TY - JOUR
T1 - Within-host microevolution of Streptococcus pneumoniae is rapid and adaptive during natural colonisation
AU - Chaguza, Chrispin
AU - Senghore, Madikay
AU - Bojang, Ebrima
AU - Gladstone, Rebecca A
AU - Lo, Stephanie W
AU - Tientcheu, Peggy-Estelle
AU - Bancroft, Rowan E
AU - Worwui, Archibald
AU - Foster-Nyarko, Ebenezer
AU - Ceesay, Fatima
AU - Okoi, Catherine
AU - McGee, Lesley
AU - Klugman, Keith P
AU - Breiman, Robert F
AU - Barer, Michael R
AU - Adegbola, Richard A
AU - Antonio, Martin
AU - Bentley, Stephen D
AU - Kwambana-Adams, Brenda A
PY - 2020/7/10
Y1 - 2020/7/10
N2 - 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.
AB - 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.
KW - Evolution, Molecular
KW - Genetics
KW - Genome, Bacterial/genetics
KW - Humans
KW - Pneumococcal Infections/genetics
KW - Streptococcus pneumoniae/genetics
KW - Whole Genome Sequencing
U2 - 10.1038/s41467-020-17327-w
DO - 10.1038/s41467-020-17327-w
M3 - Article
C2 - 32651390
SN - 2041-1723
VL - 11
SP - 3442
JO - Nature Communications
JF - Nature Communications
IS - 1
ER -