Streptococcus pneumoniae causes a high burden of invasive pneumococcal disease (IPD) globally, especially in children from resource-poor settings. Like many bacteria, the pneumococcus can import DNA from other strains or even species by transformation and homologous recombination, which has allowed the pneumococcus to evade clinical interventions such as… (More)
FIG 2 Recombination inferred by Gubbins. Recombination events mapped onto internal nodes (red blocks) and terminal branches (blue blocks) are illustrated for a typical low-recombination serotype (serotype 1 [SC1]) (a) and a high-recombination serotype (serotype 6A [SC3]) (b). (i) Maximum likelihood phylogenetic trees of the different serotypes. Branches and tips of the phylogeny are colored according to the MLST sequence type (ST). (ii) Schematic representation of the reference S. pneumoniae genome showing all the genetic annotations and locations of some well-known genes. (iii) Matrix showing the tracks representing each genome. The locations and distribution of regions, which have acquired exogenous DNA through recombination, are colored depending on the number of strains that contain them. Recombination events in internal branches (red) were present in multiple isolates and were shared through clonal descent rather than independent acquisitions, while those in the terminal branches (blue) were isolate specific and represent independent recent acquisitions. The recombination rate ( r/m), i.e., mean number of the inferred distinct recombination events per isolate (each shared ancestral recombination event that occurred once and spread in the clone via clonal descent was counted once). The recombination frequency ( re), i.e., the mean number of SNPs introduced through recombination to those introduced through mutation, is shown. A high presence of recent rather than shared recombination events implies high re.