Molecular epidemiology of pneumococci obtained from Gambian children aged 2-29 months with invasive pneumococcal disease during a trial of a 9-valent pneumococcal conjugate vaccine

Abstract

Background: The study describes the molecular epidemiology of Streptococcus pneumoniae causing invasive disease in Gambian children

Methods: One hundred and thirty-two S. pneumoniae isolates were recovered from children aged 2-29 months during the course of a pneumococcal conjugate vaccine trial conducted in The Gambia of which 131 were characterized by serotyping, antibiotic susceptibility, BOX-PCR and MLST.

Results: Twenty-nine different serotypes were identified; serotypes 14, 19A, 12F, 5, 23F, and 1 were common and accounted for 58.3% of all serotypes overall. MLST analysis showed 72 sequence types (STs) of which 46 are novel. eBURST analysis using the stringent 6/7 identical loci definition, grouped the isolates into 17 clonal complexes and 32 singletons. The population structure of the 8 serotype 1 isolates obtained from 4 vaccinated and 2 unvaccinated children were the same (ST 618) except that one (ST3336) of the isolates from an unvaccinated child had a novel ST which is a single locus variant of ST 618.

Conclusion: We provide the first background data on the genetic structure of S. pneumoniae causing IPD prior to PC7V use in The Gambia. This data will be important for assessing the impact of PC7V in post-vaccine surveillance from The Gambia.

Figure 1

BOX-PCR fingerprint patterns of invasive paediatric S. pneumoniae isolates collected during the PVT trial. (a) PCR fingerprint patterns generated with BOX primer. Lanes 2–10 contained serotypes found in the 9-valent vaccine (1, 4, 5, 6B, 9V, 14, 18C, 19F & 23F) respectively. Lanes 1 &12 contained a molecular weight standard; 100-bp and 1 kb respectively. Lane 11; negative (no DNA) control. (b) BOX-PCR fingerprint patterns of invasive pneumococcal serotype 1 collected during the PVT trial. Lanes 2–9 &11 contained serotypes 1 isolates. Lane 1 contained a 1 kb molecular weight standard and lane 10 a negative (no DNA) control. There are two BOX-PCR fingerprint profiles designated A and B.

Figure 2

Clustering of STs by use of the minimum spanning tree. Each circle represents an ST, and the serotype number is indicated in the circle. The area of each circle corresponds to the number of isolates. Thick, short, solid lines connect single-locus variants and thin, longer, solid lines connect double-locus variants. Each colour represents the source of isolates. Source: LA (lung aspirate), CSF (cerebrospinal fluid), VB (venous blood), and PE (pleural effusion).

Figure 3

Dendrogram showing the relatedness among the STs and serotypes of S. pneumoniae by use of UPGMA from BOX-PCR. Notes: Antimicrobial patterns: pen (penicillin G); amp (ampicillin), chlo (chloramphenicol), cotr (cotrimoxazole tetr (tetracycline) and cefo (cefotaxime); Source: LA (lung aspirate), CSF (cerebrospinal fluid), VB (venous blood), and PE (pleural effusion).

Figure 4

Dendrogram showing the relatedness among the STs and serotypes of S. pneumoniae by use of UPGMA from BOX-PCR. Notes: Antimicrobial patterns: pen (penicillin G); amp (ampicillin), chlo (chloramphenicol), cotr (cotrimoxazole tetr (tetracycline) and cefo (cefotaxime); Source: LA (lung aspirate), CSF (cerebrospinal fluid), VB (venous blood), and PE (pleural effusion).