Microbiology a systems approach 3rd ed m cowan BBS part 1

This page intentionally left blank THIRD EDITION Marjorie Kelly Cowan Miami University TM TM 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 QDB/QDB 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) Microbiology I Title QR41.2.C69 2012 616.9’041 — dc22 2010037851 www.mhhe.com Brief Contents CHAPTER CHAPTER The Main Themes of Microbiology CHAPTER CHAPTER Host Defenses I: Overview and Nonspecific Defenses 397 The Chemistry of Biology CHAPTER 27 CHAPTER CHAPTER CHAPTER CHAPTER 168 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 Genetic Engineering and Recombinant DNA CHAPTER 490 Infectious Diseases Affecting the Nervous System 550 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 An Introduction to the Viruses CHAPTER 80 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 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 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 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 352 Chapter 12 Drugs, Microbes, Host—The Elements of Chemotherapy 12.4 Interaction Between Drug and Host Until now, this chapter has focused on the interaction between antimicrobials and the microorganisms they target During an infection, the microbe is living in or on a host; therefore, the drug is administered to the host though its target is the microbe Therefore, the effect of the drug on the host must always be considered Although selective antimicrobial toxicity is the ideal constantly being sought, chemotherapy by its very nature involves contact with foreign chemicals that can harm human tissues In fact, estimates indicate that at least 5% of all persons taking an antimicrobial drug experience some type of serious adverse reaction to it The major side effects of drugs fall into one of three categories: direct damage to tissues through toxicity, allergic reactions, and disruption in the balance of normal microbial biota The damage incurred by antimicrobial drugs can be short term and reversible or permanent, and it ranges in severity from cosmetic to lethal Table 12.6 summarizes drug groups and their major side effects Toxicity to Organs Drugs can adversely affect the following organs: the liver (hepatotoxic), kidneys (nephrotoxic), gastrointestinal tract, cardiovascular system and blood-forming tissue (hemotoxic), nervous system (neurotoxic), respiratory tract, skin, bones, and teeth Because the liver is responsible for metabolizing and detoxifying foreign chemicals in the blood, it can be damaged by a drug or its metabolic products Injury to liver cells can result in enzymatic abnormalities, fatty liver deposits, hepatitis, and liver failure The kidney is involved in excreting drugs and their metabolites Some drugs irritate the nephron tubules, creating changes that interfere with their filtration abilities Drugs such as sulfonamides can crystallize in the kidney and form stones that can obstruct the flow of urine The most common complaint associated with oral antimicrobial therapy is diarrhea, which can progress to severe intestinal irritation or colitis Although some drugs directly irritate the intestinal lining, the usual gastrointestinal complaints are caused by disruption of the intestinal microbiota (discussed in a subsequent section) Many drugs given for parasitic infections are toxic to the heart, causing irregular heartbeats and even cardiac arrest in extreme cases Some drugs hemolyze the red blood cells, others reduce white blood cell counts, and still others damage platelets or interfere with their formation, thereby inhibiting blood clotting Certain antimicrobials act directly on the brain and can cause seizures Others, such as aminoglycosides, damage nerves (very commonly, the eighth cranial nerve), leading to dizziness, deafness, or motor and sensory disturbances When drugs block the transmission of impulses to the diaphragm, respiratory failure can result The skin is a frequent target of drug-induced side effects The skin response can be a symptom of drug allergy or a direct toxic effect Some drugs interact with sunlight to cause Table 12.6 Major Adverse Toxic Reactions to Common Drug Groups Antimicrobial Drug Primary Damage or Abnormality Produced Antibacterials Penicillin G Skin Carbenicillin Abnormal bleeding Ampicillin Diarrhea and enterocolitis Cephalosporins Inhibition of platelet function Decreased circulation of white blood cells Nephritis Tetracyclines Diarrhea and enterocolitis Discoloration of tooth enamel Reactions to sunlight (photosensitization) Chloramphenicol Injury to red and white blood cell precursors Aminoglycosides (streptomycin, gentamicin, amikacin) Diarrhea and enterocolitis Malabsorption Loss of hearing, dizziness, kidney damage Isoniazid Hepatitis Seizures Dermatitis Sulfonamides Formation of crystals in kidney; blockage of urine flow Hemolysis Reduction in number of red blood cells Polymyxin Kidney damage Weakened muscular responses Quinolones (ciprofloxacin, norfloxacin) Headache, dizziness, tremors, GI distress Rifampin Damage to hepatic cells Dermatitis Antifungals Amphotericin B Disruption of kidney function Flucytosine Decreased number of white blood cells Antiprotozoan Drugs Metronidazole Nausea, vomiting Chloroquine Vomiting Headache Itching Antihelminthics Niclosamide Nausea, abdominal pain Pyrantel Irritation Headache, dizziness Antivirals Acyclovir Seizures, confusion Rash Amantadine Nervousness, light-headedness Nausea AZT Immunosuppression, anemia 12.4 photodermatitis, a skin inflammation Tetracyclines are contraindicated (not advisable) for children from birth to years of age because they bind to the enamel of the teeth, creating a permanent gray to brown discoloration (figure 12.16) Pregnant women should avoid tetracyclines because they can cause liver damage They also cross the placenta and can be deposited in the developing fetal bones and teeth Allergic Responses to Drugs One of the most frequent drug reactions is heightened sensitivity, or allergy This reaction occurs because the drug acts as an antigen (a foreign material capable of stimulating the immune system) and stimulates an allergic response This response can be provoked by the intact drug molecule or by substances that develop from the body’s metabolic alteration of the drug In the case of penicillin, for instance, it is not the penicillin molecule itself that causes the allergic response but a product, benzylpenicilloyl Allergic reactions have been reported for every major type of antimicrobial drug, but the penicillins account for the greatest number of antimicrobial allergies, followed by the sulfonamides People who are allergic to a drug become sensitized to it during the first contact, usually without symptoms Once the immune system is sensitized, a second exposure to the drug can lead to a reaction such as a skin rash (hives), respiratory inflammation, and, rarely, anaphylaxis, an acute, overwhelming allergic response that develops rapidly and can be fatal (This topic is discussed in greater detail in chapter 16.) 353 pathogens Although we defer a more detailed discussion of this topic to chapter 13 and later chapters, here we focus on the general effects of drugs on this population If a broad-spectrum antimicrobial is introduced into a host to treat infection, it will destroy microbes regardless of their roles as normal biota, affecting not only the targeted infectious agent but also many others in sites far removed from the original infection (figure 12.17) When this therapy destroys beneficial resident species, other microbes that were once in small numbers begin to overgrow and cause disease This complication is called a superinfection Some common examples demonstrate how a disturbance in microbial biota leads to replacement biota and superinfection A broad-spectrum cephalosporin used to treat a urinary tract infection by Escherichia coli will cure the infection, but it will also destroy the lactobacilli in the vagina that normally maintain a protective acidic environment there The drug has no effect, however, on Candida albicans, a yeast that also resides in normal vaginas Released from the inhibitory environment provided by lactobacilli, the yeasts proliferate and cause symptoms Candida can cause similar superinfections of the oropharynx (thrush) and the large intestine Infection Drug Superinfection Circulating drug Suppression and Alteration of the Microbiota by Antimicrobials Most normal, healthy body surfaces, such as the skin, large intestine, outer openings of the urogenital tract, and oral cavity, provide numerous habitats for a virtual “garden” of microorganisms These normal colonists or residents, called the biota or microbiota, consist mostly of harmless or beneficial bacteria, but a small number can potentially be Interaction Between Drug and Host (b) (a) Intestine Potential pathogen resistant to drug but held in check by other microbes (c) Intestine Drug destroys beneficial flora Intestine Pathogen overgrows Normal flora important to maintain intestinal balance Figure 12.17 The role of antimicrobials in disrupting microbial biota and causing superinfections (a) A primary Figure 12.16 Drug-induced side effect An adverse effect of tetracycline given to young children is the permanent discoloration of tooth enamel infection in the throat is treated with an oral antibiotic (b) The drug is carried to the intestine and is absorbed into the circulation (c) The primary infection is cured, but drug-resistant pathogens have survived and create an intestinal superinfection 354 Chapter 12 Drugs, Microbes, Host—The Elements of Chemotherapy Oral therapy with tetracyclines, clindamycin, and broadspectrum penicillins and cephalosporins is associated with a serious and potentially fatal condition known as antibioticassociated colitis (pseudomembranous colitis) This condition is due to the overgrowth in the bowel of Clostridium difficile, an endospore-forming bacterium that is resistant to the antibiotic It invades the intestinal lining and releases toxins that induce diarrhea, fever, and abdominal pain (You’ll learn more about infectious diseases of the gastrointestinal tract, including C difficile, in chapter 22.) 12.4 Learning Outcomes—Can You 24 distinguish between drug toxicity and allergic reactions to drugs? 25 explain what a superinfection is and how it occurs? 12.5 Considerations in Selecting an Antimicrobial Drug Before actual antimicrobial therapy can begin, it is important that at least three factors be known: the nature of the microorganism causing the infection, the degree of the microorganism’s susceptibility (also called sensitivity) to various drugs, and the overall medical condition of the patient Identifying the Agent Streptococcus pneumoniae, Enterococcus faecalis, and the aerobic gram-negative enteric bacilli However, not all infectious agents require antimicrobial sensitivity testing Drug testing in fungal or protozoan infections is difficult and is often unnecessary When certain groups, such as group A streptococci and all anaerobes (except Bacteroides), are known to be uniformly susceptible to penicillin G, testing may not be necessary unless the patient is allergic to penicillin Selection of a proper antimicrobial agent begins by demonstrating the in vitro activity of several drugs against the infectious agent by means of standardized methods In general, these tests involve exposing a pure culture of the bacterium to several different drugs and observing the effects of the drugs on growth The Kirby-Bauer technique is an agar diffusion test that provides useful data on antimicrobial susceptibility In this test, the surface of a plate of special medium is spread with the test bacterium, and small discs containing a premeasured amount of antimicrobial are dispensed onto the bacterial lawn After incubation, the zone of inhibition surrounding the discs is measured and compared with a standard for each drug (table 12.7 and figure 12.18) The profile of antimicrobial sensitivity, or antibiogram, provides data for drug selection The Kirby-Bauer procedure is less effective for bacteria that are anaerobic, highly fastidious, or slowgrowing (Mycobacterium) An alternative diffusion system that provides additional information on drug effectiveness is the E-test (figure 12.19) More sensitive and quantitative results can be obtained with tube dilution tests First the antimicrobial is diluted serially in tubes of broth, and then each tube is inoculated with a small uniform sample of pure culture, incubated, and Identification of infectious agents from body specimens should be attempted as soon as possible It is especially important that such specimens be taken before any antimicrobial drug is given, just in case the drug Table 12.7 Results of a Sample Kirby-Bauer Test eliminates the infectious agent Direct examinaZone Sizes (mm) Example tion of body fluids, sputum, or stool is a rapid Required for: Results (mm) initial method for detecting and perhaps even for identifying bacteria or fungi A doctor often Susceptibility Resistance Staphylococcus begins the therapy on the basis of such immedi(S) (R) aureus Drug ate findings, or even on the basis of an informed Bacitracin 15 best guess For instance, if a sore throat appears >13 18 18 13 18 17 29 12 15 12 19