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Includes cutting-edge methods for the epidemiology of microorganisms
Provides a comparative overview of methods best adapted to species diversity
Includes tools for advanced data analyses and interpretation
The development of molecular genotyping methods has revolutionized the possibility for classification of microorganisms at the sub-species level. This investigation of species diversity is crucial for deciding the molecular relatedness of isolates for epidemiological studies. In Molecular Epidemiology of Microorganisms: Methods and Protocols, readers will find readily reproducible methods for determining the molecular epidemiology of microorganisms, all of which provide effective discrimination of unrelated strains. This volume covers a wide range of techniques which can be easily applied to the investigation of transmissible diseases, directing researchers towards the most effective methods based on the particular information to be obtained. Describing both traditional and novel techniques, expert researchers present a series of methods-based chapters with applications to some of the most important microbes. Composed in the highly successful Methods in Molecular Biology series format, each chapter contains a brief introduction, step-by-step methods, a list of necessary materials, and a Notes section which shares tips on troubleshooting and avoiding known pitfalls.
Comprehensive and practical, Molecular Epidemiology of Microorganisms: Methods and Protocols provides state-of-the-art techniques which will prove to be critical in unraveling the routes of spread of pathogens for humans, animals, and plants.
Table of Contents Preface Contributors 1. Microbial Molecular Epidemiology: an Overview Michel Tibayrenc 2. Multilocus Enzyme Electrophoresis for Parasites and other Pathogens Michel Tibayrenc 3. Plasmid Replicon Typing Timothy J. Johnson and Lisa K. Nolan 4. The Application of Randomly Amplified DNA Analysis in the Molecular Epidemiology of Microorganisms Alex van Belkum, Elisabeth van Pelt-Verkuil, and John P. Hays 5. Use of Repetitive Element Palindromic-PCR (rep-PCR) for the Epidemiological Discrimination of Foodborne Pathogens Kelli L. Hiett and Bruce S. Seal 6. Pulsed-Field Gel Electrophoresis for Molecular Epidemiology of Food Pathogens Tansy M. Peters 7. Molecular Genotyping of Microbes by Multilocus PCR and Mass Spectrophotometry: a New Tool for Hospital Infection Control and Public Health Surveillance David J. Ecker, Christian Massire, Lawrence B. Blyn, Steven A. Hofstadler, James C. Hannis, Mark W. Eshoo, Thomas A. Hall, and Rangarajan Sampath 8. Amplified Fragment Length Polymorphism Analysis Norman K. Fry, Paul H. M. Savelkoul, and Paolo Visca 9. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) for the Genotyping of Bacterial Pathogens Ibtissem Grissa, Gilles Vergnaud, and Christine Pourcel 10. Spoligotyping for Molecular Epidemiology of the Mycobacterium tuberculosis Complex Jeffrey R. Driscoll 11. Multilocus Sequence Typing Ana Belén Ibarz Pavòn and Martin C. J. Maiden 12. Multiple Locus VNTR (Variable Number of Tandem Repeat) Analysis (MLVA) Gilles Vergnaud and Christine Pourcel 13. Comparison of Molecular Typing Methods Applied to Clostridium difficile Ed J. Kuiper, Renate J. van den Berg, and Jon S. Brazier 14. Genotyping of Mycobacterium tuberculosis Clinical Isolates using IS6110-BasedRestriction Fragment Length Polymorphism Analysis Pablo Bifani, Natalia Kurepina, Barun Mathema, Xiao-Ming Wang, and Barry Kreiswirth 15. spa Typing for Epidemiological Surveillance of Staphylococcus aureus Marie Hallin, Alexander W. Friedrich, and Marc J. Struelens 16. Sequencing of Viral Genes Carol Holm-Hansen and Kirsti Vainio 17. Full Sequencing of Viral Genomes: Practical Strategies used for the Amplification and Characterisation of Foot-and-Mouth Disease Virus Eleanor M. Cottam, Jemma Wadsworth, Nick J. Knowles, and Donald P. King 18. Bacterial Genome Sequencing Hervé Tettelin and Tamara Feldblyum 19. DNA Microarray for Molecular Epidemiology of Salmonella Stephan Hühn and Burkhard Malorny 20. Methods for Data Analysis William Paul Hanage and David Michael Aanensen 21. Internet-based Sequence Typing Databases for Bacterial Molecular Epidemiology Keith A. Jolley