Dense genomic sampling identifies highways of pneumococcal recombination

Chewapreecha, Claire, Harris, Simon R, Croucher, Nicholas J, Turner, Claudia, Marttinen, Pekka, Cheng, Lu, Pessia, Alberto, Aanensen, David M, Mather, Alison E, Page, Andrew J, Salter, Susannah J, Harris, David, Nosten, Francois, Goldblatt, David, Corander, Jukka, Parkhill, Julian, Turner, Paul and Bentley, Stephen D (2014) Dense genomic sampling identifies highways of pneumococcal recombination. Nature Genetics, 46 (3). pp. 305-309. ISSN 1061-4036

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Abstract

Evasion of clinical interventions by Streptococcus pneumoniae occurs through selection of non-susceptible genomic variants. We report whole-genome sequencing of 3,085 pneumococcal carriage isolates from a 2.4-km2 refugee camp. This sequencing provides unprecedented resolution of the process of recombination and its impact on population evolution. Genomic recombination hotspots show remarkable consistency between lineages, indicating common selective pressures acting at certain loci, particularly those associated with antibiotic resistance. Temporal changes in antibiotic consumption are reflected in changes in recombination trends, demonstrating rapid spread of resistance when selective pressure is high. The highest frequencies of receipt and donation of recombined DNA fragments were observed in non-encapsulated lineages, implying that this largely overlooked pneumococcal group, which is beyond the reach of current vaccines, may have a major role in genetic exchange and the adaptation of the species as a whole. These findings advance understanding of pneumococcal population dynamics and provide information for the design of future intervention strategies.

Item Type: Article
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Depositing User: LivePure Connector
Date Deposited: 24 Apr 2019 11:30
Last Modified: 13 May 2020 23:58
URI: https://ueaeprints.uea.ac.uk/id/eprint/70671
DOI: 10.1038/ng.2895

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