Lyme patients are immunocompremised. Whatever pathogens we have acquired and harbored in our body and that were kept in check, will now become an opportunist infection and will reactivate and flourish. We are susceptible to most of these; https://en.m.wikipedia.org/wiki/Opportunistic_infection
You can never elimate pathogens from the human body. A strong and healthy immune system is the strategy.
All protocols should include healthy diet, proper sleep cycles, antimicrobials, antivirals, ( herbs or pharma), supplements, alleviate stress, exercise, detox, proper hygiene, clean water and organic foods, and clean air.