I believe that when the chicken eats the contaminated feed, the chicken then becomes toxic with salmonella. I think that the ovaries pass the salmonella on to the eggs when they are developing.
Hopefully someone will get on here and explain this to us!
This is a very good article. And, btw, free range and organic chicken eggs can STILL harbor salmonella. I have always known that and have treated eggs carefully. Cooking will kill the organisms. And I never use an egg that is already cracked (I check them when I buy them, but sometimes one gets thru my inspection).
http://news.discovery.com/human/egg-salmonella-bacteria.html