My wife is 51 and very healthy non smoker. She has had extreme fatigue, blood in urine, localized left flank pain. Ct scan was neg for kidney stones?

Infection or tumor. The most likely reason is infection of the kidney...Your doctor will check the urine and prescribe antibiotics. A less likely reason is a tumor in the kidney or nearby. This may need a urologists help. It could still be a kidney stone that was not seen on the ct, which also needs a urologists help.