The phylogenetic structure of Bhutanese S. sonnei in the context of the global phylogeny and Central Asia clade. (A) Midpoint rooted maximum-likelihood phylogenetic tree of 183 S. sonnei strains (135 from global collection and 48 from Bhutan) reconstructed using 5393 SNPs; asterisks indicate bootstrap support values ≥ 98 % on major branches. Numbers above major branches represent ones leading to major lineages (I, II, III and IV). The light blue box highlights the Global III clade; the dark grey box overlaid on the tree highlights strains belonging to the Central Asia clade; the smaller, light grey box highlights the primarily Bhutanese Central Asia clade. (B) Magnified view of the maximum-likelihood phylogenetic tree of the Central Asia clade, including 74 S. sonnei strains (54 from Bhutan and 20 others for phylogenetic context), reconstructed using 996 SNPs; asterisks indicate bootstrap support values ≥ 80 %. The tree is midpoint rooted for purposes of clarity. Columns to the right of the phylogenetic tree show isolate metadata including: country of isolation (colours indicated in the key); the presence (dark blue) or absence (light blue) of specific genetic elements and mutations [ln2, spA, pSSE3, gyrA (S83L), gyrA (D87G), parC(S80I)], or the presence of an alternative mutation (yellow) [gyrA (D87Y)]; and resistance profiles against ciprofloxacin (CIP) and trimethoprim/sulfamethoxazole (SXT), where resistance is indicated in dark red, susceptibility in light red and missing data in grey.