Dissemination of various NDM-type metallo-beta-lactamases producing multidrug-resistant Escherichia coli clinical isolates in Nepal

A total of 250 E. coli isolates obtained from different patients were screened for carbapenem-resistant isolates by microdilution methods. The whole genomes of the carbapenem-resistant isolates were sequenced by MiSeq (Illumina). Phylogenetic trees were constructed from single nucleotide polymorphism concatemers. Multilocus sequence types were deduced and drug resistance genes were identified. Of the 250 E. coli isolates, 39 (15.6%) were cabapenem-resistant isolates, with the majority resistant to aminoglycosides, carbapenems, and fluoroquinolones but not to colistin and tigecycline. Of the all carbapenem-resistant E. coli, 97.5% of the isolates harbored blaNDMs. A majority of these isolates harbored 16S rRNA methylase genes. The present study suggests that the majority of carbapenem-resistant E. coli produced various NDM-type metallo-beta-lactamases in medical settings in Nepal. The antibiotics usages in Nepal seem to contribute to evolve NDMs.