You're confused? I'm confused too. Two men cannot share a urethral infection through oral sex or any of the other usual modes of contact. I suppose if the two urethral openings were directly and vigorously opposed, it might be possible. Your partner's urethral chlamydial infection cannot explain your NGU. And chlamydia doesn't infect the throat, or only rarely. And transmission of chlamydia from mouth to genitals has never been documented--if it occurs, it is very rare. In any case, only 30% of NGU is due to chlamydia--and in gay men, it's probably closer to 15-20%. Normal oral bacteria probably cause some cases.
Having said all that, I doubt you have urethritis at all. I'm not sure what is causing your "urethral irritation", but you are correct that onset a few days after azithromycin is peculiar. Herpes is a theoretical possibility. Or irritation from lubricant (especially spermicide). Adenovirus causes a few percent of NGU cases, often in association with a common cold in the infected person, a sex partner, or both.
Bottom line: You might or might not have NGU; if so, it isn't chlamydia, but could be due to the other things I mentioned. Or nothing at all--some sort of irritation that will clear up on its own. Unless your own doctors disagree, I suggest just sitting tight for a week or two; see a provider if your symptoms don't go away by then, or if they get worse at any time. Protected sex or masturbation won't hurt anything.
Bottom line 2: Somebody brought chlamydia into your relationoship. There is a third party somewhere who needs evaluation and treatment.
Good luck-- HHH, MD
If I did have NGU, would the antibiotics have taken care of it?
HHH, MD