Definition of <i>K</i>. <i>pneumoniae</i> clones investigated in this study.

a) Phylogenetic tree inferred using maximum likelihood for K. pneumoniae genomes selected from our curated collection to represent the 509 distinct 7-gene chromosomal multi-locus sequence types. Phylogenetic clusters (monophyletic groups) were defined using patristic distance (cut-off = 0.04). Clusters corresponding to clones included in comparative analyses are marked; blue, hypervirulent; grey, unassigned; red, multi-drug resistant. b) Total number of genomes included in comparative analyses, coloured by clone type as above. Note that sample sizes exceed the number of isolates shown in the tree for the corresponding clones. c) Distribution of virulence and resistance determinants by clone. Intensity of box shading indicates the proportion of genomes harbouring the key virulence loci (blue) or acquired genes conferring resistance to different classes of antimicrobials (red), as per inset legends. Hypervirulent (Hvir) clones were defined by hierarchical clustering of virulence locus data. Multi-drug resistant (MDR) clones were defined by hierarchical clustering of resistance data. AMR, antimicrobial resistance; rmpA/A2, regulators of mucoid phenotype; ESBLs, extended spectrum beta-lactams; MLS, macrolide, lincosamide and streptogramin B antibiotics.