Emergence of a novel hypervirulent extensively drug-resistant ST383 Klebsiella pneumoniae lineage carrying ICEKp5 in Lebanon

Abstract

Klebsiella pneumoniae ST383 has emerged as a high-risk clone, characterized by carbapenem resistance and increasing detection of hypervirulence determinants. We describe a novel ST383 lineage in Lebanon, defined by the acquisition of ICEKp5, which carries the yersiniabactin locus. Three ST383 K. pneumoniae clinical isolates (LBN_CAKp91, LBN_CTKp3, LBN_CTKp11) recovered from a Lebanese medical center were subjected to whole-genome sequencing. Comparative genomic analysis included regional ST383 strains and previously characterized Lebanese isolates. The study isolates formed a tight, monophyletic cluster (3-9 SNPs) that is phylogenetically distinct from the previously reported Lebanese ST383 clone (>164 SNPs) and grouped most closely to an Egyptian ST383 strain (59-65 SNPs). All three isolates carried ICEKp5 with yersiniabactin lineage ybt14, a feature absent in the earlier Lebanese ST383 clone. The isolates were the only ST383 strains to harbor the full spectrum of hypervirulence determinants to date, including capsule regulators (rmpA, rmpA2), aerobactin (iucABCD, iutA), yersiniabactin, and the hypervirulence biomarker peg-344. All isolates carried dual carbapenemases (blaOXA-48 and blaNDM-5) in addition to blaCTX-M-15 and blaCTX-M-14b. The genetic environments of blaOXA-48 and blaNDM-5 were highly conserved across geographically diverse ST383 isolates, indicating common plasmid origins. This study documents the emergence of a novel hypervirulent extensively drug-resistant (XDR) ST383 K. pneumoniae lineage in Lebanon. The acquisition of ICEKp5, combined with plasmid-borne hypervirulence and resistance determinants, reveals the concerning convergence of hypervirulence and XDR. Enhanced surveillance and infection control measures are urgently needed to monitor this emerging high-risk clone.