In the ongoing battle against antimicrobial resistance (AMR), a new study published in *Scientific Reports* challenges conventional wisdom about the risks posed by organic farming practices. The research, led by Colette A. Nickodem of the Department of Pathobiological Sciences at the University of Wisconsin-Madison, reveals that non-organic soil management practices may inadvertently heighten the risk of transmitting antimicrobial resistance genes (ARGs) and human pathogens.
The study, conducted on a large scale, sought to understand how different soil management strategies influence the resistome—the collection of genes involved in resistance to antimicrobial agents—and the overall microbiome of agricultural soils. Specifically, the researchers investigated whether the use of composted poultry manure in organic farming practices increases the risk of spreading ARGs and drug-resistant pathogens.
Contrary to expectations, the findings suggest that non-organic practices, which do not involve the application of poultry manure, pose a greater risk. This is due to a significantly higher co-occurrence of ARGs with mobile genetic elements (MGEs), which facilitate the horizontal transfer of resistance genes. “Our results indicate that the mobility and diversity of resistance genes are critical factors in assessing AMR risks,” Nickodem explained. “Focusing solely on the abundance of ARGs can misrepresent the actual hazards.”
In contrast, organic practices that applied composted poultry manure increased the overall abundance of ARGs and metal resistance genes (MRGs), but these genes were found to be less diverse and less mobile. This nuanced understanding underscores the importance of evaluating gene mobility and management context when assessing AMR hazards.
The implications for the agriculture sector are profound. As the global push for sustainable and organic farming practices gains momentum, this research provides a crucial perspective on the unintended consequences of different soil management strategies. “This study highlights how soil management can be strategically leveraged to mitigate AMR transmission,” Nickodem noted. “It offers actionable insights for sustainable agriculture, environmental stewardship, and public health protection.”
The findings suggest that a more holistic approach to soil management is necessary, one that considers not just the presence of resistance genes but also their mobility and the broader ecological context. This could lead to the development of new guidelines and best practices for farmers, ensuring that efforts to promote sustainable agriculture do not inadvertently exacerbate the AMR crisis.
As the agriculture sector continues to evolve, this research serves as a reminder of the complex interplay between farming practices, environmental health, and public safety. By understanding and addressing these complexities, the industry can take meaningful steps toward a more sustainable and resilient future.