We just did battle with some rats, or perhaps chipmunks (we never saw them, just their tunnels). They actually dug down 18 inches to get under the hardware cloth, and came up in the run. We think they are gone now, as we haven't seen a tunnel in a while now.
Here's what we did: we put a chicken-proof bait station in the run. We also threw a little bait under the coop (the chickens have no access there). And one time we threw a little bait down a particularly deep tunnel and filled it with dirt and put a cinder block on top. In addition, we took their feeder out of the run each night and locked it in the coop with them (pop doors closed). Each morning, I look around for a dead rodent before the chickens go out, but I never saw one. I don't think the rats ever got into the coop itself. The entire coop is lined with 1/4 inch hardware cloth, although I know rats are very crafty.
I would probably eat the eggs, but you are smart to go on rat patrol before it gets worse.
Good luck!
Robin