There's multiple things required for AIEC colonization. You need the actual bacteria, AIEC, found in many people with CD, but also in a number without CD. Regular non-pathogenic E. Coli do not bind to epithelial cells, it does not invade the intestine, they're harmless commensal bacteria. AIEC are not, but they need a specific molecule to adhere to and invade epithelial cells, specifically ileal enterocyte, AIEC's forte is the ileum. That molecule is called CEACAM6, AM stands for adhesion molecule. CEACAM6 is seen a lot in patients with CD, not nearly as much in patients without CD.
One theory is that, not only AIEC uses CEACAM6, but the body can also use soluble CEACAM6 as a decoy binding protein preventing AIEC from invading the intestine. And for some reason, EN formulas, increase the amount of soluble CEACAM6 that are released.
There's also been a good study that showed that EN exclusivity is not why EN seems to help some people with CD. EN in addition to a normal diet gave the same results. So it's not the absence of X or Y in a normal diet that is of importance when taking EN, EN itself seems to help people for some reason.
It also doesn't hurt that EN formulas like 028 and Modulen contain all the nutrients people need, diverse amino acid profile, glutamine used extensively by the small intestine, vitamins like B12 and vitamin D, which tend to be lacking in people with CD, etc.