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

Abstract

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 blaNDM-5 carrying Citrobacter freundii (C. freundii) isolates from a patient with bloodstream and urinary tract infections. Results Antimicrobial susceptibility testing showed that both blaNDM-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 blaNDM-5 positive. Genotyping and comparative genomics analyses revealed that both isolates exhibited a high level of genetic similarity. Plasmid analysis confirmed that the blaNDM-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-blaNDM-5-trpF-IS26-umuD-ISKox3) was found in the upstream and downstream of the blaNDM-5 gene. Conclusions The data presented in this study showed that the conjugative blaNDM-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 blaNDM-5 gene from one single patient with multiple infections.

Coexistence of a novel NDM-1-encoding MDR plasmid and an IMP-4-encoding IncN-IncU hybrid plasmid in a clinical isolate of Citrobacter freundii BC73

“…Interestingly, these isolates all belonged to the ST22 C. freundii strain and were distributed in different countries over the span of a decade, which suggested that the ST22 C. freundii strains have disseminated globally and they may be highly clonal. Notably, C. freundii BC73 co-carrying bla NDM-1 and bla IMP-4 and C. freundii DY2007 harboring bla NDM-5 , isolated from dongyang, China in 2020 ( Ye et al, 2023 ), were found to be the most closely related isolates. Previous report has described that the differences between bla NDM-1 and bla NDM-5 were represented by mutations at only two specific sites (88, 154) ( Sun et al, 2019 ).…”

“…It was isolated from the urine of a 64-year-old patient with urinary tract infections resulting from total cystotomy and abdominal fistula drainage. Carbapenems resistant Citrobacter freundii isolates, especially multidrug-resistant strains, were gradually being found in urinary tract infections, which may cause the extension of infection and the increase of patients’ suffering ( Prussing et al, 2020 ; Zhang et al, 2021 ; Ye et al, 2023 ). The AST results presented in Table 1 showed that C. freundii BC73 and transconjugant BC73-J53 were resistance to all β-lactams, chloramphenicol, minocycline, azithromycin, and gentamicin antibiotics tested.…”

“…Recently, IncX3 plasmids carrying bla NDM have commonly been identified in different species of the Enterobacteriaceae ( Ye et al, 2023 ), implying their significant role in bla NDM transfer. Furthermore, a study from Zhang et al showed a high transfer frequency were observed in pZY-NDM1, a IncX3 plasmid harboring bla NDM-1 gene ( Zhang et al, 2021 ).…”