Background: Staphylococcus aureus is a major agent of mastitis in ruminants worldwide. Symptoms observed in ewe S.aureus intramammary infections (IMI) are very different from one case to another: IMI ranges from subclinical mastitis to lethal gangrenous mastitis. Neither the S. aureus nor the host - factors contributing to the different outcomes are known. Objectives: Identify differences between S. aureus strains implied in the acuteness of IMI. Methods: Two S. aureus strains isolated from subclinical mastitis (O46) and gangrenous mastitis (O11) were compared by using PFGE, MLST, Micro - array, spa type, s as type, SNP, MLVA type, and RAPD. Proteomic profiles of these strains were also compared. After growth in iron depleted RPMI with low oxygen, conditions that mimic IMI context, cell wall, cytoplasmic and secreted proteins were extracted and ran on 2D gels . Results: O11 and O46 were genetically closely related. They had identical PFGE patterns (OV/OV', the main pattern in South East of France), were in the same MLST cluster. They shared 3615 identical targets using a pangenomic microarray. The core genes, the core variable genes, and the mobile genetic elements were essentially the same in both strains. The major differences were in spa type, sdrD , splE , fnbB , and the presence of the prophage genes (SAS0897, SAR1558, SAR0940, SAR2100, SACOL0343). RAPD show ed the presence of an unknown gene SAB 1979 in O11. Comparative proteomic revealed over secretion of some proteins ( hlg , isdB ,hly , lukF - PV, lukM, enolase) by O11. Conclusions: Absence of a prophage as well as surface protein variants were associated with enhanced virulence. Differences can either be explained by over expression of some virulence factors. This study shows that IMI acuteness can partly be explained by strain genetic content. The impact of host factors on ewe susceptibility to IMIs still remains to be determined.