Global biogeography and projection of soil antibiotic resistance genes

Although edaphic antibiotic resistance genes (ARGs) pose serious threats to human well-being, their spatially explicit patterns and responses to environmental constraints at the global scale are not well understood. This knowledge gap is hindering the global action plan on antibiotic resistance launched by the World Health Organization. Here, a global analysis of 1088 soil metagenomic samples detected 558 ARGs in soils, where ARG abundance in agricultural habitats was higher than that in nonagricultural habitats. Soil ARGs were mostly carried by clinical pathogens and gut microbes that mediated the control of climatic and anthropogenic factors to ARGs. We generated a global map of soil ARG abundance, where the identified microbial hosts, agricultural activities, and anthropogenic factors explained ARG hot spots in India, East Asia, Western Europe, and the United States. Our results highlight health threats from soil clinical pathogens carrying ARGs and determine regions prioritized to control soil antibiotic resistance worldwide.

Automated summary

This study conducted a global analysis of soil samples and found that agricultural habitats had higher abundance of soil antibiotic resistance genes (ARGs). The soil ARGs were mainly carried by clinical pathogens and gut microbes, and their abundance was influenced by climatic and anthropogenic factors. By creating a global map of soil ARG abundance, the study identified hot spots of soil antibiotic resistance in India, East Asia, Western Europe, and the United States, highlighting the health threats posed by clinical pathogens carrying ARGs and providing important information for global control of soil antibiotic resistance.