more lymph nodes due to inflammation. bubonic plague The form of plague in which bacterial growth is primarily restricted to the lymph and is characterized by the appearance of a swollen lymph node referred to as a bubo. budding See exocytosis. bulbar poliomyelitis Complication of polio infection in which the brain stem, medulla, or cranial nerves are affected. Leads to loss of respiratory control and paralysis of the trunk and limbs. bullous Consisting of fluid-filled blisters.

C calculus Dental deposit formed when plaque becomes mineralized with calcium and phosphate crystals. Also called tartar. Calvin cycle A series of reactions in the second phase of photosynthesis that generates glucose. cancer Any malignant neoplasm that invades surrounding tissue and can metastasize to other locations. A carcinoma is derived from epithelial tissue, and a sarcoma arises from proliferating mesodermal cells of connective tissue. capsid The protein covering of a virus’s nucleic acid core. Capsids exhibit symmetry due to the regular arrangement of subunits called capsomers. See icosahedron. capsomer A subunit of the virus capsid shaped as a triangle or disc. capsular staining Any staining method which highlights the outermost polysaccharide and/or protein structure on a bacterial, fungal or protozoal cell. capsule In bacteria, the loose, gel-like covering or slime made chiefly of polysaccharides. This layer is protective and can be associated with virulence. carbohydrate A compound containing primarily carbon, hydrogen, and oxygen in a 1:2:1 ratio. carbohydrate fermentation medium A growth medium that contains sugars that

are converted to acids through fermentation. Usually contains a pH indicator to detect acid protection. carbon cycle That pathway taken by carbon from its abiotic source to its use by producers to form organic compounds (biotic), followed by the breakdown of biotic compounds and their release to a nonliving reservoir in the environment (mostly carbon dioxide in the atmosphere). carbon fixation Reactions in photosynthesis that incorporate inorganic carbon dioxide into organic compounds such as sugars. This occurs during the Calvin cycle and uses energy generated by the light reactions. This process is the source of all production on earth. carbuncle A deep staphylococcal abscess joining several neighboring hair follicles. carotenoid Yellow, orange, or red photosynthetic pigments. carrier A person who harbors infections and inconspicuously spreads them to others. Also, a chemical agent that can accept an atom, chemical radical, or subatomic particle from one compound and pass it on to another. caseous lesion Necrotic area of lung tubercle superficially resembling cheese. Typical of tuberculosis. catabolism The chemical breakdown of complex compounds into simpler units to be used in cell metabolism. catalyst A substance that alters the rate of a reaction without being consumed or permanently changed by it. In cells, enzymes are catalysts. catalytic site The niche in an enzyme where the substrate is converted to the product (also active site). catarrhal A term referring to the secretion of mucus or fluids; term for the first stage of pertussis. cation A positively charged ion. cell An individual membrane-bound living entity; the smallest unit capable of an independent existence. cell wall In bacteria, a rigid structure made of peptidoglycan that lies just outside the cytoplasmic membrane; eukaryotes also have a cell wall but may be composed of a variety of materials. cell-mediated immunity The type of immune responses brought about by T cells, such as cytotoxic and helper effects. cellulitis The spread of bacteria within necrotic tissue. cellulose A long, fibrous polymer composed of β-glucose; one of the most common substances on earth. cephalosporins A group of broad-spectrum antibiotics isolated from the fungus Cephalosporium. cercaria The free-swimming larva of the schistosome trematode that emerges from the snail host and can penetrate human skin, causing schistosomiasis.

cestode The common name for tapeworms that parasitize humans and domestic animals. chancre The primary sore of syphilis that forms at the site of penetration by Treponema pallidum. It begins as a hard, dull red, painless papule that erodes from the center. chancroid A lesion that resembles a chancre but is soft and is caused by Haemophilus ducreyi. chemical bond A link formed between molecules when two or more atoms share, donate, or accept electrons. chemical mediators Small molecules that are released during inflammation and specific immune reactions that allow communication between the cells of the immune system and facilitate surveillance, recognition, and attack. chemiosmosis The generation of a concentration gradient of hydrogen ions (called the proton motive force) by the pumping of hydrogen ions to the outer side of the membrane during electron transport. chemoautotroph An organism that relies upon inorganic chemicals for its energy and carbon dioxide for its carbon. Also called a chemolithotroph. chemoheterotroph Microorganisms that derive their nutritional needs from organic compounds. chemokine Chemical mediators (cytokines) that stimulate the movement and migration of white blood cells. chemostat A growth chamber with an outflow that is equal to the continuous inflow of nutrient media. This steady-state growth device is used to study such events as cell division, mutation rates, and enzyme regulation. chemotactic factors Chemical mediators that stimulate the movement of white blood cells. See chemokines. chemotaxis The tendency of organisms to move in response to a chemical gradient (toward an attractant or to avoid adverse stimuli). chemotherapy The use of chemical substances or drugs to treat or prevent disease. chemotroph Organism that oxidizes compounds to feed on nutrients. chitin A polysaccharide similar to cellulose in chemical structure. This polymer makes up the horny substance of the exoskeletons of arthropods and certain fungi. chloramphenicol Antibiotic that inhibits protein synthesis by binding to the 50S subunit of the ribosome. chlorophyll A group of mostly green pigments that are used by photosynthetic eukaryotic organisms and cyanobacteria to trap light energy to use in making chemical bonds. chloroplast An organelle containing chlorophyll that is found in photosynthetic eukaryotes.

Glossary cholesterol Best-known member of a group of lipids called steroids. Cholesterol is commonly found in cell membranes and animal hormones. chromatin The genetic material of the nucleus. Chromatin is made up of nucleic acid and stains readily with certain dyes. chromosome The tightly coiled bodies in cells that are the primary sites of genes. chronic Any process or disease that persists over a long duration. cilium (plural: cilia) Eukaryotic structure similar to a flagellum that propels a protozoan through the environment. class In the levels of classification, the division of organisms that follows phylum. classical pathway Pathway of complement activation initiated by a specific antigenantibody interaction. clonal selection theory A conceptual explanation for the development of lymphocyte specificity and variety during immune maturation. clone A colony of cells (or group of organisms) derived from a single cell (or single organism) by asexual reproduction. All units share identical characteristics. Also used as a verb to refer to the process of producing a genetically identical population of cells or genes. cloning host An organism such as a bacterium or a yeast that receives and replicates a foreign piece of DNA inserted during a genetic engineering experiment. coagulase A plasma-clotting enzyme secreted by Staphylococcus aureus. It contributes to virulence and is involved in forming a fibrin wall that surrounds staphylococcal lesions. coccobacillus An elongated coccus; a short, thick, oval-shaped bacterial rod. coccus A spherical-shaped bacterial cell. codon A specific sequence of three nucleotides in mRNA (or the sense strand of DNA) that constitutes the genetic code for a particular amino acid. coenzyme A complex organic molecule, several of which are derived from vitamins (e.g., nicotinamide, riboflavin). A coenzyme operates in conjunction with an enzyme. Coenzymes serve as transient carriers of specific atoms or functional groups during metabolic reactions. coevolution A biological process whereby a change in the genetic composition in one organism leads to a change in the genetics of another organism. cofactor An enzyme accessory. It can be organic, such as coenzymes, or inorganic, such as Fe2+, Mn2+, or Zn2+ ions. cold sterilization The use of nonheating methods such as radiation or filtration to sterilize materials. coliform A collective term that includes normal enteric bacteria that are gramnegative and lactose-fermenting.

colony A macroscopic cluster of cells appearing on a solid medium, each arising from the multiplication of a single cell. colostrum The clear yellow early product of breast milk that is very high in secretory antibodies. Provides passive intestinal protection. commensalism An unequal relationship in which one species derives benefit without harming the other. common source epidemic An outbreak of disease in which all affected individuals were exposed to a single source of the pathogen, even if they were exposed at different times. communicable infection Capable of being transmitted from one individual to another. community The interacting mixture of populations in a given habitat. competitive inhibition Control process that relies on the ability of metabolic analogs to control microbial growth by successfully competing with a necessary enzyme to halt the growth of bacterial cells. complement In immunology, serum protein components that act in a definite sequence when set in motion either by an antigenantibody complex or by factors of the alternative (properdin) pathway. complementary DNA (cDNA) DNA created by using reverse transcriptase to synthesize DNA from RNA templates. compounds Molecules that are a combination of two or more different elements. concentration The expression of the amount of a solute dissolved in a certain amount of solvent. It may be defined by weight, volume, or percentage. condyloma acuminata Extensive, branched masses of genital warts caused by infection with human papillomavirus. congenital Transmission of an infection from mother to fetus. congenital rubella Transmission of the rubella virus to a fetus in utero. Injury to the fetus is generally much more serious than it is to the mother. congenital syphilis A syphilis infection of the fetus or newborn acquired from maternal infection in utero. conidia Asexual fungal spores shed as free units from the tips of fertile hyphae. conidiospore A type of asexual spore in fungi; not enclosed in a sac. conjugation In bacteria, the contact between donor and recipient cells associated with the transfer of genetic material such as plasmids. Can involve special (sex) pili. Also a form of sexual recombination in ciliated protozoans. conjunctiva The thin fluid-secreting tissue that covers the eye and lines the eyelid. consortium A group of microbes that includes more than one species. constitutive enzyme An enzyme present in bacterial cells in constant amounts, regardless of the presence of substrate.

G-5

Enzymes of the central catabolic pathways are typical examples. consumer An organism that feeds on producers or other consumers. It gets all nutrients and energy from other organisms (also called heterotroph). May exist at several levels, such as primary (feeds on producers) and secondary (feeds on primary consumers). contagious Communicable; transmissible by direct contact with infected people and their fresh secretions or excretions. contaminant An impurity; any undesirable material or organism. contaminated culture A medium that once held a pure (single or mixed) culture but now contains unwanted microorganisms. convalescence Recovery; the period between the end of a disease and the complete restoration of health in a patient. corepressor A molecule that combines with inactive repressor to form active repressor, which attaches to the operator gene site and inhibits the activity of structural genes subordinate to the operator. covalent A type of chemical bond that involves the sharing of electrons between two atoms. covalent bond A chemical bond formed by the sharing of electrons between two atoms. Creutzfeldt-Jakob disease (CJD) A spongiform encephalopathy caused by infection with a prion. The disease is marked by dementia, impaired senses, and uncontrollable muscle contractions. crista The infolded inner membrane of a mitochondrion that is the site of the respiratory chain and oxidative phosphorylation. cryptosporidiosis A gastrointestinal disease caused by Cryptosporidium parvum, a protozoan. culture The visible accumulation of microorganisms in or on a nutrient medium. Also, the propagation of microorganisms with various media. curd The coagulated milk protein used in cheese making. cutaneous Second level of skin, including the stratum corneum and occasionally the upper dermis. cyanosis Blue discoloration of the skin or mucous membranes indicative of decreased oxygen concentration in blood. cyst The resistant, dormant but infectious form of protozoans. Can be important in spread of infectious agents such as Entamoeba histolytica and Giardia lamblia. cystine An amino acid, HOOC—CH(NH2)— CH2—S—S—CH2—CH(NH2)COOH. An oxidation product of two cysteine molecules in which the OSH (sulfhydryl) groups form a disulfide union. Also called dicysteine. cytochrome A group of heme protein compounds whose chief role is in electron and/or hydrogen transport occurring in the last phase of aerobic respiration.

G-6

Glossary

cytokine A chemical substance produced by white blood cells and tissue cells that regulates development, inflammation, and immunity. cytopathic effect The degenerative changes in cells associated with virus infection. Examples: the formation of multinucleate giant cells (Negri bodies), the prominent cytoplasmic inclusions of nerve cells infected by rabies virus. cytoplasm Dense fluid encased by the cell membrane; the site of many of the cell’s biochemical and synthetic activities. cytoplasmic membrane Lipid bilayer that encloses the cytoplasm of bacterial cells. cytosine (C) One of the nitrogen bases found in DNA and RNA, with a pyrimidine form. cytotoxicity The ability to kill cells; in immunology, certain T cells are called cytotoxic T cells because they kill other cells.

D daptomycin A lipopetide antibiotic that disrupts the cytoplasmic membrane. deamination The removal of an amino group from an amino acid. death phase End of the cell growth due to lack of nutrition, depletion of environment, and accumulation of wastes. Population of cells begins to die. debridement Trimming away devitalized tissue and foreign matter from a wound. decomposer A consumer that feeds on organic matter from the bodies of dead organisms. These microorganisms feed from all levels of the food pyramid and are responsible for recycling elements (also called saprobes). decomposition The breakdown of dead matter and wastes into simple compounds that can be directed back into the natural cycle of living things. decontamination The removal or neutralization of an infectious, poisonous, or injurious agent from a site. deduction Problem-solving process in which an individual constructs a hypothesis, tests its validity by outlining particular events that are predicted by the hypothesis, and then performs experiments to test for those events. deductive approach Method of investigation that uses deduction. See deduction. definitive host The organism in which a parasite develops into its adult or sexually mature stage. Also called the final host. degerm To physically remove surface oils, debris, and soil from skin to reduce the microbial load. degranulation The release of cytoplasmic granules, as when cytokines are secreted from mast cell granules. dehydration synthesis During the formation of a carbohydrate bond, the step in which one carbon molecule gives up its OH group and the other loses the H from its OH group, thereby producing a water molecule. This

process is common to all polymerization reactions. denaturation The loss of normal characteristics resulting from some molecular alteration. Usually in reference to the action of heat or chemicals on proteins whose function depends upon an unaltered tertiary structure. dendritic cell A large, antigen-processing cell characterized by long, branchlike extensions of the cell membrane. denitrification The end of the nitrogen cycle when nitrogen compounds are returned to the reservoir in the air. dental caries A mixed infection of the tooth surface that gradually destroys the enamel and may lead to destruction of the deeper tissue. deoxyribonucleic acid (DNA) The nucleic acid often referred to as the “double helix.” DNA carries the master plan for an organism’s heredity. deoxyribose A 5-carbon sugar that is an important component of DNA. dermatophytes A group of fungi that cause infections of the skin and other integument components. They survive by metabolizing keratin. dermolytic Capable of damaging the skin. desensitization See hyposensitization. desiccation To dry thoroughly. To preserve by drying. desquamate To shed the cuticle in scales; to peel off the outer layer of a surface. diabetes mellitus A disease involving compromise in insulin function. In one form, the pancreatic cells that produce insulin are destroyed by autoantibodies, and in another, the pancreas does not produce sufficient insulin. diapedesis The migration of intact blood cells between endothelial cells of a blood vessel such as a venule. dichotomous keys Flow charts that offer two choices or pathways at each level. differential medium A single substrate that discriminates between groups of microorganisms on the basis of differences in their appearance due to different chemical reactions. differential stain A technique that utilizes two dyes to distinguish between different microbial groups or cell parts by color reaction. diffusion The dispersal of molecules, ions, or microscopic particles propelled down a concentration gradient by spontaneous random motion to achieve a uniform distribution. DiGeorge syndrome A birth defect usually caused by a missing or incomplete thymus gland that results in abnormally low or absent T cells and other developmental abnormalities. dimorphic In mycology, the tendency of some pathogens to alter their growth form from mold to yeast in response to rising temperature.

diplococci Spherical or oval-shaped bacteria, typically found in pairs. direct or total cell count 1. Counting total numbers of individual cells being viewed with magnification. 2. Counting isolated colonies of organisms growing on a plate of media as a way to determine population size. disaccharide A sugar containing two monosaccharides. Example: sucrose (fructose + glucose). disease Any deviation from health, as when the effects of microbial infection damage or disrupt tissues and organs. disinfection The destruction of pathogenic nonsporulating microbes or their toxins, usually on inanimate surfaces. division In the levels of classification, an alternate term for phylum. DNA See deoxyribonucleic acid. DNA polymerase Enzyme responsible for the replication of DNA. Several versions of the enzyme exist, each completing a unique portion of the replication process. DNA profiling A pattern of restriction enzyme fragments that is unique for an individual organism. DNA sequencing Determining the exact order of nucleotides in a fragment of DNA. Most commonly done using the Sanger dideoxy sequencing method. DNA vaccine A newer vaccine preparation based on inserting DNA from pathogens into host cells to encourage them to express the foreign protein and stimulate immunity. domain In the levels of classification, the broadest general category to which an organism is assigned. Members of a domain share only one or a few general characteristics. doubling time Time required for a complete fission cycle—from parent cell to two new daughter cells. Also called generation time. droplet nuclei The dried residue of fine droplets produced by mucus and saliva sprayed while sneezing and coughing. Droplet nuclei are less than 5 μm in diameter (large enough to bear a single bacterium and small enough to remain airborne for a long time) and can be carried by air currents. Droplet nuclei are drawn deep into the air passages. drug resistance An adaptive response in which microorganisms begin to tolerate an amount of drug that would ordinarily be inhibitory. dysentery Diarrheal illness in which stools contain blood and/or mucus. dyspnea Difficulty in breathing.

E echinocandins antifungal drugs that inhibit the manufacture of fungal cell walls. ecosystem A collection of organisms together with its surrounding physical and chemical factors.

Glossary ectoplasm The outer, more viscous region of the cytoplasm of a phagocytic cell such as an amoeba. It contains microtubules, but not granules or organelles. eczema An acute or chronic allergy of the skin associated with itching and burning sensations. Typically, red, edematous, vesicular lesions erupt, leaving the skin scaly and sometimes hyperpigmented. edema The accumulation of excess fluid in cells, tissues, or serous cavities. Also called swelling. electrolyte Any compound that ionizes in solution and conducts current in an electrical field. electron A negatively charged subatomic particle that is distributed around the nucleus in an atom. electrophoresis The separation of molecules by size and charge through exposure to an electrical current. electrostatic Relating to the attraction of opposite charges and the repulsion of like charges. Electrical charge remains stationary as opposed to electrical flow or current. element A substance comprising only one kind of atom that cannot be degraded into two or more substances without losing its chemical characteristics. ELISA Abbreviation for enzyme-linked immunosorbent assay, a very sensitive serological test used to detect antibodies in diseases such as AIDS. emerging disease Newly identified diseases that are becoming more prominent. emetic Inducing to vomit. encephalitis An inflammation of the brain, usually caused by infection. endemic disease A native disease that prevails continuously in a geographic region. endergonic reaction A chemical reaction that occurs with the absorption and storage of surrounding energy. Antonym: exergonic. endocytosis The process whereby solid and liquid materials are taken into the cell through membrane invagination and engulfment into a vesicle. endoenzyme An intracellular enzyme, as opposed to enzymes that are secreted. endogenous Originating or produced within an organism or one of its parts. endoplasmic reticulum (ER) An intracellular network of flattened sacs or tubules with or without ribosomes on their surfaces. endospore A small, dormant, resistant derivative of a bacterial cell that germinates under favorable growth conditions into a vegetative cell. The bacterial genera Bacillus and Clostridium are typical sporeformers. endosymbiosis Relationship in which a microorganism resides within a host cell and provides a benefit to the host cell. endotoxic shock A massive drop in blood pressure caused by the release of endotoxin from gram-negative bacteria multiplying in the bloodstream.

endotoxin A bacterial toxin that is not ordinarily released (as is exotoxin). Endotoxin is composed of a phospholipidpolysaccharide complex that is an integral part of gram-negative bacterial cell walls. Endotoxins can cause severe shock and fever. energy of activation The minimum energy input necessary for reactants to form products in a chemical reaction. energy pyramid An ecological model that shows the energy flow among the organisms in a community. It is structured like the food pyramid but shows how energy is reduced from one trophic level to another. enriched medium A nutrient medium supplemented with blood, serum, or some growth factor to promote the multiplication of fastidious microorganisms. enteric Pertaining to the intestine. enteroaggregative The term used to describe certain types of intestinal bacteria that tend to stick to each other in large clumps. enterohemorrhagic E. coli (EHEC) A group of E. coli species that induce bleeding in the intestines and also in other organs; E. coli O157:H7 belongs to this group. enteroinvasive Predisposed to invade the intestinal tissues. enteropathogenic Pathogenic to the alimentary canal. enterotoxigenic Having the capacity to produce toxins that act on the intestinal tract. enterotoxin A bacterial toxin that specifically targets intestinal mucous membrane cells. Enterotoxigenic strains of Escherichia coli and Staphylococcus aureus are typical sources. enumeration medium Microbiological medium that does not encourage growth and allows for the counting of microbes in food, water or environmental samples. enveloped virus A virus whose nucleocapsid is enclosed by a membrane derived in part from the host cell. It usually contains exposed glycoprotein spikes specific for the virus. enzyme A protein biocatalyst that facilitates metabolic reactions. enzyme induction One of the controls on enzyme synthesis. This occurs when enzymes appear only when suitable substrates are present. enzyme repression The inhibition of enzyme synthesis by the end product of a catabolic pathway. eosinophil A leukocyte whose cytoplasmic granules readily stain with red eosin dye. eosinophilia An increase in eosinophil concentration in the bloodstream, often in response to helminth infection. epidemic A sudden and simultaneous outbreak or increase in the number of cases of disease in a community. epidemiology The study of the factors affecting the prevalence and spread of disease within a community. epitope The precise molecular group of an antigen that defines its specificity and triggers the immune response.

G-7

Epstein-Barr virus (EBV) Herpesvirus linked to infectious mononucleosis, Burkitt’s lymphoma, and nasopharyngeal carcinoma. erysipelas An acute, sharply defined inflammatory disease specifically caused by hemolytic Streptococcus. The eruption is limited to the skin but can be complicated by serious systemic symptoms. erythroblastosis fetalis Hemolytic anemia of the newborn. The anemia comes from hemolysis of Rh-positive fetal erythrocytes by anti-Rh maternal antibodies. Erythroblasts are immature red blood cells prematurely released from the bone marrow. erythrocytes (red blood cells) Blood cells involved in the transport of oxygen and carbon dioxide. erythrogenic toxin An exotoxin produced by lysogenized group A strains of β-hemolytic streptococci that is responsible for the severe fever and rash of scarlet fever in the nonimmune individual. Also called a pyrogenic toxin. eschar A dark, sloughing scab that is the lesion of anthrax and certain rickettsioses. essential nutrient Any ingredient such as a certain amino acid, fatty acid, vitamin, or mineral that cannot be formed by an organism and must be supplied in the diet. A growth factor. ester bond A covalent bond formed by reacting carboxylic acid with an OH group: O (R

C

O

R9)

Olive and corn oils, lard, and butter fat are examples of triacylglycerols—esters formed between glycerol and three fatty acids. ethylene oxide A potent, highly water-soluble gas invaluable for gaseous sterilization of heat-sensitive objects such as plastics, surgical and diagnostic appliances, and spices. etiologic agent The microbial cause of disease; the pathogen. eubacteria Term used for nonarchaea prokaryotes, means “true bacteria.” Eukarya One of the three domains (sometimes called superkingdoms) of living organisms, as proposed by Woese; contains all eukaryotic organisms. eukaryotic cell A cell that differs from a prokaryotic cell chiefly by having a nuclear membrane (a well-defined nucleus), membrane-bounded subcellular organelles, and mitotic cell division. eutrophication The process whereby dissolved nutrients resulting from natural seasonal enrichment or industrial pollution of water cause overgrowth of algae and cyanobacteria to the detriment of fish and other large aquatic inhabitants. evolution Scientific principle that states that living things change gradually through hundreds of millions of years, and these changes are expressed in structural and

G-8

Glossary

functional adaptations in each organism. Evolution presumes that those traits that favor survival are preserved and passed on to following generations, and those traits that do not favor survival are lost. exanthem An eruption or rash of the skin. exergonic A chemical reaction associated with the release of energy to the surroundings. Antonym: endergonic. exfoliative toxin A poisonous substance that causes superficial cells of an epithelium to detach and be shed. Example: staphylococcal exfoliatin. Also called an epidermolytic toxin. exocytosis The process that releases enveloped viruses from the membrane of the host’s cytoplasm. exoenzyme An extracellular enzyme chiefly for hydrolysis of nutrient macromolecules that are otherwise impervious to the cell membrane. It functions in saprobic decomposition of organic debris and can be a factor in invasiveness of pathogens. exogenous Originating outside the body. exon A stretch of eukaryotic DNA coding for a corresponding portion of mRNA that is translated into peptides. Intervening stretches of DNA that are not expressed are called introns. During transcription, exons are separated from introns and are spliced together into a continuous mRNA transcript. exotoxin A toxin (usually protein) that is secreted and acts upon a specific cellular target. Examples: botulin, tetanospasmin, diphtheria toxin, and erythrogenic toxin. exponential Pertaining to the use of exponents, numbers that are typically written as a superscript to indicate how many times a factor is to be multiplied. Exponents are used in scientific notation to render large, cumbersome numbers into small workable quantities. exponential growth phase The period of maximum growth rate in a growth curve. Cell population increases logarithmically. extrapulmonary tuberculosis A condition in which tuberculosis bacilli have spread to organs other than the lungs. extremophiles Organisms capable of living in harsh environments, such as extreme heat or cold.

F facilitated diffusion The passive movement of a substance across a plasma membrane from an area of higher concentration to an area of lower concentration utilizing specialized carrier proteins. facultative Pertaining to the capacity of microbes to adapt or adjust to variations; not obligate. Example: the presence of oxygen is not obligatory for a facultative anaerobe to grow. See obligate. family In the levels of classification, a midlevel division of organisms that groups more closely related organisms than previous levels. An order is divided into families.

fastidious Requiring special nutritional or environmental conditions for growth. Said of bacteria. fecal coliforms Any species of gramnegative lactose-positive bacteria (primarily Escherichia coli) that live primarily in the intestinal tract and not the environment. Finding evidence of these bacteria in a water or food sample is substantial evidence of fecal contamination and potential for infection (see coliform). feedback inhibition Temporary end to enzyme action caused by an end product molecule binding to the regulatory site and preventing the enzyme’s active site from binding to its substrate. fermentation The extraction of energy through anaerobic degradation of substrates into simpler, reduced metabolites. In large industrial processes, fermentation can mean any use of microbial metabolism to manufacture organic chemicals or other products. fermentor A large tank used in industrial microbiology to grow mass quantities of microbes that can synthesize desired products. These devices are equipped with means to stir, monitor, and harvest products such as drugs, enzymes, and proteins in very large quantities. fertility (F′) factor Donor plasmid that allows synthesis of a pilus in bacterial conjugation. Presence of the factor is indicated by F+, and lack of the factor is indicated by F –. filament A helical structure composed of proteins that is part of bacterial flagella. fimbria A short, numerous-surface appendage on some bacteria that provides adhesion but not locomotion. Firmicutes Taxonomic category of bacteria that have gram-positive cell envelopes. flagellar staining A staining method which highlights the flagellum of a bacterium. flagellum A structure that is used to propel the organism through a fluid environment. fluid mosaic model A conceptualization of the molecular architecture of cellular membranes as a bilipid layer containing proteins. Membrane proteins are embedded to some degree in this bilayer, where they float freely about. fluorescence The property possessed by certain minerals and dyes to emit visible light when excited by ultraviolet radiation. A fluorescent dye combined with specific antibody provides a sensitive test for the presence of antigen. fluoroquinolones Synthetic antimicrobial drugs chemically related to quinine. They are broad spectrum and easily adsorbed from the intestine. focal infection Occurs when an infectious agent breaks loose from a localized infection and is carried by the circulation to other tissues. folliculitis An inflammatory reaction involving the formation of papules or pustules in clusters of hair follicles.

fomite Virtually any inanimate object an infected individual has contact with that can serve as a vehicle for the spread of disease. food chain A simple straight-line feeding sequence among organisms in a community. food fermentations Addition to and growth of known cultures of microorganisms in foods to produce desirable flavors, smells, or textures. Includes cheeses, breads, alcoholic beverages, and pickles. food poisoning Symptoms in the intestines (which may include vomiting) induced by preformed exotoxin from bacteria. food web A complex network that traces all feeding interactions among organisms in a community (see food chain). This is considered to be a more accurate picture of food relationships in a community than a food chain. formalin A 37% aqueous solution of formaldehyde gas; a potent chemical fixative and microbicide. fosfomycin trimethamine Antibiotic that inhibits an enzyme necessary for cell wall synthesis. frameshift mutation An insertion or deletion mutation that changes the codon reading frame from the point of the mutation to the final codon. Almost always leads to a nonfunctional protein. free energy energy in a chemical system that can be used to do work. fructose One of the carbohydrates commonly referred to as sugars. Fructose is commonly fruit sugars. functional group In chemistry, a particular molecular combination that reacts in predictable ways and confers particular properties on a compound. Examples: — COOH, —OH, —CHO. fungemia The condition of fungi multiplying in the bloodstream. fungi Macroscopic and microscopic heterotrophic eukaryotic organisms that can be uni- or multicellular. fungus Heterotrophic unicellular or multicellular eukaryotic organism that may take the form of a larger macroscopic organism, as in the case of mushrooms, or a smaller microscopic organism, as in the case of yeasts and molds. furuncle A boil; a localized pyogenic infection arising from a hair follicle. fuzeon Anti-HIV drug that inhibits viral attachment to host cells.

G Gaia Theory The concept that biotic and abiotic factors sustain suitable conditions for one another simply by their interactions. Named after the mythical Greek goddess of earth. gamma globulin The fraction of plasma proteins high in immunoglobulins (antibodies). Preparations from pooled human plasma containing normal antibodies make useful passive immunizing

Glossary agents against pertussis, polio, measles, and several other diseases. gas gangrene Disease caused by a clostridial infection of soft tissue or wound. The name refers to the gas produced by the bacteria growing in the tissue. Unless treated early, it is fatal. Also called myonecrosis. gastritis Pain and/or nausea, usually experienced after eating; result of inflammation of the lining of the stomach. gel electrophoresis A laboratory technique for separating DNA fragments according to length by employing electricity to force the DNA through a gel-like matrix typically made of agarose. Smaller DNA fragments move more quickly through the gel, thereby moving farther than larger fragments during the same period of time. gene A site on a chromosome that provides information for a certain cell function. A specific segment of DNA that contains the necessary code to make a protein or RNA molecule. gene probe Short strands of single-stranded nucleic acid that hybridize specifically with complementary stretches of nucleotides on test samples and thereby serve as a tagging and identification device. gene therapy The introduction of normal functional genes into people with genetic diseases such as sickle cell anemia and cystic fibrosis. This is usually accomplished by a virus vector. generation time Time required for a complete fission cycle—from parent cell to two new daughter cells. Also called doubling time. genetic engineering A field involving deliberate alterations (recombinations) of the genomes of microbes, plants, and animals through special technological processes. genetics The science of heredity. genital warts A prevalent STD linked to some forms of cancer of the reproductive organs. Caused by infection with human papillomavirus. genome The complete set of chromosomes and genes in an organism. genomics The systematic study of an organism’s genes and their functions. genotype The genetic makeup of an organism. The genotype is ultimately responsible for an organism’s phenotype, or expressed characteristics. genus In the levels of classification, the second most specific level. A family is divided into several genera. geomicrobiology A branch of microbiology that studies the role of microorganisms in the earth’s crust. germ free See axenic. germ theory of disease A theory first originating in the 1800s that proposed that microorganisms can be the cause of diseases. The concept is actually so well established in the present time that it is considered a fact. germicide An agent lethal to nonendospore-forming pathogens.

giardiasis Infection by the Giardia flagellate. Most common mode of transmission is contaminated food and water. Symptoms include diarrhea, abdominal pain, and flatulence. gingivitis Inflammation of the gum tissue in contact with the roots of the teeth. gluconeogenesis The formation of glucose (or glycogen) from noncarbohydrate sources such as protein or fat. Also called glyconeogenesis. glucose One of the carbohydrates commonly referred to as sugars. Glucose is characterized by its 6-carbon structure. glycerol A 3-carbon alcohol, with three OH groups that serve as binding sites. glycocalyx A filamentous network of carbohydrate-rich molecules that coats cells. glycogen A glucose polymer stored by cells. glycolysis The energy-yielding breakdown (fermentation) of glucose to pyruvic or lactic acid. It is often called anaerobic glycolysis because no molecular oxygen is consumed in the degradation. glycosidic bond A bond that joins monosaccharides to form disaccharides and polymers. gnotobiotic Referring to experiments performed on germ-free animals. Golgi apparatus An organelle of eukaryotes that participates in packaging and secretion of molecules. gonococcus Common name for Neisseria gonorrhoeae, the agent of gonorrhea. Gracilicutes Taxonomic category of bacteria that have gram-negative envelopes. graft Live tissue taken from a donor and transplanted into a recipient to replace damaged or missing tissues such as skin, bone, blood vessels. graft versus host disease (GVHD) A condition associated with a bone marrow transplant in which T cells in the transplanted tissue mount an immune response against the recipient’s (host) normal tissues. Gram stain A differential stain for bacteria useful in identification and taxonomy. Gram-positive organisms appear purple from crystal violet mordant retention, whereas gram-negative organisms appear red after loss of crystal violet and absorbance of the safranin counterstain. gram-negative A category of bacterial cells that describes bacteria with an outer membrane, a cytoplasmic membrane, and a thin cell wall. gram-positive A category of bacterial cells that describes bacteria with a thick cell wall and no outer membrane. grana Discrete stacks of chlorophyllcontaining thylakoids within chloroplasts. granulocyte A mature leukocyte that contains noticeable granules in a Wright stain. Examples: neutrophils, eosinophils, and basophils. granuloma A solid mass or nodule of inflammatory tissue containing modified

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macrophages and lymphocytes. Usually a chronic pathologic process of diseases such as tuberculosis or syphilis. granzymes Enzymes secreted by cytotoxic T cells that damage proteins of target cells. Graves’ disease A malfunction of the thyroid gland in which autoantibodies directed at thyroid cells stimulate an overproduction of thyroid hormone (hyperthyroidism). greenhouse effect The capacity to retain solar energy by a blanket of atmospheric gases that redirects heat waves back toward the earth. group translocation A form of active transport in which the substance being transported is altered during transfer across a plasma membrane. growth curve A graphical representation of the change in population size over time. This graph has four periods known as lag phase, exponential or log phase, stationary phase, and death phase. growth factor An organic compound such as a vitamin or amino acid that must be provided in the diet to facilitate growth. An essential nutrient. guanine (G) One of the nitrogen bases found in DNA and RNA in the purine form. Guillain-Barré syndrome A neurological complication of infection or vaccination. gumma A nodular, infectious granuloma characteristic of tertiary syphilis. gut-associated lymphoid tissue (GALT) A collection of lymphoid tissue in the gastrointestinal tract that includes the appendix, the lacteals, and Peyer’s patches. gyrase The enzyme responsible for supercoiling DNA into tight bundles; a type of topoisomerase.

H HAART Highly active antiretroviral therapy; three-antiviral treatment for HIV infection. habitat The environment to which an organism is adapted. halogens A group of related chemicals with antimicrobial applications. The halogens most often used in disinfectants and antiseptics are chlorine and iodine. halophile A microbe whose growth is either stimulated by salt or requires a high concentration of salt for growth. Hansen’s disease A chronic, progressive disease of the skin and nerves caused by infection by a mycobacterium that is a slowgrowing, strict parasite. Hansen’s disease is the preferred name for leprosy. hapten An incomplete or partial antigen. Although it constitutes the determinative group and can bind antigen, hapten cannot stimulate a full immune response without being carried by a larger protein molecule. Hashimoto’s thyroiditis An autoimmune disease of the thyroid gland that damages the thyroid follicle cells and results in decreased production of thyroid hormone (hypothyroidism).

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Glossary

hay fever A form of atopic allergy marked by seasonal acute inflammation of the conjunctiva and mucous membranes of the respiratory passages. Symptoms are irritative itching and rhinitis. helical Having a spiral or coiled shape. Said of certain virus capsids and bacteria. helminth A term that designates all parasitic worms. helper T cell A class of thymus-stimulated lymphocytes that facilitate various immune activities such as assisting B cells and macrophages. Also called a T helper cell. hemagglutinin A molecule that causes red blood cells to clump or agglutinate. Often found on the surfaces of viruses. hematopoiesis The process by which the various types of blood cells are formed, such as in the bone marrow. hemoglobin A protein in red blood cells that carries iron. hemolysin Any biological agent that is capable of destroying red blood cells and causing the release of hemoglobin. Many bacterial pathogens produce exotoxins that act as hemolysins. hemolytic disease Incompatible Rh factor between mother and fetus causes maternal antibodies to attack the fetus and trigger complement-mediated lysis in the fetus. hemolytic uremic syndrome (HUS) Severe hemolytic anemia leading to kidney damage or failure; can accompany E. coli O157:H7 intestinal infection. hemolyze When red blood cells burst and release hemoglobin pigment. hepatitis Inflammation and necrosis of the liver, often the result of viral infection. hepatitis A virus (HAV) Enterovirus spread by contaminated food responsible for shortterm (infectious) hepatitis. hepatitis B virus (HBV) DNA virus that is the causative agent of serum hepatitis. hepatocellular carcinoma A liver cancer associated with infection with hepatitis B virus. herd immunity The status of collective acquired immunity in a population that reduces the likelihood that nonimmune individuals will contract and spread infection. One aim of vaccination is to induce herd immunity. heredity Genetic inheritance. hermaphroditic Containing the sex organs for both male and female in one individual. herpes zoster A recurrent infection caused by latent chickenpox virus. Its manifestation on the skin tends to correspond to dermatomes and to occur in patches that “girdle” the trunk. Also called shingles. heterotroph An organism that relies upon organic compounds for its carbon and energy needs. hexose A 6-carbon sugar such as glucose and fructose. hierarchies Levels of power. Arrangement in order of rank.

histamine A cytokine released when mast cells and basophils release their granules. An important mediator of allergy, its effects include smooth muscle contraction, increased vascular permeability, and increased mucus secretion. histiocyte Another term for macrophage. histone Proteins associated with eukaryotic DNA. These simple proteins serve as winding spools to compact and condense the chromosomes. HLA An abbreviation for human leukocyte antigens. This closely linked cluster of genes programs for cell surface glycoproteins that control immune interactions between cells and is involved in rejection of allografts. Also called the major histocompatibility complex (MHC). holoenzyme An enzyme complete with its apoenzyme and cofactors. hops The ripe, dried fruits of the hop vine (Humulus lupulus) that are added to beer wort for flavoring. horizontal gene transfer transmission of genetic material from one cell to another through non-reproductive mechanisms; i.e., from one organism to another living in the same habitat. host Organism in which smaller organisms or viruses live, feed, and reproduce. host range The limitation imposed by the characteristics of the host cell on the type of virus that can successfully invade it. human diploid cell vaccine (HDCV) A vaccine made using cell culture that is currently the vaccine of choice for preventing infection by rabies virus. human immunodeficiency virus (HIV) A retrovirus that causes acquired immunodeficiency syndrome (AIDS). Human Microbiome Project a project of the National Institutes of Health to identify microbial inhabitants of the human body and their role in health and disease; uses metagenomic techniques instead of culturing. human papillomavirus (HPV) A group of DNA viruses whose members are responsible for common, plantar, and genital warts. humoral immunity Protective molecules (mostly B lymphocytes) carried in the fluids of the body. hybridization A process that matches complementary strands of nucleic acid (DNA-DNA, RNA-DNA, RNA-RNA). Used for locating specific sites or types of nucleic acids. hybridoma An artificial cell line that produces monoclonal antibodies. It is formed by fusing (hybridizing) a normal antibody-producing cell with a cancer cell, and it can produce pure antibody indefinitely. hydration The addition of water as in the coating of ions with water molecules as ions enter into aqueous solution.

hydrogen bond A weak chemical bond formed by the attraction of forces between molecules or atoms—in this case, hydrogen and either oxygen or nitrogen. In this type of bond, electrons are not shared, lost, or gained. hydrologic cycle The continual circulation of water between hydrosphere, atmosphere, and lithosphere. hydrolysis A process in which water is used to break bonds in molecules. Usually occurs in conjunction with an enzyme. hydrophilic The property of attracting water. Molecules that attract water to their surface are called hydrophilic. hydrophobic The property of repelling water. Molecules that repel water are called hydrophobic. hydrosphere That part of the biosphere that encompasses water-containing environments such as oceans, lakes, rivers. hypertonic Having a greater osmotic pressure than a reference solution. hyphae The tubular threads that make up filamentous fungi (molds). This web of branched and intertwining fibers is called a mycelium. hypogammaglobulinemia An inborn disease in which the gamma globulin (antibody) fraction of serum is greatly reduced. The condition is associated with a high susceptibility to pyogenic infections. hyposensitization A therapeutic exposure to known allergens designed to build tolerance and eventually prevent allergic reaction. hypothesis A tentative explanation of what has been observed or measured. hypotonic Having a lower osmotic pressure than a reference solution.

I icosahedron A regular geometric figure having 20 surfaces that meet to form 12 corners. Some virions have capsids that resemble icosahedral crystals. immune complex reaction Type III hypersensitivity of the immune system. It is characterized by the reaction of soluble antigen with antibody, and the deposition of the resulting complexes in basement membranes of epithelial tissue. immunity An acquired resistance to an infectious agent due to prior contact with that agent. immunoassays Extremely sensitive tests that permit rapid and accurate measurement of trace antigen or antibody. immunocompetence The ability of the body to recognize and react with multiple foreign substances. immunodeficiency Immune function is incompletely developed, suppressed, or destroyed. immunodeficiency disease A form of immunopathology in which white blood cells are unable to mount a complete,

Glossary effective immune response, which results in recurrent infections. Examples would be AIDS and agammaglobulinemia. immunogen Any substance that induces a state of sensitivity or resistance after processing by the immune system of the body. immunoglobulin (Ig) The chemical class of proteins to which antibodies belong. immunology The study of the system of body defenses that protect against infection. immunopathology The study of disease states associated with overreactivity or underreactivity of the immune response. immunotherapy Preventing or treating infectious diseases by administering substances that produce artificial immunity. May be active or passive. in utero Literally means “in the uterus”; pertains to events or developments occurring before birth. in vitro Literally means “in glass,” signifying a process or reaction occurring in an artificial environment, as in a test tube or culture medium. in vivo Literally means “in a living being,” signifying a process or reaction occurring in a living thing. incidence In epidemiology, the number of new cases of a disease occurring during a period. incineration Destruction of microbes by subjecting them to extremes of dry heat. Microbes are reduced to ashes and gas by this process. inclusion A relatively inert body in the cytoplasm such as storage granules, glycogen, fat, or some other aggregated metabolic product. inclusion body One of a variety of different storage compartments in bacterial cells. incubate To isolate a sample culture in a temperature-controlled environment to encourage growth. incubation period The period from the initial contact with an infectious agent to the appearance of the first symptoms. index case The first case of a disease identified in an outbreak or epidemic. indicator bacteria In water analysis, any easily cultured bacteria that may be found in the intestine and can be used as an index of fecal contamination. The category includes coliforms and enterococci. Discovery of these bacteria in a sample means that pathogens may also be present. induced mutation Any alteration in DNA that occurs as a consequence of exposure to chemical or physical mutagens. inducible enzyme An enzyme that increases in amount in direct proportion to the amount of substrate present. inducible operon An operon that under normal circumstances is not transcribed. The presence of a specific inducer molecule can cause transcription of the operon to begin. induction The process whereby a bacteriophage in the prophage state is

activated and begins replication and enters the lytic cycle. induration Area of hardened, reddened tissue associated with the tuberculin test. infection The entry, establishment, and multiplication of pathogenic organisms within a host. infectious disease The state of damage or toxicity in the body caused by an infectious agent. inflammation A natural, nonspecific response to tissue injury that protects the host from further damage. It stimulates immune reactivity and blocks the spread of an infectious agent. inoculation The implantation of microorganisms into or upon culture media. inorganic chemicals Molecules that lack the basic framework of the elements of carbon and hydrogen. integument The outer surfaces of the body: skin, hair, nails, sweat glands, and oil glands. interferon (IFN) Natural human chemical that inhibits viral replication; used therapeutically to combat viral infections and cancer. interferon gamma A protein produced by a virally infected cell that induces production of antiviral substances in neighboring cells. This defense prevents the production and maturation of viruses and thus terminates the viral infection. interleukins A class of chemicals released from host cells that have potent effects on immunity. intermediate filament proteinaceous fibers in eukaryotic cells that help provide support to the cells and their organelles. intoxication Poisoning that results from the introduction of a toxin into body tissues through ingestion or injection. intron The segments on split genes of eukaryotes that do not code for polypeptide. They can have regulatory functions. See exon. iodophor A combination of iodine and an organic carrier that is a moderate-level disinfectant and antiseptic. ion An unattached, charged particle. ionic bond A chemical bond in which electrons are transferred and not shared between atoms. ionization The aqueous dissociation of an electrolyte into ions. ionizing radiation Radiant energy consisting of short-wave electromagnetic rays (X ray) or high-speed electrons that cause dislodgment of electrons on target molecules and create ions. irradiation The application of radiant energy for diagnosis, therapy, disinfection, or sterilization. irritability Capacity of cells to respond to chemical, mechanical, or light stimuli. This property helps cells adapt to the environment and obtain nutrients. isograft Transplanted tissue from one monozygotic twin to the other; transplants

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between highly inbred animals that are genetically identical. isolation The separation of microbial cells by serial dilution or mechanical dispersion on solid media to create discrete colonies. isoniazid Older drug that targets the bacterial cell wall; used against M. tuberculosis. isotonic Two solutions having the same osmotic pressure such that, when separated by a semipermeable membrane, there is no net movement of solvent in either direction. isotope A version of an element that is virtually identical in all chemical properties to another version except that their atoms have slightly different atomic masses.

J jaundice The yellowish pigmentation of skin, mucous membranes, sclera, deeper tissues, and excretions due to abnormal deposition of bile pigments. Jaundice is associated with liver infection, as with hepatitis B virus and leptospirosis. JC virus (JCV) Causes a form of encephalitis (progressive multifocal leukoencephalopathy), especially in AIDS patients.

K Kaposi sarcoma A malignant or benign neoplasm that appears as multiple hemorrhagic sites on the skin, lymph nodes, and viscera and apparently involves the metastasis of abnormal blood vessel cells. It is a clinical feature of AIDS. keratin Protein produced by outermost skin cells that provide protection from trauma and moisture. killed or inactivated vaccine A whole cell or intact virus preparation in which the microbes are dead or preserved and cannot multiply but are still capable of conferring immunity. killer T cells A T lymphocyte programmed to directly affix cells and kill them. See cytotoxicity. kingdom In the levels of classification, the second division from more general to more specific. Each domain is divided into kingdoms. Koch’s postulates A procedure to establish the specific cause of disease. In all cases of infection: (1) The agent must be found; (2) inoculations of a pure culture must reproduce the same disease in animals; (3) the agent must again be present in the experimental animal; and (4) a pure culture must again be obtained. Koplik’s spots Tiny red blisters with central white specks on the mucosal lining of the cheeks. Symptomatic of measles. Krebs cycle or tricarboxylic acid cycle (TCA) The second pathway of the three pathways that complete the process of primary catabolism. Also called the citric acid cycle.

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Glossary

L L form a stage in the lives of some bacteria in which they have no peptidoglycan. labile In chemistry, molecules, or compounds that are chemically unstable in the presence of environmental changes. lactoferrin A protein in mucosal secretions, tears and milk that contains iron molecules and has antimicrobial activity. lactose One of the carbohydrates commonly referred to as sugars. Lactose is commonly found in milk. lactose (lac) operon Control system that manages the regulation of lactose metabolism. It is composed of three DNA segments, including a regulator, a control locus, and a structural locus. lag phase The early phase of population growth during which no signs of growth occur. lager The maturation process of beer, which is allowed to take place in large vats at a reduced temperature. lagging strand The newly forming 5′ DNA strand that is discontinuously replicated in segments (Okazaki fragments). lantibiotics Short peptides produced by bacteria that inhibit the growth of other bacteria. latency The state of being inactive. Example: a latent virus or latent infection. leading strand The newly forming 3′DNA strand that is replicated in a continuous fashion without segments. leaven To lighten food material by entrapping gas generated within it. Example: the rising of bread from the CO2 produced by yeast or baking powder. Legionnaire’s disease Infection by Legionella bacterium. Weakly gram-negative rods are able to survive in aquatic habitats. Some forms may be fatal. legumes Plants that produce seeds in pods. Examples include soybeans and peas. lepromas Skin nodules seen on the face of persons suffering from lepromatous leprosy. The skin folds and thickenings are caused by the overgrowth of Mycobacterium leprae. lepromatous leprosy Severe, disfiguring leprosy characterized by widespread dissemination of the leprosy bacillus in deeper lesions. leprosy See Hansen’s disease. lesion A wound, injury, or some other pathologic change in tissues. leukocidin A heat-labile substance formed by some pyogenic cocci that impairs and sometimes lyses leukocytes. leukocytes White blood cells. The primary infection-fighting blood cells. leukocytosis An abnormally large number of leukocytes in the blood, which can be indicative of acute infection. leukopenia A lower-than-normal leukocyte count in the blood that can be indicative of blood infection or disease. leukotriene An unsaturated fatty acid derivative of arachidonic acid. Leukotriene

functions in chemotactic activity, smooth muscle contractility, mucus secretion, and capillary permeability. ligase An enzyme required to seal the sticky ends of DNA pieces after splicing. light-dependent reactions The series of reactions in photosynthesis that are driven by the light energy (photons) absorbed by chlorophyll. They involve splitting of water into hydrogens and oxygen, transport of electrons by NADP, and ATP synthesis. light-independent reactions The series of reactions in photosynthesis that can proceed with or without light. It is a cyclic system that uses ATP from the light reactions to incorporate or fix carbon dioxide into organic compounds, leading to the production of glucose and other carbohydrates (also called the Calvin cycle). lipase A fat-splitting enzyme. Example: triacylglycerol lipase separates the fatty acid chains from the glycerol backbone of triglycerides. lipid A term used to describe a variety of substances that are not soluble in polar solvents such as water but will dissolve in nonpolar solvents such as benzene and chloroform. Lipids include triglycerides, phospholipids, steroids, and waxes. lipopolysaccharide A molecular complex of lipid and carbohydrate found in the bacterial cell wall. The lipopolysaccharide (LPS) of gram-negative bacteria is an endotoxin with generalized pathologic effects such as fever. lipoteichoic acid Anionic polymers containing glycerol that are anchored in the cytoplasmic membranes of gram-positive bacteria. liquid media growth-supporting substance in fluid form. lithoautotroph Bacteria that rely on inorganic minerals to supply their nutritional needs. Sometimes referred to as chemoautotrophs. lithosphere That part of the biosphere that encompasses the earth’s crust, including rocks and minerals. lithotroph An autotrophic microbe that derives energy from reduced inorganic compounds such as N2S. lobar pneumonia Infection involving whole segments (lobes) of the lungs, which may lead to consolidation and plugging of the alveoli and extreme difficulty in breathing. localized infection Occurs when a microbe enters a specific tissue, infects it, and remains confined there. locus A site on a chromosome occupied by a gene. Plural: loci. log phase Maximum rate of cell division during which growth is geometric in its rate of increase. Also called exponential growth phase. lophotrichous Describing bacteria having a tuft of flagella at one or both poles. lumen The cavity within a tubular organ. lymphadenitis Inflammation of one or more lymph nodes. Also called lymphadenopathy.

lymphatic system A system of vessels and organs that serve as sites for development of immune cells and immune reactions. It includes the spleen, thymus, lymph nodes, and GALT. lymphocyte The second most common form of white blood cells. lyophilization A method for preserving microorganisms (and other substances) by freezing and then drying them directly from the frozen state. lyse To burst. lysin A complement-fixing antibody that destroys specific targeted cells. Examples: hemolysin and bacteriolysin. lysis The physical rupture or deterioration of a cell. lysogenic conversion A bacterium acquires a new genetic trait due to the presence of genetic material from an infecting phage. lysogeny The indefinite persistence of bacteriophage DNA in a host without bringing about the production of virions. lysosome A cytoplasmic organelle containing lysozyme and other hydrolytic enzymes. lysozyme An enzyme found in sweat, tears, and saliva that breaks down bacterial peptidoglycan.

M macromolecules Large, molecular compounds assembled from smaller subunits, most notably biochemicals. macronutrient A chemical substance required in large quantities (phosphate, for example). macrophage A white blood cell derived from a monocyte that leaves the circulation and enters tissues. These cells are important in nonspecific phagocytosis and in regulating, stimulating, and cleaning up after immune responses. macroscopic Visible to the naked eye. major histocompatibility complex A set of genes in mammals that produces molecules on surfaces of cells that differentiate among different individuals in the species. malt The grain, usually barley, that is sprouted to obtain digestive enzymes and dried for making beer. maltose One of the carbohydrates referred to as sugars. A fermentable sugar formed from starch. Mantoux test An intradermal screening test for tuberculin hypersensitivity. A red, firm patch of skin at the injection site greater than 10 mm in diameter after 48 hours is a positive result that indicates current or prior exposure to the TB bacillus. mapping Determining the location of loci and other qualities of genomic DNA. marine microbiology A branch of microbiology that studies the role of microorganisms in the oceans. marker Any trait or factor of a cell, virus, or molecule that makes it distinct and recognizable. Example: a genetic marker.

Glossary mash In making beer, the malt grain is steeped in warm water, ground up, and fortified with carbohydrates to form mash. mass number (MN) Measurement that reflects the number of protons and neutrons in an atom of a particular element. mast cell A nonmotile connective tissue cell implanted along capillaries, especially in the lungs, skin, gastrointestinal tract, and genitourinary tract. Like a basophil, its granules store mediators of allergy. matrix The dense ground substance between the cristae of a mitochondrion that serves as a site for metabolic reactions. matter All tangible materials that occupy space and have mass. maximum temperature The highest temperature at which an organism will grow. MDRTB Multidrug-resistant tuberculosis. mechanical vector An animal that transports an infectious agent but is not infected by it, such as houseflies whose feet become contaminated with feces. medium (plural, media) A nutrient used to grow organisms outside of their natural habitats. meiosis The type of cell division necessary for producing gametes in diploid organisms. Two nuclear divisions in rapid succession produce four gametocytes, each containing a haploid number of chromosomes. membrane In a single cell, a thin doublelayered sheet composed of lipids such as phospholipids and sterols and proteins. memory (immunologic memory) The capacity of the immune system to recognize and act against an antigen upon second and subsequent encounters. memory cell The long-lived progeny of a sensitized lymphocyte that remains in circulation and is genetically programmed to react rapidly with its antigen. Mendosicutes Taxonomic category of bacteria that have unusual cell walls; archaea. meninges The tough tri-layer membrane covering the brain and spinal cord. Consists of the dura mater, arachnoid mater, and pia mater. meningitis An inflammation of the membranes (meninges) that surround and protect the brain. It is often caused by bacteria such as Neisseria meningitidis (the meningococcus) and Haemophilus influenzae. merozoite The motile, infective stage of an apicomplexan parasite that comes from a liver or red blood cell undergoing multiple fission. mesophile Microorganisms that grow at intermediate temperatures. messenger RNA (mRNA) A single-stranded transcript that is a copy of the DNA template that corresponds to a gene. metabolic analog Enzyme that mimics the natural substrate of an enzyme and vies for its active site.

metabolism A general term for the totality of chemical and physical processes occurring in a cell. metabolites Small organic molecules that are intermediates in the stepwise biosynthesis or breakdown of macromolecules. metabolomics The study of the complete complement of small chemicals present in a cell at any given time. metachromatic Exhibiting a color other than that of the dye used to stain it. metachromatic granules A type of inclusion in storage compartments of some bacteria that stain a contrasting color when treated with colored dyes. metagenomics The study of all the genomes in a particular ecological niche, as opposed to individual genomes from single species. methanogens Methane producers. MHC Major histocompatibility complex. See HLA. MIC Abbreviation for minimum inhibitory concentration. The lowest concentration of antibiotic needed to inhibit bacterial growth in a test system. microaerophile An aerobic bacterium that requires oxygen at a concentration less than that in the atmosphere. microbe See microorganism. microbial antagonism Relationship in which microorganisms compete for survival in a common environment by taking actions that inhibit or destroy another organism. microbial ecology The study of microbes in their natural habitats. microbicides Chemicals that kill microorganisms. microbiology A specialized area of biology that deals with living things ordinarily too small to be seen without magnification, including bacteria, archaea, fungi, protozoa, and viruses. microbistatic the quality of inhibiting the growth of microbes. microfilaments Cellular cytoskeletal element formed by thin protein strands that attach to cell membrane and form a network through the cytoplasm. Responsible for movement of cytoplasm. micronutrient A chemical substance required in small quantities (trace metals, for example). microorganism A living thing ordinarily too small to be seen without magnification; an organism of microscopic size. microscopic Invisible to the naked eye. microscopy Science that studies structure, magnification, lenses, and techniques related to use of a microscope. microtubules Long hollow tubes in eukaryotic cells; maintain the shape of the cell and transport substances from one part of cell to another; involved in separating chromosomes in mitosis. miliary tuberculosis Rapidly fatal tuberculosis due to dissemination of mycobacteria in the blood and formation of

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tiny granules in various organs and tissues. The term miliary means resembling a millet seed. mineralization The process by which decomposers (bacteria and fungi) convert organic debris into inorganic and elemental form. It is part of the recycling process. minimum inhibitory concentration (MIC) The smallest concentration of drug needed to visibly control microbial growth. minimum temperature The lowest temperature at which an organism will grow. miracidium The ciliated first-stage larva of a trematode. This form is infective for a corresponding intermediate host snail. missense mutation A mutation in which a change in the DNA sequence results in a different amino acid being incorporated into a protein, with varying results. mitochondrion A double-membrane organelle of eukaryotes that is the main site for aerobic respiration. mitosis Somatic cell division that preserves the somatic chromosome number. mixed acid fermentation An anaerobic degradation of pyruvic acid that results in more than one organic acid being produced (e.g., acetic acid, lactic acid, succinic acid). mixed culture A container growing two or more different, known species of microbes. mixed infection Occurs when several different pathogens interact simultaneously to produce an infection. Also called a synergistic infection. molecule A distinct chemical substance that results from the combination of two or more atoms. molluscum contagiosum Poxvirus-caused disease that manifests itself by the appearance of small lesions on the face, trunk, and limbs. Can be associated with sexual transmission. monoclonal antibodies (MAbs) Antibodies that have a single specificity for a single antigen and are produced in the laboratory from a single clone of B cells. monocyte A large mononuclear leukocyte normally found in the lymph nodes, spleen, bone marrow, and loose connective tissue. This type of cell makes up 3% to 7% of circulating leukocytes. monomer A simple molecule that can be linked by chemical bonds to form larger molecules. mononuclear phagocyte system A collection of monocytes and macrophages scattered throughout the extracellular spaces that function to engulf and degrade foreign molecules. monosaccharide A simple sugar such as glucose that is a basic building block for more complex carbohydrates. monotrichous Describing a microorganism that bears a single flagellum. morbidity A diseased condition. morbidity rate The number of persons afflicted with an illness under question or with illness in general, expressed as a

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Glossary

numerator, with the denominator being some unit of population (as in x/100,000). mordant A chemical that fixes a dye in or on cells by forming an insoluble compound and thereby promoting retention of that dye. Example: Gram’s iodine in the Gram stain. morphology The study of organismic structure. mortality rate The number of persons who have died as the result of a particular cause or due to all causes, expressed as a numerator, with the denominator being some unit of population (as in x/100,000). most probable number (MPN) Test used to detect the concentration of contaminants in water and other fluids. motility Self-propulsion. mumps Viral disease characterized by inflammation of the parotid glands. must Juices expressed from crushed fruits that are used in fermentation for wine. mutagen Any agent that induces genetic mutation. Examples: certain chemical substances, ultraviolet light, radioactivity. mutant strain A subspecies of microorganism that has undergone a mutation, causing expression of a trait that differs from other members of that species. mutation A permanent inheritable alteration in the DNA sequence or content of a cell. mutualism Organisms living in an obligatory but mutually beneficial relationship. mycelium The filamentous mass that makes up a mold. Composed of hyphae. mycoplasma A genus of bacteria; contain no peptidoglycan/cell wall, but the cytoplasmic membrane is stabilized by sterols. mycorrhizae Various species of fungi adapted in an intimate, mutualistic relationship to plant roots. mycosis Any disease caused by a fungus. myonecrosis Death of muscle tissue.

N NAD/NADH Abbreviations for the oxidized/ reduced forms of nicotinamide adenine dinucleotide, an electron carrier. Also known as the vitamin niacin. nanobacteria (also nanobes) Bacteria that are up to 100 times smaller than average bacteria. nanobes Cell-like particles found in sediments and other geologic deposits that some scientists speculate are the smallest bacteria. Short for nanobacteria. narrow spectrum Denotes drugs that are selective and limited in their effects. For example, they inhibit either gram-negative or gram-positive bacteria but not both. natural immunity Any immunity that arises naturally in an organism via previous experience with the antigen. natural selection A process in which the environment places pressure on organisms to adapt and survive changing conditions. Only the survivors will be around to continue the life cycle and contribute their genes to future generations. This is

considered a major factor in evolution of species. necrosis A pathologic process in which cells and tissues die and disintegrate. negative stain A staining technique that renders the background opaque or colored and leaves the object unstained so that it is outlined as a colorless area. nematode A common name for helminths called roundworms. nephritis Inflammation of the kidney. neurotropic Having an affinity for the nervous system. Most likely to affect the spinal cord. neutralization The process of combining an acid and a base until they reach a balanced proportion, with a pH value close to 7. neutron An electrically neutral particle in the nuclei of all atoms except hydrogen. neutrophil A mature granulocyte present in peripheral circulation, exhibiting a multilobular nucleus and numerous cytoplasmic granules that retain a neutral stain. The neutrophil is an active phagocytic cell in bacterial infection. niche In ecology, an organism’s biological role in or contribution to its community. nitrification Phase of the nitrogen cycle in which ammonium is oxidized. nitrogen base A ringed compound of which pyrimidines and purines are types. nitrogen cycle The pathway followed by the element nitrogen as it circulates from inorganic sources in the nonliving environment to living things and back to the nonliving environment. The longtime reservoir is nitrogen gas in the atmosphere. nitrogen fixation A process occurring in certain bacteria in which atmospheric N2 gas is converted to a form (NH4) usable by plants. nitrogenous base A nitrogen-containing molecule found in DNA and RNA that provides the basis for the genetic code. Adenine, guanine, and cytosine are found in both DNA and RNA while thymine is found exclusively in DNA and uracil is found exclusively in RNA. nomenclature A set system for scientifically naming organisms, enzymes, anatomical structures, and so on. noncommunicable An infectious disease that does not arrive through transmission of an infectious agent from host to host. noncompetitive inhibition Form of enzyme inhibition that involves binding of a regulatory molecule to a site other than the active site. nonionizing radiation Method of microbial control, best exemplified by ultraviolet light, that causes the formation of abnormal bonds within the DNA of microbes, increasing the rate of mutation. The primary limitation of nonionizing radiation is its inability to penetrate beyond the surface of an object. nonpolar A term used to describe an electrically neutral molecule formed by

covalent bonds between atoms that have the same or similar electronegativity. nonself Molecules recognized by the immune system as containing foreign markers, indicating a need for immune response. nonsense codon A triplet of mRNA bases that does not specify an amino acid but signals the end of a polypeptide chain. nonsense mutation A mutation that changes an amino-acid-producing codon into a stop codon, leading to premature termination of a protein. normal biota The native microbial forms that an individual harbors. nosocomial infection An infection not present upon admission to a hospital but incurred while being treated there. nucleocapsid In viruses, the close physical combination of the nucleic acid with its protective covering. nucleoid The basophilic nuclear region or nuclear body that contains the bacterial chromosome. nucleolus A granular mass containing RNA that is contained within the nucleus of a eukaryotic cell. nucleosome Structure in the packaging of DNA. Formed by the DNA strands wrapping around the histone protein to form nucleus bodies arranged like beads on a chain. nucleotide The basic structural unit of DNA and RNA; each nucleotide consists of a phosphate, a sugar (ribose in RNA, deoxyribose in DNA), and a nitrogenous base such as adenine, guanine, cytosine, thymine (DNA only), or uracil (RNA only). numerical aperture In microscopy, the amount of light passing from the object and into the object in order to maximize optical clarity and resolution. nutrient Any chemical substance that must be provided to a cell for normal metabolism and growth. Macronutrients are required in large amounts, and micronutrients in small amounts. nutrition The acquisition of chemical substances by a cell or organism for use as an energy source or as building blocks of cellular structures.

O obligate Without alternative; restricted to a particular characteristic. Example: an obligate parasite survives and grows only in a host; an obligate aerobe must have oxygen to grow; an obligate anaerobe is destroyed by oxygen. Okazaki fragment In replication of DNA, a segment formed on the lagging strand in which biosynthesis is conducted in a discontinuous manner dictated by the 5′Æ 3′ DNA polymerase orientation. oligodynamic action A chemical having antimicrobial activity in minuscule amounts. Example: certain heavy metals are effective in a few parts per billion.

Glossary oligonucleotides Short pieces of DNA or RNA that are easier to handle than long segments. oligotrophic Nutrient-deficient ecosystem. oncogene A naturally occurring type of gene that when activated can transform a normal cell into a cancer cell. oncovirus Mammalian virus capable of causing malignant tumors. oocyst The encysted form of a fertilized macrogamete or zygote; typical in the life cycles of apicomplexan parasites. operator In an operon sequence, the DNA segment where transcription of structural genes is initiated. operon A genetic operational unit that regulates metabolism by controlling mRNA production. In sequence, the unit consists of a regulatory gene, inducer or repressor control sites, and structural genes. opportunistic In infection, ordinarily nonpathogenic or weakly pathogenic microbes that cause disease primarily in an immunologically compromised host. opsonization The process of stimulating phagocytosis by affixing molecules (opsonins such as antibodies and complement) to the surfaces of foreign cells or particles. optimum temperature The temperature at which a species shows the most rapid growth rate. orbitals The pathways of electrons as they rotate around the nucleus of an atom. order In the levels of classification, the division of organisms that follows class. Increasing similarity may be noticed among organisms assigned to the same order. organelle A small component of eukaryotic cells that is bounded by a membrane and specialized in function. organic chemicals Molecules that contain the basic framework of the elements carbon and hydrogen. osmophile A microorganism that thrives in a medium having high osmotic pressure. osmosis The diffusion of water across a selectively permeable membrane in the direction of lower water concentration. osteomyelitis A focal infection of the internal structures of long bones, leading to pain and inflammation. Often caused by Staphylococcus aureus. outer membrane An additional membrane possessed by gram-negative bacteria; a lipid bilayer containing specialized proteins and polysaccharides. It lies outside of the cell wall. oxidation In chemical reactions, the loss of electrons by one reactant. oxidation-reduction Redox reactions, in which paired sets of molecules participate in electron transfers. oxidative phosphorylation The synthesis of ATP using energy given off during the electron transport phase of respiration.

oxidizing agent An atom or a compound that can receive electrons from another in a chemical reaction. oxygenic Any reaction that gives off oxygen; usually in reference to the result of photosynthesis in eukaryotes and cyanobacteria.

P palindrome A word, verse, number, or sentence that reads the same forward or backward. Palindromes of nitrogen bases in DNA have genetic significance as transposable elements, as regulatory protein targets, and in DNA splicing. palisades The characteristic arrangement of Corynebacterium cells resembling a row of fence posts and created by snapping. PAMPs Pathogen-associated molecular patterns. Chemical signatures present on many different microorganisms but not on host which are recognized by host as foreign. pandemic A disease afflicting an increased proportion of the population over a wide geographic area (often worldwide). papilloma Benign, squamous epithelial growth commonly referred to as a wart. parasite An organism that lives on or within another organism (the host), from which it obtains nutrients and enjoys protection. The parasite produces some degree of harm in the host. parasitism A relationship between two organisms in which the host is harmed in some way while the colonizer benefits. parenteral Administering a substance into a body compartment other than through the gastrointestinal tract, such as via intravenous, subcutaneous, intramuscular, or intramedullary injection. paroxysmal Events characterized by sharp spasms or convulsions; sudden onset of a symptom such as fever and chills. passive carrier Persons who mechanically transfer a pathogen without ever being infected by it. For example, a health care worker who doesn’t wash his/her hands adequately between patients. passive immunity Specific resistance that is acquired indirectly by donation of preformed immune substances (antibodies) produced in the body of another individual. passive transport Nutrient transport method that follows basic physical laws and does not require direct energy input from the cell. pasteurization Heat treatment of perishable fluids such as milk, fruit juices, or wine to destroy heat-sensitive vegetative cells, followed by rapid chilling to inhibit growth of survivors and germination of spores. It prevents infection and spoilage. pathogen Any agent (usually a virus, bacterium, fungus, protozoan, or helminth) that causes disease. pathogen-associated molecular patterns molecules on the surfaces of

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many types of microbes that are not present on host cells that mark the microbes as foreign; PAMPs. pathogenicity The capacity of microbes to cause disease. pathogenicity islands areas of the genome containing multiple genes which contribute to a new trait for the organism that increases its ability to cause disease. pathognomic Distinctive and particular to a single disease, suggestive of a diagnosis. pathologic Capable of inducing physical damage on the host. pathology The structural and physiological effects of disease on the body. pattern recognition receptors molecules on the surface of host defense cells that recognize pathogen-associated molecular patterns on microbes; PRRs. pellicle A membranous cover; a thin skin, film, or scum on a liquid surface; a thin film of salivary glycoproteins that forms over newly cleaned tooth enamel when exposed to saliva. pelvic inflammatory disease (PID) An infection of the uterus and fallopian tubes that has ascended from the lower reproductive tract. Caused by gonococci and chlamydias. penetration (viral) The step in viral multiplication in which virus enters the host cell. penicillinase An enzyme that hydrolyzes penicillin; found in penicillin-resistant strains of bacteria. penicillins A large group of naturally occurring and synthetic antibiotics produced by Penicillium mold and active against the cell wall of bacteria. pentose A monosaccharide with five carbon atoms per molecule. Examples: arabinose, ribose, xylose. peptide Molecule composed of short chains of amino acids, such as a dipeptide (two amino acids), a tripeptide (three), and a tetrapeptide (four). peptide bond The covalent union between two amino acids that forms between the amine group of one and the carboxyl group of the other. The basic bond of proteins. peptidoglycan A network of polysaccharide chains cross-linked by short peptides that forms the rigid part of bacterial cell walls. Gram-negative bacteria have a smaller amount of this rigid structure than do grampositive bacteria. perforin Proteins released by cytotoxic T cells that produce pores in target cells. perinatal In childbirth, occurring before, during, or after delivery. period of invasion The period during a clinical infection when the infectious agent multiplies at high levels, exhibits its greatest toxicity, and becomes well established in the target tissues. periodontal Involving the structures that surround the tooth.

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Glossary

periplasmic space The region between the cell wall and cell membrane of the cell envelopes of gram-negative bacteria. peritrichous In bacterial morphology, having flagella distributed over the entire cell. petechiae Minute hemorrhagic spots in the skin that range from pinpoint- to pinheadsize. Peyer’s patches Oblong lymphoid aggregates of the gut located chiefly in the wall of the terminal and small intestine. Along with the tonsils and appendix, Peyer’s patches make up the gut-associated lymphoid tissue that responds to local invasion by infectious agents. pH The symbol for the negative logarithm of the H ion concentration; p (power) or [H+]10. A system for rating acidity and alkalinity. phage A bacteriophage; a virus that specifically parasitizes bacteria. phagocyte A class of white blood cells capable of engulfing other cells and particles. phagocytosis A type of endocytosis in which the cell membrane actively engulfs large particles or cells into vesicles. phagolysosome A body formed in a phagocyte, consisting of a union between a vesicle containing the ingested particle (the phagosome) and a vacuole of hydrolytic enzymes (the lysosome). phase variation The process of bacteria turning on or off a group of genes that changes its phenotype in a heritable manner. phenotype The observable characteristics of an organism produced by the interaction between its genetic potential (genotype) and the environment. phosphate An acidic salt containing phosphorus and oxygen that is an essential inorganic component of DNA, RNA, and ATP. phospholipid A class of lipids that compose a major structural component of cell membranes. phosphorylation Process in which inorganic phosphate is added to a compound. photoactivation (light repair) A mechanism for repairing DNA with ultraviolet-lightinduced mutations using an enzyme (photolyase) that is activated by visible light. photoautotroph An organism that utilizes light for its energy and carbon dioxide chiefly for its carbon needs. photolysis The splitting of water into hydrogen and oxygen during photosynthesis. photon A subatomic particle released by electromagnetic sources such as radiant energy (sunlight). Photons are the ultimate source of energy for photosynthesis. photophosphorylation The process of electron transport during photosynthesis that results in the synthesis of ATP from ADP. photosynthesis A process occurring in plants, algae, and some bacteria that traps the sun’s

energy and converts it to ATP in the cell. This energy is used to fix CO2 into organic compounds. phototrophs Microbes that use photosynthesis to feed. phycobilin Red or blue-green pigments that absorb light during photosynthesis. phylum In the levels of classification, the third level of classification from general to more specific. Each kingdom is divided into numerous phyla. Sometimes referred to as a division. physiology The study of the function of an organism. phytoplankton The collection of photosynthetic microorganisms (mainly algae and cyanobacteria) that float in the upper layers of aquatic habitats where sun penetrates. These microbes are the basis of aquatic food pyramids and, together with zooplankton, make up the plankton. pili Small, stiff filamentous appendages in gram-negative bacteria that function in DNA exchange during bacterial conjugation. pilus A hollow appendage used to bring two bacterial cells together to transfer DNA. pinocytosis The engulfment, or endocytosis, of liquids by extensions of the cell membrane. plague Zoonotic disease caused by infection with Yersinia pestis. The pathogen is spread by flea vectors and harbored by various rodents. plankton Minute animals (zooplankton) or plants (phytoplankton) that float and drift in the limnetic zone of bodies of water. plantar warts Deep, painful warts on the soles of the feet as a result of infection by human papillomavirus. plaque In virus propagation methods, the clear zone of lysed cells in tissue culture or chick embryo membrane that corresponds to the area containing viruses. In dental application, the filamentous mass of microbes that adheres tenaciously to the tooth and predisposes to caries, calculus, or inflammation. plasma The carrier fluid element of blood. plasma cell A progeny of an activated B cell that actively produces and secretes antibodies. plasmids Extrachromosomal genetic units characterized by several features. A plasmid is a double-stranded DNA that is smaller than and replicates independently of the cell chromosome; it bears genes that are not essential for cell growth; it can bear genes that code for adaptive traits; and it is transmissible to other bacteria. platelet-activating factor A substance released from basophils that causes release of allergic mediators and the aggregation of platelets. platelets Formed elements in the blood that develop when megakaryocytes disintegrate. Platelets are involved in hemostasis and blood clotting.

pleomorphism Normal variability of cell shapes in a single species. pluripotential Stem cells having the developmental plasticity to give rise to more than one type. Example: undifferentiated blood cells in the bone marrow. pneumococcus Common name for Streptococcus pneumoniae, the major cause of bacterial pneumonia. pneumonia An inflammation of the lung leading to accumulation of fluid and respiratory compromise. pneumonic plague The acute, frequently fatal form of pneumonia caused by Yersinia pestis. point mutation A change that involves the loss, substitution, or addition of one or a few nucleotides. point source epidemic An outbreak of disease in which all affected individuals were exposed to a single source of the pathogen at a single point in time. polar Term to describe a molecule with an asymmetrical distribution of charges. Such a molecule has a negative pole and a positive pole. poliomyelitis An acute enteroviral infection of the spinal cord that can cause neuromuscular paralysis. polyclonal In reference to a collection of antibodies with mixed specificities that arose from more than one clone of B cells. polyclonal antibodies A mixture of antibodies that were stimulated by a complex antigen with more than one antigenic determinant. polymer A macromolecule made up of a chain of repeating units. Examples: starch, protein, DNA. polymerase An enzyme that produces polymers through catalyzing bond formation between building blocks (polymerization). polymerase chain reaction (PCR) A technique that amplifies segments of DNA for testing. Using denaturation, primers, and heat-resistant DNA polymerase, the number can be increased severalmillion-fold. polymicrobial Involving multiple distinct microorganisms. polymorphonuclear leukocytes (PMNLs) White blood cells with variously shaped nuclei. Although this term commonly denotes all granulocytes, it is used especially for the neutrophils. polymyxin A mixture of antibiotic polypeptides from Bacillus polymyxa that are particularly effective against gramnegative bacteria. polypeptide A relatively large chain of amino acids linked by peptide bonds. polyribosomal complex An assembly line for mass production of proteins composed of a chain of ribosomes involved in mRNA transcription. polysaccharide A carbohydrate that can be hydrolyzed into a number of

Glossary monosaccharides. Examples: cellulose, starch, glycogen. population A group of organisms of the same species living simultaneously in the same habitat. A group of different populations living together constitutes the community level. porin Transmembrane proteins of the outer membrane of gram-negative cells that permit transport of small molecules into the periplasmic space but bar the penetration of larger molecules. portal of entry Route of entry for an infectious agent; typically a cutaneous or membranous route. portal of exit Route through which a pathogen departs from the host organism. positive stain A method for coloring microbial specimens that involves a chemical that sticks to the specimen to give it color. potable Describing water that is relatively clear, odor-free, and safe to drink. PPNG Penicillinase-producing Neisseria gonorrhoeae. prebiotics Nutrients used to stimulate the growth of favorable biota in the intestine. prevalence The total number of cases of a disease in a certain area and time period. primary infection An initial infection in a previously healthy individual that is later complicated by an additional (secondary) infection. primary response The first response of the immune system when exposed to an antigen. primary structure Initial protein organization described by type, number, and order of amino acids in the chain. The primary structure varies extensively from protein to protein. primers Synthetic oligonucleotides of known sequence that serve as landmarks to indicate where DNA amplification will begin. prion A concocted word to denote “proteinaceous infectious agent”; a cytopathic protein associated with the slow-virus spongiform encephalopathies of humans and animals. probes Small fragments of single-stranded DNA (RNA) that are known to be complementary to the specific sequence of DNA being studied. probiotics Preparations of live microbes used as a preventive or therapeutic measure to displace or compete with potential pathogens. prodromal stage A short period of mild symptoms occurring at the end of the period of incubation. It indicates the onset of disease. producer An organism that synthesizes complex organic compounds from simple inorganic molecules. Examples would be photosynthetic microbes and plants. These organisms are solely responsible for originating food pyramids and are the basis for life on earth (also called autotroph).

product(s) In a chemical reaction, the substance(s) that is(are) left after a reaction is completed. proglottid The egg-generating segment of a tapeworm that contains both male and female organs. progressive multifocal leukoencephalopathy (PML) An uncommon, fatal complication of infection with JC virus (polyoma virus). prokaryotic cells Small cells, lacking special structures such as a nucleus and organelles. All prokaryotes are microorganisms. promastigote A morphological variation of the trypanosome parasite responsible for leishmaniasis. promoter Part of an operon sequence. The DNA segment that is recognized by RNA polymerase as the starting site for transcription. promoter region The site composed of a short signaling DNA sequence that RNA polymerase recognizes and binds to commence transcription. propagated epidemic An outbreak of disease in which the causative agent is passed from affected persons to new persons over the course of time. prophage A lysogenized bacteriophage; a phage that is latently incorporated into the host chromosome instead of undergoing viral replication and lysis. prophylactic Any device, method, or substance used to prevent disease. prostaglandin A hormonelike substance that regulates many body functions. Prostaglandin comes from a family of organic acids containing 5-carbon rings that are essential to the human diet. protease Enzymes that act on proteins, breaking them down into component parts. protease inhibitors Drugs that act to prevent the assembly of functioning viral particles. protein Predominant organic molecule in cells, formed by long chains of amino acids. proteomics The study of an organism’s complement of proteins (its proteome) and functions mediated by the proteins. proton An elementary particle that carries a positive charge. It is identical to the nucleus of the hydrogen atom. protoplast A bacterial cell whose cell wall is completely lacking and that is vulnerable to osmotic lysis. protozoa A group of single-celled, eukaryotic organisms. provirus The genome of a virus when it is integrated into a host cell’s DNA. PRRs Pattern recognition receptors. Molecules on the surface of host cells that recognize pathogen-associated molecular patterns (PAMPs) on microbial cells. pseudohypha A chain of easily separated, spherical to sausage-shaped yeast cells partitioned by constrictions rather than by septa.

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pseudomembrane A tenacious, noncellular mucous exudate containing cellular debris that tightly blankets the mucosal surface in infections such as diphtheria and pseudomembranous enterocolitis. pseudopodium A temporary extension of the protoplasm of an amoeboid cell. It serves both in amoeboid motion and for food gathering (phagocytosis). pseudopods Protozoan appendage responsible for motility. Also called “false feet.” psychrophile A microorganism that thrives at low temperature (0°C–20°C), with a temperature optimum of 0°C–15°C. pulmonary Occurring in the lungs. Examples include pulmonary anthrax and pulmonary nocardiosis. pure culture A container growing a single species of microbe whose identity is known. purine A nitrogen base that is an important encoding component of DNA and RNA. The two most common purines are adenine and guanine. pus The viscous, opaque, usually yellowish matter formed by an inflammatory infection. It consists of serum exudate, tissue debris, leukocytes, and microorganisms. pyogenic Pertains to pus formers, especially the pyogenic cocci: pneumococci, streptococci, staphylococci, and neisseriae. pyrimidine Nitrogen bases that help form the genetic code on DNA and RNA. Uracil, thymine, and cytosine are the most important pyrimidines. pyrimidine dimer The union of two adjacent pyrimidines on the same DNA strand, brought about by exposure to ultraviolet light. It is a form of mutation. pyrogen A substance that causes a rise in body temperature. It can come from pyrogenic microorganisms or from polymorphonuclear leukocytes (endogenous pyrogens).

Q quaternary structure Most complex protein structure characterized by the formation of large, multiunit proteins by more than one of the polypeptides. This structure is typical of antibodies and some enzymes that act in cell synthesis. quats A word that pertains to a family of surfactants called quaternary ammonium compounds. These detergents are only weakly microbicidal and are used as sanitizers and preservatives. quinine A substance derived from cinchona trees that was used as an antimalarial treatment; has been replaced by synthetic derivatives. quinolone A class of synthetic antimicrobic drugs with broad-spectrum effects. quorum sensing The ability of bacteria to regulate their gene expression in response to sensing bacterial density.

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Glossary

R rabies The only rhabdovirus that infects humans. Zoonotic disease characterized by fatal meningoencephalitis. radiation Electromagnetic waves or rays, such as those of light given off from an energy source. radioactive isotopes Unstable isotopes whose nuclei emit particles of radiation. This emission is called radioactivity or radioactive decay. Three naturally occurring emissions are alpha, beta, and gamma radiation. rales Sounds in the lung, ranging from clicking to rattling; indicate respiratory illness. reactants Molecules entering or starting a chemical reaction. real image An image formed at the focal plane of a convex lens. In the compound light microscope, it is the image created by the objective lens. receptor Cell surface molecules involved in recognition, binding, and intracellular signaling. recombinant An organism that contains genes that originated in another organism, whether through deliberate laboratory manipulation or natural processes. recombinant DNA technology A technology, also known as genetic engineering, that deliberately modifies the genetic structure of an organism to create novel products, microbes, animals, plants, and viruses. recombination A type of genetic transfer in which DNA from one organism is donated to another. recycling A process that converts unusable organic matter from dead organisms back into their essential inorganic elements and returns them to their nonliving reservoirs to make them available again for living organisms. This is a common term that means the same as mineralization and decomposition. redox Denoting an oxidation-reduction reaction. reducing agent An atom or a compound that can donate electrons in a chemical reaction. reducing medium A growth medium that absorbs oxygen and allows anaerobic bacteria to grow. reduction In chemistry, the gain of electrons. redundancy The property of the genetic code that allows an amino acid to be specified by several different codons. refraction In optics, the bending of light as it passes from one medium to another with a different index of refraction. regulated enzymes Enzymes whose extent of transcription or translation is influenced by changes in the environment. regulator DNA segment that codes for a protein capable of repressing an operon. regulatory B cells (Breg cells) a type of activated B cell that controls the immune response.

regulatory site The location on an enzyme where a certain substance can bind and block the enzyme’s activity. rennin The enzyme casein coagulase, which is used to produce curd in the processing of milk and cheese. replication In DNA synthesis, the semiconservative mechanisms that ensure precise duplication of the parent DNA strands. replication fork The Y-shaped point on a replicating DNA molecule where the DNA polymerase is synthesizing new strands of DNA. reportable disease Those diseases that must be reported to health authorities by law. repressible operon An operon that under normal circumstances is transcribed. The buildup of the operon’s amino acid product causes transcription of the operon to stop. repressor The protein product of a repressor gene that combines with the operator and arrests the transcription and translation of structural genes. reservoir In disease communication, the natural host or habitat of a pathogen. resident biota The deeper, more stable microbiota that inhabit the skin and exposed mucous membranes, as opposed to the superficial, variable, transient population. resistance (R) factor Plasmids, typically shared among bacteria by conjugation, that provide resistance to the effects of antibiotics. resolving power The capacity of a microscope lens system to accurately distinguish between two separate entities that lie close to each other. Also called resolution. respiratory chain A series of enzymes that transfer electrons from one to another, resulting in the formation of ATP. It is also known as the electron transport chain. The chain is located in the cell membrane of bacteria and in the inner mitochondrial membrane of eukaryotes. respiratory syncytial virus (RSV) An RNA virus that infects the respiratory tract. RSV is the most prevalent cause of respiratory infection in newborns. restriction endonuclease An enzyme present naturally in cells that cleaves specific locations on DNA. It is an important means of inactivating viral genomes, and it is also used to splice genes in genetic engineering. reticuloendothelial system Also known as the mononuclear phagocyte system, it pertains to a network of fibers and phagocytic cells (macrophages) that permeates the tissues of all organs. Examples: Kupffer cells in liver sinusoids, alveolar phagocytes in the lung, microglia in nervous tissue. retrovirus A group of RNA viruses (including HIV) that have the mechanisms for converting their genome into a double strand of DNA that can be inserted on a host’s chromosome.

reverse transcriptase (RT) The enzyme possessed by retroviruses that carries out the reversion of RNA to DNA—a form of reverse transcription. Reye’s syndrome A sudden, usually fatal neurological condition that occurs in children after a viral infection. Autopsy shows cerebral edema and marked fatty change in the liver and renal tubules. Rh factor An isoantigen that can trigger hemolytic disease in newborns due to incompatibility between maternal and infant blood factors. rhizobia Bacteria that live in plant roots and supply supplemental nitrogen that boosts plant growth. rhizosphere The zone of soil, complete with microbial inhabitants, in the immediate vicinity of plant roots. ribonucleic acid (RNA) The nucleic acid responsible for carrying out the hereditary program transmitted by an organism’s DNA. ribose A 5-carbon monosaccharide found in RNA. ribosomal RNA (rRNA) A single-stranded transcript that is a copy of part of the DNA template. ribosome A bilobed macromolecular complex of ribonucleoprotein that coordinates the codons of mRNA with tRNA anticodons and, in so doing, constitutes the peptide assembly site. ribozyme A part of an RNA-containing enzyme in eukaryotes that removes intervening sequences of RNA called introns and splices together the true coding sequences (exons) to form a mature messenger RNA. rickettsias Medically important family of bacteria, commonly carried by ticks, lice, and fleas. Significant cause of important emerging diseases. ringworm A superficial mycosis caused by various dermatophytic fungi. This common name is actually a misnomer. RNA editing The alteration of RNA molecules before translation, found only in eukaryotes. RNA polymerase Enzyme process that translates the code of DNA to RNA. rolling circle An intermediate stage in viral replication of circular DNA into linear DNA. root nodules Small growths on the roots of legume plants that arise from a symbiotic association between the plant tissues and bacteria (Rhizobia). This association allows fixation of nitrogen gas from the air into a usable nitrogen source for the plant. rosette formation A technique for distinguishing surface receptors on T cells by reacting them with sensitized indicator sheep red blood cells. The cluster of red cells around the central white blood cell resembles a little rose blossom and is indicative of the type of receptor.

Glossary rough endoplasmic reticulum (RER) Microscopic series of tunnels that originates in the outer membrane of the nuclear envelope and is used in transport and storage. Large numbers of ribosomes, partly attached to the membrane, give the rough appearance. rubeola (red measles) Acute disease caused by infection with Morbillivirus.

S saccharide Scientific term for sugar. Refers to a simple carbohydrate with a sweet taste. salpingitis Inflammation of the fallopian tubes. sanitize To clean inanimate objects using soap and degerming agents so that they are safe and free of high levels of microorganisms. saprobe A microbe that decomposes organic remains from dead organisms. Also known as a saprophyte or saprotroph. sarcina A cubical packet of 8, 16, or more cells; the cellular arrangement of the genus Sarcina in the family Micrococcaceae. satellitism A commensal interaction between two microbes in which one can grow in the vicinity of the other due to nutrients or protective factors released by that microbe. saturation The complete occupation of the active site of a carrier protein or enzyme by the substrate. schistosomiasis Infection by blood fluke, often as a result of contact with contaminated water in rivers and streams. Symptoms appear in liver, spleen, or urinary system depending on species of Schistosoma. Infection may be chronic. schizogony A process of multiple fission whereby first the nucleus divides several times, and subsequently the cytoplasm is subdivided for each new nucleus during cell division. scientific method Principles and procedures for the systematic pursuit of knowledge, involving the recognition and formulation of a problem, the collection of data through observation and experimentation, and the formulation and testing of a hypothesis. scolex The anterior end of a tapeworm characterized by hooks and/or suckers for attachment to the host. sebaceous glands The sebum- (oily, fatty) secreting glands of the skin. sebum Low pH, oil-based secretion of the sebaceous glands. secondary infection An infection that compounds a preexisting one. secondary response The rapid rise in antibody titer following a repeat exposure to an antigen that has been recognized from a previous exposure. This response is brought about by memory cells produced as a result of the primary exposure. secondary structure Protein structure that occurs when the functional groups on the

outer surface of the molecule interact by forming hydrogen bonds. These bonds cause the amino acid chain to either twist, forming a helix, or to pleat into an accordion pattern called a β-pleated sheet. secretory antibody The immunoglobulin (IgA) that is found in secretions of mucous membranes and serves as a local immediate protection against infection. selective media Nutrient media designed to favor the growth of certain microbes and to inhibit undesirable competitors. selectively toxic Property of an antimicrobial agent to be highly toxic against its target microbe while being far less toxic to other cells, particularly those of the host organism. self Natural markers of the body that are recognized by the immune system. self-limited Applies to an infection that runs its course without disease or residual effects. semiconservative replication In DNA replication, the synthesis of paired daughter strands, each retaining a parent strand template. semisolid media Nutrient media with a firmness midway between that of a broth (a liquid medium) and an ordinary solid medium; motility media. semisynthetic Drugs that, after being naturally produced by bacteria, fungi, or other living sources, are chemically modified in the laboratory. sensitizing dose The initial effective exposure to an antigen or an allergen that stimulates an immune response. Often applies to allergies. sepsis The state of putrefaction; the presence of pathogenic organisms or their toxins in tissue or blood. septic shock Blood infection resulting in a pathological state of low blood pressure accompanied by a reduced amount of blood circulating to vital organs. Endotoxins of all gram-negative bacteria can cause shock, but most clinical cases are due to gram-negative enteric rods. septicemia Systemic infection associated with microorganisms multiplying in circulating blood. septicemic plague A form of infection with Yersinia pestis occurring mainly in the bloodstream and leading to high mortality rates. septum A partition or cellular cross wall, as in certain fungal hyphae. sequela A morbid complication that follows a disease. sequencing Determining the actual order and types of bases in a segment of DNA. serology The branch of immunology that deals with in vitro diagnostic testing of serum. seropositive Showing the presence of specific antibody in a serological test. Indicates ongoing infection. serotonin A vasoconstrictor that inhibits gastric secretion and stimulates smooth muscle.

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serotyping The subdivision of a species or subspecies into an immunologic type, based upon antigenic characteristics. serum The clear fluid expressed from clotted blood that contains dissolved nutrients, antibodies, and hormones but not cells or clotting factors. serum sickness A type of immune complex disease in which immune complexes enter circulation, are carried throughout the body, and are deposited in the blood vessels of the kidney, heart, skin, and joints. The condition may become chronic. severe acute respiratory syndrome (SARS) A severe respiratory disease caused by infection with a newly described coronavirus. severe combined immunodeficiencies A collection of syndromes occurring in newborns caused by a genetic defect that knocks out both B- and T-cell types of immunity. There are several versions of this disease, termed SCIDS for short. sex pilus A conjugative pilus. sexually transmitted disease (STD) Infections resulting from pathogens that enter the body via sexual intercourse or intimate, direct contact. shiga toxin Heat-labile exotoxin released by some Shigella species and by E. coli O157:H7; responsible for worst symptoms of these infections. shingles Lesions produced by reactivated human herpesvirus 3 (chickenpox) infection; also known as herpes zoster. siderophores Low-molecular-weight molecules produced by many microorganisms that can bind iron very tightly. sign Any abnormality uncovered upon physical diagnosis that indicates the presence of disease. A sign is an objective assessment of disease, as opposed to a symptom, which is the subjective assessment perceived by the patient. silent mutation A mutation that, because of the degeneracy of the genetic code, results in a nucleotide change in both the DNA and mRNA but not the resultant amino acid and thus, not the protein. simple stain Type of positive staining technique that uses a single dye to add color to cells so that they are easier to see. This technique tends to color all cells the same color. slime layer A diffuse, unorganized layer of polysaccharides and/or proteins on the outside of some bacteria. smooth endoplasmic reticulum (SER) A microscopic series of tunnels lacking ribosomes that functions in the nutrient processing function of a cell. solute A substance that is uniformly dispersed in a dissolving medium or solvent. solution A mixture of one or more substances (solutes) that cannot be separated by filtration or ordinary settling.

G-20

Glossary

solvent A dissolving medium. somatic (O or cell wall antigen) One of the three major antigens commonly used to differentiate gram-negative enteric bacteria. source The person or item from which an infection is directly acquired. See reservoir. Southern blot A technique that separates fragments of DNA using electrophoresis and identifies them by hybridization. species In the levels of classification, the most specific level of organization. specificity In immunity, the concept that some parts of the immune system only react with antigens that originally activated them. spheroplast A gram-negative cell whose peptidoglycan, when digested by lysozyme, remains intact but is osmotically vulnerable. spike A receptor on the surface of certain enveloped viruses that facilitates specific attachment to the host cell. spirillum A type of bacterial cell with a rigid spiral shape and external flagella. spirochete A coiled, spiral-shaped bacterium that has endoflagella and flexes as it moves. spontaneous generation Early belief that living things arose from vital forces present in nonliving, or decomposing, matter. spontaneous mutation A mutation in DNA caused by random mistakes in replication and not known to be influenced by any mutagenic agent. These mutations give rise to an organism’s natural, or background, rate of mutation. sporadic Description of a disease that exhibits new cases at irregular intervals in unpredictable geographic locales. sporangiospore A form of asexual spore in fungi; enclosed in a sac. sporangium A fungal cell in which asexual spores are formed by multiple cell cleavage. spore A differentiated, specialized cell form that can be used for dissemination, for survival in times of adverse conditions, and/or for reproduction. Spores are usually unicellular and may develop into gametes or vegetative organisms. sporicide A chemical agent capable of destroying bacterial endospores. sporozoite One of many minute elongated bodies generated by multiple division of the oocyst. It is the infectious form of the malarial parasite that is harbored in the salivary gland of the mosquito and inoculated into the victim during feeding. sporulation The process of spore formation. start codon The nucleotide triplet AUG that codes for the first amino acid in protein sequences. starter culture The sizable inoculation of pure bacterial, mold, or yeast sample for bulk processing, as in the preparation of fermented foods, beverages, and pharmaceuticals. stasis A state of rest or inactivity; applied to nongrowing microbial cultures. Also called microbistasis.

stationary growth phase Survival mode in which cells either stop growing or grow very slowly. stem cells Pluripotent, undifferentiated cells. sterile Completely free of all life forms, including spores and viruses. sterilization Any process that completely removes or destroys all viable microorganisms, including viruses, from an object or habitat. Material so treated is sterile. STORCH Acronym for common infections of the fetus and neonate. Storch stands for syphilis, toxoplasmosis, other diseases (hepatitis B, AIDS, and chlamydiosis), rubella, cytomegalovirus, and herpes simplex virus. strain In microbiology, a set of descendants cloned from a common ancestor that retain the original characteristics. Any deviation from the original is a different strain. streptolysin A hemolysin produced by streptococci. strict or obligate anaerobe An organism that does not use oxygen gas in metabolism and cannot survive in oxygen’s presence. stroma The matrix of the chloroplast that is the site of the dark reactions. structural gene A gene that codes for the amino acid sequence (peptide structure) of a protein. subacute Indicates an intermediate status between acute and chronic disease. subacute sclerosing panencephalitis (SSPE) A complication of measles infection in which progressive neurological degeneration of the cerebral cortex invariably leads to coma and death. subcellular vaccine A vaccine preparation that contains specific antigens such as the capsule or toxin from a pathogen and not the whole microbe. subclinical A period of inapparent manifestations that occurs before symptoms and signs of disease appear. subculture To make a second-generation culture from a well-established colony of organisms. subcutaneous The deepest level of the skin structure. substrate The specific molecule upon which an enzyme acts. subunit vaccine A vaccine preparation that contains only antigenic fragments such as surface receptors from the microbe. Usually in reference to virus vaccines. sucrose One of the carbohydrates commonly referred to as sugars. Common table or cane sugar. sulfonamide Antimicrobial drugs that interfere with the essential metabolic process of bacteria and some fungi. superantigens Bacterial toxins that are potent stimuli for T cells and can be a factor in diseases such as toxic shock. superficial mycosis A fungal infection located in hair, nails, and the epidermis of the skin.

superinfection An infection occurring during antimicrobial therapy that is caused by an overgrowth of drug-resistant microorganisms. superoxide A toxic derivative of oxygen; (O2−). surfactant A surface-active agent that forms a water-soluble interface. Examples: detergents, wetting agents, dispersing agents, and surface tension depressants. sylvatic Denotes the natural presence of disease among wild animal populations. Examples: sylvatic (sylvan) plague, rabies. symbiosis An intimate association between individuals from two species; used as a synonym for mutualism. symptom The subjective evidence of infection and disease as perceived by the patient. syncytium A multinucleated protoplasmic mass formed by consolidation of individual cells. syndrome The collection of signs and symptoms that, taken together, paint a portrait of the disease. synergism The coordinated or correlated action by two or more drugs or microbes that results in a heightened response or greater activity. syngamy Conjugation of the gametes in fertilization. synthesis (viral) The step in viral multiplication in which viral genetic material and proteins are made through replication and transcription/translation. synthetic biology The use of known genes to produce new applications. syntrophy The productive use of waste products from the metabolism of one organism by a second organism. syphilis A sexually transmitted bacterial disease caused by the spirochete Treponema pallidum. systemic Occurring throughout the body; said of infections that invade many compartments and organs via the circulation.

T T lymphocyte (T cell) A white blood cell that is processed in the thymus gland and is involved in cell-mediated immunity. Taq polymerase DNA polymerase from the thermophilic bacterium Thermus aquaticus that enables high-temperature replication of DNA required for the polymerase chain reaction. tartar See calculus. taxa Taxonomic categories. taxonomy The formal system for organizing, classifying, and naming living things. teichoic acid Anionic polymers containing glycerol that appear in the walls of grampositive bacteria. temperate phage A bacteriophage that enters into a less virulent state by becoming incorporated into the host genome as a prophage instead of in the vegetative or lytic form that eventually destroys the cell.

Glossary template The strand in a double-stranded DNA molecule that is used as a model to synthesize a complementary strand of DNA or RNA during replication or transcription. Tenericutes Taxonomic category of bacteria that lack cell walls. teratogenic Causing abnormal fetal development. tertiary structure Protein structure that results from additional bonds forming between functional groups in a secondary structure, creating a three-dimensional mass. tetanospasmin The neurotoxin of Clostridium tetani, the agent of tetanus. Its chief action is directed upon the inhibitory synapses of the anterior horn motor neurons. tetracyclines A group of broad-spectrum antibiotics with a complex 4-ring structure. tetrads Groups of four. theory A collection of statements, propositions, or concepts that explains or accounts for a natural event. theory of evolution the evidence cited to explain how evolution occurs. therapeutic index The ratio of the toxic dose to the effective therapeutic dose that is used to assess the safety and reliability of the drug. thermal death point The lowest temperature that achieves sterilization in a given quantity of broth culture upon a 10-minute exposure. Examples: 55°C for Escherichia coli, 60°C for Mycobacterium tuberculosis, and 120°C for spores. thermal death time The least time required to kill all cells of a culture at a specified temperature. thermocline A temperature buffer zone in a large body of water that separates the warmer water (the epilimnion) from the colder water (the hypolimnion). thermoduric Resistant to the harmful effects of high temperature. thermophile A microorganism that thrives at a temperature of 50°C or higher. thrush Candida albicans infection of the oral cavity. thylakoid Vesicles of a chloroplast formed by elaborate folding of the inner membrane to form “discs.” Solar energy trapped in the thylakoids is used in photosynthesis. thymine (T) One of the nitrogen bases found in DNA but not in RNA. Thymine is in a pyrimidine form. thymus Butterfly-shaped organ near the tip of the sternum that is the site of T-cell maturation. tincture A medicinal substance dissolved in an alcoholic solvent. tinea Ringworm; a fungal infection of the hair, skin, or nails. tinea versicolor A condition of the skin appearing as mottled and discolored skin pigmentation as a result of infection by the yeast Malassezia furfur.

titer In immunochemistry, a measure of antibody level in a patient, determined by agglutination methods. toll-like receptors (TLRs) a category of pattern recognition receptors that binds to pathogenassociated molecular patterns on microbes. tonsils A ring of lymphoid tissue in the pharynx that acts as a repository for lymphocytes. topoisomerases Enzymes that can add or remove DNA twists and thus regulate the degree of supercoiling. toxemia Condition in which a toxin (microbial or otherwise) is spread throughout the bloodstream. toxigenicity The tendency for a pathogen to produce toxins. It is an important factor in bacterial virulence. toxin A specific chemical product of microbes, plants, and some animals that is poisonous to other organisms. toxinosis Disease whose adverse effects are primarily due to the production and release of toxins. toxoid A toxin that has been rendered nontoxic but is still capable of eliciting the formation of protective antitoxin antibodies; used in vaccines. trace elements Micronutrients (zinc, nickel, and manganese) that occur in small amounts and are involved in enzyme function and maintenance of protein structure. transamination The transfer of an amino group from an amino acid to a carbohydrate fragment. transcript A newly transcribed RNA molecule. transcription mRNA synthesis; the process by which a strand of RNA is produced against a DNA template. transduction The transfer of genetic material from one bacterium to another by means of a bacteriophage vector. transferrin A protein in the plasma fraction of blood that transports iron. transfer RNA (tRNA) A transcript of DNA that specializes in converting RNA language into protein language. transformation In microbial genetics, the transfer of genetic material contained in “naked” DNA fragments from a donor cell to a competent recipient cell. transfusion Infusion of whole blood, red blood cells, or platelets directly into a patient’s circulation. translation Protein synthesis; the process of decoding the messenger RNA code into a polypeptide. transposon A DNA segment with an insertion sequence at each end, enabling it to migrate to another plasmid, to the bacterial chromosome, or to a bacteriophage. transport medium Microbiological medium that is used to transport specimens. traveler’s diarrhea A type of gastroenteritis typically caused by infection with enterotoxigenic strains of E. coli that are ingested through contaminated food and water.

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trematode A category of helminth; also known as flatworm or fluke. trichinosis Infection by the Trichinella spiralis parasite, usually caused by eating the meat of an infected animal. Early symptoms include fever, diarrhea, nausea, and abdominal pain that progress to intense muscle and joint pain and shortness of breath. In the final stages, heart and brain function are at risk, and death is possible. trichomoniasis Sexually transmitted disease caused by infection by the trichomonads, a group of protozoa. Symptoms include urinary pain and frequency and foulsmelling vaginal discharge in females or recurring urethritis, with a thin milky discharge, in males. triglyceride A type of lipid composed of a glycerol molecule bound to three fatty acids. triplet See codon. trophozoite A vegetative protozoan (feeding form) as opposed to a resting (cyst) form. true pathogen A microbe capable of causing infection and disease in healthy persons with normal immune defenses. trypomastigote The infective morphological stage transmitted by the tsetse fly or the reduviid bug in African trypanosomiasis and Chagas disease. tubercle In tuberculosis, the granulomatous well-defined lung lesion that can serve as a focus for latent infection. tuberculin A glycerinated broth culture of Mycobacterium tuberculosis that is evaporated and filtered. Formerly used to treat tuberculosis, tuberculin is now used chiefly for diagnostic tests. tuberculin reaction A diagnostic test in which PPD, or purified protein derivative (of M. tuberculosis), is injected superficially under the skin and the area of reaction measured; also called the Mantoux test. tuberculoid leprosy A superficial form of leprosy characterized by asymmetrical, shallow skin lesions containing few bacterial cells. tubulin protein component of long filaments of protein arranged under the cell membrane of bacteria; contribute to cell shape and division. turbid Cloudy appearance of nutrient solution in a test tube due to growth of microbe population. tyndallization Fractional (discontinuous, intermittent) sterilization designed to destroy spores indirectly. A preparation is exposed to flowing steam for an hour, and then the mineral is allowed to incubate to permit spore germination. The resultant vegetative cells are destroyed by repeated steaming and incubation. typhoid fever Form of salmonellosis. It is highly contagious. Primary symptoms include fever, diarrhea, and abdominal pain. Typhoid fever can be fatal if untreated.

G-22

Glossary

U ubiquitous Present everywhere at the same time. ultraviolet (UV) radiation Radiation with an effective wavelength from 240 nm to 260 nm. UV radiation induces mutations readily but has very poor penetrating power. uncoating The process of removal of the viral coat and release of the viral genome by its newly invaded host cell. undulant fever See brucellosis. universal donor In blood grouping and transfusion, a group O individual whose erythrocytes bear neither agglutinogen A nor B. universal precautions (UPs) Centers for Disease Control and Prevention guidelines for health care workers regarding the prevention of disease transmission when handling patients and body substances. uracil (U) One of the nitrogen bases in RNA but not in DNA. Uracil is in a pyrimidine form. urinary tract infection (UTI) Invasion and infection of the urethra and bladder by bacterial residents, most often E. coli.

V vaccination Exposing a person to the antigenic components of a microbe without its pathogenic effects for the purpose of inducing a future protective response. vaccine Originally used in reference to inoculation with the cowpox or vaccinia virus to protect against smallpox. In general, the term now pertains to injection of whole microbes (killed or attenuated), toxoids, or parts of microbes as a prevention or cure for disease. vacuoles In the cell, membrane-bounded sacs containing fluids or solid particles to be digested, excreted, or stored. valence The combining power of an atom based upon the number of electrons it can either take on or give up. van der Waals forces Weak attractive interactions between molecules of low polarity. vancomycin Antibiotic that targets the bacterial cell wall; used often in antibioticresistant infections. variable region The antigen binding fragment of an immunoglobulin molecule, consisting of a combination of heavy and light chains whose molecular conformation is specific for the antigen. varicella Informal name for virus responsible for chickenpox as well as shingles; also known as human herpesvirus 3 (HHV-3).

variolation A hazardous, outmoded process of deliberately introducing smallpox material scraped from a victim into the nonimmune subject in the hope of inducing resistance. vector An animal that transmits infectious agents from one host to another, usually a biting or piercing arthropod like the tick, mosquito, or fly. Infectious agents can be conveyed mechanically by simple contact or biologically whereby the parasite develops in the vector. A genetic element such as a plasmid or a bacteriophage used to introduce genetic material into a cloning host during recombinant DNA experiments. vegetative In describing microbial developmental stages, a metabolically active feeding and dividing form, as opposed to a dormant, seemingly inert, nondividing form. Examples: a bacterial cell versus its spore; a protozoan trophozoite versus its cyst. vehicle An inanimate material (solid object, liquid, or air) that serves as a transmission agent for pathogens. vesicle A blister characterized by a thinskinned, elevated, superficial pocket filled with serum. viable nonculturable (VNC) Describes microbes that cannot be cultivated in the laboratory but that maintain metabolic activity (i.e., are alive). vibrio A curved, rod-shaped bacterial cell. viremia The presence of viruses in the bloodstream. virion An elementary virus particle in its complete morphological and thus infectious form. A virion consists of the nucleic acid core surrounded by a capsid, which can be enclosed in an envelope. viroid An infectious agent that, unlike a virion, lacks a capsid and consists of a closed circular RNA molecule. Although known viroids are all plant pathogens, it is conceivable that animal versions exist. virtual image In optics, an image formed by diverging light rays; in the compound light microscope, the second, magnified visual impression formed by the ocular from the real image formed by the objective. virucide A chemical agent that inactivates viruses, especially on living tissue. virulence In infection, the relative capacity of a pathogen to invade and harm host cells. virulence factors A microbe’s structures or capabilities that allow it to establish itself in a host and cause damage. virus Microscopic, acellular agent composed of nucleic acid surrounded by a protein coat. virus particle A more specific name for a virus when it is outside of its host cells. vitamins A component of coenzymes critical to nutrition and the metabolic function of coenzyme complexes.

W wart An epidermal tumor caused by papillomaviruses. Also called a verruca. Western blot test A procedure for separating and identifying antigen or antibody mixtures by two-dimensional electrophoresis in polyacrylamide gel, followed by immune labeling. wheal A welt; a marked, slightly red, usually itchy area of the skin that changes in size and shape as it extends to adjacent area. The reaction is triggered by cutaneous contact or intradermal injection of allergens in sensitive individuals. whey The residual fluid from milk coagulation that separates from the solidified curd. whitlow A deep inflammation of the finger or toe, especially near the tip or around the nail. Whitlow is a painful herpes simplex virus infection that can last several weeks and is most common among health care personnel who come in contact with the virus in patients. whole blood A liquid connective tissue consisting of blood cells suspended in plasma. Widal test An agglutination test for diagnosing typhoid. wild type The natural, nonmutated form of a genetic trait. wort The clear fluid derived from soaked mash that is fermented for beer.

X XDRTB Extensively drug-resistant tuberculosis (worse than multidrug-resistant tuberculosis). xenograft The transfer of a tissue or an organ from an animal of one species to a recipient of another species.

Z zoonosis An infectious disease indigenous to animals that humans can acquire through direct or indirect contact with infected animals. zooplankton The collection of nonphotosynthetic microorganisms (protozoa, tiny animals) that float in the upper regions of aquatic habitat and together with phytoplankton comprise the plankton. zygospore A thick-walled sexual spore produced by the zygomycete fungi. It develops from the union of two hyphae, each bearing nuclei of opposite mating types.

Photographs Chapter 1 Opener: © Jim Kidd/Alamy; Table1.1A: James Gathany/Centers for Disease Control; Table1.1B: Centers for Disease Control, Division of Vector Borne Infectious Diseases; Table1.1C: © James King-Holmes/ Photo Researchers; Table1.1D: Photo by Keith Weller/ USDA, ARS, IS Photo Unit; Table1.1E: Photo by Scott Baue/USDA, ARS, IS Photo Unit; Table1.1F: © Christopher Berkey/epa/Corbis; 1.2a: © Doug Sokell/Tom Stack & Associates; 1.2b: © Michel & Christine Denis-Huot/Photolibrary; 1.3a: © Corale L. Brierley/Visuals Unlimited; 1.3b: © Bloomberg via Getty Images; 1.3c: NOAA; Insight 1.1 (left): National Institutes of Health (NIH)/U.S. National Library of Medicine; Insight 1.1 (right): © Ron Edmonds/AP Photo; 1.6 (Taenia solium): Centers for Disease Control; 1.6 (Syncephalastrum): © Dr. Arthur Siegelman/ Visuals Unlimited; 1.6 (Vorticella): © Carolina Biological Supply/Phototake; 1.6 (E. coli): Janice Carr/ Public Health Image Library; 1.6 (Herpes): Centers for Disease Control; 1.7a: © Biophoto Associates/ Photo Researchers; 1.7b: Centers for Disease Control/ Dr. Lucille K. Georg; 1.8a ((both)): © Kathy Park Talaro/Visuals Unlimited; 1.8b: © Science VU/ Visuals Unlimited; 1.9: © Steve Gschmeissner/Photo Researchers; 1.10 (left): © Tom Grill/Corbis RF; p. 423 (left): © Koester Axel/Corbis; p. 423 (middle): © Milton P. Gordon, Department of Biochemistry, University of Washington; p. 423 (right): Courtesy of Richard Shade, Purdue University; 1.10 (right): © Tom Grill/Corbis RF; 1.11: © AKG/Photo Researchers; Insight 1.3 (left): David McKay/NASA; Insight 1.3 (right): Courtesy of Renno et al., J. Geophys. Res. (2009).

Chapter 2 Opener “b”: © Vo Trung Dung/Look at Sciences/SPL/ Photo Researchers; Insight 2.1 (left): © Joe Donohue; Insight 2.1 (top): © PJ Stewart, 2007, translated into digital form by Carl Wenczek of Born Digital Ltd.; Insight 2.1 (bottom): © 2010 periodictable.com; 2.7d: © Kathy Park Talaro; 2.11a-c: © John W. Hole; Insight 2.3a: © Donald Fawcett/Visuals Unlimited.

Chapter 3 Opener: © AP Photo/Steve Pope; 3.3b, d, f: © Kathy Park Talaro; Insight 3.1: Courtesy of Charles River Lab; 3.4b: © Kathy Park Talaro; 3.5a: © Fundamental Photographs; 3.5b, 3.6b, 3.7a-b, 3.9a-b, 3.10a-b: © Kathy Park Talaro; 3.11: © Harold J. Benson; 3.12a-c: © Kathy Park Talaro; 3.14: © Kathy Park Talaro/Visuals Unlimited; 3.15: Courtesy of Leica Microsystems Inc.; Table3.5a: © Carolina Biological Supply, Co/ Visuals Unlimited; Table3.5b-d: © Michael Abbey/ Visuals Unlimited; Table3.5e: © Molecular Probes, Inc.; Table3.5f: Courtesy of Dr. Jeremy Allen/University of Salford, Biosciences Research Institute; Table3.5g: © Billy Curran, Department of Veterinary Science. Queen’s University Belfast; Table3.5h: © Science Photo Library RF/Getty Images; Table3.5i: Courtesy of Dr Valerie Sim; Table3.5j: “Electronic structure of single DNA molecules resolved by transverse

scanning tunneling spectroscopy,” Nature Materials 7, 68–74 (2008) Published online: 25 November 2007. Errez Shapir, Hezy Cohen, Arrigo Calzolari, Carlo Cavazzoni, Dmitry A. Ryndyk, Gianaurelio Cuniberti, Alexander Kotlyar, Rosa Di Felice & Danny Porath; 3.21a (top): © Kathy Park Talaro; 3.21a (bottom): © Harold J. Benson; 3.21b (top & middle): © Jack Bostrack/Visuals Unlimited; 3.21b (bottom): © Manfred Kage/Peter Arnold/Photolibrary; 3.21c (top): © A.M. Siegelman/Visuals Unlimited; 3.21c (bottom): © David Frankhauser; Insight 3.2a: Courtesy of IBM Research/Almaden Research Center; Insight 3.2b: Courtesy of Dr. Karl-Heinz Rieder, Institut für Experimentalphysik, Berlin; p. 79, 1b: © Kathy Park Talaro; p. 79, 2 (top left): Janice Carr/Public Health Image Library; p. 79, 2 (top right): © Dr. Arthur Siegelman/Visuals Unlimited; p. 79, 2 (bottom left): Centers for Disease Control; p. 79, 2 (bottom right): © Carolina Biological Supply/Phototake.

Chapter 4 Opener: Dr. David Phillips/Visuals Unlimited; 4.2b: Journal of Molecular Biology, Volume 235, Issue 4, 27 January 1994, Pages 1261-1270. “Isolation, Characterization and Structure of Bacterial Flagellar Motors Containing the Switch Complex,” Noreen R. Francis, Gina E. Sosinsky, Dennis Thomas and David J. DeRosier; 4.3a: Courtesy of Dr. Jeffrey C. Burnham; 4.3b: Reichelt and Baumann, “Taxonomy of the marine, luminous bacteria,” ARCHIVES OF MICROBIOLOGY Vol 94, No 4, 283-330; fig 19. © Springer-Verlag 1973. With kind permission of Springer Science and Business Media; 4.3c: From Noel R. Krieg in Bacteriological Reviews, March 1976, Vol. 40(1):87 fig 7; 4.3d: From Preer et al., Bacteriological Review, June 1974, 38(2);121, fig 7. © ASM; 4.6c: Stanley F. Hayes, Rocky Mountain Laboratories, NIAID, NIH; 4.7a: © Eye of Science/ Photo Researchers; 4.7b: Dr. S. Knutton from D.R. Lloyd and S. Knurron, Infection and Immunity, January 1987, p 86-92. © ASM; 4.8: © L. Caro/SPL/Photo Researchers; Insight 4.1 (all): Courtesy of D.G. Allison and I.W. Sutherland; 4.10a: © John D. Cunningham/ Visuals Unlimited; 4.10b1-2: Courtesy of Graham C. Walker; 4.11: © Science VU-Charles W. Stratton/ Visuals Unlimited; 4.12a: © S.C Holt/Biological Photo Service; 4.12b: © T. J. Beveridge/Biological Photo Service; 4.15: © David M. Phillips/Visuals Unlimited; 4.17: © E.S. Anderson/Photo Researchers; 4.19a: © Paul W. Johnson/Biological Photo Service; 4.19b: © D. Balkwill and D. Maratea; 4.20: © Rut CarballidoLopez/I.N.R.A. Jouy-en-Josas, Laboratoire de Génétique Microbienne; 4.21-22: © George Chapman/ Visuals Unlimited; Insight 4.3: © Max Planck Institute for Marine Microbiology, Germany; 4.23a: © J.T. Staley, M.P. Bryant, N. Pfennining and J.G. Holt, Bergey Manual of Systematic Bacteriology, Vol 3 © 1989 Williams and Wilkins Co. Baltimore; 4.23b: Courtesy of Jeff Broadbent; 4.23c: From Jacob S. Teppema, “In Vivo Adherence and Colonization of Vibro Cholerae Strains that differ in Hemagglutinating Activity and Motility” Journal of Infection and Immunity, 55(9): 20932102, Sept. 1987. Reprinted by permission of American Society for Microbiology.; 4.23d: Photo by De Wood. Digital colorization by Chris Pooley; 4.23e: © VEM/

Photo Researchers; 4.23f: Centers for Disease Control/ Dr. David Berd; 4.24: Centers for Disease Control/Dr. William Kaplan; 4.25a: © Wayne P. Armstrong, Palomar College; 4.25b: Dr. Mike Dyall-Smith, University of Melbourne; p. 107: © Kathy Park Talaro.

Chapter 5 Opener “a”: © D. Trozzo/Alamy; 5.1a-b: © Andrew Knoll; Insight 5.1: Courtesy of Lynn Margulis; 5.3a: © Scientifica/RMF/Visuals Unlimited, Inc.; 5.3b: © RMF/FDF/Visuals Unlimited; 5.5a: © John J. Cardamone, Jr./Biological Photo Service. All rights reserved.; 5.6: © Donald Fawcett/Visuals Unlimited; 5.7b: © Science VU/Visuals Unlimited; 5.12b: © Donald Fawcett/Visuals Unlimited; 5.14b: © Albert Tousson/PhotoTake; 5.15a-b: Courtesy of Dr. Judy A. Murphy, San Joaquin Delta College, Department of Microscopy, Stocton, CA; 5.16b: © David M. Phillips/ Visuals Unlimited; 5.17a: © Kathy Park Talaro; 5.17b: © Everett S. Beneke/Visuals Unlimited; 5.18d: © Dr. George L. Barron; Insight 5.2a: © Dennis Kunkel Microscopy, Inc./Visuals Unlimited; Insight 5.2b: Kelly Cheng Travel Photography/Getty Images; 5.20a: © Kathy Park Talaro; 5.20b: © William Marin, Jr./ The Image Works; 5.21a: © A.M. Siegelman/Visuals Unlimited; 5.21b: © John D. Cunningham/Visuals Unlimited; 5.21c: Courtesy of Neil Carlson, Department of Environmental Health and Safety; 5.22a: © David M. Phillips/Visuals Unlimited; 5.22b: © Stephen Durr; 5.22c: © BioMEDIA ASSOCIATES; 5.22d: © Yuuji Tsukii, Protist Information Server, http:// protist.i.hosei.ac.jp/protist_menuE.html; 5.25b: © Carol Geake/Animals Animals; 5.25d: © Arthur Siegelman/ Visuals Unlimited; p. 138: © Wayne P. Armstrong, Palomar College.

Chapter 6 Opener: © WoodyStock/Alamy; Insight 6.1: © Science VU/Wayside/Visuals Unlimited; 6.2a: © K.G. Murti/Visuals Unlimited; 6.2b: © Centers for Disease Control/Phototake; 6.2c: © A.B. Dowsette/ SPL/Photo Researchers; 6.3: © Omnikron/Photo Researchers; 6.6b: © Dennis Kunkel/CNRI/Phototake; 6.6d: © K.G. Murti/Visuals Unlimited; 6.7d: © Dr. Linda M. Stannard, University of Cape Town/ Photo Researchers; 6.8a (top): Fred P. Williams, Jr./ EPA; 6.8a (bottom): © Dr Linda Stannard, Uct/Photo Researchers; 6.8b: © Eye of Science/Photo Researchers; 6.9a: © Harold Fisher; 6.10a: © Lennart Nilsson/ Scanpix; 6.10b: © Kathy Park Talaro; 6.15: © K.G. Murti/Visuals Unlimited; 6.16b: © Chris Bjornberg/ Photo Researchers; 6.17a: © Patricia Barber/Custom Medical Stock; 6.17b: Courtesy of Massimo Battaglia, INeMM CNR, Rome Italy; 6.21: © K.G. Murti/Visuals Unlimited; 6.23a: Courtesy of Ted Heald, State of Iowa Hygienic Laboratory; 6.24a-b: Centers for Disease Control; 6.24c: © Visuals Unlimited; Insight 6.2: © Dr. Dennis Kunkel/Visuals Unlimited.

Chapter 7 Opener: © Hiroya Minakuchi/Minden Pictures; 7.1a: © Ralph Robinson/Visuals Unlimited; 7.1b: Jack Jones/ EPA; Insight 7.1a: Courtesy of E.E. Adams, Montana

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State University/National Science Foundation, Office of Polar Programs; Insight 7.1b: © Ralph Robinson/ Visuals Unlimited; 7.9a: © Pat Armstrong/Visuals Unlimited; 7.9b: Image courtesy Nozomu Takeuchi; Insight 7.2: © Michael Milstein; 7.10a: © Hank Morgan/SPL/Photo Researchers; 7.11: © Terese M. Barta, Ph.D.; Insight 7.3a: © Dr. Ken MacDonald/ SPL/Photo Researchers; Insight 7.3b: © Mike Abbey/ Visuals Unlimited; 7.12: © Science VU-Fred Marsik/ Visuals Unlimited; 7.13a: Courtesy of Ellen Swogger and Garth James, Center for Biofilm Engineering, Montana State University; 7.17a: © Kathy Park Talaro/ Visuals Unlimited.

Chapter 8 Opener: © Gordon M. Grant/Alamy; Insight 8.4: © David Tietz/Editorial Image, LLC.

Chapter 9 Opener: © AP Photo/Jacob Silberberg; 9.1: © PhotoDisc VO6, Nature, Wildlife and the Environment; 9.3: © K.G. Murti/Visuals Unlimited; Insight 9.1 (left): © A. Barrington Brown/Photo Researchers; Insight 9.1 (right): © Lawrence Livermore Laboratory/SPL/Custom Medical Stock Photo; 9.12b: © Center for Molecular Biology of RNA, UC-Santa Cruz; 9.16c: Courtesy of Steven McKnight and Oscar L Miller, Department of Biology, University of Virginia; Insight 9.3: © Getty Images; p. 267: © Eye of Science/ Photo Researchers.

Chapter 10 Opener: © AFP/Getty Images; 10.3b: © Kathy Park Talaro; Insight 10.1: © Stephen Jaffe/AFP/ Getty Images; 10.8 (left): © Koester Axel/Corbis; 10.8 (middle): © Milton P. Gordon, Department of Biochemistry, University of Washington; 10.8 (right): © Andrew Brookes/Corbis; Insight 10.2: © Marilyn Humphries; Insight 10.3: © AP Photo/Noah Berger; Table 10.3 (top): Courtesy of David M. Stalker; Table10.3 (middle): Courtesy of Richard Shade, Purdue University; Table 10.3 (bottom): Courtesy of Peter Beyer, UNI-Freiburg; 10.15: Courtesy of Dr. Michael Baird.

Chapter 11 Opener: © Douglas R. Clifford/Times/Newscom; Insight 11.1: © Bettmann/Corbis; Insight 11.2: © Stephen Jaffe/AFP/Getty Images; 11.5a: © Science VU/Visuals Unlimited; 11.6: © Raymond B. Otero/ Visuals Unlimited; 11.8: Photo courtesy of Dr. Brendan A. Niemira/U.S. Department of Agriculture; 11.10: © Tom Pantages; 11.11: © Fred Hossler/Visuals Unlimited; Insight 11.3: © Plush Studios/Bill Reitzel/ Getty Images RF; 11.13: STERIS Corporation. System 1 ® is a registered trademark of STERIS Corporation; Insight 11.4a: © David M. Phillips/Visuals Unlimited; Insight 11.4b: © Kathy Park Talaro; 11.16: © Kathy Park Talaro/Visuals Unlimited; p. 326: © George Chapman/ Visuals Unlimited.

Chapter 12 Opener: © Konrad Wothe/Minden Pictures; Insight 12.1: © Bettmann/Corbis; 12.2 (top): © David Scharf/ Peter Arnold/Photolibrary; 12.2 (bottom): © CNRI/ Photo Researchers; Insight 12.2: © Kathy Park Talaro/ Visuals Unlimited; 12.9: © Cabisco/Visuals Unlimited; 12.15: © Kathy Park Talaro; 12.16: © Kenneth E. Greer/ Visuals Unlimited; 12.18b: © Kathy Park Talaro; 12.19: Etest® is a registered trademark belonging to AB BIODISK, Sweden, and the product and underlying technologies are patented by AB BIODISK in all major markets; 12.20: Image courtesy David Ellis.

Chapter 13 Opener: © AFP/Getty Images; Insight 13.1: © Eurelios/Phototake; Insight 13.2: Centers for Disease Control; 13.13: Marshall W. Jennison, Massachusetts Institute of Technology, 1940; p. 396 (left): © Kathy Park Talaro; p. 396 (right): © Science VU-Charles W. Stratton/Visuals Unlimited.

Chapter 14 Opener: © John Moore/Getty Images; 14.3b: © Ellen R. Dirksen/Visuals Unlimited; 14.10d: © Gunilla Elam/ Photo Researchers; 14.12a: © David M. Phillips/Visuals Unlimited; 14.15b: Courtesy of Steve Kunkel; 14.17: © Dennis Kunkel/Phototake; 14.20: © 1966 Rockefeller University Press. The Journal of Experimental Medicine, June 1966, Vol 123, p. 969-984.

Chapter 15 Opener: © Watney Collection/Phototake; 15.11b: U.S. National Library of Medicine; 15.16: © Lennart Nilsson, “The Body Victorious”/Scanpix; 15.17 (all): © Photodisc/Getty RF; 15.17 (right): © Creatas/ PictureQuest RF; Insight 15.2: James Gillray (English, 1757-1815), The Cow-Pock, Gift of Thomas F. Furness in memory of William McCallin McKee, 1928.1407, The Art Institute of Chicago. Photography © The Art Institute of Chicago.; Insight 15.3: © Brand X Pictures/ PunchStock RF.

Chapter 16 Opener: © Keith Brofsky/Getty Images RF; 16.2b: © SPL/Photo Researchers; 16.2c: © David M. Phillips/ Visuals Unlimited; 16.5a: © Kenneth E. Greer/Visuals Unlimited; 16.5b: © Kathy Park Talaro; 16.6a: © STU/ Custom Medical Stock; 16.10a-b: © Stuart I. Fox; 16.14: © Kathy Park Talaro; 16.15b: © Kenneth E. Greer/ Visuals Unlimited; Insight 16.3 (left): © Renee Lynn/ Photo Researchers; Insight 16.3 (middle): © Walter H. Hodge/Peter Arnold/Photolibrary; Insight 16.3 (right): © Runk/Schoenberger/Grant Heilman Photography; 16.16a: © Diepgen TL, Yihume G et al. Dermatology Online Atlas published online at: www. dermis.net. Reprinted with permission.; 16.16b: © SIU/Visuals Unlimited; 16.19: Reprinted from R. Kretchmer et. al, “Congenital Aplasia of the Thymus Gland (DiGeorge’s Syndrome),” New England Journal Of Medicine, 279:1295, Dec. 12, 1968 Massachusetts Medical Society. All rights reserved.; Insight 16.5: Courtesy of Baylor College of Medicine, Public Affairs.

Chapter 17 Opener: © By Ian Miles-Flashpoint Pictures/Alamy; Insight 17.1: NIH Roadmap for Medical Research website—Source: http://nihroadmap.nih.gov/; 17.4b: © Fred Marsik/Visuals Unlimited; 17.5: © LeBeau/ Custom Medical Stock Photo; 17.7: Image provided by AdvanDx, Inc.; 17.11: © Joel Gordon; 17.12: Genelabs Diagnostics Pte Ltd; 17.14c: CHEMICON® International, Inc; 17.15b: © Hank Morgan/Science Source/Photo Researchers; 17.16a: © Carroll H. Weiss/ Camera M.D. Studios; 17.16b1: © A.M. Siegelman/ Visuals Unlimited; 17.16b2: © Science VU/CDC/ Visuals Unlimited; 17.16c1: © K.G. Murti/Visuals Unlimited; 17.16c2: © Dr. Linda M. Stannard, University of Cape Town/Photo Researchers; 17.16d: Rigurat; p. 511 (left): © Kathy Park Talaro; p. 511 (right): © Kenneth E. Greer/Visuals Unlimited.

Chapter 18 Opener: © Brand X Pictures/PunchStock RF; 18.3: © Dr. Ken Greer/Visuals Unlimited; 18.4a: © David M. Phillips/Visuals Unlimited; 18.4b: © Kathy Park Talaro/Visuals Unlimited; Insight 18.1(left & second): © Carroll H. Weiss/Camera M.D. Studios; Insight 18.1(third): © ISM/Phototake; Insight 18.1(right):

© Biomedical Communications/Custom Medical Stock Photo; 18.6: Analytab Products, a division of Sherwood Medical; 18.8a: National Institute Slide Bank/The Welcome Centre for Medical Sciences; 18.8b: © Dr. Ken Greer/Visuals Unlimited; 18.9: © John Watney/ Photo Researchers; 18.10: © Biophoto Associates/Photo Researchers; 18.11a-b: Centers for Disease Control; 18.12b: © Logical Images, Inc. All rights reserved; Insight 18.2: © AP Photo/Damian Dovarganes; Table18.6 (left): © Phil Degginger; Table 18.6 (right): © World Health Org./Peter Arnold/Photolibrary; 18.13: © Kenneth E. Greer/Visuals Unlimited; 18.14: © James Stevenson/Photo Researchers; Table 18.7 (measles): © Lennart Nilsson/Scanpix; Table 18.7 (rubella): Centers for Disease Control; Table 18.7 (fifth disease): © Jack Ballard/Visuals Unlimited; Table 18.7 (roseola): © Scott Camazine/Phototake; Table 18.7 (scarlet fever): © Mediscan/Corbis; Table18.8 (left): © Kenneth E. Greer/Visuals Unlimited; Table18.8 (right): © Charles Stoer/Camera M.D. Studios; Table 18.9 (left): Centers for Disease Control; Table18.9 (right): © Science VU-Charles W. Stratton/ Visuals Unlimited; 18.15: © Everett S. Beneke/Visuals Unlimited; 18.16, 18.17a: © Kenneth E. Greer/Visuals Unlimited; 18.17b: Reprinted from J. Walter Wilson, Fungous Diseases of Man, Plate 42 (middle right), © 1965, The Regents of the University of California; 18.18a, c: From Elmer W. Koneman and Roberts, Practical Laboratory Mycology, 1985, pages 133, 134 © Williams and Wilkins Co., Baltimore, MD; 18.18b: © A.M. Siegelman/Visuals Unlimited; 18.19: © Carroll H. Weiss/Camera M.D. Studios; 18.22: © Science VUBascom Palmer Institute/Visuals Unlimited; 18.23: Armed Forces Institute of Pathology; 18.24: © ISM/ Phototake.

Chapter 19 Opener: © Matt Bowman/Getty Images; 19.3: © Kwangshin Kim/Photo Researchers; 19.5: © Kathy Park Talaro/Visuals Unlimited; 19.6: © Dr. Gary Gaugler/Visuals Unlimited; 19.7 (both): © Gordon Love, M.D. VA, North CA Healthcare System, Martinez, CA; 19.8: Reprinted from J. Walter Wilson, Fungous Diseases of Man, Plate 21, © 1965, The Regents of the University of California; 19.9a: Centers for Disease Control/Dr. Hardin; 19.9b: Centers for Disease Control/Mercy Hosp Toledo OH; Brian J. Harrington; Insight 19.1: © Royalty-Free/Corbis/Vol. 124; 19.11: Centers for Disease Control; 19.14a: © M. Abbey/Photo Researchers; 19.14b: © Pr. J.J. Hauw/ ISM/Phototake; 19.15a: © Tektoff RM/CNRI/SPL/ Custom Medical Stock Photo; 19.17b: © Science VUCDC/Visuals Unlimited; Insight 19.4: © AP Photo/ Chet Magnuson; 19.20: © John D. Cunningham/Visuals Unlimited; 19.21: Courtesy of Dr. T. F. Sellers, Jr.; 19.24: © Biophoto Associates/Photo Researchers; p. 583: Centers for Disease Control/Dr. Leanor Haley.

Chapter 20 Opener: © Nigel Hicks/Getty Images; 20.4: Centers for Disease Control; 20.5: © JAMA; 20.7: © CDC/Peter Arnold/Photolibrary; 20.8: © Science VU-Charles W. Stratton/Visuals Unlimited; Insight 20.2a: © Dwight Kuhn; Insight 20.2b: © Science VU/Visuals Unlimited; Insight 20.2c: © A.M. Siegelman/Visuals Unlimited; Insight 20.2d: © George D. Lepp/Corbis; 20.9b: © Scott Camazine/Photo Researchers; 20.11a: © Dr. John Cunningham/Visuals Unlimited; 20.11b: Research originally published in Blood. Peter Maslak and Susan McKenzie, “Infectious Mononucleosis” Blood. 2002; © American Society of Hematology; 20.13: McCaul and Williams, “Development Cycle of C. Burnetii,” Journal of Bacteriology, 147:1063, 1981. Reprinted with permission of American Society for Microbiology; 20.14: © Kenneth E. Greer/Visuals Unlimited; 20.15:

Credits Centers for Disease Control; 20.17: Courtesy of Stephen B. Aley, PhD., University of Texas at El Paso; 20.19: © Roll Back Malaria Partnership; 20.20: © A.M. Siegelman/Visuals Unlimited; Insight 20.3: © Thierry Berrod, Mona Lisa Production/Photo Researchers; Insight 20.4: © SPL/Photo Researchers; p. 621: Courtesy of Steve Kunkel.

Chapter 21 Opener: © Ariel Skelley/Corbis; 21.1b: © Ellen R. Dirksen/Visuals Unlimited; 21.3: © Pulse Picture Library/CMP Images/PhotoTake; 21.4a: Multimedia Library, Congenital Heart Disease, Children’s Hospital, Boston. Editor: Robert Geggel, MD. www. childrenshospital.org/mml/cvp; 21.4b: © Dr. E. Walker/Photo Researchers; 21.6a (both): Diagnostic Products Corporation; 21.6b: © Dr. David Schlaes/ John D. Cunningham/Visuals Unlimited; 21.7: Federal Agriculture Research Centre; 21.8: Centers for Disease Control; Insight 21.1 (Johnstown): © Library of Congress Prints & Photographs Division [LC-USZ62-60959]; Insight 21.1 (1918 flu): © Corbis; Insight 21.1 (WWI troops): U.S. Army Signal Corps/ Library of Congress; Insight 21.1 (Capone, MLK Jr., Kosovo): © Getty Images; Insight 21.1 (AB): © ABC via Getty Images; Insight 21.1 (Carter): Trikosko, Marion S., photographer/Library of Congress; Insight 21.1 (Tsunami, swine flu): © AFP/Getty Images; Insight 21.1 (stock market): © Getty Images; 21.13: © John D. Cunningham/Visuals Unlimited; 21.15: © Elmer Koneman/Visuals Unlimited; 21.16: © CDC/ PhotoTake; 21.17: © SIU Bio Med/Custom Medical Stock Photo; 21.18: © Dr. Leonid Heifets, National Jewish Medical Research Center; 21.19a: From Nester et al. Microbiology: A Human Perspective, 4th ed. © Evans Roberts; 21.19b: © L.M. Pope and D.R. Grote/ Biological Photo Service; 21.21: Centers for Disease Control; 21.22: © NPS photo by John Good; Insight 21.3 (left): Centers for Disease Control; Insight 21.3 (right): © JAMA; 21.23: © Tom Volk; p. 659: © Jack Bostrack/ Visuals Unlimited.

Chapter 22 Opener: FEMA Photo/Andrea Booher; Insight 22.1: © AP Photo/Damian Dovarganes; 22.4a: © R. Gottsegen/Peter Arnold/Photolibrary; 22.4b: © Stanley Flegler/Visuals Unlimited; 22.6: © Science VU-Max A. Listgarten/Visuals Unlimited; 22.7: Centers for Disease Control; 22.8a: Exeen M. Morgan and Fred Rapp, “Measles Virus and Its Associates Disease,” Bacteriological Reviews, 41(3):636-666, 1977. Reprinted by permission of American Society for Microbiology; 22.9a: © PhotoTake; 22.13: R.R. Colwell and D.M. Rollins, “Viable but Nonculturable Stage of Campylobacter jejuni and its Role in Survival in the Natural Aquatic Environment,” Applied and Environmental Microbiology, 52(3): 531-538, 1986. Reprinted with permission of American Society for Microbiology; 22.14a: © David Musher/Photo Researchers; 22.14b: Courtesy of Fred Pittman; 22.14c: Farrar and Lambert: Pocket Guide for Nurses: Infectious Diseases. © 1984, Williams and Wilkins, Baltimore, MD; 22.15: Centers for Disease Control; 22.16: © Moredun Animal Health Ltd./Photo Researchers; Insight 22.2: © Kathleen Jagger; 22.17a: © Custom Medical Stock Photo; 22.18: © K.G. Murti/ Visuals Unlimited; Insight 22.3: © Tom Pantages; 22.19: © Iruka Okeke; 22.20: © Ynes R. Ortega; 22.21: Centers for Disease Control/Dr. Stan Erlandsen; 22.22d: © Science VU-Charles W. Stratton/Visuals Unlimited; 22.22e: © Eye of Science/Photo Researchers; Insight 22.4: © Sinclair Stammers/Photo Researchers; 22.24a: © Stanley Flegler/Visuals Unlimited; 22.24b: Katz et al., “Parasitic Diseases,” 1982 © Springer-Verlag. With

kind permission of Springer Science and Business Media; 22.25: Centers for Disease Control/Henry Bishop; 22.26a: © R. Calentine/Visuals Unlimited; 22.26b: © Science VU-Fred Marsik/Visuals Unlimited; 22.27: © Carroll H. Weiss/Camera M.D. Studios; 22.28: © A.M. Siegelman/Visuals Unlimited; 22.29a: © Cabisco/Visuals Unlimited; 22.29b: Courtesy of Harvey Blankespoor; 22.29c: © Science VU/Visuals Unlimited.

Chapter 23 Opener: © AP Photo/Honolulu Star-Bulletin, Richard Walker; 23.4: © Science VU/Fred Marsik/Visuals Unlimited; 23.5: Courtesy Danny L. Wiedbrauk; 23.6: © Custom Medical Stock Photo; 23.7: © David M. Phillips/The Population Council/Photo Researchers; 23.9: James Bingham, Pocket Guide for Clinical Medicine: Sexually Transmitted Diseases. © 1984 Williams and Wilkins Co., Baltimore, MD; 23.10: © George J. Wilder/ Visuals Unlimited; 23.12: Courtesy Morris D. Cooper, Ph.D., Professor of Medical Microbiology, Southern Illinois University School of Medicine, Springfield, IL; 23.13a: © Science VU/Visuals Unlimited; 23.13b: © Martin M. Rotke/Photo Researchers; 23.14: Centers for Disease Control/J. Pledger; 23.15a-b: © Science VU/CDC/Visuals Unlimited; 23.16: © Custom Medical Stock Photo, Inc; 23.17: © Science VU/CDC/ Visuals Unlimited; 23.18: © Kenneth E. Greer/Visuals Unlimited; 23.19: © Carroll H. Weiss/Camera M.D. Studios; 23.21: © Dr. Walker/Photo Researchers; 23.22: © Chor Sokunthea/Reuters/Corbis; Table23.7 (all): © Carroll H. Weiss/Camera M.D. Studios; Table23.8 (left): © Kenneth E. Greer/Visuals Unlimited; Table23.8 (right): © Charles Stoer/Camera M.D. Studios; Insight 23.2: © Martin Rotker/Phototake; p. 740 (left): Department of Health and Human Resources, Courtesy of Dr. W. Burgdorfer; p. 740 (right): © Science VU/Visuals Unlimited.

Chapter 24 Opener: © Vanessa Vick/Photo Researchers; 24.1: Reprinted Cover image from December 1, 2000 Science with permission from Jillian Banfield, Vol 290, 12/1/2000. © 2000 American Association for the Advancement of Science; Image courtesy of Jillian Banfield; 24.8b: © John D. Cunningham/Visuals Unlimited; 24.9a-b: © Sylvan Wittwer/Visuals Unlimited; Insight 24.2 (top): © Gorm Kallestad/ AP Photo; Insight 24.2 (bottom): © Kevin Schafer/ Peter Arnold/Photolibrary; 24.11a-d: Jo Handelsman, “Metagenomics: Application of Genomics to Uncultured Microorganisms,” Microbiology and Molecular Biology Reviews, December 2004, p. 669-685, Vol. 68, fig 3 page 674; 24.13: © John D. Cunningham/ Visuals Unlimited; Insight 24.3: © Mark Lewis/ Getty Images; 24.16a: © Dr. David Phillips/Visuals Unlimited/Getty Images; 24.16b: © Carleton Ray/ Photo Researchers; 24.16c: © Phillip Slattery/Visuals Unlimited; 24.17: © John D. Cunningham/Visuals Unlimited.

Chapter 25 Opener: © Bruce Chambers, The Orange County Register/Newscom; Insight 25.1 (both): © Carl Oppenheimer; 25.2: © Getty Images; 25.4a-b: Courtesy of Sanitation Districts of Los Angeles County; 25.5c: © Kathy Park Talaro; Insight 25.2: © Renee Comet/ National Cancer Institute; 25.5d (both): Reprinted from EPA Method 1604 (EPA-821-R-02-024) courtesy of Dr. Kristen Brenner from the Microbial Exposure Research Branch, Microbiological and Chemical Exposure Assessment Research Division, National Exposure Research Laboratory, Office of Research and Development, U.S Environmental Protection Agency;

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25.6: © John D. Cunningham/Visuals Unlimited; 25.7: © Ryan Hatch; 25.8a: © Kevin Schafer/Peter Arnold/ Photolibrary; 25.9: © Kathy Park Talaro/Visuals Unlimited; 25.10: © Joe Munroe/Photo Researchers; Insight 25.3a-b, 25.13: © Kathy Park Talaro; 25.15: © Volker Steger/SPL/Photo Researchers; 25.17: © J.T. MacMillan; Insight 25.4(top): © R H Productions/ Robert Harding World Imagery/Getty Images; Insight 25.4a: Giancarlo Ranalli et. al, “Biotechnology applied to cultural heritage: biorestoration of frescoes using viable bacterial cells and enzymes,” Journal of Applied Microbiology, Volume 98, Issue 1, pages 73–83, January 2005; Insight 25.4b-c: © Giancarlo Ranalli/Journal of Applied Microbiology; p. 785 (both): © Kathy Park Talaro.

Line Art Chapter 1 Table 1.2: Data from latest “World Health Report”

Chapter 6 Figure 6.9: Detailed Structure of Complex Viruses, from Westwood, et al., Journal of Microbiology, 34:67. Reprinted with permission of the Society of General Microbiology.

Chapter 8 Figure 8.18: The reactions of a single turn of the Krebs cycle, adapted from Life: The Science of Biology, 7/e, by Purfes, Sadava, Orions, & Heller. © Sinauer Associates, Inc. Reprinted with permission.

Chapter 10 Figure 10.16: © New Scientist Magazine. Reprinted by permission

Chapter 11 Figure 11.05b: From Perkins, Principles and Methods of Sterilization in Health Science, 2nd ed. Courtesy of Charles C. Thomas Publisher, Ltd., Springfield, Illinois; Figure 11.15: From Nolte, et al., Oral Microbiology, 4e. © 1982 Mosby

Chapter 13 Continuing the Case File: Graph is a screenshot from Google Flu Trends. Reprinted by permission

Chapter 15 Figure 15.14: From Joseph A. Bellanti, MD. Immunology III. (Philadelphia, PA: W.B. Saunders, 1985). Reprinted by permission; Insight Box 15.4: Data from the Organisation for Economic Co-operation and Development; OECD Health Statistics Online Database, 2008

Chapter 22 Figure 22.12: From American Scientist, 95:6, 2007; “Safer Salads” by Fonseca and Ravishankar. Reprinted by permission

Chapter 23 Figure 23.11: Data from AVERT organization; Figure 23.20: From www.infectiousdiseasenews. com/200007alexander1aCREAM.gif. Reprinted by permission

Inside Back Cover Figures 1–4: from abstract by Nicole P. Lindsey, MS, J. Erin Staples, MD, PhD, Jennifer A. Lehman, and Marc Fischer, MD; Division of Vector-Borne Infectious Diseases, National Center for Emerging and Zoonotic Infectious Diseases, CDC

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Note: In this index, page numbers followed by a t refer to tables, page numbers followed by an f refer to figures, page numbers set in boldface refer to boxed material, and page numbers set in italics refer to definitions or introductory discussions. Abatement programs, and malaria, 604 Abiogenesis, 12, 13 Abiotic factors, 743 ABO blood groups, 459, 470–74 Abscesses, 378, 411, 518 Absolute alcohol, 317 A-B toxins, 607, 632, 633f, 673 ACAM 2000, 530 Acanthamoeba, 131t, 542, 561 Accessory molecules, 438–39 Accutane, 516 Acetaminophen, 417 Acetic acid, 322, 779t Acetone, 779t Acetylcholine, 574 Acetyl coenzyme A (acetyl CoA) Acid(s) and acidity, 39–40, 322 Acid-fast staining, 74–75, 92, 641f, 643 Acidic fermentation, 221 Acidophiles, 185 Acinobacter baumanii, 232, 263, 264 Acne, 515–16 Acquired immunodeficiency syndrome (AIDS), 485. See also AIDSdefining illnesses (ADIs); Human immunodeficiency virus cat-scratch disease, 601 causative agent, 610 chronic diarrhea, 684 cryptococcal meningitis, 556 diagnosis of, 61314 drug resistance, 348 epidemiology, 612–13 genetics, 369 normal microbiota as pathogens, 365 prevention of, 614 recombinant HGH, 283 signs and symptoms of, 608, 610 treatment of, 614–16 tuberculosis, 644 Acquired specific immunity, 425 Acquisition, of infectious agents, 382 Acridine dyes, 256t Acriflavine, 322 Actin cytoskeleton, 82f, 96 Actin filaments, 120 Active immunity, 443, 444–45, 447–50 Active site, of enzyme, 201 Active transport, 178–80

Active viruses, 141 Acute diarrhea, 671–83 Acute encephalitis, 562–64 Acute endocarditis, 588, 589t Acute glomerulonephritis (AGN) Acute hemorrhagic cystitis Acute infections, 377 Acute necrotizing ulcerative gingivitis (ANUG), 668 Acute respiratory distress (ARDS), 648 Acyclovir, 344, 345t, 527, 542, 558, 563, 731 Adefovir dipivoxil, 690 Adenine (A), 50, 235 Adeno-associated virus (AAV), 145f, 150t, 164 Adenoids, 661 Adenosine deaminase (ADA), 288, 485 Adenosine diphosphate. See ADP Adenosine triphosphate. See ATP Adenoviruses, 153f, 156t, 541, 625, 653, 682. See also Adeno-associated virus Adhesins, 712 Adhesion, of pathogen, 372–73 Adjuvant, and vaccines, 450–51 Administration, of vaccines, 450–51 ADP, 51 ADP-ribosylation, 632 Adsorption, of viruses, 151, 160t Adults. See also Age; Elderly pertussis, 634 staphylococcal scalded skin syndrome, 522 recommended vaccinations, 454t Adult T-cell leukemia, 616 Advisory Committee on Immunization Practices (ACIP), 455 Aedes aegyptii, 597 Aero-, 174t Aerobes, 183 Aerobic bacteria, 102 Aerobic respiration, 172, 211, 212–14, 219–20 Aerosols, 384 Aerotolerant anaerobes, 184 Aflatoxin, 126 Africa Ebola and Marburg viruses, 598 Lassa fever, 599 malaria, 604

meningococcal epidemics, 554 plague, 591 river blindness, 543 sleeping sickness, 132, 577–78 tuberculosis, 644 African-Americans, and Tuskegee Study, 724 Agammaglobulinemia, 484 Agar, 43, 60 Age, at onset of subacute endocarditis, 589. See also Adults; Aging; Elderly; Children; Infants Agglutination and agglutination testing, 437f, 438, 500, 502 Aggregatibacter actinomycetemcomitans, 587, 666 Aging, and inflammation, 410. See also Age Agranulocytes, 406, 408–409 Agricultural microbiology, 5t Agriculture. See also Animals; Food(s); Plants; U. S. Department of Agriculture anthrax in livestock, 606 botulism in livestock, 574 brucellosis in livestock, 599 chicken production and salmonellosis, 139 fungi, 126 genetically modified organisms, 284, 286 humus content of soil, 754 phosphates as fertilizers, 751 plant-bacteria associations, 749 Agrobacterium rhizogenes, 284 Agrobacterium tumefaciens, 284, 286 AIDS. See Acquired immunodeficiency syndrome AIDS-defining illnesses (ADIs), 609, 614 Air, and transmission of infectious disease, 384 Airborne allergens, 462, 463t Airborne contaminants, 124 Air sanitization, 301 Ajax antibacterial hand soap, 323t Alanine, 48f Alaska Division of Public Health, 168 Albendazole, 343 Alcohol(s), and microbial control, 314t, 315, 317 Alcoholic beverages, 220, 770–72

I-1

I-2

Index

Alcoholic fermentation, 220–21 Aldehydes, 321 Alexander the Great, 299 Alexandrium, 108 Algae, 113, 127–28, 181f, 779–80 Alimentary tract, 661 Alkalines and alkalinity, 40, 322 Alkalinophiles, 185 Alleles, 470 Allergan eye drops, 323t Allergens, 433, 462–63. See also Allergy Allergy, 461. See also Allergens antimicrobial drugs, 353 cytokines and symptoms of, 465–66 diagnosis, 468 epidemiology and modes of contact, 461–62 evolutionary value of, 466 fungi, 126 hypersensitivity, 461 nature of allergens and portals of entry, 462–63 mistaken for infections, 461 sensitization and provocation as mechanisms of, 463–65 sinusitis, 626 treatment and prevention of, 469–70 Alloantigens, 433 Allografts, 478 Allosteric site, 252 Alpha-ketoglutaric acid, 216 Alpha toxin, 524 Alpha–2a interferon, 280, 282 Alternative pathway, of complement, 418, 419t Alternative splicing, 250–51 Alzheimer’s disease, 288, 289 Amantadine, 345t, 639 American Society for Microbiology, 313 American Type Culture Collection, 66, 182 Ames test, 257–58 Amination, 224 Amino acids, 48, 224f, 225, 779t Aminoglycosides, 332, 339–40, 342, 346, 352t, 357 Aminopenicillanic acid, 334 Aminotransferases, 205 Ammonification, 749 Ammonium hydroxide, 322 Amnesiac shellfish poisoning, 108 Amoebas, 129f, 132. See also Entamoeba(s) Amoeba proteus, 72t Amoebiasis, 131t, 686–88. See also Entamoeba histolytica Amoebic dysentery, 132 Amoxicillin, 337t, 596, 714 Amphibolism, 223 Amphipathic ions, 38 Amphitrichous flagellum, 84 Amphotericin B, 342, 352t, 357, 557, 558, 651 Ampicillin, 337t, 352t, 355f, 556

Amplicons, 278 Amplifying host, 592 Amylase, 203, 779t Anabolism, 199, 224–25 Anaerobes, 183–84 Anaerobic bacteria, 102 Anaerobic respiration, 211, 220 Anamnestic response, to antigens, 440 Anaphylaxis, 461, 468 Anaplasma phagocytophilum, 601 Anatomical diagnosis, of pneumonia, 645 Ancylostoma duodenale, 697, 698t Anemia, 696 Angiotensin, 447 Animal(s). See also Agriculture; Animal inoculation; Reservoirs; Zoonosis; specific animals drug resistance and feeds for, 348 melamine in pet foods, 285 plague, 591, 592 rabies, 569 reservoirs for disease, 381–82, 530, 569 transgenic, 286 Animalia (Kingdom), 20, 21f Animal inoculation, 59, 160–61, 496 Animal rights movement, 59 Anions, 36 Ankylosing spondylitis, 480t Annotating, of genome, 290 Anopheles mosquito, 603, 604 Anoxygenic photosynthesis, 6 Antacids, 357 Antagonism, 188 Antarctica, 173 Anthrax, 302, 535t, 536, 606–607, 608t, 616. See also Bacillus anthracis Antiallergy medication, 469 Antibiosis, 188 Antibiotic(s). See also Antimicrobial therapy; Cephalosporins; Penicillin(s); Tetracyclines allergies, 467 characteristics of ideal, 328t DNA transcription and translation, 254–55 drug resistance, 348–49, 516, 713 fungal infections, 649 natural compounds as sources of, 327 viral infections, 357 Antibiotic-associated colitis, 354, 676, 677f Antibody, 408. See also IgG blocking antibodies; Monoclonal antibodies A and B antigens, 471–73 events in B-cell activation and synthesis of, 435f immune testing, 500, 501f macromolecules, 49 structure and functions of, 436–40 Antibody-mediated hypersensitivity, 461t Antibody-mediated immunity, 408

Anticodon, 244 Antifungal drugs, 342–43, 352t, 652 Antigen(s) clonal selection, 426 cooperation in immune reactions, 433 enteric bacteria, 672 entrance and processing of, 432–33 immune disorders and overreactions to, 461 immune testing, 500, 501f lymphocyte receptors and specificity to, 428 presentation of, 433–35 specific immunity, 425 Antigen-binding fragments (Fabs), 436, 437–38 Antigen binding sites, 431 Antigenic drift, 636, 637 Antigenicity, 432 Antigenic shift, 578, 636, 637 Antigen-presenting cells (APCs), 426, 434, 442f Antihelminthic drugs, 343, 352t, 692–93 Antihistamines, 469, 625 Antimalarial drugs, 343 Antimicrobial chemicals, in consumer products, 313, 323t Antimicrobial peptides, 419, 421, 514 Antimicrobial proteins, 417–19, 421 Antimicrobial sensitivity tests, 496 Antimicrobial therapy. See also Antibiotic(s) allergies, 467 considerations in selection of, 354–57 dilemmas in approaches to, 357–58 drug resistance, 344, 346–50, 346 history of, 329 interactions between drug and host, 352–54 interactions between drug and microbe, 330–35 new approaches to, 350–51 origins of, 330 principles of, 328, 330 survey of major drug groups, 335–51 Antiparallel arrangement, of DNA, 235 Antiparasitic chemotherapy, 343 Antiphagocytic factors, 373 Antiprotozoan drugs, 352t Antisense DNA, 242 Antisepsis and antiseptics, 300. See also Asepsis and aseptic techniques Antistreptolysin O (ASO) titer test, 504 Antitoxin, 438, 577 Antiviral drugs, 165, 332, 343–44, 345t, 352t, 639 Antiviral interferon, 417–18 Apicomplexa, 131, 603 Apoenzymes, 201 Apolipoprotein, 283t Apoptosis, 443 Appendages, of cell, 83–86, 112–13 Appendicitis, 676

Index

Applied microbiology. See also Biotechnology; Environmental microbiology food and food spoilage, 769–78 industrial products, 778–83 wastewater treatment, 763–69 Applied science, 269 Aquaspirillum, 84f, 95f Aquatic microbiology, 5t, 755–58. See also Ocean; Water and water supplies Aqueous solutions, 314 Aquifer, 756 Arber, Werner, 14 Arboviruses, 562–64. See also Yellow fever Archaea, 23, 92, 102, 104–105, 228 Arctic, 173 Arenaviridae, 151t Aretino, Spinello, 782 Argentine hemorrhagic fever, 599 Arginine (arg), 253–54 Arg operon, 253–54 Argyll-Robertson pupil, 725 Arizona hinshawi, 672 Arizona State University, 254 Arrangement, of bacterial cells, 98–101 Arsenic, 727 Art, and biodegradation, 782 Artemisinin, 605–606 Arteries, 586 Arthroconidia, 557 Arthropod(s), 381, 594 Arthrospores, 125f Arthus, Maurice, 475 Arthus reaction, 475–76 Artificial immunity, 443, 445–46 Artificial viruses, 163 Ascariasis, 135t Ascaris spp., 134 A. lumbricoides, 135t, 696–97, 698t Asepsis and aseptic techniques, 17, 300. See also Antisepsis and antiseptics Asexual phase, of malarial parasite, 603 Asexual spore formation, 125 Asian influenza, 638 Aseptic meningitis, 558 Aspergillus spp., 649 A. fumigatus, 626 Aspirin, 417, 527 Assay media, 65 Assembly of cell, 225, 242–43 of viruses, 155, 159, 160t Asthma, 462, 466–67, 624–25 Astromicrobiology, 5t, 19, 747 Astroviruses, 682 Asymptomatic carriers, 380 Asymptomatic infections, 378 Atherosclerosis, 587 Athlete’s foot, 537 Atlantis (space shuttle), 254 Atmosphere, 743 Atmospheric cycles, 747–49

Atom, 28–29, 31 Atomic force microscope (APM), 73t, 76 Atomic weight, 31 Atopic allergy, 462 Atopic dermatitis, 467 Atopic diseases, 466–67 Atopy, 461 ATP (adenosine triphosphate), 210–11, 218–19 ATP synthase complex, 218 Atria, 586 Attachment, of pathogens to host, 372–73, 377f Attenuated vaccines, 448–49 Atypical squamous cells, 733 Australia, 104f Autism, and vaccinations, 452 Auto-, 174t Autoantibodies, 479 Autoclave, 307 Autograft, 478 Autoimmune diseases, 479 Autoimmune regulator (AIRE), 481 Autoimmunity, 461, 479–82 Autosplenectomy, 80 Autotrophs, 170, 171t, 172, 745 Avery, Oswald, 236, A3 Avian influenza, 162 Axenic animals, 368 Axenic culture, 66 Axial filaments, 85 Azidothymide (AZT), 165, 344, 614 Azithromycin, 340, 542, 723 Azlocillin, 337 Azoles, 342–43, 716 Azorhizobium, 748 Aztreonam, 339 Baby food and formulas. See Infant(s) Babylonians, 770 Bacillus, 98, 100f Bacillus spp., 75, 96, 97f, 98, 309, 764 B. anthracis, 88, 98, 301, 536, 584, 606. See also Anthrax B. cereus, 682–83, 684t B. coagulans, 775 B. polymyxa, 341 B. stearothermophilus, 302 B. subtilis, 339 B. thuringiensis, 97f, 284, 783 Bacitracin, 339, 354t Bacitracin disc test, 631f Back-mutation, 257 Bacon, Francis, 16 Bacteremia, 375, 378, 587 Bacteria. See also Normal microbiota; Prokaryotes Archaea and Eukarya compared to, 104t cell envelope, 89–98 domain, 23 enumeration, 193–94 genetically modified organisms, 284

I-3

medically important families and genera of, 103t structure of cell, 82f, 83 viruses, 157–59 Bacterial artificial chromosomes (BACs), 280 Bacterial chromosome, 94–95 Bacterial vaginosis (BV), 716 Bactericide, 300 Bacteriochlorophyll, 227 Bacteriophages, 157–59, 160t, 350–51, 756, 778 Bacteriorhodopsin, 228 Bacteristatic agents, 300, 301 Bacteroides fragilis, 368 Balantidiosis, 131t Balantidium coli, 131t Bang, B. L., 599 Bang’s disease, 599 Barber’s itch, 536 Bare lymphocyte syndrome, 485 Barophiles, 185 Barr, Yvonne, 596 Barr bodies, 480 Barrier(s) and barrier protection first line of host defense, 398–400 herpes prevention, 730f, 731 HIV prevention, 614 syphilis prevention, 727 Universal Precautions, 386 Bartonella henselae, 600 Bartonella quintana, 601 Basement membranes, 475 Basic science, 269 Basic solution, 39 Basophils, 408, 464 Batch culture method, 192 Batch fermentation, 783 B cells, 408 antibody structure and functions, 426, 436–40 clonal expansion and antibody production, 435–36 immunodeficiency diseases, 483t, 484 specific events in maturation, 428–29, 430f specific receptors, 431 BCG vaccine, 643, 644 Bed nets, and malaria abatement, 604 Beer, 770–71 Bee venom, 468 Beijerinck, M., 140, A3 Benzoic acid, 322 Berg, Paul, A3 Bergey’s Manual of Determinative Bacteriology, 101, 102 Bergey’s Manual of Systematic Bacteriology, 101 Berkelic acid, 27 Berkeley Pit (Montana), 27, 34 Betadine, 316 Beta-lactamases, 336–37, 346

I-4

Index

Beta oxidation, 222, 223–24 Bifidobacterium, 351 Bile, 661 Binary fission, 189 Binomial system of nomenclature, 18 Bioaccumulation, 752 Biochemistry and biochemical tests, 41, 491, 496 Biodegradation, 764, 782. See also Bioremediation Bioelements, recycling of, 747–52 Bioengineering, 334 Biofilms, 14, 15f, 87, 88f, 187–88, 342, 766 Biofuels, 779–80 Biogenesis, 12–13 Biogeochemical cycles, 747–52 “Biohackers,” 285 Bioinformatics, 290 Biological vector, 381 Biomedicine. See Medical microbiology; Medicine Biomes, 743 Biopesticides, 783 Bioremediation, 7, 34, 284, 746, 758, 764. See also Biodegradation Biosafety, 370 Biosensor, 498 Biosynthesis, 199 pathways of metabolism, 223–25 prokaryotes, eukaryotes, and viruses compared, 120t Biotechnology, 7, 182, 763. See also Applied microbiology; Genetic engineering Bioterrorism, 527, 536, 600, 607, 650–51 Biotic factors, 743 Biotransformation, 780 Bird(s) B-cell maturation, 428–29 botulism, 574 Cryptococcus neoformans, 556 influenza, 636, 638 West Nile virus, 563 Bird embryos, 161, 496 Birdseed agar, 64t Bisphenols, 317 Bishop, J. Michael, A3 Bismuth subsalicylate, 671 1,3-Bisphosphoglyceric acid (BPG), 227 Bisulfite, 256t Black death. See Plague Black fly, 543 Bladder, 709, 715 Blastomyces dermatitidis, 649 Blastospores, 125f Blindness, 542 Blister formation, 514 Blood. See also ABO blood groups; Blood transfusions; Red blood cells; Septicemias; White blood cells bloodstream and lymphatic system, 404 origin, composition, and functions of, 405–409

portals of exit for infection, 379 signs of infection in, 378 Blood agar, 61–62, 64t Blood-brain barrier, 552 Blood cells, 405. See Red blood cells; White blood cells Blood pressure, 447, 589 Bloodstream, and systemic infections, 586 Blood transfusions, 379, 459, 471–73, 486, 568, 613, 673 Bloom, on grapes, 771 B lymphocytes. See B cells Body compartments, and host defenses, 402–409 Boiling water, 308 Bolivian hemorrhagic fever, 599 Bonds. See Chemical bonds Bone(s), and tuberculosis, 641 Bone marrow and bone marrow transplantation, 429, 479, 615 Bortedella pertussis, 634 Borrelia burgdorferi, 500, 593, 594. See also Lyme disease Botox, 576 Botulinum toxin, 574 Botulism, 550, 574–77, 650 Bovine growth hormone (BGH), 283t Bovine somatotropin (BST), 283t Bovine spongiform encephalopathy (BSE), 163–64, 568 Boyer, Herb, A3 Bradykinin, 412, 466 Bradyrhizobium, 748 Brain protozoa and infection of, 131t side effects of antimicrobial therapy, 352 Brain heart infusion broth, 61t Branching filaments, 100f Brandy, 772 Bread and breadmaking, 770 Brewer’s yeast, 6, 770 Bright-field microscopy, 72t Broad spectrum drugs, 330t, 336 Brock, Thomas, 182 Bronchial-associated lymphoid tissue (BALT), 405 Brucella spp., 599 B. abortus, 599 B. suis, 599 Brucellosis, 599–600, 602t Bubble boy mystery, 485 Bubo, 590 Bubonic plague, 590. See also Plague Budding, of viruses, 155 Bulbar poliomyelitis, 570 Bulk transport, 180t Bulla, 528 Bullous lesions, 522 Bunsen burner, 308 Bunyaviruses, 150t Burgdorfer, Willy, 593 Burkholderia, 764

Burkitt, Michael, 596 Burkitt’s lymphoma, 596, 609 Bursa of Fabricius, 408, 428 Bush, George W., 527 Calcium, 29t, 169t, 171 Calcium carbonate, 748 Calciviridae, 150t Calculus, 666–67 California, 384, 558, 600 California encephalitis, 563 Calor, 410 Calvin cycle, 227 Campylobacter spp., 675–76, 680t C. jejuni, 20, 675, 676 Campylobacteriosis, 675–76 Canada, 555, 752 Cancer. See also Cervical cancer DNA microarrays, 292 genetic medicine, 288 genome analysis, 289 Helicobacter pylori and stomach, 670 hepatitis C, 691 recombinant HGH, 283 retroviruses, 616 secondary autoimmune diseases, 485–86 T cells, 443 vaccines, 447 viruses, 141, 156–57 Candida albicans, 353, 649, 715–16 Candidiasis, 127t Canning, of foods, 306, 575, 576, 775 Capillaries, 586 Capnophiles, 185 Capsid, 143–46 Capsomers, 144 Capsule staining, 75–76 Car accidents, and toxoplasmosis, 566 Carbapenems, 336t, 339 Carbenicillin, 337t, 352t Carbohydrase, 203 Carbohydrate(s), 42–45, 224 Carbohydrate fermentation media, 64 Carbon atomic structure, 28f carbon fixation, 227 chemistry of, 40, 41f elements of life, 29t, 30 microbial nutrition, 169, 170 Carbon cycle, 747–48 Carbon dioxide, 37f, 185, 747–48 Carbonyl, 41f Carboxyl, 41f Carbuncle, 518 Cardinal temperature, 180, 181 Cardiolipin, 727 Cardiovascular syphilis, 725 Cardiovascular system. See also Heart and heart disease AIDS-defining illnesses, 609 infectious diseases, 587–616, 617t, 618f structure and defenses of, 585–87

Index

Carotenoids, 225 Carrier(s), of infectious disease, 380 Carrier-mediated active transport, 180t Carter, Jimmy, 543 Carter Center, 543 Cascade reaction, 418 Cat(s), 565, 600 Catabolism, 199, 211, 222–23 Catalase, 220, 721 Catalysts, 38, 199 Catalytic site, of enzyme, 201 Catarrhal stage, of pertussis, 634 Catheter, 492 Cathode rays, 310 Cation(s), 36 Cat-scratch disease (CSD), 600–601, 602t Cattle, 566, 599, 663, 750. See also Bovine spongiform encephalopathy Caudovirales, 149t Caulobacter, 758 Causative agent, of infection, 386–87 CD3 molecules, 429 CD4 cells, 429, 434, 442f CD8 cells, 429, 441, 442f Cefepime, 338f Cefotaxime, 355f, 555, 560 Cefotiam, 338f Ceftobiprole, 338 Ceftriaxone, 338, 541 Celera Genomics, 274 Cell(s). See also Cell membrane; Cell wall chemistry of, 52 energy in, 208–209 external structure, 111–14 internal structure, 94–98, 114–20 shapes, arrangements, and sizes, 98–101 structure of bacterial, 82f, 83 viruses and destruction of, 160t Cell culture, 161–62 Cell envelope, 89–98 Cell-mediated immunity (CMI), 408, 426, 440–41, 443 Cell-mediated reactions, 476–79 Cell membrane, 46–47, 82f, 93–94, 304, 332–33, 341–42. See also Cytoplasmic membrane Cellular organization, 10 Cellulase, 779t Cellulitis, 521–22 Cellulose, 43, 44f Cell wall, 82f algae, 113 antimicrobial drugs, 304, 331–32, 336–39 characteristics of prokaryotes and eukaryotes, 81 fungi, 113 osmosis, 177f structure of, 89–92 transport mechanisms for nutrient absorption, 175f Cell-wall-deficient bacteria, 92–93

Centers for Disease Control and Prevention (CDC) AIDS-defining illnesses, 609 anthrax, 341, 607 baby food and meningitis, 560 biosafety procedures, 369, 370 botulism, 550, 577 chlamydial infections, 723 data collection, 362, 388 drug-resistant strains of tuberculosis, 644 epidemiology, 388 food-borne diseases, 683, 774 Gonococcal Isolate Surveillance Project (GISP), 721 group B Streptococcus colonization, 734 HIV testing, 613 influenza epidemic of 1918, 163 measles and measles vaccine, 455 methicillin-resistant Staphylococcus aureus, 521 prions and sterilization procedures, 300 public health microbiology, 4t report on leading causes of death, 8 screening of refugees, 408 smallpox, 527 streptococcal infections, 15 West Nile virus, 563 Central Dogma of Biology, 15, 241 Central nervous system (CNS), 551, 552. See also Nervous system Centripetal lesions, 525 Cephalosporin(s) cell wall, 332, 336t designer drugs, 334 group A streptococci, 631 industrial products, 779t superinfections, 353 toxic reactions to, 352t, 357 Cephalosporinase, 346 Cephalothin, 338f Cercaria, 700, 701f Cerebral malaria, 603 Cerebrospinal fluid (CSF), 80, 105, 551–52 Cervical cancer, 447, 732, 733 Cervical carcinoma, 609 Cervical intraepithelial neoplasia (CIN), 733 Cervicitis, 722 Cervix, 710. See also Cervical cancer Cestodes, 133, 135t Chagas, Carlos, 132 Chagas disease, 132 Chain, Ernst, 329, A3 Chalazion, 541 Chancre, 724 Chancroid, 727, 730t Charon phage, 279 Cheese, 7, 773 Chemical agents, in microbial control, 313–22, 323t Chemical analysis, and diagnosis, 491–92

I-5

Chemical bonds, 31–41 Chemical composition, of media, 59t, 61 Chemical mediators, 410 Chemical mutagenic agents, 256 Chemical preservatives, for foods, 778 Chemiclave, 322 Chemiosmosis, 218–19 Chemistry atoms and elements, 28–31 bonds and bonding, 31–40 carbon and organic compounds, 40–41 cells, 52 macromolecules, 41–51 molecules, 31 Chemo-, 174t Chemoautotroph, 171t, 172 Chemoheterotroph, 171t Chemokine(s), 410, 412 Chemokine inhibitors, 411 Chemolithoautotrophs, 747 Chemostat, 193 Chemotactic factors, 410 Chemotaxis, 84, 85f, 413, 414–15 Chemotherapy. See Antimicrobial drugs Chemotrophs, 171 Chicken(s), 139 Chickenpox, 377, 522, 524–26, 529t Chikungunya, 598 Children. See also Infants aspirin and Reye’s syndrome, 527 cat-scratch disease, 600 dental caries, 664 diarrhea, 671 E. coli O157:H7, 674 enteroaggregative E. coli, 684 food-borne botulism, 575 gonorrhea, 720 impetigo, 521 otitis media, 627 pertussis, 634 recommended vaccinations, 453t respiratory syncytial virus, 635 roseola, 532 viral meningitis, 558 Chills, and fever, 417 China folk remedies, 329 immunization, 446 zoonoses, 382 Chlamydial infections, 720, 721–23 Chlamydia tranchomatis, 540, 541, 722 Chlamydomonas nivalis, 181f Chlamydophila pneumoniae, 587, 645 Chlamydospores, 125f Chloramines, 315, 316 Chloramphenicol, 304, 352t, 354t, 355f Chlorhexadine, 314t, 317 Chloride, 169t Chlorine, 29t, 30f, 34–35, 314t, 315–16 Chlorine dioxide, 302, 322 Chlorophyll, 128, 225 Chloroplasts, 119

I-6

Index

Chloroquinine, 332, 343, 352t, 605, 688 Chocolate agar, 62f Cholera, 677–78, 679. See also Vibrio cholerae Cholera toxin (CT), 678 Cholesterol, 47 CHONPS, 170 Chordata (Phylum), 20, 21f CHROMagar Orientation, 64f Chromatin, 114 Chromobacterium violaceum, 339 Chromosomes, 82f, 94–95, 114, 234. See also Bacterial chromosome Chronic carriers, 380f, 381, 687 Chronic diarrhea, 684–91 Chronic infections, 377 Chronic latent state, of infection, 156 Chronic otitis media, 627 Chronic pulmonary histoplasmosis, 650 -cidal agents, 301 Cidofovir, 530 Cigarette smoking, 447, 626 Ciguatera, 128 Cilia, 112–13, 129, 623f, 624 Ciliophora (Phylum), 21f, 131 Ciprofloxacin, 341, 536, 541, 607 Circinella, 126f Circulatory system, 403f, 404, 405 Citric acid, 214, 216, 779t Clarithromycin, 340, 671 Class, and classification, 20 Classical pathway, of complement, 418, 419, 420f Classification. See also Taxonomy of enzyme functions, 203 of fungus, 121 of helminths, 135 of microorganisms, 18, 20–24, 101–102 of protozoa, 130–31 of viruses, 149 Clavulanic acid, 337 “Clean catch,” and urine specimens, 492 Clindamycin, 340, 348, 717 Clinton, Bill, 724 Clonal deletion, 430 Clonal expansion, 426, 436 Clonal selection, 426, 429–30, 435f Clonal selection theory, 431f, 480 Clones and cloning, 278, 429 Cloning host, 278, 280 Clonorchis sinensis, 698–99 Clorox, 323t Clostridial septicemia, 523 Clostridium spp., 75, 96, 309 C. botulinum, 98, 160, 306, 550, 575. See also Botulism C. difficile, 354, 676–77, 680t C. perfringens, 66, 74, 98, 205–206, 524, 683, 684t. See also gas gangrene C. tetani, 98, 573–74, 575. See also Tetanus Clotting factor VIII, 283 Cloverleaf structure, of tRNA, 244 Coagulase, 374, 517

Coagulase-negative staphylococci (CNS) Coagulase test, 518 Cobalt, 29t Cocaine, 447 Coccidioides immitis, 557–58, 649 Coccidioidomycosis, 127t, 384, 557–58 Coccobacillus, 98 Coccus, 98, 100f Cockroach, 381 Codons, 243, 246t Coenzymes, 201, 202–203 Coevolution, 188, 364, 368 Cofactors, 201, 202–203 Cohen, Stanley, A3 Cohn, Ferdinand, 17 Cold. See also Common cold; Freezing; Refrigeration; Temperature extreme habitats, 173 microbial control, 309 Cold enrichment, 555–56 Cold sores, 728, 731 Cold sterilization, 310 Coliform(s), 767 Coliform enumeration, 767 Collagenase, 374 Collins, Francis, 274 Colloidal silver preparations, 321 Colony, 57 Colony-forming unit (CFU), 74, 192 Colostrum, 438 Comedo, 515 Commensalism, 187, 662 Common cold, 624–25 Common source, of infection, 390 Common vehicle, 383 Communicable disease, 382–83 Communities, and ecosystems, 744 Community-acquired MRSA, 512, 521, 543 Community-acquired pneumonia, 645 Community-acquired UTIs, 712 Competent cells, and DNA recombination, 262 Competitive inhibition, 206, 333 Complement antimicrobial proteins, 418 immunodeficiency diseases, 483t Complement cascade, 418–19 Complementary DNA (cDNA), 271, 292 Complementary fixation, 437f, 503–504 Complete blood count (CBC), 397, 408 Complexity, of eukaryotes, prokaryotes, and viruses, 120t Complex viruses, 145–46 Complex medium, 61 Composting, 754 Compound(s), 31 Computerized tomography (CT), 507 Concentration, of solution, 39 Concept mapping, A6-A8 Condoms. See Barriers and barrier protection Condylomata acuminata, 732

Confirmatory data, 494 Confocal microscope, 71, 73t Congenital rubella, 531–32 Congenital syphilis, 725 Conidia, 125 Conidiospores, 125 Conjugation, 86, 130, 259–61, 263 Conjunctiva, 539 Conjunctivitis, 540–41, 722 Consolidation, of pneumonia, 646 Consortium, 746 Constitutive enzymes, 204 Consumers, and ecosystems, 745 Contactants, and allergens, 463 Contact dermatitis, 476, 477f, 478 Contact lenses, 540–41 Contact transmission, of disease, 383 Contagious disease, 382 Contaminated culture, 66 Contaminated materials, and transmission of disease, 383–84 Continuous feed systems, of fermentation, 783 Contrast, of microscope image, 71 Control locus, 251 Convalescent carriers, 380–81 Convalescent period, of infection, 376 Convalescent phase, of pertussis, 634 Coombs, R., 461 Copper, 29t Cord factor, 642 Corepressor, 253 Cornea, 539 Coronavirus, 150t, 625 Corticosteroids, 783 Corynebacterium diphtheriae, 94, 96, 100, 160, 632. See also Diphtheria Cosmetic use, of botox, 576 Coulter counter, 194 Counterstain, 74 Covalent bonds, 32–34 Cowpox, 445, 446, 529–30 Coxiella burnetti, 600 Coyotes, and rabies, 569 Cranberry juice, 713 Credé, Carl Siegmund Franz, 320 Creolin, 317 Creutzfeldt-Jakob syndrome (CJS), 163, 283, 566–68 Crick, Francis, 235, 236, A3 Crime. See Forensics Cristae, 118 Crohn’s disease, 663, 684, 694 Crown gall disease, 284 Cruise ships, and gastroenteritis, 682, 685 Cryptococcal meningitis, 556–57 Cryptococcosis, 127t, 556–57 Cryptococcus spp., 76 C. neoformans, 174, 556–57, 559t, 649 Cryptosporidiosis, 131t, 297, 322, 678–80 Cryptosporidium spp., 129f , 131t, 316, 322, 678–80, 681t, 766

Index

C. parvum, 297 Crystallizable fragment, 436 Crystal violet, 75f, 90, 322 Cultures and culturing methods anaerobes, 184f animal viruses, 160–62 fungi, 126 overview of laboratory techniques, 57–66 phenotypic methods of diagnosis, 495–97, 508f protozoa, 131 Staphylococcus aureus, 517–18 Curd, 773 Cutaneous anaphylaxis, 468 Cutaneous anthrax, 535t, 606 Cutaneous leishmaniasis, 535–36 Cutaneous mycosis, 536. See also Ringworm Cutaneous T-cell lymphoma, 616 Cutting boards, for food preparation, 776 Cyanide, 220 Cyanobacteria, 227, 756 Cycloserine, 332 Cyclospora cayetanensis, 131t, 685, 688t Cyclosporiasis, 131t Cyst, 515, 528 Cysteine, 48f Cystic acne, 515 Cysticerci, 695 Cystitis, 712 Cytoadherence, 603 Cytochrome oxidase, 721 Cytokine(s), 410, 412, 465–66, 481 Cytokine storm, 637 Cytololysin, 503 Cytomegalovirus, 156f, 288 Cytopathic effects (CPEs),156, 162 Cytoplasm, 82f, 94–96, 169–70 Cytoplasmic membrane, 93, 113–14 Cytosine (C), 50, 235 Cytoskeleton, 96, 119–20 Cytotoxic T cells, 426, 441, 443 Dairy products, 772–73. See also Cheese; Milk Dalton (Da), 31 Daptomycin, 342 Dark-field microscope, 72t Darwin, Charles, 21, 22, 188 Daschle, Tom, 302 Dawn antibacterial hand soap, 323t DDT, 605 Dead Sea, 178 Deamination, 222–23, 224 Death, infectious disease as cause of, 8t. See also Microbial death; Mortality rates; Thermal death point; Thermal death time Death phase, of growth curve, 192 Decarboxylases, 205 Decomposers, 745–46

Decomposition, 6 Decomposition reactions, 38 Decongestants, 625 Decontamination, 298, 301, 312 Deductive reasoning, 16 Deep subsurface microbiology, 755 Deer, and Lyme disease, 595 DEET, 595 Defense mechanisms. See Host defenses Definitive host, 134, 692 Degermation, 301 Degranulation, of mast cells and basophils, 464 Dehydration synthesis, 43, 204 Dehydroemetine, 688 Dehydrogenases, 203 Delavirdine, 345t Delayed-type hypersensitivity, 476 Delta agent, 164 Denaturation of DNA, 276, 278 of enzyme, 206 of protein, 49, 304 Dendritic cells, 409, 434 Dengue fever, 597–98, 605 Denitrification, 220, 749 Dental caries, 664–66 Dental plaque. See Teeth Dentistry, and Universal Precautions, 386 Deoxyribonuclease, 203 Deoxyribose sugar, 235 Department of Defense, 163 Dermatology, 528 Dermatomes, 526 Dermatophagoides, 463f Dermatophytes, 536, 538 Dermatophytosis, 127t Dermis, 514 Desensitization, to allergens, 469 Desiccation food preservation, 778 microbial control, 309 Designer drugs, 334 Desquamated cells, 399 Desquamation, 522, 709 Desulforudis audaxviator, 744 Desulfovibrio, 751 Desulfuromonas, 751 Detergents, 318–19 Developing countries, and tuberculosis, 642. See also Africa; Emerging diseases; Globalization Dextran, 779t d’Herelle, Felix, 157 Dhurnadha, Nikhil, 164 Diabetes, 9, 287, 480t, 482 Diagnosis. See also Identification; specific diseases of AIDS, 614 of allergy, 468 genotypic methods, 491, 497–98 helminthic infections, 692

I-7

immunologic methods, 491–92, 499–507 phenotypic methods, 491 specimen collection, 492–95 of viral infections, 507, 508f Dial antibacterial hand soap, 323t Diapedesis, 413 Diarrhea and diarrheal diseases, 352, 671–91 Diatom(s), 127f Diatomic elements, 34 Dichotomous keys, 496 Dicloxacillin, 337t Didanosine (ddl), 345t, 614 Dideoxynucleotide (dd), 276 Differential interference contract (DIC) microscope, 72t Differential media, 62, 63–64, 74 Differential stains, 74–76 Differentiation, of stem cells, 406 Diffusion, 175–76, 180t DiGeorge syndrome, 404, 484 Digestive tract, 661 Dihydroxyacetone phosphate (DHAP), 227 Dimer, 438 Dimorphic fungi, 122 Dinoflagellates, 757f, 758 Diphtheria, 160, 632–33. See also Corynebacterium diphtheriae Diphyllobothrium latum, 135t, 695–96 Dipicolinic acid, 97 Diplodia maydis, 121f Diploid chromosome, 234 Direct antigen testing, 495, 504 Direct cell count, of bacteria, 193–94 Direct ELISA, 507 Direct fluorescent antibody (DFA) tests, 495 Directly observed therapy (DOT), 644 Disaccharides, 42, 43f Disc diffusion tests, 355f Discharge diseases, of reproductive tract, 715, 718–23 Disease(s). See also Diagnosis; Infection(s) acquisition and transmission of, 382–84 archaea, 105 biofilms, 14, 15f causes of, 373–75 enzymes, 205–206 epidemiology, 388–92 eye, 539–43, 544t, 545f gastrointestinal tract, 664–701, 703f, 704t human condition, 8–9 human hosts for, 363–66 inflammation, 411 lysogeny, 160 nervous system, 552–78, 579t, 580f nosocomial infections, 384–85 parasitic, 692–701 persistence of, 379–82 process of, 375–77 reproductive tract, 715–34, 735t, 736f, 737f

I-8

Index

Disease(s) (continued) respiratory tract, 624–54, 655t, 656f signs and symptoms, 378 skin, 515–38, 544t, 545f urinary tract, 712–15, 735t, 736f, 737f Disinfection, 298, 300, 308. See also Antisepsis and antiseptics; Asepsis and aseptic techniques Disposal, of cultures, 66 Distilled liquors, 772 Division, and classification, 20 DIYers, 285 DNA (deoxyribonucleic acid). See also Genetics; Nucleic acids; Recombinant DNA technology analysis using genetic probes, 497–98 antibacterial drugs, 341 genetic analysis, 268, 292 genetic engineering, 270–78 genetic medicine, 288–89 macromolecules, 42t prokaryotes and eukaryotes compared, 81 recombination events, 259–64 replication, 238–40 structure and function of, 49–51, 235, 237–38 transcription and translation, 240–51 viruses, 147–48 DNA fingerprinting, 164, 683 DNA microarray analysis, 292, 293f DNA polymerases, 203, 238t, 239, 240, 276 DNA profiles, 290–92 DNase, 342 DNA vaccines, 450 DNA viruses, 147–48, 150–51t Dogs, 532, 594 Dolly (sheep), 279 Dolor, 410 Dolphins, 752 Domagk, Gerhard, 329, A3 Domain, and classification, 20 , 23 Domoic acid, 108 Double helix, of DNA, 50, 51f, 237f Doubling time, and population growth, 189–90 Downstream processing, 781 Doxycycline, 341, 536, 596, 600, 602, 607, 714 Dracunculus medinensis, 135t Droplet contact, 383, 384, 625, 634, 635, 642 Drug abuse, 369, 447 Drug allergy, 467 Drug resistance. See also Antibiotics E. coli, 713 gonorrhea, 721 impact of on antimicrobial therapy, 344, 346–50 infectious diseases, 232, 264 rise of, 346, 348–49 skin bacteria, 516

Dry habitats, 173, 185 Dry heat, 306, 308–309 Drying, of foods, 778 Dry oven, 308–309 dsDNA, 242 DTaP vaccine, 454, 632, 634 Dual lymphocyte system, 426 Dumb form, of rabies, 568 Duodenum, 661 Dust mites, 462, 463t Dwarfism, 282 Dyes culture media, 63, 64 microbial control, 314t, 322 rRNA analysis, 498 Dysentery, 673, 686. See also Amoebiasis; Shigella dysenteriae Dysplasia, 733 Dyspnea, 635 Dysuria, 712 Ear infection, 627, 628t Earth’s crust, and extreme habitats, 173 Earthquakes, and coccioidomycosis, 384, 558 Eastern equine encephalitis (EEE), 563 Ebola virus, 143f, 351, 598–99 Echinocandins, 343 Ecology associations among microbes, 185–88 basic principles, 742–43 structure of ecosystems, 743–46 Economics, and infectious disease, 8, 9 EcoRI, 271 Ecosystems, 743–46 Ectopic pregnancy, 720 Ectoplasm, 128 Eczema, 467 Edelman, Gerald, A3 Edema, 378, 410, 413 Edema factor, 606 Education, and genetic engineering, 284–85 Efavirenz, 345t Effusion, and otitis media, 627 Eflornithine, 578 Egg hatching test, 701 Egypt, ancient, 7, 299, 474, 640 Ehrlich, Paul, 329, 727, A3 Ehrlichia chaffeensis, 601 Elderly. See also Age; Aging E. coli O157:H7, 674 pneumonia, 646, 647 Electrolytes, 36 Electromagnetic radiation, 185 Electron(s), 28, 30–31 Electron carriers, 209–10 Electronegativity, 34 Electron microscopy, 143, 508f Electron transport system (ETS), 217–19 Elements, 28–29, 32, 169t. See also Bioelements

Elephants, 512, 521, 543 Elongation, and DNA replication, 240, 247, 249 El Salvador, and histoplasmosis, 622, 648, 654 Embryos. See Bird embryos Emerging diseases, 8, 9, 653 Emetic disease, 682–83 -Emia (suffix), 375, 587 Encephalitis, 375, 561, 562–68, 728 Encephalopathy, 525 Endemic disease, 390, 391f Endemic reservoirs, 592 Endergonic reaction, 208 Endocarditis, 588–89 Endocardium, 586 Endocrine glands, 481–82 Endocytosis, 152, 154f, 179f, 180 Endoenzymes, 204 Endogenous pyrogens, 416 Endogenous retroviruses (ERVs), 364 Endonucleases, 271 Endoplasm, 128 Endoplasmic reticulum (ER), 116, 117 Endoscopy, 671 Endospore(s), 82f, 96–98, 299–300, 306, 309 Endospore stain, 75 Endosymbiosis, 110 Endotoxic shock, 589 Endotoxins, 93, 374, 375, 416, 634 Energy autotrophs, 172 heterotrophs, 172, 174 metabolic processes, 208–23 nutritional flow in ecosystems, 744–46 photosynthesis, 225–28 Energy cascade, 217–18 Energy pyramid, 744 Enfavirenz, 615 Enfuvirtide, 345t, 615 Enriched medium, 61, 62f Enrofloxacin, 355f Entamoeba(s), 132 Entamoeba histolytica, 130, 131, 132, 686–88. See also Amoebas; Amoebiasis Entecavir, 690 Enteroaggregative E. coli (EAEC), 675, 684–85, 688t Enterobacter sakazakii, 560 Enterobacteriaceae, 221 Enterobiasis, 134 Enterobius vermicularis, 134, 135t, 695, 696t Enterococcus faecalis, 181 Enterococcus faecalis broth media, 63t Enterohemorrhagic E. coli (EHEC), 674–75 Enteroinvasive E. coli (EIEC), 675 Enteropathogenic E. coli (EPEC), 675 Enterotoxigenic E. coli (ETEC), 675 Enterotoxin, 673 Enumeration, of bacteria, 193–94 Enumeration media, 65

Index

Enveloped viruses, 144f, 145f, 146–47 Environment. See also Ecology; Environmental microbiology; Pollution fungi, 126 infectious diseases and destruction of, 382 microbial adaptations to, 180–88 sensitivity of enzymes to, 206 Environmental germicides, 313 Environmental microbiology, 5t aquatic microbiology, 755–58 deep surface microbiology, 755 environmental sampling, 753 natural recycling of bioelements, 747–52 principles of ecology, 742–46 soil microbiology, 753–55 Environmental Protection Agency (EPA), 284, 766, 767 Environmental sampling, 753 Enzyme(s), 199 active or catalytic site, 201 as biochemical levers, 201 characteristics of, 200 classification of functions, 203 cofactors, 202–203 genetic engineering, 270–71 industrial microbiology, 779t, 783 location and regularity of action, 204– 205 macromolecules, 49 mechanisms of action, 199–200 metabolic pathways and regulation of, 206–208 recombinant DNA technology, 283t repression of, 208 role in disease, 205–206 structure of, 201 substrate interactions, 202 unconventional forms of, 202 Enzyme induction, 207–208 Enzyme-linked immunosorbent assay (ELISA), 506–507, 508f Eosinophils, 397, 408, 414, 692 Epicardium, 586 Epidemic(s), 390, 391f, 392 AIDS, 612 cholera, 678 cryptosporidiosis, 680 dengue fever, 598 diphtheria, 632 plague, 591 Epidemiology, 4t, 388–92. See also Centers for Disease Control and Prevention; Public health; specific diseases Epidermis, 513–14 Epidermophyton, 537, 538 Epididymitis, 669, 709, 722 Epilimnion, 757, 758 Epinephrine, 469 Epithelial cells, 709

Epitope, 433 Epstein, Michael, 596 Epstein-Barr virus (EBV), 596–97 Epulopiscium fishelsoni, 99 Ergosterol, 348 Erysipelas, 518 Erythema infectiosum, 532 Erythema migrans, 593 Erythrocytes, 409 Erythrocytic phase, of malaria, 603 Erythrogenic toxin, 630 Erythromycin, 340, 348, 354t, 541, 556, 634 Erythropoietin (EPO), 283t Eschar, 536 Escherichia coli adhesive properties, 372t anaerobic respiration, 220 bacteriophages, 158–59 cell composition, 169, 170t cloning hosts, 280 culturing and media, 64, 65f enzyme induction, 207–208 f factor, 260 fimbriae, 86 genetics, 147, 235 meningitis, 560 normal microbiota, 188, 353, 663 urinary tract infections, 712, 713 Escherichia coli O157:H7, 9, 560, 672, 674–75, 680t, 683 Escherichi hermannii, 355f Essential nutrients, 169, 170–74 Ester(s), 41f Estrogen, 516, 710, 712 E-test, 355f Ethanol, 779t Ethics, and genetic engineering, 284–85 Ethidium bromide, 256t Ethyl alcohol, 315t, 317 Ethylene oxide (ETO), 299t, 314t, 315t, 321–22, 778 Etiology, of infectious diseases, 386–87. See also specific diseases Euglena mutabilis, 185 Eukarya (Domain), 23 Eukaryotes (Eurkaryotic), 3 bacteria and archaea compared to, 104t cell structure, 10, 111–20 characteristics of, 52 DNA transcription and translation, 249–50 evolution and history of, 109–11 prokaryotes compared to, 81, 104t, 120t taxonomy of, 121 Eutrophication, 758 Evolution, 3. See also Coevolution; Natural selection allergies, 466 eukaryotes, 109, 110 prokaryotes, 81 taxonomy and classification, 20–21

I-9

viruses, 141, 142 Ewald, Paul, 492 Exanthems, 530 Exchange reactions, 38 Excision repair, 257 Exergonic reaction, 208 Exfoliative toxins, 522, 523f Exocystosis, 155 Exoenzymes, 204, 373–75 Exogenous infections, 369 Exogenous pyrogens, 416 Exons, 250 Exotoxins, 374–75, 606, 632, 682–83 Exponent(s), A1-A2 Exponential growth, 190, 191 Extensively drug-resistant tuberculosis (XDR-TB), 644 Extracellular fluid (ECF), 402 Extracellular sources, of carbon, 170 Extracellular toxins, 630 Extrapulmonary tuberculosis, 641 Extreme habitats, 173 Extremozymes, 182 Exudate, 410, 413 Exxon Valdez (oil spill, 1989), 741, 744, 758 Eye and eye infections, 369, 539–43, 544t, 545f Facilitated diffusion, 178, 180t Factor VIII and IX, 283t Facultative aerobe, 183 Facultative coliforms, 767 Facultative bacteria, 102 Facultative halophiles, 185 Facultative parasites, 174 Facultative psychrophiles, 181 Falciparum malaria, 603 Fallopian tubes, 710 Familial CJD, 568 Famiciclovir, 344 Family, and classification, 20 Fasciola hepatica, 699 Fastidious bacteria, 61 Fatty acids, 45–46 Fc fragment, 438 Fecal coliforms, 767 Feces, and portals of exit for infection, 379 Female reproductive system, 710, 711f Fermentation, 220–23, 763, 769–72, 781, 783 Fermentors, 781, 783 Fertility (F factor), 259 Fever, 416–18, 589 Fever blisters, 728 Fevers of unknown origin (FUO), 416 Field, of microscope, 71 Fifth disease, 532, 533t Filament, 83–84 Filamentous hemagglutinin (FHA), 634 Filoviridae, 150t Filterable virus, 140 Filtration, and decontamination, 312

I-10

Index

Fimbria, 82f, 85–86, 720 Fire, Andrew, 242 Firmicutes, 102, 365 Fish, 128, 695–96, 699, 752, 757f. See also Shellfish Fixed, stained smears, 71, 74 Flagella (flagellum), 82f, 83–85, 112, 129 Flagellar stain, 75f, 76 Flagyl, 688 Flatworms, 133, 135t Flavin adenine dinucleotide (FAD), 205 Flaviviridae, 150t Fleas, 591, 594 Fleming, Sir Alexander, 329, A3 Flesh-eating disease, 519 Floppy baby syndrome, 575 Florey, Howard, 329, A3 Florida, 459, 471 Flow cytometer, 194 Fluconazole, 357, 557 Flucytosine, 343, 349, 352t Fluid mosaic model, of cell membrane, 46 Flukes. See Liver flukes FluMist, 639 Fluorapatite, 751 Fluorescence microscope, 71, 72t Fluorescent antibodies (FABs), 504 Fluorescent in situ hybridization (FISH), 272, 274, 498 Fluorescent staining, 508f, 641f, 643 Fluoride, 666 Fluoroquinolones, 341 Focal infection, 376, 377f Folic acid synthesis, 333, 335, 341 Folk medicines, 329 Folliculitis, 518 Fomites, 383 Fonseca pedrosoi, 123f Food(s). See also Dairy products; Foodborne diseases; Food chain; Food poisoning; Food web additives, 779t allergy, 467 applied microbiology, 769–78 canning of, 306 microorganisms as, 774 prebiotics and probiotics, 351 transmission of disease, 384 Food-borne diseases, 55, 66. See also Food poisoning acute diarrhea, 671 botulism, 574–75 brucellosis, 599 E. coli O157:H7, 674–75 hepatitis, 689 listeriosis, 555, 556 microbial involvement in, 774 salmonellosis, 673 toxoplasmosis, 566 trichinosis, 699 Yersinia spp., 676 Food chain, 744, 745f

Food and Drug Administration (FDA), 183, 313, 340, 560, 774, 775, 776, 778 Food poisoning, 128, 682–83, 774–78. See also Food-borne diseases; Salmonellosis Food web, 746f Forbidden clones, 480 Forensics, and DNA profiles, 290. See also DNA fingerprinting Formaldehyde, 314t, 321 Formalin, 321 Formula weight, 31 Formyl methionine, 247 Fosfomycin trimethamine, 339 Fossil record, 2–3 Fossil fuels, 748, 750 Fox, George, 23 Foxes, and rabies, 569 Fracastorius, Girolamo, 724, A3 Frameshift, 257 Francisella tularensis, 592–93. See also Tularemia Franklin, Rosalind, 236, A3 Free energy, 170 French and Indian Wars (1754–1767), 527 Freezing of foods, 777 microbial control, 309 French and Indian Wars (1754–1767) Frosch, Paul, 140 Frostban, 284 Fructans, 664 Fructose, 42, 43f F spikes, 669 FTA-ABS (Fluorescent Treponemal Antibody Absorbance) test, 727 Fumaric acid, 216 Fumigation, 302 Functional groups, of organic compounds, 40, 41t Functional types, of culture media, 59t Fungemia, 375, 587 Fungicide, 300 Fungistatic chemicals, 301 Fungus (fungi) antifungal drugs, 342–43 characteristics of, 121–22, 124 cell wall, 113 culture and identification, 126 drug resistance, 348, 349 human infections, 127t lung diseases, 649 microbial control, 309 nutrition, 122 organization of microscopic, 122–23 reproduction and spore formation, 125–26 roles in nature and industry, 126 sinusitis, 626 Furuncle, 518 Fusarium spp., 124 F. graminearum, 774

Fusobacterium spp., 668 F. necrophorum, 628–29 Fuzeon, 344 Galactose, 43, 44f Galen, Claudius, 719 Gallo, Robert, A3 GALT (gut-associated lymphoid tissue), 402, 405 Gamma rays, 310 Gardasil, 732 Gardnerella, 716 Gas(es). See also Ethylene dioxide; Methane; Nitrous oxide microbial control, 299t, 321–22 requirements for microbial growth, 183–85 Gas gangrene, 523–24 Gastric acid inhibitors, 676 Gastric ulcers, 8, 670–71 Gastritis, 670–71 Gastroenteritis, 660, 682 Gastrointestinal tract AIDS-defining illnesses, 609 diseases caused by helminths, 692–701 infectious diseases, 664–91, 703f, 704t normal microbiota, 364t, 365t, 663 portals of entry for infection, 369 structure and defenses of, 661–62 Gates Foundation, 570, 697 Gelatin media, 60f Gel electrophoresis, 271, 272f, 276 Gelidium, 60 Gell, P., 461 Gender, and autoimmune disease, 480. See also Female reproductive system; Male reproductive system Gene, 234 Gene cloning, 278–80 Gene expression, 87, 244–46 Gene probes, 271–74, 497–98 Generalized transduction, 262 General-purpose media, 61, 62f Generation time, and population growth, 189–90 Gene silencing, 288–89 Gene therapy, 287–88 Genetic(s). See also DNA; Genetic engineering; Genome; RNA of animal viruses, 251 autoimmune disease, 480 B cell deficiencies, 484 drug resistance, 346 host defenses, 400 immunoglobulins, 430f influenza virus, 636 introduction to, 233 major histocompatibility complex, 428 meningitis, 553 mutations, 255–58 nature of material, 234–35

Index

organ transplantation and graft rejection, 477 prokaryotes, eukaryotes, and viruses compared, 120t regulation of protein synthesis, 251–55 susceptibility of allergies, 462 susceptibility to disease, 369 Genetically modified organisms (GMOs), 7, 283–87 Genetic analysis, 268, 508f Genetic code, 274–76 Genetic engineering, 7. See also Biotechnology; Recombinant DNA technology basic elements and applications, 269 genetically modified organisms, 283–87 genetic treatments, 287–89 tools and techniques, 270–78 vaccines, 450 Genital herpes, 727–31 Genital tuberculosis, 641 Genital ulcer diseases, 723–31 Genitourinary tract. See also Reproductive tract; Urinary tract; Urogenital tract AIDS-defining illnesses, 609 barriers as host defenses, 400 normal microbiota, 364t, 365t, 711–12 structure and defenses of, 709–10 Genome, 147, 234, 235 Genome analysis, 289–92 Genomic(s), 290 Genomic libraries, 279 Genotype, 235 Genotypic methods, of diagnosis, 491 Gentamicin, 354t, 355f, 541, 588, 600 Genus, and classification, 20 Geobacter, 764 Geomicrobiology, 5t, 747 Geothermal radiation, 228 Geotrichum candidum, 649 Germ-free animals, 368 Germicidal lamps, 311 Germicide, 300 Germination, of endospores, 98 Germ theory of disease, 17 Giardia lamblia, 20, 130, 131t, 372t, 685–86, 688t Giardiasis, 131t, 685–86 Gingivitis, 666 Girard, Alfred, 20 Globalization, drug resistance, 349, 357. See also Immigration; Travel Global Malaria Action Plan, 604 Global warming, 750 Glomerulonephritis, 629–31 Glucans, 664 Gluconeogenesis, 223 Glucose aerobic respiration, 172, 212 glycosidic bonds, 43, 44f space-filling model of, 37f Glutaraldehyde, 299t, 314, 321

Glycan chains, 89, 91f Glyceraldehyde–3-phosphate (PGAL), 223, 227 Glycerol, 45, 779t Glycocalyx, 44, 82f, 86, 88, 113 Glycogen, 44, 432–33 Glycolysis, 211, 212–14 Glycoproteins, 636, 637 Glycosidic bonds, 42–43, 44f Glycosyl-phosphatidyl inositol (GPI), 604 Glycylcyclines, 340 Golgi, C., 116 Golgi apparatus, 116–18 Gonococcal Isolate Surveillance Project (GISP), 721 Gonorrhea, 719–21, 723t. See also Neisseria gonorrhoeae Google, and Flu Trends, 362, 388, 392 Government. See also Centers for Disease Control and Prevention; Department of Defense; Environmental Protection Agency; Food and Drug Administration; U. S. Department of Agriculture; U. S. Public Health Service decontamination of congressional office building, 302 hospitals and nosocomial infections, 385 Gracilicutes, 102 Graft rejection, 477 Graft versus host disease (GVHD), 478 Gram, Hans Christian, 74, 89, 90, A3 Gram-negative bacteria cell envelope, 89 cell wall, 92 gram staining, 74, 90 medically important, 103t outer membrane, 93 Gram-positive bacteria cell envelope, 89 cell wall, 91–92 gram staining, 74, 90 medically important, 103t Gram’s iodine, 90 Gram staining, 74, 75f, 89, 90 Grana, 119 Granules, 82f Granulocyte(s), 406, 408 Granulocyte colony-stimulating factor (GCSF), 283t, 412 Granulocyte-macrophage-colonystimulating factor (GM-CSF), 283t Granulomas, 378, 411 Granulomatous amoebic meningoencephalitis (GAM), 561 Granzymes, 441 Grapes, 772 Grassi, G., A3 Graves’ disease, 480t, 481–82 Gravity, 31 Grays, of radiation, 310 Great Britain, 568, 584, 607

I-11

Great Salt Lake (Utah), 178 Greece, ancient, 299 Greenhouse effect and greenhouse gases, 750 Green sulfur bacteria, 228, 756 Griffith, Frederick, 261, A3 Griseofulvin, 343, 538 Ground itch, 697 Group B streptococcus “colonization” neonatal disease, 733–34 Group translocation, 178, 179f, 180t Growth, study of microbial, 189–94 Growth curve, 191–93 Growth factors, 61, 171 Guanine (G), 50, 235 Guanosine triphosphate (GTP), 51 Guillain-Barré syndrome, 572, 638, 676 Guinea worm, 135t Gulf of Mexico (oil spill, 2010), 758 Gummas, 725 Gut-associated lymphoid tissue (GALT), 661 Gut microflora, 400 Gymnodinium, 757f HAART (highly active anti-retroviral therapy), 615, 684 Habitats. See also Osmotic pressure; pH; Temperature ecosystems, 744 extreme, 173 protozoa, 128–29 HacIII endonuclease, 271 Haeckel, Ernst, 22 Haemophilus ducreyi, 727 Haemophilus influenzae, 88, 540, 555, 559t, 627, 645 Hair follicles, 399, 514 Hairpin loops, of tRNA, 244 Halo-, 174t Halobacteria, 178 Halogens, 315 Halophiles, 104, 185 Hand, and ringworm, 537 Hand scrubbing, 313, 319, 320f, 386 Hanging drop preparation, 71 Hansen’s disease (leprosy), 75 Hantavirus, 645, 648, 653t Haploid chromosome, 234 Haptens, 433 Hart Senate Office Building (Washington DC), 301, 302 Havrix, 699 Hawaii, 762, 769, 783. See also University of Hawaii Hay fever, 466 Hazard Analysis and Critical Control Point (HACCP), 774 Health care personnel. See also Hospitals; Medicine brucellosis, 599 Creutzfeldt-Jakob disease, 568

I-12

Index

Health care personnel (continued) hepatitis, 690 HIV transmission, 613 symptoms of smallpox, 528 Universal Precautions, 386 Heart and heart disease, 352, 585–86. See also Cardiovascular system Heat. See also Temperature extreme habitats, 173 microbial control, 299t, 305–309 Heat resistance, of spores, 96–97 Heavy metal compounds, and microbial control, 320–21. See also Mercury Hektoen enteric (HE) agar, 64t Helical capsids, 144, 145f Helicases, 238t, 239 Helicobacter spp., 8 H. pylori, 670, 676 Helium, 30 Helminths, 133–35, 343, 692–701 Helper T cells, 426 Hemagglutinin (H), 636 Hematopoiesis, 405–406 Hematuria, 712 Hemodialysis, 504, 507 Hemoglobins, 419 Hemolysins, 374 Hemolysis, 471, 472 Hemolytic disease of the newborn (HDN), 473–74 Hemolytic transfusion reactions, 459, 486 Hemolytic uremic syndrome (HUS), 674 Hemophilia, 283, 288, 613, 691 Hemorrhagic fevers, 345t, 597–99, 650 Hepadnaviridae, 150t Hepatitis, 389f, 688–91 Hepatitis A virus (HAV), 376, 688–89, 691t Hepatitis B immune globulin (HBIG), 690 Hepatitis B virus (HBV), 689–90 Hepatitis C virus (HCV), 490, 504, 690–91 Hepatitis D virus (HDV), 690 Hepatitis E virus (HEV), 689, 691t Hepatocellular carcinoma, 689 Herd immunity, 451, 452, 455, 670 Heredity, 233 Hermaphroditism, 134 Herpes simplex viruses (HSVs), 146f, 156, 542, 564, 727 Herpesviruses, 147f, 150t, 345t, 532–33. See also Human herpesvirus–3; Human herpesviruses–6 and –7 Herpes zoster virus, 156, 526 Hetero-, 174t Heterolactic fermentation, 221 Heterophile antibodies, 597 Heterotroph(s), 122, 170, 171t, 172, 174 Hexachlorophene, 317 Hexoses, 42, 43f Hierarchy, and classification, 20 High-efficiency particulate air (HEPA) filters, 312 High-frequency recombination (Hfr), 260

High-level germicides, 314–15 High-performance liquid chromatography (HPLC), 643 High-temperature short-time (HTST) pasteurization, 776 HindIII endonuclease, 271 Hippocrates, 417, 668 Histamine, 412, 466 Histiocytes, 414 Histone, 114 Histoplasma capsulatum, 645, 648, 649, 650–51, 653t Histoplasmosis, 127t, 648, 650–51, 654 History antimicrobial therapy, 328, 329 beer-making, 770 diphtheria, 632 epidemiology, 388 fever, 417 gonorrhea, 719 immunization, 446, 529–30 influenza, 638 malaria, 602 microbial control, 299 microbiology, 11–18 mumps, 668 plague, 590 smallpox, 527, 529–30 syphilis, 724 tuberculosis, 640 HIV. See Human immunodeficiency virus HKO antigens, 672 HN spikes, 669 Hodgkin’s lymphoma, 596 Hoffman, E., A3 Holmes, Oliver Wendell, 17 Holoenzyme, 201 Holophrya, 113f Hominoidea (Family), 20, 21f Homo sapiens, 20, 21f H1N1 influenza, 637, 638, 639 Hong Kong flu pandemic, 638 Hooke, Robert, 12, A3 Hookworms, 697 Hops, 770 Hordeolum, 541 Horizontal gene transfer, 259–64 Horizontal transmission, of infectious disease, 382 Hormones, and recombinant DNA technology, 283t. See also Estrogen Horses, 445, 446, 447, 476, 633 Hospital(s). See also Health care personnel; Medicine; Nosocomial infections blood transfusions, 486 Clostridium difficile diarrhea, 676 drug resistance, 348 fungal infections, 649 Hospital-acquired MRSA, 512 Host defenses bacterial toxins, 375 barriers as first line of, 398–400

B-cell response, 435–40 definitions of terms, 398 factors weakening, 367t lymphocyte development, 428–30 overview of second and third lines of, 401 second line of defense, 410–16 skin, 513–14 specific immunity as third line of, 425–27 specific immunity and vaccination, 443–52 steps in progress of infection, 377f summary of major components, 399f systems involved in immune defenses, 402–409 T-cell response, 440–43 Host range, of viruses, 151 Hot-air oven, 308 Houseflies, 381 HpSA (H. pylori stool antigen test), 671 Huber, Robert, A3 Human(s). See also Adults; Children; Elderly; Infants genome mapping, 290, 292 as hosts for disease, 363–66 infectious diseases and condition of, 8–9 interrelationships with microbes, 188 number of genes, 147 taxonomy, 20, 21f use of microorganisms, 6–7 Human diploid cell vaccine (HDCV), 569 Human Genome Project, 242, 274 Human granulocytic ehrlichiosis (HE), 601 Human growth hormone (HGH), 282, 283 Human herpesvirus–3, 526 Human herpesviruses–6 and –7 (HHVs), 532–33 Human immunodeficiency virus (HIV). See also Acquired immunodeficiency syndrome adhesive properties, 372t antiviral drugs, 344, 345t maturation and release of cells, 155f pathogenesis and virulence factors, 610–11 plasma-derived factor VIII and transmission of, 283 transmission of, 611–12 Human Microbiome Project, 363, 492, 514 Human monocytic erhlichiosis (HME), 601 Human papillomavirus (HPV), 389f, 447, 534, 731–32 Human rabies immune globulin (HRIG), 569 Human T cell leukemia viruses (HTLVs), 157, 364, 610 Humus, 754 Hurricane Katrina (2005), 660, 682, 701 Hutchinson’s teeth, 725 Hyaluronidase, 374, 779t Hybridization, and DNA analysis, 271–74, 497–98

Index

Hybridoma, 444 Hydra, 327 Hydramacin, 327, 330 Hydrated ions, 38 Hydrogen atomic structure, 28f covalent bonding, 33f elements of life, 29t, 30f microbial nutrition, 169t, 170 Hydrogen bonds, 33f, 36–37, 170 Hydrogen peroxide, 183, 314, 315t, 317–18 Hydrogen sulfide, 750 Hydrolases, 203 Hydrologic cycle, 755 Hydrolysis reactions, 45, 204, 205f Hydrophilic ions, 38 Hydrophobia, 568 Hydrophobic ions, 38 Hydrosphere, 743 Hydrothermal vents, 173, 186, 228, 756 Hydroxyl, 41f Hygiene hypothesis, for allergies, 462 Hymenolepis diminuta, 696 Hymenolepis nana, 696 Hymenostomatida (Order), 21f Hymenostomea (Class), 21f Hyperbaric oxygen therapy, 524 Hypersensitivities, and allergy, 461t, 470–79 Hyperthermophiles, 105 Hypertonic conditions, 176, 177 Hypervariable regions, 437 Hyphae, 121 Hyphomicrobium, 758 Hypochlorites, 315, 316 Hypochlorous cid (HOCI), 315 Hypogammaglobulinemia, 484 Hypolimnion, 757 Hyposensitization, to allergens, 469 Hypothalamus, 416 Hypothesis, and scientific method, 15 Hypotonic conditions, 176, 177 -Iasis (suffix), 375 Iceberg effect, in epidemiology, 390–91 Icosahedral viruses, 144–45, 146f Identification, of microorganisms, 18. See also Diagnosis animal viruses, 160–62 fungi, 126 helminths, 135 overview of laboratory techniques, 56f, 65–66 protozoa, 131 selection of antimicrobial drugs, 354 IgA, 438, 439f, 484, 720 IgD, 438, 439f IgE, 438–39 IgE-mediated allergies, 463–64, 466–67 IgG, 438, 439f IgG blocking antibodies, 470 IgM, 438, 439, 531

Imipenem, 357 Immediate hypersensitivity, 461t Immigration. See also Travel health care for refugees, 397 helminthic infections, 692 tuberculosis, 642 Immune complex-mediated hypersensitivity, 461t Immune complex reactions, 474–76 Immune deficiency, theory of, 480 Immune disorders autoimmunity, 479–82 immune response, 460–61 immunodeficiency diseases, 482–86 type II hypersensitivities, 470–74 type III hypersensitivities, 474–76 type IV hypersensitivities, 476–79 Immune privilege, 540 Immune response atopy and anaphylaxis as type I allergic reactions, 461–70 bacterial toxins, 375t immune disorders, 460–61 Immune serum globulin (ISG), 446 Immune system. See Host defenses; Immune disorders; Immune response; Immunology; Immunotherapy; Specific immunity Immune testing, 499–502 Immunity, 398, 425 Immunization, 446–47. See also vaccination and vaccines Immunoassays, 504–507 Immunocompetence, 425 Immunocompromised patients, and chickenpox, 525 Immunodeficiency diseases, 461, 482–86. See also Acquired immunodeficiency syndrome Immunofluorescence testing, 504, 505f Immunogens, 425, 432, 436 Immunoglobulins, 430f, 431, 438–39, 484 Immunologic methods, of diagnosis, 491– 92, 499–507 Immunologic privilege, 552 Immunologic reactions, and viral encephalitis, 564t Immunology, 4t, 401 Immunopathology, 460 Immunosuppressant agents and immunosuppressed patients, 483t, 649 Immunotherapy, 445 Impellers, of fermentor, 781 Impetigo, 516–18, 520–21 Inactivated vaccines, 449t, 571 Inactive viruses, 141 Inappropriate expression of MHC II markers, 480 Incidence, of infectious disease, 389 Incineration, and microbial control, 308 Inclusion bodies, 82f, 95–96, 156 Incubating carriers, 380

I-13

Incubation, of cultures, 56f, 57, 65–66 Incubation period, of infection, 376 Index case, 390 India, and plague epidemics, 591 India ink, 74, 75f Indiana State Department of Health, 424, 455, 550, 576 Indicator bacteria, 767 Indinavir, 345t Indirect ELISA, 506–507 Indirect testing methods, 504 Indirect transmission, 383 Induced mutations, 256 Induction, of bacteriophage, 159 Inductive reasoning, 16 Induration, and diagnosis of tuberculosis, 642–43 Industry and industrial microbiology, 5t, 126, 778–83. See also Mining industry; Pharmaceutical industry Infant(s). See also Children; Pregnancy botulism, 574, 575–76 chlamydial infections, 722 congenital rubella, 531–32 gonorrhea, 719–20 group B streptococcus “colonization” neonatal disease, 733–34 herpes, 728 HIV transmission, 611 “hygiene hypothesis” for allergies, 462 melamine in formulas, 285 neonatal conjunctivitis, 540, 541t neonatal meningitis, 558–60 normal microbiota, 365–66 pertussis, 634 pneumonia, 646 respiratory syncytial virus, 635 rotavirus, 681 staphylococcal scalded skin syndrome, 522 TORCH infections, 372 Infantile paralysis, 570, 572 Infection(s). See also Diseases; Infectious diseases allergies mistaken for, 461 attachment, 372–73 biofilm, 87 classic stages of, 376 establishment of, 373 fungi, 127t Koch’s postulates and etiology of, 386–87 progress of, 366–87 protozoa, 131–32 viral, 165 Infection control officer, 385 Infectious, use of term, 382 Infectious allergy, 476 Infectious disease, 363. See also Disease(s); Infection(s) Infectious dose (ID), 372 Infectious mononucleosis, 596–97

I-14

Index

Infectious particles, 141 Infertility, and pelvic inflammatory disease, 720 Inflammation pelvic inflammatory disease, 720 signs and symptoms, 378 stages of, 410–14 Inflammatory bowel disease (IBD), 400, 663, 694 Inflammatory mediators, 412 Inflammatory response, 410 Influenza, 635–39 adhesive properties, 372t antiviral drugs, 345t, 639 causative agent, 636–37 creation of artificial viruses, 163 culture and diagnosis, 162, 637, 639 cytopathic changes in cells, 156t epidemiology, 637 Google Flu Trends, 362, 388, 392 history of, 636 importance of study, 635 pathogenesis and virulence factors, 637 prevention, 639 signs and symptoms, 635 transmission, 637 treatment, 345t, 639 Ingestants, and allergens, 463 Inhalants, and allergens, 462, 463f Injectant allergies, 463 Inoculating loop, 57 Inoculation, 56f, 57 Inoculum, 372 Inorganic nutrients, 169 Insect(s). See Arthropods; Black flies; Fleas; Houseflies; Insecticides; Mosquitoes; Sand fly; Ticks Insecticides. See Bioinsecticides; DDT; DEET Insertion elements, 263–64 Inspection, of cultures, 56f, 65–66 Insulin, 282, 287 Integrase inhibitors, 165, 615 Integration, of viruses, 155 Integument, 513 Interferon (IFN), 165, 283t, 344, 412, 417–18 Interferon alpha and beta, 417 Interferon gamma, 412, 417 Interleukin (IL), 283t, 412 Interleukin–1 (IL–1), 416 Interleukin–2 (IL–2), 412, 434 Interleukin–4, 412 Interleukin–5, 412 Interleukin–6, 412 Interleukin–10, 412 Interleukin–12, 412 Intermediate filaments, 120 Intermediate-level germicides, 315 Intermittent sterilization, 307–308 International Committee on the Taxonomy of Viruses, 149 Internet, 362, 388, 392

Interphase, of mitosis, 115f Intoxications, 374 Intracellular function, of carbon compounds, 170 Intrauterine devices (IUDs), 717 Introns, 250 In vitro and in vivo cultures, 160 In vivo testing, 507 Iodine, 29t, 314t, 316 Iodophors, 316 Iodoquinol, 688 Ion(s), 36 Ionic bonds, 33f, 34–36 Ionization, 35–36 Ionizing radiation, 256t, 310 Iron, 29t, 169t, 171 Iron-binding proteins, 419, 421 Irradiation, 309–10 Irritable bowel syndrome, 684 Isocitric acid, 216 Isodine, 316 Isograft, 478 Isolation, of cultures, 56f, 57–58, 495–96 Isomerases, 203 Isoniazid (IHN), 336t, 339, 349, 352t, 644 Isopropyl alcohol, 317 Isotonic conditions, 176–77 Isotopes, 30 Isotypes, of immunoglobulins, 438 -Itis (suffix), 375, 411 Itraconazole, 538, 558, 651 Ivanovski, D., 140, A3 Ivermectin, 343, 543 Ixodes pacificus, 594 Ixodes scapularis, 594 Jablot, Louis,, 12 Jacob, Francois, 251 Janthinobacterium, 514 Jaundice, 688 JC virus, 564 Jeffreys, Alex, 290 Jejunum, 661 Jenner, Edward, 446, 529–30, A3 Jock itch, 537 Johne’s disease, 663 “Jumping genes,” 263 Kajander, Olavi, 99 Kanamycin, 354t Karposi’s sarcoma, 608, 609 Kell blood groups, 474 Keratin, 399, 514, 538 Keratinase, 374, 779t Keratinized surface, of skin, 514 Keratitis, 542 Ketoconazole, 342 Ketolides, 340 Kidneys, 352, 490, 709 Killed vaccines, 448 Killer whale, 752 KiloGrays, 310

Kinases, 374 Kingdom, and classification, 20 Kirby-Bauer technique, 354 Klebsiella pneumoniae, 652 Koch, Robert, 17–18, 329, 386–87, 606, 642, A3 Koch’s postulates, 17, 59, 386–87, 663 Komodo dragon, 673 Koplik’s spots, 530 Krebs, Sir Hans, 211 Krebs cycle, 214–16, 223 Labile, enzymes as, 206 Laboratory techniques. See also Cultures and culturing methods; Identification; Incubation; Microscope overview of methods, 56f specimen analysis, 493–95 LaCrosse strain, of California encephalitis, 563 Lactase, 203 Lactate dehydrogenase, 203 Lactic acid, 322 Lactobacillus spp., 188, 712 L. acidophilus, 773 L. plantarum, 770, 772 L. sanfrancisco, 20, 770 Lactoferrin, 419, 709 Lactose, 42, 43, 44f Lactose operon, 251–53 Lagered beer, 770–71 Lagging strand, 240 Lag phase, of growth curve, 191 Lakes, 141, 757f. See also Aquatic microbiology Lambl, Vilem, 20 Lamivudine, 345t, 614, 690 Lancet, The (journal), 679 Landfills, and bioremediation, 764 Large intestine, 365t, 661, 663 Large pustular skin lesions, 535–36 Lassa fever, 598t, 599 Latent infections, 379, 725, 729 Latent period, of antigen response, 439 “Lawnmower” tularemia, 592 Leading strand, 240 Leavening, of bread, 770 Lectin pathway, of complement, 418, 419t Lederberg, Joshua, 255f, A3 Leeuwenhoek, Antonie van, 12–14, 66, 68, 685, A3 Legionella pneumophila, 646–47, 652t Legionellosis, 646–47 Legumes, 748–49 Leishmania brasiliensis, 131t, 535 Leishmania donovani, 131t Leishmania tropica, 131t, 535 Leishmaniasis, 131t, 535–36 Lemierre’s syndrome, 628–29 Leptospira interrogans, 714 Leptospirosis, 713–14, 734 Lethal factor, 606

Index

Leuconostoc mesenteroides, 772 Leucovorin, 566 Leukemia, 485–86, 616 Leukocidins, 373 Leukocytes, 406 Leukocytosis, 378 Leukopenia, 378, 611 Leukotrienes, 412, 466 Levofloxacin, 341, 536 L forms, 93 Lice, 594 Life basic characteristics of, 120t major elements of, 29t Life cycles Chlamydia, 722f helminths, 134, 693f liver fluke, 699 Lyme disease, 595f Plasmodium spp., 603f protozoa, 130 Toxoplasma, 565–66 viruses, 160 Lifestyles, of microorganisms, 10 Ligases, 203, 238t, 271 Light-dependent reactions, 225, 226 Light-independent reactions, 225, 227 Limestone, 748 Linezolid, 341 Linkage maps, 290 Linolenic acid, 45f Lipids, 42t, 45–47 Lipmann, F. A., 211 Lipopolysaccharide (LPS), 44, 93, 375 Lipoteichoic acid (LTA), 91, 630 Liquid(s), ultraviolet irradiation of, 311 Liquors, 772 Lister, Joseph, 17, 316, A3 Listeria monocytogenes, 181, 447, 555–56, 559t, 560t, 777 Listeriosis, 555–56 Lithoautotrophs, 172 Lithosphere, 743, 753–55 Lithotrophs, 745 Liver and liver disease, 352, 490, 686, 689, 690, 691, 700–701 Liver flukes, 133f, 698–99 Lobar pneumonia, 646 Localized infection, 376, 377f “Lock-and-key” fit, of enzyme, 202 Locomotion, of protozoa, 129 Loeffler, Friedrich, 140 Logarithms, 191, 303 Loop dilution technique, 57–58 Lophotrichous arrangement, of flagella, 84 Louisiana State University, 164, 756 Low-density lipoproteins (LDLs), 587 Lowenstein-Jensen (LJ) media, 63t Lower respiratory tract infectious diseases, 633–37, 639, 640–54, 655t, 656f normal microbiota, 365t

structure and defenses of, 624 Lumen, 661 Lung(s). See also Respiratory tract fungal diseases, 649 tuberculosis, 640 Lyases, 203 Lyme disease, 593–96. See also Borrelia burgdorferi Lymphadenitis, 378 Lymphangitis, 521 Lymphatic fluid, 404 Lymphatic system, 585 AIDS-defining illnesses, 609 infectious diseases, 587–616, 617t, 618f structure and defenses of, 402–405, 586–87 Lymphatic vessels, 403f, 404 Lymph nodes, 403f, 404, 405 Lymphocytes, 426, 427f, 428–32, 434–35. See also B cells; T cells Lymphocytic choriomeningitis, 599 Lymphogranuloma venerum (LGV), 722 Lymphoid tissue, 402 Lyophilization, 309 Lysin, 503 Lysis, 90, 159 Lysogenic conversion, 160 Lysogeny, 159–60 Lysol, 315, 317, 323t Lysosomes, 117, 416 Lysozyme, 90, 400, 514, 709 Lyssavirus, 568–69. See also Rabies MacConkey agar (MAC), 63t, 64 MacLeod, Colin, 236, A3 Macroconidia, 125f Macrogametocytes, 604 Macrolides and macrolide polyenes, 340, 342 Macromolecules, 41–51, 432 Macronutrients, 169 Macrophage(s), 409, 414, 552 Macrophage colony-stimulating factor (MCSF), 412 Macroscopic fungi, 121 Macroscopic morphology, 491 Macule, 528 Maculopapular rash, 528, 530–33 Mad cow disease, 163 Magnesium, 29t, 30, 169t, 171 Magnetic resonance imaging (MRI), 80, 88, 507 Magnetotactic bacteria, 96 Magnification, and microscope design, 68 , 70f Maine Department of Health and Human Services, 139, 164 Maintenance, of cultures, 66 Major histocompatibility complex (MHC), 428 Malachite green, 322

I-15

Malaria, 8, 131t, 343, 368–69, 602–606, 727. See also Plasmodium spp. Malassezia furfur, 538 Male reproductive system, 709–10 Malic acid, 216 Malnutrition, and enteroaggregative E. coli, 685 MALT (mucosa-associated lymphoid tissue), 402, 404, 405 Malting, of beer, 770 Maltase, 203 Maltose, 42, 43 Mammalia (Class), 20, 21f Manganese, 29t Mannitol salt agar (MSA), 63, 64t Mantoux test, 642 Mapping, of genomes, 289–90 Marburg virus, 598–99 March of Dimes, 572 Margulis, Lynn, 110 Marine environments, 756. See also Aquatic microbiology; Oceans Marine microbiology. See also Aquatic microbiology Markers, and immune system, 401 Mars, 19 Marshall, Barry J., 670 Mash, and beer brewing, 770 Mass, 31 Massachusetts Institute of Technology, 644 Mast cells, 408, 464, 466–67 Mastigophora, 130–31 Matrix, 118 Matter, 28 Maximum temperature, 180–81 McCarthy, Jenny, 452 McCarty, Maclyn, 236, A3 Measles, 156t, 424, 451, 455, 530–31, 533t, 566–68. See also Morbillivirus; Subacute sclerosing panencephalitis Mebendazole, 343, 692t Mechanical vectors, 381 Mechanical ventilation, and pneumonia, 652 Mediastinum, 650 Medical asepsis, 385 Medical microbiology, 4t, 17–18 Medical significance. See also Medicine bacterial spores, 98 biofilms, 87 DNA and RNA viruses, 148t families and genera of bacteria, 103t viruses, 163 Medicare and Medicaid, 385 Medicine. See also Diseases; Health care personnel; Hospitals; Medical significance; Nosocomial infections antimicrobial therapy and history of previous conditions, 357 bacterial meningitis as emergency, 554 concepts of fever, 417 drug resistance, 349 genetic treatments, 287–89

I-16

Index

Medium (media), 57, 58–65 Meiosis, 116 Melamine, 285 Melarsoprol, 578 Mello, Craig, 242 Membrane. See Cell membrane Membrane attack complex, 419, 420f Membrane filtration, 312f, 768 Membrane lipids, 46–47 Memory, and host defenses, 425 Memory cells, 436, 442f Mendeleev, Dimitri, 32 Mendosicutes, 102 Meninges, 551 Meningitis, 375, 522, 552–58, 641, 669. See also Neisseria meningitidis Meningococcal meningitis, 553–54 Meningococcemia, 553 Meningoencephalitis, 561 Mercurochrome, 320 Mercury and mercurial compounds, 314t, 320, 727, 752 Merozoites, 603–604 Mesophiles, 182 Messenger RNA (mRNA), 51, 154, 243–44, 246–47 Metabacterium polyspora, 96 Metabolic analog, 333 Metabolic pathways, 206–208 Metabolism, 40, 199 biosynthesis, 223–25 drug resistance, 348 enzymes, 199–208 pursuit and utilization of energy, 208–23 Metabolites, 780 Metabolomics, 290 Metachromatic granules, 96 Metagenomics, 290, 363, 753 Metaphase, of mitosis, 115f Metchnikoff, Elie, A3 Meteorites, 19 Methane, 33f, 104, 172 , 748 Methanococcus jannaschi, 172f Methanogens, 104, 172, 748 Methanosarcina, 172f Methicillin, 337t Methicillin-resistant Staphylococcus aureus (MRSA) , 341, 348, 512, 521, 543 Methyl alcohol, 317 Methylene blue and methylene blue reductase test (MBRT), 75f, 216, 228 Methylophilus methylotrophus, 774 Methyltransferases, 205 Metronidazole, 343, 352t, 671, 677, 688, 717, 718 Mezlocillin, 337 MIC. See Minimum inhibitory concentration Michel, Harmut, A3 Miconazole, 538 Microaerophile, 183 Microarray analysis, 292, 293f

Microbes, 2. See also Microorganisms dimensions, 67–68, 99 ecological associations, 185–88 impact of on Earth, 2–3, 6 interrelationships with humans, 188 Microbial antagonism, 365, 624 Microbial control chemical agents, 313–22, 323t decontamination by filtration, 312 general considerations in, 298 history of, 299 methods of, 298f, 301 microbial death, 301–304 modes of action of antimicrobial agents, 304–305 osmotic pressure, 312 physical methods of, 305–309 radiation, 309–11 relative resistance of microbial forms to, 299–300 selection of, 301 terminology, 300–301 Microbial death, 301–304 Microbial ecology, 742 Microbicide, 300 Microbiology, 2 historical foundations of, 11–18 scope of, 2 subdivisions of, 4–5t Microbiota. See Normal microbiota Microbistatic effects, 301 Micrococcus spp., 518 M. luteus, 65f Microconidia, 125f Microenvironment, 744 Microgametocytes, 604 Microglia, 552 Micronutrients, 169 Microorganisms, 2. See also Bacteria; Microbes; Protozoa; Viruses classification of, 18, 20–24 as food, 774 general characteristics of, 10 human use of, 6–7 Micro RNAs, 242, 243t Microscope development of, 11–15, 66–67 magnification and design of, 68 microbial dimensions, 67–68 principles of light microscopy, 69–71 Microscopic fungi, 121 Microscopic morphology, 491 Microscopy, 68 Microsporum spp., 1, 537, 538 Microtubules, 112 Middle Ages, and malaria, 602 Military, and vaccinations, 454 Milk, 198, 216, 308, 384, 642, 673, 772–73. See also Dairy products Mimiviruses, 143 Mineralization, 746 Miniaturized test system, 519f

Minimum inhibitory concentration (MIC), 355f, 356–57 Minimum temperature, 180 Mining industry, 27 Mini short tandem (DNA) repeats (miniSTR), 291 Miracidium, 700, 701f Missense mutation, 256 “Misspelling,” of DNA, 240 Mitochondria, 118 Mitosis, 114, 115f Mixed acid fermentation, 221 Mixed culture, 66 Mixed infection, 377 MMR vaccine, 450, 452, 531, 670 MN blood groups, 474 Mobiluncus, 716 Moist heat, and microbial control, 305–308 Molarity (M), 39 Mold spores, 462, 463t Molecular formula, 37 Molecular genetics, 22–23 Molecular mimicry, 480 Molecular weight (W), 31, 432 Molecule, 31 antigens, 432 chemical bonds, 33 polarity, 34 solutions, 38 structure of ATP, 210 Molluscum contagiosum, 534–35, 731t, 733 Monkeypox, 530 Monoclonal antibodies (MABs), 444 Monocytes, 409 Monod, Jacques, 251 Monolayer, and cell culture, 151–52 Monomers, 41–42, 438 Mononegavirales, 149t Mononucleosis, 596–97 Monosaccharide, 42, 43f Monospot test, 597 Monotrichous arrangement, of flagella, 84 Montagnier, Luc, A3 Montagu, Lady Mary, 446 Moraxella spp., 540 Morbidity and Mortality Weekly Report (CDC), 388 Morbidity rates, 390 Morbillivirus, 531 Morphology, 491 Mortality rates, 389 Mosquitoes, 381, 563, 597, 598, 603, 604, 605 Most probable number (MPN), 768 Motility, of microorganisms, 83, 84, 112, 120t Mouse neutralization test, 59 Mouth, and normal biota, 663 Moxalactam, 338f M protein, 520, 630 MRSA. See Methicillin-resistant Staphylococcus aureus

Index

Mucinase, 373 Mucocutaneous leishmaniasis, 536 Mucor spp., 626 Mucous membranes, 399 Mueller tellurite, 63t Mullis, Kary, 14, 182, A3 Multicloning site (MCS), 280 Multidrug-resistant (MDR) pumps, 347 Multidrug-resistant tuberculosis (MDR-TB), 644 Multimammate rat, 599 Multiple sclerosis (MS), 480t, 482 Multiplication, of viruses, 151–60 Mumps, 668–70 Mupirocin, 521 Muramic acid, 91f Murray, Polly, 593 Must, and wine production, 771 Mutagens, 256 Mutant strain, 255 Mutations, genetic, 255–58, 346 Mutualism, 186, 187 Myastentia gravis, 480t, 482 Mycelium, 122 Mycobacterium spp., 92, 94, 96 M. avium, 642, 644, 663. See also Mycobacterium avium complex M. bovis, 642 M. leprae, 190 M. tuberculosis, 74–75 , 507, 640, 641–42. See also Tuberculosis Mycobacterium avium complex (MAC), 642, 644 Mycolic acid, 92 Mycoplasma(s), 92–93, 103t Mycoplasma spp., 372t M. pneumoniae, 93, 645, 647, 652t. See also Pneumonia Mycoprotein, 774 Mycorrhizae, 754, 755f Mycosis (mycoses), 122, 126 Myeloperoxidase, 416 Myocarditis, 632 Myocardium, 586 Myonecrosis, 523, 524 NADH, 210, 214 Naegleria fowleri, 131t, 561 Nafcillin, 337t, 588 Nails, and ringworm, 537 Naked viruses, 144, 145f Names and naming. See also Terminology of enzymes, 203 of microorganisms, 18, 20 of viruses, 149 Nanobacteria, 99 Nanotechnology, 76 Narrow-spectrum drugs, 330t, 336 Nasal vaccines, 450 Nathans, Daniel, 14 National Aeronautics and Space Administration (NASA), 19

National Allergy Bureau Pollen and Mold Report, 463f National Center for Health Statistics, 720 National Institutes of Health, 288 National Oceanic and Atmospheric Agency (NOAA), 7f National Park Service, 182 Native state, of protein, 49, 304 Natromonas spp., 185 Natural immunity, 443 Natural killer (NK) cells, 418, 443, 466 Natural selection, 21, 258, 349–50 Nature (journal), 392 NDM–1, 339 Necator americanus, 697, 698t Necrosis, 376 Necrotizing fasciitis, 15, 519, 629 Necrotizing ulcerative gingivitis (NUG), 668 Necrotizing ulcerative periodontitis (NUP), 668 Needlesticks. See Health care workers; Safety Negative exponents, A2 Negative results, of serological tests, 500 Negative-sense RNA, 148 Negative staining, 71, 74 Neisseria gonorrhoeae, 254, 306, 309, 372t, 540, 554, 559t. See also Gonorrhea Neisseria meningtidis, 553–54. See also Meningitis Nematodes, 133, 135t, 697 Neomycin, 354t Neonatal meningitis, 558–60 Neonatal tetanus, 573f Nephritis, 629 Nervous system AIDS-defining illnesses, 609 antimicrobial therapy, 352 infectious diseases, 552–78, 579t, 580f structure and defenses of, 551–52 tuberculosis, 641 Neuraminidase, 636 Neuritis, 632 Neuromuscular autoimmunities, 482 Neurosyphilis, 725 Neurotoxins, 575 Neurotropic virus, 570 Neutralization reactions, 40, 438 Neutrons, 28, 551 Neutrophil(s), 406, 408 , 414 Nevirapine, 345t, 615 New Mexico, 648 Newton, Isaac, 16 New York City medical examiner, 268 New York State Health Department, 293, 297, 322, 490, 507 Niche, 744 Nicholson, C. K., 47 Nickerson, Cheryl, 254 Niclosamide, 352t Nicotiana tabacum, 287t

I-17

Nicotinamide adenine dinucleotide (NAD), 205, 210 Nidovirales, 149t Nightingale, Florence, 388 Nigrosin, 74 Nipahvirus, 382 Nitrate(s), 748, 778 Nitric oxide (NO), 416 Nitrification, 749 Nitrites, 748, 778 Nitrogen elements of life, 29t, 30f microbial nutrition, 169t, 170 Nitrogen cycle, 748–49 Nitrogenous base, 50, 235 Nitro-mersol, 320 Nitrous acid, 256t Nocardia, 75, 92 Nomenclature, 18 Noncommunicable infectious disease, 382 Noncompetitive inhibition, 207 Nongonococcal urethritis (NGU), 721 Nonhemorrhagic fever diseases, 599–606 Nonionizing radiation, 310–11 Non-nucleoside reverse transcriptase inhibitors, 344 Nonpolar molecules, 34 Nonpressurized steam, and sterilization, 307–308 Nonprogressors, and HIV infection, 613 Nonsense codons, 247 Nonsense mutation, 257 Normal microbiota, 188, 363 acquisition of, 363–65 antimicrobial drugs, 353–54 barriers to infection, 400 commercial antimicrobial chemicals, 312 eye, 540 gastrointestinal tract, 663 genitourinary tract, 364t, 365t, 711–12 initial colonization of newborn, 365–66 respiratory tract, 624 skin, 514–15 viable noncultured (VNC) microbes, 492 Norovirus, 682, 701 North American blastomycosis, 127t Norway, 752 Nosocomial infections, 232, 384–85, 521, 645, 652, 713 Notifiable diseases, 388, 391t, 612, 721, 729 Noxzema triple clean, 323t Nucleators, 756 Nucleic acid(s), 42t, 49–51, 147–48, 225. See also DNA; RNA Nucleic acid sequencing, 498 Nucleic acid synthesis, 304, 332, 345t Nucleocapsid, 144, 145 Nucleoid, 94 Nucleolus, 114 Nuceloside reverse transcriptase inhibitors, 344, 345t, 614–15 Nucleotides, 50, 235

I-18

Index

Nucleus of atom, 28 of cell, 114–16, 117 Numerical aperture (NA), 70 Nursing bottle caries, 664 Nutrient agar, 60 Nutrient broth, 60 Nutrition. See also Food(s); Malnutrition; Vitamins cytoplasm, 169–70 defined, 169 fungi, 122 nutritional flow in ecosystems, 744–46 protozoa, 128–29 sources of essential nutrients, 170–74 transport, 174–80 -Obe, 174t Obesity normal microbiota, 365 vaccine, 164 Objective, of microscope, 69 Obligate aerobe, 183 Obligate halophiles, 185 Obligate parasites, 142, 174 Obligate saprobes, 174 Oceans aquatic microbiology, 756 extreme habitats, 173, 185 viruses, 141 O’Connor, Basil, 572 Ohio State Department of Health, 424, 455 Ohio Valley, and histoplasmosis, 650, 654 Oil immersion lens, 70 Oil spills, and bioremediation, 7, 741, 744, 758 Okazaki fragments, 240 O’Leary, Paul A., 727 Oligodynamic action, 320 Oligotrophic ecosystems, 758 -Oma (suffix), 375 Omeprazole, 671 -Omics (suffix), 290 Onchocerca volvulus, 135t, 543. See also River blindness Onchocerciasis, 543 Oncogenic viruses, 157, 732 Oncoviruses, 157 Oocyst, 566, 678–79 Operator, and gene regulation, 251 Operons, 251 Opisthorchis sinensis, 698–99 Opportunistic pathogens, 126, 174, 366–67, 649 Opsonization, 437–38 Optical microscope, 71 Optimum temperature, 181 Oral cavity, and normal flora, 365t Oral contraceptives, 357, 516 Oral-fecal route, of disease transmission, 384 Oral hygiene, 667

Oral poliovirus vaccine (OPV), 571 Oral rehydration therapy (ORT), 679, 682 Oral vaccines, 450 Orbitals, of electrons, 30–31 Orchitis, 669 Order, and classification, 20 Oregon, 653 Oregon Harmful Algal Bloom Monitoring, 108, 128 Orfvirus, 143f Organelles, 10, 52, 109 Organic acids, 322, 778 Organic compounds, 40, 41t Organic nutrients, 169 Organ-specific autoimmune diseases, 479 Organ transplantation, and organ donation, 476–79, 569, 613. See also Bone marrow and bone marrow transplantation Orthomyxoviridae, 150t, 626 Orthophenyl phenol, 317 Ortho-phthalaldehyde (OPA), 321 Orthopoxvirus, 528 Oryza sativa, 287t -Osis (suffix), 375 Osmosis, 176–80 Osmotic pressure, 177, 185, 312, 778 Otitis media, 627, 628t Outer membrane (OM), 82f, 93 Ovaries, 710 Owens Lake (California), 104f Oxacillin, 337t, 588 Oxaloacetic acid, 214, 216 Oxazolidones, 340–41 Oxidase, 203 Oxidase detection test, 220 Oxidation-reduction (redox) reactions, 35 Oxidative phosphorylation, 211, 217–19 Oxidizing agent, 35 Oxidoreductases, 203 Oxygen aquatic microbiology, 758 covalent bonding, 33f electron shells, 30f elements of life, 29t microbial growth, 183–84 microbial nutrition, 169t, 170 Oxygenic photosynthesis, 6, 227 Oxytetracycline, 355f Pacemaker enzymes, 206 Palindromes, 271 Palisades arrangement, 101 Palmitic acid, 45f Pan American Health Organization, 598 Pancreas, 661 Pancreatitis, 669 Pandemics, 163, 299, 391f, 638 Pannus, 542 Papanicolaou, George, 733 Papillomas, 534

Papillomavirus, 147f, 150t. See also Human papillomavirus (HPV) Papovaviridae, 150t Pap smear, 729, 732, 733 Papule, 528 Paracoccidioides brasiliensis, 649 Paracoccidioidomycosis, 127t Parainfluenza, 155f Paralytic shellfish poisoning, 108, 128, 758 Parameciidae (Family), 21f Paramecium spp., 72t, 84f P. caudatum, 21f Paramyxoviruses, 150t, 669. See also Measles; Mumps Parasites, 10. See also Helminths; Malaria; Parasitism; Parasitology antimicrobial drugs, 343 fungi, 122 microbial nutrition, 171t, 172, 174 protozoa, 132 Parasitism, 187 Parasitology, 132 Parenteral administration, of drugs, 338 Park’s method, 319 Parotitis, 669 Paroxysmal stage, of pertussis, 634 Parvoviruses (PVs), 143, 150t, 532 Passive antibody preparation, 635 Passive carrier, 381 Passive immunity, 443, 445–46 Passive transport, 180t Pasteur, Louis, 9, 13, 17, 140, 220, 222, 319, 606, A3 Pasteur Institute (France), 608 Pasteurization, 216, 222, 308, 775–76 Pathogen(s) and pathogenesis, 8, 366. See also Pathogenicity; specific diseases biosafety levels and classes of, 370 fungi, 126 parasites, 174 Pathogen-associated molecular patterns (PAMPs), 415–16, 425 Pathogenicity, 366, 367 Pathogenicity islands, 264 Pathognomic diseases, 650 Patient chart, and specimen analysis, 494 Patient history, and brucellosis, 600 Pattern recognition receptors (PRRs), 415–16 Patterson, Meredith, 285 Payne, Roger, 752 P blood groups, 474 PCBs (polychlorinated biphenyls), 752 Pectinase, 779t Pediatrix, 454 Pediococcus cervisiae, 772 Pegylated interferon, 691 PEG-SOD, 283t Pellicle, 663 Pelvic inflammatory disease (PID), 719, 720, 722 Penetration, of virus, 151–53, 159, 160t

Index

Penicillin(s) cell wall, 332, 336–37 designer drugs, 334 discovery of, 329 drug allergies, 467 drug resistance, 348 industrial products, 779t, 780, 783 Kirby-Bauer test, 354t meningococcal infections, 554 Streptococcus pyogenes, 631 syphilis, 727 toxic reactions to, 352t Penicillinase, 203, 346 Penicillium spp., 27, 34 P. chrysogenum, 336, 783 P. roqueforti, 773 Pennsylvania Department of Health (PDH) and Department of Agriculture (PDA), 198, 228 Pentamidine, 578 Pentoses, 42, 50 Peptic ulcers, 670 Peptidase, 203 Peptide(s), 48, 350 Peptide bond, 48 Peptidoglycan (PG), 43, 89–90, 91f Perforins, 441, 443 Pericardium, 586 Periodic table, 31f, 32 Period of invasion, 376 Periodontal disease, 666–68 Peripheral nervous system (PNS), 551, 552. See also Nervous system Periplasmic flagella, 85 Peritrichous arrangement, of flagella, 84, 85 Persistent infections, 156, 160t Pertussis, 451, 633–35 Peru, 124, 640 Petechiae, 528, 553 Petri dish, 57 Peyer’s patches, 405 Pfiesteria piscicida, 127f, 128 pH scale, 39–40, 185. See also Acid(s) and acidity; Alkalines and alkalinity Phage. See Bacteriophages Phage type and phage typing, 157, 164, 496 Phagocytes, 373, 414–16, 483t Phagocytosis, 179f, 180, 414–16 Phagolysosome, 416 Phagosome, 416 Pharmaceutical industry, 282–83, 348, 779t, 783 Pharyngitis, 628–31. See also Streptococcus pyogenes Pharynx, 663 Phase-contrast microscopy, 72t Phase variation, and genetic regulation, 254 Phenazopyridine, 713 Phenol, and phenolics, 314t, 316–17 Phenol coefficient, 316

Phenotype, 235 Phenotypic methods, of diagnosis, 491, 495–97 Phenylalanine, 48f Phenylethanol agar (PEA), 63t Phialospores, 125f -Phile, 174t Philippines, 714 Phosphates, 41f, 50, 171, 235 3-Phosphoglyceric acid (PGA), 227 Phospholipids, 42t, 46 Phosphorus, 29t, 30f, 169t, 171 Phosphorus cycle, 751 Phosphorylation, 209 Phosphotransferases, 205 Photo-, 174t Photoautotrophs, 171t, 172, 747 Photocenter, 225 Photoheterotroph, 171t Photolithotrophs, 227 Photons, 225 Photophosphorylation, 211, 227 Photosynthesis, 3, 6, 225–28, 747, 756 Photosystem I (P700) and Photosystem II (P680), 226–27 Phototaxis, 85 Phototrophs, 171 Phycobilins, 225 Phylogeny, 20, 22–24 Phylum, and classification, 20 Physical agents, and genetic mutations, 256 Physical maps, of genomes, 290 Physical methods, of microbial control, 305–309 Physical state, of culture media, 59t, 60 Physiology, 491 Phytoplankton, 756–57 Pickling, of foods, 772 Picornaviridae, 150t, 570f Picrophilus, 185 Pig(s), 636, 637f, 638, 695. See also Swine flu Pilin, 86 Pilus, 82f, 85, 86, 259 Pine-Sol, 323t Pinocytosis, 179f, 180 Pinworms, 134, 135t, 695 Piperacillin, 337 Piperazine, 692t Pisum sativum, 287t Pithomyces, 34 Placenta, 371 Plague, 299, 590–92. See also Yersina pestis Plankton, 128, 756–57 Plant(s). See also Agriculture; Photosynthesis contact dermatitis, 476 fungi, 124 mycorrhizae, 754, 755f nitrogen cycle, 748–49 transgenic, 284, 286, 287t Plantar warts, 534 Plaque, 162, 528, 664, 665f. See also Teeth

I-19

Plasma, of blood, 405 Plasma cells, 408 Plasmids, 82f, 95, 259 Plasmodium spp., 131, 343, 603. See also Malaria P. falciparum, 131t P. malariae, 131t P. ovale, 604 P. vivax, 131t, 604 Plastic, and cutting boards, 776 Platelet(s), 409 Platelet-activating factor, 412, 466 Pleomorphism, 100, 727 Pleuromutilins, 341 Pluripotential stem cells, 406 Pneumococcal meningitis, 554–55 Pneumococcal pneumonia, 554 Pneumocystis (carninii) jiroveci, 608, 649, 651–52, 653t Pneumocystis pneumonia (PCP), 651–52 Pneumonia, 370, 645–54 Pneumonic plague, 590, 650, 651 Point mutations, 256 Point source, of infection, 390 Poison ivy, poison oak, and poison sumac, 476, 478 Polar arrangement, of flagella, 84, 85 Polar bears, 752 Polarity, in molecules, 34 Poliomyelitis, 451, 570–71, 572 Poliovirus, 143f, 156t, 372t Pollen, 462, 463t Pollution, and genetically modified organisms, 284. See also Bioremediation; Oil spills; Water and water supplies Polyacrylamide gel, 276 Polyclonal antibodies, 444 Polyenes, 342 Polyhydroxyalkanoate (PHA), 95f Polymer(s), 41–42, 438 Polymerase(s), 149, 203 Polymerase chain reaction (PCR) DNA analysis, 276–78 identification of pathogens, 498, 508f invention of, 14 Mycobacterium tuberculosis, 643 oral bacteria in coronary arteries, 587 real-time PCR and enumeration of bacteria, 194 Taq polymerase and improvement of, 182 viable noncultured (VNC) microbes, 492 Polymerization, and complement cascade, 420f Polymicrobial diseases, 377 Polymorphonuclear neutrophils (PMNs), 406, 408 Polymyxins, 332–33, 336t, 341–42, 352t, 354t Polypeptides, 48 Polyribosomal complex, 249

I-20

Index

Polysaccharides, 42, 43–45 Pontiac fever, 647 Population(s), and ecological communities, 744 Population growth, 189–91 Porin proteins, 93 Porospore, 125f Porphyrin, 225 Porphyromonas gingivalis, 587, 666 Portals of entry for allergens, 462–63 for infection, 369–72, 377f, 383 Portals of exit, for infection, 377f, 378–79, 383 Porter, Rodney, A3 Positive results, of serological tests, 500 Positive-sense RNA, 147 Positive staining, 71, 74 Positron emission tomography (PET), 507 Postal Service, and irradiation of mail, 310 Postexposure prophylaxis, for anthrax, 616 Postinfection encephalitis (PIE), 564 Postnatal rubella, 531 Post-polio syndrome (PPS), 570 Posttranslational modifications, and protein synthesis, 249 Potassium, 29t, 30f, 169t, 171 Potassium hydroxide, 538 Poverty, and tuberculosis, 642 Povidone (PVP), 316 Pox, 524 Poxviruses, 150t, 535 PPNG. See Penicillinase-producing Neisseria gonorrhoeae Prairie dogs, 530 Praziquantel, 343, 692t, 696, 701, 715 Prebiotics, 351 Precipitation, and bacteria in rain and snow, 756 Precipitation reactions, 437f, 500, 502 Pre-erythrocytic development, of malaria, 603 Prefixes, 174t Pregnancy. See also Infants chickenpox, 525–26 herpes, 728 HIV and perinatal prevention strategies, 613 maculopapular rash diseases, 530 portals of entry for infection, 371–72 side effects of antibiotics, 353, 516 toxoplasmosis, 565 Universal Precautions, 386 Pressure, and steam sterilization, 306–307 Presumptive data, 494 Prevalence, of infectious disease, 389 Prevention. See Centers for Disease Control and Prevention; Public health; specific diseases Prevotella intermedia, 668 Primaquine, 343

Primary amoebic meningoencephalitis (PAM), 561 Primary cell cultures, 162 Primary chancre, and sleeping sickness, 578 Primary consumers, 745 Primary dye, 74 Primary immunodeficiency diseases, 482–85 Primary infection, 377 Primary metabolites, 780 Primary pathogens, 649 Primary phase, of wastewater treatment, 765–66 Primary response, to antigens, 439 Primary structure, of protein, 49 Primary syphilis, 724 Primary tuberculosis, 640 Primase, 238t Primates (Order), 20, 21f Primer(s), 243t Prince William Sound (Alaska), 168, 741, 744, 758 Prions, 163–64, 300, 566, 567t Probiotics, 351 Prodomal stage, of infection, 376 Producers, and ecosystems, 745 Products, of chemical reactions, 37 Professional phagocytes, 414 Proflavine, 322 Progressive multifocal leukoencephalopathy (PML), 564 Prokaryotes, 3 Archaea compared to, 104t cell structure, 10, 111f characteristics of, 52 classification, 101–102 DNA transcription and translation, 249–50 eukaryotes compared to, 81, 104t, 120t form and function, 81–88 shapes, arrangements, and sizes of cells, 98–101 Proliferative stage, of lymphocyte development, 429 Promoter region, 244, 251 Proof, of liquor, 772 Propagated epidemic, 390 Prophage, 159 Prophylaxis, 330t Propionibacterium spp., 221, 773 P. acnes, 514, 515–16 Propionic acid, 322 Propylene oxide, 322, 778 Prostaglandins, 412, 466 Prostate cancer, 447 Prostate gland, 710 Prostatitis, 718 Prosthetic valves, 588 Protease(s), 203, 222 , 779t Protease inhibitors, 344, 345t, 615 Protective antigen, 606

Protein(s). See also Protein synthesis cell composition, 169 genetics, 234, 241–42 macromolecules, 42t, 47–49 microbial control, 304–305 Proteinaceous infectious particles, 566 Proteinase, 203 Protein synthesis anabolism and formation of macromolecules, 225 antimicrobial drugs, 304, 332 events in process of, 247, 248f genetic regulation of, 251–55 ribosomes, 95 RNA and organization of, 51 Proteomics, 290 Proteorhodopsin, 228 Proteus spp., 185 P. mirabilis, 712, 713t Protista (Kingdom), 20, 21f, 23, 127–32 Proton(s), 28 Proton motive force (PMF), 218 Protoplast, 93 Prototheca, 128 Protozoa, 20, 21f, 128–32, 186, 343 Provenge, 447 Provirus, 156 Provocation, and type I allergy, 463–65 Pruteen, 774 Pseudocyst, 565 Pseudohypha, 121–22 Pseudomembranes, 632, 633 Pseudomembranous colitis, 676 Pseudomonas spp., 514, 764 P. aeruginosa, 174, 205, 350, 372t P. fluorescens, 284 P. stutzeri, 782 P. syringae, 284 Pseudo-nitzschia, 108 Pseudopods, 129 Psychro-, 174t Psychrophiles, 105, 181 Psychrotrophs, 181 Public health, 388, 452, 622, 639, 644, 727. See also U. S. Public Health Service Public health microbiology, 4t Pulmonary amoebiasis, 686 Pulmonary anthrax, 606, 650 Pulse-field gel electrophoresis (PFGE), 683 PulseNet, 683 Pure cultures, 65–66, 744 Purell Instant hand sanitizer, 323t Purines, 50, 235 Purpura, 528 Pus, 413 Pustule, 528 Pyelonephritis, 712 Pyogenic bacteria, 413 Pyrantel, 343, 352t, 692t Pyrazinamide, 644 Pyretotherapy, 417 Pyrimethamine, 566

Index

Pyrimidine(s), 50, 235 Pyrimidine dimers, 311 Pyruvic acid (Pyruvate), 214 Q fever, 384, 600, 602t Quarantines, 592 Quaternary ammonium compounds (quats), 314t, 315t, 318–19 Quaternary consumers, 745 Quaternary structure, of protein, 49 Quellung test, 504 Quick test kits, 495 Quinine, 605 Quinolones, 332, 341, 352t Quorum sensing, 188 Rabbits, and tularemia, 592–93 Rabies, 156t, 376, 568–70 Racoons, and rabies, 569 Radiation. See also Ultraviolet radiation food preservation, 777–78 genetic mutations, 256 microbial control, 299t, 309–11 microbial environments, 185 Radioactive isotopes, 30 Radioallergosorbent (RAST) test, 468, 505 Radio-frequency identification (RFID), 486 Radioimmunoassay (RIA), 505 Radioimunosorbent test (RIST), 505 Rales, 466, 635 Rapid diagnostic test kits, 630, 631f Rapid multitest systems, 518 Rapid plasma reagin (RPR) test, 500, 502 Rashes, 524–30 Reactants, and chemical reactions, 37 Real image, 69 Receptors B-cell, 431 drug resistance, 347–48 lymphocytes, 428 T-cell, 431–32 Recombinant DNA technology, 7, 278–83. See also Genetic engineering Recombinant human interferon, 690 Recombination, of DNA, 259–64 Recycling, of bioelements, 747–52 Red blood cells (RBCs), 503–504, 603–604 Redi, Francesco, 12, A3 Redox pair, 209 Redox reactions, 35, 205, 209–10 Red Sea, 104 Red snow, 181f Red tide, 128, 757–58 Reducing agent, 35 Reducing media, 64 Redundancy, in genetic code, 246 Reduviid bug, 132 Reemerging diseases, 8 Refraction, 68 Refractive index, 71 Refrigeration, of foods, 777 Refugees, and infectious disease, 397

Regulation of enzymatic activity, 204, 206–208 of protein synthesis, 251–55 Regulator, of lactose operon, 251 Regulatory B cells, 436, 442f Regulatory genes, 235 Regulatory T cells, 426, 441, 447 Relaxin, 283t Release, of viruses, 155, 160t Relenza, 344, 345t, 639 Renal tuberculosis, 641 Rennet, 779t ReNu contact lens solution, 323t Reoviruses, 151t, 156t Replica plating technique, 255f Replication of DNA, 238–40 of viruses, 153–55, 159 Replication forks, 240 Reportable diseases. See Notifiable diseases Repressible operon, 253–54 Repressor, and gene regulation, 251 Reproduction. See also Reproductive tract eukaryotes, prokaryotes, and viruses compared, 120t fungi, 125–26 helminths, 134 protozoa, 130 Reproductive tract, 709, 715–34, 735t, 736f, 737f. See also Genitourinary tract; Sexually transmitted diseases Reservoirs, of infectious disease, 379–82. See also Animal(s); Zoonosis; specific diseases Resident flora. See Normal flora Resistance, of microbes to control, 299–300 Resistance (R) factors, 260–61, 346 Resolution, of microscope, 69–70, 76 Respiration, of prokaryotes, eukaryotes, and viruses compared, 120t. See also Respiratory tract Respiratory syncytial virus (RSV), 289, 345t, 625, 635 Respiratory tract AIDS-defining illnesses, 609 barriers as host defenses, 399–400 infectious diseases, 624–54, 655t, 656f normal microbiota, 365t, 624 portals of entry for infection, 369–71 portals of exit for infection, 379 structure and defenses of, 623–24 Restriction endonucleases, 270–71 Restriction enzymes, 14, 290 Restriction fragment(s), 271 Restriction fragment length polymorphisms (RFLPs), 271 Retapamulin, 341, 521 Reticuloendothelial system (RES), 402, 403f Retrotransposon, 264 Retroviruses, 148, 151t, 344, 610, 616 Reverse transcriptase, 149, 271, 344

I-21

Reverse transcriptase inhibitors, 344, 614–15 Reversible reactions, 38 Rhabdoviridae, 150t rHDNase (Pulmozyme), 283t Rheumatic fever, 629 Rheumatoid arthritis, 480t, 481, 593 Rh factor, 473–74 Rhinitis, 624–25 Rhizobia, 748–49 Rhizobium, 748 Rhizopus spp., 123f Rhizosphere, 754 Rhodococcus, 764 RhoGAM, 474 Ribavirin, 345t, 635, 691 Ribonucleic acid. See RNA Ribose, 243 Ribosomal RNA (rRNA), 51, 95, 101, 243t, 244 Ribosomes, 82f, 95, 119, 244 Riboswitches, 242, 243t Ribozymes, 202, 243t Rickettsia rickettsii, 601. See also Rocky Mountain spotted fever Ricord, Phillipe, A3 Rifampin, 352t, 644 Rifamycin, 341 Rifkin, Jeremy, 284 Riftia, 186 Rimantidine, 639 Ringworm, 536–38, 539t Risk factors, for endocarditis, 588 River blindness, 135t, 543 Rivers, T. M., 387 RNA (ribonucleic acids) alternative splicing and editing of, 250–51 antibacterial drugs, 341 cell assembly, 242–43 drug resistance, 350 importance of small, 15 macromolecules, 42t nucleic acid sequencing, 498 structure and functions of, 49–51 types of, 243t viruses, 147–48 RNA-induced silencing complex (RISC), 289 RNA polymerase, 244 RNA primer, 239 RNA viruses, 147–48, 150–51t, 152f Rock decomposition, 753–54 Rocky Mountain spotted fever (RMSF), 601–602. See also Rickettsia ricksettsii Roferon-A, 280, 282 Roman Empire, 299 Roosevelt, Franklin Delano, 572 Root nodules, 748–49 Roseola, 532–33 Ross, R., A3 Rotavirus, 146f, 451, 680–82

I-22

Index

Rough endoplasmic reticulum (RER), 116 Rounding off, of numbers, A1-A2 Roundworms, 133, 135t, 696–97 Rous, Francis, A3 Rubella, 153–54, 531–32, 533t Rubivirus, 532 Rubor, 410 Runs, of flagella, 84–85 Ruska, Ernst, A3 Russia. See Soviet Union Sabin, Albert, 571, 572 Sabouraud’s agar, 63t Saccharide, 42 Saccharomyces spp., 126 S. cerevisiae, 122f, 280, 770, 772 S. uvarum (carlsbergensis), 770 Safety. See also Health care personnel biosafety levels and classes of pathogens, 369, 370 food handling, 671, 774 Hazard Analysis and Critical Control Point, 774 Universal Precautions, 385–86 St. Helens, Mount (volcano eruption, 1980), 647 St. Louis encephalitis (SLE), 88, 563 Saliva. See also Oral cavity antimicrobial properties, 661 portals of exit for infection, 379 specimen collection, 492 Salk, Jonas, 571, 572, A3 Salmonella spp., 63, 64, 672–73, 777. See also Salmonellosis S. enterica, 139, 164, 198, 228, 672 S. enteriditis, 94f, 190. See also Typhoid fever S. hirschfeldii, 672 S. paratyphi, 672 S. typhimurium, 254, 258, 672 Salmonella/Shigella (SS) agar, 63t Salmonellosis, 139, 157, 198, 228, 672–73, 680t. See also Salmonella spp. Salpingitis, 719 Salt. See also Sodium chloride adaptations to extreme habitats, 104, 173, 178 food preservation, 778 microbial growth, 185 Salvarsan, 329, 727 Sand fly, 535, 536 San Diego Zoo, 512 Sanger, Frederick, 274 Sanger method, of DNA sequencing, 275f, 276 Sanitization, 301 Sapro-, 174t Saprobes, 122, 171t, 172, 174 Saquinavir, 345t Sarcina, 100 Sarcodina, 131 Sargasso Sea, 756

SARS. See Severe acute respiratory syndrome Satcher, David, 9 Satellite viruses, 164 Satellitism, 187 Saturated fatty acids, 45–46 Saturation, and facilitated diffusion, 178 Sauerkraut, 772 Saxitoxins, 108, 128 Scale, 528 Scalp, and ringworm, 536, 538 Scanning confocal microscope, 73t Scanning electron microscope (SEM), 73t Scanning probe microscopes, 76 Scanning tunneling microscope (STM), 73t, 76 Scarlet fever, 533, 629 Schatz’s method, 319 Schaudinn, Fritz, A3 Schistosoma haematobium, 715 Schistosoma japonicum, 135t, 700–701, 702t Schistosoma mansoni, 700–701, 702t Schistosomiasis, 700–701, 714–15 Schizogony, 603 Schizophrenia, 9 Schizont, 603–604 Schultz, Heide, 99 Schwann, Theodor, 13 Scientific method, 15 Scope mouthwash, 323t Scorpion venom, 330 Seasonal influenza, 635–36 Sebaceous glands, 514 Sebum, 514 Secondary consumers, 745 Secondary immunodeficiency diseases, 483t, 485–86 Secondary infections, 377, 525, 530 Secondary metabolites, 780 Secondary phase, of wastewater treatment, 766 Secondary response, to antigens, 440 Secondary structure, of protein, 49 Secondary syphilis, 724–25 Secondary tuberculosis, 640–41, 643 Secretory IgA, 438 Sedimentary cycles, 749–51 Seed warts, 534 Segmented RNA, 148 Selective medium, 62, 63t, 74 Selective permeability, of cell membrane, 94, 176 Selective toxicity, of antimicrobial drugs, 330–35 Self, reaction of lymphocytes to, 430 Semiconservative replication, 238 Semisolid media, 60 Semisynthetic drugs, 330t, 334, 336 Semmelweis, Ignaz, 17, A3 Sensitivity, in immune testing, 500, 501f Sensitization, and type I allergy, 463–65 Sensitizing dose, 463

Sepsis, 300 Septa, 122–23 September 11, 2001 (terrorist attacks), 268, 291, 292 Septicemia, 375 , 378, 587, 589–90, 762 Septicemic anthrax, 606 Septic shock, 15 Sequelae, of infection, 379 Sequence maps, 290 Sequencing, of DNA, 274–76 Sequestered antigen theory, 480 Serology and serological tests, 499–500, 508f Serotonin, 412, 466 Serotype and serotyping, 102, 504 Serous exudate, 413 Serratia marcescens, 65f Serum, of blood, 405 Serum hepatitis, 690 Serum sickness, 475, 476 Severe acute respiratory syndrome (SARS), 387, 653 Severe combined immunodeficiency disease (SCID), 290, 484–85 Sewage treatment, 678, 715 Sexual intercourse, and HIV transmission, 611, 613, 614 Sexual phase, of malaria, 604 Sexually transmitted diseases (STDs), 371, 379, 388, 611, 613, 715, 721. See also Gonorrhea; Syphilis Sexual spore formation, 125–26 Shapes, of prokaryotes, 98, 100–101 , 120t Sheep, 364, 503, 566 Shell(s), of electrons, 30–31 Shellfish, and food poisoning, 108, 128, 135, 168, 678, 758 Shiga toxin, 673, 674, 675 Shiga-toxin-producing E. coli (STEC), 674, 680t Shigella spp., 372t S. dysenteriae, 673 S. flexneri, 673 S. sonnei, 673 Shigellosis, 673–74, 680t Shingles, 526–27 Shultze, Franz, 13 “Sick building syndrome,” 124 Sickle cell disease, 368–69 Side effects of antimicrobial therapy, 352–54 of vaccines, 450–51 Siderophores, 419 Signs, of disease, 378, 508f. See also Symptoms Silent mutation, 257 Silver compounds, and microbial control, 314t, 320–21 Silver nitrate, 320 Silver sulfadiazine ointment, 320–21 Simian immunodeficiency viruses (SIVs), 614

Index

Simple stains, 74 Singer, S. J., 47 Single-cell protein (SCP), 774 Single nucleotide polymorphism (SNP), 290, 292 Single-stranded (ss) DNA viruses, 155 Single-stranded (ss) RNA, 154 Sinorhizobium, 88f Sinusitis, 626 Size of genomes, 235 of microbes, 67–68 of prokaryotes, 98, 99 of viruses, 142f, 143 Skin. See also Skin testing AIDS-defining illnesses, 609 allergies, 466, 468 barriers and host defenses, 398–99 diseases and infections of, 512, 515–38 hookworms, 697 naming of lesions, 528 normal microbiota, 364t, 365t, 514–15 portals of entry for infection, 369 portals of exit for infection, 379 side effects of antimicrobial therapy, 352–53 sterility, 319 structure and defenses, 513–14 Universal Precautions, 386 Skin testing allergies, 468 coccidioidomycosis, 557–58 tuberculosis, 641f, 642–43 Skunks, and rabies, 569 Sleeping sickness, 132, 577–78 Slime layer, 86, 88 Sludge, 766 Small interfering (si) RNAs, 242, 243t, 289 Small intestine, 661 Smallpox, 156t, 446, 527–30, 650 Smith, Hamilton, 14 Smooth endoplasmic reticulum (SER), 116 Snow, John, A3 Soap and Detergent Association, 313 Soaps, 314t, 318–19, 320f, 323t Sodium elements of life, 29t, 30f ionic bonds, 34–35 microbial nutrition, 169t Sodium chloride, 35 Sodium stibogluconate, 536 Soil and soil microbiology, 5t, 382, 753–55 Solid media, 60 Solutions, 38–39 Solvents, 38 Sorbic acid, 322 Southern, E. M., 272 Southern blot test, 272, 273f Soviet Union, and diphtheria epidemic, 632 Space-filling models, 37 Spanish flu pandemic (1918), 638

Sparger, of fermentor, 781 Specialized transduction, 262 Species, 20, 102, 149, 400, 492 Specific immune globulin (SIG), 446–47 Specific immunity, 425–27, 443–52 Specificity antigens, 428 apoenzymes, 201 host defenses, 425–26 immune testing, 500, 501f osmosis, 178 Specimen collection and preparation, 56f, 492–95 Spheroplast, 93 Spine, and tuberculosis, 641 Spirillium, 98, 100f Spirochetes, 85, 98, 100f Spirogyra, 127f Spiroketal, 27 Spirulina, 774 Spleen, 80, 88, 405 Spliceosome, 250 Split gene, 250 Spongiform encephalopathies, 163–64 Spontaneous generation, 12–13 Spontaneous mutation, 256, 258 Sporadic CJD, 568 Sporadic disease, 390, 391f Sporangium, 96, 125 Spore(s), 17, 96, 123, 125–26. See also Endospores Spore stain, 75f Sporicidal liquid, 299t Sporocarcina, 96 Sporozoites, 131, 603 Sporulation, 96, 97f Spread plate technique, 58 Sputum, and specimen collection, 492–93 Squamous intraepithelial lesion (SIL), 733 Ss blood groups, 474 ssRNA. See Single-stranded RNA Stains and staining, 71, 74–76. See also Acid-fast staining; Dyes; Gram staining Stanford University, 492, 566 Staphylococcal scalded skin syndrome (SSSS), 522–24 Staphylococcus spp., 63 S. aureus. See also Staphylococcal scalded skin syndrome antimicrobial therapy, 350 endocarditis, 588 food poisoning, 682, 684t heat resistance and thermal death, 306 impetigo, 516–18 names and naming, 20 osmotic pressure, 185 parasitic microorganisms, 174 PNA FISH testing for, 498f population growth and generation time, 190–91 temperature range for growth, 181

I-23

S. epidermidis, 514, 518 S. saprophyticus, 712, 713t Starch, 44f Start codon, 247 Starter cultures, 769 State University of New York at Stony Brook, 163 Stationary growth phase, 191–92 Stavudine (d4T), 345t, 614 Steam sterilization, 306–307 Stem cells, 406, 407f, 429, 479 Stentor, 129f Sterilants, 300 Sterile, 17, 57, 300, 319 Sterile milk, 308 Sterilizing gas, 299t Sterilization, 17, 298, 300. See also Asepsis and aseptic techniques Steroids, 42t, 47, 779t, 783 Sterols, 113 Stierle, Andrea, 27, 34 Stock cultures, 66 Stomach antimicrobial properties of fluid, 661 Helicobacter pylori and cancer of, 670 normal biota, 663 Strains, of bacteria, 102 Stratum basale, 514 Streak plate method, 57 Streptococcal infections, 15 Streptococcus spp., 15 S. agalactiae, 559, 560t S. mutans, 372t, 664 S. pneumoniae. See also Pneumonia cold and desiccation, 309 conjunctivitis, 540 glycocalyx, 88 otitis media, 627 phase variation, 254 pneumococcal meningitis, 554–55, 559t transformation of DNA, 261 S. pyogenes. See also Pharyngitis; Scarlet fever adhesive properties, 372t cell envelope structure, 94 conjunctivitis, 540 erysipelas, 518–19 impetigo, 516–17, 520–21 parasitic microorganisms, 174 role of enzymes in disease, 205 S. sobrinus, 372t, 664 S. thermophilus, 770 Streptokinase, 374, 520, 779t Streptolysins, 205, 374, 630 Streptomycin, 336t, 354t Stress hormones, 369 Stroke, and nosocomial pneumonia, 652 Stroma, 119 Strongyloides stercoralis, 698 Structural formulas, 37f Structural genes, 234

I-24

Index

Structural locus, and gene regulation, 251 Sty, in eye, 541 Subacute encephalitis, 564–68 Subacute endocarditis, 589 Subacute sclerosing panencephalitis (SSPE), 530, 567t Subclinical infections, 378 Subculture, 66 Subspecies, 102 Substrate(s), 122, 200 Substrate-level phosphorylation, 211 Subunit vaccines, 449 Succinic acid, 216 Succinyl CoA, 216 Sucrose, 42, 43 Suffixes, 174t, 375, 587 Sugars, and food preservation, 778 Sulfadiazine, 566 Sulfa drugs, 329, 335f Sulfamethoxazole-trimethoprim (TMP-SMZ). See Trimethoprimsulfamethoxazole Sulfate, 750 Sulfhydryl, 41f Sulfisoxazole, 341 Sulfites, 778 Sulfolobus, 173 Sulfonamides, 329, 333, 335, 336t, 341, 349, 352t Sulfur, 29t, 30f, 169t, 171 Sulfur cycle, 749–51 Sulfur indole motility (SIM), 60f, 64t Sumerians, 770 Sun, as source of energy, 225–28 Superantigens, 433, 517, 518, 630 Superficial mycoses, 538, 539t Superinfection, 353, 357 Superoxide dismutase, 183, 220 Suramin, 578 Surfactants, 304, 318 Surgical asepsis, 385 Surgical debridement, 522 Susceptibility allergy, 462 infectious disease and host defenses, 400 of microorganisms to drugs, 354–56 Svedberg (S), 95 Sweat glands, 514 Swimming pool(s), and infectious disease, 561, 680 Swine. See Pig(s) Swine flu, 636, 637f, 638 Sydenham, Sir Thomas, 417 Symbiosis, 186, 187 Symptoms, of disease, 378, 508f. See also specific diseases Syncephalastrum, 123f Syncytium (syncytia), 156, 531, 669 Syndrome, 378 Synercid, 340 Synergism, 187, 335

Synthesis. See also Protein synthesis regulation of enzymes, 207 of viruses, 153–55, 160t Synthesis reaction, 37 Synthetic biology, 286–87 Synthetic drugs, 330t Synthetic medium, 61 Syphilis, 329, 502, 724–27, 730t. See also Treponema pallidum Systemic anaphylaxis, 468 Systemic autoimmune diseases, 479, 481 Systemic infections, 376, 377f, 586 Systemic leishmaniasis, 535 Systemic lupus erythematosus (SLE), 80, 480t, 481 Tachyzoite, 565 Taenia saginata, 695 Taenia solium, 135t, 695, 696t Tamiflu, 344, 345t, 639 Tannerella forsythia, 666 Tapeworm, 133, 135t, 695–96 Taq polymerase, 182, 276 Target cells, and cytotoxic T cells, 443 Taste, and normal microbiota, 368 Tatum, E. L., A3 Taxa (taxon), 18 Taxonomy, 18, 102, 121. See also Classification T cell(s), 408 B-cell recognition and cooperation, 436 cell-mediated immunity, 440–41, 443 foreign MHC receptors, 477–78 immunodeficiency diseases, 483t, 484 organ transplantation, 476–79 receptors, 431–32, 434 specific events in maturation, 429, 430f T-cell-mediated hypersensitivity, 461t Tears, and eye, 539 Teeth diseases and infections, 664–68 normal biota, 663 side effects of antibiotics, 353 Teichoic acid, 91 Telithromycin, 340 Temperate phages, 159 Temperature. See also Cold; Heat food preservation, 775–77 microbial adaptations, 180–82 microbial control, 306t, 309 Template strand, 244 Teratogenic effects, 516, 531 Terbinafine, 538 Termination, of DNA replication, 240, 247, 249 Terminology. See also Names and naming antisense in molecular genetics, 288 antitoxins, 438 of chemotherapy, 330t, 331 clones and cloning, 279 epitopes and antigens, 433

infection and disease, 375, 382 microbial adaptations, 174t microbial control, 300–301 skin lesions, 528 spores and sporulation, 96 use of “transformation,” 262 Termites, 186, 750 Terrorism. See Bioterrorism; World Trade Center attacks Terry, Luther, 9 Tertiary consumers, 745 Tertiary structure, of protein, 49 Tertiary syphilis, 725 Testes, 709 Tetanospasmin, 573 Tetanus, 573–74. See also Clostridium tetani Tetanus immune globulin (TIG), 574 Tetracycline(s), 332, 334, 336t, 340, 352t, 353, 354t Tetrads, 100 Tetrapeptide, 91f T-even bacteriophages, 158–59 Texas , 576, 600 Texas A & M University, 364 Thailand, and dengue fever, 598 Thayer-Martin medium, 62, 721 T helper cells, 441 Theory, and scientific method, 3, 16 Therapeutic index, 356–57 Thermal death point (TDP), 306 Thermal death time (TDT), 306, 775 Thermal springs, 182 Thermo-, 174t Thermocline, 757 Thermococcus litoralis, 276 Thermoduric microbes, 182 Thermophiles, 182 Thermoplasma, 105, 185 Thermus aquaticus, 182, 276 Thiabendazole, 538, 692t Thimerosal, 320, 452 Thiobacillus spp., 750–51 T. ferrooxidans, 751 T. thiooxidans, 750–51 Thioglycollate broth, 184f Thiomargarita namibia, 99 Thiosulfate, 750 Third World. See Africa; Developing countries Threadworm, 698 Thylakoid(s), 119, 226 Thymidine kinase. 344 Thymine (T), 50, 235 Thymus, 402, 404–405, 484 Ticarcillin, 337t, 355f Ticks, 594, 601 Tigecycline, 340 Tilex mildew remover, 323t Time, and microbial control, 306t Tinctures, 314 Tinea, 536

Index

Tinea versicolor, 127t, 536, 539t TI (tumor-inducing) plasmid, 286 Tissue culture, 161–62 Tissue plasminogen activator (tPA), 283t Titer, and antigen-antibody interactions, 500 T lymphocytes. See T cell(s) Tobacco mosaic virus, 144–45 Tobramycin, 336t Togaviridae, 150t Toll-like receptors, 416 Tolnaftate, 538 Tomato juice agar, 63t Tonsil(s), 661 Tonsillitis, 628 Topoisomerases I and II, 238t Topsoil, 754 TORCH, 372 Total cell count, 193–94 Toxemias, 374, 376–77 Toxic epidermal necrolysis (TEN), 523 Toxicity. See also Toxins antimicrobial drugs, 330, 352–53 heavy metals, 320 Toxicodendron, 478 Toxic shock syndrome (TS), 629 Toxigenicity, 374 Toxin(s). See also A-B toxins; Endotoxins; Exotoxins; Toxicity bacterial and cellular damage, 374–75 biogeochemical cycling, 751 fungi, 122, 126 specialized transduction, 263 Toxin neutralization test, 504 Toxinoses, 374 Toxoid vaccines, 449 Toxoplasma gondii, 131, 564, 565, 567t Toxoplasmosis, 131t , 565 Trace elements, 169 Tracheal cytotoxin, 634 Tracheotomy, 574 Trachoma, 541–42. See also Chlamydia trachomatis Transamination, 224 Transcription, of DNA, 240–51 Transduction, and DNA recombination, 259, 262–64 “Trans fat,” 46 Transferases, 203 Transfer reactions, by enzymes, 205 Transferrin, 419 Transfer RNA (tRNA), 51, 243t, 244 Transformation DNA recombination events, 259, 261–62 of viruses, 157 Transgenic animals, 286 Transgenic plants, 284, 286, 287t Translation, of DNA code, 240–51 Translocation, of RNA, 247 Transmissible agent, 567

Transmissible spongiform encephalopathies (TSEs), 566 Transmission, of infectious agents, 382–84. See also Droplet contact; specific diseases Transmission electron microscope (TEM), 73t Transport cell membrane, 94 nutrient absorption, 174–80 Transport media, 64–65 Transposons, 263–64 Travel, and infectious disease, 604, 622, 675, 689, 692 Treatment. See specific diseases Tree of life, 22–24 Trematodes, 133, 135t Trench fever, 601, 602t Treponema pallidum, 495f, 725, 726. See also Syphilis Treponema vincentii, 668 Trichinella spiralis, 135t Trichinosis, 695, 699–700 Trichomonas vaginalis, 129f, 130, 717–18 Trichomoniasis, 131t Trichophyton spp., 537 Trichuris suis, 694 Trichuris trichiura, 694, 696t Triclosan (Irgasan), 313, 317 Trifluridine, 542 Triglycerides, 42t , 45 Trimethoprim, 333, 335, 341, 349 Trimethoprim-sulfamethoxazole, 556, 634, 652, 673 Triple-sugar iron agar (TSIA), 64t Triplet code, 241 Trojan horse vaccine, 450 Troph-, 174t Trophozoite, 130, 685, 686 Tropisms, 151 Trovafloxacin, 341 True pathogens, 366 Trypanosoma spp., 132 T. brucei, 131t , 132, 577–78. See also Sleeping sickness T. b. gambiense, 578 T.b. rhodesiense, 578 T. cruzi, 131t, 132 Trypanosomes, 132 Trypanosomiasis, 131t, 577–78 Trypticase soy agar (TSA), Tsetse fly, 577–78 TSG101, 351 Tube agglutination test, 501f Tube dilution tests, 354, 356 Tubercle(s), 640 Tuberculin test, 507 Tuberculosis, 449, 476, 640–44, 645t. See also Mycobacterium tuberculosis Tube worms, 186 Tubulin, 96

I-25

Tularemia, 592–93, 650, 651. See also Francisella tularensis Tulip(s), 141 Tumbles, of flagella, 84–85 Tumor(s), 410 Tumor necrosis factor (TNF), 283t, 412, 416, 481, 630 Turbidity, and measurement of growth, 193 Turgid cytoplasmic membrane, 178 Tuskegee Study, 724 Twinrix, 689 Twort, Frederick, 157 Tyndall, John, 17, 307 Tyndallization, 307–308 Type(s), of bacteria, 102 Typhoid fever, 381, 672, 673. See also Salmonella enteritidis Typhoid Mary, 381 Tyrosine, 48f Ubiquitous, microbes as, 3 Ulcerative colitis, 684, 694 Ulcer diseases, of reproductive tract, 715, 723–31 Ulcers. See Gastric ulcers Ultrahigh-temperature (UHT) pasteurization, 776 Ultraviolet radiation (UV), 72t, 185, 256, 257, 310, 322 Unclotted blood, 405 Uncoated viruses, 152–53, 159 Undulant fever, 599 Undulating membrane, 129 UNICEF, 452, 679 Unified atomic mass unit (U), 31 United Nations, 382, 604 U. S. Department of Agriculture (USDA), 286, 774, 775, 776 U. S. Department of Health and Human Services, 455 U. S. Public Health Service (USPHS), 4t, 388, 650 Universal donor, 472 Universal Precautions (UPs), 385–86 University of Hawaii, 708, 734, 769 University of Iowa, 694 University of Keil (Germany), 327 University of Montana, 27, 34 University of Tennessee, 289 University of Wisconsin, 776 Unsaturated fatty acids, 45–46 Upper respiratory tract infectious diseases, 624–37, 639 normal microbiota, 365t structure and defenses of, 623, 624 Upwelling, 757 Uracil (U), 50, 243 Urea, 185 Urea breath test, 671 Urea broth, 60f, 64t Urease, 670, 671

I-26

Index

Urethra, 709 Urethritis, 712 Urinary schistosomiasis, 714–15 Urinary tract, 709. See also Genitourinary tract; Urogenital tract infectious diseases, 712–15, 735t, 736f, 737f normal microbiota, 364t, 365t specimen collection, 492 Urinary tract infections (UTIs), 712–13 Urine, 709 Urogenital tract portals of entry for infection, 371 portals of exit for infection, 379 Urushiol, 478 Uterus, 710 Vaccination and vaccines. See also Immunization; specific diseases allergy, 469–70 characteristics of effective, 448t chickens and infectious diseases, 139 dental caries, 666 development of new, 450 genetic engineering, 141, 283 HIV, 614 meningitis, 554 obesity, 164 otitis media, 627 recommended, 451–52, 453t, 454t rhinitis, 625 routes of administration and side effects, 450–51 salmonellosis, 673 specific immunity, 443–52 Streptococcus pneumoniae, 555 Vaccinia virus, 143f Vacuoles, 117–18 Vagina, 710, 712 Vaginitis and vaginosis, 715–18 Valacyclovir, 344 Valence, 31 Valine, 48f Valves, of heart, 588 Vampirovibrio chlorellavorus, 20 Vancomycin, 339, 348, 354t, 588, 677 Vancomycin intermediate Staphylococcus aureus (VISA), 348 Vancomycin-resistant Enterococcus faecalis (VRE), 341 Vancomycin-resistant Staphylococcus aureus (VRSA), 348 Van der Waals forces, 36–37 Variable (V) regions, 431 Variant form of CJD (VCJD), 568 Varicella-zoster virus (VZV), 526 Variola minor and major, 527–28. See also Smallpox Variolation, 446, 529–30 Varmus, Harold, A3 Vas deferens, 709–10 Vasoactive mediators, 410, 412

VDRL (Venereal Disease Research Laboratory) test, 502 Vector(s) for cloning, 278, 279–80 for disease, 381 Vegetations, on heart valves, 588 Vegetative cells, 75 , 306 Vegetative hyphae, 123f Vehicle, for infectious disease, 383–84 Veins, 586 Venter, J. Craig, 274, 286, 756 Vent polymerase, 276 Ventricles, of heart, 586 Vesicle, 528 Vesicular or pustular rash diseases, 524–30 Vesicular stomatitis virus (VSV), 141 Vetter, David, 485 Viable noncultured (VNC) microbes, 492 Viable plate count, 192 Vibrio, 98, 100f Vibrio cholerae, 160, 677–78, 681t. See also Cholera Vibrio fischeri, 84f Vibrio parahaemolyticus, 168, 183, 777 Vibrio vulnificus, 762, 769, 783 Vidarabine, 345t Viking Explorer spacecraft, 19 Vinegar, 222, 772 Viremia, 375, 378, 587 Virion, 10, 144 Viroids, 164 Virtual image, 69 Virucide, 300 Virulence, of infectious disease, 367 Virulence factors, 367, 373. See also specific diseases Virus(es), 10. See also specific diseases antibiotics, 357 antiviral drugs, 165, 332, 343–44, 345t artificial, 163 autoimmune disorders, 481 biological spectrum, 141–42 classification and naming of, 149 conjunctivitis, 541 cultivation and identification of, 160–62 diagnosis of infections, 507, 508f dimensions, 67 discovery of, 140 eukaryotes and prokaryotes compared to, 120t gastroenteritis, 682 gastrointestinal tract as portal of entry, 369 general structure, 143–49 genetically modified organisms, 284 genetics of, 251 important families, genera, names, and diseases of, 150–51t interferon, 418 medical importance of, 163 meningitis, 558, 559t microbial control, 309

multiplication, 151–60 normal microbiota, 364 in oceans, 756 positive view of, 141 properties of, 142t size of, 142f, 143 treatment of infections, 165 Vitamins, 203, 531, 779t Vitravene, 288 Vodka, 772 Von Borries, B., A3 Von Linné, Carl (Linnaeus), 18 Vulvovaginal candidiasis, 716 Waksman, Selman, A3 Walking pneumonia, 645, 647 Warren, J. Robert, 670 Wart(s), and wartlike eruptions, 534–35 Wart diseases, of reproductive tract, 715, 731–33 Water and water supplies. See also Aquatic microbiology cell composition, 169 cholera, 678 Cryptosporidium spp. and contamination, 316, 322, 680 distribution of on Earth’s surface, 755t environmental influences on microbes, 185 fertilizer runoff into, 751 filtration for purification of, 312 giardiasis, 686 hepatitis, 689 hydrogen bonding, 36f on Mars, 19 microbial contamination of, 297 monitoring to prevent disease, 766–68 polar nature of, 34 reservoirs for disease, 382 solutions, 38 space-filling model of, 37f ultraviolet treatment system for disinfection, 311f wastewater treatment, 763–69 Water quality assays, 767 Watson, James, 235, 236, 284, A3 Wavelength, of light, 69–70 Waxes, 42t, 47 Websites, 274 Weight, 31 Weil-Felix reaction, 502 Weil’s syndrome, 713 Weiss, Benjamin, 19 Western blot analysis, 502–503, 614 Western equine encephalitis (WEE), 563 West Nile virus, 563, 564 Wet Ones antibacterial moist towellettes, 323t Whales, 752 Wheal and flare reaction, 466 Whey, 773 Whipworm, 694

Index

Whiskey, 772 White blood cells (WBCs), 401f, 406, 413 Whittaker, Robert, 22 Whole blood, 405 Whooping cough, 633–35 Wilkins, Maurice, 236, A3 Wine, 222, 771–72 Wisconsin Division of Public Health, 55, 680, 766 Wobble, and genetic code, 247 Woese, Carl, 22–23 Wood, and cutting boards, 776 World Health Organization (WHO) emerging pneumonias, 653 epidemiology, 388 H1N1 flu epidemic, 638 malaria, 604, 606 oral rehydration therapy, 679 poliomyelitis, 570, 572 public health microbiology, 4t

report on leading causes of death, 8 smallpox, 446, 527 World Trade Center terrorist attack, 268, 291, 292 World War II, 774 Wort, 770 Wound botulism, 574, 576–77 Wright, James, A3 Xanthan, 779t Xenograft, 478 Xeroderma pigmentosa, 257 Xifaxan, 341 X-linked severe combined immunodeficiency disease (SCID), 288 X rays, 310, 643 Xylose, 42 Yahoo, 392

I-27

Yeast(s), 6, 122f. See also Saccharomyces spp.; Yeast infections Yeast artificial chromosomes (YACs), 280 Yeast infections, 715 Yellow fever, 597, 598t. See also Arboviruses Yellowstone National Park, 182 Yersinia spp., 676, 681t Y. enterocolitica, 676 Y. pestis, 590–91. See also Plague Y. pseudotuberculosis, 676 Yogurt, 285, 351, 773 Zalcitabine, 345t Zidovudine (AZT), 345t, 352t Zinc, 29t, 171 Zoonosis, 381–82, 592, 713 Zooplankton, 757 Zostavax, 527 Zosyn, 337