Comparative genomic and resistome analysis of Citrobacter koseri: first genome report from Egypt
6 affiliations
- 1Microbiology and Immunology Department, October University for Modern Sciences and Arts (MSA), Giza, Egypt
- 2Medical Microbiology and Immunology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
- 3School of Science, Faculty of Engineering and Science, University of Greenwich (Medway campus, Kent), London and Southeast (LASE) University Group, London, UK
- 4Department of Zoonoses, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
- 5National Institute of Diabetes and Endocrinology (NIDE), Cairo, Egypt
- 6PharmD Students Program, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Giza, Egypt
Abstract
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 (blaCKO, blaTEM, blaOXA−9, blaCTX−M−15, and blaCMY−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, blaCKO and blaMAL, 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 blaKPC 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 blaKPC−2, which was embedded within an IS26-bracketed transposon (IS26–recA–ISKpn27–blaKPC−2–ISKpn6–IS26) 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.
Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1186/s12866-026-05726-w.
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BibTeX
@article{hamed2026comparative,
title = {{Comparative genomic and resistome analysis of Citrobacter koseri: first genome report from Egypt}},
author = {Samira M. Hamed and Manal M. Darwish and Mohamed Samir and Reham Monir and Ahmed Al Taweel and Ayat I. Ghanem and Ihab N. Hanna and Aya H. Hefnawy and Nada S. Gebreel and Noha M. Soltan and Yara H. Aboudewan and Mai A. Amer},
journal = {BMC Microbiology},
year = {2026},
month = nov,
doi = {10.1186/s12866-026-05726-w},
url = {https://doi.org/10.1186/s12866-026-05726-w},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Comparative genomic and resistome analysis of Citrobacter koseri: first genome report from Egypt
AU - Samira M. Hamed
AU - Manal M. Darwish
AU - Mohamed Samir
AU - Reham Monir
AU - Ahmed Al Taweel
AU - Ayat I. Ghanem
AU - Ihab N. Hanna
AU - Aya H. Hefnawy
AU - Nada S. Gebreel
AU - Noha M. Soltan
AU - Yara H. Aboudewan
AU - Mai A. Amer
PY - 2026
DA - 2026/11/05
JO - BMC Microbiology
DO - 10.1186/s12866-026-05726-w
UR - https://doi.org/10.1186/s12866-026-05726-w
AB - 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 (blaCKO, blaTEM, blaOXA−9, blaCTX−M−15, and blaCMY−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, blaCKO and blaMAL, 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 blaKPC 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 blaKPC−2, which was embedded within an IS26-bracketed transposon (IS26–recA–ISKpn27–blaKPC−2–ISKpn6–IS26) 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. Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1186/s12866-026-05726-w.
SN - 1471-2180
ER -