First emergence of genetically related concurrently producing KPC-2 and VIM-1 ST39 carbapenem-resistant Klebsiella pneumoniae strains isolated in Greece.

The aim of the current study is the genetic characterization through whole-genome sequencing (WGS) of four ST39 CRKP strains simultaneously producing KPC-2 and VIM-1, isolated in an intensive care unit (ICU) and pediatric ICU (PICU) of an endemic country.Identification and antimicrobial susceptibility testing of CRKP strains were performed through VITEK 2. A multiplex PCR, a multiplex lateral flow immunoassay (LFIA), phenotypic tests, and WGS were applied. The sequence reads were de novo assembled and annotated using Geneious Prime version 2021.2.1 and BLAST Ring Image Generator (BRIG) software. MLST assignment, antimicrobial resistance genes, and plasmid detection were assessed. Genomic comparison and core genome single-nucleotide polymorphism (cgSNP)-based phylogenetic analysis was also performed.All four CRKP strains (C2482, Z508, D1598, and D2452) were resistant to most antimicrobials, they carried concurrently blaKPC-2 and blaVIM-1 genes and were assigned to ST39. BlaVIM-1 was integrated into a class 1 integron. All strains produced a 1000bp amplicon of the mgrB gene. They all harbored many antimicrobial resistance genes and various plasmids. Genome comparison and cgSNP-based phylogenetic analysis revealed that all strains were closely related to each other.