For many Americans, the Trump administration’s firing of the head of the Centers for Disease Control and Prevention is about the clash between establishment science and the anti-vaccination movement fronted by Health Secretary Robert F. Kennedy Jr.

But for President Donald Trump, who has embraced the vaccine skepticism of his MAGA base while touting the delivery of Covid-19 vaccines under his first-term Operation Warp Speed program, the fight over Susan Monarez is mostly about stamping out dissent.

While Trump has not spoken about the gutting of CDC leadership — several of Monarez’s deputies resigned after Kennedy announced she had been axed earlier this week — White House officials have defended the move, which was precipitated by Monarez’s refusal to sign off on upcoming vaccine recommendations from a panel that Kennedy stacked with skeptics.

“The president was elected for a reason,” a senior White House official said in a telephone interview with NBC News. “He has a view on all these areas, and he wants to execute on those views. If there are people who don’t believe in democracy, then they shouldn’t be working in a democratic government.”

In that context, the firing of Monarez is part of a larger effort by Trump, his Cabinet and his aides to consolidate power inside the executive branch and at its margins. In many cases, the targets are experts in their fields, people Trump appointed himself or both.

In just the past week, Defense Secretary Pete Hegseth sacked several senior Pentagon officials, Trump has tried to fire Federal Reserve governor Lisa Cook and Surface Transportation Board member Robert Primus, and FEMA staff who signed a letter criticizing Trump’s cuts to the agency have been put on administrative leave.

Monarez, Cook and Primus are all fighting their dismissals.

Some CDC employees see the president as waging a war of political ideology against empirical science.

“This truly feels like the beginning of the end of objective science,” said one CDC employee who spoke on the condition of anonymity to avoid retribution. “I feel physically ill. I used to feel proud to work for CDC, and now I am scared.”

The risk for Trump in shaking up the CDC is as plain as the Covid-19 outbreak that bedeviled him — and harmed the nation’s health and economy — in the final year of his first term: Americans may blame him for shedding expertise if there is another pandemic. Because he is not eligible to run for re-election, any electoral damage would likely fall on the shoulders of fellow Republicans.

One former senior Trump campaign official who works on congressional campaigns said that Trump won’t lose any base support for firing the CDC director but that independent voters may question whether it’s a wise move — especially if another disease rips through the country. That could bolster Democratic criticism of Trump and Kennedy.

“No matter what, let’s say the director was there and there’s an outbreak a month ago, Democrats are still saying RFK is a bats— crazy person,” the former campaign official said. “It doesn’t change the response. It just gives a data point.”

At the same time, there are signs that Trump will get pushback from within his own party over the hollowing out of CDC’s leadership, which included the resignations of Debra Houry, the agency’s chief medical officer; Demetre Daskalakis, director of the National Center for Immunization and Respiratory Diseases; Daniel Jernigan, the director of the National Center for Emerging and Zoonotic Infectious Diseases; and Jen Layden, director of the Office of Public Health Data, Surveillance and Technology.

Sen. Bill Cassidy, R-La., who delivered a key vote in favor of Kennedy’s confirmation after he said he secured a series of promises from Kennedy that amounted to a validation of the efficacy of vaccines, called this week for the postponement of a Sept. 18 meeting of the Health and Human Services Department’s visory Committee on Immunization Practices. That’s the panel at the center of the Monarez story.

“Serious allegations have been made about the meeting agenda, membership, and lack of scientific process being followed for the now announced September ACIP meeting,” Cassidy said Thursday in a statement.

In February, when he voted to advance Kennedy’s nomination to the Senate floor, Cassidy said Kennedy had promised not to reconstitute the panel — which Kennedy has since done.

“If the meeting proceeds, any recommendations made should be rejected as lacking legitimacy given the seriousness of the allegations and the current turmoil in CDC leadership,” Cassidy said in Thursday’s statement.

The White House official said no one should be surprised by Kennedy’s approach to vaccines — or Trump’s desire to make sure that his agenda is not met with resistance at any level.

“Bobby’s view and position on this has been very clear on this the whole time,” the White House official said. “Generally, there’s people buried in government who think they can overrule or defy the will of the elected president.”

Trump chafed at inertia in his first term.

“This is a different administration — it’s being handled differently,” the White House official said. “There’s a belief that, ‘We’re still going to get our person through and it’s going to be good and we’ll resist.’ That’s not a thing.”