Effect of antibiotics on livestock or merely correlation?

Antibiotic resistance of bacteria such as staphylococcus aureus is a serious problem in medical care.  This study fearlessly investigates our primary food supply for contamination with staphylococcus aureus and the resistance of these bacteria to multiple drugs.

Multi-drug-Resistant Staphylococcus Aureus in US Meat and Poultry

The study looked at turkey, pork, chicken, and beef.  Contamination was highest in turkey (77%) and lowest in beef (37%).  Overall 47% of samples were contaminated.   The authors acknowledge that the impact of this contamination on our health is unknown but at the same time they don't hesitate to point out that

"Conventional concentrated animal feeding operations (CAFOs) provide all the necessary components for the emergence and proliferation of multidrug-resistant zoonotic pathogens. In the United States, billions of food animals are raised in densely stocked CAFOs, where antibiotics are routinely administered in feed and water for extended periods to healthy animals."

What the study lacks is analysis of meats from local farmers, Amish communities, and others who choose to raise animals naturally. 

Regardless of where your meat comes from handle it carefully, cook it well, and make sure you wash your hands and dirty utensils.