Molecular Epidemiology of mcr-1, blaKPC-2, and blaNDM-1 Harboring Clinically Isolated Escherichia coli from Pakistan.

Purpose The multiple-drug resistant Escherichia coli are among the deadliest pathogens causing life-threatening infections. This study was planned to determine the molecular epidemiology of mcr-1, blaKPC-2, and blaNDM-1 harboring clinically isolated E. coli from Pakistan. Methods In total, 545 strains of E. coli from clinical samples were collected from June 2018 to September 2019. All the isolates were screened for colistin-resistance, extended-spectrum-β-lactamases (ESBL), and carbapenemases through the micro-dilution method, Double-Disk-Synergy-Test (DDST), and Modified-Hodge-Test (MHT). The detection, sequence-typing, conjugal transfer, S1-PFGE, plasmid-replicon-typing, and southern-blotting for mcr, ESBL, and carbapenemase-encoding genes were performed. Findings A total of four (0.73%) colistin-resistant strains carrying alongside mcr-1 and blaCTX-M-15 genes, three of these strains also had the blaTEM-1 gene. The presence of ESBL genes was detected in 139 (25.5%) isolates harboring blaCTXM-15 (74.82%), blaTEM (34.53%), blaSHV (28.06%) and blaOXA-1 (28.78%). In 129 carbapenemase-producers, 35.83% possessed blaNDM-1, 26.67% blaKPC-2, 8.3% blaOXA-48, 25% blaVIM-1, and 20.83% blaIMP-1 genes. The sequence typing revealed that mcr-1 harboring isolates belonged to ST405, ST117, and ST156. Fifty percent of blaKPC-2 and 48.83% of blaNDM-1 were found on ST131 and ST1196, respectively. Two rare types of STs, ST7584, and ST8671 were also identified in this study. The mcr-1 gene was located on Incl2 (60-kb) plasmid. The blaKPC-2 was present on (140-kb) IncH12, (100-kb) IncN, (90-kb) Incl1, while blaNDM-1 was located on (70-kb) IncFIIK, (140-kb) IncH12, (100-kb) IncN, (60-kb) IncA/C, and (45-kb) IncFII plasmids, which were successfully trans-conjugated. Among the plasmid types, the Incl1 carrying blaKPC-2, IncH12 harboring blaKPC-2 and blaNDM-1, and IncFIIK carrying blaNDM-1 were for the first time detected in Pakistan. Conclusion The mcr-1, blaKPC-2, and blaNDM-1 genes finding in various clonal and plasmids types indicate that a substantial selection of the resistance genes had occurred in our clinical strains.