Molecular microbiology : diagnostic principles and practice

 Content: 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. Moller, Bjorn Herrmann, Jorgen 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       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, 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