Comparative genomic and resistome analysis of Citrobacter koseri: first genome report from Egypt

Background Citrobacter koseri is increasingly implicated in healthcare- and community-associated infections, with multidrug-resistant (MDR) strains posing a growing clinical concern. However, its population structure and resistome dynamics remain incompletely understood. Here, we report the first draft genome sequence of an MDR C. koseri isolate (DFU32) from Egypt, recovered from a patient with a diabetic foot ulcer (DFU). We also present a comparative genomic and resistome analysis of 518 publicly available C. koseri genomes available at the time of the study. Results The isolate exhibited resistance to multiple antimicrobial classes, including β-lactams, aminoglycosides, fluoroquinolones, and sulfonamides, as well as tigecycline and colistin. MLST assigned DFU32 to sequence type (ST) 1172. Genomic analysis identified 21 antimicrobial resistance (AMR) genes, including multiple β-lactamases ( bla CKO , bla TEM , bla OXA−9 , bla CTX−M−15 , and bla CMY−2 ) and aminoglycoside resistance determinants, including armA . Colistin resistance was associated with the presence of a PhoQ V381I substitution. Comparative analysis of 518 publicly available genomes revealed 140 unique AMR genes across the species, with 73.6% of genomes carrying acquired resistance determinants. The population comprised two major lineages, bla CKO and bla MAL , with the MAL lineage, particularly MAL-2, carrying significantly more AMR genes. Carbapenemase genes were identified in 29.1% of genomes and were distributed across nearly half of the detected STs, with bla KPC variants predominating. Mobilized colistin resistance ( mcr ) genes were detected in 2.5% of genomes. Both carbapenemase and mcr genes were predominantly located on plasmid-associated contigs. Notably, chromosomal integration events were observed. These included mcr-9.1 , which was associated with IS26 and IS903B, and bla KPC−2 , which was embedded within an IS26-bracketed transposon (IS 26 – recA –IS Kpn27 – bla KPC−2 –IS Kpn6 –IS 26 ) in novel STs. These findings underscore the genomic plasticity of C. koseri and the potential for stable, plasmid-independent maintenance of colistin and carbapenem resistance. Among the identified STs, ST690 displayed a particularly high resistance gene load, including carbapenemase and mcr genes, suggesting that it may represent a high-risk lineage. Conclusion This study provides the first genome-based characterization of an MDR C. koseri isolate from Egypt. The results highlight the potential genetic mobility and global spread of AMR determinants in this emerging pathogen. Notably, the studied isolate was recovered from DFU, underscoring the increasing clinical relevance of C. koseri in chronic wound infections.