He also has direct ties to the White House and Capitol Hill. He worked as an investigator for Rep. Henry Waxman, D-Calif., now chairman of the powerful House Energy and Commerce Committee, before becoming Baltimore's health chief. Under Waxman, Sharfstein investigated tobacco companies, and in Baltimore he has fought to reduce smoking, experience that could be vital with Congress considering giving the FDA authority to regulate cigarettes as drug-delivery devices.
Sharfstein had also been floated as a possible commissioner of the agency but vigorous opposition to his nomination was possible due to his reputation as a crusader against drug companies. The deputy position does not require confirmation.
Ensuring the safety of the country's food and drug supply is a daunting task. Many observers have said the FDA does not have enough people or money to do the job well.
"The system is not set up to catch bad actors, at least not until the problem has already erupted, really on a nationwide level," Caroline Smith DeWaal, food safety director for the Center for Science in the Public Interest, told ABC News in January during a peanut recall.
"I believe it is broken, I believe it needs to be fixed," Tom Nassif, president and CEO of Western Growers, told ABC News in July 2008 when the FDA was trying to determine what was contaminating tomatoes. "I know that FDA and CDC must be tremendously frustrated by their inability to trace back the source."
David Acheson, FDA's assistant commissioner for food safety, explained the enormity of the job in January during the peanut recall.
"Clearly in the context of a global food supply, the more integrated the system is, the more standardized it is, the better," Acheson said. "And there's definitely significant moves in that direction. Not just from the FDA but from the states as well. So we're moving in that direction, but FDA doesn't have a mandate to require every state to do exactly what FDA tells it to do."
Consumers and lawmakers alike have also worried the FDA is not doing enough to inspect foreign food and drug plants. In addition to domestic health scares, the FDA has recently dealt with blocking the import of Chinese milk products and zeroing in on where along its international supply chain the blood thinner heparin became tainted.
The agency has also confronted controversy about the safety of diabetes drug Avandia and recalls of the painkiller Vioxx -- flaps that left some wondering whether the FDA is effectively regulating drugmakers.
"We want to work with Dr. Hamburg to reform the way FDA approves medicines," said Consumers Union health analyst Bill Vaughan in a March 11 statement. "Between contaminated imports and the use of dishonest research results, the American medicine cabinet has become a little shop of horrors. In recent years, the agency has been too slow to protect consumers and too willing to give industries a pass on safety."
Lawmakers have repeatedly voiced their frustrations with the FDA.
"Either you don't have the resources, or you are incompetent to do the job you're supposed to do," Rep. John Dingell said to FDA food safety director Stephen Sundlof at a February hearing on the peanut recall. "Which conclusion am I to arrive at?"