I personally believe that Lyme, like Syphilis, can remain in the body and cause symptoms long-term. Many viruses are able to do this, too (EBV, CMV, HH6, Polio, etc.). The film, Under Our Skin, showed research proving the presence of a viable Lyme infection in the brains of 7 out of 10 alzheimer's patients at the time of their death (he obtained samples from a brain bank).
The negative tests are primarily due to the elusive nature of the Borellia bergdorferi bacteria, the suppression of the immune system, and the poor quality of the tests.
Those who do not see improvement after long-term treatment have not been given the proper treatment, have a coinfection that has not been treated, or have damage that their body is unable to repair (nutritional imbalance plays a role in this). Can Lyme disease trigger autoimmunity? I do not believe it is "true" autoimmunity. I think the body's immune system is recognizing cells that have been damaged or altered by the Lyme bacteria and is trying to remove those cells. This is just my own theory. I came up with this theory because of the brain research from Under Our Skin. The research showed Lyme-human hybrid cells in the brain samples. If Lyme can do it in the brain, it can do it elsewhere. What if the body isn't attacking healthy cells, but rather is attacking Lyme-human hybrid cells? Medical science just isn't advanced enough right now to understand how all this stuff works or how to really test for it in live human beings.
Just my $.02...
Chronic Lyme Disease, Gluten & Sulfite Sensitivity, Many Food/Inhalant/Medication/Chemical Allergies & Intolerances, Asthma, Gut issues (dysmotility, non-specific inflammation), UCTD ("Secondary Lupus-Like Syndrome"), Osteoporosis, Pancytopenia, chronic malabsorption/malnutrition, etc.; G-Tube; Currently TPN-dependent.
Meds: Zofran, Pulmicort, Heparin (to flush PICC line), Claritin, Colloidal Silver (used topically), IV Milk Thistle, probiotics.