{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,26]],"date-time":"2026-03-26T05:28:06Z","timestamp":1774502886119,"version":"3.50.1"},"reference-count":31,"publisher":"Cambridge University Press (CUP)","issue":"7","license":[{"start":{"date-parts":[[2018,5,9]],"date-time":"2018-05-09T00:00:00Z","timestamp":1525824000000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/www.cambridge.org\/core\/terms"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Infect. Control Hosp. Epidemiol."],"published-print":{"date-parts":[[2018,7]]},"abstract":"<jats:sec id=\"S0899823X18001010_abs1\" sec-type=\"general\"><jats:title>OBJECTIVE<\/jats:title><jats:p>We report the utility of whole-genome sequencing (WGS) conducted in a clinically relevant time frame (ie, sufficient for guiding management decision), in managing a <jats:italic>Streptococcus pyogenes<\/jats:italic> outbreak, and present a comparison of its performance with <jats:italic>emm<\/jats:italic> typing.<\/jats:p><\/jats:sec><jats:sec id=\"S0899823X18001010_abs2\" sec-type=\"general\"><jats:title>SETTING<\/jats:title><jats:p>A 2,000-bed tertiary-care psychiatric hospital.<\/jats:p><\/jats:sec><jats:sec id=\"S0899823X18001010_abs3\" sec-type=\"methods\"><jats:title>METHODS<\/jats:title><jats:p>Active surveillance was conducted to identify new cases of <jats:italic>S. pyogene<\/jats:italic>s. WGS guided targeted epidemiological investigations, and infection control measures were implemented. Single-nucleotide polymorphism (SNP)\u2013based genome phylogeny, <jats:italic>emm<\/jats:italic> typing, and multilocus sequence typing (MLST) were performed. We compared the ability of WGS and <jats:italic>emm<\/jats:italic> typing to correctly identify person-to-person transmission and to guide the management of the outbreak.<\/jats:p><\/jats:sec><jats:sec id=\"S0899823X18001010_abs4\" sec-type=\"results\"><jats:title>RESULTS<\/jats:title><jats:p>The study included 204 patients and 152 staff. We identified 35 patients and 2 staff members with <jats:italic>S. pyogenes.<\/jats:italic> WGS revealed polyclonal <jats:italic>S. pyogenes<\/jats:italic> infections with 3 genetically distinct phylogenetic clusters (C1\u2013C3). Cluster C1 isolates were all <jats:italic>emm<\/jats:italic> type 4, sequence type 915 and had pairwise SNP differences of 0\u20135, which suggested recent person-to-person transmissions. Epidemiological investigation revealed that cluster C1 was mediated by dermal colonization and transmission of <jats:italic>S. pyogenes<\/jats:italic> in a male residential ward. Clusters C2 and C3 were genomically diverse, with pairwise SNP differences of 21\u201345 and 26\u201358, and <jats:italic>emm<\/jats:italic> 11 and mostly <jats:italic>emm<\/jats:italic>120, respectively. Clusters C2 and C3, which may have been considered person-to-person transmissions by <jats:italic>emm<\/jats:italic> typing, were shown by WGS to be unlikely by integrating pairwise SNP differences with epidemiology.<\/jats:p><\/jats:sec><jats:sec id=\"S0899823X18001010_abs5\" sec-type=\"conclusions\"><jats:title>CONCLUSIONS<\/jats:title><jats:p>WGS had higher resolution than <jats:italic>emm<\/jats:italic> typing in identifying clusters with recent and ongoing person-to-person transmissions, which allowed implementation of targeted intervention to control the outbreak.<\/jats:p><jats:p><jats:italic>Infect Control Hosp Epidemiol<\/jats:italic> 2018;852\u2013860<\/jats:p><\/jats:sec>","DOI":"10.1017\/ice.2018.101","type":"journal-article","created":{"date-parts":[[2018,5,9]],"date-time":"2018-05-09T06:44:21Z","timestamp":1525848261000},"page":"852-860","source":"Crossref","is-referenced-by-count":14,"title":["An Outbreak of <i>Streptococcus pyogenes<\/i> in a Mental Health Facility: Advantage of Well-Timed Whole-Genome Sequencing Over <i>emm<\/i> Typing"],"prefix":"10.1017","volume":"39","author":[{"given":"Sarah M.","family":"Bergin","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Balamurugan","family":"Periaswamy","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Timothy","family":"Barkham","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hong Choon","family":"Chua","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yee Ming","family":"Mok","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel Shuen Sheng","family":"Fung","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alex Hsin Chuan","family":"Su","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yen Ling","family":"Lee","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ming Lai Ivan","family":"Chua","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Poh Yong","family":"Ng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wei Jia Wendy","family":"Soon","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Collins Wenhan","family":"Chu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Siyun Lucinda","family":"Tan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mary","family":"Meehan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Brenda Sze Peng","family":"Ang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yee Sin","family":"Leo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthew T. 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