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

Globalization has made agricultural commodities more accessible, available, and affordable. But their global movement increases the potential for invasion by pathogens and necessitates development and implementation of sensitive, rapid, and scalable surveillance methods. Here, we used 35 strains, isolated by multiple diagnostic laboratories, as a case study for using whole genome sequence data in a plant disease diagnostic setting. Twenty-seven of the strains were isolated in 2022 and identified as Xanthomonas hortorum pv. pelargonii. Eighteen of these strains originated from material sold by a plant breeding company that had notified clients following a release of infected geranium cuttings. Analyses of whole genome sequences revealed epidemiological links among the 27 strains from different growers that confirmed a common source of the outbreak and uncovered likely secondary spread events within facilities that housed plants originating from different plant breeding companies. Whole genome sequencing data were also analyzed to reveal how preparatory and analytical methods can impact conclusions on outbreaks of clonal pathogenic strains. Results demonstrate the potential power of using whole genome sequencing among a network of diagnostic labs and highlight how sharing such data can help shorten response times to mitigate outbreaks more expediently and precisely than standard methods.