Introduction: Due to the increasing trend of antibiotic resistance in the Enterobacteriaceae family, treatment of infections caused by these bacteria has been difficult. The aim of this study was to identify of class I and II integrons and associated gene cassettes in clinical isolates of Escherichia coli and Klebsiella pneumonia.

Methods: In this cross-sectional study, of 500 strains isolated from clinical samples of hospitals in Hamadan, Iran, in 2015, 129 K. pneumoniae and 118 E. coli isolates were isolated and examined. Then, the isolates were verified by standard biochemical methods and PCR was performed on class I and II integron genes using specific primers.

Results: The results of this study showed that the prevalence of class I integrons was more than class II integrons. The most frequent class I integron gene cassettes were aadA1 and dfrA7 respectively, which are resistance encoding genes for kanamycin and trimethoprim.

Conclusions: The result of this study indicated a high prevalence of class I integrons in E. coli and K. pneumonia isolates. Thus, the identification of these resistance genes for infection control programs and to prevent the spread of resistant strains is very important