Does inflammatory colitis and infection come out through defecation?

I was at the ER department recently of a hospital in New Jersey and I was diagnosed with inflammatory colitis and an infection of the right side of the ascending colon and transverse colon being identified as a "wall" that was thickening. I am currently on the second day of two antibiotics, Levaquin and Flagyl, 750 milligrams and 500 milligrams. I was wondering, by the end of my infection and inflammation, does the parasite or bacterial infection come out through defecation (or, excuse my language, "pooping") or is it eliminated from the colon in a different way that the Levaquin and Flagyl team up on chemically? Thanks and ten points for best answer.