Coexistence of blaKPC-2-IncN and mcr-1-IncX4 plasmids in a ST48 Escherichia coli strain in China

Abstract

Objectives: The aim of this study was to explore the genomic content of a bla_KPC-2- and mcr-1-harbouring Escherichia coli strain and to clarify the molecular mechanism for the transmission of multidrug resistance.

Methods: Antimicrobial susceptibility testing was conducted by the broth microdilution method to determine the resistance profile. Filter-mating conjugation assays were performed to confirm the plasmid transfer ability. Whole-genome sequence data were acquired by a combination of Illumina paired-end reads and Nanopore long-read sequencing.

Results: Escherichia coli strain QE11-421 was an mcr-1-positive colistin-resistant isolate that co-harboured the bla_KPC-2 gene conferring carbapenem resistance. Genome sequence data confirmed QE11-421 as a sequence type 48 (ST48) E. coli that harboured five large conjugative plasmids encoding several multidrug resistance genes. The bla_KPC-2 gene was located on a Tn3-Tn4401 composite transposon, which is part of a 65-kb multidrug-resistant IncN plasmid. The mcr-1 gene was harboured on another 33-kb IncX4 plasmid that was more conserved and presented few antimicrobial resistance determinants. No copies of insertion sequence ISApl1 were found flanking the mcr-1 gene, decreasing the mobility of mcr-1 based on its original Tn6330 transposon.

Conclusions: Horizontal transfer of multidrug resistance plasmids or resistance-related transposon units was responsible for the emergence of this notorious superbug. The coexistence of bla_KPC-2-IncN and mcr-1-IncX4 plasmids in a ST48 E. coli strain in humans poses a great threat.

Keywords: Carbapenemase; Colistin; Plasmid; bla(KPC-2); mcr-1.