Abstract

Introduction: Carbapenem- and third-generation cephalosporin-resistant Enterobacterales, including the Citrobacter freundii complex, are classified as a World Health Organization ‘critical priority’ due to their public health threat. This study reports a C. freundii complex isolate (Cit-107) co-harbouring the blaNDM-1, blaCTX-M-30, armA, rmtC, and rmtD genes, recovered from a rectal swab in 2022 in Concepción, Chile. Methods: Antimicrobial susceptibility was assessed via disk diffusion. Whole-genome sequencing 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. Results: 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: blaNDM-1, blaCTX-M-30, mcr-9.1, armA, rmtC, and rmtD. The blaNDM-1 gene was embedded in a Tn125-like transposon contained in an IncC-type plasmid alongside the blaCTX-M-30, rmtC, and tet(G) genes. The blaCTX-M-30 was harboured 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. Conclusions: This is the first report of a carbapenem-resistant C. freundii complex isolate carrying blaNDM-1 in Chile alongside multiple antibiotic-resistance genes harboured 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. © 2025