Soil plays an overlooked role in antibiotic resistance

Soil, often perceived as lifeless dirt, is a dynamic ecosystem teeming with bacteria, many of which naturally carry antibiotic resistance genes (ARGs). These tiny genetic codes enable bacteria to resist antibiotics, posing a significant challenge when they spread to harmful bacteria capable of infecting humans. 

Human activities like pollution and land-use changes disturb soil ecosystems, facilitating the transfer of these genes from soil bacteria to pathogens, which could exacerbate the global antibiotic resistance crisis.

Jingqiu Liao, an assistant professor in civil and environmental engineering, has led a new study to understand how soil bacteria contribute to the growing issue of antibiotic resistance. 

The findings emphasize that once bacteria acquire ARGs, they can rapidly transmit them to other species. This process transforms antibiotic resistance into an escalating public health concern. 

By deciphering these mechanisms, scientists hope to develop strategies to control ARG spread, protecting human health and preserving antibiotics’ efficacy.

The threat of antibiotic resistance in soil 

Soil is a vibrant environment filled with diverse bacterial communities. While some bacteria naturally carry ARGs as a defense mechanism against antibiotics, the situation becomes dangerous when these genes spread to pathogenic bacteria. 

Listeria monocytogenes, a bacterium found in soil, exemplifies this threat. When it infiltrates the food chain, it can cause listeriosis, a severe illness with fatality rates of 20–30% in vulnerable populations. 

The ability of listeria to spread ARGs and infect humans makes it a critical model for studying the dynamics of antibiotic resistance in soil and its potential to spread to other environments.

According to Liao, soil is a crucial reservoir for ARGs, with environmental factors such as pollution and land use amplifying their prevalence. These factors create conditions that promote the survival, spread, and exchange of ARGs among bacteria. 

However, the ecological and evolutionary mechanisms driving ARG dynamics in soil remain poorly understood. To address this gap, her team used listeria as a model organism to unravel the emergence and development of ARGs in soil ecosystems.

Antibiotic resistance in listeria

Liao’s team comprises a multidisciplinary group of researchers, including doctoral student Ying-Xian Goh, the study’s lead author. 

Supported by Virginia Tech’s Center for Emerging, Zoonotic, and Arthropod-borne Pathogens Interdisciplinary Team-building Pilot Grant, the team is conducting comprehensive genetic and ecological analyses of ARGs. 

This project builds on earlier research, such as Liao’s previous study published in Nature Microbiology, which analyzed nearly 600 listeria genomes from soil samples across the United States.

The findings identify five primary ARGs prevalent nationwide and shed light on how these genes spread between bacteria. 

Transformation, a process where bacteria acquire free-floating DNA containing ARGs from their environment, plays a key role. 

Once a bacterium picks up an ARG, it can pass it to others, even across species. This rapid transfer of resistance genes underscores the urgency of the antibiotic resistance problem. 

By studying ARG transmission in listeria, the team gained crucial insights into how resistance develops and propagates through ecosystems.

Liao highlighted the relevance of listeria as a model organism. Although clinical cases of listeria with antibiotic resistance remain low, the bacterium naturally resists several antibiotics and is showing signs of increased resistance. This makes it an ideal candidate for tracking ARG development before it becomes a widespread clinical issue.

The impact of soil and land use

The study also examined how soil properties and land use shape ARG diversity and distribution. For instance, soils rich in aluminum tend to encourage greater ARG diversity. 

Aluminum stress may prompt bacteria to retain resistance genes. In contrast, magnesium-rich soils seem to reduce ARG diversity, likely by lowering bacterial competition. 

Wildlife presence in forested areas contributes to higher ARG prevalence as animals introduce these genes into the environment. Conversely, agricultural activities can alter soil composition and microbial communities, influencing ARG dynamics in bacteria like listeria.

Liao underscored the importance of minimizing activities that disturb soil conditions, such as improper waste disposal that may lead to metal contamination. She advises practicing good sanitation after activities like gardening to avoid potential exposure to ARGs and resistant bacteria in soil. 

Understanding how environmental factors affect ARG spread is critical for developing strategies to mitigate antibiotic resistance and protect public health.

The future of combating antibiotic resistance

The study highlights the vital role of protecting natural ecosystems to curb ARG spread. Soil health preservation not only benefits the environment but also plays a crucial role in safeguarding future medical care. 

Building on these findings, Liao aims to explore new strategies for controlling antibiotic resistance, ensuring that antibiotics remain effective against infections for generations to come.

Liao believes that a deeper understanding of the ecological drivers of ARGs in soil is essential to tackling this urgent global health threat. 

“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,” she concluded.

The study is published in the journal Nature Communications.

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