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The presence of Staphylococcus aureus and methicillin-resistant S. aureus (MRSA) in raw milk is a challenge for veterinarians and public health professionals. In this study, we investigated the presence and clonality of S. aureus and MRSA in milk of individual dairy goats with subclinical mastitis reared under the low-input farming system in Greece and determined the isolates' enterotoxin gene carriage and their ability to form biofilms. S. aureus was isolated from 162 out of the 559 milk samples examined (29 %) and one isolate per S. aure