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My son is 4. He has had normal bowel movement since he was tested positive for c diff on 2nd June but the toxins a and B came positive yesterday that is 7th June. He does get a loose stool every once in a while if he is out in the sun stressing himself or eats something fatty but it would be once in a week or two. My question is can immunity start working and making him better but still the toxins are positive? And will remain positive for a while? If so how long?

If someone has a degree of immunity to c.diff the toxins do not make them sick, that's exactly how the vaccine will work.
Testing positive for toxin is not unusual, c.diff is a normal gut flora in many people and it does not make them sick. That's why testing to see if its gone is next to useless.
If theres no symptoms there's no disease and no treatment needed.
It's possible to test toxin positive for life and never have c.diff as a disease.

Thanks Roy.