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
