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

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


Title: Genomic Analyses of >3,100 Nasopharyngeal Pneumococci Revealed Significant Differences Between Pneumococci Recovered in Four Different Geographical Regions
Author: van Tonder, Andries J.
Bray, James E.
Jolley, Keith A.
Jansen van Rensburg, Melissa
Quirk, Sigríður Júlía   orcid.org/0000-0002-8254-9720
Haraldsson, Gunnsteinn   orcid.org/0000-0002-9897-0384
Maiden, Martin   orcid.org/0000-0001-6321-5138
Bentley, Stephen D.
Haraldsson, Ásgeir   orcid.org/0000-0001-5364-7877
Erlendsdóttir, Helga
... 2 more authors Show all authors
Date: 2019-02-25
Language: English
Scope: 317
University/Institute: Háskóli Íslands
University of Iceland
School: Heilbrigðisvísindasvið (HÍ)
School of Health Sciences (UI)
Series: Frontiers in Microbiology;10(FEB)
ISSN: 1664-302X
DOI: 10.3389/fmicb.2019.00317
Subject: Microbiology; Accessory genome; Bacterial population structure; Core genome; Next generation sequencing; Pan-genome; Pneumococcus; Genarannsóknir; Erfðarannsóknir; Pneumókokkar; Gerlar; Örverufræði
URI: https://hdl.handle.net/20.500.11815/2057

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Citation:

van Tonder, A. J., et al. (2019). "Genomic Analyses of >3,100 Nasopharyngeal Pneumococci Revealed Significant Differences Between Pneumococci Recovered in Four Different Geographical Regions." 10(317).

Abstract:

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.

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This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms

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