The recent shakeup within the Centers for Disease Control and Prevention (CDC) under the Trump administration has left many employees stunned and uncertain about the future. Late Friday marked the beginning of a series of dismissals that swept across more than a dozen divisions, affecting critical teams responsible for investigating infectious disease outbreaks, chronic disease management, respiratory disease surveillance, and immunization efforts.

In a surprising twist, the administration has been scrambling to reverse some of these terminations, adding another layer of confusion to an already tumultuous situation. This upheaval coincided with the second week of a government shutdown and is seen as part of President Trump’s broader agenda to reduce the size of the federal workforce. Administration officials have pointed fingers at Democrats, suggesting these actions are meant as a reprisal against them.

Yet in an apparent reversal, the administration has been racing to rescind some of those firings, leading to even more confusion. 

The moves came in the second week of a government shutdown and are part of President Trump’s efforts to slash the government workforce. Top administration officials blame Democrats and say the firings are meant to punish them. 

Trump said at the White House last week that the firings, which are not typical during a shutdown, would target primarily “Democrat” programs.  

“HHS employees across multiple divisions have received reduction-in-force notices as a direct consequence of the Democrat-led government shutdown,” Health and Human Services (HHS) spokesperson Andrew Nixon said in a statement Friday. 

“All HHS employees receiving reduction-in-force notices were designated non-essential by their respective divisions. HHS continues to close wasteful and duplicative entities, including those that are at odds with the Trump administration’s Make America Healthy Again agenda.” 

Here’s what to know: 

More than a thousand fired; hundreds brought back 

The Trump administration said in court filings Friday that about 4,200 federal employees across seven different agencies would begin receiving reduction-in-force notices. An estimated 1,100 to 1,200 employees from the Department of Health and Human Services are expected to be affected. 

The notices were emailed shortly after 9 p.m. EDT on a holiday weekend. 

The American Federation of Government Employees (AFGE) Local 2883, which represents workers at the CDC’s Atlanta headquarters, said the HHS fired more than 1,300 CDC federal employees during the government shutdown, citing retaliatory reasons for their removal.  

But within 24 hours of receipt of the original reduction-in-force notices, around 700 employees received emails rescinding their terminations. The administration claimed these employees were “mistakenly” placed on notice because of a coding error.  

Before Friday’s cuts, there were 11,400 employees at the CDC.  

Among the people who were initially fired and then brought back were leaders in the Global Health Center, including all six of the CDC’s regional offices around the world; the team that produces the Morbidity and Mortality Weekly Report; and some of the Epidemic Intelligence Service (EIS) employees, known as “disease detectives.” EIS employees are typically the first responders in an outbreak. 

Gutting public health  

“This Administration continues to destroy critical pillars of America’s already wounded public health system,” said Richard Besser, a former acting director of the CDC. “Using a government shutdown as a pretense to fire hundreds of critically important health officials and thousands of additional government staffers is the height of cruelty and recklessness. The damage this will do to our nation is incalculable.“ 

A coalition of infectious disease expert organizations, led by the Infectious Disease Society of America, said in a statement that targeting the CDC’s core functions and scientific leadership “will cripple the agency that keeps our country safe by monitoring and preventing disease and saving lives in every community across the country.”    

“Uncertainty around which staff have been fired or rehired leaves health professionals and the public in a state of complete confusion about which longstanding public health services they can rely upon,” the groups said. 

The damage to the CDC has been wide-ranging and far from consistent.  

“Did they really not know they were firing the people tracking Ebola? Did they not care enough to find out who they were firing and what they did before sending termination letters?” said Gregg Gonsalves, Coordinating Committee member of the Defend Public Health network.   

The CDC’s entire Washington, D.C., office was eliminated, which may alarm lawmakers. Agency officials describe that office as the conduit for congressional briefings and congressional inquiries.   

Leadership eliminated 

Some divisions have been left untouched, while others have had their leadership eliminated, according to Debra Houry, who was the agency’s chief medical officer before she resigned in protest in August. 

Houry said the agency’s ethics office was completely eliminated.  

“The secretary has talked about conflicts of interest, and the ethics office is the one that reviews all CDC leaders and advisory committees for conflicts of interest. So you think that would be an office they would want to keep,” Houry said. 

Some divisions were protected by a court injunction stemming from earlier firings, though there will be new lawsuits over the latest round of layoffs.  

CDC has been a target 

The CDC has been in tumult since HHS Secretary Robert F. Kennedy Jr. was sworn in as head of the department.   

Kennedy has been highly critical of CDC staff, and the agency previously lost about a third of its staff to massive layoffs in April. The latest round of firings came about a month after Kennedy in a congressional hearing called for “new blood” at the CDC.  

In August, a gunman fired more than 500 rounds at buildings on the agency’s primary Atlanta campus, killing a police officer. Weeks later, Kennedy ousted then-agency Director Susan Monarez after less than a month on the job, installing one of his top deputies as her interim replacement.  

There has been little information publicly released by the HHS since the firings began. The Hill has reached out to the department for comment. 

“The carelessness and callousness with which this administration handles life and death matters is unbelievable. The CDC was already decimated earlier this year, and those who were left behind work every day to protect us all. If these new firings aren’t all reversed, people are going to suffer and very likely some will die,” Gonsalves said. 

Houry said she doesn’t trust that the people who were brought back are safe from further reductions. 

“I would be concerned that these are areas that, should HHS do a reorganization, they may be looking at changes [to the impacted offices and divisions],” Houry said. “If they wanted to look at restructuring, I think those could be potentially early signals.” 

One newly fired agency employee said they had been bracing for a layoff notice ever since Trump’s budget request called for eliminating many of the agency centers. 

“It’s been a rollercoaster,” the employee said.