7 weeks is a very long time to have been on Baytril. I’m not familiar with the typical course for Metronidizole, but that also seems very long as well.
It’s true that stopping antibiotics early can lead to resistance, but I’m also wondering about the length of treatment. My thinking is that if you have a bacteria that is not responding to the current antibiotics, it will show up in the culture even if you keep using them. Unless the bacteria is responding very slowly… Personally I would call the specialist and ask them what to do. They should be able to advise you whether to stop the medicines before coming in or not.
Usually when an animal needs to come back for labs, vaccines, etc, it’s easier to schedule than a new patient appointment because they will just bring the bun to the back and the technicians can handle it, so I wouldn’t worry too much about getting everything done in one go.
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The answers provided in this discussion are for general guideline purposes only. The information is not intended to diagnose or treat your pet. Seek the advice of your veterinarian or a qualified behaviorist.