Staphylococcus aureus is a major etiological agent of mastitis in ruminants. We report here the genome sequences of two ovine strains that were isolated from gangrenous (strain O11) and subclinical (strain O46) ewe mastitis. Both strains belong to the same clonal complex. Despite this close genotypic relationship, the two isolates were shown to reproducibly induce highly divergent types of infections, either severe (O11) or mild (O46) mastitis, in an experimental ewe model.Staphylococcus aureus is one of the main pathogens involved in ruminant mastitis. Staphylococcal mastitis severity is highly variable, ranging from subclinical to gangrenous mastitis. Severity partly relies on bacterial factors. S. aureus strains isolated from bovine or ovine-caprine hosts differ from human isolates, as revealed previously (3), and genomic data regarding ruminant isolates are still scarce (4, 6). There is thus a need for more genomic data to better understand mastitis and identify bacterial factors involved in the severity of the infection.We characterized two S. aureus ovine strains, which were shown to be clonally related (9) and reproducibly induced severe (strain O11) and mild (strain O46) mastitis in experimental ewe mastitis (8).We sequenced the two genomes by using an Illumina Genome Analyzer GAII (Fasteris, Geneva, Switzerland).Base calling was performed with GAPipeline 1.4.0 software; a total of 27.6 million reads (pass filter) were obtained. After bar code selection, 13.9 and 11.8 million reads of 71 bases in length were obtained for O11 and O46, respectively. Sequence reads were de novo assembled with the Edena assembler (5), version 3.0. Assembly resulted in 87 contigs (sum, 2.77 Mbp; N 50 , 92.2 kbp; maximum, 266 kbp; minimum, 211 bp) and 96 contigs (sum, 2.81 Mbp; N 50 , 76.5 kbp; maximum, 209 kbp; minimum, 228 bp) for O11 and O46, respectively. (N 50 is contig size such that 50% of the entire assembly is contained in contigs equal to or larger than this size.) Totals of 2,787 and 2,822 coding sequences were detected for O11 and O46, respectively, by using Glimmer3 (PMID no. 17237039). Sequence comparison and single nucleotide polymorphism (SNP) calling were performed with MUMmer (7). Over 53% of the genes were assigned to specific subsystem categories by RAST (1). Gene products were submitted to protein location prediction using the software package SurfGϩ (2).The overall O11 and O46 genomes share high similarity to the ED133 genome. The great majority of the genes were common to both strains, except for an additional prophage (containing 42 coding sequences [CDSs]) detected in the O46 genome, which was not found in ED133 either. The putative O46 prophage genes are functionally unknown.