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 blaNDM-9-carrying and two blaNDM-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 blaNDM-9 and blaNDM-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 blaNDM 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 blaNDM-9 genes were carried by IncHI2-type plasmids (n = 4) or IncK2-type plasmids (n = 2), while all blaNDM-13 genes were exclusively carried by IncX3-type plasmids (n = 2). Both variants were associated with Tn125-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 blaNDM-13-carrying isolates differed by only two SNPs. Conjugation experiments confirmed the successful transfer of blaNDM-9 and blaNDM-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.

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

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2026年1月19日

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

摘要

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 Tn125-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.