The federal government allows factory farms to administer antibiotics to animals raised for human consumption. These antibiotics (the same ones used in humans) are given every time an animal eats. This leads to drug resistance in humans and is a serious public health threat.
The only reason antibiotics are used in animals is due to the fact that they are kept in unsanitary conditions to begin with, often standing in their own waste.
Read more here: http://www.pbs.org/wgbh/pages/frontline/shows/meat/safe/overview.html