Phylogenomic analysis of the sequenced isolates. (A) Maximum likelihood phylogeny of the isolates based on likely point mutations. The branches of the phylogeny are coloured according to the geographical location of the isolates, as reconstructed through the tree on the basis of maximum parsimony. The PMEN2 and PMEN22 clades are indicated by the black vertical bars; the grey shaded box marks the ‘Outgroup’ clade. Isolates from Iceland are indicated by the orange boxes highlighting clades IC1 and IC2. Isolates from Spain previously providing evidence of transmission from continental Europe are marked with single asterisks; the German isolate most closely related to clade IC1 is marked with a double asterisk. The PMEN22 isolate that has become resistant to β-lactams is marked by the † symbol. (B) Simplified annotation of the reference genome against which sequence reads were mapped. The positions of putative mobile genetic elements (MGEs) is marked, along with the capsule polysaccharide synthesis locus (cps), Pneumococcal Pathogenicity Island 1 (PPI-1), the gene for penicillin-binding protein 2B (pbp2b), and the antigen-encoding genes pspA and pspC. (C) Density of recombination events across the genome: (i) across the entire collection, (ii) within only the PMEN2 clade. (D) Distribution of recombination events. The dashed line defines a panel consisting of a row for each of the sequenced isolates in the collection, with a column for each base in the reference sequence. Putative recombination events are indicated by the coloured blocks: red events are reconstructed as occurring on internal branches and are, therefore, shared by multiple isolates through common descent, whereas blue blocks are recombinations occurring on terminal branches, which are unique to individual isolates.