Tackling Soil ARG-Carrying Pathogens with Global-Scale Metagenomics

Area of Science:

• Environmental microbiology
• Public health
• Genomics

Background:

• Antibiotic overuse and environmental contamination accelerate antibiotic resistance genes (ARGs) spread via horizontal gene transfer.
• While ARG distribution in soils is studied, the global antibiotic resistance of soilborne pathogens remains largely unknown.
• This knowledge gap hinders effective global strategies against antibiotic resistance.

Purpose of the Study:

• To investigate the global distribution and characteristics of antibiotic-resistant pathogens (APs) in soils.
• To identify factors influencing AP hotspots and inform targeted control measures.
• To advance understanding of soilborne APs and their public health implications.

Main Methods:

• Assembled metagenomic contigs from 1643 global soil samples.
• Identified and characterized 407 ARG-carrying pathogens (APs).
• Mapped global AP richness and analyzed contributing anthropogenic and climatic factors.

Main Results:

• APs were detected in 87.8% of samples, with higher richness in agricultural soils.
• Agricultural soils showed a prevalence of clinical APs (e.g., Escherichia, Enterobacter).
• APs frequently co-occurred with multidrug resistance genes and bacA; hotspots identified in Asia and the US.

Conclusions:

• Soilborne APs are globally distributed, with agricultural soils being significant reservoirs.
• Anthropogenic and climatic factors drive AP hotspots, necessitating regional control strategies.
• Mapping AP distribution aids in prioritizing global efforts to mitigate antibiotic resistance.