Frustrating Rat Respiratory Symptoms?

So I have treated my one boy Smokey, with Doxycycline which ended up not lasting the whole time that it was supposed to happen and he got much better after the treatment. Then he picked up the symptoms again so I put him and his brothers on the same regimen this time for 4 weeks straight. Well he just started slightly wheezing again (I guess you could call it that, when he inhales he makes a funny sound) He isn't sneezing, he has had a myco test and it was negative, none of the others show symptoms at all. What could this mean? Is he allergic to something? I use unscented Yesterdays news (maybe it is gettind dusty? it seems to be) I mean his initial myco test showed that there was lots of bacteria in his upper tract so I'm uming its bacterial but it seems to keep coming back. I'm starting to run out of money and I can't keep taking him in and getting antibiotics. I've read stories of people talking to their vets about using echinacea and it seems to work, any one tried it? Sorry so many questions but trying to give history so I can try to figure out why he has continued to be sick.