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If they were struvite crystals, and he thinks this is what has caused a stone (if this does turn out to be the case), then he will likely prescribe more antibiotics. Struvite stones are caused by infection and to clear the infection up requires antibiotics.
However, since the culture came back negative, it makes it unlikely this to be the case......Except that sometime a free catch culture won't show anything when there really is an infection there. Sometimes a guided C&S has to be done. This happened with my boy. Free catches on him showed no bacteria, but there was an infection there. A guided C&S is where they use ultrasound and with the ultrasound, it helps them guide a needle directly into the bladder and they take a sample this way. I made sure my dog drank fluids well in advance and would carry him in so he wouldn't pee before getting this procedure done. (I was told they could add saline to the bladder if it wasn't full enough, but I didn't like that idea and didn't trust it not to dilute the sample more). So, my boy did have an infection that only showed up by culturing a sample retrieved directly from the bladder (whereas it did not show from a free catch) Can't explain why this is, but it does happen.
So, if the struvites were crystal, then doing a guided C&S (cultrue and sensitivity) and getting the urine directly from the bladder should show the type of infection and then also which antibiotics to use. You have to repeat this procedure a few weeks after stopping the antibiotics to make sure the infection is all gone.. Again, I can't explain why this is sometimes necessary, but it can happen this way.
IF the crystals were oxalate and that has caused an oxalate stone, then we're talking a whole 'nother ballgame. Oxalate stones are formed b/c of the body's inability to properly digest oxalate containing foods. IF this be the case, then I recommend joining K9KidneyDiet yahoo group and strictly follow their guidelines for the FuzzerFood diet. Introduce yourself and they can walk you thru stuff. It is a diet to be followed for life, but is apparently very effective. This is only necessary if the stone was oxalate. From what I have read, using prescription food is ineffective for this purpose.
Lastly, about my boy. He did have blood in his urine, but no stones. His blood was from the infection (again, only found from a urine sample taken directly from the bladder, and not found by free catch). So, it is possible that there are not any stones involved.
Oh, I re-read and it was someone else who mentioned crystals. It's late, and I didn't catch that early on. Still, it could just be an infection, or there could be a stone there. We didn't do x-rays, we did an ultrasound to look for stones. When a stone was not found in the bladder (not one in the shaft, either, since he is a male), then we did the needle draw from the bladder. Some vets don't use a guided needle to draw urine......but my comfort zone wouldn't allow it to be done without using an ultrasound and having it done by someone comfortable with doing the procedure that does it regularly enough. To me, it was a big deal puting a needle into a bladder and not missing. I wasn't comfortable with it at all, but am more comfortable with it now that it has been done twice (by vets that I trusted).