Every year, nearly 5 million people die from causes related to antimicrobial resistance (AMR), the phenomena by which microorganisms like bacteria evolve to resist the drugs designed to kill them. AMR poses a growing threat to global human health, as it diminishes the ability of common antibiotics to treat infections.
Microorganisms become impervious to such treatments when they encounter snippets of DNA called antibiotic resistance genes (ARGs) and incorporate them into their own genetic material, often receiving them from other bacteria. ARGs are exchanged in environments where bacteria come into close contact with one another: runoff from farms, running water, and sewage. An emerging challenge for public health is tracking and treating ARGs in wastewater.
“Antibiotic resistance is a big issue; it doesn’t see borders and it potentially impacts all of us,” said Kyle Bibby, the Keating-Crawford Collegiate Professor of Environmental Engineering in the Department of Civil and Environmental Engineering and Earth Sciences. “We all benefit from strong monitoring of ARGs.”
Bibby’s research group designs systems for monitoring and quantifying biological materials, including ARGs, in liquid waste. A recent study published by Bibby’s research group—with support from the Berthiaume Institute for Precision Health (BIPH)—explores the effectiveness of a novel indicator for tracking the presence of common ARGs throughout the treatment process for wastewater.
“In order to keep ARGs from spreading and bestowing antibiotic resistance on their hosts, we can start by making sure they’re being treated properly in wastewater,” said Bibby, who leads the Genomics & Environmental Research in Microbiology (GERM) Lab in the College of Engineering. “Traditional treatment plants don’t target ARGs, and targeting begins with tracking.”
Since ARGs are small pieces of genetic material, they can move through waterways independent of a living host, freewheeling until they are snatched up by passing bacteria. At any given time, thousands of important ARGs could be present in wastewater systems.
“ARGs are incredibly diverse, and there are thousands of potentially important ones,” Bibby said. “How important varies depending on the host class, and it’s not realistic to simultaneously monitor for thousands of genes on the level of a municipal plant.”
The study, published in the journal ACS ES&T Water, examines the efficacy of a new broad-class indicator for tracking the general presence of ARGs wastewater.
The indicator of interest is a plasmid—a little slice of DNA—called pBI143. Recently, pBI143 was flagged by researchers at the University of Chicago as being more plentiful in the human gut than previously realized. Bibby’s group selected it as a promising candidate for its human specificity and abundance.
“Traditional wastewater treatment does reduce ARGs to a certain extent, but using a tracker like pBI143 helps us to really visualize at what stage ARGs are reduced while also estimating how much ARG material is leftover at the end of the whole treatment cycle,” said Bethany Oceguera Johnson, co-lead author and 2026 doctoral graduate from the Department of Civil and Environmental Engineering and Earth Sciences. “From there, new treatments can be piloted and their effectiveness can be tracked.”
Oceguera Johnson and co-author Marlee Shaffer, who received her doctorate from the Department of Civil and Environmental Engineering and Earth Sciences in 2025, worked with a wastewater treatment plant in northern Indiana to collect wastewater samples at various stages in the treatment cycle, screening them for specific ARGs and indicators along the way. They tracked pBI143 levels alongside three widely used indicators for fecal matter, as well as a group of ARGs selected for their clinical and agricultural importance.
The researchers found that the amount of pBI143 in the samples at each collection point most closely correlated with the levels of selected ARGs. This is the first study to explore pBI143 as a dedicated indicator for ARGs.
“If we know that we’re reducing pBI143, we can then use that information to say we’ve reduced our antibiotic resistance by a certain amount,” Shaffer, the co-lead author, explained. “But testing for multiple genes is time consuming and costly, so having just one marker to show how efficient a treatment plant is at removing ARGs is less taxing on the individual municipality.”
Bibby’s research group is now working on a dedicated assay for pBI143 detection, which would be of use in field testing of wastewater and runoff for ARGs as a category. This marks the first phase of research Bibby is undertaking with support from the BIPH-led Notre Dame Biothreat Surveillance, Containment, & Operational Preparedness Engine (ND-BIOSCOPE). Intended to strengthen global health resilience, ND-BIOSCOPE announced its inaugural round of awardees, including Bibby, in early 2026 — advancing Notre Dame’s contributions to next-generation sensor technologies, artificial intelligence-driven analytics, biosurveillance networks, and rapid therapeutic countermeasure development pipelines.
“BIOSCOPE is taking a holistic approach to the globally important challenge of emerging biological threats,” said Matthew Webber, the Keating-Crawford Collegiate Professor of Engineering, ND-BIOSCOPE’s principal investigator, and acting director of BIPH. “By supporting innovative approaches to antibiotic resistance, novel sensors, and enhanced surveillance networks, our researchers can build capacity in the areas of greatest need.”
ND-BIOSCOPE is a cross-disciplinary initiative led by BIPH, in collaboration with the Notre Dame Sensor Initiative, Warren Center for Drug Discovery, Remote Emerging Disease Intelligence Network (REDI-NET), and the Bioengineering & Life Sciences (BELS) initiative. Working with partners from the College of Science and College of Engineering, Bibby intends to develop two integrated, high-throughput analytical platforms based on proprietary nanoparticle technology: the first for environmental disease surveillance via wastewater, and the second to screen and detect immune signatures of infection and latent viruses.
“Instead of needing a fancy lab to run this, an assay would let us detect pBI143—and, therefore, ARGs—in the field,” said Bibby, who is an affiliate of Notre Dame’s Eck Institute for Global Health and Environmental Change Initiative. “It would also enable us to more effectively track ARGs in other countries that are less likely than the United States to have centralized wastewater treatment facilities.”
Overall, having better tools for measuring the presence of ARGs in water systems worldwide will enable the reduction of free-floating genetic material from the environment, and, ultimately, a reduction in the proliferation of antibiotic-resistant pathogens.
“Antibiotic resistance is a public health threat and a growing one,” Shaffer said. “Projections show that by 2050, about 10 million deaths will be either directly attributed to antibiotic resistance or associated with it, which is about a 70 percent increase from what we are currently seeing in the medical field.”
“10 to 15 years ago antibiotic resistance was often considered almost too complicated to tackle, but our work with pBI143 shows that the field is capable of finding actionable solutions,” added Bibby.
At the intersection of public health and environmental engineering, Bibby and his research group have found a supportive partner in BIPH.
“I’m really appreciative that BIPH recognizes the importance of environmental work,” Bibby said. “Some might find it odd that an environmental engineer is involved with BIPH, but diving in, one can appreciate how understanding the spread of antibiotic resistance is critical for the field of precision health.”
Shaffer, now a postdoctoral scholar at Carnegie Mellon University, was supported by a Berry Family Foundation Graduate Fellowship from BIPH. The annual fellowship funds two outstanding graduate students at the University who are investigating issues of high interest to the Institute, and supported Shaffer’s work on the pBI143 study from the formulation of the research question to publication.
“I think we’re just scratching the surface of antibiotic resistance, especially in terms of what we can do now with more advanced molecular detection,” Shaffer said. “There are so many important future research ideas that will change how we manage the impact that antibiotic resistance is having on our clinicians and our health systems.”
Shaffer was also involved as Vice President of the BIPH Graduate Student Group, and helped to plan the Institute’s Annual Symposium.
“The hands-on experience I gained while planning the symposium has proven invaluable in my next phase as a postdoctoral scholar and working towards a career in academia,” Shaffer said. “I’m grateful to BIPH for the support and formation I received during my years as a graduate student.”
Originally published by Erin Fennessy Lawlor at precisionhealth.nd.edu on August 13, 2026.