I purchased a rather large quanity of rats to start breeding as well. They came from a reptile breeder who was downsizing. They were all very thin and many were sneezing and had runny noses. I have a friend who runs a rat rescue. Though she is not happy that I breed them for food she gave me some advice to hep the sick rats. Out of about 30 rats, only 3 ended up dying.
I was told to supply them with a good quality rodent lab block, alfalfa and suppliment with infant similac formula mixed with oatmeal to a thick consistency. I was also informed that an RI in rats is not usually passed from rat to rat if the conditions are clean and correct. They can be kept with healthy rats as they help take care of eachother if one is sick thereby reducing the amount of stress.
I followed these steps and lost only 3. All the others were fattened up before being split into M/F colonies. They are all doing fine now.