The Senate on Tuesday narrowly confirmed Dr. Robert Califf as commissioner of the Food and Drug Administration, a key federal agency that has been without a permanent chief for more than a yearlong stretch of the coronavirus pandemic.
The vote was 50-46, with six Republicans crossing the aisle to support him while five Democrats opposed him. One senator voted present.
In recent weeks, Dr. Califf’s odds of a second confirmation looked increasingly long as opposition mounted over concerns about how he would respond to the opioid epidemic and the agency’s handling of abortion drug rules. The White House responded by trying to rally support in Congress and among other allies, with mainstream medical societies and a bipartisan group of six former F.D.A. commissioners coming to Dr. Califf’s defense.
Senator Richard Burr, Republican of North Carolina, was one of a handful of G.O.P. senators who backed Dr. Califf and offset some Democrats’ opposition. On Tuesday, Mr. Burr called on other senators to confirm Dr. Califf, saying the F.D.A. had gone 391 days without a permanent leader.
“I urge my colleagues to support Dr. Califf’s nomination because he will provide the leadership needed to promote today’s biomedical advancements and help to pave the way for tomorrow’s innovation,” Mr. Burr said.
Despite some Republican support, senators in both parties, ranging from liberal Democrats leery of his ties to the pharmaceutical industry to conservative Republicans in lock step with the anti-abortion movement, posed formidable opposition.
By contrast, Dr. Califf breezed into the commissioner role in 2016 in a vote of 89 to 4, with strong support from both sides of the aisle. Some of the headwinds he has faced since President Biden nominated him in November are from the same Democratic senators who opposed him six years ago. Back then, Senator Joe Manchin III, Democrat of West Virginia, voiced concerns about Dr. Califf’s ties to the pharmaceutical industry amid the opioid epidemic that by 2016 had already killed thousands.
On Friday, Mr. Manchin called on Mr. Biden to withdraw the nomination in an opinion essay, noting that while Dr. Califf pledged to make changes the last time he was commissioner, the F.D.A. approved five new opioids in 2016 and 2017.
“I have never been more profoundly confident of a vote I’m going to cast than I am right now,” Mr. Manchin said in a fiery floor speech on Monday, directly placing partial blame for the worsening epidemic on Dr. Califf. Opposition to his nomination, Mr. Manchin added, would “send a message to this administration, to our president, that we need a new direction at the F.D.A.”
“We need people who want to protect us,” he concluded, “not people who allow drugs to destroy us.”
Just before the vote on Tuesday, Senator Edward Markey, Democrat of Massachusetts, denounced the F.D.A.’s role in becoming the “country’s biggest pill pusher” and said Dr. Califf did little to address the problem in his previous stint as commissioner.
“There was no real commitment to reforming the F.D.A. or to learning from the mistakes that enabled this public health crisis,” Mr. Markey said.
Dr. Califf also faced pressure from abortion foes over the F.D.A.’s risk-management policies related to abortion medications. The influential Susan B. Anthony List organization, which opposes abortion, has canvassed lawmakers about changes made during Dr. Califf’s prior tenure as commissioner that eased access to medication abortion pills.
During a Senate hearing in December, Dr. Califf expressed confidence in the agency’s ability to handle decisions about the medications again. Two days after that hearing, the F.D.A. announced that women could receive the pills by mail after a telehealth appointment, eliminating a requirement for an in-person evaluation.
The Susan B. Anthony List announced that it would “score” the vote on Dr. Califf’s nomination, meaning it will be considered in the organization’s assessments for lawmakers’ “pro-life scorecard.” Republicans up for re-election often seek the group’s endorsement.
Senator Steve Daines, Republican of Montana, spoke in opposition before the vote, criticizing Dr. Califf’s role in the abortion medication changes.
“Dr. Califf has refused to distance himself from the F.D.A. decision to abandon vulnerable pregnant women to the reckless and predatory actions of the abortion industry,” Mr. Daines said.
Dr. Califf’s backers argued that the agency was long overdue for permanent leadership, particularly as the agency wrestles with the review of coronavirus vaccines for young children on top of other health crises.
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“Dr. Califf’s previous service in this role, his career as one of the nation’s leading research scientists, gives him the experience to take on this challenge,” said Senator Patty Murray of Washington, the chairwoman of the Senate Committee on Health, Education, Labor and Pensions.
“It is critically important to have confirmed leadership at the F.D.A. in the middle of the pandemic,” Karine Jean-Pierre, the White House deputy press secretary, said on Monday. She underscored the meetings and phone calls Dr. Califf, the White House and their allies had undertaken to shore up support for his confirmation.
The agency plays a key role as gatekeeper to the vaccines, tests and treatments Americans have access to, and regulates food, drugs, cosmetics and tobacco products that account for 20 cents of each dollar of U.S. consumer spending.
The incoming commissioner will have plenty of work to do. The agency is facing high-profile decisions on e-cigarette marketing applications, with tobacco opponents watching in concern over the persistent lure of youth vaping. Lawmakers are eager to see changes in how the agency fast-tracks drugs to the market after the controversial approval of the Alzheimer’s drug Aduhelm. And the agency has a lengthy backlog of foreign inspections to contend with, as roughly 80 percent of active drug ingredients come in from overseas.
Dr. Califf spent most of his career at Duke University, where he served as a professor of medicine and founding director of the Duke Clinical Research Institute. He led numerous clinical trials in cardiology, gained experience working with the pharmaceutical industry and drew widespread respect in the field of medicine.
That standing is crucial, said Dr. David J. Skorton, president of the Association of American Medical Colleges.
“The decisions that are made by an F.D.A. commissioner or the F.D.A. in general are not always going to please everybody,” Dr. Skorton said. “They are very, very difficult decisions,” he said. Noting that he had followed Dr. Califf’s career for decades, Dr. Skorton described him as “the person for the hour.”