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Background    Staphylococcus argenteus  and  S. schweitzeri , were recently proposed as novel species within  S. aureus  complex (SAC).  S. argenteus  has been reported in many countries and can threaten human health.  S. schweitzeri  has not been associated with human infections, but has been isolated from non-human primates. Questions regarding the evolution of pathogenicity of these two species will remain elusive until an exploratory evolutionary framework is established.    Results  We present genomic comparison analysis among members of SAC based on a pan-genome definition, which included 15  S. argenteus  genomes (five newly sequenced), six  S. schweitzeri  genomes and 30 divergent  S. aureus  genomes. The three species had divergent core genomes and rare interspecific recombination was observed among the core genes. However, some subtypes of staphylococcal cassette chromosome  mec  (SCC mec ) elements and prophages were present in different species. Of 111 tested virulence genes of  S. aureus , 85 and 86 homologous genes were found in  S. argenteus  and  S. schweitzeri , respectively. There was no difference in virulence gene content among the three species, but the sequence of most core virulence genes was divergent. Analysis of the  agr  locus and the genes in the capsular polysaccharides biosynthetic operon revealed that they both diverged before the speciation of SAC members. Furthermore, the widespread geographic distribution of  S. argenteus , sequence type 2250, showed ambiguous biogeographical structure among geographically isolated populations, demonstrating an international spread of this pathogen.    Conclusions    S. argenteus  has spread among several countries, and invasive infections and persistent carriage may be not limited to currently reported regions.  S. argenteus  probably had undergone a recent host adaption and can cause human infections with a similar pathogenic potential.    Electronic supplementary material  The online version of this article (10.1186/s12864-017-4149-9) contains supplementary material, which is available to authorized users.

Preliminary comparative genomics revealed pathogenic potential and international spread of Staphylococcus argenteus