The main problem I'm seeing is the vets aren't prescribing the antibiotics for nearly long enough, espeicially if this is pasteurella. Minimum will usually be 4 weeks, though several months treatment isn't unheard of. 10 days of durapen is not even long enough. I would expect to do at least a month of injections.
Medirabbit: respiratory issues in rabbits
http://www.bio.miami.edu/hare/jawab...n Effective,acidic environment of the stomach.
I had infection spread through my group of 7 rabbits. A few got eye infections and a few got respiratory infections. I didn't have a culture done, but because of it being highly contagious and affecting most of the rabbits in my group, it was presumed to be pasteurella.
Initially baytril and smz was tried and didn't produce improvement. Next they were put on azithromycin(at my request) 30mg/kg, and they started improving after a few days. After 3 weeks they all seemed to be better so the antibiotic was stopped. After about a week, symptoms started to return. So they were put back on azithromycin at the higher dose of 50mg/kg, but for 4 weeks this time. They all got better and the symptoms didn't ever return, except for one rabbit. After about 2 years an eye infection returned, which may have been a reemergence or just a different infection due to old age and a poor immune system. The rest of the rabbits had already passed from old age at this point.
So that antibiotic worked really well for my rabbits, with immediate improvement within days of starting the oral dosing. But the highest dose did need to be given, and for an extended length of time. And this was with an antibiotic that is considered to be pretty 'heavy duty' as it is. But it's a good antibiotic for respiratory and head infections, because it has good tissue and bone penetration, but only if the bacteria is sensitive to it. One caution though, is it can be hard on some rabbits, and rarely can result in serious digestive upset for a few. The only side effect I saw in my rabbits was some initial stomach cramping in a few, that occurred in the first few days(and only for a few hours after oral administration), but then subsided after those first few days.
A culture and sensitivity may help, though they can sometimes come back with inaccurate results. But I would certainly consider having that done over surgery right now. And I would want to try other antibiotics before opting for a risky surgery.
I can't say anything as to the problems with nebulizing. I'm not sure why your vet has had issues arise, unless something was done incorrectly or the rabbits were just already too ill for it to help. But nebulizing with gentamicin is something that is done with rabbits, as you can see in some of these nebulizing videos in the link below.
If your rabbit is to the point of respiratory distress, with struggling to breath and possibly mouth breathing, I would be inclined to try the nebulizing immediately. But also if he was at this stage, he should also be hospitalized and on oxygen, and probably IV antibiotics as well. If he's not in respiratory distress and doesn't need hospitalization and isn't struggling to breath, then instead of doing the nebulizing at this point, it might be worth either continuing with the penicillin injections for a much longer course than 10 days if you see improvement on it. If not, having a culture/sensitivity done may be a good idea. Or consider trialing azithromycin.
If you do decide to try the azithromycin, the best cost I found for the suspension, was getting a prescription for it from costco or walmart, and using goodrx to further reduce the cost. It ended up being about $23 a 15ml bottle, which lasted 2 weeks(small rabbit), and I needed 2 bottles per rabbit for the whole month treatment.
https://wabbitwiki.com/wiki/Medicating_your_rabbit