ABSTRACT
The Escherichia genus comprises four 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 multi-drug resistance plasmid using Illumina and Nanopore whole-genome sequencing (WGS). Strain OPT1704T can be differentiated from existing Escherichia spp. using biochemical (VITEK2) and genomic tests (average nucleotide identity [ANI] and digital DNA:DNA hybridisation [dDDH]). Phylogenetic analysis based on alignment of 16S rRNA sequences and 682 concatenated core genes showed similar results. Our analysis further revealed that strain OPT1704T 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 E. ruysiae sp. nov. as a novel species, encompassing Escherichia cryptic clades III and IV (type strain OPT1704T = NCCB 100732T = NCTC 14359T).
Author notes The Genbank accession number for the 16S rRNA gene sequence of strain OPT1704T is LR745848. The Genbank accession number for the complete genome sequence of strain OPT1704T is CABVLQ000000000.
Footnotes
↵† Members listed in supplementary file 1
Extensive restructuring of the paper, with a lot more focus on Escherichia ruysiae as a novel species. The analysis of the Escherichia genus has been removed from this version as this did not carry enough scientific value.
ABBREVIATIONS
- ONT
- Oxford Nanopore Technologies
- MIC
- Minimum Inhibitory Concentration
- COS
- Columbia agar + Sheep blood
- dDDH
- digital DNA:DNA hybridisation
- ANI
- Average Nucleotide Identity
- SNP
- Single Nucleotide Polymorphism