Characterization of Plasmid Co-Harboring NDM-1 and SHV-12 from a Multidrug-Resistant Citrobacter freundii Strain ZT01-0079 in China

BACKGROUND: The emergence of multidrug-resistant Citrobacter freundii poses daunting challenges to the treatment of clinical infections. The purpose of this study was to characterize the genome of a C. freundii strain with an IncX3 plasmid encoding both the bla(NDM-1) and bla(SHV-12) genes. METHODS: Strain ZT01-0079 was isolated from a clinical urine sample. The Vitek2 system was used for identification and antimicrobial susceptibility testing. The presence of bla(NDM-1) was detected by PCR and sequencing. Conjugation experiments and Southern blotting were performed to determine the transferability of the bla(NDM-1)- carrying plasmid. Nanopore and Illumina sequencing were performed to better understand the genomic characteristics of the strain. RESULTS: Strain ZT01-0079 was identified as C. freundii, and the coexistence of bla(NDM-1) and multiple drug resistance genes was confirmed. Electrophoresis and Southern blotting showed that bla(NDM-1) was located on a ~53kb IncX3 plasmid. The NDM-1-encoding plasmid was successfully transferred at a frequency of 1.68×10(−3). Both the bla(NDM-1) and bla(SHV-12) genes were located on the self-transferable IncX3 plasmid. CONCLUSION: The rapid spread of the IncX3 plasmid highlights the importance of continuous monitoring of the prevalence of NDM-1-encoding Enterobacteriaceae. Mutations of existing carbapenem resistance genes will bring formidable challenges to clinical treatment.