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

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Senghore, Madikay 
Bojang, Ebrima 
Gladstone, Rebecca A 
Lo, Stephanie W 


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.


Funder: Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)


Evolution, Molecular, Genetics, Genome, Bacterial, Humans, Pneumococcal Infections, Streptococcus pneumoniae, Whole Genome Sequencing

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Nat Commun

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Springer Science and Business Media LLC
Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation) (OPP1034556, OPP1034556, OPP1034556)