In order to place the Bhutanese isolates in the context of global diversity, we aligned the Bhutanese S. sonnei sequences with publicly available sequences utilized in a previous global analysis (Holt et al., 2012). An initial phylogeny was inferred with these data using RAxML under the GTRGAMMA model. To further assess the relationship of the Bhutanese isolates within Central Asia, the previous alignment was then subsampled to include only the 71 Bhutanese sequences along with 20 other closely related Central Asia sequences. Previously described mobile genetic elements (Holt et al., 2012) and potential recombinant regions were removed from the alignment using Gubbins (Croucher et al., 2014). Further removal of gaps, indeterminate bases, invariant sites and 17 Bhutanese sequences that were identical to others in the dataset resulted in a final alignment of 996 SNPs across 74 taxa. A maximum-likelihood phylogeny was inferred from these sequences using garli (Zwickl, 2006) with 1000 bootstrap replicates under the TVM (transversion) model of nucleotide substitution, which was determined to be the best-fit model using jModelTest (Posada, 2008).