Overnight death of chicken concerned for the rest of the flock

About 1 month ago we had a 2 year old NH red that died. She started to have some runny poo, then started to sit on the floor of the coop instead of the perch. We seperated her but by this time she would not eat or drink and died the next day. That was 1 month ago. Last night my wife noticed that another of our 2 year old NH reds looked like she had some runny poo. She told me about it just before bed. We got up this morning and I went to check on them. She was dead on the floor face down. We live in northern VT. It is averaging 20 degrees out. Our Coop has been maintaining around 40 degrees. We keep it very clean, change the water everyday and make sure the food is clean. There is an outside pen that is covered and we have it wrapped in clear plastic to keep the weather out over the winter. It has been very wet this year and the floor of the outside pen is not drying out well and keeps forming puddles. We try to clean it up but it is tough since it is staying wet. We are starting to think this could have something to do with it. But, could there be something else going on? Should we start them on an antibiotic? Keep them out of the outside pen till it dries up? The rest of the flock is 1 NH red, 5 Plymouth rocks, 5 golden Wyndottes, 5 Silver Wyndottes, 5 buff orpinghams, and 1 sussex. The red is 2 years old all others are around 8 months old.