Fig. 1

Recombination events affecting genomes of Polish invasive S. pneumoniae isolates of ST320 and serotypes 19A and 19F elucidated using Gubbins and visualized in PHANDANGO. The annotated 3238/09 genome used as reference, with short vertical blue lines of various thickness representing CDSs; phylogenetic trees on the left; pink bars, recombinations shared by clusters of isolates; violet bars, recombinations unique for isolates at terminal branches. A Analysis of the 3238/09 and 3641/15 genomes from this study and the complete SP64 and TCH8431-19A genomes of ST320 and serotype 19A from GenBank (CP018138.1 and CP001993.1, respectively). Recombination blocks, distinguishing the 3641/15 genome from the 3238/09 genome indicated above the reference genome; the approximately 161-kb cps region shadowed. B Details of the cps region from (A) depicted for the 3238/09 and 3641/15 genomes. The putative mobile genetic element (MGE) [49] and the cps operon marked by thick black bars; localization of pbp2x, dexB, aliA, pbp1a indicated with thin arrows; recombination blocks, distinguishing the 3641/15 genome from the 3238/09 genome indicated below. C Analysis of the approximately 0.3 Mb contig harbouring the cps operon from the SN39039 isolate [49] and the corresponding parts of the 3238/09, 3641/15, SP64 and TCH8431-19A genomes. MGE, cps, pbp2x, dexB, aliA, pbp1a indicated as in (B); the 76.5 kb recombining fragment, acquired by the SN39039 isolate [49] indicated by a thick double-headed arrow; recombination blocks upstream and downstream cps specific for the 3641/15 isolate described in the lower part of the figure, with the recombining segment R3 shadowed in grey