Claire ChewapreechaSimon R. HarrisNicholas J. CroucherClaudia TurnerPekka MarttinenLu ChengAlberto PessiaDavid M. AanensenAlison E. MatherAndrew J. PageSusannah J. SalterDavid HarrisFrancois NostenDavid GoldblattJukka CoranderJulian ParkhillPaul TurnerStephen D. BentleyWellcome Trust Sanger InstituteSt Mary's Hospital LondonMahidol UniversityNuffield Department of Clinical MedicineAalto UniversityHelsingin YliopistoUCL Institute of Child HealthAbo Akademi UniversityUniversity of Cambridge2018-11-092018-11-092014-01-01Nature Genetics. Vol.46, No.3 (2014), 305-30915461718106140362-s2.0-84895858474https://repository.li.mahidol.ac.th/handle/20.500.14594/33502Evasion 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. © 2014 Nature America, Inc. © 2014 Nature America, Inc.Mahidol UniversityBiochemistry, Genetics and Molecular BiologyArticleSCOPUS10.1038/ng.2895