In reply to your follow-up question in a new thread, which I deleted: I agree with your doctor that the IgA test is meaningless. No blood tests are useful in diagnosing chlamydia. However, the negative PCR tests prove that you do not have chlamydia at this time.
HHH, MD
Thank you for using the forum. I will try to help. But the main thing to know is that you probably do not have any continuing STD or any other serious infection. You have been more than adequately treated for all possible STDs that might have been present at the start. There are some major differences in the beliefs about STDs, their causes, and treatments between countries. For example, unlike your doctors, most STD experts believe that Candida rarely causes urethritis in men and that Ureaplasma is not an STD (we never even test for it in my clinic).
However, as I already said, there is no realistic possibility that any STD explains the symptoms you still have. In some cases, an abnormal immune reaction might cause symptoms that persist even though the infection has cleared up. Another possible explanation for symptoms like yours is the male chronic pelvic pain syndrome, which used to be considered a form of prostate gland inflammation -- but the prostate may not be involved at all. If you Google "chronic pelvic pain syndrome", you will find lots of information about it. Start your reading with the Wikipedia article, which is very good; I believe you will find your symptoms fit pretty well. CPPS is uncomfortable but not dangerous.
You might return to your urologist; or if not certain he understands these issues well, perhaps see a different one. But whatever happens, you can be certain you do not have continuing chlamydia or any other STD. And you have nothing that will ever seriously harm your health or that of your current or future sex partners.
Best wishes-- HHH, MD