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

Abstract

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.

Keywords: Escherichia coli; IncX3 type plasmid; ST410; blaNDM-7; carbapenem resistant.

Figure 1

Profile of the bla_NDM-7-encoding plasmid pEC25_NDM-7.

Figure 2

Phylogenetic relationship between E. coli ST410 strain EC25 and other E. coli strains. Twenty-one phylogenetically related strains were identified in the BacWGSTdb server. All of these strains belonged to ST410. Seven strains were isolated from Germany, five from the USA, four from China, two from Norway, and one each from Argentina, Brazil, and India.