Fig. 8: Phylogenetic relationship of invasive S. Typhimurium clades in the global population structure of S. Typhimurium.

a Maximum likelihood phylogenetic tree containing 10 isolates from each invasive S. Typhimurium clade (blue branches) and a representative collection of 131 global S. Typhimurium isolates (black branches). The tree was constructed using sequence variation (SNPs) in the core genome with reference to S. Typhimurium strain SL1344. The root was identified using S. Heidelberg (accession number NC_011083.1) as the outgroup (not shown). The heatmap to the right of the tree highlights the invasive S. Typhimurium clades and the 19 previously determined population structure groups of the 131 strains (Bawn et al.,³⁰). Isolate names are shown as branch labels where high-quality long-read reference sequences, clonal complexes described in literature are also shown. The bifurcations giving rise to S. Typhimurium clade-α and clade-β are annotated. b Box plots of the geometric mean Delta Bitscore (DBS: bitscore SL1344 (FQ312003)—test strain bitscore) of proteomes of the same representative collection of 131 S. Typhimurium isolates are shown. Centres represent the geometric mean DBS, minima and maxima of the boxes represent the first and third quartiles, vertical lines indicate first or second quartile + 1.5× the interquartile range, and outliers > or less than these values plotted as points. The number of genomes (biological replicates) analysed in each group are indicated within the figure (n = ). Boxes are coloured to indicate phylogroups in (a). Basally rooted population structure group 1 not shown.