Genomic analyses of >3,100 nasopharyngeal pneumococci revealed significant differences between pneumococci recovered in four different geographical regions
File(s)
Published version
Author(s)
Type
Journal Article
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.
Date Issued
2019-02-25
Date Acceptance
2019-02-06
Citation
Frontiers in Microbiology, 2019, 10
ISSN
1664-302X
Publisher
Frontiers Media
Journal / Book Title
Frontiers in Microbiology
Volume
10
Copyright Statement
© 2019 van Tonder, Bray, Jolley, Jansen van Rensburg, Quirk, Haraldsson, Maiden, Bentley, Haraldsson, Erlendsdóttir, Kristinsson and Brueggemann. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY) (https://creativecommons.org/licenses/by/4.0/). 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.
Identifier
http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000459595900002&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=1ba7043ffcc86c417c072aa74d649202
Subjects
Science & Technology
Life Sciences & Biomedicine
Microbiology
next generation sequencing
bacterial population structure
core genome
accessory genome
pan-genome
pneumococcus
SEROTYPE REPLACEMENT
VACCINE
SEQUENCES
CARRIAGE
CHILDREN
DISEASE
Publication Status
Published
Article Number
317
Date Publish Online
2019-02-25