Temporal phylogenetic reconstruction of Bhutanese Shigella sonnei between 2011 and 2013.Image shows a maximum clade credibility phylogenetic reconstruction of S. sonnei isolated primarily in Bhutan over the study period. Distinct subpopulations of Bhutanese S. sonnei are highlighted and indicated by letters. Black circles indicate posterior probability support ≥ 80 % on internal nodes. The asterisk indicates the branch leading to the Bhutanese S. sonnei clade, which represents 22 lineage-defining SNPs. Arrows denote branches characterized by select substitution events. Columns to the right of the phylogeny show metadata including: season (dark red, monsoon season: June–September; light red, other), and presence (dark blue) or absence (light blue) of mobile genetic elements, including specific genes (qnrS1, blaCTXM-15, pilL–V locus) and plasmids (pHUSEC41-1-like, pSH146_65-like, pHUSEC2011-1-like, IncK). Grey bars in metadata columns indicate sequences from S. sonnei isolated outside of Bhutan.