Fig. 1

Phylogenetic relationships within CG23. Time-calibrated Bayesian phylogeny (left) showing the relationships between 97 CG23 Kp, their sequences types (STs), the presence of chromosomal virulence loci (ybt, yersiniabactin; clb, colibactin; iro, salmochelin; rmpA, regulator of mucoid phenotype; mcc, microcin E492), plasmid virulence loci (iro salmochelin, iuc aerobactin, rmpA/rmpA2 regulator of mucoid phenotype), and the virulence plasmid backbone (pK2044-like, see Supplementary Fig. 6). Grey shading indicate partial mcc deletions (see Supplementary Fig. 7). Tips are coloured by region of isolate origin as indicated. In addition to SGH10, complete genomes for which chromosomes are shown in Fig. 2 are marked A-F as per inset legend. * indicates three human-associated multidrug resistant isolates. Subclades containing ICEKp are indicated by shading, labelled with the corresponding ICEKp and ybt lineages; the pink shaded clade carrying ICEKp10 (ybt 1) is the dominant lineage, CG23-I. Putative ICEKp acquisition events by a lineage or single strain are indicated by triangles at the corresponding node or next to a strain, and are shaded by chromosomal tRNA-Asn insertion site. Bayesian molecular dating estimates are shown for the most recent common ancestor of all isolates (i.e. the tree root), the CG23-I lineage, and the horse lineage (nodes as marked with white circles). The number of SNPs unique to CG23-I and the horse lineage are indicated on the relevant branches