Carbapenem resistant Klebsiella sp. Slovenian isolates

The first Slovenian hospital outbreak with carbapenemase producing Klebsiella pneumoniae (CP-KP) was detected using classical epidemiological research in 2014-2016. The aim of the study was to perform whole genome sequencing (short read Illumina and long read Oxford Nanopore Technologies) to analyse the epidemiology and antimicrobial resistance markers of 13 CP-KP strains isolated during the hospital outbreak, 16 CP-KP strains unrelated to the outbreak, 5 carbapenem-sensitive K. pneumoniae and ATCC 700603 strain as a reference strain. Using long read sequencing on selected isolates, we wanted to confirm that the resistance markers were spreading between different clones in the outbreak through plasmids.