I've read that it is actually the process of "forced molting" in the commercial industry that causes the occurance of salmonella. Forced molting depresses the cellular immune response and increases the severity of a concurrent intestinal Salmonella enteritidis (SE) infection.
At one point, salmonella infections were traced to dirty or cracked eggs. Just be sure to clean your eggs in water that is hotter than the temperature of the egg. Only wash them if they are soiled, as the egg is sealed in a "cuticle" that protects the egg from the entry of bacteria. Washing the egg washes the cuticle off, so unless you are using the egg immediately, you may want to wipe a very light layer of oil on the egg (vegetable, olive, etc.). If I have to do this I put a pea sized drop of oil on a paper towel, rub the egg down with the oil, then follow with a clean paper towel to remove any excess.
Salmonella is a disease born from filth. If you are keeping your coop clean, the occurance of salmonella will probably never happen.