Sometimes floroquinolones like cipro and levaquin have side effects too.
I had the flu (confirmed with nasal swab) in January of 2012. I ended up going to the emergency room because I felt so bad and I was afraid that it would push my 17% gfr to a point where I would need dialysis. My kidney function did drop to around 10% and I did end up being admitted to the hospital for 2 nights as a cautionary measure. I was treated with IV fluids and an anti-viral. This episode also caused me to have to start taking phosphate binders. They also with held my lisinopril while I was sick. I'm a little fuzzy on the reasoning for it but it had something to do with actually hurting the kidney while I was sick. My gfr did recover. My kidney function has continued to slowly decline, but that was the way it was heading before I got the flu anyways.
There is no real medication treatment for viruses. Bacteria require antibiotics, but the antibiotic has to match the sensitivity of the bacteria. It will be a different antibiotic for different bacteria. Generally antibiotics dont damage kidneys except for aminoglycosides like gentamycin. Sometimes floroquinolones like cipro and levaquin have side effects too. Most cephalosporins like cefazolin (kefzol) are safe for the kidneys and are the first line choice for bacteremia that is NOT MRSA. Autoimmune disease is not really a compomised immune system. It is the immune system attacking the person . The immune system is actually over active. Compromised immune systems occur with kidney disease and especially diabetes. In these cases the immune system is underactive. If you have specific questions on these, please ask.