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Can you ask your vet to evaluate his blood pressure if s/he hasn't already done so? Hypertension would increase protein traffic across the kidneys, which could lead to proteinuria. If that is the case, it will be important to determine the cause of hypertension (and while there are many causes of hypertension, one cause is kidney disease).

Bloodwork also may not catch a problem , particularly with serum creatinine, until a lot of damage has already been done to the kidneys. The normal ranges of bloodwork/urinalysis can be pretty wide depending on the lab your vet uses, so the creatinine values could be still be in the normal range, but I would also look at these numbers over the course of several months. Have they been staying the same, or have they been going up?

Was the ultrasound normal? When was it done?
Have all tick borne diseases been ruled out?
Has a culture and sensitivity test been done on his urine?

If this was my dog, I would ask for a referral to a specialist at this point (board certified veterinary internist).
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