PRJNA734902
Salmonella enterica subsp. enterica Welikade phylogenetic analysis
Clustering studies by single nucleotide polymorphism (SNP) core-genome phylogenetic analysis of outbreaks due to major serovars are simplified by the availability of many complete genomes in the free access databases. This is not the case for outbreaks due to less common serovars, such as Welikade, for which no reference genomes are available. In this study, we propose a method to solve this problem and we applied it to a retrospective analysis of a Salmonella enterica serovar Welikade (S. Welikade) foodborne outbreak that occurred in France in 2016.