Can NGU be caused by HPV?

[kzn123]

I had unprotected sex almost 3 years ago with a girl, and I was in a stable relationship for 2.5 years with no symptoms or any health issues. However, three months ago months ago I had treatment (Liquid Nitrogen) for two small bumps around my genital area that I noticed this last december. I have also taken many STDs tests (urine and blood) and all of them came back negative, however, two days ago i noticed a milky discharge in the morning. The same day, I went to the STI clinic to get tested. I was diagnosed with NGU which made me very confused because I had only had one PROTECTED encounter with a female 3 weeks before this happened. The nurse took a swab of my urethra and told me that there was evidence of bacteria and that it was probably that what couldve caused the discharge. She gave me 6 pills to take all at once at the clinic, and told me to wait 7 days with no sex and after that, wait another 7 days to see if the symptoms persisted. Today  is the third day after I took the medication at the clinic but lately I have been feeling a burning sensation at the top of my penis while doing my daily activities. No burning when i pee and havent noticed the milky discharge lately. Although, there is a clear discharge once in a while that is very hard to differentiate from urine and i usually have to milk my penis to be able to see it. Ive also noticed redness inside my urethra (only inside the left side lip). The sensation comes and goes but at this point I dont know what really caused my NGU infection. I dont think it is Herpes because i havent developed any sores or blisters and it definielty doesnt burn when i pee, but im still worried about it. Perhaps if HPV could have caused this?? Also, i havent had any recurrences of any bumps or warts in my genitals.
is the treatment going to be effective even if my tests previous came back negative?
is NGU going to clear up?

Please help me with this, it has been the worst time of my life.

Thank you!