Definition of the species Escherichia coli: problems of taxonomy and phylogeny

Escherichia coli is a component of the normal intestinal microbiota of humans and animals. Phenotypic and genotypic characteristics allow the identification of pathogenic E. coli strains. Numerous pathotypes, representing groups of strainswith specific pathogenic characteristics, have been described based on heterogeneous criteria. The use of whole-genome sequencing has led to the accumulation of genomic data that enable a population-phylogenetic approach to the emergence of virulence, thus allowing E. coli to be further classified into phylogenetic groups. An analysis of the literature data revealed that non-pathogenic E. coli living in the gastrointestinal tract of animals belong to group A, commensal and some pathogenic strains belong to group B1, InPEC belong to groups D1, D2 and E, most ExPEC belong to group B2, and strains that are phenotypically indistinguishable and genetically diverse, belong to Clade I. Emerging multidrug-resistant E. coli strains are more difficult to treat and pose a higher risk of bacteremia. Effective prevention and treatment of E. coli infections requires distinguishing between strains (pathotypes, phylogenetic groups) of the microorganism that cause disease in animals and strains that infect humans through the food chain, as animals serve as their reservoir. The development and implementation of effective preventive strategies requires a better understanding of the current taxonomy of the pathogen, as well as tracing its genomic evolution to generate fundamental knowledge for the development of not only effective vaccines but also new therapeutics to combat this diverse group of pathogens within the framework of a One Health approach.

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