Nature Communications (Sep 2024)

Impact of pneumococcal conjugate vaccines on invasive pneumococcal disease-causing lineages among South African children

  • Cebile Lekhuleni,
  • Kedibone Ndlangisa,
  • Rebecca A. Gladstone,
  • Sopio Chochua,
  • Benjamin J. Metcalf,
  • Yuan Li,
  • Jackie Kleynhans,
  • Linda de Gouveia,
  • Scott Hazelhurst,
  • Ana D. S. Ferreira,
  • Happy Skosana,
  • Sibongile Walaza,
  • Vanessa Quan,
  • Susan Meiring,
  • Paulina A. Hawkins,
  • Lesley McGee,
  • Stephen D. Bentley,
  • Cheryl Cohen,
  • Stephanie W. Lo,
  • Anne von Gottberg,
  • Mignon du Plessis

DOI
https://doi.org/10.1038/s41467-024-52459-3
Journal volume & issue
Vol. 15, no. 1
pp. 1 – 12

Abstract

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Abstract 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.