Raw milk Cheeses as Reservoirs of Antimicrobial-Resistant Bacteria: A Comparative Study of Goat and Sheep Milk Products

Raw milk cheeses represent complex microbial ecosystems that may act as reservoirs of antimicrobial-resistant bacteria. This study investigated the microbiological characteristics, bacterial community structure, and antimicrobial resistance (AMR) profiles of artisanal goat and sheep cheeses produced by regional manufacturers in Poland. A total of ten cheeses, including five goat cheeses and five sheep oscypek-type cheeses, were analysed. Culture-dependent enumeration and isolation were combined with molecular identification via 16S rRNA gene sequencing and antimicrobial susceptibility testing by disk diffusion. Total viable bacterial counts ranged from 105 to 108 CFU/mL, revealing considerable variability among individual samples. Microbiological profiling indicated the predominance of lactic acid bacteria, with Lactococcus, Lactobacillus, and Streptococcus representing the dominant genera. Multivariate analysis (PCoA) demonstrated substantial intra-group dispersion and overlapping clustering patterns between goat and sheep cheeses, suggesting that sample-specific ecological factors exerted a stronger influence on microbial composition than milk origin. Among 150 bacterial isolates, multidrug resistance (MDR) was detected in 28.7% of strains. MDR prevalence varied markedly between bacterial groups, reaching 100.0% in Enterobacterales, 73.3% in Enterococcus spp., and 16.2% in lactic acid bacteria. Resistance was most frequently observed for aminoglycosides and β-lactam antibiotics, particularly streptomycin and gentamicin. The results indicate that artisanal cheeses constitute heterogeneous microbial niches and may serve as potential reservoirs of antimicrobial-resistant bacteria. Integrating microbiological and AMR analyses provides valuable insight into the ecological determinants of resistance in traditional dairy products. These findings indicate that artisanal cheeses may represent heterogeneous microbial niches and potential reservoirs of AMR bacteria. The integration of microbiome profiling and phenotypic AMR assessment provides valuable insight into the ecological drivers of resistance in traditional dairy products.