Pip overlooked the fact that Art and Kat do encounter plague rats out there and, while the two may be healthy enough to not come down with something, they can still be carriers. Pip will have a relatively weakened immune system due to his sedentary and less healthy lifestyle.
It might sound strange, but the ones most at risk might be the squirrels, depending on how clean their environment was at Quentin. If it was too clean, they might end up like American Indians versus smallpox, a fatal combination. On the other hand, I suspect they aren't that likely to get sick because they already would have during previous outbreaks since they left the lab, especially Scarlet. We don't need to invoke genetic engineering, either. All that's necessary is a strong enough immune system and that's cheaply done by maintaining good health and exposing them to pathogens when growing up to build up their immunity.
Lastly, the Denizens might get sick, but probably only out of curiosity. I figure they're immune to everything but the Rule of Funny. (Besides, they're already supposed to have died out from really common diseases alá The War of the Worlds, or so them rilly smat scien-teest guys sayed. :p )