Complete-genome sequencing and comparative genomic characterization of bla 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 carrying Citrobacter freundii (C. freundii) isolates from a patient with bloodstream and urinary tract infections.

Results: Antimicrobial susceptibility testing showed that both bla 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 positive. Genotyping and comparative genomics analyses revealed that both isolates exhibited a high level of genetic similarity. Plasmid analysis confirmed that the bla 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-trpF-IS26-umuD-ISKox3) was found in the upstream and downstream of the bla gene.

Conclusions: The data presented in this study showed that the conjugative bla 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 gene from one single patient with multiple infections.