Antibiotic Resistance of Enterobacteriaceae in Microbiomes Associated with Poultry Farming

Antibiotics have long been overused for non-therapeutic purposes. As a result, Escherichia, Enterobacter, Klebsiella, and Proteus in avian microbiomes have become reservoirs for genetic determinants of resistance, thus spreading resistance to antibiotics and contaminating raw materials and finished products. The food industry is looking for alternative means to preserve health and maintain high productivity of commercial poultry, e.g., probiotics, phytobiotics, organic acids, etc. The research featured the effect of antibiotics and phytobiotics on enteropathogenic bacteria in the microbiomes of broiler chicken. Escherichia coli bacteria were cultivated in vitro in subthreshold concentrations on nutrient media with antibiotics for 37 days to study the effect of low doses of antibiotics on the sensitivity of isolates. The study involved microbiocenoses of broiler chicken that received avilamycin A and a phytobiotic based on Brassica juncea, Linum usitatissimum, and Nigella sativa L. A set of experiments covered the species composition of opportunistic Enterobacteriaceae, the phenotypic sensitivity to antibiotics, and the genetic determinants of resistance, as well as the antimicrobial potential of phytobiotics. E. coli developed no resistance for 37 days when the antibiotic dose remained below minimal inhibitory. Opportunistic gram-negative Enterobacterales predominated in all litter samples. E. coli, Klebsiella pneumoniae, and Proteus mirabilis accounted for more than 30% of all isolated strains. Avilamycin A and the phytobiotic affected the coccal microflora but had no effect on the genus-species composition of Enterobacteriaceae. Litter samples from both experimental and control groups demonstrated K. pneumoniae with severe phenotypic resistance to ciprofloxacin, as well as blaDHA genes. In broiler farming, maintenance and circulation of resistance agents depends on litter microbiota. In this research, the chicken that received the phytobiotic showed the lowest level of resistance to ciprofloxacin while the groups that received avilamycin A had the highest resistance results. During a broiler’s life span, bacteria with no active resistance determinants in their genome remained sensitive to antibiotics, even though the contact with the latter was constant. Phytobiotics showed good prospects for broiler farming as food additive that could reduce and eventually eliminate the intake of antibiotics.