Whole genome sequencing-based tracing of a 2022 introduction and outbreak of Xanthomonas hortorum pv. pelargonii

Authors: BOCARDO, FERNANDA IRUEGA - Oregon State University; WEISBERG, ALEXANDRA - Oregon State University; RIUTTA, ELIZABETH - Oregon State University; KILDAY, KAMERON - Oregon State University; BONKOSWKI, JOHN - Purdue University; CRESSWELL, TOM - Purdue University; DAUGHTREY, M - Cornell University; RANE, KAREN - University Of Maryland; Grunwald, Niklaus - Nik; CHANG, JEFF - Oregon State University; PUTNAM, MELODIE - Oregon State University

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/11/2022
Publication Date: 12/14/2022
Citation: Bocardo, F.S., Weisberg, A.J., Riutta, E., Kilday, K., Bonkoswki, J.C., Cresswell, T., Daughtrey, M.L., Rane, K., Grunwald, N.J., Chang, J.H., Putnam, M.L. 2022. Whole genome sequencing-based tracing of a 2022 introduction and outbreak of Xanthomonas hortorum pv. pelargonii. Phytopathology. https://doi.org/10.1094/PHYTO-09-22-0321-R.
DOI: https://doi.org/10.1094/PHYTO-09-22-0321-R

Interpretive Summary: Globalization has made agricultural commodities more accessible, available, and affordable. But global trade increases the potential for invasion by pathogens and necessitates development and implementation of sensitive, rapid, and scalable surveillance methods. In 2022, a producer notified clients of a release of stock plants of garden geranium infected with a pathogern that causes bacterial blight on Pelargonium and Geranium hosts Here, we generated and analyzed whole genome sequences from pathogen strains isolated by three different plant diagnostic clinics. We first developed guidelines for using whole genome sequencing for plant disease diagnostics. Next, we analyzed genome sequences and revealed epidemiological links among strains from different growers that supported an outbreak and secondary spread within facilities that house plants originating from different producers. Results demonstrate the power for using whole genome sequencing to diagnose and mitigate outbreaks more expediently and precisely than traditional methods.

Technical Abstract: Globalization has made agricultural commodities more accessible, available, and affordable. But global trade increases the potential for invasion by pathogens and necessitates development and implementation of sensitive, rapid, and scalable surveillance methods. In 2022, a producer notified clients of a release of stock plants of garden geranium infected with Xanthomonas hortorum pv pelargonii, a species with members that cause bacterial blight on host plants of the Pelargonium and Geranium genera. Here, we generated and analyzed whole genome sequences from X. hortorum pv pelargonii strains isolated by three different diagnostic clinics. We first developed guidelines for using whole genome sequencing for plant disease diagnostics. Next, we analyzed X. hortorum pv pelargonii sequences and revealed epidemiological links among strains from different growers that supported an outbreak and secondary spread within facilities that house plants originating from different producers. Results demonstrate the power for using whole genome sequencing among a network of diagnostic labs and highlight the potential for such data to help shorten response times to mitigate outbreaks more expediently and precisely than traditional methods.