P-201 - BacPath and BacPathDB: Bacterial plant pathogen identification through metagenomics

Rapid and accurate identification of pathogens is crucial for safeguarding crops by providing essential information for disease management and protection. BacPath is a field-deployable bioinformatics pipeline designed for on-site pathogen identification that integrates portable metagenomic long-read sequencing and cloud-based analysis. To ensure accurate identification, BacPathDB was developed as a comprehensive database containing over 400 high-quality complete genomes of all known species of Pectobacterium, Dickeya, Clavibacter, and other important and closely related bacterial species. To demonstrate the accuracy of BacPath in a field setting, potato plants were inoculated with D. dianthicola strain PL25. DNA extraction, Flongle library-prep, sequencing, and data upload to the server were performed on-site. Processing time, ease of library preparation and sequencing, and portability were evaluated. In all samples, BacPath accurately identified D. dianthicola, with no false positives (other Dickeya species) or false negatives recorded. No pathogens were found in the control plants. Additionally, field-grown potato and kale plants were collected and analyzed with BacPath. The casual pathogen was isolated in CVP media and identified by Sanger-seq as gold-standards. BacPath identified pathogens as P. brasiliense in potatoes and P. atrosepticum in kale, supported by sequencing results. This analysis provided promising results for BacPath to be used in the field, and enhance routine and regulatory diagnostics, biosecurity, disease management, and epidemiological studies.