Textbook of Diagnostic Microbiology

by Mahon & Manuselis

• ISBN13: 9780721679174
• ISBN10: 072167917X
• Edition: 2nd
• Format: Hardcover
• Copyright: 2000-04-27
• Publisher: Saunders

Summary

This 2nd Edition offers students a comprehensive approach to the essential information they need in identifying etiologic agents of infectious diseases. New content has been added on emerging viral pathogens, newly recognized parasitic agents, emerging resistance, and emerging technologies. Pedagogical features include tables, procedures, case studies, and illustrations. Information is presented to beginning level students in a logical approach to microbiology progressing from core principles and concepts to systematic identification of etiologic agents of infectious disease. A saleable instructor's CD-ROM is also available.

Table of Contents

PART I Introduction to Clinical Microbiology	1	(326)
Bacterial Cell Structure, Physiology, Metabolism, and Genetics	2	(23)
George Manuselis
Connie R. Mohon
Significance	4	(1)
Classification	4	(3)
Taxonomy	4	(1)
Nomenclature	5	(1)
Classification by Phenotypic and Genotypic Characteristics	5	(1)
Classification by Cellular Type: Prokaryotes, Eukaryotes, and Archaeobacteria	5	(2)
Comparison of Eukaryotic and Prokaryotic Cell Structure	7	(3)
Eukaryotic Cell Structure	7	(1)
Prokaryotic Cell Structure	7	(3)
Bacterial Morphology	10	(3)
Microscopic Shapes	10	(1)
Common Stains Used for Microscopic Visualization	11	(2)
Microbial Growth and Nutrition	13	(3)
Nutritional Requirements for Growth	14	(1)
Environmental Factors Influencing Growth	14	(1)
Bacterial Growth	15	(1)
Bacterial Biochemistry and Metabolism	16	(4)
Metabolism	16	(1)
Fermentation and Respiration	16	(1)
Biochemical Pathways from Glucose to Pyruvic Acid	17	(1)
Anaerobic Utilization of Pyruvate Acid (Fermentation)	18	(1)
Aerobic Utilization of Pyruvate (Oxidation)	19	(1)
Carbohydrate Utilization and Lactose Fermentation	19	(1)
Bacterial Genetics	20	(5)
Terminology	20	(1)
Genetic Elements and Alterations	21	(1)
Mechanisms of Gene Transfer	21	(4)
Control of Microorganisms	25	(27)
Disinfection and Sterilization	25	(1)
Connie R. Mahon
Sterilization Versus Disinfection	26	(1)
Factors that Influence the Degree of Killing	27	(1)
Types of Organisms	27	(1)
Number of Organisms	27	(1)
Concentration of Disinfecting Agent	27	(1)
Organic Soil Present	27	(1)
Nature of Surface to Be Disinfected	28	(1)
Methods of Disinfection and Sterilization	28	(7)
Physical Methods	28	(2)
Chemical Methods	30	(4)
Microbiology Laboratory Safety	34	(1)
Margaret Gregory
General Safety Principles	35	(1)
Safety Program for the Microbiology Laboratory	35	(1)
Handling of Biologic Hazards	35	(6)
Major Sources of Biologic Hazards	35	(4)
OSHA Regulations for Blood-Borne Pathogens	39	(2)
Disposal of Infectious Waste	41	(1)
Chemical Safety	41	(6)
Employee Right-to-Know	41	(1)
Material Safety Data Sheets	41	(5)
Hazardous Chemicals Inventory	46	(1)
Laboratory Safety for Hazardous Chemicals	46	(1)
Hazardous Waste Reduction	47	(1)
Fire Safety	47	(1)
Thermal Injuries	47	(1)
Electrical Safety	48	(1)
Miscellanous Safety Considerations	48	(1)
Back Safety	48	(1)
Storage of Gases	48	(1)
First Aid Training	48	(1)
Immunizations	49	(1)
Safety Training	49	(3)
Concepts in Antimicrobial Therapy	52	(53)
Antimicrobial Mechanisms of Action	52	(2)
Susan L. Koletar
Effects on Cell Wall Integrity	54	(3)
β-Lactam Antibacterial Agents	55	(1)
β-Lactamase Inhibitors	56	(1)
Other Antimicrobial Agents Whose Primary Site of Action Is the Cell Wall	57	(1)
Interruption of Cell Membrane Structure and Function	57	(1)
Inhibition of Protein Synthesis	57	(1)
Inhibition of Essential Metabolites	58	(1)
Interference with Nucleic Acid Metabolism	59	(1)
Resistance to Antibacterial Agents	59	(5)
Procedures in Antimicrobial Susceptibility Testing	62	(2)
Janet A. Hindler
James H. Jorgensen
Reasons and Indications for Performing Antimicrobial Susceptibility Tests	64	(1)
Factors to Consider When Determining Whether Testing Is Warranted	64	(1)
Selecting Antimicrobial Agents for Testing and Reporting	65	(2)
Selection of Test Batteries	65	(1)
Reporting of Susceptibility Test Results	65	(2)
Traditional Antimicrobial Susceptibility Test Methods	67	(17)
Inoculum Preparation and Use of McFarland Standards	67	(2)
Dilution Methods	69	(4)
Disk Diffusion Testing	73	(4)
Modified Methods for Testing Slow-Growing or Fastidious Bacteria	77	(4)
Additional Organism and Antimicrobial Agent Testing Concerns	81	(3)
Automated Antimicrobial Susceptibility Test Methods	84	(4)
Principles of Technologies Used	84	(1)
Currently Available Automated Systems	85	(2)
Nonautomated Antimicrobial Susceptibility Test Method: E Test	87	(1)
Interpretation of In Vitro Antimicrobial Susceptibility Test Results	88	(1)
Methods of Detecting Antimicrobial-Inactivating Enzymes	89	(1)
β-Lactamase Tests	89	(1)
Quality Control of Antimicrobial Susceptibility Tests	90	(3)
Selecting an Antimicrobial Susceptibility Test Method	93	(5)
Special Antimicrobial Susceptibility Tests	97	(1)
Janet A. Hindler
Minimum Bactericidal Concentration (MBC) Test	98	(2)
Controlling Test Variables	100	(1)
Interpretation Concerns	100	(1)
Time-Kill Assays	100	(1)
Synergy Tests	100	(2)
Serum Bactericidal Test	102	(1)
Molecular Probes for Identifying Determinants of Antimicrobial Resistance	103	(1)
Measurement of Antimicrobial Agents in Serum and Body Fluids	103	(2)
Biologic Assays	103	(1)
Immunoassays	103	(1)
Chromatographic Assays	104	(1)
Performance Improvement in the Microbiology Laboratory	105	(24)
Quality Issues in Clinical Microbiology	105	(2)
Merrily Rausch
General Guidelines for Establishing Quality Control	107	(9)
Temperatures	107	(1)
Thermometer Calibration	108	(1)
Equipment QC	108	(4)
Reagent QC	112	(1)
Antimicrobial Susceptibility QC	112	(1)
Personnel Competency	112	(2)
Use of Stock Cultures	114	(1)
QC Manual	114	(2)
Performance Improvement (PI)	116	(5)
Mission Statement	116	(1)
Indicators of PI: Process Versus Outcome	116	(1)
Establishing Performance Monitors	116	(1)
Problem/Action Form	116	(1)
The Customer Concept	117	(1)
Fixing the Process	117	(1)
Benchmarking	117	(1)
Commercially Purchased Monitors	118	(3)
Putting the Laboratory Test to the Test	121	(1)
Frederic J. Marsik
Analytical Analysis of Tests	121	(1)
Analytical (Technical) Sensitivity	122	(1)
Analytical (Technical) Specificity	122	(1)
Accuracy	122	(1)
Clinical Analysis of Tests	122	(1)
Clinical (Diagnostic) Sensitivity	122	(1)
Clinical (Diagnostic) Specificity	122	(1)
Operational Analysis of Tests	123	(2)
Incidence of Disease	123	(1)
Prevalence of Disease	123	(1)
Predictive Values of Tests	123	(2)
Efficiency of Tests	125	(1)
Other Concepts	125	(1)
Choosing a Laboratory Method	125	(2)
Test Validation	127	(2)
Emergent Technologies	129	(82)
Direct Microbial Antigen Detection	129	(2)
David W. Craft
Historical Perspective	131	(2)
Antigen Detection Methods	133	(12)
Precipitin Tests	133	(2)
Particle Agglutination	135	(4)
Immunofluorescent Assays	139	(2)
Enzyme Immunoassays	141	(4)
Optical Immunoassays	145	(1)
Other Immunoassays	145	(1)
Current Clinical Applications	145	(6)
Respiratory Tract Infections	145	(4)
Meningitis and Sepsis	149	(1)
Gastrointestinal Tract Infections	149	(1)
Sexually Transmitted Diseases	150	(1)
Blood-Borne and Body Fluid-Borne Diseases	151	(1)
Future Applications	151	(5)
Serologic Diagnosis of Infectious Diseases	154	(2)
Ronald H. Holton
Immune Response to Infectious Agents	156	(6)
Host Resistance to Infection	156	(2)
Nature of the Immune Response to Infectious Agents	158	(1)
Antigens and Antibodies	159	(2)
Primary and Secondary Antibody Responses	161	(1)
Interpreting Serologic Test Data	162	(3)
Acute and Convalescent Antibody Titers	162	(1)
Antibody Specificity and Cross-Reactivity	162	(1)
False-Negative and False-Positive Serologic Test Results	163	(1)
Value of Serologic Tests	164	(1)
Antibody Detection Methods and Applications	165	(12)
Particle Agglutination Assays	165	(2)
Precipitation Assays	167	(1)
Complement Fixation Test	168	(2)
Neutralization Tests	170	(1)
Microscope-Assisted Labeled-Reagent Techniques	171	(2)
Enzyme-Linked Immunosorbent Assay and Related Techniques	173	(2)
Western Blotting	175	(2)
Use of Serologic Testing in Specific Diseases	177	(6)
Serologic Testing of Syphilis	177	(1)
Serologic Testing for Streptococcal Infections	177	(1)
Serologic Testing of Toxoplasmosis	178	(1)
Serologic Testing of Important Viral Diseases	178	(2)
Serologic Diagnosis of Fungal Infection	180	(2)
Rapid Methods and Automation in the Microbiology Laboratory	182	(1)
David W. Craft
The Term Rapid	183	(1)
Microscopic Methods for Rapid Detection	183	(1)
Rapid Biochemical Tests Performed on Isolated Colonies	184	(1)
Identification Systems Relying Upon Carbohydrate Utilization or Chromogenic Substrates	184	(8)
Principles of Identification	184	(1)
Manual Rapid Tests	185	(3)
Automated Rapid Tests	188	(1)
Evaluation of Rapid Methods	189	(2)
Molecular Applications in the Clinical Laboratory	191	(1)
Gerri S. Hall
Hybridization Formats	192	(2)
Probe Labels	193	(1)
Probe Target	194	(1)
Applications for Probe Technology	194	(10)
Probes for Culture Confirmation	194	(1)
Probes for Rapid Diagnosis of Infectious Diseases	195	(4)
Amplification	199	(1)
Detection of the Amplicon	200	(4)
Clinical Applications of Amplification	204	(7)
Technical Considerations for Implementation of Amplification	205	(1)
Measures to Control Contamination	205	(1)
Commercially Available Amplification Systems	205	(2)
Detection of Mycobacterium tuberculosis	207	(1)
Other Available Assays	207	(4)
Host-Parasite Interaction	211	(26)
Indigenous Microbial Flora	211	(1)
Hal S. Larsen
Flora	212	(1)
Origin of Microbial Flora	212	(1)
Characteristics of Indigenous Microbial Flora	212	(1)
Usual Flora at Different Body Sites	213	(6)
Usual Flora of the Skin	213	(1)
Usual Flora of the Mouth	213	(1)
Usual Flora of the Respiratory Tract	214	(1)
Usual Flora of the Gastrointestinal Tract	214	(1)
Usual Flora of the Genitourinary Tract	215	(3)
Pathogenesis of Infection	218	(1)
Hal S. Larsen
Pathogenicity	219	(1)
Pathogens	219	(1)
Opportunistic Pathogens	219	(1)
Virulence	220	(1)
Host Resistance Factors	220	(7)
Physical Barriers	220	(1)
Cleansing Mechanisms	221	(1)
Antimicrobial Substances	222	(1)
Indigenous Microbial Flora	222	(1)
Phagocytosis	222	(2)
Inflammation	224	(2)
Immune Responses	226	(1)
Infectious Agent Factors	227	(3)
Adherence	227	(1)
Proliferation	227	(1)
Tissue Damage	228	(1)
Invasion	228	(1)
Dissemination	228	(2)
Routes of Transmission	230	(3)
Airborne Transmission	230	(1)
Transmission by Food and Water	231	(1)
Close Contact	232	(1)
Cuts and Bites	232	(1)
Arthropods	232	(1)
Zoonoses	232	(1)
Epidemiology	233	(4)
Definitions	233	(1)
Surveillance and Reporting	234	(3)
General Concepts in Specimen Collection and Handling	237	(24)
Merrily Rausch
Joy G. Remley
Basic Principles of Specimen Collection	239	(1)
Appropriate Collection Techniques	239	(1)
Patient Education and Preparation	240	(2)
Patient Education: Patient-Collected Samples	240	(1)
Patient or Site Preparation	241	(1)
Preservation, Storage, and Transport of Specimens	242	(3)
Use of Preservatives	242	(1)
Use of Anticoagulants	242	(1)
Use of Holding and Transport Media	243	(1)
Unprotected Specimens	243	(1)
Storage of Specimens	243	(1)
Mailing Etiologic Agents	244	(1)
Safety	245	(1)
Protection of the Specimen Transporter	245	(1)
Protection of the Specimen Processor	245	(1)
Labeling and Rejection of Specimens	245	(2)
Requisitions	245	(2)
Unacceptable Specimens	247	(1)
Processing of Clinical Samples for Optimal Organism Recovery	247	(14)
Prioritization During Processing	247	(1)
Gross Examination of Specimens	248	(1)
Direct Examination Techniques	248	(2)
Primary Inoculation of Routine Specimens	250	(5)
Processing Nonroutine Specimens	255	(6)
Microscopic Examination of Infected Materials	261	(50)
Leona W. Ayers
Preparation of Samples	263	(3)
Smears from Swabs	263	(1)
Smears from Thick Liquids or Semisolids	263	(1)
Smears from Thick, Granular, or Mucoid Materials	264	(1)
Smears from Thin Fluids	265	(1)
Cytocentrifuge Preparations	265	(1)
Stains	266	(1)
Microscopes	266	(5)
Terminology for Direct Examinations	271	(2)
Examination of Prepared Material	273	(2)
Characterization of Background Materials	273	(1)
Search for Microorganisms	274	(1)
Evaluation of Choice of Antibiotic	275	(1)
Direct Examination Summary	275	(1)
Initiation of Special Handling for Unsuspected or Special Pathogens	275	(1)
Grading or Classifying Materials	275	(2)
Contaminating Materials	276	(1)
Local Materials	276	(1)
Purulence	277	(1)
Mixed Materials	277	(1)
Reports of Direct Examinations	277	(1)
Examples of Sample Observations and Reports	278	(1)
Quality Control in Direct Microscopic Interpretations	278	(4)
Direct Examination Showing Local and Contaminating Materials	282	(2)
Direct Examination in Common Bacterial Infections	284	(2)
Direct Examination in Gram-Positive Bacillary Infections	286	(2)
Direct Examination in Uncommon Gram-Positive Bacilli	288	(2)
Direct Examination in Gram-Positive Bacilli with Filaments and Branches	290	(2)
Direct Examination in Selected Gram-Negative Bacterial Infections	292	(2)
Direct Examination in Selected Gram-Negative Bacillary Infections	294	(4)
Direct Examination in Polymicrobial Infections	298	(2)
Direct Examination in Fungal Infections	300	(4)
Direct Examination in Parastic Infections	304	(4)
Direct Examination in Viral Infections	308	(3)
Use of Colonial Morphology for the Presumptive Identification of Microorganisms	311	(16)
George Manuselis
Importance of Colonial Morphology as a Diagnostic Tool	313	(1)
Initial Observation and Interpretation of Cultures	313	(3)
Gross Colony Characteristics Used to Differentiate and Presumptively Identify Microorganisms	316	(5)
Hemolysis	316	(1)
Size	317	(1)
Form or Margin	317	(1)
Elevation	317	(2)
Density	319	(1)
Color	319	(1)
Consistency	319	(1)
Pigment	319	(1)
Odor	319	(2)
Colonies with Multiple Characteristics	321	(1)
Growth of Organisms in Liquid Media	321	(6)
PART II Laboratory Identification of Significant Isolates	327	(548)
Staphylococci	329	(16)
Hal S. Larsen
Connie R. Mahon
General Characteristics	330	(2)
Clinically Significant Species	332	(3)
Staphylococcus aureus	332	(3)
Staphylococcus epidermidis	335	(1)
Staphylococcus saprophyticus	335	(1)
Other Coagulase-Negative Staphylococci	335	(1)
Laboratory Diagnosis	335	(6)
Specimen Collection and Handling	335	(1)
Microscopic Examination	335	(1)
Isolation and Identification	336	(5)
Antimicrobial Susceptibility	341	(1)
Methicillin-Resistant Staphylococci	341	(4)
Streptococcaceae	345	(28)
Hal S. Larsen
Streptococcus and Enterococcus: General Characteristics	347	(11)
Cell Wall Structure	347	(1)
Classification	347	(9)
Noncultural Identification	356	(2)
Clinically Significant Streptococci and their Associated Diseases	358	(10)
Streptococcus pyogenes (Group A Streptococci)	358	(3)
Streptococcus agalactiae (Group B Streptococci)	361	(1)
Other Groups	362	(2)
Enterococcus	364	(1)
Streptococcus pneumoniae	364	(3)
Viridans Streptococci	367	(1)
Nutritionally Variant Streptococci	368	(1)
Streptococcus-like Oganisms	368	(5)
Aerococcus	369	(1)
Leuconostoc	369	(1)
Pediococcus	369	(1)
Gemella	370	(3)
Corynebacterium and Other Non-Spore-Forming Gram-Positive Rods	373	(16)
Hal S. Larsen
Corynebacterium	375	(7)
General Characteristics	375	(1)
Corynebacterium diphtheriae	375	(5)
Other Corynebacteria	380	(1)
Arcanobacterium	381	(1)
Rhodococcus	381	(1)
Undesignated CDC Coryneform Groups	381	(1)
Rothia dentocariosa	381	(1)
Listeria monocytogenes	382	(3)
General Characteristics	382	(1)
Physiology	382	(1)
Virulence Factors	382	(1)
Clinical Infections	382	(1)
Laboratory Diagnosis	383	(2)
Erysipelothrix rhusiopathiae	385	(4)
General Characteristics	385	(1)
Clinical Infections	385	(1)
Laboratory Diagnosis	385	(4)
Aerobic Gram-Positive Bacilli	389	(12)
Hal S. Larsen
Bacillus	390	(5)
General Characteristics	390	(2)
Bacillus anthracis	392	(2)
Other Bacillus Species	394	(1)
Aerobic Actinomycetes	395	(6)
Nocardia Species	396	(3)
Other Actinomycetes	399	(2)
Neisseria Species and Moraxella catarrhalis	401	(24)
Karen S. Long
John G. Thomas
Jean Barnishan
General Characteristics	404	(1)
Pathogenic Neisseria Species	404	(14)
Neisseria gonorrhoeae	404	(11)
Neisseria meningitidis	415	(2)
Moraxella catarrhalis	417	(1)
Nonpathogenic Neisseria Species	418	(7)
Identification	418	(1)
Neisseria polysaccharea	418	(3)
Neisseria cinerea	421	(1)
Kingella denitrificans	421	(1)
Neisseria lactamica	421	(1)
Neisseria mucosa	422	(1)
Neisseria sicca	422	(1)
Neisseria subflava	422	(1)
Neisseria flavescens	422	(1)
Neisseria elongata	422	(1)
Neisseria weaveri	422	(3)
Haemophilus and Other Fastidious Gram-Negative Rods	425	(1)
A. Haemophilus Species, Hacek Group Pasteurella, Brucella, and Francisella Species	425	(38)
George Manuselis
Jean Barnishan
Haemophilus Species	426	(10)
General Characteristics	426	(2)
Haemophilus influenzae	428	(1)
Infections Associated with Other Haemophilus Species	429	(1)
Laboratory Diagnosis	430	(4)
Treatment	434	(2)
HACEK Group and Capnocytophaga Species	436	(5)
Haemophilus aphrophilus	436	(1)
Actinobacillus actinomycetemcomitans	436	(2)
Cardiobacterium hominis	438	(1)
Eikenella corrodens	439	(1)
Kingella Species	439	(1)
Capnocytophaga Species	440	(1)
Pasteurella Species	441	(2)
General Characteristics	441	(1)
Pasteurella multocida	441	(2)
Brucella Species	443	(1)
General Characteristics	443	(1)
Francisella Species	444	(4)
Francisella tularensis	444	(3)
Legionella Species	447	(1)
A. Christian Whelen
Epidemiology	448	(1)
Clinical Infections	448	(1)
Legionnaires' Disease	448	(1)
Pontiac Fever	449	(1)
Laboratory Diagnosis	449	(8)
Specimen Collection and Handling	449	(1)
Direct Microscopic Examination	449	(2)
DNA Probe	451	(1)
Culture and Identification	451	(2)
Urine Antigen Test	453	(1)
Serology	454	(1)
Antimicrobial Susceptibility	455	(2)
Bordetella	457	(1)
A. Christian Whelen
General Characteristics	457	(1)
Epidemiology	457	(1)
Virulence Factors	458	(1)
Clinical Infections	458	(1)
Laboratory Diagnosis	458	(3)
Specimen Collection and Transport	458	(1)
Direct Fluorescent Antibody Test	459	(1)
Nucleic Acid Detection	459	(1)
Culture and Identification	459	(1)
Serology	460	(1)
Antimicrobial Susceptibility	461	(2)
Enterobacteriaceae	463	(52)
Connie R. Mahon
George Manuselis
General Characteristics	465	(3)
Microscopic and Colonial Morphology	465	(1)
Classification	465	(1)
Virulence and Antigenic Factors	465	(1)
Clinical Significance	465	(3)
Opportunistic Members of the Family Enterobacteriaceae and Associated Infections	468	(11)
Escherichia coli	468	(5)
Other Escherichia Species	473	(1)
Klebsiella, Enterobacter, Serratia, and Hafnia Species	473	(4)
Proteus, Morganella, and Providencia Species	477	(1)
Edwardsiella Species	478	(1)
Erwinia and Pectobacterium Species	478	(1)
Citrobacter Species	478	(1)
Primary Intestinal Pathogens and Related Human Infections	479	(11)
Salmonella Species	479	(5)
Shigella Species	484	(2)
Yersinia Species	486	(2)
New Genera and Biotypes	488	(2)
Laboratory Diagnosis	490	(6)
Specimen Collection and Transport	490	(1)
Isolation and Identification	490	(6)
Biochemical Principles and Reactions on Conventional Media	496	(10)
Lactose Fermentation and Utilization of Carbohydrates	496	(2)
Glucose Metabolism and Its Metabolic Products	498	(8)
Screening Stool Cultures for Pathogens	506	(2)
Serologic Grouping	508	(7)
Salmonella Species	508	(1)
Shigella Species	508	(7)
Vibrio, Aeromonas, Plesiomonas, and Campylobacter Species	515	(24)
Amy M. Carnahan
Gerald Andrews
Vibrio	516	(8)
General Characteristics	517	(2)
Vibrio cholerae	519	(1)
Vibrio parahaemolyticus	520	(1)
Vibrio vulnificus	521	(1)
Vibrio alginolyticus	521	(1)
Laboratory Diagnosis	521	(3)
Antimicrobial Susceptibility	524	(1)
Aeromonas	524	(4)
General Characteristics	524	(1)
Clinical Infection	525	(1)
Laboratory Diagnosis	526	(1)
Antimicrobial Susceptibility	526	(2)
Plesiomonas	528	(2)
Epidemiology	528	(1)
General Characteristics	529	(1)
Clinical Infections	529	(1)
Laboratory Diagnosis	529	(1)
Antimicrobial Susceptibility	530	(1)
Campylobacter and Campylobacter-like Species	530	(9)
Epidemiology	530	(2)
General Characteristics	532	(1)
Clinical Infection	532	(1)
Laboratory Diagnosis	532	(4)
Antimicrobial Susceptibility	536	(3)
Nonfermenting Gram-Negative Bacilli and Miscellaneous Gram-Negative Rods	539	(26)
Gerri S. Hall
General Characteristics of Nonfermenters	540	(7)
Clinical Infections	541	(1)
Biochemical Characteristics	541	(1)
Initial Clues to Nonfermenters	542	(1)
Identification Methods	543	(4)
Most Commonly Encountered Nonfermentative Organisms	547	(7)
The Pseudomonads	547	(2)
Stenotrophomonas maltophilia	549	(1)
Acinetobacter Species	549	(1)
Other Pseudomonads	550	(1)
Pseudomonads and Other Nonfermenters Whose Names Have Been Changed	551	(3)
Miscellaneous Nonfermenting Gram-Negative Bacilli	554	(11)
Nonfermenters with Peritrichous Flagellation	554	(2)
Nonmotile Gram-Negative Bacilli	556	(3)
Other Gram-Negative Nonfermenters	559	(6)
Anaerobes of Clinical Importance	565	(58)
Paul G. Engelkirk
Janet Duben-Engelkirk
Important Concepts in Anaerobic Bacteriology	567	(6)
Anaerobes Defined	567	(1)
Why Are They Anaerobes?	568	(1)
Where Anaerobes Are Found	568	(1)
Anaerobes at Specific Anatomic Sites	569	(2)
Factors that Predispose Patients to Anaerobic Infections	571	(1)
Indications of Anaerobe Involvement in Human Disease	571	(2)
Specimen Selection, Collection, Transport, and Processing	573	(10)
Specimen Quality	573	(1)
Specimen Transport and Processing	573	(2)
Processing Clinical Samples for Maximum Recovery of Anaerobic Pathogens	575	(8)
Procedures for Identifying Anaerobic Isolates	583	(11)
Preliminary Procedures	583	(4)
Identification of Anaerobic Isolates	587	(7)
Frequently Encountered Anaerobes and their Associated Diseases	594	(24)
Gram-Positive Spore-Forming Anaerobic Bacilli	594	(5)
Gram-Positive Non-Spore-Forming Anaerobic Bacilli	599	(7)
Anaerobic Gram-Negative Bacilli	606	(5)
Anaerobic Cocci	611	(7)
Susceptibility and β-Lactamase Testing	618	(3)
Anaerobe Resistance to Antimicrobial Agents	618	(1)
Susceptibility Testing of Anaerobes	619	(1)
Problems in Susceptibility Testing of Anaerobic Isolates	620	(1)
Susceptibility Testing Options	620	(1)
Quality-Assurance Considerations Pertaining to Susceptibility Testing	620	(1)
β-Lactamase Testing	620	(1)
Treating Anaerobe-Associated Diseases	621	(2)
The Spirochetes	623	(12)
A. Christian Whelen
Leptospires	625	(1)
General Characteristics	625	(1)
Virulence Factors and Pathogenicity	625	(1)
Clinical Infections	625	(1)
Laboratory Diagnosis	626	(1)
Treatment and Prevention	626	(1)
Borreliae	626	(2)
General Characteristics	626	(1)
Borrelia recurrentis and Other Borreliae	627	(1)
Borrelia burgdorferi	628	(1)
Treponemes	628	(7)
General Characteristics	629	(1)
Clinical Infections	629	(2)
Other Treponemal Diseases	631	(4)
Chlamydia, Mycoplasma, and Ureaplasma Species	635	(32)
Chlamydia Species	635	(1)
John G. Thomas
Karen S. Long
General Characteristics	636	(3)
Chlamydia pneumoniae	639	(3)
Clinical Infections	639	(1)
Laboratory Diagnosis	640	(2)
Chlamydia trachomatis	642	(7)
Clinical Infections	642	(2)
Laboratory Diagnosis	644	(2)
Culture	646	(1)
Nonculture, Nonamplified	647	(1)
Nonculture, Amplified	647	(2)
Results Reporting	649	(1)
Chalamydia psittaci	649	(4)
Mycoplasma and Ureaplasma Species	652	(1)
John G. Thomas
Karen S. Long
General Characteristics	653	(2)
Clinical Infections	655	(3)
Mycoplasma pneumoniae	655	(1)
Mycoplasma hominis and Ureaplasma urealyticum	656	(1)
Emerging Mycoplasma Pathogens	657	(1)
Laboratory Diagnosis	658	(5)
Specimen Collection and Transport	658	(1)
Culture	658	(5)
Serologic Diagnosis	663	(1)
Antimicrobial Susceptibility	663	(1)
Interpretation of Laboratory Results	663	(4)
Mycobacterium tuberculosis and Other Nontuberculous Mycobacteria	667	(42)
James L. Vossler
General Characteristics	670	(1)
Safety Considerations	671	(1)
Personnel Safety	671	(1)
Proper Ventilation	671	(1)
Proper Use of Biologic Safety Cabinet	671	(1)
Use of Proper Disinfectant	671	(1)
Other Precautions	672	(1)
Specimen Collection and Processing	672	(5)
Sputum and Other Respiratory Secretions	672	(1)
Gastric Aspirates and Washings	673	(1)
Urine	673	(1)
Stool	674	(1)
Blood	674	(1)
Tissue and Other Body Fluids	674	(3)
Digestion and Decontamination of Specimens	677	(1)
Decontamination and Digestion Agents	675	(2)
Concentration	677	(1)
Staining for Acid-Fast Bacteria	677	(1)
Examination and Interpretation of Smears	677	(1)
Culture Media and Isolation Methods	677	(4)
Egg-Based Media	678	(1)
Serum-or Agar-Based Media	678	(1)
Liquid Media	679	(1)
Other Culture Media for Recovery of Mycobacteria	680	(1)
Isolator Lysis-Centrifugation System	681	(1)
Identification	681	(11)
Laboratory Levels or Extents of Service	681	(1)
Identification of Mycobacteria	682	(1)
Biochemical Identification	682	(7)
Chromatography	689	(1)
Amplification for Mycobacterium tuberculosis	690	(1)
Serology	691	(1)
Susceptibility of Mycobacterium tuberculosis	691	(1)
Mycobacterium tuberculosis Complex	692	(4)
Mycobacterium tuberculosis	692	(3)
Mycobacterium bovis	695	(1)
Nontuberculous Mycobacteria: Clinical Significance and Differentiation	696	(8)
Mycobacterium avium Complex	696	(1)
Mycobacterium kansasii	697	(1)
Mycobacterium fortuitum-chelonei Complex	698	(1)
Mycobacterium marinum	699	(1)
Mycobacterium scrofulaceum	699	(1)
Mycobacterium xenopi	700	(1)
Mycobacterium szulgai	701	(1)
Mycobacterium malmoense	701	(1)
Mycobacterium simiae	701	(1)
Mycobacterium ulcerans	702	(1)
Mycobacterium haemophilum	702	(1)
Mycobacterium gordonae	702	(1)
Mycobacterium asiaticum	702	(1)
Mycobacterium thermoresistibile	703	(1)
Mycobacterium terrae-triviale Complex	703	(1)
Mycobacterium nonchromogenicum	703	(1)
Mycobacterium flavescens	703	(1)
Mycobacterium smegmatis	703	(1)
Mycobacterium phlei	704	(1)
Mycobacterium vaccae	704	(1)
Mycobacterium gastri	704	(1)
Mycobacterium paratuberculosis	704	(1)
Mycobacterium genavense	704	(1)
Mycobacterium leprae	704	(5)
Medically Significant Fungi	709	(46)
Linda A. Smith
Annette W. Fothergill
Deanna A. Sutton
James L. Harris
General Characteristics	711	(3)
Yeasts versus Molds	711	(1)
Septate versus Sparsely Septate	712	(1)
Hyaline versus Dematiaceous	712	(1)
Dimorphism	713	(1)
Reproduction	713	(1)
Taxonomy	714	(1)
Zygomycota	714	(1)
Ascomycota	714	(1)
Basidiomycota	714	(1)
Fungi Imperfecti	714	(1)
Clinical Sites of Infection	715	(1)
Superficial Mycoses	715	(1)
Cutaneous Mycoses	715	(1)
Subcutaneous Mycoses	715	(1)
Systemic Mycoses	716	(1)
Specimen Collecting, Handling, and Transport	716	(1)
Hair	716	(1)
Skin	716	(1)
Nails	716	(1)
Blood and Bone Marrow	717	(1)
Cerebrospinal Fluid	717	(1)
Abscess Fluid and Wound Exudates	717	(1)
Respiratory Specimens	717	(1)
Urogenital and Fecal Specimens	717	(1)
Methods of Identifying Fungal Agents	717	(2)
Direct Microscopic Examination of Specimens	717	(1)
Culture	718	(1)
Beginning the Identification	719	(3)
Gross Examination of the Culture	719	(2)
Microscopic Examination for Fungal Structures	721	(1)
Safety Issues	722	(1)
Agents of Superficial Mycoses	722	(2)
Malassezia furfur	722	(1)
Piedraia hortae	723	(1)
Trichosporon beigelli	723	(1)
Phaeoannellomyces werneckii	724	(1)
Agents of Dermatophytoses	724	(5)
Epidemiology	724	(1)
Clinical Infections	724	(2)
Treatment	726	(1)
Commonly Encountered Dermatophytes	726	(2)
Laboratory Diagnosis	728	(1)
Agents of Subcutaneous Mycoses	729	(5)
Sporotrichosis	729	(1)
Chromoblastomycosis	730	(1)
Eumycotic Mycetoma	731	(2)
Subcutaneous Phaeohyphomycosis	733	(1)
Agents of Systemic Mycoses	734	(8)
Blastomyces dermatitidis	735	(2)
Histoplasma capsulatum var. capsulatum	737	(3)
Coccidioides immitis	740	(1)
Paracoccidioides brasiliensis	741	(1)
Agents of Opportunistic Fungal Infections: the Saprobes	742	(6)
Agents of Yeast Infections	748	(7)
General Characteristics	748	(1)
Clinically Significant Yeast Species	748	(1)
Methods of Yeast Identification	749	(6)
Diagnostic Parasitology	755	(78)
Linda A. Smith
General Concepts in Parasitology Laboratory Methods	757	(7)
Fecal Specimens	757	(4)
Other Specimens Examined for Intestinal Parasites	761	(1)
Examination of Specimens for Blood and Tissue Parasites	762	(1)
Immunologic Diagnosis	763	(1)
Quality Assurance in the Parasitology Laboratory	763	(1)
Medically Important Parasitic Agents	764	(69)
Protozoa	764	(19)
Apicomplexa	783	(16)
Microsporidia	799	(1)
Helminths	800	(33)
Clinical Virology	833	(42)
William F. Nauschuetz
Viruses	834	(1)
Structure	834	(1)
Taxonomy	835	(1)
Laboratory Diagnosis of Viral Infections	835	(5)
Specimen Collection and Transport	835	(2)
Appropriate Specimens for Maximum Recovery	837	(1)
Methods in Diagnostic Virology	837	(3)
Cell Culture for Viral Isolation	840	(2)
Cytopathic Effect on Cell Cultures for Presumptive Identification of Viral Agents	840	(2)
Centrifugation-Enhanced Shell Vial Culture	842	(1)
Respiratory Viruses	842	(3)
Influenza Viruses	842	(1)
Parainfluenza Viruses	843	(1)
Respiratory Syncytial Virus	844	(1)
Adenoviruses	844	(1)
Rhinoviruses	845	(1)
Coronaviruses	845	(1)
Exanthemas	845	(2)
Mumps	845	(1)
Measles (Rubeola)	845	(1)
Rubella	846	(1)
Hand, Foot, and Mouth Disease	846	(1)
Parvovirus B19	847	(1)
Immunodeficiency Viruses: Human Immunodeficiency Virus Type 1	847	(2)
Central Nervous System Viruses: Enteroviruses	849	(1)
Agents of Gastrointestinal Infections	850	(1)
Rotaviruses	850	(1)
Norwalk and Norwalk-Like Agents	850	(1)
Enteric Adenoviruses	851	(1)
Other Viruses	851	(1)
Arboviruses	851	(4)
Family Bunyaviridae	852	(1)
Family Togaviridae	853	(1)
Family Flaviviridae	853	(1)
Family Reoviridae	854	(1)
Laboratory Diagnosis of Arboviral Infections	855	(1)
Family Arenaviridae	855	(1)
Genus Hantavirus	856	(1)
Family Filoviridae	857	(1)
Rabies	858	(1)
Human Papillomaviruses	859	(1)
Hepatitis Viruses	859	(7)
Hepatitis A	859	(2)
Hepatitis B	861	(1)
Hepatitis D (Delta Hepatitis)	862	(2)
Hepatitis C	864	(1)
Hepatitis E	864	(2)
Herpesviruses	866	(5)
Herpes Simplex Virus	866	(2)
Human Cytomegalovirus	868	(1)
Epstein-Barr Virus	868	(2)
Varicella-Zoster Virus	870	(1)
Human Herpesvirus 6	870	(1)
Human Herpesvirus 7	870	(1)
Human Herpesvirus 8	870	(1)
Antiviral Therapy	871	(4)
Absorption	871	(1)
Penetration	872	(1)
Uncoating	872	(1)
Eclipse/Synthesis	872	(1)
Maturation/Release	872	(3)
Part III Laboratory Diagnosis of Infectious Diseases: an Organ System Approach to Diagnostic Microbiology	875	(240)
Upper and Lower Respiratory Tract Infections	877	(42)
James L. Cook
General Concepts of Infectious Diseases of the Respiratory Tract	879	(4)
The Role of Normal Flora	879	(1)
The Immune Status of the Host	880	(2)
Seasonal and Community Trends in Infections	882	(1)
Empiric Antimicrobial Therapy	882	(1)
Anatomic Characterization of the Respiratory Tract	883	(1)
Anatomy of the Respiratory Tract	883	(1)
Barriers to Infection	883	(1)
Virulence Factors of Pathogenic Organisms	884	(1)
Adherence	884	(1)
Toxin Elaboration	884	(1)
Evasion of Host Defenses	884	(1)
Upper Respiratory Tract Infections	885	(10)
Pharyngitis	885	(2)
Sinusitis	887	(4)
Otitis Media	891	(1)
Epiglottitis	892	(2)
Pertussis	894	(1)
Lower Respiratory Tract Infections	895	(17)
Bronchitis and Bronchiolitis	896	(3)
Acute Pneumonia	899	(5)
Aspiration Pneumonia	904	(3)
Chronic Pneumonia	907	(4)
Empyema	911	(1)
Opportunistic Infections of the Respiratory Tract	912	(7)
Granulocytopenic Patients	912	(1)
Patients with Defects in Cellular Immunity	913	(1)
Patients with Defects in Humoral Immunity	914	(1)
Diagnosis	914	(5)
Skin and Soft-Tissue Infections	919	(26)
Raymond A. Smego, Jr.
Skin and Skin Structures	920	(1)
Anatomy of the Skin	920	(1)
Usual Skin Flora	921	(1)
Clinical Infections	921	(24)
Bacterial Skin Infections	921	(10)
Cutaneous Infections Caused by Miscellaneous Agents	931	(1)
Spirochetal Infections	931	(1)
Mycoplasmal Infections	932	(1)
Viral Skin Diseases	933	(3)
Fungal Skin Infections	936	(4)
Parasitic Skin Infections	940	(5)
Gastrointestinal Infections and Food Poisoning	945	(28)
Connie R. Mahon
George Manuselis
General Concepts in Evaluating Gastrointestinal Infections and Food Poisoning	946	(1)
Anatomic Considerations	947	(1)
The Role of the Usual Flora	948	(1)
A Practical Approach to Diagnosis of the Patient with Diarrhea	949	(1)
History	949	(1)
Physical Examination	950	(1)
Laboratory Studies	950	(1)
Pathogenic Mechanisms and Clinical Presentations of Acute Diarrhea	950	(2)
Enterotoxin-Mediated Diarrhea	950	(1)
Diarrhea Mediated by Invasion of Bowel Mucosal Surface	951	(1)
Diarrhea Mediated by Invasion of Full Bowel Thickness with Lymphatic Spread	952	(1)
Common Bacterial, Viral, and Parasitic Gastrointestinal Infections and Their Agents	952	(8)
Bacterial Agents	953	(5)
Viral Agents	958	(1)
Parasitic Agents	958	(2)
Complications of Diarrheal Infections	960	(1)
Newly Recognized Agents of Acute Diarrhea	960	(1)
Agents of Food Poisoning	961	(2)
Laboratory Diagnosis of Gastrointestinal Pathogens	963	(4)
Specimen Collection and Handling	963	(1)
Direct Microscopic Examination	963	(1)
Culture	963	(4)
Treatment of Diarrhea	967	(6)
Infections of the Central Nervous System	973	(24)
Kirk M. Doing
David P. Marmaduke
General Concepts Related to Infections of the Central Nervous System	975	(2)
Anatomic Organization	975	(1)
Cerebrospinal Fluid Characteristics	976	(1)
Host-Pathogen Relationships	976	(1)
Infections of the Central Nervous System	977	(13)
Bacterial Infections	977	(4)
Brain Abscesses	981	(1)
Spirochetal Infections	982	(1)
Fungal Meningitis	982	(2)
Viral Infections	984	(4)
Parasitic Infections	988	(2)
Laboratory Diagnosis of Central Nervous System Infections	990	(7)
Specimen Collection: Lumbar Puncture	990	(1)
Laboratory Evaluation	991	(6)
Bacteremia	997	(14)
Sherry Trevino
Connie R. Mahon
General Concepts Related to Bacteremic Infections	999	(1)
Bacteremia Versus Septicemia	999	(1)
Forms of Bacteremia	999	(1)
Bacteremic Episodes	999	(1)
Other Conditions	999	(1)
Epidemiology	999	(1)
Risk Factors	1000	(1)
Pathogenesis	1000	(2)
Sources of Bacteremic Spread	1000	(1)
Clinical Signs and Symptoms	1001	(1)
Complications	1002	(1)
Laboratory Diagnosis	1002	(5)
Specimen Collection	1002	(1)
Blood Culture Methods	1003	(4)
Treatment	1007	(4)
Urinary Tract Infections	1011	(22)
John G. Thomas
Overview	1012	(2)
The Urinary System	1013	(1)
Epidemiology and Risk Factors	1014	(2)
Age	1014	(2)
Clinical Signs and Symptoms	1016	(2)
Etiology of Urinary Tract Infections	1018	(3)
Pathogenesis of Urinary Tract Infections	1018	(1)
Etiologic Agents of Urinary Tract Infections	1018	(3)
Laboratory Diagnosis	1021	(3)
Significance of Colony Counts: A Historical Background	1021	(1)
Specimen Collection	1022	(2)
Additives	1024	(1)
Specimen Transport	1024	(1)
Microbial Detection	1024	(4)
Specimen Screening: Rapid, Nonculture Methodologies	1024	(3)
Rejection Criteria	1027	(1)
Culture for Etiologic Agents of Urinary Tract Infections	1027	(1)
Interpretation of Results	1028	(3)
Susceptibility Reporting	1031	(2)
UTI Antibiograms	1031	(2)
Sexually Transmitted Diseases	1033	(12)
William F. Nauschuetz
Common Exudative Sexually Transmitted Infections	1035	(4)
Gonorrhea	1035	(2)
Genital Chlamydiosis	1037	(1)
Bacterial Vaginosis	1038	(1)
Common Ulcerative Sexually Transmitted Infections	1039	(6)
Syphilis	1039	(2)
Chancroid	1041	(1)
Genital Herpes	1042	(3)
Infections in Special Patient Populations	1045	(8)
James T. Griffith
Malignancy	1047	(2)
Decrease in Humoral and Cellular Immune Response	1047	(1)
Granulocytopenia	1048	(1)
Decrease in Leukocyte Function	1048	(1)
Infections in Neutropenic Patients	1048	(1)
Infections in Cancer Patients	1048	(1)
Infections in Patients with Hodgkin's Disease	1049	(1)
Burns and Surgery	1049	(1)
Antimicrobial Therapy	1050	(1)
Organ Transplantation	1050	(1)
Aging	1050	(3)
Zoonotic and Rickettsial Infections	1053	(30)
William F. Nauschuetz
Robert G. Whiddon
Zoonotic Infections Transmitted by Scratches and Bites	1056	(9)
Plague	1056	(2)
Lyme Borreliosis	1058	(2)
Pasteurellosis	1060	(2)
Erysipeloid	1062	(1)
Capnocytophaga canimorsus Infection (Formerly CDC Group DF-2)	1063	(1)
Bacillary and Spirillary Rat-Bite Fevers	1064	(1)
Zoonotic Infections Transmitted by Direct Contact or Inhalation	1065	(9)
Anthrax	1065	(3)
Tularemia	1068	(2)
Brucellosis	1070	(3)
Leptospirosis	1073	(1)
The Rickettsiae	1074	(9)
Rickettsia	1075	(3)
Ehrlichiosis	1078	(5)
Ocular Infections	1083	(32)
Darlene Miller
Ocular Structures	1084	(2)
Conjunctiva	1084	(1)
Lids	1085	(1)
Cornea	1085	(1)
Sclera	1086	(1)
Orbit	1086	(1)
Lacrimal Apparatus	1086	(1)
Anterior Chamber	1086	(1)
Vitreous Chamber	1086	(1)
Uveal Tract	1086	(1)
Retina	1086	(1)
Pathogenesis of Ocular Infections	1086	(2)
Usual Ocular Flora	1088	(1)
Infections of the Conjunctivae (Conjunctivitis)	1089	(4)
Bacteria	1089	(2)
Viruses	1091	(1)
Rickettsia	1092	(1)
Fungi	1092	(1)
Parasites	1092	(1)
Infections of the Lids (Blepharitis)	1093	(1)
Bacteria	1093	(1)
Viruses	1094	(1)
Fungi	1094	(1)
Parasites	1094	(1)
Infections of the Cornea (Keratitis)	1094	(4)
Bacteria	1094	(1)
Viruses	1095	(2)
Fungi	1097	(1)
Parasites	1097	(1)
Infections of the Sclera and Episclera (Scleritis and Episcleritis)	1098	(1)
Infections of the Orbit (Preseptal and Orbital Cellulitis)	1098	(2)
Infections of the Lacrimal Apparatus	1100	(1)
Infections of the Intraocular Chambers (Endophthalmitis)	1101	(1)
Bacteria	1101	(1)
Infections of the Uveal Tract (Uveitis)	1102	(1)
Infections of the Retina (Retinitis)	1102	(1)
Viruses	1103	(1)
Parasites	1103	(1)
Scleral Buckle Infections	1103	(1)
Ocular Manifestations in Patients with Human Immunodeficiency Virus	1104	(1)
Laboratory Diagnosis of Ocular Infections	1104	(7)
Specimen Collection	1104	(1)
Direct Smear Examination	1105	(2)
Culture	1107	(2)
Special Procedures for Recovering Ocular Pathogens	1109	(1)
Special Culture Techniques	1109	(2)
Ocular Therapy	1111	(4)
Appendixes	1115	(52)
Appendix A Selected Bacteriologic Culture Media	1117	(24)
Patricia K. Hargrave
Shirley Adams
Appendix B Selected Mycology Media, Fluids, and Stains	1141	(4)
Patricia K. Hargrave
Shirley Adams
Appendix C Nomenclature Changes for the Enterobacteriaceae and Nonfermentative Bacilli	1145	(2)
Appendix D Answers to Learning Assessment Questions	1147	(20)
Index	1167