Carbapenemase-producing Klebsiella pneumoniae lineages over a 15-year period in a Greek hospital

Local genomic surveillance is useful for characterizing the circulating lineages of carbapenemase-producing Klebsiella pneumoniae (CPKP) - an increasing threat to patient safety. We retrospectively characterized CPKP circulating within 12 wards in a Greek hospital with the aim of investigating the dynamics of circulating clones, the extent, and the complexity of carbapenem resistance. Between 2003 and 2018, 392 CPKP blood isolates were recovered from patients, epidemiological data were retrieved, and carbapenem resistance genes were determined using PCR. We whole genome-sequenced 209 of these and analyzed the sequence data using publicly available tools. We demonstrate that ST258 (n =108), ST147 (n = 29), and ST11 (n = 18) are the major lineages of CPKP K. pneumoniae circulating within this Greek hospital, where blaVIM-1-carrying ST147 strains first emerged during the early sampling period (2003), followed by the emergence of dominant blaKPC-2-carrying ST258 strains (2006), and blaNDM-1-carrying ST11 strains (2013). More than 25% of CPKP belonging to the major lineages (n = 153) co-carried mgrB truncated genes (56.2%) and extended spectrum beta-lactamase genes (blaCTX-M-15, blaCTX-M-3, blaSHV-5, blaSHV-12, 26.797%), but blaVEB-1 was uncommon (3.921%). When contextualizing the current collection with published data from Pathogenwatch, ST147 reflected the global diversity, ST258 co-segregated with isolates representing the first introduction into Europe, and ST11 partitioned into a geographically restricted lineage indicative of local spread. This study demonstrates the changing profile of CPKP in a Greek tertiary care hospital over 15 years, and underlines the explanatory power of local surveillance when combined with WGS in characterizing clones with high dissemination potential.