Fig. 3

Maximum-likelihood phylogeny of the ST22 S. aureus lineage and temporal phylogenetic reconstruction of the ST22-PT hypervirulent MRSA clone. (A) Maximum-likelihood tree of 1,051 ST22 isolates (8 from this study) based on 21,413 non-recombinant core genome SNPs. Rings 1 to 8 (from inside to outside) indicate the presence of QRDR mutations, with colored cells indicating presence and white cells indicating absence. Rings 9 and 10 indicate the presence of PVL and TSST-1 virulence factors, respectively. The tree is midpoint-rooted, and the scale bar represents the number of substitutions. (B) Bayesian phylogenetic reconstruction of the ST22-PT hypervirulent MRSA clone using 818 non-recombinant core SNPs from 29 ST22-PT isolates (7 from this study). Isolates are represented by dots at the tree tips, colored by isolation country. Strain names of EIA-MRSA isolates are colored in red. (C) Linear regression plot showing the relationship between date (x-axis) and root-to-tip divergence (y-axis), used to assess the correspondence between phylogenetic and temporal signals. (D) Comparison of the number of acquired antimicrobial resistance genes in ST22-PT-eQR isolates versus ST22-PT isolates without eQR genotypes