Comparative analysis of the caecal tonsil transcriptome in two chicken lines experimentally infected with Salmonella Enteritidis

Abstract

Managing Salmonella enterica Enteritidis (SE) carriage in chicken is necessary to ensure human food safety and enhance the economic, social and environmental sustainability of chicken breeding. Salmonella can contaminate poultry products, causing human foodborne disease and economic losses for farmers. Both genetic selection for a decreased carriage and gut microbiota modulation strategies could reduce Salmonella propagation in farms. Two-hundred and twenty animals from the White Leghorn inbred lines N and 61 were raised together on floor, infected by SE at 7 days of age, transferred into isolators to prevent oro-fecal recontamination and euthanized at 12 days post-infection. Caecal content DNA was used to measure individual Salmonella counts (ISC) by droplet digital PCR. A RNA sequencing approach was used to measure gene expression levels in caecal tonsils after infection of 48 chicks with low or high ISC. The analysis between lines identified 7516 differentially expressed genes (DEGs) corresponding to 62 enriched Gene Ontology (GO) Biological Processes (BP) terms. A comparison between low and high carriers allowed us to identify 97 DEGs and 23 enriched GO BP terms within line 61, and 1034 DEGs and 288 enriched GO BP terms within line N. Among these genes, we identified several candidate genes based on their putative functions, including FUT2 or MUC4, which could be involved in the control of SE infection, maybe through interactions with commensal bacteria. Altogether, we were able to identify several genes and pathways associated with differences in SE carriage level. These results are discussed in relation to individual caecal microbiota compositions, obtained for the same animals in a previous study, which may interact with host gene expression levels for the control of the caecal SE load.

Fig 1. Summary of the results of comparisons between lines and between low and high carrier classes within lines according to the experiment.

Mean (red points) and standard deviation (SD; red bars) of the Salmonella Enteritidis abundance at 12 dpi in caecal contents (log10/g of caceal contents) of chicken groups infected with SE according to the line and experiment. Difference in mean between low and high carriers according to the line and experiment and t-test p-value. Difference in mean between lines and t-test p-value. Results of the DEG and BP GO term enrichment analyses. Results of the 16S analysis from the study [17].

Fig 2. Principal component analysis of the gene expression in caecal tonsils in all samples.

The first principal component contains 29% of the variance and may be attributed to the line effect and the second principal component contains 25% of the variance and may be attributed to the sex effect.

Fig 3. Principal component analysis of the gene expression in caecal tonsils from experiment 1 in each line.

(A) Principal component analysis (PCA) of the gene expression in caecal tonsils within line 6₁ in experiment 1. (B) PCA of the gene expression in caecal tonsils within line N in experiment 1.

Fig 4. Venn diagram.

Differentially expressed genes identified by comparing different groups of animals: (A) L6L1/L6H1 and LNL1/LNH1 (low vs high carriers of lines 6₁ and N, respectively, in experiment 1), (B) L6L1/L6H1 and LN/L6 (low vs high carriers of line 6₁ in experiment 1, and line N vs line 6₁), and (C) LNL1/LNH1 and LN/L6 (low vs high carriers of line N in experiment 1, and line N vs line 6₁).