This was on the Washington thread...
http://www.countrysidemag.com/issues/96/96-2/chicken_crimes.html
It's a bit long but worth a read.
I wonder if we just vaccinated chicks at the hatchery for Cocci, MG, Fowl Pox, if we could control disease with vaccines. That has worked in humans. All the tracking sounds cumbersome and probably would not work as long as we backyard chicken farmers are shipping birds and eggs around the country.