Molecular Epidemiology of mcr-1, bla KPC-2, and bla NDM-1 Harboring Clinically Isolated Escherichia coli from Pakistan

The multiple-drug resistant are among the deadliest pathogens causing life-threatening infections. This study was planned to determine the molecular epidemiology of , and harboring clinically isolated from Pakistan. In total, 545 strains of 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 , ESBL, and carbapenemase-encoding genes were performed. A total of four (0.73%) colistin-resistant strains carrying alongside and genes, three of these strains also had the gene. The presence of ESBL genes was detected in 139 (25.5%) isolates harboring (74.82%), (34.53%), (28.06%) and (28.78%). In 129 carbapenemase-producers, 35.83% possessed , 26.67% , 8.3% , 25% , and 20.83% genes. The sequence typing revealed that harboring isolates belonged to ST405, ST117, and ST156. Fifty percent of and 48.83% of were found on ST131 and ST1196, respectively. Two rare types of STs, ST7584, and ST8671 were also identified in this study. The gene was located on Incl2 (60-kb) plasmid. The was present on (140-kb) IncH12, (100-kb) IncN, (90-kb) Incl1, while 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 , IncH12 harboring and , and IncFIIK carrying were for the first time detected in Pakistan. The , and genes finding in various clonal and plasmids types indicate that a substantial selection of the resistance genes had occurred in our clinical strains.