The Spatiotemporal Dynamics and Microevolution Events That Favored the Success of the Highly Clonal Multidrug-Resistant Monophasic Circulating in Europe.

The European epidemic monophasic variant of enterica serovar (. 1,4,[5],12:i:-) characterized by the multi sequence type ST34 and the antimicrobial resistance ASSuT profile has become one of the most common serovars in Europe (EU) and the United States (US). In this study, we reconstructed the time-scaled phylogeny and evolution of this in Europe.

A Simple and Robust Statistical Method to Define Genetic Relatedness of Samples Related to Outbreaks at the Genomic Scale - Application to Retrospective Foodborne Outbreak Investigations.

The investigation of foodborne outbreaks (FBOs) from genomic data typically relies on inspecting the relatedness of samples through a phylogenomic tree computed on either SNPs, genes, kmers, or alleles (i.e., cgMLST and wgMLST).