Identification of Bovine Genotypes Conferring Diminished Susceptibility to Salmonellosis and Colonization by Salmonella and E. coli O157:H7

Salmonella and E. coli O157:H7 are two of the most important problems for the beef industry. Cattle can develop salmonellosis and persistently harbor Salmonella, or they can asymptomatically shed Salmonella and/or E. coli O157:H7 resulting in contamination of the hide and carcass surfaces during processing. Additionally, Salmonella infiltrates lymph nodes that get incorporated into ground beef. In this study, we investigated the possibility of identifying cattle with reduced susceptibility to one or both of these infections. Empirical observations from previous studies suggested that a diminished susceptibility was possible in amelanotic cattle, i.e., cattle bearing the mcr1/mcr1 genotype and lacking overt black pigmentation. By searching for single nucleotide polymorphisms (SNP) present in the 34 genes encoding the Salmonella interactome, we identified a SNP that was consistently present in amelanotic cattle with diminished susceptibility to Salmonella. Specifically, we used an ex vivo assay to screen 500 cattle blood samples for the diminished ability of Salmonella to penetrate peripheral leukocytes. Diminished Salmonella penetration was observed in 150 of these blood samples and 147 of these samples harbored two alleles bearing a SNP that introduces a miRNA cleavage site (bta-let-7b) in the 3’UTR of the bsynJ1 gene, which we designate as the SYNJ1/SNYJ1 genotype. Further ex vivo studies revealed a decreased expression of SYNJ1 in leukocytes bearing the SYNJ1/SNYJ1 genotype. In vivo experimental challenge studies revealed a diminished susceptibility to salmonellosis in cattle with the SYNJ1/SNYJ1::mcr1/mcr1 genotype. Additional in vivo challenge studies revealed that SYNJ1/SNYJ1::mcr1/mcr1 cattle have a decreased susceptibility to lymph node infiltration by two Salmonella serotypes (S. Anatum and S. Montevideo) implicated in this lymph node problem, and a decreased susceptibility to E. coli O157:H7 colonization of the recto-anal junction. A field study revealed that the SYNJ1/SNYJ1::mcr1/mcr1 genotype was five times more prevalent, when compared to the SYNJ1/synj1::mcr1/mcr1 and synj1/ synj1::mcr1/mcr1 genotypes, in Salmonella-free lymph nodes. Small-scale genetic surveys revealed that the SYNJ1/SNYJ1 genotype was present in the following mcr1/mcr1 breeds: Akaushi, Barzona, Braunvieh, Hereford, Piedmontese, Red and White Holsteins, Red Angus, Red Poll, Shorthorn, Simmental (Red), and Tarentaise. Studies using the aforementioned ex vivo penetration assay, which putatively predicts the diminished susceptibility phenotype, revealed that the penetrance of the diminished susceptibility is >99% in SYNJ1/SNYJ1::mcr1/mcr1 cattle but only ∼1% in SYNJ1/SNYJ1 cattle with at least one MCR1 allele. Further studies with the ex vivo assay revealed that three additional SNPs are part of a genotype conferring diminished susceptibility to a broad array of Salmonella serotypes commonly associated with cattle. In summary, the studies presented herein reveal a bovine genotype associated with decreased susceptibility to Salmonella and E. coli O157:H7. PSR Genetics LLC holds a U.S. patent on testing for the SYNJ1/SNYJ1 genotype (patent number 9,049,848) while the three complementary SNPs are under further investigation.