Dense genomic sampling identifies highways of pneumococcal recombination

Claire Chewapreecha, Simon R. Harris, Nicholas J. Croucher, Claudia Turner, Pekka Marttinen, Lu Cheng, Alberto Pessia, David M. Aanensen, Alison E. Mather, Andrew J. Page, Susannah J. Salter, David Harris, Francois Nosten, David Goldblatt, Jukka Corander, Julian Parkhill, Paul Turner, Stephen D. Bentley

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267 Citations (Scopus)


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.
Original languageEnglish
Pages (from-to)305-309
Number of pages5
JournalNature Genetics
Issue number3
Early online date9 Feb 2014
Publication statusPublished - 1 Mar 2014

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