Effects of two Salmonella Typhimurium vaccination programs and their interaction with coccidiosis vaccination on intestinal health of broilers

Experiment 2; Data: RNAseq dataset for transcriptome analysis; Sample names (x+day+group+pen): x42/35 = day 42 or 35 + A/B/C/D/E/F = group + pen number; Groups: Control (A=Ctrl), Coccidia (B=C), Coccidia + ST on day 1 and day 14 (C=CST1ST14), Coccidia + ST on day 14 (D=CST14), ST on day 1 and day 14 (E=ST1ST14), ST on day 14 (F=ST14); Samples: cecal walls, 6 birds per group, on day 35 (x35...) and on day 42 (x35), in total 72 samples. Abstract: Salmonellosis and coccidiosis are common intestinal diseases in the poultry industry. Antibiotic-free and organic production have increased the use of vaccines against both pathogens to minimize the zoonotic risk of salmonellosis for consumers and to reduce economic losses by coccidiosis. Results of chapter 3 indicated that in broilers a systemic infection with Salmonella Typhimurium (ST) was more frequently found after vaccination against coccidiosis. In addition, the two vaccines showed interactions in their effect on the number of differentially expressed genes at 28 days of age. In the present study, a 2 x 3 experimental design with different vaccination schedules on day 1 and 14 was used to further investigate the interactions between both vaccines in two experiments. Experiment 1 ended after 28 days, while in experiment 2 birds were challenged with a ST marker strain on day 28 and kept until day 42. In both experiments, groups not vaccinated against coccidia had an impaired performance, likely due to the inclusion of 0.02% of the anticoccidial feed additive nicarbazin in the feed of the unvaccinated groups. The results of the re-isolation of the ST marker strain from the environment, the cecal content and liver tissue confirmed the efficacy of the ST vaccine when given on the day of hatch, followed by a booster vaccine on day 14, but a lesser efficacy when birds were only vaccinated on day 1. The ST vaccine was found to decrease microbial diversity and express altered pathway abundance in the ceca on day 35 and 42 after challenge with ST. Additionally, the analysis of bacterial metabolic pathways showed significantly higher abundances of detoxification, energy and growth-related pathways in groups vaccinated against coccidiosis. The analysis of the transcriptome in the cecal wall revealed potential implications for cell-cell junction upregulation and intestinal epithelial integrity in response to the ST vaccine. Overall, the results indicated the potential influence of the coccidiosis vaccine, which becomes apparent after the ST challenge and the importance of the booster vaccine. Data: RNAseq dataset for transcriptome analysis Sample names (x+day+group+pen): x42/35 = day 42 or 35 + A/B/C/D/E/F = group + pen number Groups: Control (A=Ctrl), Coccidia (B=C), Coccidia + ST on day 1 and day 14 (C=CST1ST14), Coccidia + ST on day 14 (D=CST14), ST on day 1 and day 14 (E=ST1ST14), ST on day 14 (F=ST14) Samples: cecal walls, 6 birds per group, on day 35 (x35...) and on day 42 (x35), in total 72 samples