Days after a division chief at the Food and Drug Administration resigned amid accusations that he used his federal power to seek revenge on a former business associate, the scandal took on a new life.
Robert F. Kennedy Jr., the nation’s health secretary, and his top deputies brought the matter to the White House as evidence that the F.D.A.’s leadership was in chaos.
The group, led by Jim O’Neill, the deputy health secretary and a former Silicon Valley investor, aired their grievances to Susie Wiles, the chief of staff for President Trump, according to people familiar with the meeting. They then turned to staff members of the Domestic Policy Council, the people said.
The meetings took aim at Dr. Marty Makary, the commissioner of the F.D.A. who was appointed by Mr. Kennedy. But the White House rebuffed what some have viewed as a coup attempt against him, according to those who have knowledge of the sessions.
The result was a fragile truce, but it offered a window into the turmoil at the top reaches of the Department of Health and Human Services, where Mr. Kennedy’s niche projects and infighting among staff members have taken precedence over seismic policy problems, like the looming expiration of Obamacare subsidies.
The tumult at the F.D.A., though, reflects a jarring year defined by the loss of thousands of agency staff members, a rapidly spinning door of top leaders and conflicting statements and actions related to drug approvals. The biotech industry has also pressured the White House about the agency’s refusal to approve a number of drugs.
The meetings also occurred against the backdrop of opposing forces buffeting the F.D.A. At times, Mr. Trump’s corporate-friendly goals have clashed with the agenda of the Make America Healthy Again movement that supports business-wary initiatives.
Officials from the Department of Health and Human Services declined a request for an interview with Dr. Makary for this article.
Asked about the meetings with Trump officials, Kush Desai, a White House spokesman, said the administration fully backed Dr. Makary.
“The White House maintains complete confidence in Marty Makary and the entire team at H.H.S. and F.D.A.,” Mr. Desai said. He cited the “near-weekly flow of groundbreaking F.D.A. announcements” on removing artificial food ingredients and cutting red tape as “proof that Commissioner Makary and his team are delivering for the American people.”
Mr. Kennedy also has full confidence in Dr. Makary, Andrew Nixon, a spokesman for H.H.S., said, adding that Mr. Kennedy had a close working relationship with the commissioner.
Despite those statements of support, agency actions continue to alarm public health experts.
A memo leaked from the agency the day after Thanksgiving made unsupported claims linking Covid vaccines to a small number of children’s deaths, drawing fire from outside and within the agency. The memo, written by Dr. Vinay Prasad, the agency’s top vaccine regulator, also proposed policy changes that brokered no dissent; he invited resignations from staff members who disagreed.
In a year of steep government cutbacks, the F.D.A. has been especially hard-hit, despite its relatively lean federal budget and crucial role in safeguarding the nation’s food and drug supply. The agency’s oversight can have life-or-death consequences, and it regulates products that drive roughly 20 percent of consumer spending.
The agency has lost about 4,000 employees, or 20 percent of its work force, to layoffs, buyouts and other departures this year, slimming the ranks of inspectors and scientists who ensure that drugs are free of toxins. An internal presentation showed that staffing at the drug division alone had fallen to 2016 levels, shedding nearly 1,400 jobs, with the work force reduced to 4,650 from more than 6,000 employees.
“The loss of talent is setting the agency back a decade plus,” said David Kessler, a former agency commissioner. “It is not going to be fixable in the short term.”
The agency has also performed far fewer inspections at food and drug manufacturing plants that ship tons of products to the United States, records show. So far this year, inspection numbers — which were also hindered by the government shutdown — are at levels not seen for more than a decade, aside from the pandemic years.
Staff members in food and drug labs are still dealing with spending limits that have left them idle, rather than scrutinizing food ingredients, packaging and drug safety.
Though Dr. Makary has worked behind the scenes to retain staff members and improve agency operations, he has also stumbled in introducing some policy changes.
From the start, Dr. Makary planned to roll out big announcements at a rapid clip. His office staff is known to push around a white board on wheels speckled with sticky notes planning the next media splash.
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Some of his changes have been well-received, including one to remove the agency’s strictest warning from hormone replacement therapy for women in menopause. His team has led a charge to reduce drug testing on animals, to hasten approvals for less expensive biologic drugs and to warn drugmakers against making unsupported claims on televised drug ads.
When President Trump insisted that pregnant women “tough it out” rather than take Tylenol, warning them of what is still an unproven link between the drug and autism, Dr. Makary took a more reasoned tone. He signed an F.D.A. letter to doctors that said such a link was an “ongoing area of scientific debate.”
Dr. Makary worked internally to get approval in July to hire 1,000 staff members, according to people familiar with the move, with about 500 inspectors and product reviewers coming onboard. In recent days, he has taken steps to keep existing staff members from leaving, promising bonus payments to inspectors and reviewers in an internal F.D.A. video viewed by The New York Times.
But Dr. Makary has also pushed some initiatives with little follow-up, including an event meant to draw attention to the dangers of cancer-causing asbestos in talc used in food and medications. It was followed with the revocation of a rule meant to make talc safer. Though he endorsed the drug leucovorin as a potential aid for some children with autism, such prescribing remains off-label.
He made divisive personnel choices and advanced conspiratorial claims, including that “mad scientists” played a role in lab leaks of H.I.V. in Africa and ticks infected with Lyme disease. And he has fanned flames of distrust over mRNA technology in vaccines, despite its success in reducing Covid deaths and its potential to combat some forms of cancer.
“I think it’s very hard to see the future of these technologies moving forward when it probably was one of the brighter beacons in cancer research two or three years ago,” said Jeff Allen, chief executive of the Friends of Cancer research.
A number of decisions on drug approvals has highlighted internal disputes and roiled agency critics. Dr. Prasad, the agency’s chief scientific and medical officer, has overruled staff vaccine recommendations several times. He has also slammed the door on a series of companies’ drugs by saying they had not demonstrated a clear benefit for patients.
Mr. Nixon, the H.H.S. spokesman, said Dr. Prasad’s decisions on drugs “represented the recommendation of each review team of career scientists.”
Before joining the F.D.A., Dr. Prasad had been critical of the agency, saying it was too willing to approve questionable medications.
But these recent decisions have deflated the hopes of families of people with rare diseases, who are desperate for investment in what may be even marginal therapies for deadly conditions. Biotech companies and their investors have protested, pressing the agency and White House over the agency’s stances on certain drugs.
Other moves have also put pressure on the agency. On Nov. 2, Dr. George Tidmarsh, who was then the head of the F.D.A.’s drug division, resigned under pressure, saying he was being targeted by agency officials over his concerns about a plan to expedite certain drug approvals. Hours later, a drug company sued Dr. Tidmarsh, claiming that he had tried to extort the company’s chairman. Dr. Tidmarsh has denied the accusation and not yet responded to the legal claim.
These events spurred the trip to the White House by Mr. O’Neill, the acting director of the Centers for Disease Control and Prevention, and others. Mr. Kennedy, and two of his top advisers, Stefanie Spear, and Matt Buckham attended the sessions with administration officials. Though Mr. Kennedy has a good relationship with Dr. Makary, he has privately expressed concerns about the agency’s management, according to people familiar with the conversations.
Mr. O’Neill, the deputy health secretary who was said to initiate the White House meetings, has a longstanding interest in the F.D.A. and its dealings with drug companies.
A federal health official during George W. Bush’s presidency, Mr. O’Neill was an unsuccessful candidate to run the F.D.A. in 2017, apparently because of a position he voiced in 2014 that drugs should be approved if they are deemed safe — with effectiveness proved later.
That view goes far beyond the deregulation policies favored by most pharmaceutical executives, who see the F.D.A.’s two-pronged standard of safety and efficacy as crucial to blocking untested products. Mr. O’Neill has not spoken publicly about the issue in the years since and did not respond to requests for comment.
Although Dr. Makary has survived the recent complaints raised at the White House, upheaval at the agency has not let up.
For example, after Dr. Tidmarsh left, Dr. Makary made a house call to Dr. Rick Pazdur, the longtime leader of that agency’s cancer drug center. Dr. Makary convinced him to take the job running the larger drug division, a global operation with a mandate touching on approvals, drug manufacturing and supply chain security.
“A true innovator, an academic, he’s excited about the role,” Dr. Makary said of Dr. Pazdur on an episode of the F.D.A. Direct podcast in mid-November.
Less than three weeks later, Dr. Pazdur announced his retirement, frustrated that Dr. Makary was interviewing a candidate for a key role overseeing the unit that regulates over-the-counter drugs without consulting him, according to people close to the matter. His rapid departure drew rebukes.
“We are at a tipping point,” said John F. Crowley, chief executive of BIO, a trade organization representing the biotech industry, in a statement at the time. “It is time to right this ship.”
Dr. Makary quickly named Dr. Tracy Beth Hoeg, a sports medicine doctor and epidemiologist, to replace Dr. Pazdur. Her criticisms of pandemic policies resemble the views of Dr. Makary and Dr. Prasad during the Biden administration.
But her lack of experience in drug development and management has again put a spotlight on the agency.
“One of the concerns overall is that more and more decision-making is in the hands of people influenced by politics,” said Dr. Robert Califf, the F.D.A. commissioner under President Biden. “I saw the most important part of my job was to take the calls and say: ‘It’s in the hands of civil servants.’”
Rebecca Robbins contributed to this article.
Christina Jewett covers the Food and Drug Administration, which means keeping a close eye on drugs, medical devices, food safety and tobacco policy.
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