The second edition presents the latest molecular diagnostic techniques to support clinical care and basic and clinical research. The authors all experienced researchers and diagnosticians have conducted a comprehensive review and evaluation of this rapidly evolving field and provide the new material in an easy-to-read summary format. Moreover, the book offers a broad range of practical advice, such as determining the appropriate type and quantity of a specimen, releasing and concentrating the targets, and eliminating inhibitors. David Persing not only examines techniques to detect individual pathogens, but also explores the growing trend toward a systems approach for diagnosing infectious diseases, with chapters covering gastrointestinal infections, sepsis, meningitis, and encephalitis. In short, this text not only encapsulates the current state of the science, but also points to new avenues for research that will broaden the application and usefulness of molecular diagnostics.

Diagnostic Principles -- I. Molecular Hybridization for 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. Nucleic 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 and et al. -- 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 "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, and et al. -- 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 D. Zink, Nick M. Cirino, and Christina Egan -- 22. Detection of Emerging Antimicrobial Resistance by Use of the Ibis T5000 Universal Biosensor / David J. ecker and et al. -- 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. Moller and et al. -- 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 / 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 / Stephane 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 and et al. -- 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.