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Using Whole Genome Analysis to Examine Recombination across Diverse Sequence Types of Staphylococcus aureus

Staphylococcus aureus is an important clinical pathogen worldwide and understanding this organism's phylogeny and, in particular, the role of recombination, is important both to understand the overall spread of virulent lineages and to characterize outbreaks. To further elucidate the phylogeny...

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Autores principales: Driebe, Elizabeth M., Sahl, Jason W., Roe, Chandler, Bowers, Jolene R., Schupp, James M., Gillece, John D., Kelley, Erin, Price, Lance B., Pearson, Talima R., Hepp, Crystal M., Brzoska, Pius M., Cummings, Craig A., Furtado, Manohar R., Andersen, Paal S., Stegger, Marc, Engelthaler, David M., Keim, Paul S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4498916/
https://www.ncbi.nlm.nih.gov/pubmed/26161978
http://dx.doi.org/10.1371/journal.pone.0130955
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author Driebe, Elizabeth M.
Sahl, Jason W.
Roe, Chandler
Bowers, Jolene R.
Schupp, James M.
Gillece, John D.
Kelley, Erin
Price, Lance B.
Pearson, Talima R.
Hepp, Crystal M.
Brzoska, Pius M.
Cummings, Craig A.
Furtado, Manohar R.
Andersen, Paal S.
Stegger, Marc
Engelthaler, David M.
Keim, Paul S.
author_facet Driebe, Elizabeth M.
Sahl, Jason W.
Roe, Chandler
Bowers, Jolene R.
Schupp, James M.
Gillece, John D.
Kelley, Erin
Price, Lance B.
Pearson, Talima R.
Hepp, Crystal M.
Brzoska, Pius M.
Cummings, Craig A.
Furtado, Manohar R.
Andersen, Paal S.
Stegger, Marc
Engelthaler, David M.
Keim, Paul S.
author_sort Driebe, Elizabeth M.
collection PubMed
description Staphylococcus aureus is an important clinical pathogen worldwide and understanding this organism's phylogeny and, in particular, the role of recombination, is important both to understand the overall spread of virulent lineages and to characterize outbreaks. To further elucidate the phylogeny of S. aureus, 35 diverse strains were sequenced using whole genome sequencing. In addition, 29 publicly available whole genome sequences were included to create a single nucleotide polymorphism (SNP)-based phylogenetic tree encompassing 11 distinct lineages. All strains of a particular sequence type fell into the same clade with clear groupings of the major clonal complexes of CC8, CC5, CC30, CC45 and CC1. Using a novel analysis method, we plotted the homoplasy density and SNP density across the whole genome and found evidence of recombination throughout the entire chromosome, but when we examined individual clonal lineages we found very little recombination. However, when we analyzed three branches of multiple lineages, we saw intermediate and differing levels of recombination between them. These data demonstrate that in S. aureus, recombination occurs across major lineages that subsequently expand in a clonal manner. Estimated mutation rates for the CC8 and CC5 lineages were different from each other. While the CC8 lineage rate was similar to previous studies, the CC5 lineage was 100-fold greater. Fifty known virulence genes were screened in all genomes in silico to determine their distribution across major clades. Thirty-three genes were present variably across clades, most of which were not constrained by ancestry, indicating horizontal gene transfer or gene loss.
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spelling pubmed-44989162015-07-17 Using Whole Genome Analysis to Examine Recombination across Diverse Sequence Types of Staphylococcus aureus Driebe, Elizabeth M. Sahl, Jason W. Roe, Chandler Bowers, Jolene R. Schupp, James M. Gillece, John D. Kelley, Erin Price, Lance B. Pearson, Talima R. Hepp, Crystal M. Brzoska, Pius M. Cummings, Craig A. Furtado, Manohar R. Andersen, Paal S. Stegger, Marc Engelthaler, David M. Keim, Paul S. PLoS One Research Article Staphylococcus aureus is an important clinical pathogen worldwide and understanding this organism's phylogeny and, in particular, the role of recombination, is important both to understand the overall spread of virulent lineages and to characterize outbreaks. To further elucidate the phylogeny of S. aureus, 35 diverse strains were sequenced using whole genome sequencing. In addition, 29 publicly available whole genome sequences were included to create a single nucleotide polymorphism (SNP)-based phylogenetic tree encompassing 11 distinct lineages. All strains of a particular sequence type fell into the same clade with clear groupings of the major clonal complexes of CC8, CC5, CC30, CC45 and CC1. Using a novel analysis method, we plotted the homoplasy density and SNP density across the whole genome and found evidence of recombination throughout the entire chromosome, but when we examined individual clonal lineages we found very little recombination. However, when we analyzed three branches of multiple lineages, we saw intermediate and differing levels of recombination between them. These data demonstrate that in S. aureus, recombination occurs across major lineages that subsequently expand in a clonal manner. Estimated mutation rates for the CC8 and CC5 lineages were different from each other. While the CC8 lineage rate was similar to previous studies, the CC5 lineage was 100-fold greater. Fifty known virulence genes were screened in all genomes in silico to determine their distribution across major clades. Thirty-three genes were present variably across clades, most of which were not constrained by ancestry, indicating horizontal gene transfer or gene loss. Public Library of Science 2015-07-10 /pmc/articles/PMC4498916/ /pubmed/26161978 http://dx.doi.org/10.1371/journal.pone.0130955 Text en © 2015 Driebe et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Driebe, Elizabeth M.
Sahl, Jason W.
Roe, Chandler
Bowers, Jolene R.
Schupp, James M.
Gillece, John D.
Kelley, Erin
Price, Lance B.
Pearson, Talima R.
Hepp, Crystal M.
Brzoska, Pius M.
Cummings, Craig A.
Furtado, Manohar R.
Andersen, Paal S.
Stegger, Marc
Engelthaler, David M.
Keim, Paul S.
Using Whole Genome Analysis to Examine Recombination across Diverse Sequence Types of Staphylococcus aureus
title Using Whole Genome Analysis to Examine Recombination across Diverse Sequence Types of Staphylococcus aureus
title_full Using Whole Genome Analysis to Examine Recombination across Diverse Sequence Types of Staphylococcus aureus
title_fullStr Using Whole Genome Analysis to Examine Recombination across Diverse Sequence Types of Staphylococcus aureus
title_full_unstemmed Using Whole Genome Analysis to Examine Recombination across Diverse Sequence Types of Staphylococcus aureus
title_short Using Whole Genome Analysis to Examine Recombination across Diverse Sequence Types of Staphylococcus aureus
title_sort using whole genome analysis to examine recombination across diverse sequence types of staphylococcus aureus
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4498916/
https://www.ncbi.nlm.nih.gov/pubmed/26161978
http://dx.doi.org/10.1371/journal.pone.0130955
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