Background: CNF are single-chain proteins that are created by some uropathogenic Escherichia coli.There are three types of CNFs detected in E.coli, but CNF1 represent more frequently. Objective: The purposes of this study were to determine the prevalence of cnf1 and cnf2 genes in  E. coli isolates by using specific primers. Materials and Methods: The sensitivity test was evaluated by using different types of antibiotics in the current study, and the cnf1 and cnf2 genes were detected by PCR in all bacterial isolates. Results: The antibiotics sensitivity test show variable degrees of sensitivity and resistance. The high percentage of sensitivity was achieved against amikacin at a percentage of 86% and ciprofloxacin, ceftazidime, gentamicin, and tobramycin at a percentage of 80%, whereas trimethoprim and aztreonam at 64%and 60% respectively. In this study, most isolates were resistant to Amoxicillin (92%);  while showing different degrees of resistance against other types of antibiotics ranging from Tetracycline (62%) to amikacin 4%.  The frequency of MDR bacteria was about 64 % (32 isolates), 30 from urine, and 2 others from stool. The results revealed that the cnf1 gene was found in Five bacterial isolates (10%), whereas the other 45 (90%) isolates don't have this gene, while cnf2 wasn't found in any one of the bacterial isolates. Conclusion: E.coli was recorded as multidrug resistance (MDR) and the cnf1 gene was found only in uropathogenic isolates.