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Genome-Wide Patterns of Recombination in the Opportunistic Human Pathogen Pseudomonas aeruginosa
The bacterium Pseudomonas aeruginosa is a significant cause of acute nosocomial infections as well as chronic respiratory infections in patients with cystic fibrosis (CF). Recent reports of the intercontinental spread of a CF-specific epidemic strain, combined with high intrinsic levels of antibioti...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4316616/ https://www.ncbi.nlm.nih.gov/pubmed/25480685 http://dx.doi.org/10.1093/gbe/evu260 |
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author | Dettman, Jeremy R. Rodrigue, Nicolas Kassen, Rees |
author_facet | Dettman, Jeremy R. Rodrigue, Nicolas Kassen, Rees |
author_sort | Dettman, Jeremy R. |
collection | PubMed |
description | The bacterium Pseudomonas aeruginosa is a significant cause of acute nosocomial infections as well as chronic respiratory infections in patients with cystic fibrosis (CF). Recent reports of the intercontinental spread of a CF-specific epidemic strain, combined with high intrinsic levels of antibiotic resistance, have made this opportunistic pathogen an important public health concern. Strain-specific differences correlate with variation in clinical outcomes of infected CF patients, increasing the urgency to understand the evolutionary origin of genetic factors conferring important phenotypes that enable infection, virulence, or resistance. Here, we describe the genome-wide patterns of homologous and nonhomologous recombination in P. aeruginosa, and the extent to which the genomes are affected by these diversity-generating processes. Based on whole-genome sequence data from 32 clinical isolates of P. aeruginosa, we examined the rate and distribution of recombination along the genome, and its effect on the reconstruction of phylogenetic relationships. Multiple lines of evidence suggested that recombination was common and usually involves short stretches of DNA (200–300 bp). Although mutation was the main source of nucleotide diversity, the import of polymorphisms by homologous recombination contributed nearly as much. We also identified the genomic regions with frequent recombination, and the specific sequences of recombinant origin within epidemic strains. The functional characteristics of the genes contained therein were examined for potential associations with a pathogenic lifestyle or adaptation to the CF lung environment. A common link between many of the high-recombination genes was their functional affiliation with the cell wall, suggesting that the products of recombination may be maintained by selection for variation in cell-surface molecules that allows for evasion of the host immune system. |
format | Online Article Text |
id | pubmed-4316616 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-43166162015-02-19 Genome-Wide Patterns of Recombination in the Opportunistic Human Pathogen Pseudomonas aeruginosa Dettman, Jeremy R. Rodrigue, Nicolas Kassen, Rees Genome Biol Evol Research Article The bacterium Pseudomonas aeruginosa is a significant cause of acute nosocomial infections as well as chronic respiratory infections in patients with cystic fibrosis (CF). Recent reports of the intercontinental spread of a CF-specific epidemic strain, combined with high intrinsic levels of antibiotic resistance, have made this opportunistic pathogen an important public health concern. Strain-specific differences correlate with variation in clinical outcomes of infected CF patients, increasing the urgency to understand the evolutionary origin of genetic factors conferring important phenotypes that enable infection, virulence, or resistance. Here, we describe the genome-wide patterns of homologous and nonhomologous recombination in P. aeruginosa, and the extent to which the genomes are affected by these diversity-generating processes. Based on whole-genome sequence data from 32 clinical isolates of P. aeruginosa, we examined the rate and distribution of recombination along the genome, and its effect on the reconstruction of phylogenetic relationships. Multiple lines of evidence suggested that recombination was common and usually involves short stretches of DNA (200–300 bp). Although mutation was the main source of nucleotide diversity, the import of polymorphisms by homologous recombination contributed nearly as much. We also identified the genomic regions with frequent recombination, and the specific sequences of recombinant origin within epidemic strains. The functional characteristics of the genes contained therein were examined for potential associations with a pathogenic lifestyle or adaptation to the CF lung environment. A common link between many of the high-recombination genes was their functional affiliation with the cell wall, suggesting that the products of recombination may be maintained by selection for variation in cell-surface molecules that allows for evasion of the host immune system. Oxford University Press 2014-12-04 /pmc/articles/PMC4316616/ /pubmed/25480685 http://dx.doi.org/10.1093/gbe/evu260 Text en © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Research Article Dettman, Jeremy R. Rodrigue, Nicolas Kassen, Rees Genome-Wide Patterns of Recombination in the Opportunistic Human Pathogen Pseudomonas aeruginosa |
title | Genome-Wide Patterns of Recombination in the Opportunistic Human Pathogen Pseudomonas aeruginosa |
title_full | Genome-Wide Patterns of Recombination in the Opportunistic Human Pathogen Pseudomonas aeruginosa |
title_fullStr | Genome-Wide Patterns of Recombination in the Opportunistic Human Pathogen Pseudomonas aeruginosa |
title_full_unstemmed | Genome-Wide Patterns of Recombination in the Opportunistic Human Pathogen Pseudomonas aeruginosa |
title_short | Genome-Wide Patterns of Recombination in the Opportunistic Human Pathogen Pseudomonas aeruginosa |
title_sort | genome-wide patterns of recombination in the opportunistic human pathogen pseudomonas aeruginosa |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4316616/ https://www.ncbi.nlm.nih.gov/pubmed/25480685 http://dx.doi.org/10.1093/gbe/evu260 |
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