Impact of Exposure to Disinfectants on Presence of Efflux Pump Genes and Antibiotic Resistance Profiles in Escherichia coli Isolates

Disinfectant tolerance in bacteria may be related to exposure to subinhibitory concentrations of disinfectants, which may activate efflux pumps capable of expelling antimicrobial compounds. The aim of this study was to evaluate the impact of disinfection on the presence of efflux pump genes and the resistance profile of <i>Escherichia coli</i> from commercial laying farms employing different disinfection protocols. The <i>emrE</i>, <i>qacE</i>, <i>qacEΔ1</i>, <i>qacH</i>, <i>sugE(c)</i>, <i>ydgE</i>, <i>ydgF</i>, and class 1 integron (<i>intl1</i>) genes were investigated using PCR. Susceptibility to 17 antibiotics was assessed, including β-lactams, fluoroquinolones, aminoglycosides, and tetracyclines. Disinfectant exposure was significantly associated with higher frequencies of <i>qacE</i> and <i>qacH</i>, and a reduced frequency of <i>ydgF</i>. Moreover, resistance to ampicillin, trimethoprim-sulfamethoxazole, and doxycycline was significantly more frequent in <i>E. coli</i> isolated from chickens exposed to disinfectants. These findings indicate that disinfectant use can select for <i>E. coli</i> carrying efflux pump genes and resistance genes, favoring the survival and dissemination of tolerant and resistant strains in poultry production. Continuous monitoring and the development of disinfection strategies that minimize selective pressures are crucial for limiting the spread of antimicrobial resistance at the animal-human-environment interface.