Phylogenetic analysis of invasive serotype 1 pneumococcus in South Africa, 1989 to 2013

Abstract

Serotype 1 is an important cause of invasive pneumococcal disease in South Africa and has declined following the introduction of the 13-valent pneumococcal conjugate vaccine in 2011. We genetically characterized 912 invasive serotype 1 isolates from 1989 to 2013. Simpson's diversity index (D) and recombination ratios were calculated. Factors associated with sequence types (STs) were assessed. Clonal complex 217 represented 96% (872/912) of the sampled isolates. Following the introduction of the 13-valent pneumococcal conjugate vaccine (PCV13), ST diversity increased in children<5 years (D, 0.39 to 0.63, P=0.002) and individuals> 14 years (D, 0.35 to 0.54, P<0.001): ST-217 declined proportionately in children<5 years (153/203 [75%] versus 21/37 [57%], P=0.027) and individuals>14 years (242/305 [79%] versus 96/148 [65%], P=0.001), whereas ST-9067 increased (4/684 [0.6%] versus 24/228 [11%], P<0.001). Three subclades were identified within ST-217: ST-217C1 (353/382 [92%]), ST-217C2 (15/ 382 [4%]), and ST-217C3 (14/382 [4%]). ST-217C2 ST-217C3, and single-locus variant (SLV) ST-8314 (20/912 [2%]) were associated with nonsusceptibility to chloramphenicol, tetracycline, and co-trimoxazole. ST-8314 (20/912 [2%]) was also associated with increased nonsusceptibility to penicillin (P<0.001). ST-217C3 and newly reported ST-9067 had higher recombination ratios than those of ST-217C1 (4.344 versus 0.091, P<0.001; and 0.086 versus 0.013, P<0.001, respectively). Increases in genetic diversity were noted post-PCV13, and lineages associated with antimicrobial nonsusceptibility were identified.