The winner of this week’s presidential contest, regardless of the outcome, will be faced next year with the challenge of leading agencies whose reputations have suffered badly during the pandemic under the direction of President Donald Trump.

Two agencies in particular, the Centers for Disease Control and Prevention and the Food and Drug Administration, have been among the most high-profile during the COVID-19 pandemic, and have also been among the most heavily politicized, scrutinized, and criticized — even by Trump himself.

Polling shows that the public trusts the CDC less now than at the beginning of the pandemic. The same polling finds worries the FDA is facing political pressure on vaccine approvals.

[Experts: Public trust in science, data key to COVID-19 vaccine credibility]

Experts say that in order to rebuild trust in agencies like the FDA and CDC, they need to act independently, show a commitment to science and be transparent in their decision-making.

“Trust is tested during any national health emergency. Trust can be repaired and maintained through consistent, honest, and direct communication, daily publicized briefings, and laying out simple steps that everyone can take to protect themselves, their families and communities,” said Tom Frieden, a former CDC director and director of Resolve to Save Lives, a global health initiative.

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From April to October, the percentage of people reporting trust in the CDC dropped from 83 percent to 72 percent, according to the Kaiser Family Foundation’s health tracking poll.

The survey didn’t ask about the FDA earlier this year, but as of October, there was a similar level of confidence, with 71 percent saying they trust the agency to ensure a COVID-19 vaccine is safe and effective.

Around half of the country sees Trump as interfering in the work of the FDA and CDC. More than 60 percent say they are worried a vaccine may be rushed. And while trust in the CDC has fallen among Democrats, given the perception of political interference, it has dropped even more sharply among Republicans.

“I think what we’re seeing with declining Republican trust in the CDC is a reflection of President Trump’s public statements calling CDC leaders and CDC guidance into question,” said Liz Hamel, Kaiser Family Foundation’s director of public opinion and survey research. “Trump is by far the most trusted source of coronavirus information for Republicans.”

But that’s a problem when Trump, according to a study by Cornell University researchers, is the biggest source of misinformation about the virus.

The Trump administration contends that its decisions were based on science, and that the president listens to the experts. But Trump routinely contradicts leaders of the CDC, FDA, National Institutes of Health, and others during press briefings or campaign speeches. In contrast, former Vice President Joe Biden has pledged to listen to scientists and let their expertise guide his pandemic response.

“Even when the health officials were saying the right things, publicly, that medically made sense and were in line with the science, the politicians got in the way and said something very different,” said Georges Benjamin, executive director of the American Public Health Association.

Medical providers and other public health experts also have been forced to question the decision-making of the agencies they often rely upon. In order to win back public trust, the agencies also should focus on doctors and local health officials, said former Baltimore Health Commissioner Leana Wen, a professor of public health at the George Washington University.

“Whatever administration comes in, they need to first convince those of us who are experts in this field, because right now we don’t trust the decisions that are coming out of the administration,” she said.

In addition to mixed messages sowing confusion among health practitioners, there is also a risk that the frequent controversies could inspire non-political career scientists to take their expertise elsewhere.

“If you start to allow the expertise to dwindle, or if you sort of do things that begin to erode trust, then you have, I think, a really potentially big problem where you won’t get people to do the things that need to be done,” said Stephanie Zaza, president of the American College of Preventive Medicine, formerly a longtime medical officer at the CDC.

Credibility concerns

A commitment to transparency also could help the public understand that decisions are being made for public health reasons rather than political reasons. Political appointees reportedly tried to edit scientific CDC reports presenting data that wouldn’t make the administration’s response look good.

Around the same time, the CDC updated testing guidance that would have resulted in fewer people being tested. Given frequent statements by Trump that the United States was testing too much and that that was making the numbers look worse, the guidance change was met with extreme skepticism. Later, the CDC pulled off its website guidance that suggested infectious particles could linger in the air for long periods — a finding that would make it harder to justify reopening indoor spaces like restaurants and gyms.

Naturally, questions arose about whether the agency’s changes were truly based on new scientific knowledge or if they were politically motivated.

“The guidance sort of comes out and everybody reads it, and you don’t seem to be hearing the why,” said Josh Sharfstein, a vice dean of the Johns Hopkins University Bloomberg School of Public Health. “The explanation should come with it: ‘Here is what we’ve learned that’s new, and here’s what we’re doing based on that knowledge.’”

That kind of messaging could be particularly important once COVID-19 vaccines are approved. The public will need to understand that new information about their safety and effectiveness will come to light once more people begin taking them.

“You’re going to have to be flexible. That adds to the challenge, which is really why you do want to be transparent about these sorts of issues,” Sharfstein said.

The FDA and CDC have different missions, and will likely take different approaches to restoring any credibility that’s been lost.

Sharfstein, also a former deputy FDA commissioner, said the FDA is more used to confronting outside interference, given the powerful industries that it regulates, including pharmaceuticals, food and tobacco. For much of the pandemic, the agency has been clouded by murky communication around the issuance of emergency use authorizations for potential COVID-19 treatments that had minimal evidence supporting their use.

But in recent weeks, Sharfstein and others say that Commissioner Stephen Hahn has helped demonstrate more independence, making clear that a vaccine is going to go through rigorous approval standards without outside pressure, and letting career officials speak out about the process as well.

“He hasn’t gotten in the way of his own career scientists, who have committed themselves, and in some cases even written publicly, about the rigor of the procedures that they’re going to use,” said Daniel Carpenter, a government professor at Harvard University who studies the FDA and its history. “And that, I think, has been really crucial.”

The CDC is less accustomed to the kind of pressure it has been faced under the Trump administration, according to Sharfstein and Zaza. To help fix that going forward, Zaza said, the agency needs a leader who can say: “‘This is what we know, and this is what we need to be doing,’ and to not back away from that, those hard truths.”