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Forecasting Pathogen Dynamics with Bayesian Model-Averaging: Application to Xylella fastidiosa

Authors: Candy Abboud, Eric Parent, Olivier Bonnefon & Samuel Soubeyrand
Date Published: 10/06/2023
Via: Springer

Abstract

Forecasting invasive-pathogen dynamics is paramount to anticipate eradication and containment strategies. Such predictions can be obtained using a model grounded on partial differential equations (PDE; often exploited to model invasions) and fitted to surveillance data. This framework allows the construction of phenomenological but concise models relying on mechanistic hypotheses and real observations. However, it may lead to models with overly rigid behavior and possible data-model mismatches. Hence, to avoid drawing a forecast grounded on a single PDE-based model that would be prone to errors, we propose to apply Bayesian model averaging (BMA), which allows us to account for both parameter and model uncertainties. Thus, we propose a set of different competing PDE-based models for representing the pathogen dynamics, we use an adaptive multiple importance sampling algorithm (AMIS) to estimate parameters of each competing model from surveillance data in a mechanistic-statistical framework, we evaluate the posterior probabilities of models by comparing different approaches proposed in the literature, and we apply BMA to draw posterior distributions of parameters and a posterior forecast of the pathogen dynamics. This approach is applied to predict the extent of Xylella fastidiosa in South Corsica, France, a phytopathogenic bacterium detected in situ in Europe less than 10 years ago (Italy 2013, France 2015). Separating data into training and validation sets, we show that the BMA forecast outperforms competing forecast approaches.

Complete circularized genome resources for Xylella fastidiosa subsp. sandyi strains CO33 and CFBP8478

Authors: María Pilar Velasco-Amo, Luis F. Arias-Giraldo, Miguel Román-Écija, Annalisa Giampetruzzi, Maria Saponari, and Blanca B. Landa

Date: 04/03/24

Xylella fastidiosa (Xf) is a vascular phytopathogenic bacterium native to the Americas, known for causing severe diseases and significant economic losses in important crops. In Europe, Xf is considered a quarantine pathogen. Since its first detection in 2013 in Italy,...

Complete circularized genome resources for Xylella fastidiosa subsp. sandyi strains CO33 and CFBP8478

Authors: María Pilar Velasco-Amo, Luis F. Arias-Giraldo, Miguel Román-Écija, Annalisa Giampetruzzi, Maria Saponari, and Blanca B. Landa

Date: 04/03/24

Xylella fastidiosa (Xf) is a vascular phytopathogenic bacterium native to the Americas, known for causing severe diseases and significant economic losses in important crops. In Europe, Xf is considered a quarantine pathogen. Since its first detection in 2013 in Italy,...

Genealogical tracing of Olea europaea species and pedigree relationships of var. europaea using chloroplast and nuclear markers

Authors: Roberto Mariotti, Angjelina Belaj, Raúl de la Rosa, Rosario Muleo, Marco Cirilli, Ivano Forgione, Maria Cristina Valeri & Soraya Mousavi

Date: 26/09/23

Background Olive is one of the most cultivated species in the Mediterranean Basin and beyond. Despite being extensively studied for its commercial relevance, the origin of cultivated olive and the history of its domestication remain open questions. Here, we present a...