Xylella

Xylella detects and identifies Xylella fastidiosa (Xf), a polyphagous gram-negative bacterial plant pathogen, directly from infected plant material using Oxford Nanopore Technologies (ONT) MinION amplicon sequencing to enable rapid species, subspecies and Sequence Type (ST) identification.

Key Features:

• Direct Detection and Identification: Detects and identifies Xylella fastidiosa at species, subspecies and Sequence Type (ST) levels directly from plant samples without prior DNA purification.
• High Sensitivity: Demonstrates sensitivity exceeding conventional real-time PCR, enabling detection in samples with low contamination levels.
• Rapid Results: Produces diagnostic results within a few hours using Oxford Nanopore Technologies (ONT) MinION sequencing.
• Amplicon Sequencing Workflow: Employs a multiple PCR strategy followed by Nanopore amplicon sequencing using primers targeting the seven Multilocus Sequence Typing (MLST) loci officially adopted for Xf typing at the type strain level.
• Ad Hoc Pipeline Development: Implements an ad hoc computational pipeline to generate MLST consensus sequences from Nanopore data for accurate strain identification.

Scientific Applications:

• Outbreak Management: Enables rapid detection and identification to support management of current and future Xf outbreaks, including in regions where the pathogen is not endemic.
• Research on Vascular Pathogens: Provides a sensitive, amplicon-based sequencing approach that can inform development of similar diagnostics for other challenging vascular pathogens.

Methodology:

An ad hoc computational pipeline processes Nanopore amplicon sequencing data to generate MLST consensus sequences used for species, subspecies and Sequence Type (ST) identification.