Hello and welcome, Flagyl (Metronidazol) is used to treat amoebiasis. Amoebiasis presents mostly with cramping abdominal pain, watery or bloody diarrhea. There are majority of diseases that can present with foul smell & mucus in the stool (malabsorbtion etc). It is not specific for certain disease (it might be amoebiasis). Before starting the treatment with Flagyl (Metronidazol) amoebiasis should be confirmed. His stool should be examined for amoebiasis. His body will not become immune or resistant to antibiotics if you take the medicine as prescribed by your doctor. Antibiotics might not work if the infection becomes resistant. I hope the above information will be helpful for you. Please, feel free to ask me if there is anything else you need to know. Thank you, Malik Amonov MD