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Abstract

(the pneumococcus) is a leading cause of childhood mortality globally and in Cambodia. It is commensal in the human nasopharynx, occasionally resulting in invasive disease. Monitoring population genetic shifts, characterized by lineage and serotype expansions, as well as antimicrobial-resistance (AMR) patterns is crucial for assessing and predicting the impact of vaccination campaigns. We sought to elucidate the genetic background (global pneumococcal sequence clusters; GPSCs) of pneumococci carried by Cambodian children following perturbation by pneumococcal conjugate vaccine (PCV) 13. We sequenced pre-PCV13 (01/2013–12/2015, =258) and post-PCV13 carriage isolates (01/2016–02/2017, =428) and used PopPUNK and SeroBA to determine lineage prevalence and serotype composition. Following PCV13 implementation in Cambodia, we saw expansions of non-vaccine type (NVT) serotypes 23A (GPSC626), 34 (GPSC45) and 6D (GPSC16). We predicted antimicrobial susceptibility using the CDC-AMR pipeline and determined concordance with phenotypic data. The CDC-AMR pipeline had >90 % concordance with the phenotypic antimicrobial-susceptibility testing. We detected a high prevalence of AMR in both expanding non-vaccine serotypes and residual vaccine serotype 6B. Persistently high levels of AMR, specifically persisting multidrug-resistant lineages, warrant concern. The implementation of PCV13 in Cambodia has resulted in NVT serotype expansion reflected in the carriage population and driven by specific genetic backgrounds. Continued monitoring of these GPSCs during the ongoing collection of additional carriage isolates in this population is necessary.

Funding
This study was supported by the:
  • Wellcome Trust (Award 220211)
    • Principle Award Recipient: PaulTurner
  • Wellcome Trust (Award 206194)
    • Principle Award Recipient: StephenD Bentley
  • Wellcome Trust (Award 098051)
    • Principle Award Recipient: StephenD Bentley
  • Bill and Melinda Gates Foundation (Award OPP1034556)
    • Principle Award Recipient: StephenD Bentley
  • This is an open-access article distributed under the terms of the Creative Commons Attribution NonCommercial License.
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2022-06-28
2024-06-13
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