Flawed prescription practices are fueling the growing threat of antimicrobial resistance, the top U.S. public health agency official said today.

“We estimate about half of all the antibiotics used among people in the United States are either unnecessary or inappropriate. We are taking this precious resource and squandering it,” Thomas Frieden, director of the U.S. Centers for Disease Control and Prevention, told the President’s Council on Advisors on Science and Technology in Washington, D.C. “To be frank, there’s a very poor state of practice in terms of antimicrobial prescribing,” he said.

Past studies have already shown how the use of prescription drugs in humans and antimicrobials on the farm can promote conditions allowing drug-resistant bacteria to proliferate, rendering front-line drugs that treat disease ineffective. But early next week the CDC will weigh in with its first report taking stock of the pressing issues in this area and review what organisms pose imminent threats and what steps must be taken. “We’re sounding the alarm because it’s not too late,” Frieden said. Right now there is little data on global trends for antimicrobial resistance and there is no comprehensive picture of the issue in the U.S., he added. Compounding the challenge of tracking these emerging concerns are reductions in public health jobs in recent years due to budget cuts and sequestration.

One threat Frieden highlighted today is carbapenem-resistant Enterobacteriaceae, or CRE. This family of germs, which includes Escherichia coli, is particularly difficult to treat because of its high levels of resistance to antibiotics. CRE usually strikes patients in long-term health settings like nursing homes if they are dependent on ventilators, catheters or intravenous treatments to help with basic bodily functions. “The key fact to remember is even though it’s a really bad problem, it’s not too late to stop it,” he said.

Ramping up tracking of antimicrobial resistance and implementing programs that would help detect and protect against antimicrobial resistance will be key, he said in his testimony. Shoring up collaboration between public health and clinical medicine will be the “most important challenge for public health to deal with in the next decade,” he said. “I don’t think there are quick answers. I don’t think there are simple answers, but I think there are emerging answers.”

The CDC expects that genomic sequencing of microbes will be a key tool in the fight against antimicrobial resistance. Sequencing the genomes of microbes and gleaning more information about them and how they interact with human genomes provides a new level of data that could fuel stronger action against antimicrobial resistance, Frieden said. Combining bioinformatics, genomic sequencing and traditional epidemiological methods will give researchers new power to find, stop and prevent outbreaks, he said. Better data tracking and rewarding institutions for strong performance could also promote better conditions in long-term care facilities.

Simple steps that amount to antibiotic stewardship programs will also play an essential part, he said. Getting bacterial cultures from patients before starting a course of antibiotics and taking an “antibiotic time out” to reassess how antibiotics are working after 48 to 72 hours of use, for example, will help stem the tide of unnecessary drug use. Ensuring all orders have dose, duration and indications for prescription will be another part of that stewardship.

Frieden’s comments highlighting drug resistance from human antibiotic use comes on the heels of repeated calls for action in the public health community regarding curtailing antimicrobial use among livestock. Currently, no farm regulation limits the use of antimicrobials on livestock, and large farms typically administer low doses of antibiotics to healthy animals, which enable them to grow quickly but heighten the risk of breeding drug-resistant bacteria. Already, about 80 percent of antibiotics sold in the U.S. are intended for food animals instead of people, according to recent estimates. The U.S. Food and Drug Administration does not have the authority to collect data on exactly how antibiotics are being used.

Guidance issued by the FDA asks livestock producers to voluntarily curtail their antibiotic use for growth promotion among livestock whereas other FDA guidance (which has not yet been finalized) also asks drug manufacturers to stop marketing their products for animal production purposes. Public health groups maintain only mandatory requirements will effectively limit antimicrobial use among farm animals.