Phylogenetic Analysis of Invasive Serotype 1 Pneumococcus in South Africa, 1989-2013.

du Plessis M1, Allam M2, Tempia S3, Wolter N4, de Gouveia L2, Mollendorf CV5, Jolley KA6, Mbelle N7, Wadula J8, Cornick JE9, Everett DB9, McGee L10,Breiman RF11, Gladstone RA12, Bentley SD12, Klugman KP13, von Gottberg A4.

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Abstract

BACKGROUND:

Serotype 1 is an important cause of invasive pneumococcal disease in South Africa and has declined following introduction of the 13-valent pneumococcal conjugate vaccine in 2011.

METHODS:

We genetically characterized 912 invasive serotype 1 isolates from 1989-2013. Simpson's diversity index and recombination ratios were calculated. Factors associated with sequence types (ST) were assessed.

RESULTS:

Clonal complex 217 represented 96% (872/912) of sampled isolates. Post PCV13, ST diversity increased in children <5 years (0.39 to 0.63, p=0.002) and individuals >14 years (0.35 to 0.54, p<0.001): ST-217 declined proportionately in children <5 years [153/203 (75%) vs. 21/37 (57%), p=0.027], and individuals >14 years [242/305 (79%) vs. 96/148 (65%), p=0.001], whereas ST-9067 increased [4/684 (0.6%) vs. 24/228 (11%), p<0.001]. Three sub-clades 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 non-susceptibility to chloramphenicol, tetracycline and co-trimoxazole. ST-8314 (20/912, 2%) was also associated with increased non-susceptibility to penicillin (p<0.001). ST-217C3 and newly reported ST-9067 had higher recombination ratios compared to ST-217C1 (4.344 vs. 0.091, p<0.001 and 0.086 vs. 0.013, p<0.001, respectively).