President Donald Trump’s new choice to lead the US Food and Drug Administration (FDA) faces a tough road ahead, after several foodborne illness outbreaks this summer left many Americans sick and frustrated with their government.

Trump has picked White House aide and doctor Heidi Overton to lead the agency. But former and current FDA officials fear the Trump ally will prioritise loyalty to the president over rebuilding an agency that has lost much of its leadership and many members of staff.

“She’s taking over an agency where the morale is low,” said John Swartzberg, a professor emeritus of infectious diseases UC Berkeley’s School of Public Health. “This is going to be very difficult for her to improve.”

She was nominated to the post after a particularly bad summer of foodborne illnesses. While such outbreaks occur each year, when warmer conditions fuel growth of bacteria, experts say the cyclospora infections have been unprecedented and health officials have seemed slower to identify contamination issues.

She must be confirmed to the post by the Senate. No date for her hearing has been set.

This summer, the US saw over 17,000 confirmed cases of explosive diarrhoea caused by cyclospora – linked to lettuce from Taylor Farms – up from 1,180 cases last summer. There have also been outbreaks of E. coli and salmonella from alfalfa sprouts, eggs, jalapenos, frozen blueberries and a number of other products.

The recalls have left Americans baffled about what is safe to consume, as public health experts say the slow response to the outbreaks is a symptom of a depleted FDA.

“People are definitely upset about the outbreaks this summer, and they have a reason to be,” said Sarah Sorscher, a food safety advocate with nonprofit Center for Science in the Public Interest.

“This is already a system that was teetering on the brink, and the cuts from the past year and the disruptions from the past year are pushing it over the edge.”

The Health and Human Services department contests this.

“The Trump Administration has mounted a robust response to each outbreak,” a spokesperson said.

“FDA has the staff needed to continue investigating outbreaks, as no FDA investigators were affected by staffing changes or reductions in force.”

While some Americans are willing to give Trump’s new FDA leader a shot, others worry the Trump administration’s policies at the FDA have put their health at risk this summer.

Texas resident David Hargrave is on edge after having had diarrhoea every single day for the past month and a half, since the 59-year-old contracted cyclospora around the Fourth of July.

“It puts the scare into you,” Hargrave said about knowing what to eat.

Food regulation experts say that a major contributing factor in these outbreaks has been deep cuts at the FDA, which they say has led to fewer food inspections and poor communication about outbreaks.

“If we had had better boots on the ground in that [cyclospora] outbreak, we could have potentially solved it,” Sorscher said.

In the case of cyclospora, the US Centers for Disease Control and Prevention (CDC) issued its first health alert on 14 July, 10 weeks after the first cases began in early May.

“It’s resulted in a public that’s a little more on edge and panic about what’s going on because of the poor communication,” said Jerold Mande, a former FDA and USDA official and a professor of nutrition at Harvard TH Chan School of Public Health.

Toby Davis got the parasite too after eating at Taco Bell, sending him to the emergency room.

Davis said he knows foodborne outbreaks happen every summer, but he believes the firings of agency workers with years of expertise slowed down the response to the parasite that sickened him and thousands of others.

“This is the result of those bad mistakes,” the independent voter said. ” Do I believe we’ll contract more things from their negligence? Absolutely.”

Even some supporters of the current health agenda are wary about whether the Trump administration cuts were helpful. Jacqueline Capriotti, who identifies with the “Make America Healthy Again” (MAHA) movement started by Health Secretary Robert F Kennedy Jr, said food safety must be a priority for the FDA.

“We’re encouraging – ‘eat real food’ – well we have to make sure that that food is safe,” Capriotti said, referencing Kennedy’s nutritional message to Americans.

The FDA has been without a commissioner for nearly 3.5 months, after former leader Marty Makary resigned over a reported clash with the White House. Makary had reportedly refused to support Trump’s plan to lift a ban on flavoured vapes, over concern it would encourage addiction amongst youths. Soon after his exit, several senior leaders also left the agency.

The wave of departures follows deep staffing cuts the previous year, when Health Secretary Robert F Kennedy fired 20% of employees at the FDA as part of the administration’s widespread efforts to slash the civil service.

For years, many food scientists and health activists have tried to argue for more FDA funding, not less. And the cuts and leadership uncertainty have not helped fuel trust in the organisation that is in charge of regulating 80% of America’s food supply.

Trump has praised Overton, a former general surgery resident at Johns Hopkins University School of Medicine and chief policy officer at conservative think tank America First Policy Institute, as a “rockstar” future leader of the FDA.

But her nomination to the top job comes at a time where Trump officials are attempting to take steps on a number of controversial issues regulated by the agency, including vaccines and abortion medication.

As an insider in Trump’s orbit, some public health experts, including Swartzberg, are afraid she will put his agenda first, and the science second.

In a statement to the BBC, White House spokesperson Kush Desai said Overton “has been integral to ensuring that the Administration’s policies are correct, consistent, and grounded in Gold Standard Science.

“The White House looks forward to her swift confirmation by the Senate.”

But to be confirmed, Overton must first get the support of the Senate’s health committee, chaired by Republican Senator and doctor Bill Cassidy. It’s unclear whether Cassidy will back the president’s pick, after he expressed “strong concerns” about Overton because of her support for Trump’s orders to overhaul the childhood vaccine schedule.

Her nomination is also viewed sceptically by some in MAHA movement, because of Trump’s order to increase domestic production of glyphosate, which they argue causes cancer.

One prominent MAHA influencer, Alex Clark, took to social media last week to accuse Overton of being heavily involved in the executive order, an allegation the White House denies.

Yet Capriotti said some in the movement were too quick to raise concerns.

“She’s a well-respected doctor,” Capriotti said. “I would like to give her a chance.”