Hello and thank you for your post on e health forum.
MRSA infection in the kidney can result in a number of conditions including pyelonephritis, renal abscess, recurrent urinary infections, etc.
You might with progressive damage of renal tissue and loss of renal function.
You might benefit by taking a second opinion from a urologist and get tests like kidney ultrasound done for proper evaluation of the current status.
I hope this helps.