Background: Citrobacter freundii is an emerging nosocomial pathogen, yet its transmission dynamics remain poorly characterized.

Methods: We conducted a retrospective genomic and epidemiological study to investigate the transmission chains of extended-spectrum beta-lactamase (ESBL) and carbapenemase producing C. freundii collected at Geneva University Hospitals during a six-year period (2017-2022). Whole genome sequencing (WGS) using Nanopore long-read sequencing, MLST and plasmid typing, and resistome profiling were performed. Transmission events were defined based on genetic relatedness, plasmid similarity and patient trajectories.

Results: A total of 103 cases of ESBL and carbapenemase-producing C. freundii were identified, of which 79% were hospital-acquired, 72% were isolated from rectal swabs, and bacteremia occurred in six patients. Among 90 isolates available for WGS, 73% were confirmed as C. freundii, whereas the remaining belonged to other Citrobacter species. A high genetic diversity was observed among C. freundii sensu stricto, with 29 distinct sequence types, including predominant ST114, ST98, and ST22. We identified 10 clusters involving multiple Citrobacter species among 35 patients. Transmission chain analysis revealed that 37% of patients were involved in putative clonal transmission and 21% in putative plasmid-mediated dissemination events, particularly in abdominal surgery, geriatrics and septic orthopedics, often involving C. freundii harboring blaCTX-M-15, blaOXA-48/CTX-M-14b and blaOXA-181 on IncHI2-IncHI2A, IncM1 and IncX3 plasmids, respectively.

Conclusions: Our study highlights the role of C. freundii as a vector of both clonal and plasmid-mediated, nosocomial transmission of antimicrobial resistance. It emphasizes the need to include C. freundii in genomic and epidemiological surveillance to detect its silent spread.