Population genomics of pneumococcal carriage in South Africa following the introduction of the 13-valent pneumococcal conjugate vaccine (PCV13) immunization

Nida Javaid, Courtney Olwagen, Susan Nzenze, Paulina Hawkins, Rebecca Gladstone, Lesley McGee, Robert F Breiman, Stephen D Bentley, Shabir A Madhi, Stephanie Lo

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6 Citations (SciVal)


Streptococcus pneumoniae is a major human pathogen responsible for over 317000 deaths in children <5 years of age with the burden of the disease being highest in low- and middle-income countries including South Africa. Following the introduction of the 7-valent and 13-valent pneumococcal conjugate vaccine (PCV) in South Africa in 2009 and 2011, respectively, a decrease in both invasive pneumococcal infections and asymptomatic carriage of vaccine-type pneumococci were reported. In this study, we described the changing epidemiology of the pneumococcal carriage population in South Africa, by sequencing the genomes of 1825 isolates collected between 2009 and 2013. Using these genomic data, we reported the changes in serotypes, Global Pneumococcal Sequence Clusters (GPSCs), and antibiotic resistance before and after the introduction of PCV13. The pneumococcal carriage population in South Africa has a high level of diversity, comprising of 126 GPSCs and 49 serotypes. Of the ten most prevalent GPSCs detected, six were predominantly found in Africa (GPSC22, GPSC21, GPSC17, GPSC33, GPSC34 and GPSC52). We found a significant decrease in PCV7 serotypes (19F, 6B, 23F and 14) and an increase in non-vaccine serotypes (NVT) (16F, 34, 35B and 11A) among children <2 years of age. The increase in NVTs was driven by pneumococcal lineages GPSC33, GPSC34, GPSC5 and GPSC22. Overall, a decrease in antibiotic resistance for 11 antimicrobials was detected in the PCV13 era. Further, we reported a higher resistance prevalence among vaccine types (VTs), as compared to NVTs; however, an increase in penicillin resistance among NVT was observed between the PCV7 and PCV13 eras. The carriage isolates from South Africa predominantly belonged to pneumococcal lineages, which are endemic to Africa. While the introduction of PCV resulted in an overall reduction of resistance in pneumococcal carriage isolates, an increase in penicillin resistance among NVTs was detected in children aged between 3 and 5 years, driven by the expansion of penicillin-resistant clones associated with NVTs in the PCV13 era.

Original languageEnglish
Article number000831
Number of pages9
JournalMicrobial Genomics
Issue number6
Publication statusPublished - 23 Jun 2022

Bibliographical note

Acknowledgements: We would like to acknowledge Higher Education Commission, Pakistan and Lahore University of Management Sciences for funding Nida Javaid during her fellowship at Wellcome Sanger Institute through international Research Support Initiative Programme and Dr. Shaper Mirza’s grant, respectively. We would also like to thank all members of The Global Pneumococcal Sequencing Consortium for their collaborative spirit and determination during the monumental task of sampling, extracting and sequencing this dataset, and all contributions to experimental design and input into this manuscript. We also would like to thank Wellcome Sanger Institute sequencing facility and Pathogen Informatics Team at the Wellcome Sanger Institute for their technical supports. For the purpose of Open Access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.

Data statement: All supporting data, code and protocols have been provided within the article or through supplementary data files. Ten supplementary
tables and four supplementary figures are available with the online version of this article.


  • Carrier State/epidemiology
  • Child
  • Child, Preschool
  • Humans
  • Immunization
  • Metagenomics
  • Nasopharynx
  • South Africa/epidemiology
  • Streptococcus pneumoniae/genetics
  • Vaccines, Conjugate


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