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

Abstract

The genus Escherichia comprises five species and at least five lineages currently not assigned to any species, termed 'Escherichia cryptic clades'. We isolated an Escherichia 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 Escherichia 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 Escherichia 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 Escherichia ruysiae sp. nov. as a novel species, encompassing Escherichia cryptic clades III and IV (type strain OPT1704^T=NCCB 100732^T=NCTC 14359^T).

Keywords: Enterobacteriaceae; Escherichia; bacterial taxonomy.

Fig. 1.

16S phylogeny of Escherichia ruysiae sp. nov. OPT1704^T with type strains of other Escherichia species, other Escherichia cryptic clades and Salmonella enterica serovar Typhimurium as the outgroup. Numbers indicate bootstraps on a scale of 0 to 1. Phylogeny available at https://itol.embl.de/tree/14511722611226771596704407.

Fig. 2.

Phylogeny based on 682 concatenated core genes including Escherichia ruysiae OPT1704^T with type strains of other Escherichia species, other Escherichia cryptic clades and Salmonella enterica serovar Typhimurium as outgroup. Numbers indicate bootstraps on a scale of 0 to 100. Phylogeny available at https://itol.embl.de/tree/14511722611160731596708541.