PART 1 FOODBORNE PATHOGEN SURVEILLANCE AND OUTBREAK INVESTIGATION

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1 Contents PART 1 FOODBORNE PATHOGEN SURVEILLANCE AND OUTBREAK INVESTIGATION PART 2 SUBTYPING OF FOODBORNE PATHOGENS PART 3 MOLECULAR METHODS, GENOMICS AND OTHER EMERGING APPROACHES IN THE SURVEILLANCE AND STUDY OF FOODBORNE PATHOGENS PART 4 TRACING PATHOGENS IN PARTICULAR FOOD CHAINS Introduction S Brul, University of Amsterdam, The Netherlands, P Fratamico, United States Department of Agriculture, Agricultural Research Service (USDA-ARS), USA and T McMeekin, University of Tasmania, Australia - Microbes and the food chain - Where and in what state are noxious microbes in our food chain? - Towards integration PART 1 FOODBORNE PATHOGEN SURVEILLANCE AND OUTBREAK INVESTIGATION Surveillance for foodborne pathogens in humans I S T Fisher, HPA Centre for Infections, UK - Methods for the surveillance of foodborne pathogens - National and international surveillance systems in use - Limitations to surveillance activities - Conclusion Systems for real-time, linked foodborne pathogen surveillance P Gerner-Smidt, Centers for Disease Control and Prevention, USA - 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 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 - 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

2 - Acknowledgements and useful reading Attributing the burden of foodborne disease to specific sources of infection T Hald and S M Pires, Technical University of Denmark, Denmark - Definitions - Approaches for source attribution - Conclusions and recommendations Determining the economic costs and global burden of foodborne disease J C Buzby, US Department of Agriculture, Economic Research Service (USDA-ERS), USA - 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 PART 2 SUBTYPING OF FOODBORNE PATHOGENS Phenoytypic subtyping of foodborne pathogens W A Gebreyes, 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 - Hemagglutination - Conclusions 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 - Technical overview - Comparison of molecular methods - Library subtyping - Data interpretation for foodborne disease surveillance and outbreak investigation Emerging methods for foodborne bacterial subtyping F Pagotto and A Reid, Health Canada, Canada - Nucleic acid-based technologies - Protein-based technologies - Other emerging technologies - Conclusions and future trends

3 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 - Strain selection for protocol development and validation - Protocol development - Internal validation - External validation - Establishment of reference databases and a QA/QC program 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 - 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 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 - Methodologies for tracing and/or understanding strain properties - Conclusion 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 - Molecular typing systems in tracking bacterial pathogens in the food chain - Whole genome approaches using microarrays - Conclusions and future trends 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 - 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

4 - Electrophysiology - Proteomics - Applications of proteomics for detection of foodborne pathogens - Metabolomics Virulotyping of foodborne pathogens T M Wassenaar, Molecular Microbiology and Genomic Consultants, Germany - Defining and identifying virulence genes - Virulotyping: advantages and disadvantages - Examples of specific pathogens 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 - 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 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 - Acknowledgements 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 - 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

5 Tracing pathogens in fish production chains B T Lunestad and A Levsen, NIFES and J T Rosnes, NOFIMA Norconserv, Norway - 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 Tracing pathogens in poultry and egg production and at the abattoir K L Hiett, United States Department of Agriculture, USA - 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 Tracing zoonotic pathogens in dairy production J S Van Kessel, M Santin-Duran and J S Karns, United States Department of Agriculture and Y Schukken, Cornell University, USA - 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 Tracing pathogens in molluscan shellfish production chains R J Lee and R E Rangdale, Centre for Environment, Fisheries and Aquaculture Science, UK - Overview of shellfish production chains - Foodborne pathogens in shellfish - Typing methods for tracking pathogens in shellfish production chains

6 - Pathogen monitoring strategies - Pathogen typing strategies - Improving pathogen control Tracing pathogens in fruit and vegetable production chains R E Mandrell, US Department of Agriculture, USA - 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 - Microbial source tracking in recent produce outbreak investigations - Next generation Microbial source tracking - Conclusions - Acknowledgements