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Painful urination when finishing for female

I have been having painful urination when finishing since end of July. I went to GP, he prescribed me a bunch of antibiotics (Cipro, Bactrim, Macrobid), none of them work. Fast forward, went to see my GYN, she did a urethral swab and urine culture. My right part of urethra feels tender per GYN. The swab for STD/STI were negative. However, my urine came back positive for E.Coli. So I was prescribed Cipro, but I had an allergic reaction to it. So now I am on Keflex 4x a day for 7 days. Today is 2nd day, I still feel the pain. I am thinking that my bacteria is now resistant to antibiotics after taking so many. Does anyone have experience with this? Could it be a kidney stone lodge in the right part of my urethra?
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