Human intestinal colonization by Escherichia coli ST4014 co-harboring tet(X4) and blaNDM-1 gene: a potential reservoir for antimicrobial resistance dissemination.

UNLABELLED: This study aims to elucidate the genomic characteristics of three Escherichia coli strains isolated from stool specimens of healthy individuals co-carrying tet(X4) and blaNDM-1 gene, which confer resistance to tigecycline and carbapenems, respectively. Whole-genome sequencing (WGS) and bioinformatic analysis were conducted to identify the genomic characteristics. Fourteen E. coli strains belonging to the same sequence type (ST) 4014, comprising eleven strains retrieved from public databases and three strains from this study, were integrated into a phylogenetic analysis. Conjugation experiments were conducted to evaluate the transferability of the resistance plasmids. Three E. coli strains exhibited resistance to both tetracyclines and carbapenems, consistent with the presence of tet(X4) and blaNDM-1 genes in their genomes. All strains belonged to the rare ST 4014 and were identified in healthy individuals within a 1-week period. WGS revealed that tet(X4) and blaNDM-1 genes were each located on separate plasmids, both exhibiting 100% sequence identity to others previously reported in various bacterial species. Conjugation experiments confirmed the transferability of both tet(X4) and blaNDM-1-carrying plasmids. Phylogenetic analysis based on cgSNPs revealed limited genetic diversity among the three strains (2-6 SNPs), but substantial differences compared to 11 publicly available ST4014 strains (116-172 SNPs). This study reports E. coli ST4014 strains from healthy individuals harboring conjugative plasmids carrying tet(X4) and blaNDM-1 genes, conferring resistance to tigecycline and carbapenems, respectively. These findings highlight the silent spread of multidrug-resistant strains in community populations and emphasize the need for enhanced surveillance of antimicrobial resistance beyond clinical settings.

IMPORTANCE: The emergence of Escherichia coli strains co-harboring tet(X4) and blaNDM-1 genes in healthy individuals represents a critical public health concern. These genes mediate resistance to tigecycline and carbapenems, two of the few remaining options for treating infections caused by multidrug-resistant gram-negative bacteria. The detection of clonally related ST4014 strains carrying conjugative plasmids encoding both resistance determinants highlights the potential for horizontal gene transfer and silent dissemination of dual-resistance plasmids in community settings. Such colonization among healthy individuals suggests that antimicrobial resistance may be spreading unnoticed beyond hospitals, driven by environmental or foodborne transmission routes. These findings emphasize the urgent need for integrated genomic surveillance and One Health-based interventions encompassing human, animal, and environmental reservoirs to prevent the expansion of high-risk resistance genes and safeguard the clinical efficacy of last-line antibiotics.