Well, all the times I have got bladder infection and doctors don't know the type of bacteria, they do request a special lab test to identify the bacteria. The proccess is the same, you just provide another urine sample and the lab is in charge to detect which bacteria is showing up there, at least the one in the bladder is going to be detected this way, and since I have heard that some bladder infections do spread to your kidneys too (is not common, but it does happens sometimes) this could be your case, but is very probably that the bacteria that they're going to found on your urine could be the same one of your kidneys.
Last year I got a bladder infection, and also I have bad stomach symptoms , they test my urine and my stools, and both showed the same bacteria *E.Coli* it spread from my bowel to my urine tract causing infection on both (and even my kidneys were mild compromise too).
So, keep waiting
at least they're not longer thinking is you been hypochondriac.