The discharge most likely is secondary from the pemphigus
, though this could be due to something different such as a fungal disease in the nasal passages or unfortunately a tumor in the nasal passages. IF your vet has checked an x-ray, checked for a fungal disease and everything was normal then this is then probably due to pemphigus.
At this point, I would definitely consider having your vet switch antibiotics as the bacteria that is causing this discharge may be resistant to the Doxycycline. If the prednisone was causing much weight gain you, which it does unfortunately, I would suggest asking your vet about a medication called Imuran or Azathioprine to help control the pemphigus foliaceous. This drug has a similar effect on the immune system to try to control this immune mediated skin disease and may help reduce the amount of discharge from the nose also. Imuran does not cause any weight gain in dogs compared to the prednisone. If you and your vet do decide to try this medication instead you will have to have his cell counts checked in the blood to make sure that the medication does not suppress his immune system too much. Here is a link for further information.
If the culture results are not back yet then I would wait for these before deciding which antibiotic to use. If the results are back and are not helpful, then I would suggest trying a combination of antibiotics as this can help reduce an resistance. My suggestion would be a fluroquinolone antibiotic such as Zeniquin and a Penicillin type antibiotic such as Amoxicillin
. Together these antibiotics should clear out most infections.
If this is not working and you haven't had him tested for a fungal disease or a tumor then you may have to talk to your vet about this also.
Hope this helps - please feel free to reply if you have any other questions.