Integrated OMICs approach reveals energy metabolism pathway is vital for Salmonella Pullorum survival within the egg white

Purpose: To elucidate the survival strategies in egg white of Salmonella Pullorum, a host-restricted pathogen with vertical transmission capability. Methods: The logarithmic-phase wild-type and ?fim mutant strains were inoculated into LB medium and egg white (final concentration 80%) and statically cultured at 42°C for 6 hours. RNA samples were then extracted for sequencing. Three biological replicates were carried out per sample. RNA sample was sequenced with Illumina HiSeq 2000 System. EdgeR method was used to calculate the differentially expressed genes. qRT–PCR and gene mutation were used to validate RNA-seq result. Results: A total of 12 samples were sequenced. The average clean bases of each sample was 3.63 Gb, and the average comparison rate with the reference genome was more than 90%. Compared with LB broth, there were 1606 differentially expressed genes (FDR =0.05 and |Log2Fold change| =1) in egg white with 762 genes upregulated and 844 genes downregulated. These accounted for about 35% of the whole genome indicating a large shift in the transcriptional response to egg white. qRT–PCR result of 7 selected genes highly consistent with the RNA-seq results. Five mutants showed decreased survival ability in egg white, suggested that the DEGs from the RNAseq results correlated significantly with the egg white resistance phenotype.Moreover, a significant downregulation of all genes within the fim gene cluster was observed and the RNA-seq analysis of ?fim mutant in the egg white was further conducted. In comparison with wild-type in egg white, the fim mutant showed 36 differentially expressed genes, with most of them associated with energy metabolism pathways. Overall design: To understand the mechanisms employed by Salmonella Pullorum to withstand the challenging environment in egg white, three biological replicates of wild-type and ?fim mutant incubated in LB broth and egg white (totally 12 samples) were conducted RNA sequncing.