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

• Type of Material: Article
• Authors: Mignon du Plessis, National Institute for Communicable Diseases, South Africa; Mushal Allam, National Institute for Communicable Diseases, South Africa; Stefano Tempia, National Institute for Communicable Diseases, South Africa; Nicole Wolter, National Institute for Communicable Diseases, South Africa; Linda de Gouveia, National Institute for Communicable Diseases, South Africa; Claire von Mollendorf, National Institute for Communicable Diseases, South Africa; Keith A. Jolley, University of Oxford; Nontombi Mbelle, Tshwane Academic Hospital; Jeannette Wadula, Chris Hani Baragwanath Academic Hospital; Jennifer E. Cornick, University of Liverpool; Dean B. Everett, University of Liverpool; Lesley McGee, Centers for Disease Control and Prevention; Robert Breiman, Emory University; Rebecca A. Gladstone, Wellcome Trust Sanger Institute; Stephen D. Bentley, Wellcome Trust Sanger Institute; Keith Klugman, Emory University; Anne von Gottberg, National Institute for Communicable Diseases, South Africa
• Language: English
• Date: 2016-05-01
• Publisher: American Society for Microbiology
• Publication Version: Final Published Version
• Copyright Statement: © 2016 du Plessis et al.
• License: Creative Commons Attribution 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.1128/JCM.00055-16
• Title of Journal or Parent Work: Journal of Clinical Microbiology
• ISSN: 0095-1137
• Volume: 54
• Issue: 5
• Start Page: 1326
• End Page: 1334
• Grant/Funding Information: National IPD surveillance was funded by the National Health Laboratory Service, Centers for Disease Control and Prevention (CDC), National Centre for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention (NCHHSTP), and Global AIDS Program Cooperative agreement no. U62/PSO022901.; Whole-genome sequencing was supported through the Pneumococcal African Genomics Consortium (PAGe) and the Global Pneumococcal Sequencing (GPS) project. Both projects were funded by the Bill & Melinda Gates Foundation (PAGe, grant OPP1023440; GPS, grant OPP1034556).; MLST was funded by Pfizer Vaccines Research through an Investigator-Initiated Research grant entitled “Investigation of vaccine effectiveness and the molecular epidemiology of Streptococcus pneumoniae causing disease in children before and after the introduction of the 7-valent pneumococcal vaccine in South Africa” and the Robert Austrian Research Award in Pneumococcal Vaccinology awarded at the 8th International Symposium on Pneumococci and Pneumococcal Diseases, Iguaçu Falls, Brazil, 11 to 15 March 2012.
• Keywords: MENINGITIS; UNITED-STATES; CONJUGATE VACCINE; CLONES; DISEASE; CHILDREN; EPIDEMIOLOGY; STREPTOCOCCUS-PNEUMONIAE; Microbiology; SEQUENCE TYPING DATA; ANTIBIOTIC-RESISTANCE; Life Sciences & Biomedicine
• Research Categories: Biology, Microbiology; Health Sciences, Public Health

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.