In-Depth Genome-Based Analysis of Shigella spp. and Escherichia spp.: Resolving Ambiguities and Unveiling Phylogenetic Relationships.

Abstract

Although traditionally classified as distinct genera, recent genomic analyses suggest that Shigella species may represent pathogenic clones of Escherichia coli. In this study, we investigated the genetic relationships between Shigella and Escherichia species through comprehensive phylogenomic and taxonomic analyses. Genomic datasets for all validly named species within both genera were retrieved from GenBank. Multiple methods, including 16S rRNA gene sequence analysis, digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI), Genome BLAST Distance Phylogeny (GBDP), and percentage of conserved proteins (POCP), were employed. These results reveal a high genetic similarity between Shigella species and E. coli, with ANI values exceeding 96% and dDDH values above 70%, indicating that Shigella species fall within the same species as E. coli. Phylogenomic trees, generated from whole-genome sequences and core genes, further corroborated the close evolutionary relationship between these taxa. Furthermore, these analyses challenge the reclassification of Atlantibacter hermannii and Pseudescherichia vulneris, supporting their retention within the genus Escherichia. Based on these findings, we propose the reclassification of Shigella species as subspecies within E. coli and recommend revisiting the taxonomic status of other related species.