Abbott shut down production at the plant last year amid “shocking” sanitation lapses, touching off a disruptive infant supply formula shortage.The U.S. Department of Justice has opened an investigation into operations at the Abbott Nutrition infant formula plant in Michigan that shut down over sanitation problems early last year, causing a lengthy and widespread infant formula shortage.The company confirmed the investigation in an email but offered no further details, other than that it was “cooperating fully,” according to an Abbott spokesman.The plant, in Sturgis, Mich., came to national attention in 2022 after the Food and Drug Administration, while fielding reports of infants sickened by formula produced there, found strikingly unsanitary conditions, including puddles of water on the floor near production lines. In February, the agency urged the company to recall Similac and other widely used infant formulas, F.D.A. records show. Abbott voluntarily ceased production at the plant for several months.Baby formula was already somewhat scarce because of pandemic-related supply chain issues, but the Abbott recall made the situation much worse. Stunned parents reported hunting for hours to find formula needed to feed their infants. By May, President Biden was deploying military planes to airlift infant formula into the United States.The investigation was previously reported by The Wall Street Journal. The Department of Justice declined to comment.Four infants in three states — Minnesota, Ohio and Texas — fell ill with the dangerous Cronobactor sakazakii bacteria starting in September 2021, and two of them died. Though F.D.A. inspectors who swabbed the area near production lines at the Sturgis plant found samples of the bacteria, F.D.A. records show, no strain associated with an infant was directly linked to the facility.Lawmakers held hearings about the crisis, discussing the F.D.A.’s fumbling of a whistle-blower complaint from an Abbott insider who asserted that the plant did not destroy a batch of formula found to include micro-organisms because “senior management was under significant pressure to meet its ‘numbers.’”In one House hearing in May, Dr. Robert Califf, the F.D.A. commissioner, acknowledged that the agency moved too slowly to address the supply chain crisis and made “decisions that were suboptimal along the way.”He also described “shocking” and “egregiously unsanitary” conditions at the Sturgis plant, including a leaking roof and pooled water near production areas.The F.D.A. released a review of its response in September, noting that the agency needs better information technology and visibility into the supply chain, even as formula supply remained low. Dr. Califf commissioned a more sweeping review of the F.D.A. food division, released last month, which called for a stronger new leadership structure.Glenn Thrush

The proposed deal would resolve thousands of lawsuits in multidistrict litigation based in Northern California.Juul Labs has agreed to pay $1.7 billion to settle more than 5,000 lawsuits by school districts, local governments and individuals who claimed that its e-cigarettes were more addictive than advertised, according to people with knowledge of the deal.The amount for the deal, which involves a consolidation of cases centered in Northern California, is more than three times the sum reported for other Juul settlements in other state and local cases thus far.The settlement amount was reported earlier by The Wall Street Journal.In September, the company agreed to pay $438.5 million to settle a multistate investigation into whether the company had targeted young people. States investigating the company bristled at ads featuring young models and fruit and dessert flavors that appealed to adolescents. The resulting settlement restricted Juul from aiming marketing of its products at young people.Full terms of the settlement, reached earlier this week, have not been disclosed. But Juul has repeatedly denied targeting minors and has not admitted wrongdoing in reaching other agreements with plaintiffs.Juul continues to sell its products in the United States while awaiting a decision by the Food and Drug Administration, which regulates e-cigarettes. In June, the agency denied the company’s application to allow its vapes and pods to remain on the market. Juul went to court and received a temporary reprieve; the F.D.A. then put its decision on hold for further review, which is continuing.The new settlement does not put an end to claims against Altria, which owned a 35 percent stake in Juul, according to lawyers for the plaintiffs. The agreement does not offer funds immediately, but will open up a claims process for the 10,000 plaintiffs to apply for distribution of the funds.

The deal is the latest in the company’s efforts to resolve litigation over its marketing of products that some contend fueled the teenage vaping crisis.Juul Labs announced on Tuesday that it had agreed to settle about 5,000 lawsuits in a Northern California court case for an undisclosed sum, resolving one more legal battle over its sale and marketing of e-cigarettes blamed for the teenage vaping crisis.The proposed agreement on the multidistrict litigation would wrap up personal injury, consumer class action, government and Native American tribe cases in a deal that the company said it had secured an investment to fund.“These settlements represent a major step toward strengthening Juul Labs’ operations and securing the company’s path forward to fulfill its mission to transition adult smokers away from combustible cigarettes while combating underage use,” a company spokesman said in a statement.In September, the company settled an investigation by three dozen states for $438.5 million. That investigation focused on the company’s early marketing of its products, including the use of young models and the sale of flavors like mango and crème brûlée that many contended were deliberately aimed at underage youths. That settlement set terms for Juul’s marketing that prohibited the company from targeting young people.Juul has repeatedly denied targeting minors, and in other rounds of settlements the company has not admitted wrongdoing in reaching agreements with the plaintiffs. The latest settlement does not end claims against Altria, which owned a 35 percent stake in Juul, according to lawyers for the plaintiffs. The agreement does not offer funds immediately but will open up a claims process.“The scope of these suits is enormous,” Sarah R. London, a co-lead counsel for the plaintiffs, said in a statement. “These settlements will put meaningful compensation in hands of victims and their families, get real funds to schools for abatement programs, and help government and tribal entities prevent youth use of e-cigarettes across the U.S.”The company is still awaiting a decision by the Food and Drug Administration over permanent authorization for sale of its vaping devices and pods. In June, the agency denied the company’s application to allow its e-cigarettes to remain on the market. Juul received a temporary court reprieve, and then the F.D.A. put its decision on hold for further review, which is continuing.Juul said the agreement reached on Tuesday involved about 10,000 plaintiffs, many of whom claimed they had not been aware that the product could be more addictive than cigarettes. The plaintiffs, which included school districts, also argued that the e-cigarettes were unreasonably dangerous because of their attractiveness to young people. They made a wide range of claims, from racketeering to fraud and unjust enrichment.Meredith Berkman, a co-founder of Parents Against Vaping E-Cigarettes, said she hoped the settlement was large enough “to compensate millions of American families whose lives have been upended by the youth vaping epidemic created by Juul.” The group is not a plaintiff in this multidistrict litigation.She said she was troubled by the lack of details initially released by Juul and hoped the judge overseeing the litigation would require Juul to produce documents showing whether the company had deliberately targeted adolescents.

Spurred by the infant formula crisis, a panel found that the agency shied away from tough decisions, sometimes fearing confrontations with industry over enforcement of critical public health issues.The Food and Drug Administration’s food division has no clear leadership, avoids bold policy or enforcement actions, and fosters a culture that doesn’t adequately protect public health, according to a report issued on Tuesday by an agency-related group.Experts with the group, the Reagan-Udall Foundation, which was asked to examine the food division after widespread criticism stemming from the infant formula crisis, concluded in the report that the division’s management structure and mission should be overhauled.Dr. Robert Califf, the agency commissioner, released a statement Tuesday saying he would form a group to advise him on the findings and on how to put the recommendations in place. The infant formula crisis was the first major challenge that Dr. Califf confronted this year as commissioner, although the agency has also faced criticism over the regulation of vaping and tobacco products, which prompted a similar review of its tobacco division.“I expect this leadership group to be bold and focused on the transformative opportunities ahead for the F.D.A.’s food program,” Dr. Califf said. “I will be fully engaged to ensure that the program comes out of this transition with the resources, tools and visibility it warrants given how critical its work is to every American.”Congressional lawmakers and others have long called for strengthening the authority and influence of the agency’s food division, given the effects of foods like added sugar and salt on deadly chronic diseases and the toll of food-borne illnesses that account for an estimated 128,000 U.S. hospitalizations and 3,000 deaths each year.The report followed years of complaints that the food unit was toothless, a criticism that was amplified by what critics viewed as the agency’s plodding and disorganized response to reports of infant illness and death and unsanitary conditions at the Abbott Nutrition infant formula plant in Michigan. The agency’s shutdown of the factory in February aggravated an infant formula shortage that left parents scrambling to feed their babies for months earlier this year.A New York Times review found that the F.D.A. had fielded a complaint in September 2021 about a Minnesota infant hospitalized with the deadly Cronobactor sakazakii bacteria, reportedly after consuming formula from the plant. Yet even though agency inspectors inspected the plant in Sturgis, Mich., at the time, it was not until February that the authorities swabbed the plant and discovered the bacteria near production areas. Abbott has said that genetic sequencing did not connect bacteria found in the plant to the deaths of infants infected with Cronobactor.Representative Rosa DeLauro, Democrat of Connecticut and chairwoman of the House Appropriations Committee, which oversees the agency, said in a statement that she was “pleasantly surprised by the formal acknowledgment of the issues that plague the F.D.A. foods program.”“I look forward to working with the F.D.A. on how they intend to implement the positive reforms in this report,” Ms. DeLauro said.Food safety advocates who have been harsh critics of the agency said the report appeared detailed and strong enough to pave the way for needed change.“It’s very significant and encouraging from that standpoint, because for them to outline the findings that they did is important, because it’s a critical acknowledgment that things definitely need to change,” Brian Ronholm, director of food policy for Consumer Reports, said. “Now it comes down to: How does F.D.A. process this report and the information contained in it, and how does that translate to meaningful reform?”Some critics, however, pointed to the relationship the report’s authors have with the agency. The Reagan-Udall Foundation is funded by the F.D.A. and major corporations like Pfizer, AbbVie and Nestle USA, which makes infant formula. The foundation sought the views of food safety and nutrition experts and collated the comments of agency staff members, but has since removed the feedback from its website.The staff comments, reviewed by The Times, showed some discontent with how the division was run. Some employees repeatedly complained that division managers stopped short of enforcing food-safety laws out of fear of complaints or lawsuits. Others said that input from industry consultants and special advisers from industry added little value. And some others chafed about a lack of clear priorities, or personality politics and favoritism that trumped a focus on protecting the nation’s food supply.Four former F.D.A. food center directors submitted a statement calling for the division to be better protected from budget cuts and for giving its officials more control over food facility inspections.The report underscores that concern about lack of leadership, noting that three food division officials have competing levels of authority. The report recommends a structural change, laying out several options that would make leadership more centralized. It also recommended more funding to enhance the division’s operations, although congressional approval for budgetary increases might prove difficult now that inflation and the economy may force cutbacks.

Especially for Black patients, inaccurate readings have imperiled care and may have contributed to deaths during the pandemic, experts told an advisory panel.Researchers warned an expert panel of the Food and Drug Administration on Tuesday that flawed readings on devices measuring oxygen levels in the blood — especially among Black and dark-skinned patients — might have contributed to deaths during the coronavirus pandemic. Panelists, in turn, urged the federal agency to raise accuracy standards and to alert doctors and consumers of the potential risks.The devices that measure blood oxygen typically on the fingertip, known as pulse oximeters, can be cheap, small products sold over the counter or medical devices used in hospitals and clinics.Decades before the pandemic, studies showed that they were less accurate on darker skin, often giving a healthy reading when blood tests showed more concerning levels.But in recent years, experts said the flawed readings might have driven some of the racial and ethnic disparities exposed in studies reviewing access to Covid treatments. Authors of the studies emphasized that blood-oxygen levels were often a key factor in deciding who would receive certain medicines, oxygen therapies and even hospital beds at times when all were in short supply.Dr. Amal Jubran, a pulmonary critical care doctor at Loyola Medicine in Chicago, one of the first physicians to identify the problem in 1990, testified on Tuesday that flawed readings were “hazardous” during the height of the pandemic.They “most likely contributed to the several-fold greater number of deaths in Covid-19 in ethnic minority patients than in white patients,” Dr. Jubran told the panel.The F.D.A. reviews prescription pulse oximeters and those used in hospitals under its so-called 510K program, which clears devices that are similar to existing ones — with some additional scrutiny. The over-the-counter versions are deemed “wellness” devices and are subject to virtually no agency oversight.Read More on the Coronavirus PandemicWarnings of a ‘Tripledemic’: An expected winter rise in Covid cases appears poised to collide with a resurgent flu season and a third pathogen straining pediatric hospitals in some states.Updated Boosters for Kids: The Food and Drug Administration broadened access to updated Covid booster shots to include children as young as 5.A Decline Among Seniors: Americans over 65 remain the demographic most likely to have received the original series of Covid vaccinations. But fewer are getting booster shots, surveys indicate.Personality Changes: New research suggests that Covid’s disruption of social rituals and rites of passage have made people less extroverted, creative, agreeable and conscientious.The accuracy concerns, which the agency flagged in 2021, led to a 10-hour meeting Tuesday of an F.D.A. advisory panel involving doctors and advisers. They did not formally vote on specific ways that the agency might address the issue, but several suggested measures like adding warnings to product labels and raising the bar manufacturers need to reach — in terms of correct readings — to get new devices approved. Doctors testifying to the panel also said studies gauging device performance on people with a range of skin tones and chronic medical conditions were needed.Veverly Edwards, a community representative and the only African American on the panel of mainly white male doctors, called for manufacturers to be held accountable. She said Black people should have a sustained voice on the matter that also affects people of many ethnicities with dark skin.“I guess my fear is that historically that the disparity in health care is like it never stops,” said Ms. Edwards, who is an assistant professor at the University of Memphis. “When you lump African Americans in with everyone else, we end up on the short end — because this started 30 years ago and here we are today addressing it.”During the hearing, F.D.A. officials said the pulse oximeters used in hospitals were marketed based on studies of as few as 10 healthy people. And the devices that people buy online or at retail pharmacies are not scrutinized by the F.D.A.Panelists agreed that the current rules were too lax for devices that had become a key driver of patient-care decisions, such as prescribing or ending the use of supplemental oxygen.“That should be held to a very different standard,” said Dr. Hugh Cassiere, an adviser and critical care chief at North Shore University Hospital in New York. “We really need to tighten that up.”Doctors who appeared before the panel cited a series of studies that showed how inaccurate readings from the devices used in hospitals affected people with darker skin during the pandemic and were associated with inadequate medical care.One University of Michigan study found that the devices that squeeze the finger gave elevated readings in Black people when a blood test showed a lower rate, suggesting “hidden” hypoxemia, or significantly low blood oxygen. The discrepancy was found in nearly 12 percent of Black people and in nearly four percent of white people.Dr. Ian Wong, a Duke University researcher, confirmed elevated levels of hidden hypoxemia in Black and Hispanic patients. He also told the panel that he found that all patients who had hidden hypoxemia had a risk of in-hospital death that was 70 percent higher than those with accurate readings.Doctors at the Johns Hopkins University School of Medicine confirmed the disparity again and noted the result: Black and Hispanic patients were 29 and 23 percent less likely to be recognized as candidates for Covid treatments.The studies were largely based on self-identified race, and researchers are still looking into the degree that melanin in the skin — which lends the darker pigmentation — affects pulse oximeter performance.The findings underscore the importance of testing the devices on sick patients and those with a range of skin tones, said Dr. Eric Gartman, a Brown University assistant professor testifying for the American College of Chest Physicians. Currently those devices are tested in healthy people in a lab.“We wouldn’t tolerate that in a medicine,” he said, “so I’m not sure we should tolerate that in a device, either.”Dr. Jesse Ehrenfeld, president-elect of the American Medical Association and an anesthesiologist, testified that he wondered if the pulse oximeter he used on a patient Tuesday morning was going to be accurate.“We need to take appropriate steps to remove the growing uncertainty around these devices and ensure the health and safety of the public,” he said.Dr. Ehrenfeld said the F.D.A. should put specific warnings on devices that produce biased readings, make health providers aware of the limitations and increase testing of devices that were already cleared by the agency.For the oximeters that people buy online or from retail stores, the lack of regulation is troubling, said one agency adviser, Dr. Murad Alam, a medicine professor at Northwestern University. People use them, he noted, to monitor oxygen levels at home and decide if they need urgent medical attention.“This is a misclassification problem,” Dr. Alam said. “I don’t know how it happened, but this is not shampoo. So F.D.A. will need to find a way to regulate these.”Advisers urged the agency to provide prominent warnings that the retail devices are not for medical use and are not approved by the F.D.A. The agency said it was working with researchers from Stanford and the University of California, San Francisco, on real-world studies of device performance.

The agency cited Teva’s continuing supply problems as well as those of other drug makers struggling to fill the gap.The Food and Drug Administration has declared a nationwide shortage of Adderall, a medication used to treat A.D.H.D. that has had surging demand in recent years.The F.D.A. noted that one maker of the drug, Teva Pharmaceuticals, has had continuing manufacturing delays, and other manufacturers of generic versions or alternatives have also reported periodic problems with meeting demand.The agency recommended that patients taking Adderall talk to their doctors to find alternative treatments.Adderall, which contains the stimulant amphetamine, is a controlled substance and highly regulated, so it is difficult for pharmacies to quickly pivot and carry new brands, analysts said. Further muddying the picture is the recent popularity of telehealth services. A crop of telehealth start-up companies flourished during the pandemic, with some prescribing Adderall and other drugs to patients in unknown quantities.The number of Adderall and generic-equivalent prescriptions has been rising in recent years, according to figures from IQVIA, a data analytics company. Total prescriptions rose by about 16 percent, to 41.2 million last year from 35.5 million in 2019.Over the years, concerns have been raised about the overprescribing of Adderall for children and young adults with A.D.H.D., and about its abuse as a study aid among college students. The teenage mental health crisis that exploded during the pandemic put a spotlight on sharp increases in some prescriptions, like Adderall.Dr. David Goodman, director of the Adult Attention Deficit Disorder Center of Maryland, said about 4 percent of adults and 8 percent of children have attention deficit hyperactivity disorder, and large numbers of them go untreated — roughly 70 percent of adults and 40 percent of children. He said growing awareness about the condition appears to be leading to a surge in demand for medications.In addition, he said, the telehealth start-ups made it cheaper and less time-consuming to get a diagnosis, although he questioned whether all of those were accurate.“I can understand why there are shortages, because there’s an increased demand of people who are seeking these medications,” said Dr. Goodman, who is also an assistant professor of psychiatry at Johns Hopkins University School of Medicine. He received $18,000 in 2021 as a consultant for drug companies.While a number of companies make Adderall and generic versions, pharmacies may find it difficult to pivot to other suppliers because of amphetamine’s status as a controlled substance that typically includes restrictions on its use and monitoring of prescription orders. Any given pharmacy might risk raising red flags with the Drug Enforcement Administration by doubling its supply, said Erin Fox, an expert on drug shortages at the University of Utah.“With a controlled substance, it’s harder for patients to call around and find a pharmacy that has product for them,” Ms. Fox said.Dr. Goodman said patients report almost every day that they are unable to get prescriptions filled. He said his office has had to reissue them in different dosages to help patients receive treatment. Even then, some come up short and, without their medications, may miss deadlines or forget important tasks if they are working in a high-pressure situation.There is little data on start-up telehealth companies that have drawn criticism for rapidly prescribing a variety of medications, including Adderall.One such company is Cerebral, which is based in San Francisco. A former vice president of Cerebral, Matthew Truebe, filed a wrongful termination suit against his former employer, claiming that a company goal was to prescribe stimulants to 100 percent of the company’s A.D.H.D. patients, something he considered “not safe or legal,” according to court records. Mr. Truebe also claimed the company had duplicate patients in its database, suggesting that some were seeking prescriptions to resell.Cerebral, valued at over $1.2 billion this summer, said in a court filing that Mr. Truebe was not fired as an act of retaliation, but because he was a “poor performer.” The company has received a subpoena from federal investigators reviewing its compliance with the Controlled Substances Act. A Cerebral rival, called Done, is also facing Drug Enforcement Administration scrutiny, The Wall Street Journal reported.Chris Savarese, a spokesman for Cerebral, said the company had ceased prescribing controlled substances to new patients and had not been accused by any government agency of wrongdoing.

While use among youths has fallen since the peaks of 2018-19, resumption of in-school classes this year shows students still have access to flavored, disposable vapes.High school students resumed taking the annual National Youth Tobacco Survey in school this year and 14 percent of them reported using e-cigarettes, underscoring how an upstart industry is dodging regulators’ efforts to spare a generation from nicotine addiction.The number shows a slight change from 11 percent last year, but researchers cautioned against drawing comparisons to 2021’s survey, which was conducted differently because it took place when many schools were closed during the pandemic. The latest results were released by the Centers for Disease Control and Prevention on Thursday.Though the age-old force of peer pressure may still be encouraging use, the percent of high school students who reported vaping in the last 30 days was still far lower than record-high levels reached in 2019 of nearly 28 percent.Overall, the survey found that 2.5 million middle and high school students, or about 9 percent, used e-cigarettes in the last 30 days. That puts their overall rate of use several times higher than that of adults, which is estimated at about 3 percent.In the survey, which was conducted from January through May of this year, high school students reported strongly favoring fruit- and candy-flavored vapes. Some mentioned PuffBar, Vuse and Juul as their favorite brand among those on the survey’s list.Read More on Smoking, Vaping and E-CigarettesThe Business of Addiction: McKinsey’s ties to opioid makers are well known, but for decades the consulting giant worked with Big Tobacco and has also advised Juul.Youth Vaping Settlement: Juul tentatively agreed to pay $438.5 million to settle an investigation by nearly three dozen states over marketing and sales practices that they contend set off the teen vaping crisis.Ban Suspension: The Food and Drug Administration ordered Juul to stop selling e-cigarettes on the U.S. market, though it later suspended the ban citing “scientific issues” that warrant a review of the decision.Nicotine Levels: The F.D.A. is planning to require tobacco companies to slash the amount of nicotine in their cigarettes. But experts warn that drastic cuts could prove disruptive and fuel underground markets.But many said their favored e-cigarette brand was not one of the 13 listed. That finding highlights how nimble the industry has been in stamping an array of brand names on vapes with flavors like strawberry ice cream and fresh vanilla that are largely made in China and shipped from warehouses to corner stores and into e-commerce.“What that shows is that playing Whac-A-Mole with a few products is not going to solve the problem,” said Vince Willmore, a spokesman for the Campaign for Tobacco-Free Kids. “As long as any flavored products are still on the market, kids are going to shift to them. To solve the problem, you have to clear the market of all flavored products.”One stark finding was that one in four of the high school students who were e-cigarette users reported vaping every day. Groups opposed to e-cigarettes and tobacco products were particularly troubled by one other result that reflected the highest frequency-of-use to date: Nearly half of the high school students who were vaping said they were doing so 20 to 30 days a month.“That’s a real signal of addiction and setting up young people for a lifetime of addiction which they don’t want, they didn’t choose and they don’t like,” said Robin Koval, president of the Truth Initiative, a nonprofit organization aimed at eliminating youth tobacco use.The Food and Drug Administration considers e-cigarettes to be generally beneficial, because they can provide an alternative to adult users of traditional cigarettes, which coat the lungs in tar. The agency’s hope for health gains, though, has existed in the shadow of a youth vaping crisis that exploded in 2018-19, prompting an outcry from parents, schools, lawmakers and public health experts.The F.D.A. began to crack down on vape makers in 2019, banning many flavors and ordering manufacturers to apply for marketing authorization to keep their products on the market — an ongoing process. That effort has been challenged by e-cigarette makers who saw a loophole in making e-cigarettes with synthetic nicotine and jumped into the market with blueberry, kiwi and candy-flavored vapes.This spring Congress gave the F.D.A. the authority to rein in those devices. The agency said it was reviewing about one million applications to sell synthetic nicotine products. In July, the agency gained authority to remove unauthorized nontobacco products from the market but has said it needs to move methodically as it enforces the law.The consequences for teens who develop a nicotine addiction are just beginning to be understood. Dr. Rose Marie Robertson, science and medicine officer with the American Heart Association, said scientists were seeing toxic effects from the inhaled flavoring ingredients. She said researchers were also detecting signs of e-cigarette use on the heart and lungs.“It took us 40 years to show that women would develop lung cancer more readily if they smoked,” Dr. Robertson said. “The fact that we’re seeing any effects at an early stage is very worrisome.”The persistent rate of e-cigarette use among teenagers also concerns experts who were thrilled to see youth cigarette smoking rates fall steadily for years.“To have decades of progress wiped away by e-cigarettes has been astonishing to us who’ve been there all along,” Dr. Robertson said.

The pharmaceutical industry finances about 75 percent of the agency’s drug division, through a controversial program that Congress must reauthorize by the end of this month.Every five years, top officials of the Food and Drug Administration go behind closed doors to negotiate the terms of its core budget — about $3 billion this year.But the F.D.A. is not at the table with members of Congress or with White House officials. Instead, it’s in dozens of meetings with representatives of the giant pharmaceutical companies whose products the agency regulates. The negotiations are a piece of the “user fee” program in which drug, device and biotech companies make payments to the agency partly to seek product approvals. The fees have soared since the program’s inception three decades ago and now make up nearly half of the F.D.A.’s budget and finance 6,500 jobs at the agency.The pharmaceutical industry funding alone has become so dominant that last year it accounted for three-quarters — or $1.1 billion — of the agency’s drug division budget.Details of the program are being debated in Congress as a Sept. 30 deadline for reauthorization nears. The powerful pharmaceutical lobby says its role in funding the agency has helped speed approvals of lifesaving drugs to the market by providing it with the resources to do the work. But advocates for patients and doctors say the agreements have enabled the industry to weaken the approval process meant to ensure that drugs are safe and effective.“It’s kind of like a devil’s bargain,” said Dr. Joseph Ross, a professor at the Yale School of Medicine who has studied F.D.A. policies, “that I think is not in the best interest of the agency, because it turns this every-five-year cycle into the F.D.A. essentially asking industry, ‘What can we do to secure this money?’ ”In recent weeks, the user fee bill in Congress became snagged by added provisions, including over an effort to speed approval of generic drugs that could cut into the big companies’ profits and make the drugs less expensive for consumers and insurers. A key Republican senator and the major pharmaceutical lobby opposed that provision.Versions of the bills in the House and Senate also included a raft of extra proposals that would require annual inspections of infant formula makers and increase oversight of cosmetics, diagnostic tests, dietary supplements and food packaging.Those measures may not survive final haggling over reauthorizing the program in Congress, where the drug and device industries spend hundreds of millions on lobbying and campaign contributions. Senator Richard Burr, Republican of North Carolina and the leading member of the main Senate committee overseeing the agency, opposed the amendment that would allow the F.D.A. to help generic drug makers replicate an off-patent drug with specifics on the ingredients, which for years had tended to be more of a guessing game.The Congressional Budget Office estimated that the generic drug measure could save taxpayers $546 million over 10 years by speeding those versions to market. But Mr. Burr argued that it would hamper innovation and, objecting to another amendment limiting drug exclusivity, voted against the bill in June. In July, he introduced a stripped-down user fee bill to reset negotiations.Senator Richard Burr of North Carolina, a leading member of the Senate committee that oversees the F.D.A., voted against a user fee bill in June.Al Drago for The New York TimesSenator Patty Murray, Democrat of Washington and chairwoman of the Senate committee that oversees the F.D.A., issued a statement Wednesday underscoring the urgency of the moment.“At every single phase in this process, I‘m laser focused on patients—and making sure F.D.A. works for families, not pharmaceutical companies’ bottom lines,” Ms. Murray said. “We absolutely can’t let Congressional inaction force F.D.A. to send out pink slips. But we also can’t, and I won’t, stop pushing for the kind of reforms families need to see from the drug industry and this critical agency.”In committee hearings this summer, senators debated the merits of the user fee program.Senator Bernie Sanders, an independent of Vermont and a longtime critic of the drug industry, suggested that the pharmaceutical companies’ tendency to charge “outrageous” prices was related to their significant role in funding and advancing policy goals of the F.D.A.’s drug division.“So the industry, in a sense, is regulating itself,” Mr. Sanders said during a hearing on June 14 of the Senate Health, Education, Labor & Pensions Committee. “May make sense to somebody — but not to me.”Mr. Burr, a business-focused conservative, complained that the program burdens companies with negotiating with the agency over the fees, which he predicted would rise even higher. He has also complained about how the high costs of the program limit opportunity for small businesses; new-drug application fees are $1.5 million to $3.1 million.“In a perfect world, I hope we would all be here lobbying that there are going to be no user fees paid to the F.D.A. by anybody,” he said during the hearing. Ultimately, the White House and Congress have final say over the agency’s priorities.Even Dr. Robert Califf, the F.D.A. commissioner, acknowledged in a news briefing this summer that the program was not ideal. “Philosophically, I wish the taxpayer paid for all the F.D.A. and there weren’t user fees,” he said.A spokeswoman for the F.D.A. said agency policy prohibited officials from commenting on pending legislation.The user fee program traces its roots to 1992, when AIDS activists pressed the F.D.A. to hasten drug approvals. About a decade later, drugs moved through the pipeline more quickly, averaging about 10 months from roughly 19 months.Over the years, the program’s scope and funding grew. Annual “performance reports” detail the F.D.A.’s efforts to make quick decisions, hold routine meetings with drug companies and approve products under fast-track pathways.User fees were added for medical devices, generic drugs and biologics, which include vaccines and gene therapies. (The tobacco division and its 1,200 employees are entirely user-fee funded, though the industry has no say in how the dollars are spent.) By 2012, drug companies accounted for half of the F.D.A. drug division budget, through fees for new-drug applications and annual payments for approved drugs.“Philosophically, I wish the taxpayer paid for all the F.D.A. and there weren’t user fees,” said Dr. Robert Califf, the F.D.A. commissioner.Anna Rose Layden for The New York TimesDr. Aaron Mitchell, an oncologist and researcher at Memorial Sloan Kettering Cancer Center, recently wrote that the fee program’s policy changes had “favored industry through decreasing regulatory standards, shortening approval times and increasing industry involvement in F.D.A. decision making.”He said he was surprised that user fee negotiations in 1997 led to reducing the number of clinical trials for drug approval to one, from the longtime standard of two trials. He said it was also notable that the 2012 user fee law allowed “fewer, smaller or shorter clinical trials” for therapies for life-threatening conditions.“The faster you’re rushing to approval and the less clinical evidence that you’re requiring,” Dr. Mitchell said, “the greater the chances that you’re going to miss something” that could harm patients.Some F.D.A. drug approvals based on uncertain evidence have proved highly controversial. Medicare refused to routinely pay for the Alzheimer’s drug Aduhelm, citing little evidence of benefit and serious safety risks. Another approval of a medication for a deadly muscle disease — over the objections of agency experts — drew scrutiny when insurers refused to pay for it, calling the therapy “investigational.” The agency issued those approvals on the condition that further study prove a benefit, though such reviews take years to complete.For its part, the F.D.A. said the user fee process had given it authority to improve public health by expanding oversight of foreign drugmakers, allowing hearing aids to be sold over the counter and monitoring drug shortages.The user fee process “revolutionized” the F.D.A.’s drug approval process, Dr. Peter Marks, director of the agency vaccine and gene therapy division, told a Senate panel in April.“It’s not an understatement to say that there are many people with us today who would not be here without the program, which has dramatically reshaped drug development and approval in the United States,” Dr. Marks said.Those testifying from industry groups PhRMA, AdvaMed and BIO, which represents the biotech industry, have noted the program’s value in ensuring the F.D.A. has the staff and technology to review a growing number of rapidly changing gene and cell therapies, novel medical devices and rare-disease therapies. The Pharmaceutical Research Manufacturers of America, known as PhRMA, called the program a “success” and said the funding made the F.D.A. a global leader in approving three-fourths of new medicines before any other nation.The growth of the program “reflects the robust innovation and timely access to safe and effective medicines required for an appropriately staffed and funded F.D.A.,” Priscilla VanderVeer, PhRMA vice president of public affairs, said in a statement.“It’s a great example of a meaningful public, private collaboration to get patients the products that they need,” said Scott Whitaker, president of AdvaMed, which represents medical device makers.Dr. Reshma Ramachandran, a professor of medicine at Yale University, said doctors often don’t recognize the pressure the drug industry exerts over the F.D.A.Christopher Capozziello for The New York TimesThe pace of approvals often appears too hasty for Dr. Sanket Dhruva, a cardiologist and an assistant professor of medicine at the University of California, San Francisco. One cardiac device he recently encountered was approved after a study followed patients for only 30 days and offered no comparison against the standard treatment. It was not enough information for him to use the device on the patients he treats, he said.Generally, he said that doctors could earn more money by adopting the newest technologies and that hospitals liked to advertise them, though clear evidence of safety and effectiveness was often lacking.“What we end up going on is hype,” Dr. Dhruva said.Dr. Mitchell expressed concern that new cancer drugs had been approved using tests that compared a new treatment with a placebo, a practice that F.D.A. guidance has deemed unethical, instead of testing them against standard therapies. That leaves him uncertain whether the new drugs for the cancer patients he treats are better than the old ones.Dr. Reshma Ramachandran, co-director of the Yale Collaboration for Research Integrity and Transparency, said that doctors were not trained to sift through F.D.A. records to scrutinize the quality of the studies that led to approvals. Nor do many recognize the pressure the drug industry exerts on the F.D.A. to meet approval decision deadlines.“And that just seems like the wrong metric to care about,” said Dr. Ramachandran, who has tracked the user fee process and testified to Congress for Doctors for America. “It should be: ‘Are patients healthier? Are patients safe?’ And that just seems like an afterthought.”The latest negotiation cycle over prescription drug user fees involved about 100 meetings between the F.D.A. and drug company representatives and six meetings with groups like Dr. Ramachandran’s.The concerns expressed about the imbalance of access — that the drug and device industries hold outsize sway compared with patient groups and public-interest advocates — have led to calls for Congress to find a way to fully fund the agency through a tax on sales or by federal appropriations.While few see that change as likely, Dr. Mikkael Sekeres, a former F.D.A. oncology adviser who is a professor of medicine at the University of Miami, said that the F.D.A. should match its brisk pace of approvals with a system that could identify problems just as quickly.“They don’t have a good mechanism to monitor the side effects of these drugs once they’re on the market,” said Dr. Sekeres, who recently wrote a book about the F.D.A. “So the post-marketing approval surveillance mechanism isn’t as good as it should be to guarantee the safety of the public.”