First report of a blaVIM-1 metallo-β-lactamase-possessing Klebsiella michiganensis

Abstract

Background: Klebsiella michiganensis is an emerging pathogen. As for Klebsiella pneumoniae, this species is able to acquire antibiotic resistance genes (ARGs) via mobile genetic elements. In this context, K. michiganensis isolates producing carbapenemases of KPC, NDM, IMP and OXA-48-like types have been already reported. Here, we characterized a strain (BD-50-Km) isolated from the rectal swab of a Turkish patient hospitalized in Switzerland.

Methods: Species identification was initially obtained by using the MALDI-TOF MS. Susceptibility tests were done by the microdilution method. Whole-genome sequencing (WGS) was performed with both Illumina and Nanopore platforms and used to confirm ID, characterize plasmids and perform core-genome analyses.

Results: BD-50-Km was initially identified as Klebsiella oxytoca and showed a reduced susceptibility to imipenem. However, WGS indicated that the isolate was actually K. michiganensis. BD-50-Km carried the blaVIM-1 associated to a rare class 1 integron (In87) located in a pST1 196kb IncC plasmid. This plasmid shared its backbone with many other IncC plasmids found in different species (including 5 K. michiganensis), but not the same In87 and the remaining region harboring various ARGs. BD-50-Km belonged to the novel ST342. Moreover, core-genome analysis (single nucleotide variants analysis) showed that BD-50-Km was not closely-related to any of the K. michiganensis strains deposited in NCBI (n=212), including the 38 so far reported as possessing carbapenemase genes.

Conclusions: This is the first report of a blaVIM-possessing K. michiganensis clinical isolate. The spread of plasmid-mediated VIM carbapenemases in this emerging pathogen represent an additional threat to our therapeutic armamentarium.