Salmonella enterica infections result in substantial morbidity and mortality in humans and livestock worldwide. While most S. enterica serovars such as Typhimurium, Enteritidis and Newport remain restricted to the intestine and primarily cause gastroenteritis after ingestion, those that are well adapted to a host, including Typhi in humans (the agent of typhoid fever), Choleraesuis in pigs, Dublin in cattle and Gallinarum in poultry, have evolved to spread systemically, promoting sepsis that can lead to death if left untreated. These systemic Salmonella have undergone extensive loss-of-function mutations, mainly in genes that are no longer needed outside of the anaerobic intestinal environment. Although a few newly acquired genes and host-adapted allelic variants promoting virulence in systemic Salmonella have been identified, a comprehensive analysis of genes and/or alleles unique to systemic serovars has not yet been undertaken. In preliminary studies, we have identified only three genes shared by systemic Salmonella, but have identified many unique allelic variants shared among all or most of these septicemic serovars. Based on this finding and the additional exciting observation that newly described systemically invasive non-typhoidal Salmonella share many virulence protein alleles with systemic Salmonella and not with intestinal Salmonella, we will test the hypothesis that allelic variants are major determinants of the systemic pathotype. An innovative and unbiased genome wide association study will specifically compare the genomes of the four systemic/host-adapted serovars with those of the three typical intestinal serovars, all mentioned above, to identify unique nonsynonymous single nucleotide polymorphisms for allelic variants that promote systemic spread and host adaptation. Metabolic pathways potentially involved in promoting systemic Salmonella dissemination will be determined by gene enrichment analysis. The biological relevance of the most statistically significant unique alleles detected in systemic/host-adapted Salmonella will be further investigated in functional assays. Particular attention will be given to virulence factors, such as adhesins and type 3 effector proteins, with a focus on those participating in bacterial invasion and host inflammation. Additional scrutiny will be given to proteins involved in metabolic pathways that would provide a selective advantage in the systemic environment, which is better oxygenated and provides a different complement of nutrients and metabolites. Bacterial binding, invasion, survival/ replication and host cell lethality will be evaluated with corresponding host-specific cells and knock out- mutants, allelic substitutions and/or recombinants. Determining which animal specific Salmonella share(s) human-adapted alleles will inform future in vivo studies by providing more relevant animal models for systemic salmonellosis in humans. Identification of specific sets of alleles that dictate a septicemic pathotype in humans will highlight new targets for combatting or preventing the systemic forms of Salmonella infections.