Fig. 1: Phylogenetic tree of ST131 clade C.

Maximum-likelihood phylogenetic tree of 1338 clade C0, C1, and C2 isolates based on 10,904 variable sites in a 2.5 Mb core genome alignment. Each isolate is annotated with ST131 subclade affiliation (ring 1), presence of selected IncF plasmid replicon types (pMLST; ring 2), blaCTX-M allele (ring 3), and papGII gene (ring 4). ST131 papGII-containing sublineages discussed in the text are shaded in grey. Those of clade C2 are annotated with L1, L2, and L3. The scale bar indicates the number of substitutions per site. The tree was visualized using iTOL⁷⁴. Supplementary Fig. 2 shows this tree with additional information.