{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T13:25:49Z","timestamp":1791293149370,"version":"4.1.0"},"reference-count":154,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2014,9,1]],"date-time":"2014-09-01T00:00:00Z","timestamp":1409529600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["International Journal of Food Microbiology"],"published-print":{"date-parts":[[2014,9]]},"DOI":"10.1016\/j.ijfoodmicro.2014.07.002","type":"journal-article","created":{"date-parts":[[2014,7,11]],"date-time":"2014-07-11T16:03:26Z","timestamp":1405094606000},"page":"57-72","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":79,"special_numbering":"C","title":["Exploiting the explosion of information associated with whole genome sequencing to tackle Shiga toxin-producing Escherichia coli (STEC) in global food production systems"],"prefix":"10.1016","volume":"187","author":[{"given":"Eelco","family":"Franz","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pascal","family":"Delaquis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefano","family":"Morabito","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lothar","family":"Beutin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kari","family":"Gobius","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David A.","family":"Rasko","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jim","family":"Bono","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nigel","family":"French","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacek","family":"Osek","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bj\u00f8rn-Arne","family":"Lindstedt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maite","family":"Muniesa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shannon","family":"Manning","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeff","family":"LeJeune","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Todd","family":"Callaway","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Scott","family":"Beatson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark","family":"Eppinger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tim","family":"Dallman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ken J.","family":"Forbes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Henk","family":"Aarts","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David L.","family":"Pearl","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Victor P.J.","family":"Gannon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chad R.","family":"Laing","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Norval J.C.","family":"Strachan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0005","doi-asserted-by":"crossref","first-page":"535","DOI":"10.2752\/175174413X13758634981976","article-title":"Horsemeat-gate the discursive production of a neoliberal food scandal","volume":"16","author":"Abbots","year":"2013","journal-title":"Food Cult. Soc."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0010","series-title":"The Evolution of Foodborne Pathogens","author":"Abu-Ali","year":"2011"},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0015","doi-asserted-by":"crossref","first-page":"165","DOI":"10.2217\/17460913.2.2.165","article-title":"Stx-phages: drivers and mediators of the evolution of STEC and STEC-like pathogens","volume":"2","author":"Allison","year":"2007","journal-title":"Future Microbiol"},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0020","doi-asserted-by":"crossref","first-page":"1906","DOI":"10.3201\/eid1710.111027","article-title":"Timeliness of surveillance during outbreak of Shiga toxin-producing Escherichia coli infection, Germany, 2011","volume":"17","author":"Altmann","year":"2011","journal-title":"Emerg. Infect. Dis."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0025","doi-asserted-by":"crossref","first-page":"370","DOI":"10.1128\/JCM.01361-06","article-title":"Fast DNA serotyping of Escherichia coli by use of an oligonucleotide microarray","volume":"45","author":"Ballmer","year":"2007","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0030","doi-asserted-by":"crossref","first-page":"e00066-13","DOI":"10.1128\/mBio.00066-13","article-title":"Bloody coli: A Gene Cocktail in Escherichia coli O104:H4","volume":"4","author":"Baquero","year":"2013","journal-title":"mBio"},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0035","doi-asserted-by":"crossref","first-page":"3013","DOI":"10.1128\/JCM.32.12.3013-3017.1994","article-title":"Laboratory investigation of a multistate food-borne outbreak of Escherichia coli O157-H7 by using pulsed-field gel-electrophoresis and phage typing","volume":"32","author":"Barrett","year":"1994","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0040","doi-asserted-by":"crossref","first-page":"4302","DOI":"10.1128\/IAI.70.8.4302-4311.2002","article-title":"Identification of an aggregative adhesion fimbria (AAF) type III-encoding operon in enteroaggregative Escherichia coli as a sensitive probe for detecting the AAF-Encoding operon family","volume":"70","author":"Bernier","year":"2002","journal-title":"Infect. Immun."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0045","doi-asserted-by":"crossref","first-page":"803","DOI":"10.1111\/1469-0691.12217","article-title":"Rapid bacterial genome sequencing: methods and applications in clinical microbiology","volume":"19","author":"Bertelli","year":"2013","journal-title":"Clin. Microbiol. Infect."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0050","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1128\/AEM.01035-06","article-title":"Greater diversity of Shiga toxin-encoding bacteriophage insertion sites among Escherichia coli O157: H7 isolates from cattle than in those from humans","volume":"73","author":"Besser","year":"2007","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0055","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1007\/BF00193627","article-title":"Virulence factors and phenotypical traits of verotoxigenic strains of Escherichia coli isolated from human patients in Germany","volume":"183","author":"Beutin","year":"1994","journal-title":"Med. Microbiol. Immunol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0060","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1016\/j.ijmm.2013.08.001","article-title":"Shiga toxin-producing Escherichia coli strains from cattle as a source of the Stx2a bacteriophages present in enteroaggregative Escherichia coli 0104:H4 strains","volume":"303","author":"Beutin","year":"2013","journal-title":"Int. J. Med. Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0065","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1016\/S1473-3099(11)70165-7","article-title":"Characterisation of the Escherichia coli strain associated with an outbreak of haemolytic uraemic syndrome in Germany, 2011: a microbiological study","volume":"11","author":"Bielaszewska","year":"2011","journal-title":"Lancet Infect. Dis."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0070","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1128\/JCM.37.3.497-503.1999","article-title":"Associations between virulence factors of Shiga toxin-producing Escherichia coli and disease in humans","volume":"37","author":"Boerlin","year":"1999","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0080","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1186\/1471-2334-7-98","article-title":"Association of Escherichia coli O157: H7 tir polymorphisms with human infection","volume":"7","author":"Bono","year":"2007","journal-title":"BMC Infect. Dis."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0085","doi-asserted-by":"crossref","first-page":"2047","DOI":"10.1093\/molbev\/mss072","article-title":"Phylogeny of Shiga toxin-producing Escherichia coli O157 isolated from cattle and clinically ill humans","volume":"29","author":"Bono","year":"2012","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0090","doi-asserted-by":"crossref","first-page":"2458","DOI":"10.1128\/AEM.02322-10","article-title":"Molecular risk assessment and epidemiological typing of Shiga toxin-producing Escherichia coli by using a novel PCR binary typing system","author":"Brandt","year":"2011","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0095","doi-asserted-by":"crossref","first-page":"1422","DOI":"10.1086\/466536","article-title":"Non-O157 Shiga toxin-producing Escherichia coli infections in the United States, 1983\u20132002","volume":"192","author":"Brooks","year":"2005","journal-title":"J. Infect. Dis."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0100","doi-asserted-by":"crossref","first-page":"3780","DOI":"10.1128\/AEM.72.5.3780-3784.2006","article-title":"Development and validation of an oligonucleotide microarray for detection of multiple virulence and antimicrobial resistance genes in Escherichia coli","volume":"72","author":"Bruant","year":"2006","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0105","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1016\/j.tifs.2012.04.004","article-title":"\u2018Omics\u2019 technologies in quantitative microbial risk assessment","volume":"27","author":"Brul","year":"2012","journal-title":"Trends Food Sci. Technol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0110","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1128\/AEM.01921-09","article-title":"Low-density macroarray targeting non-locus of enterocyte effacement effectors (nle genes) and major virulence factors of Shiga toxin-producing Escherichia coli (STEC): a new approach for molecular risk assessment of STEC isolates","volume":"76","author":"Bugarel","year":"2010","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0115","article-title":"Subtyping of STEC by MLVA in Argentina. Frontiers in cellular and infection","volume":"2","author":"Bustamante","year":"2012","journal-title":"Microbiology"},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0120","doi-asserted-by":"crossref","first-page":"1336","DOI":"10.1128\/JCM.05317-11","article-title":"Incidence and virulence determinants of verocytotoxin-producing Escherichia coli infections in the Brussels-capital region, Belgium, in 2008\u20132010","volume":"50","author":"Buvens","year":"2012","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0125","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1016\/S1369-5274(03)00086-9","article-title":"Phage as agents of lateral gene transfer","volume":"6","author":"Canchaya","year":"2003","journal-title":"Curr. Opin. Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0130","doi-asserted-by":"crossref","DOI":"10.3389\/fcimb.2012.00057","article-title":"A framework for assessing the concordance of molecular typing methods and the true strain phylogeny of Campylobacter jejuni and C. coil using draft genome sequence data","volume":"2","author":"Carrillo","year":"2012","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0135","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1016\/j.meegid.2012.01.005","article-title":"The evolution of the Escherichia coli phylogeny","volume":"12","author":"Chaudhuri","year":"2012","journal-title":"Infect. Genet. Evol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0140","doi-asserted-by":"crossref","first-page":"e8801","DOI":"10.1371\/journal.pone.0008801","article-title":"Complete genome sequence and comparative metabolic profiling of the prototypical enteroaggregative Escherichia coli strain 042","volume":"5","author":"Chaudhuri","year":"2010","journal-title":"PLoS One"},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0145","doi-asserted-by":"crossref","first-page":"579","DOI":"10.3109\/00365548.2011.568953","article-title":"MLVA is a valuable tool in epidemiological investigations of Escherichia coli and for disclosing multiple carriage","volume":"43","author":"Christiansson","year":"2011","journal-title":"Scand. J. Infect. Dis."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0150","doi-asserted-by":"crossref","DOI":"10.1016\/S0140-6736(10)62261-1","article-title":"Ciprofloxacin-resistant campylobacteriosis in the UK","volume":"376","author":"Cody","year":"2010","journal-title":"Lancet"},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0155","doi-asserted-by":"crossref","first-page":"3121","DOI":"10.1111\/1462-2920.12236","article-title":"Sigma factors in a thousand E. coli genomes","volume":"15","author":"Cook","year":"2013","journal-title":"Environ. Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0160","doi-asserted-by":"crossref","first-page":"2153","DOI":"10.1128\/AEM.02566-07","article-title":"Molecular analysis as an aid to assess the public health risk of non-O157 Shiga toxin-producing Escherichia coli strains","volume":"74","author":"Coombes","year":"2008","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0165","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1186\/1471-2164-15-17","article-title":"Comparative genomics of enterohemorrhagic Escherichia coli O145:H28 demonstrates a common evolutionary lineage with Escherichia coli O157:H7","volume":"15","author":"Cooper","year":"2014","journal-title":"BMC Genomics"},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0170","doi-asserted-by":"crossref","first-page":"1083","DOI":"10.1128\/JCM.02864-12","article-title":"Towards a molecular definition of enterohemorrhagic Escherichia coli (EHEC): detection of genes located on O island 57 as markers to distinguish EHEC from closely related enteropathogenic E. coli strains","volume":"51","author":"Delannoy","year":"2013","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0175","doi-asserted-by":"crossref","first-page":"887","DOI":"10.1128\/IAI.00882-09","article-title":"Role of RpoS in virulence of pathogens","volume":"78","author":"Dong","year":"2010","journal-title":"Infect. Immun."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0180","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1186\/2042-5783-3-2","article-title":"Beginner's guide to comparative bacterial genome analysis using next-generation sequence data","volume":"3","author":"Edwards","year":"2013","journal-title":"Microb. Inform. Exp."},{"issue":"12","key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0185","doi-asserted-by":"crossref","first-page":"3502","DOI":"10.2903\/j.efsa.2013.3502","article-title":"Scientific Opinion on the evaluation of molecular typing methods for major food-borne microbiological hazards and their use for attribution modelling, outbreak investigation and scanning surveillance: Part 1 (evaluation of methods and applications)","volume":"11","author":"EFSA","year":"2013","journal-title":"EFSA J."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0195","doi-asserted-by":"crossref","first-page":"2916","DOI":"10.1128\/AEM.02554-10","article-title":"Genome signatures of Escherichia coli O157:H7 isolates from the bovine host reservoir","volume":"77","author":"Eppinger","year":"2011","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0200","doi-asserted-by":"crossref","first-page":"20142","DOI":"10.1073\/pnas.1107176108","article-title":"Genomic anatomy of Escherichia coli O157:H7 outbreaks","volume":"108","author":"Eppinger","year":"2011","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0205","doi-asserted-by":"crossref","first-page":"3148","DOI":"10.1128\/AEM.00256-13","article-title":"High-throughput sequencing and metagenomics: moving forward in the culture-independent analysis of food microbial ecology","volume":"79","author":"Ercolini","year":"2013","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0210","doi-asserted-by":"crossref","first-page":"1085","DOI":"10.1093\/molbev\/msh118","article-title":"A specific genetic background is required for acquisition and expression of virulence factors in Escherichia coli","volume":"21","author":"Escobar-Paramo","year":"2004","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0215","doi-asserted-by":"crossref","first-page":"842","DOI":"10.3201\/eid1005.030576","article-title":"Virulence factors for hemolytic uremic syndrome, Denmark","volume":"10","author":"Ethelberg","year":"2004","journal-title":"Emerg. Infect. Dis."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0220","series-title":"Codex Alimentarius Commission: Procedural Manual","author":"FAO","year":"1997"},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0225","doi-asserted-by":"crossref","first-page":"1750","DOI":"10.1086\/517438","article-title":"Genotypic and phenotypic changes in the emergence of Escherichia coli O157: H7","volume":"177","author":"Feng","year":"1998","journal-title":"J. Infect. Dis."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0230","unstructured":"Flynn, D.,2013. Letter from the Editor: IT Risks in the Metadata World. Food Safety News, 1-1."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0235","doi-asserted-by":"crossref","first-page":"1771","DOI":"10.1056\/NEJMoa1106483","article-title":"Epidemic profile of Shiga-Toxin-producing Escherichia coli O104:H4 outbreak in Germany","volume":"365","author":"Frank","year":"2011","journal-title":"N. Engl. J. Med."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0240","doi-asserted-by":"crossref","first-page":"8088","DOI":"10.1128\/AEM.00745-11","article-title":"Variability of Escherichia coli O157 strain survival in manure-amended soil in relation to strain origin, virulence profile, and carbon nutrition profile","volume":"77","author":"Franz","year":"2011","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0245","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1128\/JCM.05964-11","article-title":"Genetic features differentiating bovine, food, and human isolates of Shiga toxin-producing Escherichia coli O157 in the Netherlands","volume":"50","author":"Franz","year":"2012","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0255","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1086\/338115","article-title":"Escherichia coli harboring Shiga toxin 2 gene variants: frequency and association with clinical symptoms","volume":"185","author":"Friedrich","year":"2002","journal-title":"J. Infect. Dis."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0260","doi-asserted-by":"crossref","first-page":"1329","DOI":"10.1128\/IAI.01182-10","article-title":"Shiga toxin subtypes display dramatic differences in potency","volume":"79","author":"Fuller","year":"2011","journal-title":"Infect. Immun."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0265","series-title":"Modern Infectious Disease Epidemiology","author":"Giesecke","year":"2002"},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0270","doi-asserted-by":"crossref","first-page":"222","DOI":"10.1016\/j.mcp.2011.08.004","article-title":"A high-throughput open-array qPCR gene panel to identify, virulotype, and subtype O157 and non-O157 enterohemorrhagic Escherichia coli","volume":"25","author":"Gonzales","year":"2011","journal-title":"Mol. Cell. Probes"},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0275","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1089\/fpd.2012.1401","article-title":"Increased recognition of non-O157 Shiga toxin-producing Escherichia coli infections in the United States during 2000\u20132010: epidemiologic features and comparison with E. coli O157 infections","volume":"10","author":"Gould","year":"2013","journal-title":"Foodborne Pathog. Dis."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0280","doi-asserted-by":"crossref","first-page":"e00452-12","DOI":"10.1128\/mBio.00452-12","article-title":"Comparative genomics of recent Shiga toxin-producing Escherichia coli O104:H4: short-term evolution of an emerging pathogen","volume":"4","author":"Grad","year":"2013","journal-title":"mBio"},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0285","first-page":"33","article-title":"The significance of non-O157 Shiga toxin-producing Escherichia coli in food","author":"Grant","year":"2011","journal-title":"Food Prot. Trends"},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0290","doi-asserted-by":"crossref","first-page":"E2010","DOI":"10.1073\/pnas.1207359109","article-title":"Genomic diversity of 2010 Haitian cholera outbreak strains","volume":"109","author":"Hasan","year":"2012","journal-title":"Proc. Nat. Acad. Sci. U.S.A."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0295","doi-asserted-by":"crossref","first-page":"S79","DOI":"10.1016\/j.ijfoodmicro.2009.10.015","article-title":"Future challenges to microbial food safety","volume":"139","author":"Havelaar","year":"2010","journal-title":"Int. J. Food Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0300","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1093\/dnares\/8.1.11","article-title":"Complete genome sequence of enterohemorrhagic Escherichia coli O157: H7 and genomic comparison with a laboratory strain K-12","volume":"8","author":"Hayashi","year":"2001","journal-title":"DNA Res."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0305","doi-asserted-by":"crossref","first-page":"12810","DOI":"10.1073\/pnas.1306836110","article-title":"Refining the pathovar paradigm via phylogenomics of the attaching and effacing Escherichia coli","volume":"110","author":"Hazen","year":"2013","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0310","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1016\/j.ijmm.2004.06.023","article-title":"Shiga toxin-encoding bacteriophages \u2014 genomes in motion","volume":"294","author":"Herold","year":"2004","journal-title":"Int. J. Med. Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0315","series-title":"USDA's New Shiga Toxin-Producing Escherichia coli Policy","first-page":"17","author":"Hodges","year":"2012"},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0320","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1111\/j.1574-695X.2009.00545.x","article-title":"Asymptomatic healthy slaughterhouse workers in South Korea carrying Shiga toxin-producing Escherichia coli","volume":"56","author":"Hong","year":"2009","journal-title":"FEMS Immunol. Med. Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0325","doi-asserted-by":"crossref","first-page":"5693","DOI":"10.1128\/AEM.00107-10","article-title":"Quantification of Shiga toxin-converting bacteriophages in wastewater and in fecal samples by real-time quantitative PCR","volume":"76","author":"Imamovic","year":"2010","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0330","doi-asserted-by":"crossref","first-page":"450","DOI":"10.1186\/1471-2334-13-450","article-title":"A prospective case\u2013control and molecular epidemiological study of human cases of Shiga toxin-producing Escherichia coli in New Zealand","volume":"13","author":"Jaros","year":"2013","journal-title":"BMC Infect. Dis."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0335","doi-asserted-by":"crossref","first-page":"1587","DOI":"10.1086\/509573","article-title":"The emerging clinical importance of non-O157 Shiga toxin-producing Escherichia coli","volume":"43","author":"Johnson","year":"2006","journal-title":"Clin. Infect. Dis."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0340","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1186\/1471-2105-11-595","article-title":"BIGSdb: Scalable analysis of bacterial genome variation at the population level","volume":"11","author":"Jolley","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0345","doi-asserted-by":"crossref","first-page":"990-U4","DOI":"10.1038\/nature06536","article-title":"Global trends in emerging infectious diseases","volume":"451","author":"Jones","year":"2008","journal-title":"Nature"},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0350","doi-asserted-by":"crossref","first-page":"3406","DOI":"10.1128\/AEM.03661-12","article-title":"Distribution of pathogenicity islands OI-122, OI-43\/48, and OI-57 and a high-pathogenicity island in Shiga toxin-producing Escherichia coli","volume":"79","author":"Ju","year":"2013","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0355","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1002\/emmm.201201662","article-title":"The enemy within us: lessons from the 2011 European Escherichia coli O104:H4 outbreak","volume":"4","author":"Karch","year":"2012","journal-title":"EMBO Mol. Med."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0360","doi-asserted-by":"crossref","first-page":"4930","DOI":"10.1128\/JCM.41.11.4930-4940.2003","article-title":"Association of genomic O(\u2212)island 122 of Escherichia coli EDL 933 with verocytotoxin-producing Escherichia coli seropathotypes that are linked to epidemic and\/or serious disease","volume":"41","author":"Karmali","year":"2003","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0365","doi-asserted-by":"crossref","first-page":"360","DOI":"10.1016\/j.vetmic.2009.04.011","article-title":"Verocytotoxin-producing Escherichia coli (VTEC)","volume":"140","author":"Karmali","year":"2010","journal-title":"Vet. Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0370","doi-asserted-by":"crossref","first-page":"13288","DOI":"10.1073\/pnas.96.23.13288","article-title":"Octamer-based genome scanning distinguishes a unique subpopulation of Escherichia coli O157: H7 strains in cattle","volume":"96","author":"Kim","year":"1999","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0375","doi-asserted-by":"crossref","first-page":"5614","DOI":"10.1128\/JB.186.17.5614-5620.2004","article-title":"A regulatory trade-off as a source of strain variation in the species Escherichia coli","volume":"186","author":"King","year":"2004","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0380","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1186\/1471-2164-14-211","article-title":"Genome sequencing of bacteria: sequencing, de novo assembly and rapid analysis using open source tools","volume":"14","author":"Kisand","year":"2013","journal-title":"BMC Genomics"},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0390","doi-asserted-by":"crossref","first-page":"1873","DOI":"10.1128\/JB.184.7.1873-1879.2002","article-title":"Strains of Escherichia coli O157: H7 differ primarily by insertions or deletions, not single-nucleotide polymorphisms","volume":"184","author":"Kudva","year":"2002","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0400","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1186\/1471-2164-10-287","article-title":"In silico genomic analyses reveal three distinct lineages of Escherichia coli O157:H7, one of which is associated with hyper-virulence","volume":"10","author":"Laing","year":"2009","journal-title":"BMC Genomics"},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0395","doi-asserted-by":"crossref","DOI":"10.1186\/1471-2105-11-461","article-title":"Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions","volume":"11","author":"Laing","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0825","doi-asserted-by":"crossref","first-page":"210","DOI":"10.1111\/j.1365-2672.2006.03214.x","article-title":"Multilocus sequence typing performed on Campylobacter coli isolates from humans, broilers, pigs and cattle originating in Denmark","volume":"103","author":"Litrup","year":"2007","journal-title":"J. Appl. Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0410","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1017\/S0950268801006045","article-title":"Risk factors for sporadic cases of Escherichia coli O157 infection: the importance of contact with animal excreta","volume":"127","author":"Locking","year":"2001","journal-title":"Epidemiol. Infect."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0415","doi-asserted-by":"crossref","first-page":"524","DOI":"10.3201\/eid1703.100167","article-title":"Escherichia coli O157 infection and secondary spread, Scotland, 1999-2008","volume":"17","author":"Locking","year":"2011","journal-title":"Emerg. Infect. Dis."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0420","doi-asserted-by":"crossref","first-page":"4868","DOI":"10.1073\/pnas.0710834105","article-title":"Variation in virulence among clades of Escherichia coli O157: H7, associated with disease outbreaks","volume":"105","author":"Manning","year":"2008","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0425","doi-asserted-by":"crossref","first-page":"4862","DOI":"10.1128\/AEM.01158-13","article-title":"Shiga toxin 2-encoding bacteriophages in human fecal samples from healthy individuals","volume":"79","author":"Martinez-Castillo","year":"2013","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0430","doi-asserted-by":"crossref","first-page":"1514","DOI":"10.1126\/science.1240578","article-title":"Distinguishable epidemics of multidrug-resistant Salmonella Typhimurium DT104 in Different Hosts","volume":"341","author":"Mather","year":"2013","journal-title":"Science"},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0435","doi-asserted-by":"crossref","first-page":"1721","DOI":"10.4315\/0362-028X-73.9.1721","article-title":"Non-O157 Shiga toxin-producing Escherichia coli in foods","volume":"73","author":"Mathusa","year":"2010","journal-title":"J. Food Prot."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0440","doi-asserted-by":"crossref","first-page":"3348","DOI":"10.1128\/AAC.00419-13","article-title":"The comprehensive antibiotic resistance database","volume":"57","author":"McArthur","year":"2013","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0445","doi-asserted-by":"crossref","first-page":"1287","DOI":"10.3201\/eid1408.071082","article-title":"Analysis of collection of hemolytic uremic syndrome-associated enterohemorrhagic Escherichia coli","volume":"14","author":"Mellmann","year":"2008","journal-title":"Emerg. Infect. Dis."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0450","doi-asserted-by":"crossref","first-page":"e22751","DOI":"10.1371\/journal.pone.0022751","article-title":"Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology","volume":"6","author":"Mellmann","year":"2011","journal-title":"PLoS One"},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0455","doi-asserted-by":"crossref","first-page":"4724","DOI":"10.1128\/AEM.00365-12","article-title":"Phylogenetically related Argentinean and Australian Escherichia coli O157 isolates are distinguished by virulence clades and alternative Shiga toxin 1 and 2 prophages","volume":"78","author":"Mellor","year":"2012","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0460","doi-asserted-by":"crossref","first-page":"5050","DOI":"10.1128\/AEM.01525-13","article-title":"Multilocus genotype analysis of Escherichia coli O157 isolates from Australia and the United States provides evidence of geographic divergence","volume":"79","author":"Mellor","year":"2013","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0465","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1016\/j.ijfoodmicro.2013.10.022","article-title":"Comparative evaluation of eleven commercial DNA extraction kits for real-time PCR detection of Bacillus anthracis spores in spiked dairy samples","volume":"170","author":"Mertens","year":"2014","journal-title":"Int. J. Food Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0470","doi-asserted-by":"crossref","first-page":"7","DOI":"10.3201\/eid0101.950102","article-title":"Factors in the emergence of infectious-diseases","volume":"1","author":"Morse","year":"1995","journal-title":"Emerg. Infect. Dis."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0475","doi-asserted-by":"crossref","first-page":"37","DOI":"10.2807\/ese.18.03.20365-en","article-title":"Molecular-based surveillance of campylobacteriosis in New Zealand \u2014 from source attribution to genomic epidemiology","volume":"18","author":"Muellner","year":"2013","journal-title":"Eurosurveillance"},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0480","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0042599","article-title":"Risk factors for campylobacteriosis of chicken, ruminant, and environmental origin: a combined case\u2013control and source attribution analysis","volume":"7","author":"Mughini Gras","year":"2012","journal-title":"PLoS One"},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0485","series-title":"Pathogenic Escherichia coli","article-title":"Shiga toxin-encoding phages: multifunctional gene ferries","author":"Muniesa","year":"2014"},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0490","doi-asserted-by":"crossref","first-page":"716","DOI":"10.1111\/j.1462-2920.2004.00604.x","article-title":"Free Shiga toxin bacteriophages isolated from sewage showed diversity although the stx genes appeared conserved","volume":"6","author":"Muniesa","year":"2004","journal-title":"Environ. Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0495","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1128\/CMR.11.1.142","article-title":"Diarrheagenic Escherichia coli","volume":"11","author":"Nataro","year":"1998","journal-title":"Clin. Microbiol. Rev."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0500","doi-asserted-by":"crossref","first-page":"466","DOI":"10.1016\/j.micpath.2011.07.009","article-title":"Shiga toxin 2 overexpression in Escherichia coil O157:H7 strains associated with severe human disease","volume":"51","author":"Neupane","year":"2011","journal-title":"Microb. Pathog."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0505","doi-asserted-by":"crossref","first-page":"S3","DOI":"10.1016\/j.ijfoodmicro.2010.01.021","article-title":"Food-borne diseases \u2014 the challenges of 20years ago still persist while new ones continue to emerge","volume":"139","author":"Newell","year":"2010","journal-title":"Int. J. Food Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0510","doi-asserted-by":"crossref","first-page":"e00280-12","DOI":"10.1128\/mBio.00280-12","article-title":"Virulence meets metabolism: Cra and KdpE gene regulation in enterohemorrhagic Escherichia coli","volume":"3","author":"Njoroge","year":"2012","journal-title":"mBio"},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0515","doi-asserted-by":"crossref","first-page":"675","DOI":"10.1128\/JCM.41.2.675-679.2003","article-title":"Multilocus sequence typing reveals a lack of diversity among Escherichia coli O157: H7 isolates that are distinct by pulsed-field gel electrophoresis","volume":"41","author":"Noller","year":"2003","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0520","doi-asserted-by":"crossref","first-page":"6689","DOI":"10.1128\/AEM.01259-12","article-title":"Association of nucleotide polymorphisms within the O-Antigen gene cluster of Escherichia coli O26, O45, O103, O111, O121, and O145 with serogroups and genetic subtypes","volume":"78","author":"Norman","year":"2012","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0525","doi-asserted-by":"crossref","first-page":"R138","DOI":"10.1186\/gb-2007-8-7-r138","article-title":"Extensive genomic diversity and selective conservation of virulence-determinants in enterohemorrhagic Escherichia coli strains of O157 and non-O157 serotypes","volume":"8","author":"Ogura","year":"2007","journal-title":"Genome Biol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0535","doi-asserted-by":"crossref","first-page":"D206","DOI":"10.1093\/nar\/gkt1226","article-title":"The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST)","volume":"42","author":"Overbeek","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0550","doi-asserted-by":"crossref","first-page":"699","DOI":"10.1017\/S0950268805005741","article-title":"The use of outbreak information in the interpretation of clustering of reported cases of Escherichia coli O157 in space and time in Alberta, Canada, 2000\u20132002","volume":"134","author":"Pearl","year":"2006","journal-title":"Epidemiol. Infect."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0545","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1017\/S0950268806006650","article-title":"The use of randomization tests to assess the degree of similarity in PFGE patterns of E. coli O157 isolates from known outbreaks and statistical space-time clusters","volume":"135","author":"Pearl","year":"2007","journal-title":"Epidemiol. Infect."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0555","doi-asserted-by":"crossref","first-page":"240-240","DOI":"10.1038\/35065664","article-title":"Genome sequence of enterohaemorrhagic Escherichia coli O157: H7 (vol 409, pg 529, 2001)","volume":"410","author":"Perna","year":"2001","journal-title":"Nature"},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0560","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1089\/fpd.2008.0208","article-title":"Attributing the human disease burden of foodborne infections to specific sources","volume":"6","author":"Pires","year":"2009","journal-title":"Foodborne Pathog. Dis."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0565","doi-asserted-by":"crossref","first-page":"2118","DOI":"10.1128\/AEM.02688-07","article-title":"Molecular analysis of Shiga toxin-producing Escherichia coli strains isolated from hemolytic-uremic syndrome patients and dairy samples in France","volume":"74","author":"Pradel","year":"2008","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0570","doi-asserted-by":"crossref","first-page":"e78180","DOI":"10.1371\/journal.pone.0078180","article-title":"Shiga toxin-producing Escherichia coli O157 is more likely to lead to hospitalization and death than non-O157 serogroups \u2014 except O104","volume":"8","author":"Preussel","year":"2013","journal-title":"PLoS One"},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0575","doi-asserted-by":"crossref","first-page":"945","DOI":"10.1093\/genetics\/155.2.945","article-title":"Inference of population structure using multilocus genotype data","volume":"155","author":"Pritchard","year":"2000","journal-title":"Genetics"},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0580","doi-asserted-by":"crossref","first-page":"1530","DOI":"10.1128\/JCM.40.4.1530-1533.2002","article-title":"Four strains of Escherichia coli O157: H7 isolated from patients during an outbreak of disease associated with ground beef: Importance of evaluating multiple colonies from an outbreak-associated product","volume":"40","author":"Proctor","year":"2002","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0585","series-title":"IEEE Computer Society, 10662 Los Vaqueros Circle, PO Box 3014, Los Alamitos, CA 90720-1264 USA","article-title":"EcMLST: an online database for multi locus sequence typing of pathogenic Escherichia coli","author":"Qi","year":"2004"},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0590","doi-asserted-by":"crossref","first-page":"6881","DOI":"10.1128\/JB.00619-08","article-title":"The pangenome structure of Escherichia coli: Comparative genomic analysis of E. coli commensal and pathogenic isolates","volume":"190","author":"Rasko","year":"2008","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0595","doi-asserted-by":"crossref","first-page":"709","DOI":"10.1056\/NEJMoa1106920","article-title":"Origins of the E. coli strain causing an outbreak of hemolytic\u2013uremic syndrome in Germany","volume":"365","author":"Rasko","year":"2011","journal-title":"N. Engl. J. Med."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0600","doi-asserted-by":"crossref","first-page":"e26907","DOI":"10.1371\/journal.pone.0026907","article-title":"Rates of mutation and host transmission for an Escherichia coli clone over 3years","volume":"6","author":"Reeves","year":"2011","journal-title":"PLoS One"},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0605","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1038\/35017546","article-title":"Parallel evolution of virulence in pathogenic Escherichia coli","volume":"406","author":"Reid","year":"2000","journal-title":"Nature"},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0610","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1089\/fpd.2006.3.88","article-title":"Characterization and epidemiologic subtyping of Shiga toxin-producing Escherichia coli strains isolated from hemolytic uremic syndrome and diarrhea cases in Argentina","volume":"3","author":"Rivas","year":"2006","journal-title":"Foodborne Pathog. Dis."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0615","doi-asserted-by":"crossref","first-page":"718","DOI":"10.1056\/NEJMoa1107643","article-title":"Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4","volume":"365","author":"Rohde","year":"2011","journal-title":"N. Engl. J. Med."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0620","doi-asserted-by":"crossref","first-page":"4884","DOI":"10.1128\/AEM.00929-12","article-title":"Phylomark, a tool to identify conserved phylogenetic markers from whole-genome alignments","volume":"78","author":"Sahl","year":"2012","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0630","doi-asserted-by":"crossref","first-page":"7","DOI":"10.3201\/eid1701.P11101","article-title":"Foodborne illness acquired in the United States\u2014major pathogens","volume":"17","author":"Scallan","year":"2011","journal-title":"Emerg. Infect. Dis."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0635","doi-asserted-by":"crossref","first-page":"123","DOI":"10.4315\/0362-028X.JFP-11-058","article-title":"Economic burden from health losses due to foodborne illness in the United States","volume":"75","author":"Scharff","year":"2012","journal-title":"J. Food Prot."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0640","doi-asserted-by":"crossref","first-page":"5","DOI":"10.2807\/ese.16.24.19889-en","article-title":"Characteristics of the enteroaggregative Shiga toxin\/verotoxin-producing Escherichia coli O104:H4 strain causing the outbreak of haemolytic uraemic syndrome in Germany, May to June 2011","volume":"16","author":"Scheutz","year":"2011","journal-title":"Eurosurveillance"},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0650","doi-asserted-by":"crossref","first-page":"1205","DOI":"10.1128\/AEM.66.3.1205-1208.2000","article-title":"A new Shiga toxin 2 variant (Stx2f) from Escherichia coli isolated from pigeons","volume":"66","author":"Schmidt","year":"2000","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0655","doi-asserted-by":"crossref","first-page":"601","DOI":"10.4315\/0362-028X-72.3.601","article-title":"Escherichia coli O157:H7 lineages in healthy beef and dairy cattle and clinical human cases in Alberta, Canada","volume":"72","author":"Sharma","year":"2009","journal-title":"J. Food Prot."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0660","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.1086\/597402","article-title":"Campylobacter genotyping to determine the source of human infection","volume":"48","author":"Sheppard","year":"2009","journal-title":"Clin. Infect. Dis."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0665","doi-asserted-by":"crossref","first-page":"e51572","DOI":"10.1371\/journal.pone.0051572","article-title":"Carriage of stx2a differentiates clinical and bovine-biased strains of Escherichia coli O157","volume":"7","author":"Shringi","year":"2012","journal-title":"PLoS One"},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0670","doi-asserted-by":"crossref","first-page":"915","DOI":"10.1017\/S0950268804002390","article-title":"Asymptomatic carriage of verocytotoxin-producing Escherichia coli O157 in farm workers in Northern Italy","volume":"132","author":"Silvestro","year":"2004","journal-title":"Epidemiol. Infect."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0675","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1186\/1471-2164-13-311","article-title":"Comparative genomics of Shiga toxin encoding bacteriophages","volume":"13","author":"Smith","year":"2012","journal-title":"BMC Genomics"},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0680","doi-asserted-by":"crossref","first-page":"346","DOI":"10.1016\/j.ijheh.2012.07.005","article-title":"Escherichia coli O104:H4 outbreak from sprouted seeds","volume":"216","author":"Soon","year":"2013","journal-title":"Int. J. Hyg. Environ. Health"},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0685","doi-asserted-by":"crossref","first-page":"2097","DOI":"10.1007\/s00467-012-2383-6","article-title":"Long-term outcomes of Shiga toxin hemolytic uremic syndrome","volume":"28","author":"Spinale","year":"2013","journal-title":"Pediatr. Nephrol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0690","doi-asserted-by":"crossref","first-page":"322","DOI":"10.1016\/j.diagmicrobio.2012.05.004","article-title":"Evaluation of the Meridian Premier EHEC assay as an indicator of Shiga toxin presence in direct faecal specimens","volume":"73","author":"Staples","year":"2012","journal-title":"Diagn. Microbiol. Infect. Dis."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0700","doi-asserted-by":"crossref","DOI":"10.3389\/fcimb.2012.00133","article-title":"Comparative genomics and stx phage characterization of LEE-negative Shiga toxin-producing Escherichia coli","volume":"2","author":"Steyert","year":"2012","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0705","doi-asserted-by":"crossref","first-page":"282","DOI":"10.1136\/vr.156.9.282","article-title":"Quantification of the Escherichia coli O157 reservoir in Grampian, Scotland","volume":"156","author":"Strachan","year":"2005","journal-title":"Vet. Rec."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0710","doi-asserted-by":"crossref","first-page":"1260","DOI":"10.1038\/nprot.2012.068","article-title":"A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs","volume":"7","author":"Swain","year":"2012","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0715","first-page":"1073","article-title":"Shiga-toxin-producing Escherichia coli and haemolytic uraemic syndrome","volume":"365","author":"Tarr","year":"2005","journal-title":"Lancet"},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0720","series-title":"Epidemiologic Methods for the Study of Infectious Diseases","author":"Thomas","year":"2001"},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0725","doi-asserted-by":"crossref","first-page":"14941","DOI":"10.1073\/pnas.0604891103","article-title":"An extensive repertoire of type III secretion effectors in Escherichia coli O157 and the role of lambdoid phages in their dissemination","volume":"103","author":"Tobe","year":"2006","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0730","doi-asserted-by":"crossref","first-page":"e1000344","DOI":"10.1371\/journal.pgen.1000344","article-title":"Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths","volume":"5","author":"Touchon","year":"2009","journal-title":"PLoS Genet."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0735","doi-asserted-by":"crossref","first-page":"3950","DOI":"10.1128\/JCM.01930-13","article-title":"Precise dissection of an Escherichia coli O157:H7 outbreak by single nucleotide polymorphism analysis","volume":"51","author":"Turabelidze","year":"2013","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0740","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1128\/JCM.01696-12","article-title":"Public health value of next-generation DNA sequencing of enterohemorrhagic Escherichia coli isolates from an outbreak","volume":"51","author":"Underwood","year":"2013","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0745","first-page":"58157","article-title":"Shiga toxin-producing Escherichia coli in certain raw beef products","volume":"78","author":"USDA-FSIS","year":"2011","journal-title":"Fed. Regist."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0750","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1111\/1574-6968.12024","article-title":"The role of rpoS in Escherichia coli O157 manure-amended soil survival and distribution of allelic variations among bovine, food and clinical isolates","volume":"338","author":"van Hoek","year":"2013","journal-title":"FEMS Microbiol. Lett."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0755","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1128\/AEM.01666-09","article-title":"Differential expression of virulence and stress fitness genes between Escherichia coli O157:H7 strains with clinical or bovine-biased genotypes","volume":"76","author":"Vanaja","year":"2010","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0760","doi-asserted-by":"crossref","first-page":"1160","DOI":"10.1096\/fj.09-144972","article-title":"Multiple antibiotic resistance gene recruitment onto the enterohemorrhagic Escherichia coli virulence plasmid","volume":"24","author":"Venturini","year":"2010","journal-title":"FASEB J."},{"issue":"D1","key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0765","doi-asserted-by":"crossref","first-page":"D581","DOI":"10.1093\/nar\/gkt1099","article-title":"PATRIC, the bacterial bioinformatics database and analysis resource","volume":"42","author":"Wattam","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0770","doi-asserted-by":"crossref","first-page":"298","DOI":"10.1016\/S0140-6736(11)60090-1","article-title":"Watch out for the even eviler cousin-sorbitol-fermenting E. coil O157","volume":"377","author":"Werber","year":"2011","journal-title":"Lancet"},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0775","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1128\/AEM.01761-09","article-title":"Diverse genetic markers concordantly identify bovine origin Escherichia coli O157 genotypes underrepresented in human disease","volume":"76","author":"Whitworth","year":"2010","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0780","doi-asserted-by":"crossref","first-page":"741","DOI":"10.4315\/0362-028X-72.4.741","article-title":"Evaluation of three commercially available enzyme-linked immunosorbent assay kits for detection of Shiga toxin","volume":"72","author":"Willford","year":"2009","journal-title":"J. Food Prot."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0785","doi-asserted-by":"crossref","first-page":"e1000203","DOI":"10.1371\/journal.pgen.1000203","article-title":"Tracing the source of campylobacteriosis","volume":"4","author":"Wilson","year":"2008","journal-title":"PLoS Genet."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0790","doi-asserted-by":"crossref","first-page":"1930","DOI":"10.1056\/NEJM200006293422601","article-title":"The risk of the hemolytic\u2013uremic syndrome after antibiotic treatment of Escherichia coli O157: H7 infections","volume":"342","author":"Wong","year":"2000","journal-title":"N. Engl. J. Med."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0795","doi-asserted-by":"crossref","first-page":"e1002672","DOI":"10.1371\/journal.ppat.1002672","article-title":"Lysogeny with Shiga toxin 2-encoding bacteriophages represses type III secretion in enterohemorrhagic Escherichia coli","volume":"8","author":"Xu","year":"2012","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0800","doi-asserted-by":"crossref","first-page":"6846","DOI":"10.1128\/AEM.70.11.6846-6854.2004","article-title":"Identification of common subpopulations of non-sorbitol-fermenting, beta-glucuronidase-negative Escherichia coli O157:H7 from bovine production environments and human clinical samples","volume":"70","author":"Yang","year":"2004","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0805","doi-asserted-by":"crossref","first-page":"7282","DOI":"10.1128\/IAI.72.12.7282-7293.2004","article-title":"Regulators encoded in the Escherichia coli type III secretion system 2 gene cluster influence expression of genes within the locus for enterocyte effacement in enterohemorrhagic E. coli O157: H7","volume":"72","author":"Zhang","year":"2004","journal-title":"Infect. Immun."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0815","doi-asserted-by":"crossref","first-page":"4314","DOI":"10.1128\/AEM.02821-07","article-title":"Genotypic characterization and prevalence of virulence factors among Canadian Escherichia coli O157: H7 strains","volume":"74","author":"Ziebell","year":"2008","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.ijfoodmicro.2014.07.002_bb0820","doi-asserted-by":"crossref","first-page":"328","DOI":"10.1016\/j.vetmic.2006.06.017","article-title":"Virulence profiles of Shiga toxin 2e-producing Escherichia coli isolated from healthy pig at slaughter","volume":"117","author":"Zweifel","year":"2006","journal-title":"Vet. Microbiol."}],"updated-by":[{"DOI":"10.1016\/j.ijfoodmicro.2014.09.026","type":"erratum","label":"Erratum","source":"publisher","updated":{"date-parts":[[2015,1,16]],"date-time":"2015-01-16T00:00:00Z","timestamp":1421366400000}}],"container-title":["International Journal of Food Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0168160514003328?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0168160514003328?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2022,4,10]],"date-time":"2022-04-10T23:40:46Z","timestamp":1649634046000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0168160514003328"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,9]]},"references-count":154,"alternative-id":["S0168160514003328"],"URL":"https:\/\/doi.org\/10.1016\/j.ijfoodmicro.2014.07.002","relation":{"erratum":[{"id-type":"doi","id":"10.1016\/j.ijfoodmicro.2014.09.026","asserted-by":"object"}]},"ISSN":["0168-1605"],"issn-type":[{"value":"0168-1605","type":"print"}],"subject":[],"published":{"date-parts":[[2014,9]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Exploiting the explosion of information associated with whole genome sequencing to tackle Shiga toxin-producing Escherichia coli (STEC) in global food production systems","name":"articletitle","label":"Article Title"},{"value":"International Journal of Food Microbiology","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.ijfoodmicro.2014.07.002","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"Copyright \u00a9 2014 Published by Elsevier B.V.","name":"copyright","label":"Copyright"}]}}