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An injection of Cetriaxone or a single dose of 400mg of cefixime is highly effective against gonorrhea, and treatment failure is very unlikely. If you still have a burning sensation, you may have a different infection( e.g. chlamydia), especially if you also have a penile discharge.
The gonorrhea bacteria can be resistant to other antibiotics. If you did not recieve the treatment I mentioned, then you should be screened for gonorrhea again.
Yes, the gonorrhea should be completely cured by now. Doxycycline is effective against chlamydia as well. I doubt that the burning sensation you have is associated with any infection. The bumps in your thigh are lymph nodes. The fact that the lymph nodes are smaller is another indication that your infection is treated.
You may have a tiny tear within the urethra that is stimulated/exacerbated by masterbation.
if the lesions are not painful, then they are unlikely from herpes infection.
the best way to find out if you are infected is by a blood test. People can be carriers of teh virus without having any skin lesions.