Non-parametric approaches to investigate food poisoning outbreaks at the core, accessory and pangenome scales independently of phylogenomic inference applied on Salmonella enterica subsp. enterica serovars Typhimurium and monophasic variants

Based on retrospective epidemiological investigations of four outbreaks of Salmonella enterica subsp. enterica serovar Typhimurium and monophasic variants of Typhimurium (i.e. S. 4,[5],12:i:-) , we propose in this manuscript to estimate the most appropriated non-parametric tests (i.e. in term as alpha risk to incorrectly reject the null hypothesis) applied to pairwise differences measured at the coregenome (i.e. SNPs or wgMLST), accessory genome (i.e. genes) and pangenome (i.e. kmers or wgMLST) scales, in order to distinguish between related (i.e. null hypothesis) and unrelated bacterial genomes without computing necessarily time consuming phylogenomic inferences.