Genomic Analyses of >3,100 Nasopharyngeal Pneumococci Revealed Significant Differences Between Pneumococci Recovered in Four Different Geographical Regions.

• Published in: Frontiers in Microbiology
• Main Authors: van Tonder, Andries J, Bray, James E, Jolley, Keith A, Jansen van Rensburg, Melissa, Quirk, Sigríður J, Haraldsson, Gunnsteinn, Maiden, Martin C J, Bentley, Stephen D, Haraldsson, Ásgeir, Erlendsdóttir, Helga, Kristinsson, Karl G, Brueggemann, Angela B
• Other Authors: 1 Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom. 2 Parasites and Microbes, Wellcome Sanger Institute, Hinxton, United Kingdom. 3 Department of Zoology, University of Oxford, Oxford, United Kingdom. 4 Department of Medicine, Imperial College London, London, United Kingdom. 5 Clinical Microbiology, University of Iceland and Landspitali University Hospital, Reykjavik, Iceland. 6 Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom. 7 Department of Pathology, University of Cambridge, Cambridge, United Kingdom. 8 Children's Hospital Iceland, Landspitali University Hospital, Reykjavik, Iceland.
• Format: Article in Journal/Newspaper
• Language: English
• Published: Frontiers Research Foundation 2019
• Subjects: accessory genome; bacterial population structure; core genome; next generation sequencing; pan-genome; pneumococcus; Gerlar; Landfræðileg útbreiðsla; Bakteríusjúkdómar; Streptococcus pneumoniae; Bacterial Structures; Geographic Locations; Iceland
• Online Access: http://hdl.handle.net/2336/620887; https://doi.org/10.3389/fmicb.2019.00317

To access publisher's full text version of this article, please click on the hyperlink in Additional Links field or click on the hyperlink at the top of the page marked Download Understanding the structure of a bacterial population is essential in order to understand bacterial evolution. Estimating the core genome (those genes common to all, or nearly all, strains of a species) is a key component of such analyses. The size and composition of the core genome varies by dataset, but we hypothesized that the variation between different collections of the same bacterial species would be minimal. To investigate this, we analyzed the genome sequences of 3,118 pneumococci recovered from healthy individuals in Reykjavik (Iceland), Southampton (United Kingdom), Boston (United States), and Maela (Thailand). The analyses revealed a "supercore" genome (genes shared by all 3,118 pneumococci) of 558 genes, although an additional 354 core genes were shared by pneumococci from Reykjavik, Southampton, and Boston. Overall, the size and composition of the core and pan-genomes among pneumococci recovered in Reykjavik, Southampton, and Boston were similar. Maela pneumococci were distinctly different in that they had a smaller core genome and larger pan-genome. The pan-genome of Maela pneumococci contained several >25 Kb sequence regions (flanked by pneumococcal genes) that were homologous to genomic regions found in other bacterial species. Overall, our work revealed that some subsets of the global pneumococcal population are highly heterogeneous, and our hypothesis was rejected. This is an important finding in terms of understanding genetic variation among pneumococci and is also an essential point of consideration before generalizing the findings from a single dataset to the wider pneumococcal population. Wellcome Trust Biomedical Research Fund award Wellcome Trust Research Fellowship University of Oxford John Fell Fund award Wellcome Trust Eimskipa University Fund GlaxoSmithKline Biologicals SA Landspitali University ...