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Antibiotic resistance in avian pathogenic Escherichia coli (APEC) is a common problem in the Indonesian poultry industry. Zoo birds have been postulated as sentinels, reservoirs, and potential spreaders of antibiotic resistance, although much is still unknown about the strains of zoo birds. Disinfection can reduce the infection burden. However, little is known about the presence of resistance against these products. Sixty one APEC strains were isolated from Indonesian zoo birds. The resistance to different classes of antibiotics as well as the minimum inhibitory concentrations (MIC) and minimum bactericidal concentrations (MBC) of five disinfectants most often used in the poultry industry was determined. Resistance to tetracycline (42.6%), sulfonamides (24.5%), ampicillin (22.9%), gentamicin (19.6), nalidixic acid (18.03%) and streptomycin (16.3%) was high, but resistance to other tested antibiotics was low and none of the isolates were resistant to extended spectrum beta-lactamase (ESBL) producers. Sixteen strains (26.2%) were found positive for multi drug resistance. The MIC of the disinfectants for the APEC strains showed normal distribution, indicating that there was no acquired resistance. MBCs were similar to MICs using the broth dilution method, showing the bactericidal effect of the disinfectants. Phenotypic resistance to commonly used disinfectants could not be found, indicating that the current use of disinfectants in the zoo and aviaries did not select for resistance. Significantly high resistance rates against commonly used antibiotics in Indonesian zoos is worrisome and indicates that widespread use of antibiotics could have negative implications for animal health and the environment. Proper use of antibiotics and surveillance programs to monitor antimicrobial resistance in pathogenic bacteria are warranted.