That's further evidence that you have no bacterial infectionand almost certainly no STD. A good bet is prostatitis -- most cases are not caused by known bacteria. Antibiotics often are tried, but usually don't make much difference.
Or maybe you have an adenovirus infection. Adenovirus usually causes colds, bronchitis, etc but can be transferred to the penis by oral sex. Do you by any chance also have cold symptoms or itchy/red eyes? If so, no antibiotics will have any effect, but it will clear up on its own.
Continue to work with your urologist on it.
My urologist prescribed me doxycycline but it seems as if it's not working but getting more painful.
The tests are very accurate; you can be certain you don't have those STDs. Conceivably you have nongonococcal urethritis (NGU). However, your symptoms don't fit well with any of these STDs, nor for HIV. And you can't catch HIV from receiving oral sex.
What to do now? Keep working with your doctor. But in the meantime, don't worry. This doesn't sound at all serious.