What Causes Pain During Urination Along With Penile Discharge?

Hi, I have been experiencing pain during urinating and penile discharge for about 4 days now. My discharge is sometimes clear and sometimes with a pus. I had a urinalysis and gram stain penile discharge done yesterday and from the results everything is normal. I took a picture of the tip of my penis and showed it to my doctor, he then observed 2 small pus filled bumps just outside the opening of my urethra. So he said the infection was just outside and not my bladder or the inside of my urinary tract. He prescribe cefaclor 500mg 3x a day for 10days and mupirocin. Now for the first time I took cefaclor last night, then I had a fever, and when I wokeup today the pus filled discharge is gone. And it doesn t hurt no more. My question is, is it safe to apply mupirocin on the opening of my urethra/meatus? Since they ve indicated for external use only?