title: Population genomic datasets describing the post-vaccine evolutionary epidemiology of Streptococcus pneumoniae.
abstract: Streptococcus pneumoniae is common nasopharyngeal commensal bacterium and important human pathogen. Vaccines against a subset of pneumococcal antigenic diversity have reduced rates of disease, without changing the frequency of asymptomatic carriage, through altering the bacterial population structure. These changes can be studied in detail through using genome sequencing to characterise systematically-sampled collections of carried S. pneumoniae. This dataset consists of 616 annotated draft genomes of isolates collected from children during routine visits to primary care physicians in Massachusetts between 2001, shortly after the seven valent polysaccharide conjugate vaccine was introduced, and 2007. Also made available are a core genome alignment and phylogeny describing the overall population structure, clusters of orthologous protein sequences, software for inferring serotype from Illumina reads, and whole genome alignments for the analysis of closely-related sets of pneumococci. These data can be used to study both bacterial evolution and the epidemiology of a pathogen population under selection from vaccine-induced immunity.
authors.affiliation: Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus , London W2 1pg, UK.
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Croucher
authors.affiliation: Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute , Boston, Massachusetts 02215, USA ; Division of General Pediatrics, Boston Children's Hospital , Boston, Massachusetts 02215, USA.
authors.forename: Jonathan A
authors.initials: JA
authors.lastname: Finkelstein
authors.affiliation: Maxwell Finland Laboratory for Infectious Diseases, Boston University Medical Center , Boston, Massachusetts 02118, USA.
authors.forename: Stephen I
authors.initials: SI
authors.lastname: Pelton
authors.affiliation: Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus , Cambridge CB10 1SA, UK.
authors.forename: Julian
authors.identifier: 0000-0002-7069-5958
authors.initials: J
authors.lastname: Parkhill
authors.affiliation: Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus , Cambridge CB10 1SA, UK.
authors.forename: Stephen D
authors.initials: SD
authors.lastname: Bentley
authors.affiliation: Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health , 677 Huntington Avenue, Boston, Massachusetts 02115, USA.
authors.forename: Marc
authors.initials: M
authors.lastname: Lipsitch
authors.affiliation: Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health , 677 Huntington Avenue, Boston, Massachusetts 02115, USA.
authors.forename: William P
authors.initials: WP
authors.lastname: Hanage
mesh_terms: D002648:Child; D002675:Child, Preschool; D019143:Evolution, Molecular; D016680:Genome, Bacterial; D006801:Humans; D007223:Infant; D056186:Metagenomics; D010802:Phylogeny; D011008:Pneumococcal Infections / Q000382:microbiology / Q000517:prevention & control; D022242:Pneumococcal Vaccines / Q000008:administration & dosage / Q000276:immunology; D013296:Streptococcus pneumoniae / Q000235:genetics* / Q000276:immunology; D018074:Vaccines, Conjugate / Q000008:administration & dosage / Q000276:immunology
chemical_list: D022242:Pneumococcal Vaccines; D018074:Vaccines, Conjugate
keywords: Bacterial genetics; Genetic variation; Molecular evolution; Respiratory tract diseases