Improved subtyping of Staphylococcus aureus clonal complex 8 strains based on whole-genome phylogenetic analysis

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 S Keim, Brandi M. Limbago

Research output: Contribution to journalArticle

5 Citations (Scopus)

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 wellknown 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.

Original languageEnglish (US)
Article numbere00464-17
JournalmSphere
Volume3
Issue number3
DOIs
StatePublished - May 1 2018
Externally publishedYes

Fingerprint

Staphylococcus aureus
Genome
Methicillin
Methicillin-Resistant Staphylococcus aureus
Clone Cells
Phylogeny
Terminology
Single Nucleotide Polymorphism
Real-Time Polymerase Chain Reaction
Epidemiology
Delivery of Health Care

Keywords

  • Assay development
  • CC8
  • MRSA
  • MSSA
  • Phylogeny
  • Staphylococcus aureus
  • Strain typing
  • Whole genome

ASJC Scopus subject areas

  • Microbiology
  • Molecular Biology

Cite this

Bowers, J. R., Driebe, E. M., Albrecht, V., McDougal, L. K., Granade, M., Roe, C. C., ... Limbago, B. M. (2018). Improved subtyping of Staphylococcus aureus clonal complex 8 strains based on whole-genome phylogenetic analysis. mSphere, 3(3), [e00464-17]. https://doi.org/10.1128/mSphere.00464-17

Improved subtyping of Staphylococcus aureus clonal complex 8 strains based on whole-genome phylogenetic analysis. / Bowers, Jolene R.; Driebe, Elizabeth M.; Albrecht, Valerie; McDougal, Linda K.; Granade, Mitchell; Roe, Chandler C.; Lemmer, Darrin; Rasheed, J. Kamile; Engelthaler, David M.; Keim, Paul S; Limbago, Brandi M.

In: mSphere, Vol. 3, No. 3, e00464-17, 01.05.2018.

Research output: Contribution to journalArticle

Bowers, JR, Driebe, EM, Albrecht, V, McDougal, LK, Granade, M, Roe, CC, Lemmer, D, Rasheed, JK, Engelthaler, DM, Keim, PS & Limbago, BM 2018, 'Improved subtyping of Staphylococcus aureus clonal complex 8 strains based on whole-genome phylogenetic analysis', mSphere, vol. 3, no. 3, e00464-17. https://doi.org/10.1128/mSphere.00464-17
Bowers, Jolene R. ; Driebe, Elizabeth M. ; Albrecht, Valerie ; McDougal, Linda K. ; Granade, Mitchell ; Roe, Chandler C. ; Lemmer, Darrin ; Rasheed, J. Kamile ; Engelthaler, David M. ; Keim, Paul S ; Limbago, Brandi M. / Improved subtyping of Staphylococcus aureus clonal complex 8 strains based on whole-genome phylogenetic analysis. In: mSphere. 2018 ; Vol. 3, No. 3.
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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 wellknown 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.",
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