SPREAD: Spatiotemporal Pathogen Relationships and Epidemiological Analysis Dashboard.

In the scope of public health, the rapid identification and control of infectious disease outbreaks are a paramount concern. Traditional surveillance methods often face challenges in effectively combining genetic, geographical, and temporal data, which is crucial for a comprehensive understanding of disease transmission dynamics. Addressing this critical need, the Spatiotemporal Phylogenomic Research and Epidemiological Analysis Dashboard (SPREAD) emerges as an innovative standalone web-based application.

Spatial and temporal dynamics of West Nile virus between Africa and Europe.

It is unclear whether West Nile virus (WNV) circulates between Africa and Europe, despite numerous studies supporting an African origin and high transmission in Europe. We integrated genomic data with geographic observations and phylogenetic and phylogeographic inferences to uncover the spatial and temporal viral dynamics of WNV between these two continents. We focused our analysis towards WNV lineages 1 (L1) and 2 (L2), the most spatially widespread and pathogenic WNV lineages.

Harmonization of supervised machine learning practices for efficient source attribution of Listeria monocytogenes based on genomic data.

Background: Genomic data-based machine learning tools are promising for real-time surveillance activities performing source attribution of foodborne bacteria such as Listeria monocytogenes. Given the heterogeneity of machine learning practices, our aim was to identify those influencing the source prediction performance of the usual holdout method combined with the repeated k-fold cross-validation method.

Methods: A large collection of 1 100 L.