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L

ABORATORY

D

IAGNOSIS

OF

I

NFECTIOUS

D

ISEASES

Essentials of Diagnostic Microbiology

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L

ABORATORY

D

IAGNOSIS

OF

I

NFECTIOUS

D

ISEASES

Essentials of Diagnostic Microbiology

Paul G. Engelkirk,

Ph.D., MT(ASCP), SM(AAM)

President, Biomed Ed

(Biomedical Educational Services)

Belton, Texas

Janet Duben-Engelkirk,

Ed.D., MT(ASCP), CLS(NCA)

Chair, Biotechnology Department

Temple College and the Texas Bioscience Institute

Temple, Texas

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Acquisitions Editor: Peter Sabatini Managing Editor: Kevin C. Dietz Marketing Manager: Alison M. Noplock Production Editor: Julie Montalbano Designer: Doug Smock

Compositor: Aptara, Inc.

Copyright © 2008 Lippincott Williams & Wilkins, a Wolters Kluwer business 351 West Camden Street 530 Walnut Street

Baltimore, MD 21201 Philadelphia, PA 19106

All rights reserved. This book is protected by copyright. No part of this book may be reproduced or transmitted in any form or by any means, including as photocopies or scanned-in or other electronic copies, or utilized by any information storage and retrieval system without written permission from the copyright owner, except for brief quotations embodied in critical articles and reviews. Materials appearing in this book prepared by individuals as part of their official duties as U.S. government employees are not covered by the above-mentioned copyright. To request permission, please contact Lippincott Williams & Wilkins at 530 Walnut Street, Philadelphia, PA 19106, via email at permissions@lww.com, or via website at lww.com (products and services).

9 8 7 6 5 4 3 2 1

Library of Congress Cataloging-in-Publication Data

Engelkirk, Paul G.

Laboratory diagnosis of infectious diseases : essentials of diagnostic microbiology / Paul G. Engelkirk, Janet Duben-Engelkirk.

p. ; cm.

Includes bibliographical references. ISBN-13: 978-0-7817-9701-6

1. Diagnostic microbiology. 2. Communicable Diseases—Diagnosis—Laboratory manuals. I. Duben-Engelkirk, Janet L. II. Title.

[DNLM: 1. Communicable Diseases—diagnosis. 2. Microbiological Techniques—methods. QW 25 E57L 2008]

QR67.E54 2008 616.9’0475—dc22

2007019766 DISCLAIMER

Care has been taken to confirm the accuracy of the information present and to describe generally accepted prac-tices. However, the authors, editors, and publisher are not responsible for errors or omissions or for any consequences from application of the information in this book and make no warranty, expressed or implied, with respect to the cur-rency, completeness, or accuracy of the contents of the publication. Application of this information in a particular situ-ation remains the professional responsibility of the practitioner; the clinical treatments described and recommended may not be considered absolute and universal recommendations.

The authors, editors, and publisher have exerted every effort to ensure that drug selection and dosage set forth in this text are in accordance with the current recommendations and practice at the time of publication. However, in view of ongoing research, changes in government regulations, and the constant flow of information relating to drug therapy and drug reactions, the reader is urged to check the package insert for each drug for any change in indications and dosage and for added warnings and precautions. This is particularly important when the recommended agent is a new or infrequently employed drug.

Some drugs and medical devices presented in this publication have Food and Drug Administration (FDA) clear-ance for limited use in restricted research settings. It is the responsibility of the health care provider to ascertain the FDA status of each drug or device planned for use in their clinical practice.

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Visit Lippincott Williams & Wilkins on the Internet: http://www.lww.com. Lippincott Williams & Wilkins customer service representatives are available from 8:30 am to 6:00 pm, EST.

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This Book is Dedicated to . . .

Paul’s sister Sue, her husband Bob, and Jan’s brother Ken, in

appreciation for the love and kindness that they unselfishly

contributed to our mothers’ care during their final days,

and

the many heroes—both the praised and the unsung—who

have devoted their lives to the diagnosis and treatment of infectious

diseases worldwide and to the equally important

professionals who educated them.

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Paul G. Engelkirk, Ph.D., MT(ASCP), SM(AAM) Dr. Engelkirk has been engaged in various aspects of clin-ical microbiology for more than 40 years and is a Past President of the Rocky Mountain Branch of the American Society for Microbiology. He received his bachelor’s degree (in Biology) from New York University and his master’s and doctoral degrees (both in Microbiology and Public Health) from Michigan State University. He received additional medical technology and tropical medi-cine training at Walter Reed Army Hospital in Washington, D.C., and specialized training in anaerobic bacteriology, mycobacteriology, and virology at the Centers for Disease Control and Prevention in Atlanta, Georgia.

Dr. Engelkirk served 22 years as an officer in the U.S. Army Medical Department supervising a variety of immunology, clinical pathology, and microbiology laboratories in Germany, Vietnam, and the United States. He retired with the rank of Lieutenant Colonel. Following his military service, he devoted 20 years to microbi-ology education, including 8 years as an Associate Professor at the University of Texas Health Science Center in Houston, Texas, teaching diagnostic microbiology to medical technology students, and 12 years as a Profes-sor of Biological Sciences in the Science Department at Central Texas College in Killeen, Texas, teaching intro-ductory microbiology to nursing students.

Dr. Engelkirk is the author or co-author of four microbiology textbooks, ten additional book chapters, five medical laboratory-oriented self-study courses, and many scientific articles. Over the years, he and his wife, Janet, have edited and published a variety of educational newsletters for clinical microbiology labora-tory personnel on such topics as anaerobic bacteriology, clinical parasitology, medical mycology, and diag-nostic microbiology. He and Janet currently provide biomedical educational services through their consult-ing firm (Biomed Ed), located in Belton, Texas. Dr. Engelkirk’s hobbies include RVconsult-ing, hikconsult-ing, kayakconsult-ing, nature photography, and working in his yard.

Janet Duben-Engelkirk, Ed.D., MT(ASCP), CLS(NCA)

Dr. Duben-Engelkirk has over 30 years of experience in clinical laboratory science and higher education. She received bachelor’s degrees in biology and medical technology and a master’s degree in technical edu-cation from the University of Akron, and her doctorate in allied health eduedu-cation and administration from a combined program through the University of Houston and Baylor College of Medicine in Houston, Texas.

Dr. Duben-Engelkirk began her career in clinical laboratory science education teaching students “on the bench” in a community hospital in Akron, Ohio. She then became Education Coordinator for the Clin-ical Laboratory Science Program at the University of Texas Health Science Center at Houston, where she taught clinical chemistry and related subjects for 12 years. In 1992, Dr. Duben-Engelkirk assumed the position of Director of Allied Health and Clinical Laboratory Science Education at Scott and White Hos-pital in Temple, Texas, where her responsibilities included teaching microbiology and clinical chemistry. She also served as Interim Program Director for the Medical Laboratory Technician program at Temple College. Currently, Dr. Duben-Engelkirk is the Chair of the Biotechnology Department at Temple College and the Texas Bioscience Institute in Temple, where she is responsible for the administration of the biotechnology degree and certificate programs. The Biotechnology Programs and the Texas Bioscience

About the Authors

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Institute recently received the prestigious Bellwether Award for community colleges. Dr. Duben-Engelkirk was co-editor of a widely used clinical chemistry textbook and co-authored a clinical anaerobic bacteriol-ogy textbook with her husband, Paul. She has authored or co-authored numerous book chapters, journal articles, self-study courses, newsletters, and other educational materials.

Dr. Duben-Engelkirk has received many awards during her career, including Outstanding Young Leader in Allied Health, the American Society for Clinical Laboratory Science’s Omicron Sigma Award for outstanding service, and Teaching Excellence Awards. Her professional interests include instructional tech-nology, web-based instruction, and computer applications. Outside of the office and classroom, Dr. Duben-Engelkirk enjoys taking cruises, reading, music, yoga, movies, and hiking and RVing with Paul and their miniature schnauzer, Lacy.

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Microbiology—the study of microbes—is a fascinating and extremely important subject. We are sur-rounded by microscopic critters that impact our daily lives in a variety of ways. In addition to the numerous beneficial aspects of microbes, many of them cause disease. In recent years, the public has been bombarded by news reports about microbe-associated medical problems such as bird flu, SARS, monkeypox, flesh-eat-ing bacteria, mad cow disease, superbugs, black mould in buildflesh-eat-ings, West Nile virus, Ebola virus, bioter-rorism, anthrax, smallpox, food recalls due to the presence of bacterial pathogens, and epidemics of menin-gitis, hepatitis, influenza, tuberculosis. and diarrheal diseases.

Imagine how rewarding it would be to play a major role in the diagnosis of microbial diseases. Laboratory Diagnosis of Infectious Diseases is intended for both teaching and learning about diagnostic microbiology. Although laboratory professionals do not actually diagnose diseases, they provide valuable assistance to clini-cians by furnishing them with accurate and timely laboratory observations and test results. Throughout this book, the term “laboratory diagnosis of infectious diseases” refers to the various laboratory observations and test results, which, when received and evaluated by clinicians, assist them to correctly diagnose infectious diseases and initiate appropriate therapy.

This book, unlike some of the other books on the market, focuses on the essentials of diagnostic microbiology and, therefore, its entire contents can be taught in a one-semester course. The book contains many pedagogical features designed to make the text student friendly and its contents easily learned. Each chapter contains an outline, learning objectives, study aids, key points reemphasized in the margins, a list of new terms, a chapter review, and self-assessment exercises. Also included in the book are numerous full-color illustrations, an extensive glossary, and appendices containing detailed clinical microbiology labora-tory procedures, useful conversion formulas, and answers to self-assessment exercises.

Much of the material contained in more lengthy diagnostic microbiology textbooks has been omitted in an effort to provide a concise presentation of the information required by those who will be performing clinical microbiology laboratory procedures. However, each chapter also contains a list of References and Suggested Reading, where students may find more in-depth information on specific topics.

The first seven chapters provide a background on pathogens, infectious diseases, host defense mecha-nisms, clinical specimens, and the organization and responsibilities of the clinical microbiology laboratory. Chapters 8 through 25 discuss the most important bacterial, fungal, parasitic, and viral pathogens as well as the infectious diseases that they cause and how clinical laboratory professionals assist in the diagnosis of these diseases. Chapter 26 contains timely information regarding the role of the clinical microbiology lab-oratory in healthcare epidemiology and the hospital’s response to bioterrorist attacks.

A variety of pedagogical features, such as additional self-assessment exercises and answers, case stud-ies, puzzles, and in-depth discussions of selected topics, can be found on the accompanying Student CD-ROM. Appendices on the Student CD-ROM provide useful information on topics such as microbial intoxi-cations and choice of culture media and guidance regarding the work-up of colonies that are present on primary isolation plates. At the Lippincott Williams & Wilkins Web site (www.thePoint.com), instructors will find a comprehensive test generator and an image bank.

This book has been written in response to numerous requests for a concise, understandable, and easy-to-use text that covers only the basics of diagnostic microbiology. The authors welcome comments from users of the book as to how future editions might be improved.

Our sincere thanks to Robert C. Fader, Ph.D., Thomas W. Huber, Ph.D., Dale D. Dingley, M.P.H., and all others who contributed to the reviewing, editing, and production of this book. Special thanks to the authors of other Lippincott Williams & Wilkins textbooks whose illustrations appear throughout the book and to Pat Hidy, Ed.D., and the LWW artists for their excellent drawings.

—P.G.E. —J.D.E.

Preface

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Robert C. Fader, Ph.D., D(ABMM)

Section Chief, Microbiology/Virology Laboratories Scott and White Hospital

Temple, Texas Assistant Professor Department of Pathology

Texas A&M System Health Science Center, College of Medicine Temple, Texas

Thomas W. Huber, Ph.D., D(ABMM)

Microbiologist, Pathology and Laboratory Medicine

Central Texas Veterans Health Care System, Olin E. Teague Medical Center Temple, Texas

Associate Professor

Department of Pathology and Department of Medical Microbiology and Immunology Texas A&M System Health Science Center, College of Medicine

Temple, Texas

Consultants

Dale D. Dingley, M.P.H., M(ASCP)

Former Chief Parasitologist for the State of Texas Austin, Texas

Patrick K. Hidy, RN, Ed.D.

Former Chairman, Science Department Central Texas College

Killeen, Texas

Mary Ruth Beckham, M.Ed., MT(ASCP) Director, Program in Clinical Laboratory Science Scott and White Hospital

Temple, Texas

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Contents

SECTION I Introduction to Microbes and the Diseases They Cause

Chapter 1 Microbes and the Science of Microbiology 3

Chapter 2 Understanding Infectious Diseases 18

Chapter 3 Combating Pathogens and Infectious Diseases 43

SECTION II Introduction to the Clinical Microbiology Laboratory

Chapter 4 Organization and Responsibilities of the Clinical Microbiology Laboratory 71 Chapter 5 Clinical Specimens Used for the Diagnosis of Infectious Diseases 96

Chapter 6 General Clinical Microbiology Laboratory Methods 124

Chapter 7 Antimicrobial Agents and Antimicrobial Susceptibility Testing 153

SECTION III Bacterial Infections

Chapter 8 Introduction to Medical Bacteriology 185

Chapter 9 Gram-Positive Cocci 213

Chapter 10 Gram-Positive and Acid-Fast Bacilli 240

Chapter 11 Gram-Negative Cocci and Related Bacteria 272

Chapter 12 Gram-Negative Bacilli: The Family Enterobacteriaceae 292

Chapter 13 Gram-Negative Bacilli: Nonfermenters 319

Chapter 14 Fastidious and Miscellaneous Gram-Negative Bacilli 335

Chapter 15 Curved and Spiral-Shaped Bacilli 363

Chapter 16 Obligate Intracellular Bacteria 381

Chapter 17 Anaerobic Bacteria 392

Chapter 18 Laboratory Diagnosis of Selected Bacterial Infections 444

SECTION IV Fungal Infections

Chapter 19 Introduction to Medical Mycology 489

Chapter 20 Laboratory Diagnosis of Selected Fungal Infections 507

SECTION V Parasitic Infections

Chapter 21 Introduction to Medical Parasitology 543

Chapter 22 Laboratory Diagnosis of Selected Protozoal Infections 553

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xiv Contents

SECTION VI Viral Infections

Chapter 24 Introduction to Medical Virology 621

Chapter 25 Laboratory Diagnosis of Selected Viral Infections 640

SECTION VII Additional Responsibilities of the Clinical Microbiology Laboratory

Chapter 26 Health Care Epidemiology and Bioterrorism 667

Appendix A Clinical Microbiology Laboratory Procedures 683

Appendix B Useful Conversions 712

Appendix C Answers to Self-Assessment Exercises 713

Glossary 719

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I

Introduction

to Microbes

and the

Diseases

They Cause

CHAPTER 1

Microbes and the Science of

Microbiology

CHAPTER 2

Understanding Infectious Diseases

CHAPTER 3

Combating Pathogens and Infectious

Diseases

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AIDS. Malaria. Tuberculosis. Collectively, these

infec-tious diseases cause about 5 million deaths each year. Yet they are only three of hundreds of infectious diseases— diseases that maim, cripple, and kill; diseases that can strike anyone, at anytime, and in any part of the world; diseases that may occur naturally or may be spread by carelessness or design. To compound matters, previously unrecognized infectious diseases are constantly emerging. Imagine how exciting and rewarding it would be to play a role in diagnos-ing these terrible diseases.

TERMS AND DEFINITIONS

Microbiologyis the study of microbes. Microbesconsist of t w o m a j o r g r o u p s :

(1) cellular microbes, a n d ( 2 ) a c e l l u l a r microbes (Fig. 1-1).

Cellular microbes are composed of cells; t h e r e f o r e , t h e y a r e

considered living organisms and are usually referred to as microorganisms(tiny organisms).1Examples of cellular microorganisms are bacteria, archaea, microscopic algae, protozoa, and microscopic fungi (yeasts and moulds).2

Microbes and the Science

of Microbiology

Chapter Outline

Terms and Definitions

Diseases Caused by Pathogens Nonliving, Acellular Infectious Agents Living, Cellular Microorganisms

■ Procaryotic Genome ■ Eucaryotic Genome

Taxonomy, Microbial Classification, and Binomial Nomenclature

Careers in Microbiology

LEARNING OBJECTIVES

After studying this chapter, you should be able to:

Define the terms and abbreviations introduced in this chapter (e.g., bacteriology, capsule, cell membrane)

Differentiate between microbial intoxications and infectious diseases

Compare and contrast acellular and cellular microbes, and cite an example of each

Given diagrams of procaryotic and eucaryotic microorganisms, label the structural components

Cite a function for each of the following parts of a eucaryotic cell: cell membrane, nucleus, ribosomes, Golgi apparatus, lysosomes, mitochondria, plastids, cytoskeleton, cell wall, flagella, cilia

Cite a function for each of the following parts of a bacterial cell: cell membrane, chromosome, cell wall, capsule, flagella, pili, endospores

Identify the genus and specific epithet portions of the names of species (e.g., Escherichia coli)

Compare the five-kingdom and three-domain systems of classification with regard to categories of procary-otes and eucaryprocary-otes

Microbiology is the study of microbes. The two major categories of microbes are

acellular microbes and microorganisms.

1 The cell theory states that all living organisms are composed of cells. It was first proposed in the late 1830s by Matthias Schleiden (a German botanist) and

Theodor Schwann (a German zoologist).

2 The term for single-celled fungi may be spelled moulds or molds. Mycologists prefer moulds; therefore, that spelling is used throughout the book.

C H A P T E R

1

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4 SECTION I: Introduction to Microbes and the Diseases They Cause

Acellular microbes, on the other hand, are not com-posed of cells. They are smaller than cells, and their structures are far less complex than those of cells. Because they are not composed of cells, the acellular microbes are considered by most scientists to be nonliving entities. They are often referred to as infectious agents or infectious particles. Viruses and prions are examples of acellular microbes. Virtually all microbes, both the cellular and acellular types, are micro-scopic, meaning that a microscope is required to see them.3

Some microbes cause disease, whereas others do not. Although sometimes referred to as “germs,” the technical term for the microbes that cause disease is pathogens. The microbes that do not cause disease are called nonpathogens. For humans, some nonpathogens are beneficial and some have no effect. (Beneficial aspects of nonpathogens are briefly discussed on the CD-ROM that accompanies this book.) Other microbes, many of which live on and in the human body,4are called opportunisticpathogens (or oppor-tunists). They usually do not cause any health problems, but they have the potential to cause disease if they gain access to a part of the anatomy where they do not belong. One example i s t h e b a c t e r i u m Escherichia coli, which lives in the human intesti-nal tract. This organism does not cause any harm as long as it stays in the intestinal tract, but it can cause disease if it gains

access to the urinary bladder, the bloodstream, or a wound. Some opportunistic pathogens strike when a person becomes run down, stressed, or debilitated (weakened) as a result of some disease or condition. Opportunistic pathogens can be thought of as microbes awaiting the opportunity to cause disease.

DISEASES CAUSED

BY PATHOGENS

In his discussion of Anton van Leeuwenhoek,5thought by many to be the father of microbiology, Paul de Kruif (see “References and Suggested Reading”) described pathogens as follows:

[Leeuwenhoek] had stolen and peeped into a fantastic sub-visible world of little things, creatures that had lived, had bred, had battled, had died, completely hidden from and unknown to all men from the beginning of time. Beasts these were of a kind that ravaged and annihilated whole races of men ten million times larger than they were themselves. Beings these were, more terrible than fire-spitting dragons or hydra-headed monsters. They were silent assassins that mur-dered babes in warm cradles and kings in sheltered places. It was this invisible, insignificant, but implacable—and some-times friendly—world that Leeuwenhoek had looked into for the first time of all men of all countries.

Pathogens cause two categories of diseases: infectious diseases and microbial intoxications (Fig. 1-2). An infec-tious diseaseresults when a pathogen invades the body and subsequently causes

dis-ease. A microbial intoxi-cation results when a per-s o n i n g e per-s t per-s a t o x i n (poisonous substance) that has been produced by a

pathogen. Of the two categories, infectious diseases cause far more illnesses and deaths.

NONLIVING, ACELLULAR

INFECTIOUS AGENTS

The nonliving, acellular infectious agents discussed in this book include viruses and prions. Viruses and the diseases they cause are discussed in detail in Chapters 24 and 25.

Microbes Acellular Infectious Agents

Prions Viruses Cellular Microorganisms Procaryotes Archaea Bacteria Eucaryotes Algae Fungi Protozoa

Figure 1-1. Acellular and cellular microbes. Acellular microbes include prions and viruses. Cellular microbes include the less com-plex procaryotes (archaea and bacteria) and the more comcom-plex eucaryotes (algae, protozoa, and fungi).

3 Helminths(parasitic worms) are described in Chapters 21 and 23. Helminths are multicellular animals and, although they are microscopic at some

stage(s) in their life cycles, they are not considered microorganisms. In fact, some adult helminths are extremely long—up to 10 meters in some cases. Helminths are included in this book because information obtained in the clinical microbiology laboratory is used in the diagnosis of helminth infections.

4Microbes that live on and in the human body are collectively referred to as the indigenous microflora. The older term, normal flora, is still in common

usage. It has been estimated that the indigenous microflora of humans may number as high as 100 trillion organisms, consisting of as many as 500 to 1,000 species. Many of these microbes are beneficial. They inhibit the growth of pathogens in areas of the body where they live by occupying space, depleting the food supply, and secreting materials (waste products, toxins, antibiotics, etc.) that may prevent or reduce the growth of pathogens.

5During the mid-to-late 1600s, a Dutchman named Anton van Leeuwenhoek was the first person to observe live bacteria and protozoa, using simple

micro-scopes he had constructed.

Microbes cause two categories of diseases: infectious diseases and microbial intoxications.

The microbes that cause disease are called pathogens. If they only cause disease under certain

conditions, they are called opportunistic pathogens.

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LIVING, CELLULAR

MICROORGANISMS

According to the cell theory, all living organisms are com-posed of cells. Considerable evidence exists to indicate that between 3.5 billion and 4 billion years ago, the first bit of life to appear on the earth was a very primitive cell similar to the simple bacteria of today. Bacterial cells exhibit all the characteristics of life, although they do not have the com-plex system of membranes and organelles (tiny organlike structures) found in the

more advanced organisms. These less complex cells, which include bacteria and a r c h a e a , a r e c a l l e d procaryotesor procaryotic cells (Fig. 1-3). The more complex cells—those con-taining a true nucleus and many membrane-bound o rg a n e l l e s — a r e c a l l e d

eucaryotes or eucaryotic cells (Fig. 1-4).7 Eucaryotes include organisms like algae, protozoa, fungi, plants, ani-mals, and humans.

Some microbes are procaryotic, some are eucaryotic, and as previously dis-cussed, some are n o t c e l l s a t a l l . Learning the differ-ences in the

struc-tures of these diverse groups of microbes helps us to better understand pathogenic (disease-causing) mechanisms and why some drugs are effective against one group but not oth-ers. Table 1-1 summarizes key differences between procary-otic and eucaryprocary-otic cells.

Procaryotic Genome

Bacterial cells usually contain only one chromosome, which consists of a long, supercoiled, circular, deoxyri-bonucleic acid (DNA) molecule. The bacterial chromo-some serves as the control center of the bacterial cell. It is capable of duplicating itself, guiding cell division, and directing cellular activities. A procaryotic cell contains neither nucleoplasm nor a nuclear membrane. The chromo-some is suspended or embedded in the cytoplasm. The DNA-occupied space within a bacterial cell is sometimes referred to as the bacterial nucleoid. (The suffix -oid means “like” or “similar to”; nucleoid means “like or similar to a nucleus.”)

CHAPTER 1: Microbes and the Science of Microbiology 5

Prions(pronounced “pree-ons”) are small infectious pro-teins (i.e., protein molecules capable of causing diseases). Prions cause fatal neuro-logical diseases in ani-m a l s ,6 s u c h a s s c r a p i e (pronounced “scrape-ee”) in sheep and goats; bovine spongiform encephalopa-thy (“mad cow disease”); and kuru, Creutzfeldt-Jakob dis-ease, Gerstmann-Sträussler-Scheinker disdis-ease, and fatal familial insomnia in humans. Similar diseases in mink, mule deer, western whitetail deer, elk, and cats may also be caused by prions. The term scrapie comes from the observation that infected animals scrape themselves against fence posts and other objects in an effort to relieve the intense itching (pruritus) associated with the disease. The disease in deer and elk is called chronic wasting dis-ease, in reference to the irreversible weight loss the ani-mals experience. All these prion diseases are fatal spongi-form encephalopathies—diseases of the brain, in which the brain becomes spongelike, filled with amyloid pro-teins that replace the neurons that are normally found there.

The mechanism by which prions cause disease remains a mystery, although it is thought that prions convert func-tional protein molecules into nonfuncfunc-tional ones by causing the functional molecules to change their shape. Many scien-tists remain unconvinced that proteins alone can cause dis-ease. Because the clinical microbiology laboratory cur-rently does not play a role in the diagnosis of prion diseases, prions will not be discussed further in this book. It is possible that laboratory tests will become available in the future to diagnose prion diseases, at which time, clinical microbiology laboratory professionals may perform those procedures.

Infectious Disease Process Microbial Intoxication

A pathogen colonizes the body

A pathogen produces a toxin in vitro

This type of disease is an infectious disease

The pathogen causes disease

This type of disease is a microbial intoxication A person ingests the toxin, and

the toxin causes a disease

Figure 1-2. The two categories of diseases caused by

pathogens. An infectious disease results when a pathogen

colo-nizes (inhabits) the body and subsequently causes disease. Micro-bial intoxication results when a person ingests a toxin (poisonous substance) that has been produced by a microorganism in vitro (outside the body).

6 Although humans are technically animals, the word animals is used in this book in reference to animals other than humans. 7Alternate spellings of procaryote/procaryotic and eucaryote/eucaryotic are prokaryote/prokaryotic and eukaryote/eukaryotic.

Cellular microorganisms are divided into two major categories: procaryotes and

eucaryotes.

Eucaryotic cells possess a true nucleus, whereas procaryotic cells do not.

Eucaryotic cells possess numerous membranes and membrane-bound structures. The only membrane possessed by a procaryotic cell is the cell

membrane or cytoplasmic membrane. The two groups of

acellular microbes that cause human disease are

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6 SECTION I: Introduction to Microbes and the Diseases They Cause

Structure or Component Procaryotic Cells Eucaryotic Cells

TABLE 1 - 1

Key Differences Between Procaryotic and Eucaryotic Cells

Cell membrane: also known as the cellular, plasma, or

cytoplasmic membrane; separates the contents of the cell from the “outer world”; its function is selective permeability, meaning that it regulates the passage of materials into and out of the cell; some materials will be able to pass through the cell membrane, whereas others will not (Fig. 1-5)

Cytoplasm: the semifluid, gelatinous, nutrient matrix

enclosed by the cell membrane; within which are found various structures and components

Nucleus: a true nucleus consists of three components—

a gelatinous matrix known as nucleoplasm,

chromosomes, and a nuclear membrane; the nucleus serves as the “command center” of eucaryotic cells

Endoplasmic reticulum (ER): a highly convoluted system

of membranes running throughout the cytoplasm; ribosomes are attached to some areas of the ER, giving it a rough appearance (rough ER) when observed with an electron microscope; sections of ER where ribosomes are not attached are referred to as smooth ER

Ribosomes: the sites of protein synthesis; clusters of

ribosomes are referred to as polyribosomes or polysomes; ribosomes are composed of proteins and rRNA molecules

Golgi apparatus (also known as the Golgi complex or

Golgi body): connects with the ER; where newly synthesized proteins are transformed into mature, functional proteins, which are then packaged into membrane-bound vesicles for storage within the cell or transport out of the cell; sometimes referred to as “packaging plants”

Lysosomes: membrane-bound vesicles containing

digestive enzymes

Mitochondria (sing. mitochondrion): sometimes referred

to as “power plants,” “powerhouses,” or “energy factories”; structures within which a great deal of energy is produced

Plastids: the sites of photosynthesis, a process by which

light energy is converted into chemical energy; a chloroplast is an example

Possessed by all

Possessed by all

Not found in procaryotic cells

Not found in procaryotic cells

Possessed by all

Not found in procaryotic cells

Not found in procaryotic cells

Not found in procaryotic cells

Not found in procaryotic cells

Possessed by all

Possessed by all

Possessed by all (although rare, some eucaryotic cells possess more than one nucleus)

Possessed by all Possessed by all Possessed by all Possessed by all Possessed by all Possessed by cells of photosynthetic eucaryotes, such as algae and plants

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CHAPTER 1: Microbes and the Science of Microbiology 7

Cell wall: rigid structure lying outside of the cell

membrane; provides rigidity, shape, and protection

Glycocalyx: slimy, gelatinous, polysaccharide material

found outside of the cell wall; there are two types of glycocalyx—a slime layer, which consists of

unorganized, loosely attached material, and a capsule, which consists of organized, firmly attached material

Flagella (sing. flagellum): long appendages that enable

cells to be motile; they move in a whiplike manner; the internal structure of procaryotic flagella is much different than that of eucaryotic flagella

Cilia (sing. cilium): short, hairlike appendages that

enable cells to be motile

Pili (sing. pilus): long, thin appendages that enable cells

to attach to surfaces; a special type of pilus known as a sex pilus is described later in the book; pili are also referred to as fimbriae

Spores: thick-walled structures, usually produced within

cells

Possessed by virtually all; notable exceptions are bacteria in the genus

Mycoplasma (discussed

later in the book)

Some procaryotes possess a slime layer, others possess a capsule, and others possess neither; the capsule serves an

antiphagocytic function, meaning that it protects encapsulated bacteria from being phagocytized by white blood cells

Possessed by some; composed of threads of a protein called flagellin

Not found on procaryotic cells

Possessed by some

Possessed by some; bacterial spores are technically known as

endospores; produced by

some bacteria as a means of survival

Possessed by algal, fungal, and plant cells, but not by protozoal, animal, or human cells

Not found in eucaryotes

Possessed by some; protozoa with flagella are referred to as flagellates; a eucaryotic flagellum contains microtubules that run the length of the flagellum

Possessed by some; protozoa that possess cilia are referred to as ciliates; a eucaryotic cilium contains microtubules that run the length of the cilium

Not found in eucaryotes

Possessed or produced by some (e.g., moulds); their function is reproduction

Structure or Component Procaryotic Cells Eucaryotic Cells

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Inclusion Cell wall Ribosomes Cytoplasm Cell membrane Chromosome Plasmid Flagella Capsule Capsule Cell wall Cell membrane Pili

Figure 1-3. A typical procaryotic cell.

Centriole Golgi apparatus Nucleolus Nuclear membrane Rough endoplasmic reticulum (ER) Cytosol Microvilli Cilia Lysosome Mitochondrion Peroxisome Ribosomes Vesicle Nucleus Smooth endoplasmic reticulum (ER) Cell membrane

Figure 1-4. A typical eucaryotic cell. (From Cohen BJ, Taylor JJ. Memmler’s The Human Body in Health and Disease. 10th Ed. Philadelphia: Lippincott Williams & Wilkins, 2005.)

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CHAPTER 1: Microbes and the Science of Microbiology 9

Genes are located along the bacterial chromosome. Although genes are sometimes described as “beads on a string,” each bead (gene) is actually a particular segment of the DNA molecule. Each gene contains the genetic informa-tion (or genetic code) that enables the cell to produce a gene product. Most gene products are proteins, but some genes code for the production of two types of ribonucleic acid (RNA): ribosomal ribonucleic acid (rRNA) and transfer ribonucleic acid (tRNA) molecules. The organ-ism’s complete collection of genes is referred to as that organism’s genotypeor genome.

Gene products influence the organism’s phenotype, which can be thought of as all the attributes, characteristics, or properties of the organism. An organism’s phenotype is a manifestation of that organism’s genotype. Phenotypic character-i s t character-i c s o f h u m a n s include such attrib-utes as eye, hair, and s k i n c o l o r, a n d genetic tendencies to develop various hereditary diseases. Phenotypic characteristics of bacteria include the following: • Cell shape and morphologic arrangement (grouping) of

the cells

• The organism’s Gram reaction (i.e., what color the cells stain in the Gram staining procedure, which is described later in the book)

• Composition of the cell wall

• Presence or absence of a capsule

• Presence or absence of flagella and, if present, their num-ber and location on the cell

• Ability to sporulate (produce endospores) • Presence or absence of pili (including a sex pilus) • Presence or absence of various enzymes

The thin and tightly folded chromosome of an E. coli cell is about 1.5 mm (1,500 m) long and only 2 nm wide. Because a typical E. coli cell is about 2 to 3 m long, its chromosome is approximately 500 to 750 times longer than the cell itself—quite a packaging feat. Bacterial chromo-somes contain between 450 and 8,000 genes, depending on the species. Thus, a bacterial chromosome contains suffi-cient genetic information to code for between 450 and 8,000 gene products (enzymes, other proteins, rRNA, and tRNA molecules). In comparison, the chromosomes within a human cell contain about 25,000 to 30,000 genes— enough to code for approximately 25,000 to 30,000 gene products.

Small, circular molecules of double-stranded DNA that are not part of the chromosome (referred to as extrachromo-somal DNA or plasmids) may also be present in the cyto-plasm of procaryotic cells. A cyto-plasmid may contain anywhere from fewer than 10 genes to several hundred genes. A bacte-rial cell may contain one plasmid, multiple copies of the same plasmid, or more than one type of plasmid (i.e., plas-mids containing different genes). Thus, a bacterial cell’s complete genome consists of the genes located on its chro-mosome plus the genes located on any plasmids that it possesses.

Phosphate “head”

Lipid “tail”

Cytoplasm

Proteins

Figure 1-5. The lipid bilayer structure of cell membranes, showing the hydrophilic heads

and hydrophobic tails of phospholipid molecules. Cell membranes also contain protein

mole-cules, which have been described as resembling “icebergs floating in a sea of lipids.”

An organism’s complete collection of genes is referred to as its genotype

or genome.

An organism’s phenotype includes all the attributes, characteristics, or properties of

the organism. Phenotype is determined by genotype.

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10 SECTION I: Introduction to Microbes and the Diseases They Cause

Eucaryotic Genome

As previously mentioned, the primary difference between procaryotic and eucaryotic cells is that eucaryotic cells pos-sess a “true nucleus,” whereas procaryotic cells do not. The nucleusunifies, controls, and integrates the functions of the entire cell and can be thought of as the “command center” of the cell. The nucleus has three components: nucleoplasm, chromosomes, and a nuclear membrane. Nucleoplasmis the gelatinous matrix or base material of the nucleus; like cyto-plasm, nucleoplasm is a type of protoplasm. The chromo-somes are embedded or suspended in the nucleoplasm. The membrane that serves as a “skin” around the nucleus is called the nuclear membrane; it contains holes (nuclear pores) through which large molecules can enter and exit the nucleus.

Eucaryotic chromosomes consist of linear DNA mole-cules and proteins (histones and nonhistone proteins). The number and composition of chromosomes and the number of genes on each chromosome are characteristic of the par-ticular species of organism. Different species have different numbers and sizes of chromosomes. Human diploid cells, for example, have 46 chromosomes (23 pairs), each consist-ing of thousands of genes. As previously mentioned, it has been estimated that the human genome consists of about 25,000 to 30,000 genes.

When observed using a transmission electron micro-scope (see Chapter 6), a dark (electron-dense) area can be seen within the nucleus. This area is called the nucleolus; it is here that rRNA molecules are manufactured. The rRNA molecules then exit the nucleus to become part of the structure of ribosomes (ribosomes are described in Table 1-1).

TAXONOMY, MICROBIAL

CLASSIFICATION, AND BINOMIAL

NOMENCLATURE

Taxonomyis the science of classification of living organ-isms. According to Bergey’s Manual of Systematic Bacteri-ology (see “References and Suggested Reading”), taxonomy consists of three separate but interrelated areas: classifica-tion, nomenclature, and identification. Classification is the arrangement of organisms into taxonomic groups (known as taxa) on the basis of similarities or relationships. Taxa include kingdoms or domains, divisions or phyla, classes, orders, families, genera, and species (see the Study Aid). Closely related organisms (i.e., organisms having similar characteristics) are placed into the same taxon.

Nomencla-ture is the assignment of names to the various taxa

accord-ing to international rules. Identification is the process of determining whether an isolate belongs to one of the estab-lished, named taxa or represents a previously unidentified species.

A Way to Remember the Sequence of Taxa from Kingdom to Species. Phrases

are often helpful when trying to learn new material. A former student used the phrase “ K i n g D av i d C a m e O ve r Fo r G o o d Spaghetti” (KDCOFGS) to help her remem-ber the sequence of taxa from Kingdom to Species (K for Kingdom, D for Division, C for Class, O for Order, F for Family, G for Genus, and S for Species.) If phylum is preferred over division, King Philip can substitute for King David (KPCOFGS).

When attempting to learn the identity of a microorgan-ism that has been isolated from a clinical specimen, person-nel working in clinical microbiology laboratories are very much like detectives or crime scene investigators (Fig. 1-6). They gather “clues” (characteristics, attributes, properties, traits) about the organism until they have a sufficient number of clues to identify (speciate) the culprit. In most cases, the “clues” gathered will match the characteristics of an estab-lished species. (Note: Throughout this book, the phrase “to identify an organism” means to learn the organism’s species name—i.e., to speciate it.) Consult the CD-ROM for more information about the connection between laboratory professionals and crime scene investigators.

The science of taxonomy is based on the binomial system developed in the 18th century by the Swedish scientist Carolus L i n n a e u s . I n t h e

binomial system, each organism is given two names (e.g.,Homo sapiens for humans). The fi r s t n a m e i s t h e genus (pl. genera), and the second name is the specific

epi-thet. The first and second names together are referred to as the species. Thus,Homo is a genus and Homo sapiens is a species.

In the binomial system of nomenclature, the first name (e.g., Escherichia) is the genus, and the second name (e.g., coli)

is the specific epithet. When used together, the first and second names (e.g., Escherichia

coli) are referred to as a species.

Figure 1-6. Clinical microbiology laboratory professionals are

very much like detectives or crime scene investigators. They

gather “clues” about the organism until they have a sufficient num-ber of clues to identify (speciate) the culprit.

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Bacterium Disease

CHAPTER 1: Microbes and the Science of Microbiology 11

Because written reference is often made to genera and species, biologists throughout the world have adopted a standard method of expressing these names. To express the genus, the first letter of the word is capitalized and the whole word underlined or italicized—for example,Escherichia. To express the species, the first letter of the genus name is cap-italized (the specific epithet is not capcap-italized) and then the entire species name is underlined or italicized—for exam-ple,Escherichia coli. Frequently, the genus is designated by a single-letter abbreviation, as in E. coli. In an essay or arti-cle about Escherichia coli, Escherichia would be spelled out the first time the organism is mentioned; thereafter, the abbreviated form,E. coli, could be used. The abbreviation sp. indicates a single species, and the abbreviation spp. indi-cates more than one species.

In addition to proper scientific names for bacteria, acceptable names like staphylococci (for Staphylococcus spp.), streptococci (for Streptococcus spp.), clostridia (for Clostridium spp.), pseudomonads (for Pseudomonas spp.), mycoplasmas (for Mycoplasma spp.), rickettsias (for Rick-ettsia spp.), and chlamydiae (for Chlamydia spp.) are

com-monly used in health care settings. Bacterial nicknames and slang frequently used within hospitals are GC and gono-cocci (for Neisseria gonorrhoeae), meningococci (for Neis-seria meningitidis), pneumococci (for Streptococcus pneu-moniae), staph (for Staphylococcus or staphylococcal), and strep (for Streptococcus or streptococcal). It is common to hear health care professionals using names like meningo-coccal meningitis, pneumomeningo-coccal pneumonia, staph infec-tion, and strep throat.

Quite often, bacteria are named for the disease that they cause (see Table 1-2 for examples). However, in a few cases, bacteria are misnamed. For example, the bacterium Haemophilus influenzae does not cause influenza. Influenza is a respiratory disease caused by influenza viruses.

Each organism is categorized into larger groups based on their similarities and differences. In 1969, Robert H. Whittaker proposed a five-kingdom system of classification, in which all organisms are placed into five kingdoms: • Bacteria and archaea (which in many ways are similar to

bacteria) are in the Kingdom Procaryotae(or Kingdom

Bacillus anthracis Anthrax

Chlamydophila pneumoniae Pneumonia

Chlamydophila psittaci Psittacosis (parrot fever)

Chlamydia trachomatis Trachoma

Clostridium botulinum Botulism

Clostridium tetani Tetanus

Corynebacterium diphtheriae Diphtheria

Francisella tularensis Tularemia (rabbit fever)

Klebsiella pneumoniae Pneumonia

Mycobacterium leprae Leprosy (Hansen disease)

Mycobacterium tuberculosis Tuberculosis

Mycoplasma pneumoniae Pneumonia

Neisseria gonorrhoeae Gonorrhea

Neisseria meningitidis Meningitis

Streptococcus pneumoniae Pneumonia

Vibrio cholerae Cholera

TABLE 1 - 2

Examples of Bacteria Named for the Diseases They Cause

a

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12 SECTION I: Introduction to Microbes and the Diseases They Cause

Monera). All organisms in this kingdom are procaryotic. Nearly all are unicellular and considered microorgan-isms. Many bacteria cause infections in humans; bacterial infections are discussed in Chapters 8 through 18. Archaea are common in nature but are thought not to cause any type of human disease and, for that reason, are not described in this book.

• Algae and protozoa are in the Kingdom Protista. All organisms in this kingdom are eucaryotic; they are referred to as protists. Some algae are

microorgan-isms, whereas oth-ers (e.g., certain “seaweeds”) are quite large. Although algae cause various microbial intoxica-tions, they are only rarely associated with infectious diseases. Algal infections are discussed briefly in Chapter 2. Most protozoa are unicellular, and all are considered microorganisms. Various protozoa cause human infections, which are discussed in Chapters 21 and 22.

• Fungi are in the Kingdom Fungi. All organisms in this kingdom are eucaryotic. Some fungi (e.g., yeasts and moulds) are microorganisms, whereas others (e.g., mush-rooms and toadstools) are not. Many yeasts and moulds are human pathogens; fungal infections are discussed in Chapters 19 and 20.

• Plants are in the Kingdom Plantae. All organisms in this kingdom are eucaryotic. This kingdom contains no microorganisms.

• Animals are in the Kingdom Animalia. All organisms in this kingdom are eucaryotic. This kingdom contains no microorganisms. As previously mentioned, although humans are in the Kingdom Animalia, in this book the word animals refers to animals other than humans.

Each kingdom consists of divisions or phyla, which in turn are divided into classes, orders, families, genera, and species (Table 1-3). In some cases, species are divided into subspecies, their names consisting of a genus, a specific epi-thet, and a subspecific epithet (abbreviated ssp. or subsp.); an example would be the bacterium Haemophilus influenzae ssp. aegyptius, the most common cause of the medical con-dition referred to as pink eye. Although Whittaker’s

five-In the five-kingdom system of classification, procaryotic microorganisms are in the

Kingdom Procaryotae. Eucaryotic microorganisms

are in the Protista and Fungi kingdoms.

TABLE 1 - 3

Comparison of Human and Bacterial Classifications

a

Escherichia coli (a Staphylococcus aureus

medically important (a medically important Classification Human Gram-negative bacillus)b Gram-positive coccus)b

Kingdom (Domain) Animalia (Eucarya) Procaryotae (Bacteria) Procaryotae (Bacteria)

Phylum Chordata Proteobacteria Firmicutes

Class Mammalia Gammaproteobacteria Bacilli

Order Primates Enterobacteriales Bacillales

Family Hominidae Enterobacteriaceae Staphylococcaceae

Genus Homo Escherichia Staphylococcus

Species (a species

Homo sapiens Escherichia coli Staphylococcus aureus

has 2 names; the first name is the genus; the second name is the specific epithet)

aThe bacteriology classification is based on Boone DR, Castenholz RW, eds. The Archaea and the Deeply Branching and Phototrophic Bacteria. New York: Springer-Verlag, 2001. Garrity GM, ed. Bergey’s Manual of Systematic Bacteriology, vol 1. 2nd Ed.

bThe terms Gram-negative and Gram-positive relate to the colors of bacteria at the end of the Gram staining procedure (see Chapter 6). If the bacteria are pink to red, they are referred to as Gram-negative bacteria. If they are blue to purple, they are referred to as Gram-positive bacteria. A bacillus is a rod-shaped bacterium, and a coccus is a round bacterium.

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CHAPTER 1: Microbes and the Science of Microbiology 13

kingdom system of classification has been the most popular classification system for the past 30 years or so, not all sci-entists agree with it; other taxonomic classification schemes exist. For example, some scientists do not agree that algae and protozoa should be placed into the same kingdom, and in some classification schemes, protozoa are placed into a subkingdom of the Kingdom Animalia. Prions and viruses are not included in the five-kingdom system of classification because they are not living cells; they are acellular.

In the late 1970s, Carl R. Woese devised a three-domain system of classification that is gaining in popularity among scientists. In this sys-t e m , sys-t h e r e a r e sys-t wo domains of procary-o t e s (A rch a e a a n d B a c t e r i a ) a n d o n e domain (Eucarya or Eukarya) that includes all eucaryotic organisms. The word Archaea comes from archae, meaning “ancient.” Note that the domain names are italicized. Domain Archaea contains two phyla and Domain Bacteria contains 23 phyla. The three-domain system is based on differences in the structure of cer-tain rRNA molecules among organisms in the three domains.

CAREERS IN MICROBIOLOGY

Many career fields are possible within the science of micro-biology. For example, a person may specialize in the study of just one category of microbe. A bacteriologist is a scientist who specializes in bacteriology—the study of the structure, functions, and activities of bacteria. Scientists specializing in the field of phycologystudy the various types of algae and are called phycologists. Protozoologists explore the area of protozoology—the study of protozoa and their activities. Those who specialize in the study of fungi, or mycology, are called mycologists.Virology encompasses the study of viruses and their effects on living cells of all types. Virolo-gists and cell bioloVirolo-gists may become genetic engineers who transfer genetic material (DNA) from one cell type to another. Virologists may also study prions. A parasitologist is one who specializes in parasitology—the study of parasites. The parasites usually studied by parasitologists include para-sitic protozoa, helminths, and certain arthropods.

Other career fields in microbiology pertain more to applied microbiology—that is, how knowledge of

microbi-ology can be applied to different aspects of society, medi-cine, and industry. One such career field is the exciting and rewarding field of clinical microbiology(also called diag-nostic microbiology), which is the focus of this book. Clini-cal microbiology is the subdiscipline of microbiology that is associated with the diagnosis of human infectious diseases. Procedures performed

in the clinical micro-biology laboratory include the isolation of pathogens from human clinical

speci-mens, tests to identify or speciate pathogens, and tests used to determine the susceptibility or resistance of pathogens to drugs. These are the laboratory procedures described in this book. The results of these tests assist clinicians in the diag-nosis, treatment, and management of infectious diseases. People working in clinical microbiology must possess an extensive knowledge of pathogens and the laboratory methods required to diagnose infectious diseases. They must not only have a genuine desire to assist clinicians and patients but also enjoy detective work. Additional infor-mation about this career field can be found on the Web sites of the American Society for Microbiology (http:// www.asm.org/), the American Society for Clinical Pathol-ogy (http://www.ascp.org/) and the American Society for Clinical Laboratory Science (http://www.ascls.org/).

Information about other areas of specialization in applied microbiology can be found on the CD-ROM that accompanies this book and the Web site of the American Society for Microbiology (http://www.asm.org/). Exam-ples of other microbiology career fields include

agricul-tural microbiology, biotechnology (the use of microbes

to make useful products), environmental microbiology and bioremediation (the use of microbes to decompose wastes, including industrial and toxic wastes), microbial

genetics and genetic engineering (inserting genes into

microorganisms to enable them to produce important prod-ucts they previously were unable to produce), microbial

physiology, paleomicrobiology (the study of ancient

microbes), parasitology, sanitary microbiology, and

vet-erinary microbiology. Another career field that

incorpo-rates an interest in and knowledge of microbiology is

epi-demiology (see Chapter 26). The scope of microbiology

has broad, far-reaching effects on human beings and their environment.

In the three-domain system of classification, procaryotic microorganisms are in the

Bacteria and Archaea domains.

Clinical microbiology is the subdiscipline of microbiology associated with the diagnosis of

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Chapter Review

• Microbes include viruses, prions, bacteria, archaea, certain algae, protozoa, and certain fungi.

• Because viruses and prions are acellular (not com-posed of cells), they are often referred to as infectious agents or infectious particles, rather than microorgan-isms.

• Microbes that live on and in various parts of the human body are called indigenous microflora (or indigenous microbiota).

• Only a small percentage of known microbes cause disease. Those that do are called pathogens, and the diseases they cause are referred to as infectious dis-eases and microbial intoxications. Microbes that do not cause disease are called nonpathogens. Oppor-tunistic pathogens do not cause disease under ordi-nary circumstances; however, they have the potential to cause disease if they gain access to the “wrong place” at the “wrong time.”

• The cell is the fundamental unit of any living organ-ism; it exhibits the basic characteristics of life. All liv-ing organisms are composed of one or more cells. • Complex eucaryotic cells contain membrane-bound

organelles and a true nucleus, containing DNA. Pro-caryotic cells (archaea and bacteria) exhibit all the characteristics of life but do not have a true nucleus or a complex system of membranes and membrane-bound organelles.

• Some eucaryotic cells have cell walls to provide rigidity, shape, and protection; these simple cell walls may contain cellulose, pectin, lignin, chitin, or min-eral salts. Procaryotic bacterial cell walls are more complex, containing peptidoglycan and, in some cases, lipopolysaccharides.

• In eucaryotic cells, energy is produced within mito-chondria (“energy factories”). Energy-producing reactions occur at the cell membranes of procaryotic cells.

• External to the cell wall, some bacteria have either a capsule or a slime layer. Capsules serve an antiphago-cytic function and have been used in the production of certain vaccines. Determining whether a bacterium possesses a capsule or not is of value when attempting to identify the organism.

• Many bacteria have flagella that enable motility and some produce spores for survival. Determining whether a bacterium possesses flagella or not is of value when attempting to identify the organism, as are the number and location of the flagella. Likewise, the

presence or absence of spores is of value when identi-fying bacteria.

• In the binomial system of nomenclature, the first name is the genus, the second name is the specific epithet, and the two names together represent the species.

• Taxonomic classification of organisms separates them into kingdoms, divisions, orders, classes, families, genera, and species, based on their characteristics, attributes, properties, and traits.

• In the five-kingdom system of classification, microor-ganisms are found in the first three kingdoms— Procaryotae (bacteria), Protista (algae and protozoa), and Fungi. In the three-domain system of classifica-t i o n , m i c r o o rg a n i s m s a r e f o u n d i n a l l classifica-t h r e e domains—Archaea, Bacteria, and Eucarya.

New Terms and Abbreviations

After studying Chapter 1, you should be familiar with the following terms, which are defined within the chapter and in the Glossary at the back of the book:

Acellular microbe Bacteriology Capsule Cell membrane Cell wall Chromosome Cilium (pl. cilia) Cytoplasm

Endoplasmic reticulum (ER) Endospore Eucaryote Flagellum (pl. flagella) Gene Gene product Genotype Genus (pl. genera) Glycocalyx Golgi apparatus Indigenous microflora Infectious disease 14

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15 Lysosome Microbial intoxication Microbiology Microorganism Mitochondrion (pl. mitochondria) Mycology Nonpathogen Nuclear membrane Nucleolus Nucleoplasm Nucleus (pl. nuclei) Opportunistic pathogen Organelle Pathogen Parasitology Phenotype Phycology Pilus (pl. pili) Plasmid Plastid Prion Procaryote Protist Protoplasm Protozoology Ribosomes Slime layer Species (pl. species) Specific epithet Spore Taxon (pl. taxa) Taxonomy Toxin Virology

References and Suggested Reading

Boone DR, Castenholz RW, eds. The Archaea and the Deeply Branching and Phototrophic Bacteria. New York: Springer-Verlag, 2001. Garrity GM, ed. Bergey’s Manual of Systematic Bacteriol-ogy, vol 1. 2nd Ed.

De Kruif P. Microbe Hunters. New York: Harcourt Brace, 1926.

On the CD-ROM

• How Microbes Affect Our Lives • The CSI Connection

• Careers in Microbiology

• Additional Self-Assessment Exercises • Puzzle

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Self-Assessment Exercises

After studying Chapter 1, answer the following questions.

1. In the five-kingdom system of classification, bacteria are found in which of the following kingdoms? A.Animalia

B.Plantae C.Procaryotae D.Protista

2. The microbes that usually live on or within a person are collectively referred to as A.germs.

B.indigenous microflora. C.nonpathogens.

D.opportunistic pathogens.

3. The field of parasitology involves the study of which of the following types of organisms? A.Arthropods, bacteria, fungi, protozoa, and viruses

B.Arthropods, helminths, and certain protozoa C.Bacteria, fungi, and protozoa

D.Bacteria, fungi, and viruses

4. Which of the following are even smaller than viruses? A.Bacteria

B.Fungi C.Prions D.Protozoa

5. Molecules of extrachromosomal DNA are also known as A.the Golgi apparatus.

B.plasmids. C.plastids. D.lysosomes.

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6.Of the following, which one is not found in procaryotic cells?

A.Chromosome B.Plasmid C.Mitochondrion D.Ribosome

7.The three-domain system of classification is based on differences in which one of the following molecules?

A.DNA

B.mRNA

C.tRNA

D.rRNA

8.Which of the following is in the correct sequence? A.Kingdom, Division, Order, Class, Family, Genus B.Kingdom, Order, Division, Class, Family, Genus C.Kingdom, Division, Class, Order, Family, Genus D.Kingdom, Class, Division, Order, Family, Genus

9.The semipermeable structure controlling the transport of materials between the cell and its external environment is the

A.cell wall. B.cytoplasm. C.cell membrane. D.nuclear membrane.

10.Which one of the following statements about opportunistic pathogens is true? A.They always cause disease.

B.They never cause disease.

C.They have the potential to cause disease but usually do not. D.They usually cause disease but sometimes do not.

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C H A P T E R

2

Chapter Outline

Infectious Diseases Versus Microbial Intoxications Colonization, Infection, and Infectious Disease Biofilms and Polymicrobial (Synergistic) Infections Interactions Among Pathogens, Hosts, and the Environment

The Chain of Infection Reservoirs of Infection ■ Living Reservoirs ■ Nonliving Reservoirs

Modes of Transmission

Communicable, Contagious, and Noncommunicable Infectious Diseases

Sporadic, Endemic, Epidemic, and Pandemic Diseases The Four Periods in the Course of an

Infectious Disease

Localized and Systemic Infections Acute, Subacute, and Chronic Diseases Symptoms and Signs of a Disease Latent Infections

Primary and Secondary Infections

Steps in the Pathogenesis of Infectious Diseases Mechanisms by Which Pathogens Cause Disease

■ Virulence ■ Virulence Factors

Examples of Infectious Diseases of Humans ■ Infectious Diseases Caused by Bacteria ■ Infectious Diseases Caused by Algae ■ Infectious Diseases Caused by Fungi ■ Infectious Diseases Caused by Protozoa ■ Infectious Diseases Caused by Helminths ■ Infectious Diseases Caused by Viruses

LEARNING OBJECTIVES

After studying this chapter, you should be able to:

Define the terms and abbreviations introduced in this chapter (e.g., acute disease, adhesin [ligand],

arthropod-borne disease)

Describe a biofilm, including its biological makeup, medical significance, and susceptibility to antibiotics

Identify three factors that influence the development of an infectious disease, including one pathogen fac-tor, one host facfac-tor, and one environmental factor

List the six components or “links” in the chain of infection, in the proper order

Identify three examples of living reservoirs of infec-tion and three examples of nonliving reservoirs

List five principal modes of transmission of pathogens

Differentiate among a communicable disease, a con-tagious disease, and a noncommunicable disease

Differentiate among sporadic, endemic, nonendemic, epidemic, and pandemic diseases, and cite an exam-ple of each

Name and discuss the four periods or phases in the course of an infectious disease

Differentiate between localized and systemic infections, including the sites and severity of both types of diseases

Understanding

Infectious Diseases

References

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