The Food and Drug Administration called on drug companies Wednesday to help limit the use of antibiotics in farm animals, a decades-old practice that scientists say has contributed to a surge in dangerous, drug-resistant bacteria.

Antibiotic drugs like penicillin are routinely mixed with animal feed and water to help livestock, pigs and chickens put on weight and stay healthy in crowded feeding lots. Scientists have warned that such use leads to the growth of antibiotic-resistant germs that can be passed on to humans.

The FDA has struggled for decades with how to tackle the problem because the powerful agriculture industry argues the drugs are a key part of modern meat production.

Under the new FDA guidelines, the agency recommends antibiotics be used “judiciously,’’ or only when necessary to keep animals healthy. The agency also wants to require a veterinarian to prescribe the drugs. They can currently be purchased over-the-counter by farmers.

“Now you have a veterinarian who will be consulting and providing advice to these producers, and we feel that is an important element to assure that they are in fact using these drugs appropriately,’’ said William Flynn, a deputy director in FDA’s veterinary medicine center.

The draft recommendations by the FDA are not binding, and the agency is asking drug manufacturers’ to voluntarily put the proposed limits in place. Drug companies would need to adjust the labeling of their antibiotics to remove so-called production uses of the drugs. Production uses include increased weight gain and accelerated growth, which helps farmers save money by reducing feed costs.

The FDA hopes drugmakers will phase out language promoting non-medical uses within three years.