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It appears that the vast majority of U.S. antibiotic use is for animals, the commission noted, adding that because of the lack of oversight by the Food and Drug Administration and other agencies, even regulators can only estimate how many drugs are being given to animals.

The commission urges stronger reporting requirements for companies and a phaseout and then ban on antibiotics in farm animals except as treatments for disease, a policy already initiated in some European countries.

"That's a good recommendation. A strong recommendation," said Margaret Mellon of the Union of Concerned Scientists, which released its own report last week documenting billions of dollars in farm subsidies to factory farming operations and annual federal expenditures of $100 million to clean up their ongoing environmental damage.

Factory farming takes a big, hidden toll on human health and the environment, is undermining rural America's economic stability and fails to provide the humane treatment of livestock increasingly demanded by American consumers, concludes an independent, 2 1/2 -year analysis that calls for major changes in the way corporate agriculture produces meat, milk and eggs.

The report released yesterday, sponsored by the Pew Charitable Trusts and Johns Hopkins Bloomberg School of Public Health, finds that the "economies of scale" used to justify factory farming practices are largely an illusion, perpetuated by a failure to account for associated costs.

Among those costs are human illnesses caused by drug-resistant bacteria associated with the rampant use of antibiotics on feedlots and the degradation of land, water and air quality caused by animal waste too intensely concentrated to be neutralized by natural processes.

Several observers said the report, by experts with varying backgrounds and allegiances, is remarkable for the number of tough recommendations that survived the grueling research and review process, which participants said was politically charged and under constant pressure from powerful agricultural interests.

In the end, however, even industry representatives on the panel agreed to such controversial recommendations as a ban on the nontherapeutic use of antibiotics in farm animals -- a huge hit against veterinary pharmaceutical companies -- a phaseout of all intensive confinement systems that prevent the free movement of farm animals, and more vigorous enforcement of antitrust laws in the increasingly consolidated agricultural arena.

The report acknowledges that the decades-long trend toward reliance on "concentrated animal feeding operations," or CAFOs, has brought some benefits, including cheaper food. In 1970, the average American spent 4.2 percent of his or her income to buy 194 pounds of red meat and poultry annually. By 2005, typical Americans were spending 2.1 percent of their income for 221 pounds per year.

But the system has brought unintended consequences. With thousands of animals kept in close quarters, diseases spread quickly. To prevent some of those outbreaks -- and to spur faster growth -- factory farms routinely treat animals with antibiotics, speeding the development of drug-resistant bacteria and in some cases rendering important medications less effective in people.