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

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.

Back to Previous Page

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

Published Date:

July 10 2020

Source:

Nat Commun. 11

Language:

English

[PDF-1.62 MB]

Details:

Alternative Title:

Nat Commun

Personal Author:

Chaguza, Chrispin ; Senghore, Madikay ; Bojang, Ebrima ; Gladstone, Rebecca A. ; Lo, Stephanie W. ; ... More ▼

Description:

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.

Subject:

[+]

Pubmed ID:

32651390

Pubmed Central ID:

PMC7351774

Document Type:

Journal Article

Funding:

WT_/Wellcome Trust/United Kingdom ; MRC_/Medical Research Council/United Kingdom ;

Collection(s):

CDC Public Access

Main Document Checksum:

[+]

File Type:

Supporting Files:

	41467_2020_17327_Fig5_HTML.gif	image/gif
	41467_2020_17327_Fig5_HTML.jpg	image/jpeg
	41467_2020_17327_Fig6_HTML.gif	image/gif
	41467_2020_17327_Fig6_HTML.jpg	image/jpeg
	41467_2020_17327_Fig7_HTML.gif	image/gif
	41467_2020_17327_Fig7_HTML.jpg	image/jpeg
	41467_2020_17327_Fig8_HTML.gif	image/gif
	41467_2020_17327_Fig8_HTML.jpg	image/jpeg
	41467_2020_17327_MOESM10_ESM.xlsx	application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
	41467_2020_17327_MOESM11_ESM.xlsx	application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
	41467_2020_17327_Fig1_HTML.gif	image/gif
	41467_2020_17327_MOESM12_ESM.xlsx	application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
	41467_2020_17327_MOESM1_ESM.pdf	application/pdf
	41467_2020_17327_MOESM2_ESM.pdf	application/pdf
	41467_2020_17327_MOESM3_ESM.pdf	application/pdf
	41467_2020_17327_MOESM4_ESM.pdf	application/pdf
	41467_2020_17327_MOESM5_ESM.xlsx	application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
	41467_2020_17327_MOESM6_ESM.xlsx	application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
	41467_2020_17327_MOESM7_ESM.xlsx	application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
	41467_2020_17327_MOESM8_ESM.xlsx	application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
	41467_2020_17327_MOESM9_ESM.xlsx	application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
	41467_2020_17327_Fig1_HTML.jpg	image/jpeg
	41467_2020_Article_17327.nxml	text/xml
	41467_2020_17327_Fig2_HTML.gif	image/gif