Genetic variation in the Staphylococcus aureus 8325 strain lineage revealed by whole-genome sequencing.

Staphylococcus aureus strains of the 8325 lineage, especially 8325-4 and derivatives lacking prophage, have been used extensively for decades of research. We report herein the results of our deep sequence analysis of strain 8325-4. Assignment of sequence variants compared with the reference strain 8...

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Autores principales:	Kristoffer T Bæk, Dorte Frees, Adriana Renzoni, Christine Barras, Natalia Rodriguez, Caroline Manzano, William L Kelley
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/edfec67169144303aec63448fe1f7ce0
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spelling	oai:doaj.org-article:edfec67169144303aec63448fe1f7ce02021-11-18T08:53:22ZGenetic variation in the Staphylococcus aureus 8325 strain lineage revealed by whole-genome sequencing.1932-620310.1371/journal.pone.0077122https://doaj.org/article/edfec67169144303aec63448fe1f7ce02013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24098817/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Staphylococcus aureus strains of the 8325 lineage, especially 8325-4 and derivatives lacking prophage, have been used extensively for decades of research. We report herein the results of our deep sequence analysis of strain 8325-4. Assignment of sequence variants compared with the reference strain 8325 (NRS77/PS47) required correction of errors in the 8325 reference genome, and reassessment of variation previously attributed to chemical mutagenesis of the restriction-defective RN4220. Using an extensive strain pedigree analysis, we discovered that 8325-4 contains 16 single nucleotide polymorphisms (SNP) arising prior to the construction of RN4220. We identified 5 indels in 8325-4 compared with 8325. Three indels correspond to expected Φ11, 12, 13 excisions, one indel is explained by a sequence assembly artifact, and the final indel (Δ63bp) in the spa-sarS intergenic region is common to only a sub-lineage of 8325-4 strains including SH1000. This deletion was found to significantly decrease (75%) steady state sarS but not spa transcript levels in post-exponential phase. The sub-lineage 8325-4 was also found to harbor 4 additional SNPs. We also found large sequence variation between 8325, 8325-4 and RN4220 in a cluster of repetitive hypothetical proteins (SA0282 homologs) near the Ess secretion cluster. The overall 8325-4 SNP set results in 17 alterations within coding sequences. Remarkably, we discovered that all tested strains of the 8325-4 lineage lack phenol soluble modulin α3 (PSMα3), a virulence determinant implicated in neutrophil chemotaxis, biofilm architecture and surface spreading. Collectively, our results clarify and define the 8325-4 pedigree and reveal clear evidence that mutations existing throughout all branches of this lineage, including the widely used RN6390 and SH1000 strains, could conceivably impact virulence regulation.Kristoffer T BækDorte FreesAdriana RenzoniChristine BarrasNatalia RodriguezCaroline ManzanoWilliam L KelleyPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 9, p e77122 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Kristoffer T Bæk Dorte Frees Adriana Renzoni Christine Barras Natalia Rodriguez Caroline Manzano William L Kelley Genetic variation in the Staphylococcus aureus 8325 strain lineage revealed by whole-genome sequencing.
description	Staphylococcus aureus strains of the 8325 lineage, especially 8325-4 and derivatives lacking prophage, have been used extensively for decades of research. We report herein the results of our deep sequence analysis of strain 8325-4. Assignment of sequence variants compared with the reference strain 8325 (NRS77/PS47) required correction of errors in the 8325 reference genome, and reassessment of variation previously attributed to chemical mutagenesis of the restriction-defective RN4220. Using an extensive strain pedigree analysis, we discovered that 8325-4 contains 16 single nucleotide polymorphisms (SNP) arising prior to the construction of RN4220. We identified 5 indels in 8325-4 compared with 8325. Three indels correspond to expected Φ11, 12, 13 excisions, one indel is explained by a sequence assembly artifact, and the final indel (Δ63bp) in the spa-sarS intergenic region is common to only a sub-lineage of 8325-4 strains including SH1000. This deletion was found to significantly decrease (75%) steady state sarS but not spa transcript levels in post-exponential phase. The sub-lineage 8325-4 was also found to harbor 4 additional SNPs. We also found large sequence variation between 8325, 8325-4 and RN4220 in a cluster of repetitive hypothetical proteins (SA0282 homologs) near the Ess secretion cluster. The overall 8325-4 SNP set results in 17 alterations within coding sequences. Remarkably, we discovered that all tested strains of the 8325-4 lineage lack phenol soluble modulin α3 (PSMα3), a virulence determinant implicated in neutrophil chemotaxis, biofilm architecture and surface spreading. Collectively, our results clarify and define the 8325-4 pedigree and reveal clear evidence that mutations existing throughout all branches of this lineage, including the widely used RN6390 and SH1000 strains, could conceivably impact virulence regulation.
format	article
author	Kristoffer T Bæk Dorte Frees Adriana Renzoni Christine Barras Natalia Rodriguez Caroline Manzano William L Kelley
author_facet	Kristoffer T Bæk Dorte Frees Adriana Renzoni Christine Barras Natalia Rodriguez Caroline Manzano William L Kelley
author_sort	Kristoffer T Bæk
title	Genetic variation in the Staphylococcus aureus 8325 strain lineage revealed by whole-genome sequencing.
title_short	Genetic variation in the Staphylococcus aureus 8325 strain lineage revealed by whole-genome sequencing.
title_full	Genetic variation in the Staphylococcus aureus 8325 strain lineage revealed by whole-genome sequencing.
title_fullStr	Genetic variation in the Staphylococcus aureus 8325 strain lineage revealed by whole-genome sequencing.
title_full_unstemmed	Genetic variation in the Staphylococcus aureus 8325 strain lineage revealed by whole-genome sequencing.
title_sort	genetic variation in the staphylococcus aureus 8325 strain lineage revealed by whole-genome sequencing.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/edfec67169144303aec63448fe1f7ce0
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Genetic variation in the Staphylococcus aureus 8325 strain lineage revealed by whole-genome sequencing.

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