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This serogroup was initially feared to represent a new, emerging <jats:italic>V<\/jats:italic>. <jats:italic>cholerae<\/jats:italic> clone that would lead to an eighth cholera pandemic. However, these concerns were ultimately unfounded. The majority of clinically relevant <jats:italic>V<\/jats:italic>. <jats:italic>cholerae<\/jats:italic> O139 isolates are closely related to serogroup O1, biotype El Tor <jats:italic>V<\/jats:italic>. <jats:italic>cholerae<\/jats:italic>, and comprise a single sublineage of the seventh pandemic El Tor lineage. Although related, these <jats:italic>V<\/jats:italic>. <jats:italic>cholerae<\/jats:italic> serogroups differ in several fundamental ways, in terms of their O-antigen, capsulation phenotype, and the genomic islands found on their chromosomes. Here, we present four complete, high-quality genomes for <jats:italic>V<\/jats:italic>. <jats:italic>cholerae<\/jats:italic> O139, obtained using long-read sequencing. Three of these sequences are from toxigenic <jats:italic>V<\/jats:italic>. <jats:italic>cholerae<\/jats:italic>, and one is from a bacterium which, although classified serologically as <jats:italic>V<\/jats:italic>. <jats:italic>cholerae<\/jats:italic> O139, lacks the CTX\u03c6 bacteriophage and the ability to produce cholera toxin. We highlight fundamental genomic differences between these isolates, the <jats:italic>V<\/jats:italic>. <jats:italic>cholerae<\/jats:italic> O1 reference strain N16961, and the prototypical O139 strain MO10. These sequences are an important resource for the scientific community, and will improve greatly our ability to perform genomic analyses of non-O1 <jats:italic>V<\/jats:italic>. <jats:italic>cholerae<\/jats:italic> in the future. These genomes also offer new insights into the biology of a <jats:italic>V<\/jats:italic>. <jats:italic>cholerae<\/jats:italic> serogroup that, from a genomic perspective, is poorly understood.<\/jats:p>","DOI":"10.1038\/s41598-019-41883-x","type":"journal-article","created":{"date-parts":[[2019,4,10]],"date-time":"2019-04-10T10:18:48Z","timestamp":1554891528000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":19,"title":["High quality reference genomes for toxigenic and non-toxigenic Vibrio cholerae serogroup O139"],"prefix":"10.1038","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7064-6163","authenticated-orcid":false,"given":"Matthew J.","family":"Dorman","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5389-9185","authenticated-orcid":false,"given":"Daryl","family":"Domman","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Muhammad Ikhtear","family":"Uddin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Salma","family":"Sharmin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9627-7877","authenticated-orcid":false,"given":"Mokibul Hassan","family":"Afrad","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yasmin Ara","family":"Begum","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Firdausi","family":"Qadri","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4432-8505","authenticated-orcid":false,"given":"Nicholas R.","family":"Thomson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2019,4,10]]},"reference":[{"key":"41883_CR1","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1007\/BF01571061","volume":"28","author":"T Shimada","year":"1994","unstructured":"Shimada, T. et al. 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