I've had to real with serious funk after a week of solid fishing in hot weather. It smelled like a hockey bag, and there was no amount of shampoo or cleaner that would get the sweat stench out. I hung them inside out at the end of each day. The smell took over and only got worse. It was sweat, and bacteria, and I thought I was going to have to throw them out.
I ended up spraying "Nature's Miracle" on them. It's an enzyme cleaner.
I use it to get rid of dog pee when I foster greyhounds. Amazing stuff. I put a couple cap fulls in a spray bottle, maybe 2 cups of water and spray it all over the inside of my waders (well, insides-out). Let it sit. Reapply as necessary. It will remove the offensive odor, and the bacteria that is causing it.
I've also used nature's miracle skunk odor-remover with good results.
It's available at decent pet supply stores, and most vet offices in my area have it.