Antibiotic Resistance and Zoonotic Potential of Escherichia coli Strains Isolated from Birds in the Poultry Agro-Industrial Complex

Commercial poultry is a source of antibiotic-resistant and potentially pathogenic Escherichia coli, which can circulate in enterprises and enter the environment through organic waste. The objective of the study is to analyze the antibiotic resistance profiles, virulence-associated genes, and phylogroups of E. coli strains circulating on the poultry farms in Perm Krai. Thus, the strains detected in the samples of three different groups, including healthy poultry (n = 16), chickens with colibacillosis (n = 28), and organic waste samples (n = 19), were studied. The PCR method was used to detect the antibiotic resistance and virulence genes. The prevalence of the multidrug-resistant E. coli strains comprised 18.8, 75, and 73.7% of strains found in the first, second, and third groups, respectively. In the E. coli DNA, up to six antibiotic resistance genes were detected. The beta-lactamase (blaTEM) gene was found to be most prevalent in all the groups. More than half of E. coli strains isolated from sick birds carried blaCTX–M. In organic waste samples, a high proportion of E. coli harbored the blaSHV gene (63.2%) was revealed. In this same group, the tetA efflux pump gene was detected more frequently. In addition, more than 20% of E. coli strains in that category group carried the genes encoding QnrB and QnrS proteins responsible for plasmid-mediated resistance to fluoroquinolones. Most isolates from healthy poultry, sick birds, and organic waste samples were assigned to phylogroups E, B1, and C or E, respectively. Avian pathogenic E. coli (APEC), including high-risk clones, were found at high frequency in the group of strains isolated from sick birds (75%). In addition, they were found in the group of strains isolated from healthy birds (6.3%) and organic waste samples (63.2%). Most of the analyzed E. coli (54%) combinations of genetic markers for both extraintestinal and intestinal pathotypes E. coli, indicating their high zoonotic potential.