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Pneumococcal prophages are diverse, but not without structure or history

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Title: Pneumococcal prophages are diverse, but not without structure or history
Authors: Brueggemann, AB
Harrold, CL
Javan, RR
Van Tonder, AJ
McDonnell, AJ
Edwards, BA
Item Type: Journal Article
Abstract: Bacteriophages (phages) infect many bacterial species, but little is known about the diversity of phages among the pneumococcus, a leading global pathogen. The objectives of this study were to determine the prevalence, diversity and molecular epidemiology of prophages (phage DNA integrated within the bacterial genome) among pneumococci isolated over the past 90 years. Nearly 500 pneumococcal genomes were investigated and RNA sequencing was used to explore prophage gene expression. We revealed that every pneumococcal genome contained prophage DNA. 286 full-length/putatively full-length pneumococcal prophages were identified, of which 163 have not previously been reported. Full-length prophages clustered into four major groups and every group dated from the 1930–40 s onward. There was limited evidence for genes shared between prophage clusters. Prophages typically integrated in one of five different sites within the pneumococcal genome. 72% of prophages possessed the virulence genes pblA and/or pblB. Individual prophages and the host pneumococcal genetic lineage were strongly associated and some prophages persisted for many decades. RNA sequencing provided clear evidence of prophage gene expression. Overall, pneumococcal prophages were highly prevalent, demonstrated a structured population, possessed genes associated with virulence, and were expressed under experimental conditions. Pneumococcal prophages are likely to play a more important role in pneumococcal biology and evolution than previously recognised.
Issue Date: 20-Feb-2017
Date of Acceptance: 17-Jan-2017
URI: http://hdl.handle.net/10044/1/45698
DOI: https://dx.doi.org/10.1038/srep42976
ISSN: 2045-2322
Publisher: NATURE PUBLISHING GROUP
Journal / Book Title: SCIENTIFIC REPORTS
Volume: 7
Issue: 2017
Copyright Statement: © 2017 The Author(s). This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
Keywords: Science & Technology
Multidisciplinary Sciences
Science & Technology - Other Topics
STREPTOCOCCUS-PNEUMONIAE
SEQUENCE
BACTERIOPHAGE
CARRIAGE
PHAGE
VISUALIZATION
ALIGNMENT
LYSOGENY
GENOMICS
DISEASE
Publication Status: Published
Article Number: ARTN 42976
Appears in Collections:Department of Medicine
Faculty of Medicine



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