Microbiology with diseases by body system 3rd ed r bauman (pearson, 2012) 1

Chapter-by-Chapter Revisions • Four new photos • Thirteen figures revised and enhanced for better clarity and pedagogy CHAPTER 5 MICROBIAL METABOLISM • New “Clinical Case” and “Clinical

Cecily D Cosby, PhD, FNP-C, PA-C

Samuel Merritt College

Janet Fulks, EdD

Executive Editor: Leslie Berriman

Associate Editor: Katie Seibel

Director of Development: Barbara Yien

Editorial Assistant: Nicole McFadden

Art Development Manager: Laura Southworth

Art Development Editor: Elisheva Marcus

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Cover Photo Credit: Visuals Unlimited/Corbis.

Credits and acknowledgments borrowed from other sources and reproduced, with

permission, in this textbook appear on the appropriate page within the text or on p CR-1.

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Library of Congress Cataloging-in-Publication Data

Bauman, Robert W.

Microbiology : with diseases by body system / Robert W Bauman ; contributions by

Elizabeth Machunis-Masuoka, Jean E Montgomery ; clinical consultants, Cecily D Cosby,

Janet Fulks, John M Lammert – 3rd ed.

p ; cm.

Includes index.

ISBN-13: 978-0-321-71271-4 (Student ed : hardcover : alk paper)

ISBN-10: 0-321-71271-4 (Student ed : hardcover : alk paper)

1 Microbiology I Machunis-Masuoka, Elizabeth II Montgomery, Jean E III Title.

[DNLM: 1 Microbiological Phenomena 2 Bacterial Infections–microbiology QW 4]

1 2 3 4 5 6 7 8 9 10—CRK—13 12 11 10

To Michelle— I’m glad you are my partner and best friend

I look forward to another 25 years.

—Robert

About the Author

ROBERT W BAUMANis a professor of biology and past chairman of the Department ofBiological Sciences at Amarillo College in Amarillo,Texas He teaches microbiology, human anatomy and physiology, and botany In 2004, the students ofAmarillo College selected Dr Bauman as the recipient

of the John F Mead Faculty Excellence Award Hereceived an MA degree in botany from the University

of Texas at Austin and a PhD in biology from StanfordUniversity His research interests have included themorphology and ecology of freshwater algae, the cellbiology of marine algae (particularly the deposition ofcell walls and intercellular communication), andenvironmentally triggered chromogenesis in butterflies He is a member of the American Society

of Microbiology (ASM), Texas Community College Teacher’s Association (TCCTA), American

Association for the Advancement of Science (AAAS), Human Anatomy and Physiology Society

(HAPS), and The Lepidopterist’s Society When he is not writing books, he enjoys spending time

with his family and chocolate Labrador retriever: gardening, hiking, camping, rock climbing,

mountaineering, skiing, and reading classics out loud by a crackling fire

About the Clinical Consultants

CECILY D COSBYis nationally certified as both a family nurse practitioner and physician

assistant She is a professor of nursing at Samuel Merritt College in Oakland, California, and has

been in clinical practice since 1980, most recently at the University of California, San Francisco, in

a preoperative practice She received her PhD and MS from the University of California, San

Francisco; her BSN from California State University, Long Beach; and her PA certificate from the

Stanford Primary Care program

JANET FULKS is a professor of microbiology at Bakersfield College and a clinical laboratory

scientist She received her MA in Biology with an Emphasis in Microbiology from University of

Pacific, and her EdD in Higher Education Leadership from Nova Southeastern University Dr Fulks

and her husband spent six years in Nepal, working with doctors to diagnose diseases and train

Nepalese hospital workers She has also worked at the CDC and at a variety of clinical microbiology

labs Currently the college-wide curriculum chair, Dr Fulks has taught at Bakersfield College for

15 years and previously served as the biology department chair Her primary research areas are

student learning outcomes assessment, and student success and educational accountability

JOHN M LAMMERT is a professor of biology at Gustavus Adolphus College He teaches

courses in microbiology, immunology, and introductory biology In 1998, he received the Edgar M

Carlson Award for Distinguished Teaching at Gustavus Adolphus College Dr Lammert received

an MA in biology from Valparaiso University and a PhD in immunology from the University of

Illinois-Medical Center, Chicago He is the author of Techniques in Microbiology: A Student Handbook,

and three books on science fair projects (microbes, plants, and the human body)

understand, while at the same time presenting a thorough and accurate overview of microbiology.

I also wished to highlight the many positive effects of microorganisms on our lives, along withthe medically important microorganisms that cause disease

NEW TO THIS EDITION

In approaching the third edition, my goal was to build upon the strengths and success of theprevious edition by updating it with the latest scientific and educational research and data availableand by incorporating the many helpful suggestions I have received from colleagues and studentsalike The result is, once again, a collaborative effort of educators, students, editors, and topscientific illustrators, and a textbook that continues to improve upon conventional explanationsand illustrations in substantive and effective ways In this new edition:

• NEW Engaging, story-based Clinical Cases hook students at the beginning of the chapter and keep them curious until the Clinical Case Follow-Up at the end of the chapter Each chapter-

opening Clinical Case relates a compelling patient dilemma The Clinical Case Follow-Up revealsthe source of the patient illness and asks students to apply concepts covered in the chapter

• NEW Emerging Diseases boxes reflect this edition’s emphasis on cutting-edge clinical content.

Written in an engaging narrative voice that focuses on a patient’s experience, these boxes describe

diseases such as Hantavirus pulmonary syndrome, babesiosis, and MRSA (see p xxxvi for a full list).

• NEW Concept Mapping activity in the end-of chapter sections provide students with

hands-on practice for organizing the information they have learned, helping them to betterunderstand the connections between concepts

• IMPROVED Lab equipment illustrations feature increased dimensionality and realism to

help students get prepared for their lab course Glassware, such as test tubes, flasks, and Petriplates, look more authentic, allowing students to make a stronger connection between whatthey learn in their textbook and the experiments they perform in the lab

• Immunology chapters (Chapters 15–18) reflect the most current understanding of this rapidly

evolving field Immunology is also woven into student and instructor media through dynamicMicroFlix that bring immunology to life in 3-D animations The material in these chapters iscontinually reviewed in depth by immunology specialists

• Chapter 3 (Cell Structure and Function) has been reorganized to follow the latest taxonomic

research The discussion deemphasizes the term prokaryote and emphasizes the three domains

of living organisms The newly separate section on the Archaea can be covered or easilyskipped over, depending on instructor preference

• MasteringMicrobiology (www.masteringmicrobiology.com) provides unprecedented,

cutting-edge assessment resources for instructors as well as self-study tools for several textfeatures, including “Emerging Diseases” boxes and “Concept Mapping” exercises

The following section provides a detailed outline of this edition’s chapter-by-chapter

revisions followed by a visual walkthrough of its main themes and features

Chapter-by-Chapter Revisions

• Four new photos

• Thirteen figures revised and enhanced for better clarity and pedagogy

CHAPTER 5 MICROBIAL METABOLISM

• New “Clinical Case” and “Clinical Case Follow-Up” on botulism intoxication

• Clarified definitions of aerobic respiration versus anaerobic tion versus fermentation in text, figures, and critical thinking questions

respira-• Expanded coverage of vitamins as enzymatic cofactors

• New art to illustrate relationships of catabolism, anabolism, ADP energy cycle, use of nutrients, precursor metabolites, and macromolecules

ATP-• Alternatives to Embden-Meyerhof glycolysis (pentose phosphate pathway and Entner-Doudoroff pathway) rearranged for greater clarity and better pedagogy

• Twenty-two figures upgraded for greater clarity and better pedagogy

• One new figure

• Simplified longer figure legends, at request of reviewers

• New critical thinking question regarding photosynthesis

CHAPTER 6 MICROBIAL NUTRITION AND GROWTH

• New “Clinical Case” and “Clinical Case Follow-Up” on septicemia

• Added material concerning definition, development, and prevalence

of biofilms and quorum sensing

• Increased coverage of serial dilutions, viable plate counting, the contrast between lithotrophy and organotrophy, nonculturable microbes, continuous culture in a chemostat, and methods to obtain pure cultures

• Four new photos, one new figure

• Fifteen figures revised for greater clarity, ease of reading, and better pedagogy

• Five new questions for review at the end of the chapter, including three critical thinking questions

CHAPTER 7 MICROBIAL GENETICS

• New “Clinical Case” and “Clinical Case Follow-Up” on hepatitis C

• New “Clinical Applications” box on horizontal gene transfer

• New “Emerging Diseases” box on Vibrio vulnificus infection

• Revised discussion that more clearly explains the differences among archaeal, bacterial, and eukaryotic genetics

• Updated sections on bacterial chromosome number and bacterial plasmids

• Extended coverage of the difference between nucleoside and cleotide (many antimicrobial drugs are the former, not the latter)

nu-• Added discussion of the actions of topoisomerase and gyrase

• Expanded discussion of regulation of genetic expression—antisense RNA, RNA interference (RNAi), riboswitches—and CAP/cAMP-

mediated, positive regulation of the lac operon, and quorum sensing

as it relates to genetic control in infection

• Inclusion of newly discovered codons and tRNAs for 21st and 22nd amino acids

Every chapter in this edition has been thoroughly revised, and

data in the text, tables, and figures have been updated The

main changes for each chapter are summarized below

THROUGHOUT THE DISEASE CHAPTERS (CHAPTERS 19–24)

• Updated disease diagnoses, treatments, and incidence and prevalence

data

• Updated immunization recommendations and suggested treatments

for all diseases

CHAPTER 1 A BRIEF HISTORY OF MICROBIOLOGY

• New “Clinical Case” and “Clinical Case Follow-Up” on cholera

• New “Clinical Applications” box on a yellow fever epidemic in the

18th century

• New “Emerging Diseases” box on variant Creutzfeldt-Jakob disease

(prion disease)

• Four figures revised for better clarity and pedagogy

• Two new photos, two new figures

CHAPTER 2 THE CHEMISTRY OF MICROBIOLOGY

• New “Clinical Case” and “Clinical Case Follow-Up” on stomach ulcers

• Expanded coverage of role of manganese as an antioxidant in bacteria

• Expanded coverage of nucleosides, which are used as nucleotide

analogs in treating a number of diseases

• Seventeen figures revised for better pedagogy

• One new figure

CHAPTER 3 CELL STRUCTURE AND FUNCTION

• New “Clinical Case” and “Clinical Case Follow-Up” on streptococcal

infection

• New sections on Domain Archaea examining these microbes in

more detail and independently from Domain Bacteria, emphasizing

that “prokaryote” is not a taxonomic grouping

• Expanded coverage of bacterial shapes and arrangements, but kept

at level appropriate for this early chapter

• Reorganized discussion of eukaryotic flagella and cilia to emphasize

that these structures are internal to the cytoplasmic membrane

• Incorporation of new discoveries concerning cell structure and

function For example:

✓ Electrical signaling among bacteria via conductive fimbriae

✓ Archaeal hami—fimbriae-like cell extensions shaped like Ninja

grappling hooks on barbed wire

• Ten new photos, nine new figures

• Revised and enhanced artwork in nineteen figures

CHAPTER 4 MICROSCOPY, STAINING, AND CLASSIFICATION

• New “Clinical Case” and “Clinical Case Follow-Up” on cystic fibrosis

• New “Emerging Diseases” box on necrotizing fasciitis

• Added coverage of histological stains: Gomori methenamine silver

(GMS) stain and hematoxylin and eosin (HE) stain

• Updated coverage of taxonomy to be more current; for example,

expanded definitions of microbial species

• Three new figure legend questions and critical thinking questions

• Added material on transfer of resistance genes between and among bacteria and on research to discover novel antimicrobials

CHAPTER 11 CHARACTERIZING AND CLASSIFYING

PROKARYOTES

• New “Clinical Case” and “Clinical Case Follow-up” on diabetic foot syndrome

• New “Emerging Diseases” box on whooping cough

• New “Highlight” box on the possible connection between teria and neurological disorders such as amyotrophic lateral sclerosis, Parkinson’s disease, and Alzheimer’s disease

cyanobac-• Eight new photos

• Four figures revised for better pedagogy

CHAPTER 12 CHARACTERIZING AND CLASSIFYING

EUKARYOTES

• New “Clinical Case” and “Clinical Case Follow-Up” on dengue fever

• New “Emerging Diseases” box on aspergillosis

• Updated taxonomy of algae, fungi, protozoa, water molds, and slime molds

• Added discussion of the use by fungi of radiation as an energy source

• Ten new photos

• Thirteen figures upgraded for greater clarity, accuracy, ease of ing, and better pedagogy

read-CHAPTER 13 CHARACTERIZING AND CLASSIFYING VIRUSES,

VIROIDS, AND PRIONS

• New “Clinical Case” and “Clinical Case Follow-Up” on Ebola hemorrhagic fever

• New “Emerging Diseases” box on chikungunya

• Updated viral nomenclature to correspond to changes approved by the International Committee on Taxonomy of Viruses

• Expanded coverage of prions

• Four new TEMs of viruses

• Three new photos

• Three figures upgraded for better pedagogy

CHAPTER 14 INFECTION, INFECTIOUS DISEASES,

AND EPIDEMIOLOGY

• New “Clinical Case” and “Clinical Case Follow-Up” on urinary tract infection

• New “Emerging Diseases” box on Hantavirus pulmonary syndrome

• Incidence and prevalence figure redrawn to reflect current AIDS data in U.S.

• Updated epidemiology charts, tables, and graphs

• Updated list of nationally notifiable infectious diseases

• Expanded coverage of roles of public health agencies

• Seven figures revised for better pedagogy

• Two new photos

CHAPTER 15 INNATE IMMUNITY

• New “Clinical Case” and “Clinical Case Follow-Up” on mycoplasmal pneumonia

• New coverage of antimicrobial peptides and bradykinins (act in inflammation)

• Greatly enhanced coverage of Toll-like receptors (TLRs)

CHAPTER-BY-CHAPTER REVISIONS vii

• Coverage of new research showing that DNA moves through

hollow pili even over great distances

• Modified artwork to reflect changes in our understanding of

molec-ular biology: for example, where possible enzyme shapes are based

upon actual 3-D profiles as revealed by X-ray crystallography (e.g.,

Figures 7.5, 7.8, 7.20, and 7.27)

• Two new photos and three new art figures

• Twenty-seven upgraded figures for greater clarity, accuracy, ease of

reading, and better pedagogy

• New critical thinking questions

CHAPTER 8 RECOMBINANT DNA TECHNOLOGY

• New “Clinical Case” and “Clinical Case Follow-Up” on gene therapy

for SCID

• Expanded coverage of the use of recombinant DNA technology to

produce antisense nucleic acid molecules for research and genetic

modification of crops

• New coverage of DNA microarrays and fluorescent in situ

hybridiza-tion (FISH)

• Added coverage of new recombinant agricultural crops, including

potato-blight-resistant potatoes and deadly ringspot-virus-resistant

papayas

• New section discussing use of recombinant DNA techniques to

address environmental problems

• Increased coverage of the debate concerning genetic modification of

agricultural products

• Two new photos, four new figures

• Nine modified, updated, or pedagogically enhanced figures

CHAPTER 9 CONTROLLING MICROBIAL GROWTH IN

THE ENVIRONMENT

• New “Clinical Case” and “Clinical Case Follow-Up” on parasitic worm

infection

• New “Emerging Diseases” box on Acanthamoeba keratitis

• Three figures revised for better pedagogy

• Added descriptions of four biosafety levels as established by the

CDC

• Two new photos

• New critical thinking questions, including one based on the 2008

Salmonella outbreak associated with tomatoes and peppers

CHAPTER 10 CONTROLLING MICROBIAL GROWTH IN

THE BODY: ANTIMICROBIAL DRUGS

• New “Clinical Case” and “Clinical Case Follow-up” on drug-resistant

bacteria infection

• New “Emerging Diseases” box on community-associated MRSA

• Clarified etymology and use of the terms antimicrobial, antibiotic,

and semisynthetic

• Expanded discussion of use of RNA interference (RNAi) and antisense

nucleic acids as antimicrobial therapy

• Increased discussion of biofilms as they relate to drug resistance

• Updated and revised tables of antimicrobials to include all

antimi-crobials mentioned in pathogen chapters

• Added coverage of the new anti-HIV drug tenofovir and of the new

antibacterial drug mupirocin

• Four new photos, seven new figures

• Twelve figures revised for greater clarity, accuracy, ease of reading,

and better pedagogy, including correct shapes for anti-transcription

antimicrobials

viii CHAPTER-BY-CHAPTER REVISIONS

• Expanded coverage of pathogen-associated molecular patterns

(PAMPs)

• Discussion of neutrophil extracellular traps (NETs)

• Presentation of NOD receptor proteins

• Added discussion of the latest discoveries in iron usage among

pathogenic bacteria and sequestration of iron in the body as a defense

• Enhanced coverage of steps involved in phagocytosis

• Clarified artwork and discussion of pathways of complement

acti-vation, including the lectin pathway

• Six figures modified for enhanced clarity and better pedagogy,

in-cluding new hybrid TEM/artist’s rendition of phagocytosis

• Two new photos

CHAPTER 16 ADAPTIVE IMMUNITY

• New “Clinical Case” and “Clinical Case Follow-Up” on HPV

vaccination

• New “Emerging Diseases” box on microsporidiosis

• Updated information on adaptive T cell cancer therapy

• One new figure, seven revised pieces of art, two new photos for

better pedagogy

CHAPTER 17 IMMUNIZATION AND IMMUNE TESTING

• New “Clinical Case” and “Clinical Case Follow-Up” on whooping

cough

• Updated coverage of types of vaccines, including newly approved

combination vaccines

• Updated coverage of passive immunotherapy

• Added information regarding vaccines against agents of Japanese

encephalitis and typhoid fever

• Inclusion of newly revised CDC 2010 vaccination schedule for

children, adolescents, and adults

• Updated table of vaccine-preventable diseases in the U.S.

• Added discussion of methods of vaccine administration

• Expanded and clarified definitions of contact immunity, immunization,

vaccination, vaccine, titer, direct immune testing, and indirect immune

testing

• Fourteen figures revised for better pedagogy

CHAPTER 18 AIDS AND OTHER IMMUNE DISORDERS

• New “Clinical Case” and “Clinical Case Follow-up” on poison ivy

hypersensitivity

• Updated, simplified, and corrected material on Graves’ disease,

tissue transplants, and multiple sclerosis

• Eleven revised figures and two new photographs for more effective

• New “Clinical Case” and “Clinical Case Follow-Up” on severe acne

• New “Clinical Applications” box on a child with unsightly warts

• New “Clinical Applications” box on shingles

• New “Clinical Applications” box on athlete’s foot

• New “Clinical Applications” box on leishmaniasis revealed in

archaeological discoveries in Chile

• New “Emerging Diseases” box on Buruli ulcer

• New “Emerging Diseases” box on monkeypox

• Updated disease diagnoses, treatments, and incidence and lence data

preva-• Expanded coverage of methicillin-resistant and

vancomycin-resistant Staphylococcus aureus (MRSA, VRSA), necrotizing fasciitis,

and multi-drug-resistant tuberculosis (MDR-TB)

• Expanded and updated coverage of action of anthrax toxins

• Added coverage of extensively drug-resistant TB (XDR-TB)

• Four new photos

• Two figures revised for enhanced accuracy and pedagogy

• Five new end-of-chapter questions

CHAPTER 20 MICROBIAL DISEASES OF THE NERVOUS

SYSTEM AND EYES

• New “Clinical Case” and “Clinical Case Follow-up” on meningitis

• New “Clinical Applications” box on a trypanosome disease

• New “Emerging Diseases” box on tick-borne encephalitis

• New “Emerging Diseases” box on melioidosis

• Updated disease diagnoses, treatments, and incidence and lence data

preva-• Added discussion of blebbing as it relates to meningococcal disease

• Discussion of the action of tetanospasmin (tetanus toxin) revised for clarity, succinctness, and better pedagogy

• Expanded discussion of prion diseases

• Ten new figures

• Five figures revised for better pedagogy

CHAPTER 21 CARDIOVASCULAR AND SYSTEMIC DISEASES

• New “Clinical Case” and “Clinical Case Follow-Up” on tularemia

• New “Emerging Diseases” box on schistosomiasis

• Four new figures

• Five figures revised for greater visual contrast, pedagogy, accuracy, currency, and general interest

CHAPTER 22 MICROBIAL DISEASES OF

THE RESPIRATORY SYSTEM

• New “Clinical Case” and “Clinical Case Follow-Up” on tuberculosis

• New “Emerging Diseases” box on pulmonary blastomycosis

• New “Emerging Diseases” box on H1N1 influenza

• Text altered to reflect that Chlamydia pneumoniae and C psittaci are now classified as Chlamydophila spp.

• Twelve new figures

• Seven figures revised for enhanced pedagogy

CHAPTER 23 MICROBIAL DISEASES OF THE DIGESTIVE SYSTEM

• New “Clinical Case” and “Clinical Case Follow-Up” on giardiasis

• New “Clinical Applications” box examining cases of bacterial gastorenteritis

• New “Emerging Diseases” box on Norovirus gastroenteritis

• Expanded coverage of dental diseases, probiotics, and hepatitis viruses C and E

• Extensive coverage of pseudomembranous colitis (Clostridium difficile diarrhea)

• Added coverage of the connection between esophageal cancer and

the use of antibiotics to treat Helicobacter infection

• Reporting of the end of the cholera pandemic in South America in 2002

• Four new figures

• Four revised, updated, or enhanced figures

CHAPTER 25 INDUSTRIAL AND ENVIRONMENTAL

MICROBIOLOGY

• New “Clinical Case” and “Clinical Case Follow-Up” on salmonellosis

• Clarified use of the term fermentation in biochemistry, food

produc-tion, and industry

• Expanded coverage of pharmaceutical products produced by combinant DNA technology

re-• One revised figure

• One new photo

CHAPTER-BY-CHAPTER REVISIONS ix

• Seven new figures

• Seven revised, updated, enhanced, and pedagogically more effective

figures

CHAPTER 24 MICROBIAL DISEASES OF THE URINARY

AND REPRODUCTIVE SYSTEMS

• New “Clinical Case” and “Clinical Case Follow-Up” on genital herpes

• New “Clinical Applications” box examining a case of AIDS

• New “Clinical Applications” box examining a case of gonorrhea

• Expanded discussion of the fact that male circumcision reduces the

spread of sexually transmitted and urinary tract diseases

• Updated and expanded coverage of papillomaviruses, their

treat-ment, and prevention of their diseases

Reviewers For The Third Edition

Wendy Owen Dusek

Wisconsin Indianhead Technical College

First, I heartily thank the hundreds of instructors and students who participated in reviews, class

tests, and focus groups for earlier editions of the textbook Your comments have informed this

book from beginning to end, and I am deeply grateful For the third edition, I extend my deepest

appreciation to the following reviewers:

Tarrant County College

Gina Marie Morris

Frank Phillips College

American River College

Stephanie Rena Songer

North Georgia College & State University

Valencia Community College

University of New Mexico

Acknowledgments

As was the case with the first two editions, this book has truly been a team effort I am deeplygrateful to Leslie Berriman of Pearson Science and to the team she gathered to produce the thirdedition, foremost of whom is the wonderful Katie Seibel Leslie and Katie helped develop thevision for the third edition, constantly coming up with ideas for making it more effective andcompelling As project editor, Katie also had the unenviable task of coordinating everything andkeeping me on track—thank you, Katie! This edition wouldn’t have been possible without thediligent support, hard work, care, and friendship of Barbara Yien, who developed the first edi-tion, taught me patiently about book publishing, and introduced me to chocolate truffles Thankyou, dear friend Many thanks to Robin Pille, whose work on the Taxonomy version of this bookcontinues in this edition I am grateful to Frank Ruggirello for his support of my work and thisbook I am also indebted to Daryl Fox, whose early support for this book never wavered

Sally Peyrefitte edited the manuscript thoroughly and meticulously, suggesting important

changes for clarity, accuracy, and consistency Elisheva Marcus did a superb job as art

development editor, helping to conceptualize illustrations and suggesting ways to improve theart overall—thank you, Ellie My friend Ken Probst is responsible for originally creating many

of this book’s amazingly beautiful biological illustrations My thanks to Precision Graphics forrendering the art in this edition Michele Mangelli and David Novak of Mangelli Productionsexpertly guided the project through production Maureen “Mo” Spuhler did an incredible jobresearching the photos for this text Rich Robison and Brent Selinger supplied a variety of thetext’s wonderful and unique micrographs, while Travis Amos suggested ways to enhance thephoto selections Yvo Riezebos created the beautiful interior design and the stunning cover Thanks to Nichol Dolby of Amarillo College, Mindy Miller-Kittrell of University of Tennessee,Knoxville, Christopher Thompson of Loyola College, and Todd Primm of Sam Houston StateUniversity, for their work on the media and print supplements for this edition Thanks to CecilyCosby of Samuel Merritt College, Janet Fulks of Bakersfield College, and John Lammert of

Gustavus Adolphus College for their contributions to the chapter-opening Clinical Cases Thanks

to Suzanne Long, who created the concept maps that appear at the end of each chapter in thisedition Thanks also to Nan Kemp, Kelly Reed, Jacob Price, Jordan Roeder, and Nicole McFaddenfor their administrative, editorial, and research assistance Betsy Dietrich proofread and checkedpages, and Kathy Pitcoff indexed—without their help the book would be less useful Thanks toLucinda Bingham for her excellent work on the media program, especially MasteringMicrobiology.Finally, thanks to Neena Bali and the wonderful Pearson Science sales reps for continuing to do aterrific job of keeping in touch with the professors and students who provided suggestions tomake this edition better

I am especially grateful to Phil Mixter of Washington State University, John Lammert of GustavusAdolphus College, Mary Jane Niles of the University of San Francisco, Benjamin Wise of KeeneState College, Bronwen Steele of Estrella Mountain Community College, and Jane Reece for theirexpertise and advice on the cell and immunology chapters

On the home front, I am grateful for Chris Gilbert and Jordan Roeder, dear friends and formerstudents; Vance Esler, MD; John Curry, DDS; Dan Meddor, DDS; and Andy Roller, Larry Latham,and Mike Isley—all of whom are always supportive and helpful My “secretarial staff,” Michelle,Jennie, Elizabeth, and Jeremy, are always here to photocopy, type, file, surf the web, run to theFedEx box, and provide emotional support Thank you, dear ones My life isn’t my own—I oweeverything to others

Robert W Bauman

Amarillo, Texas

NEW Clinical Cases pique students’

curiosity at the beginning of each chapter and

keep them intrigued until the Clinical Case

Follow-Up at the end of the chapter Each

chapter-opening Clinical Case presents a

compelling patient story at just the right level

of student understanding The Clinical Case

Follow-Up reveals the source of the patient

illness and asks students to apply content in the

chapter to the Clinical Case.

Real-World Clinical

THE SALTY TODDLER

page 96

A SOUVENIR FROM PARADISE

page 347

RAW FISH, RAW DEAL?

page 261

TROUBLE AT THE REC CENTER

engaging narrative voice that focuses on a patient’s experience with

a key emerging or reemerging disease such as Hantavirus pulmonary

syndrome, babesiosis, and MRSA See page xxxvi for a full list of the Emerging Diseases boxes.

page 618

xiii

BOTULISMAND BOTOX

page 330

PLASTICS MADE PERFECT?

page 74

GOLD-MININGMICROBES

A full list of these Benefi cial Microbes boxes can be found on page xxxv.

SLIME MATTERS

HYDROGEN-LOVINGMICROBES

page 170

Highlight boxes focus on applied topics in microbiology

and help demonstrate the relevance of microbiology to everyday life

A full list of these Highlight boxes can be found on page xxxiv.

Critical Thinking questions , located throughout and at the end of each chapter, encourage students to apply what they have just

xvi

Real-World Practice

Disease at a Glance

boxes feature succinct

summaries of selected diseases

in each of the disease chapters

(Chs 19–24) These boxed

“snapshots” include the cause,

portal of entry, symptoms, and

treatment of the disease and

provide students with a

ready-made study tool.

Clinical Applications

boxes appear throughout the

book and are particularly helpful

to pre-nursing and allied health

students They ask students to

apply material they have learned

in the text to clinical scenarios

and often feature a micrograph

or clinical photo to interpret.

in the Book

Mapping activities

in the end-of-chapter sections

provide students with

hands-on practice for organizing

the information they have

learned Students can also

complete interactive concept

maps in the Study Area of

fi gures from the chapter.

Assign quizzes and activities on 3-D movie- quality animations

to help students understand and visualize tough topics.

xviii

You can now easily assign powerful online tools—

and have your assignments automatically graded!

Assign quizzes on

Get Ready For Microbiology

topics so that your students come to your course prepared.

Assign quizzes

on the opening Clinical Cases to encourage students to connect the case scenario to the larger themes explored in the chapter.

chapter-An Assignment and

Assign quizzes

on the Concept Mapping activities

to check and assess students’

conceptual understanding.

Grade assignments

automatically Shades

of red highlight students who

are struggling or assignments

that are diffi cult for the class as

a whole Easily export grades to

a course management system

or spreadsheet.

Other assignable features:

• Pre-lecture reading quizzes ensure that your students read the textbook before coming to class.

• Post-lecture quizzes check your students’ understanding.

• Pre-lab quizzes with accompanying lab techniques videos prepare your students for the lab.

• Post-lab quizzes check that your lab objectives were met.

Assessment System

Tools to Make the Grade

MasteringMicrobiology includes a Study Area that will help students get ready for tests with its simple, three-step approach:

Take a Pre-Test and obtain a personalized Study Plan.

Learn & Practice with animations, activities, and MP3 Tutor Sessions.

Test Yourself with quizzes and a chapter post-test.

Online Concept

Mapping activities help

students practice building maps to

organize concepts in a meaningful,

visual way These concept maps

also appear in the end-of-chapter

sections in the textbook.

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1 2 3

Study Area

115 multi-step

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References to the Microbiology

Animations appear throughout

the chapters of the book.

MicroFlixTM are 3-D

movie-quality animations with

self-paced tutorials and gradable

quizzes that help students master

the three toughest topics in

microbiology: metabolism, DNA

replication, and immunology

Students can view the animations,

complete the tutorial, print a

study sheet, and take the quiz

Students also have access to BioFlix

animations to help them review

relevant concepts from general

biology.

Support for Instructors

xxii

MasteringMicrobiologyTM

This website (www.masteringmicrobiology.com) helps

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for more information

eText with Whiteboard Mode

The Microbiology with Diseases by Body System, Third

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Study Guide

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Get Ready for Microbiology

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This new brief primer saves classroom time and frustration by helping students quickly prepare for their microbiology course

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Concise & Investigative

Laboratory Experiments

in Microbiology,

Ninth Edition

by Ted R Johnson and Christine L Case978-0321-56028-5 • 0-321-56028-0

This manual offers 57 exercises that encourage students to evaluate their results and draw conclusions Questions placed within the procedure require students to pause and recall what they have learned

Critical thinking questions in the Laboratory Reports

further promote analytical reasoning

Rich, vibrant photographs and illustrations appear within the relevant exercise, allowing students to better interpret their results

Comprehensive & Versatile

Microbiology:

A Laboratory Manual,

Ninth Edition

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This manual offers 75 straightforward, clearly explained experiments with minimal equipment requirements Instructors can pick and choose from a variety of diverse experiments, including labs in the areas of biotechnology, genetics, immunology, and medical microbiology

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An excellent companion for your laboratory manual

Techniques in Microbiology: A Student Handbook

by John M Lammert978-0-13-224011-6 • 0-13-224011-4

An ideal complement to a complete lab manual, this vivid, full-color handbook guides students in manipulations and preparations that are fundamental to the microbiology laboratory.

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Table of Contents

CHAPTER 1

A Brief History of

The Early Years of Microbiology 2

What Does Life Really Look Like? 2

How Can Microbes Be Classified? 3

The Golden Age of Microbiology 7

Does Microbial Life Spontaneously Generate? 7

What Causes Fermentation? 10

What Causes Disease? 11

How Can We Prevent Infection and Disease? 16

The Modern Age of Microbiology 18

What Are the Basic Chemical Reactions of Life? 18

How Do Genes Work? 19

What Roles Do Microorganisms Play in

the Environment? 20

How Do We Defend Against Disease? 20

What Will the Future Hold? 21

Chapter Summary 22 • Questions for Review 23

Critical Thinking 24 • Concept Mapping 25

Nonpolar Covalent Bonds 30

Polar Covalent Bonds 32

Carbohydrates 42Proteins 46Nucleic Acids 49Chapter Summary 52 • Questions for Review 53Critical Thinking 54 • Concept Mapping 55

CHAPTER 3

Cell Structure and

Processes of Life 57Prokaryotic and Eukaryotic Cells: An Overview 58External Structures of Bacterial Cells 59

Glycocalyces 59Flagella 61Fimbriae and Pili 64

Bacterial Cell Walls 65

Gram-Positive Bacterial Cell Walls 66Gram-Negative Bacterial Cell Walls 68Bacteria Without Cell Walls 68

Bacterial Cytoplasmic Membranes 68

Structure 68Function 69

Cytoplasm of Bacteria 73

Cytosol 73Inclusions 74Endospores 75Nonmembranous Organelles 76

External Structures of Archaea 76

Glycocalyces 76Flagella 77Fimbriae and Hami 77

Archaeal Cell Walls and Cytoplasmic Membranes 77Cytoplasm of Archaea 78

External Structure of Eukaryotic Cells 78

Glycocalyces 78

Eukaryotic Cell Walls and Cytoplasmic Membranes 79

xxv

xxvi TABLE OF CONTENTS

Chapter Summary 89 • Questions for Review 92

Critical Thinking 94 • Concept Mapping 95

Staining for Electron Microscopy 113

Classification and Identification of Microorganisms 114

Linnaeus and Taxonomic Categories 114

Domains 117

Taxonomic and Identifying Characteristics 117

Taxonomic Keys 120

Chapter Summary 122 • Questions for Review 123

Critical Thinking 124 • Concept Mapping 125

CHAPTER 5

Basic Chemical Reactions Underlying Metabolism 127

Catabolism and Anabolism 127

Oxidation and Reduction Reactions 128

ATP Production and Energy Storage 129

The Roles of Enzymes in Metabolism 129

Carbohydrate Catabolism 135

Glycolysis 136Cellular Respiration 136Alternatives to Glycolysis 144Fermentation 144

Other Catabolic Pathways 148

Lipid Catabolism 148Protein Catabolism 148

Photosynthesis 149

Chemicals and Structures 150Light-Dependent Reactions 151Light-Independent Reactions 152

Other Anabolic Pathways 154

Carbohydrate Biosynthesis 155Lipid Biosynthesis 155

Amino Acid Biosynthesis 156Nucleotide Biosynthesis 157

Integration and Regulation of Metabolic Functions 158

Chapter Summary 160 • Questions for Review 162Critical Thinking 164 • Concept Mapping 165

Special Culture Techniques 182Preserving Cultures 182

Growth of Microbial Populations 183

Mathematical Considerations in Population Growth 183Generation Time 184

Phases of Microbial Population Growth 184Continuous Culture in a Chemostat 185Measuring Microbial Reproduction 186Chapter Summary 191 • Questions for Review 192Critical Thinking 194 • Concept Mapping 195

CHAPTER 7

The Structure and Replication of Genomes 197

The Structure of Nucleic Acids 197

The Structure of Prokaryotic Genomes 197

The Structure of Eukaryotic Genomes 199

DNA Replication 201

Gene Function 206

The Relationship Between Genotype and Phenotype 206

The Transfer of Genetic Information 206

The Events in Transcription 207

Identifying Mutants, Mutagens, and Carcinogens 225

Genetic Recombination and Transfer 227

Horizontal Gene Transfer Among Prokaryotes 227

Transposons and Transposition 232

Chapter Summary 234 • Questions for Review 236

Critical Thinking 237 • Concept Mapping 238

The Use of Reverse Transcriptase to Synthesize cDNA 240

Synthetic Nucleic Acids 241

Restriction Enzymes 242

Vectors 244

Gene Libraries 245

Techniques of Recombinant DNA Technology 245

Multiplying DNA in vitro: The Polymerase Chain

Reaction (PCR) 245

Selecting a Clone of Recombinant Cells 247

Separating DNA Molecules: Gel Electrophoresis and the

Southern Blot 247

DNA Microarrays 248Inserting DNA into Cells 249

Applications of Recombinant DNA Technology 249

Genetic Mapping 249Environmental Studies 251Pharmaceutical and Therapeutic Applications 252Agricultural Applications 254

The Ethics and Safety of Recombinant DNATechnology 255

Chapter Summary 257 • Questions for Review 258Concept Mapping 259 • Critical Thinking 260

CHAPTER 9

Controlling Microbial Growth

Basic Principles of Microbial Control 262

Terminology of Microbial Control 262Microbial Death Rates 263

Action of Antimicrobial Agents 264

The Selection of Microbial Control Methods 264

Factors Affecting the Efficacy of AntimicrobialMethods 264

Methods for Evaluating Disinfectants and Antiseptics 266

Physical Methods of Microbial Control 267

Heat-Related Methods 267Refrigeration and Freezing 270Desiccation and Lyophilization 270Filtration 271

Osmotic Pressure 272Radiation 272

Biosafety Levels 274

Chemical Methods of Microbial Control 275

Phenol and Phenolics 275Alcohols 276

Halogens 276Oxidizing Agents 277Surfactants 277Heavy Metals 278Aldehydes 279Gaseous Agents 279Enzymes 280Antimicrobials 280Development of Resistant Microbes 280Chapter Summary 282 • Questions for Review 283Critical Thinking 285 • Concept Mapping 286

TABLE OF CONTENTS xxvii

xxviii TABLE OF CONTENTS

CHAPTER 10

Controlling Microbial

Growth in the Body:

The History of Antimicrobial Agents 288

Mechanisms of Antimicrobial Action 289

Inhibition of Cell Wall Synthesis 290

Inhibition of Protein Synthesis 291

Disruption of Cytoplasmic Membranes 293

Inhibition of Metabolic Pathways 294

Inhibition of Nucleic Acid Synthesis 295

Prevention of Virus Attachment 297

Clinical Considerations in Prescribing

Antimicrobial Drugs 297

Spectrum of Action 297

Efficacy 298

Routes of Administration 299

Safety and Side Effects 300

Resistance to Antimicrobial Drugs 301

The Development of Resistance in Populations 301

Mechanisms of Resistance 302

Multiple Resistance and Cross Resistance 303

Retarding Resistance 304

Chapter Summary 314 • Questions for Review 315

Critical Thinking 316 • Concept Mapping 317

CHAPTER 11

Characterizing and Classifying

General Characteristics of Prokaryotic Organisms 319

Morphology of Prokaryotic Cells 319

Reproduction of Prokaryotic Cells 319

Arrangements of Prokaryotic Cells 321

Deeply Branching and Phototrophic Bacteria 326

Low Gram-Positive Bacteria 328

High Gram-Positive Bacteria 331

Protozoa 353

Distribution of Protozoa 353Morphology of Protozoa 353Nutrition of Protozoa 354Reproduction of Protozoa 354Classification of Protozoa 355

Fungi 360

The Significance of Fungi 360Morphology of Fungi 361Nutrition of Fungi 362Reproduction of Fungi 363Classification of Fungi 364Lichens 367

Algae 370

Distribution of Algae 370Morphology of Algae 371Reproduction of Algae 371Classification of Algae 371

Water Molds 375Other Eukaryotes of Microbiological Interest:

Parasitic Helminths and Vectors 375

Arachnids 375Insects 376Chapter Summary 377 • Questions for Review 379Critical Thinking 380 • Concept Mapping 381

CHAPTER 13

Characterizing and Classifying Viruses,

Characteristics of Viruses 383

Genetic Material of Viruses 383Hosts of Viruses 384

Sizes of Viruses 384

Replication of Animal Viruses 394

The Role of Viruses in Cancer 399

Culturing Viruses in the Laboratory 400

Culturing Viruses in Mature Organisms 400

Culturing Viruses in Embryonated Chicken Eggs 401

Culturing Viruses in Cell (Tissue) Culture 401

Are Viruses Alive? 402

Other Parasitic Particles: Viroids and Prions 402

Characteristics of Viroids 402

Characteristics of Prions 403

Chapter Summary 406 • Questions for Review 407

Concept Mapping 408 • Critical Thinking 409

CHAPTER 14

Infection, Infectious Disease,

Symbiotic Relationships Between Microbes

and Their Hosts 411

Types of Symbiosis 411

Normal Microbiota in Hosts 412

How Normal Microbiota Become Opportunistic

The Movement of Microbes into Hosts: Infection 416

Exposure to Microbes: Contamination and Infection 416

Portals of Entry 416

The Role of Adhesion in Infection 418

The Nature of Infectious Disease 419

Manifestations of Disease: Symptoms, Signs,

and Syndromes 419

Causation of Disease: Etiology 419

Virulence Factors of Infectious Agents 422

The Stages of Infectious Diseases 425

The Movement of Pathogens Out of Hosts:

Portals of Exit 426Modes of Infectious Disease Transmission 427

Contact Transmission 427Vehicle Transmission 427Vector Transmission 428

Classification of Infectious Diseases 429Epidemiology of Infectious Diseases 430

Frequency of Disease 430Epidemiological Studies 433Hospital Epidemiology: Nosocomial Infections 435Epidemiology and Public Health 437

Chapter Summary 440 • Questions for Review 441Critical Thinking 443 • Concept Mapping 444

Immunity 449The Role of Normal Microbiota in Innate Immunity 449Other First-Line Defenses 449

The Body’s Second Line of Defense 450

Defense Components of Blood 450Phagocytosis 453

Nonphagocytic Killing 455Nonspecific Chemical Defenses Against Pathogens 455Inflammation 461

Fever 463Chapter Summary 466 • Questions for Review 467Critical Thinking 468 • Concept Mapping 469

B Lymphocytes (B Cells) and Antibodies 475

TABLE OF CONTENTS xxix

xxx TABLE OF CONTENTS

T Lymphocytes (T Cells) 480

Clonal Deletion 482

Immune Response Cytokines 484

Preparation for an Adaptive Immune Response 485

The Roles of the Major Histocompatibility Complex 485

Antigen Processing 486

Cell-Mediated Immune Responses 487

Activation of T Cell Clones and Their Functions 488

The Perforin-Granzyme Cytotoxic Pathway 489

The CD95 Cytotoxic Pathway 489

Memory T Cells 490

T Cell Regulation 490

Humoral Immune Responses 490

Inducement of T-Independent Humoral Immunity 490

Inducement of T-Dependent Humoral Immunity with

Clonal Selection 491

Memory B Cells and the Establishment of Immunological

Types of Acquired Immunity 495

Naturally Acquired Active Immunity 495

Naturally Acquired Passive Immunity 495

Artificially Acquired Active Immunity 495

Artificially Acquired Passive Immunotherapy 496

Chapter Summary 497 • Questions for Review 499

Critical Thinking 500 • Concept Mapping 501

The Complement Fixation Test 515

Labeled Antibody Tests 515

Recent Developments in Antibody-Antigen Immune

Testing 518

Chapter Summary 520 • Questions for Review 521

Critical Thinking 522 • Concept Mapping 523

Type IV (Delayed or Cell-Mediated) Hypersensitivity 535

Folliculitis 558Staphylococcal Scalded Skin Syndrome 560Impetigo (Pyoderma) and Erysipelas 561Necrotizing Fasciitis 562

Acne 564Cat Scratch Disease 565

Chickenpox and Shingles 576Rubella 578

Measles (Rubeola) 579Other Viral Rashes 581

Mycoses of the Hair, Nails, and Skin 582

Chapter Summary 591 • Questions for Review 592

Concept Mapping 595 • Critical Thinking 596

CHAPTER 20

Microbial Diseases of the

Structure of the Nervous System 598

Structures of the Central Nervous System 598

Structures of the Peripheral Nervous System 598

Cells of the Nervous System 598

Portals of Infection of the Nervous System 600

Bacterial Diseases of the Nervous System 600

Protozoan Diseases of the Nervous System 620

African Sleeping Sickness 620

Primary Amebic Meningoencephalopathy 622

Prion Disease 622

Variant Creutzfeldt-Jakob Disease (vCJD) 623

Microbial Diseases of the Eyes 624

Structure of the Eye 624

Trachoma 624

Other Microbial Diseases of the Eyes 625

Chapter Summary 626 • Questions for Review 627

Critical Thinking 629 • Concept Mapping 630

CHAPTER 21

Microbial Cardiovascular and

Structures of the Cardiovascular System 632

Structure of the Heart 632Movement of Blood and Lymph 632

Bacterial Cardiovascular and Systemic Diseases 632

Septicemia, Bacteremia, and Toxemia 632Endocarditis 636

Brucellosis 638Tularemia 639Plague 640Lyme Disease 642Ehrlichiosis and Anaplasmosis 644

Viral Cardiovascular and Systemic Diseases 646

Infectious Mononucleosis 646

Cytomegalovirus Disease 648

Yellow Fever 648Dengue Fever and Dengue Hemorrhagic Fever 649African Viral Hemorrhagic Fevers 651

Protozoan and Helminthic Cardiovascular and SystemicDiseases 653

Malaria 653Toxoplasmosis 655Chagas’ Disease 657Schistosomiasis 659Chapter Summary 662 • Questions for Review 663Critical Thinking 665 • Concept Mapping 666

CHAPTER 22

Microbial Diseases of the

Structures of the Respiratory System 668

Structures of the Upper Respiratory System, Sinuses, and Ears 668

Structures of the Lower Respiratory System 668Normal Microbiota of the Respiratory System 668

Bacterial Diseases of the Upper Respiratory System,Sinuses, and Ears 670

Streptococcal Respiratory Diseases 670Diphtheria 671

Sinusitis and Otitis Media 672

TABLE OF CONTENTS xxxi

xxxii TABLE OF CONTENTS

Viral Diseases of the Upper Respiratory System 674

Severe Acute Respiratory Syndrome (SARS) 689

Respiratory Syncytial Virus Infection 690

Hantavirus Pulmonary Syndrome 692

Other Viral Respiratory Diseases 693

Mycoses of the Lower Respiratory System 693

Coccidioidomycosis 693

Blastomycosis 695

Histoplasmosis 696

Pneumocystis Pneumonia (PCP) 698

Chapter Summary 699 • Questions for Review 701

Concept Mapping 703 • Critical Thinking 704

CHAPTER 23

Microbial Diseases of the

Structures of the Digestive System 706

The Gastrointestinal Tract 706

The Accessory Digestive Organs 706

Normal Microbiota of the Digestive System 707

Bacterial Diseases of the Digestive System 707

Dental Caries, Gingivitis, and Periodontal Disease 708

Peptic Ulcers 710

Bacterial Gastroenteritis 711

Bacterial Food Poisoning (Intoxication) 719

Viral Diseases of the Digestive System 720

Helminthic Infestations of the Intestinal Tract 731

Tapeworm Infestations 731Pinworm Infestations 733Chapter Summary 734 • Questions for Review 736Critical Thinking 737 • Concept Mapping 738

CHAPTER 24

Microbial Diseases of the Urinary and Reproductive

Structures of the Urinary and Reproductive Systems 740

Structures of the Urinary System 740Structures of the Reproductive Systems 740Normal Microbiota of the Urinary and ReproductiveSystems 742

Bacterial Diseases of the Urinary System 742

Bacterial Urinary Tract Infections 742Leptospirosis 743

Streptococcal Acute Glomerulonephritis 744

Nonvenereal Diseases of the Reproductive Systems 744

Staphylococcal Toxic Shock Syndrome 745Bacterial Vaginosis 745

Viral STDs 757

Genital Herpes 757Genital Warts 758

Protozoan STDs 760

Trichomoniasis 760Chapter Summary 761 • Questions for Review 763Critical Thinking 765 • Concept Mapping 766

CHAPTER 25

Applied and Environmental

Food Microbiology 768

The Roles of Microorganisms in Food Production 768

The Causes and Prevention of Food Spoilage 771

Foodborne Illnesses 775

Industrial Microbiology 775

The Roles of Microbes in Industrial Fermentations 776

Industrial Products of Microorganisms 776

Water Treatment 779

Environmental Microbiology 786

Microbial Ecology 786

Bioremediation 787

The Problem of Acid Mine Drainage 787

The Roles of Microorganisms in Biogeochemical

Cycles 788

Soil Microbiology 791

Aquatic Microbiology 792

Biological Warfare and Bioterrorism 794

Assessing Microorganisms as Potential Agents of Warfare

or Terror 794Known Microbial Threats 795Defense Against Bioterrorism 796The Roles of Recombinant Genetic Technology inBioterrorism 796

Chapter Summary 798 • Questions for Review 800Critical Thinking 802 • Concept Mapping 803

Answers to Chapter Review and Practice A-1Appendix A Metabolic Pathways A-5Appendix B Some Mathematical Considerations

in Microbiology A-13Glossary G-1

Credits CR-1Index I-1

TABLE OF CONTENTS xxxiii

Clinical Cases and Feature Boxes

Antibiotics: Friend or Foe? 410

A Stealth Invader in the Lungs 445

A Vaccine Against Cancer? 470Outbreak in the Inner City 502

A Simple Case of Bug Bites? 524

A Bad Case of Acne 555Under Pressure and Under-the-Weather 597Rabbit Fever 631

This Cough Can Kill 667Trouble at the Rec Center 705Picture-Perfect Romance? 739Food Poisoning at a Five-Star Restaurant? 767

CLINICAL CASES

A Simple Case of Traveler’s Diarrhea? 1

Can Spicy Food Cause Ulcers? 26

The Big Game 56

The Salty Toddler 96

What’s Lurking in the Fitness Center? 126

Can a Trip to the Dentist Be Life Threatening? 166

The Case of the Matching Tattoos 196

Can a “Bad” Gene be Replaced with a “Good” Gene? 239

Raw Fish, Raw Deal? 261

Battling a Microscopic Enemy 287

Can Diabetes Cause a Foot Infection? 318

A Souvenir from Paradise 347

Outbreak in the Jungle 382

HIGHLIGHTS

“The New Normal”: The Challenge of Emerging

and Reemerging Diseases 8

It’s Alive? Maybe 58

Giant Bacteria 61

Biofilms: Slime Matters 65

Studying Biofilms in Plastic “Rocks” 106

Glowing Bacteria 143

What’s That Fishy Smell? 149

Hydrogen-Loving Microbes in Yellowstone’s Hot Springs 170

Flipping the Switch: RNA Interference 220

Nature’s Own Decaf Machine 243

Vaccines on the Menu 254

Brass to the Rescue 279

Antibacterial Soap: Too Much of a Good Thing? 281

Microbe Altruism: Why Do They Do It? 289

From Cyanobacteria to Bats to Brain Disease? 328

Streptomyces and the European Beewolf 333

Amoeba Midwives 360The Threat of Avian Influenza 394How Do Viruses Thwart Interferon? 460BCR Diversity: The Star of the Show 479The Loss of Helper T Cells in AIDS Patients 482Attacking Cancer with Lab-Grown T Cells 490Why Isn’t There a Cold Vaccine? 504

Can Pets Help Decrease Children’s Allergy Risks? 528When Kissing Triggers Allergic Reactions 529

SCID: “Bubble Boy” Disease 542

In Search of a Malaria Vaccine 656Making Blue Jeans “Green” 778Bacterial Batteries 779

Could Bioterrorists Manufacture Viruses from Scratch? 797

TABLE OF CONTENTS xxxv

Good Viruses? Who Knew? 386Prescription Bacteriophages? 390

A Bioterrorist Worm 414What Happens to All That Skin? 447Smallpox: To Vaccinate or Not To Vaccinate? 509New Vessels Made from Scratch? 569

Cocaine No Brainer 611When a Bacterial Infection Is a Good Thing 636Microbes to the Rescue? 708

Pharmacists of the Future 748Oil-Eating Bacteria to the Rescue in the Gulf 788

Probiotics: The New Sheriff in Town 302

Botulism and Botox 330

A Microtube of Superglue 337

Fungi for $3000 a Pound 370

CLINICAL APPLICATIONS

Remedy for Fever or Prescription for Death? 16

Raw Oysters and Antacids: A Deadly Mix? 39

Deadly Horizontal Gene Transfer 233

Antibiotic Overkill 288

To Treat or Not to Treat? 304

Invasion from Within or Without? 404

A Deadly Carrier 416

TB in the Nursery 428

Unusual Transmission of West Nile Virus 430

Legionella in the Produce Aisle 436

Diagnosis in the Desert 588

The Frowning Actor 609

A Man with No Feelings 615

A Threat from the Wild 622

A Blue Baby 693When “Health Food” Isn’t 720The Case of the Lactovegetarians 722Painful Dysentery 731

A Painful Problem 751

A Sick Mother-to-Be 755

A Case of Genital Sores 756

A Very Sick Man 759

Hantavirus Pulmonary Syndrome 693

Histoplasmosis 697Peptic Ulcers 711Cholera 713Bacterial Diarrhea 716Typhoid Fever and Salmonellosis 719Staphylococcal Intoxication (Food Poisoning) 720

Hepatitis 726Giardiasis 728Amebiasis 730Leptospirosis 744Toxic Shock Syndrome 746Candidiasis 747

Pelvic Inflammatory Disease (PID) 748Gonorrhea 750

Syphilis 753Genital Warts 760

Microsporidiosis 495Buruli Ulcer 559Monkeypox 590Melioidosis 600Tick-Borne Encephalitis 618Snail Fever in China 659H1N1 Influenza 689Pulmonary Blastomycosis 696

Martin is a nurse in Chicago Every summer, he spends a few

weeks in Africa volunteering in a rural village in Zambia The

village has no sanitationsystem and gets its water from a

nearby shallow well Over time, Martin has gained the

villagers’ trust and demonstrated handwashing technique,

safer food preparation, and other ways to prevent infectious

disease Water purificationis especially a challenge:

boiling water requires fuel that isn’t always available, and

chemicals that make water safer to drink are often in short

supply

During the last week of Martin’s most recent Africa trip,

torrentialrains hit the country, causing flash floods and

extensive damage to the village Despite the conditions, Martin

Clinical Case:

A SIMPLE CASE OF TRAVELER’S DIARRHEA?

History of Microbiology

Take the pre-test for this chapter online Visit the Study Area at www.masteringmicrobiology.com

manages to return to Chicago on schedule A day later, he begins experiencing diarrhea At first, he brushes it off as

“traveler’sdiarrhea,” which can be caused by a change indiet and usually goes away quickly However, over the followingdays, Martin’s symptoms worsen The diarrheais muchmore severe than anything Martin has experienced before; it ismilky, with flecks of mucus, and frightening-looking Martin also develops nausea, vomiting, and muscle cramps

He drinks massive amounts of water and tries over-the-counterdiarrhea medicine, but nothing he does relieves the symptoms

Is Martin suffering from a simple case of “traveler’sdiarrhea”? Or is something more serious going on? Turn

to page 22 to find out

2 CHAPTER 1 A Brief History of Microbiology

Science is the study of nature that proceeds by posing questions

about observations Why are there seasons? What is the

func-tion of the nodules at the base of this plant? Why does this

bread taste sour? What does plaque from between teeth look

like when magnified? Why are so many crows dying this

win-ter? What causes new diseases?

Many early written records show that people have always

asked questions like these For example, the Greek physician

Hippocrates (ca 460–ca 377 B.C.) wondered whether there is a

link between environment and disease, and the Greek historian

Thucydides (ca 460–ca 404 B.C.) questioned why he and other

survivors of the plague could have intimate contact with

vic-tims and not fall ill again For many centuries, the answers to

these and other fundamental questions about the nature of life

remained largely unanswered But about 350 years ago, the

in-vention of the microscope began to provide some clues

In this chapter we’ll see how one man’s determination to

answer a fundamental question about the nature of life—What

does life really look like?—led to the birth of a new science called

microbiology We’ll then see how the search for answers to other

questions, such as those concerning spontaneous generation, the

reason fermentation occurs, and the cause of disease, prompted

advances in this new science Finally, we’ll look briefly at some of

the key questions microbiologists are asking today

The Early Years of Microbiology

The early years of microbiology brought the first observations

of microbial life and the initial efforts to organize them into

✓ Define microbes in the words of Leeuwenhoek and as we

know them today

A few people have changed the world of science forever We’ve

all heard of Galileo, Newton, and Einstein, but the list also

in-cludes Antoni van Leeuwenhoek (la¯¿ve˘n-huk; 1632–1723), a

Dutch tailor, merchant, and lens grinder, and the man who first

discovered the bacterial world (Figure 1.1)

Leeuwenhoek was born in Delft, the Netherlands, and

lived most of his 90 years in the city of his birth What set

Leeuwenhoek apart from most other men of his generation was

an insatiable curiosity coupled with an almost stubborn desire

to do everything for himself His journey to fame began simply

enough, when as a tailor he needed to examine the quality of

cloth Rather than merely buying one of the magnifying lenses

already available, he learned to make glass lenses of his own

(Figure 1.2) Soon he began asking, “What does it really look

like?” of everything in his world: the stinger of a bee, the brain

of a fly, the leg of a louse, a drop of blood, flakes of his own

skin To find answers, he spent hours examining, reexamining,

and recording every detail of each object he observed

Figure 1.1 Antoni van Leeuwenhoek Leeuwenhoek reported the existence of protozoa in 1674 and of bacteria in 1676 Why did Leeuwenhoek discover protozoa before bacteria?

Figure 1.2 Reproduction of Leeuwenhoek’s microscope This simple device is little more than a magnifying glass with screws for manipulating the specimen; yet with it, Leeuwenhoek changed the way

we see our world The lens, which is convex on both sides, is about the size of a pinhead The object to be viewed was mounted either directly

on the specimen holder or inside a small glass tube, which was then mounted on the specimen holder.

Figure 1.1 Protozoa ar

e generally larger than bacteria.

Making and looking through his simple microscopes, mostreally no more than magnifying glasses, became the over-whelming passion of his life His enthusiasm and dedication are evident from the fact that he sometimes personally ex-tracted the metal for his microscope from ore Further, he often

CHAPTER 1 A Brief History of Microbiology 3

made a new microscope for each specimen, which remained

mounted so that he could view it again and again Then one

day, he turned a lens onto a drop of water We don’t know what

he expected to see, but certainly he saw more than he had

antici-pated As he reported to the Royal Society of London1 in 1674,

he was surprised and delighted by

some green streaks, spirally wound serpent-wise, and

or-derly arranged Among these there were, besides, very

many little animalcules, some were round, while others a

bit bigger consisted of an oval On these last, I saw two

lit-tle legs near the head, and two litlit-tle fins at the hind most

end of the body And the motion of most of these

animalcules in the water was so swift, and so various,

upwards, downwards, and round about, that ‘twas

won-derful to see

Leeuwenhoek had discovered a previously unknown microbial

world, which today we know to be populated with tiny

ani-mals, fungi, algae, and single-celled protozoa (Figure 1.3) In a

later report to the Royal Society, he noted that

the number of these animals in the plaque of a man’s

teeth, are so many that I believe they exceed the number

of men in a kingdom I found too many living animals

therein, that I guess there might have been in a quantity

of matter no bigger than the 1/100 part of a [grain of]

sand

From the figure accompanying this report and the precise

de-scription of the size of these organisms from between his teeth,

we know that Leeuwenhoek was reporting the existence of

bacteria By the end of the 19th century, Leeuwenhoek’s

“beasties,” as he sometimes dubbed them, were called

microorganisms, and today we also know them as microbes.

Both terms include all organisms that are too small to be seen

without a microscope

Because of the quality of his microscopes, his profound

ob-servational skills, his detailed reports over a 50-year period,

and his report of the discovery of many types of

microorgan-isms, Antoni van Leeuwenhoek was elected to the Royal

Society in 1680 He and Isaac Newton were probably the most

famous scientists of their time

How Can Microbes Be Classified?

Learning Objectives

✓ List six groups of microorganisms

✓ Explain why protozoa, algae, and nonmicrobial parasitic

worms are studied in microbiology

✓ Differentiate prokaryotic from eukaryotic organisms

Shortly after Leeuwenhoek made his discoveries, the Swedish

botanist Carolus Linnaeus (1707–1778) developed a taxonomic

system—a system for naming plants and animals and grouping

similar organisms together For instance, Linnaeus and other

scientists of the period grouped all organisms into either the

an-imal kingdom or the plant kingdom Today, biologists still usethis basic system, but they have modified Linnaeus’s scheme byadding categories that more realistically reflect the relation-ships among organisms For example, scientists no longer clas-sify yeasts, molds, and mushrooms as plants, but instead asfungi We examine taxonomic schemes in more detail inChapter 4

The microorganisms that Leeuwenhoek described can begrouped into six basic categories: bacteria, archaea, fungi, pro-tozoa, algae, and small multicellular animals The only type of

microbes not described by Leeuwenhoek are viruses,2which aretoo small to be seen without an electron microscope We brieflyconsider organisms in the first five categories in the followingsections

Bacteria and Archaea

Bacteria and archaea are prokaryotic;3 meaning that they lacknuclei; that is, their genes are not surrounded by a membrane.Bacterial cell walls are composed of a polysaccharide called

peptidoglycan (Some bacteria, however, lack cell walls.) The cell

walls of archaea lack peptidoglycan and instead are composed

of other chemicals Members of both groups reproduce ally Chapters 3, 4, and 11 examine other differences betweenbacteria and archaea, and Chapters 19–24 discuss pathogenic(disease-causing) bacteria

asexu-50 μm

LM

Figure 1.3 The microbial world Leeuwenhoek reported seeing a

1 The Royal Society of London for the Promotion of Natural Knowledge, granted a royal charter in 1662, is one of the older and more prestigious scientific groups in Europe.

2 Technically, viruses are not “organisms,” because they neither replicate themselves nor carry on the chemical reactions of living things See Chapter 3 for a fuller discussion of this issue.

3 From Greek pro, meaning before, and karyon, meaning kernel (which in this case refers to the nucleus of a cell).