Microbiological Biodiversity of Regional Cow, Goat and Ewe Milk Cheeses Produced in Poland and Antibiotic Resistance of Lactic Acid Bacteria Isolated from Them

SIMPLE SUMMARY: Traditional and regional cheeses are becoming more and more popular among consumers. Usually, they are produced in small dairy plants which are characterized by a unique microbiota of the processing area. The unique microbiota determines both the microbial quality and safety of the final products. Another issue related to the microbiological safety of food products is the presence of antibiotic resistance (AR) in microbiota, which is a potential health issue for humans. The AR was mainly investigated in pathogenic bacteria as a direct risk for effective antimicrobial therapy. However, the AR phenomenon is also present in desired food bacteria participating in the production of dairy products. These bacteria can be a reservoir of antibiotic resistance genes (ARG) in the environment, therefore monitoring AR in LABs seems to be an urgent need for ensuring the safety of food. In this work, we investigated the microbial diversity of ripened and unripened cheeses produced from cow, ewe, and goat milk in Poland, and identified LAB typical for cheeses and microbiota characteristic of the investigated types of cheese. Moreover, we assessed the phenotypic AR and the presence of ARG in lactic acid bacteria. ABSTRACT: (1) Unique sensory values of traditional and regional dairy products made them more and more popular among consumers. Lactic acid bacteria naturally occurring in these products can express antibiotic resistance and be a reservoir of antibiotic resistance genes (ARG) in the environment. The aim of the study was to characterize the microbial diversity of twenty regional cheeses produced from non-pasteurized cow, goat and ewe milk, and investigate the phenotypic and genotypic antibiotic resistance (AR) of lactic acid bacteria isolated from these products. (2) Conventional microbiological methods were applied for the enumeration of lactic acid bacteria (lactobacilli and lactococci) and their isolation, and for the enumeration of Enterococcus, Staphylococcus, Enterobacteriaceae and spores. The disc diffusion method was applied for phenotypic AR. The PCR-based methods were used for strain identification, microbiological diversity of cheeses (PCR-DGGE), and for AR gene detection. (3) Among 79 LAB isolates the most frequent species were L. plantarum (n = 18), Leuc. lactis (n = 17), Lc. lactis (n = 11), Leuc. mesenteroides (n = 9) and L. pentosus (n = 8). Additionally, by using the PCR-DGGE method, DNA of L. casei was found in nine products. Lactobacilli (5.63–8.46 log cfu/g) and lactococci (6.15–8.41 log cfu/g) predominated over Enterococcus (max. 4.89 log cfu/g), Staphylococcus (max. 4.18 log cfu/g), and Enterobacteriaceae (mostly up to 4.88 log cfu/g). Analysis of phenotypic resistance to tetracycline (30 µg), erythromycin (15 µg), and chloramphenicol (30 µg) showed that 29% of LAB isolates were resistant to one antibiotic, 8%—to two, and 12%—to all tested antibiotics. Antibiotic resistance genes (AGR) for tetracycline (tet(M), tet(L), tet(W)), erythromycin (erm(B)) and chloramphenicol (cat-TC) were detected in 30 (38%), 29 (36.7%) and 33 (43.4%) LAB isolates, respectively. Among 31 LAB isolates phenotypically susceptible to all tested antibiotics, only 5 (16%) had no ARGs. (4) The results obtained in our work shed light on the potential threat posed by the widespread presence of ARGs in LAB present in regional cheeses.