High Levels of Recombination among Streptococcus pneumoniae Isolates from the Gambia

We carried out multilocus sequence typing (MLST) on 148 pneumococcal carriage isolates collected from children <24 months old in the Upper River Division, the Gambia. MLST revealed a diverse population. Seventy-six different sequence types (STs) were found, the most common of which were 802 and 919, associated with 23F and 6A serotypes, respectively. Comparison with the MLST database showed that only 11 of the STs found in the present sample had been reported outside Africa. Six STs showed evidence of capsular switching (172, 802, 847, 1730, 1736, and 1737). Serotype switches were confirmed by microarrays that detected capsule genes. Of isolates analyzed by using microarrays, 40/69 (58%) harbored the tetM resistance determinant. A statistical genetic analysis to detect recombination found that 49/144 (34%) isolates showed significant (P < 0.05) evidence of admixture, which is greater than that observed in similar samples from the United Kingdom (5%) and Finland (2%). We hypothesize that large amounts of admixture could reflect the high prevalence of multiple carriage in this region, leading to more opportunities for homologous recombination between strains. This could have consequences for the population response to conjugate vaccination.