Bailey & Scott's Diagnostic Microbiology, 15th Edition (Complete PDF)

Front Cover
IFC
Bailey & Scott’s DIAGNOSTIC MICROBIOLOGY
Copyright
Dedication
Reviewers
Contributors
Preface
Acknowledgments
Contents
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 Elements (Mobilome)
DNA Replication
Replication
Expression of Genetic Information
Transcription
Translation
Regulation and Control of Gene Expression
Genetic Exchange and Diversity
Mutation
Genetic Recombination
Genetic Exchange
Transformation
Transduction
Conjugation
Bacterial Metabolism
Fueling
Acquisition of Nutrients
Production of Precursor Metabolites
Energy Production
Oxidative Phosphorylation
Biosynthesis
Polymerization and Assembly
Structure and Function of the Bacterial Cell
Eukaryotic and Prokaryotic Cells
Bacterial Morphology
Bacterial Cell Components
Cell Envelope
Outer Membrane
Cell Wall (Murein Layer)
Periplasmic Space
Cytoplasmic (Inner) Membrane
Cellular Appendages
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
General Protective Characteristics
Specific Protective Characteristics
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
Nonspecific Responses
Phagocytes
Inflammation
Specific Responses—The Immune System
Components of the Immune System
Two Branches of the Immune System
The Microorganism’s Perspective
Colonization and Infection
Pathogens and Virulence
Microbial Virulence Factors
Attachment
Invasion
Survival Against Inflammation
Survival Against the Immune System
Microbial Toxins
Genetics of Virulence: Pathogenicity Islands
Biofilm Formation
Outcome and Prevention of Infectious Diseases
Outcome of Infectious Diseases
Prevention of Infectious Diseases
Immunization
Epidemiology
II - General Principles in Clinical Microbiology
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
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
Biological Safety Levels
Biologic Safety Cabinets
Personal Protective Equipment
Postexposure Control
Mailing 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 Work-Up
Extent of Identification Required
Communication of Laboratory Findings
Critical (Panic) Values
Expediting Results Reporting: Computerization
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
Procedure Overview
Principle
Gram Stain Examination (Direct Smear)
Gram Stain of Bacteria Grown in Culture (Indirect Smear)
Acid-Fast Stains
Principle
Procedure Overview
Phase-Contrast Microscopy
Fluorescent Microscopy
Principle of Fluorescent Microscopy
Staining Techniques for Fluorescent Microscopy
Fluorochroming
Acridine Orange
Auramine-Rhodamine
Calcofluor White
Immunofluorescence
Dark-Field Microscopy
Digital Automated Microscopy
Digital Holographic Microscopy
7 - Overview of Conventional Cultivation and Systems for Identification
Organism Identification
Principles of Bacterial Cultivation
Nutritional Requirements
General Concepts of Culture Media
Phases of Growth Media
Media Classifications and Functions
Summary of Artificial Media for Routine Bacteriology
Blood Agar
Brain-Heart Infusion
Chocolate Agar
Columbia Colistin-Nalidixic Acid With Blood
Eosin Methylene Blue Agar, Levine
Gram-Negative Broth
Hektoen Enteric Agar
MacConkey Agar
Phenylethyl Alcohol Agar
Modified Thayer-Martin Agar
Thioglycollate Broth
Xylose-Lysine-Deoxycholate Agar
Preparation of Artificial Media
Media Sterilization
Cell Cultures
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
Establishing Enzymatic Capabilities
Types of Enzyme-Based Tests
Single Enzyme Tests
Catalase Test
Oxidase Test
Indole Test
L-pyroglutamyl-aminopeptidase Test
Tests for the Presence of Metabolic Pathways
Oxidation and Fermentation Tests
Amino Acid Degradation
Single Substrate Utilization
Establishing Inhibitor Profiles
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 Utilization
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
Use of the Database to Identify Unknown Isolates
Confidence in Identification
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
Production and Labeling of Nucleic Acid Probe
Preparation of Target Nucleic Acid
Mixture and Hybridization of Target and Probe
Detection of Hybridization
Hybridization Formats
Liquid Format
Solid Support Format
In Situ Hybridization
Peptide Nucleic Acid Fluorescence In Situ Hybridization
Hybridization With Signal Amplification
Amplification Methods—Polymerase Chain Reaction–Based
Overview of Polymerase Chain Reaction and Derivations
Extraction and Denaturation of the Target Nucleic Acid
Primer Annealing
Extension of the Primer-Target Duplex
Detection of Polymerase Chain Reaction Products
Derivations of the Polymerase Chain Reaction Method
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
Enzymatic Digestion and Electrophoresis of Nucleic Acids
Applications of Nucleic Acid–Based Methods
Direct Detection of Microorganisms
Advantages and Disadvantages
Analytical Specificity
Analytical Sensitivity
Applications for Direct Molecular Detection of Microorganisms
Identification of Microorganisms Grown in Culture
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
Features of the Immune Response
Characteristics of Antibodies
Features of the Humoral Immune Response Useful in Diagnostic Testing
Interpretation of Serologic Tests
Production of Antibodies for Use in Laboratory Testing
Polyclonal Antibodies
Monoclonal Antibodies
Immunoglobulin M Clinical Significance
Separating Immunoglobulin M from Immunoglobulin G for Serologic Testing
Principles of Immunochemical Methods Used for Organism Detection
Precipitation Tests
Double Immunodiffusion
Single Immunodiffusion
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
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
Fosfomycin
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
Methods That Directly Measure Antimicrobial Activity
Conventional Testing Methods: General Considerations
Inoculum Preparation
Selection of Antimicrobial Agents for Testing
Conventional Testing Methods: Broth Dilution
Procedures
Medium and Antimicrobial Agents. With in vitro susceptibility testing methods, certain conditions must be altered when examining...
Inoculation and Incubation. Standardized bacterial suspensions that match the turbidity of the 0.5 McFarland standard (i.e., 1.5...
. After incubation, the microdilution trays are examined for bacterial growth. Each tray should include a growth (i.e., Positive...
Conventional Testing Methods: Agar Dilution
Conventional Testing Methods: Disk Diffusion
Procedures
. The Mueller-Hinton preparation is the standard agar-base medium used for testing most bacterial organisms, although certain su...
. Before disk placement, the plate surface is inoculated using a swab that has been submerged in a bacterial suspension standard...
. Before results with individual antimicrobial agent disks are read, the plate is examined to confirm that a confluent lawn of g...
. Two important advantages of the disk diffusion test are convenience and user friendliness. Up to 12 antimicrobial agents can b...
Commercial Antimicrobial Susceptibility Testing Systems
Rapid ID/Antimicrobial Susceptibility Testing Systems
Gradient Diffusion Testing
Alternative Approaches for Enhancing Resistance Detection
Supplemental Testing Methods
Predictor Antimicrobial Agents
Methods That Directly Detect Specific Resistance Mechanisms
Phenotypic Methods
Beta-Lactamase Detection
Penicillin-Binding Protein 2a
Chloramphenicol Acetyltransferase Detection
Genotypic Methods
Special Methods for Complex Antimicrobial/Organism Interactions
Bactericidal Tests
Minimal Bactericidal Concentration
Time-Kill Studies
Serum Bactericidal Test (Schlichter Test)
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 Results Review Strategies
Data Review
Resolution
Accuracy and Antimicrobial Resistance Surveillance
Communication
III - Bacteriology
1 - Principles of Identification
12 - Overview of Bacterial Identification Methods and Strategies: Acetamide Utilization
Rationale for Approaching Organism Identification
Future Trends of Organism Identification
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
Serodiagnosis
Matrix-Assisted Desorption Ionization Time of Flight
Antimicrobial Susceptibility Testing and Therapy
Prevention
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
Serodiagnosis
Antimicrobial Susceptibility Testing and Therapy
Prevention
4 - Non-Branching, Catalase-Positive, Gram-Positive Bacilli
15 - Bacillus and Similar Organisms
General Characteristics
Bacillus 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
Cultivation
Media of Choice
Incubation Conditions and Duration
Colonial Appearance
Approach to Identification
Serodiagnosis
Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry
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
Serodiagnosis
Comments on Specific Organisms
Antimicrobial Susceptibility Testing and Therapy
Prevention
Treatment
5 - Non-Branching, 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
Serodiagnosis
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
Antimicrobial Susceptibility Testing and Therapy
Prevention
6 - Branching or Partially Acid-Fast, Gram-Positive Bacilli
18 - Nocardia, Streptomyces, Rhodococcus, and Similar Organisms: GENERA AND SPECIES TO BE CONSIDERED
General Characteristics
Acid-Fast Aerobic Actinomycetes
Partially Acid-Fast Aerobic Actinomycetes
Nocardia spp
Rhodococcus, Gordonia, and Tsukamurella 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, Pseudonoca...
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, Pseudonoca...
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
Serodiagnosis
Antimicrobial Susceptibility Testing and Therapy
Prevention
7 - Gram-Negative Bacilli and Coccobacilli (MacConkey-Positive, Oxidase-Negative)
19 - Enterobacterales
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Diseases
Specific Organisms
Opportunistic Human Pathogens
Citrobacter spp
Cronobacter spp
Edwardsiella spp
Enterobacter spp
Escherichia coli
Erwinia spp
Hafnia spp
Klebsiella spp
Morganella spp
Pantoea spp
Plesiomonas shigelloides
Proteus spp. and Providencia spp
Raoultella spp
Serratia spp
Other Enterobacterales
Primary Intestinal Pathogens
Salmonella
Shigella spp
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
Serodiagnosis
Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry
Antimicrobial Susceptibility Testing and Therapy
Extended Spectrum Beta-Lactamase–Producing Enterobacterales
Expanded-Spectrum Cephalosporin Resistance 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
Serodiagnosis
Antimicrobial Resistance and Antimicrobial Susceptibility Testing
Antimicrobial Therapy
Prevention
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
Other Identification Methods
Comments Regarding Specific Organisms
Serodiagnosis
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
Serodiagnosis
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
Serodiagnosis
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
Serodiagnosis
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
Serodiagnosis
Antimicrobial Susceptibility Testing and Therapy
Prevention
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
Serodiagnosis
Cultivation
Media of Choice
Incubation Conditions and Duration
Colonial Appearance
Approach to Identification
Comments Regarding Specific Organisms
Sphingobacterium mizutaii
Sphingomonas paucimobilis
Sphingomonas parapaucimobilis
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
Serodiagnosis
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
Serodiagnosis
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
Serodiagnosis
Cultivation
Media of Choice
Incubation Conditions and Duration
Colonial Appearance
Approach to Identification
Comments Regarding Specific Organisms
Serodiagnosis
Prevention
30 - Actinobacillus, Kingella, Cardiobacterium, Capnocytophaga, and Similar Organisms
General Characteristics
Epidemiology, Pathogenesis, and Spectrum of Disease and Antimicrobial Therapy
Laboratory Diagnosis
Specimen Collection and Transport
Specimen Processing
Direct Detection Methods
Nucleic Acid Detection
Serodiagnosis
Cultivation
Media of Choice
Incubation Conditions and Duration
Colonial Appearance
Approach to Identification
Comments Regarding Specific Organisms
Prevention
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 Detection
Nucleic Acid Detection
Cultivation
Media of Choice
Incubation Conditions and Duration
Colonial Appearance
Approach to Identification
Serotyping
Serodiagnosis
Antimicrobial Susceptibility Testing and Therapy
Prevention
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
Serodiagnosis
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
Stool
Blood
Atmosphere
Approach to Identification
Serodiagnosis
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
Serodiagnosis
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
Nucleic Acid Detection
Cultivation
Approach to Identification
Serodiagnosis
Antimicrobial Susceptibility Testing and Therapy
Prevention
35 - Brucella
General Characteristics
Epidemiology and Pathogenesis
Spectrum of Disease
Laboratory Diagnosis
Specimen Collection, Transport, and Processing
Direct Detection Methods
Nucleic Acid Detection
Serodiagnosis
Cultivation
Approach to Identification
Antimicrobial Susceptibility Testing and Therapy
Prevention
36 - Bordetella pertussis, Bordetella parapertussis, and Related Species
General Characteristics
Epidemiology and Pathogenesis
Pathogenesis
Spectrum of Disease
Laboratory Diagnosis
Specimen Collection, Transport, and Processing
Direct Detection Methods
Cultivation
Approach to Identification
Serodiagnosis
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
Serodiagnosis
Cultivation
Approach to Identification
Antimicrobial Susceptibility Testing and Therapy
Prevention
38 - Streptobacillus spp. and Spirillum minus
Streptobacillus spp
General Characteristics
Epidemiology and Pathogenesis
Spectrum of Disease
Laboratory Diagnosis
Specimen Collection, Transport, and Processing
Direct Detection Methods
Cultivation
Approach to Identification
Serodiagnosis
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
Serodiagnosis
Antimicrobial Susceptibility Testing and Therapy
Prevention
12 - Gram-Negative Bacilli
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
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: GENERA AND SPECIES TO BE CONSIDERED
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
Anaerobic Gram-Positive and Gram-Negative Cocci
Laboratory Diagnosis
Nucleic Acid Detection and MALDI-TOF MS
Prevention
14 - Mycobacteria and Other Bacteria With Unusual Growth Requirements
42 - Mycobacteria
Mycobacterium tuberculosis Complex
General Characteristics
Epidemiology and Pathogenesis
Epidemiology
Pathogenesis
Spectrum of Disease
Nontuberculous Mycobacteria
Slow-Growing Nontuberculous Mycobacteria
Photochromogens
Scotochromogens
Nonphotochromogens
Mycobacterium avium Complex
. Taxonomically, MAC comprises M. avium, Mycobacterium intracellulare, M. avium subsp. avium, M. avium subsp. paratuberculosis, ...
. MAC is an important pathogen in both immunocompromised and immunocompetent populations. These organisms are among the most com...
. The clinical manifestations of MAC infections are summarized in Table 42.5
Other Nonphotochromogens
Rapidly Growing Nontuberculous Mycobacteria
General Characteristics
Epidemiology and Pathogenesis
Spectrum of Disease
Noncultivatable Nontuberculous Mycobacteria—Mycobacterium leprae
General Characteristics
Epidemiology and Pathogenesis
Epidemiology
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
Overview
Special Considerations
Specimens Not Requiring Decontamination
Direct Detection Methods
Microscopy
Acid-Fast Stains
Methods
. Fluorochrome staining is the screening procedure recommended for laboratories that have a fluorescent (ultraviolet) microscope...
. The classic carbolfuchsin stain (Ziehl-Neelsen) requires heating of the slide for better penetration of the stain into the myc...
Examination, Interpretation, and Reporting of Smears
Antigen-Protein Detection
Immunodiagnostic Testing
Nucleic Acid Detection
Genetic Sequencing and Nucleic Acid Amplification
DNA Microarrays
Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry
Cultivation
Solid Media
Liquid Media
Interpretation
Approach to Identification
Conventional Phenotypic Tests
Growth Characteristics
. The rate of growth is an important criterion for determining the initial category of an isolate. Rapid growers usually produce...
. As previously discussed, mycobacteria can be categorized into three groups based on pigment production. Evolve Procedure 42.5 ...
Biochemical Testing
. Niacin (nicotinic acid) plays an important role in the oxidation-reduction reactions that occur during mycobacterial metabolis...
. A nitrate reduction test is valuable for identifying M. tuberculosis, M. kansasii, M. szulgai, and M. fortuitum. The ability o...
. Most species of mycobacteria except for certain strains of M. tuberculosis complex (some isoniazid-resistant strains) and M. g...
. The commonly nonpathogenic, slow-growing scotochromogens and nonphotochromogens produce a lipase that can hydrolyze Tween 80 (...
. Some species of mycobacteria reduce potassium tellurite at variable rates. The ability to reduce tellurite in 3 to 4 days dist...
. The enzyme arylsulfatase is present in most mycobacteria. Test conditions can be varied to distinguish the different forms of ...
. The thiophene-2-carboxylic acid hydrazide (TCH) growth-inhibition test is used to distinguish M. bovis from M. tuberculosis be...
. Other tests are often performed to make more subtle distinctions between species (Table 42.10). However, performing all the pr...
Antimicrobial Susceptibility Testing and Therapy
M. tuberculosis Complex
Direct Versus Indirect Susceptibility Testing
Conventional Methods
Molecular Methods for the Determination of Susceptibility
Therapy
Nontuberculous Mycobacteria
Prevention
43 - Obligate Intracellular and Nonculturable Bacterial Agents
Chlamydia
Chlamydia trachomatis
General Characteristics
Epidemiology and Pathogenesis
Spectrum of Disease
Trachoma
Lymphogranuloma Venereum
Oculogenital Infections
Perinatal Infections
Laboratory Diagnosis
Specimen Collection and Transport
Direct Detection Methods
. Cytologic examination of cell scrapings from the conjunctiva of newborns or persons with ocular trachoma can be used to detect...
. Fluorescent monoclonal specific antibody antigen detection of C. trachomatis species-specific outer membrane proteins makes it...
. FDA-approved NAATs for the laboratory diagnosis of C. trachomatis infection use three different formats: polymerase chain reac...
Serodiagnosis
Cultivation
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
Direct Detection Methods
Serodiagnosis
Cultivation
Antibiotic Susceptibility Testing and Therapy
Prevention
Rickettsia, Orientia, Anaplasma, and Ehrlichia
General Characteristics
Epidemiology and Pathogenesis
Spectrum of Disease
Laboratory Diagnosis
Direct Detection Methods
Serodiagnosis
Cultivation
Antibiotic Susceptibility Testing and Therapy
Prevention
Coxiella
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
Serodiagnosis
Susceptibility Testing and Therapy
Prevention
45 - The Spirochetes
Treponema
General Characteristics
Epidemiology and Pathogenesis
Spectrum of Disease
Laboratory Diagnosis
Specimen Collection
Direct Detection
Nucleic Acid Detection
Serodiagnosis
Rapid Syphilis Tests
Nontreponemal Antibody Tests
Treponemal Serologic Tests
Antimicrobial Susceptibility Testing and Therapy
Prevention
Borrelia
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
Relapsing Fever
Nucleic Acid Detection
Serodiagnosis
Relapsing Fever
Lyme Disease
Cultivation
Antimicrobial Susceptibility Testing and Therapy
Prevention
Brachyspira
General Characteristics
Epidemiology and Pathogenesis
Laboratory Diagnosis
Specimen Collection and Direct Detection
Cultivation
Approach to Identification
Antimicrobial Susceptibility Testing and Therapy
Leptospira
General Characteristics
Epidemiology and Pathogenesis
Spectrum of Disease
Laboratory Diagnosis
Specimen Collection, Transport, and Processing
Direct Detection
Nucleic Acid Detection
Cultivation
Approach to Identification
Serodiagnosis
Molecular Typing Methods
Antimicrobial Susceptibility Testing and Therapy
Prevention
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
Ova and Parasite Examination
Recovery of the Tapeworm Scolex
Examination for Pinworm
Sigmoidoscopy Material
Duodenal Drainage
Duodenal Capsule Technique (Entero-Test)
Urogenital Tract Specimens
Sputum
Aspirates
Biopsy Specimens
Blood
Thin Blood Films
Thick Blood Films
Buffy Coat Films
Direct Detection Methods
Intestinal Parasites
Blood Parasites
Cultivation
Larval-Stage Nematodes
Blood Protozoa
Serodiagnosis
Prevention
Ectoparasites
47 - Intestinal Protozoa
Amoebae
Entamoeba histolytica
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Asymptomatic Infection
Intestinal Disease
Hepatic Disease
Metastatic Amebiasis
Laboratory Diagnosis
Routine Methods
Antigen Detection
Histology
Nucleic Acid Detection
Antibody (Serologic) Detection
Reporting of Results
Therapy
Asymptomatic Infection
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
Routine Methods
Antigen Detection
Antibody (Serologic) Detection
Reporting of Results
Therapy
Prevention
Flagellates
Giardia duodenalis
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Asymptomatic Infection
Intestinal Disease
Chronic Disease
Antigenic Variation
Laboratory Diagnosis
Routine Methods
Antigen Detection
Antibody Detection
Histology
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
Routine Methods
Antigen Detection
Antibody Detection
Therapy
Prevention
Pentatrichomonas hominis
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Therapy
Prevention
Retortamonas intestinalis
Ciliates
Neobalantidium 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
Immunocompetent Individuals
Immunocompromised Individuals
Laboratory Diagnosis
Routine Methods
Antigen Detection
Nucleic Acid Detection
Antibody Detection
Histology
Results Reporting
Therapy
Prevention
Cyclospora cayetanensis
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Special Stains
Nucleic Acid Detection and Serologic Tests
Results and Reporting
Therapy
Prevention
Cystoisospora belli
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Nucleic Acid Detection
Histology
Results and Reporting
Therapy
Prevention
Sarcocystis spp
General Characteristics
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
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
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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
Automated Instruments
Serologic Tests
Results Reporting
Therapy
Babesia spp
General Characteristics
Organism
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Routine Methods
Nucleic Acid Detection
Serologic Tests
Results Reporting
Therapy
Prevention
Trypanosoma spp
African Trypanosomiasis
General Characteristics
Pathogenesis and Spectrum of Disease
Trypanosoma brucei gambiense
Trypanosoma brucei rhodesiense
Laboratory Diagnosis (All Species)
Routine Methods
Nucleic Acid Detection
Antigen Detection
Antibody Detection
Therapy
American Trypanosomiasis
Trypanosoma cruzi
General Characteristics
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
. Trypomastigotes may be detected in blood by using thick and thin blood films or the buffy coat concentration technique (QBC). ...
. Referral laboratories have used molecular methods to detect infections with as few as one trypomastigote in 20 mL of blood, bu...
. In endemic areas where reduviid bugs are readily available, xenodiagnosis can be used to detect light infections; this techniq...
. Immunoassays have been used to detect antigens in urine and sera in patients with congenital infections and those with chronic...
. Serologic tests for antibody detection include complement fixation, IFA, indirect hemagglutination tests, and ELISA. The use o...
. In tissue, amastigotes can be differentiated from fungal organisms because they will not stain positive with periodic acid-Sch...
Therapy
Leishmania spp
General Characteristics
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Nucleic Acid Detection
Serologic Tests
Therapy
49 - Protozoa From Other Body Sites
Free-Living Amoebae
Naegleria fowleri
General Characteristics
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Routine Methods
Other Methods
Therapy
Acanthamoeba spp
General Characteristics
Pathogenesis and Spectrum of Disease
Granulomatous Amoebic Encephalitis
Keratitis
Cutaneous Infections
Laboratory Diagnosis
Routine Methods
Other Methods
Therapy
Disseminated Infections
Acanthamoeba Keratitis
Balamuthia mandrillaris
General Characteristics
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
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
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
Therapy
Prevention
Enterobius vermicularis
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Therapy
Prevention
Strongyloides stercoralis
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Serologic Testing
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
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, Ancylostoma braziliense, and Ancylostoma caninum
General Characteristics
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Therapy
Prevention
Results and Reporting
51 - Tissue Nematodes
Trichinella spp
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Serologic Testing
Nucleic Acid 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
Serologic Testing
Nucleic Acid Detection
Therapy
Prevention
Baylisascaris procyonis (Neural Larva Migrans)
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Serologic Testing
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 (Cerebral 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
Serologic Testing
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
Serologic Testing
Antigen 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
Serologic Testing
Nucleic Acid Detection
Therapy
Prevention
Onchocerca volvulus
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Direct Detection
Serologic Testing
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
Diphyllobothrium latum
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
Echinostoma spp
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Therapy and Prevention
Fasciolopsis buski General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Therapy and Prevention
Gastrodiscoides hominis
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Therapy and Prevention
Heterophyes: Metagonimus yokogawai, Centrocestus spp., Haplorchis spp., Stellantchamus spp., and Pygidiopsis spp.General Charact...
Heterophyes heterophyes
Epidemiology
Metagonimus yokogawai
Adult
Epidemiology
Centrocestus spp
Epidemiology
Haplorchis spp
Epidemiology
Stellantchamus spp
Epidemiology
Pygidiopsis spp
Epidemiology
Pathogenicity and Spectrum of Disease
Prevention
Laboratory Diagnosis
Nucleic Acid Detection
Treatment
56 - Liver and Lung Trematodes
The Liver Flukes
General Characteristics
Epidemiology and Life Cycle
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Serologic Testing
Nucleic Acid Detection
Therapy and Prevention
The Lung Flukes
General Characteristics
Epidemiology and Life Cycle
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Serologic Testing
Nucleic Acid Detection
Treatment and Prevention
57 - Blood Trematodes
General Characteristics
Epidemiology
Pathology and Spectrum of Disease
Laboratory Diagnosis
Antigen Detection
Serologic Testing
Therapy
Prevention
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
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
Direct Microscopic Examination
Serologic Testing
(1,3)-β-d-Glucan Detection
Molecular Methods
Matrix-Assisted Laser Desorption Ionization Mass Spectrometry
General Considerations for the Identification of Yeasts
General Considerations for the Identification of Molds
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
Stains
Antigen-Protein
Nucleic Acid–Based Testing
Cultivation
Approach to Identification
Serologic Testing
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
Antigen-Protein
Nucleic Acid–Based Testing
Cultivation
Approach to Identification
Serologic Testing
The Dermatophytes
General Characteristics
Epidemiology and Pathogenesis
Spectrum of Disease
Trichophyton spp
Laboratory Diagnosis
Specimen Collection, Transport, and Processing
Direct Detection Methods
Stains
Antigen-Protein
Nucleic Acid–Based Testing
Cultivation
Approach to Identification
Trichophyton spp
Microsporum spp
Epidermophyton sp
Serologic Testing
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
Stains
Antigen-Protein
Nucleic Acid–Based Tests
Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry
Cultivation
Approach to Identification
Aspergillus spp
Serologic Testing
Fusarium spp
Geotrichum candidum
Acremonium spp
Penicillium spp. and Talaromyces marneffei
Paecilomyces spp
Purpureocillium spp
Scopulariopsis spp
Serologic Testing
Systemic Mycoses
General Characteristics
Epidemiology
Blastomyces spp
Coccidioides spp
Emmonsia spp
Emergomyces spp
Histoplasma capsulatum
Paracoccidioides brasiliensis and P. lutzi
Talaromyces marneffei
Sporothrix spp
Pathogenesis and Spectrum of Disease
Blastomyces spp
Coccidioides spp
Emergomyces spp
Emmonsia spp
Histoplasma capsulatum
Paracoccidioides spp
Talaromyces marneffei
Sporothrix spp
Laboratory Diagnosis
Specimen Collection, Transport, and Processing
Direct Detection Methods
Stains
. The diagnosis of blastomycosis may easily be made when a clinical specimen is observed by direct microscopy. Blastomyces spp. ...
. In direct microscopic examinations of sputum or other body fluids, Coccidioides spp. appear as a nonbudding, thick-walled sphe...
. Emergomyces spp. can be differentiated from Emmonsia by the presence of budding yeasts and the absence of adiaspores
. Emmonsia spp. have not been successfully cultured from human specimens. Therefore, diagnosis is dependent on the histologic ap...
. Direct microscopic examination of respiratory tract specimens and other similar specimens often fails to reveal the presence o...
. Specimens submitted for direct microscopic examination are important for the diagnosis of paracoccidioidomycosis. Large, round...
. Direct examination of infected tissues and exudates reveals that T. marneffei produces small, yeastlike cells (2 to 6 μm) that...
. Exudate aspirated from unopened subcutaneous nodules or from open draining lesions often is submitted for culture and direct m...
Antigen-Protein
Nucleic Acid Testing
Cultivation
Approach to Identification
Blastomyces dermatitidis–B. gilchristii
Coccidioides spp
Emmonsia spp. and Emergomyces spp
Histoplasma capsulatum
Paracoccidioides spp
Talaromyces marneffei
Sporothrix spp
Serologic Testing
60 - Dematiaceous (Melanized) Molds
General Characteristics
Epidemiology and Pathogenesis Superficial Infections
Mycetoma
Chromoblastomycosis
Phaeohyphomycosis
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Specimen Collection, Transport, and Processing
Direct Detection Method
Stains
Superficial Infections
Chromoblastomycosis
Mycetoma and Phaeohyphomycosis
Serologic Testing
Nucleic Acid–Based Tests
Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry
Cultivation
Superficial Infections
Mycetoma
. Scedosporium spp. grow rapidly (5 to 10 days) on common laboratory media. Initial growth begins as a white, fluffy colony that...
. Colonies of Madurella spp. and E. jeanselmei (Fig. 60.3) are slow growing, unlike colonies of Curvularia spp. Colonies of Madu...
Chromoblastomycosis
Phaeohyphomycosis
Approach to Identification
Superficial Infections
Mycetoma
White Grain Mycetoma: Scedosporium apiospermum complex and Acremonium spp
Black Grain Mycetoma: Exophiala jeanselmei, Curvularia spp., and Madurella spp
Chromoblastomycosis: Cladosporium, Phialophora, and Fonsecaea spp
Phaeohyphomycosis: Alternaria, Bipolaris, Clado phialophora, Curvularia, Exophiala, Exserohilum, and Phialophora spp
. Microscopically, hyphae are septate and golden-brown pigmented; conidiophores are simple but sometimes branched. Conidiophores...
. Hyphae are dematiaceous and septate. However, conidiophores are characteristically bent (geniculate) at the locations where co...
. Microscopically, hyphae are septate and brown. Conidiophores are long, branched, and give rise to branching chains of darkly p...
. Microscopically, hyphae are dematiaceous and septate. Conidiophores are geniculate (i.e., bent where conidia are attached). Co...
. Only the Exophiala species E. jeanselmei and E. dermatitidis are considered here; although other species exist, they are recov...
. Hyphae are septate and dematiaceous. Conidiophores are geniculate, and conidia are produced sympodically. Conidia are elongate...
Antifungal Susceptibilities
61 - Atypical and Parafungal Agents
PNEUMOCYSTIS
General Characteristics
Epidemiology
Pathogenesis and Spectrum of Disease
Laboratory Diagnosis
Specimen Collection and Transport
Specimen Processing
Direct Detection Methods
Stains
Direct Detection of (1-3)-Beta-D-Glucan
Nucleic Acid Detection
Serologic Testing
Cultivation
Approach to Identification
Treatment
Rare Atypical and Parafungal Agents
Lacazia loboi
Laboratory Diagnosis and Treatment
Pythium insidiosum
Laboratory Diagnosis and Treatment
Treatment
Lagenidium spp
Laboratory Diagnosis
Treatment
Rhinosporidium seeberi
Laboratory Diagnosis
Treatment
62 - The Yeasts and Yeastlike Organisms
General Characteristics
Epidemiology
Candida spp
Cryptococcus spp
Filobasidium sp., Hannaella sp., Naganishia spp., Papiliotrema spp., and Solicoccozyma sp
Geotrichum sp
Malassezia spp
Prototheca spp
Rhodotorula spp
Saccharomyces sp
Saprochaete spp
Sporobolomyces spp
Trichosporon spp., Apiotrichum spp., and Cutaneotrichosporon spp
Ustilago spp
Pathogenesis and Spectrum of Disease
Candida albicans Complex
Nonalbicans 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
Ustilago spp
Laboratory Diagnosis
Specimen Collection, Transport, and Processing
Stains
Candida spp
Cryptococcus spp
Malassezia spp
Trichosporon spp., Cutaneotrichosporon spp., and Apiotrichum sp
Other Organisms Resembling Yeasts (Geotrichum, Prototheca, and Ustilago spp.)
Antigen Detection
Nucleic Acid Detection
Cultivation
Candida spp
Cryptococcus spp
Trichosporon spp., Cutaneotrichosporon spp., and Apiotrichum sp
Malassezia spp
Approach to Identification
Candida spp
Germ Tube Test
Cryptococcus neoformans
Rapid Urease Test
Rapid Trehalose 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
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
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
VI - Virology
64 - Overview of the Methods and Strategies in Virology: Processing Blood for Viral Culture: Leukocyte Separation Using Polymorphprep
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
Bronchial and Bronchoalveolar Washes
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
Serum for Antibody Testing
Specimen Transport and Storage
Specimen Processing
General Principles
Processing Based on Requests for Specific Viruses
Arboviruses
Cytomegalovirus
Enteroviruses and Parechoviruses
Epstein-Barr Virus
Hepatitis Viruses
Herpes Simplex and Herpes B Virus
Human Immunodeficiency Virus and Other Retroviruses
Influenza A and B Viruses
Pediatric Respiratory Viruses
Gastroenteritis Viruses
TORCH
Varicella-Zoster Virus
Virus Detection Methods
Cytology and Histology
Immunodiagnostics (Antigen Detection)
Enzyme-Linked Virus-Inducible System
Nucleic Acid Based Methods
Cell Culture
Conventional Cell Culture
Shell Vial Cell Culture
Identification of Viruses Detected in Cell Culture
Matrix-Assisted Desorption Ionization Time-of-Flight Mass Spectrometry
Serologic Testing
General Principles
Immune Status Testing
Serology Panels
Preservation and Storage of Viruses
65 - Viruses in Human Disease
Viruses in Human Disease
Adenoviridae
Arenaviridae
Astroviridae
Caliciviridae
Coronaviridae
Filoviridae
Flaviviridae
Yellow Fever
Dengue
West Nile Virus
Zika Virus
Hepatitis C Virus
Hantaviridae
Hepadnaviridae
Hepeviridae
Herpesviridae
Herpesviruses
Varicella-Zoster Virus
Epstein-Barr Virus
Cytomegalovirus
Orthomyxoviridae
Papillomaviruses
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
Dye Uptake Assay
Enzyme Immunoassay
Neuraminidase Inhibition Assay
Recombinant Virus Assays
Genotypic Susceptibility Assays
Pyrosequencing
Next Generation Sequencing
Human Immunodeficiency Virus
Influenza
Prevention of Other Viral Infections
Vaccination
Immune Prophylaxis and Therapy
Eradication
VII - Diagnosis by Organ System
67 - Bloodstream Infections: Drawing Blood for Culture
General Considerations
Etiology
Bacteria
Fungi
Parasites
Viruses
Types of Bacteremia
Types of Bloodstream Infections
Intravascular Infections
Endocarditis
Mycotic Aneurysm and Suppurative Thrombophlebitis
. IV catheters are an integral part of the care for many hospitalized patients. For example, central venous catheters are used t...
Extravascular Infections
Clinical Manifestations
Immunocompromised Patients
Detection of Bacteremia
Specimen Collection
Preparation of the Site
Antisepsis
Precautions
Specimen Volume
Adults
Children
Number of Blood Cultures
Timing of Collection
Miscellaneous Matters
Anticoagulation
Dilution
Blood Culture Media
Types of Blood Culture Bottles
Culture Techniques
Conventional Blood Cultures
Incubation Conditions
Self-Contained Manual Culture Systems
Lysis Centrifugation
Instrument-Based Systems
BACTEC Systems
BacT/ALERT Microbial Detection System
Versa TREK System
Non–Culture Based Methods for the Identification of Bacteremia or Sepsis
Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry
Intravenous Catheter–Associated Infections
Handling Positive Direct Detection and Indirect Detection From Culture
Direct Rapid Tests from 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
Diseases of the Lower Respiratory Tract
Bronchitis
Acute
Chronic Versus Acute
Bronchiolitis
Pneumonia
Pathogenesis
Clinical Manifestations
Epidemiology and Etiologic Agents
Community-Acquired Pneumonia
. Community-acquired pneumonia in children is a common and potentially serious infection. Determining the cause of pneumonia is ...
. The most common etiologic agent of lower respiratory tract infection among adults younger than 30 years of age is M. pneumonia...
Adults (Viral Pneumonia)
Adults (Fungal Pneumonia)
Chronic Lower Respiratory Tract Infections
Immunocompromised Patients
. Patients with cancer are at high risk to become infected because of either granulocytopenia or other defects in phagocytic def...
. For successful organ transplantation, the recipient’s immune system must be suppressed. As a result, these patients are predis...
. Patients who are infected with human immunodeficiency virus (HIV) are at high risk for developing pneumonia. As discussed in t...
Pleural Infections
Laboratory Diagnosis of Lower Respiratory Tract Infections
Specimen Collection and Transport
Sputum
Expectorated
Induced
Endotracheal or Tracheostomy Suction Specimens
Bronchoscopy
Transtracheal Aspirates
Other Invasive Procedures
Specimen Processing
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
Laryngitis
Laryngotracheobronchitis
Epiglottitis
Pharyngitis, Tonsillitis, and Peritonsillar Abscesses
Pharyngitis and Tonsillitis
. Infection of the pharynx is associated with pharyngeal pain. Visualization of the pharynx reveals erythematous (red) and swoll...
. Pathogenic mechanisms differ and depend on the organism causing the pharyngitis. For example, some organisms directly invade t...
. Most cases of pharyngitis occur during the colder months (winter to early spring) and often accompany other infections, primar...
Peritonsillar Abscesses
Rhinitis
Miscellaneous Infections Caused by Other Agents
Corynebacterium diphtheriae
Bordetella pertussis
Klebsiella spp
Oral Cavity
Stomatitis
Thrush
Periodontal Infections
Etiologic Agents
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
Purulent Meningitis
. The outcome of a host-microbe interaction depends on the characteristics of both the host and the microorganism. As previously...
. Meningitis can be classified as either an acute or a chronic disease in the onset and overall progression within the host. It ...
. Classical symptoms of acute meningitis include fever, stiff neck, headache, nausea and vomiting, neurologic abnormalities, and...
. Chronic meningitis is common in patients who are immunocompromised, although this is not always the case. Patients experience ...
. The cause of acute meningitis depends on the age of the patient. Most cases in the United States occur in children younger tha...
Aseptic Meningitis
Encephalitis/Meningoencephalitis
Viral Encephalitis
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
Stained Smear of Sediment
Wet Preparation
India Ink Stain
Direct Detection of Etiologic Agents
Antigen
. Rapid antigen detection from CSF has been largely accomplished by the techniques of latex agglutination (Chapter 9). All comme...
. Reagents for the detection of the polysaccharide capsular antigen of Cryptococcus spp. are available commercially. CSF specime...
Nucleic Acid Detection
Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry
Culture
Bacteria and Fungi
Parasites and Viruses
Brain Abscess/Biopsies
. Whenever possible, biopsy specimens or aspirates from brain abscesses should be submitted to the laboratory under anaerobic co...
71 - Infections of the Eyes, Ears, and Sinuses
Eyes
Anatomy
Resident Microbiota
Diseases
Pathogenesis
Epidemiology and Etiology of Disease
Blepharitis and Hordeolum
Conjunctivitis
Keratitis
Endophthalmitis
Periocular
Uveitis
Other Infections
Laboratory Diagnosis
Specimen Collection and Transport
Direct Visual Examination
Nucleic Acid Testing Methods
Other Nonculture Methods
Culture
Ears
Anatomy
Resident Microbiota
Diseases, Epidemiology, and Etiology of Disease
Otitis Externa (External Ear Infections)
Otitis Media (Middle Ear Infections)
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
Urosepsis
Laboratory Diagnosis of Urinary Tract Infections
Specimen Collection
Clean-Catch Midstream Urine
Straight Catheterized Urine
Suprapubic Bladder Aspiration
Indwelling Catheter
Specimen Transport
Screening Procedures
Gram or Methylene Blue Stain
Pyuria
Indirect Indices
Nitrate Reductase (Griess) Test
Leukocyte Esterase Test
Catalase
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
Sexually Transmitted
Other Routes
Clinical Manifestations
Asymptomatic
Dysuria
Urethral Discharge
Lesions of the Skin and Mucous Membranes
Vaginitis
Cervicitis
Anorectal Lesions
Bartholinitis
Infections of the Reproductive Organs and Other Upper Genital Tract Infections
Females
Pelvic Inflammatory Disease
Infections After Gynecologic Surgery
Infections Associated With Pregnancy
Males
Gonorrhea
Syphilis
Laboratory Diagnosis of Genital Tract Infections
Lower Genital Tract Infections
Urethritis, Cervicitis, and Vaginitis
Specimen Collection
. Urethral discharge may occur in both males and females infected with pathogens, such as N. gonorrhoeae, N. meningitidis, and T...
. Organisms that cause purulent vaginal discharge (vaginitis) include T. vaginalis, gonococci, Candida spp. and, rarely, beta-he...
. Swabs collected for isolation of gonococci may be transported to the laboratory in modified Stuart’s or Amie’s charcoal transp...
Direct Microscopic Examination
Culture
Nonculture Methods
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
Primary Pathogenic Mechanisms
Toxins
Enterotoxins. Enterotoxins alter the metabolic activity of intestinal epithelial cells, resulting in an outpouring of electrolyt...
Cytotoxins. Cytotoxins, which constitute the second category of toxins, disrupt the structure of individual intestinal epithelia...
Neurotoxins. Food poisoning, or intoxication, may occur as a result of ingesting toxins produced by microorganisms. The microorg...
. An organism’s ability to cause disease can also depend on its ability to colonize and adhere to the bowel. To illustrate, ETEC...
. After initial and essential adherence to GI mucosal cells, some enteric pathogens can gain access to the intracellular environ...
Miscellaneous Virulence 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
Organisms for Routine Culture
Routine Culture Methods
. Maximum recovery of Salmonella and Shigella is obtained when inoculating an enrichment broth in addition to primary direct pla...
. Cultures for isolation of C. jejuni and Campylobacter coli should be inoculated to a combination of at least two selective aga...
. As previously indicated, enrichment broths are sometimes used for enhanced recovery of Salmonella, Shigella, Campylobacter, an...
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
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
Primary Peritonitis
Secondary and Tertiary Peritonitis
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
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
Antisera
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 Control
Incidence of Health Care–Associated Infections
Types of Health Care–Associated Infections
Catheter-Associated Urinary Tract Infections
Ventilator-Associated Pneumonia (VAP)
Surgical Site Infections
Central Line–Associated Bloodstream Infections
Emergence of Antibiotic-Resistant Microorganisms
Hospital Infection Control 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
Index
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
Q
R
S
T
U
V
W
X
Y
Z