Genomic characterization of Enterobacter hormaechei subsp. xiangfangensis isolated from a urinary tract infection: insights into antibiotic resistance determinant and mobile genetic elements

Urinary tract infections (UTIs) remain a major public health concern in resource-limited settings, where reliance on conventional urine culture and sensitivity testing may result in misdiagnosis and inappropriate antibiotic prescriptions. This study aimed to provide the first genomic characterization of Enterobacter hormaechei subsp. xiangfangensis isolated from a UTI case in Côte d’Ivoire, focusing on antimicrobial resistance, mobile genetic elements, and epidemiological relevance. A bacterial isolate (20LM111) was recovered from a UTI patient at Daloa Regional Hospital. Antimicrobial susceptibility testing was performed, followed by genomic DNA extraction, Illumina NextSeq sequencing, and de novo genome assembly. In silico analyses were conducted to identify antimicrobial resistance genes, plasmid replicons, prophage regions, virulence factors, and multilocus sequence type. The isolate exhibited resistance to doxycycline, tetracycline, ampicillin, amoxicillin–clavulanate, nalidixic acid, cefuroxime, ceftriaxone, and cefoxitin. Genomic analysis identified the resistance genes dfrA14, blaACT-16_1, and fosA_7, while no virulence-associated genes were detected. The draft genome size was 4,697,941 bp with a GC content of 55.42 % and was assigned to sequence type ST114. Two plasmids (IncFIB[pQil] and IncR) and four prophage regions were identified. This study highlights the value of whole-genome sequencing for improving UTI diagnostics, monitoring antimicrobial resistance, and enhancing surveillance of high-risk Enterobacter clones in resource-limited settings. • First genomic characterization of Enterobacter hormaechei subsp. xiangfangensis causing a urinary tract infection in Côte d’Ivoire. • The isolate belongs to the high-risk international clone ST114, previously associated with multidrug-resistant Enterobacter outbreaks. • Whole-genome sequencing revealed multiple antibiotic resistance determinants, including dfrA14 , blaACT-16 , and fosA7. • Two plasmid replicons (IncFIB[pQil] and IncR) and four prophage regions were identified, highlighting substantial genomic plasticity. • No virulence genes were detected, but the presence of diverse mobile genetic elements suggests a potential for horizontal gene transfer.