{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,20]],"date-time":"2026-02-20T21:44:45Z","timestamp":1771623885417,"version":"3.50.1"},"reference-count":40,"publisher":"American Society for Microbiology","issue":"11","license":[{"start":{"date-parts":[[2023,11,21]],"date-time":"2023-11-21T00:00:00Z","timestamp":1700524800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2023,11,21]],"date-time":"2023-11-21T00:00:00Z","timestamp":1700524800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["J Clin Microbiol"],"published-print":{"date-parts":[[2023,11,21]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:p>\n            The recently observed increase in invasive\n            <jats:italic>Streptococcus pyogenes<\/jats:italic>\n            infections causes concern in Europe. However, conventional molecular typing methods lack discriminatory power to aid investigations of outbreaks caused by\n            <jats:italic>S. pyogenes<\/jats:italic>\n            . Therefore, there is an urgent need for high-resolution molecular typing methods to assess genetic relatedness between\n            <jats:italic>S. pyogenes<\/jats:italic>\n            isolates. In the current study, we aimed to develop a novel high-resolution core-genome multilocus sequence typing (cgMLST) scheme for\n            <jats:italic>S. pyogenes<\/jats:italic>\n            and compared its discriminatory power to conventional molecular typing methods. The cgMLST scheme was designed with the commercial Ridom SeqSphere+ software package. To define a cluster threshold, the scheme was evaluated using publicly available data from nine defined\n            <jats:italic>S. pyogenes<\/jats:italic>\n            outbreaks in the United Kingdom. The cgMLST scheme was then applied to 23 isolates from a suspected\n            <jats:italic>S. pyogenes<\/jats:italic>\n            outbreak and 117\n            <jats:italic>S<\/jats:italic>\n            .\n            <jats:italic>pyogenes<\/jats:italic>\n            surveillance isolates both from the Netherlands. MLST and\n            <jats:italic>emm<\/jats:italic>\n            -typing results were used for comparison to cgMLST results. The allelic differences between isolates from defined outbreaks ranged between 6 and 31 for isolates with the same\n            <jats:italic>emm-<\/jats:italic>\n            type, resulting in a proposed cluster threshold of\n            <jats:underline>&lt;<\/jats:underline>\n            5 allelic differences out of 1,095 target loci. Seven out of twenty-three (30%) isolates from the suspected outbreak had an allelic difference of\n            <jats:underline>&lt;<\/jats:underline>\n            2, thereby identifying a potential cluster that could not be linked to other isolates. The proposed cgMLST scheme shows a higher discriminatory ability when compared to conventional typing methods. The rapid and simple analysis workflow allows for extended detection of clusters of potential outbreak isolates and surveillance and may facilitate the sharing of sequencing results between (inter)national laboratories.\n          <\/jats:p>","DOI":"10.1128\/jcm.00558-23","type":"journal-article","created":{"date-parts":[[2023,10,10]],"date-time":"2023-10-10T13:03:51Z","timestamp":1696943031000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":7,"title":["A core-genome multilocus sequence typing scheme for the detection of genetically related\n            <i>Streptococcus pyogenes<\/i>\n            clusters"],"prefix":"10.1128","volume":"61","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3348-2419","authenticated-orcid":false,"given":"Myrthe M. A.","family":"Toorop","sequence":"first","affiliation":[{"name":"Department of Medical Microbiology, Leiden University Medical Center , Leiden, the Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Margriet E. M.","family":"Kraakman","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, Leiden University Medical Center , Leiden, the Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Irene V.","family":"Hoogendijk","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, Leiden University Medical Center , Leiden, the Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joffrey","family":"van Prehn","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, Leiden University Medical Center , Leiden, the Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eric C. J.","family":"Claas","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, Leiden University Medical Center , Leiden, the Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6707-2311","authenticated-orcid":true,"given":"Els","family":"Wessels","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, Leiden University Medical Center , Leiden, the Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1560-6799","authenticated-orcid":false,"given":"Stefan A.","family":"Boers","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, Leiden University Medical Center , Leiden, the Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"235","reference":[{"key":"e_1_3_5_2_2","doi-asserted-by":"publisher","DOI":"10.1084\/jem.57.4.571"},{"key":"e_1_3_5_3_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13054-020-03008-z"},{"key":"e_1_3_5_4_2","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/cir084"},{"key":"e_1_3_5_5_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmi.2018.04.034"},{"key":"e_1_3_5_6_2","doi-asserted-by":"publisher","DOI":"10.1093\/ofid\/ofy145"},{"key":"e_1_3_5_7_2","unstructured":"Rijksinstituut voor Volksgezondheid en Milieu (RIVM)\n. 2022. Meldingen van invasieve GAS-infecties in Nederlan. Available from: https:\/\/wwwrivmnl\/groep-a-streptokokkeninfecties-gas\/meldingen-van-invasieve-gas-infecties-in-nederland. Accessed 19 Dec 2022."},{"key":"e_1_3_5_8_2","doi-asserted-by":"publisher","DOI":"10.2807\/1560-7917.ES.2023.28.1.2200941"},{"key":"e_1_3_5_9_2","unstructured":"World Health Organization (WHO)\n. Increase in invasive group A streptococcal infections among children in Europe including fatalities. Available from: https:\/\/wwwwhoint\/europe\/news\/item\/12-12-2022-increase-in-invasive-group-a-streptococcal-infections-among-children-in-europe--including-fatalities. Accessed 19 December 2022"},{"key":"e_1_3_5_10_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.43.9.4369-4376.2005"},{"key":"e_1_3_5_11_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.69.4.2416-2427.2001"},{"key":"e_1_3_5_12_2","unstructured":"Pubmlst scheme information S. Pyogenes. Available from: https:\/\/pubmlstorg\/bigsdb?db=pubmlst_spyogenes_seqdef&page=schemeInfo&scheme_id=1. Accessed 1 April 2023"},{"key":"e_1_3_5_13_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-08914-x"},{"key":"e_1_3_5_14_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro3093"},{"key":"e_1_3_5_15_2","doi-asserted-by":"publisher","DOI":"10.1186\/s42522-020-0010-1"},{"key":"e_1_3_5_16_2","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa1109910"},{"key":"e_1_3_5_17_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-019-0214-5"},{"key":"e_1_3_5_18_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01145-17"},{"key":"e_1_3_5_19_2","doi-asserted-by":"publisher","DOI":"10.3390\/genes3020261"},{"key":"e_1_3_5_20_2","doi-asserted-by":"publisher","DOI":"10.1128\/jcm.00315-22"},{"key":"e_1_3_5_21_2","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.2522"},{"key":"e_1_3_5_22_2","unstructured":"NCBI RefSeq database. Available from: https:\/\/wwwncbinlmnihgov\/refseq. 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Accessed 4 May 2023"}],"container-title":["Journal of Clinical Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/jcm.00558-23","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/jcm.00558-23","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,21]],"date-time":"2023-11-21T15:28:15Z","timestamp":1700580495000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/jcm.00558-23"}},"subtitle":[],"editor":[{"given":"Alexander","family":"Mellmann","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2023,11,21]]},"references-count":40,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2023,11,21]]}},"alternative-id":["10.1128\/jcm.00558-23"],"URL":"https:\/\/doi.org\/10.1128\/jcm.00558-23","relation":{},"ISSN":["0095-1137","1098-660X"],"issn-type":[{"value":"0095-1137","type":"print"},{"value":"1098-660X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,11,21]]},"assertion":[{"value":"2023-05-04","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2023-08-07","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2023-10-10","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e00558-23"}}