Characteristics of Extended-Spectrum β-Lactamase Genes in Escherichia coli Isolated from Different Animal Sources.

Antimicrobial resistance associated with the spread of the plasmid-encoded extended-spectrum b-lactamase (ESBL) genes, conferring resistance to third-generation cephalosporins is a major concern in global public health. The purpose of this study was to investigate the molecular characteristics of ESBL-encoding genes identified in Escherichia coli isolated from swine, beef, dairy, and poultry etc. collected from different regions of the United States. Three hundred samples were typed into different phylogroups, characterized by REP-PCR and PCR was performed to identify the corresponding ESBL genes followed by susceptibility testing by the disk diffusion method. Of the 300 isolates, 59.7% were resistant to sulfsoxazole, 49.3% to tetracycline, 32.3% to cephalothin, 22.3% to ampicillin, 20% to streptomycin, 16% to ticarallin, and the remaining 12 antimicrobials carried less than 10 % resistance. A total of 81 E. coli were confirmed as ESBL producers by double-disk synergy testing. Of the 81 ESBL-positive isolates identified 11 were from beef, 27 from dairy, 31 from swine, 6 from poultry, 2 from fish, 2 from horse, 1 from lamb, 1 from sediment, and 0 from river samples. ESBL-positive isolates identified, bla_CTX-M, bla_TEM, bla_OXA, and bla_SHV in 25.3%, 22.3%, 0%, and 13% of these isolates, respectively. Shotgun metagenomics analysis produced high levels of tetracycline, multidrug, erythromycin, and aminoglycoside resistance genes. The results demonstrated that bacteria in swine, chicken, dairy and beef fecal were assigned to 28, 21, 32, and 35 phyla, respectively. Significantly, higher levels of ARGs were detected in chicken and dairy feces than others, suggesting higher ARG contamination. This study provides evidence of the main sources of ARGs/ARBs from different animal environments in the watershed.