Recommendations from Euphresco projects
The following research project has recently been carried out in the framework of Euphresco (network for phytosanitary research coordination - hosted by EPPO). A report presenting the main objectives and results of this project, as well as recommendations made, can be viewed on the Euphresco website.
Rapid identification of plant-health related bacteria by MALDI-TOF mass spectrometry (MALD-ID)
MALDI-TOF mass spectrometry is a powerful analytical method that can be used to identify molecules and organisms: it is rapid (less than 1 hour), can be high-throughput, cheap and accurate. Correct identification relies on reliable databases of spectra, however, the available databases are commercial (maintained by the companies that produce the mass spectrometers), and they lack spectra for the identification of plant pests. The project (MALD-ID) aimed to produce reference spectra to support the identification of plant pathogenic bacteria (Clavibacter spp., Curtobacterium spp., Erwinia spp., Pantoea spp., Pectobacterium spp., Pseudomonas spp., Ralstonia spp. and Xylophilus spp.) and to validate their use amongst the project partner laboratories. 117 reference spectra were obtained in the framework of the project activities. The reference spectra proved to be sufficient, when used alongside the commercial databases, to reliably identify bacteria from the eight studied taxa to at least genus level. However, the efficiency of the method to identify strains differs from genus to genus. MALDI-TOF MS is reliable for identification of some bacteria at species level (e.g. species belonging to Pantoea, Ralstonia and Xylophilus), but it is not precise enough to discriminate between closely related species, such those belonging to Curtobacterium, Pectobacterium and Pseudomonas. For these three latter genera, the identification at the is reliable to genus level. In plant health, the relevant taxonomic level for the diagnosis of bacteria is often at the infra-specific level. For example, Pantoea stewartii subsp. stewartii is a quarantine pest while Pantoea stewartii subsp. indologenes is not. In these cases, it is essential to discriminate between the subspecies. The project partners recommend that MALDI-TOF mass spectrometry is used as a first step in the diagnostic workflow. By providing identification these bacteria to genus level, MALDI-TOF mass spectrometry can help users choose the most relevant test for the identification of the pathogen at a lower taxonomic level.
Duration of the project: 2019-02-01 to 2022-03-31.
Authors: Perrine Portier, Jeroen van der Bilt, Annette Wensing.
Link: https://drop.euphresco.net/data/aead15b6-34ac-4fc0-8111-e0b83fd893c3/
Sources
Euphresco (2023-03).