Co-occurrence of blaKPC−3 and blaNDM−1 in an ST167 Escherichia coli isolate from a patient with urinary tract infection

The coexistence of bla KPC and bla NDM carbapenemase genes in Escherichia coli is extremely rare and poses a serious threat to clinical treatment and infection control. This study aimed to characterize the antimicrobial resistance profile, plasmid features, and genetic background of a carbapenem-resistant E. coli isolate co-harboring bla KPC−3 and bla NDM−1 recovered from a urinary tract infection patient. A carbapenem-resistant E. coli isolate, designated TZ-1, was recovered from the urine of a hospitalized patient with urinary tract infection. Antimicrobial susceptibility testing was performed using the broth microdilution method according to CLSI guidelines. Whole-genome sequencing combining Illumina and Oxford Nanopore platforms was conducted to determine the genomic characteristics, resistance genes, virulence-associated factors, and plasmid structures. Conjugation experiments were performed using sodium azide-resistant E. coli J53 as the recipient to evaluate the transferability of carbapenem resistance determinants. Transconjugants were selected under different antimicrobial conditions and confirmed by PCR. Escherichia coli TZ-1 belonged to sequence type ST167 and a multidrug-resistant phenotype, including high-level resistance to meropenem (128 mg/L), ceftazidime-avibactam (> 64/4 mg/L), and aztreonam (> 128 mg/L), and co-harbored bla KPC−3 and bla NDM−1 together with multiple additional resistance and virulence-associated genes. Whole-genome sequencing revealed the coexistence of bla KPC−3 and bla NDM−1 located on two distinct plasmids, designated pTZ_KPC and pTZ_NDM, respectively. Comparative genomic analysis revealed that pTZ_KPC shared 95% query coverage and 99.98% nucleotide identity with pSZN_KPC, whereas pTZ_NDM showed 100% query coverage and 100% nucleotide identity with pF621_NDM. Conjugation assays yielded three transconjugants (J-TZ-1, JK-TZ-1, and JN-TZ-1) under different selective conditions. Notably, PCR analysis demonstrated that all transconjugants simultaneously carried bla KPC−3 and bla NDM−1 . The frequencies of transconjugant recovery under ceftazidime-avibactam- and meropenem-selective conditions were 1.2 × 10^-4 and 3.2 × 10^-4 per recipient cell, respectively, indicating efficient horizontal transfer and stable establishment of both resistance plasmids. This study reports a rare ST167 E. coli isolate co-harboring bla KPC−3 and bla NDM−1 on transferable IncN and IncX3 plasmids from a urinary tract infection patient. Comparative genomic analysis demonstrated that both resistance plasmids possessed highly conserved epidemic backbones, while conjugation experiments confirmed their horizontal transfer capability. The coexistence of two carbapenemase genes within a globally disseminated ST167 lineage highlights the ongoing convergence of major resistance determinants in high-risk E. coli clones and underscores the urgent need for continuous genomic surveillance and strengthened infection control strategies.