Applied Genomics of Foodborne Pathogens

1. Front Matter

   Pages i-xi

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2. Role of Whole Genome Sequencing in the Public Health Surveillance of Foodborne Pathogens

   • Peter Gerner-Smidt, Heather Carleton, Eija Trees

   Pages 1-11

3. Global Microbial Identifier

   • Peter R. Wielinga, Rene S. Hendriksen, Frank M. Aarestrup, Ole Lund, Saskia L. Smits, Marion P. G. Koopmans et al.

   Pages 13-31

4. The Use of Whole Genome Sequencing for Surveillance of Enteric Organisms by United States Public Health Laboratories

   • David Boxrud, William J. Wolfgang

   Pages 33-50

5. Bioinformatics Aspects of Foodborne Pathogen Research

   • Henk C. den Bakker, Laura K. Strawn, Xiangyu Deng

   Pages 51-64

6. The CGE Tool Box

   • Mette Voldby Larsen, Katrine G. Joensen, Ea Zankari, Johanne Ahrenfeldt, Oksana Lukjancenko, Rolf Sommer Kaas et al.

   Pages 65-90

7. Genomic Diversity in Salmonella enterica

   • John Wain, Justin O’Grady

   Pages 91-107

8. Verocytotoxin-Producing Escherichia coli in the Genomic Era: From Virulotyping to Pathogenomics

   • Valeria Michelacci, Rosangela Tozzoli, Alfredo Caprioli, Stefano Morabito

   Pages 109-126

9. Campylobacter

   • Noel McCarthy

   Pages 127-143

10. Genomics and Foodborne Viral Infections

    • Saskia L. Smits, Marion P. G. Koopmans

    Pages 145-166

11. Transcriptomics and Proteomics of Foodborne Bacterial Pathogens

    • Joelle K. Salazar, Yun Wang, Wei Zhang

    Pages 167-200

12. Back Matter

    Pages 201-205

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This book provides a timely and thorough snapshot into the emerging and fast evolving area of applied genomics of foodborne pathogens. Driven by the drastic advance of whole genome shot gun sequencing (WGS) technologies, genomics applications are becoming increasingly valuable and even essential in studying, surveying and controlling foodborne microbial pathogens. The vast opportunities brought by this trend are often at odds with the lack of bioinformatics know-how among food safety and public health professionals, since such expertise is not part of a typical food microbiology curriculum and skill set. Further complicating the challenge is the large and ever evolving body of bioinformatics tools that can obfuscate newcomers to this area. Although reviews, tutorials and books are not in short supply in the fields of bioinformatics and genomics, until now there has not been a comprehensive and customized source of information designed for and accessible to microbiologists interested inapplying cutting-edge genomics in food safety and public health research.  This book fills this void with a well-selected collection of topics, case studies, and bioinformatics tools contributed by experts at the forefront of foodborne pathogen genomics research.

• Bioinformatics
• Food Safety
• Food Microbiology
• Foodborne Pathogens
• Genomics
• Sequencing

• Center for Food Safety, University of Georgia, Griffin, USA

  Xiangyu Deng

• Department of Animal and Food Sciences, Texas Tech University, Lubbock, USA

  Henk C. den Bakker

• National Food Institute, Technical University of Denmark, Copenhagen, Denmark

  Rene S. Hendriksen

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