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We obtained 42 and 50 <jats:italic>S. suis<\/jats:italic> isolates from lesions of porcine endocarditis and palatine tonsils, respectively, of clinically healthy pigs in Japan; we then determined their sequence types (STs) by multilocus sequence typing (MLST), <jats:italic>cps<\/jats:italic> genotypes, serotypes, and presence of classical major virulence-associated marker genes (<jats:italic>mrp<\/jats:italic>, <jats:italic>epf<\/jats:italic>, and <jats:italic>sly<\/jats:italic>). The 42 isolates from endocarditis lesions were assigned to a limited number of STs and clonal complexes (CCs). On the other hand, the 50 isolates from tonsils were diverse in these traits and seemingly in the degree of virulence, suggesting that tonsils can accommodate a variety of <jats:italic>S. suis<\/jats:italic> isolates. The goeBURST full algorithm using tonsil isolates obtained in this study and those retrieved from the database showed that major CCs as well as many other clusters were composed of isolates originating from different countries, and some of the STs were very similar to each other despite the difference in country of origin. These findings indicate that <jats:italic>S. suis<\/jats:italic> with not only different but also similar mutations in the genome have survived in tonsils independently across different geographical locations. Therefore, unlike the lesions of endocarditis, the tonsils of pigs seemingly accommodate various <jats:italic>S. suis<\/jats:italic> lineages. The present study suggests that <jats:italic>S. suis<\/jats:italic> acquired its diversity by natural mutations during colonization and persistence in the tonsils of pigs.<\/jats:p>","DOI":"10.1186\/s13567-024-01270-5","type":"journal-article","created":{"date-parts":[[2024,2,6]],"date-time":"2024-02-06T17:38:08Z","timestamp":1707241088000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Characterization of pig tonsils as niches for the generation of\u00a0Streptococcus suis\u00a0diversity"],"prefix":"10.1186","volume":"55","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4524-284X","authenticated-orcid":false,"given":"Kai","family":"Kobayashi","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hiroaki","family":"Kubota","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mari","family":"Tohya","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Megumi","family":"Ushikubo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Miki","family":"Yamamoto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tsukasa","family":"Ariyoshi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yumi","family":"Uchitani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Morika","family":"Mitobe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rumi","family":"Okuno","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ichiro","family":"Nakagawa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tsutomu","family":"Sekizaki","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun","family":"Suzuki","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kenji","family":"Sadamasu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,2,6]]},"reference":[{"key":"1270_CR1","doi-asserted-by":"publisher","DOI":"10.1038\/emi.2014.45","volume":"3","author":"G Goyette-Desjardins","year":"2014","unstructured":"Goyette-Desjardins G, Auger JP, Xu J, Segura M, Gottschalk M (2014) Streptococcus suis, an important pig pathogen and emerging zoonotic agent-an update on the worldwide distribution based on serotyping and sequence typing. 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