What makes an E.coli an E.coli, genotype or phenotype?
The context for identifying E. coli is primarily clinical Microbiology, and in the clinical lab the identification is primarily phenotypic, based on various properties such as growth and morphology on selective media, Gram stain appearance, biochemical characteristics, etc - only under unusual circumstances is genetic testing done. The latter is problematic because of extreme genetic diversity within the species and some overlap with others (even other genera).

The problems with the notion of "species" in E. coli in the context of 16s sequencing, horizontal gene transfer, mobile genetic elements, plasmids, etc is discussed at some length in Quammen's recent book The Tangled Tree.

For now, phenotypic species identification is the norm, as illustrated by the "Nomenclature" guidance to authors of the Journal of Bacteriology, a publication of the American Society for Microbiology.