Coexistence of a blaNDM-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

Yefu Han,1 Xiaobin Li,2 Jing Yang2 1Department of Orthopedics, Gong An County People’s Hospital, Jingzhou, 434300, People’s Republic of China; 2Department of Pulmonary and Critical Care Medicine, Zhuhai People’s Hospital (The Affiliated Hospital of Beijing Institute of Technology, Zhuhai Clinical Medical College of Jinan University), Zhuhai, 519000, People’s Republic of ChinaCorrespondence: Jing Yang, Email [email protected]: 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 blaNDM-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 blaNDM-5 on IncHI2/IncHI2A plasmid pEC6622-1. blaNDM-5 was embedded in ΔISKox3-IS 3000-ΔISAba125-IS 5-blaNDM-5-bleMBL-trpF-dsbC-ΔcutA-IS 26-ΔISVsa5-IS 3000-IS 1A. 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 Tn 3-like region containing mer operon and blaTEM-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 blaNDM-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 blaNDM-harboring E. coli.Keywords: E. coli, IncHI2/IncHI2A plasmid, blaNDM-5, Tn 3000, IncFIBAP001918/IncFII plasmid