Genetic diversity of Streptococcus pneumoniae causing meningitis and sepsis in Singapore during the first year of PCV7 implementation

Figures & data

Figure 1 Serotype incidence among age groups. Total number of isolates 156. Vaccine coverage would be: PCV—38% (n=60, including the cross-protection for serotype 6A), PCV10—50% (n=79) and PCV13—74% (n=116). NT, non-typable by Pneumotest kit or mPCR method; UC, uncapsulated (cpsA not present, ply gene present, MLST indicated S. pneumoniae).

Table 1 ST and serotype/serogroup distribution within age groups

Serotype/serogroup ST
Children: ≤5 years (n=12)
Serotype 6B	315 (n=1); 2782 (n=1); 6198 (n=1); unavailable (n=1)
Group 11	6191 (n=1)
Serotype 14	9 (n=1)
Serotype 15B/C	6192 (n=1)
Serotype 19A	320 (n=2)
Serotype 19F	236 (n=1); 320 (n=1)
Serotype 23F	311 (n=1)
Children: 6–18 years (n=2)
Serotype 4	5275 (n=1)
Serotype 23F	81 (n=1)
Adults: 19–64 years (n=82)
Serotype 1	217 (n=1); 303 (n=1); 5044 (n=1); 5254 (n=1)
Serotype 3	458 (n=3); 505 (n=1); 4389 (n=1); 6193 (n=2); 3805 (n=1); 63 (n=1)
Serotype 6A	5832 (n=1)
Serotype 6B	386 (n=1); 1518 (n=3); 2779 (n=1); 6206 (n=1)
Serotype 6C	6209 (n=1)
Serotype 7F	218 (n=1); 3545 (n=5); 5265 (n=2); 5441 (n=1)
Serotype 8	5039 (n=4); 5291 (n=1); 6197 (n=2)
Serotype 9V	156 (n=1)
Serogroup 12	989 (n=1)
Serotype 14	9 (n=1); 143 (n=1); 200 (n=1); 876 (n=1); 6196 (n=1)
Serotype 15A	1591 (n=1); 6202 (n=1); 6204 (n=1)
Serogroup 18F	291 (n=1); 2711 (n=1)
Serotype 19A	230 (n=1); 320 (n=2); 416(n=3); 847 (n=1); 1848 (n=1); 2013 (n=2); 3781 (n=1); 3111 (n=1)
Serotype 19F	9 (n=1); 5260 (n=1); 5278 (n=1);3791 (n=1); 6199 (n=1); 5297 (n=1)
Serogroup 20	4901 (n=1); 5190 (n=1)
Serogroup 22	6194 (n=1)
Serotype 23A	338 (n=1)
Serotype 23F	81 (n=3); 361 (n=1); 6195 (n=1); 6200 (n=2)
Non-typable	6207 (n=1); 6210 (n=1); 5292 (n=1)
Uncapsulated	6201 (n=1)
Adults: 65 years and above (n=60)
Serotype 3	180 (n=2); 4655 (n=1); 4909 (n=1); 5255 (n=1); 5267 (n=1); 5299 (n=1)
Serotype 4	4127 (n=3); 5872 (n=1)
Serotype 6A	81 (n=2); 5272 (n=1)
Serotype 6B	95 (n=2); 3114 (n=1); 5241 (n=1)
Serotype 6C	224 (n=1); 5295 (n=1)
Serotype 7F	191 (n=1); 218 (n=1); 3544 (n=2); 3545(n=1)
Serotype 8	2234 (n=1); 6197 (n=1); 6203 (n=1)
Serotype 9V	156 (n=2)
Serotype 14	9 (n=2); 200 (n=2); 782 (n=1); 876 (n=1)
Serotype 15A	1591 (n=1)
Serotype 15B/C	199 (n=1)
Serotype 19A	199 (n=2); 2013 (n=1); 2102 (n=1); 4904 (n=1); 4937 (n=1)
Serotype 19F	81 (n=1); 320 (n=1)
Serogroup 20	235 (n=1); 4901 (n=1); 5289 (n=1)
Serogroup 22	433 (n=1)
Serotype 23A	338 (n=2)
Serotype 23F	242 (n=1) 5273 (n=1) 5296 (n=1) 6205 (n=1) 6212 (n=1)
Serotype 34	2832 (n=1)
Non-typable	5893 (n=1); 6208 (n=1)

Non-typable by Pneumotest and mPCR methods.

In bold: novel STs assigned in this study.

One pneumococcal sample did not generate MLST profile.

Figure 2 goeBURST (PHYLOViZ) analysis of 18 CCs. Population snapshot based on goeBURST analysis of 155 pneumococcal isolates. 18 CCs were formed. Each colour represents a different serotype.

Figure 3 Clonal diversity. Total number of isolates n=155; 102 STs; 24 serotypes/serogroups. Clonal diversity within serotype/serogoup. Number above the column is SID. No SID value shows that three or less isolates were available of that serotype/serogroup. A slightly greater clonal diversity was within PCV-vaccine serotypes (number of different STs n=71) than within non-PCV—non-vaccine serotypes (number of different STs n=31). NT, non-typable by Pneumotest kit and mPCR method; UC, uncapsulated (cpsA not present, ply gene present, MLST indicates S. pneumoniae).

Figure 4 The same STs as PMEN clones within Singaporean isolates (n=31). Serotypes are shown next to the corresponding ST.