autoimmune disease is when the body makes antibodies to an invader that has peptide sequences in its cell walls that resemble those of the antibodies. When the invader is gone, those antibodies for some reason linger and start attacking tissues of the host, and nerve tissue is often commonly attacked. In some people these antibodies do not shut off and the body continues to make them. It is thought that some autoimmune processes are inherited.

The vaccine for Lyme only caused attacks on hosts' joints, that carried certain markers on their white cells.

I used to have a very old cat..who had terrible arthritis...and our vet at the time told us that AUTOIMMUNE disease is
becoming epidemic in cats. (today our poor pets are vaccinated to death IMO) Pet vaccines were causing sarcomas in cats, so now they vaccinate in the leg...so if the sarcoma (cancer) occurs the vets can amputate the leg and save the cat. Some compassion? Think about that.

Infections can also trigger autoimmunity in those who have certain genetic markers making them at risk.

Historically rabies vaccines, have been the worst offenders, until that Lyme vaccine showed up. Even the newer rabies types have studies on PubMed about reactions. If you search
"rabies" on PN you will find the posters here over the years who have gone into detail about neurological reactions.

So today there is quite a bit of concern about too many vaccines. I am sure you could Google to find the process by which micro-organisms trigger autoimmunity, but the ones I have seen are very complex explanations and involve genetic data and terminology.