Are Factory Farms the cause of disease?

From the Daily Green, environmental news:

Swine Flu, Factory Pig Farms, and the Pandemic waiting to happen.

Hmm. Makes plenty of sense to me, nevermind the horrible environmental impact of Factory Farming, and not to mention the terrible mistreatment the animals suffer in such an environment. Factory Farms in the USA are not a pretty picture, I cannot imagine what they are like in Mexico, where horse slaughter means a man with a knife stabs the animal repeatedly until he manages (miraculously!) to severe its spine and paralyze it.

Factory Farming is just evil. And that's all I have to say about it.