All S. sonnei (n = 74) isolated during this study were subjected to WGS; 71 isolates produced sufficient sequence for analysis. To contextualize the Bhutanese S. sonnei within the known global S. sonnei population structure, we constructed a phylogeny that included the Bhutanese sequences and those from a previous global S. sonnei sequencing project (Holt et al., 2012); within this phylogeny, all Bhutanese S. sonnei fell into a single clade within lineage III (Central Asia clade), which is a sister clade to the intercontinental expanding Global III clade (Fig. 1A). To investigate the phylogenetic relationships within the Central Asia clade, we concatenated 74 of the non-duplicate whole-genome sequences, including 54 from Bhutan and 20 selected from other countries. A maximum-likelihood phylogeny reconstructed from this alignment showed a close clonal relationship between the Bhutanese S. sonnei. Showing a similarly close relationship to the Bhutanese isolates, and interspersed within this clade, were also two isolates from Thailand and Cambodia, likely representing importations following regional travel (Fig. 1B).