Coexistence of a bla NDM-5-Harboring IncHI2 Plasmid and an IncF Multidrug-Resistance Plasmid in a Clinical Escherichia coli Strain from Urine Sample of a Patient with Lower Limb Fracture.

OBJECTIVE

This study aimed to report the genome of carbapenem-resistant ST58 Escherichia coli strain EC6622, isolated from the urine sample of a patient with lower limb fracture, and to explore the genomic characteristics of the bla NDM-5-harboring IncHI2/IncHI2A plasmid and the multi-resistance IncF plasmid carried by strain EC6622.

METHODS

The genome of E. coli strain EC6622 was fully sequenced using the Illumina and PacBio platforms, followed by hybrid assembly of the genome sequences. The identification of antibiotic resistance genes (ARGs) and the genetic context of ARGs were accomplished using bioinformatics tools. Comparative genomic analyses of the resistance plasmids carried by E. coli strain EC6622 were performed.

RESULTS

E. coli strain EC6622, belonging to ST58 (Achman scheme) or ST87 (Pasteur scheme), harbored bla NDM-5 on IncHI2/IncHI2A plasmid pEC6622-1. bla NDM-5 was embedded in ΔISKox3-IS3000-ΔISAba125-IS5-bla NDM-5-ble MBL-trpF-dsbC-ΔcutA-IS26-ΔISVsa5-IS3000-IS1A. In addition, two class 1 integrons were also found in the IncHI2/IncHI2A plasmid pEC6622-1. IncFIBAP001918/IncFII plasmid pEC6622-2 carried one 23-kb multidrug-resistant (MDR) region, including tet(A)-tetR(A), class 1 integron, and a Tn3-like region containing mer operon and bla TEM-1B gene, which were nearly identical to those of seven IncF plasmids distributed in E. coli strains.

CONCLUSION

In the carbapenem-resistant E. coli strain EC6622 isolated from the urine sample of a 70-year-old patient with a lower limb fracture, the carbapenemase gene bla NDM-5 was carried by the IncHI2/IncHI2A plasmid (pEC6622-1), while a coexisting IncFIBAP001918/IncFII hybrid multidrug-resistance plasmid (pEC6622-2) was also identified. These findings provide detailed genetic information that enhances our understanding of the resistance mechanisms and potential dissemination routes of bla NDM-harboring E. coli.