Nitrite and Leukocyte Esterase can indicate an infection, but the absence of either in the urine test doesn't mean that no infection is present. I'd ask them to look for white blood cells specifically, either from a urine sample or the swab or PCR, like klamidia suggests. The PCR will take it further, so that's the best idea.
Since it gets worse as you sit, talk to them about prostatitis, too.
Good luck, and let us know.
Hi,
urine culture in men will show bacteria only after the infection has progressed substantially, please ask either for a swab, or a pcr analyses