Note: Intro -- Advanced Techniquesin Diagnostic Microbiology -- Preface -- Contents -- Contributors -- Part I: Methods -- Chapter 1: Automated Blood Cultures -- Introduction -- Principles -- Automated Culturing Systems -- Blood Culture and CMBCS for Mycobacteria -- Concluding Remarks -- References -- Chapter 2: Breath Tests for Detection of Helicobacter pylori and Aspergillus fumigatus -- Introduction -- Helicobacter pylori -- Aspergillus spp. -- Conventional Diagnostic Tests -- Detection of H. pylori -- Detection of Aspergillus spp. -- Breath Tests -- Introduction -- Sample Collection -- Urea Breath Test for H. pylori -- Breath Test for Aspergillosis -- Conclusions -- References -- Chapter 3: Rapid Antigen Tests -- Introduction -- Principles of the Techniques -- Agglutination -- Immuno uorescence -- Enzyme Immunoassay -- Chemiluminescent Methods -- Lateral Flow Immunochromatography and Fluoroimmunoassay -- Characteristics of the Techniques -- Applications of the Techniques -- Bacteria -- Fungi -- Parasites -- Viruses -- References -- Chapter 4: Antibody Detection: Principles and Applications -- Introduction -- Principles and Characteristics of Techniques -- Colorimetric or Chromogenic Substrate -- Radioimmunoassay -- Chemiluminescence-Immunoassay -- Electrochemiluminescent -- Fluorescent Immunoassays -- Multi-Analyte Pro le Technology -- Contrast of These Techniques -- Application of the Techniques in the Diagnostic Microbiology -- Clinical Applications -- Automation -- Summary -- References -- Chapter 5: Cytometry-Based Antimicrobial Resistance Techniques -- Introduction -- Flow Cytometry Setup -- Antimicrobial Resistance Measurements -- Assay Turnaround Time -- Comparator Methods -- Flow Cytometry Challenges -- Conclusions and Future Prospects -- References -- Chapter 6: Biochemical Pro le-Based Microbial Identi cation Systems. , Introduction -- Conventional Microbial Identi cation Systems -- Single Enzyme Rapid Tests -- Catalase Test -- Oxidase Test -- Spot Indole Test -- Slide Coagulase Test -- Microdase -- Bile Solubility Test -- PYR -- Leucine Aminopeptidase Test -- MUG Test -- Indoxyl Butyrate Disk -- Chromogenic Enzyme Substrate Test -- Gonocheck II -- Bacticard Neisseria -- Hippurate -- Lysostaphin -- CLO Test -- Overnight Biochemical Tests -- Tube Coagulase Test -- DNA Hydrolysis -- Vancomycin Disk Test -- Bacitracin Inhibition Test (Taxo A Disk) -- Bacitracin and STX Susceptibility Test -- Taxo P Disks (Optochin) -- CAMP Test -- Reverse CAMP Test -- Bile Esculin Agar Slant -- 6.5 % Salt Broth -- Indole Test -- Nitrite Test -- ALA ( Haemophilus in uenzae Porphyrin Test) -- Motility Indole Lysine Sul de (MILS) Medium -- O -Nitrophenyl-b- d -Galactopyranoside Test -- Methyl Red Test -- Voges-Proskauer Test -- Pseudosel Agar Slant -- Urea Agar Slant -- Citrate Agar Slant -- Cetrimide Agar -- Gelatin -- Acetate Utilization -- Lead Acetate for Hydrogen Sul de Detection -- Lysine Iron Agar -- Triple Sugar Iron Agar Slant -- Phenylalanine Deaminase -- Decarboxylase (Moeller's Method) -- OF Glucose Medium -- OF Sugars -- Commercial Microbial Identi cation System -- API Identi cation System -- API Gram-Negative Identi cation -- API Gram-Positive Identi cation -- API Anaerobe Identi cation -- BBL™ Crystal™ Identi cation System -- BBL Phoenix Identi cation and Susceptibility System -- VITEK and VITEK 2 Identi cation System -- MicroScan WalkAway -- Sensititre ® Microbiology Systems -- MIDI Sherlock -- BioLog ID System -- References -- Chapter 7: Infectious Disease Biomarkers: Non-Antibody-Based Host Responses -- Introduction -- Procalcitonin -- The Roles of PCT and Other Biomarkers in Sepsis -- The Roles of PCT in Sepsis -- The Roles of CRP in Sepsis. , The Roles of CRP and PCT in Infectious States Other than Sepsis -- The Roles of Miscellaneous and Novel Biomarkers in Infectious States -- Serum Amyloid A -- Lipopolysaccharide-Binding Protein -- Coagulation Markers -- Angiopoietins -- Neopterin -- Toll-Like Receptor-2 -- Triggering Receptor Expressed on Myeloid Cells-1 -- Soluble Urokinase-Type Plasminogen Activator Receptor -- Soluble Receptor for Advanced Glycation End Products -- CD64 -- HLA-DR -- Presepsin -- Cytokines -- Proadrenomedullin -- Alpha-1 Antitrypsin and Other Hepatitis Biomarkers -- Gelsolin -- Interferon-Gamma-Inducible Protein-10 -- Neutrophil Distribution Width -- Regulatory T Lymphocytes (Treg) -- Summary of Miscellaneous Biomarkers -- Newer Platforms for Measurement of Biomarkers -- Conclusions and Future Directions -- References -- Chapter 8: Functional Assessment of Microbial and Viral Infections by Real-Time Cellular Analysis System -- Introduction -- RTCA and Its Principle of Detection Using Impedance Microelectrode Sensor Arrays -- Analysis of Host Cell Responses to Bacterial Infections on RTCA System -- Detection of Clostridium dif cile Toxin -- Detection of Clostridium botulinum Toxin -- Detection of Meningococcal Infection -- Virus-Induced CPE and Neutralizing Antibody Detection on RTCA System -- West Nile Virus and St. Louis Encephalitis Virus CEP and Neutralizing Antibody Detection -- In uenza Virus and Neutralizing Antibody Detection -- Hand-Foot-Mouth Virus Detection -- Helminth Motility and Egg Hatching Activity on RTCA System -- Host Immune Function Assessment on RTCA: Nature Killer Cells and T Cells -- Natural Killer Cell Function Assessment -- T Cell Surface Receptor Detection -- Perspectives -- References -- Chapter 9: Cellular Fatty Acid-Based Microbial Identi cation and Antimicrobial Susceptibility Testing -- Introduction. , General Principles and Methods of Cellular Fatty Acid Analysis -- CFA Testing Platforms for Bacterial Identi cation -- Library Expansion and Fatty Acid Polymorphisms -- Identi cation of Agents of Bioterrorism and Other Select Agents -- Mycolic Acid Analysis for Identi cation of Mycobacteria -- HPLC and Susceptibility Testing -- Advantages and Disadvantages of Fatty Acid-Based Identi cation Methods -- References -- Chapter 10: MALDI-TOF Mass Spectrometry-Based Microbial Identi cation -- Introduction -- General Remarks on Mass Spectrometry -- MALDI and ESI MS -- Species Identi cation Using MALDI-TOF MS -- Limitations and Shortcomings of MALDI-TOF MS -- Further Challenges Approaching MALDI-TOF MS for Species Diagnosis -- Conclusion -- References -- Chapter 11: Nucleic Acid Extraction Techniques -- Introduction -- Nucleic Acid Extraction Techniques -- Cesium Chloride/Ethidium Bromide Density Gradient Centrifugation -- Phenol-Chloroform Extraction -- Solid-Phase Extraction -- Magnetic Bead Method -- Applications to Clinical Specimens -- Cellular Component -- Serum, Plasma, and Whole Blood -- In uence of Speci c Pathogen -- PCR Inhibitors -- Measurement of DNA Quality -- Comparison of Nucleic Acid Extraction Methods -- Manual Method -- Automatic Methods -- Conclusion -- References -- Chapter 12: Nonampli ed Probe-Based Microbial Detection and Identi cation -- Introduction -- Probe-Based Assay Design -- Target Selection -- Probe Selection -- Nucleic Acid Hybridization Formats -- Clinical Application of Nonampli ed Probe-Based Assays -- Gen-Probe Nucleic Acid Detection Methods -- Hybrid Capture Assay -- Af rm DNA Assay -- Line Probe Assay -- In Situ Hybridization Assays -- Peptide Nucleic Acid FISH Assays -- Future Considerations -- References -- Chapter 13: Molecular Typing Techniques: State of the Art -- Introduction. , What Does "State of the Art" Mean? -- The Ultimate Foundation for Epidemiological Comparison: The Bacterial Genome -- Methods with Electrophoretic Output -- Pulsed-Field Gel Electrophoresis -- Optical Mapping -- PCR-Based -- Repetitive Sequence-Based PCR -- PCR Ribotyping -- Staphylococcal Cassette Chromosome mec Typing -- Multiple-Locus VNTR Analysis -- DNA Sequence-Based Methods -- Single-Locus Sequence Typing -- S. aureus Protein A Typing -- Strepcococcus pyogenes M Protein ( emm) Typing -- mec -Associated Direct Repeat Unit Typing -- Multi-Locus Sequence Typing -- Other Multi-Locus Approaches: Hybridization-Based Typing -- Whole Genome Sequence Typing -- Non-Sequence-Based Whole Cell Typing -- Strain Typing in the Context of the Epidemiological Window -- References -- Chapter 14: An Introduction to In Vitro Nucleic Acid Ampli cation Techniques -- Target Ampli cation Systems -- Probe Ampli cation Systems -- Signal Ampli cation Systems -- References -- Chapter 15: PCR and Its Variations -- PCR: The Quintessential Nucleic Acid Ampli cation Method -- Principles of PCR -- Enzymatic Ampli cation of DNA: Components of the PCR -- The PCR Cycle -- Denaturation -- Annealing -- Extension -- Detection and Analysis of the PCR Product -- Conventional PCR -- Real-Time PCR -- PCR Variations -- Allele-Speci c PCR -- Hot-Start PCR -- Touchdown PCR -- Degenerate PCR -- Nested and Heminested PCR -- Multiplex PCR -- Reverse Transcription-PCR -- Quantitative PCR -- Real-Time PCR -- PCR-Based Strain Typing Techniques -- Arbitrarily Primed-PCR and Random Ampli ed Polymorphic DNA -- Ampli ed Fragment-Length Polymorphism -- ERIC-, Rep-, BOX-, IS-, and VNTR-PCR -- Appendix -- Primer Design Resources -- References -- Chapter 16: Non-PCR Target Ampli cation Techniques -- Introduction -- Isothermal Transcription-Based Ampli cation. , Strand Displacement Ampli cation.