DNA Methods in Food Safety: Molecular Typing of Foodborne and Waterborne Bacterial Pathogens

Molecular typing of foodborne pathogens has become an indispensable tool in epidemiological studies. Thanks to these techniques, we now have a better understanding of the distribution and appearance of bacterial foodborne diseases and have a deeper knowledge of the type of food products associated with the major foodborne pathogens. Within the molecular techniques, DNA–based techniques have prospered for more than 40 years and have been incorporated in the first surveillance systems to monitor bacterial foodborne pathogens in the United States and other countries. However, DNA techniques vary widely and many microbiology laboratory personnel working with food and/or water face the dilemma of which method to incorporate.

DNA Methods in Food Safety: Molecular Typing of Foodborne and Waterborne Bacterial Pathogens succinctly reviews more than 25 years of data on a variety of DNA typing techniques, summarizing the different mathematical models for analysis and interpretation of results, and detailing their efficacy in typing different foodborne and waterborne bacterial pathogens, such as Campylobacter, Clostridium perfringens, Listeria, Salmonella, among others. Section I describes the different DNA techniques used in the typing of bacterial foodborne pathogens, whilst Section II deals with the application of these techniques to type the most important bacterial foodborne pathogens. In Section II the emphasis is placed on the pathogen, and each chapter describes some of the most appropriate techniques for typing each bacterial pathogen.

The techniques presented in this book are the most significant in the study of the molecular epidemiology of bacterial foodborne pathogens to date. It therefore provides a unique reference for students and professionals in the field of microbiology, food and water safety and epidemiology and molecular epidemiology.

List of Contributors vii

Preface xiii

Section I Typing Method, Analysis, and Applications 1

1 Polymerase Chain Reaction–Based Subtyping Methods 3
Yi Chen and Insook Son

2 Pulsed–Field Gel Electrophoresis and the Molecular Epidemiology of Foodborne Pathogens 27
Mohana Ray and David C. Schwartz

3 Multilocus Sequence Typing: An Adaptable Tool for Understanding the Global Epidemiology of Bacterial Pathogens 47
Stephen J. Knabel

4 High–Throughput Sequencing 65
Xiangyu Deng, Lee S. Katz, Patricia I. Fields, and Wei Zhang

5 Analysis of Typing Results 85
João André Carriço and Mário Ramirez

6 Databases and Internet Applications 113
G. Gopinath, K. Hari, R. Jain, M. H. Kothary, K. G. Jarvis, A. A. Franco, C. J. Grim, V. Sathyamoorthy, M. K. Mammel, A. R. Datta, B. A. McCardell, M. D. Solomotis, and Ben D. Tall

7 The Transformation of Disease Surveillance, Outbreak Detection, and Regulatory Response by Molecular Epidemiology 133
David A. Sweat

Section II Pathogens 163

8 The Genus Bacillus 165
Monika Ehling–Schulz and Ute Messelhäusser

9 Molecular Typing of Campylobacter jejuni 185
Catherine D. Carrillo and Omar A. Oyarzabal

10 DNA Typing Methods for Members of the Cronobacter Genus 205
Susan Joseph and Stephen Forsythe

11 Molecular Subtyping Approaches for Pathogenic Clostridium spp. Isolated from Foods 249
Brian H. Raphael, Deborah F. Talkington, Carolina Lúquez, and Susan E. Maslanka

12 Molecular Characterization of Shiga Toxin–Producing Escherichia coli 275
Pallavi Singh and Shannon D. Manning

13 Molecular Subtyping Methods for Listeria monocytogenes: Tools for Tracking and Control 303
Sara Lomonaco and Daniele Nucera

14 Salmonella 337
Aaron M. Lynne, Jing Han, and Steven L. Foley

15 Vibrio cholerae 359
Dong Wook Kim

Index 381

Dr Omar A. Oyarzabal is Vice President of Technical Services at IEH Laboratories and Consulting Group, Seattle, WA

Dr Sophia Kathariou is Professor of Bioprocessing and Nutrition Sciences at the Department of Food, North Carolina State University, Raleigh, USA