The federal government shutdown has suspended key scientific operations—including FDA application processing, EPA inspections, NIH and NSF grant reviews, CDC reporting, and OSHA enforcement—resulting in significant delays for laboratories.
As of October 1, 2025, a lapse in federal funding has forced many U.S. science-relevant agencies to curtail nonessential operations, leaving laboratory leaders to manage uncertainty, delays, and compliance risks.
What’s Happening Across Agencies
Lab Manager reported that the FDA warned that “new drug, biologics, and device applications that require user fees are not being accepted during the shutdown.”
In an official message, FDA Commissioner Marty Makary, MD, MPH, stated that while “many employees will be furloughed during the lapse period,” the agency will “continue to fully execute our public health mission to the extent permitted by law.”
FDA Commissioner Marty Makary, MD, MPH, noted in the FDA’s official message, “I am disappointed that Congress failed to reach a budget agreement. As a result, the FDA is now faced with a lapse in appropriations and will be forced to shut down certain operations of the agency.” (Photo credit: FDA)
The Los Angeles Times reported that EPA will see a sweeping reduction in capacity, with nearly 90 % of its workforce being furloughed.
Lab Manager also reported that new permits, inspections, and compliance enforcement are largely frozen.
HHS Contingency Plan
Under the HHS contingency plan, which covers NIH, CDC, and other health agencies:
Out of ~79,717 employees, 32,460 are estimated to be furloughed under the plan.
HHS will continue only “exempt or excepted” activities, such as outbreak monitoring by CDC and “core functions” at the FDA.
All non-exempt NIH extramural research, grant oversight, and data collection will be suspended.
The Occupational Safety and Health Administration (OSHA) has largely ceased routine enforcement and consultation activities during the shutdown, with only emergency inspections continuing. According to Lab Manager, the agency has suspended “most programmed inspections and compliance assistance,” retaining only personnel necessary to respond to “imminent danger situations” and fatalities. This means laboratory safety programs will receive no regular oversight until funding is restored, placing greater responsibility on lab leaders to maintain compliance and documentation internally.
Key Impacts for Laboratory Leaders
While grant proposals may still be submitted in some cases, their review and processing are stalled, according to Lab Manager. Further, labs awaiting FDA approvals or oversight (e.g. for devices, reagents, protocols) may see deliverables and timelines move unpredictably.
Without regular EPA permitting, inspections, or enforcement, labs that rely on environmental permits must sustain internal compliance vigilance in the absence of federal oversight.
Agencies that supply routine safety, epidemiological, or environmental data are scaling back to minimal essential operations, potentially leaving labs with delayed access to critical datasets.
In many agencies, core capabilities are cut to only those functions required to protect human life or property.
What Lab Leaders Should Do Now
Revisit project timelines: Recognize that regulatory submission dates, funding disbursements, and permit cycles may shift.
Document internal compliance: Maintain logs, audits, and safety checks independent of federal interaction.
Communicate with stakeholders: Funders, collaborators, and regulatory bodies should be notified of possible delays.
Prioritize essential operations: Identify which experiments, sample storage, or assays must continue even under constrained oversight.
Monitor agency updates: Shutdowns evolve, and agencies may alter which functions are considered “essential” or “excepted.”
With recruitment pressures mounting, national pathology societies are aligning on a unified approach that could benefit both applicants and clinical lab leadership.
Laboratory leaders play a central role in shaping the future pathology workforce—not only through daily operations and training, but by supporting broader efforts that impact recruitment, equity, and retention across the field. As workforce challenges continue to affect many institutions, a new joint statement from the College of American Pathologists (CAP) and 12 other national pathology organizations highlights an important step forward: standardizing the fellowship recruitment process across subspecialties.
“Our residents and fellows deserve a recruitment process that puts their needs first,” said CAP President Donald S. Karcher, MD, FCAP.
“By supporting this match effort, we’re advancing fairness, transparency, and a more unified future for our profession,” noted Donald S. Karcher, MD, FCAP. (Photo copyright: GW Cancer Center.)
Spearheaded by the Association for Academic Pathology (AAPath) Fellowship Directors Committee, the joint statement recommends participation in the 2027 match cycle, placing fellows into programs for the 2028–29 academic year. Several subspecialties—including Hematopathology, Molecular Genetic Pathology, and Forensic Pathology—have already committed to joining by the 2026–27 cycle.
Future Workforce Planning
For clinical lab leaders involved in workforce planning, aligning recruitment timelines may offer benefits such as improved coordination, greater equity for applicants, and a more structured approach to fellow selection. Survey data cited in the joint statement indicate that “a substantial majority (~85%) of trainees desire a standardized timeline for fellowship recruitment,” with a similar percentage of program directors supporting broader interview opportunities before applicants make decisions.
Additionally, programs that bypass a coordinated process “are discouraged from asking for a commitment from any applicant before the common date chosen by the subspecialty”—a recommendation designed to curb early-offer dynamics that “harm, or perceive harm,” to programs aligned with the common timeline.
CAP emphasizes that this move is part of its larger workforce strategy. “This initiative builds on its broader advocacy to improve training, recruitment, and retention across the specialty,” the organization stated.
Given ongoing concerns about trainee experience and consistency across programs, clinical laboratory leaders may be encouraged to support efforts that promote fair and sustainable fellowship recruitment practices across pathology subspecialties.
New AI tool doubled efficiency in busy university radiology department
Creative artificial intelligence (AI) solutions are being developed to address critical staffing shortages in radiology that could help with similar shortages in overworked pathology and clinical laboratories as well.
In a recent clinical study at 11-hospital Northwestern Medicine, researchers developed a new generative AI radiology tool to assist radiologists that demonstrates high accuracy and efficiency rates when working with multiple types of imaging scans.
For the study, approximately 24,000 radiology reports were analyzed and then compared for clinical accuracy with and without the AI tool. The tool evaluates an entire scan and generates a report that is 95% complete and personalized to each patient. A template based on that report is then provided to radiologists for review, according to a Northwestern Medicine Feinberg School of Medicine news release.
The study reported an average 15.5% increase in radiograph efficiency without compromising accuracy. Some radiologists even produced gains as high as 40%. The radiology reports were scrutinized during a five-month period last year and enabled radiologists to improve the time it took to return a diagnosis.
“This is, to my knowledge, the first use of AI that demonstrably improves productivity, especially in healthcare. Even in other fields, I haven’t seen anything close to a 40% boost,” said the study’s senior author Mozziyar Etemadi, MD, PhD, assistant professor of anesthesiology and biomedical engineering at Northwestern University McCormick School of Engineering, in the news release. (Photo copyright: Northwestern University.)
Doubled Efficiency for One Radiology Team
“For me and my colleagues, it’s not an exaggeration to say that it doubled our efficiency. It’s such a tremendous advantage and force multiplier,” said study co-author Samir Abboud, MD, emergency radiology in the department of radiology at Northwestern Medicine, in the news release.
“Having a draft report available, even before it is viewed by the radiologist, offers a simple, actionable datapoint that can be quickly and efficiently acted upon” added study senior author Mozziyar Etemadi, MD, PhD, assistant professor of anesthesiology and biomedical engineering at Northwestern University McCormick School of Engineering, in the news release. “This is completely different than traditional triage systems, which need to meticulously be trained one by one on each and every diagnosis.”
The AI tool can also alert radiologists to life-threatening conditions.
“On any given day in the ER, we might have 100 images to review, and we don’t know which one holds a diagnosis that could save a life,” Abboud said. “This technology helps us triage faster—so we catch the most urgent cases sooner and get patients to treatment quicker.”
Relying on In-house Data
Engineers at Northwestern developed the AI model using clinical data within the university’s own network, emphasizing that such tools can be created without assistance from other organizations.
“Our study shows that building custom AI models is well within reach of a typical health system, without reliance on expensive and opaque third-party tools like ChatGPT,” Etemadi noted.
The Journal of the American College of Radiology states the supply of radiologists is expected to increase by approximately 26% over the next 30 years. However, the need for radiologists is expected to grow between 17% and 27% over the same period. Becker’s Hospital Review reports there will be a shortage of up to 42,000 radiologists in the US by 2033.
Some health organizations are using a mixed model of permanent employees and contracted radiologists to meet the increasing demand for services. Others are also looking at options such as internal training programs, better benefits for workers, teleradiology, and remote radiologists to fulfill radiology needs.
“You still need a radiologist as the gold standard,” Abboud said. “Medicine changes constantly—new drugs, new devices, new diagnoses—and we have to make sure the AI keeps up. Our role becomes ensuring every interpretation is right for the patient.”
Can pathology practices and clinical laboratories learn from radiology’s situation? Development of AI solutions for those fields would likely have similar effects on workloads and overworked personnel.
Exploring the benefits of AI may be one way of helping meet clinical laboratory and pathology practice staff shortages.
Some of the former employees worked for public health labs involved in tracking HIV, hepatitis, and STDs
More than 450 federal employees who were laid off from the Centers for Disease Control and Prevention (CDC) during the April cutbacks are being reinstated by the Department of Health and Human Services (HHS).
Nearly half (214) worked for the National Center for HIV, Viral Hepatitis, STD, and Tuberculosis Prevention (NCHHSTP), which includes specialized public health laboratories. Another 158 worked at the National Center for Environmental Health (NCEH). Others were employed by the Immediate Office of the Director and Global Health Center.
“I think people are very tacitly hopeful that this means they can get their jobs back and continue serving in ways that they love,” NCEH health scientist Kathryn Sisler, MPH, told NPR. “But there has been so much instability and chaos that I think a lot of people would hesitate to say it is good news.”
Sisler, who works in NCEH’s Division of Environmental Health Science and Practice, received an email notification of her reinstatement on June 11, NPR reported.
She described the rehiring as “a step in the right direction,” but noted that she was among some employees in her division who had moved away from Atlanta, where the CDC is based. “Other employees had taken other jobs or had been offered them,” NPR reported.
In an interview with NPR, Scott Becker, CEO of the Association of Public Health Laboratories, admitted to being “happily flabbergasted” to hear about HHS’ offer to rehire the former federal workers. (Photo copyright: Association of Public Health Laboratories.)
Impact at Critical Labs
As part of the cutbacks, the CDC shut down two laboratories at NCHHSTP that were involved in tracking viral hepatitis and sexually transmitted diseases, even as “some of those scientists performed disease surveillance work unlike any other labs in the world,” NPR noted.
NCHHSTP staffers told NPR that some of the division’s labs were damaged due to the “lapse in activity” during April and May, and that “some disease outbreaks had not been properly tracked.” One employee said that, due to the cutbacks, the division’s hepatitis lab was unable to assist health workers tracking a hepatitis C outbreak in Florida. The CDC employees requested anonymity.
“It’s great to see that there is some recognition of the importance of these workers and that being in those positions is critical for the public health of America and that they are being reinstated in order to continue their important work,” Carmen J. Marsit, PhD, of Emory University’s Rollins School of Public Health, told NPR. He added, however, that “there’s still a lot of people that are not being reinstated.”
HIV Not Being Tracked
KFF Health News reported that the reinstatements included “dozens of HIV experts” who were laid off in April. At the time, they were working on a national survey conducted among 30,000 individuals at risk of acquiring the infection. They haven’t been told if the project will resume.
Public health departments use data from the survey as part of their efforts to reduce spread of the disease, KFF Health News stated, noting that “preventing HIV is far cheaper than treating people once they’re infected.”
Since the cutbacks, many HIV researchers at CDC have obtained new jobs or moved. Some employees “called the reinstatements perplexing because the notices don’t say what they’ll be doing when they return and for how long,” KFF Health News reported.
“I am concerned about how many of the people have already moved on or might move on and the trauma that they really must be going through with the uncertainty,” Scott Becker, CEO of the Association of Public Health Laboratories, told NPR about the reinstatements at CDC. “But all in all, it’s good news and I’ll take it.”
Programs Cut by Mistake
The reinstatements amount to approximately 20% of the 2,400 CDC employees laid off following the March 27 announcement of a massive restructuring at HHS.
HHS secretary Robert F. Kennedy, Jr. told ABC News in early April that some programs had been cut by mistake. “Personnel that should not have been cut were cut—we’re reinstating them, and that was always the plan,” he said.
In May, Kennedy said that 328 employees of the CDC’s National Institute for Occupational Safety and Health (NIOSH) would be reinstated, NPR reported, following “considerable pushback from labor organizations and congressional lawmakers.”
NPR and other outlets had earlier reported that HHS planned to cut at least 900 NIOSH employees, amounting to 90% of the institute’s workforce.
Industry commenters point to a void since the federal government shuttered the Clinical Laboratory Improvement Advisory Committee
For readers wondering what has happened to the Clinical Laboratory Improvement Advisory Committee (CLIAC), the bottom line is the panel has been terminated, causing a significant void for the lab industry at the federal level.
Dark Daily’s sibling brands, including The Dark Report, G2 Intelligence, and Today’s Clinical Lab, have been exploring various aspects about the demise of CLIAC.
The Centers for Disease Control and Prevention (CDC) confirmed to G2 Intelligence that CLIAC was terminated as of March 31, citing an executive order from President Donald Trump intended to reduce federal advisory committees. The decision blindsided even those closest to CLIAC. Incoming committee chairman Jordan Laser, MD, revealed in an email to colleagues that he did not have more insight into CLIAC’s demise beyond media reports, G2 reported.
Since its founding in 1992, CLIAC has played an influential—though non-regulatory—role in shaping updates to the Clinical Laboratory Improvement Amendments of 1988 (CLIA). The committee brought together pathologists, lab directors, public health leaders, and representatives from federal agencies such as the CDC, Centers for Medicare and Medicaid Services, and Food and Drug Administration.
The federal government’s decision to eliminate CLIAC “risks stalling progress in laboratory medicine, which could ultimately hinder efforts to improve patient care,” CAP President Donald Karcher, MD, FCAP, told The Dark Report. (Photo copyright: College of American Pathologists.)
‘Critical Venue’ for Labs Has Been Eliminated
Industry groups are sounding alarms about what comes next. In an interview with Today’s Clinical Lab, Anthony Killeen, MD, PhD, president of the Association for Diagnostics and Laboratory Medicine (ADLM), said CLIAC was an important forum for medical lab scientists to discuss CLIA.
“[CLIAC] served as a critical venue for working through current problems with the rule and also for expert input on how new technologies—such as next-generation sequencing, digital pathology, and artificial intelligence-assisted diagnostics—should be assessed and integrated under CLIA,” Killeen said.
ADLM has formally urged Department of Health and Human Services Secretary Robert F. Kennedy, Jr. to reverse the CLIAC decision. In a May letter, the association emphasized that CLIAC’s work was funded entirely through user fees paid by clinical laboratories rather than taxpayer dollars—a point many in the lab industry say underscores CLIAC’s value.
CAP President Wonders about Future Communication Gaps
The Dark Report noted that the disbanding of CLIAC may cost labs time in certain cases, a commodity that few diagnostic settings have in abundance.
“The absence of this advisory body may lead to gaps in communication and slower response times in addressing [industry] challenges,” Donald Karcher, MD, FCAP, president of the College of American Pathologists (CAP), told The Dark Report.
The absence of CLIAC raises uncertainty for clinical labs because federal agencies have lost a prime source to gather specialized input on complex scientific and operational issues facing the lab industry. Dark Daily’s partner brands will continue to track this matter closely. If you’re not a subscriber, you can check out The Dark Report’s insider coverage with a 14-day free trial.
Clinical laboratories should take a proactive approach to ensure compliance with current price transparency regulations
Price transparency in healthcare continues to be a focus of the Centers for Medicare and Medicaid Services (CMS). As of this ebrief, the agency has cited nearly a dozen hospitals this year that failed to, wholly or in part, follow through with federal legislation due to technical issues.
The citations, paired with President Trump’s executive order from February on price transparency, demonstrates a growing trend toward costly enforcement.
It’s not clear from the documentation posted by CMS if any of this involves price transparency with clinical laboratory tests. Labs that operate within hospitals or health systems are subject to the executive order; thus, diagnostic test pricing estimates are subject to transparency mandates.
Based on enforcement actions posted online by CMS, it’s clear that the agency is looking into technical issues of price transparency requirements that have little to do with diagnostic medicine. From that perspective, clinical laboratory teams may want to pass this Dark Daily ebrief along to their IT department and business analysts, whose work is drawing criticism from CMS at some hospitals.
The entire lab team should be proactive on the issue of price transparency.
“Imagine how a one-on-one conversation with a patient would go if a physician explained that a routine cholesterol test sent to Lab A would cost five times that of Lab B. Anyone think the patient would choose Lab A?” wrote Bryan Vaughn, senior vice president, health systems and mid-America division, Labcorp, in an article he penned for the lab company’s website. (Photo copyright: Labcorp.)
Hefty Fines and Warnings from CMS
According to CMS, already in 2025, 10 hospitals have received civil monetary penalty (CMP) notices of hefty fines for non-compliance. They include:
Arkansas Methodist Medical Center, Paragould, Ark. $309,738
Northlake Behavioral Health System, Mandeville, La. $257,180
Lawrence Rehabilitation Hospital, Brick, N.J. $120,120
Community Care Hospital, New Orleans, La. $93,214
Hill Hospital of Sumter County, York, Ala. $84,216
Bucktail Medical Center, Renovo, Pa. $75,582
D.W. McMillan Memorial Hospital, Brewton, Ala. $71,852
First Surgical Hospital, Bellaire, Texas $62,016
CCM Health, Montevideo, Minn. $55,611
Southeast Regional Medical Center, Kentwood, La. $32,301
Payments for citations are due 60 days after receiving the CMP notice.
Trump’s Executive Order
CMS’ price transparency focus comes alongside President Trump’s Executive Order 14221, “Making America Healthy Again by Empowering Patients with Clear, Accurate, and Actionable Healthcare Pricing Information,” which the administration put out in February of this year, CMS noted.
As covered in the March 31 issue of The Dark Report, a sister publication to Dark Daily, Trump’s order is an expansion of his previous price transparency ruling, which went into effect at the start of 2021.
At that time, hospitals were required to “provide clear, accessible pricing information online about the items and services they provide” that was easy understand and to use, and machine-readable files listing all services and items available, CMS noted.
Impact on Clinical Laboratories
CMS’ updated requirements and refreshed reinforcement against healthcare organizations remain pertinent to hospital laboratories mostly due to extreme variations in test pricing.
“Reports continue to point out wide differences in the prices of routine laboratory testing across settings. Yet, routine lab testing may be some of the most comparable procedures in healthcare, with minimal differences in methods or quality,” wrote Bryan Vaughn, senior vice president of health systems and the mid-America division at Labcorp, in an article he penned for the lab company’s website.
Vaughn cited as much as a $600 difference found between metabolic or lipid panels and other standard lab tests.
It behooves clinical labs to verify that the information they provide to consumers online about test prices is indeed easy to understand and meets the spirit of the executive order and CMS. Failure to do so could be costly to a health system or hospital.
