Researchers in Oregon say yes. They have built an open-source pipeline that identifies pathogens in minutes, helping agriculture respond faster to emerging threats.
Scientists with the U.S. Department of Agriculture Agricultural Research Service (USDA-ARS) in Corvallis, Oregon, working alongside Oregon State University, have developed a new disease surveillance platform designed to help agriculture stay ahead of emerging plant health threats.
The open-source tool, called PathogenSurveillance, analyzes DNA sequences to quickly identify microbes, pests and emerging pathogen variants. Researchers say the automated pipeline could help scientists respond in real time to invasive threats across agronomic, urban and forest ecosystems.
“This genomics pipeline allows us to identify any microbe, pest, or pathogen in just minutes-to-hours once there is a genome sequence,” USDA-ARS plant pathologist Nik Grunwald said in a USDA news release. “The genomic pipeline can be used for real-time biosurveillance of known, or unknown, pathogens relatively quickly, which lessens the barrier to adoption and use of PathogenSurveillance drastically.”
Grunwald says the platform’s sequence-based approach makes it possible to monitor how pest and pathogen populations evolve over time. That includes tracking new invasions, emerging variations and shifts in genetic diversity.
“Samples are sent to a local lab, and the resulting genome is sequenced and uploaded to the pipeline software system for identification,” Grunwald said. “Variation in genomes can thus be monitored over time and space by comparing genomes.”
Because the workflow is designed to be accessible, PathogenSurveillance can be used by disease clinics or diagnostic labs with limited computational experience. The platform supports analysis of bacteria, fungi, insects and nematodes, and can process one to several hundred samples at a time.
The output includes visual graphs of genetic diversity and interactive HTML reports designed to help users interpret results quickly.
“This will be a benefit to researchers, disease clinics, and diagnosticians in their work to identify clonal, or other types of variants such as the UG99 stem rust, or NA2 of sudden oak death,” Grunwald said.
