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Chlamydia not cured?

A few weeks ago, I was diagnosed with chlamydia and I got treated for it with azithromycin.
At the same time my partner had gotten tested twice and both came back negative.
I went back for a re-test a week after I took the pills and it was positive but my doctor assumed it was a false positive so I went back for another test a week later. That test came back negative and I was told I am all clear.
However, before I went back for my very last test after the false positive, I started to notice some symptoms again.
My vaginal area is itchy, I noticed some discharge which does not have any odor, and pain during intercourse with some mild mild blood in the fluids.
Does this mean I still have chlamydia even though the last test came back as negative?
Should I go back and get re-tested?
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I have been trying to cure my chlamydia for over a month now. I have taken 2 grams of azithromycin all at once about a month ago. My symptoms went away for about 3 weeks and returned. I'm on a 7 day course of minocycline, which doesn't seem to be helping.  

I believe I might have a super strain of chlamydia here in Japan. I will be getting a new urine/swab test tomorrow and I will have to get more anitbiotics as well.
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