Multiple regional outbreaks caused by global and local VIM-producing Klebsiella pneumoniae clones in Poland, 2006–2019

This study was aimed at comprehensive genomic analysis of VIM-type carbapenemase-producing Klebsiella pneumoniae species complex (KpSC) in Poland.

All non-duplicate 214 VIM-producing KpSC isolates reported in Poland in 2006–2019 were short-read sequenced and re-identified by the average nucleotide identity scoring. Their clonality/phylogeny was assessed by cgMLST and SNP in comparison with genomes from international databases. Serotypes, VIM-encoding integrons, resistomes, virulomes and plasmid replicons were identified by various bioinformatic tools. Structures of plasmids and genomic islands with VIM integrons were analysed for representative long-read sequenced isolates.

The KpSC isolates were the second most prevalent VIM-positive Enterobacterales (23.1%) in Poland in 2006–2019, following Enterobacter spp. (40.1%). Their significance emerged in 2014 and then grew consequently, owing to eight regional outbreaks of K. pneumoniae sequence types (STs) ST437, ST147, ST15, ST277 and ST392. These carried different VIM integrons, mainly In238 and In916 types, located on IncFIB + IncHI2 (pNDM-MAR)-, IncA- or IncM-like plasmids, or clc-type integrative and conjugative elements. Despite relatedness of the outbreak clusters to isolates from other countries, e.g. Greece, Spain, Slovakia or Germany, most of them have apparently emerged on site by horizontal acquisition of resistance determinants from other species, including Enterobacter spp. and Pseudomonas spp.

This work shows dynamic epidemiology of VIM-producing organisms, driven by a mix of circulation of different VIM-encoding elements, and parallel clonal spread of multiple organisms.