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

Mignon Du Plessis, Mushal Allam, Stefano Tempia, Nicole Wolter, Linda De Gouveia, Claire Von Mollendorf, Keith A. Jolley, Nontombi Mbelle, Jeannette Wadula, Jennifer E. Cornick, Dean B. Everett, Lesley McGee, Robert F. Breiman, Rebecca A. Gladstone, Stephen D. Bentley, Keith P. Klugman, Anne Von Gottberg

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14 Scopus citations

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.

Original languageBritish English
Pages (from-to)1326-1334
Number of pages9
JournalJournal of Clinical Microbiology
Volume54
Issue number5
DOIs
StatePublished - May 2016

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