Journal Article

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

Barer, Michael R., Worwui, Archibald, Bojang, Ebrima, Senghore, Madikay, Okoi, Catherine, Tientcheu, Peggy-Estelle, Bancroft, Rowan E., Chaguza, Chrispin, Gladstone, Rebecca A., Kwambana-Adams, Brenda A., Breiman, Robert F., Ceesay, Fatima, McGee, Lesley, Adegbola, Richard A., Bentley, Stephen D., Antonio, Martin, Lo, Stephanie W., Foster-Nyarko, Ebenezer, Klugman, Keith P.

2020

Overview

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. Streptococcus pneumoniae is an opportunistic pathogen and asymptomatic colonization is a precursor for invasive disease. Here the authors show rapid within-host evolution of naturally acquired pneumococci in ninety-eight infants driven by high nucleotide substitution rates and intra-host homologous recombination.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 13 / 45 / 45/23 / 631/208/212/2304 / 631/208/325/2482 / 631/326/107 / 692/308/3187 / Antibiotic resistance / Antibiotics / Colonization / Divergence / Drug resistance / Evolution / Evolution, Molecular / Evolutionary genetics / Gene sequencing / Genetic diversity / Genetics / Genome, Bacterial - genetics / Genomes / Genomics / Homologous recombination / Homology / Humanities and Social Sciences / Humans / Infants / multidisciplinary / Nucleotides / Opportunist infection / Pathogenesis / Pathogens / Pneumococcal Infections - genetics / Science / Science (multidisciplinary) / Streptococcus infections / Streptococcus pneumoniae / Streptococcus pneumoniae - genetics / Substitutes / Whole Genome Sequencing