Baytril certainly needs to be prescribed because it's a prescription drug. All antibiotics (except some topical) are.
Baytril is not a magic, cure-all drug that works for every infection. Actually, if the same type of microbes are causing this URI a second time, then Baytril will be even LESS effective because the microbes that are left are the ones that survived the first round of Baytril, so they are resistant to it. Overzealous use of antibiotics is how antimicrobial resistance occurs, and this is what creates "superbugs" that are very, very tough to kill.
If the URI is caused by something fungal or viral, which you cannot tell at home, then Baytril will have zero effectiveness.
Have you double-checked your husbandry? If cage temps are too low (which often happens in the winter and we don't realize it), this could weaken your collared's immune system, making him more susceptible to things like respiratory infections. Is the ambient humidity appropriate for a desert species? Does he have a humid microhabitat (humid hide) he can retreat to for hydration?
You did the right thing by bringing him into the vet for the first URI, but you'll need to see the vet again to have it treated. Make sure the vet knows that the first infection was treated with Baytril, and give him the time frame that it came back in.
You might want to ask to have a culture and sensitivity done. They would do a lung/tracheal wash to retrieve a sample of the gunk in your lizard's respiratory tract, then send it to a lab to grow whatever is in there, and they test to see what antibiotic will work best, and which will not work at all. Vets do not always opt to do this in the first place because of the extra costs involved for the owner, and because often one round of an antibiotic works pretty well.
I'm not a big fan of herpers buying medication and treating their herps themselves. There are certainly herpers with decades of experience on these boards that would argue this point, because some of them know more about herps than any general practice vet, but nothing compares to that 5 years of intensive schooling plus extra learning to specialize in herps. Doctors are vastly underappreciated, because infections are not nearly as simple as taking an antibiotic off the shelf and giving some injections... just because it works like that sometimes, that doesn't mean there is not a long, calculated thought process behind it.
To summarize:
-Double check your temps. For now, you can up the warm end of his tank by a few degrees to give his immune system a boost (just make sure he has a cool end to retreat to if he gets too warm).
-Call up the vets, explain the situtation and ask if they would do a culture and sensitivity before the next trial of antibiotics. If money is not a big issue, bloodwork and/or an x-ray would not be a bad idea, either, to check his general health status.
Keep us posted!
Christina Miller, CAHT
www.herptiles.net