With this type of infection [re: lyme type] it is very difficult to determine exactly what is the primary infective agent. The neuro toxin is the main cause of symptoms, but the organism[s] are the source. In my case, I have observed the commensal e-coli is contaminated with several mutant forms. Since the e-coli has compatible sero-type to my body, the immune-reactions are only directed at forms which present unusual antigens.
This keeps the reactions in perpetuity. Meanwhile, the toxins insure certain systems which are essential to immune functions are continuously impeded.
I very much suspect that SIgA is being crippled, which causes weak immune response in gut and other mucus membranes which may be affected.
This is what I would check, plus testosterone levels and aMSH if possible. Shroom