Whole Genome Sequencing of Danish Staphylococcus argenteus Reveals a Genetically Diverse Collection with Clear Separation from Staphylococcus aureus

Abstract

Staphylococcus argenteus (S. argenteus) is a newly identified Staphylococcus species that has been misidentified as Staphylococcus aureus (S. aureus) and is clinically relevant. We identified 25 S. argenteus genomes in our collection of whole genome sequenced S. aureus. These genomes were compared to publicly available genomes and a phylogeny revealed seven clusters corresponding to seven clonal complexes. The genome of S. argenteus was found to be different from the genome of S. aureus and a core genome analysis showed that ~33% of the total gene pool was shared between the two species, at 90% homology level. An assessment of mobile elements shows flow of SCCmec cassettes, plasmids, phages, and pathogenicity islands, between S. argenteus and S. aureus. This dataset emphasizes that S. argenteus and S. aureus are two separate species that share genetic material.

Keywords: S. argenteus; S. aureus; SargPI; SargPID7903; Staphylococcus; phage; plasmid.

Figure 1

Phylogenetic comparison of S. argenteus with S. aureus and of S. argenteus isolates alone. (A) SNP analysis of 34 S. argenteus genomes with a representative set of 22 genomes of S. aureus all with different sequence types. (B) Maximum likelihood phylogenetic tree of S. argenteus isolates. The tree is made from multiple sequence alignment of assemblies from 25 isolates from Denmark and 9 references of S. argenteus assemblies. One Hundred bootstraps were performed. Prefix of Sa indicates S. argenteus reference genomes downloaded from NCBI, O- prefix are Odense isolates and the remaining isolates are from Copenhagen. Bootstrap values are shown at the major breakpoints. The scale bar represents the mean number of nucleotide substitutions per site. The tree is midpoint rooted.

Figure 2

Pan-genome analysis, plasmid identification, and identification of mecA antibiotic resistance genes. The y-axis portrays the isolates. Two dimensional clustering of genes and isolates shows the genes of the pan-genome as present (red) or absent (white) in each isolate with a BLASTp similarity of 90%. The plasmid replicon genes are shown as purple and the absence of replicon gene is shown as yellow. The presence of mecA in the isolates is shown to the right. Blue is presence of mecA and green denotes absence of mecA.