Title Page -- Table of Contents -- Important Notice -- Preface to the Second Edition -- Foreword -- Acknowledgments -- Rising Sun Chair -- Contributors -- CHAPTER 1: Role of the US Food and Drug Administration in the Regulation of Clinical Microbiology Devices -- 1.1 Historical overview of in vitro diagnostics -- 1.2 Current microbiology device review regulatory pathways: practical considerations -- 1.3 Assay performance characteristics: "Statistics 101" for diagnostic device developers[1] -- 1.4 Common issues with new FDA submissions -- Appendix: web sites -- References -- CHAPTER 2: Commercial Blood Culture Systems and Methods -- 2.1 Manual blood cultures -- 2.2 Automated blood culture systems -- 2.3 Molecular and other methods -- 2.4 Future directions -- References -- CHAPTER 3: Rapid Devices and Instruments for the Identification of Aerobic Bacteria -- 3.1 Introduction -- 3.2 Major methods currently available -- 3.3 Commercial systems for identification of Gram-positive organisms -- 3.4 Commercial systems for identification of Gram-negative organisms -- 3.5 Commercial methods for identification of microorganisms directly in blood culture bottles -- 3.6 Commercial molecular methods for identification of bacteria isolated in culture -- 3.7 Emerging technologies for the identification of organisms: mass spectrometry -- References -- CHAPTER 4: Rapid Devices and Instruments for the Identification of Anaerobic Bacteria -- 4.1 Introduction and clinical considerations -- 4.2 Steps in the diagnosis of anaerobic bacterial infections -- 4.3 Commercial kit requiring 24 h of anaerobic incubation -- 4.4 Commercial enzyme kits for identification after four hours ofaerobic incubation -- 4.5 Identification by gene sequencing -- 4.6 Identification by chemical methods.

4.7 Immunodiagnostic and molecular methods for diagnosis of Clostridium difficile infection -- References -- CHAPTER 5: Rapid Antigen Devices and Instruments for the Detection and Identification of Viruses -- 5.1 Influenza viruses -- 5.2 Respiratory syncytial virus -- 5.3 Immunofluorescence staining of respiratory viruses -- 5.4 Herpes simplex virus, varicella zoster virus, cytomegalovirus -- 5.5 Gastrointestinal viruses -- References -- CHAPTER 6: Molecular Tests for the Identification of Viruses -- 6.1 Introduction -- 6.2 Respiratory viral infections -- 6.3 Enteric viruses -- 6.4 Enterovirus and parechovirus -- 6.5 Herpesviruses -- 6.6 Viral infections associated with transplantation -- 6.7 Implementation and additional considerations -- References -- CHAPTER 7: Viral Hepatitis -- 7.1 Introduction/background -- 7.2 Clinical manifestations, epidemiology, and diagnostic considerations by virus -- 7.3 Commercial methods -- 7.4 Summary -- References -- CHAPTER 8: Human Papillomaviruses -- 8.1 Background -- 8.2 Commercial assays -- 8.3 Current challenges and future directions -- References -- CHAPTER 9: Human Immunodeficiency Virus -- 9.1 Introduction -- 9.2 Markers of HIV infection -- 9.3 HIV screening -- 9.4 Laboratory-based immunoassays -- 9.5 Rapid, less-sophisticated immunoassays -- 9.6 Specimen matrices for HIV screening -- 9.7 Confirmatory and supplemental tests -- 9.8 Serological testing of neonates -- 9.9 p24 Antigen detection -- 9.10 Qualitative molecular detection -- 9.11 Quantification of HIV RNA -- 9.12 Phenotypic and genotypic assays for drug resistance -- References -- CHAPTER 10: Chlamydia -- 10.1 Introduction -- 10.2 Epidemiology -- 10.3 Biology -- 10.4 Natural history -- 10.5 Clinical symptoms and sequelae -- 10.6 Treatment -- 10.7 Laboratory testing for C. trachomatis -- References -- CHAPTER 11: Rickettsiae and Tick-borne Diseases.

11.1 Introduction -- 11.2 Overview of tick-borne diseases -- 11.3 Newly emerging tick-borne disease -- References -- CHAPTER 12: Mycoplasma -- 12.1 Introduction and clinical considerations -- 12.2 Culture-based diagnosis -- 12.3 Serological diagnosis -- 12.4 Molecular detection systems -- 12.5 Antimicrobial susceptibility testing -- 12.6 Future directions -- References -- CHAPTER 13: Commercial Methods for Identification and Susceptibility Testing of Fungi -- 13.1 Direct examination and detection methods -- 13.2 Culture and detection -- 13.3 Identification systems -- 13.4 Molecular testing -- 13.5 Susceptibility testing -- References -- CHAPTER 14: Mycobacteria -- 14.1 Introduction -- 14.2 Specimen processing -- 14.3 Acid-fast staining reagents -- 14.4 Direct detection of mycobacteria from clinical specimens -- 14.5 Blood-culture recovery of mycobacteria -- 14.6 Mycobacteria-culturing methods and systems -- 14.7 Identification of mycobacteria -- 14.8 Susceptibility tests for mycobacteria -- 14.9 Immunodiagnosis of tuberculosis -- 14.10 Conclusion -- References -- CHAPTER 15: Diagnostic Medical Parasitology -- 15.1 Diagnostic parasitology testing -- 15.2 Solicitation of product information -- 15.3 Specimen collection systems -- 15.4 Fresh stool specimen collection -- 15.5 Preservation of stool specimens -- 15.6 Intestinal tract specimens (stool) -- 15.7 Ova and parasite examination -- 15.8 Molecular methods -- 15.9 Other diagnostic methods -- 15.10 Collection of specimens from other body sites -- 15.11 Blood collection -- 15.12 Malaria rapid diagnostic tests -- References -- CHAPTER 16: Molecular Microbiology -- 16.1 Introduction -- 16.2 Specimen processing and nucleic acid extraction platforms -- 16.3 Amplification methods and platforms -- 16.4 Amplicon detection and identification platforms -- 16.5 Future directions -- 16.6 Summary -- References.

CHAPTER 17: Automated Immunoassay Analyzers -- References -- CHAPTER 18: Molecular Typing Instruments and Methods -- 18.1 Introduction -- 18.2 Background -- 18.3 Current molecular typing methodologies -- 18.4 Comparison of typing techniques -- 18.5 Summary -- References -- CHAPTER 19: Commercial Methods in Clinical Veterinary Microbiology -- 19.1 Collection and transportation of clinical samples -- 19.2 Selection of diagnostic laboratories and tests -- 19.3 Pathology and histopathology -- 19.4 Quality control of veterinary diagnostic assays: sensitivity and specitivity -- 19.5 Veterinary virology -- 19.6 Veterinary bacteriology -- 19.7 Veterinary mycology -- 19.8 Veterinary parasitology -- Acknowledgements -- References -- CHAPTER 20: Microbiology Laboratory Information Systems -- 20.1 In general, microbiology laboratory information systems fit one of three categories -- 20.2 What are the key features of software to support management of microbiology? -- 20.3 Microbiology information systems have evolved over several decades -- 20.4 Criteria for comparison of current systems -- 20.5 Specialized software -- 20.6 Selecting an information system for your laboratory -- 20.7 Cases -- 20.8 Management of the laboratory information system -- 20.9 Personnel management -- References -- CHAPTER 21: Emerging Infectious Diseases -- 21.1 Introduction -- 21.2 Plasmodium knowlesi -- 21.3 Clostridium difficile -- 21.4 Pandemic H1N1 influenza -- 21.5 Escherichia coliO104:H4 -- 21.6 Cryptococcus gattii -- 21.7 Borrelia miyamotoi -- 21.8 Rickettsia parkeri -- 21.9 Mycobacterium lepromatosis -- 21.10 Bocavirus -- 21.11 Human metapneumovirus -- 21.12 Severe fever with thrombocytopenia syndrome virus -- 21.13 Zika virus -- References -- CHAPTER 22: Automated and Manual Systems for Antimicrobial Susceptibility Testing of Bacteria -- 22.1 Introduction.

22.2 Evaluation of commercial AST performance -- 22.3 Automated broth microdilution AST systems -- 22.4 Semiautomated and manual broth microdilution AST systems -- 22.5 Manual and semiautomated agar antimicrobial gradient diffusion and disk diffusion susceptibility tests -- 22.6 Phenotypic detection of antimicrobial resistance using chromogenic media -- 22.7 Genotypic detection of antimicrobial resistance determinants in positive blood cultures -- 22.8 Next generation methods for antimicrobial susceptibility testing -- References -- CHAPTER 23: Bioterrorism -- 23.1 Introduction -- 23.2 History of bioterrorism -- 23.3 Bioterrorism in the future -- 23.4 Laboratory Response Network -- 23.5 Rapid methods -- 23.6 Conclusion -- References -- CHAPTER 24: Clinical Microbiology -- 24.1 Introduction -- 24.2 Connectivity between extraction and amplification platforms -- 24.3 Polymerase chain reaction and RT-PCR: detection and characterization -- 24.4 Other amplification methods -- 24.5 Probe technology -- 24.6 Mass spectrometry -- 24.7 DNA sequencing -- 24.8 Emerging technology -- 24.9 Other strategies and concepts that will impact clinical microbiology -- 24.10 Some new responsibilities for the coming years -- 24.11 Summary -- References -- CHAPTER 25: Clinical Microbiology In Vitro Diagnostic Medical Devices in Argentina -- 25.1 History -- 25.2 Regulation of clinical microbiology in vitro diagnostic medical devices in Argentina -- References -- CHAPTER 26: Clinical Microbiology In Vitro Diagnostics in Australia -- 26.1 The Therapeutic Goods Administration -- 26.2 National Pathology Accreditation Advisory Council -- 26.3 National Association of Testing Authorities -- 26.4 RCPA quality assurance programs -- 26.5 Manufacturers and suppliers of IVDs -- References -- CHAPTER 27: Clinical Microbiology In Vitro Diagnostic Devices in Canada -- References.

CHAPTER 28: Clinical Microbiology In Vitro Diagnostics in China.