Chronic clamydia infection. Solution?

I had protected sex in 2017, against most of the theories I can say I got clamydial infection through kissing. Because 2.5 half months after the sexual contact when I used saliva during masturbation which I never did in my life before, I saw redness and itching the very next day. On getting Naat test from Dr path lab, my report was +ve for clamydia and gonorrhoea. I was given azythromyin which did not help. I suffered reactive arthritis for 1-2 days where all my joints were swollen, also faced swelling in testicles. Then I was given ceftriaxone injection along with doxycycline for 21 days which helped. But since then I see some white patches in my throat and also got hypothyroidism as if something destroyed my thyroid and the most disturbing thing is my new partner now has got burning sensation very next day after only oral sex. There is no history of any sexual contact of mine or her in last 2 years. I feel clamydia is still present in my throat but couldn't fine any testing center.