Functional features of KPC-109, a novel 270-loop KPC-3 mutant mediating resistance to avibactam-based β-lactamase inhibitor combinations and cefiderocol

  • Int J Antimicrob Agents. 2023 Nov 4:107030. doi: 10.1016/j.ijantimicag.2023.107030.
Vincenzo Di Pilato  1 ,  Giulia Codda  2 ,  Claudia Niccolai  3 ,  Edward Willison  4 ,  Joshua Lc Wong  5 ,  Erika Coppo  4 ,  Gad Frankel  5 ,  Anna Marchese  6 ,  Gian Maria Rossolini  7
Affiliations
  • 1. Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, Genoa, Italy. Electronic address: [email protected].
  • 2. Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, Genoa, Italy.
  • 3. Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.
  • 4. Microbiology Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy.
  • 5. Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom.
  • 6. Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, Genoa, Italy; Microbiology Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy.
  • 7. Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy; Clinical Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy.
PMID: 37931849 DOI: 10.1016/j.ijantimicag.2023.107030
Abstract

Objectives: This study investigated a ceftazidime/avibactam (CZA)-resistant K. pneumoniae (NE368), isolated from a patient exposed to CZA, expressing a novel KPC-3 variant, named KPC-109.

Methods: Antimicrobial susceptibility testing was performed by reference broth microdilution. WGS analysis of NE368 was performed combining a short- and long-reads approach by Illumina and Nanopore technologies. Functional characterization of KPC-109 was performed investigating the impact of KPC-109 production on the β-lactam resistance phenotype of various Escherichia coli and Klebsiella pneumoniae strains, including derivatives of K. pneumoniae with OmpK35 and OmpK36 porin alterations. Horizontal transfer of the KPC-109-encoding plasmid was investigated by conjugation and transformation experiments.

Results: K. pneumoniae NE368 was isolated from a patient after repeated CZA exposure, and showed resistance to CZA, fluoroquinolones, piperacillin-tazobactam, expanded-spectrum cephalosporins, amikacin, carbapenems, and cefiderocol. WGS revealed the presence of a large chimeric plasmid of original structure (pKPN-NE368), encoding a novel 270-loop mutated KPC-3 variant, named KPC-109 (ins_270_KYNKDD). KPC-109 production mediated resistance/decreased susceptibility to avibactam-based combinations (with ceftazidime, cefepime and aztreonam) and cefiderocol, with a trade-off on carbapenem resistance. However, in the presence of porin alterations commonly encountered in high-risk clonal lineages of K. pneumoniae, KPC-109 was able to confer clinical-level resistance to carbapenems as well. Resistance to cefiderocol in NE368 was likely contributed by KPC-109 production acting in concert with a mutated EnvZ sensor kinase. The KPC-109-encoding plasmid was apparently not conjugative.

Conclusions: Present findings expanded current knowledge about the diversity of emerging KPC Enzymes variants with 270-loop alterations that can be encountered in the clinical setting.

Keywords
Klebsiella pneumoniae; OmpK35; OmpK36; carbapanemase-producing Enterobacterales; resistance mechanism; β-lactamase inhibitor combinations.
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