Genomic Epidemiology of Carbapenemase Producing Klebsiella pneumoniae Strains at a Northern Portuguese Hospital Enables the Detection of a Misidentified Klebsiella variicola KPC-3 Producing Strain

The evolutionary epidemiology, resistome, virulome and mobilome of thirty-one multidrug resistant Klebsiella pneumoniae clinical isolates from the northern Vila Real region of Portugal were characterized using whole-genome sequencing and bioinformatic analysis. The genomic population structure was dominated by two main sequence types (STs): ST147 (n = 17; 54.8%) and ST15 (n = 6; 19.4%) comprising four distinct genomic clusters. Two main carbapenemase coding genes were detected (bla(KPC-3) and bla(OXA-48)) along with additional extended-spectrum β-lactamase coding loci (bla(CTX-M-15), bla(SHV-12), bla(SHV-27), and bla(SHV-187)). Moreover, whole genome sequencing enabled the identification of one Klebsiella variicola KPC-3 producer isolate previously misidentified as K. pneumoniae, which in addition to the bla(KPC-3) carbapenemase gene, bore the chromosomal broad spectrum β-lactamase bla(LEN-2) coding gene, oqxAB and fosA resistance loci. The bla(KPC-3) genes were located in a Tn4401b transposon (K. variicola n = 1; K. pneumoniae n = 2) and Tn4401d isoform (K. pneumoniae n = 28). Overall, our work describes the first report of a bla(KPC-3) producing K. variicola, as well as the detection of this species during infection control measures in surveillance cultures from infected patients. It also highlights the importance of additional control measures to overcome the clonal dissemination of carbapenemase producing clones.