Urethral inflammation after urethritis.

I had unprotected sex in Feb. Soon started having symptoms: 1. Pain/burning sensation while peeing 2. Yellow discharge from penis 3. Frequent urination I did a urine test and culture test. Culture test didn't show any bacteria presence. But urine sample showed presence of pus cells and leucocytes. For one week I took OFLOX, but symptoms reappeared after 4 days. Next I took Macrobid. Symptoms reappeared after 4days. I consulted a urologist who diagnosed it as Urethritis due to STI. He didn't mention which STI it is. Now I was suggested Amykacin 500mg injection and Ceftum500mg both tablet twice a day for 1 week. All symptoms disappeared. After 2 weeks I did urine test which showed everything as normal. After 25days I had sex (protected) and observed a sharp pain while ejaculation, and pain lasted for 30 min after . Could this be because the inflammation has not healed completely?