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Staphylococcus aureus (S.aureus)2 is a common pathogen that can cause serious infections, even death.Because of the horizontal gene transfer (HGT) of antibiotic resistance genes, the drug resistant condition is becoming increasingly prevalent.Recently, an adaptive immunity system, named clustered regularly interspaced short palindromic repeats (CRISPR), was discovered and demonstrated to confer a defense against foreign invading elements that may carry the antibiotic resistance genes.In this study, we reveal the features of 45 identified CRISPR loci and the CRISPR associated gene (Cas) in 32 S.aureus strains from CRISPR database.Five spacers of S.aureus 08BA02176 and MSHR1132 were homologous with foreign genetic sequences from phages or plasmids, even containing a spacer sequence identical to part of some phages genomes containing lukPV gene that encodes the PVL toxin.Many S.aureus strains with the same CRISPR type shared the same MLST type.CRISPR loci that had 3 or more similar protein loci mostly belonged to the same CRISPR type.We came to the conclusion that the CRISPR/Cas of strains 08BA02176 and MSHR1132 were inherited from a common ancestor or recombined from S.lugdunensis.CRISPR loci can be mobilized and can transfer among different but closely related species, and the same types of MLST strains exhibit a higher affinity to the same types of CRISPR loci.Bacteriophages may be the predominant challenge facing S.aureus.The CRISPR/Cas structure may limit the transmission of bacterial virulence among S.aureus.