I'm currently nursing 2 through a bout with pneumonia, and have a tiny one (that should not have been separated from her mother) quarantined against them.
MB
Most of the time this sickness you see them getting is from a tiny bacteria, that resides in the lungs of essentially every domestic rat, called
Myscoplasma pulmonaris. This mycoplasma usually just takes advantage of a weakened immune system, typically late in life or induced by some other stress.
I almost lost a rat recently to respiratory illness and I searched fervently and found what I found to be an absolute miracle treatment for rats.
I tried treating my rat with Baytril, and not only was it difficult to get her to take it, it didn't seem to be working fantastically. So, I ended up doing the following (getting the vet to agree to the following treatment that is):
Subcutaneous (at the scruff, given perpendicular to the body length) injections of Gentomycin at 2-4mg/lb per day, spread out over two injections--I gave 4mg on the first dose.
Usually gentomycin comes in a rather large dose (100mg/ml) so you'll have to get some sterile saline and dilute it, but your vet should be able to supply you with this. I diluted to 10mg/ml and just used a diabetic syringe (1mg) to administer the dose.
Again, the first dose was what would have been double the normal dose for my female. My female was 1lb, and I was giving her 2mg 2x daily, so her very first dose was 4mg and I continued regularly. More info here:
Rat & Mouse Gazette: Medical Corner: Gentamicin and Tylan
I also prepared a solution of .083% albuterol / gentomycin / sterile saline that I administered to relieve bronchiol inflammation via a nebulizer. It seemed to really help the wheezing bouts and deliver antibiotic directly to the lungs. I was giving these 3x daily for two weeks for 15 minutes (consumed about 6ml of solution each session)
The solution was prepared as described by this site:
Medication Guide: Albuterol Sulfate
So, to summarize, here is an awesome treatment for rats--most vets don't do well with rats because they so rarely get them as patients, so you have to really dig deep to find appropriate treatments.
* 2-4mg/lb of injectable (subcutaneous) gentamicin, dose split into two administrations. I continued this for about 5 days, but there was research I discovered that had found up to 20mg/day for nearly a month had no adverse side effects in rats.
* albuterol nebulizer treatment--diluted accordingly--given 3-5x daily for up to two weeks.
I thought my rat (she's my favorite, too!) was going to die after a few days of no improvement...actually, she got worse! Then, I swear, withing 4-6 hours of her 4mg dose of subcutaneous gentamicin she was eating, drinking, and playing again. You HAVE to keep up on it though because that mycoplasma (and accompanying virulent bugs) will come back quick--your rate may hate you after their skin gets a bit sensitive from getting poked 2x/day, but this treatment works incredibly.
Best of luck to you!