Most pet store rats are kept overly crowded, stressed from fighting for food and space and sharing every germ they have amongst themselves...hence they will often sneeze, have crappy coats, the runs, and excessive red discharge (porphyrin) from the eyes and nose, etc. Those issues can be addressed with better husbandry, less crowding and good eats.
Many rats are born with mycoplasmosis - I think that's what you are referring to. I do not have a vet license LOL nor do I have any rats with active myco in my colony, so what I know of this is only what I've read but here is a link I have that I thought explained it quite well. It is an older article but was one of the more clear, concise ones I found when I was doing research.
http://www.rmca.org/Articles/myco.htm
Basically from what I gather this is a latent disease that will flare up under certain conditions that can be somewhat controlled.
To try and avoid the whole issue I am careful to only buy rats from the pet store that in decent shape (I spend quite some time checking them out first) and only buy from good pet stores. I'm now working on the future so I will end up only using my own stock as much as possible w/o inbreeding too much (2nd generations breeders are in the tubs growing up now). I don't breed from any rat that exhibits symptoms of active myco outbreak and would euthanize and discard it (not feed it off). Again, that's just my way of managing my colony, not the only or best way...just my way.
~~Jo~~