Vibrio cholerae and other Vibrio spp. isolates analysed in this study.

*Genome strains 1587 (GenBank Accession No. AAUR00000000); 623-39 (Accession No. AAWG00000000); AM-19226 (Accession No. AATY00000000); BX330286 (Accession No. ACIA00000000); CMCP6 (Accession No. AE016795.3); CT5369-93 (Accession No. ADAL00000000); M66-2 (Accession No. CP001233); MB451 (Accession No. ADAF00000000); MZO-2 (Accession No. AAWF00000000); MZO-3 (Accession No. AAUU00000000); N16961 (Accession No. AE003852); M1616/O395 (Accession No. CP000626); RC341 (Accession No. ACZT00000000); RC385 (Accession No. AAKH00000000); RC586 (Accession No. ADBD00000000); SX-4 (Accession No. ADOO00000000); TM11079-80 (Accession No. ACHW00000000); TMA21 (Accession No. ACHY00000000); V51 (Accession No. AAKI00000000); V52 (Accession No. AAKJ00000000); VL426 (Accession No. ACHV00000000); VM223 (Accession No. ADAJ00000000); VM573 (Accession No. ACYV00000000); VM603 (Accession No. ACYU00000000); 12129 (Accession No. ACFQ00000000).†Two primer pairs were used as previously described in Tay et al. [44] to amplify divergent tcpA genes.§Two primer pairs were used for typing the type III secretion system (T3SS), one for vcsC2 and one for vcsV2.‡N/A: Data not available.#Clonal complex (CC) as defined by eBURST analysis.¶Subpopulations are derived from STRUCTURE analysis.