Table of Contents

Table of Contents DIAGNOSTIC PRINCIPLES I. Molecular Hybridization for Microbial Identification 1. Applications of Fluorescence In Situ Hybridization in Diagnostic Microbiology Stefan Juretschko and Thomas R. Fritsche 2. DNA Probes for Culture Confirmation and Direct Detection of Bacterial and Fungal Infections: a Review of Current Technologies and Assays Julie Kingery and Karen C. Carroll II. Nucleid Acid Amplification Methods 3. In Vitro Nucleic Acid Amplification Techniques Vivekanand Datta and Randall T. Hayden 4. Real Time PCR and Melting Analysis Carl T. Wittwer and Noriko Kusukawa 5. Quantitative Molecular Methods Donna M. Wolk and Randall T. Hayden 6. Use of Commercial Amplification Tests in the Clinical Microbiology Laboratory: Test Selection and Quality Assurance Gerri S. Hall, Mark Katanik, Marion Tuohy, and Mary Sholtis III. Laboratory Operations 7. Nucleic Acid Isolation: Overview of Sample Preparation Methods Charles E. Hill 8. Laboratory Design and Operations P. Shawn Mitchell, Jeffrey J. Germer, and Joseph D. C. Yao IV. Molecular Typing Methods 9. Molecular Phylogenetic Analysis Les Dethlefsen, Paul W. Lepp, and David A. Relman 10. Pulsed-Field Gel Electrophoresis: Laboratory and Epidemiologic Considerations for Interpretation of Data Richard V. Goering, Efrain M. Ribot, and Peter Gerner-Smidt 11. Strain Typing Using Multiple Loci “Variable Number of Tandem Repeat” Analysis and Genetic Element CRISPR Christine Pourcel and Gilles Vergnaud 12. Repetitive Sequence-Based PCR Typing of Bacteria and Fungi Stacie R. Frye and Mimi Healy 13. Molecular Typing Methods for Analysis of Extraintestinal Pathogenic Escherichia coli James R. Johnson V. Detection Methodology 14. Fluorescence Resonance Energy Transfer J. R. Uhl, Y.-W. Tang, and F. R. Cockerill III 15. Detection of Pathogenic Organisms with Multicolor Molecular Beacons Fann Wu, Phyllis Della-Latta, Sanjay Tyagi, and Fred Russell Kramer 16. Microwell Plate Detection Systems for Amplicon Detection and Characterization Jiang Fan and Michael J. Loeffelholz 17. Detection Methodology: Pyrosequencing Liying Yan and Robert Slinger 18. Solid- and Liquid-Phase Array Technologies Melissa B. Miller VI. New Technologies 19. Next Generation DNA Sequencing and Microbiology Russell Higuchi, Ulf Gyllensten and David H. Persing 20. Raman Spectroscopy for Bacterial Strain Typing Diana Willemse-Erix, Alex van Belkum, and Kees Maquelin 21. Multiplex PCR Product Detection and Discrimination Steven Zink, Nick M. Cirino, and Christina Egan 22. Detection of Emerging Antimicrobial Resistance by Use of the Ibis T5000 Universal Biosensor David J. Ecker, Rangarajan Sampath, Christian Massire, Lawrence B. Blyn, Mark W. Eshoo, Thomas A. Hall, and Steven Hofstadler DIAGNOSTIC APPLICATIONS VII. Molecular Detection of Bacterial Organisms 23. Update on the Detection and Characterization of Bacterial Pathogens by Nucleic Acid Amplification K. Loens, H. Goossens, and M. Ieven 24. Molecular Detection of Chlamydia trachomatis and Neisseria gonorrhoeae Jens K. Møller, Björn Herrmann, Jørgen Skov Jensen, and Henrik Westh 25. PCR Detection of Haemophilus ducreyi, Treponema pallidum and Mycoplasma genitalium Patricia A. Totten, Lisa E. Manhart, and Arturo Centurion-Lara 26. Molecular Detection and Characterization of Mycobacterium tuberculosis Betty A. Forbes 27. Sequence-Based Identification and Characterization of Mycobacteria Nancy L. Wengenack and Leslie Hall 28. Molecular Detection of Group B Streptococcus Elizabeth M. Marlowe and Preeti Pancholi 29. Molecular Detection and Identification of Methicillin-Resistant Staphylococcus aureus Willem van Leeuwen and Alex van Belkum 30. Identification of Bacteria by DNA Target Sequencing in a Clinical Microbiology Laboratory Rosemary C. She, Keith E. Simmon, and Cathy A. Petti 31. Broad-Range PCR for Detection and Identification of Bacteria Matthias Maiwald 32. Detection of Antimicrobial Resistance Genes and Mutations Associated with Antimicrobial Resistance in Bacteria Fred C. Tenover and J. Kamile Rasheed 33. Detection of Agents Associated with Bioterrorism Paul Keim, Victor Waddell, and David M. Engelthaler VIII. Molecular Detection and Characterization of Viruses 34. Diagnostic Molecular Virology: Current Practice and Future Trends Frederick S. Nolte 35. Molecular Detection and Characterization of HIV-1 Angela M. Caliendo and Colleen S. Kraft 36. Molecular Detection and Characterization of Hepatitis C Virus Michael S. Forman and Alexandra Valsamakis 37. Molecular Detection and Characterization of Hepatitis B Virus David R. Hillyard 38. Molecular Detection of Human Papillomaviruses Denise I. Quigley and Elizabeth R. Unger 39. Molecular Detection of Respiratory Viruses Richard S. Buller and Max Q. Arens 40. Viral Infections in Transplant Recipients Robin Patel and Frederick S. Nolte 41. New Virus Discovery in the 21st Century Stacy Finkbeiner and David Wang IX. Detection and Characterization of Fungal Pathogens 42. Molecular Detection and Characterization of Fungal Pathogens Stéphane Bretagne 43. Sequence-Based Fungal Identification and Classification Jianli Dong, Michael J. Loeffelholz, and Michael R. McGinnis 44. Molecular Detection of Antifungal Resistance Thomas D. Edlind X. Detection and Characterization of Parasitic Protozoa 45. Overview of the Development, Utility, and Future of Molecular Diagnostics for Parasitic Diseases Bobbi Pritt and Jon Rosenblatt 46. Molecular Approaches for Diagnosis of Malaria and Characterization of Genetic Markers of Drug Resistance Laura K. Erdman, Michael Hawkes, and Kevin C. Kain 47. Molecular Approaches for Diagnosis of Chagas’ Disease and Genotyping of Trypanosoma cruzi Michal Svoboda, Myrna Virreira, Carine Truyens, Faustino Torrico, and Yves Carlier XI. Systems Microbiology 48. Molecular Diagnosis of Gastrointestinal Infections Benjamin A. Pinsky and Niaz Banaei 49. Molecular Approaches to the Diagnosis of Sepsis Paul H. M. Savelkoul and Remco P. H. Peters 50. Molecular Approaches to the Diagnosis of Meningitis and Encephalitis Karen C. Bloch and Yi-Wei Tang XII. The Pathogen/Host Interface 51. Genomics and DNA Variation: Determinants of Susceptibility and Outcomes in Microbial Diseases Chiea-Chuen Khor, Stephen J. Chapman, and Adrian V. S. Hill 52. Genetically Polymorphic Cytochrome P450s and Transporters and Personalized Antimicrobial Chemotherapy Hong-Guang Xie 53. Host Genomic Profiling in Human Immunodeficiency Virus Infection Kevin V. Shianna and Amalio Telenti 54. Innate Immunity and Host Defense against Microbial Infection Markus Schnare and Salman Qureshi XIII. Laboratory Standardization, Proficiency-Testing Programs, Quality-Control Standards, and Monitoring 55. Molecular Method Verification Donna M. Wolk and Elizabeth M. Marlowe 56. Molecular Test Validation, Monitoring, and Quality Control Matthew J. Bankowski 57. External Quality Assessment and Proficiency Testing in Diagnostic Molecular Microbiology Michael J. Mitchell 58. Laboratory Controls and Standards Maurice Exner