Immune-mediated inflammatory diseases (IMIDs) are a heterogeneous group of diseases that have common pathogenic mechanisms. Among them, ailments such as colitis ulcerosa, Crohn's disease, celiac disease, collagenous colitis, rheumatoid arthritis, psoriatic arthritis, psoriasis, chronic urticaria, vitiligo or multiple sclerosis are mentioned. In the emergence of these diseases, the dysregulation of the host's immune response and chronic inflammation are involved.
Article Immune-mediated inflammatory diseases (IMIDs) and biologic t...
Article Immune-mediated inflammatory diseases: Progress in molecular...
It is also suggested that human microflora may play a role in the development of IMIDs.
and a case report from 1992: http://adc.bmj.com/content/archdischild/67/12/1475.full.pdf as well as http://www.who.int/medicines/publications/pharmacopoeia/2012-04-04TestsforParticulateContamination_QAS11-405_Final.pdf to understand the scope of the problem and how to address it.
Persistent viruses such as cytomegalovirus (CMV) can be a source of inflammation. The pathogen burden (of which CMV is a key component) has also been linked to some inflammatory diseases. In my own research I have been looking for outbreaks of an unknown pathogen which appears to work via sub-acute immune manipulation. Have a look at the relevant sections at http://www.hcaf.biz/2010/Publications_Full.pdf