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Corresponding authors: E-mails: cc19@sanger.ac.uk; Martin.Antonio@lshtm.ac.uk; sdb@sanger.ac.uk.
C.C., M.A., and S.D.B. conceived the analysis. B.A.K.-A., C.E., M.S., P.-E.T., and M.A. conducted the field studies and sample collection. C.E., P.-E.T., M.S., B.A.K.-A., and M.A. conducted the surveillance and bacteriology work. S.D.B. led the genome sequencing work and supervised data analysis. R.A.G. and S.W.L. performed quality checks and genomic-based serotyping and sequence typing work. C.C. performed data analysis. G.T.-H., N.J.C., and S.D.B. contributed to the discussions on the GWAS analysis. C.C. and S.D.B. wrote the initial draft of the manuscript. C.C., C.E., M.Y., P.-E.T., G.T.-H., M.S., S.W.L., J.E.C., A.W., R.A.G., R.F.B., L.M., K.P.K., D.B.E., G.M., N.J.C., A.R., A.K., B.A.K.-A., M.A., and S.D.B. reviewed the manuscript.
The authors thank the study participants and guardians, microbiology team at the Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, and the library construction, sequence, and core informatics teams, and the pathogen informatics for their technical support, and the Bentley lab team at the Wellcome Sanger Institute for discussions.
We would also like to thank Dr. Claire Chewapreecha from Mahidol-Oxford Tropical Medicine Research Unit (MORU) for the advice regarding ancestral state reconstruction, and Dr. Yuan Li at the US Centers for Disease Control and Prevention (CDC) for providing feedback on the manuscript.
We acknowledge funding from the MRC The Gambia @LSHTM and the Bill and Melinda Gates Foundation (grant numbers: OPP1023440 and OPP1034556), the Joint Programme Initiative for Antimicrobial Resistance (JPIAMR) (grant no. MR/R003076/1), and Wellcome Trust (2016–2021 core award grant no. 206194).
© The Author(s) 2022. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.