Thanks for the additonal information. With this information, I would now focus on the comments I made in my second paragraph of my original answer. You need more tests. Sometimes nucleic acids from dead organisms can still be detected for weeks following successful therapy although that for your second positive test to be still positive six weeks following therapy would be quite unusual. Thus I'd start with another test for chlamydia. If it is now negative for chlamydia, I suspect your second test may have detected dead chlamydia and that what you are now seeing is normal genital secretions that you are simply more attuned to. On the other hand, if your test is still positive and/or if there are signs of inflammation, then you need further tests by an expert to address the concerns mentioned in my original reply. EWH
My partner was treated with expedited partner therapy following my initial diagnosis on 1/14/2014. She was treated with a single dose of azithromycin 1g. She received her first test results in later January and was again treated prophylactically with 100 mg doxycycline BID x 7 days and another single dose of azithromycin 1 g. We weren't intimate again until completion of my antibiotic therapy on 2/9/2014. Again both of her tests, the first being culture (late January) and the later a PCR test (3/4/2014) we're negative. This has been emotionally exhausting. I just don't understand why my test results for NAAT urethral swab is still positive and hers negative after 3-4 episodes of unprotected sex. She hasn't received as many antibiotics as I have, but she has been treated. Also, I would conclude that two false negatives would be unlikely. What are your thoughts Dr. Hook?
Welcome back to the problem. I remember and have reviewed our earlier exchange. Before I comment on your continuing symptoms, I have a question to ask. You mention that your partner was tested but do not mention that she has been treated. The standard of care is that if you have been tested and have had unprotected sex with your partner within the 30-45 days preceding your diagnosis, she should be treated using the same therapy as you have. There is a (small) chance that her test was falsely negative and, as a result, infections are being passed back and forth in "ping pong" fashion. If she was not treated, you both need to be evaluated and, based on the findings, treated with the same therapy before you have sex again.
A few more comments. It sounds like that your discharge has changed in character with treatment. Is this correct? If so, I would strongly suggest you see a provider who can perform a Gram stain test on a specimen taken of the discharge to look for signs of inflammation. If the are no polymorphonuclear leukocytes present, what you may be noticing could be normal urethral secretions. This is not uncommon and you are almost certainly more attuned to the possibility of urethral discharge, leading you to notice normal secretions that you would normally overlook. On the other hand, if there are PMNs present you should be tested further for other pathogens, for a non-STI urinary tract infection, or for prostate infection. You have now been treated with treatment which should be highly effective for chlamydia, Mycoplasma genitalium, and trichomonas. Had these been present , you should have been successfully treated.
I hope these suggestions are helpful. EWH