Clonal outbreak of NDM-1 producing Enterobacter hormaechei belonging to high-risk international clone ST78 with the coexistence of tmexCD2-toprJ2 and mcr-9  in China.

The emergence of the carbapenem-resistant Enterobacter cloacae complex (CR-ECC) has posed significant challenges to the clinical treatment of healthcare-associated infections globally. Herein, we report the clonal outbreak of NDM-1-producing Enterobacter hormaechei with the coexistence of tmexCD2-toprJ2 and mcr-9 in China. During the outbreak (January 2018-December 2021), a total of fifteen non-repetitive multidrug-resistant E. hormaechei strains were obtained from thirteen patients in a tertiary hospital. The 15 E. hormaechei strains belonged to the high-risk international clone ST78 and co-harbored tmexCD2-toprJ2 and blaNDM-1 , of which 12 E. hormaechei strains carried the mcr-9 gene. Whole-genome sequencing analysis revealed that tmexCD2-toprJ2 and blaNDM-1 coexisted on the IncFIB/IncFII type plasmid, which could be transferred to E. coli J53 by conjugation and had a significant effect on host fitness. The mcr-9 gene is located between two insertion sequences, IS903B and IS1R, but lacks the two-component system regulatory genes qseBC, which might be the reason for all mcr-9-positive E. hormaechei strains remained susceptible to colistin. Besides, the expression of mcr-9 is not inducible in strains confirmed by colistin induction assays. Furthermore, the phylogenetic analysis illustrated the silent spread and rapid evolution of mcr-9-carrying E. hormaechei worldwide. Collectively, this study enriched the epidemiological and genomic characterization of the coexistence of tmexCD2-toprJ2 and mcr-9 in ST78 CR-ECC isolates and demonstrated that they could prolong clonal dissemination in a tertiary hospital in China. Hence, continuous epidemiological surveillance and molecular characterization of CR-ECC should be conducted to monitor the evolution of CR-ECC around the world.