Genomic characterization of a bla KPC-2-producing IncM2 plasmid harboring transposon ΔTn 6296 in Klebsiella michiganensis

Abstract

Klebsiella michiganensis is an emerging hospital-acquired bacterial pathogen, particularly strains harboring plasmid-mediated carbapenemase genes. Here, we recovered and characterized a multidrug-resistant strain, bla _KPC-2-producing Klebsiella michiganensis LS81, which was isolated from the abdominal drainage fluid of a clinical patient in China, and further characterized the co-harboring plasmid. K. michiganensis LS81 tested positive for the bla _KPC-2 genes by PCR sequencing, with bla _KPC-2 located on a plasmid as confirmed by S1 nuclease pulsed-field gel electrophoresis combined with Southern blotting. In the transconjugants, the bla _KPC-2 genes were successfully transferred to the recipient strain E. coli EC600. Whole-genome sequencing and bioinformatics analysis confirmed that this strain belongs to sequence type 196 (ST196), with a complete genome comprising a 5,926,662bp circular chromosome and an 81,451bp IncM2 plasmid encoding bla _KPC-2 (designated pLS81-KPC). The IncM2 plasmid carried multiple β-lactamase genes such as bla _TEM-1B, bla _CTX-M-3, and bla _KPC-2 inserted in truncated Tn6296 with the distinctive core structure ISKpn27-bla _KPC-2-ISKpn6. A comparison with 46 K. michiganensis genomes available in the NCBI database revealed that the closest phylogenetic relative of K. michiganensis LS81 is a clinical isolate from a wound swab in the United Kingdom. Ultimately, the pan-genomic analysis unveiled a substantial accessory genome within the strain, alongside significant genomic plasticity within the K. michiganensis species, emphasizing the necessity for continuous surveillance of this pathogen in clinical environments.

Keywords: ISKpn27-blaKPC-2-ISKpn6; Klebsiella michiganensis; blaKPC-2 carbapenemases; carbapenem-resistant Enterobacteriaceae; phylogenetics; whole genome sequencing.