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Volume 7, Issue 7

Phylogeography and resistome of pneumococcal meningitis in West Africa before and after vaccine introduction Open Access

Abstract

Despite contributing to the large disease burden in West Africa, little is known about the genomic epidemiology of which cause meningitis among children under 5 years old in the region. We analysed whole-genome sequencing data from 185 . isolates recovered from suspected paediatric meningitis cases as part of the World Health Organization (WHO) invasive bacterial diseases surveillance from 2010 to 2016. The phylogeny was reconstructed, accessory genome similarity was computed and antimicrobial-resistance patterns were inferred from the genome data and compared to phenotypic resistance from disc diffusion. We studied the changes in the distribution of serotypes pre- and post-pneumococcal conjugate vaccine (PCV) introduction in the Central and Western sub-regions separately. The overall distribution of non-vaccine, PCV7 (4, 6B, 9V, 14, 18C, 19F and 23F) and additional PCV13 serotypes (1, 3, 5, 6A, 19A and 7F) did not change significantly before and after PCV introduction in the Central region (Fisher's test value 0.27) despite an increase in the proportion of non-vaccine serotypes to 40 % (=6) in the post-PCV introduction period compared to 21.9 % (=14). In the Western sub-region, PCV13 serotypes were more dominant among isolates from The Gambia following the introduction of PCV7, 81 % (=17), compared to the pre-PCV period in neighbouring Senegal, 51 % (=27). The phylogeny illustrated the diversity of strains associated with paediatric meningitis in West Africa and highlighted the existence of phylogeographical clustering, with isolates from the same sub-region clustering and sharing similar accessory genome content. Antibiotic-resistance genotypes known to confer resistance to penicillin, chloramphenicol, co-trimoxazole and tetracycline were detected across all sub-regions. However, there was no discernible trend linking the presence of resistance genotypes with the vaccine introduction period or whether the strain was a vaccine or non-vaccine serotype. Resistance genotypes appeared to be conserved within selected sub-clades of the phylogenetic tree, suggesting clonal inheritance. Our data underscore the need for continued surveillance on the emergence of non-vaccine serotypes as well as chloramphenicol and penicillin resistance, as these antibiotics are likely still being used for empirical treatment in low-resource settings. This article contains data hosted by Microreact.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): antibiotic resistance , genomic epidemiology , paediatric meningitis , pneumococcus and West and Central Africa
Funding
This study was supported by the:
  • Bill and Melinda Gates Foundation (Award OPP1034556)
    • Principal Award Recipient: StephenD. Bentley
© 2021 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2021-07-30
2025-12-16

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Phylogeography and resistome of pneumococcal meningitis in West Africa before and after vaccine introduction
M Gen 7, 000506 (2021); https://doi.org/10.1099/mgen.0.000506
/content/journal/mgen/10.1099/mgen.0.000506
/content/journal/mgen/10.1099/mgen.0.000506
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