Salmonella Mbandaka, Typhimurium and its monophasic variant are prevalent serovars in dairy and pork food sectors. Faced with industrial limits and lack of knowledge of the mechanisms and determinants of the dissemination, the persistence and the resistance of these strains, whole genome sequencing approaches gained interest from both food sectors.
In this thesis, I have developed an innovative methodology, called "pan-genome" in order to take into account all single nucleotide polymorphisms within a considered set of Salmonella genomes, including the accessory and coregenome from coding and non-coding DNA fragments. In addition to have demonstrated that my developments allowed the inference of a phylogenomic tree in agreement with the epidemiological data through several datasets (Salmonella Typhimurium and its monophasic variant, Escherichia coli and Neisseria meningitidis), this work also revealed that the pangenomic inference produced new reconciliations between strains compared to the coregenome-based inference. These developments provided a pangenomic method with a higher discriminatory power than the usual methods based on core or accessory genomes, and consequently brought a potential solution for the improvement of outbreak investigations.
In addition, I studied in detail genomes to detect firstly host markers, and secondly geographical markers, on the French and global scales. I demonstrated that genomic clusters are harbored by Salmonella Mbandaka isolated from poultry and cattle. For Salmonella Typhimurium and its monophasic variant, I observed an absence of geographical distinction of strains isolated from pig herds, and that a single genomic profile was found dispersed in France, while a geographical segregation worldwide was observed.
Overall this research provided a solid overview of the genomic of Salmonella Mbandaka, Typhimurium and its monophasic variant in dairy and pig and pork food sectors, and a pangenomic method to bring further resolution in future bacterial epidemiological investigations.