Characterization of a NDM-7 carbapenemase-producing Escherichia coli ST410 clinical strain isolated from a urinary tract infection in China

Purpose: The emergence of New Delhi metallo-beta-lactamase (NDM) carbapenemase-producing Escherichia coli leaves few therapeutic options. Infections due to NDM-7 carbapenemase-producing E. coli are infrequent. In this study, we report the whole-genome sequence of an NDM-7 carbapenemase-producing E. coli belonging to sequence type (ST) 410 isolated from a patient with a urinary tract infection in China. Patients and methods: The NDM-7 producing E. coli strain EC25 was isolated from a urine sample of a male patient hospitalized in a tertiary hospital in Zhejiang Province of China. Susceptibility assay of antibiotics was performed according to the guidelines of the Clinical and Laboratory Standards Institute (CLSI). The whole genome of the strain was sequenced, and the bla(NDM-7)-harboring plasmid was analyzed. The genomic characterization and molecular epidemiology of the strain were further elucidated. Results: E. coli EC25 was resistant to all antimicrobials tested, except tigecycline and colistin. The whole genome of E. coli EC25 was composed of one chromosomal DNA and five plasmids. Four virulence factors and twenty-five antimicrobial resistance genes, including bla(NDM-7), were identified. Resistance genes were all located in an IncF-type plasmid (pEC25-1), except bla(NDM-7), which was located in an individual IncX3-type plasmid (pEC25_NDM-7). Twenty-one phylogenetically related strains were identified. The phylogenetically related E. coli ST410 strains exist globally. The closest relative strain of EC25 was a strain isolated from Sichuan province of China in 2016, with a similar IncX3-type plasmid that encoded bla(NDM-5). Conclusion: Our study reports the emergence of an E. coli ST410 strain harboring bla(NDM-7) in China. This strain may evolve as a successful epidemic clone of NDM-producing E. coli in China, and the bla(NDM) gene is prone to mutate during its dissemination.