Co-Occurrence of NDM-9 and MCR-1 in a Human Gut Colonized Escherichia coli ST1011

BACKGROUND: The emergence of the plasmid-borne colistin-resistant gene (mcr-1) poses a great threat to human health. What is worse, the recent observations of the coexistence of mcr-1 with carbapenemase encoding genes in some bacteria caused even more concern. Yet, there is a lack of observations of such strains in the human gut. METHODS: The isolation of E. coli L889 was performed on selective medium plates. Antibiotic susceptibilities were determined by an agar dilution and a broth microdilution method. Multi-locus sequence typing (MLST) and acquired resistance genes were also characterized. Transferability of bla(NDM-9)/mcr-1-carrying plasmids was determined by conjugation, replicon typing and S1-Pulsed-field gel electrophoresis (S1-PFGE), and Southern blotting. The sequences of these plasmids were analyzed by using whole-genome sequencing with Illumina Novaseq and Nanopore platforms. RESULTS: E. coli L889 was identified as ST1101 concomitantly carrying bla(NDM-9) and mcr-1 from a stool sample. Antimicrobial susceptibility tests showed that it was resistant to various antimicrobial agents and only susceptible to tigecycline. Notably, bla(NDM-9) was located on a ~114-kb untypable plasmid, while mcr-1 was located on a ~63-kb IncI2 plasmid. CONCLUSION: Our research, to our knowledge, first reported an ST1101 E. coli strain with an untypeable bla(NDM-9)-harbouring plasmid and an IncI2 mcr-1-carrying plasmid. The colonized E. coli strains potentially contribute to the dissemination and transfer of bla(NDM-9) and mcr-1 to clinical isolates, which is a considerable threat to public health and should be closely monitored.