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Pneumococcal within-host diversity during colonization, transmission and treatment

Tonkin-Hill, Gerry; Ling, Clare; Chaguza, Chrispin; Salter, Susannah J; Hinfonthong, Pattaraporn; Nikolaou, Elissavet; Tate, Natalie; ... Bentley, Stephen D; + view all (2022) Pneumococcal within-host diversity during colonization, transmission and treatment. Nature Microbiology , 7 pp. 1791-1804. 10.1038/s41564-022-01238-1. Green open access

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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.

Type: Article
Title: Pneumococcal within-host diversity during colonization, transmission and treatment
Location: England
Open access status: An open access version is available from UCL Discovery
DOI: 10.1038/s41564-022-01238-1
Publisher version: https://doi.org/10.1038/s41564-022-01238-1
Language: English
Additional information: This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
Keywords: Science & Technology, Life Sciences & Biomedicine, Microbiology, STREPTOCOCCUS-PNEUMONIAE, HAEMOPHILUS-INFLUENZAE, POPULATION, EVOLUTION, CHILDREN, AGGLUTINATION, MECHANISMS, SEROTYPES, SELECTION, PATHOGEN
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Div of Infection and Immunity
URI: https://discovery.ucl.ac.uk/id/eprint/10160970
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