I had Lyme diagnosed in the acute phase, back in 1994. Tick bite, EM rash, arthralgia, rising lyme titer. I was likely undertreated.

I now run a +ANA and am diagnosed with autoimmune problems, including small fiber neuropathy and dysautonomia due to the SFN.

I believe my first treatment of 20 days of amoxicillin was not adequate.

I was retreated years later with doxy, azith and amox, not concurrently, not for more than 6 months and at reasonable doses. I didn't see any difference in how I felt.

I was retreated again with doxy a few years ago, and again, felt no difference.

I don't plan on any more antibiotic treatment, and other than catching it in the active phase, I don't think this long term treatment really does much. I think the side effects of the antibiotics and the possibility that one can get C. Difficile from all this, isn't worth it.

If there is evidence of active infection, then it should be treated, but in later phases, I don't know of many cases really get better from prolonged antibiotic treatment. As to whether Lyme caused the autoimmune problem, the jury is out, and probably will be.