Purpose: To investigate the prevalence of qnr, intI, and intII genes in extended spectrum betalactamase (ESBL)-producing Escherichia coli isolated from clinical samples in Kerman, Iran. Methods: A total of 127 E. coli were collected from clinical samples in Kerman hospitals. The antibiotic susceptibility test was performed using disc diffusion method, while the presence of ESBL-producing E. coli was determined by phenotypic confirmatory test. Furthermore, the presence of qnrA, qnrB, qnrS, intI,

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... intII, and β-lactamase-encoding genes was detected by polymerase chain reaction (PCR). Finally, the data were analyzed and associations between different genes and antibiotic resistance were evaluated. Results: The highest and lowest rates of resistance were observed against ampicillin (72.4 %) and imipenem (2.3 %), respectively. Also, 41.7 % of the isolates produced ESBL-enzymes. The qnrS and genes were detected in 6.3 and 0.78 %, respectively, of the isolates, while qnrA gene was not detected in the current study. The results revealed that 64.5 and 10.2 % of isolates carried intI and intII genes, respectively. Data analysis showed a significant association between ESBL production and class I integrin gene in E. coli isolates. Conclusions: Due to the variation in the resistance patterns of E. coli against antibiotics in different geographical regions, antimicrobial treatments should be based on local experience. Also, the coexistence of ESBL and intI gene in the majority of E. coli isolates suggests that care should be taken in choosing antibiotic therapy.