To demonstrate the resistance of antibiotics and disinfectants to Escherichia coli isolates, 255 E. coli strains were isolated from 328 retail meat samples in this study. Susceptibility testing results showed that 85.5% isolates were resistant to at least one antibiotic drug. The E. coli isolates showed the highest resistance to sulfamethoxazole (61.6%), followed by tetracycline (61.2%), ampicillin (48.2%), cefalotin (29.8%), and kanamycin (22.4%). The minimum inhibitory concentrations of the disinfectants cetyltrimethylammonium bromide, N,N-didecyl-N,N-dimethylammonium chloride, cetyltrimethylammonium bromide, and cetylpyridinium chloride for E. coli were 16-1,024, 4-1,024, 16-512, and 8-512 mg/L, respectively. The emrE, ydgE/ydgF, mdfA, and sugE(c) genes were commonly present (53.7-83.1%), but the qac and sugE(p) genes were less prevalent (0.0-14.9%). The qac genes were highly associated with antimicrobial resistance. Conjugative transfer experiment indicated that the disinfectant resistance genes, qacF, sugE(p), and qacEΔ1, were located on conjugative plasmids. Pulsed-field gel electrophoresis revealed that the antimicrobial-resistant isolates were associated with the sampling supermarkets or groceries. This study indicated that using quaternary ammonium compounds to decontaminate food processing environments may be ineffective and even provide a selective pressure for strains with acquired resistance to other antimicrobials.