Tracing Pathogens in the Food Chain

Successful methods for the detection and investigation of outbreaks of foodborne disease are essential for ensuring consumer safety. Increased understanding of the transmission of pathogens in food chains will also assist efforts to safeguard public health. Tracing Pathogens in the Food Chain reviews key aspects of the surveillance, analysis, and spread of foodborne pathogens at different stages of industrial food production and processing. The first section of this work provides an introduction to foodborne pathogen surveillance, outbreak investigation, and control. The second concentrates on subtyping of foodborne pathogens, with chapters on phenoytypic subtyping, pulsed-field gel electrophoresis, and other emerging methods. The vital topics of method validation and quality assurance are also covered. The focus in the third section is on particular techniques for the surveillance and study of pathogens, such as protein-based analysis, ribotyping, and comparative genomics. Finally, the fourth section focuses on tracing pathogens in specific food chains, such as red meat and game, dairy, fish, and shellfish.

Table of Contents:
PART 1 FOODBORNE PATHOGEN SURVEILLANCE AND OUTBREAK INVESTIGATION Surveillance for foodborne pathogens in humans I S T Fisher, HPA Centre for Infections, UK Introduction. Methods for the surveillance of foodborne pathogens. National and international surveillance systems in use. Limitations to surveillance activities. Future trends. Conclusion. References. Systems for real-time, linked foodborne pathogen surveillance P Gerner-Smidt, Centers for Disease Control and Prevention, USA Introduction. Models for real-time linked foodborne pathogen surveillance: the Salm-net/Enter-net model. Models for real-time linked foodborne pathogen surveillance: the PulseNet model. Future trends. Sources of further information and advice. References. Detection, investigation and control of outbreaks of foodborne disease C Stein and A Ellis, World health Organization, Switzerland and T Jones, Tennessee Department of Health, USA Introduction. Planning and preparation. Outbreak detection. Outbreak investigation: epidemiological investigations. Descriptive epidemiological investigations. Analytical epidemiological investigations. Environmental and food investigations. Laboratory investigations. Control measures. Control of transmission. End of outbreak. Acknowledgements. References. Attributing the burden of foodborne disease to specific sources of infection T Hald and S M Pires, Technical University of Denmark Introduction. Definitions. Approaches for source attribution. Conclusions and recommendations. References. Determining the economic costs and global burden of foodborne disease J C Buzby, US Department of Agriculture, Economic Research Service (USDA-ERS), USA Introduction. Challenges faced in estimating the impact of foodborne disease. Methods used to value the impact of foodborne disease. Examples of the economic costs of foodborne disease and their use in cost-benefit analyses of food safety interventions. Future trends. Sources of further information and advice. References. PART 2 SUBTYPING OF FOODBORNE PATHOGENS Phenoytypic subtyping of foodborne pathogens W A Gebreyes, The Ohio State University and S Thakur, North Carolina State University, USA Overview of phenotypic subtyping. Serogrouping and serotyping. Biotyping. Phage typing. Antibiotyping (Antibiogram). Multi-locus enzyme electrophoresis (MLEE). Hemagglutination. Conclusions. References. Pulsed-field gel electrophoresis and other commonly used molecular methods for subtyping of foodborne bacteria K L F Cooper, Centers for Disease Control and Prevention, USA Introduction. Technical overview. Comparison of molecular methods. Library subtyping. Data interpretation for foodborne disease surveillance and outbreak investigation. Future trends. References. Emerging methods for foodborne bacterial subtyping F Pagotto and A Reid, Health Canada, Canada Introduction. Nucleic acid-based technologies. Protein-based technologies. Other emerging technologies. Conclusions and future trends. References. Development, validation and quality assurance of methods for subtyping of foodborne pathogens E K Hyytia-Trees and E M Ribot, Centers for Disease Control and Prevention, USA Introduction. Strain selection for protocol development and validation. Protocol development. Internal validation. External validation. Establishment of reference databases and a QA/QC program. Future trends. Sources of further information and advice. References. PART 3 MOLECULAR METHODS, GENOMICS AND OTHER EMERGING APPROACHES IN THE SURVEILLANCE AND STUDY OF FOODBORNE PATHOGENS Sample preparation for the detection of foodborne pathogens by molecular biological methods P Rossmanith, Christian-Doppler Laboratory for Molecular Biological Food Analytics and M Wagner, Department for Farm Animals and Public Veterinary Health, Austria Introduction. Physical separation methods used in sample preparation. Biochemical and biological separation methods used in sample preparation. Chemical and enzymatic pre-separation methods for sample treatment. Related approaches and combined sample preparation and detection methods. Conclusion and future trends. Acknowledgements. References. A comparison of molecular technologies and genomotyping for tracing and strain characterization of Campylobacter isolates J van der Vossen, B Keijser, F Schuren, A Nocker and R Montijn, TNO Quality of Life, The Netherlands Introduction. Methodologies for tracing and/or understanding strain properties. Conclusion. References. Investigating foodborne pathogens using comparative genomics R A Stabler, E S Nalerio, P C Strong and B W Wren, London School of Hygiene and Tropical Medicine, UK Introduction. Molecular typing systems in tracking bacterial pathogens in the food chain. Whole genome approaches using microarrays. Conclusions and future trends. References. Protein-based analysis and other new and emerging non-nucleic acid based methods for tracing and investigating food-borne pathogens J P Bowman, University of Tasmania, Australia Introduction. Distinguishing live from dead cells: viability and pH sensitive stains for assessing cell physiology. Rapid sample scanning: fluorescent in situ hybridization (FISH) coupled to secondary ion mass spectrometry (SIMS), Fourier transform and Raman spectroscopy. Electrophysiology. Proteomics. Applications of proteomics for detection of foodborne pathogens. Metabolomics. Sources of further information and advice. References. Virulotyping of foodborne pathogens T M Wassenaar, Molecular Microbiology and Genomic Consultants, Germany Introduction. Defining and identifying virulence genes. Virulotyping: advantages and disadvantages. Examples of specific pathogens. Future trends. References. Using ribotyping to trace foodborne aerobic sporeforming bacteria in the factory: a case study A C M van Zuijlen, Unilever R&D Vlaardingen, The Netherlands Introduction. Ingredients as a source of bacterial spores. Growth of bacterial spores in line. Identifying relevant sporeformers. Tracking sources of relevant sporeformers. Controlling levels of sporeformers in production. Future trends. References. Biotracing: a novel concept in food safety integrating microbiology knowledge, complex systems approaches and probabilistic modelling J Hoorfar, Technical University of Denmark, Denmark, M Wagner, Department of Farm Animal and Veterinary Public Health, Austria, K Jordan, Teagasc, Ireland and G C Barker, Institute of Food Research, UK What is BIOTRACER? Definition of biotracing. Fundamental concepts of biotracing. Why is biotraceability needed? What are the gaps in biotraceability? How can these gaps be closed? What are the achievements so far? Specific achievements to date. Future trends. Acknowledgements. References. PART 4 TRACING PATHOGENS IN PARTICULAR FOOD CHAINS Tracing pathogens in red meat and game production chains and at the abattoir P Whyte, S Fanning, S O’Brien, L O’Grady and K Solomon, University College Dublin, Ireland Introduction. Foodborne pathogens in red meat and their public health significance. Potential amplification steps and control of enteropathogens in red meat and game production chains. Antimicrobial resistance in red meat pathogens. Future trends. Sources of further information and advice. References. Tracing pathogens in fish production chains B T Lunestad and A Levsen, NIFES and J T Rosnes, NOFIMA Norconserv, Norway Introduction. Foodborne pathogens in the fish production chains. Bacteria. Biogenic amines. Parasites. Fungi and mycotoxins. Tracking the sources, reservoirs, survival and potential amplification steps of human pathogens in fish production chains. Pathogen monitoring and control strategies. New preservation strategies. HACCP. Microbial modelling. Future trends. Sources of further information and advice. References. Tracing pathogens in poultry and egg production and at the abattoir K L Hiett, United States Department of Agriculture, Agricultural Research Service (USDA-ARS)) Introduction. Pathogens associated with broiler meat. Source tracking. Phenotypic based tracking methods. Nucleic acid based methods. Reservoirs and potential amplification steps of human pathogens in poultry production chains. Pathogen monitoring strategies. Improving pathogen control. Antimicrobial resistance. Future trends. Sources of further information and advice. References. Tracing zoonotic pathogens in dairy production J S Van Kessel, M Santin-Duran and J S Karns, United States Department of Agriculture, Agricultural Research Service (USDA-ARS) and Y Schukken, Cornell University Introduction. Foodborne pathogens in dairy production chains and their significance for public health. Tracking the sources, reservoirs and potential amplification steps of human pathogens in dairy production. Pathogen monitoring strategies. Improving pathogen control. Future trends. References. Tracing pathogens in molluscan shellfish production chains R J Lee and R E Rangdale, Centre for Environment, Fisheries and Aquaculture Science, UK Introduction. Overview of shellfish production chains. Foodborne pathogens in shellfish. Typing methods for tracking pathogens in shellfish production chains. Pathogen monitoring strategies. Pathogen typing strategies. Improving pathogen control. Future trends. Sources of further information and advice. References. Tracing pathogens in fruit and vegetable production chains R E Mandrell, United States Department of Agriculture, Agricultural Research Service (USDA-ARS) Introduction. Summary of major outbreaks linked to pre-harvest contamination of produce. Incidence of human pathogens on fresh produce. Incidence of generic E. coli on produce. Animal sources of enteric foodborne pathogens relevant to produce contamination. Pathogens in municipal and agricultural watersheds. Fitness of human pathogens in the environment. Fecal indicators of contamination in watersheds. Survival of human pathogens on pre-harvest plants. Hydrology and microorganisms. Microbial source tracking (MST). MST in recent produce outbreak investigations. Next generation MST. Conclusions. Acknowledgements. References.