First documentation of a clinical multidrug-resistant Enterobacter chuandaensis ST2493 isolate co-harboring blaNDM-1 and two blaKPC-2 bearing plasmids

The increasing prevalence of carbapenem-resistant Enterobacter cloacae complex (CREC) poses great challenges to infection treatment in the clinical setting. In this study, we reported the emergence of carbapenemase in a rare species, Enterobacter chuandaensis, belonging to the Enterobacter cloacae complex (ECC). We elucidated the genetic characteristics of carbapenem-resistant isolate FAHZZU5885, co-harboring bla(NDM-1) and bla(KPC-2). Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and average nucleotide identity (ANI) analysis were used to identify E. chuandaensis. S1 nuclease pulsed-field gel electrophoresis (S1-PFGE) and Southern blotting were used to clarify the number and size of the plasmids in FAHZZU5885. Antimicrobial phenotypes were identified by antimicrobial susceptibility testing (AST), and the characteristics of the strain were examined with whole-genome sequencing (WGS). The conjugation experiment and stability assay were conducted to verify the transferability and stability of the plasmid carrying carbapenemase-encoding genes. E. chuandaensis FAHZZU5885 was isolated from a perianal swab of a patient admitted to the ICU. This strain simultaneously carried bla(NDM-1) and two bla(KPC-2) genes. FAHZZU5885 was resistant to most of the tested antibiotics except for amikacin, tigecycline, and colistin. Two bla(KPC-2) were located separately on two different plasmids, the similar to 120 kb IncFIA-IncFII plasmid and the similar to 80 kb IncR plasmid. Both plasmids shared the conserved sequence klcA-korC-ISkpn6-bla(KPC-2)-ISkpn27-tnpR-tnpA. The bla(NDM-1)-bearing plasmid had the potential to transfer and can remain stable after successive passages. In addition, the bla(NDM-1) was carried on a similar to 80 kb IncFII plasmid with the conserved sequence ISAba125-bla(NDM-1)-ble-trpF-dsbD-cutA-groS-groL. In summary, this study marks the first report of the multidrug-resistant E. chuandaensis strain FAHZZU5885 harboring two bla(KPC-2)-bearing plasmids, indicating the potential for the further dissemination of carbapenemase-encoding genes in novel species. The findings contribute to enhancing our understanding of CREC strains, emphasizing the need for continued and comprehensive surveillance of this species.