You have to realize thought that resistance is not something an animal is born with in many instances. You develop resistance by being exposed to the elements in your environment, both good and bad. It's like you getting the cold, once you've had it your body develops a resistance to it and until that virus mutates again into a strain the body does not recognize you will not get sick from the same strain again. The white blood cells recognize the attacking strain and launch a counter attack before the virus can make you sick again.
Vaccination simply introduces a dead version of a virus, or a modified live virus into the system of the bird so that the white blood cells can develop a 'template' if you will to help combat that virus in the future. This same process would happen if the bird were exposed to the virus in small quantities in the natural environment and survived the infection. The birds has now developed antibodies. This will happen whether it's by natural exposure, or through vaccination.
The advantage of the vaccination is that the exposure is very controlled and the bird is likely to survive the infection. In the natural environment this may not be the case.
Many years ago when Europeans first landed in America they brought disease that the Native people could not fight off and they died in huge numbers. The native people were strong, fit and healthy and yet they still scummed to the common cold, and flu. If they had been vaccinated they may not have.
I guess my point to all this is you can breed fit, healthy, strong birds, but it doesn't necessarily mean they will be disease resistant....especially if they have never been exposed to the disease before and had a chance to build up an immunity. This is what vaccination does, it kick starts the immunity process.
Just something to think about.
Urban Coyote