Omics, Microbial Modeling and Technologies for Foodborne Pathogens
DEStech Publications, Inc, January 2012, Pages: 643
This book provides comprehensive information on genetic analysis and multiple “omics” methods, microbial modeling, and other technologies used for the analysis of foodborne pathogens.
Part I details the use of genomics and other omics technologies to study and classify foodborne bacteria, viruses, fungi and protozoa. Part II covers microbial growth, modeling, and risk assessment and how these contribute to improving food safety. In this section new tools are described for representing and deploying digital data about microbe strains of interest. Part III provides guidance on creating a new food safety database infrastructure, which can improve how food safety and foodborne pathogen data are correlated and shared among epidemiologists, microbiologists and regulating agencies. Here, design information is given for a surveillance network to detect and limit outbreaks of foodborne disease.
The text offers a systematic presentation of advanced food safety tools, including microarrays, next-generation sequencers, biometric methods, and wireless technologies.
Some of the highlights of the book include:
- Expands detection knowledge and classification of foodborne pathogens
- Connects omics methods, modeling, data and food safety databases
- Offers framework for risk assessment and rapid online surveillance and analysis
Preface
PART I: OMICS OF FOOD-BORNE PATHOGENS
1. Omics, Microbial Modeling, and Food Safety Information Infrastructure: A Food Safety Perspective
- Introduction Omics in Food Safety
- Microbial Modeling
- Food Safety Information Infrastructure
- Summary Points
- References
2. Non-O157 Shiga Toxin-producing Escherichia coli
- Introduction
- Molecular Serotyping of E. Coli
- Epidemiology of Non-O157 STEC
- STEC Virulence Factors
- "Omics" Technologies
- Stress Tolerance in STEC
- Quorum Sensing in STEC
- Detection and Identification of STEC
- Molecular Analysis of STEC and SNP Typing
- Conclusions
- References
3. Pathogenic Salmonella
- Introduction
- Epidemiology, Pathogenesis and Drug Resistance
- Genomics
- SNP
- Transcriptomics
- Proteomics
- Application: Detection by Microarray
- Future Trends/Issues
- Conclusions
- References
4. Campylobacter and Arcobacter
- Introduction
- Clinical Symptoms
- Discovery and Background of Campylobacter and Arcobacter
- Detecting Campylobacter Spp. and Arcobacter Spp. From Food or Environmental Samples by Molecular Techniques
- Summary and Further Views
- References
5. Listeria monocytogenes
- Introduction
- Evolution-Adaptability, Epidemiology and Pathogenicity
- Genome, Genomics, Transcriptomics, Proteomics and Metabolomics
- Applications and Case Studies
- Future Trends
- Summary Points
- Suggested Websites and Key References
- Proteomes/gene-Genome Information Databases
- References
6. Shigella Species
- Introduction
- Evolution, Adaptability and Epidemiology
- Genome, Genomics, Transcriptomics, Metabolomics, and Proteomics
- Applications and Case Studies
- Future Trends/Issues
- Summary Points
- References
7. Pathogenic Yersinia Species
- Introduction
- Evolution, Adaptability and Epidemiology
- Genomics
- Applications and Case Studies
- Future Trends/Issues
- References
8. Emerging Foodborne Pathogens
- Introduction
- Hepatitis E Virus
- Conclusions
- References
9. Pathogenic Vibrio
- Introduction
- Vibrio Bacteria Genome and Genomics
- Microarray Analysis of Vibrio Bacteria
- Vibrio Genome Evolution and Emergence of New Strains
- Adaptability of Vibrio Bacteria to the Environment
- Pathogenicity
- Genotyping and Surveillance of Vibrios
- Proteomics of Vibrio Bacteria
- Concluding Remarks
- Acknowledgements
- References
10. Norovirus and Hepatitis A Virus
- Introduction
- Key Notes from the Norovirus and HAV Genomes
- Applications and Case Studies for Norovirus
- Future Trends/Issues
- References
11. Fungi: Microsporidia
- Introduction
- Evolution, Adaptability, and Epidemiology
- Genomics
- Proteomics
- Transcriptomics
- Application and Case Studies
- Future Trends/Issues
- Summary Points
- Suggested Reading and Key References
12. Foodborne Protozoa
- Introduction
- Diversity and Life Cycles
- Epidemiology
- Detection Methods of (Parasitic) Protozoa in Food Matrices
- Genomics and Functional Genomics
- Future Trends and Issues
- Summary Points
- References
PART II: MICROBIAL MODELING AND RISK ASSESSMENT OF FOOD-BORNE PATHOGENS
13. Methods for Mathematical Modeling of Microbial Growth in Food Systems
- Introduction
- Primary Models
- Secondary Models
- Summary
- References
14. Innovative Modeling Approaches for Risk Assessments in Food Safety
- Introduction
- Recent Advances
- Methods and/or Software
- Case Studies
- Future Trends/Issues
- Summary Points
- Suggested Reading and Key References
15. Microbial Quantitative Risk Assessment
- Introduction
- Survey of Existing QMRAS
- Selected Components of QMRA
- Perspectives on QMRA
- Future Directions
- Conclusions
- References
PART III: TECHNOLOGIES AND INFORMATION RESOURCES FOR FOOD-BORNE PATHOGENS
16. Epidemiological Surveillance: Tracking Foodborne Pathogens and Their Diseases from Farm-to-Fork
- Introduction
- Subtyping Schemes for the Surveillance of Foodborne Pathogens
- Conclusion
- Epidemiological Surveillance Systems for Foodborne Diseases and Pathogens
- Conclusions
- References
17. Monitoring and Surveillance: Epidemiology of Foodborne Pathogens and Food Safety
- Introduction
- Recent Advances
- Typing Methods
- Case Studies
- Antimicrobial Resistance of Foodborne Bacterial Pathogens
- Future Trends/Issues
- Summary Points
- References
18. Next Generation Sequencers: Methods and Applications in Foodborne Pathogens
- Introduction
- Next Generation Sequencing Technologies
- Applications of Next Generation Sequencers
- Future Development
- Acknowledgements
- Conflict of Interest
- References
19. Utilization of Optical Forward Scatter Image Biological Database: Foodborne Pathogen Colony Differentiation and Detection
- Summary
- Introduction
- Recent Advances
- Light-Scattering Technology
- Scatter Image Signatures of Foodborne Pathogens and Validation of Bardot-Based Detection using Inoculated Food Samples
- Conclusions and Future Perspectives
- Acknowledgements
- References
20. DNA Microarray Technology for the Detection of Foodborne Viral Pathogens
- Introduction
- DNA Microarray Technology
- Application of DNA Microarrays for Foodborne Virus Detection
- Conclusions and Future Prospects
- Summary Points
- Acknowledgements
- References
21. RFID Technologies for Inspection of Imported Foods
- Introduction
- Background
- Food Safety Information System
- Conclusion
- References
Contributor Contact Details
Index
Omics, Microbial Modeling and Technologies for Foodborne Pathogens
The editors’ preface and introductory chapter present the book as a comprehensive source of “omics,” microbial modeling and microbial technologies that can be used to understand, detect, and control foodborne organisms such as the bacterial, protozoan, fungal, and viral pathogens of humans. Use of the term “omics” apparently originated with Kandpal et al. in 2009. It is a blanket term for the phases of information-flow from the genetic material of an organism through to its realization as a biological entity and its interaction with host defenses and environmental stresses. As such it then includes the fundamental phases of genomics (including specifically pathogenomics in the book), transcriptomics, and proteomics. However, the book also considers supplementary “omics”: metabolomics, interactomics, fluxomics, and metagenomics.
The 21 chapters of the text, which are written by notable experts including the editors, are distributed into three parts. Chapters 2-7 and 9 of Part I cover the “omics” of the following bacterial genera with foodborne pathogenic members: Escherichia (Shiga-toxigenic non-O157), Salmonella, Campylobacter and Arcobacter, Listeria, Shigella, Yersinia, and Vibrio. In addition, Part I includes chapters on the “omics” of pathogenic foodborne fungi (the microsporidia), protozoa, and viruses. The viral “omics” are covered in two chapters, one on norovirus and hepatitis A virus and in Chapter 8 on emerging pathogens, which include hepatitis E virus. Looking at the Table of Contents and the running title for Chapter 8, one is not informed that it also covers the “omics” of Arcobacter spp. (which itself is also covered with Campylobacter), Cronobacter (formerly Enterobacter) sakazakii, Streptococcus suis, and sorbitol-fermenting Shiga-toxigenic E. coli (O157:H-). Readers of the book might well puzzle over the multichapter treatments for Escherichia and Arcobacter. The lack of mention of E. coli O157:H+ is only apparent as it is basically covered in the chapter on Shiga-toxigenic non-O157 E. coli since “omics” studies of the non-O157 strains are sparse. However it is helpful to have the available information on them collated as awareness of the significance of this group continues to increase. An apparent omission is that the non-Shiga-toxigenic pathogenic strains of E. coli are not considered at all. Even though there is wealth of bibliographic detail in the chapters on the various pathogens in Part I, their narratives are generally not reader friendly. Some of the figures are difficult to resolve.
Part II contains three interesting chapters on the mathematical modeling of microbial growth, the modeling of food safety risk assessments, and quantitative risk assessment. Being mathematical in approach, one might expect difficult going for the reader but that is not the case. The mathematics does not impede the narrative flow.
Part III has six chapters. Two are useful epidemiological treatments of food safety from farm-to-fork. Two more have valuable discussions of next generation sequencers (NGS) and of DNA microarray technology. NGS methodology is expected to be the cutting-edge technology for microbial strain typing and fully understanding the basis of pathogenicity. Finally there are two valuable chapters on noninvasive methods for direct typing of isolated colonies isolates (by optical forward scattering) and for tracking food lots through international and national commerce (by radio frequency IDs).
Not many readers will read such a technical text from cover to cover as this reviewer did. Rather it is suggested that they first read the introductory chapter, followed by Chapters 15-17 since these are the most reader friendly and provide an overview of food safety, modeling, and epidemiology, as well as, importantly the molecular typing methods used in the studies of the pathogens reviewed in the various chapters of Part I. Then those chapters can be profitably mined for finding out what “omics” studies have been done and what the conclusions were with the pathogens of particular interest to the reader.
The text is a valuable source of information on the current status of the “omics,” modeling and developing technologies for foodborne pathogens. Food safety microbiologists and students will want to have this text handy for reference, at least in their institutional or departmental libraries, if not at their desk sides.
- Anthony D. Hitchins
U.S. Food and Drug Administration, Retired
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