Table 2_Molecular epidemiology and genomic evolution mechanism of carbapenemase-resistant Enterobacter cloacae complex in Northeast China from July 2019 to March 2025.xlsx

The rise of carbapenem-resistant Enterobacteriaceae (CRE), particularly the Enterobacter cloacae complex (ECC), poses a significant global health threat. However, the genomic evolution and transmission mechanisms of CRECC remain insufficiently understood. This study aimed to characterize the genotypes, resistance determinants, and transmission dynamics of clinical CRECC isolates using whole-genome sequencing (WGS) to inform infection control strategies. A total of 123 clinical CRECC isolates were subjected to species identification, antimicrobial susceptibility testing, WGS, plasmid analysis, and conjugation experiments. Taxonomic classification was refined based on an Average Nucleotide Identity (ANI) threshold of ≥95%, and phenotypic confirmation of carbapenemase production was performed using the combined disc test. Enterobacter hormaechei was the predominant species (n = 114, 92.7%), comprising three major subspecies: xiangfangensis, steigerwaltii, and hoffmannii. ST171 (30.1%) and ST1120 (21.1%) emerged as the dominant clonal lineages. The primary resistance genes were blaNDM − 5 (55.3%) and blaNDM − 1 (39.0%), with a subset of isolates co-harboring blaKPC − 2. All isolates were resistant to meropenem and imipenem (MIC90 ≥16 μg/ml). Genomic analysis revealed that the IncX3 plasmid was the principal vector for blaNDM, facilitating its dissemination. Minimal SNP differences between isolates within the same clonal group suggested recent transmission events. Conjugation experiments confirmed the horizontal transferability of blaNDM-carrying plasmids, with a success rate of 28.0% (7/25). This study reveals that the regional epidemiology of CRECC is driven by the clonal expansion of E. hormaechei ST171 and ST1120, coupled with the efficient horizontal transfer of blaNDM genes via IncX3 plasmids. These findings provide a crucial molecular basis for targeted surveillance and infection control measures to mitigate the spread of high-risk CRECC clones.