To identify potential genetic mechanisms associated with diversification of the Bhutanese S. sonnei, we compared their content of unique SNPs in comparison with the three most closely related outgroup isolates, taken from global isolates belonging to the same global lineage but collected outside of Bhutan (Fig. 2). The Bhutanese isolates were distinguished from these by the presence of 22 lineage-specific consensus SNPs. Of these 22 SNPs, five fell in intergenic regions and 17 mapped within predicted coding sequences; 11 represented non-synonymous and six were synonymous mutations. The genes bearing non-synonymous mutations are summarized in Table 1 together with their predicted impact on function. These include mutations in gyrA and parC associated with antimicrobial resistance, as well as those located in ycgB, mppA, hisC and rbsK, as determined by in silico sift (see Methods) analysis. With the exception of ycgB encoding a protein with unknown function, these genes all encode proteins predicted to be involved in the metabolism of histidine, ribose and formate, as well as transport of murein tripeptide (Table 1).