This paper contains the results of complex microbiological studies (culture method, real-time PCR) of biological material from cows affected by inflammatory diseases of reproductive organs and mammary gland. Milk microbiota with underlying subclinical mastitis was represented by pathogenic (S. aureus, enteropathogenic E. coli), opportunistic bacteria (Staphylococcus spp., E. coli, E. faecium, Streptococcus spp., S. agalactiae, P. aeruginosa) and yeast-like fungi of Candida spp. in association. Combined infectious and inflammatory diseases of genital tract and mammary gland in cows resulted in the same types of microorganisms in microflora composition, which confirms information obtained by other researchers on associated microbiota during inflammatory processes. S. aureus, P. aeruginosa, E. coli, E. faecium, E. faecalis, S. epidermidis, S. saprophyticus, Bacillus spp., and yeast-like fungi of Candida spp. were obtained from milk samples from cows with acute clinical mastitis and in vaginal washes from cows with acute postpartum endometritis. In the course of defining the sensitivity to antibiotics and identifying genes of antimicrobial resistance, multidrug resistance was established in most part of obtained strains, which should be taken into account when planning treatment measures.
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