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Background   Salmonella  is a Gram-negative bacterium causing a wide range of clinical syndromes ranging from typhoid fever to diarrheic disease. Non-typhoidal  Salmonella  (NTS) serovars infect humans and animals, causing important health burden in the world. Susceptibility to salmonellosis varies between individuals under the control of host genes, as demonstrated by the identification of over 20 genetic loci in various mouse crosses. We have investigated the host response to  S.  Typhimurium infection in 35 Collaborative Cross (CC) strains, a genetic population which involves wild-derived strains that had not been previously assessed.    Results  One hundred and forty-eight mice from 35 CC strains were challenged intravenously with 1000 colony-forming units (CFUs) of  S.  Typhimurium. Bacterial load was measured in spleen and liver at day 4 post-infection. CC strains differed significantly ( P  < 0.0001) in spleen and liver bacterial loads, while sex and age had no effect. Two significant quantitative trait loci (QTLs) on chromosomes 8 and 10 and one suggestive QTL on chromosome 1 were found for spleen bacterial load, while two suggestive QTLs on chromosomes 6 and 17 were found for liver bacterial load. These QTLs are caused by distinct allelic patterns, principally involving alleles originating from the wild-derived founders. Using sequence variations between the eight CC founder strains combined with database mining for expression in target organs and known immune phenotypes, we were able to refine the QTLs intervals and establish a list of the most promising candidate genes. Furthermore, we identified one strain, CC042/GeniUnc (CC042), as highly susceptible to  S.  Typhimurium infection.    Conclusions  By exploring a broader genetic variation, the Collaborative Cross population has revealed novel loci of resistance to  Salmonella  Typhimurium. It also led to the identification of CC042 as an extremely susceptible strain.    Electronic supplementary material  The online version of this article (10.1186/s12864-018-4667-0) contains supplementary material, which is available to authorized users.

Identification of new loci involved in the host susceptibility to Salmonella Typhimurium in collaborative cross mice