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

This study investigated the microbiological composition and antimicrobial resistance (AMR) profiles of artisanal goat and sheep milk cheeses produced in Poland. Ten raw milk cheeses (five each from goat and sheep milk) were analyzed using a combined approach involving culture-dependent enumeration, 16S rRNA gene sequencing, and antibiotic susceptibility testing. Microbial counts revealed substantial variability among the samples, with lactic acid bacteria (LAB) dominating the microbiota. Taxonomic analysis confirmed the predominance of Lactococcus, Streptococcus, and lactobacilli, although marked intra-group heterogeneity was observed. Multivariate analyses indicated that sample-specific factors had a greater influence on microbiome composition than milk origin. Among 170 isolates, 28.7% were classified as multidrug-resistant (MDR), being most prevalent in Enterobacterales (100%) and Enterococcus spp. (73%), whereas LAB exhibited low resistance levels (16.2%). Resistance was most frequently associated with aminoglycosides and β-lactams. The resistance results were interpreted according to CLSI guidelines. These findings demonstrate that artisanal cheeses harbor complex, dynamic microbial ecosystems that may serve as reservoirs of antimicrobial resistance. The results highlight that environmental and technological factors, rather than milk source alone, are key drivers of both microbiome structure and resistance distribution, underscoring the need for targeted AMR monitoring in traditional dairy products.