Three years of Klebsiella pneumoniae in intensive care units: Epidemiological trends and rapid typing via Multiplex PCR

A genome wide association study was conducted to identify genes specifically associated with the most relevant STs circulating in Italy ST11, ST37, ST101, ST147, ST258, ST512, ST307, ST395. Molecular typing methods including multiplex PCR, multi locus sequence typing MLST and pulsed field gel electrophoresis PFGE were applied. Whole genome sequencing WGS was performed on representative strains. A total of 179 strains collected over four years were analysed, of these 125 were carbapenem resistant. Multiplex PCR assays were developed as a pre screening tool to rapidly identify the most relevant STs and were applied on the 125 KPC producing strains. MLST was performed for validate multiplex PCR results. Almost perfect matches were identified for ST37, ST101, ST307 and ST512. WGS enabled the genomic characterization of antimicrobial resistance determinants, virulence genes, and the identification of multiple outbreaks. We developed multiplex PCRs that allowed us to select strains for WGS. The identified outbreaks resulted from multiple independent introductions of different STs, some of which led to prolonged ward colonization lasting several years. Outbreaks frequently spread across different wards notably, some involved both SARS CoV 2 positive and negative dedicated wards, highlighting possible cross contamination routes.