Figure 3

Phylogeny and temporal changes in population structure of CC1, CC10 and CC19 lineages. (a) Mid-point rooted maximum likelihood phylogenetic tree of CC1. Branches are coloured according to phylogenetic clade assignment. (b) Number of isolates from CC1 over time stratified by clade assignment. (c) Mid-point rooted maximum likelihood phylogenetic tree of CC10. Branches are coloured according to phylogenetic clade assignment. (d) Number of isolates from CC10 over time stratified by clade assignment. (e) Mid-point rooted maximum likelihood phylogenetic tree of CC19. Branches are coloured according to phylogenetic clade assignment. (f) Number of isolates from CC19 over time stratified by clade assignment. The exact number of isolates in each year is available in Supplementary Data S1. Isolates from 2016 were excluded from trend analyses as study sampling ended in May of that year.