Microbiology : with diseases by body system

928 Pages·2012·64.473 MB·English

by  Robert W Bauman, Elizabeth Machunis-Masuoka, Jean E Montgomery

THIRD EDITION
M I C RO B I O LO GY
WITH DISEASES BY BODY SYSTEM
ROBERT W. BAUMAN, PhD
Amarillo College
Clinical Consultants: Contributions by:
Cecily D. Cosby, PhD, FNP-C, PA-C Elizabeth Machunis-Masuoka, PhD
Samuel Merritt College University of Virginia
Janet Fulks, EdD Jean E. Montgomery, MSN, RN
Bakersfield College Austin CommunityCollege
John M. Lammert, PhD
Gustavus Adolphus College
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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]
QR41.2.B383 2012
579–dc22
2010044963
ISBN 10: 0-321-71271-4 (Student edition)
ISBN 13: 978-0-321-71271-4 (Student edition)
ISBN 10: 0-321-71636-1 (Professional copy)
ISBN 13: 978-0-321-71636-1 (Professional copy)
1 2 3 4 5 6 7 8 910—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. BAUMAN
is a professor of
biology and past chairman of the Department of
Biological Sciences at Amarillo College in Amarillo,
Texas. He teaches microbiology, human anatomy
and physiology, and botany. In 2004, the students of
Amarillo College selected Dr. Bauman as the recipient
of the John F. Mead Faculty Excellence Award. He
received an MAdegree in botany from the University
of Texas at Austin and a PhD in biology from Stanford
University. His research interests have included the
morphology and ecology of freshwater algae, the cell
biology of marine algae (particularly the deposition of
cell walls and intercellular communication), and
environmentally 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. COSBY
is 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 PAcertificate from the
Stanford Primary Care program.
JANET FULKS
is a professor of microbiology at Bakersfield College and a clinical laboratory
scientist. She received her MAin 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 MAin 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: AStudent Handbook,
and three books on science fair projects (microbes, plants, and the human body).
Preface
The threat of bird flu and other emerging diseases; the progress of cutting-edge research into
microbial genetics; the challenge of increasingly drug-resistant pathogens; the continual discovery
of microorganisms previously unknown—these are just a few examples of why the study of
microbiology has never been more exciting, or more important. Welcome!
I have taught microbiology to undergraduates for over 20 years and witnessed firsthand how
students struggle with the same topics and concepts year after year. Students invariably come to
class with different levels of preparation—while some have strong science backgrounds, others
lack a foundation in chemistry and/or biology, making it a challenge to decide how to gear the
course. In creating this textbook, my goal was to write a text that explains complex topics—
especially metabolism, genetics, and immunology—in a way that beginning students can
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 with
the 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 the
previous edition by updating it with the latest scientific and educational research and data available
and by incorporating the many helpful suggestions I have received from colleagues and students
alike. The result is, once again, a collaborative effort of educators, students, editors, and top
scientific illustrators, and a textbook that continues to improve upon conventional explanations
and illustrations in substantive and effective ways. In this new edition:
• NEW Engaging, story-based Clinical Caseshook students at the beginning of the chapter and
keep them curious until the Clinical Case Follow-Upat the end of the chapter. Each chapter-
opening Clinical Case relates a compelling patient dilemma. The Clinical Case Follow-Up reveals
the source of the patient illness and asks students to apply concepts covered in the chapter.
• NEW Emerging Diseases boxesreflect 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 Hantaviruspulmonary syndrome, babesiosis, and MRSA(see p. xxxvifor a full list).
• NEW Concept Mapping activityin the end-of chapter sections provide students with
hands-on practice for organizing the information they have learned, helping them to better
understand the connections between concepts.
• IMPROVED Lab equipment illustrationsfeature increased dimensionality and realism to
help students get prepared for their lab course. Glassware, such as test tubes, flasks, and Petri
plates, look more authentic, allowing students to make a stronger connection between what
they learn in their textbook and the experiments they perform in the lab.
• Immunology chapters (Chapters 15–18) reflect the most current understandingof this rapidly
evolving field. Immunology is also woven into student and instructor media through dynamic
MicroFlix that bring immunology to life in 3-D animations. The material in these chapters is
continually reviewed in depth by immunology specialists.
• Chapter 3(Cell Structure and Function) has been reorganizedto follow the latest taxonomic
research. The discussion deemphasizes the term prokaryoteand emphasizes the three domains
of living organisms. The newly separate section on the Archaea can be covered or easily
skipped 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 text
features, 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.
vi
Chapter-by-Chapter Revisions
Every chapter in this edition has been thoroughly revised, and • Four new photos
data in the text, tables, and figures have been updated. The • Thirteen figures revised and enhanced for better clarity and pedagogy
main changes for each chapter are summarized below.
CHAPTER 5MICROBIAL METABOLISM
• New “Clinical Case” and “Clinical Case Follow-Up” on botulism
THROUGHOUT THE DISEASE CHAPTERS (CHAPTERS 19–24)
intoxication
• Updated disease diagnoses, treatments, and incidence and prevalence
• Clarified definitions of aerobic respiration versus anaerobic respira-
data
tion versus fermentation in text, figures, and critical thinking
• Updated immunization recommendations and suggested treatments
questions
for all diseases
• Expanded coverage of vitamins as enzymatic cofactors
• New art to illustrate relationships of catabolism, anabolism, ATP-
CHAPTER 1A BRIEF HISTORY OF MICROBIOLOGY
ADP energy cycle, use of nutrients, precursor metabolites, and
• New “Clinical Case” and “Clinical Case Follow-Up” on cholera
macromolecules
• New “Clinical Applications” box on a yellow fever epidemic in the
• Alternatives to Embden-Meyerhof glycolysis (pentose phosphate
18th century
pathway and Entner-Doudoroff pathway) rearranged for greater
• New “Emerging Diseases” box on variant Creutzfeldt-Jakob disease
clarity and better pedagogy
(prion disease)
• Twenty-two figures upgraded for greater clarity and better
• Four figures revised for better clarity and pedagogy
pedagogy
• Two new photos, two new figures
• One new figure
• Simplified longer figure legends, at request of reviewers
CHAPTER 2THE CHEMISTRY OF MICROBIOLOGY • New critical thinking question regarding photosynthesis
• New “Clinical Case” and “Clinical Case Follow-Up” on stomach ulcers
• Expanded coverage of role of manganese as an antioxidant in bacteria
CHAPTER 6MICROBIAL NUTRITION AND GROWTH
• Expanded coverage of nucleosides, which are used as nucleotide
• New “Clinical Case” and “Clinical Case Follow-Up” on septicemia
analogs in treating a number of diseases
• Added material concerning definition, development, and prevalence
• Seventeen figures revised for better pedagogy
of biofilms and quorum sensing
• One new figure
• Increased coverage of serial dilutions, viable plate counting, the
contrast between lithotrophy and organotrophy, nonculturable
CHAPTER 3CELL STRUCTURE AND FUNCTION
microbes, continuous culture in a chemostat, and methods to obtain
• New “Clinical Case” and “Clinical Case Follow-Up” on streptococcal pure cultures
infection • Four new photos, one new figure
• New sections on Domain Archaea examining these microbes in • Fifteen figures revised for greater clarity, ease of reading, and better
more detail and independently from Domain Bacteria, emphasizing pedagogy
that “prokaryote” is not a taxonomic grouping • Five new questions for review at the end of the chapter, including
• Expanded coverage of bacterial shapes and arrangements, but kept three critical thinking questions
at level appropriate for this early chapter
• Reorganized discussion of eukaryotic flagella and cilia to emphasize
CHAPTER 7MICROBIAL GENETICS
that these structures are internal to the cytoplasmic membrane
• New “Clinical Case” and “Clinical Case Follow-Up” on hepatitis C
• Incorporation of new discoveries concerning cell structure and
• New “Clinical Applications” box on horizontal gene transfer
function. For example:
• New “Emerging Diseases” box on Vibrio vulnificusinfection
✓
Electrical signaling among bacteria via conductive fimbriae
• Revised discussion that more clearly explains the differences among
✓
Archaeal hami—fimbriae-like cell extensions shaped like Ninja
archaeal, bacterial, and eukaryotic genetics
grappling hooks on barbed wire
• Updated sections on bacterial chromosome number and bacterial
• Ten new photos, nine new figures
plasmids
• Revised and enhanced artwork in nineteen figures
• Extended coverage of the difference between nucleoside and nu-
cleotide (many antimicrobial drugs are the former, not the latter)
CHAPTER 4MICROSCOPY, STAINING, AND CLASSIFICATION • Added discussion of the actions of topoisomerase and gyrase
• New “Clinical Case” and “Clinical Case Follow-Up” on cystic fibrosis • Expanded discussion of regulation of genetic expression—antisense
• New“Emerging Diseases” box on necrotizing fasciitis RNA, RNA interference (RNAi), riboswitches—and CAP/cAMP-
• Added coverage of histological stains: Gomori methenamine silver mediated, positive regulation of the lacoperon, and quorum sensing
(GMS) stain and hematoxylin and eosin (HE) stain as it relates to genetic control in infection
• Updated coverage of taxonomy to be more current; for example, • Inclusion of newly discovered codons and tRNAs for 21st and 22nd
expanded definitions of microbial species amino acids
CHAPTER-BY-CHAPTER REVISIONS vii
• Coverage of new research showing that DNA moves through • Three new figure legend questions and critical thinking questions
hollow pili even over great distances • Added material on transfer of resistance genes between and among
• Modified artwork to reflect changes in our understanding of molec- bacteria and on research to discover novel antimicrobials
ular biology: for example, where possible enzyme shapes are based
upon actual 3-D profiles as revealed by X-ray crystallography (e.g., CHAPTER 11CHARACTERIZING AND CLASSIFYING
Figures 7.5, 7.8, 7.20, and 7.27) PROKARYOTES
• Two new photos and three new art figures • New “ClinicalCase” and “ClinicalCase Follow-up” on diabetic foot
• Twenty-seven upgraded figures for greater clarity, accuracy, ease of syndrome
reading, and better pedagogy • New “Emerging Diseases” box on whooping cough
• New critical thinking questions • New “Highlight” box on the possible connection between cyanobac-
teria and neurological disorders such as amyotrophic lateral sclerosis,
CHAPTER 8RECOMBINANT DNA TECHNOLOGY Parkinson’s disease, and Alzheimer’s disease
• New “Clinical Case” and “Clinical Case Follow-Up” on gene therapy • Eight new photos
for SCID • Four figures revised for better pedagogy
• Expanded coverage of the use of recombinant DNAtechnology to
produce antisense nucleic acid molecules for research and genetic CHAPTER 12 CHARACTERIZING AND CLASSIFYING
modification of crops EUKARYOTES
• New coverage of DNAmicroarrays and fluorescent in situ hybridiza- • New “ClinicalCase” and “ClinicalCase Follow-Up” on dengue fever
tion (FISH) • New “Emerging Diseases” box on aspergillosis
• Added coverage of new recombinant agricultural crops, including • Updated taxonomy of algae, fungi, protozoa, water molds, and
potato-blight-resistant potatoes and deadly ringspot-virus-resistant slime molds
papayas • Added discussion of the use by fungi of radiation as an energy
• New section discussing use of recombinant DNA techniques to source
address environmental problems • Ten new photos
• Increased coverage of the debate concerning genetic modification of • Thirteen figures upgraded for greater clarity, accuracy, ease of read-
agricultural products ing, and better pedagogy
• Two new photos, four new figures
• Nine modified, updated, or pedagogically enhanced figures CHAPTER 13CHARACTERIZING AND CLASSIFYING VIRUSES,
VIROIDS, AND PRIONS
CHAPTER 9 CONTROLLING MICROBIAL GROWTH IN • New “Clinical Case” and “Clinical Case Follow-Up” on Ebola
THE ENVIRONMENT
hemorrhagic fever
• New “ClinicalCase” and “ClinicalCase Follow-Up” on parasitic worm • New “Emerging Diseases” box on chikungunya
infection • Updated viral nomenclature to correspond to changes approved by
• New “Emerging Diseases” box on Acanthamoebakeratitis the International Committee on Taxonomy of Viruses
• Three figures revised for better pedagogy • Expanded coverage of prions
• Added descriptions of four biosafety levels as established by the • Four new TEMs of viruses
CDC • Three new photos
• Two new photos • Three figures upgraded for better pedagogy
• New critical thinking questions, including one based on the 2008
Salmonellaoutbreak associated with tomatoes and peppers CHAPTER 14INFECTION, INFECTIOUS DISEASES,
AND EPIDEMIOLOGY
CHAPTER 10CONTROLLING MICROBIAL GROWTH IN • New “ClinicalCase” and “ClinicalCase Follow-Up” on urinary tract
THE BODY: ANTIMICROBIAL DRUGS
infection
• New “ClinicalCase” and “ClinicalCase Follow-up” on drug-resistant • New “Emerging Diseases” box on Hantaviruspulmonary syndrome
bacteria infection • Incidence and prevalence figure redrawn to reflect current AIDS
• New “Emerging Diseases” box on community-associated MRSA data in U.S.
• Clarified etymology and use of the terms antimicrobial, antibiotic, • Updated epidemiology charts, tables, and graphs
andsemisynthetic • Updated list of nationally notifiable infectious diseases
• Expanded discussion of use of RNAinterference (RNAi) and antisense • Expanded coverage of roles of public health agencies
nucleic acids as antimicrobial therapy • Seven figures revised for better pedagogy
• Increased discussion of biofilms as they relate to drug resistance • Two new photos
• Updated and revised tables of antimicrobials to include all antimi-
crobials mentioned in pathogen chapters CHAPTER 15INNATE IMMUNITY
• Added coverage of the new anti-HIV drug tenofovir and of the new
• New “ClinicalCase” and “ClinicalCase Follow-Up” on mycoplasmal
antibacterial drug mupirocin
pneumonia
• Four new photos, seven new figures
• New coverage of antimicrobial peptides and bradykinins (act in
• Twelve figures revised for greater clarity, accuracy, ease of reading,
inflammation)
and better pedagogy, including correct shapes for anti-transcription
• Greatly enhanced coverage of Toll-like receptors (TLRs)
antimicrobials
viii CHAPTER-BY-CHAPTER REVISIONS
• Expanded coverage of pathogen-associated molecular patterns • New “Emerging Diseases” box on monkeypox
(PAMPs) • Updated disease diagnoses, treatments, and incidence and preva-
• Discussion of neutrophil extracellular traps (NETs) lence data
• Presentation of NOD receptor proteins • Expanded coverage of methicillin-resistant and vancomycin-
• Added discussion of the latest discoveries in iron usage among resistant Staphylococcus aureus (MRSA, VRSA), necrotizing fasciitis,
pathogenic bacteria and sequestration of iron in the body as a defense and multi-drug-resistant tuberculosis (MDR-TB)
• Enhanced coverage of steps involved in phagocytosis • Expanded and updated coverage of action of anthrax toxins
• Clarified artwork and discussion of pathways of complement acti- • Added coverage of extensively drug-resistant TB (XDR-TB)
vation, including the lectin pathway • Four new photos
• Six figures modified for enhanced clarity and better pedagogy, in- • Two figures revised for enhanced accuracy and pedagogy
cluding new hybrid TEM/artist’s rendition of phagocytosis • Five new end-of-chapter questions
• Two new photos
CHAPTER 20MICROBIAL DISEASES OF THE NERVOUS
CHAPTER 16ADAPTIVE IMMUNITY SYSTEM AND EYES
• New “Clinical Case” and “Clinical Case Follow-Up” on HPV • New “Clinical Case” and “Clinical Case Follow-up” on meningitis
vaccination • New “Clinical Applications” box on a trypanosome disease
• New “Emerging Diseases” box on microsporidiosis • New “Emerging Diseases” box on tick-borne encephalitis
• Updated information on adaptive T cell cancer therapy • New “Emerging Diseases” box on melioidosis
• One new figure, seven revised pieces of art, two new photos for • Updated disease diagnoses, treatments, and incidence and preva-
better pedagogy lence data
• Added discussion of blebbing as it relates to meningococcal disease
CHAPTER 17IMMUNIZATION AND IMMUNE TESTING • Discussion of the action of tetanospasmin (tetanus toxin) revised for
• New “Clinical Case” and “Clinical Case Follow-Up” on whooping clarity, succinctness, and better pedagogy
cough • Expanded discussion of prion diseases
• Updated coverage of types of vaccines, including newly approved • Ten new figures
combination vaccines • Five figures revised for better pedagogy
• Updated coverage of passive immunotherapy
• Added information regarding vaccines against agents of Japanese CHAPTER 21CARDIOVASCULAR AND SYSTEMIC DISEASES
encephalitis and typhoid fever • New “Clinical Case” and “Clinical Case Follow-Up” on tularemia
• Inclusion of newly revised CDC 2010 vaccination schedule for • New “Emerging Diseases” box on schistosomiasis
children, adolescents, and adults • Four new figures
• Updated table of vaccine-preventable diseases in the U.S. • Five figures revised for greater visual contrast, pedagogy, accuracy,
• Added discussion of methods of vaccine administration currency, and general interest
• Expanded and clarified definitions of contact immunity, immunization,
vaccination, vaccine, titer, direct immune testing, and indirect immune CHAPTER 22MICROBIAL DISEASES OF
testing THE RESPIRATORY SYSTEM
• Fourteen figures revised for better pedagogy • New “Clinical Case” and “Clinical Case Follow-Up” on tuberculosis
• New “Emerging Diseases” box on pulmonary blastomycosis
CHAPTER 18AIDS AND OTHER IMMUNE DISORDERS • New “Emerging Diseases” box on H1N1 influenza
• New “Clinical Case” and “Clinical Case Follow-up” on poison ivy • Text altered to reflect that Chlamydia pneumoniae and C. psittaci are
hypersensitivity now classified as Chlamydophilaspp.
• Updated, simplified, and corrected material on Graves’ disease, • Twelve new figures
tissue transplants, and multiple sclerosis • Seven figures revised for enhanced pedagogy
• Eleven revised figures and two new photographs for more effective
pedagogy CHAPTER 23MICROBIAL DISEASES OF THE DIGESTIVE SYSTEM
• Updated discussion of AIDS prevalence, transmission, prevention, • New “Clinical Case” and “Clinical Case Follow-Up” on giardiasis
and treatment • New “Clinical Applications” box examining cases of bacterial
gastorenteritis
CHAPTER 19MICROBIAL DISEASES OF THE SKIN • New “Emerging Diseases” box on Norovirusgastroenteritis
AND WOUNDS • Expanded coverage of dental diseases, probiotics, and hepatitis
• New “Clinical Case” and “Clinical Case Follow-Up” on severe acne viruses C and E
• New “Clinical Applications” box on a child with unsightly warts • Extensive coverage of pseudomembranous colitis (Clostridium
• New “Clinical Applications” box on shingles difficilediarrhea)
• New “Clinical Applications” box on athlete’s foot • Added coverage of the connection between esophageal cancer and
• New “Clinical Applications” box on leishmaniasis revealed in the use of antibiotics to treat Helicobacterinfection
archaeological discoveries in Chile • Reporting of the end of the cholera pandemic in South America in
• New “Emerging Diseases” box on Buruli ulcer 2002
CHAPTER-BY-CHAPTER REVISIONS ix
• Seven new figures • Four new figures
• Seven revised, updated, enhanced, and pedagogically more effective • Four revised, updated, or enhanced figures
figures
CHAPTER 25INDUSTRIAL AND ENVIRONMENTAL
CHAPTER 24MICROBIAL DISEASES OF THE URINARY MICROBIOLOGY
AND REPRODUCTIVE SYSTEMS • New “ClinicalCase” and “ClinicalCase Follow-Up” on salmonellosis
• New “Clinical Case” and “Clinical Case Follow-Up” on genital herpes • Clarified use of the term fermentationin biochemistry, food produc-
• New “Clinical Applications” box examining a case of AIDS tion, and industry
• New “Clinical Applications” box examining a case of gonorrhea • Expanded coverage of pharmaceutical products produced by re-
• Expanded discussion of the fact that male circumcision reduces the combinant DNAtechnology
spread of sexually transmitted and urinary tract diseases • One revised figure
• Updated and expanded coverage of papillomaviruses, their treat- • One new photo
ment, and prevention of their diseases