Impact of pneumococcal conjugate vaccines on invasive pneumococcal disease-causing lineages among South African children
Invasive pneumococcal disease (IPD) due to non-vaccine serotypes after the introduction of pneumococcal conjugate vaccines (PCV) remains a global concern. This study used pathogen genomics to evaluate changes in invasive pneumococcal lineages before, during and after vaccine introduction in South Africa. We included genomes (N = 3104) of IPD isolates from individuals aged <18 years (2005-20), spanning four periods: pre-PCV, PCV7, early-PCV13, and late-PCV13. Significant incidence reductions occurred among vaccine-type lineages in the late-PCV13 period compared to the pre-PCV period. However, some vaccine-type lineages continued to cause invasive disease and showed increasing effective population size trends in the post-PCV era. A significant increase in lineage diversity was observed from the PCV7 period to the early-PCV13 period (Simpson's diversity index: 0.954, 95% confidence interval 0.948-0.961 vs 0.965, 0.962-0.969) supporting intervention-driven population structure perturbation. Increases in the prevalence of penicillin, erythromycin, and multidrug resistance were observed among non-vaccine serotypes in the late-PCV13 period compared to the pre-PCV period. In this work we highlight the importance of continued genomic surveillance to monitor disease-causing lineages post vaccination to support policy-making and future vaccine designs and considerations.
Authors
- Scott Hazelhurst (ORCID: https://orcid.org/0000-0002-0581-149X)
- Jackie Kleynhans (ORCID: https://orcid.org/0000-0001-7081-6273)
- Linda de Gouveia (ORCID: https://orcid.org/0000-0002-1418-8468)
- Stephanie W. Lo (ORCID: https://orcid.org/0000-0002-2182-0222)
- Susan Meiring (ORCID: https://orcid.org/0000-0003-4508-5469)
- Lesley McGee (ORCID: https://orcid.org/0000-0001-8214-921X)
- Vanessa Quan (ORCID: https://orcid.org/0000-0003-1666-4752)
- Cebile Lekhuleni (ORCID: https://orcid.org/0000-0002-1264-2284)
- Kedibone Ndlangisa (ORCID: https://orcid.org/0000-0001-6441-2539)
- Rebecca Ashley Gladstone (ORCID: https://orcid.org/0000-0002-7993-3051)
- Benjamin J. Metcalf (ORCID: https://orcid.org/0000-0002-9628-2051)
- Anne von Gottberg (ORCID: https://orcid.org/0000-0002-0243-7455)
- Mignon du Plessis (ORCID: https://orcid.org/0000-0001-9186-0679)
- Sopio Chochua (ORCID: https://orcid.org/0000-0001-8222-7353)
- Sibongile Walaza (ORCID: https://orcid.org/0000-0001-7588-2480)
- Stephen D. Bentley (ORCID: https://orcid.org/0000-0001-8094-3751)
- Paulina A. Hawkins (ORCID: https://orcid.org/0000-0001-5096-392X)
- Happy Skosana
- Cheryl Cohen (ORCID: https://orcid.org/0000-0003-0376-2302)
- Yuan Li (ORCID: https://orcid.org/0000-0002-2331-2694)
- Ana D S Ferreira
Institutions
- National Health Laboratory Service (ZA)
- Centers for Disease Control and Prevention (US)
- University of Cape Town (ZA)
- University of Oslo (NO)
- University of the Witwatersrand (ZA)
- Wellcome Sanger Institute (GB)
- University of Bath (GB)
Publication Details
- Journal
- Nature Communications
- Published
- 2024-09-27
- DOI
- https://doi.org/10.1038/s41467-024-52459-3
- Citations
- 15
- Primary Topic
- Pneumonia and Respiratory Infections
- Type
- article
- Field-Weighted Citation Impact
- 5.80
Funders
- Bill and Melinda Gates Foundation
- Wellcome
- University of Pittsburgh
- Wellcome Trust
- Department of Health and Social Care
- National Institutes of Health
- Fogarty International Center