Whole Genome Analysis of Diverse Sequence Types Advances Our Understanding of Population Genetics and Evolution of Staphylococcus aureus

Staphylococcus aureus is an important clinical pathogen worldwide and understanding this organism''s phylogeny and evolution 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 next generation technologies. 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. However, when the core genome SNP phylogeny was compared to a phylogeny based on concatenated multilocus sequence typing (MLST) markers, there were significant differences. 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 two clonal lineages we found much less recombination. These data demonstrate that in S. aureus, recombination occurs across major lineages that subsequently expand in a clonal manner. 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. Additionally, a set of lineage-specific SNPs for possible use in tracing outbreaks were identified in the analysis, and real-time PCR assays were developed and validated for use in identifying strains that belong to the important clonal S. aureus groups USA100 (CC5), USA300 (CC8), and USA600 (CC45).