Journal Article

Clinical and molecular characterization of NDM-9 and NDM-13 producing multidrug-resistant Escherichia coli strains in China

Yv, Hua, Jia, Wei, Chen, Liang, Li, Gang, Shan, Bin, Du, Hong, Tao, Jia, Wang, Wen, Fu, Hui, Wang, Liru, Tang, Yiwei, Zhu, Zhichen, Zhu, Jie

2026

Overview

Objectives The continuous evolution of NDM variants, some of which exhibit enhanced hydrolytic activity, poses a serious public health threat and necessitates ongoing surveillance. This study aimed to investigate the clinical and molecular characteristics of Escherichia coli strains producing NDM-9 and NDM-13 variants. Methods Six bla NDM-9 -carrying and two bla NDM-13- carrying E. coli strains were isolated from six hospitals in China. MALDI-TOF MS and Vitek-2 systems were used for identification and antimicrobial susceptibility testing (AST). Phenotypic detection of carbapenemases was conducted using a combined disc test. Multi-locus sequence typing (MLST) was used to assess clonal relatedness among the eight E. coli isolates. Whole genome sequencing (WGS) and bioinformatics analysis were used to characterize the bla NDM-9 and bla NDM-13 -carrying strains. Phylogenetic trees and core SNP comparisons were generated using isolates from this study and publicly available sequences from the GenBank database. Conjugation experiments were performed to evaluate the horizontal transferability of bla NDM genes. Plasmid stability was assessed by serial passage for 10 days without antibiotic selection. Results All E. coli isolates exhibited a multiple drug resistance phenotype, but remained susceptible to amikacin and tigecycline. The E. coli types were diverse by MLST, including ST1 ( n  = 2), ST19 ( n  = 2), ST2 ( n  = 1), ST664 ( n  = 2), and one novel ST type. WGS analysis identified 41 and 49 resistance genes and virulence factor genes. The bla NDM-9 genes were carried by IncHI2-type plasmids ( n  = 4) or IncK2-type plasmids ( n  = 2), while all bla NDM-13 genes were exclusively carried by IncX3-type plasmids ( n  = 2). Both variants were associated with Tn 125 -related transposons. Phylogenetic analysis of core SNPs revealed that 52 E. coli strains (including 44 genome sequences from GenBank) were divided into six clustering clades with SNP differences ranging from 2 to 10,625. Two bla NDM-13 -carrying isolates differed by only two SNPs. Conjugation experiments confirmed the successful transfer of bla NDM-9 and bla NDM-13 to E. coli C600, and plasmids remained stable after 10 days of passage. Conclusions The detailed clinical and molecular characteristics of NDM-9 and NDM-13 producing CR-EC enhance our understanding of the evolution and dissemination of NDM variants. These insights highlight the further comprehensive surveillance to evaluate the public-health risk of NDM variants producing strains.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Amikacin / Analysis / Anopheles / Anti-Bacterial Agents - pharmacology / Antibacterial agents / Antibiotics / Beta lactam antibiotics / Beta lactamases / beta-Lactamases - genetics / beta-Lactamases - metabolism / Bioinformatics / Biological Microscopy / Biomedical and Life Sciences / Bla NDM-13 / Bla NDM-9 / Carbapenemase / China / Clustering / Conjugation / DNA sequencing / Dosage and administration / Drug resistance / Drug Resistance, Multiple, Bacterial - genetics / E coli / Environmental aspects / Escherichia coli / Escherichia coli - classification / Escherichia coli - drug effects / Escherichia coli - enzymology / Escherichia coli - genetics / Escherichia coli - isolation & purification / Escherichia coli Infections - microbiology / Ethylenediaminetetraacetic acid / Evolution / Evolutionary biology / Females / Gene sequencing / Genes / Genetic aspects / Genomes / Genomics / Health aspects / Health risks / Humans / Life Sciences / Microbial Sensitivity Tests / Microbiology / Multidrug resistance / Multilocus Sequence Typing / Mycology / Nucleotide sequencing / Parasitology / Phenotypes / Phylogenetics / Phylogeny / Plasmids / Plasmids - genetics / Public health / Single-nucleotide polymorphism / Surgery / Surveillance / Tetracycline / Tetracyclines / Tigecycline / Transposons / Urine / Virology / Virulence (Microbiology) / Virulence factors / Whole Genome Sequencing