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

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 wi...

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Bibliographic Details
Published in:Nature communications Vol. 11; no. 1; pp. 3442 - 14
Main Authors: Chaguza, Chrispin, Senghore, Madikay, Bojang, Ebrima, Gladstone, Rebecca A., Lo, Stephanie W., Tientcheu, Peggy-Estelle, Bancroft, Rowan E., Worwui, Archibald, Foster-Nyarko, Ebenezer, Ceesay, Fatima, Okoi, Catherine, McGee, Lesley, Klugman, Keith P., Breiman, Robert F., Barer, Michael R., Adegbola, Richard A., Antonio, Martin, Bentley, Stephen D., Kwambana-Adams, Brenda A.
Format: Journal Article
Language:English
Published: London Nature Publishing Group UK 10.07.2020
Nature Publishing Group
Nature Portfolio
Subjects:
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
ISSN:2041-1723, 2041-1723
Online Access:Get full text
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Summary: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.
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ISSN:2041-1723
2041-1723
DOI:10.1038/s41467-020-17327-w