Genomic characterization of a novel multidrug-resistant plasmid harboring bla NDM5 in Escherichia coli sequence type 167 isolate from Zhongshan, China

Abstract

Abstract Background The dissemination of carbapenem-resistant Enterobacteriaceae represents an emerging challenge in infection control because carbapenems are the last-resort antibiotics for treating multidrug-resistant (MDR) bacterial infections. In recent years, New Delhi metallo-β-lactamase (NDM) has become a widespread carbapenem-resistance gene that needs active surveillance. Results In this study, the MDR Escherichia coli (E. coli) strain GZ04-0083 carrying the blaNDM−5 plasmid was identified from the stools of a patient with diarrhea using pulsed-field gel electrophoresis (S1-PFGE) and southern blot. A conjugation experiment was conducted to assess the transferability of the resistance plasmid. Second-generation and nanopore sequencing were performed to assemble the genomics and plasmid sequence. Multi-locus sequence typing (MLST) results showed that GZ04-0083 belonged to the ST167 isolate, and a novel 146,950-bp IncF plasmid harboring the blaNDM−5 gene was identified and named pNDM-5-0083. An additional β-lactamase gene (blaTEM−1B) and five other resistance genes (sul2, dfrA12, tetA, aadA2, and rmtB) were also detected in pNDM-5-0083. The plasmid’s key elements might play significant roles in plasmid stability and resistance genes transmission, including integrator and transposon elements (Intl1, Tn21, and Tn3), a replication protein (RepA), stabilization proteins (ParA and ParB), insertion sequences (Is26, Is30, Is91, and Ins gene cluster), iron transporters (Iro, Luc, and Sit) and conjugative splice transfer systems of plasmids (Tra and Trb gene cluster). The basic local alignment search tool (BLAST) revealed that pNDM-5-0083 shared the conserved sequence RepA-blaTEM−1B-blaNDM−5-bleMBL-Is91-SuI2-addA2-dfrA12 with three other plasmids. Conclusion In conclusion, the results imply that the newly discovered pNDM-5-0083 plasmid could be a co-vector mediating the spread of blaNDM−5, leading to widespread β-lactam antibiotic resistance.