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

Publication subTitle :Molecular Typing of Foodborne and Waterborne Bacterial Pathogens

Author: Omar A. Oyarzabal  

Publisher: John Wiley & Sons Inc‎

Publication year: 2014

E-ISBN: 9781118278642

P-ISBN(Hardback):  9781118278673

Subject: R155 dietetic hygiene and food inspection

Language: ENG

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Description

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.

Chapter

PCR-restriction fragment length polymorphism (PCR-RFLP)

PCR melting profile analysis

References

Chapter 2 Pulsed-Field Gel Electrophoresis and the Molecular Epidemiology of Foodborne Pathogens

Background

Theory

Parameters critical to PFGE separations

Instrumentation

Epidemiological applications of PFGE

Conclusion

Acknowledgments

References

Chapter 3 Multilocus Sequence Typing: An Adaptable Tool for Understanding the Global Epidemiology of Bacterial Pathogens

Multilocus sequence typing

MLST databases

Advantages of MLST

Types of MLST schemes

Discriminatory power and epidemiologic concordance

Clonal complexes, epidemic clones, and outbreak clones

Conclusions

Acknowledgments

References

Chapter 4 High-Throughput Sequencing

Introduction

Existing subtyping methods

WGS: A comprehensive platform for molecular subtyping

MLST versus WGS

SNP analysis versus WGS

Hypervariable markers

Phenotypic markers versus WGS

Technical process of WGS

Computational tools for WGS analysis

WGS in recent foodborne outbreak investigations

Challenges and future prospects of WGS in molecular subtyping

References

Chapter 5 Analysis of Typing Results

Introduction

Measuring similarity

Creating groupings of related isolates

Comparison of typing methods

References

Chapter 6 Databases and Internet Applications

Introduction

Existing online networks and resources

Current challenges, possible solutions, and future trends

GeoGenomic identification and an integrated Web-based global infrastructure

References

Chapter 7 The Transformation of Disease Surveillance, Outbreak Detection, and Regulatory Response by Molecular Epidemiology

Epidemiology and surveillance

Outbreaks

PulseNet

From steps to principles

The end of the culture era?

Summary

Acknowledgments

References

Section II Pathogens

Chapter 8 The Genus Bacillus

Bacillus: A highly heterogeneous genus challenging food quality and safety

Bacillus toxins are gaining increasing prominence as causative agents of foodborne diseases

Polymerase chain reaction methods

Multilocus sequence typing (MLST) and amplified fragment length polymorphism (AFLP): The “golden standards” for population analysis of the B. cereus group

Pulsed-field gel electrophoresis

Microarrays and high-throughput sequencing: From genotyping to genomotyping

Conclusions and future direction

References

Chapter 9 Molecular Typing of Campylobacter jejuni

Introduction

Brief history of typing methods to study C. jejuni

Most common methods to type C. jejuni

Less commonly used typing methods

Comparative genomic fingerprinting

Combination of techniques

References

Chapter 10 DNA Typing Methods for Members of the Cronobacter Genus

Introduction

Cronobacter pathogenicity and virulence

Taxonomy and genomic diversity of the Cronobacter genus

Cronobacter and the food industry

Biotyping of Cronobacter strains

DNA-based typing of Cronobacter strains

Multilocus sequence typing of Cronobacter spp.

Case studies of using DNA sequence–based typing of Cronobacter spp.

Current issues in the application of DNA typing methods for Cronobacter spp.

Conclusions

Acknowledgments

References

Chapter 11 Molecular Subtyping Approaches for Pathogenic Clostridium spp. Isolated from Foods

Introduction

Concluding remarks

Disclaimer

References

Chapter 12 Molecular Characterization of Shiga Toxin-Producing Escherichia coli

Introduction

DNA fingerprinting

Sequence-based genotyping

Virotyping

Conclusions

References

Chapter 13 Molecular Subtyping Methods for Listeria monocytogenes: Tools for Tracking and Control

Introduction

Fragment-based methods

Hybridization-based methods

DNA sequence-based subtyping methods

Acknowledgments

References

Chapter 14 Salmonella

Introduction

Restriction analysis-based genotyping

PCR-based typing methods

DNA sequencing-based typing methods

Comparison of molecular subtyping methods for Salmonella

Conclusions

Disclaimer

References

Chapter 15 Vibrio cholerae

Introduction

CTX Phage

CTXcla (classical type CTX) and CTX-1 (El Tor type CTX or CTXEl Tor)

CTX-2

CTX-3

ctxB Typing

TLC element

Genotyping of V. cholerae

MLVA analysis of V. cholerae O1 strains

Conclusions

References

Index

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