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Rachelle, mommy to 8 year old boys!
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In my experience stuff that goes on that long was parasitic. Unfortunately, we didn't catch them in pediatrician stool samples. They only tests for certain ones. Not the most common actually (b. hominus, d. fragilis, etc.) that continue indefintiely, not generally cryptosporidium, etc.
If you don't "catch" it and this goes on (note: many/most of the lasting parasitic infections are acute initially and then form a come and go pattern) I strongly recommend metametrix comprehensive stool test. It will catch it as they use DNA and test for all of them including b. hominus, crypto, fragilis, etc. Genova also tests for all of them but they don't use DNA so you'll want two samples to be sure to catch anything. Whatever stool test you use collect from beginning, middle, and end of stool. Some are only carried in certain portions. This is especially important with the culture types (all except metametrix).