Here, we have used WGS to define a population of S. sonnei causing disease in the South Asian land-locked nation of Bhutan. These strains belong to an expansion of lineage III, which we have named the Central Asia clade, which was introduced into Bhutan around 2006. To the best of our knowledge, this is the first time that WGS has been used on this scale to study a population of S. sonnei in South Asia, a region with a substantial burden of diarrhoeal disease. In contrast to recent observations from Vietnam, the sequenced S. sonnei in Bhutan demonstrated no evidence of a single clonal expansion. This is perhaps due to the short sampling time frame or other factors such as the lack of a definitive selective sweep event. However, the evolution history of Central Asia clade S. sonnei resembles the two initial sweep events observed in Vietnam [associated with fixation of a colicin plasmid and mutation(s) in gyrA] (Holt et al., 2013), showing that the two geographically and phylogenically unrelated S. sonnei populations followed a similar evolutionary trajectory. After its introduction to Bhutan, our data predict that these S. sonnei had access to a substantial gene pool, as indicated by the sporadic acquisition of ESBL plasmids and type IV pili. The gains of ESBL plasmids, although infrequent, could potentially become the next selective sweep for the Bhutan's S. sonnei population as observed in Vietnam, given the selection path toward resistance is maintained. The characteristically thin type IV pilus has been shown to improve the efficiency and specificity of conjugation in liquid environments (Kim & Komano, 1997), and also facilitates adherence, interbacterial contact and twitching motility (Berry & Pelicic, 2015). Although this structure is known to be widespread in prokaryotes, its impact on the lifestyle of Shigella is not well described and requires further experimental investigation (Holt et al., 2013; Rohmer et al., 2014).