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

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 bla NDM−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 bla NDM−5 gene was identified and named pNDM-5-0083. An additional β-lactamase gene ( bla TEM−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-bla TEM−1B -bla NDM−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 bla NDM−5 , leading to widespread β-lactam antibiotic resistance.