Genomic characterization of clinical Enterobacter roggenkampii co-harbouring bla- and bla-encoding IncP6 and mcr-9-encoding IncHI2 plasmids isolated in Japan.

Objectives: The spread of carbapenemase-producing Enterobacterales (CPE) with colistin resistance is a critical public health issue. We genetically characterized the clinical isolate Enterobacter roggenkampii OIPH-N260, which harboured carbapenemase genes bla and bla with multiple resistance genes, including mcr-9 and bla.

Methods: This isolate was characterized by whole-genome sequencing, comparative analysis of resistance plasmids, susceptibility tests, bacterial conjugation, S1-nuclease digested pulsed-field-gel electrophoresis, and Southern blot hybridization.

Results: The OIPH-N260 isolate exhibited resistance to most β-lactams and colistin. It co-harboured two resistance plasmids, the bla- and bla-encoding IncP6 plasmid pN260-3 and mcr-9- and bla-encoding IncHI2 plasmid pN260-1. The comparative analysis of pN260-3 indicated that a unique bla-surrounding region was inserted into the bla-encoding plasmid with the mobile element IS26, which plays an important role in the spread of resistance genes. pN260-1 did not possess the mcr-9 expression regulative gene qseBC. Both plasmids were transferable into other bacterial species via conjugation.

Conclusions: This is the first study to report not only a bla and bla co-encoding plasmid, but also the co-harbouring of another plasmid carrying mcr-9 and bla in Enterobacter cloacae complex. The development of advanced resistance via IS26-mediated insertion and the co-harbouring of resistance plasmids highlights the need to monitor for resistance genes in CPE.