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Here, we interrogated a collection of 1,804 <jats:italic>Shigella<\/jats:italic> whole genome sequences from organisms isolated in four continental Southeast Asian countries (Thailand, Vietnam, Laos, and Cambodia) over three decades to characterise the evolution of both <jats:italic>S. flexneri<\/jats:italic> and <jats:italic>S. sonnei<\/jats:italic>. We show that <jats:italic>S. sonnei<\/jats:italic> and each major <jats:italic>S. flexneri<\/jats:italic> serotype are comprised of genetically diverse populations, the majority of which were likely introduced into Southeast Asia in the 1970s\u20131990s. Intranational and regional dissemination allowed widespread propagation of both species across the region. Our data indicate that the epidemiology of <jats:italic>S. sonnei<\/jats:italic> and the major <jats:italic>S. flexneri<\/jats:italic> serotypes were characterised by frequent clonal replacement events, coinciding with changing susceptibility patterns against contemporaneous antimicrobials. We conclude that adaptation to antimicrobial pressure was pivotal to the recent evolutionary trajectory of <jats:italic>Shigella<\/jats:italic> in Southeast Asia.<\/jats:p>","DOI":"10.1038\/s42003-021-01905-9","type":"journal-article","created":{"date-parts":[[2021,3,19]],"date-time":"2021-03-19T13:04:20Z","timestamp":1616159060000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":36,"title":["Evolutionary histories and antimicrobial resistance in Shigella flexneri and Shigella sonnei in Southeast Asia"],"prefix":"10.1038","volume":"4","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4028-4074","authenticated-orcid":false,"given":"Hao","family":"Chung The","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ladaporn","family":"Bodhidatta","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Duy Thanh","family":"Pham","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3676-2811","authenticated-orcid":false,"given":"Carl J.","family":"Mason","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tuyen","family":"Ha Thanh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Phat","family":"Voong Vinh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1013-7815","authenticated-orcid":false,"given":"Paul","family":"Turner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sopheak","family":"Hem","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9189-7244","authenticated-orcid":false,"given":"David A. 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