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

Abstract

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.

Keywords: Escherichia coli; ST1101; blaNDM-9; gut; mcr-1.

Figure 1

S1-PFGE pattern for E. coli L889 and Southern blot analysis indicating the bla_NDM-9-and mcr-1-carrying plasmids. Lane marker, Salmonella serotype Braenderup strain H9812 as a reference size standard; L889, PFGE result of S1-digested plasmid DNA of strain E. coli L889; NDM-9, Southern blotting of L889 with the probes specific to the bla_NDM-9; MCR-1, Southern blotting of L889 with the probes specific to the mcr-1.

Figure 2

Comparative analysis of plasmids pL889-NDM9 and pL889-MCR1 detected in E. coli L889. (A) Comparison of bla_NDM-9 coding region of plasmid pL889-NDM9 with plasmid pHNTH02-1 (MG196294), pEC013 (MG545909), pNDM-T2 (MN335919), and pHNSD138-1 (MG271839). (B) Comparison of mcr-1-carrying plasmid pL889-MCR1 with plasmids pHNTH02-1 (KY693674), pHLJ179-34 (MN232213), and p5CRE51-MCR-1 (CP021176). The circular map was generated with the BLAST Ring Image Generator (http://brig.sourceforge.net/).