Laura Uelze

TL;DR: The relevant approaches for phylogenomic studies for outbreak studies are described and an overview of selected tools for the characterization of foodborne pathogens based on WGS data are given.

TL;DR: Although the accuracy of computational serovar predictions is still not quite on par with traditional serotyping by Salmonella reference laboratories, the command-line tools investigated in this study perform a rapid, efficient, inexpensive, and reproducible analysis, which can be integrated into in-house characterization pipelines.

TL;DR: ChewieSnake as discussed by the authors is a simple and simple-to-use cgMLST workflow that combines the concept of allele hashing with the chewBBACA algorithm for the analysis of whole-genome sequencing.

TL;DR: Investigation of next-generation short read sequencing between ten laboratories involved in food safety from Germany and Austria found Illumina short read data to be more accurate and consistent and consistent than Ion Torrent sequence data, with little variation between the different Illumina instruments.

TL;DR: In this article, the authors present a working solution for cross-sector interpretation of sequencing data from different sources (such as human, veterinarian, food, feed and environmental) and outline how a decentralised data analysis can contribute to a uniform cluster detection and facilitate outbreak investigations.