Cuts to Federal Funding Threaten Clostridioides Difficile Research and Prevention Efforts

The infections caused by Clostridioides difficile (C difficile) can be painful and difficult to manage, especially for those who get recurrent infections. The bacteria cause diarrhea and colitis, accompanied by severe abdominal pain that could lead to more serious complications, such as toxic megacolon or sepsis. Though it often occurs following frequent use of antibiotic medications, C difficile has become more commonly spread in community and health care settings, making thorough surveillance, accurate diagnoses, and effective treatments critical to preventing illness.¹

C difficile causes an immense burden to patients impacred. | Image Credit: © jumrass khlongkhaew - stock.adobe.com

How Federal Funding Ensures Comprehensive C difficile Monitoring and Research

Much of the ability to track and research C difficile comes from federal funding. The CDC’s National Healthcare Safety Network (NHSN) comprises much of the United States’ monitoring and reporting ability, and it received $24 million in 2024 to capture and analyze infection data. Meanwhile, the federal government—through the Biomedical Advanced Research and Development Authority (BARDA) and National Institute of Allergy and Infectious Diseases (NIAID)—issue grants to companies developing treatments and preventatives for C difficile, while providing funding to researchers to better understand the bacteria.¹

According to Christian John Lillis, cofounder and CEO of the Peggy Lillis Foundation, recent cuts to the Department of Health and Human Services outlined in the recently signed “One Big, Beautiful Bill Act” (OBBBA) and the proposed fiscal year 2026 (FY26) budget could be detrimental to agencies that provide this funding. Because of these legislative initiatives, millions could lose access to preventative C difficile care and result in strained hospitals across the country. Further, research to better understand and monitor C difficile and develop more effective treatments would halt.¹

“To see these potential cuts is devastating, and they will have a devastating effect on people,” Lillis explained. Lillis spoke during a webinar hosted by the Peggy Lillis Foundation, titled “C. diff and the Federal Budget.” During the webinar, Lillis and Kevin Brennan, principal of Bluebird Strategies, a health care consulting and advocacy firm, explained the cuts described in the OBBBA and FY26 budget and the possible ramifications of approving such cuts to C difficile monitoring, research, and prevention.¹

Research Towards New Agents Against C difficile

Some of the major recipients of federal funding are biomedical companies seeking to develop innovative new treatments for rare diseases. For C difficile, federal funding is often required to jumpstart the development of new treatments; as Lillis states in his presentation, this is because these drugs are less likely to achieve “blockbuster” status, such as semaglutide (Ozempic, Wegovy; Novo Nordisk) or atorvastatin calcium (Lipitor; Pfizer).¹

"These kinds of [drugs for rare] diseases are often more reliant on federal funding to reach approval because private investors want to fund the next Lipitor or the next Ozempic,” Lillis outlined. “They want to get a big return on their investment, and the government doesn't have to make a return on its investment."¹

Accordingly, the federal government through BARDA has allotted millions of dollars in funding to various companies developing novel C difficile treatments. For example, BARDA granted $62.4 million to Summit Therapeutics for the development of ridinilazole, a C difficile-specific antibiotic. Funding for agents like ridinilazole goes towards the initiation and conduction of phase 3 trials; one such trial of ridinilazole found that the drug significantly reduced recurrent C difficile infection and resulted in an earlier gut microbiome recovery compared with vancomycin.^1,2

Understanding the nature of C difficile is another pertinent concern addressed by federal funding by the National Institutes of Health (NIH), which received $96.7 million in funding for C diff research from 2021 to 2025, according to Lillis. These initiatives included $6.5 million to University of Oklahoma College of Medicine to work towards a C difficile vaccine and $3.3 million for NIH funding of the Fecal Microbiota Transplant (FMT) National Registry, which tracks recipients of FMT to assess its short- and long-term safety and efficacy.^1,3,4

Tracking, Surveillance Efforts Bolstered by Federal Involvement

Like associated research and development initiatives, efforts to track, surveil, and report C difficile infections are mostly conducted on behalf of the federal government. Primarily, surveillance is done through the NHSN. The millions that initiative receives in 2024 was not just a blanket grant for any purpose, as Lillis explained. Rather, this funding gets disseminated down to individual health systems and hospitals, which each use the funding to contribute to monitoring efforts.¹

Lillis explained the process from the perspective of individual hospitals and infections. The $24 million NHSN received in 2024 was disseminated to 38,000 hospitals that use the system, accounting for $631 per hospital. With these surveillance efforts, over 179,000 C difficile infections were successfully tracked by the NHSN, or $134 per infection, according to Lillis.¹

With state and local municipalities often raising little taxes and spending little money on their public health infrastructure, money from the federal government towards hospitals and other agencies goes a long way to tracking C difficile infections and preventing further spread. Not only does federal funding enable these entities to repot C difficile cases, but it allows for faster and more efficient reporting. Lillis recalled an example from many years ago in which agencies received reports of C difficile cases through paper faxing to local health departments. Thanks to federal funding, Lillis said these processes are now much more streamlined.¹

By analyzing C difficile incidences for trends in transmission, scientists, researchers, and public health authorities can garner important insights. The data can help guide antibiotic sewage programs, identify hospitals that may have more C difficile cases than others, and allow academics to have a robust trove of information to conduct studies and analyses towards novel strategies.¹

“That, in turn, has led to us being able to save tens of thousands of lives,” Lillis stated.¹

Anticipated Funding Cuts Pose Threats to C difficile Prevention

The budget cuts proposed by the OBBBA and FY26 stand to total the largest ever cuts to Medicaid, with cuts encompassing $1.02 trillion over the next decade, according to Brennan. Further cuts are expected to the Children’s Health Insurance Program, Affordable Care Act (ACA), and Medicare programs. In all, almost 12 million Americans are expected to lose their health insurance in the next 10 years.¹

Concurrently, Brennan described the immense cuts to HHS agencies, including the CDC, NIH, and FDA that have occurred since the beginning of the second Trump administration and stand to continue based on the 2 legislative packages. Funding for the CDC stands to be reduced by 44% in the FY26 budget, from $9.2 billion to $5.2 billion; NIH funding will decrease by about 40% from $47 billion to $27.5 billion; and FDA funding will be reduced by 5.5%. Additionally, 2400, 1200, and 1900 staff members will be terminated from the CDC, NIH, and FDA respectively, whereas the entirety of BARDA would be eliminated and folded into a new HHS office.¹

Brennan spoke about the great risks of so many Americans losing their health insurance, discussing the possibility of overwhelmed and strained hospitals and health care centers, especially in rural areas. Although he noted that legislators added a hospital stabilization fund to account for the anticipated increased demand, Brennan noted that it pales in comparison to the trillions in cuts mandated by the laws. The impacts to C difficile prevention could be immense, and thousands more patients could end up hospitalized with the bacteria than they would have before the cuts.¹

"By increasing the number of people who are uninsured, you're going to increase the number of people who seek care in a hospital emergency room,” Brennan explained. “Folks who are in dire straits will not get the preventative care they need; they'll end up in emergency situations or seeking care in these settings."¹

Although the OBBBA has already been signed into law, Lillis told the audience to advocate for changes to the FY26 budget resolution before it is adopted in the fall. He called on the audience to contact their representative or senator to let them know of the C difficile-related impacts that stand to occur if the budget were to be adopted.¹

"We're at a critical moment for you all to be engaged and you to be communicating with your lawmakers about how you feel about these issues,” Brennan said.¹

Ultimately, without proper federal funding, Lillis said that there is a “very good chance” the developmental drugs he previously mentioned will never come into existence, emphasizing the imperative nature of the moment.¹

“We need many, many more tools in the toolbox,” concluded Lillis.¹

REFERENCES

1. Lillis CJ, Brennan K. C diff and the federal budget. Peggy Lillis Foundation for C. Diff Education & Advocacy. Presented July 1, 2025. Accessed July 24, 2025. https://www.youtube.com/watch?v=Y8bVp9T0hQw

2. Okhuysen PC, Ramesh MS, Louie T, et al. A Randomized, Double-Blind, Phase 3 Safety and Efficacy Study of Ridinilazole Versus Vancomycin for Treatment of Clostridioides difficile Infection: Clinical Outcomes With Microbiome and Metabolome Correlates of Response. Clin Infect Diseases. 2024;78(6):1462-1472. doi:10.1093/cid/ciad792

3. University of Oklahoma. OU College of Medicine researchers earn $6.5 million grant to work towards C. difficile vaccine. News Release. Released September 15, 2023. Accessed July 24, 2025. https://www.ou.edu/news/articles/2023/september/ou-college-of-medicine-researchers-earn-6-point-5-million-grant-to-work-toward-c-difficile-vaccine

4. Fecal Microbiota Transplant National Registry (FMT). National Library of Medicine. ClinicalTrials.gov Identifier: NCT03325855. Last Updated January 29, 2025. Accessed July 24, 2025. https://clinicaltrials.gov/study/NCT03325855