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. 2019 Apr 10;9:5865. doi: 10.1038/s41598-019-41883-x

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© The Author(s) 2019

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Phylogenetic analysis. (A) A total of 168,476 variable sites from a core-gene alignment of 2,103 genes from 65 genomes were used to generate a maximum-likelihood phylogenetic tree of the V. cholerae species, rooted on Vibrio metoecus and Vibrio sp. RC586. Two genomes that are representative of the 7PET lineage were included. The non-toxigenic isolate 48853_F01 clustered together with other non-toxigenic, non-O1/O139 V. cholerae. (B) A maximum-likelihood phylogeny of the 7PET lineage constructed using 1,629 non-recombinant variable sites across 117 V. cholerae genomes, rooted on M66-2. The three toxigenic samples in this study clustered together with other toxigenic O139 genome sequences, all of which form a discrete sub-lineage within 7PET. Hatch marks denote branches that were shortened artificially for illustrative purposes; an unedited tree is presented in Supplementary Fig. S5. Trees were also computed using an ascertainment bias correction model (see Methods). These are presented in Supplementary Fig. S6.