Escherichia ruysiae sp. nov., a novel Gram-stain-negative bacterium, isolated from a faecal sample of an international traveller

Abstract

The genus <i>Escherichia</i> comprises five species and at least five lineages currently not assigned to any species, termed '<i>Escherichia</i> cryptic clades'. We isolated an <i>Escherichia</i> strain from an international traveller and resolved the complete DNA sequence of the chromosome and an IncI multidrug resistance plasmid using Illumina and Nanopore whole-genome sequencing (WGS). Strain OPT1704^T can be differentiated from existing <i>Escherichia</i> species using biochemical (VITEK2) and genomic tests [average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH)]. Phylogenetic analysis based on alignment of 16S rRNA sequences and 682 concatenated core genes showed similar results. Our analysis further revealed that strain OPT1704^T falls within <i>Escherichia</i> cryptic clade IV and is closely related to cryptic clade III. Combining our analyses with publicly available WGS data of cryptic clades III and IV from Enterobase confirmed the close relationship between clades III and IV (>96 % interclade ANI), warranting assignment of both clades to the same novel species. We propose <i>Escherichia ruysiae</i> sp. nov. as a novel species, encompassing <i>Escherichia</i> cryptic clades III and IV (type strain OPT1704^T=NCCB 100732^T=NCTC 14359^T).