UrbanHomesteadTX
Songster
If it feels that overwhelming to deal with right now, I honestly wouldn't worry about it. Yes rats, oppossums and other critters can carry diseases and parasites, and it's always best to keep a coop as clean as possible. But odds are higher than not that nothing bad will result from your night visitor's intrusion. Aiming for perfection is great, but sometimes we are forced to settle for good enough. If your coop and run were totally rat-infested, that would be a different story, but I think your current situation will be ok. By far the most important thing is to make sure the critter(s) don't gain access again.

If you are worried about it, then I'd suggest just focusing your efforts on the coop, where you know it's been and any likelihood of poop or parasites that may affect your hens would be there. Otherwise, I believe you'd be fine to just leave it be. Do make sure you have things secured to ensure rats and/or opossums can't get back in though.
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