Recent advances in whole-genome sequencing (WGS) and analytical methodologies have enhanced our understanding of the epidemiology, international spread and antimicrobial susceptibility trends of S. sonnei (Holt et al., 2012, 2013). We now know that S. sonnei is formed of three main lineages (I, II and III), which are all related to a common ancestor that arose in Europe ∼400 years ago (Holt et al., 2012). Lineage III, which is multidrug-resistant (MDR), now dominates globally (Holt et al., 2012). We have also previously shown that once introduced into a new geographical region, into an apparently naive human population, S. sonnei can establish new isolated clonal populations which evolve locally (Holt et al., 2013). Antimicrobial resistance is a key driver of the recent S. sonnei global expansions marked by the acquisition of antimicrobial resistance genes and/or mutations in genes encoding the target proteins for antimicrobials (Pu et al., 2015).