What question did this study set out to answer?

The study aims to analyze the genomic features of a multidrug-resistant E. coli strain co-harboring resistance genes.

April 1, 2026Open Access

Genomic Characteristics of a Carbapenem-Resistant Escherichia coli Co-Carrying blaNDM-5 and mcr-1.1 from a Urinary Tract Infection in China

JJJuan JinChildren's Hospital of Zhejiang University LHLing HuangChildren's Hospital of Zhejiang University DBDanni BaoNantong University

Puntos clave

The study aims to analyze the genomic features of a multidrug-resistant E. coli strain co-harboring resistance genes.
Conducted antimicrobial susceptibility testing using broth microdilution assay.
Employed Clermont Typing platform for phylogenetic classification.
Utilized BacWGSTdb 2.0 for sequence typing and core genome analysis.
Identified resistance genes via SerotypeFinder, CHTyper, PlasmidFinder, and ResFinder databases.
E. coli strain SM107 showed resistance to nearly all antibiotics except nitrofurantoin.
Complete genome analysis revealed a single chromosome and six plasmids, assigned to sequence type ST1011.
The bla NDM-5 gene was found on a 119,850 bp IncI1-1-type plasmid, while mcr-1.1 was on a 111,450 bp IncI2-type plasmid.
cgMLST analysis highlighted the emergence of ST1011 strains harboring both colistin and carbapenem resistance genes.

Resumen

Objective: The global emergence of multidrug-resistant Escherichia coli strains, particularly those co-carrying plasmid-mediated colistin and carbapenemase genes, represents a significant public health concern. The coexistence of these resistance determinants severely limits the therapeutic options available for treating infections caused by MDR pathogens. Methods: Antimicrobial susceptibility testing was performed by broth microdilution assay. Clermont Typing platform was employed to classify the phylogenetic group. The BacWGSTdb 2.0 online platform was utilized to determine sequence types and perform the core genome cgMLST analysis by comparing with publicly available E. coli isolates. Serotype, FimH type, Inc groups and antimicrobial resistance genes were carried out using SerotypeFinder 2.0, CHTyper 1.0, PlasmidFinder 2.1 and ResFinder 3.2 databases, respectively. Results: E. coli SM107 was resistant to nearly all the tested antibiotics excluding nitrofurantoin. The complete genome sequence comprises a single chromosome along with six plasmids and was assigned to sequence type (ST)1011. The bla NDM-5 gene was discovered in a 119,850 bp IncI1-1-type plasmid with IS 26 , IS 3000 , IS 30 and IS 5 exist downstream of the bla NDM-5 gene with IS 26 situated upstream as a truncated fragment. The mcr-1.1 gene in a 111,450 bp IncI2-type plasmid. cgMLST analysis highlighting the emergence of multidrug-resistant E. coli ST1011 strains that harbor both colistin and carbapenem resistance genes. Conclusion: We report the emergence of a ST1011 E. coli strain in China co-carrying the mcr-1.1 and bla NDM-5 genes. This highlights the urgent need for alternative therapeutic strategies, strengthened antimicrobial stewardship, and enhanced genomic surveillance to curb the dissemination of high-risk resistance plasmids and safeguard the effectiveness of last-resort antibiotics. Keywords: Escherichia coli , bla NDM-5 , mcr-1.1 , whole genome sequencing, antimicrobial resistance, nitrofurantoin

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