Colistin-Resistant Escherichia coli Isolated from Houseflies and Feces of Cattle and Pigs at a Slaughterhouse in Lima, Peru

Background: Pigs and cattle have been implicated as reservoirs of antimicrobial resistance genes (ARGs) that can spread to humans, and houseflies are considered potential carriers of bacteria with ARGs that could contribute to their spread to the environment, including food, animals, and humans. Methods: In this study, 107, 145, and 127 Escherichia coli strains were isolated from houseflies, pigs, and cattle, respectively, from a slaughterhouse in Lima, Peru. Antimicrobial susceptibility testing was performed using the Kirby–Bauer method, where thirteen antibiotics were used. Strains were also plated on CHROMagar COL-APSE agar, and colistin’s minimum inhibitory concentration (MIC) was determined. Colistin-resistant E. coli strains were subjected to whole genome sequencing. Results: 7.8% (8/107), 1.38% (2/145), and 0.79% (1/127) of E. coli strains isolated from houseflies, pigs, and cattle, respectively, were resistant to colistin (MIC ≥ 4 µg/mL). ARGs associated with resistance to more than 6 different antibiotic classes were identified, including tetracyclines, beta-lactams, fluoroquinolones, nitroimidazoles, trimethoprim and amphenicols. Conclusions: This study suggests that flies could contribute to the dissemination of ARG carrying bacteria and shows the potential risk of animals and meat production systems as reservoirs of ARG carrying bacteria.