Some people say not to clean eggs before incubation, others swear by it. The general idea is that mother nature doesn't clean her eggs before incubation and there's actually a protective layer around the eggs (called the cuticle) that protects them by preventing bacteria from entering the egg through the pores of the shell. I have tried both methods and have to admit that if done properly, cleaning and disinfecting eggs does seem to work and gives me a far higher hatch rate but there are a few things to consider.
1There is absolutely no point in cleaning and sterilising your eggs if you are then going to put them in an incubator that hasn't also been sterilised. Remember incubators operate around 37 degrees - THE perfect temperature for bacteria to multiply on your eggs.
2There is also no point in cleaning and sterilising eggs if you then handle them with dirty hands. By that I mean contaminated hands, not just dirt you can see. Use an antibacterial hand wash every time you open the lid and touch your eggs.
3Everything else that comes into contact with your eggs also has to be sterile - so if you candle eggs, you should wipe the end of your candler with antibacterial wipes.
Always keep the pointed end down. Pointing the blunt end down strains the membranes in the egg so should be avoided.
Start by getting the cleanest eggs you can for incubation. Nest box hygiene is very important. Don't allow chickens to sleep in their nest boxes at night otherwise they will soil them. Scrape any obvious muck or dirt off (you can do this gently with the edge of a knife). Dip your eggs into warm egg disinfectant. I use one made by Brinsea but there are many others.
Ensure you follow the instructions on the side of the bottle carefully - if the solution is too strong, it could kill the embryo of your eggs! Make sure the solution is warmer than your eggs because this will cause the pores of the egg shell to push bacteria out, rather than suck it in. The cuticle (on the shell) gets very slippery when wet so be careful you don't drop your eggs.
Congratulations you now have a clean egg. But WAIT! Don't put it down on anything that hasn't been sterilised. Put it into your clean incubator or onto a tray that has first been sterilised.