Rapid typing of Staphylococcus aureus CC8 strains

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 healthcare settings. Methods for typing CC8 strains are becoming obsolete as the strains evolve and diversify, and whole genome sequencing has shown that some strains have been misclassified by previous methods. In this study, we attempt to clarify the strain typing 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 clone 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 modern Iberian clone clade diverged. We also show that a USA500 strain gave rise to the USA300 lineage, 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 these stable genomic markers based on evolutionary lineages over traditional S. aureus typing techniques. This more accurate and accessible S. aureus strain typing system will improve and may increase surveillance and better inform the epidemiology of this very important pathogen.