{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T15:36:55Z","timestamp":1790696215496,"version":"4.1.0"},"reference-count":40,"publisher":"Elsevier BV","issue":"6","license":[{"start":{"date-parts":[[2023,6,1]],"date-time":"2023-06-01T00:00:00Z","timestamp":1685577600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2023,6,1]],"date-time":"2023-06-01T00:00:00Z","timestamp":1685577600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2023,3,10]],"date-time":"2023-03-10T00:00:00Z","timestamp":1678406400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000272","name":"NIHR","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000272","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Journal of Food Protection"],"published-print":{"date-parts":[[2023,6]]},"DOI":"10.1016\/j.jfp.2023.100074","type":"journal-article","created":{"date-parts":[[2023,4,6]],"date-time":"2023-04-06T21:06:05Z","timestamp":1680815165000},"page":"100074","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":7,"title":["Foodborne Outbreak of Extended Spectrum Beta-lactamase Producing Shigella sonnei Associated with Contaminated Spring Onions in the United Kingdom"],"prefix":"10.1016","volume":"86","author":[{"given":"Claire","family":"Jenkins","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philippa","family":"Griffith","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ann","family":"Hoban","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claire","family":"Brown","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joanna","family":"Garner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Megan","family":"Bardsley","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Caroline","family":"Willis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Frieda","family":"Jorgensen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew","family":"Bird","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David R.","family":"Greig","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matt","family":"Edmunds","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charles","family":"Beck","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lesley","family":"Larkin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.jfp.2023.100074_b0005","doi-asserted-by":"crossref","first-page":"e1010174","DOI":"10.1371\/journal.pgen.1010174","article-title":"Dynamics of Salmonella enterica and antimicrobial resistance in the Brazilian poultry industry and global impacts on public health","volume":"18","author":"Alikhan","year":"2022","journal-title":"PLoS Genetics"},{"key":"10.1016\/j.jfp.2023.100074_b0010","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1016\/S1473-3099(16)30319-X","article-title":"Import and spread of extended-spectrum \u03b2-lactamase-producing Enterobacteriaceae by international travellers (COMBAT study): A prospective, multicentre cohort study","volume":"17","author":"Arcilla","year":"2016","journal-title":"The Lancet Infectious Diseases"},{"key":"10.1016\/j.jfp.2023.100074_b0015","doi-asserted-by":"crossref","first-page":"e1752","DOI":"10.7717\/peerj.1752","article-title":"Identification of Salmonella for public health surveillance using whole genome sequencing","volume":"4","author":"Ashton","year":"2016","journal-title":"PeerJ"},{"key":"10.1016\/j.jfp.2023.100074_b0020","doi-asserted-by":"crossref","first-page":"e01692","DOI":"10.1128\/JCM.01692-19","article-title":"Persistent Transmission of Shigellosis in England Is Associated with a Recently Emerged Multidrug-Resistant Strain of Shigella sonnei","volume":"58","author":"Bardsley","year":"2020","journal-title":"Journal of Clinical Microbiology"},{"key":"10.1016\/j.jfp.2023.100074_b0025","doi-asserted-by":"crossref","first-page":"e02408-18","DOI":"10.1128\/mBio.02408-18","article-title":"Acquisition and Loss of CTX-M-Producing and Non-Producing Escherichia coli in the Fecal Microbiome of Travelers to South Asia","volume":"9","author":"Bevan","year":"2018","journal-title":"MBio"},{"key":"10.1016\/j.jfp.2023.100074_b0030","doi-asserted-by":"crossref","first-page":"e52","DOI":"10.1017\/S0950268822000206","article-title":"The epidemiology of Shiga toxin-producing Escherichia coli serogroup O157 in England, 2009\u20132019","volume":"150","author":"Butt","year":"2022","journal-title":"Epidemiology and Infection"},{"key":"10.1016\/j.jfp.2023.100074_b0035","doi-asserted-by":"crossref","first-page":"1161","DOI":"10.4315\/0362-028X.JFP-15-580","article-title":"Epidemiological and Microbiological Investigation of an Outbreak of Severe Disease from Shiga Toxin-Producing Escherichia coli O157 Infection Associated with Consumption of a Slaw Garnish","volume":"79","author":"Byrne","year":"2016","journal-title":"Journal of Food Protection"},{"key":"10.1016\/j.jfp.2023.100074_b0040","doi-asserted-by":"crossref","first-page":"1503","DOI":"10.1016\/S1473-3099(22)00370-X","article-title":"Outbreak of sexually transmitted, extensively drug-resistant Shigella sonnei in the UK, 2021\u201322: A descriptive epidemiological study","volume":"22","author":"Charles","year":"2022","journal-title":"The Lancet Infectious Diseases"},{"key":"10.1016\/j.jfp.2023.100074_b0045","doi-asserted-by":"crossref","first-page":"1667","DOI":"10.1080\/15287390490492313","article-title":"Vulnerability of waterborne diseases to climate change in Canada: A review","volume":"67","author":"Charron","year":"2004","journal-title":"Journal of Toxicology and Environmental Health"},{"key":"10.1016\/j.jfp.2023.100074_b0050","doi-asserted-by":"crossref","first-page":"616","DOI":"10.1128\/JCM.01790-16","article-title":"Identification of Escherichia coli and Shigella Species from Whole-Genome Sequences","volume":"55","author":"Chattaway","year":"2017","journal-title":"Journal of Clinical Microbiology"},{"key":"10.1016\/j.jfp.2023.100074_b0055","doi-asserted-by":"crossref","first-page":"e15","DOI":"10.1093\/nar\/gku1196","article-title":"Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins","volume":"43","author":"Croucher","year":"2015","journal-title":"Nucleic Acids Research."},{"key":"10.1016\/j.jfp.2023.100074_b0060","doi-asserted-by":"crossref","first-page":"882","DOI":"10.1099\/jmm.0.000296","article-title":"Use of whole-genome sequencing for the public health surveillance of Shigella sonnei in England and Wales, 2015","volume":"65","author":"Dallman","year":"2016","journal-title":"Journal of Medical Microbiology"},{"key":"10.1016\/j.jfp.2023.100074_b0065","doi-asserted-by":"crossref","first-page":"3028","DOI":"10.1093\/bioinformatics\/bty212","article-title":"SnapperDB: A database solution for routine sequencing analysis of bacterial isolates","volume":"34","author":"Dallman","year":"2018","journal-title":"Bioinformatics"},{"key":"10.1016\/j.jfp.2023.100074_b0070","doi-asserted-by":"crossref","first-page":"2569","DOI":"10.1111\/jam.15728","article-title":"Whole genome sequencing reveals antimicrobial resistance determinants (AMR genes) of Salmonella enterica recovered from raw chicken and ready-to-eat leaves imported into England between 2014 and 2019","volume":"133","author":"Davies","year":"2022","journal-title":"Journal of Applied Microbiology"},{"key":"10.1016\/j.jfp.2023.100074_b0075","doi-asserted-by":"crossref","first-page":"26","DOI":"10.3201\/eid0101.950105","article-title":"An outbreak of Shigella sonnei infection associated with consumption of iceberg lettuce","volume":"1","author":"Frost","year":"1995","journal-title":"Emerging Infectious Diseases"},{"key":"10.1016\/j.jfp.2023.100074_b0080","first-page":"1700627","article-title":"Use of an ingredient-based analysis to investigate a national outbreak of Escherichia coli O157, United Kingdom, July 2016","volume":"23","author":"Gardiner","year":"2018","journal-title":"Euro Surveillance"},{"key":"10.1016\/j.jfp.2023.100074_b0085","doi-asserted-by":"crossref","first-page":"mgen000545","DOI":"10.1099\/mgen.0.000545","article-title":"Analysis of a small outbreak of Shiga toxin-producing Escherichia coli O157: H7 using long-read sequencing","volume":"7","author":"Greig","year":"2021","journal-title":"Microbial Genomics"},{"key":"10.1016\/j.jfp.2023.100074_b0090","series-title":"Shigella, Encyclopedia of Food and Health","first-page":"785","author":"Jenkins","year":"2016"},{"key":"10.1016\/j.jfp.2023.100074_b0095","first-page":"1800346","article-title":"Impact of whole genome sequencing on the investigation of food-borne outbreaks of Shiga toxin-producing Escherichia coli serogroup O157:H7, England, 2013 to 2017","volume":"24","author":"Jenkins","year":"2019","journal-title":"Euro Surveillance"},{"key":"10.1016\/j.jfp.2023.100074_b0100","doi-asserted-by":"crossref","first-page":"1950","DOI":"10.4315\/0362-028X.JFP-19-014","article-title":"Outbreaks of Shiga Toxin-Producing Escherichia coli Linked to Sprouted Seeds, Salad, and Leafy Greens: A Systematic Review","volume":"82","author":"Kintz","year":"2019","journal-title":"Journal of Food Protection"},{"key":"10.1016\/j.jfp.2023.100074_b0105","first-page":"83","article-title":"The selection and use of cephalosporins: A review","volume":"12","author":"Klein","year":"1995","journal-title":"Advances in Therapy"},{"key":"10.1016\/j.jfp.2023.100074_b0110","first-page":"2200314","article-title":"Investigation of an international outbreak of multidrug-resistant monophasic Salmonella Typhimurium associated with chocolate products, EU\/EEA and United Kingdom, February to April 2022","volume":"27","author":"Larkin","year":"2022","journal-title":"Euro Surveillance"},{"key":"10.1016\/j.jfp.2023.100074_b0115","doi-asserted-by":"crossref","first-page":"326","DOI":"10.1017\/S0950268808001829","article-title":"Outbreaks of Shigella sonnei infections in Denmark and Australia linked to consumption of imported raw baby corn","volume":"137","author":"Lewis","year":"2009","journal-title":"Epidemiology and Infection"},{"key":"10.1016\/j.jfp.2023.100074_b0120","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1093\/bioinformatics\/btp698","article-title":"Fast and accurate long-read alignment with burrows-wheeler transform","volume":"26","author":"Li","year":"2010","journal-title":"Bioinformatics"},{"key":"10.1016\/j.jfp.2023.100074_b0125","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"10.1016\/j.jfp.2023.100074_b0130","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1101\/gr.107524.110","article-title":"The genome analysis toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data","volume":"20","author":"McKenna","year":"2010","journal-title":"Genome Research"},{"key":"10.1016\/j.jfp.2023.100074_b0135","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1016\/j.puhe.2022.01.036","article-title":"Lessons learned from the investigation and management of an outbreak of Shigella flexneri associated with a restaurant in London, 2019\u20132020","volume":"205","author":"McLarty","year":"2022","journal-title":"Public Health"},{"key":"10.1016\/j.jfp.2023.100074_b0140","doi-asserted-by":"crossref","DOI":"10.1017\/S0950268821000509","article-title":"Utility of whole-genome sequencing during an investigation of multiple foodborne outbreaks of Shigella sonnei","volume":"149","author":"Mikhail","year":"2021","journal-title":"Epidemiology and Infection"},{"key":"10.1016\/j.jfp.2023.100074_b0145","first-page":"19241","article-title":"Imported fresh sugar peas as suspected source of an outbreak of Shigella sonnei in Denmark, April-May 2009","volume":"14","author":"Muller","year":"2009","journal-title":"Euro Surveillance"},{"key":"10.1016\/j.jfp.2023.100074_b0150","doi-asserted-by":"crossref","first-page":"848","DOI":"10.1016\/j.aogh.2016.10.007","article-title":"Incidences of Waterborne and Foodborne Diseases After Meteorologic Disasters in South Korea","volume":"82","author":"Na","year":"2016","journal-title":"Annals of Global Health"},{"key":"10.1016\/j.jfp.2023.100074_b0155","doi-asserted-by":"crossref","first-page":"e000257","DOI":"10.1099\/mgen.0.000257","article-title":"LiSEQ - whole-genome sequencing of a cross-sectional survey of Listeria monocytogenes in ready-to-eat foods and human clinical cases in Europe","volume":"5","author":"Painset","year":"2019","journal-title":"Microbial Genomics"},{"key":"10.1016\/j.jfp.2023.100074_b0160","doi-asserted-by":"crossref","first-page":"e000170","DOI":"10.1099\/mgen.0.000170","article-title":"Whole-genome sequencing revealed concurrent outbreaks of shigellosis in the English Orthodox Jewish Community caused by multiple importations of Shigella sonnei from Israel","volume":"4","author":"Rew","year":"2018","journal-title":"Microbial Genomics"},{"key":"10.1016\/j.jfp.2023.100074_b0165","doi-asserted-by":"crossref","first-page":"2496","DOI":"10.1093\/jac\/dkx170","article-title":"Comparison of phenotypic and WGS-derived antimicrobial resistance profiles of Shigella sonnei isolated from cases of diarrhoeal disease in England and Wales","volume":"72","author":"Sadouki","year":"2015","journal-title":"The Journal of Antimicrobial Chemotherapy"},{"key":"10.1016\/j.jfp.2023.100074_b0170","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","article-title":"RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies","volume":"30","author":"Stamatakis","year":"2014","journal-title":"Bioinformatics"},{"key":"10.1016\/j.jfp.2023.100074_b0175","doi-asserted-by":"crossref","first-page":"1022","DOI":"10.1099\/jmm.0.000779","article-title":"Antimicrobial resistance profiles of Shigella dysenteriae isolated from travellers returning to the UK, 2004\u20132017","volume":"67","author":"Terry","year":"2018","journal-title":"Journal of Medical Microbiology"},{"key":"10.1016\/j.jfp.2023.100074_b0180","doi-asserted-by":"crossref","first-page":"e2308","DOI":"10.7717\/peerj.2308","article-title":"MOST: A modified MLST typing tool based on short read sequencing","volume":"4","author":"Tewolde","year":"2016","journal-title":"PeerJ"},{"key":"10.1016\/j.jfp.2023.100074_b0185","doi-asserted-by":"crossref","first-page":"1596","DOI":"10.1099\/jmm.0.000832","article-title":"An outbreak of Shigella boydii serotype 20 in January 2015 amongst United Kingdom healthcare workers involved in the Ebola response in Sierra Leone","volume":"67","author":"Todkill","year":"2018","journal-title":"Journal of Medical Microbiology"},{"key":"10.1016\/j.jfp.2023.100074_b0190","doi-asserted-by":"crossref","first-page":"1079","DOI":"10.3390\/antibiotics11081079","article-title":"Antibiotic Resistance in Bacteria-A Review","volume":"11","author":"Urban-Chmiel","year":"2022","journal-title":"Antibiotics"},{"key":"10.1016\/j.jfp.2023.100074_b0195","doi-asserted-by":"crossref","first-page":"2775","DOI":"10.1128\/IAI.71.5.2775-2786.2003","article-title":"Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457 T","volume":"71","author":"Wei","year":"2003","journal-title":"Infection and Immunity"},{"key":"10.1016\/j.jfp.2023.100074_b9000","doi-asserted-by":"crossref","unstructured":"Torpdahl M, White ED, Schj\u00f8rring S, S\u00f8by M, Engberg J, Engsbro AL, Holt HM, Lemming L, L\u00fctzen L, Olesen B, Coia JE, Kjels\u00f8 C, M\u00fcller L. Imported spring onions related to the first recorded outbreak of enteroinvasive Escherichia coli in Denmark, November to December 2021. Euro Surveill. 2023 Apr; 28(15). doi: 10.2807\/1560-7917.ES.2023.28.15.2200572.","DOI":"10.2807\/1560-7917.ES.2023.28.15.2200572"}],"container-title":["Journal of Food Protection"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0362028X23067467?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0362028X23067467?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,10,6]],"date-time":"2025-10-06T22:32:52Z","timestamp":1759789972000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0362028X23067467"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,6]]},"references-count":40,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2023,6]]}},"alternative-id":["S0362028X23067467"],"URL":"https:\/\/doi.org\/10.1016\/j.jfp.2023.100074","relation":{},"ISSN":["0362-028X"],"issn-type":[{"value":"0362-028X","type":"print"}],"subject":[],"published":{"date-parts":[[2023,6]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Foodborne Outbreak of Extended Spectrum Beta-lactamase Producing Shigella sonnei Associated with Contaminated Spring Onions in the United Kingdom","name":"articletitle","label":"Article Title"},{"value":"Journal of Food Protection","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.jfp.2023.100074","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"Crown Copyright \u00a9 2023 Published by Elsevier Inc. on behalf of International Association for Food Protection.","name":"copyright","label":"Copyright"}],"article-number":"100074"}}