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2 year old Great Pyrenees has Blood in Urine, Vets can’t Diagnose...

My 2 year old female (not fixed) has been experiencing blood in her urine for the past two months. As soon as we notice we took her to the vet the next day. They performed a urinalysis and saw bacteria so they started her on 1-2 weeks of amoxicillin, nothing happened. This led them to perform a urine culture which came up with nothing but they admitted it was likely mishandled. In the mean time I started her on a week of ciprofloxacin, once again no results. They then said an x ray might be needed to check for kidney/bladder stones but again nothing showed up. After this they recommended an ultrasound and everything came back normal. Then they performed another urine culture and were able to identify E. coli and acinetobacter lwoffii, they immediately started her on two weeks of simplicef antibiotics. Towards the end of the two weeks we noticed noticeable improvement, she went a whole 2-3 days with no sign of blood. However, by the end of the antibiotic she still had blood in her urine. Now they recommend we either spay her or do an endoscopy which can easily run up to $2k. I will do the endoscopy if we must but I was curious if anyone has ever heard of anything like this?
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