Yellow-green fluorescence of Clostridium difficile under long-wave UV irradiation. (CDC)

After years of warnings from the science and medical communities about the depletion of the world’s arsenal of effective antibiotics, President Obama directed federal agencies Thursday to significantly ramp up their efforts to deal with the threat.

The administration also released a national strategy with a five-year plan and called for a new presidential advisory council to make specific recommendations to the White House by February 2015.

Antibiotic resistance causes 2 million illnesses a year in the United States and 23,000 deaths, “and those are conservative estimates,” said Tom Frieden, director of the Centers for Disease Control and Prevention, who joined administration officials in a conference call with reporters.

The strategy calls for a 50 percent reduction in the overall incidence of Clostridium difficile, also known as C-diff, and to cut in half the number of methicillin-resistant Staphylococcus aureus (MRSA) infections by 2020.

In the pharmaceutical industry, the antibiotic pipeline has been relatively dry, experts say, because the investment in developing drugs that will only lose effectiveness the more they’re used is simply not worth the time and money.

Along with the White House directive, the President’s Council of Advisors on Science and Technology (PCAST) released a 78-page report detailing practical steps the government can take to both track resistant germs and develop novel antibiotics to treat bacterial infections.

Eric S. Lander, the council’s co-chairman and one of the participants in the call, said he thinks some of the recommendations could help turn that tide.

“There are ‘push’ mechanisms — like partnerships with government — [that] make co-founding [new drugs] attractive,” he said. “There are also ‘pull’ recommendations — successful development will involve some reward, such as higher reimbursements, for instance.”

Several medical and scientific organizations, including the Pew Charitable Trusts and the Society for Healthcare Epidemiology of America, applauded the announcements. Others faulted the council’s report.

“It’s a disappointment,” said Mae Wu, health attorney at the Natural Resources Defense Council, who said there are huge loopholes in the restrictions supported by the Food and Drug Administration, which is phasing out the use of antibiotics to promote growth in farm animals but continues to allow their use to prevent disease in those same animals.

According to the NRDC and others, 70 percent of all medically important antibiotics for humans are sold for use in animals.

Antibiotic resistance isn’t just a hospital phenomenon.

“The problem with PCAST’s recommendations is they’re too weak and we won’t see any change,” she said. “The FDA is still going to allow huge misuses of antibiotics.”

Rep. Louise Slaughter (D-N.Y.), who has pushed for legislation limiting antibiotic use in animals for 15 years, said she had “pretty well decided the American government is not going to provide food safety. . . . The loophole [in the FDA restrictions] is as big as a truck.”

Slaughter said she was glad the government has acknowledged the problem but added that the United States is behind Europe and China when it comes to restricting antibiotic use in animals.

“The FDA has known there was a problem since 1977, and we’re reaching the tipping point,” she said.

Wu acknowledged, however, that there has been some positive movement in the agriculture industry. She cited Perdue’s recent decision to not feed their chickens human antibiotics.

“They heard it from their customers,” she said. “Maybe people will call their Tyson’s or Foster Farms and if they demand it, they would get something done faster than the federal government. Companies actually listen to consumers. It’s a real opportunity.”

The White House directive was coupled with the announcement of a $20 million prize from the National Institutes of Health and Biomedical Advanced Research and Development Authority for the development of a rapid diagnostics test for highly resistant bacteria.