I couldn't find anything definitive on the net to back this up, but tea tree oil is what popped into my head. Or perhaps soaking what you can in vinegar? Bac Out? Maybe all of the above mixed together w/ water in a big tub? I, myself, might make an exception in the case of coxsackie and use chlorine bleach. I heard that if left in the sun that the harmful components are rendered inert and you're left with salt water, but my scientist friend and I couldn't find anything to prove that 100%, either.
Confession: DH just had food poisoning and I made an exception and used bleach water to clean the 2 bathrooms he was in.