Emergence of NDM-1 and KPC-3 carbapenemases in Kluyvera cryocrescens: Investigating genetic heterogeneity and acquisition routes of blaNDM-1 in Enterobacterales species in Portugal

Abstract

Objectives: A higher diversity of species, clones and genes have been increasingly implicated in carbapenemases spread, though the mobile genetic elements responsible for their acquisition and dispersion at local and global levels are less explored, particularly in species other than Klebsiella pneumoniae or Escherichia coli. We aim to explain the emergence of NDM-1 and KPC-3 carbapenemases in a Kluyvera cryocrescens isolate, and to shed light on the heterogeneity of genetic platforms and acquisition routes of bla_NDM-1 in diverse Enterobacterales species in Portugal.

Methods: A KPC-3 and NDM-1-producing K. cryocrescens colonizing a hospitalized patient in 2019 was characterized by whole-genome sequencing and antibiotic resistance profiling following standard methods. Conjugative transfer of carbapenemases genes was assessed by filter mating. Plasmids were reconstructed with in silico and in vitro approaches. bla_NDM-1 genetic context was compared with that of diverse NDM-1-producing Enterobacterales species, previously described in Portugal.

Results: K. cryocrescens K629 showed a multidrug resistance profile. Resistance gene bla_KPC-3 was harboured by a Tn4401d transposon within a worldwide-spread IncN-ST15 plasmid (pKLU-KPC3), whereas bla_NDM-1 was located in a Tn3000 within a non-typeable mosaic plasmid (pKLU-NDM1). The heterogeneous bla_NDM-1 genetic platforms and variable plasmid backbones identified in various Enterobacterales species suggested multiple introductions of bla_NDM-1 in Portugal, mediated by variable insertion sequences.

Conclusions: We report the convergence of KPC-3 and NDM-1 in K. cryocrescens and the variable dissemination modes of these carbapenemases in different Enterobacterales species, underlining the need to track down genetic platforms responsible for carbapenemases diffusion.

Keywords: Carbapenemase; Carbapenemase-producing Enterobacterales (CPE); IncN; Multidrug resistance (MDR); Tn3000; Tn4401; Whole genome sequencing (WGS).