Scientists launch open-source plant pathogen surveillance platform

USDA-ARS scientists in Corvallis, Oregon, in collaboration with Oregon State University, developed a disease surveillance platform that could improve U.S. agriculture by unlocking the future of plant health. PathogenSurveillance is an innovative, open-source software tool that can quickly analyze and identify novel microbial variants based on DNA sequences.

The automated PathogenSurveillance pipeline is an innovative workflow tool to help scientists respond in real-time to emerging, or re-emerging, invasive pathogens and pests. The surveillance platform will improve plant health and aid in reducing the spread of new and emerging diseases in agronomic, urban and forest ecosystems.

“This genomics pipeline revolutionizes plant health, allowing us to identify any microbe, pest or pathogen in just minutes-to-hours once there is a genome sequence,” said Nik Grunwald, ARS research plant pathologist at the Horticultural Crops Disease and Pest Management Research Unit in Corvallis. “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 added that, since everything is sequence-based, the tool can be used to monitor the evolution of pest/pathogens in real-time, providing insights into how populations change, variations emerge and new invasions occur. The platform can also be deployed to identify a specific pathogen or to monitor the emergence of new disease strains or variants.

“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.”

This allows PathogenSurveillance to be used by labs or clinics with little computational experience, and it provides “unprecedented capability for in-field or point-of-care diagnosis of pests and pathogens,” according to Grunwald.

The PathogenSurveillance platform also enables scientists to input one to several hundred population samples of small-to-modest genome sizes, including bacteria, fungi, insects and nematodes for pathogen surveillance and identification.The program output is also intuitive for the user because it can provide graphs of genetic diversity and create reports in the form of an interactive HTML document.

“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.

Plant researchers can download the PathogenSurveillance software tool at: https://nf-co.re/pathogensurveillance/1.0.0/.

FAQs

Who developed PathogenSurveillance?

USDA-ARS scientists in Corvallis, Oregon, collaborated with Oregon State University to develop the platform.

What is PathogenSurveillance?

PathogenSurveillance is an open-source workflow tool designed to analyze and identify microbial variants using DNA sequences.

What can the platform detect?

The system can identify bacteria, fungi, insects, nematodes and emerging pathogen variants.

How does the tool help plant health?

It supports real-time biosurveillance and rapid pathogen identification to reduce disease spread.