Soil plays a much bigger role in the spread of antibiotic resistance than one might imagine.
Surprisingly, the ground beneath us is packed with antibiotic resistance genes (ARGs) — tiny codes that allow bacteria to resist antibiotics. Human activities, such as pollution and changing land use, can disturb soil ecosystems and make it easier for resistance genes to transfer from soil bacteria and infect humans.
Jingqiu Liao, assistant professor in civil and environmental engineering, is on a mission to understand how soil bacteria contribute to the growing global issue of antibiotic resistance through a study recently published in Nature Communications. Her team’s findings show that once bacteria acquire these resistant genes, they can be rapidly transmitted to other species as well, making this such a pressing public health threat.
Understanding these patterns can help scientists find ways to control the spread of antibiotic resistance, protecting human health and preserving the effectiveness of antibiotics for future generations.
Why antibiotic resistance in soil matters
Soil isn’t just dirt — it’s a bustling ecosystem filled with bacteria. Some of these bacteria naturally carry ARGs, which help them fight off antibiotics. While this might not seem like a big deal at first, it becomes dangerous when these ARGs end up in harmful bacteria that infect humans.
One such bacterium is Listeria monocytogenes. This soil dweller can make its way into the food chain and cause a serious illness called listeriosis. For people with weakened immune systems, listeriosis can be deadly, with fatality rates as high as 20 to 30 percent. Because of its ability to spread ARGs and infect humans, listeria is an important model for studying how antibiotic resistance develops in soil and spreads to other environments.
“Soil is an important reservoir of resistant bacteria and ARGs,” Liao said. “Environmental factors can amplify ARGs by creating conditions that promote the survival, spread, and exchange of these genes among bacteria. The ecological and evolutionary mechanisms underlying the dynamics of ARGs in soils remain inadequately explored. In this project, we use listeriaas a key model to understand the emergence and development of ARGs in soils.”
Using listeria to study resistance
Liao’s team includes several students along with:
- Ying-Xian Goh, doctoral student and lead author
- Amy Pruden, University Distinguished Professor, civil and environmental engineering
- Leigh-Anne Krometis, professor, biological systems engineering
- Hailong Zhang, assistant professor, business information technology
- Monica Ponder, professor, food science and technology
The researchers will continue to work together to perform comprehensive population genetics and ecological analyses on this nationwide set of data. The project, which builds on the group’s former research, is funded by aCenter for Emerging, Zoonotic, and Arthropod-borne Pathogens Interdisciplinary Team-building Pilot Grant at Virginia Tech.
“Virginia Tech has played a pivotal role in supporting and enabling this research,” said Goh. “The university’s commitment to interdisciplinary research creates an environment that inspires innovation and promotes impactful research like this.”
For the findings published in Nature Communications team members analyzed close to 600 listeria genomes from soil samples that Liao collected in a previous study, published in Nature Microbiology. They identified five main ARGs from across the United States.
The study also revealed how ARGs spread between bacteria. A process called transformation allows bacteria to pick up loose pieces of DNA containing ARGs from their surroundings. Once a bacterium acquires these genes, it can pass them along to others — even to different species. This rapid sharing of resistance genes is a major reason why antibiotic resistance is such a challenging problem.
The team focuses on listeria because it isn’t just another soil bacterium — it’s a key player in understanding antibiotic resistance. Studying how ARGs spread in soil bacteria like listeria gives scientists valuable insights into how resistance develops and moves through ecosystems.
“Although resistance in clinical listeria cases is currently low, these bacteria naturally resist several antibiotics and are showing increased resistance to others,” Liao said. “This makes listeriaa good model for tracking ARG development before it becomes a widespread clinical issue.”
How soil properties and land use shape ARG spread
The study also highlighted how the soil’s properties and land use can affect ARG spread. For example:
- Aluminum-rich soil encourages more ARG diversity, possibly because it stresses bacteria, making them more likely to keep resistance genes.
- Magnesium-rich soil lowers ARG diversity, potentially by reducing competition among bacteria.
- Forested areas tend to have more ARGs likely because wildlife naturally introduce these genes to the environment.
- On the other hand, agricultural fields can change the soil’s makeup and microbial communities, influencing ARG diversity in bacteria like listeria.
For households, it is important for people to avoid activities that may disturb soil conditions, such as improperly disposing of waste that may cause metal contamination. Liao said it is also important to maintain good sanitation practices after contact with soils, such as after gardening, given the possible presence of ARGs and resistant bacteria.
By revealing how ARGs spread and how environmental factors influence this process, Liao’s study highlights the importance of protecting natural ecosystems. Preserving soil health isn’t just good for the environment — it’s vital for our future medical care.
Building off of this research, Liao hopes to find new strategies to control antibiotic resistance, ensuring antibiotics remain effective in treating infections for years to come.
“Establishing a fundamental understanding of the ecological drivers of these bacteria in the soil could help us better understand the emergence, evolution, and spread of antibiotic resistance,” said Liao. “This is an urgent, global public health threat.”
