Work

Genomic characterization of a carbapenem-resistant Citrobacter freundii complex strain co-carrying blaNDM-1, blaCTX-M-30, armA, rmtC, and rmtD from Chile

Year: 2025

Type: article

Abstract: • C. freundii strain Cit-107 harbors a broad resistome, including bla NDM-1 , bla CTX-M-30 , armA, rmtC and rmtD . • The C. freundii strain Cit-107 belongs to sequence type ST112, not previously reported in clinical settings. • bla NDM-1 , rmtC and rmtD were located on an IncC-type plasmid, previously described in Providencia vermicola isolated in 2017 in Congo. • The Chilean strain Cit-107 may represent a distinct and underrepresented lineage of C. freundii complex. Carbapenem- and third-generation cephalosporin-resistant Enterobacterales , including the Citrobacter freundii complex, are classified as a WHO ‘critical priority’ due to their public health threat. This study reports a C. freundii complex isolate (Cit-107) co-harboring the bla NDM-1 , bla CTX-M-30 , armA, rmtC , and rmtD genes, recovered from a rectal swab in 2022 in Concepción, Chile. Antimicrobial susceptibility was assessed via disk diffusion. Whole-genome sequencing (WGS) was performed using the Illumina NextSeq 2000 platform and annotated with Bakta. In silico analyses included JSpeciesWS, PubMLST, ABRicate, AMRFinderPlus, and MOB-suite. Phylogenetic analysis of Cit-107 and 50 C. freundii complex genomes from the Americas was conducted using IQ-TREE and visualized with iTOL. Cit-107 was resistant to clinically relevant antibiotics, such as carbapenems, cephalosporins, aminoglycosides, and fluoroquinolones. It belongs to Sequence Type (ST) ST112 and carries multiple resistance genes: bla NDM-1 , bla CTX-M-30 , mcr-9.1, armA, rmtC , and rmtD . The bla NDM-1 gene was embedded in an Tn 125 -like transposon contained in an IncC-type plasmid alongside the bla CTX-M-30 , rmtC , and tet(G) genes. The bla CTX-M-30 was harbored in an IncN-type plasmid, while armA, msr(E) , and mph(E) were co-carried in an IncHI2A-type plasmid. Phylogenetic analysis revealed Cit-107 as a divergent lineage within the C. freundii complex. This is the first report of a carbapenem-resistant C. freundii complex isolate carrying bla NDM-1 in Chile alongside multiple antibiotic-resistance genes harbored in several plasmid types. Its unique resistome and phylogenetic profile underscore the need for surveillance of emerging multidrug-resistant C. freundii strains in clinical settings.

Source: Journal of Global Antimicrobial Resistance

DOI: 10.1016/j.jgar.2025.10.021