I went to one nutriopathic lecture where they suggested that many autoimmune diseases were a result of a previous infection from a stealth, or long term infection. This is the same way that lymes disease is a stealth pathogen that causes an autoimmune disease. The lecturer spoke of having strong results when treating autoimmune diseases similarly to ways you would treat a stealth pathogen infection and that he had had much success with this.
Do you have an experience with this?
This is another hypothesis of how autoimmune diseases arise known as the cryptic infection hypothesis. As far as I am aware the current evidence is now swaying in favour of the hygiene hypothesis as opposed to the cryptic infection hypothesis.
Here is a link to more information on this hypothesis: https://www.ncbi.nlm.nih.gov/pubmed/12848953