title: Diversification of bacterial genome content through distinct mechanisms over different timescales.
abstract: Bacterial populations often consist of multiple co-circulating lineages. Determining how such population structures arise requires understanding what drives bacterial diversification. Using 616 systematically sampled genomes, we show that Streptococcus pneumoniae lineages are typically characterized by combinations of infrequently transferred stable genomic islands: those moving primarily through transformation, along with integrative and conjugative elements and phage-related chromosomal islands. The only lineage containing extensive unique sequence corresponds to a set of atypical unencapsulated isolates that may represent a distinct species. However, prophage content is highly variable even within lineages, suggesting frequent horizontal transmission that would necessitate rapidly diversifying anti-phage mechanisms to prevent these viruses sweeping through populations. Correspondingly, two loci encoding Type I restriction-modification systems able to change their specificity over short timescales through intragenomic recombination are ubiquitous across the collection. Hence short-term pneumococcal variation is characterized by movement of phage and intragenomic rearrangements, with the slower transfer of stable loci distinguishing lineages.
authors.affiliation: 1] Centre for Communicable Disease Dynamics, Harvard School of Public Health, 677 Huntington Avenue, Boston, Massachusetts 02115, USA [2] Department of Infectious Disease Epidemiology, St. Mary's Campus, Imperial College, London W2 1PG, UK.
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Croucher
authors.affiliation: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Paul G
authors.initials: PG
authors.lastname: Coupland
authors.affiliation: Centre for Communicable Disease Dynamics, Harvard School of Public Health, 677 Huntington Avenue, Boston, Massachusetts 02115, USA.
authors.forename: Abbie E
authors.initials: AE
authors.lastname: Stevenson
authors.affiliation: Centre for Communicable Disease Dynamics, Harvard School of Public Health, 677 Huntington Avenue, Boston, Massachusetts 02115, USA.
authors.forename: Alanna
authors.initials: A
authors.lastname: Callendrello
authors.affiliation: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Stephen D
authors.initials: SD
authors.lastname: Bentley
authors.affiliation: Centre for Communicable Disease Dynamics, Harvard School of Public Health, 677 Huntington Avenue, Boston, Massachusetts 02115, USA.
authors.forename: William P
authors.initials: WP
authors.lastname: Hanage
mesh_terms: D015280:DNA Restriction-Modification Enzymes / Q000235:genetics; D014644:Genetic Variation; D016680:Genome, Bacterial; D044404:Genomic Islands; D039002:Prophages / Q000235:genetics*; D013296:Streptococcus pneumoniae / Q000235:genetics*; D013997:Time Factors
chemical_list: D015280:DNA Restriction-Modification Enzymes