Three carbapenem-resistant Escherichia coli were recovered from rectal swabs of different patients in a tertiary hospital and were found carrying bla NDM-4, an uncommon bla NDM variant. Genome sequences of the isolates were obtained using Illumina technology and the long-read MinION sequencer. The isolates belonged to ST405 and phylogenetic group D, a globally distributed lineage associated with antimicrobial resistance. In addition to bla NDM-4, the three isolates carried 14 known resistance genes including the extended-spectrum β-lactamase gene bla CTX-M-15. There were only 1 or 2 SNPs between the isolates, suggesting a common origin and cryptic transmission in hospital. bla NDM-4 was located on a 46.5-kb IncFIA self-transmissible plasmid, which may facilitate further dissemination of bla NDM-4. Two copies of IS26 bracketed a 14.6-kb region containing bla NDM-4 and have the potential to form a composite transposon for mediating the mobilization of bla NDM-4.