Clinical, Microbiological and Genomic Characterization of OXA-48-Producing Klebsiella pneumoniae ST395 Circulating in a Secondary-Care Hospital in North-Eastern Italy, 2024–2025

Abstract

Background/Objectives: This study aimed to characterize the epidemiology, resistance, virulence determinants, and genomic relatedness of OXA-48-producing Klebsiella pneumoniae in a secondary-care hospital in north-eastern Italy, and to assess the in vitro activity of cefepime-based β-lactam/β-lactamase inhibitor combinations. Methods: We performed a retrospective observational study of consecutive, non-duplicate isolates (September 2024–January 2025). Susceptibility testing was performed using VITEK® 2 and MIC TestStrip. All isolates underwent single-read Nanopore whole-genome sequencing, with assembly and in silico detection of resistance genes, porin alterations, plasmid replicons and virulence loci. Core-genome single-nucleotide polymorphism analysis with recombination filtering assessed genetic relatedness. Results: Thirteen isolates were recovered from elderly, highly comorbid inpatients, mainly from urine (46.2%) and rectal/fecal screening (38.5%). Twelve patients were classified as colonized, whereas one patient had an infection due to OXA-48-producing K. pneumoniae, with the organism recovered from both blood and urine cultures. All belonged to sequence type 395 and carried blaOXA-48 and blaCTX-M-15, together with a truncated OmpK35 and an OmpK36 loop-3 GD insertion. The yersiniabactin locus ybt16 within integrative conjugative element ICEKp12 was detected in 92.3% of isolates. Core-genome analysis showed high genomic similarity among isolates, consistent with local circulation of an ST395 lineage. Although yersiniabactin may contribute to iron acquisition and bacterial fitness, its presence alone does not establish a hypervirulent phenotype or predict clinical virulence. In the absence of aerobactin, salmochelin, rmpADC, and rmpA2, and without phenotypic virulence testing, these isolates should be regarded as yersiniabactin-positive but non-hypervirulent based on their genomic profile. Core-genome analysis indicated close genetic relatedness among the isolates, consistent with possible local clonal circulation. In a subset, cefepime/enmetazobactam and especially cefepime/zidebactam substantially reduced cefepime minimum inhibitory concentrations. Conclusions: We identified a multidrug-resistant OXA-48-producing K. pneumoniae ST395 lineage circulating locally, predominantly in colonization contexts. Active screening and genomic surveillance may support infection control and inform the potential role of emerging cefepime-based inhibitor combinations.