Clinical Microbiology Procedures Handbook, Multi-Volume -  - E-Book

Clinical Microbiology Procedures Handbook, Multi-Volume E-Book

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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.

If you are looking for online access to the latest from this reference or site access for your lab, please visit https://www.wiley.com/shop/clinmicronow".

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Table of Contents

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

List of Appendixes

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)

List of Tables

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)