Hi pickles97 -
Thanks for answering my questions.
Although I am sure that your vet has already done this, make sure that she has been tested for both feline leukemia virus and feline immunodeficiency virus. Both of these can suppress a cat's immune system and result in stubborn bacterial infections. It would be very routine to have these tests done, especially sine the kitty started as a stray, but it would be good to verify these indeed have been done.
Many times when cats have chronic nasal discharge it is because there is some underlying problem. These may include a polyp present within the nasopharyngeal area. It could be a latent viral infection that then allows for secondary bacterial infection. It could be a fungal infection that destroys the turbinates, making them more susceptible to a bacterial infection.
Diagnostic testing that would be appropriate here (besides the FeLV/FIV test I mentioned above) would be rhinoscopy (looking at the nasal passages with an endoscope - requires very specialized equipment because of the small size of the cat), biopsying the nasal passages and CT scan (expensive I know). These tests would help you find out if there is indeed some underlying cause present.
As far as treatment goes - if the antibiotic has helped in the past, I would keep the kitty on it for a minimum of 8 weeks continuously. Two weeks is standard for many respiratory infections, but this one is much more stubborn, so longer course would be better. The problem with oral antibiotics in these situations is that it is very difficult to get the antibiotic to the area that is infected as they just don't penetrate into the nasal cavitiy that well. Therefore, it may be worth trying nebulization therapy with an antibiotic, which means the antibiotic is dissolved in water and then aerosolized with an nebulizer and the cat is made to breath this in through their nose. This would deliver the antibiotic directly to the nasal passages rather than it having to be delivered by the blood stream.
If there is an underlying herpes virus infection (this is common) you may consider starting your cat on lysine, which is an amino acid that makes it so the virus cannot replicate very well. This is a very safe treatment and certainly wouldn't hurt anything. There is an an anti-inflammatory medication called piroxicam that has been used in these cases that sometimes helps that could be tried.
I hope this information is useful. If so, please click Accept. If you have additional questions, please let me know.