Factory farms have been around for almost a century and that hasn't happened. Nothing's changed now, there's absolutely no empirical evidence that such a thing is happening.
you cannot be serious. disease among husbanded animal populations has been a problem since mankind began keeping animals. before vaccines, the only options available were cleanliness, inoculation, and culling, to include killing entire herds when even a single individual was found to carry a disease.
https://ourworldindata.org/how-rinderpest-was-eradicated