{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T14:41:48Z","timestamp":1788878508518,"version":"build-2803163510"},"reference-count":18,"publisher":"Cambridge University Press (CUP)","license":[{"start":{"date-parts":[[2021,6,28]],"date-time":"2021-06-28T00:00:00Z","timestamp":1624838400000},"content-version":"unspecified","delay-in-days":178,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["cambridge.org"],"crossmark-restriction":true},"short-container-title":["Epidemiol. Infect."],"published-print":{"date-parts":[[2021]]},"abstract":"<jats:title>Abstract<\/jats:title>\n\t  <jats:p>An outbreak surveillance system for <jats:italic>Salmonella<\/jats:italic> integrating whole genome sequencing (WGS) and epidemiological data was developed in South East and London in 2016\u201317 to assess local WGS clusters for triage and investigation. Cases genetically linked within a 5 single-nucleotide polymorphism (SNP) single linkage cluster were assessed using a set of locally agreed thresholds based on time, person and place, for reporting to local health protection teams (HPTs). Between September 2016 and September 2017, 230 unique 5-SNP clusters (442 weekly reports) of non-typhoidal <jats:italic>Salmonella<\/jats:italic> 5-SNP WGS clusters were identified, of which 208 unique 5-SNP clusters (316 weekly reports) were not reported to the HPTs. In the remaining 22 unique clusters (126 weekly clusters) reported to HPTs, nine were known active outbreak investigations, seven were below locally agreed thresholds and six exceeded local thresholds. A common source or vehicle was identified in four of six clusters that exceeded locally agreed thresholds. This work demonstrates that a threshold-based surveillance system, taking into account time, place and genetic relatedness, is feasible and effective in directing the use of local public health resources for risk assessment and investigation of non-typhoidal <jats:italic>Salmonella<\/jats:italic> clusters.<\/jats:p>","DOI":"10.1017\/s0950268821001400","type":"journal-article","created":{"date-parts":[[2021,6,28]],"date-time":"2021-06-28T08:10:09Z","timestamp":1624867809000},"update-policy":"https:\/\/doi.org\/10.1017\/policypage","source":"Crossref","is-referenced-by-count":11,"title":["Development and evaluation of an outbreak surveillance system integrating whole genome sequencing data for non-typhoidal <i>Salmonella<\/i> in London and South East of England, 2016\u201317"],"prefix":"10.1017","volume":"149","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5633-8559","authenticated-orcid":false,"given":"Karthik","family":"Paranthaman","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Piers","family":"Mook","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniele","family":"Curtis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Edward-Wynne","family":"Evans","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emma","family":"Crawley-Boevey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Girija","family":"Dabke","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5095-4169","authenticated-orcid":false,"given":"Kevin","family":"Carroll","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacquelyn","family":"McCormick","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Timothy J.","family":"Dallman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4965-2619","authenticated-orcid":false,"given":"Paul","family":"Crook","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"56","published-online":{"date-parts":[[2021,6,28]]},"reference":[{"key":"S0950268821001400_ref2","first-page":"212","article-title":"Epidemic intelligence: a new framework for strengthening disease surveillance in Europe","volume":"11","author":"Paquet","year":"2006","journal-title":"Euro Surveillance"},{"key":"S0950268821001400_ref9","doi-asserted-by":"publisher","DOI":"10.1089\/fpd.2019.2650"},{"key":"S0950268821001400_ref5","doi-asserted-by":"publisher","DOI":"10.3389\/fpubh.2019.00317"},{"key":"S0950268821001400_ref6","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(19)30047-7"},{"key":"S0950268821001400_ref14","unstructured":"14. R core team (2020). R: A language and environment for statistical computing. Available at (https:\/\/www.R-project.org\/). Accessed 24 June 2021."},{"key":"S0950268821001400_ref18","unstructured":"18. Food Standards Agency and Public Health England. Rise in cases of Salmonella Typhimurium. Available at (https:\/\/www.gov.uk\/government\/news\/rise-in-cases-of-salmonella-typhimurium). Accessed 24 June 2021."},{"key":"S0950268821001400_ref16","unstructured":"16. Food Standards Agency. FSA issues precautionary egg safety and handling advice concerning one flock code. Available at (https:\/\/www.food.gov.uk\/news-alerts\/alert\/fsa-fafa-02-2019). 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Monitoring the use of whole-genome sequencing in infectious disease surveillance in Europe 2015\u20132017. Available at (https:\/\/www.ecdc.europa.eu\/en\/publications-data\/monitoring-use-whole-genome-sequencing-infectious-disease-surveillance-europe). Accessed 24 June 2021."},{"key":"S0950268821001400_ref12","unstructured":"12. Public Health England. Salmonella data 2007 to 2016. Available at (https:\/\/assets.publishing.service.gov.uk\/government\/uploads\/system\/uploads\/attachment_data\/file\/711972\/salmonella_data_2007_to_2016_may_2018.pdf). Accessed 24 June 2021."},{"key":"S0950268821001400_ref13","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty212"},{"key":"S0950268821001400_ref10","doi-asserted-by":"publisher","DOI":"10.1017\/S0950268818001589"},{"key":"S0950268821001400_ref17","unstructured":"17. Animal and Plant Health Agency Salmonella. New strain in sheep. Available at (http:\/\/apha.defra.gov.uk\/documents\/surveillance\/diseases\/salmonella-in-sheep-info-note.pdf). Accessed 24 June 2021."},{"key":"S0950268821001400_ref1","doi-asserted-by":"publisher","DOI":"10.1086\/650733"},{"key":"S0950268821001400_ref11","unstructured":"11. Office for National Statistics. Population estimates for the UK, England and Wales, Scotland and Northern Ireland: mid-2017. Available at (https:\/\/www.ons.gov.uk\/peoplepopulationandcommunity\/populationandmigration\/populationestimates\/bulletins\/annualmidyearpopulationestimates\/mid2017). Accessed 24 June 2021."}],"container-title":["Epidemiology and Infection"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.cambridge.org\/core\/services\/aop-cambridge-core\/content\/view\/S0950268821001400","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,7,16]],"date-time":"2021-07-16T05:58:15Z","timestamp":1626415095000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.cambridge.org\/core\/product\/identifier\/S0950268821001400\/type\/journal_article"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021]]},"references-count":18,"alternative-id":["S0950268821001400"],"URL":"https:\/\/doi.org\/10.1017\/s0950268821001400","relation":{},"ISSN":["0950-2688","1469-4409"],"issn-type":[{"value":"0950-2688","type":"print"},{"value":"1469-4409","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021]]},"assertion":[{"value":"Copyright \u00a9 The Author(s), 2021. Published by Cambridge University Press","name":"copyright","label":"Copyright","group":{"name":"copyright_and_licensing","label":"Copyright and Licensing"}},{"value":"This is an Open Access article, distributed under the terms of the Creative Commons Attribution licence (http:\/\/creativecommons.org\/licenses\/by\/4.0\/), which permits unrestricted re-use, distribution, and reproduction in any medium, provided the original work is properly cited.","name":"license","label":"License","group":{"name":"copyright_and_licensing","label":"Copyright and Licensing"}},{"value":"This content has been made available to all.","name":"free","label":"Free to read"}],"article-number":"e164"}}