How dirty are they? Whether it is guinea, duck, chicken, or turkey, the last thing that goes on the egg is a clear wet substance we call bloom. This quickly dries and forms a barrier that helps stop bacteria from getting inside the egg yet allows the developing embryo to breathe through the porous shell. It’s not perfect but it does a really good job. If you wash, rub, or sand-paper the egg to remove “dirt” you will be removing bloom.
If the eggs are extremely dirty I would not set them to start with. If the eggs just have a light bit of poop or dirt on them, gently (very gently) rub that off with your thumb after washing and drying your hands so you don’t add bacteria to the mix. If they are not dirty or very dirty do not wash them.
A poultry science professor once showed a chart at a talk about washing eggs and hatching eggs at home. You get the best success with unwashed clean eggs. Slightly dirty eggs were not that much worse, pretty good really. Next was washed eggs. There was a significant drop-off here. Worst of all was really dirty eggs, eggs with clumps of poop or mud on them. A lot of times when the egg is laid in poop or mud the bloom does not dry on it and protect it and the poop especially can harbor bacteria that gets inside the egg through that unprotected area.
It’s also extremely important that the incubator be really clean when you start. You don’t want bacteria living in there. And keep your hands clean and oil-free when handle them.
Commercial hatcheries wash their eggs before they incubate them but then they coat them with a special substance to help replace that bloom. They are also germ-a-phobes. They keep everything extremely sterile. It’s a different environment than us hatching at home.
Good luck!
