title: Dense genomic sampling identifies highways of pneumococcal recombination.
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-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.
authors: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
authors: Claire
authors: C
authors: Chewapreecha
authors: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
authors: Simon R
authors: SR
authors: Harris
authors: Department of Infectious Disease Epidemiology, Imperial College London, St. Mary's Hospital, London, W2 1PG, UK.
authors: Nicholas J
authors: NJ
authors: Croucher
authors: 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.
authors: Claudia
authors: C
authors: Turner
authors: Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University, 00076, Finland.
authors: Pekka
authors: P
authors: Marttinen
authors: Department of Mathematics and Statistics, University of Helsinki, 00014, Finland.
authors: Lu
authors: L
authors: Cheng
authors: Department of Mathematics and Statistics, University of Helsinki, 00014, Finland.
authors: Alberto
authors: A
authors: Pessia
authors: Department of Infectious Disease Epidemiology, Imperial College London, St. Mary's Hospital, London, W2 1PG, UK.
authors: David M
authors: DM
authors: Aanensen
authors: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
authors: Alison E
authors: AE
authors: Mather
authors: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
authors: Andrew J
authors: AJ
authors: Page
authors: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
authors: Susannah J
authors: SJ
authors: Salter
authors: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
authors: David
authors: D
authors: Harris
authors: Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Maesot 63110, Thailand.|Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7LJ, UK.
authors: Francois
authors: F
authors: Nosten
authors: Immunobiology Unit, Institute of Child Health, University College London, WC1N 1EH, UK.
authors: David
authors: D
authors: Goldblatt
authors: Department of Mathematics and Statistics, University of Helsinki, 00014, Finland.|Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK.
authors: Jukka
authors: J
authors: Corander
authors: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
authors: Julian
authors: J
authors: Parkhill
authors: 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.
authors: Paul
authors: P
authors: Turner
authors: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.|Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK.
authors: Stephen D
authors: SD
authors: Bentley
mesh_terms: D000328:Adult; D015331:Cohort Studies; D004269:DNA, Bacterial / Q000235:genetics; D024881:Drug Resistance, Bacterial / Q000235:genetics; D005260:Female; D051456:Gene Flow; D016680:Genome, Bacterial; D055106:Genome-Wide Association Study; D006801:Humans; D007223:Infant; D008297:Male; D010802:Phylogeny; D011008:Pneumococcal Infections / Q000188:drug therapy / Q000382:microbiology; D020641:Polymorphism, Single Nucleotide; D011995:Recombination, Genetic; D012036:Refugees; D013296:Streptococcus pneumoniae / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification
chemical_list: D004269:DNA, Bacterial