Female dog urinary issues

We have a young rescued female rottie cross who was spayed @ 8 wks of age by the shelter we got her from. She is now 16 months old, we got her as a pup - right after she was spayed. She has had a number iof issues since we got her including incontinence, which we are treating with Prion; we have taken numerous urine samples to our vet in which the bacteria levels have been very high, the PH has been high 7.75 - 8.5, and she has had crystals in her urine, some time the crystals have been extremely high in number. She often is licking her genital area. Our vet has put her on anti-biotics 4-5 times when the bacteria, crstals & PH has been high, but my concern is that this appears to work for awhile but does not ever solve the problem. A month ago they did a culture and thought she might have e.coli in her urine, which they  treated with anti-biotics.
Her vulva is tucked up and not very easy to see-someone suggested that she may not be able to empty her bladder when she urinates which may be promoting the bacteria growth, but what about the PH & crystal? She is on Science Diet - adult, per our vet recommendation; I have also started adding a teaspoon of crushed cranberries to each of her meals to promote a higher acid level in her urine; she gets very little else as far as treats due to trying to conntrol her diet. Should I get a second opinion, and perhaps have an ultra-sound done to see if there is something anatomically wrong that could be causing this? Should I change her dog food?  I want to give her a good and comfortable life. I am a little disappointed in the lack of "proactiveness on behalf of our vet, as his method of treatment only consists of antibiotics, nothing furture. Please advise. Thank you.  

[Dan Sims, DVM]

There are 2 types of crystals:one indicates an infection in the urinary tract and the other is the result of diet.
I would switch her to so diet which can help with both crystals types and xray her bladder for bladder stones.
The vaginal conformation may be leading to the problem.If I knew which type of crystal she had it would be helpful along with the culture results.