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Methicillin-resistant Staphylococcus aureus (MRSA) poses a serious challenge to both human and veterinary health. The pathogen has been present almost continuously at the Department and Clinic of Equine Medicine at the University of Veterinary Medicine since at least 2008. Due to a Salmonella outbreak in the summer of 2024, a thorough cleaning and disinfection were carried out. Subsequently, no MRSA infections were identified at the clinic for a long period (7 months), until the end of April 2025. The aim of the study was to investigate the effect of epidemiological measures on the MRSA population.

In the spring of 2024, MRSA screening tests were conducted on staff (n =48) and in the environment (n = 23). Following the Salmonella outbreak, samples were also collected from horses (n =211) admitted to the clinic through December. In early 2025, to assess the impact of the intervention, the previous human (n = 44) and environmental (n = 16) screening tests were repeated. In addition, samples from MRSA-infected horses were preserved from 2024 through September 2025 (n = 15). After pre-enrichment, the received samples were cultured on selective differential media and then identified using PCR. For MRSA isolates, disk diffusion susceptibility testing was performed according to EUCAST recommendations. We used the MLSTFinder, ResFinder, SCCmecFinder, and BioNumerics software to analyze data from whole-genome sequencing of the isolates.

A total of 39 samples collected during the study tested positive for MRSA. Prior to the intervention, 16.7% of human samples and 47.8% of environmental samples were positive; afterward, 6.8% of human samples were positive, while no MRSA was detected in the environment. Only 2 (0.9%) of the nasal swab samples from incoming horses tested positive. Most isolates (35/39) were of the ST398 sequence type, which predominantly carried the SCCmec cassette gene type IVa. We identified 94.3% (n=33) of the ST398 isolates as equine hospital-associated (EHA-)MRSA, all of which carried the lukPQ and horse-specific scn virulence genes. In 4 staff isolates, we identified the human-specific scn gene. Based on whole-genome MLST analysis, the isolates—with 3 exceptions—can be classified into two main clusters. All isolates were multidrug-resistant.

Given the minor differences among the EHA-MRSA strains isolated in 2024 and 2025, we were unable to determine the source of reinfection. Greater genetic diversity was observed in 2024 prior to the intervention, suggesting the parallel accumulation of multiple MRSA strains over a longer period. In contrast, the narrow genetic variability of the 2025 clinical isolates suggests the spread of a dominant clone. The decrease in environmental load and the rate of human carriage can be explained by the effectiveness of comprehensive disinfection. Given the low rate of MRSA carriage among incoming horses, it is unlikely that they play a significant role in maintaining the equine clinical MRSA population.