Fig. 6: Population structure of S. Kentucky ST198 strains isolated from Zimbabwe in the context of 364 globally sourced S. Kentucky strains.
a Maximum likelihood phylogenetic tree constructed based on recombination-purged SNPs in the shared genome with reference to S. Kentucky strain 201001922 (GenBank accession number CP028357). The tree was rooted on S. Typhimurium SL1344 strain SL1344 as an outgroup (not shown). The region (inner circle) and year (middle circle) and presence of a blaCTXM-14 gene (outer circle) are indicated by colors (inset key). Deeply rooted lineages (gray lines), lineages of strains isolated from Zimbabwe (red lines) and closely related strains isolated elsewhere (blue lines) are indicated to assist interpretation. b A subtree extracted from that shown above including strains isolated from Zimbabwe (red lines) and closely related strains isolated elsewhere (blue lines). Colored boxes indicate the country of isolation and country implicated through recent travel, if known (inset key), and the presence of AMR genes are indicated (inset key).
