Complete-genome sequencing and comparative genomic characterization of bla(NDM-5) carrying Citrobacter freundii isolates from a patient with multiple infections

BACKGROUND: The emergence and wide spread of carbapenemase-producing Enterobacteriaceae (CPE) poses a growing threat to global public health. However, clinically derived carbapenemase-producing Citrobacter causing multiple infections has rarely been investigated. Here we first report the isolation and comparative genomics of two bla(NDM-5) carrying Citrobacter freundii (C. freundii) isolates from a patient with bloodstream and urinary tract infections. RESULTS: Antimicrobial susceptibility testing showed that both bla(NDM-5) carrying C. freundii isolates were multidrug-resistant. Positive modified carbapenem inactivation method (mCIM) and EDTA-carbapenem inactivation method (eCIM) results suggested metallo-carbapenemase production. PCR and sequencing confirmed that both metallo-carbapenemase producers were bla(NDM-5) positive. Genotyping and comparative genomics analyses revealed that both isolates exhibited a high level of genetic similarity. Plasmid analysis confirmed that the bla(NDM-5) resistance gene is located on IncX3 plasmid with a length of 46,161 bp, and could successfully be transferred to the recipient Escherichia coli EC600 strain. A conserved structure sequence (ISAba125-IS5-bla(NDM-5)-trpF-IS26-umuD-ISKox3) was found in the upstream and downstream of the bla(NDM-5) gene. CONCLUSIONS: The data presented in this study showed that the conjugative bla(NDM-5) plasmid possesses a certain ability to horizontal transfer. The dissemination of NDM-5-producing C. freundii isolates should be of close concern in future clinical surveillance. To our knowledge, this is the first study to characterize C. freundii strains carrying the bla(NDM-5) gene from one single patient with multiple infections. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-023-09579-9.