The president also is creating a special advisory group to coordinate food safety laws and recommend how to update them. Many of these laws have not changed since they were written early in the last century, he said.
Obama said too many agencies are responsible for food safety, making it difficult to share information and stop problems from falling through the cracks.
The FDA does not have enough money or workers to conduct annual inspections at more than a fraction of the 150,000 food processing plants and warehouses in the country, Obama said.
"That is a hazard to public health. It is unacceptable. And it will change under the leadership of Dr. Margaret Hamburg," he pledged.
Hamburg, 53, is a bioterrorism expert. She was an assistant health secretary under President Bill Clinton and helped lay the groundwork for the government's bioterrorism and flu pandemic preparations.
As New York City's top health official in the early 1990s, she created a program that cut high rates of drug-resistant tuberculosis. She is the daughter of two doctors. Her mother was the first black woman to earn a medical degree from Yale University, and she credits her father for instilling in her a passion for public health.
Sharfstein, 39, is a pediatrician who has challenged the FDA on the safety of over-the-counter cold medicines for children. He also served as a health policy aide to Rep. Henry Waxman, D-Calif., who plays a leading role in overseeing the pharmaceutical industry.
Both are doctors and outsiders to the troubled agency and will face the challenge of trying to turn it around.
Those with a stake in the FDA's work, from health and consumer groups to the food and drug industries, said Obama made good choices.
The Trust for America's Health said Hamburg is a proven manager who turned around the ailing health department in New York City.
"She restored both morale among workers and the agency's credibility among citizens," said Lowell Weicker Jr., a former Connecticut senator and president of the trust's board. "And she has shown she can reach across party lines, having worked for both Democratic and Republican mayors in New York City."
Gail Cassell, an Eli Lilly & Co. vice president who once served on a government advisory board with Hamburg, said Hamburg "is a big believer" in backing up policy with the best scientific evidence and data.
"She is very balanced and thoughtful about the actions that she takes and certainly has had the experience of running a very complex organization," Cassell said.
Ellen Bloom of Consumers Union said Sharfstein's experience is "just what the doctor ordered for FDA," and Carol Tucker Foreman of Consumer Federation of America said, "Their resumes are extremely impressive."
The main food industry group said Obama seems committed to overhauling the agency.
"The president's appointment of these two prominent public health professionals is a clear signal that this administration has placed a priority on bolstering FDA's food safety role," said Pamela Bailey, president and chief executive of the Grocery Manufacturers Association.
Hamburg's appointment requires Senate confirmation; Sharfstein's does not.
Obama said while he doesn't believe government has the answer to every problem, there are certain things that only government can do such as "ensuring that the foods we eat and the medicines we take are safe and don't cause us harm."
"Protecting the safety of our food and drugs is one of the most fundamental responsibilities government has," he said.
Obama cited a string of breakdowns in assuring food safety in recent years, from contaminated spinach in 2006 to salmonella in peppers and possibly tomatoes last year. This year, a massive salmonella outbreak in peanut products has sickened more than 600 people, is suspected of causing nine deaths and led to one of the largest product recalls in U.S. history.
These cases are a "painful reminder of how tragic the consequences can be when food producers act irresponsibly and government is unable to do its job," Obama said, noting that contaminated food outbreaks have more than tripled to nearly 350 a year from 100 incidents annually in the early 1990s.
Separately, Obama announced a ban on the slaughter of "downer" cows, which are too sick or weak to stand on their own, to keep them out of the food supply. These animals pose a higher risk of having mad cow disease, E. coli and other infections.
Obama said he takes food safety seriously, not just as a president but also as the parent of two young daughters.
"No parent should have to worry that their child is going to get sick from their lunch," he said.
Also awaiting the next FDA chief is a renewed effort in Congress to require government regulation of cigarettes and other tobacco products, to reduce the harm from smoking.
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