I agree with you on high density confinement livestock production. But is there evidence of antibiotic resistant strains in animals causing issues for humans?
Much of modern medicine depends on antibiotics. The above resources give clear and compelling evidence that overuse of antibiotics in livestock is associated with increases in drug-resistant infections in humans.
There are a number of bacteria that have made the jump from animals to people so creating a huge breeding pool for very antibiotic resistant bacteria that have generated human viruses in the past seems like a poor choice.