Whole-genome sequencing and antibiotic resistance analysis of a clinical carbapenem-resistant Enterobacter chuandaensis

ABSTRACT This study aimed to characterize a rare clinical isolate, Enterobacter chuandaensis , carrying the carbapenem resistance gene bla NDM-1 . The antimicrobial susceptibility analysis revealed that E. chuandaensis EC001 was resistant to the majority of commonly used antimicrobial agents, except for amikacin, chloramphenicol, and minocycline. The results of the modified carbapenem inactivation method and EDTA-modified carbapenem inactivation method confirmed that E. chuandaensis EC001 produces metallo-β-lactamase. E. chuandaensis EC001 was typed as sequence type 2493 and presented an extensive drug-resistant profile. Whole-genome sequencing analysis demonstrated that the strain harbors two plasmids (p1_EC001 and p2_EC001), among which bla NDM-1 is located on the conjugative plasmid p1_EC001 of IncFIB/IncFII-type. Plasmid p1_EC001 could be transferred into Escherichia coli , indicating its interbacterial horizontal transmission potential. The majority of plasmid-mediated resistance genes reside within or adjacent to various mobile genetic elements in p1_EC001. In addition, an IS 3000 element (3,018 bp) was detected upstream of bla NDM-1 , while the bleomycin resistance-related gene ble MBL was located downstream of bla NDM-1 , followed by trpF , dsbD , cutA , groS , groL , and IS Kpn19. Moreover, one class 1 integron harboring the genetic array intI1-dfrA12-aadA2-qacEdeltal-sul1 was identified on p1_EC001. The plasmid p2_EC001 was characterized as a mobilizable plasmid, and two key genes, mbeA and mbeC , were detected, which encode the plasmid mobilization relaxase MbeA and the accessory protein MbeC, respectively. In summary, this study demonstrated the antimicrobial susceptibility, plasmid features, and potential transmission mechanisms of E. chuandaensis EC001, which serve as evidence for controlling and prevention of clinical E. chuandaensis . IMPORTANCE Current research on carbapenem resistance in E. chuandaensis remains relatively limited. This study performed detailed genome characterization of the two plasmids (p1_EC001 and p2_EC001) carried by E. chuandaensis EC001 and analyzed their resistance gene profiles, plasmid features, and potential transmission mechanisms. The findings provide a theoretical foundation for the formulation of hospital infection control strategies, improve the capability for early warning and prevention of carbapenem-resistant Enterobacterales , and exhibit substantial scientific significance, as well as promise clinical application value.