Identification of a hypervirulent extensively drug-resistant ST383 Klebsiella pneumoniae sub-lineage carrying ICEKp5 in Lebanon

Klebsiella pneumoniae ST383 has emerged as a high-risk clone, characterized by carbapenem resistance and increasing detection of hypervirulence determinants. We describe a phylogenetically distinct ST383 sub-lineage in Lebanon, defined by the acquisition of ICEKp5, which carries the yersiniabactin locus. Three ST383 K. pneumoniae clinical isolates (LBN_CAKp91, LBN_CTKp3, and 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 (three to nine single-nucleotide polymorphisms [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 and rmpA2 ), aerobactin ( iucABCD and iutA ), yersiniabactin, and the hypervirulence biomarker peg-344 . All isolates carried dual carbapenemases ( bla OXA-48 and bla NDM-5 ) in addition to bla CTX-M-15 and bla CTX-M-14b . The genetic environments of bla OXA-48 and bla NDM-5 were highly conserved across geographically diverse ST383 isolates, indicating common plasmid origins. This study describes a phylogenetically distinct hypervirulent extensively drug-resistant (XDR) ST383 K. pneumoniae sub-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.