{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T06:35:05Z","timestamp":1789022105396,"version":"build-2803163510"},"reference-count":14,"publisher":"Cambridge University Press (CUP)","issue":"11","license":[{"start":{"date-parts":[[2018,7,2]],"date-time":"2018-07-02T00:00:00Z","timestamp":1530489600000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/www.cambridge.org\/core\/terms"}],"content-domain":{"domain":["www.cambridge.org"],"crossmark-restriction":true},"short-container-title":["Epidemiol. Infect."],"published-print":{"date-parts":[[2018,8]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Since April 2014 all presumptive <jats:italic>Salmonella<\/jats:italic> isolates received by Public Health England (PHE) have been characterised using whole genome sequencing (WGS) and the genomic data generated used to identify clusters of infection. To inform the implementation and development of a national gastrointestinal infection surveillance system based on WGS we have retrospectively identified genetically related clusters of <jats:italic>Salmonella<\/jats:italic> Enteritidis and <jats:italic>Salmonella<\/jats:italic> Typhimurium infection over a one year period and determined the distribution of these clusters by PHE operational levels. Using a constrained WGS cluster definition based on single nucleotide polymorphism distance, case frequency and temporal spread we demonstrate that the majority of clusters spread to multiple PHE operational levels. The greatest investigative burden is on national level staff investigating small, geographically dispersed clusters. We also demonstrate that WGS identifies long-running, slowly developing clusters that may previously have remained undetected. This analysis also indicates likely increased workload for local health protection teams and will require an operational strategy to balance limited human resources with the public health importance of investigating small, geographically contained clusters of highly related cases. While there are operational challenges to its implementation, integrated cluster detection based on WGS from local to international level will provide further improvements in the identification of, response to and control of clusters of <jats:italic>Salmonella<\/jats:italic> spp. with public health significance.<\/jats:p>","DOI":"10.1017\/s0950268818001589","type":"journal-article","created":{"date-parts":[[2018,7,2]],"date-time":"2018-07-02T03:24:22Z","timestamp":1530501862000},"page":"1452-1460","update-policy":"https:\/\/doi.org\/10.1017\/policypage","source":"Crossref","is-referenced-by-count":25,"title":["Operational burden of implementing <i>Salmonella<\/i> Enteritidis and Typhimurium cluster detection using whole genome sequencing surveillance data in England: a retrospective assessment"],"prefix":"10.1017","volume":"146","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8661-4606","authenticated-orcid":false,"given":"Piers","family":"Mook","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel","family":"Gardiner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Neville Q.","family":"Verlander","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacquelyn","family":"McCormick","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martine","family":"Usdin","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"}]},{"given":"Claire","family":"Jenkins","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Timothy J.","family":"Dallman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"56","published-online":{"date-parts":[[2018,7,2]]},"reference":[{"key":"S0950268818001589_ref1","article-title":"Revolutionising public health reference microbiology using whole genome sequencing: Salmonella as an exemplar","author":"Ashton","year":"2015","journal-title":"bioRxiv"},{"key":"S0950268818001589_ref4","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1002776"},{"key":"S0950268818001589_ref11","doi-asserted-by":"publisher","DOI":"10.1017\/S0950268810002281"},{"key":"S0950268818001589_ref5","unstructured":"OpenEpi Menu. Available at http:\/\/www.openepi.com\/Menu\/OE_Menu.htm (Accessed 1 May 2017)."},{"key":"S0950268818001589_ref7","unstructured":"European Centre for Disease Prevention and Control (2016) Salmonellosis \u2013 Annual Epidemiological Report 2016 [2014 data]. Available at http:\/\/ecdc.europa.eu\/en\/publications-data\/salmonellosis-annual-epidemiological-report-2016-2014-data (Accessed 12 December 2017)."},{"key":"S0950268818001589_ref2","doi-asserted-by":"publisher","DOI":"10.1016\/j.fm.2017.02.012"},{"key":"S0950268818001589_ref3","unstructured":"Annual Mid-year Population Estimates \u2013 Office for National Statistics. Available at https:\/\/www.ons.gov.uk\/peoplepopulationandcommunity\/populationandmigration\/populationestimates\/bulletins\/annualmidyearpopulationestimates\/2015-06-25 (Accessed 1 May 2017)."},{"key":"S0950268818001589_ref6","unstructured":"Foodborne and non-foodborne gastrointestinal outbreaks surveillance \u2013 GOV.UK. Available at https:\/\/www.gov.uk\/guidance\/foodborne-and-non-foodborne-gastrointestinal-outbreaks-surveillance (Accessed 30 June 2017)."},{"key":"S0950268818001589_ref10","doi-asserted-by":"publisher","DOI":"10.1017\/S0950268813001210"},{"key":"S0950268818001589_ref12","doi-asserted-by":"publisher","DOI":"10.1017\/S0950268816001941"},{"key":"S0950268818001589_ref13","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/cis967"},{"key":"S0950268818001589_ref9","article-title":"A multi-country Salmonella Enteritidis phage type 14b outbreak associated with eggs from a German producer: \u2018near real-time\u2019 application of whole genome sequencing and food chain investigations, United Kingdom, May to September 2014","volume":"20","author":"Inns","year":"2015","journal-title":"Euro Surveillance: Bulletin Europeen Sur Les Maladies Transmissibles = European Communicable Disease Bulletin"},{"key":"S0950268818001589_ref14","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365-2672.94.s1.13.x"},{"key":"S0950268818001589_ref8","unstructured":"Public Health England (2016) Salmonella data 2006 to 2015. Available at https:\/\/www.gov.uk\/government\/uploads\/system\/uploads\/attachment_data\/file\/598401\/Salmonella_2016_Data.pdf (Accessed 28 June 2017)."}],"container-title":["Epidemiology and Infection"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.cambridge.org\/core\/services\/aop-cambridge-core\/content\/view\/S0950268818001589","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,4,13]],"date-time":"2019-04-13T18:22:03Z","timestamp":1555179723000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.cambridge.org\/core\/product\/identifier\/S0950268818001589\/type\/journal_article"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,7,2]]},"references-count":14,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2018,8]]}},"alternative-id":["S0950268818001589"],"URL":"https:\/\/doi.org\/10.1017\/s0950268818001589","relation":{},"ISSN":["0950-2688","1469-4409"],"issn-type":[{"value":"0950-2688","type":"print"},{"value":"1469-4409","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,7,2]]},"assertion":[{"value":"Copyright \u00a9 Cambridge University Press 2018\u00a0","name":"license","label":"License","group":{"name":"copyright_and_licensing","label":"Copyright and Licensing"}}]}}