Genomic and virulence characterization of OXA-48-producing Klebsiella pneumoniae causing urinary tract infections and their susceptibility to lytic bacteriophages.

INTRODUCTION

Klebsiella pneumoniae (Kpn) is the second most frequent cause of urinary tract infections (UTIs) and represents a major concern in the context of antimicrobial resistance (AMR); nevertheless, the phenotypic and genomic traits that define uropathogenic Kpn strains are not clear.

METHODS

In this study, 24 carbapenemase-producing Kpn strains, most of them (23/24) carrying bla OXA-48, isolated from urine samples of nosocomial or community origin in northwest Spain, were characterized in terms of antibiotic resistance, virulence traits and biofilm-forming capacity to identify UTI-associated traits. Additionally, the susceptibility to bacteriophages, both in planktonic cultures and biofilms, was assessed.

RESULTS AND DISCUSION: High levels of resistance to other antibiotics were also observed, with 83.3% of strains classified as multidrug-resistant. Most isolates belonged to ST15 (n = 11) and ST147 (n = 8), representing high-risk clones, all of them harboring bla OXA-48. Strain 6022, belonging to ST307, represented a third high-risk clone. Principal component analysis (PCA) revealed clustering of strains into two main groups according to antibiotic resistance and virulence genes, corresponding to the two predominant STs. None of the urine strains carried hypervirulence-associated genetic markers, despite the high proportion of hypermucoviscous isolates. Six lytic bacteriophages belonging to the genera Webervirus, Jiaodavirus, and Druslisvirus, were evaluated against the Kpn isolates. All six phages lysed at least one strain. None of the phages lysed ST15 isolates, confirming previously reported specificity associated with ST and capsule locus types. The combination of Webervirus kpv33d1 and Jiaodavirus kpv33d6 completely inhibited planktonic growth of selected strains, even at low multiplicities of infection (MOI = 0.01). Importantly, this low MOI was sufficient to significantly reduce colony-forming unit counts in preformed biofilms, a key factor in infection persistence and antibiotic resistance in Kpn. These results indicate that some genomic and phenotypic traits seem to be associated with UTI Kpn strains, even though a higher number of strains should be analyzed. The isolation of wide-spectrum phages for the treatment of Kpn UTI infections is demonstrated to be feasible, but our results emphasize the need to assess biofilm-disrupting activity when selecting phages for therapeutic applications against K. pneumoniae.