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 OPT1704T 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 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 Escherichia ruysiae sp. nov. as a novel species, encompassing Escherichia cryptic clades III and IV (type strain OPT1704T=NCCB 100732T=NCTC 14359T).
BrennerDJ, DavisBR, SteigerwaltAG, RiddleCF, McWhorterAC et al. Atypical biogroups of Escherichia coli found in clinical specimens and description of Escherichia hermannii sp. nov. J Clin Microbiol1982; 15:703–713 [View Article]
FarmerJJ, FanningGR, DavisBR, O'HaraCM, RiddleC et al.Escherichia fergusonii and Enterobacter taylorae, two new species of Enterobacteriaceae isolated from clinical specimens. J Clin Microbiol1985; 21:77–81 [View Article]
HataH, NatoriT, MizunoT, KanazawaI, EldesoukyI et al. Phylogenetics of family Enterobacteriaceae and proposal to reclassify Escherichia hermannii and Salmonella subterranea as Atlantibacter hermannii and Atlantibacter subterranea gen. nov., comb. nov. Microbiol Immunol2016; 60:303–311 [View Article]
AlnajarS, GuptaRS. Phylogenomics and comparative genomic studies delineate six main clades within the family Enterobacteriaceae and support the reclassification of several polyphyletic members of the family. Infection, Genetics and Evolution2017; 54:108–127 [View Article]
PriestFG, BarkerM. Gram-Negative bacteria associated with brewery yeasts: reclassification of Obesumbacterium proteus biogroup 2 as Shimwellia pseudoproteus gen. nov., sp. nov., and transfer of Escherichia blattae to Shimwellia blattae comb. nov. Int J Syst Evol Microbiol2010; 60:828–833 [View Article]
LiuS, FengJ, PuJ, XuX, LuS et al. Genomic and molecular characterisation of Escherichia marmotae from wild rodents in Qinghai-Tibet plateau as a potential pathogen. Sci Rep2019; 9:1–9 [View Article]
RussoT, JohnsonJR. Medical and economic impact of extraintestinal infections due to Escherichia coli: focus on an increasingly important endemic problem. Microbes Infect2003; 5:449–456 [View Article]
GangiredlaJ, MammelMK, BarnabaTJ, TarteraC, GebruST et al. Draft genome sequences of Escherichia albertii, Escherichia fergusonii, and strains belonging to six cryptic lineages of Escherichia spp. Genome Announc2018; 6:e00271–18 [View Article][PubMed]
ArcillaMS, van HattemJM, HaverkateMR, BootsmaMCJ, van GenderenPJJ et al. Import and spread of extended-spectrum β-lactamase-producing Enterobacteriaceae by international travellers (combat study): a prospective, multicentre cohort study. Lancet Infect Dis2017; 17:78–85 [View Article][PubMed]
SundinGW, BenderCL. Ecological and genetic analysis of copper and streptomycin resistance in Pseudomonas syringae pv. syringae. Appl Environ Microbiol1993; 59:1018–1024 [View Article]
OjdanaD, SieńkoA, SachaP, MajewskiP, WieczorekP et al. Genetic basis of enzymatic resistance of E. coli to aminoglycosides. Adv Med Sci2018; 63:9–13 [View Article]
MitchellAL, AttwoodTK, BabbittPC, BlumM, BorkP et al. InterPro in 2019: improving coverage, classification and access to protein sequence annotations. Nucleic Acids Res2019; 47:D351–D360 [View Article]
ZhouZ, AlikhanN-F, MohamedK, FanY, AchtmanM et al. The EnteroBase user’s guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity. Genome Res2020; 30:138–152 [View Article]
YoonS-H, HaS-M, LimJ, KwonS, ChunJ. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek2017; 110:1281–1286 [View Article][PubMed]
Rodriguez-RLM, KonstantinidisKT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Prepr2016; 4:e1900v1
ChunJ, OrenA, VentosaA, ChristensenH, ArahalDR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol2018; 68:461–466 [View Article]
KimM, OhH-S, ParkS-C, ChunJ. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol2014; 64:346–351 [View Article][PubMed]
QinQ-L, XieB-B, ZhangX-Y, ChenX-L, ZhouB-C et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol2014; 196:2210–2215 [View Article]
Redondo-SalvoS, Fernández-LópezR, RuizR, VielvaL, de ToroM et al. Pathways for horizontal gene transfer in bacteria revealed by a global map of their plasmids. Nat Commun2020; 11:3602 [View Article][PubMed]
NguyenL-T, SchmidtHA, von HaeselerA, MinhBQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol2015; 32:268–274 [View Article]
KalyaanamoorthyS, MinhBQ, WongTKF, von HaeselerA, JermiinLS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods2017; 14:587–589 [View Article][PubMed]
Huerta-CepasJ, SzklarczykD, HellerD, Hernández-PlazaA, ForslundSK et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res2019; 47:D309–D314 [View Article]
VignaroliC, Di SanteL, MagiG, LunaGM, Di CesareA et al. Adhesion of marine cryptic Escherichia isolates to human intestinal epithelial cells. Isme J2015; 9:508–515 [View Article][PubMed]