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Nat Commun. 2014 Nov 19;5:5471. doi: 10.1038/ncomms6471.

Diversification of bacterial genome content through distinct mechanisms over different timescales.

Author information

1
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.
2
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
3
Centre for Communicable Disease Dynamics, Harvard School of Public Health, 677 Huntington Avenue, Boston, Massachusetts 02115, USA.

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.

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PMID:
25407023
PMCID:
PMC4263131
DOI:
10.1038/ncomms6471
[Indexed for MEDLINE]
Free PMC Article

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