Fig. 5: Phylogenetic distribution of orthologous gene clusters differentially overrepresented between IE and non-IE S. mitis isolates among invasive isolates belonging to the genetically related and more pathogenic sister species pneumococcus.
Maximum-likelihood phylogeny of invasive bacteraemia S. pneumoniae isolates is built using 141,880 SNPs out of 1,520,986 core nucleotide bases. The coloured tips of the phylogeny and the first metadata row shows the Global Pneumococcal Sequence Cluster (GPSC), while the second row shows the serotype. The subsequent 12 rows show the presence or absence of the orthologous gene clusters (with prefix SCLS for sequence cluster locus sequence) that were overrepresented in invasive or carriage S. mitis. The phylogeny shows there are a few gene clusters that are also prevalent among the invasive pneumococcal isolates, however, most gene clusters are absent among the pneumococcal isolates. The largely absent S. mitis lytA gene was further investigated among the pneumococci using the virulence finder database90, which identified the presence of pneumococcal lytA among 448 out of 493 (90.9%) isolates using pneumococcal specific lytA reference sequences in the virulence finder database90. Source data are provided as a Source Data file.
