Dr. Robert Califf spent three decades as a drug-trial researcher at Duke University, where he founded Duke’s Clinical Research Institute.

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WASHINGTON — After five months of delays, the Senate voted 89-4 on Wednesday to confirm cardiologist Dr. Robert Califf, a longtime Duke University drug-trial researcher, as the new commissioner of the Food and Drug Administration (FDA).

Califf was nominated to the post by President Obama in September, but concerns about his ties to the pharmaceutical industry and some of the FDA’s practices tied up his confirmation.

“Dr. Califf is the right person with the right experience to build on the FDA’s unsurpassed record of protecting public health while encouraging innovation and the introduction of new lifesaving therapies to the market,” Health and Human Services Secretary Sylvia Burwell said Wednesday.

The position has been open since Dr. Margaret Hamburg stepped down in February 2015. Califf already was serving as deputy commissioner of the agency, its No. 2 spot, when he was nominated last year.

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Several senators held up the confirmation over concerns ranging from the FDA’s approval and labeling processes to doubts about the candidate’s ties to the drug industry.

Califf spent three decades as a drug-trial researcher at Duke University, where he founded Duke’s Clinical Research Institute. He forged close relationships with the pharmaceutical industry that some critics say are too close for comfort. Opponents to his confirmation have pointed out that as head of the FDA, Califf would be in charge of regulating former clients.

The strongest pushback against Califf’s nomination came from Sens. Edward Markey, D-Mass., and Joe Manchin, D-W.Va., who said the candidate’s industry ties make him a poor choice to reform problematic practices in the agency. They expressed frustration with the FDA’s approval of pediatric opioids and said the agency needs to change its process for approving opioid painkillers.

Markey pointed out that 80 percent of heroin overdoses in 2014 happened to people who started out on prescription opioids.

Others, like Sen. Bernie Sanders, I-Vt., objected to Califf himself.

“His extensive ties to the pharmaceutical industry give me no reason to believe that he would make the FDA work for ordinary Americans, rather than pharmaceutical CEOs who are more focused on making obscene profits than saving lives,” Sanders, who is also a candidate for the Democratic presidential nomination, said last month.

Even so, Califf has broad bipartisan support in Congress and sailed through an initial vote by the Senate health committee last month. The Senate cleared the way for Califf’s nomination on Monday, overwhelmingly backing a motion to prevent lawmakers from further blocking the vote and limiting the debate on the decision to 30 hours. Only six senators voted against it, though some advocacy groups still tried to rally opposition to the nomination before Wednesday’s vote.

As the new chief of the FDA, Califf is inheriting an agency that faces a slate of challenges in the final year of the Obama administration. Under his leadership, the agency will continue to be under pressure to speed the drug-approval process and to extend its regulation of tobacco to include electronic cigarettes.

The FDA also is in the middle of overhauling how it controls companies’ food-safety practices to prevent foodborne illnesses, and under pressure to end delays on labeling cheaper copies of biologic drugs, known as biosimilars.