Fig. 2: Phylogenetic and spatiotemporal dynamics of V. cholerae 7PET O139.

a Maximum likelihood phylogenetic tree of the V. cholerae 7PET O139 sublineage, constructed from whole-genome SNPs relative to the [H01] reference genome. Tree tips are colored by place of isolation (see key). Color strips and heat map depict the year of isolation, O139 wave, and AMR profile, respectively (see keys). The scale bar represents the number of substitutions per site per genome. b–d Spatiotemporal distribution of the three waves of V. cholerae 7PET O139 V. cholerae between 1992 and 2015. Solid circles represent the cities in which the clades were first observed, while dashed circles represent locations of secondary dominance. Dashed lines represent putative spread and circulation of the O139 waves. Map tiles were obtained from Stamen Design, under CC BY 3.0. Data by OpenStreetMap, under ODbL. e The number of genomes corresponding to each wave, over time. Points are colored by place of isolation and size of the point is relative to the number of genomes (see keys). Locations labeled on the Y axis with no corresponding X axis point are locations in which the O139 waves were observed, but for which the year of isolation is unknown and hence cannot be plotted. Where available, we have used higher resolution city information, but were restricted to country-level information for some of the samples.