Region-specific diversification of the highly virulent serotype 1 Streptococcus pneumoniae

Abstract

Serotype 1 Streptococcus pneumoniae is a leading cause of invasive pneumococcal disease (IPD) worldwide, with the highest burden in developing countries. We report the whole-genome sequencing analysis of 448 serotype 1 isolates from 27 countries worldwide (including 11 in Africa). The global serotype 1 population shows a strong phylogeographic structure at the continental level, and within Africa there is further region-specific structure. Our results demonstrate that region-specific diversification within Africa has been driven by limited cross-region transfer events, genetic recombination and antimicrobial selective pressure. Clonal replacement of the dominant serotype 1 clones circulating within regions is uncommon; however, here we report on the accessory gene content that has contributed to a rare clonal replacement event of ST3081 with ST618 as the dominant cause of IPD in the Gambia.

Keywords: Africa; Antibiotic Resistance; Genomics; PAGe; Phylogeny; Pneumococcal Disease; Recombination.

Fig. 1.

Phylogeography of serotype 1 S. pneumoniae isolates. Maximum-likelihood phylogenetic tree based on the whole genome SNPs of serotype 1 isolates annotated with country of origin. The colour of each isolate indicates the continent of origin: red, Africa; orange, Asia; green, Europe; blue, South America (the Brazilian group is highlighted by a circle, the Argentinian and Peruvian isolates are highlighted by a star); purple, Oceania. Specific lineages referred to in the text are labelled: A (lineage A, Europe, South America & Oceania), B (lineage B, Africa), C, (lineage C, South America), D (lineage D, Asia). Note that Asian isolates are present in all of the lineages.

Fig. 2.

Reconstructed maximum-likelihood phylogeny of serotype 1, lineage B isolates. The phylogeny is solely reconstructed using SNPs outside of recombinant blocks. The scale bar represents substitutions per SNP. The colour of each isolate indicates the country of origin. The panel next to the phylogeny shows the genomic locations of putative recombination events detected in each terminal taxon. Red blocks indicate recombination events that have occurred in multiple isolates. Blue blocks indicate recombination events that have occurred in a single isolate. The background colour of the panel indicates the region of origin.

Fig. 3.

Recombination dynamics of serotype 1 pneumococci. The mean rec/m (number of homologous recombination events/ number of SNPs introduced through spontaneous mutation) for the lineage B African clades. Error bars represent the 95 % confidence interval.

Fig. 4.

(a). Genomic regions recombination in the 376 lineage B isolates. The genes subject to the highest number of independent recombination events are named. (b). Genomic regions under recombination within the five lineage B Africa clades. folP, dihydropteroate synthase; pep, aminopeptidase; man, mannose PTS system component; adhP, alcholol dehydrogenase; PTS; phosphotransferase system protein; glyA, serine hydroxymethyltransferase; dnaG, DNA primase; rpoB, RNA polymerase beta subunit; folA, dihyrdofolate reductase; clpX, CLP protease; engB, STP binding protein; nan, neuraminidase; arc, arginine deiminase; fuc, fuculose kinase.

Fig. 5.

Association between clade-specific recombination events involving folA and folP and co-trimoxazole resistance. (a) The centre phylogeny is based on the SNP differences between folA from 210 lineage B isolates. (b) The centre phylogeny is based on the SNP differences between folP from the same dataset. The inner circles represent the lineage B clades from which the genes were isolated. The middle circles are coloured according to the co-trimoxazole resistance phenotype. The outer ring indicates if folA or folP was involved in a clade-specific recombination event. The scale bar represents substitutions per SNP.

Fig. 6.

Distribution of the antimicrobial resistance proteins Tet and Cat in serotype 1 pneumococci. The centre phylogeny is based on the whole genome SNP differences between 210 lineage B isolates, the inner rings are annotated with the country of origin and coloured according to the lineage B clade which the isolate belongs to. (a) The middle ring is coloured according to the tetracycline resistance phenotype, the outer ring according to the absence/presence of Tet. (b) The middle ring is coloured according to the chloramphenicol resistance phenotype, the outer ring according to the absence/presence of Cat. The scale bar represents substitutions per SNP.

Fig. 7.

Reconstructed maximum-likelihood phylogeny of serotype 1, lineage B isolates. The phylogeny is solely reconstructed using SNPs outside of recombinant blocks. The scale bar represents substitutions per SNP. The colour of each isolate indicates the country of origin. The panel next to the phylogeny shows the absence/presence of accessory genes in each isolate. Red blocks indicate an accessory gene is present (blue blocks indicate an antimicrobial resistant accessory gene is present). Putative or hypothetical accessory genes are not included in this figure.

Fig. 8.

Phylogeny of ST618 and ST3081 serotype 1 S. pneumoniae isolates recovered from the Gambia. Maximum-likelihood phylogenetic tree based on the whole genome SNPs of serotype 1 isolates annotated with ST. The scale bar represents substitutions per SNP. The colour of each isolate indicates its ST: blue, ST3081; red, ST217; purple, novel ST; orange, ST303; green, ST618; turquoise, ST2084. The panel next to the phylogeny shows the presence (red) or absence (blue) of accessory genes for each of the study isolates.