Improved Subtyping of <named-content content-type="genus-species">Staphylococcus aureus</named-content> Clonal Complex 8 Strains Based on Whole-Genome Phylogenetic Analysis

ABSTRACT Strains of Staphylococcus aureus in clonal complex 8 (CC8), including USA300, USA500, and the Iberian clone, are prevalent pathogens in the United States, both inside and outside health care settings. Methods for typing CC8 strains are becoming obsolete as the strains evolve and diversify,...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Jolene R. Bowers, Elizabeth M. Driebe, Valerie Albrecht, Linda K. McDougal, Mitchell Granade, Chandler C. Roe, Darrin Lemmer, J. Kamile Rasheed, David M. Engelthaler, Paul Keim, Brandi M. Limbago
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2018
Materias:	CC8 MRSA MSSA phylogeny Staphylococcus aureus strain typing Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/8838d2d457554ee1941466c409a2277f
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:8838d2d457554ee1941466c409a2277f
record_format	dspace
spelling	oai:doaj.org-article:8838d2d457554ee1941466c409a2277f2021-11-15T15:24:23ZImproved Subtyping of <named-content content-type="genus-species">Staphylococcus aureus</named-content> Clonal Complex 8 Strains Based on Whole-Genome Phylogenetic Analysis10.1128/mSphere.00464-172379-5042https://doaj.org/article/8838d2d457554ee1941466c409a2277f2018-06-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSphere.00464-17https://doaj.org/toc/2379-5042ABSTRACT Strains of Staphylococcus aureus in clonal complex 8 (CC8), including USA300, USA500, and the Iberian clone, are prevalent pathogens in the United States, both inside and outside health care settings. Methods for typing CC8 strains are becoming obsolete as the strains evolve and diversify, and whole-genome sequencing has shown that some strain types fall into multiple sublineages within CC8. In this study, we attempt to clarify the strain nomenclature of CC8, classifying the major strain types based on whole-genome sequence phylogenetics using both methicillin-resistant S. aureus (MRSA) and methicillin-susceptible S. aureus (MSSA) genomes. We show that isolates of the Archaic and Iberian clones from decades ago make up the most basal clade of the main CC8 lineages and that at least one successful lineage of CC8, made up mostly of MSSA, diverged before the other well-known strain types USA500 and USA300. We also show that the USA500 type includes two clades separated by the previously described “Canadian epidemic MRSA” strain CMRSA9, that one clade containing USA500 also contains the USA300 clade, and that the USA300-0114 strain type is not a monophyletic group. Additionally, we present a rapid, simple CC8 strain-typing scheme using real-time PCR assays that target single nucleotide polymorphisms (SNPs) derived from our CC8 phylogeny and show the significant benefit of using more stable genomic markers based on evolutionary lineages over traditional S. aureus typing techniques. This more accurate and accessible S. aureus typing system may improve surveillance and better inform the epidemiology of this very important pathogen. IMPORTANCE Staphylococcus aureus is a major human pathogen worldwide in both community and health care settings. Surveillance for S. aureus strains is important to our understanding of their spread and to informing infection prevention and control. Confusion surrounding the strain nomenclature of one of the most prevalent lineages of S. aureus, clonal complex 8 (CC8), and the imprecision of current tools for typing S. aureus make surveillance and source tracing difficult and sometimes misleading. In this study, we clarify the CC8 strain designations and propose a new typing scheme for CC8 isolates that is rapid and easy to use. This typing scheme is based on relatively stable genomic markers, and we demonstrate its superiority over traditional typing techniques. This scheme has the potential to greatly improve epidemiological investigations of S. aureus.Jolene R. BowersElizabeth M. DriebeValerie AlbrechtLinda K. McDougalMitchell GranadeChandler C. RoeDarrin LemmerJ. Kamile RasheedDavid M. EngelthalerPaul KeimBrandi M. LimbagoAmerican Society for MicrobiologyarticleCC8MRSAMSSAphylogenyStaphylococcus aureusstrain typingMicrobiologyQR1-502ENmSphere, Vol 3, Iss 3 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	CC8 MRSA MSSA phylogeny Staphylococcus aureus strain typing Microbiology QR1-502
spellingShingle	CC8 MRSA MSSA phylogeny Staphylococcus aureus strain typing Microbiology QR1-502 Jolene R. Bowers Elizabeth M. Driebe Valerie Albrecht Linda K. McDougal Mitchell Granade Chandler C. Roe Darrin Lemmer J. Kamile Rasheed David M. Engelthaler Paul Keim Brandi M. Limbago Improved Subtyping of <named-content content-type="genus-species">Staphylococcus aureus</named-content> Clonal Complex 8 Strains Based on Whole-Genome Phylogenetic Analysis
description	ABSTRACT Strains of Staphylococcus aureus in clonal complex 8 (CC8), including USA300, USA500, and the Iberian clone, are prevalent pathogens in the United States, both inside and outside health care settings. Methods for typing CC8 strains are becoming obsolete as the strains evolve and diversify, and whole-genome sequencing has shown that some strain types fall into multiple sublineages within CC8. In this study, we attempt to clarify the strain nomenclature of CC8, classifying the major strain types based on whole-genome sequence phylogenetics using both methicillin-resistant S. aureus (MRSA) and methicillin-susceptible S. aureus (MSSA) genomes. We show that isolates of the Archaic and Iberian clones from decades ago make up the most basal clade of the main CC8 lineages and that at least one successful lineage of CC8, made up mostly of MSSA, diverged before the other well-known strain types USA500 and USA300. We also show that the USA500 type includes two clades separated by the previously described “Canadian epidemic MRSA” strain CMRSA9, that one clade containing USA500 also contains the USA300 clade, and that the USA300-0114 strain type is not a monophyletic group. Additionally, we present a rapid, simple CC8 strain-typing scheme using real-time PCR assays that target single nucleotide polymorphisms (SNPs) derived from our CC8 phylogeny and show the significant benefit of using more stable genomic markers based on evolutionary lineages over traditional S. aureus typing techniques. This more accurate and accessible S. aureus typing system may improve surveillance and better inform the epidemiology of this very important pathogen. IMPORTANCE Staphylococcus aureus is a major human pathogen worldwide in both community and health care settings. Surveillance for S. aureus strains is important to our understanding of their spread and to informing infection prevention and control. Confusion surrounding the strain nomenclature of one of the most prevalent lineages of S. aureus, clonal complex 8 (CC8), and the imprecision of current tools for typing S. aureus make surveillance and source tracing difficult and sometimes misleading. In this study, we clarify the CC8 strain designations and propose a new typing scheme for CC8 isolates that is rapid and easy to use. This typing scheme is based on relatively stable genomic markers, and we demonstrate its superiority over traditional typing techniques. This scheme has the potential to greatly improve epidemiological investigations of S. aureus.
format	article
author	Jolene R. Bowers Elizabeth M. Driebe Valerie Albrecht Linda K. McDougal Mitchell Granade Chandler C. Roe Darrin Lemmer J. Kamile Rasheed David M. Engelthaler Paul Keim Brandi M. Limbago
author_facet	Jolene R. Bowers Elizabeth M. Driebe Valerie Albrecht Linda K. McDougal Mitchell Granade Chandler C. Roe Darrin Lemmer J. Kamile Rasheed David M. Engelthaler Paul Keim Brandi M. Limbago
author_sort	Jolene R. Bowers
title	Improved Subtyping of <named-content content-type="genus-species">Staphylococcus aureus</named-content> Clonal Complex 8 Strains Based on Whole-Genome Phylogenetic Analysis
title_short	Improved Subtyping of <named-content content-type="genus-species">Staphylococcus aureus</named-content> Clonal Complex 8 Strains Based on Whole-Genome Phylogenetic Analysis
title_full	Improved Subtyping of <named-content content-type="genus-species">Staphylococcus aureus</named-content> Clonal Complex 8 Strains Based on Whole-Genome Phylogenetic Analysis
title_fullStr	Improved Subtyping of <named-content content-type="genus-species">Staphylococcus aureus</named-content> Clonal Complex 8 Strains Based on Whole-Genome Phylogenetic Analysis
title_full_unstemmed	Improved Subtyping of <named-content content-type="genus-species">Staphylococcus aureus</named-content> Clonal Complex 8 Strains Based on Whole-Genome Phylogenetic Analysis
title_sort	improved subtyping of <named-content content-type="genus-species">staphylococcus aureus</named-content> clonal complex 8 strains based on whole-genome phylogenetic analysis
publisher	American Society for Microbiology
publishDate	2018
url	https://doaj.org/article/8838d2d457554ee1941466c409a2277f
work_keys_str_mv	AT jolenerbowers improvedsubtypingofnamedcontentcontenttypegenusspeciesstaphylococcusaureusnamedcontentclonalcomplex8strainsbasedonwholegenomephylogeneticanalysis AT elizabethmdriebe improvedsubtypingofnamedcontentcontenttypegenusspeciesstaphylococcusaureusnamedcontentclonalcomplex8strainsbasedonwholegenomephylogeneticanalysis AT valeriealbrecht improvedsubtypingofnamedcontentcontenttypegenusspeciesstaphylococcusaureusnamedcontentclonalcomplex8strainsbasedonwholegenomephylogeneticanalysis AT lindakmcdougal improvedsubtypingofnamedcontentcontenttypegenusspeciesstaphylococcusaureusnamedcontentclonalcomplex8strainsbasedonwholegenomephylogeneticanalysis AT mitchellgranade improvedsubtypingofnamedcontentcontenttypegenusspeciesstaphylococcusaureusnamedcontentclonalcomplex8strainsbasedonwholegenomephylogeneticanalysis AT chandlercroe improvedsubtypingofnamedcontentcontenttypegenusspeciesstaphylococcusaureusnamedcontentclonalcomplex8strainsbasedonwholegenomephylogeneticanalysis AT darrinlemmer improvedsubtypingofnamedcontentcontenttypegenusspeciesstaphylococcusaureusnamedcontentclonalcomplex8strainsbasedonwholegenomephylogeneticanalysis AT jkamilerasheed improvedsubtypingofnamedcontentcontenttypegenusspeciesstaphylococcusaureusnamedcontentclonalcomplex8strainsbasedonwholegenomephylogeneticanalysis AT davidmengelthaler improvedsubtypingofnamedcontentcontenttypegenusspeciesstaphylococcusaureusnamedcontentclonalcomplex8strainsbasedonwholegenomephylogeneticanalysis AT paulkeim improvedsubtypingofnamedcontentcontenttypegenusspeciesstaphylococcusaureusnamedcontentclonalcomplex8strainsbasedonwholegenomephylogeneticanalysis AT brandimlimbago improvedsubtypingofnamedcontentcontenttypegenusspeciesstaphylococcusaureusnamedcontentclonalcomplex8strainsbasedonwholegenomephylogeneticanalysis
_version_	1718427961431949312

Improved Subtyping of <named-content content-type="genus-species">Staphylococcus aureus</named-content> Clonal Complex 8 Strains Based on Whole-Genome Phylogenetic Analysis

Ejemplares similares