Genomic insights into replicons and conjugative transfer systems of blaNDM-positive plasmids in the Enterobacter cloacae complex
5 affiliations
- 1Clinical Laboratory Medicine Department, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260 China
- 2Department of Radiation Oncology, Zhuhai People’s Hospital (The Affiliated Hospital of Beijing Institute of Technology, Zhuhai Clinical Medical College of Jinan University), Zhuhai, 519000 China
- 3Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People’s Hospital (The Affiliated Hospital of Beijing Institute of Technology, Zhuhai Clinical Medical College of Jinan University), Zhuhai, 519000 China
- 4Department of Pulmonary and Critical Care Medicine, Zhuhai People’s Hospital, (The Affiliated Hospital of Beijing Institute of Technology, Zhuhai Clinical Medical College of Jinan University), Zhuhai, 519000 China
- 5School of Basic Medicine, Guangzhou Medical University, Guangzhou, 511436 China
Abstract
The Enterobacter cloacae complex (ECC) represents a prominent opportunistic pathogen associated with multidrug-resistant nosocomial infections. The emergence of New Delhi metallo-β-lactamase (NDM)-producing ECC isolates presents a significant threat to public health, owing to the restricted available treatment regimens. Here, we identified a clinical E. hormaechei strain E20590 carrying the blaNDM-1 gene from Guangdong Province, South China, and combined it with 259 non-redundant blaNDM-harboring ECC plasmid sequences retrieved from the NCBI GenBank database (2009–2025) to form a cohort of 260 plasmids for systematic genomic characterization. Analyses of blaNDM variants, replicon types, conjugative transfer systems, clustering dendrograms and geographic distributions revealed that blaNDM was present in four ECC species, with E. hormaechei (77.31%, 201/260) as the predominant host, and blaNDM-1 (81.15%) and blaNDM-5 (14.62%) as the dominant variants. Gene-content clustering divided these plasmids into eight distinct clades, primarily differentiated by replicon types (IncX3 ~ 40%, IncF ~ 30%, IncH ~ 8%) and conjugative transfer modules. The largest clade (Clade I) comprised IncX3 single-replicon plasmids (~ 50 kb) encoding MOBP family relaxases, T4CP2 family coupling proteins and Type T T4SS, which were mainly distributed in Sichuan and Guangdong Provinces of China. The IncF-like plasmid pE20590-1 from strain E20590 belonged to Clade VIII (~ 100 kb), carrying MOBF family relaxases, T4CP2 and Type F T4SS, and was the only isolate from Guangdong in this clade with unique regional distribution characteristics. Among the analyzed GenBank-derived ECC plasmid records, China accounted for the largest proportion (49.6%), followed by Canada, Bangladesh, and Poland. Within the analyzed Chinese plasmid records, Sichuan, Guangdong, and Zhejiang contributed the largest numbers of submissions. Conjugation experiments confirmed the functional transfer of pE20590-1, and most plasmids harbored intact conjugative transfer elements, highlighting the high horizontal transmission potential of blaNDM in ECC. Our results systematically illustrate the genetic diversity, structural characteristics, and distribution patterns of blaNDM-carrying plasmids within the ECC, offering key genomic evidence to support the surveillance and control of NDM-mediated carbapenem resistance spread in clinical environments.
Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1186/s12866-026-05489-4.
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BibTeX
@article{chen2026genomic,
title = {{Genomic insights into replicons and conjugative transfer systems of blaNDM-positive plasmids in the Enterobacter cloacae complex}},
author = {Mingxiao Chen and Wei Zhang and Jingyi Zhang and Canbo Fan and Tingting Deng and Pei Yu and Meifang Lin and Jianqiang Zhu and Qiwen Xiao and Minling Wang and Xiaobin Li and Qiyong Zhang and Miaoshan Luo and Qiang Zhou},
journal = {BMC Microbiology},
year = {2026},
month = aug,
doi = {10.1186/s12866-026-05489-4},
url = {https://doi.org/10.1186/s12866-026-05489-4},
note = {CC BY-NC-ND 4.0},
}
RIS
TY - JOUR
TI - Genomic insights into replicons and conjugative transfer systems of blaNDM-positive plasmids in the Enterobacter cloacae complex
AU - Mingxiao Chen
AU - Wei Zhang
AU - Jingyi Zhang
AU - Canbo Fan
AU - Tingting Deng
AU - Pei Yu
AU - Meifang Lin
AU - Jianqiang Zhu
AU - Qiwen Xiao
AU - Minling Wang
AU - Xiaobin Li
AU - Qiyong Zhang
AU - Miaoshan Luo
AU - Qiang Zhou
PY - 2026
DA - 2026/08/07
JO - BMC Microbiology
DO - 10.1186/s12866-026-05489-4
UR - https://doi.org/10.1186/s12866-026-05489-4
AB - The Enterobacter cloacae complex (ECC) represents a prominent opportunistic pathogen associated with multidrug-resistant nosocomial infections. The emergence of New Delhi metallo-β-lactamase (NDM)-producing ECC isolates presents a significant threat to public health, owing to the restricted available treatment regimens. Here, we identified a clinical E. hormaechei strain E20590 carrying the blaNDM-1 gene from Guangdong Province, South China, and combined it with 259 non-redundant blaNDM-harboring ECC plasmid sequences retrieved from the NCBI GenBank database (2009–2025) to form a cohort of 260 plasmids for systematic genomic characterization. Analyses of blaNDM variants, replicon types, conjugative transfer systems, clustering dendrograms and geographic distributions revealed that blaNDM was present in four ECC species, with E. hormaechei (77.31%, 201/260) as the predominant host, and blaNDM-1 (81.15%) and blaNDM-5 (14.62%) as the dominant variants. Gene-content clustering divided these plasmids into eight distinct clades, primarily differentiated by replicon types (IncX3 ~ 40%, IncF ~ 30%, IncH ~ 8%) and conjugative transfer modules. The largest clade (Clade I) comprised IncX3 single-replicon plasmids (~ 50 kb) encoding MOBP family relaxases, T4CP2 family coupling proteins and Type T T4SS, which were mainly distributed in Sichuan and Guangdong Provinces of China. The IncF-like plasmid pE20590-1 from strain E20590 belonged to Clade VIII (~ 100 kb), carrying MOBF family relaxases, T4CP2 and Type F T4SS, and was the only isolate from Guangdong in this clade with unique regional distribution characteristics. Among the analyzed GenBank-derived ECC plasmid records, China accounted for the largest proportion (49.6%), followed by Canada, Bangladesh, and Poland. Within the analyzed Chinese plasmid records, Sichuan, Guangdong, and Zhejiang contributed the largest numbers of submissions. Conjugation experiments confirmed the functional transfer of pE20590-1, and most plasmids harbored intact conjugative transfer elements, highlighting the high horizontal transmission potential of blaNDM in ECC. Our results systematically illustrate the genetic diversity, structural characteristics, and distribution patterns of blaNDM-carrying plasmids within the ECC, offering key genomic evidence to support the surveillance and control of NDM-mediated carbapenem resistance spread in clinical environments. Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1186/s12866-026-05489-4.
SN - 1471-2180
ER -