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

<i>Escherichia ruysiae</i> is a recently characterized species within the <i>Escherichia</i> genus, often misclassified as <i>E. coli</i> due to limitations in existing operating procedures and diagnostic databases. In this study, we report the first isolation and genomic characterization of <i>E. ruysiae</i> 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 <i>E. coli</i>, but phylogenomic and Average Nucleotide Identity (ANI) analysis confirmed it to be <i>E. ruysiae</i>, Clade IV with enteroaggregative associated genes. Whole genome sequencing of the strain FK53-34 enables the identification of resistance genes, including <i>bla_EC-15</i>, <i>eptA</i>, and <i>pmrF</i>. The virulence profile of the strain included, but was not limited to <i>aap</i>, <i>aatABC</i>, and <i>senB</i> 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 <i>Escherichia ruysiae</i>.