{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T23:48:44Z","timestamp":1787010524633,"version":"build-2736575974"},"reference-count":36,"publisher":"Microbiology Society","issue":"11","license":[{"start":{"date-parts":[[2019,11,1]],"date-time":"2019-11-01T00:00:00Z","timestamp":1572566400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,11,1]]},"abstract":"\n Since the 1970s, shigellosis has been reported as a sexually transmissible infection, and in recent years, genomic data have revealed the breadth of\n \n \n Shigella<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n spp. transmission among global networks of men who have sex with men (MSM). In 2015, Public Health England (PHE) introduced routine whole-genome sequencing (WGS) of\n \n \n Shigella<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n spp. to identify transmission clusters. However, limited behavioural information for the cases hampers interpretation. We investigated whether WGS can distinguish between clusters representing sexual transmission in MSM and clusters representing community (non-sexual) transmission to inform infection control. WGS data for\n \n \n Shigella flexneri<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n from August 2015 to July 2017 were aggregated into single linkage clusters based on SNP typing using a range of SNP distances (the standard for\n \n \n Shigella<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n surveillance at PHE is 10 SNPs). Clusters were classified as \u2018adult male\u2019, \u2018household\u2019, \u2018travel-associated\u2019 or \u2018community\u2019 using routine demographic data submitted alongside laboratory cultures. From August 2015 to March 2017, PHE contacted those with shigellosis as part of routine public-health follow-up and collected exposure data on a structured questionnaire, which for the first time included questions about sexual identity and behaviour. The questionnaire data were used to determine whether clusters classified as \u2018adult male\u2019 represented likely sexual transmission between men, thereby validating the use of the SNP clustering tool for informing appropriate public-health responses. Overall, 1006\u2009\n \n \n S<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n .\n \n \n flexneri<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n cases were reported, of which 563 clustered with at least one other case (10-SNP threshold). Linked questionnaire data were available for 106 clustered cases, of which 84.0\u200a% belonged to an \u2018adult male\u2019 cluster. At the 10-SNP threshold, 95.1\u200a% [95\u200a% confidence interval (CI) 88.0\u201398.1%] of MSM belonged to an \u2018adult male\u2019 cluster, while 73.2\u200a% (95\u200a% CI 49.1\u201387.5%) of non-MSM belonged to a \u2018community\u2019 or \u2018travel-associated\u2019 cluster. At the 25-SNP threshold, all MSM (95\u200a%\u2009CI 96.0\u2013100%) belonged to an \u2018adult male\u2019 cluster and 77.8\u200a% (95\u200a% CI 59.2\u201389.4%) of non-MSM belonged to a \u2018community\u2019 or \u2018travel-associated\u2019 cluster. Within one phylogenetic clade of\n \n \n S. flexneri<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n , 9 clusters were identified (7 \u2018adult male\u2019; 2 \u2018community\u2019) using a 10-SNP threshold, while a single \u2018adult male\u2019 cluster was identified using a 25-SNP threshold. Genotypic markers of azithromycin resistance were detected in 84.5\u200a% (294\/348) of \u2018adult male\u2019 cases and 20.9\u200a% (9\/43) of cases in other clusters (10-SNP threshold), the latter of which contained gay-identifying men who reported recent same-sex sexual contact. Our study suggests that SNP clustering can be used to identify\n \n \n Shigella<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n clusters representing likely sexual transmission in MSM to inform infection control. Defining clusters requires a flexible approach in terms of genetic relatedness to ensure a clear understanding of underlying transmission networks.\n <\/jats:p>","DOI":"10.1099\/mgen.0.000311","type":"journal-article","created":{"date-parts":[[2019,11,4]],"date-time":"2019-11-04T09:56:10Z","timestamp":1572861370000},"source":"Crossref","is-referenced-by-count":23,"title":["Use of whole-genome sequencing to identify clusters of Shigella flexneri associated with sexual transmission in men who have sex with men in England: a validation study using linked behavioural data"],"prefix":"10.1099","volume":"5","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6103-9975","authenticated-orcid":false,"given":"Holly D.","family":"Mitchell","sequence":"first","affiliation":[{"name":"Centre for Molecular Epidemiology and Translational Research, Institute for Global Health, University College London, London, UK"},{"name":"National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Blood Borne and Sexually Transmitted Infections, London, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amy F. 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