Pneumococcal within-host diversity during colonization, transmission and treatment
Issued Date
2022-11-01
Resource Type
eISSN
20585276
Scopus ID
2-s2.0-85139616122
Pubmed ID
36216891
Journal Title
Nature Microbiology
Volume
7
Issue
11
Start Page
1791
End Page
1804
Rights Holder(s)
SCOPUS
Bibliographic Citation
Nature Microbiology Vol.7 No.11 (2022) , 1791-1804
Suggested Citation
Tonkin-Hill G., Ling C., Chaguza C., Salter S.J., Hinfonthong P., Nikolaou E., Tate N., Pastusiak A., Turner C., Chewapreecha C., Frost S.D.W., Corander J., Croucher N.J., Turner P., Bentley S.D. Pneumococcal within-host diversity during colonization, transmission and treatment. Nature Microbiology Vol.7 No.11 (2022) , 1791-1804. 1804. doi:10.1038/s41564-022-01238-1 Retrieved from: https://repository.li.mahidol.ac.th/handle/20.500.14594/83570
Title
Pneumococcal within-host diversity during colonization, transmission and treatment
Author's Affiliation
Angkor Hospital for Children
Faculty of Tropical Medicine, Mahidol University
Department of Veterinary Medicine
The Peter Doherty Institute for Infection and Immunity
London School of Hygiene & Tropical Medicine
Microsoft Research
Liverpool School of Tropical Medicine
Imperial College London
Universitetet i Oslo
Murdoch Children's Research Institute
Nuffield Department of Medicine
Wellcome Sanger Institute
Yale University
Helsingin Yliopisto
Faculty of Tropical Medicine, Mahidol University
Department of Veterinary Medicine
The Peter Doherty Institute for Infection and Immunity
London School of Hygiene & Tropical Medicine
Microsoft Research
Liverpool School of Tropical Medicine
Imperial College London
Universitetet i Oslo
Murdoch Children's Research Institute
Nuffield Department of Medicine
Wellcome Sanger Institute
Yale University
Helsingin Yliopisto
Other Contributor(s)
Abstract
Characterizing the genetic diversity of pathogens within the host promises to greatly improve surveillance and reconstruction of transmission chains. For bacteria, it also informs our understanding of inter-strain competition and how this shapes the distribution of resistant and sensitive bacteria. Here we study the genetic diversity of Streptococcus pneumoniae within 468 infants and 145 of their mothers by deep sequencing whole pneumococcal populations from 3,761 longitudinal nasopharyngeal samples. We demonstrate that deep sequencing has unsurpassed sensitivity for detecting multiple colonization, doubling the rate at which highly invasive serotype 1 bacteria were detected in carriage compared with gold-standard methods. The greater resolution identified an elevated rate of transmission from mothers to their children in the first year of the child’s life. Comprehensive treatment data demonstrated that infants were at an elevated risk of both the acquisition and persistent colonization of a multidrug-resistant bacterium following antimicrobial treatment. Some alleles were enriched after antimicrobial treatment, suggesting that they aided persistence, but generally purifying selection dominated within-host evolution. Rates of co-colonization imply that in the absence of treatment, susceptible lineages outcompeted resistant lineages within the host. These results demonstrate the many benefits of deep sequencing for the genomic surveillance of bacterial pathogens.