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In response to the ever-changing needs and responsibilities of the clinical microbiology field, Clinical Microbiology Procedures Handbook, Fourth Edition has been extensively reviewed and updated to present the most prominent procedures in use today. The Clinical Microbiology Procedures Handbook provides step-by-step protocols and descriptions that allow clinical microbiologists and laboratory staff personnel to confidently and accurately 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. The collaborative efforts of over 150 experienced clinical microbiologists, medical laboratory technologists, and laboratory supervisors are included in the third edition of the Clinical Microbiology Procedures Handbook. Bibliography Includes bibliographical references and index Contents Contributors In Memoriam Contents Editorial Board How To Use This Handbook Abbreviations Preface Reader Response Form Disclaimer VOLUME 1 Procedure Coding, Reimbursement, and Billing Compliance Chapter 1.1 : Introduction / Vickie S. Baselski Chapter 1.2 : Procedure Coding, Reimbursement, and Billing Compliance / Vickie S. Baselski Specimen Collection, Transport, and Acceptability Chapter 2.1 : Collection, Transport, and Manipulation of Clinical Specimens and Initial Laboratory Concerns / Andrea J. Linscott Aerobic Bacteriology Chapter 3.1 : Introduction / Deirdre L. Church Chapter 3.2 : Staining Procedures / Wilson W. Chan Chapter 3.3 : Processing, Isolation, Detection, and Interpretation of Aerobic Bacteriology Cultures / Deirdre L. Church Chapter 3.4 : Blood Cultures Chapter 3.5 : Body Fluid Cultures (Excluding Blood, Cerebrospinal Fluid, and Urine) / Richard B. Thomson Chapter 3.6 : Diagnosis of Catheter-Related Bloodstream Infection: Differential-Time-to-Positivity Cultures and Catheter Tip Cultures / Steve Miller Chapter 3.7 : Cerebrospinal Fluid Cultures / Deirdre L. Church Chapter 3.8 : Fecal and Other Gastrointestinal Cultures and Toxin Assays / Dylan R. Pillai Chapter 3.9 : Genital Cultures Chapter 3.10 : Ocular Cultures / Deirdre L. Church Chapter 3.11 : Respiratory Tract Cultures Chapter 3.12 : Urine Cultures / Wilson W. Chan Chapter 3.13 : Wound Cultures / Julie A. Carson Chapter 3.14 : Leptospira Culture / Paul N. Levett Chapter 3.15 : Detection of Human Mycoplasmas and Ureaplasmas from Clinical Specimens by Culture and PCR / Ken B. Waites, Lynn B. Duffy, Li Xiao Chapter 3.16 : Guidelines for Biochemical Identification of Aerobic Bacteria / Deirdre L. Church Chapter 3.17 : Biochemical Tests for the Identification of Aerobic Bacteria / Deirdre L. Church Chapter 3.18 : Identification of Gram-Positive Bacteria Anaerobic Bacteriology Chapter 4.1 : Introduction / Gerri S. Hall Chapter 4.2 : Collection, Transport, and Processing of Clinical Specimens for Anaerobic Culture / Gerri S. Hall, Judith Holden Chapter 4.3 : Culture Media for Anaerobes / Gerri S. Hall, James I. Mangels Chapter 4.4 : Incubation Techniques for Anaerobic Bacteriology Specimens / Gerri S. Hall, James I. Mangels Chapter 4.5 : Examination of Primary Culture Plates for Anaerobic Bacteria / Gerri S. Hall, Linda Byrd Chapter 4.6 : Rapid Disk, Spot Tests, and Other Rapid or Primary Methods for the Identification of Anaerobes / Gerri S. Hall, Paula Summanen Chapter 4.7 : Commercial Kit Overnight Biochemical Systems for the Identification of Anaerobes / Gerri S. Hall, James I. Mangels Chapter 4.8 : Rapid Enzymatic Systems for the Identification of Anaerobes / Gerri S. Hall, James I. Mangels Chapter 4.9 : Rapid Biochemical Tests (4 Hours or Less) for the Identification of Anaerobes / Gerri S. Hall, James I. Mangels Chapter 4.10 : Use of Matrix-Assisted Laser Desorption Ionization-Time of Flight for the Identification of Anaerobic Bacteria / Gerri S. Hall Chapter 4.11 : Anaerobic Gram-Negative Bacilli / Gerri S. Hall Chapter 4.12 : Anaerobic Gram-Positive Bacilli / Gerri S. Hall Chapter 4.13 : Anaerobic Cocci / Gerri S. Hall Chapter 4.14 : Suggestions for a Practical Scheme for the Workup of Anaerobic Cultures / Gerri S. Hall Chapter 4.15 : Clostridium difficile as a Pathogen Involved in Antimicrobial Agent-Associated Diarrhea, Colitis, and Pseudomembranous Colitis / Gerri S. Hall VOLUME 2 Antimicrobial Susceptibility Testing Chapter 5.1 : Disk Diffusion Test Chapter 5.2 : Broth Microdilution Test Chapter 5.3 : Etest Chapter 5.4 : Agar Dilution MIC Test Chapter 5.5 : Beta-Lactamase Tests Chapter 5.6 : Oxacillin Salt-Agar Screen Test To Detect Oxacillin (Methicillin)-Resistant Staphylococcus aureus Chapter 5.7 : Detection of VRSA, VISA, and Vancomycin-Heteroresistant Staphylococcus aureus (hVISA) Chapter 5.8 : Screening Tests for Detection of High-Level Mupirocin Resistance in Staphylococcus aureus Chapter 5.9 : Detection of Inducible Clindamycin Resistance in Staphylococcus spp., Streptococcus pneumoniae, and Streptococcus spp. Beta-Hemolytic Group Chapter 5.10 : Screen Tests To Detect High-Level Aminoglycoside Resistance in Enterococcus spp. Chapter 5.11 : Agar Screen Test To Detect Vancomycin Resistance in Enterococcus spp. Chapter 5.12 : Extended-Spectrum Beta-Lactamase Testing for Escherichia coli, Klebsiella pneumoniae, Klebsiella oxytoca, and Proteus mirabilis Chapter 5.13 : The Modified Hodge Confirmatory Test (or the Carbapenem Inactivation Test) for Carbapenemase Production in Enterobacteriaceae Chapter 5.14 : 5.14 Tests To Assess Bactericidal Activity Chapter 5.15 : Serum Inhibitory and Bactericidal Titers Chapter 5.16 : Synergism Testing: Broth Microdilution Checkerboard and Broth Macrodilution Methods Chapter 5.17 : Quality Assurance Measures for Antimicrobial Susceptibility Testing Chapter 5.18 : Evaluation and Verification of Antimicrobial Susceptibility Test Systems Chapter 5.19 : Selecting Antimicrobial Agents for Testing and Reporting Chapter 5.20 : Preparation of Routine Media and Reagents Used in Antimicrobial Susceptibility Testing Chapter 5.21 : Preparation of Broth Microdilution MIC Trays Chapter 5.22 : Appendixes Aerobic Actinomycetes Chapter 6.1 : Introduction Chapter 6.2 : Specimen Examination and Primary Isolation Chapter 6.3 : Media and Methods Used for Phenotypic Characterization of Aerobic Actinomycetes Chapter 6.4 : Molecular Identification Chapter 6.5 : Susceptibility Testing Chapter 6.6 : Appendixes Mycobacteriology and Antimycobacterial Susceptibility Testing Chapter 7.1 : Introduction Chapter 7.2 : General Mycobacterial Procedures Chapter 7.3 : Solid Media Used for Isolation Chapter 7.4 : Liquid Media Used for Isolation Chapter 7.5 : Identification of Mycobacteria Chapter 7.6 : Nucleic Acid Amplification Procedures for Identification from Specimen Chapter 7.7 : Susceptibility Testing by Liquid Media Methods Chapter 7.8 : Susceptibility Testing by Agar Proportion Method for Mycobacterium tuberculosis Complex Chapter 7.9 : Susceptibility Testing by TREK Sensititre Microdilution Plates Mycology and Antifungal Susceptibility Testing Chapter 8.1 : Introduction and General Considerations Chapter 8.2 : Specimen Selection, Collection, and Transport Chapter 8.3 : Specimen Examination Chapter 8.4 : Processing Specimens for Fungal Culture Chapter 8.5 : Examination and Evaluation of Primary Cultures Chapter 8.6 : Presumptive Identification Tests for Yeasts Isolated on Primary Culture Chapter 8.7 : Identification of Moulds on Primary Culture Chapter 8.8 : Full Identification of Yeasts Chapter 8.9 : Mould Identification Chapter 8.10 : Antifungal Susceptibility Testing Parasitology Chapter 9.1 : Introduction Chapter 9.2 : Collection and Preservation of Fecal Specimens Chapter 9.3 : Macroscopic and Microscopic Examination of Fecal Specimens Chapter 9.4 : Special Stains for Coccidia and Microsporidia Chapter 9.5 : Additional Techniques for Stool Examination Chapter 9.6 : Other Specimens from the Intestinal Tract and the Urogenital System Chapter 9.7 : Sputum, Aspirates, and Biopsy Material Chapter 9.8 : Detection of Blood Parasites Chapter 9.9 : Culture Chapter 9.10 : Appendixes Viruses and Chlamydiae Chapter 10.1 : Laboratory Diagnosis of Viral Infections: Introduction Chapter 10.2 : Selection, Maintenance, and Observation of Uninoculated Monolayer Cell Cultures Chapter 10.3 : Cell Culture Techniques: Serial Propagation and Maintenance of Monolayer Cell Cultures Chapter 10.4 : Specimen Collection and Processing Chapter 10.5 : Viral Culture: Isolation of Viruses in Cell Cultures Chapter 10.6 : Isolation of Chlamydia spp. in Cell Culture Chapter 10.7 : Direct Detection of Viruses and Chlamydia in Clinical Samples VOLUME 3 Immunology Chapter 11.1 : Immunology Introduction Chapter 11.2 : Serologic Diagnosis of Group A Streptococcal Infections Chapter 11.3 : Detection of Legionella Antigen by Direct Immunofluorescence Chapter 11.4 : Laboratory Diagnosis of Syphilis Chapter 11.5 : Detection of Borrelia burgdorferi Antibodies Chapter 11.6 : Serodiagnosis of Rickettsial Infections Chapter 11.7 : Virology Introduction Chapter 11.8 : Human Immunodeficiency Virus Serology Chapter 11.9 : Epstein-Barr Virus Chapter 11.10 : Cytomegalovirus Serology Chapter 11.11 : Herpes Simplex Virus 1 and 2 Serology Chapter 11.12 : Flow Cytometry Chapter 11.13 : Whole-Blood Lymphocyte Immunophenotyping Using Cell Surface Markers by Flow Cytometry Chapter 11.14 : Natural Killer Cell Assays Chapter 11.15 : Dendritic Cell Assays Chapter 11.16 : Neutrophil Assays Chapter 11.17 : Peripheral Blood Mononuclear Cells Chapter 11.18 : Lymphocyte Proliferation Assay Chapter 11.19 : Measurement of Antigen-Specific Cellular Responses Using the Polychromatic Flow Cytometry Intracellular Cytokine Staining Assay Chapter 11.20 : Interferon Gamma Enzyme-Linked Immunosorbent Spot Assay Chapter 11.21 : Bead- and Plate-Based Cytokine Enzyme-Linked Immunosorbent Assays Molecular Diagnostics Chapter 12.1 : Introduction Chapter 12.2 : General Aspects of Molecular Diagnostics Chapter 12.3 : Molecular Methods for Identification of Cultured Microorganisms Chapter 12.4 : Sequence-Based Identification and Typing Chapter 12.5 : Matrix-Assisted Laser Desorption Ionization Time of Flight (MALDI-TOF) for Microorganism Identification Chapter 12.6 : Appendix 12.6-1-FDA-Cleared or Approved Nucleic Acid-Based Tests Chapter 12.7 : Appendix 12.7-1-Location in CMPH4 of Molecular Procedures Outside of Section 12 Epidemiologic and Infection Control Microbiology Chapter 13.1 : Introduction Chapter 13.2 : Laboratory Support for Infection Prevention: Collaboration with Benefits for All Chapter 13.3 : Environmental Sampling and Cultures Chapter 13.4 : Outbreak Investigations: Laboratory and Epidemiologic Concepts Chapter 13.5 : Microbial Strain Typing for Epidemiology and Infection Control Chapter 13.6 : Surveillance Cultures Chapter 13.7 : Infection Control in the Laboratory Quality Assurance, Quality Control, Laboratory Records, and Water Quality Chapter 14.1 : Quality Assessment and Improvement (Quality Assurance) Process Improvement Chapter 14.2 : Quality Control Chapter 14.3 : Laboratory Records Chapter 14.4 : Preparation and Quality Control of Laboratory Water Chapter 14.5 : Overview of Individualized Quality Control Plan (IQCP) Biohazards and Safety Chapter 15.1 : Introduction Chapter 15.2 : Biological Safety and Biohazard Prevention Chapter 15.3 : Biohazard Containment Chapter 15.4 : Laboratory Instrumentation and Equipment Chapter 15.5 : Special Pathogens and Employee Safety Chapter 15.6 : Packing and Shipping Infectious Substances Chapter 15.7 : Management of Laboratory Accidents Chapter 15.8 : Management of Infectious Waste Chapter 15.9 : Risk Assessment Bioterrorism Chapter 16.1 : General Introduction to Bioterrorism and Emerging Infectious Diseases Chapter 16.2 : Levels of Laboratory Safety Chapter 16.3 : Packing and Shipping Select Agents Chapter 16.4 : Anthrax-Bacillus anthracis Chapter 16.5 : Botulinum Toxin-Clostridium botulinum Chapter 16.6 : Brucellosis-Brucella spp. Chapter 16.7 : Plague-Yersinia pestis Chapter 16.8 : Tularemia-Francisella tularensis Chapter 16.9 : Melioidosis (Burkholderia pseudomallei) and Glanders (Burkholderia mallei) Chapter 16.10 : Smallpox-Variola Major Chapter 16.11 : Novel Influenza Viruses Chapter 16.12 : Q Fever-Coxiella burnetii Chapter 16.13 : Staphylococcal Enterotoxin B-Staphylococcus aureus Chapter 16.14 : Clinical Laboratory Bioterrorism Readiness Plan Chapter 16.15 : Biochemical Procedures Index Publisher’s summaryContinues to serve as the sole major publication providing step-by-step protocols and descriptions that enable clinical microbiologists and laboratory staff personnel to perform all analyses from the receipt of the specimen through processing, testing, interpretation, presentation of the final report, and subsequent consultation. In response to the ever-changing needs and responsibilities of the clinical microbiology field, Clinical Microbiology Procedures Handbook, Fourth Edition has been extensively reviewed and updated to present the most prominent procedures in use today. The Clinical Microbiology Procedures Handbook provides step-by-step protocols and descriptions that allow clinical microbiologists and laboratory staff personnel to confidently and accurately 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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