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Gold Standard consensus-based procedures from the experts.
The Clinical Microbiology Procedures Handbook, 5th edition, provides those engaged in microbial analysis of clinical specimens with procedures for the detection, identification, and characterization of microorganisms involved in human infections. This unique and valuable collection of step-by-step descriptions of the numerous testing modalities used in the clinical microbiology laboratory was written and edited by highly knowledgeable laboratorians. The 5th edition features two new sections, one on blood cultures and one on MALDI-TOF MS, and the sections on molecular diagnostics, virology, and serology were extensively revised and updated. Presented over multiple volumes, this handbook enables laboratory staff to perform all analyses, including appropriate quality control recommendations, from the receipt of the specimen through processing, testing, interpretation, presentation of the final report, and subsequent consultation.
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Seitenzahl: 8304
Veröffentlichungsjahr: 2024
Cover
Table of Contents
Title Page
Copyright
Dedication
VOLUME 1
Editorial Board
Contributors
Author and Editor Conflict of Interest Statements
Preface
Acknowledgments
How To Use This Handbook
Abbreviations
SECTION 1 Procedure Coding, Reimbursement, and Billing Compliance
1.1. Introduction
1.2. Procedure Coding, Reimbursement, and Billing Compliance
1.2.1. Procedure Coding
1.2.2. Procedure Billing
1.2.3. Coverage of Laboratory Services
1.2.4. Billing Compliance Programs
SECTION 2 Specimen Collection, Transport, and Acceptability
2.1. Collection, Transport, and Manipulation of Clinical Specimens and Other Preanalytical Concerns
SECTION 3 Aerobic Bacteriology
3.1. Introduction
3.2. Staining Procedures
3.2.1. Gram Stain
3.2.2. Acridine Orange Stain
3.2.3. Vaginal Wet Mount
3.2.4. Methylene Blue Stain for Fecal Leukocytes
3.2.5. Dark-Field Microscopy for
Treponema pallidum
3.3. Processing, Isolation, Detection, and Interpretation of Aerobic Bacteriology Cultures
3.3.1. Processing of Specimens for Aerobic Bacteriology
3.3.2. Interpretation and Rapid Identification of Bacterial Growth on Primary Culture Media
3.4. Body Fluid Cultures (Excluding Blood, Cerebrospinal Fluid, and Urine)
3.5. Cerebrospinal Fluid Cultures
3.6. Medical Devices: Pre- and Postimplant testing
3.7. Fecal and Other Gastrointestinal Cultures
3.7.1. Fecal Culture for Aerobic Pathogens of Gastroenteritis
3.7.2. Culture for
Campylobacter
and Related Organisms
3.7.3.
Helicobacter pylori
Cultures
3.7.4. Quantitative Culture of Small-Bowel Contents
3.8. Genital Cultures
3.8.1. Guidelines for Performance of Genital Cultures
3.8.2. Group B
Streptococcus
Cultures
3.8.3.
Neisseria gonorrhoeae
Cultures
3.8.4.
Haemophilus ducreyi
Cultures
3.9. Ocular Cultures
3.10. Respiratory Tract Cultures
3.10.1. Guidelines for Performance of Respiratory Tract Cultures
3.10.2. Lower Respiratory Tract Cultures
3.10.3. Respiratory Cultures from Cystic Fibrosis Patients
3.10.4.
Legionella
Cultures and Urinary Antigen Testing
3.10.5. Ear Cultures
3.10.6.
Bordetella
Cultures
3.10.7. Culture of
Corynebacterium diphtheriae
and Other Diphtheria Toxin-Producing Bacterial Species
3.10.8. Throat Culture and Nonculture Tests for Pharyngitis
3.10.9 Nasal Sinus Cultures
3.11. Urine Cultures
3.11.1. Urine Cultures
3.11.2. Stone Cultures
3.12. Wound Cultures
3.12.1. Wound/Abscess and Soft Tissue Cultures
3.12.2. Quantitative Cultures of Wound Tissues
3.13.
Leptospira
Culture
3.14. Detection of Human Mycoplasmas and Ureaplasmas from Clinical Specimens by Culture and PCR
3.14.1.
Mycoplasma pneumoniae, Mycoplasma hominis,
and
Ureaplasma
Cultures
3.14.2. Antimicrobial Susceptibility Testing of Mycoplasmas and Ureaplasmas
3.14.3. Detection of
Mycoplasma pneumoniae
by Nucleic Acid Amplification Tests
3.14.4. Detection of
Mycoplasma genitalium
,
Mycoplasma hominis
, and
Ureaplasma
Species by Nucleic Acid Amplification Tests
3.15.
Bartonella
Cultures
3.16. Guidelines for Biochemical Identification of Aerobic Bacteria
3.17. Biochemical Tests for the Identification of Aerobic Bacteria
3.17.1. Acetamide Utilization Test (Acetamide Agar)
3.17.2. Acetate Utilization Test (Acetate Differential Agar)
3.17.3. ALA (δ-Aminolevulinic Acid) Test for Porphyrin Synthesis—Tube or Disk Test
3.17.4. Antimicrobial Disk Tests for Identification
3.17.5. Bile-Esculin and Esculin Tests
3.17.6. Bile Solubility Test
3.17.7. Butyrate Esterase Test
3.17.8. CAMP Factor Tests (Standard/Rapid, Reverse, and Inhibition)
3.17.9. Carbohydrate Utilization Tests
3.17.10. Catalase Test
3.17.11. Cetrimide Test
3.17.12. Citrate Utilization Test (Simmons)
3.17.13. Coagulase Test—Protein A/Clumping Factor Agglutination Method
3.17.14. Coagulase Test—Rabbit Plasma Method
3.17.15. Decarboxylase-Dihydrolase Tests
3.17.16. DNase Test–Rapid Thermonuclease Test
3.17.17. Fluorescent-Pigment Agars for
Pseudomonas
Identification
3.17.18. Gelatin Liquefaction
3.17.19. Gram Reaction Enzymatic Test
3.17.20. Hippurate Hydrolysis Rapid Test
3.17.21. Hydrogen Sulfide Production
3.17.22. Indole Test
3.17.23. Indoxyl Acetate Disk Test
3.17.24. Kligler’s Iron Agar Test and Triple Sugar Iron Agar Test
3.17.25. Leucine Aminopeptidase Test
3.17.26. Lecithinase and Lipase Detection
3.17.27. Lipophilism Test for
Corynebacterium
3.17.28. Malonate Test
3.17.29. Methyl Glucopyranoside (MGP) Test
3.17.30. Motility Tests
3.17.31. MRS Broth
3.17.32. Methyl Red–Voges-Proskauer (MR-VP) Tests
3.17.33. MUG (4-Methylumbelliferyl-β-d-Glucuronide) Test
3.17.34. Nitrate/Nitrite Reduction Test
3.17.35. O/129 Disk Susceptibility Testing for
Vibrio
and
Aeromonas
spp.
3.17.36. ONPG (
o
-Nitrophenyl-β-d-Galactopyranoside) Test
3.17.37. Optochin Susceptibility Test
3.17.38. Oxidase Test
3.17.39. Phenylalanine Deaminase Test
3.17.40. PYR (l-Pyrrolidonyl-β-Naphthylamide) Test
3.17.41. Quellung Reaction for
Streptococcus pneumoniae
(Neufeld Test)
3.17.42. 6.5% Salt and Temperature Tolerance Test
3.17.43. Satellite Test
3.17.44. SPS (Sodium Polyanethol Sulfonate) Disk Test
3.17.45. Starch Hydrolysis Test
3.17.46. Urease Test
3.18. Identification of Gram-Positive Bacteria
3.19. Identification of Gram-Negative Bacteria
SECTION 4 Anaerobic Bacteriology
4.1. Introduction
4.2. Taxonomy Updates for Anaerobes
4.3. Specimen Selection, Collection, and Transport for Anaerobic Culture
4.4. Culture Media for Anaerobes
4.4.1. Primary Culture Media for Anaerobes
4.4.2. Secondary Culture Media for Anaerobes
4.5. Processing Specimens for Anaerobic Culture
4.6. Incubation Techniques for Anaerobic Bacteriology Specimens
4.7. Examination of Primary Culture Plates for Anaerobic Bacteria
4.8. A Practical Guide to the Workup of Anaerobic Cultures
4.9. Rapid Disk, Spot Tests, and Other Rapid or Primary Methods for the Identification of Anaerobes
4.9.1. Introduction
4.9.2. Indole Test
4.9.3. Nitrate Disk Reduction Test
4.9.4. Catalase Test
4.9.5. Identification by Using Special-Potency Disks
4.9.6. Sodium Polyanethol Sulfonate (SPS) Disk for Differentiation of Gram-Positive Anaerobic Cocci
4.9.7. Bile Disk Test/Bile Broth Test/
Bacteroides
Bile Esculin Agar for Differentiation of Anaerobic Gram-Negative Rods
4.9.8. Fluorescence
4.9.9. Lipase Test
4.9.10. Lecithinase Test
4.9.11. Pigment Production
4.9.12. Urease Test
4.9.13. Gelatinase Production
4.9.14. Alkaline Phosphatase
4.9.15. Glutamic Acid Decarboxylase
4.9.16. L-Alanyl-Alanylaminopeptidase
4.9.17. L-Proline-Aminopeptidase
4.9.18. 4-Methylumbelliferone Derivative Substrates
4.9.19. Combination Enzymatic Tablets for Nitrophenol, Aminopeptidase, and Glycosidases
4.10. Commercial Kit and Rapid Enzymatic Systems for the Identification of Anaerobes
4.11. Storage and Stocking of Anaerobes
4.12. Use of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry for the Identification of Anaerobic Bacteria
4.13. Anaerobic Gram-Negative Bacilli
4.14. Anaerobic Gram-Positive Bacilli
4.15. Anaerobic Cocci
4.16.
Clostridioides
(
Clostridium) difficile
as a Pathogen Involved in Antimicrobial Agent-Associated Diarrhea, Colitis, and Pseudomembranous Colitis
VOLUME 2
SECTION 5 Blood Culture
5.1. Introduction
5.2. Preanalytical Considerations and Laboratory Processing of Samples for Blood Culture
5.3. Continuous-Monitoring Blood Culture Systems for Detection of Aerobic and Anaerobic Bacteria
5.4. Lysis Centrifugation
5.5. Continuous Monitoring Blood Culture Systems for Detection of Acid-Fast Bacilli and Fungi
5.6. Quality Control and Quality Assurance for Blood Cultures
5.7. Staining, Culture, and Identification Methods for Aerobic and Anaerobic Bacteria Recovered from Positive Blood Cultures
5.8. Staining, Culture, and Identification Methods for Acid-Fast Bacilli and Fungi Recovered from Positive Blood Cultures
5.9. Blood Cultures: Postanalytical Considerations
5.10. Supplementing Blood Cultures with Chromogenic Media to Expedite Microorganism Identification and/or Antimicrobial Resistance Detection
5.11. Specialized Processing of Blood
5.11.1. Transfusion Reactions
5.11.2. Autopsy Blood Cultures
5.11.3. Special Media or Stains for Fastidious and Infrequently Encountered Organisms
5.12. Diagnosis of Catheter-Related Bloodstream Infection: Differential-Time-to-Positivity Cultures and Catheter Tip Cultures
5.13. Multiplex Molecular Panels for Positive Blood Cultures
5.14. Broad-Range PCR and Emerging Technologies for the Direct Detection of Microorganisms from Blood Specimens
SECTION 6 MALDI-TOF MS
6.1. Introduction
6.2. MALDI-TOF MS for Bacterial and Yeast Identification
6.3. Identification of Highly Pathogenic Bacteria by MALDI-TOF MS
6.4. MALDI-TOF MS for Identification of Acid-Fast Bacilli and Aerobic Actinomycetes
6.5. MALDI-TOF MS for Filamentous Fungi Identification
6.6. MALDI-TOF MS for Identification of Bacteria and Yeast from Positive Blood Culture Broth
SECTION 7 Antimicrobial Susceptibility Testing
7.1. Introduction to Antimicrobial Susceptibility Testing Methods
7.1.1. Types of Antimicrobial Susceptibility Tests
7.1.2. Selecting and Applying Clinical Breakpoints
7.2. Disk Diffusion Testing
7.3. Disk Diffusion from Positive Blood Culture
7.4. Broth Microdilution Test
7.4.1. Broth Microdilution MIC Test
7.4.2. Broth Microdilution MIC Test for Anaerobic Bacteria
7.5. Gradient Diffusion Tests
7.6. Agar Dilution MIC Test
7.6.1. Agar Dilution MIC Test for Aerobic Bacteria
7.6.2. Agar Dilution MIC Test for Anaerobic Bacteria
7.7. Beta-Lactamase Tests
7.8. Oxacillin Salt Agar Test To Detect Methicillin (Oxacillin)-Resistant
Staphylococcus aureus
7.9. Detection of VRSA, VISA, and Vancomycin-Heteroresistant
Staphylococcus aureus
(hVISA)
7.10. Screening Tests for Detection of High-Level Mupirocin Resistance in
Staphylococcus aureus
7.11. Detection of Inducible Clindamycin Resistance in
Staphylococcus
spp.,
Streptococcus pneumoniae
, and
Streptococcus
spp. Beta-Hemolytic Group
7.12. Screen Tests to Detect High-Level Aminoglycoside Resistance in
Enterococcus
spp.
7.13. Agar Screen Test To Detect Vancomycin Resistance in
Enterococcus
spp.
7.14. Extended-Spectrum Beta-Lactamase Testing for
Enterobacterales
7.15. AmpC Beta-Lactamase Testing
7.16. Phenotypic Carbapenemase Detection Methods
7.16.1. Introduction
7.16.2. Modified Hodge Test and Modified Carbapenem Inactivation Method for Phenotypic Detection of Carbapenemases
7.16.3. Carbapenemase Nordmann-Poirel (Carba NP) Test for the Phenotypic Detection of Carbapenemases
7.16.4. Phenotypic Tests for the Detection of Metallo-β-Lactamases
7.17. Tests to Assess Bactericidal Activity
7.17.1. Minimum Bactericidal Concentration Testing
7.17.2. Time-Kill Assay
7.17.3. Time-Kill Assay for Determining Synergy
7.18. Serum Inhibitory and Bactericidal Titers
7.19. Synergy Testing: Broth Microdilution and Broth Macrodilution Checkerboard Methods
7.20. Quality Assurance Measures for Antimicrobial Susceptibility Testing
7.21. Creation of an Antibiogram and Verification of Data
7.22. Evaluation and Verification of Antimicrobial Susceptibility Test Systems
7.23. Selecting Antimicrobial Agents for Testing and Reporting
7.24. Preparation of Routine Media and Reagents Used in Antimicrobial Susceptibility Testing
7.24.1. McFarland Standards
7.24.2. Antimicrobial Stock Solutions
7.24.3. Preparation of Agar and Broth Media Used in Routine Antimicrobial Susceptibility Tests
7.25. Preparation of Broth Microdilution MIC Trays
SECTION 8 Aerobic Actinomycetes
8.1. Introduction
8.2. Specimen Examination and Primary Isolation
8.3. Media and Methods Used for Phenotypic Characterization of Aerobic Actinomycetes
8.4. Definitive Identification of Aerobic Actinomycetes
8.5. Susceptibility Testing
8.6. Appendixes
8.6.1. Appendix 8.6.1–1—Human Clinical Diseases Associated with Aerobic Actinomycetes
SECTION 9 Mycobacteriology and Antimycobacterial Susceptibility Testing
9.1. Introduction
9.2. General Mycobacterial Procedures
9.2.1. Safety and Levels of Laboratory Service
9.2.2. Digestion Decontamination
9.2.3. Acid-Fast Stains
9.2.4. Reporting
9.3. Solid Media Used for Isolation
9.4. Liquid Media Used for Isolation
9.4.1. BACTEC MGIT Automated Mycobacterial Culture
9.4.2. VersaTREK Myco Culture System
9.5. Identification of Mycobacteria
9.5.1. Conventional Biochemicals
9.5.2. AccuProbe Mycobacterial Culture Identification Tests
9.5.3. INNO-LiPA MYCOBACTERIA v2 Line Probe Assay
9.6. Nucleic Acid Amplification Procedures for Identification from Specimens
9.6.1. Cepheid Xpert MTB/RIF Test
9.6.2. Cepheid Xpert MTB/RIF Tests: Xpert MTB/RIF Ultra
9.6.3. Cepheid Xpert MTB/XDR Test
9.7. Susceptibility Testing by Liquid Media Methods
9.7.1. BACTEC MGIT SIRE—Nonradiometric Susceptibility Testing for
Mycobacterium tuberculosis
Complex
9.7.2. BACTEC MGIT Pyrazinamide (PZA)—Nonradiometric Susceptibility Testing for
Mycobacterium tuberculosis
9.7.3. VersaTREK—Indirect Susceptibility Testing for
Mycobacterium tuberculosis
9.8. Susceptibility Testing by the Agar Proportion Method for
Mycobacterium tuberculosis
Complex
9.9. Susceptibility Testing by TREK Sensititre Microdilution Plates
9.9.1. Antimicrobial Susceptibility Testing for Rapidly Growing Nontuberculous Mycobacteria
9.9.2. Antimicrobial Susceptibility Testing for Slowly Growing Nontuberculous Mycobacteria
9.9.3. Antimicrobial Susceptibility Testing for the
Mycobacterium tuberculosis
Complex Using Broth Microdilution
9.10. Molecular Susceptibility Testing for
Mycobacterium tuberculosis
9.10.1. Pyrosequencing Prediction of Drug Resistance in
Mycobacterium tuberculosis
Complex-Positive Clinical Specimens
VOLUME 3
SECTION 10 Mycology and Antifungal Susceptibility Testing
10.1. Introduction and General Considerations
10.2. Fungal Taxonomy and Nomenclature
10.3. Specimen Selection, Collection, and Transport
10.4. Specimen Examination
10.4.1. Microscopic Examination of Clinical Specimens
10.4.2. Staining Procedure for Direct Microscopic Detection of
Pneumocystis jirovecii
in Respiratory Samples
10.5. Processing Specimens for Fungal Culture
10.6. Examination and Evaluation of Primary Cultures
10.7. Presumptive Identification Tests for Yeasts Isolated on Primary Culture
10.8. Identification of Molds on Primary Culture
10.9. Full Identification of Yeasts
10.10. Phenotypic Identification of Molds
10.11. Molecular Identification of Yeasts and Molds
10.12. Antifungal Susceptibility Testing
10.12.1. Broth Dilution Antifungal Susceptibility Testing
10.12.2. Disk Diffusion and Gradient Diffusion Antifungal Susceptibility Testing
10.13. Clinical Breakpoints and Epidemiological Cutoff Values
SECTION 11 Parasitology
11.1. Introduction
Part 1. Equipment
Part 2. Calibration of Microscope with an Ocular Micrometer
Part 3. Safety
Part 4. Quality Control
Part 5. Quality Assurance
Part 6. STAT Testing in Parasitology
11.2. Collection and Preservation of Fecal Specimens
11.2.1. Collection of Fresh Specimens
11.2.2. Fixation and Preservation of Specimens
11.2.3. Shipment of Specimens
11.3. Macroscopic and Microscopic Examination of Fecal Specimens
11.3.1. Macroscopic Examination of Fecal Specimens: Age and Physical Description
11.3.2. Microscopic Examination of Fecal Specimens: Direct Smears
11.3.3. Microscopic Examination of Fecal Specimens: Concentration by Formalin-Ethyl Acetate Sedimentation
11.3.4. Microscopic Examination of Fecal Specimens: Concentration by Zinc Sulfate Flotation
11.3.5. Microscopic Examination of Fecal Specimens: Permanent Stained Smear (Trichrome)
11.3.6. Microscopic Examination of Fecal Specimens: Iron Hematoxylin Stain (Modified Spencer-Monroe Method)
11.4. Special Stains for Coccidia and Microsporidia
11.4.1. Special Stains for
Cryptosporidium
and the Coccidia: Modified Kinyoun’s Acid-Fast Stain (Cold)
11.4.2. Special Stains for
Cryptosporidium
and the Coccidia: Modified Ziehl-Neelsen Acid-Fast Stain (Hot)
11.4.3. Special Stains for Microsporidia: Modified Trichrome-Weber Green
11.4.4. Special Stains for Microsporidia: Modified Trichrome-Ryan Blue
11.4.5. Special Stains for Microsporidia: Combination Acid-Fast Modified Trichrome Stain for the Apicomplexa and the Microsporidia
11.4.6. Special Stain for
Cryptosporidium
and the Coccidia: Modified Safranin Technique with Microwave Heating
11.4.7. Autofluorescence for
Cyclospora
,
Cystoisospora
, and
Sarcocystis
11.4.8. Calcofluor White for Detection of Microsporidial Spores,
Acanthamoeba
, and
Balamuthia mandrillaris
Cysts
11.5. Additional Techniques for Stool Examination
11.5.1. “Culture” of Larval-Stage Nematodes: Baermann Technique
11.5.2. “Culture” of Larval-Stage Nematodes: Harada-Mori Technique
11.5.3. “Culture” of Larval-Stage Nematodes: Petri Dish-Filter Paper Slant
11.5.4. “Culture” of Larval-Stage Nematodes: Agar Plate Culture for
Strongyloides stercoralis
11.5.5. Determination of Egg Viability: Schistosomal Egg Hatching
11.5.6. Recovery of Scolices and Proglottids of Cestodes
11.5.7. Qualitative Fecal Fat
11.5.8. Reducing Substances (AimTab)
11.6. Other Specimens from the Intestinal Tract and the Urogenital System
11.6.1. Examination for Pinworm: Cellulose Tape Preparation
11.6.2. Sigmoidoscopy Specimen: Direct Wet Smear
11.6.3. Sigmoidoscopy Specimen: Permanent Stained Smear
11.6.4. Duodenal Contents: Duodenal Aspirate
11.6.5. Urogenital Specimens: Direct Saline Mount
11.6.6. Urogenital Specimens: Permanent Stained Smear (Giemsa)
11.6.7. Urine Concentration: Centrifugation
11.6.8. Urine Concentration: Membrane Filter (Nuclepore)
11.7. Sputum, Aspirates, and Biopsy Material
11.7.1. Expectorated Sputum: Direct-Mount and Stained Preparations
11.7.2. Aspirates and Bronchoscopy Specimens
11.7.3. Biopsy Specimens
11.8. Detection of Blood Parasites
11.8.1. Detection of Blood Parasites
11.8.2. Preparation of Thin Blood Films
11.8.3. Preparation of Thick Blood Films
11.8.4. Combination Thick and Thin Blood Films
11.8.5. Giemsa Stain
11.8.6. Wright’s Stain
11.8.7. Determination of Parasitemia: Parasite Quantification
11.8.8. Delafield’s Hematoxylin Stain
11.8.9. Concentration Procedures: Buffy Coat Concentration
11.8.10. Concentration Procedures: Membrane Filtration Concentration
11.8.11. Concentration Procedures: Knott Concentration
11.8.12. Testing Modalities and Algorithms for Malaria Diagnosis
11.9. Culture
11.9.1. Parasite Culture of
Acanthamoeba
and
Naegleria
spp.
11.9.2. Parasite Culture:
Trichomonas vaginalis
11.9.3. Parasite Culture:
Leishmania
spp. and
Trypanosoma cruzi
11.10. Gross Examination of Helminths and Arthropods
11.11. Appendixes
11.11.1. Appendix 11.11.1–1—Identification Aids: Artifacts
11.11.2. Appendix 11.11.2–1—Information Tables
11.11.3. Appendix 11.11.3–1—Common Problems in Organism Identification
11.11.4. Appendix 11.11.4–1—Quality Control Recording Sheets
11.11.5. Appendix 11.11.5–1—Flowcharts for Processing Stool Specimens
11.11.6. Appendix 11.11.6–1—Current OSHA Regulations on the Use of Formaldehyde
11.11.7. Appendix 11.11.7–1—Test Report Comments
SECTION 12 Viruses and Chlamydiae
12.1. Introduction: Traditional Methods for Laboratory Diagnosis of Viral and Chlamydial Infections
12.2. Selection, Collection, Transport, and Processing of Specimens for Viral Diagnosis
12.3. Quality Control and Quality Assurance in Clinical Virology
12.4. Biosafety in the Clinical Virology Laboratory
12.5. Conventional Tube Cell Culture for Primary Virus Isolation
12.6. Shell Vial/Multiwell Plate Culture for Rapid Virus Isolation
12.7. Selection, Maintenance, and Serial Propagation of Uninoculated Monolayer Cell Cultures
12.8. Preparation of Cell Culture Media and Supplemental Components
12.9. Tests for Direct Detection of Viruses in Clinical Specimens
12.9.1. Immunofluorescence Test for Direct Detection of Viruses in Clinical Specimens
12.9.2. Rapid Solid-Phase Immunoassays for Direct Detection of Viruses in Clinical Specimens: Influenza Virus, Respiratory Syncytial Virus, and SARS-CoV-2
12.9.3. Histologic and Cytologic Procedures for Detection of Viruses in Exfoliated Cells and Tissues
12.10. Isolation of
Chlamydia
spp. in Cell Culture
12.11. Hemagglutination Inhibition Assay for Quantitative Measurement of Antibody Responses to Influenza Virus
VOLUME 4
SECTION 13 Serology
13.1. Immunoassays for Detection of Infectious Diseases
13.1.1. Introduction
13.1.2. Common Immunologic Assays Used for Detection of Antibodies to and Antigens from Infectious Pathogens
13.2. Serologic Diagnosis of Group A Streptococcal Infections
13.2.1. Serologic Evaluation for Rheumatic Fever and Poststreptococcal Glomerulonephritis
13.2.2. Anti-Streptolysin O and Anti-DNase B Tests
13.3. Detection of
Brucella
spp. Antibodies
13.3.1. Introduction
13.3.2. Detection of
Brucella
spp. by Microagglutination Test
13.3.3. Detection of
Brucella
spp. Antibodies by Tube Agglutination Test
13.4. Detection of
Francisella tularensis
Antibodies
13.4.1. Introduction
13.4.2. Detection of
Francisella tularensis
Antibodies by Agglutination
13.4.3. Detection of
Francisella tularensis
Antibodies by ELISA
13.5. Laboratory Diagnosis of Syphilis
13.5.1. Introduction
13.5.2. Venereal Disease Research Laboratory (VDRL) Tests
13.5.3. Rapid Plasma Reagin (RPR) Test
13.5.4. Automated Nontreponemal Rapid Plasma Reagin (RPR) Tests
13.5.5.
Treponema pallidum
Particle Agglutination (TP-PA) Test
13.5.6. Trep-Sure Enzyme Immunoassay
13.5.7. Automated Treponemal Tests
13.5.8. INNO-LIA Syphilis Score
13.6. Detection of
Borrelia burgdorferi
Antibodies
13.7. SARS-CoV-2 Serologic Testing
13.8. Epstein-Barr Virus Serology
13.8.1. Introduction
13.8.2. Detection of Heterophile Antibodies
13.8.3. Detection of Epstein-Barr Virus-Specific Antibodies
13.9. Cytomegalovirus Serology
13.9.1. Introduction
13.9.2. Detection of Antibodies Against Cytomegalovirus by Enzyme-Linked Immunosorbent Assays and Chemiluminescence Immunoassays
13.9.3. Cytomegalovirus IgG Avidity Testing
13.10. Human Immunodeficiency Virus Serology
13.10.1. Introduction
13.10.2. HIV Screening Immunoassays
13.10.3. HIV-1/2 Supplemental Immunoassays
13.11. Serologic Testing for Hepatitis Viruses
13.11.1. Heptatits A Virus Serology
13.11.2. Hepatitis B Virus Serology
13.11.3. Hepatitis C Virus Serology
13.12. Serologic Diagnosis of Arbovirus Infections
13.13. Serologic Tests for Diagnosis of
Histoplasma capsulatum
13.13.1. Introduction
13.13.2.
Histoplasma capsulatum
Antibody Detection by Complement Fixation
13.13.3.
Histoplasma capsulatum
Antibody Detection by Immunodiffusion (ID)
13.14. Serologic Methods for Diagnosis of
Coccidioides
Infections
13.14.1. Introduction
13.14.2. Detection of Antibodies to
Coccidioides
spp. by Immunodiffusion
13.14.3. Detection of Antibodies to
Coccidioides
spp. by Complement Fixation
13.14.4. Detection of Antibodies to
Coccidioides
spp. by EIA
13.14.5. Detection of Antibodies to
Coccidioides
spp. by Lateral Flow Assay (LFA)
13.15. Serologic Diagnosis of Chagas Disease
13.16. Serologic Testing for Toxoplasmosis
13.16.1. Introduction
13.16.2. Detection of
Toxoplasma
IgM Antibodies by ELISA (Remington Method)
13.16.3. Detection of
Toxoplasma
IgM Antibodies by the Immunoglobulin M Immunosorbent Agglutination Assay
13.16.4. Detection of
Toxoplasma
IgA Antibodies by ELISA (Remington Method)
13.16.5. Detection of
Toxoplasma
IgE Antibodies by ELISA (Remington Method)
13.16.6. Vidas Toxo IgG Avidity Assay
13.16.7. AC/HC (Differential Agglutination)
13.17. Interferon Gamma Release Assays for Latent Tuberculosis Infection
SECTION 14 Molecular Techniques
14.1. Introduction
14.2. General Aspects of Molecular Diagnostics
14.2.1. Preanalytical Considerations for Molecular Testing
14.2.2. Molecular Workflow and Contamination Control in a Clinical Microbiology Laboratory
14.2.3. Biosafety in the Molecular Microbiology Laboratory
14.2.4. Verification and Validation of Molecular Tests
14.2.5. Use of Controls and Calibrators
14.2.6. Postanalytical Considerations for Molecular Testing
14.3. Molecular Methods for Identification of Microorganisms
14.3.1. Molecular Detection of HIV-1
14.3.2. HIV Genotypic Resistance Testing
Part 1. Genotypic Assay
Part 2. Phenotypic Assay
14.3.3. Molecular Methods for Identification of High-Risk Human Papillomaviruses
14.3.4. Molecular Detection of Herpes Simplex Viruses 1 and 2 and Varicella-Zoster Virus
14.3.5. Quantitative Detection of Human Cytomegalovirus DNA by Real-Time PCR
14.3.6. Human Cytomegalovirus Drug Resistance Testing
14.3.7. Molecular Diagnostics of Epstein-Barr Virus Infections
14.3.8. Molecular Diagnostics of BK Virus Infections
14.3.9.
Chlamydia trachomatis
and
Neisseria gonorrhoeae
14.4. Syndromic Panels
14.4.1. Gastroenteritis Panels
14.4.2. Syndromic Panels: Respiratory Panels
14.4.3. Meningitis/Encephalitis Molecular Panels
14.5. Sequence-Based Identification and Typing
14.5.1. Sequencing-Based Identification of Microorganisms
14.5.2. Deep Amplicon Sequencing for Direct Microbial Detection and Identification
14.5.3. Whole-Genome Sequencing
14.5.4. Shotgun Metagenomic Next-Generation Sequencing (mNGS) for Direct Microbial Detection and Identification
SECTION 15 Epidemiologic and Infection Control Microbiology
15.1. Introduction
15.2. Laboratory Support for Infection Prevention: Collaboration with Benefits for All
15.3. Microbiological Sampling for Pharmacies that Compound Sterile Preparations
15.3.1. Environmental Monitoring by Viable Air Sampling
15.3.2. Surface Sampling
15.3.3. Gloved Fingertip Testing
15.3.4. Media Fill Test Procedure
15.3.5. USP<71> Sterility Testing
15.3.6. Endotoxin Testing
15.4. Environmental Sampling and Cultures
15.4.1. Culture of Hospital Water for
Legionellaceae
15.4.2. Heterotrophic Plate Count and Endotoxin Assay of Hemodialysis Fluids
15.4.3. Air Cultures for Fungi
15.4.4. Environmental Surface Testing
15.4.5. Culture of Blood and Cellular Therapy Products in Blood Banking
15.4.6. Culture of Human Cadaveric Tissues for Transplantation
15.4.7. Duodenoscope Surveillance
15.5. Outbreak Investigations: Laboratory and Epidemiologic
15.5.1. Collection and Tracking of Surveillance and Clinical Specimens for Outbreak Investigation
15.5.2. Collection and Storage of Outbreak Isolates
15.5.3. Systematic Analysis of Nosocomial Outbreaks
15.5.4. Public Health Reporting of Infectious Diseases: A Collaborative Approach by the Microbiology Laboratory and Clinicians
15.6. Molecular Methods for Epidemiological Typing of Microorganisms
15.6.1. Introducion
15.6.2. PCR Ribotyping
15.6.3. Molecular Strain Typing Using Pulsed-Field Gel Electrophoresis
15.6.4. Strain Typing Analysis of
Staphylococcus aureus
Isolates Using Staphylococcal Protein A (
spa
) Typing
15.6.5. Multilocus Sequence Typing
15.6.6. Strain Typing Using Next-Generation Sequencing
15.7. Surveillance Cultures for Hsopital-Associated Infections
15.7.1. CDC Antibiotic Resistance Coordination and Strategy Unit (ARX) Antibiotic Resistance Laboratory Network (AR Lab Network)
15.7.2. Screening for Methicillin-Resistant Staphylococcus aureus
15.7.3. Screening for Vancomycin-Resistant Enterococci
15.7.4. Surveillance Cultures of Multidrug-Resistant
Enterobacterales, Pseudomonas aeruginosa,
and
Acinetobacter baumannii
15.7.5. Surveillance Cultures for
Candida auris
15.7.6. Surveillance Cultures from Immunocompromised Hosts
15.7.7. Infection Surveillance Prior to Transplantation
15.8. Infection Control in the Laboratory
15.8.1. Immunization of Microbiology Laboratory Personnel
15.8.2. Laboratory Support of Blood-Borne Pathogen Exposures
15.8.3. Investigation of Laboratory Exposures
15.8.4. Laboratory Isolation Codes and Notification Fan-Out for Suspected Biosafety Risk Group 3 and 4 Microorganisms
VOLUME 5
SECTION 16 Quality Assurance, Quality Control, Laboratory Records, and Water Quality
16.1. Quality Assessment and Improvement (Quality Assurance)
16.1.1. Process Improvement
16.1.2. Quality Control and Assurance for Microbiology Full Laboratory Automation
16.2. Quality Control
16.3. Verification and Validation of Test System Performance Specifications
16.4. CLIA Certification and Accreditation, ISO 15189 Accreditation, and Proficiency Testing
16.5. Individualized Quality Control Plan
16.6. Laboratory Records
16.7. Preparation and Quality Control of Laboratory Water
16.8. Pipette and Loop Calibration
16.8.1. Use and Performance Verification of Microbiological Loops
16.8.2. Use and Performance Verification of Pipettors
SECTION 17 Biohazards and Safety
17.1. Introduction
17.2. Biological Safety and Biohazard Prevention
17.2.1. Routes of Infection and Laboratory Activities
17.2.2. Safe Work Practices
17.2.3. Decontamination
17.2.4. Biohazardous Spills
17.2.5. Hand Hygiene for Laboratory Personnel
17.3. Biohazard Containment
17.3.1. Introduction
17.3.2. Biosafety Levels
17.3.3. Biological Safety Cabinet
17.3.4. PPE and Engineering Controls
17.4. Laboratory Instrumentation and Equipment
17.4.1. Introduction
17.4.2. Autoclave
17.4.3. Centrifuge
17.4.4. Compressed Gas Cylinders
17.4.5. Pneumatic Tube System
17.4.6. Specimen/Microorganism Storage and Retention
17.4.7. Other Equipment and Devices
17.5. Special Pathogens and Employee Safety
17.5.1. Introduction
17.5.2. Early (Bench-Level) Recognition of Biothreat Agents and Laboratory-Acquired Infections
17.5.3. Select Agents
17.5.4. Environmental, Non-Human, and Suspicious Specimens and Substances
17.5.5. Prions, Prion Diseases (Including Creutzfeldt-Jakob Disease), and Safety Issues Specific to Specimens Suspected of Containing Prions
17.5.6. Resources for Information on Specific Pathogens
17.6. Packing and Shipping Infectious Substances
17.7. Management of Laboratory Accidents
17.8. Management of Infectious Waste
17.9. Risk Assessment
SECTION 18 Bioterrorism
18.1. General Introduction to Bioterrorism and Emerging Infectious Diseases
18.2. Levels of Laboratory Safety
18.3.
Bacillus anthracis
and
Bacillus cereus
biovar anthracis—Anthrax
18.4.
Brucella
spp.—Brucellosis
18.5.
Yersinia pcstis
18.6. Tularemia—
Francisclla tularensis
18.7. Melioidosis (
Burkholderia pseudomallei
) and Glanders (
Burkholderia mallei
)
18.8. Smallpox and Other Poxviruses
18.9. Novel Influenza Viruses and Highly Pathogenic Coronaviruses
18.10. Q Fever—Coxiella burnetii
18.11. Toxins: Botulinum Toxin (
Clostridium botulinum
) and Staphylococcal Enterotoxin B (
Staphylococcus aureus
)
18.12. High-C’onsequence Viral Pathogens
18.13. Eastern Equine Encephalitis Virus
18.14. Clinical Laboratory Bioterrorism Readiness Plan
18.15. Phenotypic Tests and Biochemical Procedures
18.15.1 Oxidase Test
18.15.2 Catalase Test
18.15.3 Spot Indole Test
18.15.4 Beta-Lactamase Test
18.15.5 Motility Tests
18.15.6 Urease Test
18.15.7 Antimicrobial Disk Tests for Identification
18.15.8 Satellite Test
Index
End User License Agreement
Section 1
Appendix 1.1–1. Glossary of Reimbursement and Compliance Terminology and Acronyms
Appendix 1.1–2. Websites and Guidance Documents
Appendix 1.2.4–1. Reflex and Composite Scenarios in Microbiology
Section 3
Appendix 3.2.1–1. Preparation of Gram Stain Reagents
Appendix 3.2.1–2. Rejection Criteria for Sputum Culture
Appendix 3.2.1–3. Reporting Gram-Stained Vaginal Smears to Diagnose Bacterial Vaginosis and Vaginitis
Appendix 3.2.2–1. Preparation of Acridine Orange Stain
Appendix 3.7.1–1. Detection of Somatic O Antigen Serogroups of Bacteria
Appendix 3.7.1–2. Detection of
Escherichia coli
O157 by Latex Agglutination
Appendix 3.7.1–3. Detection of Shiga Toxin by Immunochromatographic Assay
Appendix 3.7.3–1.
Helicobacter pylori
Antigen Assay
Appendix 3.10.2–1. Quantitative Culture of Protected Specimen Brush and Bronchoalveolar Lavage Fluid Specimens
Appendix 3.10.4–1. Urinary Antigen Testing
Appendix 3.10.8–1. Beta-Hemolytic Streptococcal Latex Agglutination Method
Appendix 3.11.1–1. Validation of Urine Inoculation Methods
Appendix 3.13–1. Summary of Diagnostic Tests for Leptospirosis
Appendix 3.14.1–1. Medium Formulations for Cultivation of Mycoplasmas and Ureaplasmas from Humans
Appendix 3.17.22–1. Reagent Preparation
Appendix 3.17.26–1. Preparation of Egg Yolk Agar Medium
Section 4
Appendix 4.4.1–1. Formulas of Media for Anaerobes
Section 5
Appendix 5.6–1. Serial Dilution Method for Seeded Blood Culture Studies
Section 6
Appendix 6.4–1. Databases
Section 7
Appendix 7.1.1–1. Surrogate and Equivalent Agent Tests for Commonly Isolated Bacteria that Grow Aerobically
Appendix 7.2–1. Quality Control: CLSI
Appendix 7.2–2. Quality Control: EUCAST
Appendix 7.2–3. Where to find CLSI and EUCAST Disk Diffusion Criteria for Various Organisms
Appendix 7.2–4. Zone Reading
Appendix 7.3–1. Procedures for CLIS and EUCAST Disk Diffusion from Positive Blood Cultures
Appendix 7.4.1–1. Quick Reference List for Performing Broth Microdilution MIC Tests
Appendix 7.4.1–2. Broth Microdilution QC Log Sheet
Appendix 7.4.1–3.
Haemophilus Influenzae
and
Haemophilus Parainfluenzae
Appendix 7.4.1–4.
Streptococcus Pneumoniae
and
Streptococcus
spp. (Beta Hemolytic Group and Viridans Group)
Appendix 7.4.1–5.
Neisseria meningitidis
Appendix 7.4.1–6. Breakpoint MIC Panels
Appendix 7.4.1–7. Example MIC Breakpoint Panel
Appendix 7.4.2–1. Preparation of Media and Reagents
Appendix 7.4.2–2. Anaerobe Broth Microdilution QC
Appendix 7.5–1. Gradient Test QC Table
Appendix 7.5–2. Quick Reference List for Performing Gradient Diffusion Tests
Appendix 7.5–3. Photographic Reading Guide
Appendix 7.6.1–1.
Neisseria meningitidis
Appendix 7.6.1–2.
Neisseria gonorrhoeae
Appendix 7.6.1–3.
Helicobacter pylori
Appendix 7.6.1–4. Quick Reference Guide for Performing Agar Dilution MIC Tests
Appendix 7.6.1–5. Preparation of MHA Deeps
Appendix 7.6.1–6. Volumes of Components Required for Preparation of Agar Dilution Plates When Using Round or Square Petri Plates
Appendix 7.6.1–7. Agar Dilution QC
Appendix 7.6.1–8. Timetable for Agar Dilution Susceptibility Testing of Aerobic Bacteria
Appendix 7.6.1–9. Preparation of Antimicrobial Ddilutions from Stock Solutions
Appendix 7.6.1–10. Agar Dilution MIC Worksheet
Appendix 7.6.2–1. Preparation of Media and Reagents
Appendix 7.6.2–2. Agar Dilution QC
Appendix 7.6.2–3. Timetable for Agar Dilution Susceptibility Testing of Anaerobic Bacteria
Appendix 7.6.2–4. Preparation of Antimicrobial Dilutions from Stock Solutions
Appendix 7.6.2–5. Volumes of Components Required for Preparation of Agar Dilution Plates When Using Round of Square Petri Plates
Appendix 7.6.2–6. Agar Dilution MIC Worksheet
Appendix 7.7–1. Summary of Colorimetric Beta-Lactamase Testing Methods and Method(s) Generally Satisfactory for Various Organisms
Appendix 7.7–2. Beta-Lactamase Test QC
Appendix 7.8–1.
Staphylococcus aureus
Oxacillin Salt Agar Test QC
Appendix 7.9–1. Preparation of Vancomycin (VAN) Dilutions
Appendix 7.9–2. Volumes of Components Required for Preparation of Vancomycin Agar Plates When Using 100-mm Round Petri Plates
Appendix 7.9–3. Dilutions for Each Agar Plate
Appendix 7.9–4. Example Calculations for AUC
Appendix 7.9–5. PAP-AUC Worksheet
Appendix 7.11–1. Quick Reference List to Screen for Inducible Clindamycin Resistance
Appendix 7.11–2. D-Zone Test QC
Appendix 7.11–3. Inducible Clindamycin Resistance Test—Broth Microdilution QC
Appendix 7.12–1. Aminoglycoside-Modifying Enzymes that Confer HLAR in
Enterococcus
spp.
Appendix 7.12–2.
Enterococcus
HLAR Agar Screen Test QC
Appendix 7.13–1.
Enterococcus
Vancomycin Agar Screen Test QC
Appendix 7.14–1. ESBL Disk Diffusion Test QC
Appendix 7.14–2. ESBL MIC Test QC
Appendix 7.15–1. Disk Diffusion Test QC
Appendix 7.15–2. Disk Diffusion Test Results Interpretation Examples
Appendix 7.17.1–1. MBC Testing Conditions for Various Bacteria for Microdilution and Macrodilution Procedures
Appendix 7.17.1–2. Worksheet for MIC and MBC
Appendix 7.17.1–3. Technique for Using Bent Glass Rod “Hockey Sticks” for Colony Counts
Appendix 7.17.1–4. Worksheet for MBCs
Appendix 7.17.1–5. Rejection Value and Calculated Sensitivity and Specificity for each Initial Concentration Based on Duplicate 0.01-ml Samples
Appendix 7.17.2–1. MBC Testing Conditions for Various Bacteria for Microdilution and Macrodilution Procedures
Appendix 7.17.2–2. Preparation of Inoculum for Reaction Tubes in Time-Kill Assays
Appendix 7.17.2–3. Determining Colony Counts from Control and Antimicrobial Tubes for Time-Kill Assays
Appendix 7.17.2–4. Time-Kill Assay Worksheet
Appendix 7.17.2–5. Sample Graph for Time-Kill Assay of
S. aureus
with Vancomycin
Appendix 7.17.3–1. Time-Kill Assay Worksheet
Appendix 7.17.3–2. Graphic Representation of Time-Kill Assay Showing Synergism and Antagonism
Appendix 7.17.3–3. Sample Graph of Time-Kill Assay of
P. aeruginosa
with Piperacillin and Amikacin
Appendix 7.18–1. Alternative Protocols for Variations in Sample or Diluent
Appendix 7.18–2. SIT and SBT Test Conditions and Media Used for Various Bacteria
Appendix 7.18–3. Configuration of Microdilution Plate for SIT and SBT
Appendix 7.18–4. Worksheet for SIT and SBT Tests
Appendix 7.18–5. Rejection Value and Calculated Sensitivity and Specificity for Each Initial Concentration Based on Duplicate 0.01-ml Samples
Appendix 7.19–1. Examples of Reported Combination Interactions
Appendix 7.19–2. Example of Format of Broth Microdilution Checkerboard Panel
Appendix 7.19–3. Dilution Schematics for Two-Agent Broth Microdilution Checkerboard
Appendix 7.19–4. Example of Broth Microdilution Showing Synergism, Partial Synergism, and Indifference
Appendix 7.19–5. Example of Broth Microdilution Showing indifference and Antagonism
Appendix 7.19–6. Example of Limited-Series Checkerboard Format for Broth Microdilution
Appendix 7.19–7. Dilution Schematics for Two-Agent Broth Macrodilution Limited Checkerboard
Appendix 7.19–8. Example of Broth Macrodilution Showing Synergism
Appendix 7.19–9. Example of Broth Macrodilution Showing Antagonism
Appendix 7.19–10. Representing Checkerboards as Isobolograms
Appendix 7.19–11. Synergy Testing by Disk Agar Diffusion Methods
Appendix 7.19–12. Planning Studies
Appendix 7.20–1. Suggested QC Strains for Aantimicrobial Susceptibility Tests
Appendix 7.20–2. Example for Use of QC Strains with “On-Scale” Endpoints
Appendix 7.20–3. Primary Variables that Must be Controlled When Performing Routine Disk Diffusion and Broth Microdilution MIC Tests for Nonfastidious Bacteria
Appendix 7.20–4. Competency Assessment Checklist for Antimicrobial Susceptibility Testing
Appendix 7.21–1. Stepwise Instructions for Generating Antibiogram Reports Based on Antimicrobial Susceptibility Test System
Appendix 7.22–1. Suggested Recommendations for Number of Isolates and Extent of Verification/Validation
Appendix 7.22–2. Suggested Resistant Organisms to Include in Evaluation of AST Systems
Appendix 7.22–3. Susceptibility Category Errors
Appendix 7.22–4. Example of a Correlation Table for One Antimicrobial Agent
Appendix 7.22–5. Example of an Overall Correlation Table
Appendix 7.23–1. Reference Chart for Commonly used Antimicrobial Agents
Appendix 7.24.1–1. Preparation of McFarland Standards
Appendix 7.24.1–2. Wickerham Card
Appendix 7.24.2–1. Preparation of Solvents and Diluents
Appendix 7.24.2–2. Worksheet for Antimicrobial Stock Solution QC
Appendix 7.24.2–3. Formulas for Preparation of Antimicrobial Stock Solutions
Appendix 7.24.3–1. Preparation of Additives and Supplements
Appendix 7.24.3–2. Notes and QC Parameters for Media
Appendix 7.25–1. Ordering Media for Broth Microdilution MIC Tray Preparation
Appendix 7.25–2. QC Log for Broth Microdilution MIC Tray Preparation
Appendix 7.25–3. QC of Stock Solution: Form and Example
Appendix 7.25–4. Sample Listing of Antimicrobial Agents, Abbreviations, and Concentrations that Might be Included in Microdilution MIC Trays
Appendix 7.25–5. ATCC QC Organisms that have On-Scale Endpoints for the Agents and Concentrations Depicted in Appendix 7.25–4
Appendix 7.25–6. Preparation of Antimicrobial Dilutions for Broth Microdilution MIC Trays
Appendix 7.25–7. Preparation of Individual Broth Microdilution MIC Trays
Appendix 7.25–8. Worksheet for Microdilution MIC Trays and Sample Sheet
Appendix 7.25–9. Broth Microdilution MIC Tray Preparation Checklist
Section 9
Appendix 9.10.1–1. Comparison of PyroMark (PSQ) Platforms (Qiagen)
Appendix 9.10.1–2. Primers Required for Pyrosequencing Assays
Appendix 9.10.1–3. Thermal Cycling Conditions for Pyrosequencing Assays
Appendix 9.10.1–4. Dispensation Order for Each PSQ Subassay
Appendix 9.10.1–5. Library for PSQ Subassays
Appendix 9.10.1–6. Positive Control for Each Subassay, as Shown in the Detailed Report of the IdentiFire Software
Section 10
Appendix 10.4.1–1. Reagent Preparation
Appendix 10.4.2–1. Reagents
Appendix 10.6–1. Medium and Reagent Preparation
Appendix 10.7–1. Medium Preparation, Storage, and Sources
Appendix 10.9–1. Medium Preparation and Sources
Appendix 10.10–1. Figures
Appendix 10.10–2. Media and Reagents, Sources, and Recipes
Section 12
Appendix 12.2–1. Viral Transport Medium Formula
Appendix 12.2–2. Antimicrobial Additives for Specimen Decontamination Prior to Virus Culture Inoculation
Appendix 12.2–3. NH
4
Cl Lysis Solution
Appendix 12.3–1. Example of Assay Training Checklist
Appendix 12.3–2. Example of Laboratory Procedure Format
Appendix 12.3–3. Example of Validation/Verification Form
Appendix 12.3–4. Example of an IQCP Form
Appendix 12.3–5. Example of Tracer Form
Appendix 12.5–1. Preparation of 10% RBC Suspension for Hemadsorption Test
Appendix 12.5–2. Viral Titration and Determination of TCID
50
Appendix 12.5–3. Hemadsorption Procedure
Appendix 12.5–4. Preparation and Fixation of Cell Spots on Slides
Appendix 12.5–5. Immunofluorescence Staining of Fixed Cell Spots on Slides
Appendix 12.5–6. Acid Lability Assay
Appendix 12.5–7. Preservation of Cell Culture Monolayers in Cell Culture Tubes
Appendix 12.7–1. Summary of Aseptic Technique
Appendix 12.7–2. Detection of Bacterial and Fungal Contamination in Cultured Cells
Appendix 12.7–3. Detection of Mycoplasmas in Cultured Cells
Appendix 12.7–4. Cell Counting with a Hemocytometer
Appendix 12.7–5. Samples of Forms for Recording the Preparation and QC of Monolayer Cell Cultures
Appendix 12.8–1. Composition of BSS, PBS, and Media
Appendix 12.8–2. Select Commercial Sources of Cell Culture Medium and Supplemental Components
Appendix 12.8–3. Storage Conditions and Shelf Lives of Media and Supplemental Components
Appendix 12.8–4. Procedure of Heat Inactivation of FBS
Appendix 12.8–5. Procedure for Washing and Sterilizing Glassware
Appendix 12.8–6. Samples of Report Forms for Recording the Preparation and QC of Media and Supplemental Components
Appendix 12.9.1–1. Procedures for Collection of Specimens for Immunofluorescence Testing
Appendix 12.9.2–1. Meta-analysis of RADT Performance
Appendix 12.9.2–2. Real-time Monitoring of Test Data
Appendix 12.9.2–3. Biosafety Considerations for Testing of Respiratory Viruses
Appendix 12.10–1. Preparation of
Chlamydia
Control Stock
Appendix 12.10–2. Procedure for Pretesting Swabs
Section 13
Appendix 13.16.7–1. 1.4% 2-Mercaptoethanol in Phosphate-Buffered Saline
Section 15
Appendix 15.3.1–1. Calculating Sample Results from 500 Liters or 200 Liters per Plated Medium with Two Different Media
Appendix 15.3.4–1. Media Fill Testing Procedure for Low-Risk Sterile Compounding
Appendix 15.3.4–2. Media Fill Testing Procedure for Medium-Risk Sterile Compounding
Appendix 15.3.4–3. Media Fill Testing Procedure for High-Risk Compounds
Appendix 15.3.4–4. USP <797> Sample Form 1: Assessing Hand Hygiene and Garbing Related Practices of Compounding Personnel
Appendix 15.3.4–5. USP <797< Sample Form 2: Assessing Aseptic Technique and Related Practices of
Appendix 15.3.5–1. Minimum Number of Articles to be Tested in Relation to the Number of Articles in the Batch
Appendix 15.3.5–2. Minimum Quantity to be Used for Each Medium
Appendix 15.3.5–3. Strains of the Test Microorganisms Suitable for Use in the Growth Promotion Test and the Method Suitability Test
Appendix 15.4.1–1. Reagents and Media
Appendix 15.4.3–1.Features of Mechanical Volumetric Sampling Devices
Appendix 15.7.2–1. Media Surveillance Cultures for MRSA
Appendix 15.8.3–1. Postexposure Questionnaire for Risk Assessment
Appendix 15.8.3–2. Tool for Monitoring Symptoms in the Case of Possible Exposure
Section 16
Appendix 16.1–1. List of Approved Accreditation Organizations Under the Clinical Laboratory Improvement Amendments (CLIA)
Appendix 16.1–2. List of the Clinical Laboratory Improvement Amendments (CLIA) Approved Proficiency Testing (PT) Programs for 2021
Appendix 16.1–3. Procedure for Development of a Customer Feedback Survey
Appendix 16.1–4. Procedure to Develop a Competency Assessment Program
Appendix 16.1–5. Example Draft of Bacteriology Tests Systems or Processes Grouped for Competency Assessment
Appendix 16.1–6. Competency Assessment Form
Appendix 16.1–7. Quality Indicators by Path of Workflow
Appendix 16.1–8. Quality Indicator Activities Form
Appendix 16.1–9. Example of Quality Indicator Report
Appendix 16.1–10. Nonconforming Event Form
Appendix 16.1–11. Nonconforming Event Analyzed by Path of Workflow
Appendix 16.1–12. Examples of Tools Used for Root Cause Analysis. A. Process Mapping B. Fishbone Diagram. C. Pareto Chart
Appendix 16.1.1–1. Problem-Solving PDCA-A3 Form
Appendix 16.1.2–1. Example Error Report Log
Appendix 16.1.2–2. Example Maintenance Log
Appendix 16.1.2–3. Laboratory Process Improvement Metrics Example
Appendix 16.6–1. Requirements for Laboratory Records
Appendix 16.6–2. Examples of Laboratory Forms and Records
Appendix 16.7–1. Determination of Total Bacterial Counts
Appendix 16.7–2. Resistivity Testing
Appendix 16.8.1–1. Colorimetric Quantitative Loop Calibration
Appendix 16.8.2–1. Worksheet 1: Pipette Calibration—Gravimetric
Appendix 16.8.2–2. Worksheet 2: Pipette Calibration—Spectrophotometric
Section 18
Appendix 18.14-1. (A-H)
Section 2
Table 2.1–1. “Rule-Out” Clinical Impressions and Potential Etiological Agents
Table 2.1–2 General principles for specimen collection
Table 2.1–3 Common transport media
Table 2.1–4 Collection of specimens for bacteriological analysisa,b
Table 2.1–5 Rejection criteria for microbiological specimensa,b
Table 2.1–6 Collection of specimens to detect infrequently encountered organisms
Table 2.1–7 Collection of specimen for virological analysisa
Table 2.1–8 Laboratory approaches to suspected fungal infections
Table 2.1–9 Collection of specimens to detect parasitesa
Table 2.1–10 Specimen processing triage
Table 2.1–11 Procedure for processing clinical specimens in microbiologya
Table 2.1–12 Critical values in microbiologya
Table 2.1–13 Alert request
Section 3
Table 3.2.1–1 Common descriptions of bacterial Gram staining characteristics. Note: these descriptive terms are not generally included in the patient report.
Table 3.2.1–2 Gram stain morphology for clinical report
Table 3.2.1–3 Enumeration of cells and reporting of Gram stain results from direct smearsa
Table 3.2.1–4 Direct specimen Gram stain: most common pathogens by anatomic site/specimen sourcea
Table 3.2.1–A1 Standardized scoring method for evaluation of Gram stains for BV
Table 3.3.1–1 Common laboratory media used for aerobic culturesa
Table 3.3.1–2 Order of manual specimen processing for bacteriology when multiple specimens are received at the same time
Table 3.3.1–3 Recommended aerobic culture media for inoculation of common clinical specimensa
Table 3.3.2–1 Terms to describe gross colonial morphologya
Table 3.3.2–2 Enumeration guidelines for aerobic cultures (excludes quantitative cultures)
Table 3.3.2–3 Commonly used primary plating media
Table 3.3.2–4 Colony morphology on primary mediaa
Table 3.3.2–5 Key biochemical and phenotypic characteristics of common pathogens to aid in preliminary identification when suspected from colony morphology listed in Table 3.3.2–4a
Table 3.4–1 Types of body fluids submitted for culture
Table 3.4–2 Common drainage tubes in clinical use
Table 3.4–3 Sterile fluid volume to inoculate in blood culture bottles (for pericardial, peritoneal dialysis, pleural, and synovial fluids)
Table 3.5–1 Common bacterial organisms causing acute meningitis by age or conditiona
Table 3.5–2 Collection guideline for laboratory tests performed on CSF and shunt specimens
Table 3.5–3 Common types of central nervous system devicesa
Table 3.7.1–1 Commonly used primary plating and broth media for isolation/detection of Salmonella, Shigella, and STEC
Table 3.7.1–2 Special highly selective media for specific pathogen requests
Table 3.7.1–3 QC of specialized media for detection of fecal pathogens
Table 3.7.1–4 Biochemical differentiation of selected members of the Salmonella groupa
Table 3.7.1–5 Summary of detection media and identification methods for fecal pathogensa
Table 3.7.2–1 Human disease associations of Campylobacter and related speciesa
Table 3.7.2–2 Commercial systems for generating microaerobic environments and the approximate atmospheric content
Table 3.7.2–3 QC of specialized media for detection of Campylobacter species
Table 3.7.2–4 Phenotypic reactions of clinically important Campylobacter, Arcobacter, and Helicobacter speciesa
Table 3.8.1–1 Female genital infections
Table 3.8.1–2 Female genital infectious clinical syndromes associated with intrapartum, postpartum, and postabortal infections
Table 3.8.1–3 Male genital infections
Table 3.8.3–1 Biochemical reactions of Neisseria and related oxidase‐positive diplococci and bacilli that may grow on Thayer‐Martin or similar selective agara
Table 3.9–1 Common ocular infections
Table 3.9–2 Recommended media and common pathogens detected from specimens collected for the diagnosis of ocular infections
Table 3.10.1–1 Appropriate specimens for diagnosis of bacterial and yeast upper and lower respiratory diseases
Table 3.10.2–1 Guidelines for reporting of primary pathogens for lower respiratory cultures
Table 3.10.2–2 Culture methods, colony equivalents, and thresholds for significant growth
Table 3.10.3–1 Criteria for workup of organisms
Table 3.10.4–1 Plating guidelines for Legionella culture
Table 3.10.5–1 Bacterial organisms associated with ear infections
Table 3.10.6–1 Suction pressures for collecting nasal aspirates
Table 3.10.6–2 Test organisms for medium control
Table 3.10.6–3 Biochemical differentiation of Bordetella species of importance in respiratory culturesa
Table 3.10.7–1 Expected QC results for TIN and CTBA media
Table 3.10.7–2 Key biochemical reactions to identify toxigenic Corynebacterium speciesa
Table 3.10.8–1 Overview of bacterial pharyngitis pathogens
Table 3.11.1–1 Definitions of common terms
Table 3.11.1–2 Classification and workup of potential uropathogens in nonsterile urinesa
Table 3.11.1–3 Protocol for workup and reporting of urine cultures
Table 3.11.1–4 Examples of alternative urine culture systemsa
Table 3.11.1–5 Reporting scheme for isolates with minimal testinga
Table 3.12.1–1 Common types of superficial and deep wounds and abscesses
Table 3.12.1–2 Guidance on workup of common aerobic and anaerobic isolates from wound and tissue cultures
Table 3.12.1–3 Examples of challenging clinical scenarios in wound culture
Table 3.14.3–1 Examples of commercial NAATs for detection of M. pneumoniaea
Table 3.14.4–1 Examples of commercial NAATs for detection of M. genitaliuma
Table 3.14.4–2 Characteristics of commercial NAATs for detection of M. genitalium
Table 3.16–1 Summary of commonly used commercial manual and automated bacterial identification systems
Table 3.16–2 General testing considerations for biochemical identification of aerobic bacteria
Table 3.17.4–1 QC organisms and zone sizes for antimicrobial disks used for identification testing
Table 3.17.15–1 Decarboxylase‐dihydrolase test results for QC organisms
Table 3.17.24–1 QC Organisms and test resultsa
Table 3.17.30–1 Control organisms
Table 3.17.35–1 Organisms
Table 3.18–1 Key biochemical reactions of the common and/or significant Gram‐positive cocci that are always or nearly always catalase positive with large white to yellow coloniesa
Table 3.18–2 Separation of the common groups of viridans group streptococci isolated from human clinical specimens (PYR‐negative, LAP‐positive, 6.5% NaCl‐negative cocci in chains)a
Table 3.18–3 Common species of Enterococcus and other PYR‐positive cocci in chainsa
Table 3.18–4 Phenotypic characteristics of PYR‐positive, catalase‐negative or weakly catalase‐positive, Gram‐positive cocci (excluding Streptococcus pyogenes)a,b
Table 3.18–5 Phenotypic characteristics of PYR‐negative, catalase‐negative, Gram‐positive coccia
Table 3.18–6 Catalase‐negative, Gram‐positive bacilli that can grow aerobically or as facultative anaerobesa
Table 3.18–7 Catalase‐positive, Gram‐positive bacilli which may have yellow‐ or pink‐pigmented coloniesa
Table 3.18–8 Large, regular catalase‐positive, Gram‐positive bacilli that may produce spores and are usually motilea
Table 3.18–9 Urease‐positive Corynebacterium spp. of clinical importancea
Table 3.18–10 Catalase‐positive, urease‐negative, Gram‐positive bacilli, excluding Corynebacterium spp. and yellow‐ or pink‐pigmented bacillia
Table 3.18–11 Urease‐negative Corynebacterium spp. of clinical importancea
Table 3.19–1 Biochemical reactions of Neisseria spp. and related oxidase‐positive diplococci and coccobacilli that may grow on Thayer‐Martin or similar selective agara,b
Table 3.19–2 Biochemical reactions of Haemophilus spp. that satellite on BAPa
Table 3.19–3 Differential biochemical reactions for indole‐positive, Gram‐negative bacilli that grow poorly on MAC in 48 ha
Table 3.19–4 Gram‐negative bacilli and coccobacilli that grow on BAP but are catalase negative or weak, with poor growth on MAC in 48 ha
Table 3.19–5 Biochemical differentiation of non‐yellow‐pigmented, Gram‐negative bacilli and coccobacilli that are catalase positive and indole negative but do not grow well on MACa
Table 3.19–6 Biochemical characteristics of the nonmotile, yellow, nonfermenting, Gram‐negative bacilli that are catalase positivea
Table 3.19–7 Biochemical differentiation of the motile, yellow, non‐glucose‐fermenting, Gram‐negative bacillia
Table 3.19–8 Characteristics of the common pathogenic oxidase‐positive, glucose‐fermenting bacilli that grow on MAC and are not yellow pigmenteda
Table 3.19–9 Differentiation of Yersinia pestis from similar bacteriaa
Table 3.19–10 Biochemical reactions of non‐glucose‐fermenting, Gram‐negative bacilli or coccobacilli that are catalase positive, oxidase negative or delayed, and grow well on MAC within 48 ha
Table 3.19–11 Characteristics of Burkholderia cepacia complex and related polymyxin B‐resistant organismsa
Table 3.19–12 Biochemical reactions of nonyellow Gram‐negative bacilli that are oxidase positive and grow well on MAC within 48 ha
Section 4
Table 4.2–1 Clinically relevant taxonomy updates for anaerobes
Table 4.3–1 Acceptable specimens for anaerobic culturea
Table 4.4.1–1 Primary anaerobic media and their usesa
Table 4.4.2–1 Secondary media for use in cultivating or selecting for specific anaerobes
Table 4.7–1 Anaerobic organism clues from primary anaerobic blood agar culture plates and suggestions for use of supplemental media
Table 4.8–1 Identification of anaerobic bacteria isolated from nonsterile sites when MALDI‐TOF MS is not available
Table 4.9.5–1 Identification by means of special‐potency antimicrobial agent disksa
Table 4.9.8–1 Fluorescence of anaerobic bacteria
Table 4.10–1 Characteristics of the manual biochemical system, API 20A (bioMérieux, Inc.)
Table 4.10–2 Characteristics of rapid identification systems
Table 4.10–3 Recommended QC strains for API 20A system
Table 4.13–1 Clinical significance and key biochemicals of pathogenic anaerobic Gram‐negative bacillia
Table 4.13–2 Characteristics of clinically relevant Fusobacterium spp.a
Table 4.13–3 Characteristics of select members of Bacteroides spp. and former Bacteroides species renamed into other generaa
Table 4.13–4 Characteristics of Porphyromonas spp. of human origina
Table 4.13–5 Characteristics of pigmented and saccharolytic Prevotella and Alloprevotella spp.a
Table 4.13–6 Characteristics of 20% bile‐sensitive, nonpigmented, and saccharolytic Prevotella and related spp.a
Table 4.13–7 Characteristics of other anaerobic Gram‐negative bacillia
Table 4.14–1 Clinical significance and biochemical characteristics of species of Actinomyces spp., genera formerly Actinomyces, Actinotignum spp., Cutibacterium spp., and allied generaa,
Table 4.14–2 Gram stain morphology and clinical significance of non‐spore‐forming anaerobic Gram‐positive bacilli, other than Actinomyces spp., genera formerly Actinomyces, Actinotignum spp., Cutibacterium spp., and allied genera
Table 4.14–3 Gram stain and colonial morphology of Actinomyces spp., genera formerly Actinomyces, Actinotignum spp., Cutibacterium spp., and allied generaa
Table 4.14–4 Gram stain and colonial morphology of commonly isolated and clinically relevant Clostridium spp., Clostridioides spp., Paraclostridium spp., Enterocloster spp., Hathewaya spp., and Paeniclostridium spp.a
Table 4.14–5 Biochemical characteristics of Clostridium spp., Clostridioides spp., Paraclostridium spp., Enterocloster spp., Hathewaya spp., and Paeniclostridium spp.a
Table 4.14–6 Biochemical characteristics of non‐spore‐forming anaerobic Gram‐positive bacilli, other than Actinomyces spp., genera formerly Actinomyces, Actinotignum spp., Cutibacterium spp., and allied generaa
Table 4.15–1 Classification of the major genera of clinically relevant anaerobic Gram‐positive and Gram‐negative cocci in humans
Table 4.15–2 Characteristics of commonly recovered anaerobic Gram‐positive coccia
Table 4.15–3 Characteristics of anaerobic Gram‐negative coccia
Table 4.15–4 Special‐potency disk testing of anaerobic coccia
Table 4.16–1 Available methods and algorithms for detection of Clostridioides difficile in stool specimens
Section 5
Table 5.2–1 Key points for the collection and laboratory diagnosis of bacteremiaa
Table 5.2–2 Example of weight-based blood volumes for culture from pediatric patientsa
Table 5.2–3 Example of age-based blood volumes for culture from pediatric patientsa
Table 5.3–1 Summary of automated blood culture systemsa
Table 5.5–1 Acceptable specimens for use with VersaTREK Myco and BACTEC Myco/F Lytic media
Table 5.5–2 Recommended incubation protocols for mycobacteria, yeast, and fungi
Table 5.7–1 Visible signs of growth caused by organisms commonly encountered in blood cultures
Table 5.7–2 Interpretative guide for positive blood cultures
Table 5.9–1 Commonly isolated true pathogens versus probable contaminants in blood specimens
Table 5.11.1–1 Organisms cultured from blood products in TTBI reported to the National Healthcare Safety Network Hemovigilance Module, 2010–2016
Table 5.12–1 Common types of vascular and hemodialysis access cathetersa
Table 5.13–1 Summary of commercially available blood culture panels using positive blood culture brotha
Section 6
Table 6.3–1 Summary of common misidentifications of select agents by MALDI-TOF MS
Table 6.4–A1 Databases
Table 6.5–1 Available fungal databases
Section 7
Table 7.1–1 Summary for AST testing and reporting considerations for major pathogen groups a
Table 7.1.2–1 Primary organizations involved in establishing and revising breakpoints
Table 7.1.2–2 Interpretive categories for bacterial antimicrobial susceptibility tests
Table 7.2–1 Recommended agars for testing according to CLSI and EUCASTa
Table 7.2–2 Sample QC strain recommendations
Table 7.2–3 Recommended incubation conditions according to CLSI and EUCAST
Table 7.4.1–1 Inoclum preparation method summary
Table 7.4.1–2 Example for E. coli with CLSI interpretation
Table 7.4.1–3 Methods for detection of methicillin (oxacillin)-resistant Staphylococcus spp. using CLSI methods
Table 7.4.1–4 Methods for detection of methicillin (oxacillin)-resistant Staphylococcus spp. using EUCAST methods
Table 7.5–1 Interpretive drug resistance categories
Table 7.9–1 Summary of test methods for detection of hVISA, VISA, and VRSA in Staphylococcus aureusa
Table 7.14–1 CLSI screening criteria for ESBL detection (7, 8)
Table 7.14–2 EUCAST ESBL screening criteria for ESBL detection in Enterobacteralesa
Table 7.15–1 Antimicrobial susceptibility profiles used to screen EUCAST group 1 Enterobacterales to consider testing for acquired AmpC beta-lactamasesa
Table 7.16.2–1 MHT and mCIM quality control worksheeta
Table 7.16.2–2 Capacity of 100-mm (small) and 150-mm (large) MHA plates for the MHT
Table 7.16.2–3 Interpretation and reporting of MHT results
Table 7.16.2–4 Interpretation and reporting of mCIM results
Table 7.16.3–1 Carba NP quality control worksheet
Table 7.16.3–2 Interpretation and reporting of results
Table 7.16.4–1 mCIM and eCIM quality control worksheeta
Table 7.16.4–2 Interpretation of mCIM and eCIM results
Table 7.16.4–3 Combined disk test interpretation
Table 7.25–A1 Preparation of antimicrobial dilutions: primary scheme
Table 7.25–A2 Preparation of antimicrobial dilutions: alternative schemea
Section 8
Table 8.1–1 Common genera of aerobic actinomycetes associated with disease in humans, with the number of presently recognized species in each (2)
Table 8.3–1 Results of tests used for presumptive identification of aerobic actinomycetes to genus levela,b
Table 8.3–2 Characteristics differentiating the medically important species of the genus Nocardiaa,b
Table 8.3–3 Differential characteristics of the genus Rhodococcusa,b
Table 8.3–4 Differential characteristics of the genus Tsukamurella a, b
Table 8.3–5 Differential characteristics of the genus Nocardiopsis a,b
Table 8.3–6 Differential physiological characteristics of the medically important Gordonia a speciesb
Table 8.3–7 Differentiation of commonly isolated nocardiae based on antimicrobial susceptibility patterna,b
Table 8.3–8 Susceptibility profile indexes of commonly isolated nocardiae based on antimicrobial susceptibility patternsa,b
Table 8.4–1 Gene primers for multilocus amplification and sequencing
Table 8.5–1 QC ranges of MICs a
Table 8.5–2 Broth microdilution MIC interpretational breakpoints for Nocardia spp. and other aerobic actinomycetesa
Table 8.6.1–A1 More frequently isolated Nocardia species/complexes listed by frequency
Table 8.6.1–A2 More frequently isolated species of aerobic actinomycetes and primary clinical disease association
Table 8.6.1–A3 Less frequently/infrequently isolated species of aerobic actinomycetes and primary clinical disease association
Section 9
Table 9.2.3–1 Quantitation of acid-fast staining results
Table 9.3–1 Media commonly available for recovery of mycobacteria (3)
Table 9.4.1–1 Dilutions and days to positivity
Table 9.4.2–1 Expected QC results
Table 9.5.1–1 Preparation of arylsulfatase standards (1)
Table 9.5.1–2 Distinctive properties of cultivable mycobacteria encountered in clinical specimensa
Table 9.5.1–3 Colonial morphology for selected mycobacteria (2)
Table 9.5.2–1 Suggested positive and negative control organisms
Table 9.5.2–2 Hybridization and selection step temperature ranges and selection times
Table 9.7.1–1 SIRE QC test expected results
Table 9.7.1–2 BACTEC MGIT SIRE Kit drug concentrations per susceptibility test preparation step
Table 9.7.1–3 BACTEC MGIT STR 4.0 and INH 0.4 Kits’ drug concentrations per susceptibility test preparation step
Table 9.7.2–1 QC results
Table 9.7.2–2 MGIT concentrations for PZA susceptibility testing
Table 9.7.3–1 Reagent formulations upon rehydration
Table 9.7.3–2 Drug concentrationsa
Table 9.8–1 Recommended drug concentrations in Middlebrook 7H10 and 7H11 agar (1, 4–6)
Table 9.8–2 Guidelines for selection of the dilution of a specimen concentrate prior to inoculation of 7H10 medium for susceptibility testing using the direct method
Table 9.9.1–1 Suggested QC ranges for M. peregrinum ATCC 700686
Table 9.9.1–2 Interpretation of MIC
Table 9.9.2–1 Expected MICs for M. marinum ATCC 927, M. avium ATCC 700898, and S. aureus ATCC 29213a
Table 9.9.2–2 MIC interpretations for isolates of slowly growing NTMa
Table 9.9.3–1 MIC QC ranges for testing MTBC using M. tuberculosis ATCC 27294 (H37Rv) in Middlebrook 7H9 media supplemented with OADC
Table 9.9.3–2 Interpretation of inoculum density as determined by viable countsa
Table 9.9.3–3 Broth microdilution breakpoints and interpretive categories for MTBC tested using commercially available MIC platesa
Section 10
Table 10.3–1 Site-specific specimen selection and collection guidelines
Table 10.4.1-1 Quality control standard performance of common stains and reagents used in direct microscopic examination of clinical specimens in the mycology laboratory
Table 10.5–1 Mycological media selection for the isolation of fungi
Table 10.5–2 Media for the isolation and identification of fungia
Table 10.6–1 General list of yeast and yeastlike species or genera based on colony colora
Table 10.6–2 Summary of subsequent tests
Table 10.7–1 Tests for presumptive identification of yeasts in primary culture
Table 10.7–2 Presumptive identification of C. auris is provided
Table 10.9–1 Examples of anamorph-teleomorph binomials of commonly encountered yeastsa
Table 10.9–2 General considerations of two commercial yeast identification systems
Table 10.9–3 Examples of useful supplemental tests for yeastsa
Table 10.9–4 Culture and biochemical characteristics of yeasts frequently isolated from clinical specimensa
Table 10.9–5 Characteristics of selected Trichosporon spp.a
Table 10.9–6 Key characteristics to differentiate Malassezia species
Table 10.9–7 Common yeast morphology on cornmeal agar
Table 10.10–1 Definitions of terms used to describe morphological structures
Table 10.10–2 Phenotypic characteristics useful for identification of Mucoromycetaa
Table 10.10–3 Description of terms for conidial ontogeny and reproductive structures of the Ascomycota
Table 10.10–4 Common media used for molds
Table 10.10–5 Temperature tests commonly used in identification of clinically important molds
Table 10.10–6 Cycloheximide responses of common or critical clinical laboratory molds (including abundant contaminants)
Table 10.10–7 Distinguishing features for preliminary identification of mold phases of dimorphic systemic pathogens
Table 10.10–8 Particulate phases of dimorphic fungi as seen in in vitro conversion and their differentiating characteristics
Table 10.10–9 Dermatophyte micromorphological structures
Table 10.10–10 Phenotypic identification characteristics of common and occasionally seen dermatophytes, as well as rare species
Table 10.10–11 Most common fungi other than dermatophytes and Neoscytalidium repeatedly and rigorously implicated as causal agents of onychomycosis
Table 10.11–1 Common PCR primers used for fungal DNA sequencinga
Table 10.11–2 PCR master mix components and volumes to use
Table 10.11–3 PCR submaster mix 1
Table 10.11–4 PCR submaster mix 2
Table 10.11–5 PCR cycling parameters
Table 10.11–6 Cycle sequencing PCR master mix
Table 10.11–7 Cycle sequencing PCR cycling conditions
Table 10.12.1–1 Differences between the CLSI and EUCAST methods for microdilution antifungal susceptibility testing
Table 10.12.1–2 Dilution procedures for preparing stock solutions of water-insoluble antifungals
Table 10.12.1–3 Dilution procedures for preparing stock solutions of water-soluble antifungals
Table 10.12.1–4 Final antifungal concentration ranges for susceptibility testing
Table 10.12.1–5 Examples of CLSI yeast QC isolates and MIC ranges for clinically available antifungals
Table 10.12.1–6 Examples of CLSI QC and reference isolates of filamentous fungi, and MIC/MEC ranges (μg/ml) for different clinically available antifungals
Table 10.12.1–7 Recommended absorbance ranges (OD, measured at 530 nm) per different genera of filamentous fungi used for the preparation of the inoculum
Table 10.12.1–8 Recommended incubation periods for different fungi
Table 10.12.1–9 Endpoints used for determination of antifungal activity
Table 10.12.2–1 QC zone diameters for disk diffusion testing against Candida
Table 10.12.2–2 QC and reference zone diameters for disk diffusion testing against filamentous fungi and Candida krusei
Table 10.13–1 CLSI MIC breakpoints for in vitro broth dilution susceptibility testing of Candida species and select antifungal agents after 24-hour incubationa
Table 10.13–2 CLSI zone diameter breakpoints for select antifungal agents against Candida spp. after 24-hour incubationa
Table 10.13–3 CLSI MIC breakpoints for voriconazole against Aspergillus fumigatus after 48-hour incubation
Table 10.13–4 List of Aspergillus species and antifungals for which EUCAST CBPs are available
Table 10.13–5 Species with known intrinsic resistance to certain antifungal agents
Table 10.13–6 ECVs for Candida species (without defined interpretive breakpoints)
Table 10.13–7 ECVs for Cryptococcus species (without defined interpretive breakpoints)
Table 10.13–8 ECVs for Aspergillus species (without defined interpretive breakpoints)
Section 11
Table 11.2.2–A1 Fixatives used in diagnostic parasitology (stool specimens)
Table 11.6.2–1 Quantitation of parasites, human cells, yeast cells, and artifacts in specimens from the intestinal tracta
Table 11.6.3–1 Quantitation of parasites, human cells, yeast cells, and artifacts in specimens from the intestinal tracta
Table 11.6.4–1 Quantitation of parasites, fecal leukocytes, and red blood cells in specimens from the intestinal tracta
Table 11.7.3–1 Stains for identifying parasites in various tissuesa
Table 11.8.7–1 Parasitemia determined from conventional light microscopy: clinical correlationa
Table 11.8.7–2 Malaria resistancea
Table 11.11.1–A1 Clinical specimens: summary of artifacts resembling parasites
Table 11.11.2–A1 Body sites and specimen collection
Table 11.11.2–A2 Body sites and the most common parasites recovered (trophozoites, cysts, oocysts, spores, adults, larvae, eggs, amastigotes, and trypomastigotes)a
Table 11.11.2–A3 Body sites, specimens, and recommended stainsa
Table 11.11.2–A4 Examination of tissues and body fluids
Table 11.11.2–A5 Protozoa of the intestinal tract and urogenital system: key characteristicsa
Table 11.11.2–A6 Tissue protozoa: characteristics
Table 11.11.2–A7 Helminths: key characteristicsa
Table 11.11.2–A8 Parasites found in blood: characteristicsa
Table 11.11.2–A9 Parasitic infections: clinical findings in healthy and compromised hosts
Table 11.11.2–A10 Fecal antigen detection method options
Table 11.11.7–A1 Submission of stool specimens
Table 11.11.7–A2 Examination of fecal specimensa
Table 11.11.7–A3 Examination of blood specimens
Section 12
Table 12.1–1 Clinical manifestations of human viral infections transmitted from one person to anothera
Table 12.1–2 Zoonotic viruses and clinical manifestations associated with infection spread from vertebrate animals to humans
Table 12.1–3 Laboratory methods used in clinical virology laboratory to identify viruses
Table 12.2–1 Specific clinical presentations/suspected infections for which virus/chlamydia culture may be diagnostically helpful
Table 12.2–2 Specimen collection for virus culturea
Table 12.5–1 Selected common cell types (lines) used in conventional tube cultures for virus isolation in clinical virology laboratories
Table 12.5–2 Appearance, development, and progression of CPE for select viruses that grow in tube cell culturesa
Table 12.6–1 Troubleshooting problems with shell vial or multiwell plate cultures
Table 12.7–1 Viral culture systems and availability
Table 12.7–2 Characteristics of monolayer cell cultures
Table 12.7–3 Assessment of monolayer cell cultures and troubleshooting
Table 12.7–4 Reagent volumes for trypsinization of monolayer cell cultures
Table 12.7–5 Recommended split ratios for commonly used cell linesa
Table 12.7–6 Surface area, cell yield, and final volume of growth medium for commonly used culture vesselsa
Table 12.8–1 Common components of cell culture medium and their function
Table 12.8–2 Selected common culture media and balanced salt solutions for mammalian cells
Table 12.8–A1 Composition of BSS and PBSa (1, 2, 3)
Table 12.8–A2 Compositions of commonly used cell culture media (4, 5, 6)
Table 12.9.1–1 Immunofluorescence detection of viruses in clinical specimens
Table 12.9.1–2 Troubleshooting problems with immunofluorescence assays
Table 12.9.2–1 Available FDA-cleared rapid antigen detection tests for influenza virus types A and Ba
Table 12.9.2–2 Selected SARS-CoV-2 rapid antigen detection tests with emergency use authorization by FDAa
Table 12.9.2–3 Available FDA-cleared rapid antigen detection tests for RSVa
Table 12.9.3–1 Description of inclusion morphology for selected viruses following cytologic staininga
Table 12.10–1 Human chlamydial infections
Table 12.10–2 Collection of specimens
Section 13
Table 13.1.2–1 Basic description of common immunologic assays used for detection of antibodies to and antigens from infectious pathogensa
Table 13.2.1–1 Extracellular products used in streptococcal serology assays
Table 13.2.1–2 Upper limit of normal (80th percentile) values for serum streptococcal antibody titers in children in the United Statesa
Table 13.2.1–3 Upper limit of normal (80th percentile) for serum streptococcal antibody titers in children and adults in tropical settings where GAS disease is endemica
Table 13.3.1–1 Tests commonly used in the laboratory diagnosis of brucellosisa
Table 13.4.1–1 Comparative analysis of the sensitivity and specificity of serologic tests for tularemiaa
Table 13.5.1–1 Select list of treponemal and nontreponemal syphilis diagnostic test kits and reagentsa
Table 13.5.2–1 Reporting quantitative serum resultsa
Table 13.5.2–2 Reporting quantitative CSF resultsa
Table 13.5.3–1 Reporting quantitative resultsa
Table 13.5.5–1 Reporting patterns of agglutination
Table 13.5.8–1 Rating of the antigen lines’ intensity in comparison to control lines
Table 13.6–1 Lyme disease stages
Table 13.6–2 FDA-cleared commercially available B. burgdorferi antibody assays released between 2016 and 2021a
Table 13.7–1 Summary of select serologic assays with FDA EUA for detection of IgG or total antibodies to SARS-CoV-2
Table 13.7–2 Summary of anti-spike and antinucleocapsid serologic test results and interpretationa
Table 13.8.1–1 Correlation of clinical status and characteristic EBV serologic profilesa
Table 13.9.2–1 List of commonly used serologic methods or platforms for CMV testing
Table 13.9.3–1 Commercially available CMV IgG avidity assays
Table 13.10.1–1 Relevant HIV-1 and HIV-2 proteins in diagnostic platforms
Table 13.10.1–2 FDA-approved HIV screening testsa
Table 13.10.2–1 CDC/APHL recommended language for reporting algorithm resultsa
Table 13.10.3–1 Antigens included in the Bio-Rad Geenius supplemental assay
Table 13.10.3–2 Bio-Rad Geenius supplemental assay interpretation
Table 13.11.1–1 FDA-approved serological assays for HAV detection
Table 13.11.1–2 Expected results from serologic testing
Table 13.11.2–1 Hepatitis B virus serologic profiles in different clinical scenarios
Table 13.11.2–2 Stages of chronic hepatitis B virus infection
Table 13.11.2–3 FDA-approved serological assays for HBV detection
Table 13.11.3–1 FDA-approved serological assays for HCV detection
Table 13.11.3–2 Interpretation of serological and molecular HCV test results
Table 13.12–1 ARBV endemic in the United States
Table 13.12–2 Commercially available kits and reagents for serodiagnosis of arboviruses
Table 13.14.2–1 Commercial sources for immunodiffusion reagents
Table 13.14.3–1 Conversion table to produce 2.8% SRBC suspensiona
Table 13.14.3–2 Preparing hemoglobin and SRBC solutions to make color standardsa
Table 13.14.3–3 Volumes of hemoglobin solution and 0.28% SRBC solution needed for making hemolysis color standards
Table 13.14.3–4 Preparation of hemolysin dilutions
Table 13.14.3–5 Preparation of complement for titrationa
Table 13.14.3–6 Reagent volume for the preparation of sensitized SRBCsa
Table 13.14.3–7 Complement titration setupa
Table 13.14.3–8 Complement back-titration acceptable rangesa
Table 13.14.4–1 Sources of EIA for the detection of antibodies to Coccidioides spp.
Table 13.15–1 Epidemiological and clinical indications for T. cruzi (Chagas disease) diagnostic testing
Table 13.15–2 Testing recommended for Chagas disease diagnosis by phase and context
Table 13.15–3 FDA-cleared assays for anti-T. cruzi antibody detectiona
Table 13.16.1–1 Example of interpretation of T. gondii serology in pregnant women
Table 13.16.1–2 Example of interpretation of T. gondii serology in an immunocompetent patient with clinical signs suggestive of toxoplasmosis
Table 13.16.1–3 Example of interpretation of T. gondii serology in immunocompromised patients
Table 13.16.1–4 Dilution technique summary
Table 13.16.6–1 Interpretation of avidity test results
Table 13.17–1 QFT-Plus result interpretation criteria (adapted from QFT-Plus package insert https://www.quantiferon.com/us/products/quantiferon-tb-gold-plus-us/package-inserts/)
Section 14
Table 14.2.1–1 Examples of errors in specimen collection
Table 14.2.1–2 Example lab submission guide/test menu
Table 14.2.1–3 Rejected specimen tracking and trendinga
Table 14.2.1–4 Trending a specific cause across time, from specific submitting sites, to support interventions
Table 14.2.1–5 Key considerations when testing in a public health emergency
Table 14.2.4–1 Regulatory guidance on the performance of method verification for molecular tests
Table 14.2.4–2 Guidance on data analysis following method verification
Table 14.3.1–1 Comparison of FDA-approved HIV-1 RNA tests: preanalytical considerationsa
Table 14.3.1–2 Comparison of FDA-approved HIV-1 RNA tests: analytical considerationsa
Table 14.3.2–1 Selected commercial tests
Table 14.3.3–1 Summary of characteristics of the five FDA-cleared HR HPV tests (as of September 2021)
Table 14.3.4–1 Commercially available FDA-cleared or -approved assaysa
Table 14.3.6–1 Selected CMV resistance assays using Sanger sequencinga
Table 14.3.7–1 EBV-associated lymphoid malignancies and applications of measuring EBV viral loads
Table 14.3.7–2 Selected list of commercial EBV qPCR assays
Table 14.3.8–1 Commercially available BKV PCR kits or reagents
Table 14.3.9–1 CDC 2021 testing recommendations by patient characteristics
Table 14.3.9–2 Preanalytical considerations for FDA-cleared tests (compiled based on data available August 2021)
Table 14.3.9–3 Analytic considerations for FDA-cleared tests (compiled based on data available August 2021)
Table 14.4.1–1 Commercially available multiplex gastrointestinal pathogen panel assays and platform/panel specificationsa
Table 14.4.1–2 Stool submission conditions and common fixatives and preservatives used in clinical microbiology, with intended use
Table 14.4.2–1 List of in vitro diagnostic syndromic panels for respiratory tract infectionsa
Table 14.4.2–2 Specimen collection for respiratory testing
Table 14.4.2–3 Selected third-party manufacturers of syndromic panel external quality controlsa
Table 14.5.1–1 Selected available reagents, kits, and software for sequence-based identification of bacteria and fungi
Table 14.5.1–2 Commonly used primers for broad-range bacterial PCR and sequence analysis using the 16S rRNA gene
Table 14.5.1–3 Commonly used primers for broad-range fungal PCR and sequence analysis using the ITS regions (includes ITS-1, ITS-2, and the 5.8S rRNA gene) or the D1/D2 region of the 28S rRNA gene
Table 14.5.2–1 Examples of open-source software for deep amplicon sequencing data analysis
Table 14.5.2–2 Primer sets for pan-bacterial and pan-fungal DNA amplification
Table 14.5.3–1 Examples of quality parameters and their thresholds evaluated at different steps of WGSa
Table 14.5.3–2 Troubleshooting common problems in WGS
Table 14.5.3–3 Suggested total genomic input per a MiSeq cartridge (in relation to the number of 5 Mb E. coli genomes)