TY - JOUR
T1 - Phylogenetic analysis of invasive serotype 1 pneumococcus in South Africa, 1989 to 2013
AU - Du Plessis, Mignon
AU - Allam, Mushal
AU - Tempia, Stefano
AU - Wolter, Nicole
AU - De Gouveia, Linda
AU - Von Mollendorf, Claire
AU - Jolley, Keith A.
AU - Mbelle, Nontombi
AU - Wadula, Jeannette
AU - Cornick, Jennifer E.
AU - Everett, Dean B.
AU - McGee, Lesley
AU - Breiman, Robert F.
AU - Gladstone, Rebecca A.
AU - Bentley, Stephen D.
AU - Klugman, Keith P.
AU - Von Gottberg, Anne
N1 - Funding Information:
This work, including the efforts of Mignon du Plessis, Nicole Wolter, and Anne von Gottberg, was funded by Pfizer Vaccines Reseach (IIR #WS116752). This work, including the efforts of Mignon du Plessis, Mushal Allam, Nicole Wolter, Linda de Gouveia, Jennifer Cornick, Dean Everett, Lesley McGee, Robert F. Breiman, Rebecca A Gladstone, Stephen Bentley, Keith P Klugman, and Anne von Gottberg, was funded by Bill and Melinda Gates Foundation (OPP1034556 and OPP1023440).
Publisher Copyright:
Copyright © 2016 du Plessis et al.
PY - 2016/5
Y1 - 2016/5
N2 - 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.
AB - 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.
UR - https://www.scopus.com/pages/publications/84964932893
U2 - 10.1128/JCM.00055-16
DO - 10.1128/JCM.00055-16
M3 - Article
C2 - 26962082
AN - SCOPUS:84964932893
SN - 0095-1137
VL - 54
SP - 1326
EP - 1334
JO - Journal of Clinical Microbiology
JF - Journal of Clinical Microbiology
IS - 5
ER -