Global emergence and population dynamics of divergent serotype 3 CC180 pneumococci - Fig 2

A) Rooted maximum likelihood phylogeny of S. pneumoniae serotype 3 CC180 isolates (n = 301) inferred from an alignment of 15,327 SNPs present in the core genome. Phylogeny was out-group rooted using strain AP200 (accession # CP002121) a serotype 11A, ST62 S. pneumoniae invasive isolate, which was found to be immediately basal to the CC180 clade in a global phylogeny of pneumococcal reference genomes and therefore represented the closest out-group. Bootstrap values from 100 replicates are labelled on major clades and epidemiologically relevant sub-clades. Additional values can be found in the supplemental phylogeny. Mean pairwise within- and between-clade SNP difference are presented in the grey shaded box with colors corresponding to the phylogeny. B.) World map illustrating sampled countries and regions with respective proportion of isolates belonging to Clade I-α, I-β, and II. Countries are colored according to region and pie charts represent the proportion of isolates belonging to major serotype 3 clades. The size of the pie chart is scaled to the proportion of strains sampled from each region. Mapping was performed using R package maps v3.3.0. C) Proportion of clade membership by three-year collection window. The proportion of clade membership by region over-time is displayed on the top of the figure. Pie charts are scaled by the number of isolates sampled from a geographic region by time window (i.e., column). The overall proportion of clades for each time window is presented on the bottom of the figure.