Staphylococcus aureus is a major cause of mastitis in bovine and other ruminant species. We here present the results of a comparative genomic analysis between a bovine mastitis-associated clone, RF122, and the recently sequenced human-associated clones, Mu50 and N315, of Staphylococcus aureus. A shotgun sequence survey of ϳ10% of the RF122 genome identified numerous unique sequences and those with elevated rates of nonsynonymous substitution. Taken together, these analyses show that there are notable differences in the genomes of bovine mastitis-associated and human clones of S. aureus and provide a framework for the identification of specific factors associated with host specificity in this major human and animal pathogen.Staphylococcus aureus is a widely distributed animal and human pathogen. Phenotypic analyses of S. aureus strains isolated from human and bovine hosts have revealed important differences between the two populations of isolates, but the underlying genetic basis for the variation among S. aureus strains remains unknown (10,14,15). Multilocus enzyme electrophoretic analysis of 2,077 S. aureus isolates from bovine, ovine, and human hosts showed that only 6 of the 33 clusters included isolates from more than one host species (11). Population genetic analysis of 357 S. aureus isolates recovered from cases of bovine mastitis from global sources suggested that only eight clones represented 90% of the isolates, and these clones rarely overlapped with those responsible for human disease (5). To begin identifying the nature and scope of the genetic differences between the bovine and human staphylococcal genomes, we present here a comparative analysis of the genome content of the common bovine S. aureus clone RF122 (4) and the recently sequenced human pathogenic clones Mu50 and N315 (6).A random shotgun genomic library was prepared as described previously (7), with the exception that RF122 genomic DNA was mechanically sheared with a Hydroshear device (GeneMachines, San Carlos, Calif.). The first 850 random shotgun clones of RF122, encoding 285,077 unique bases and representing approximately 10% of the total genome, were sequenced by using dideoxy terminator chemistry on ABI 3700 DNA sequencers (ABI, Foster City, Calif.) and assembled into 600 contigs consisting of one to six sequences and ranging in size from 82 to 1,828 bases using phredPhrap (P. Green, University of Washington, Seattle) (details of individual genes, gene names, and categories are available at http://www.cbc.umn .edu/ResearchProjects/AGAC/Staph/staphhome.html). The average GC content of the initial sequences was 33.95%, closely approximating the GC content of the completed S. aureus genomes (6). The range of GC contents of individual contigs was 21 to 73%. Fourteen contigs had GC contents greater than 45%. Of these, two had no significant hits (P Ͻ e-15) to any GenBank submission based on tBLASTn searches, five had significant homology to S. aureus genomic DNA, and one was homologous to an S. aureus plasmid (1). The remaining five contig...