Xylella fastidiosa (Xf) is a quarantine bacterium causing important diseases in various host plants. Since 2013 it has been intercepted in several European countries, starting from Italy. The recent rise in minimum winter temperatures, due to climate change, has extended the range of areas suitable for its establishment, in fact cold temperature is one of the main deterring factors for Xf establishment. The spread of this bacterium often comes from asymptomatic plant materials for which sensitive detection is needed. Moreover, in case of new outbreak or new host plant, the identification of the subspecies and the Sequence Type (ST) is required. With this purpose, an amplicon-Nanopore sequencing was developed for Xf detection and identification at the subspecie/ST level, even in asymptomatic conditions. The workflow foresees the amplification of seven housekeeping genes (MLST) and the sequencing based on MinION from Oxford Nanopore Technology, a portable, fast and easy-to-use device, paired with an ad hoc bioinformatics pipeline. Two host plants, grape and olive, have been spiked with the Xf subspecies fastidiosa and pauca respectively, at different known concentrations (from 107 to 10 cfu/mL). Preliminary results indicate that this approach is a promising tool to precisely detect and identify Xf and therefore can be used to monitor the spread and the evolution of this bacterium. Finally this workflow could be applied for the correct identification of other priority pathogens.

Nanopore amplicon sequencing: rapid, sensitive and specific diagnostic system to monitor and intercept Xylella fastidiosa / Crosara, V.; Scala, V.; Pucci, N.; Reverberi, M.; Tatulli, G.; Faino, L.; Loreti, S.. - (2023). (Intervento presentato al convegno 4th European conference on Xylella fastidiosa (satellite event of the 12th International Congress on Plant Pathology) tenutosi a Lione, Francia).

Nanopore amplicon sequencing: rapid, sensitive and specific diagnostic system to monitor and intercept Xylella fastidiosa

Crosara V.
;
Reverberi M.;Faino L.;
2023

Abstract

Xylella fastidiosa (Xf) is a quarantine bacterium causing important diseases in various host plants. Since 2013 it has been intercepted in several European countries, starting from Italy. The recent rise in minimum winter temperatures, due to climate change, has extended the range of areas suitable for its establishment, in fact cold temperature is one of the main deterring factors for Xf establishment. The spread of this bacterium often comes from asymptomatic plant materials for which sensitive detection is needed. Moreover, in case of new outbreak or new host plant, the identification of the subspecies and the Sequence Type (ST) is required. With this purpose, an amplicon-Nanopore sequencing was developed for Xf detection and identification at the subspecie/ST level, even in asymptomatic conditions. The workflow foresees the amplification of seven housekeeping genes (MLST) and the sequencing based on MinION from Oxford Nanopore Technology, a portable, fast and easy-to-use device, paired with an ad hoc bioinformatics pipeline. Two host plants, grape and olive, have been spiked with the Xf subspecies fastidiosa and pauca respectively, at different known concentrations (from 107 to 10 cfu/mL). Preliminary results indicate that this approach is a promising tool to precisely detect and identify Xf and therefore can be used to monitor the spread and the evolution of this bacterium. Finally this workflow could be applied for the correct identification of other priority pathogens.
2023
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11573/1725487
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