Bailey & Scott's Diagnostic Microbiology

Name: Bailey & Scott's Diagnostic Microbiology
Price: 7990 ISK
Availability: InStock
Author: Patricia M. Tille
ISBN: 9780443118920

Höfundur: Patricia M. Tille (Útgáfa: 16)

Kaup valmöguleikar

Nánar um bókina

Útgefandi: Elsevier Limited (UK)

ISBN: 9780443118920

Print ISBN: 9780443118913

Format: ePub

Útgáfa: 16

Höfundar: Patricia M. Tille

Tungumál: English

Útgefið: 2024-11-06

Prent takmörkun á líftíma: 10

Flokkar: Heilbrigðisvísindi

Efnisflokkar: Læknisfræði › Læknisfræðileg tækni

Kaflar

Title of Book
Cover image
Title page
Table of Contents
Copyright
Dedication
Reviewers
Contributors
Preface
Acknowledgments
Part I. Basic Medical Microbiology
1. Microbial Taxonomy
Classification
Family
Genus
Species
Nomenclature
Identification
Identification Methods
2. Bacterial Genetics, Metabolism, and Structure
Bacterial Genetics
Nucleic Acid Structure and Organization
Nucleotide Structure and Sequence
Deoxyribonucleic Acid Molecular Structure
Genes and the Genetic Code
Chromosomes
Nonchromosomal Mobile Genetic Elements
DNA Replication
Replication
Expression of Genetic Information
Regulation and Control of Gene Expression
Genetic Exchange and Diversity
Mutation
Genetic Recombination
Genetic Exchange
Bacterial Metabolism
Fueling
Acquisition of Nutrients
Production of Precursor Metabolites
Energy Production
Biosynthesis
Polymerization and Assembly
Structure and Function of the Bacterial Cell
Eukaryotic and Prokaryotic Cells
Bacterial Morphology
Bacterial Cell Components
Cell Envelope
Cell Interior
3. Host-Microorganism Interactions
The Encounter Between Host and Microorganism
The Human Host’s Perspective
Microbial Reservoirs and Transmission
Human and Microbe Interactions
Animals as Microbial Reservoirs
Insects as Vectors
The Environment as a Microbial Reservoir
The Microorganism’s Perspective
Microorganism Colonization of Host Surfaces
The Host’s Perspective
Skin and Skin Structures
Mucous Membranes
The Microorganism’s Perspective
Microbial Colonization
Microorganism Entry, Invasion, and Dissemination
The Host’s Perspective
Disruption of Surface Barriers
Responses to Microbial Invasion of Deeper Tissue
Specific Responses—The Immune System
The Microorganism’s Perspective
Colonization and Infection
Pathogens and Virulence
Microbial Virulence Factors
Genetics of Virulence: Pathogenicity Islands
Outcome and Prevention of Infectious Diseases
Outcome of Infectious Diseases
Prevention of Infectious Diseases
Immunization
Epidemiology
Matching
General Principles in Clinical Microbiology
Section 1. Safety and Specimen Management
4. Laboratory Safety
Sterilization, Disinfection, and Decontamination
Methods of Sterilization
Methods of Disinfection
Physical Methods of Disinfection
Chemical Methods of Disinfection
Antiseptics
Antimicrobial Material Fabrication
Chemical Safety
Fire Safety
Electrical Safety
Handling of Compressed Gases
Biosafety
Exposure Control Plan
Employee Education and Orientation
Disposal of Hazardous Waste
Standard Precautions
Laboratory Design and Engineering Controls
Laboratory Environment
Biologic Safety Levels
Biologic Safety Cabinets
Personal Protective Equipment
Postexposure Control
Transport of Biohazardous Materials
5. Specimen Management
General Concepts for Specimen Collection and Handling
Appropriate Collection Techniques
Specimen Transport
Specimen Preservation
Specimen Storage
Specimen Labeling
Specimen Requisition
Rejection of Unacceptable Specimens
Specimen Processing
Gross Examination of Specimen
Direct Microscopic Examination
Selection of Culture Media
Specimen Preparation
Inoculation on Solid Media
Incubation Conditions
Specimen Diagnostic Procedures
Extent of Identification Required
Communication of Laboratory Findings
Critical (Panic) Values
Expediting Results Reporting: Computerization
Section 2. Approaches to Diagnosis of Infectious Diseases
6. Role of Microscopy
Bright-Field (Light) Microscopy
Principles of Light Microscopy
Magnification
Resolution
Contrast
Direct and Indirect Smears
Staining Techniques
Gram Stain
Acid-Fast Stains
Fluorescence Microscopy
Principle of Fluorescence Microscopy
Staining Techniques for Fluorescence Microscopy
Fluorochroming
Immunofluorescence
Dark-Field Microscopy
Digital Automated Photomicroscopy
Digital Holographic Microscopy
7. Overview of Cultivation and Systems for Identification
Organism Identification
Principles of Bacterial Cultivation
Nutritional Requirements
General Concepts of Culture Media
Formulation of Bacterial Growth Media
Media Classifications and Functions
Quality Control of Media
Summary of Artificial Media for Routine Bacteriology
Preparation of Artificial Media
Environmental Requirements
Oxygen and Carbon Dioxide Concentration
Temperature
pH
Moisture
Methods for Providing Optimal Incubation Conditions
Bacterial Cultivation
Isolation of Bacteria From Specimens
Evaluation of Colony Morphologies
Type of Media Supporting Bacterial Growth
Relative Quantities of Each Colony Type
Colony Characteristics
Indirect Gram Stain and Subcultures
Principles of Identification
Organism Identification Using Genotypic Criteria
Organism Identification Using Phenotypic Criteria
Microscopic Morphology and Staining Characteristics
Macroscopic (Colony) Morphology
Environmental Requirements for Growth
Resistance or Susceptibility to Antimicrobial Agents
Nutritional Requirements and Metabolic Capabilities
Principles of Phenotypic Identification Schemes
Selection and Inoculation of Identification Biochemical Test Battery
Type of Bacteria to Be Identified
Clinical Significance of the Bacterial Isolate
Availability of Reliable Testing Methods
Incubation for Substrate Use
Conventional Identification
Rapid Identification
Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry
Detection of Metabolic Activity
Colorimetry
Fluorescence
Turbidity
Analysis of Metabolic Profiles
Identification Databases
Commercial Identification Systems and Automation
Advantages and Examples of Commercial System Designs
8. Nucleic Acid–Based Analytic Methods for Microbial Identification and Characterization
Overview of Nucleic Acid–Based Methods
Specimen Collection and Transport
Nucleic Acid Hybridization Methods
Hybridization Steps and Components
Hybridization Formats
Overview of Polymerase Chain Reaction and Derivations
Real-Time Polymerase Chain Reaction
Amplification Methods: Non–Polymerase Chain Reaction–Based
Coupled Target and Signal (Probe) Amplification
Isothermal (Constant Temperature) Amplification
Nicking Endonuclease Amplification
Postamplification End-Point Analysis
Nucleic Acid Electrophoresis
Sequencing and Enzymatic Digestion of Nucleic Acids
Nucleic Acid Sequencing
Pyrosequencing
Next-Generation Sequencing
Nucleic Acid and Oligonucleotide Arrays
High-Density Deoxyribonucleic Acid Probes
Low- to Moderate-Density Arrays
Magnetic Resonance
Clustered Regularly Interspersed Short Palindromic Repeats
Enzymatic Digestion and Electrophoresis of Nucleic Acids
Applications of Nucleic Acid–Based Methods
Direct Detection of Microorganisms
Analytical Specificity
Analytical Sensitivity
Applications for Direct Molecular Detection of Microorganisms
Characterization of Microorganisms Beyond Identification
Detection of Antimicrobial Resistance
Investigation of Strain Relatedness and Pulsed-Field Gel Electrophoresis
Automation and Advances in Molecular Diagnostic Instrumentation
9. Overview of Immunochemical Methods Used for Organism Detection
The Immune Response
Characteristics of Antibodies
Humoral Immune Response
Antibody (Serologic) Detection
Antibody Production
Polyclonal Antibodies
Monoclonal Antibodies
Immunoglobulin M
Separation of Immunoglobulin M and Immunoglobulin G
Immunochemical Methods
Precipitation
Double Immunodiffusion
Single Immunodiffusion
Agglutination
Particle Agglutination
Coagglutination
Hemagglutination
Hemagglutination Inhibition Assays
Flocculation Tests
Neutralization Assays
Complement Fixation Assays
Immunofluorescent Assays
Enzyme Immunoassays
Solid-Phase Immunoassay
Membrane-Bound Solid-Phase Enzyme Immunosorbent Assay
Automated Fluorescent Immunoassays
Western Blot Immunoassays
Summary
Matching:
Matching:
Section 3. Evaluation of Antimicrobial Activity
10. Principles of Antimicrobial Action and Resistance
Antimicrobial Action
Principles
Mode of Action of Antibacterial Agents
Inhibitors of Cell Wall Synthesis
Beta-Lactams
Cephalosporins
Fosfomycin
Carbapenems
Glycopeptides and Lipoglycopeptides
Inhibitors of Cell Membrane Function
Lipopeptides
Inhibitors of Protein Synthesis
Aminoglycosides
Macrolide-Lincosamide-Streptogramin Group
Ketolides
Oxazolidinones
Chloramphenicol
Tetracyclines
Glycylglycines
Mupirocin
Inhibitors of Nucleic Acid Synthesis
Fluoroquinolones
Metronidazole
Rifamycin
Inhibitors of Other Metabolic Processes
Sulfonamides
Trimethoprim
Nitrofurantoin
Mechanisms of Antibiotic Resistance
Principles
Biologic Versus Clinical Resistance
Environmentally Mediated Antimicrobial Resistance
Microorganism-Mediated Antimicrobial Resistance
Intrinsic Resistance
Acquired Resistance
Common Pathways for Antimicrobial Resistance
Resistance to Beta-Lactam Antimicrobials
Resistance to Glycopeptides
Resistance to Aminoglycosides
Resistance to Quinolones
Resistance to Other Antimicrobial Agents
Emergence and Dissemination of Antimicrobial Resistance
11. Laboratory Methods and Strategies for Antimicrobial Susceptibility Testing
Goal and Limitations
Standardization
Limitations of Standardization
Testing Methods
Principles
Conventional Testing Methods That Directly Measure Antimicrobial Activity
General Considerations
Broth Dilution
Agar Dilution
Disk Diffusion
Commercial Antimicrobial Susceptibility Testing Systems
Rapid Identification/Antimicrobial Susceptibility Testing Systems
Alternative Approaches for Enhancing Resistance Detection
Methods That Directly Detect Specific Resistance Mechanisms
Phenotypic Methods
Genotypic Methods
Special Methods for Complex Antimicrobial/Organism Interactions
Bactericidal Tests
Tests for Activity of Antimicrobial Combinations
Laboratory Strategies for Antimicrobial Susceptibility Testing
Relevance
When to Perform a Susceptibility Test
Determining Clinical Significance
Predictability of Antimicrobial Susceptibility
Availability of Reliable Susceptibility Testing Methods
Selection of Antimicrobial Agents for Testing
Accuracy
Use of Accurate Methodologies
Review of Results
Components of Result Review Strategies
Accuracy and Antimicrobial Resistance Surveillance
Communication
Bacteriology
Section 1. Principles of Identification
12. Overview of Bacterial Identification Methods and Strategies
Rationale for Approaching Organism Identification
Future Trends of Organism Identification
Section 2. Catalase-Positive, Gram-Positive Cocci
13. Staphylococcus, Micrococcus, and Similar Organisms
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Specimen Collection and Transport
Specimen Processing
Direct Detection Methods
Microscopy
Nucleic Acid Detection
Cultivation
Media of Choice
Incubation Conditions and Duration
Colonial Appearance
Approach to Identification
Comments Regarding Specific Organisms
Antibody (Serologiv) Detection
Molecular Typing
Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry
Antimicrobial Susceptibility Testing and Therapy
Prevention
Section 3. Catalase-Negative, Gram-Positive Cocci
14. Streptococcus, Enterococcus, and Similar Organisms
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Beta-Hemolytic Streptococci
Streptococcus pneumoniae
Viridans Streptococci
Enterococcus spp.
Miscellaneous Other Gram-Positive Cocci
Laboratory Diagnosis
Specimen Collection and Transport
Specimen Processing
Direct Detection Methods
Antigen Detection
Nucleic Acid Detection
Gram Stain
Cultivation
Media of Choice
Incubation Conditions and Duration
Colonial Appearance
Approach to Identification
Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry
Comments Regarding Specific Organisms
Antibody (Serologic) Detection
Molecular Typing
Antimicrobial Susceptibility Testing and Therapy
Prevention
Section 4. Non-Branching, Catalase-Positive, Gram-Positive Bacilli
15. Bacillus and Similar Organisms
General Characteristics
Bacillus anthracis and Bacillus cereus biovar Anthracis
Epidemiology
Pathogenesis and Spectrum of Disease
B. cereus Group (Not B. anthracis)
Epidemiology
Pathogenesis and Spectrum of Disease
B. thuringiensis
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Specimen Processing
Direct Detection Methods
Nucleic Acid Detection
Matrix-Assisted Laser Desorption Ionization Time of Flight
Cultivation
Media of Choice
Incubation Conditions and Duration
Colonial Appearance
Approach to Identification
Molecular Typing
Antibody (Serologic) Detection
Antimicrobial Susceptibility Testing and Therapy
Prevention
16. Listeria, Corynebacterium, and Similar Organisms
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Specimen Collection and Transport
Specimen Processing
Direct Detection Methods
Nucleic Acid Detection
Cultivation
Media of Choice
Incubation Conditions and Duration
Colonial Appearance
Approach to Identification
Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry
Antibody (Serologic) Detection
Molecular Typing
Comments on Specific Organisms
Antimicrobial Susceptibility Testing and Therapy
Prevention
Treatment
Matching:
Section 5. Nonbranching, Catalase-Negative, Gram-Positive Bacilli
17. Erysipelothrix, Lactobacillus, and Similar Organisms
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Specimen Collection and Transport
Specimen Processing
Direct Detection Methods
Nucleic Acid Detection
Antibody (Serologic) Detection
Cultivation
Incubation Conditions and Duration
Colonial Appearance
Approach to Identification
Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry
Comments Regarding Specific Organisms
Antimicrobial Susceptibility Testing and Therapy
Prevention
Section 6. Branching or Partially Acid-Fast, Gram-Positive Bacilli
18. Nocardia, Streptomyces, Rhodococcus, and Similar Organisms
General Characteristics
Acid-Fast Aerobic Actinomycetes
Partially Acid-Fast Aerobic Actinomycetes
Nocardia spp.
Rhodococcus, Gordonia, and Tsukamurella spp.
Non–Acid-Fast Aerobic Actinomycetes: Streptomyces, Actinomadura, Amycolatopsis, Dermatophilus, Dietzia, Nocardiopsis, Pseudonocardia, Saccharomonospora, Saccharopolyspora, and Williamsia spp.
Thermophilic Actinomycetes
Epidemiology and Pathogenesis
Acid-Fast Aerobic Actinomycetes
Partially Acid-Fast Aerobic Actinomycetes
Nocardia spp.
Rhodococcus, Gordonia, and Tsukamurella spp.
Non–Acid-Fast Aerobic Actinomycetes: Streptomyces, Actinomadura, Amycolatopsis, Dermatophilus, Dietzia, Nocardiopsis, Pseudonocardia, Saccharomonospora, Saccharopolyspora, Williamsia spp., and Thermophilic Actinomycetes
Acid-Fast Aerobic Actinomycetes
Partially Acid-Fast Aerobic Actinomycetes
Nocardia spp.
Rhodococcus, Gordonia, and Tsukamurella spp.
Non–Acid-Fast Aerobic Actinomycetes: Streptomyces, Actinomadura, Amycolatopsis, Dermatophilus, Dietzia, Nocardiopsis, Pseudonocardia, Saccharomonospora, Saccharopolyspora, Williamsia spp., and Thermophilic Actinomycetes
Laboratory Diagnosis
Specimen Collection, Transport, and Processing
Direct Detection Methods
Nucleic Acid Detection
Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry
Cultivation
Approach to Identification
Molecular Typing
Antibody (Serologic) Detection
Antimicrobial Susceptibility Testing and Therapy
Prevention
Matching
Section 7. Gram-Negative Bacilli and Coccobacilli (MacConkey-Positive, Oxidase-Negative)
19. Enterobacterales
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Specific Organisms: Opportunistic Human Pathogens
Family Budviciaceae
Family Enterobacteriaceae
Citrobacter spp.
Cronobacter spp.
Enterobacter spp.
Escherichia spp.
Klebsiella spp.
Raoultella spp.
Other Enterobacteriaceae
Family Erwiniaceae
Erwinia spp.
Pantoea spp.
Tatumella spp.
Family Hafniaceae
Edwardsiella spp.
Hafnia spp.
Family Morganellaceae
Morganella spp.
Proteus and Providencia spp.
Family Yersiniaceae
Ewingella and Rahnella spp.
Serratia spp.
Other Enterobacterales
Plesiomonas shigelloides
Specific Organisms: Primary Intestinal Pathogens
Family Enterobacteriaceae
Escherichia spp.
Salmonella spp.
Shigella spp.
Family Yersiniaceae
Yersinia spp.
Laboratory Diagnosis
Specimen Collection and Transport
Specimen Processing
Direct Detection Methods
Nucleic Acid Detection
Cultivation
Media of Choice
Incubation Conditions and Duration
Colonial Appearance
Approach to Identification
Specific Considerations for Identifying Enteric Pathogens
Molecular Typing
Antibody (Serologic) Detection
Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry
Antimicrobial Susceptibility Testing and Therapy
Extended Spectrum Beta-Lactamase–Producing Enterobacterales
Expanded-Spectrum Cephalosporin and Carbapenem Resistance
Multidrug-Resistant Typhoid Fever
Prevention
20. Acinetobacter, Stenotrophomonas, and Other Organisms
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Specimen Collection and Transport
Specimen Processing
Direct Detection Methods
Cultivation
Media of Choice
Incubation Conditions and Duration
Colonial Appearance
Approach to Identification
Comments Regarding Specific Organisms
Antibody (Serologic) Detection
Antimicrobial Resistance and Antimicrobial Susceptibility Testing
Antimicrobial Therapy
Prevention
Section 8. Gram-Negative Bacilli and Coccobacilli (MacConkey-Positive, Oxidase-Positive)
21. Pseudomonas, Burkholderia, and Similar Organisms
General Characteristics
Epidemiology
Burkholderia, Cupriavidus, and Ralstonia spp.
Acidovorax, Brevundimonas, and Pandoraea spp.
Pseudomonas spp.
Pathogenesis and Spectrum of Disease
Burkholderia, Cupriavidus, and Ralstonia spp.
Acidovorax, Brevundimonas, and Pandoraea spp.
Pseudomonas spp.
Laboratory Diagnosis
Specimen Collection and Transport
Specimen Processing
Direct Detection Methods
Nucleic Acid Detection
Cultivation
Media of Choice
Incubation Conditions and Duration
Colonial Appearance
Approach to Identification
Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry
Comments Regarding Specific Organisms
Antibody (Serologic) Detection
Antimicrobial Susceptibility Testing and Therapy
Prevention
22. Achromobacter, Rhizobium, Ochrobactrum, and Similar Organisms
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Specimen Collection and Transport
Specimen Processing
Direct Detection Methods
Cultivation
Media of Choice
Incubation Conditions and Duration
Colonial Appearance
Approach to Identification
Comments Regarding Specific Organisms
Antibody (Serologic) Detection
Antimicrobial Susceptibility Testing and Therapy
Prevention
23. Chryseobacterium, Sphingobacterium, and Similar Organisms
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Specimen Collection and Transport
Specimen Processing
Direct Detection Methods
Cultivation
Media of Choice
Incubation Conditions and Duration
Colonial Appearance
Approach to Identification
Comments Regarding Specific Organisms
Antibody (Serologic) Detection
Antimicrobial Susceptibility Testing and Therapy
Prevention
24. Alcaligenes, Comamonas, and Similar Organisms
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Specimen Collection and Transport
Specimen Processing
Direct Detection Methods
Cultivation
Media of Choice
Incubation Conditions and Duration
Colonial Appearance
Approach to Identification
Comments Regarding Specific Organisms
Antibody (Serologic) Detection
Antimicrobial Susceptibility Testing and Therapy
Prevention
25. Vibrio, Aeromonas, Plesiomonas shigelloides, and Chromobacterium violaceum
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Specimen Collection and Transport
Specimen Processing
Direct Detection Methods
Cultivation
Media of Choice
Incubation Conditions and Duration
Colonial Appearance
Approach to Identification
Comments Regarding Specific Organisms
Antibody (Serologic) Detection
Antimicrobial Susceptibility Testing and Therapy
Prevention
Section 9. Gram-Negative Bacilli and Coccobacilli (MacConkey-Negative, Oxidase-Positive)
26. Sphingomonas and Similar Organisms
General Considerations
Epidemiology, Spectrum of Disease, and Antimicrobial Therapy
Laboratory Diagnosis
Specimen Collection and Transport
Specimen Processing
Direct Detection Methods
Antibody (Serologic) Detection
Cultivation
Media of Choice
Incubation Conditions and Duration
Colonial Appearance
Approach to Identification
Comments Regarding Specific Organisms
Antimicrobial Susceptibility
Prevention
27. Moraxella and Neisseria spp.
General Characteristics
Epidemiology, Spectrum of Disease, and Antimicrobial Therapy
Laboratory Diagnosis
Specimen Collection and Transport
Specimen Processing
Direct Detection Methods
Cultivation
Media of Choice
Incubation Conditions and Duration
Colonial Appearance
Approach to Identification
Comments Regarding Specific Organisms
Antibody (Serologic) Detection
Antimicrobial Susceptibility
Prevention
28. Eikenella corrodens and Similar Organisms
General Characteristics
Epidemiology, Spectrum of Disease, and Antimicrobial Therapy
Laboratory Diagnosis
Specimen Collection and Transport
Specimen Processing
Direct Detection Methods
Nucleic Acid Detection
Cultivation
Media of Choice
Incubation Conditions and Duration
Colonial Appearance
Approach to Identification
Comments Regarding Specific Organisms
Antibody (Serologic) Detection
Prevention
29. Pasteurella and Similar Organisms
General Characteristics and Taxonomy
Epidemiology, Spectrum of Disease, and Antimicrobial Therapy
Laboratory Diagnosis
Specimen Collection and Transport
Specimen Processing
Direct Detection Methods
Antibody (Serologic) Detection
Cultivation
Media of Choice
Incubation Conditions and Duration
Colonial Appearance
Approach to Identification
Comments Regarding Specific Organisms
Prevention
30. Actinobacillus, Kingella, Cardiobacterium, Capnocytophaga, and Similar Organisms
General Characteristics
Epidemiology, Pathogenesis, Spectrum of Disease, and Antimicrobial Therapy
Laboratory Diagnosis
Specimen Collection and Transport
Specimen Processing
Direct Detection Methods
Nucleic Acid Detection
Antibody (Serologic) Detection
Cultivation
Media of Choice
Incubation Conditions and Duration
Colonial Appearance
Approach to Identification
Comments Regarding Specific Organisms
Prevention
Section 10. Gram-Negative Bacilli and Coccobacilli (MacConkey-Negative, Oxidase-Variable)
31. Haemophilus
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Specimen Collection and Transport
Specimen Processing
Direct Detection Methods
Direct Observation
Antigen (Serologic) Detection
Nucleic Acid Detection
Cultivation
Media of Choice
Incubation Conditions and Duration
Colonial Appearance
Approach to Identification
Serotyping
Antibody (Serologic) Detection
Antimicrobial Susceptibility Testing and Therapy
Prevention
Section 11. Gram-Negative Bacilli that are Optimally Recovered on Special Media
32. Bartonella
Bartonella
General Characteristics
Epidemiology and Pathogenesis
Spectrum of Disease
Laboratory Diagnosis
Specimen Collection, Transport, and Processing
Direct Detection Methods
Microscopy
Nucleic Acid Detection
Cultivation
Approach to Identification
Antibody (Serologic) Detection
Antimicrobial Susceptibility Testing and Therapy
Prevention
33. Campylobacter, Arcobacter, and Helicobacter
Campylobacter and Arcobacter
General Characteristics
Epidemiology and Pathogenesis
Spectrum of Disease
Laboratory Diagnosis
Specimen Collection, Transport, and Processing
Direct Detection
Antigen Detection
Nucleic Acid Detection
Media
Cultivation
Approach to Identification
Antibody (Serologic) Detection
Antimicrobial Susceptibility Testing and Therapy
Prevention
Helicobacter spp.
General Characteristics
Epidemiology and Pathogenesis
Spectrum of Disease
Laboratory Diagnosis
Specimen Collection, Transport, and Processing
Direct Detection
Nucleic Acid Detection
Cultivation
Approach to Identification
Antibody (Serologic) Detection
Antimicrobial Susceptibility Testing and Therapy
Prevention
34. Legionella
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Specimen Collection and Transport
Specimen Processing
Direct Detection Methods
Microscopy
Antigens (Serologic) Detection
Nucleic Acid Detection
Cultivation
Approach to Identification
Antibody (Serologic) Detection
Antimicrobial Susceptibility Testing and Therapy
Prevention
Matching
Short Answer
35. Brucella
General Characteristics
Epidemiology and Pathogenesis
Spectrum of Disease
Laboratory Diagnosis
Specimen Collection, Transport, and Processing
Direct Detection Methods
Nucleic Acid Detection
Antibody (Serologic) Detection
Cultivation
Approach to Identification
Antimicrobial Susceptibility Testing and Therapy
Prevention
36. Bordetella pertussis and Bordetella parapertussis
General Characteristics
Epidemiology and Pathogenesis
Pathogenesis
Spectrum of Disease
Laboratory Diagnosis
Specimen Collection, Transport, and Processing
Direct Detection Methods
Cultivation
Approach to Identification
Antibody (Serologic) Detection
Antimicrobial Susceptibility Testing and Therapy
Prevention
37. Francisella
General Characteristics
Epidemiology and Pathogenesis
Spectrum of Disease
Laboratory Diagnosis
Specimen Collection, Transport, and Processing
Direct Detection Methods
Nucleic Acid Detection
Antibody (Serologic) Detection
Cultivation
Approach to Identification
Antimicrobial Susceptibility Testing and Therapy
Prevention
38. Streptobacillus spp. and Similar Organisms
Streptobacillus and Pseudostreptobacillus spp.
General Characteristics
Epidemiology and Pathogenesis
Spectrum of Disease
Laboratory Diagnosis
Specimen Collection, Transport, and Processing
Direct Detection Methods
Cultivation
Approach to Identification
Antibody (Serologic) Detection
Antimicrobial Susceptibility Testing and Therapy
Prevention
Spirillum minus
General Characteristics
Epidemiology and Pathogenesis
Spectrum of Disease
Laboratory Diagnosis
Specimen Collection, Transport, and Processing
Direction Detection Methods
Antibody (Serologic) Detection
Antimicrobial Susceptibility Testing and Therapy
Prevention
Section 12. Gram-Negative Cocci
39. Neisseria and Moraxella catarrhalis
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Specimen Collection and Transport
Specimen Processing
Direct Detection Methods
Gram Stain
Nucleic Acid Detection
Cultivation
Media of Choice
Incubation Conditions and Duration
Colonial Appearance
Approach to Identification
Biochemical Identification
Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry
Comments About Specific Organisms
Immunoserologic Identification
Serotyping
Antimicrobial Susceptibility Testing and Therapy
Prevention
Section 13. Anaerobic Bacteriology
40. Overview and General Laboratory Considerations
General Characteristics
Specimen Collection and Transport
Macroscopic Examination of Specimens
Direct Detection Methods
Gram Staining
Specimen Processing
Anaerobe Jars or Pouches
Holding Jars
Anaerobe Chamber
Anaerobic Media
Incubation Conditions and Duration
Approach to Identification
Examination of Primary Plates
Subculture of Isolates
Presumptive Identification of Isolates
Definitive Biochemical Identification
Rapid Identification Methods
Antimicrobial Susceptibility Testing and Therapy
41. Overview of Anaerobic Organisms
Epidemiology
Pathogenesis and Spectrum of Disease
Gram-Positive, Spore-Forming Bacilli
Laboratory Diagnosis and Specimen Collection
Nucleic Acid Detection and MALDI-TOF MS (Gram-Positive)
Gram-Positive, Non–Spore-Forming Bacilli
Laboratory Diagnosis
Nucleic Acid Detection and MALDI-TOF MS (Gram-Negative)
Gram-Negative Rods
Bacteroides fragilis Group
Nonpigmented Prevotella spp.
Pigmented Porphyromonas and Prevotella spp.
Fusobacteriaceae
Proteobacteria
Other Anaerobic Gram-Negative Rods
Anaerobic Gram-Positive and Gram-Negative Cocci
Laboratory Diagnosis
Limitations of Nucleic Acid Detection and MALDI-TOF MS
Result Reporting
Prevention
Section 14. Mycobacteria and Other Bacteria with Unusual Growth Requirements
42. Mycobacteria
Mycobacterium tuberculosis Complex
General Characteristics
Epidemiology and Pathogenesis
Spectrum of Disease
Nontuberculous Mycobacteria
Slow-Growing Nontuberculous Mycobacteria
Photochromogens
Scotochromogens
Nonphotochromogens
Rapidly Growing Nontuberculous Mycobacteria
General Characteristics
Epidemiology and Pathogenesis
Spectrum of Disease
Noncultivatable Nontuberculous Mycobacteria—Mycobacterium leprae
General Characteristics
Epidemiology and Pathogenesis
Spectrum of Disease
Laboratory Diagnosis of Mycobacterial Infections
Specimen Collection and Transport
Pulmonary Specimens
Gastric Lavage Specimens
Urine Specimens
Fecal Specimens
Tissue and Body Fluid Specimens
Blood Specimens
Wounds, Skin Lesions, and Aspirates
Specimen Processing
Contaminated Specimens
Inadequate Specimens and Rejection Criteria
Specimens Not Requiring Decontamination
Direct Detection Methods
Microscopy
Acid-Fast Stains
Immunodiagnostic Testing
Nucleic Acid Detection
Cultivation
Solid Media
Liquid Media
Interpretation
Approach to Identification
Conventional Phenotypic Tests
Antimicrobial Susceptibility Testing and Therapy
M. tuberculosis complex
Susceptibility Testing
Therapy
Nontuberculous Mycobacteria
Prevention
43. Obligate Intracellular and Nonculturable Bacterial Agents
Order Chlamydiales
Family Chlamydiaceae
Chlamydia trachomatis
General Characteristics
Epidemiology and Pathogenesis
Spectrum of Disease
Perinatal Infections
Laboratory Diagnosis
Antibiotic Susceptibility Testing and Therapy
Prevention
Chlamydia psittaci
General Characteristics
Epidemiology and Pathogenesis
Spectrum of Disease
Laboratory Diagnosis
Antibiotic Susceptibility Testing and Therapy
Prevention
Chlamydia pneumoniae
General Characteristics
Epidemiology and Pathogenesis
Spectrum of Disease
Laboratory Diagnosis
Antibiotic Susceptibility Testing and Therapy
Prevention
Family Parachlamydiaceae
Family Waddliaceae
Family Simkaniaceae
Rickettsia, Orientia, Anaplasma, Ehrlichia, Neoehrlichia, and Neoreickettsia
General Characteristics
Epidemiology and Pathogenesis
Spectrum of Disease
Laboratory Diagnosis
Direct Detection Methods
Antibody (Serologic) Detection
Cultivation
Antibiotic Susceptibility Testing and Therapy
Prevention
Coxiella sp.
General Characteristics
Epidemiology and Pathogenesis
Spectrum of Disease
Laboratory Diagnosis
Antibiotic Susceptibility Testing and Therapy
Prevention
Tropheryma whipplei
General Characteristics
Epidemiology, Pathogenesis, and Spectrum of Disease
Laboratory Diagnosis
Antibiotic Susceptibility Testing and Therapy
Prevention
Klebsiella granulomatis
General Characteristics
Epidemiology and Pathogenesis
Spectrum of Disease
Laboratory Diagnosis
Antibiotic Susceptibility Testing and Therapy
44. Cell Wall–Deficient Bacteria: Mycoplasma and Ureaplasma
General Characteristics
Epidemiology and Pathogenesis
Epidemiology
Pathogenesis
Spectrum of Disease
Laboratory Diagnosis
Specimen Collection, Transport, and Processing
Direct Detection Methods
Nucleic Acid Detection
Cultivation
Approach to Identification
Antibody (Serologic) Detection
Susceptibility Testing and Therapy
Prevention
45. The Spirochetes
Family Treponemataceae
General Characteristics
Epidemiology and Pathogenesis
Spectrum of Disease
Laboratory Diagnosis
Specimen Collection
Direct Detection
Nucleic Acid Detection
Antibody (Serologic) Detection
Rapid Syphilis Tests
Nontreponemal Antibody Tests
Treponemal Serologic Tests
Antimicrobial Susceptibility Testing and Therapy
Prevention
Family Borreliaceae
General Characteristics
Epidemiology and Pathogenesis
Relapsing Fever
Lyme Disease
Spectrum of Disease
Relapsing Fever
Lyme Disease
Laboratory Diagnosis
Specimen Collection, Transport, and Processing
Direct Detection Methods
Nucleic Acid Detection
Antibody (Serologic) Detection
Cultivation
Antimicrobial Susceptibility Testing and Therapy
Prevention
Family Brachyspiraceae
General Characteristics
Epidemiology and Pathogenesis
Laboratory Diagnosis
Specimen Collection and Direct Detection
Cultivation
Approach to Identification
Antimicrobial Susceptibility Testing and Therapy
Family Leptospiraceae
General Characteristics
Epidemiology and Pathogenesis
Spectrum of Disease
Laboratory Diagnosis
Specimen Collection, Transport, and Processing
Direct Detection
Nucleic Acid Detection
Cultivation
Approach to Identification
Antibody (Serologic) Detection
Molecular Typing Methods
Antimicrobial Susceptibility Testing and Therapy
Prevention
Part IV. Parasitology
46. Overview of the Methods and Strategies in Parasitology
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Specimen Collection and Transport
Specimen Processing
Approach to Identification
Microscopic Examination
Intestinal Tract
Urogenital Tract Specimens
Sputum
Aspirates
Biopsy Specimens
Blood
Direct Detection Methods
Intestinal Parasites
Blood Parasites
Cultivation
Larval-Stage Nematodes
Blood Protozoa
Antibody (Serologic) Detection
Prevention
Ectoparasites
47. Intestinal Protozoa
Amoebae
Entamoeba histolytica
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Metastatic Amebiasis
Laboratory Diagnosis
Nucleic Acid Detection
Reporting of Results
Therapy
Prevention
Entamoeba coli
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Therapy
Prevention
Entamoeba hartmanni
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Entamoeba polecki and Entamoeba gingivalis
Endolimax nana
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Iodamoeba bütschlii (buetschlii)
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Therapy
Prevention (Nonpathogenic Entamoeba, Endolimax, and Iodamoeba spp.)
Blastocystis spp.
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Nucleic Acid Detection
Reporting of Results
Therapy
Prevention
Flagellates
Giardia duodenalis
General Characteristics
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Nucleic Acid Detection
Results and Reporting
Prevention
Treatment
Chilomastix mesnili
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Therapy
Prevention
Dientamoeba fragilis
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Therapy
Prevention
Pentatrichomonas hominis
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Therapy
Prevention
Ciliates
Balantioides coli
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Results Reporting
Therapy
Prevention
Sporozoa (Apicomplexa)
Cryptosporidium spp.
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Results Reporting
Therapy
Prevention
Cyclospora cayetanensis
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Results and Reporting
Therapy
Prevention
Cystoisospora belli
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Nucleic Acid Detection
Results and Reporting
Therapy
Prevention
Sarcocystis spp.
General Characteristics
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Serologic Detection
Nucleic Acid Detection
Results and Reporting
Therapy
Prevention
Microsporidia
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Enterocytozoon bieneusi
Encephalitozoon spp.
Encephalitozoon intestinalis
Other Microsporidia
Laboratory Diagnosis
Antigen Detection
Antibody Detection
Nucleic Acid Detection
Histology
Results and Reporting
Therapy
Prevention
48. Blood and Tissue Protozoa
Plasmodium spp.
Plasmodium vivax (Benign Tertian Malaria)
General Characteristics
Pathogenesis and Spectrum of Disease
Plasmodium ovale
General Characteristics
Pathogenesis and Spectrum of Disease
Plasmodium malariae (Quartan Malaria)
General Characteristics
Pathogenesis and Spectrum of Disease
Plasmodium falciparum (Malignant Tertian Malaria)
General Characteristics
Pathogenesis and Spectrum of Disease
Plasmodium knowlesi (Simian Malaria, The Fifth Human Malaria)
General Characteristics
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis (All Species)
Routine Methods
Antigen-Based Tests
Nucleic Acid Detection
Antibody (Serologic) Detection
Results Reporting
Therapy
Babesia spp.
General Characteristics
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Routine Methods
Nucleic Acid Detection
Antibody (Serologic) Detection
Results Reporting
Therapy
Prevention
Trypanosoma spp.
African Trypanosomiasis
General Characteristics
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis (All Species)
Therapy
American Trypanosomiasis
Trypanosoma cruzi
General Characteristics
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Therapy
Leishmania Spp.
General Characteristics
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Histologic Identification
Nucleic Acid Detection
Antibody (Serologic) Detection
Therapy
49. Protozoa From Other Body Sites
Free-Living Amoebae
Naegleria fowleri
General Characteristics
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Routine Methods and Direct Detection
Isolation and Culture
Antibody (Serologic) Detection
Therapy
Acanthamoeba spp.
General Characteristics
Pathogenesis and Spectrum of Disease
Granulomatous Amoebic Encephalitis
Keratitis
Cutaneous Infections
Acanthamoeba Pneumonia
Laboratory Diagnosis
Direct Detection and Routine Methods
Isolation and Culture
Antibody (Serology) Detection
Therapy
Acanthamoeba keratitis
Disseminated Infections
Balamuthia mandrillaris
General Characteristics
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Antibody (Serologic) Detection
Therapy
Sappinia spp.
Nucleic Acid Detection (Free-Living Amoebae)
Results Reporting (Free-Living Amoebae)
Trichomonas vaginalis
General Characteristics
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Wet Mounts
Stained Smears
Antigen Detection
Nucleic Acid Detection
Culture
Therapy
Trichomonas tenax
General Characteristics
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Therapy
Toxoplasma gondii
General Characteristics
Pathogenesis and Spectrum of Disease
Immunocompetent Individuals
Chronic Infections
Immunocompromised Individuals
Congenital Infections
Ocular Infections
Laboratory Diagnosis
Nucleic Acid Detection
Therapy
50. Intestinal Nematodes
Ascaris lumbricoides
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Nucleic Acid Detection
Therapy
Prevention
Enterobius vermicularis
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Nucleic Acid Detection
Therapy
Prevention
Strongyloides stercoralis
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Antibody (Serologic) Detection
Nucleic Acid Detection
Therapy
Prevention
Trichostrongylus spp.
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Therapy
Prevention
Trichuris trichiura
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Nucleic Acid Detection
Therapy
Prevention
Capillaria philippinensis
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Therapy
Prevention
Hookworms
Epidemiology
Ancylostoma duodenale
General Characteristics
Pathogenesis and Spectrum of Disease
Necator americanus
General Characteristics
Pathogenesis and Spectrum of Disease
Ancylostoma ceylonicum and Ancylostoma caninum
General Characteristics
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Nucleic Acid Detection
Therapy
Prevention
Results and Reporting
51. Tissue Nematodes
Trichinella spp.
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Antibody (Serologic) Detection
Therapy
Prevention
Toxocara canis (Visceral Larva Migrans) and Toxocara cati (Ocular Larva Migrans)
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Direct Microscopy
Antibody (Serologic) Detection
Therapy
Prevention
Baylisascaris procyonis (Neural Larva Migrans)
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Antibody (Serologic) Detection
Therapy
Ancylostoma braziliense and Ancylostoma caninum (Cutaneous Larva Migrans)
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Therapy and Prevention
Dracunculus medinensis
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Therapy
Parastrongylus cantonensis (Neural Angiostrongyliasis)
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Therapy
Parastrongylus costaricensis (Abdominal Angiostrongyliasis)
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Therapy
Gnathostoma spinigerum
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Antibody (Serologic) Detection
Therapy
Capillaria hepatica
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Therapy
Prevention
Dirofilaria immitis and Other Species
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Therapy
52. Blood and Tissue Filarial Nematodes
Wuchereria bancrofti
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Endosymbiont
Laboratory Diagnosis
Direct Detection
Antigen Detection
Antibody (Serologic) Detection
Nucleic Acid Detection
Brugia malayi and Brugia timori
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Therapy
Prevention
Loa loa
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Direct Detection
Antibody (Serologic) Detection
Nucleic Acid Detection
Therapy
Prevention
Onchocerca volvulus
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Direct Detection
Antibody (Serologic) Detection
Nucleic Acid Detection
Therapy
Prevention
Mansonella spp. (M. ozzardi, M. streptocerca, M. perstans)
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Nucleic Acid Detection
Therapy
Prevention
Dirofilaria spp. (D. immitis, D. repens, D. tenuis)
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Therapy
Prevention
53. Intestinal Cestodes
Dibothriocephalus latus
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Therapy
Prevention
Dipylidium caninum
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Therapy
Prevention
Hymenolepis nana
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Therapy
Prevention
Hymenolepis diminuta
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Therapy
Prevention
Taenia solium
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Therapy
Prevention
Taenia saginata
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Therapy
Prevention
Taenia asiatica
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Therapy
Prevention
Taenia crassiceps
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Therapy
Prevention
Nucleic Acid Detection (All Species)
54. Tissue Cestodes
Taenia solium
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Therapy
Prevention
Echinococcus granulosus complex
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Therapy
Prevention
Echinococcus multilocularis
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Therapy
Prevention
Echinococcus oligarthrus and Echinococcus vogeli
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Therapy
Prevention
Taenia multiceps and Other Species
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Therapy
Prevention
Taenia serialis
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Therapy and Prevention
Spirometra mansonoides
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Therapy
Prevention
55. Intestinal Trematodes
Family Echinostomatidae
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Therapy and Prevention
Family Fasciolidae
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Therapy and Prevention
Family Heterophyidae
General Characteristics
Heterophyes heterophyes
Epidemiology
Metagonimus yokogawai
Adult
Epidemiology
Centrocestus spp.
Epidemiology
Haplorchis spp.
Epidemiology
Stellantchasmus spp.
Epidemiology
Pygidiopsis spp.
Epidemiology
Pathogenicity and Spectrum of Disease
Prevention
Family Paramphistomidae: Gastrodiscoides hominis
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Therapy and Prevention
Family Troglotrematidae
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Treatment
Nucleic Acid Detection
56. Liver and Lung Trematodes
The Liver Flukes
General Characteristics
Epidemiology and Life Cycle
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Antibody (Serologic) Detection
Nucleic Acid Detection
Therapy and Prevention
The Lung Flukes
General Characteristics
Epidemiology and Life Cycle
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Antibody (Serologic) Detection
Nucleic Acid Detection
Treatment and Prevention
57. Blood Trematodes
General Characteristics
Epidemiology
Pathology and Spectrum of Disease
Laboratory Diagnosis
Antigen Detection
Antibody (Serologic) Detection
Nucleic Acid Testing
Therapy
Prevention
Part V. Mycology
58. Overview of Fungal Identification Methods and Strategies
Epidemiology
General Features of the Fungi
Taxonomy of the Fungi
Clinical Classification of the Fungi
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Collection, Transport, and Culturing of Clinical Specimens
Lower Respiratory Tract Secretions
Upper Respiratory Specimens
Sterile Body Fluids Including Cerebrospinal Fluid
Blood and Bone Marrow
Eye (Corneal Scrapings or Vitreous Humor)
Hair, Skin, and Nail Scrapings
Vaginal
Urine
Tissue
Culture Media and Incubation Requirements
Quality Control
Direct Microscopic Examination
Antibody (Serologic) Detection
(1,3)-β-d-Glucan Detection
Nucleic Acid Detection
Matrix-Assisted Laser Desorption Ionization Mass Spectrometry
General Considerations for the Identification of Yeast
General Considerations for the Identification of Molds
Microscopic Morphologic Features
General Morphologic Features of the Molds
Clinical Relevance for Fungal Identification
Laboratory Safety
Prevention
59. Hyaline Molds, Mucorales, Basidiobolales, Entomophthorales, Dermatophytes, and Opportunistic and Systemic Mycoses
The Mucorales
General Characteristics
Epidemiology and Pathogenesis
Spectrum of Disease
Laboratory Diagnosis
Specimen Collection, Transport, and Processing
Direct Detection Methods
Approach to Identification
Antibody (Serologic) Detection
Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry
The Entomophthorales and Basidiobolales
General Characteristics
Epidemiology and Pathogenesis
Spectrum of Disease
Laboratory Diagnosis
Specimen Collection, Transport, and Processing
Direct Detection Methods
Approach to Identification
Antibody (Serologic) Detection
The Dermatophytes
General Characteristics
Epidemiology and Pathogenesis
Spectrum of Disease
Trichophyton spp.
Laboratory Diagnosis
Specimen Collection, Transport, and Processing
Direct Detection Methods
Approach to Identification
Antibody (Serologic) Detection
The Opportunistic Mycoses
General Characteristics
Epidemiology and Pathogenesis
Aspergillus spp.
Pathogenesis and Spectrum of Disease
Aspergillus spp.
Fusarium spp. and Other Hyaline Septate Opportunistic Molds
Laboratory Diagnosis
Specimen Collection, Transport, and Processing
Direct Detection Methods
Approach to Identification
Antibody (Serologic) Detection
Antibody (Serologic) Detection
Systemic Mycoses
General Characteristics
Epidemiology
Blastomyces spp.
Coccidioides spp.
Emergomyces spp.
Histoplasma capsulatum
Paracoccidioides brasiliensis and Paracoccidioides lutzii
Pathogenesis and Spectrum of Disease
Blastomyces spp.
Coccidioides spp.
Emergomyces spp.
Histoplasma capsulatum
Paracoccidioides spp.
Laboratory Diagnosis
Specimen Collection, Transport, and Processing
Direct Detection Methods
Approach to Identification
Antibody (Serologic) Detection
60. Dematiaceous Molds
General Characteristics
Epidemiology, Pathogenesis, and Spectrum of Disease
Mycetoma
Chromoblastomycosis
Phaeohyphomycosis
Sporotrichosis
Laboratory Diagnosis
Specimen Collection, Transport, and Processing
Direct Detection Method
Stains
Antibody (Serologic) Detection
Nucleic Acid–Based Tests
Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry
Cultivation
Approach to Identification
Superficial Infections
Mycetoma
Antifungal Susceptibilities
61. Pneumocystis jirovecii, Lagenidium, Paralegenidium, Pythium, Rhinosporidium and Uncultivated Paracoccidioides
Pneumocystis spp.
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Specimen Collection, Processing, and Transport
Direct Detection Methods
Nucleic Acid Detection
Paracoccidioides loboi (Previously Lacazia loboi)
Laboratory Diagnosis and Treatment
Pythium insidiosum
Laboratory Diagnosis
Treatment
Lagenidium and Paralegenidium spp.
Laboratory Diagnosis
Treatment
Rhinosporidium seeberi
Laboratory Diagnosis
Treatment
62. The Yeasts and Yeastlike Organisms
General Characteristics
Epidemiology
Ascomycetous Yeasts
Candida spp.
Saccharomyces
Saprochaete spp.
Basidiomycetes Yeasts
Cryptococcus spp.
Filobasidium sp., Hannaella sp., Naganishia spp., Papiliotrema spp., and Solicoccozyma sp.
Malassezia spp.
Rhodotorula spp.
Sporobolomyces spp.
Trichosporon spp., Apiotrichum spp., and Cutaneotrichosporon spp.
Pseudozyma spp.
Yeastlike Organisms
Geotrichum sp.
Prototheca spp.
Pathogenesis and Spectrum of Disease
Candida albicans Complex
Non-Albicans Candida
Cryptococcus neoformans
Filobasidium sp., Hannaella sp., Naganishia spp., Papiliotrema spp., and Solicoccozyma sp.
Malassezia spp.
Geotrichum and Prototheca spp.
Rhodotorula spp. and Sporobolomyces spp.
Saccharomyces cerevisiae
Saprochaete spp.
Trichosporon spp., Cutaneotrichosporon spp., and Apiotrichum sp.
Pseudozyma spp.
Laboratory Diagnosis
Specimen Collection, Transport, and Processing
Stains
Antigen Detection
Nucleic Acid Detection
Cultivation
Approach to Identification
Candida spp.
Germ Tube Test
Cryptococcus neoformans
Rapid Urease Test
Trichosporon spp., Cutaneotrichosporon spp., and Apiotrichum sp.
Malassezia spp.
Commercial Yeast Identification Systems
Multiple Species Identification Systems
API-20C AUX
MicroScan Rapid Yeast Identification Panel
Vitek Biochemical Cards
Chromogenic Agars
Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry
Cornmeal Agar Morphology
Carbohydrate Utilization
Phenoloxidase Detection Using Niger Seed Agar
Nucleic Acid Sequencing Methods
63. Antifungal Susceptibility Testing, Therapy, and Prevention
Antifungal Susceptibility Testing
Broth Dilution Antifungal Susceptibility Testing for Yeast
Broth Dilution Antifungal Susceptibility Testing for Molds
Antifungal Therapy and Prevention
Azole Antifungal Drugs
Fluconazole
Itraconazole
Ketoconazole
Voriconazole
Posaconazole
Isavuconazole
Echinocandins
Polyene Macrolide Antifungals
Amphotericin B
Nystatin
Griseofulvin
5-Fluorocytosine (Flucytosine)
Allylamines
Terbinafine and Naftifine
Selenium Sulfide
Part VI. Virology
64. Overview of the Methods and Strategies in Virology
General Characteristics
Viral Structure
Virus Taxonomy
Viral Replication
Epidemiology
Pathogenesis and Spectrum of Disease
Prevention and Therapy
Antiviral Agents
Viruses That Cause Human Diseases
Laboratory Diagnosis
Designing a Clinical Virology Laboratory
Specimen Selection and Collection
General Principles
Throat, Nasopharyngeal Swab, or Aspirate (Respiratory)
Bronchial and Bronchoalveolar Washes (Lower Respiratory)
Rectal Swabs and Stool Specimens
Urine
Skin and Mucous Membrane Lesions
Sterile Body Fluids Other Than Blood
Dried Blood Spots
Bone Marrow
Tissue
Genital Specimens
Oral
Eye
Serum for Antibody Testing
Specimen Transport and Storage
Specimen Processing
General Principles
Processing Based on Requests for Specific Viruses
Virus Detection Methods
Cytology and Histology
Immunodiagnostics (Antigen Detection)
Enzyme-Linked Virus-Inducible System
Nucleic Acid–Based Methods
Cell Culture
Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry
Serologic Testing
General Principles
Immune Status Testing
Serology Panels
Preservation and Storage of Viruses
65. Viruses and Prions in Human Disease
Viruses in Human Disease
Adenoviridae
Arenaviridae
Astroviridae
Caliciviridae
Coronaviridae
Filoviridae
Flaviviridae
Yellow Fever Virus
Dengue Virus
West Nile Virus
Zika Virus
Hepatitis C Virus
Hantaviridae
Hepadnaviridae
Hepeviridae
Herpesviridae
Herpesviruses
Varicella-Zoster Virus
Epstein-Barr Virus
Cytomegalovirus
Orthomyxoviridae
Papillomaviridae
Paramyxoviridae
Measles Virus
Parvoviridae
Picornaviridae
Enteroviruses, Parechoviruses, and Polioviruses
Rhinovirus
Hepatitis A Virus
Pneumoviridae
Polyomaviridae
Poxviridae
Reoviridae
Retroviridae
Rhabdoviridae
Togaviridae
Prions in Human Disease
66. Antiviral Therapy, Susceptibility Testing, and Prevention
Antiviral Therapy
Antiviral Resistance
Methods of Antiviral Susceptibility Testing
Phenotypic Assays
Plaque Reduction Assay
Enzyme Immunoassay
Recombinant Virus Assays
Genotypic Susceptibility Assays
Pyrosequencing
Next-Generation Sequencing
Human Immunodeficiency Virus
Influenza
SARS-CoV-2
Prevention of Other Viral Infections
Vaccination
Immune Prophylaxis and Therapy
Eradication
Part VII. Diagnosis by Organ System
67. Bloodstream Infections
General Considerations
Etiology
Bacteria
Fungi
Parasites
Viruses
Types of Bacteremia
Types of Bloodstream Infections
Intravascular Infections
Extravascular Infections
Clinical Manifestations
Immunocompromised Patients
Detection of Bacteremia
Specimen Collection
Preparation of the Site
Specimen Volume
Number of Blood Cultures
Timing of Collection
Miscellaneous Matters
Types of Blood Culture Bottles
Culture Techniques
Conventional Blood Cultures
Self-Contained Manual Culture Systems
Lysis Centrifugation
Instrument-Based Systems
Non–culture-Based Methods for Identification of Bacteremia or Sepsis
Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry
Intravenous Catheter–Associated Infections
Handling Positive Indirect Detection From Culture
Rapid Tests From Positive Blood Culture Bottles
Interpretation of Blood Culture Results
Special Considerations for Other Relevant Organisms Isolated From Blood
HACEK Bacteria
Campylobacter and Helicobacter spp.
Fungi
Mycobacterium spp.
Brucella spp.
Spirochetes
Borrelia spp.
Leptospira spp.
Granulicatella and Abiotrophia spp.
Mycoplasma spp.
Bartonella spp.
68. Infections of the Lower Respiratory Tract
General Considerations
Anatomy
Pathogenesis of the Respiratory Tract: Basic Concepts
Host Factors
Microorganism Virulence Factors
Adherence
Toxins
Microorganism Growth
Avoiding the Host Response
Acute Diseases of the Lower Respiratory Tract
Bronchitis
Bronchiolitis
Pneumonia
Pathogenesis
Clinical Manifestations
Epidemiology and Etiologic Agents
Pneumonia in Children
Pneumonia in Young Adults
Pneumonia in Adults
Chronic Diseases of the Lower Respiratory Tract
Bronchitis
Pneumonia
Cystic Fibrosis
Bacterial Lung Abscess
Immunocompromised Patients
Patients With Neoplasms
Transplant Recipients
Patients With Human Immunodeficiency Virus
Pleural Infections
Laboratory Diagnosis of Lower Respiratory Tract Infections
Specimen Collection and Transport
Sputum
Endotracheal or Tracheostomy Suction Specimens
Bronchoscopy
Transtracheal Aspirates
Other Invasive Procedures
Specimen Processing
Rejection Criteria for Respiratory Samples
Direct Visual Examination
Routine Culture
69. Upper Respiratory Tract Infections and Other Infections of the Oral Cavity and Neck
General Considerations
Anatomy
Pathogenesis
Diseases of the Upper Respiratory Tract, Oral Cavity, and Neck
Upper Respiratory Tract
Common Cold
Laryngitis
Laryngotracheobronchitis
Epiglottitis
Pharyngitis, Tonsillitis, and Peritonsillar Abscesses
Rhinitis
Miscellaneous Infections Caused by Other Agents
Oral Cavity
Stomatitis
Thrush
Periodontal Infections
Salivary Gland Infections
Neck
Diagnosis of Upper Respiratory Tract Infections
Collection and Transport of Specimens
Direct Visual Examination or Detection
Culture
Streptococcus pyogenes (Beta-Hemolytic Group A Streptococci)
Corynebacterium diphtheriae
Bordetella pertussis
Neisseria spp.
Epiglottitis
Diagnosis of Infections in the Oral Cavity and Neck
Collection and Transport
Direct Visual Examination
Culture
70. Meningitis and Other Infections of the Central Nervous System
General Considerations
Anatomy
Coverings and Spaces of the Central Nervous System
Cerebrospinal Fluid
Routes of Infection
Diseases of the Central Nervous System
Meningitis
Encephalitis/Meningoencephalitis
Viral Encephalitis
Mycobacterial Infections
Fungal Infections
Parasitic Infections
Brain Abscess
Shunt Infections
Laboratory Diagnosis of Central Nervous System Infections
Meningitis
Specimen Collection and Transport
Initial Processing
Cerebrospinal Fluid Laboratory Results
Visual Detection of Etiologic Agents
Direct Detection of Etiologic Agents
Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry
Culture
71. Infections of the Eyes, Ears, and Sinuses
Eyes
Anatomy
Resident Microbiota
Diseases
Pathogenesis
Epidemiology and Etiology of Disease
Periocular Infections
Microbial Conjunctivitis
Microbial Keratitis
Endophthalmitis
Uveitis
Laboratory Diagnosis
Specimen Collection and Transport
Direct Visual Examination
Nucleic Acid–Based Methods
Other Nonculture Methods
Culture
Ears
Anatomy
Resident Microbiota
Diseases, Epidemiology, and Etiology of Disease
Otitis Externa (External Ear Infection)
Otitis Media (Middle Ear Infections)
Mastoiditis
Pathogenesis
Laboratory Diagnosis
Specimen Collection and Transport
Direct Visual Examination
Culture and Nonculture Methods
Sinuses
Anatomy
Diseases
Pathogenesis
Epidemiology and Etiology of Disease
Laboratory Diagnosis
Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry
72. Infections of the Urinary Tract
General Considerations
Anatomy
Resident Microbiota of the Urinary Tract
Infections of the Urinary Tract
Epidemiology
Etiologic Agents
Community-Acquired
Hospital- and Health Care–Associated
Miscellaneous
Pathogenesis
Routes of Infection
The Host-Pathogen Relationship
Types of Infection and Their Clinical Manifestations
Urethritis
Ureteritis
Asymptomatic Bacteriuria
Cystitis
Acute Urethral Syndrome
Pyelonephritis
Laboratory Diagnosis of Urinary Tract Infections
Specimen Collection
Clean-Catch or Clean-Voided Midstream Urine
Straight Catheterized Urine
Suprapubic Bladder Aspiration
Indwelling Catheter
Timing of Specimen Collection
Specimen Transport
Screening Procedures
Gram or Methylene Blue Stain
Pyuria
Indirect Indices
Automated and Semiautomated Systems
General Comments Regarding Screening Procedures
Urine Culture
Inoculation and Incubation of Urine Cultures
Interpretation of Urine Cultures
73. Genital Tract Infections
General Considerations
Anatomy
Resident Microbiota
Sexually Transmitted Diseases and Other Genital Tract Infections
Genital Tract Infections
Sexually Transmitted Diseases and Other Lower Genital Tract Infections
Epidemiology and Etiologic Agents
Routes of Transmission
Clinical Manifestations
Infections of the Reproductive Organs and Other Upper Genital Tract Infections
Female Patients
Male patients
Laboratory Diagnosis of Genital Tract Infections
Lower Genital Tract Infections
Urethritis, Cervicitis, and Vaginitis
Genital Skin and Mucous Membrane Lesions
Buboes
Infections of the Reproductive Organs
Pelvic Inflammatory Disease
Miscellaneous Infections
Infections of Neonates and Human Products of Conception
74. Gastrointestinal Tract Infections
Anatomy
Resident Gastrointestinal Microbiome
Gastroenteritis
Pathogenesis
Host Factors
Microbial Factors
Clinical Manifestations
Epidemiology
Institutional Settings
Traveler’s Diarrhea
Foodborne and Waterborne Outbreaks
Immunocompromised Hosts
Etiologic Agents
Other Infections of the Gastrointestinal Tract
Esophagitis
Gastritis
Proctitis
Miscellaneous
Laboratory Diagnosis of Gastrointestinal Tract Infections
Specimen Collection and Transport
General Comments
Stool Specimens for Bacterial Culture
Stool Specimens for Ova and Parasites
Stool Specimens for Viruses
Miscellaneous Specimen Types
Direct Detection of Agents of Gastroenteritis in Feces
Wet Mounts
Stains
Antigen Detection
Nucleic Acid Testing
Culture of Fecal Material for Isolation of Etiologic Agents
Bacteria
Laboratory Diagnosis of Clostridioides difficile–Associated Diarrhea
75. Skin, Soft Tissue, and Wound Infections
General Considerations
Anatomy of the Skin
Function of the Skin
Prevalence, Etiology, and Pathogenesis
Skin and Soft Tissue Infections
Infections of the Epidermis and Dermis
Infections in or Around Hair Follicles
Infections in the Keratinized Layer of the Epidermis
Infections in the Deeper Layers of the Epidermis and Dermis
Infections of the Subcutaneous Tissues
Infections of the Muscle Fascia and Muscles
Necrotizing Fasciitis
Progressive Bacterial Synergistic Gangrene
Myositis
Wound Infections
Postoperative Infections
Bites
Burns
Special Circumstances Regarding Skin and Soft Tissue Infections
Infections Related to Vascular and Neurologic Problems
Sinus Tracts and Fistulas
Systemic Infections and Skin Manifestations
Laboratory Diagnostic Procedures
Specimen Collection
Infections of the Epidermis and Dermis
Erysipeloid
Superficial Mycoses and Erythrasma
Erysipelas and Cellulitis
Vesicles and Bullae
Infections of the Subcutaneous Tissue
Infections of the Muscle Fascia and Muscles
Wound Infections
Postoperative
Bites
Burns
76. Normally Sterile Body Fluids, Bone and Bone Marrow, and Solid Tissues
Specimens From Sterile Body Sites
Fluids
Pleural Fluid
Peritoneal Fluid
Peritoneal Dialysis Fluid
Pericardial Fluid
Joint Fluid
Bone
Bone Marrow Aspiration or Biopsy
Bone Biopsy
Solid Tissues
Laboratory Diagnostic Procedures
Specimen Collection and Transport
Fluids and Aspirates
Bone
Tissue
Specimen Processing, Direct Examination, and Culture
Fluids and Aspirates
Bone
Solid Tissue
Part VIII. Clinical Laboratory Management
77. Quality in the Clinical Microbiology Laboratory
Quality Program
Specimen Collection and Transport
Standard Operating Procedure Manual
Personnel
Reference Laboratories
Patient Reports
Proficiency Testing
Performance Checks
Instruments
Commercially Prepared Media Exempt From Quality Control
User-Prepared and Nonexempt, Commercially Prepared Media
Antimicrobial Susceptibility Tests
Stains and Reagents
Kits
Maintenance of Quality Control Records
Maintenance of Reference Quality Control Stocks
Bacteriology
Mycology
Mycobacteriology
Virology
Parasitology
Quality Assurance Program
Types of Quality Assurance Audits
Conducting a Quality Assurance Audit
Continuous Daily Monitoring
78. Infection Prevention and Control
Incidence of Health Care–Associated Infections
Types of Health Care–Associated Infections
Catheter-Associated Urinary Tract Infections
Ventilator-Associated Pneumonia
Surgical Site Infections
Central Line–Associated Bloodstream Infections
Emergence of Antibiotic-Resistant Microorganisms
Hospital Infection Prevention Programs
Role of the Microbiology Laboratory
Characterizing Strains Involved in an Outbreak
Preventing Health Care–Associated Infections
Surveillance Methods
79. Sentinel Laboratory Response to Bioterrorism
General Considerations
Bio Crime
Government Laws and Regulations
Biosecurity
Laboratory Response Network
Role of the Sentinel Laboratory
Glossary
Index