Wild animals, especial bids and rodents carry al kinds of nasty stuff that can infect chickens in one way or another.
They really is not way to ever protect a flock from everything.
There are some things that can be vaccinated for though.
Sounds like you brought a respiratory disease in with the new chickens and it has now spread throughout your flock.
The only thing you can do is continue to try to ease their symptoms and from this point on breed for resistance. Meaning cull the sickest and let the strongest ones survive.
You...