Salmonella Enteritidis (SE) is a zoonotic and vertically transmitted pathogen, often colonized in the reproductive tract of adult poultry, which can result in direct contamination of eggs and threaten human health. Previous studies have revealed that some pattern recognition receptors and resistance genes were involved in regulating immune responses to SE invasion in birds. However, the role of these immune response genes was not independent, and the interactions among the genes remained to be further investigated. In this study, SE burden and colonization were determined in reproductive tissue after the ducks were SE-infected, and RNA-sequencing was performed to construct co-expression networks by weighted gene co-expression network analysis (WGCNA). The result showed that SE could be isolated from 22% of infected-birds in any segment of the reproductive tract and the SE was readily colonized in the stroma, small follicle, isthmus, and vagina of the reproductive tracts in morbid ducks. The top central, highly connected genes were subsequently identified three specific modules in the above four tissues at the defined cut-offs (P<0.01), including 60 new candidate regulators and 125 transcription factors. Moreover, those 185 differentially expressed genes (DEGs) in these modules were co-expressed. Moreover, the hub genes (TRAF3, CXCR4 and IL13RA1) were identified to act with many other genes through immune response pathways including NF-kappaB, Toll-like receptor, steroid biosynthesis, and p53 signaling pathways. These data provide references that will understand the immune regulatory relationships during SE infection, but also assist in the breeding of SE-resistant lines through potential biomarkers.
