Development of a Swiss Surveillance Database for Molecular Epidemiology of Hypervirulent and Multi-drug Resistant Pathogens

genome assembly; prediction of sequence type (MLST); core genome MLST tree to rapidly compare strains within a project; core genome single nucleotide polymorphism (SNP) tree to compare all Swiss Pathogen Surveillance Platform (SPSP) strains belonging to a same species; whole genome SNP tree to compare all SPSP strains within the same species and ST;; prediction of resistance and virulence factors within pathogen submitted genomes; time trees and calculation of transmission rates, including basic reproduction number; analysis of classical epidemiological data with advanced statistical methods including machine learning.