Global Epidemiological Survey and Genomic Analysis of Multiple Carbapenemases-Producing Citrobacter freundii

Carbapenem-resistant Citrobacter freundii (CRCF) has emerged as a growing global health concern, as it is increasingly implicated in human infections and recognized as an important reservoir of clinically significant antimicrobial resistance determinants. Although C. freundii carrying single carbapenemase genes has been widely reported, systematic global analyses of isolates harboring multiple carbapenemase genes remain limited.

Citrobacter spp. isolates were recovered and antimicrobial susceptibility testing was determined using the broth microdilution method. We further conducted a comprehensive genomic analysis of multi-carbapenem-producing C. freundii (MCP-CF). Whole-genome sequencing data were used to characterize the carbapenemase gene profiles, multi-locus sequence types (MLST), phylogenetic relationships, geographic distribution, and plasmid replicon compositions.

Through antimicrobial susceptibility testing, all MCP-CF isolates exhibited extensive resistance to β-lactams, with partial resistance to tigecycline but retained susceptibility to colistin. From the global perspective, MCP-CF isolates occurred at a low frequency but spanned multiple sequence types and geographic regions. Carbapenemase gene combinations predominantly comprised bla_KPC and bla_NDM and were associated with plasmids of heterogeneous replicon backgrounds. Phylogenetic analysis indicated that these isolates were phylogenetically dispersed rather than clonally related.

Our findings demonstrate the capacity of C. freundii to acquire and disseminate multiple carbapenemase genes and reveal the widespread, yet under-recognized, distribution of these highly resistant strains. Continuous genomic surveillance and integrated analyses of public genomic data are essential for improving early detection and informing effective infection control and antimicrobial stewardship strategies.