First Isolation and Genomic Characterization of Escherichia ruysiae in Togo from a Five-Year-Old Patient with Gastroenteritis and Bloody Diarrhea.

Escherichia ruysiae is a recently characterized species within the Escherichia genus, often misclassified as E. coli due to limitations in existing operating procedures and diagnostic databases. In this study, we report the first isolation and genomic characterization of E. ruysiae in Togo, from a five-year-old female patient who was hospitalized with gastroenteritis and bloody diarrhea and subsequently died after eight days. Biochemical tests and MALDI-TOF initially identified the microorganism as E. coli, but phylogenomic and Average Nucleotide Identity (ANI) analysis confirmed it to be E. ruysiae, Clade IV with enteroaggregative associated genes. Whole genome sequencing of the strain FK53-34 enables the identification of resistance genes, including blaEC-15, eptA, and pmrF. The virulence profile of the strain included, but was not limited to aap, aatABC, and senB genes, which may support its pathogenicity and virulence. Multilocus sequence typing (MLST) did not match any known sequence type, which is obvious for a newly characterized microorganism. This study highlights the critical need for enhanced diagnostic tools and surveillance systems to identify emerging pathogens, including Escherichia ruysiae.