The outcome was heralded for years as a victory for public health work. But earlier this month, Massachusetts officials received notification that the entire staff of the federal lab had been laid off, erasing a significant node in the nation’s network to identify and track public health threats, state officials said.

As the Trump administration reshapes how the federal government finances and communicates scientific findings, Massachusetts’ health laboratory is now at a crossroads, facing dramatic changes to its mandate and uncertainty over its future. The state is in a legal battle to protect nearly $84 million in federal funding the Trump administration is trying to claw back. Meanwhile, the state could face other significant additional cuts in Congress’ coming budget. While all of this is unfolding, the lab’s staff is struggling to figure out how to perform in-house work the feds used to reliably handle.

Congress’ budget could force some public health programs to shutter, but how widespread the cuts will be remains unknown, said Dr. Robbie Goldstein, the state’s public health commissioner.

“We can’t put anything on an untouchable list right now,” he said as he joined leading DPH staff on a recent visit to the lab building. “That’s not the happy answer the folks in this room wanted to hear.”

At stake, health officials said, is their ability to mount a well-informed, nimble response to public health challenges. Operating without the CDC’s full partnership is akin to being blindfolded.

“With their limited presence, we are limited in our understanding of what’s going on, even around us in our neighboring states,” said Nicolas Epie, the lab’s director.

The federal Department of Health and Human Services in a statement to the Globe described the layoffs and lab shutdowns as part of a streamlining effort that will ultimately strengthen the CDC.

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The Massachusetts Public Health Laboratory is the hub of the state’s public health work. Doctors, hospitals, and health officials statewide look to it for information about the germs, environmental contaminants, or food borne illnesses that might have made someone sick, how best to treat them, and what they mean for the health of the rest of the state. Each year, roughly 300,000 samples pass through the lab, tracking illnesses such as HIV, tuberculosis, avian flu, and COVID-19.

The lab is housed in a scaffolding-encased brutalist office tower in Jamaica Plain, where more than 400 epidemiologists, virologists, chemists, microbiologists and other workers help assemble microscopic clues into a coherent picture of the state of health in Massachusetts. During a visit to the lab in April, workers said they were trying to maintain a stoic focus despite the news from Washington.

“It doesn’t matter what’s going on in the country,” said Erika Buzby, a veteran microbiologist and supervisor of the 8th floor molecular biology lab. “We just have to keep going.”

One floor beneath, workers carried racks filled with dozens of samples for inspection in the sexually transmitted infections lab, the same one responsible for identifying the worrying gonorrhea infections. Next door, behind a door warning of biohazards, staff hunkered over counters to review the results of tuberculosis bacteria analysis. Cases of TB, a bacterial infection of the lungs, increased by 13 percent in Massachusetts in 2024 compared to the year before.

“Samples are coming from a lot of the hospitals all over the Commonwealth,” said Bernie Chirokas, director of sexually transmitted diseases and mycobacteriology.

Workers here raise their voices to be heard over the loud droning of air coolers that keeps machines operating smoothly.

“It’s the constant hum of public health,” said Goldstein. “What we’re nervous about is that we will be silenced here.”

The $84 million for the lab is what remains from an almost $776 million CDC grant allocated in 2019 that was expected to last into 2026.

That money is supposed to help pay for data system modernization, supply stockpiles and upgraded equipment, a needed compliment to a multi-year renovation project nearing conclusion. Near the top of the wish list is a biosafety cabinet that protects staff from samples of infectious agents. The current cabinet is so old executives fear just moving it during the renovations could break it, putting workers at risk.

The lab’s grant makes up the bulk of the more than $105 million in CDC funding for Massachusetts public health services that is at risk, according to a DPH affidavit shared with the Globe. The Trump administration announced March 26 it intended to reclaim the money by April, saying it was no longer needed because the pandemic was over. It’s loss, though, would hobble programs supporting community health, children’s vaccinations, and addressing health disparities. Nearly $5 million for substance use programs from a different federal agency is also in jeopardy.

One example of the lab’s recent pivot toward self-sufficiency is a new viral genetic sequencing program to track how different strains of hepatitis C are spreading. It’s a service the CDC used to perform through another program kneecapped by layoffs this month, according to a notification state officials received from the CDC on April 3. Massachusetts set aside funding for the testing program well before Trump’s election in part, Goldstein said, because the state foresaw what another Trump presidency might mean for public health. President Trump and Robert F. Kennedy, Jr., who now leads HHS, had campaigned on promises to shake up public health institutions.

“We didn’t know which way the November election was going to go,” said Goldstein, who worked for the CDC before joining state government. “We had to prepare for what could be a very friendly environment for public health and continued investment, or a very hostile environment.”

Another attempt to replicate federal functions locally is a proposed program to recommend vaccinations for adults and a fund to help purchase them.

To be sure, Massachusetts health leaders acknowledge the state’s lab alone can’t fully replace federal public health resources. And there are challenges ahead without an established communication workflow between various health leaders across the nation to share intel and spread warnings.

Avian flu gets attention as a possible threat, but experts said a novel virus isn’t the only worry when it comes to what public health crises may lie ahead.

“It could be a food borne pathogen,” said Dr. Larry Madoff, medical director of the bureau of infectious disease and laboratory sciences. “It could be a mosquito borne pathogen.”

“I’m actually worried about the every day suspects,” said Catherine Brown, state epidemiologist and public heath veterinarian, “measles, or the increase of tuberculosis cases that we’re seeing, drug resistant gonorrhea, or the EEE (Eastern Equine Encephalitis) outbreaks that we have regularly in Massachusetts.”

Tackling an outbreak, whether a new virus or an old foe, without the resources and reach of some cancelled CDC programs is intimidating, said Epie, the lab’s director.

“The world is not as compartmentalized as it was before,” he said. “We cannot protect ourselves without ever knowing what’s going on in other countries as well.”

Jason Laughlin can be reached at jason.laughlin@globe.com. Follow him @jasmlaughlin.