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Nat Genet. 2014 Mar;46(3):305-309. doi: 10.1038/ng.2895. Epub 2014 Feb 9.

Dense genomic sampling identifies highways of pneumococcal recombination.

Author information

The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
Department of Infectious Disease Epidemiology, Imperial College London, St. Mary's Hospital, London, W2 1PG, UK.
Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Maesot 63110, Thailand.
Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia.
Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7LJ, UK.
Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University, 00076, Finland.
Department of Mathematics and Statistics, University of Helsinki, 00014, Finland.
Immunobiology Unit, Institute of Child Health, University College London, WC1N 1EH, UK.
Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK.
Contributed equally


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-km(2) 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.

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