In the last few years, foodborne pathogens have had devastating consequences that alarmed the public. Bacteria in infant formula sickened babies. Deli meat ridden with listeria killed 10 people and led to 60 hospitalizations in 19 states. Lead-laden applesauce pouches poisoned young children.

In each outbreak, state and federal officials connected the dots from each sick person to a tainted product and ensured the recalled food was pulled off the shelves.

Some of those employees and their specific roles in ending outbreaks are now threatened by Trump administration measures to increase government efficiency, which come on top of cuts already being made by the Food and Drug Administration’s chronically underfunded food division.

Like the food safety system itself, the cutbacks and new administrative hurdles are spread across an array of federal and state agencies.

At the Food and Drug Administration, freezes on government credit card spending ordered by the Trump administration have impeded staff members from buying food to perform routine tests for deadly bacteria. In states, a $34 million cut by the F.D.A. could reduce the number of employees who ensure that tainted products — like tin pouches of lead-laden applesauce sold in 2023 — are tested in labs and taken off store shelves. F.D.A. staff members are also bracing for further Trump administration personnel reductions.

And at the Agriculture Department, a committee studying deadly bacteria was recently disbanded, even as it was developing advice on how to better target pathogens that can shut down the kidneys. Committee members were also devising an education plan for new parents on bacteria that can live in powdered infant formula. “Further work on your report and recommendations will be prohibited,” read a Trump administration email to the committee members.

Taken together, there is concern in the food safety field that the number of outbreaks could grow or evade detection. By limiting resources, the cutbacks pare back work meant to prevent problems and to focus efforts on cases in which someone was already hurt or killed, Darin Detwiler, a food safety consultant and associate professor at Northeastern University, said. His toddler son died in an E. coli outbreak in 1993.

“It’s as if someone, without enough information, has said, What’s a good way to save money on our automobiles?” he asked. “Let’s just take out the seatbelts and airbags, because do we really need them?”

Robert F. Kennedy Jr., the nation’s health secretary, has a keen interest in food. He has already pledged to get color additives out of food and started an effort called “Operation Stork Speed” to examine the nutritional content and potential toxins in infant formula. Yet some of the most dangerous food problems in recent years have been from pathogens.

Last year, nearly 500 people were hospitalized and 19 died from foodborne illnesses with a known cause, double or more than in the year before, according to the U.S. P.I.R.G. Education Fund, an advocacy group. (Most food poisoning is never reported or traced back to a particular food.)

Government cutbacks affect a number of areas that officials were shoring up to prevent repeats of recent outbreaks. Here are the details of some of the changes:

Key committees shut down

Often in response to a deadly outbreak, a joint F.D.A. and Agriculture Department committee dived into the details to seek ways to improve detection and to limit illness and death. The committee has also examined how to deploy rapidly changing technology — including artificial intelligence and genome sequencing — to protect public health.

The Trump administration abruptly shut down the committee earlier this month, citing the executive order on reducing government bureaucracy. It demanded that work stop for the panel called the National Advisory Committee on Microbiological Criteria for Foods and also for the National Advisory Committee on Meat and Poultry Inspection.

The microbial committee was studying how to more accurately identify infants who would be most at risk from cronobacter sakazakii, the deadly bacteria that contributed to the decision to temporarily shut down an Abbott Nutrition infant formula plant in Michigan in 2022. The committee planned to then provide advice to caregivers who should use sterile liquid formula instead of powdered formula, which is not sterile.

Abby Snyder, a Cornell University food scientist and co-chair of a subcommittee on infant formula, said she was disappointed by the decision to discontinue the committee’s work. “Safety of powdered formula for infants is of critical importance and I think important to most people,” Dr. Snyder said.

The F.D.A. did not respond to a question about whether Kyle Diamantas, its food division chief, was involved in the decision to axe the committee. A former corporate lawyer, Mr. Diamantas worked on cases defending Abbott over claims of harm related to infant formula.

Michael Hansen, a scientist and member of the committee from Consumer Reports, an advocacy group, said his team on the committee was trying to pinpoint certain types of E. coli that were most likely to cause bloody diarrhea and kidney failure, among other efforts.

He said the decision to end the committee was a shock and destroyed almost two years of work on harnessing genomic sequencing — technology that is now widely available and affordable — to limit outbreaks. The team leveraged hours of volunteer work from the top experts in the field, he said.

“It makes no sense that they were getting rid of this committee,” Dr. Hansen said, “because if you want to do a full cost-benefit analysis, all the work that we were doing was actually free of charge.”

Spending freezes

Scientists at the F.D.A.’s product and food testing labs said they were barred from some routine use of their government credit cards because of an executive order backing the efforts of Elon Musk’s so-called Department of Government Efficiency.

An exception has been made for “critical activities,” an F.D.A. spokeswoman said.

That has slowed or stopped some testing of grocery items for hazardous bacteria and monitoring of shellfish and food packaging for PFAS, chemicals linked to cancer and reproductive harm.

Credit cards can be used in an investigation of listeria in frozen supplemental shakes dispensed in elder care homes that have been linked to a dozen deaths. For other work, staff members have encountered red tape, agency scientists said.

“Even hours can matter in an outbreak,” said Susan Mayne, an adjunct professor at Yale School of Public Health and a former F.D.A. food official who had heard from current employees about the situation. “Any delay is unacceptable when you’re dealing with a product that can kill someone.”

Food safety inspections

In a recent letter to lawmakers, F.D.A. officials said that the agency employed about 443 food safety inspectors — far fewer than the agency needed to inspect every food processing facility at the pace Congress mandated. The agency estimated that it would need about 1,500 more workers to inspect 36,600 food facilities, foreign and domestic, once every five years or once every three years for high-risk producers.

At this time, those inspectors are largely exempted from losing their jobs.

However, one team of outbreak investigators is vulnerable, according to Jim Jones, the agency’s food division chief in the latter part of the Biden administration. This team, known as CORE, coordinates with the Centers for Disease Control and Prevention to link a cluster of sick people to a specific food plant or farmer’s field. The team tracks inspections and efforts to ensure that tainted food is removed from store shelves.

Mr. Jones said the team was recently built up as a fully remote operation that would most likely be affected when orders to return to work at federal offices were put in place this month. Workers who live more than 50 miles from an F.D.A. office have until late April to begin working at a federal site.

“So their choices will be you either move so that you can go to a federal facility, or you leave,” Mr. Jones said. “There’s nothing strategic about who gets caught in that pickle.”

Across the F.D.A., inspections plummeted during the pandemic and have not returned to the higher levels before 2020. At the same time, the amount of imported food has risen, including clams that have repeatedly found to be contaminated with PFAS.

Cutbacks to States

Once the F.D.A. identifies a factory that was the source of contamination, it often relies on state inspectors to investigate on site. In criticizing the reductions, Senator Richard Blumenthal, Democrat of Connecticut, pointed out that state inspectors performed about half of the inspections at food processing facilities, 90 percent of the produce safety inspections and all of the retail store visits.

The F.D.A. also turns to state and local public health officials to pluck potentially tainted foods from grocery store shelves and test them at a network of 55 public health labs throughout the United States. If a product is recalled, the state officials also audit grocery stores to be sure the food has been removed.

A move late in the Biden era sharply limited the funding that the F.D.A. sends to states and to the labs that do critical work. The latest $34 million funding reduction applies to states and to those public health labs. The agency said in a letter to Mr. Blumenthal that the cuts were being made because the food division had a flat budget and costs were increasing because of inflation.

Thom Petersen, commissioner of the Minnesota Department of Agriculture, said F.D.A. food safety funding had fallen steadily since 2019, with the latest cut striking deeper and possibly leading to layoffs. He said the funding loss could slow the important work of taking bad food out of stores.

That work proved particularly important after officials discovered extremely high levels of lead in cinnamon in applesauce pouch snacks for children. The F.D.A. ended up sending a warning letter to Dollar Tree over its failure to quickly pull the pouches.

“Timing is the important piece,” Mr. Petersen said. “We want to take care of those and work on that.“

The public health labs reported that the money amounted to about 30 percent of their funding, which helps them respond to outbreaks more quickly than the F.D.A.

In the Boar’s Head listeria outbreak, for instance, lab officials in Maryland and New York bought liverwurst at stores that tested positive for the same strain that sickened people. A trade group for the labs predicted that the budget cuts could delay responses — and lead to more people getting sick.