Pneumococcal capsular switching: a historical perspective

Abstract

Background: Changes in serotype prevalence among pneumococcal populations result from both serotype replacement and serotype (capsular) switching. Temporal changes in serotype distributions are well documented, but the contribution of capsular switching to such changes is unknown. Furthermore, it is unclear to what extent vaccine-induced selective pressures drive capsular switching.

Methods: Serotype and multilocus sequence typing data for 426 pneumococci dated from 1937 through 2007 were analyzed. Whole-genome sequence data for a subset of isolates were used to investigate capsular switching events.

Results: We identified 36 independent capsular switch events, 18 of which were explored in detail with whole-genome sequence data. Recombination fragment lengths were estimated for 11 events and ranged from approximately 19.0 kb to ≥ 58.2 kb. Two events took place no later than 1960, and the imported DNA included the capsular locus and the nearby penicillin-binding protein genes pbp2x and pbp1a.

Conclusions: Capsular switching has been a regular occurrence among pneumococcal populations throughout the past 7 decades. Recombination of large DNA fragments (>30 kb), sometimes including the capsular locus and penicillin-binding protein genes, predated both vaccine introduction and widespread antibiotic use. This type of recombination has likely been an intrinsic feature throughout the history of pneumococcal evolution.

Figure 1.

Temporal distribution of capsular switch variants among the historical isolate collection. Gray triangles indicate isolation dates for the oldest recombinant representatives of 36 independent capsular switch events identified among the historical pneumococcal collection. Abbreviation: PCV7, 7-valent pneumococcal conjugate vaccine.

Figure 2.

Genetic changes leading to capsular switching within clonal complexes (CCs) 66, 113, and 156/162. Bars represent the cps locus and flanking regions. Filled arrows indicate the relative positions of the dexB (left) and aliA (right) loci. Open arrows indicate the relative positions of the pbp2x (left) and pbp1a (right) loci. Vertical bisecting lines indicate single nucleotide substitutions. Recombination fragments are indicated by coloring. Identical sequences are indicated by identical coloring. Regions bounded by solid lines are depicted at their maximum length. Regions not bounded by solid lines are depicted at their minimum length (Table 2). The asterisk indicates a single-base-pair deletion. The schematic is drawn approximately to scale.

Figure 3.

Variable site maps for the cps loci of serogroups 18 and 7. Rows represent the nucleotide sequences of independent isolates and are labeled as isolate name (year). Nucleotide differences relative to row 1 are shown. Periods indicate an identical base, and hyphens indicate a missing base. Numbers above each column indicate the nucleotide position within the alignment. Nucleotide substitutions marking putative recombination regions are marked in bold and underlined. A, CC113 isolates include 1 of serotype 18B (18B/2) and 6 of serotype 18C. B, CC191 isolates include 1 of serotype 7A (7A/2) and 7 of serotype 7F. CC218 isolates all represent serotype 7F (B*). The arrow indicates the position of a single-base-pair insertion in the 7A/2 sequence, compared with the other serogroup 7 sequences.

Figure 4.

Genetic changes leading to capsular switching within clonal complexes (CCs) 191, 218, and 574. Bars represent the cps locus and flanking regions. Filled arrows indicate the relative positions of the dexB (left) and aliA (right) loci. Open arrows indicate the relative positions of the pbp2x (left) and pbp1a (right) loci. Vertical bisecting lines indicate single nucleotide substitutions. Recombination fragments are indicated by coloring. Regions bounded by solid lines are depicted at their maximum length. Regions not bounded by solid lines are represented at their minimum length (Table 2). The asterisk indicates a single-base-pair insertion. The schematic is drawn approximately to scale.

Figure 5.

Inter-clonal complex (CC) cps locus transfers inferred in this study. Circles represent pneumococcal CCs as named. Arrows indicate transfer of cps loci between CCs, as inferred from nucleotide sequence analyses for 15 capsular switching events. Donor CCs could not be predicted for a total of 7 events because donor isolates were not present among this collection. Arrow labels indicate serotypes associated with the transferred cps loci and isolation year of the oldest recombinant pneumococcus in this collection.