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.
Keywords: C. freundii , whole-genome sequencing, genomics analysis