Metagenomic Sequencing for Identification of Xylella fastidiosa from Leaf Samples

Verónica Román-Reyna, Enora Dupas, Sophie Cesbron, Guido Marchi, Sara Campigli, Mary Ann Hansen, Elizabeth Bush, Melanie Prarat, Katherine Shiplett, Melanie L. Lewis Ivey, Joy Pierzynski, Sally A. Miller, Francesca Peduto Hand, Marie Agnes Jacques, Jonathan M. Jacobs

Research output: Contribution to journalArticlepeer-review

10 Scopus citations


Xylella fastidiosa (Xf) is a globally distributed plant-pathogenic bacterium. The primary control strategy for Xf diseases is eradicating infected plants; therefore, timely and accurate detection is necessary to prevent crop losses and further pathogen dispersal. Conventional Xf diagnostics primarily relies on quantitative PCR (qPCR) assays. However, these methods do not consider new or emerging variants due to pathogen genetic recombination and sensitivity limitations. We developed and tested a metagenomics pipeline using in-house short-read sequencing as a complementary approach for affordable, fast, and highly accurate Xf detection. We used metagenomics to identify Xf to the strain level in single- and mixed-infected plant samples at concentrations as low as 1 pg of bacterial DNA per gram of tissue. We also tested naturally infected samples from various plant species originating from Europe and the United States. We identified Xf subspecies in samples previously considered inconclusive with real-time PCR (quantification cycle [Cq], .35). Overall, we showed the versatility of the pipeline by using different plant hosts and DNA extraction methods. Our pipeline provides taxonomic and functional information for Xf diagnostics without extensive knowledge of the disease. This pipeline demonstrates that metagenomics can be used for early detection of Xf and incorporated as a tool to inform disease management strategies.

Original languageEnglish (US)
Article numbere00591
Issue number5
StatePublished - Oct 2021

All Science Journal Classification (ASJC) codes

  • Microbiology
  • Physiology
  • Biochemistry
  • Ecology, Evolution, Behavior and Systematics
  • Modeling and Simulation
  • Molecular Biology
  • Genetics
  • Computer Science Applications

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