The composition of the accessory genome can be used to indicate the capacity of the host species to sample the local gene pool and also to highlight themes in the patterns of acquisition that may be under selection. We performed a comparative gene content analysis of Bhutanese and non-Bhutanese S. sonnei belonging to the Central Asia clade. These data revealed events that appear to have been pivotal in evolution and spread of the Central Asia clade. Notably, all the isolates of this clade possessed a specific class 2 integron In2 (dfrA1, sat1), conferring resistance to trimethoprim and streptothricin. These strains additionally gained the S. sonnei spA plasmid carrying sul2, strAB and tetRA genes, which further expanded the spectrum of antimicrobial resistance to incorporate sulphonamides, streptomycin and tetracycline resistance, respectively (Fig. 1B). This resistance gene profile concurs with the observation made in the previous global S. sonnei study (Holt et al., 2012). It is of note that the class 2 integron of the Central Asia clade differs from that of Global III in the absence of aadA1, which confers resistance to aminoglycosides. Moreover, it was clear that isolates within this clade have, over time, accumulated chromosomal mutations conferring fluoroquinolone resistance (Fig. 1B). From the lineage-specific phylogeny, we predicted that the first mutation in gyrA (S83L) occurred before 1996, and supplementary mutations in parC (S80I) and secondary mutations in gyrA (D87G), leading to high-level fluoroquinolone resistance, were fixed in the Bhutanese clade prior to its expansion and diversification in 2006 (Fig. 2).