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# Microbial Forensics in Food Safety

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.
Price Non-Member $15.00 • Author: • Editors: • VIEW AFFILIATIONS HIDE AFFILIATIONS Affiliations: 1: Biological Sciences Department, California Polytechnic State University, San Luis Obispo, CA 93407; 2: California Polytechnic State University, San Luis Obispo, CA; 3: University of Puerto Rico-Río Piedras, San Juan, Puerto Rico • Source: microbiolspec August 2016 vol. 4 no. 4 doi:10.1128/microbiolspec.EMF-0002-2013 • Received 18 November 2013 Accepted 16 September 2014 Published 12 August 2016 • Marie Yeung, pmyeung@calpoly.edu Preview this microbiology spectrum article: Microbial Forensics in Food Safety, Page 1 of 2 | /docserver/preview/fulltext/microbiolspec/4/4/EMF-0002-2013-1.gif /docserver/preview/fulltext/microbiolspec/4/4/EMF-0002-2013-2.gif • Abstract: Foodborne diseases represent a significant public health burden to the United States, considering that they cause illness in 1 in 6 people annually, which amounts to ∼48 million people (E. Scallan, R. M. Hoekstra, F. J. Angulo, R. V. Tauxe, M. A. Widdowson, S. L. Roy, J. L. Jones, and P. M. Griffin, 17:7–15, 2011). The average national cost of illness associated with 30 foodborne pathogens is estimated to be$55.5 to $93.2 billion based on two cost-of-illness models (R.L. Scharff, 78:1064–1071, 2015). Predominately, foodborne illnesses are the result of accidental contamination or unintentional mishandling of food materials during the farm-to-table continuum. Nevertheless, principles and methodologies derived from microbial forensics are applied in foodborne outbreaks investigation to determine the source of the pathogen. Drawing from multiple real-life examples and case studies, this review discusses how the current food industry practice, demography, and consumer preference are shaping the landscape of food safety. The approaches to source tracking, or traceback, are described, with a focus on bacterial pathogens associated with food-producing animals. Current challenges and opportunities in microbial forensics in food safety are also addressed. • Citation: Yeung M. 2016. Microbial Forensics in Food Safety. Microbiol Spectrum 4(4):EMF-0002-2013. doi:10.1128/microbiolspec.EMF-0002-2013. ## Key Concept Ranking Food Safety 0.54095554 Restriction Fragment Length Polymorphism 0.48177472 Foodborne Illnesses 0.43736115 0.54095554 ## References 1. MacDonald JM, O’Donoghue EJ, McBride WD, Nehring RF, Sandretto CL, Mosheim R. 2007. Profits, Costs, and the Changing Structure of Dairy Farming. Economic research report no. ERR-47. Economic Research Service, US Department of Agriculture, Washington, DC. http://www.ers.usda.gov/publications/err-economic-research-report/err47.aspx#.VBOMpPldWSo. 2. Government Accountability Office. 2011. Opportunities to reduce potential duplication in government programs, save tax dollars, and enhance revenue. Government Accountability Office, Washington, DC. http://www.gao.gov/assets/320/315920.pdf. 3. Boxrud D, Monson T, Stiles T, Besser J. 2010. The role, challenges, and support of PulseNet laboratories in detecting foodborne disease outbreaks. Public Health Rep 125(Suppl 2):57–62. [PubMed] 4. Scallan E, Hoekstra RM, Angulo FJ, Tauxe RV, Widdowson MA, Roy SL, Jones JL, Griffin PM. 2011. Foodborne illness acquired in the United States—major pathogens. Emerg Infect Dis 17:7–15. [PubMed][CrossRef] 5. Painter JA, Hoekstra RM, Ayers T, Tauxe RV, Braden CR, Angulo FJ, Griffin PM. 2013. Attribution of foodborne illnesses, hospitalizations, and deaths to food commodities by using outbreak data, United States, 1998–2008. Emerg Infect Dis 19:407–415. [PubMed][CrossRef] 6. Centers for Disease Control and Prevention. 1996. Outbreak of Escherichia coli O157:H7 infections associated with drinking unpasteurized commercial apple juice—British Columbia, California, Colorado, and Washington, October 1996. MMWR Morb Mortal Wkly Rep 45:975. [PubMed] 7. Flynn D. 17 September 2009. Odwalla apple juice E. coli outbreak. Food Safety News, Seattle, WA. http://www.foodsafetynews.com/2009/09/meaningful-outbreak-4-odwalla-apple-juice-e-coli-o157h7-outbreak/#.VyIjaXp6l4w. 8. Davidson K. 1996. E. coli verified in Odwalla juice. Online edition of San Francisco Chronicle (SFGate), San Francisco, CA. http://www.sfgate.com/news/article/E-coli-verified-in-Odwalla-juice-3310018.php. 9. Wall PG, Morgan D, Lamden K, Griffin M, Threlfall EJ, Ward LR, Rowe B. 1995. Transmission of multi-resistant strains of Salmonella typhimurium from cattle to man. Vet Rec 136:591–592. [PubMed][CrossRef] 10. Dechet AM, Scallan E, Gensheimer K, Hoekstra R, Gunderman-King J, Lockett J, Wrigley D, Chege W, Sobel J, Multistate Working Group. 2006. Outbreak of multidrug-resistant Salmonella enterica serotype Typhimurium Definitive Type 104 infection linked to commercial ground beef, northeastern United States, 2003-2004. Clin Infect Dis 42:747–752. [PubMed][CrossRef] 11. Mather AE, Reid SWJ, Maskell DJ, Parkhill J, Fookes MC, Harris SR, Brown DJ, Coia JE, Mulvey MR, Gilmour MW, Petrovska L, de Pinna E, Kuroda M, Akiba M, Izumiya H, Connor TR, Suchard MA, Lemey P, Mellor DJ, Haydon DT, Thomson NR. 2013. Distinguishable epidemics of multidrug-resistant Salmonella Typhimurium DT104 in different hosts. Science 341:1514–1517. [PubMed][CrossRef] 12. Bottemiller H. 28 May 2013. Putting food traceability at consumers’ fingertips. Food Safety News, Seattle, WA. http://www.foodsafetynews.com/2013/05/putting-food-traceability-at-consumers-fingertips/#.VyIjyHp6l4w. 13. Centers for Disease Control and Prevention. 2008. Outbreak of Salmonella serotype Saintpaul infections associated with multiple raw produce items—United States, 2008. MMWR Morb Mortal Wkly Rep 57:929–934. [PubMed] 14. Flynn D. 2 August 2013. Tomato growers want compensation for losses in 2008 outbreak, Food Safety News, Seattle, WA. http://www.foodsafetynews.com/2013/08/tomato-growers-want-to-be-compensated-for-losses-in-2008-outbreak/#.VyIj4Xp6l4w. 15. Pavlic M, Griffiths MW. 2009. Principles, applications, and limitations of automated ribotyping as a rapid method in food safety. Foodborne Pathog Dis 6:1047–1055. [PubMed][CrossRef] 16. Maiden MCJ. 2006. Multilocus sequence typing of bacteria. Annu Rev Microbiol 60:561–588. [PubMed][CrossRef] 17. Maiden MCJ, Bygraves JA, Feil E, Morelli G, Russell JE, Urwin R, Zhang Q, Zhou J, Zurth K, Caugant DA, Feavers IM, Achtman M, Spratt BG. 1998. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci USA 95:3140–3145. [PubMed][CrossRef] 18. Holmes EC, Urwin R, Maiden MCJ. 1999. The influence of recombination on the population structure and evolution of the human pathogen Neisseria meningitidis. Mol Biol Evol 16:741–749. [PubMed][CrossRef] 19. Keim P, Price LB, Klevytska AM, Smith KL, Schupp JM, Okinaka R, Jackson PJ, Hugh-Jones ME. 2000. Multiple-locus variable-number tandem repeat analysis reveals genetic relationships within Bacillus anthracis. J Bacteriol 182:2928–2936. [PubMed][CrossRef] 20. Pourcel C, André-Mazeaud F, Neubauer H, Ramisse F, Vergnaud G. 2004. Tandem repeats analysis for the high resolution phylogenetic analysis of Yersinia pestis. BMC Microbiol 4:22. [PubMed][CrossRef] 21. Farlow J, Smith KL, Wong J, Abrams M, Lytle M, Keim P. 2001. Francisella tularensis strain typing using multiple-locus, variable-number tandem repeat analysis. J Clin Microbiol 39:3186–3192. [PubMed][CrossRef] 22. Neil KP, Biggerstaff G, MacDonald JK, Trees E, Medus C, Musser KA, Stroika SG, Zink D, Sotir MJ. 2012. A novel vehicle for transmission of Escherichia coli O157:H7 to humans: multistate outbreak of E. coli O157:H7 infections associated with consumption of ready-to-bake commercial prepackaged cookie dough-United States, 2009. Clin Infect Dis 54:511–518. [PubMed][CrossRef] 23. Hyytia-Trees E, Lafon P, Vauterin P, Ribot EM. 2010. Multilaboratory validation study of standardized multiple-locus variable-number tandem repeat analysis protocol for Shiga toxin-producing Escherichia coli O157: a novel approach to normalize fragment size data between capillary electrophoresis platforms. Foodborne Pathog Dis 7:129–136. [PubMed][CrossRef] 24. Nadon CA, Trees E, Ng LK, Møller Nielsen E, Reimer A, Maxwell N, Kubota KA, Gerner-Smidt P, MLVA Harmonization Working Group. 2013. Development and application of MLVA methods as a tool for inter-laboratory surveillance. Euro Surveill 18:20565. [PubMed][CrossRef] 25. Kreuzer-Martin HW, Lott MJ, Dorigan J, Ehleringer JR. 2003. Microbe forensics: oxygen and hydrogen stable isotope ratios in Bacillus subtilis cells and spores. Proc Natl Acad Sci USA 100:815–819. [PubMed][CrossRef] 26. Kreuzer-Martin HW, Chesson LA, Lott MJ, Dorigan JV, Ehleringer JR. 2004. Stable isotope ratios as a tool in microbial forensics—Part 2. Isotopic variation among different growth media as a tool for sourcing origins of bacterial cells or spores. J Forensic Sci 49:961–967. [PubMed][CrossRef] 27. Loman NJ, Constantinidou C, Christner M, Rohde H, Chan JZM, Quick J, Weir JC, Quince C, Smith GP, Betley JR, Aepfelbacher M, Pallen MJ. 2013. A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4. JAMA 309:1502–1510. [PubMed][CrossRef] 28. Eppinger M, Mammel MK, Leclerc JE, Ravel J, Cebula TA. 2011. Genomic anatomy of Escherichia coli O157:H7 outbreaks. Proc Natl Acad Sci USA 108:20142–20147. [PubMed][CrossRef] 29. Gilmour MW, Graham M, Van Domselaar G, Tyler S, Kent H, Trout-Yakel KM, Larios O, Allen V, Lee B, Nadon C. 2010. High-throughput genome sequencing of two Listeria monocytogenes clinical isolates during a large foodborne outbreak. BMC Genomics 11:120. [PubMed][CrossRef] 30. den Bakker HC, Allard MW, Bopp D, Brown EW, Fontana J, Iqbal Z, Kinney A, Limberger R, Musser KA, Shudt M, Strain E, Wiedmann M, Wolfgang WJ. 2014. Rapid whole-genome sequencing for surveillance of Salmonella enterica serovar enteritidis. Emerg Infect Dis 20:1306–1314. [PubMed][CrossRef] 31. Allard MW, Luo Y, Strain E, Pettengill J, Timme R, Wang C, Li C, Keys CE, Zheng J, Stones R, Wilson MR, Musser SM, Brown EW. 2013. On the evolutionary history, population genetics and diversity among isolates of Salmonella Enteritidis PFGE pattern JEGX01.0004. PLoS One 8:e55254. [PubMed][CrossRef] 32. Bergholz TM, Moreno Switt AI, Wiedmann M. 2014. Omics approaches in food safety: fulfilling the promise? Trends Microbiol 22:275–281. [PubMed][CrossRef] 33. Institute of Food Technologists. August 2012. Pilot Projects for Improving Product Tracing along the Food Supply System—Final Report. Institute of Food Technologists, Chicago, IL. http://www.ift.org/knowledge-center/focus-areas/food-safety-and-defense/∼/media/Knowledge%20Center/Focus%20Areas/Traceability/IFT_FDA_ProductTracingPilotsFinalReport.pdf. 34. Crandall PG, O’Bryan CA, Babu D, Jarvis N, Davis ML, Buser M, Adam B, Marcy J, Ricke SC. 2013. Whole-chain traceability, is it possible to trace your hamburger to a particular steer, a U.S. perspective. Meat Sci 95:137–144. [PubMed][CrossRef] 35. USDA/Agriculture Marketing Program/Livestock Poultry and Seed Program. May 2013. Technical Requirement Schedule—Ground Beef—2013. US Department of Agriculture, Washington, DC. http://www.ams.usda.gov/AMSv1.0/getfile?dDocName=STELPRDC5066617. 36. Shackell GH, Mathias HC, Cave VM, Dodds KG. 2005. Evaluation of microsatellites as a potential tool for product tracing of ground beef mixtures. Meat Sci 70:337–345. [PubMed][CrossRef] 37. US Food and Drug Administration. 1998. Guide to Minimize Microbial Food Safety Hazards for Fresh Fruits and Vegetables. US Food and Drug Administration, Washington, DC. microbiolspec.EMF-0002-2013.citations cm/4/4 content/journal/microbiolspec/10.1128/microbiolspec.EMF-0002-2013 Citations loading... Article metrics loading... /content/journal/microbiolspec/10.1128/microbiolspec.EMF-0002-2013 2016-08-12 2017-11-19 Abstract: Foodborne diseases represent a significant public health burden to the United States, considering that they cause illness in 1 in 6 people annually, which amounts to ∼48 million people (E. Scallan, R. M. Hoekstra, F. J. Angulo, R. V. Tauxe, M. A. Widdowson, S. L. Roy, J. L. Jones, and P. M. Griffin, 17:7–15, 2011). The average national cost of illness associated with 30 foodborne pathogens is estimated to be$55.5 to \$93.2 billion based on two cost-of-illness models (R.L. Scharff, 78:1064–1071, 2015). Predominately, foodborne illnesses are the result of accidental contamination or unintentional mishandling of food materials during the farm-to-table continuum. Nevertheless, principles and methodologies derived from microbial forensics are applied in foodborne outbreaks investigation to determine the source of the pathogen. Drawing from multiple real-life examples and case studies, this review discusses how the current food industry practice, demography, and consumer preference are shaping the landscape of food safety. The approaches to source tracking, or traceback, are described, with a focus on bacterial pathogens associated with food-producing animals. Current challenges and opportunities in microbial forensics in food safety are also addressed.

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