I always ask a vet WHY they choose a particular medication for one of my furkids and I get better responses from some than others. I also look up medication in the Merck manual or an online source to find out what is in it (if I don't already know) and what it is recommended for.
One vet I use for routine things (because his fees are more reasonable than most others in this area) is not a high tech vet but has good instincts based on experience and his approach to the use of abx is to start with the one most specific to a particular condition, if possible, and if that doesn't work then go for one that is more broad-specturm and one of the "bigger" guns in the abx arsenal such as Baytril. His opinion is that if you always start with the biggest gun, if resistance becomes an issue you have no better options. If Amoxicillan (relative of penicillan) or Clavamox (combo of ) don't work, then try something like Baytril or Zeniquin (a newer relative of Baytril). Sometimes if a condition seems serious and what is going on is not clear, he'll start with a bigger gun. Last year I had a kitty who was presenting with a high fever and no other symptoms...his first choice was Baytril and when that didn't bring down the fever, he prescribed something called Delta Albaplex, which I'd never heard of before. The fever was gone in 2 days after that. I looked it up and DA is a combo of an abx (can't remember which one offhand) and a steroid. I've never had to use Doxycycline yet, so haven't looked it up, but it seems to be more specific in what it targets than Clavamox. For one thing, Doxy is prescribed for the blood parasite hemobartonella and seems to be more powerful in its action than Clavamox or Amoxicillan. But it can have a caustic effect on mucous membranes and administering it is more problematic. I guess the idea is to kill whatever bacteria may be the culprit without OVERkilling. If there is a choice that can be made, I will opt for the one with the least gnarly taste and fewest possible side-effects. Sally in San Jose