Background:  Multidrug resistant Escherichia coli (MDR-E.coli) is becoming a major public health concern worldwide causing obstruction of disease control and increased the cost of treatment because pathogens have become resistant to commercially available drugs, necessitating the use of more expensive therapies. Objectives: This study aimed to detect the presence of plasmid mediated colistin resistant mcr-1 gene in extended spectrum β-lactamase (ESβL) producing Escherichia coli from clinical samples. Methods: In this cross-sectional study a total of 88 multidrug resistant E. coli isolates were collected from different hospitals in Khartoum state. The isolates were cultured on MacConkey agar media at 37^o C for 24 hours subsequently routine bacterial identification was done by performing colonial morphology, Gram staining, and biochemical tests. Antimicrobial susceptibility testing was performed following the modified Kirby-Bauer disc diffusion method, then phenotypic confirmatory test for ESβL producers was done by using the double disc synergy test. Results: A total of 88 (100%) E. coli isolates were multi drug resistant, 7(8%) of which were phenotypically resistant to colistin. After performance of the double disc synergy test for detection of extended spectrum β lactamase, 29 (33%) isolates were positive.  PCR technique was done to detect the presence of mcr-1 gene in 7 MDR isolates, the result showed that 4 (57,1%) were carriers for mcr-1 gene. Conclusion: This study confirms the presence of mcr-1 gene in E. coli in clinical isolates and all E. coli isolates that were carriers of mcr-1 gene were confirmed to be producers of ESβL.