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Background   Staphylococcus pseudintermedius  (SP) and  Staphylococcus aureus  (SA) are common colonizers of companion animals, but they are also considered opportunistic pathogens, causing diseases of diverse severity. This study focused on the identification and characterization of 33 coagulase-positive staphylococci isolated from diseased pets (28 dogs and five cats) during 2009–2011 in a veterinary hospital in Spain in order to stablish the circulating lineages and their antimicrobial resistance profile.    Results  Twenty-eight isolates were identified as SP and five as SA. Nine methicillin-resistant (MR) isolates (27%) carrying the  mecA  gene were detected (eight MRSP and one MRSA). The 55% of SP and SA isolates were multidrug-resistant (MDR). MRSP strains were typed as ST71- agr III-SCC mec II/III-(PFGE) A ( n =5), ST68- agr IV-SCC mec V-B1/B2 ( n =2), and ST258- agr II-SCC mec IV-C ( n =1). SP isolates showed resistance to the following antimicrobials [percentage of resistant isolates/resistance genes]: penicillin [82/ blaZ ], oxacillin [29/ mecA ] erythromycin/clindamycin [43/ erm (B)], aminoglycosides [18–46/ aacA-aphD, aphA3, aadE ], tetracycline [71/ tet (M),  tet (K)], ciprofloxacin [29], chloramphenicol [29/ cat  pC221 ], and trimethoprim-sulfamethoxazole [50/ dfrG ,  dfrK ]. The  dfrK  gene was revealed as part of the  radC -integrated Tn 559  in two SP isolates. Virulence genes detected among SP isolates were as follow [percentage of isolates]:  siet  [100] , se-int  [100] , lukS/F-I  [100] , sec   canine   [7], and  expB  [7]. The single MRSA- mecA  detected was typed as t011-ST398/CC398- agr I-SCC mec V and was MDR. The methicillin-susceptible SA isolates were typed as t045-ST5/CC5 ( n =2), t10576-ST1660 ( n =1), and t005-ST22/CC22 (n=1); the t005-ST22 feline isolate was PVL-positive and the two t045-ST45 isolates were ascribed to Immune Evasion Cluster (IEC) type F. Moreover, the t10576-ST1660 isolate, of potential equine origin, harbored the  lukPQ  and  scn eq genes. According to animal clinical history and data records, several strains seem to have been acquired from different sources of the hospital environment, while some SA strains appeared to have a human origin.    Conclusions  The frequent detection of MR and MDR isolates among clinical SP and SA strains with noticeable virulence traits is of veterinary concern, implying limited treatment options available. This is the first description of MRSA-ST398 and MRSP-ST68 in pets in Spain, as well the first report of the  dfrK -carrying Tn 559  in SP. This evidences that current transmissible lineages with mobilizable resistomes have been circulating as causative agents of infections among pets for years.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12917-020-02726-4.

S. pseudintermedius and S. aureus lineages with transmission ability circulate as causative agents of infections in pets for years