Within-host microevolution of Streptococcus pneumoniae is rapid and adaptive during natural colonisation

Chrispin Chaguza (), Madikay Senghore, Ebrima Bojang, Rebecca A. Gladstone, Stephanie W. Lo, Peggy-Estelle Tientcheu, Rowan E. Bancroft, Archibald Worwui, Ebenezer Foster-Nyarko, Fatima Ceesay, Catherine Okoi, Lesley McGee, Keith P. Klugman, Robert F. Breiman, Michael R. Barer, Richard A. Adegbola, Martin Antonio, Stephen D. Bentley () and Brenda A. Kwambana-Adams ()
Additional contact information
Chrispin Chaguza: Wellcome Genome Campus
Madikay Senghore: Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine
Ebrima Bojang: Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine
Rebecca A. Gladstone: Wellcome Genome Campus
Stephanie W. Lo: Wellcome Genome Campus
Peggy-Estelle Tientcheu: Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine
Rowan E. Bancroft: Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine
Archibald Worwui: Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine
Ebenezer Foster-Nyarko: Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine
Fatima Ceesay: Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine
Catherine Okoi: Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine
Lesley McGee: Centers for Disease Control and Prevention
Keith P. Klugman: Emory University
Robert F. Breiman: Emory University
Michael R. Barer: University of Leicester
Richard A. Adegbola: RAMBICON Immunisation & Global Health Consulting, 6A Platinum Close
Martin Antonio: Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine
Stephen D. Bentley: Wellcome Genome Campus
Brenda A. Kwambana-Adams: Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine

Nature Communications, 2020, vol. 11, issue 1, 1-14

Abstract: Abstract Genomic evolution, transmission and pathogenesis of Streptococcus pneumoniae, an opportunistic human-adapted pathogen, is driven principally by nasopharyngeal carriage. However, little is known about genomic changes during natural colonisation. Here, we use whole-genome sequencing to investigate within-host microevolution of naturally carried pneumococci in ninety-eight infants intensively sampled sequentially from birth until twelve months in a high-carriage African setting. We show that neutral evolution and nucleotide substitution rates up to forty-fold faster than observed over longer timescales in S. pneumoniae and other bacteria drives high within-host pneumococcal genetic diversity. Highly divergent co-existing strain variants emerge during colonisation episodes through real-time intra-host homologous recombination while the rest are co-transmitted or acquired independently during multiple colonisation episodes. Genic and intergenic parallel evolution occur particularly in antibiotic resistance, immune evasion and epithelial adhesion genes. Our findings suggest that within-host microevolution is rapid and adaptive during natural colonisation.

Date: 2020
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DOI: 10.1038/s41467-020-17327-w

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