Figure 1.

Maximum likelihood phylogenetic tree obtained using the SNPs of the core genome of the 44 S. pneumoniae genomes. The tree has been rooted using the four S. mitis genomes as outgroup, but note that the branch connecting the S. pneumoniae clade to the S. mitis clade is not to scale. The branches are annotated with their bootstrap support (numbers in italics). Red bars indicate strains belonging to the same sequence type (ST), while blue bars indicate strains belonging to the same clonal complex (CC). The six major lineages are identified by roman numbers I to VI.