Manual of Clinical Microbiology, 4 Volume Set E-Book
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- Herausgeber: John Wiley & Sons
- Kategorie: Fachliteratur
- Serie: ASM Books
- Sprache: Englisch
Revised by a collaborative, international, interdisciplinary team of editors and authors, this edition of the Manual of Clinical Microbiology includes the latest applications of genomics and proteomics and is filled with current findings regarding infectious agents, leading-edge diagnostic methods, laboratory practices, and safety guidelines. This edition also features four new chapters: Diagnostic Stewardship in Clinical Microbiology; Salmonella; Escherichia and Shigella; and Morganellaceae, Erwiniaceae, Hafniaceae, and Selected Enterobacterales. This seminal reference of microbiology continues to set the standard for state-of-the-science laboratory practice as the most authoritative reference in the field of microbiology.
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Veröffentlichungsjahr: 2024
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Table of Contents
Cover
Table of Contents
Title Page
Copyright
Editorial Board
Contributors
Preface
Author and Editor Conflicts of Interest
Volume 1
section I DIAGNOSTIC STRATEGIES AND GENERAL TOPICS
1 Introduction to the 13th Edition of the Manual of Clinical Microbiology
2 Laboratory Accreditation and Compliance
Accreditation
Compliance
Ldts And Fda Oversight
Emergency Use Authorization Of In Vitro Diagnostics
Summary
References
3 Diagnostic Stewardship in Clinical Microbiology
Concepts In Diagnostic Stewardship
Diagnostic Stewardship Of Specific Infectious Syndromes
Diagnostic Stewardship Of Specific Pathogen Groups
Specific Testing Topics In Diagnostic Stewardship
Establishing And Sustaining A Diagnostic Stewardship Program
References
4 Microscopy
Introduction
Ongoing Utility Of Microscopy In The Molecular Era
Limitations, Sensitivity, Specificity, And Variability
Properties Of Light
Microscope Components And Functions
Microscope Types And Applications
Specific Applications
Quality Assurance
Regulatory Requirements
Photomicroscopy
Microscope Maintenance
Ergonomics
Summary
Appendix
References
5 Laboratory Detection of Bacteremia and Fungemia
Clinical Significance
Limitations Of Current Methods For Detecting Microorganisms In Blood
Laboratory Detection: Culture-Based Methods
Specimen Collection
Blood Culture Systems
Interpretation Of Blood Culture Results
Rapid Identification Of Microbial Isolates
Pna-Fish
Maldi-Tof Ms
Direct Rapid Antimicrobial Susceptibility Testing From Blood Cultures
Laboratory Detection: Non-Culture-Based Methods
Evaluating Genotypic Phenotypic Discrepancies Of Rapid Molecular Identification Systems
Clinical Impact Of Rapid Identification And Ast From Blood Culture
Communication Of Results
Quality Audits And Benchmarks
Summary
References
6 Systems for Identification of Bacteria and Fungi
Organism Identification Systems
Phenotypic Identification Systems
Proteomic Identification Systems: Maldi-Tof Ms
Genotypic Identification Systems
Selection Of An Identification System
Verification Of Identification System Performance
Limitations Of Identification Systems
Future Perspectives On Identification Systems
References
7 Laboratory Automation in Clinical Microbiology
Laboratory Automation: Historical Perspective
Description Of Laboratory Automation Systems
Automated Specimen Processing
Wasp
Digital Imaging And Image Analysis
Criteria For Evaluation And Selection Of An Automation System
How To Implement Tla
Limitations Of Automation Systems
Future Perspectives
Summary
References
8 Molecular Techniques
Probe-Based Methods Without Amplification
Signal Amplification Methods
Target Amplification Methods, Pcr Based
Target Amplification Methods, Pcr Free
Highly Multiplex Molecular Detection
Nucleic Acid Amplification Assay Formats
Nucleic Acid Sequencing
Emerging Technology: Crispr-Cas
Molecular Quality Control/Quality Assurance
Reporting Of Results
Summary
References
9 Immunoassays for the Diagnosis of Infectious Diseases
Historical Perspective On Immunoassay Development
Basic Principles Of Immunology
General Concepts Of Immunoassays
Specific Immunoassays
Summary
References
10 Prevention of Health Care-Associated Infections
Health Care-Associated Infections
The Hospital Infection Prevention Program
Hai Surveillance
Role Of The Cml In Infection Prevention
Conclusion
References
11 Investigation of Disease Outbreaks
Introduction
Disease Surveillance
Outbreak Detection
Epidemiological Approaches To An Outbreak Investigation
The Role Of The Laboratory In Outbreaks
Select Examples Of Outbreak Scenarios: Collaboration Between Health Care Facilities And Clinical And Public Health Laboratories
Resources To Stay Informed And Connected In Global Outbreaks
Summary And Evaluation
References
12 Molecular Epidemiology
Subtyping Methods
Applications
Subtyping Method Selection, Validation, And Data Interpretation
Libraries For Molecular Epidemiology
Conclusions And Future Trends
References
13 Procedures for the Storage of Microorganisms
Overview Of Preservation Methods
Procedures For Specific Organisms
Storage Of Nucleic Acids
Storage Of Patient Specimens For Verification Studies
Disaster Preparedness
Future Directions
References
14 Prevention of Laboratory-Acquired Infections
Introduction
Risk Assessment And Mitigation Of Risk
Biosafety Management Program
Key Laboratory Safety Initiatives For The Prevention Of Laboratory-Acquired Infections
Pathogens Potentially Implicated In Laboratory-Acquired Infections
Investigation And Management Of Laboratory Exposures And Infections
References
15 Disinfection and Sterilization
Principles And Definitions
Hierarchy Of Resistance
Regulatory Oversight And Practical Use
The Importance Of Cleaning
Surface Disinfection
Sterilization
Resistance And Tolerance To Biocides
Implications For The Laboratory
Summary
References
16 Biothreat Agents
The Lrn
Federal Select Agent Program
Tier 1 Select Agents
Select Non-Tier 1 Agents
Evaluation, Interpretation And Reporting Of Results
References
17 The Human Microbiome
Overview Of The Microbiota
Factors That Influence The Microbiota
Analysis Of The Microbiota
The Microbiota In Health And Disease
Perspective
References
section II BACTERIOLOGY
GENERAL
18 Taxonomy of Bacteria and Archaea
Taxonomy, Clinical Microbiology, And Health Care Professionals
Taxonomic Ranks
Species, Type Species, And Type Strains
Uncultivated Organisms
Nomenclature
Classification, Characterization, And Identification
Phenotypic Methods
Chemotaxonomy
Genotypic Methods
Other Genotypic Methods For Bacterial Identification And Classification
The Winds Of Change In The Laboratory
The Changing Face Of Taxonomy: The Age Of The Genome And Bioinformatics
Future Perspectives
References
19 Specimen Collection, Transport, and Processing: Bacteriology
General Principles Of Specimen Collection And Transport
Handling Of Specimens In The Laboratory
Laboratory Safety Issues Regarding Bacterial Pathogens
Specific Specimen Collection And Processing Recommendations (Also See Table 7)
References
GRAM-POSITIVE COCCI
20 Approaches to the Identification of Aerobic Gram-Positive Cocci
References
21 Staphylococcus, Micrococcus, and Other Catalase-Positive Cocci
Taxonomy
Description Of The Families
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Examination
Isolation Procedures
Identification
Typing Systems
Serologic Tests
Antimicrobial Susceptibilities
Evaluation, Interpretation, And Reporting Of Results
References
22 Streptococcus
Taxonomy
Description Of The Genus
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Examination
Isolation Procedures
Identification
Typing Systems
Serologic Tests
Antimicrobial Susceptibilities
Evaluation, Interpretation, And Reporting Of Results
References
23 Enterococcus
Taxonomy
Description Of The Genus
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Examination
Isolation Procedures
Identification
Typing Systems
Serologic Tests
Antimicrobial Susceptibilities
Evaluation, Interpretation, And Reporting Of Results
References
24 Aerococcus, Abiotrophia, and Other Aerobic Catalase-Negative, Gram-Positive Cocci
Taxonomy
Description Of The Genera
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Examination
Isolation Procedures
Identification
Typing Systems
Serologic Tests
Antimicrobial Susceptibilities
Evaluation, Interpretation, And Reporting Of Results
References
GRAM-POSITIVE RODS
25 General Approaches to the Identification of Aerobic Gram-Positive Rods
References
26 Bacillus and Other Aerobic Endospore-Forming Bacteria
Taxonomy
Description Of The Genera
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Examination
Isolation Procedures
Identification
Typing Systems
Serologic Tests
Antimicrobial Susceptibilities
Evaluation, Interpretation, And Reporting Of Results
References
27 Listeria and Erysipelothrix
Introduction
Listeria
Erysipelothrix
Direct Examination
References
28 Coryneform Gram-Positive Rods
Taxonomy
Description Of Genera Within Families
Epidemiology And Transmission
Clinical Significance
Diphtheria Toxin-Producing Corynebacterium Spp.
Collection, Transport, And Storage Of Specimens
Direct Examination
Isolation Procedures
Identification
Identification: Descriptions Of Corynebacterium Species
Identification Of Other Non-Corynebacterium Coryneforms In Microbiology Laboratories
Typing Systems
Serologic Tests
Antimicrobial Susceptibilities
Evaluation, Interpretation, And Reporting Of Results
Appendix
Family Bifidobactericeae, Genus Gardnerella
Collection, Transport, And Storage Of Specimens
Direct Examination, Isolation, And Identification
References
29 Nocardia, Rhodococcus, Gordonia, Actinomadura, Streptomyces, and Other Aerobic Actinomycetes
Taxonomy
Description Of The Genera
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Examination
Isolation Procedures
Identification
Typing Systems
Serologic Tests
Antimicrobial Susceptibilities
Evaluation, Interpretation, And Reporting Of Results
References
30 Mycobacterium: General Characteristics, Laboratory Processing, Staining, Isolation, and Detection Procedures
Taxonomy And Description Of The Genus
Epidemiology And Transmission
Safety, Transport, And Collection Of Specimens
Isolation And Staining Procedures
Immunodiagnostic Tests For Tuberculosis
Cross-Contamination
Quality Assurance
Summary
Appendix
References
31 Mycobacterium tuberculosis Complex
Introduction
Taxonomy
Epidemiology And Transmission
Clinical Significance
Safe Handling, Collection, And Storage Of Specimens
Igras
Direct Testing From Specimens
Culture And Identification
Nucleic Acid Amplification Tests
Antimicrobial Susceptibililty Testing
Immunodiagnostic Tests
Typing Systems
Evaluation, Interpretation, And Reporting Of Results
References
32 Mycobacterium: Laboratory Characteristics of Slowly Growing Mycobacteria Other than Mycobacterium tuberculosis
Taxonomy
Epidemiology And Transmission
Clinical Significance
Direct Examination
Identification
Mass-Spectrometric Identification
Genotypic Identification
Other Molecular Tests For Ntm
Typing Systems
Antimicrobial Susceptibility Testing
Evaluation, Interpretation, And Reporting Of Results
References
33 Mycobacterium: Clinical and Laboratory Characteristics of Rapidly Growing Mycobacteria
Taxonomy And Description Of The Agents
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Examination
Isolation Procedures
Identification
Hplc Identification
Typing Systems
Serologic Tests
Antimicrobial Susceptibilities
Evaluation, Interpretation, And Reporting Of Results
References
Volume 2
section II BACTERIOLOGY
GRAM-NEGATIVE BACTERIA
34 Approaches to the Identification of Aerobic Gram-Negative Bacteria
Prokaryotic Nomenclature
Phenotypic Test Methods And Identification Schemes
Gram-Negative Bacteria With Poor Or No Growth On Sba
Matrix-Assisted Laser Desorption Ionization–Time Of Flight Mass Spectrometry
Bacterial Identification Using Ribosomal Rna Gene Sequences
Whole-Genome Sequences
Conclusions
References
35 Neisseria
Taxonomy
Description Of The Genus Neisseria
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Laboratory Safety Issues For Handling Of Meningococcal Cultures
Direct Examination
Isolation Procedures
Identification
Molecular Typing
Serologic Tests
Antimicrobial Susceptibilities
Evaluation, Interpretation, And Reporting Of Results
References
36 Aggregatibacter, Capnocytophaga, Eikenella, Kingella, Pasteurella, and Other Fastidious or Rarely Encountered Gram-Negative Rods
Taxonomy
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Examination
Isolation Procedures
Identification
Typing Systems And Serologic Tests
Antimicrobial Susceptibility
Evaluation, Interpretation, And Reporting Of Results
References
37 Haemophilus
Taxonomy And Description Of The Genus
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Examination
Isolation Procedures
Identification
Maldi-Tof Ms
Typing Systems
Serologic Tests
Antimicrobial Susceptibilities
Evaluation, Interpretation, And Reporting Of Results
References
38 Salmonella
Taxonomy
Description Of The Genus
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Examination
Isolation Procedures
Identification
Typing Systems
Antimicrobial Susceptibilities
Evaluation, Interpretation, And Reporting Of Results
References
39 Escherichia and Shigella
Escherichia
Shigella
Collection, Transport, And Storage Of Specimens
Stool Toxin Testing For Stec
Identification
Typing Systems
Antimicrobial Susceptibilities
Summary
References
40 Klebsiella, Enterobacter, Citrobacter, and Selected Other Enterobacteriaceae
Taxonomy
Description Of The Genera
Epidemiology, Transmission, And Clinical Significance
Collection, Transport, And Storage Of Specimens
Isolation Procedures
Identification
Typing Systems
Antimicrobial Susceptibility
Evaluation, Interpretation, And Reporting Of Results
References
41 Morganellaceae, Erwiniaceae, Hafniaceae, and Selected Enterobacterales
Epidemiology, Transmission, And Clinical Significance
Collection, Transport, And Storage Of Specimens
Isolation Procedures
Identification
Typing Systems
Antimicrobial Susceptibility
Evaluation, Interpretation, And Reporting Of Results
References
42 Yersiniaceae
Taxonomy
Description Of The Agent
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Examination
Isolation Procedures
Identification
Antimicrobial Susceptibilities
Evaluation, Interpretation, And Reporting Of Results
References
43 Aeromonas
Taxonomy
Description Of The Genus
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Examination
Isolation Procedures
Rapid Detection From Samples
Identification
Typing Systems
Serologic Tests
Antimicrobial Susceptibilities
Evaluation, Interpretation, And Reporting Of Results
References
44 Vibrio and Related Organisms
Taxonomy
Description Of The Vibrionaceae
Epidemiology, Transmission, And Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Examination
Isolation Procedures
Identification
Typing Systems
Serologic Tests
Antimicrobial Susceptibilities
Evaluation, Interpretation, And Reporting Of Results
References
45 Pseudomonas
Taxonomy
Description Of The Agent
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Examination
Isolation Procedures
Identification
Typing Systems
Serologic Tests
Antimicrobial Susceptibilities
Evaluation, Interpretation, And Reporting Of Results
References
46 Burkholderia, Stenotrophomonas, Ralstonia, Cupriavidus, Pandoraea, Brevundimonas, Comamonas, Delftia, and Acidovorax
Taxonomy
Description Of The Agents
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage
Direct Examination
Culture And Isolation
Identification
Typing Systems
Serologic Tests
Antimicrobial Susceptibilities
Evaluation, Interpretation, And Reporting Of Results
References
47 Acinetobacter, Chryseobacterium, Moraxella, Branhamella, and Other Nonfermentative Gram-Negative Rods
Taxonomy
Description Of The Agents
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Examination
Isolation Procedures
Identification
Identification Of The Five Genotypic Groups
Antimicrobial Susceptibilities
Evaluation, Interpretation, And Reporting Of Results
References
48 Bordetella and Related Genera
Taxonomy
Description Of The Genera
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Examination
Isolation Procedures
Identification
Typing Systems
Serologic Tests
Antimicrobial Susceptibilities
Evaluation, Interpretation, And Reporting Of Results
References
49 Francisella
Taxonomy
Description Of The Genus
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Examination
Isolation Procedures
Identification
Typing Systems
Serologic Tests
Antimicrobial Susceptibilities
Evaluation, Interpretation, And Reporting Of Results
References
50 Brucella
Taxonomy
Description Of The Genus
Antigenic Components
Virulence Factors, Pathogenic Mechanisms, And Immune Response
Epidemiology And Transmission
Clinical Categories Of Human Brucellosis
Complications
Collection, Handling, Storage, And Transport Of Specimens
Culture
Identification
Molecular Testing
Typing Systems
Serologic Tests
Antimicrobial Susceptibilities
Anti-Brucella Therapy
Prevention
Evaluation, Interpretation, And Reporting Of Results
References
51 Bartonella
Taxonomy, And Description Of The Genus
Epidemiology And Transmission
Public Health Implications Of Bartonella Infection In Dogs, Cats, Rodents, And Bats
Clinical Significance
Sample Collection, Transport, And Storage
Direct Examination
Nucleic Acid Amplification Tests
Serology
Isolation Procedures
Identification
Typing Systems
Antimicrobial Susceptibility And Susceptibility Testing
Choice And Use Of Antimicrobials
Evaluation, Interpretation, And Reporting
References
52 Legionella
Taxonomy
Description Of The Agent
Epidemiology, Transmission, And Pathogenesis
Clinical Significance
Collection, Storage, And Transport
Direct Examination
Identification From Bacterial Colonies
Typing Systems
Antibody Determination
Antimicrobial Susceptibilities And Susceptibility Testing
Evaluation, Interpretation, And Reporting Of Results
References
ANAEROBIC BACTERIA
53 Approaches to the Identification of Anaerobic Bacteria
Significance And Medical Importance Of Anaerobes
Specimen Collection And Transport
Isolation And Identification Of Anaerobic Bacteria
Antibiotic Resistance In Anaerobes: Trends And Detection
Conclusion
References
54 Peptostreptococcus, Finegoldia, Anaerococcus, Peptoniphilus, Parvimonas, Murdochiella, Veillonella, and Other Anaerobic Cocci
Taxonomy
Description Of The Group Of Organisms
Epidemiology
Clinical Significance
Collection, Transport, And Storage Of Clinical Specimens
Direct Examination
Isolation Procedures
Identification
Antimicrobial Susceptibilities
Evaluation, Interpretation, And Reporting Of Results
References
55 Anaerobic Non-Spore-Forming Gram-Positive Rods
Taxonomy And Description Of The Agents
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Examination
Isolation Procedures
Identification
Serologic Tests
Antimicrobial Susceptibilities
Evaluation, Interpretation, And Reporting Of Results
References
56 Clostridium, Clostridioides, and Other Clostridia
Taxonomy
Description Of The Genus
Epidemiology And Transmission
Clinical Significance
Clinical Microbiology Of Clostridial Diseases
Isolation Procedures
Identification Of Other Clostridial Species
Typing Systems
Serologic Tests
Antimicrobial Susceptibilities
Evaluation, Interpretation, And Reporting Of Results
References
57 Bacteroides, Porphyromonas, Prevotella, Fusobacterium, and Other Anaerobic Gram-Negative Rods
Taxonomy And Description Of The Group
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Examination
Isolation Procedures
Identification
Antimicrobial Susceptibilities
Evaluation, Interpretation, And Reporting Of Results
References
CURVED AND SPIRAL-SHAPED GRAM-NEGATIVE RODS
58 Algorithms for Identification of Curved and Spiral-Shaped Gram-Negative Rods
59 Campylobacter and Arcobacter
Taxonomy
Description Of The Agents
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Examination
Isolation Procedures
Identification
Typing Systems
Serologic Tests
Antimicrobial Susceptibilities
Evaluation, Interpretation, And Reporting Of Results
References
60 Helicobacter
Taxonomy
Description Of The Agents
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Examination
Isolation Procedures
Identification
Typing Systems
Serologic Tests
Antimicrobial Susceptibility
Evaluation, Interpretation, And Reporting Of Results
References
61 Leptospira
Taxonomy
Description Of The Family
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Examination
Isolation Procedures
Identification
Typing Systems
Serologic Tests
Antibiotic Susceptibilities
Evaluation, Interpretation, And Reporting Of Results
References
62 Borrelia
Taxonomy
Description Of The Genus
Species
Epidemiology And Transmission
Clinical Significance
Laboratory Diagnosis
Methods
Culture
Nucleic Acid Detection
Serology
Antimicrobial Susceptibility
Evaluation, Interpretation, And Reporting Of Lyme Borreliosis Test Results
References
63 Treponema and Brachyspira
Taxonomy
Description Of The Agents
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Detection
Isolation Procedures
Identification
Typing Systems
Whole-Genome Sequencing
Serologic Tests
Antimicrobial Susceptibilities
Evaluation And Interpretation Of Results
References
MYCOPLASMAS AND OBLIGATE INTRACELLULAR BACTERIA
64 General Approaches to Identification of Mycoplasma, Ureaplasma, and Obligately Intracellular Bacteria
65 Mycoplasma and Ureaplasma
Taxonomy
Description Of Mollicutes
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Examination
Isolation Procedures
Identification
Typing Systems
Serologic Tests
Antimicrobial Susceptibilities
Evaluation, Interpretation, And Reporting Of Results
References
66 Chlamydia
Taxonomy
Description Of Genera Of Medical Importance
Clinical Significance And Epidemiology
Collection, Transport, And Storage Of Specimens
Direct Examination
Isolation Procedures
Identification
Typing Systems
Serologic Tests
Antimicrobial Susceptibilities
Evaluation, Interpretation, And Reporting Of Results
References
67 Rickettsia and Orientia
Taxonomy
Description Of The Genera
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Detection
Immunologic Detection
Molecular Detection
Isolation Procedures
Identification Of Rickettsia And Orientia Isolates
Serologic Tests
Antimicrobial Susceptibilities
Interpretation And Reporting Of Results
References
68 Ehrlichia, Anaplasma, and Related Intracellular Bacteria
Taxonomy
Description Of The Genera
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Laboratory Diagnosis
Antimicrobial Susceptibilities, Treatment, And Prevention
Evaluation, Interpretation, And Reporting Of Results
References
69 Coxiella
Taxonomy
Description Of The Agent
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Examination
Isolation Procedures
Typing Systems
Serologic Tests
Antimicrobial Susceptibilities
Evaluation, Interpretation, And Reporting Of Results
Special Considerations
References
70 Tropheryma whipplei
Taxonomy
Description Of The Agent
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Examination
Isolation Procedures, Identification, And Typing Systems
Serologic Tests
Antimicrobial Susceptibilities
Evaluation, Interpretation, And Reporting Of Results
References
section III ANTIBACTERIAL AGENTS AND SUSCEPTIBILITY TEST METHODS
71 Antibacterial Agents
Penicillins
Cephalosporins
Other β-Lactam Antibiotics
β-Lactamase Inhibitors
Quinolones
Aminoglycosides And Aminocyclitols
Macrolides
Ketolides
Fidaxomicin
Lincosamides
Tetracyclines And Glycylcyclines
Glycopeptides And Lipopeptides
Streptogramins
Oxazolidinones
Sulfonamides And Trimethoprim
Polymyxins
Chloramphenicol
Metronidazole
Rifamycins
Nitrofurantoin
Fosfomycin
Mupirocin
Lefamulin
Appendix
References
72 Mechanisms of Resistance to Antibacterial Agents
Introduction
Resistance To Broad-Spectrum Agents
Resistance Specific To Gram-Positive Agents
Resistance In Gram-Negative Agents
Resistance To Antianaerobe Agents
Conclusion
References
73 Susceptibility Test Methods: General Considerations
Selecting An Antimicrobial Susceptibility Testing Method
Selecting Antibacterial Agents For Routine Testing
Establishing Susceptibility Breakpoints
Molecular Detection Of Resistance
Selected Use Of Confirmatory And Supplementary Tests
Reporting Of Results
Role Of The Laboratory In Antimicrobial Stewardship
Future Directions And Needs In Antimicrobial Susceptibility Testing
References
74 Antimicrobial Susceptibility Test Methods: Dilution and Disk Diffusion Methods
Dilution Methods
Disk Diffusion Testing
Common Sources Of Error In Antibacterial Susceptibility Testing
Specific Susceptibility Method Preferences
Differences In Breakpoints Internationally
The Future Of Antimicrobial Susceptibility Testing
References
75 Antimicrobial Susceptibility Testing Systems
Manual Gradient Diffusion Method
Semiautomated Instrumentation For Disk Diffusion Testing
Manual Broth Microdilution Systems
Semiautomated Broth Microdilution Systems
Automated Broth Microdilution Systems
Direct From Positive Blood Culture Ast
Investigational Ast Methodologies
Computerized Expert Systems
Critical Review Of Ast Results
Selecting An Ast System
Ast System Verification
Summary And Future Directions
References
76 Special Phenotypic Methods for Detecting Antibacterial Resistance
Introduction
Phenotypic Detection Of Resistance Among Gram-Positive Organisms
Phenotypic Detection Of Resistance Among Gram-Negative Organisms
Conclusion
References
77 Susceptibility Test Methods: Fastidious Bacteria
Streptococcus Pneumoniae
Streptococci Other Than Pneumococci
Haemophilus Influenzae
Neisseria Gonorrhoeae
Neisseria Meningitidis
Potential Bacterial Agents Of Bioterrorism
Abiotrophia Species And Granulicatella Species
Aerococcus
Aeromonas
Bacillus Species
Campylobacter
Corynebacterium Species And Coryneforms
Erysipelothrix Rhusiopathiae
Gemella
Hacek Group
Helicobacter Pylori
Lactobacillus, Pediococcus, And Leuconostoc Species
Listeria Monocytogenes
Micrococcus
Moraxella Catarrhalis
Pasteurella Species
Rothia Mucilaginosa
Vibrio Species
Conclusion
References
78 Susceptibility Test Methods: Anaerobic Bacteria
Susceptibility Testing Methods And Quality Control
Resistance Patterns In Anaerobic Bacteria
Strategies For Testing And Reporting Of Susceptibility Data
Conclusions
References
79 Susceptibility Test Methods: Mycobacteria, Nocardia, and Other Actinomycetes
Antimicrobial Agents
Antimicrobial Susceptibility Testing Of Mtbc
Phenotypic Ast Methods
Molecular Ast Methods
Nontuberculous Mycobacteria
M. Avium Complex
M. Kansasii
M. Marinum
Rapidly Growing Mycobacteria
Nocardia Species And Other Aerobic Actinomycetes
Updated Testing Recommendations From Clsi
References
80 Molecular Detection of Antibacterial Drug Resistance
Technology
Resistance Targets
Other Resistance Targets
Conclusions
References
Volume 3
section IV VIROLOGY
GENERAL
81 A Practical Guide to the Taxonomy, Classification, and Characterization of Clinically Important Viruses
Defining Taxonomy
Origins Of Viruses
Classifying Viruses On The Basis Of Genetic Codes And Genomes
A Shift To Whole-Genome Characterization Of Viruses
The Baltimore And Less Used Approaches To Viral Classification
The International Committee On Taxonomy Of Viruses
The Ictv Definition Of A Viral Species
Recent Changes In Viral Taxonomy To The Level Of Species
Viral Classification Below The Level Of Species
World Health Organization Guidance On Classifying Human Infectious Diseases
Classifying Viruses And Viral Diseases Using The Icd System
Specific Changes In Approaches To Viral Taxonomy
Conclusion
References
82 Specimen Collection, Transport, and Processing: Virology
Specimen Selection
Specimen Collection
Transport Medium
Transport Conditions
Specimen Storage And Processing
Collection Methods And Processing Of Selected Specimens
Transportation Regulations
Summary
References
83 Reagents, Stains, Media, and Cell Cultures: Virology
Reagents
Virology Stains
Cell Cultures
Cell Culture Media
Qc In The Diagnostic Virology Laboratory
Appendix
References
84 Algorithms for Detection and Identification of Viruses
Introduction
Advances In Diagnostics
Impact Of Covid-19, Current Challenges, And Future Perspectives
RNA VIRUSES
85 Human Immunodeficiency Viruses
Taxonomy
Description Of The Agents
Epidemiology And Transmission
Clinical Significance
Collection, Storage, And Transport Of Specimens
Direct Detection
Hiv Rna And Dna Qualitative Assays
Hiv Rna Viral Load Assays
Isolation Procedures
Serologic Tests
Antiviral Susceptibilies
Evaluation, Interpretation, And Reporting Of Results
References
86 Human T-Cell Lymphotropic Viruses
Taxonomy
Description Of The Agent
Epidemiology And Transmission
Clinical Significance
Collection And Storage Of Specimens
Direct Examination
Virus Isolation And Identification
Typing Systems And Serologic Tests
Evaluation, Interpretation, And Reporting Of Results
References
87 Influenza Viruses
Taxonomy
Description Of The Agents
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Detection
Isolation Procedures
Identification And Typing Systems
Serologic Tests
Antiviral Susceptibilities
Evaluation, Interpretation, And Reporting Of Results
References
88 Parainfluenza and Mumps Viruses
Taxonomy
Description Of The Agents
Parainfluenza Viruses
Mumps Virus
Isolation And Identification
References
89 Respiratory Syncytial Virus and Human Metapneumovirus
Respiratory Syncytial Virus
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Examination
Isolation Procedures
Identification
Typing Systems
Serologic Tests
Antiviral Susceptibilities
Evaluation, Interpretation, And Reporting Of Results
Human Metapneumovirus
References
90 Measles and Rubella Viruses
Measles Virus
Rubella Virus
References
91 Enteroviruses and Parechoviruses
Taxonomy
Description Of The Agents
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Examination
Isolation Procedures
Identification
Typing Systems
Serologic Testing
Antiviral Susceptibilities
Evaluation, Interpretation, And Reporting Of Results
References
92 Rhinoviruses
Taxonomy
Description Of The Agent
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Detection
Isolation Procedures
Identification
Typing Systems
Serologic Tests
Antiviral Susceptibilities
Evaluation, Interpretation, And Reporting Of Results
References
93 Coronaviruses
Taxonomy
Description Of The Agent
Epidemiology And Transmission
Clinical Significance
Prevention
Collection, Transport, And Storage Of Specimens
Direct Detection
Isolation Procedures
Serological Tests
Evaluation, Interpretation, And Reporting Of Results
References
94 Hepatitis A and E Viruses
Taxonomy
Description Of The Agents
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Examination
Isolation Procedures
Identification And Typing Systems
Serologic Tests
Evaluation, Interpretation, And Reporting Of Results
References
95 Hepatitis C Virus
Taxonomy
Description Of The Agent
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Detection
Isolation Procedures And Identification
Genotyping
Antiviral Susceptibility
Evaluation, Interpretation, And Reporting Of Results
References
96 Gastroenteritis Viruses
Taxonomy
Description Of The Agents
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Detection
Isolation Procedures
Serological Tests
Evaluation, Interpretation, And Reporting Of Results
References
97 Rabies Lyssavirus
Taxonomy
Description Of The Agent
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Detection Methods
Isolation Procedures
Identification
Typing Systems
Serologic Tests
Antiviral Susceptibilities
Evaluation, Interpretation, And Reporting Of Results
References
98 Arboviruses
Taxonomy
Description Of The Agent
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Detection
Rt-Pcr
Rt-Lamp
Isolation Procedures
Identification
Serological Tests
Evaluation, Interpretation, And Reporting Of Results
References
99 Hantaviruses
Taxonomy
Description Of The Agents
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Examination
Identification
Evaluation, Interpretation, And Reporting Of Results
References
100 Arenaviruses and Filoviruses
Taxonomy And Description Of The Agents
Filoviridae
Epidemiology And Transmission
Filoviridae
Clinical Significance
Arenaviridae
Filoviridae
Collection, Transport, And Storage Of Specimens
Direct Examination
Isolation Procedures
Identification Of Virus
Serologic Diagnosis
Vaccines, Therapies, And Antiviral Susceptibilities
Evaluation And Interpretation Of Results
References
DNA VIRUSES
101 Herpes Simplex Viruses and Herpes B Virus
Taxonomy
Description Of The Agent
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Detection
Isolation Procedures
Identification And Typing
Serologic Tests
Antiviral Susceptibilities
Evaluation, Interpretation, And Reporting Of Results
Herpes B Virus
Clinical Significance
References
102 Varicella-Zoster Virus
Taxonomy
Description Of The Agent
Epidemiology And Transmission
Clinical Significance
Diagnosis Overview
Therapy Overview
Collection, Transport, And Storage Of Specimens
Direct Examination
Isolation And Identification
Serologic Tests
Antiviral Therapy And Susceptibility
Evaluation, Interpretation, And Reporting Of Results
References
103 Human Cytomegalovirus
Taxonomy
Description Of The Agent
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Examination
Histopathologic Testing
Isolation Procedures
Serologic Tests
Immunofluorescence Assays
Igm Antibody Measurements
Antiviral Susceptibility Testing
Evaluation, Interpretation, And Reporting Of Results
References
104 Epstein-Barr Virus
Taxonomy
Description Of The Agent
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Examination
Ebv Antigen Detection By Immunohistochemistry And Eber Detection By In Situ Hybridization
Isolation, Identification, And Typing Procedures
Serologic Tests And T-Cell Diagnostics
Ebv-Specific Antibodies
Evaluation, Interpretation, And Reporting Of Results
References
105 Human Herpesviruses 6A, 6B, and 7
Human Herpesvirus 6
Human Herpesvirus 7
Clinical Significance
References
106 Human Herpesvirus 8
Taxonomy
Description Of The Agent
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Examination
Isolation Procedures
Identification And Typing Systems
Serologic Tests
Antiviral Treatment
Evaluation, Interpretation, And Reporting Of Results
References
107 Adenoviruses
Taxonomy
Description Of The Agent
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Detection
Nucleic Acid Detection
Isolation Procedures
Identification
Typing Systems
Serologic Tests
Evaluation, Interpretation, And Reporting Of Results
References
108 Human Papillomaviruses
Taxonomy
Description Of The Group Of Organisms
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Examination/Microscopy
Antigen Detection
Nucleic Acid Detection
Typing
Isolation Procedures
Serologic Tests
Evaluation, Interpretation, And Reporting Of Results
References
109 Human Polyomaviruses
Taxonomy
Epidemiology Of Human Polyomaviruses
Description Of The Agents And Diagnostic Implications
Clinical Significance
Collection, Transport, And Storage Of Specimens
Virus Detection
Evaluation, Interpretation, And Reporting Of Results
References
110 Parvovirus B19V, Bocaviruses, and Other Human Parvoviruses
Taxonomy
Parvovirus B19
Human Bocaviruses
Human Parvovirus 4
Human Bufavirus, Tusavirus, And Cutavirus
References
111 Poxviruses
Taxonomy
Description Of The Agents
Epidemiology And Transmission
Clinical Significance
Collection, Handling, And Storage Of Specimens
Direct Detection
Isolation And Identification
Serologic Tests
Evaluation, Interpretation, And Reporting Of Results
References
112 Hepatitis B and D Viruses
Hepatitis B Virus
Hepatitis D Virus
References
SUBVIRAL AGENTS
113 Prion Diseases
Taxonomy
Description Of The Agent
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Identification
Evaluation, Interpretation, And Reporting Of Results
References
section V ANTIVIRAL AGENTS AND SUSCEPTIBILITY TEST METHODS
114 Antiviral Agents
Agents Against Hiv-1 And Hiv-2
Agents Against Hepatitis C Virus
Agents Against Hepatitis B Virus
Agents Against Herpesviruses
Agents Against Influenza Viruses
Agents Against Sars-Cov-2 Virus
Anti-Sars-Cov-2 Monoclonal Antibodies
Covid-19 Convalescent Plasma (Ccp)
References
115 Mechanisms of Resistance to Antiviral Agents
Herpes Viruses
Human Immunodeficiency Virus
Hepatitis B Virus
Hepatitis C Virus
Ni And Nni Rdrp Inhibitor Resistance
Ns5A Inhibitors
Influenza Virus
References
116 Susceptibility Test Methods: Viruses
Antiviral Resistance And Causes Of Drug Failure
Clinical Indications For Antiviral Susceptibility Testing
Testing Methods: Phenotypic Assays
Genotypic Assays
Applications For Genotypic Antiviral Resistance Testing
Interpretation Of Genotypic Antiviral Resistance Testing
Future Directions And Emerging Technologies
References
Volume 4
section VI MYCOLOGY
GENERAL
117 Taxonomy, Classification, and Nomenclature of Fungi
Morphological Characteristics Of The Fungi
Nomenclature Of Fungi
Taxonomy And Classification Of The Fungi
Identification Of Yeasts
Classification And Identification Of Anamorphic Molds
Identification Of Molds
Polyphasic Identification
Common Mycological Terms
References
118 Specimen Collection, Transport, and Processing: Mycology
Specimen Collection And Transport
Specimen Handling, Pretreatment, And Safety
Specimen Processing And Culture Guidelines
References
119 Reagents, Stains, and Media: Mycology
Reagents
Stains
Media
Appendix
References
120 General Approaches for Direct and Indirect Detection and Identification of Fungi
Direct Microscopic Examination
Detection Of Antibodies Targeting Fungal Pathogens
Fungal Antigen Detection
(1,3)-β-D-Glucan Detection
Fungal-Specific Metabolite Detection
Nucleic Acid Detection
References
FUNGI
121 Candida, Cryptococcus, and Other Yeasts of Medical Importance
Taxonomy And Nomenclature
Description Of The Agents
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Examination
Isolation Procedures
Identification
Organisms Resembling Yeasts
Typing Systems
Serologic Tests
Antimicrobial Susceptibilities
Evaluation, Interpretation, And Reporting Of Results
References
122 Pneumocystis jirovecii
Taxonomy
Description Of The Agent
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Examination And Identification
Isolation Procedures
Typing Systems
Serologic Tests
Antimicrobial Susceptibilities
Evaluation, Interpretation, And Reporting Of Results
References
123 Aspergillus, Talaromyces, and Penicillium
Aspergillus Species
Talaromyces And Penicillium Species
References
124 Fusarium and Other Opportunistic Hyaline Fungi
Taxonomy And Identification
Clinical Significance
Collection, Transport, And Storage Of Specimens
Fusarium Species
Other Opportunistic Hyaline Molds
References
125 Agents of Systemic and Subcutaneous Mucormycosis and Entomophthoromycosis
Taxonomy
Mucormycosis
Entomophthoromycosis
References
126 Histoplasma, Blastomyces, Coccidioides, Paracoccidioides and Other Dimorphic Fungi Causing Systemic Mycoses
Description Of The Agents
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Examination
Isolation Procedures
Identification
Typing Systems
Serologic Tests
Antimicrobial Susceptibilities
Evaluation, Interpretation, And Reporting Of Results
References
127 The Dermatophytes and Their Relatives (Trichophyton, Microsporum, Epidermophyton, Arthroderma, Nannizzia, Paraphyton, and Lophophyton) and Other Agents of Superficial Mycoses
Taxonomy
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Laboratory Testing Of Specimens
Identification
Physiological Tests
Description Of Etiologic Agents
Strain Typing Systems
Antimicrobial Susceptibilities
Evaluation, Interpretation, And Reporting Of Laboratory Results
Superficial Mycoses
References
128 Curvularia, Exophiala, Scedosporium, Sporothrix, and Other Melanized Fungi
Taxonomy And Description Of The Agents
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Examination
Isolation Procedures
Identification
Typing Systems
Serologic Tests
Antifungal Susceptibilities
Evaluation, Interpretation, And Reporting Of Results
References
129 Fungi Causing Eumycotic Mycetoma
Taxonomy And Description Of The Agents
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Examination
Isolation Procedures
Identification
Maldi-Tof Ms
Typing Systems
Serologic Tests
Antimicrobial Susceptibilities
Evaluation, Interpretation, And Reporting Of Results
References
130 Mycotoxins
Chemical Classification And Biosynthesis Of Mycotoxins
Food Safety
Bioterrorism
Sick Building Syndrome
Conclusions
References
131 Lagenidium, Paralagenidium, Pythium, Rhinosporidium, and Uncultivated Paracoccidioides Species (Formerly Lacazia loboi)
Uncultivated Paracoccidioides Species (Formerly Lacazia Loboi)
Direct Examination
Pythium Insidiosum
Lagenidium And Paralagenidium Species
Rhinosporidium Seeberi
References
132 Microsporidia
Taxonomy
Description Of The Genera And Species
Epidemiology And Transmission
Clinical Significance
Collection, Transport, And Storage Of Specimens
Detection Procedures
Isolation Of Microsporidia
Identification
Serologic Tests
Antimicrobial Susceptibility
Evaluation, Interpretation, And Reporting Of Results
References
section VII ANTIFUNGAL AGENTS AND SUSCEPTIBILITY TEST METHODS
133 Antifungal Agents
Allylamines
Azoles
Echinocandins
Polyenes
Other Miscellaneous Agents
Novel Antifungal Agents In Development
Conclusion
References
134 Mechanisms of Resistance to Antifungal Agents
Defining Clinical And Microbiological Resistance
Resistance To Azoles
Mechanisms Of Azole Resistance
Mechanisms Of Echinocandin And Enfumafungin Resistance
Mechanisms Of Polyene Resistance
Mechanisms Of Flucytosine Resistance
Microbial Drivers Of Resistance: Drug Adaptation, Tolerance, And Escape
Summary And Perspective
References
135 Susceptibility Test Methods: Yeasts and Filamentous Fungi
Antifungal Susceptibility Testing
Standardized Broth Dilution Methods For Yeasts
Yeast Genera Other Than Candida
Special Considerations
Clsi And Eucast Clinical Breakpoints And Epidemiological Cutoff Values For Candida Spp.
Alternative Approaches For Yeasts
Standardized Broth Dilution Methods For Molds
Summary And Conclusions
References
section VIII PARASITOLOGY
GENERAL
136 Taxonomy and Classification of Human Eukaryotic Parasites
Modern Classification Of Eukaryotes
Classification Of Parasitic Protists
Classification Of Parasitic Helminths And Arthropods
References
137 Specimen Collection, Transport, and Processing: Parasitology
Specimen Collection And Transport
Direct Detection By Routine Methods
Appendix
Parasite Image Libraries And Parasitological Resources
References
138 Reagents, Stains, and Media: Parasitology
Reagents
Stains
Media
Acknowledgements
References
139 General Approaches for Detection and Identification of Parasites
Stool Specimens
Additional Techniques for stool examination
Examination Of Other Specimens From The Intestinal Tract
Specimens from other Body Sites
References
PARASITES
140 Plasmodium and Babesia
Taxonomy
Plasmodium
Babesia
References
141 Leishmania and Trypanosoma
Leishmania Spp. And Leishmaniasis
Trypanosoma And Trypanosomiasis
African Trypanosomiasis
Other Trypanosomes Infecting Humans
References
142 Toxoplasma
Introduction
Taxonomy And Life Cycle
Epidemiology And Transmission
Clinical Significance
Diagnostic Methods
Clinical Use And Interpretation Of Diagnostic Tests
Treatment And Chemoprophylaxis
Acknowledgments
References
143 Pathogenic and Opportunistic Free-Living Amebae
Taxonomy
Description Of The Agents
Epidemiology
Clinical Significance
Collection, Handling, And Storage Of Specimens
Clinical And Laboratory Diagnosis
Treatment
Evaluation, Interpretation, And Reporting Of Results
References
144 Intestinal and Urogenital Amebae, Flagellates, and Ciliates
Amebae
Nonpathogenic Amebae
Blastocystis Species
Flagellates
Nonpathogenic Flagellates
Ciliates
Summary
References
145 Cystoisospora, Cyclospora, and Sarcocystis
Taxonomy
Description Of The Pathogens
Epidemiology, Transmission, And Prevention
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Examination
Serologic Tests
Genotyping
Treatment
Evaluation, Interpretation, And Reporting Of Results
References
146 Cryptosporidium
Taxonomy
Description Of Agent
Epidemiology, Transmission, And Prevention
Clinical Significance
Collection, Transport, And Storage Of Specimens
Direct Examination
Typing Systems
Isolation Procedures
Treatment And Prevention
Evaluation, Interpretation, And Reporting Of Results
References
147 Nematodes
Collection, Transport, And Storage Of Specimens
Laboratory Methods
Ascaris Lumbricoides (Roundworm)
Enterobius Vermicularis (Pinworm Or Threadworm)
Hookworms
Strongyloides Stercoralis
Strongyloides Fuelleborni Fuelleborni And Strongyloides Fuelleborni Kellyi
Trichuris Trichiura (Whipworm)
Evaluation, Interpretation, And Reporting Of Results
References
148 Filarial Nematodes
Lymphatic Filarial Parasites
Onchocerca Volvulus
Loa Loa
Mansonella Species
References
149 Cestodes
Dibothriocephalus/Diphyllobothrium/Adenocephalus
Taenia Saginata
Taenia Solium
Hymenolepis Nana
Larval Cestodes Infecting The Human Host
References
150 Trematodes
Collection, Transport, And Storage
Digeneans Of The Circulatory System: Schistosomes
Foodborne Digeneans
Acknowledgement
References
151 Less Common Helminths
Collection, Transport, And Storage Of Specimens
Less Common Nematodes
Less Common Cestodes
Summary
References
152 Arthropods of Medical Importance
Arthropods As Vectors
Arthropods As Intermediate Hosts For Parasites Via Ingestion
Endoparasitic And Ectoparasitic Arthropods
Direct Injury Due To Arthropods
Other Injury
Identifying Submitted Specimens
References
section IX ANTIPARASITIC AGENTS AND SUSCEPTIBILITY TEST METHODS
153 Antiparasitic Agents
Anthelmintic Agents
An Agent With Anthelmintic And Antiprotozoal Activities: Nitazoxanide
Antimalarials
Other Antiprotozoal Agents
Appendix National And Regional Medicine Regulatory Authorities
References
154 Mechanisms of Resistance to Antiparasitic Agents
Malaria
Trichomoniasis
Leishmaniasis
Schistosomiasis
Soil-Transmitted Helminthiases
Future Perspectives
References
155 Susceptibility Test Methods: Parasites
Malaria
Trichomoniasis
Leishmaniasis
African Trypanosomiasis
Schistosomiasis
Future Perspectives
References
Author Index
Subject Index
End User License Agreement
Guide
Cover
Table of Contents
Title Page
Copyright
Editorial Board
Contributors
Preface
Author and Editor Conflicts of Interest
Begin Reading
Author Index
Subject Index
End User License Agreement
List of Illustrations
2 Laboratory Accreditation and Compliance
FIGURE 1 Number of U.S. laboratories by CLIA certificate type, as of July 2019. PPMP, provider-performed micros-copy procedures. Source: CMS CLIA Data Base, Division of Clinical Laboratory Improvement and Quality Centers for Medicare and Medicaid Services, March 2020, cms.gov
FIGURE 2 Number of laboratories with CLIA certificates of accreditation, by accreditation organization, as of July 2019. CAP, College of American Pathologists; AAHHS/HFAP, Accreditation Association for Hospitals and Health Systems/Healthcare Facilities Accreditation Program; ASHI, American Society for Histocompatibility and Immunogenetics; A2LA, American Association for Laboratory Accreditation. Source: CMS CLIA Data Base, Division of Clinical Laboratory Improvement and Quality Centers for Medicare and Medicaid Services, March 2020, cms.gov
FIGURE 3 The plan-do-check-act (PDCA) cycle. Reproduced with permission from Richard Zarbo.
3 Diagnostic Stewardship in Clinical Microbiology
FIGURE 1 Diagnostic algorithms for (A) respiratory viruses and (B) diarrhea. Example of diagnostic stewardship algorithms for diagnosis of patients with an influenza-like illness and infectious diarrhea (courtesy Mayo Clinic).
4 Microscopy
FIGURE 1 Basic upright light microscope with labeled components. Courtesy of Nikon Instruments, Inc.
FIGURE 2 Example of a microscope optical train, including a fluorescence module. Courtesy of Olympus Microscopy Resource Center.
FIGURE 3 Objective lens labeling. Objective lenses are labeled with information about the manufacturer, correction factors, numerical aperture, tube length, coverslip thickness, working distance, and expected immersion medium. Objectives without a listed aberration correction are considered achromats. Objectives without a listed immersion medium (Oil, Oel, W, Gly) are considered dry objectives and are intended for use with air between the lens and the specimen.
FIGURE 4 Gram stain review policy. Abbreviations: BAL, bronchoalveolar lavage; QA, quality assurance; QI, quality improvement.
5 Laboratory Detection of Bacteremia and Fungemia*
FIGURE 1 Bottles from the BacT/Alert system (left to right: PF Plus, FN Plus, and FA Plus).
FIGURE 2 Bottles from the BACTEC system (Lytic/10 Anaerobic/F [left] and Plus Aerobic/F [right]).
FIGURE 3 BD Bactec Myco/F lytic culture vial.
FIGURE 4 Bottles from the VersaTREK system (aerobic Redox 1 [left] and anaerobic Redox 2 [right]).
FIGURE 5 Thermo Scientific VersaTREK Myco bottle. The cellulose sponge (yellow), used as a growth matrix in the bottle, can be seen.
6 Systems for Identification of Bacteria and Fungi*
FIGURE 1 MALDI-TOF MS workflow (from reference 163). A colony from an acceptable culture plate is picked and smeared evenly as a thin film on a spot on the target plate. The target plate can be a reusable or a disposable plate or slide, depending on the system. Formic acid is applied to the target as applicable and allowed to dry. This is followed by the addition of matrix. Once dried, the target plate is placed into the mass spectrometer, where a mass spectrum is generated and compared against the system’s database. Results are displayed as an identification (
Candida parapsilosis
in position A4 in the example).
FIGURE 2 MALDI-TOF MS (from reference 163). The target plate is placed in the mass spectrometer. Spots to be analyzed are shot by a laser, desorbing microbial and matrix molecules from the target plate. Charge is transferred from the matrix to microbial molecules, and the ionized molecules are funneled through a positively charged electrostatic field into the mass analyzer, a tube under vacuum. The ions travel toward an ion detector, with the smallest analytes traveling fastest, followed by progressively larger analytes. As ions emerge from the mass analyzer, they run into the ion detector, thereby generating a mass spectrum representing the number of ions hitting the detector over time. Although separation is by mass-to-charge ratio, since the charge is typically single for the described application, separation is by molecular weight.
7 Laboratory Automation in Clinical Microbiology
FIGURE 1 BD Kiestra TLA unit consisting of the InoqulA+ front-end processor, six work stations attached to the ProceedA tract system, and four ReadA compact incubators with internal agar plate imaging. Courtesy and © Beckton, Dickinson, and Company. Reprinted with permission.
FIGURE 2 Installed BD Kiestra TLA unit with one InoqulA processor, five ReadA compact incubators, and seven workbenches, installed at Bioscientia Labor Ingelheim, Ingelheim, Germany. Courtesy and © Beckton, Dickinson, and Company. Reprinted with permission.
FIGURE 3 BD Kiestra stand-alone InoqulA+ front-end processor. Courtesy and © Beckton, Dickinson, and Company. Reprinted with permission.
FIGURE 4 BD Kiestra work cell automation (WCA) consisting of an InoqulA+ front-end processor and two ReadA compact incubators with internal imaging. Courtesy and © Beckton, Dickinson, and Company. Reprinted with permission.
FIGURE 5 BD Kiestra ReadA compact stand-alone instrument for agar plate incubation and imaging. Courtesy and © Beckton, Dickinson, and Company. Reprinted with permission.
FIGURE 6 BD Kiestra TLA containing the IdentifA and SusceptA modules, which allow automated MALDI-TOF MS organism identification and antimicrobial susceptibility testing in conjunction with the BD Phoenix M50 system. Courtesy and © Beckton, Dickinson, and Company. Reprinted with permission.
FIGURE 7 WASPLab (Copan), including WASP (depth, 79.0 cm; width, 194.9 cm; weight, 720 to 740 kg), double incubator (depth, 83.0 cm; width, 173.8 cm; weight, 875 kg), and imaging system (depth, 121.3 cm; width, 37.5 cm; weight, 300 kg). Image courtesy of COPAN Diagnostics, Inc.
FIGURE 8 WASP Colibri (depth, 79.0 cm; width, 193.0 cm; weight, 780 kg). Image courtesy of COPAN Diagnostics, Inc.
FIGURE 9 Installed WASPLab with 2 WASP, 2 double incubators, and 10 work benches, installed at Stichting PAMM Laboratorium Medische Microbiologie, Veldhoven, The Netherlands. Image courtesy of COPAN Diagnostics, Inc.
FIGURE 10 APAS Independence Clever Culture system (Clever Culture Systems, Freienbach, Switzerland). Photo courtesy of Thermo Fisher Scientific.
FIGURE 11 InoqulA+ inoculated agar plate (chromogenic medium; CHROMagar orientation). Courtesy and © Beckton, Dickinson, and Company. Reprinted with permission.
FIGURE 12 WASP-inoculated MacConkey agar plate (
E. coli
).
8 Molecular Techniques
FIGURE 1 Probe-based methods without amplification can be utilized only in situations in which targets are biologically amplified
in vivo
(i.e., high organism burden or rRNA target) or
ex vivo
(i.e., cultured isolate).
FIGURE 2 BD Affirm VPIII assay. Following a cell lysis step, a patient sample initially reacts with beads coated by the target-specific capture probes. The specimen is then transferred to a separate reagent well, where the color development probes are added. A washing step is critical to clear the beads of any unbound target or probe. Finally, an enzyme conjugate solution (horseradish peroxidase [HRP]) followed by an indicator solution with a chemical substrate is added, which reacts with the color development probe if present, producing a colorimetric change. The BD Affirm VPIII assay is designed to have three parallel reactions that detect
Gardnerella vaginalis
,
Trichomonas vaginalis
, and
Candida
species.
FIGURE 3 (Top) Hybrid protection. Single-stranded DNA probes bound to acridine esters (AE) are first hybridized with complementary single-stranded RNA targets. The resultant hybrids protect the acridine esters from hydrolysis (during the selection process), which can be measured in a light-generating reaction. (Bottom) Hybrid capture. A similar technique, hybridization capture, utilizes RNA oligonucleotides to bind to complementary single-stranded DNA targets. The resultant duplexes are detected by antibodies that specifically bind to RNA-DNA hybrids. These antibodies are conjugated to alkaline phosphatase, which generates signal upon addition of substrate.
FIGURE 4 Branched DNA (bDNA). Target nucleic acid is first immobilized on a solid surface utilizing a sequence-specific capture extender probe. A secondary label extender probe subsequently binds in a target sequence-dependent manner. Following a washing step, a preamplifier probe designed to be homologous to the label extender probe is added. This structure in turn binds amplifier probes and alkaline phosphatase enzyme-labeled probes sequentially, allowing positivity to be determined through the addition of a developer solution.
FIGURE 5 Invader. Invader uses a series of target-specific probes that, when bound, overlap. The overlapping region is cleaved by a specialized cleavase enzyme, and the cleaved product is detected using a probe-specific fluorescence resonance energy transfer (FRET) oligonucleotide.
FIGURE 6 T2 Magnetic Resonance (T2MR). Following specimen lysis, target DNA cross-links paramagnetic particles. The change in T2, measured by clustered particles, is proportional to the quantity of target DNA.
FIGURE 7 DNA polymerase function. (A) The minimum requirements for DNA synthesis by PCR-mediated amplification include a DNA template, DNA polymerase, annealed primers, magnesium (Mg
2+
) as a cofactor, and supplied dNTPs. (B) Addition of complementary dNTPs extends the newly synthesized DNA strand. (C) If primers do not fully anneal to the target DNA, extension cannot proceed, thus allowing specificity during synthesis.
FIGURE 8 PCR. (A) The PCR process consists of serial temperature shifts, or cycles, that allow primer annealing, polymerase extension, and denaturation. Target DNA is initially denatured at temperatures exceeding 90°C, effectively dissociating all PCR components, including primers and enzymes. The subsequent annealing step decreases the temperature so that primers can specifically bind to complementary regions of the target DNA. Primers of 15 to 30 bases are annealed to target regions below the primer
Tm
, typically 50 to 65°C, based on nucleotide complementarity. DNA polymerase then binds this double-stranded complex and catalyzes phosphodiester bond formation between the 5′ phosphate groups of incoming nucleotides and the 3′ hydroxyl groups at the terminal ends of the primers (or newly incorporated nucleotides). This DNA synthesis reaction is typically performed at 68 to 72°C and results in the extension of primer-initiated DNA strands in the 5′ to 3′ direction. The polymerase will either dissociate once the 3′ end of the template strand is reached or continue synthesis if amplifying the original (native) DNA molecule. Following a temperature increase to >90°C, the primers, polymerase, and DNA strands dissociate. This completes one cycle of PCR, and both the original and newly synthesized DNA can serve as templates for the next cycle. (B) The PCR cycle is repeated multiple times to exponentially generate copies of the original and amplified target sequences. As a result, 2
n
DNA molecules can potentially be produced, where
n
is equivalent to the number of PCR cycles. With 100% PCR efficiency and unlimited reagents in a 40-cycle reaction, one molecule of DNA could theoretically generate 2
40
, or over one trillion, amplified copies.
FIGURE 9 Line probe assay (LiPA). (A) The test device is impregnated with oligonucleotide probes specific for target sequence. Shown is an assay that differentiates HCV genotypes. Patient specimen containing HCV is amplified in an endpoint PCR, incorporating a fluorescent label during the reaction. Alternatively, biotin can be incorporated; however, this requires additional streptavidin-based detection. The entire PCR is then applied to the lateral-flow assay. Following subsequent temperature changes and wash steps, only the specific target remains bound. (B) The bound target can then be detected via a streptavidin-conjugated reporter that generates a color change when a chromogenic substrate is applied. Alternatively, one primer can be labeled with a specific fluorophore and detected with a fluorescence reader. Two controls often included in LiPA identify potential PCR inhibition (internal control) and false positives from nontarget hybridization (genotype-agnostic pathogen probe). In this image, a pan-HCV probe specific for all HCV genotypes and a hybridization control (HC) are used to ensure that the lateral flow reaches the adsorbent pad.
FIGURE 10 Real-time PCR amplification plots. (A) PCR amplification is divided into four phases: baseline (blue), exponential (red), linear (green), and plateau (purple). Fluorescence on the
y
axis is a function of the cycle number on the
x
axis. A horizontal threshold line intersects the curve at the exponential phase. (B) The threshold line in panel A is visible only upon expansion of the
y
axis. (C) Log transformation of fluorescence data allows easier visualization of the
C
T
value during the exponential phase, which is now shown as a linear slope. The
C
T
value corresponds to the perpendicular intercept of the threshold line. (D) Amplification results for four different concentrations of target are shown on the aggregate plot. Note the plateau-phase fluorescence cannot be used to differentiate target concentration. (E)
C
T
values for the multiple target concentrations, visualized on a log-transformed plot. This type of concentration-dependent
C
T
value determination is the basis for real-time PCR calibration. (F) In a special application of real-time amplification, HDPCR target discrimination is facilitated by unique target plateaus. Such discrimination is accomplished by limiting primer and probe concentrations during the reaction.
FIGURE 11 Hydrolysis probes. Hydrolysis probes anneal to target DNA but do not participate in the extension phase of PCR. Hydrolysis probes remain “dark” when either in solution or bound by virtue of a closely associated quencher molecule. However, the 5′-to-3′ exonuclease activity of most DNA polymerases employed in PCR amplification results in irreversible cleavage or hydrolysis of the bound probe. Unbound probes are resistant to degradation. A consequence of probe hydrolysis is the release of the fluorophore from the proximity of the quencher, allowing it to fluoresce. In the case of multiple PCR targets, the specificity of the PCR primers, probe binding, and the fluorophores used discriminates among targets.
FIGURE 12 Primer-probes. Scorpion probes belong to a class of molecules that incorporate both a primer for PCR extension and a quenched probe for detection. The 3′ end of a Scorpion probe is very similar to that of a traditional PCR primer. (A) Primer binding to target DNA follows the same kinetics as traditional PCRs. (B) Following extension, regions of DNA complementary to the stem-loop sequence of the Scorpion probe is synthesized. The 5′ end does not specifically bind to the target sequence in its native form; however, as the temperature increases and DNA is synthesized during the elongation step, sequence complementarity allows a previously stable stem-loop structure to destabilize and the loop portion to hybridize to the newly created amplicon. (C) Following denaturation at the end of a PCR cycle, annealing of the covalently attached step-loop is favored, thus releasing the fluorophore from the quencher. The stem of the stem-loop structure is destabilized at 72°C, facilitating this reaction only during the elongation step. Note that the Scorpion probe is not degraded during this process.
FIGURE 13 Hybridization probes. (A) Molecular beacons anneal to PCR-amplified target sequences based on complementarity to the sequence contained within its stem-loop region. The annealing physically separates the fluorophore from the proximity of the quencher, allowing a fluorescence signal to be detected, but during the annealing phase only. (B) FRET-based probes require two different probe molecules that bind adjacently on the target DNA. If one probe fails to anneal or nonadjacent binding occurs, the donor fluorophore will not be in close enough proximity to the acceptor fluorophore to be excited and emit fluorescence. With FRET technology, no quencher molecule is required, as the acceptor probe will not fluoresce unless these specific conditions are met.
FIGURE 14 Intercalating dyes bind only double-stranded DNA (dsDNA). Initially and during PCR denaturation steps, all dye molecules are unbound. When dsDNA is present, the amount of dye binding and subsequent fluorescence is proportional to the target amount. Binding is sequence independent, so careful optimization of PCR condition is required.
FIGURE 15 Modified nucleotides. 2′-Deoxy-5-methyl-isocytidine (isoC) is a unique nucleotide that will pair only with isoG. Incorporation during PCR amplification is accomplished with modified primers containing a fluorescently labeled isoC nucleotide. Following the first round of extension, a dsDNA fluorescent molecule is generated. Secondary extension of this isoC-containing DNA strand proceeds in the presence of isoG conjugated to a quencher molecule. This new dsDNA no longer fluoresces; thus, as amplification proceeds, a decrease in the fluorescent signal is observed. A post-PCR melting curve analysis allows separation of the quencher from the fluorescent signal, adding specificity to the detection process.
FIGURE 16 Melting curve analysis. Following the completion of PCR, if either intercalating dyes or nonhydrolyzed probes were used to quantify product, these molecules can be used to interrogate the specificity of the amplicon based on the temperature at which the probe dissociates, or “melts,” off the target sequence. The reaction mixture is initially incubated at a low temperature; the temperature is then slowly ramped up while the fluorescent signal is continuously monitored. (A) Plot of the fluorescence measurements as a function of temperature. (B) The same plot showing the negative change in fluorescence over the change in temperature (−d
F
/d
T
) as a function of temperature. This type of plot makes it easier to visualize the results of a melting curve analysis. Vertical lines depict the
Tm
s of two different targets with unique
Tm
s.
FIGURE 17 Droplet digital PCR (ddPCR). PCR targets are amplified in droplet partitions. Partitions are generated to maximize the probability of single target molecules being amplified within the emulsion. Following endpoint PCR in these partitions, the individual droplets are scanned for the presence of particular molecules based on fluorescent probes used during PCR. The droplets are commonly detected on a flow-based instrument.
FIGURE 18 Transcription-mediated amplification (TMA). The general princple of TMA is the use of RT to reverse transcribe RNA to DNA. This DNA can then be used to transcribe additional RNA products, and the presence of transcribed RNA can be determined using sequence-specific nucleic acid probes. Some of the RNA products are also transcribed into additional DNA template (through the DNA polymerase activity of RT), allowing target amplification. Since a single DNA molecule can be used to generate hundreds of RNA molecules through transcription, the amplification achieved using TMA is more robust than PCR-based approaches, which rely on product doubling.
FIGURE 19 Strand displacement amplification (SDA) and nicking-enzyme amplification reaction (NEAR). SDA and NEAR involve the introduction of nicking enzyme sites into amplified product through initial heat denaturation and a series of primers containing the nuclease site. Upon introduction of the site, nicking enzymes can be utilized to cleave one of the DNA strands. This allows the binding of DNA polymerase, elongation of the cut strand at the nicked site, and displacement of the other single strand of nucleic acid at the other end of the nicked site.
FIGURE 20 Helicase-dependent amplification (HDA). The enzyme helicase is able to open primer binding sites without heat denaturation. Following the binding of single-stranded binding proteins, target nucleic acid binding sites can be exposed for primer annealing.
FIGURE 21 Loop-mediated amplification (LAMP). LAMP utilizes a combination of four different primers to create a dumbbell-shaped single-stranded nucleic acid intermediate with hairpin loops at either end. A key aspect of this structure is that it is self-priming at the hairpin loop sites. Elongation from these sites creates additional hairpin loops and additional primer-binding sites, all without the need for thermal separation of double-stranded nucleic acid. Whether nucleic acid amplification is occurring can then be determined utilizing precipitation of magnesium in the presence of pyrophosphate (released through nucleic acid synthesis) as an indirect measure of amplification. This allows the determination of positivity or negativity simply by measuring the change in reaction turbidity.
FIGURE 22 Multiplex target detection with color-coded beads. Beads coated with capture oligonucleotides complementary to specific targets are color coded based on unique combinations of red and infrared dyes (top). Biotinylated PCR products are mixed with beads and then labeled with streptavidin-conjugated phycoerythrin (SA-PE). Complexes are then evaluated by magnetic immobilization (left) or flow cytometry (right), in which distinct wavelengths of light are used to quantify the signal (based on PE label) associated with each target (based on bead color code).
FIGURE 23 Multiplex ligation-dependent probe amplification (MLPA). First, a pair of single-stranded oligonucleotides (half-probes) are hybridized to a target sequence, which allows them to be ligated. Template-mediated ligation generates oligonucleotides harboring fixed 5′ and 3′ sequences that can then be used for amplification. Targets are then detected by qPCR using a fluorescently labeled primer followed by hybridization probe-based melting curve analysis (left). Alternatively, oligonucleotides harboring target-specific spacer sequences (of varying lengths) are amplified and identified by capillary electrophoresis (right).
FIGURE 24 Next-generation sequencing. (A) Platform-specific adapter sequences are added to insert molecules generated by fragmentation or PCR. (B) An Illumina flow cell (top) is composed of individual lanes harboring lawns of oligonucleotides complementary to sequencing adapters. An Ion Torrent chip (bottom) is composed of an array of wells coupled to an integrated circuit of electrochemical sensors. (C) Ion Torrent uses emulsion PCR to generate clonal populations of library fragments attached to ion sphere particles. Individual ion sphere particles settle into wells on the Ion Torrent chip, which are positioned above an ion-sensitive electrode array. dNTPs are introduced one at a time, and nucleotide incorporation is electrochemically detected by hydrogen ion release. Incorporation of the same nucleotide multiple times in a row is detected by the magnitude of the observed voltage change. (D) Illumina uses bridge amplification to generate physically localized clonal populations of library fragments (clusters). Clusters are sequenced in parallel using fluorescently labeled nucleotides, whose 3′ hydroxyl groups are capped with azidomethyl groups. Sequencing is performed in cycles during which (i) individual nucleotides are incorporated into the template molecules in each cluster, (ii) the flow cell is imaged with total internal reflection microscopy, and (iii) the fluorophores are cleaved and the blocking groups are removed. Read lengths are determined by the total number of cycles (up to 300 bp using current instruments). For paired-end sequencing, bridge amplification is used to regenerate the reverse strands in each cluster, the forward strands are then cleaved, and the reverse strands are sequenced.
FIGURE 25 Pathogen detection with CRISPR-Cas systems. (A) Guide RNAs (red) mediate target-specific cleavage by Cas12a (DETECTR) or Cas13a (SHERLOCK). (B) Target-specific cleavage activates nonspecific single-stranded DNA (DETECTR) or RNA (SHERLOCK) nuclease activity, which is used to cleave quenched oligonucleotide probes (blue), generating a fluorescent signal.
FIGURE 26 Acceptable control strategies for molecular assays. External controls should be used in a way that proves that each extraction and amplification associated with a given sample is effective prior to result reporting. In the control strategies shown, the validity of each extraction and amplification run is traceable to a valid external control.
9 Immunoassays for the Diagnosis of Infectious Diseases
FIGURE 1 Precipitin curve showing the phenomenon of zone of equivalence, prozone, and postzone.
FIGURE 2 Immunodiffusion reaction.
FIGURE 3 Diagram of a direct and indirect immunofluorescence assay (IFA).
FIGURE 4 Diagram of a direct and indirect immunofluorescence assay (IFA).
FIGURE 5 Diagram of a competitive EIA.
FIGURE 6 Diagram of an IgM capture EIA.
FIGURE 7 Diagram of a noncompetitive EIA.
FIGURE 8 Diagram of a lateral-flow immunoassay (LFA).
10 Prevention of Health Care-Associated Infections
FIGURE 1 Sample chart format for reporting (a) the monthly and mean rates of CLABSI in an intensive care unit and (b) the SIR using CDC NHSN data to calculate the number of observed infections divided by the number of expected infections during each time period. The color of the bar signifies how the SIR differs from the national benchmark for similar units: red, worse; yellow, no difference; green, better. MICU, medical intensive care unit; CVC, central venous catheter.
11 Investigation of Disease Outbreaks
FIGURE 1 Epidemic curves. The
x
axis is time;
y
axis is the number of cases. The two curves contrast the distribution of cases from a point source outbreak compared to person-to-person spread.
12 Molecular Epidemiology
FIGURE 1 Hypothetical example of the subtype distribution of 100 epidemiologically unrelated microbial strains generated by two different subtyping methods.
FIGURE 2 Procedural principles of some commonly used non-target-specific subtyping methods.
FIGURE 3 Procedural principles of some commonly used target-specific subtyping methods.
FIGURE 4 Heat map showing the SNPs among 10 STEC O157 isolates belonging to the same outbreak. In order to elucidate the genetic relationships among the outbreak isolates, high-quality SNPs were called against the outbreak reference strain (index case), which appears at the far left. A total of nine SNPs were detected among the outbreak isolates. The nine outbreak isolates (2091 through 2098) differ from the index case (Ref_2090) at all nine SNP loci, but share all alleles among themselves. In this case, the putative index case is likely an inappropriate choice of reference, unless an outgroup is needed.
FIGURE 5 Genomic epidemiology of SARS-CoV-2 with North America-focused subsampling. Data from Genbank sequence submissions, visualized using Nextstrain. Nextstrain (https://doi.org/10.1093/bioinformatics/bty407) is one of several open-source platforms for visualizing phylodynamic relationships, incorporating phylogenetics, place/time, and other sample-specific metadata. This figure shows the phylogenetic relationships between SARS-CoV-2 sequences from North America, with major lineages of the virus highlighted in different colors (https://nextstrain.org/ncov/open/north-america).
14 Prevention of Laboratory-Acquired Infections
FIGURE 1 Risk assessment matrix. *, WHO classifications: 1, low (not associated with disease); 2, moderate (associated with disease that is rarely serious); 3, high (associated with disease that is serious or lethal); 4, high (associated with disease that is serious or lethal and is readily spread from person to person, and intervention not usually available). **, “Daily” is defined as 4 or more days per week; “periodically” is defined as 1 to 3 days per week; “sporadically” is defined as <4 days per month. ***, Inhalation, ingestion, percutaneous, or mucous membrane. ****, “Low” means that the organism is unlikely to infect by this route; “mod” means that the organism may infect by this route; “high” means that the organism is likely to infect by this route.
15 Disinfection and Sterilization
FIGURE 1 The typical contents of an Environmental Protection Agency (EPA)-registered environmental disinfectant label include a number of required elements: company name, product name, and product information (formulation, safety information, directions for use).
FIGURE 2 Examples of “nontouch” disinfection systems: a portable UV light system (left) and a hydrogen peroxide gas generator (right).
FIGURE 3 Examples of chemical disinfectant formulations. Use of commercial products and trade names is for identification purposes and offered as examples and does not imply endorsement by the authors or their employers.
FIGURE 4 Examples of heat-based sterilizers: a large steam sterilizer (autoclave [left]), a small bench-top autoclave (upper right), and a benchtop dry-heat sterilizer (lower right).
16 Biothreat Agents
FIGURE 1 Structure of the Laboratory Response Network (LRN).
FIGURE 2 Sentinel-level laboratory flowchart for
Bacillus anthracis
and
B. cereus
biovar
anthracis
. Note that automated identification systems, including MALDI-TOF, may misidentify potential biothreat agents. Sentinel-level laboratories should perform only necessary tests to rule out suspected biothreat agents. If a suspected biothreat agent cannot be ruled out, it should be submitted to the nearest LRN reference laboratory for confirmatory testing. Adapted from ASM’s sentinel-level clinical microbiology laboratory
Bacillus anthracis
guidelines (https://asm.org/Articles/CPHMC/Laboratory-Response-Network-LRN-Sentinel-Level-C).
FIGURE 3 Sentinel-level laboratory flowchart for suspected botulinum toxin cases. Adapted from ASM’s sentinel-level clinical microbiology laboratory botulinum toxin guidelines (https://asm.org/Articles/CPHMC/Laboratory-Response-Network-LRN-Sentinel-Level-C).
FIGURE 4 Sentinel-level laboratory flowchart for
Yersinia pestis
. Note that automated identification systems, including MALDI-TOF, may misidentify potential biothreat agents.
Y. pestis
has been misidentified as
Y. pseudotuberculosis
,
Shigella
, H
2
S-negative
Salmonella
,
Acinetobacter
, and
Pseudomonas
species. Sentinel-level laboratories should perform only necessary tests to rule out suspected biothreat agents. If a suspected biothreat agent cannot be ruled out, it should be submitted to the nearest LRN reference level laboratory for confirmatory testing. Adapted from ASM’s sentinel-level clinical microbiology laboratory
Yersinia pestis
guidelines (https://asm.org/Articles/CPHMC/Laboratory-Response-Network-LRN-Sentinel-Level-C).
FIGURE 5 Sentinel-level laboratory flowchart for
Francisella tularensis
. Note that automated identification systems, including MALDI-TOF, may misidentify potential biothreat agents. Sentinel-level laboratories should perform only necessary tests to rule out suspected biothreat agents. If a suspected biothreat agent cannot be ruled out, it should be submitted to the nearest LRN reference laboratory for confirmatory testing. Adapted from ASM’s sentinel-level clinical microbiology laboratory
Francisella tularensis
guidelines (https://asm.org/Articles/CPHMC/Laboratory-Response-Network-LRN-Sentinel-Level-C).
FIGURE 6 Sentinel-level laboratory flowchart for
Burkholderia mallei
. Note that automated identification systems, including MALDI-TOF, may misidentify potential biothreat agents. Sentinel-level laboratories should perform only necessary tests to rule out suspected biothreat agents. If a suspected biothreat agent cannot be ruled out, it should be submitted to the nearest LRN reference laboratory for confirmatory testing. Adapted from ASM’s sentinel-level clinical microbiology laboratory
Burkholderia
guidelines (https://asm.org/Articles/CPHMC/Laboratory-Response-Network-LRN-Sentinel-Level-C).
FIGURE 7 Sentinel-level laboratory flowchart for
Burkholderia pseudomallei
. Note that automated identification systems, including MALDI-TOF, may misidentify potential biothreat agents. Sentinel-level laboratories should only perform necessary tests to rule out suspected biothreat agents. If a suspected biothreat agent cannot be ruled out, it should be submitted to the nearest LRN reference laboratory for confirmatory testing. Adapted from the ASM’s sentinel-level clinical microbiology laboratory
Burkholderia
guidelines (https://asm.org/Articles/CPHMC/Laboratory-Response-Network-LRN-Sentinel-Level-C).
FIGURE 8 Sentinel-level laboratory flowchart for
Brucella
. Note that automated identification systems, including MALDI-TOF, may misidentify potential biothreat agents. Sentinel-level laboratories should perform only necessary tests to rule out suspected biothreat agents. If a suspected biothreat agent cannot be ruled out, it should be submitted to the nearest LRN reference laboratory for confirmatory testing. Adapted from ASM’s sentinel-level clinical microbiology laboratory
Brucella
species guidelines (https://asm.org/Articles/CPHMC/Laboratory-Response-Network-LRN-Sentinel-Level-C).
17 The Human Microbiome
