I have had kidney issues for several years now. Kidney/liver issues are what stopped me from being able to use antibiotics. The abx plus artemisinin made my blood tests show problems. I stopped all abx and went to a naturopath for treatment. He used natural supplements etc. to help me and my tests finally reached the normal range about 6 months later. My GFR however has never returned to normal and has remained a little low for a couple years now. The docs think I have some kind of permanent problem with the kidneys and I need to be careful with what I take and make sure I am properly hydrated. My issues could be from the infections, treatment, or even genetic tendancy. Anyway, I have remained on all natural treatments for the lyme/coinfections and a kidney doc checks my blood test every 2-3 months to make sure I am still OK.
Toxicity is a big issue with these diseases and their treatments. Using good detox methods can help as well as supplements to support the organs. I think sometimes treatment needs to stop or slow down untill the body can get rid of the bad stuff and recover. Maybe you can add in a good naturopath to your "team". I could not do this without one. They have been extremely valuable.
Wishing you all the best, bablymers mom