My father was misdiagnosed with a smaller kidney stone than it actually was. Before they found out the real size in CT scan, the doctors began the flush therapy and it apparently started to damage his kidney walls so they inserted a DJ stent. After keeping the stent for two weeks, they conducted RIRS Lithrotripsy to remove the stone. They sent him home with a stent again in the ureter. Within a week he started to suffer from high fever which has continued till date, it has been over 18 days now, still in hospital. We thought the stent was causing the fever, it was removed and fever persisted. All blood and urine cultures are negative. Anti-malarial drugs were administered, to no avail. A CT scan detected a minimal pus in the right kidney which has also now been removed through fine needle aspiration but the fever persisted. The pus biopsy was also negative. So far he has been on Meropenem (and now merobactum), PCM injections for fever relief, amikacin (restarted today), four doses of colistin in two days (suspected to cause higher fever than regular - 104° with chills and vomitting). PET CT detected a fungal infection in kidney today and he has been put on Amfocare (amphotericin) 50mg.
Complicated kidney infection. Unexplained f... - Kidney Disease
Kidney Disease
Complicated kidney infection. Unexplained fever.

So sorry to hear that your father is going through this. Try to hang in the and wait for the amphoteracin to work.
I was a respiratory therapist and I saw many people in the hospital with unexplained fevers. As long as he is in the care of a doctor and being monitored he should be fine.
I know it's really frustrating but try and hang in there.
Turns out it is a renal tuberculosis related cause. He's taking fixed dose combination of ATT (R-cinex 600mg, Benadon 40mg, combutal 1200mg, P-zide 750mg) and Omnacortil 30mg for sarcoidosis treatment. Could it be tuberculous sarcoidosis?
The fever has come down now. Any suggestions for recovery?
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So sorry your father is going though so much. Sending healing thoughts and prayers.
Thank you