Definitely check for wet under the padding.
If the subfloor is wood, once it dries out very thoroughly, you could seal it up with any kind of varnish or similar. Seal in the smell.
The carpet and padding, you can get the smell out with oxygen bleach. Then rinse with vinegar to neutralize the bleach. You can rent a carpet machine and use a bleach solution and then a vinegar solution instead of soap.
You should do this in a warm climate, even if it means waiting till summer. Technically, you can do it in cooler weather, and then have the windows open and heaters running for days until everything dries out, but it takes a lot of heat.
