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A study was conducted to evaluate the efficacy of fructooligosaccharides (FOS) in controlling the infection of Salmonella Enteritidis (SE) in White Leghorns. A total of 30 laying hens (white leghorns W-36) were challenged both orally and cloacally with approximately 108 colony-forming units of nalidxic acid resistant SE (SENAR) and divided into 3 treatments: 1) SENAR challenged + 0.0% FOS, 2) SENAR challenged + 0.5% FOS (Nutraflora), and 3) SENAR challenged + 1.0% FOS. SENAR recovery via fecal shedding was measured at 3- and 6-d post-infection (dpi), whereas in the ceca and internal organs, SENAR recovery was measured at 7-d post-infection. In the first experiment, there was a 1.0 log10 and a 1.3 log10 reduction in cecal SENAR by supplementation of FOS at 0.5 and 1.0%, respectively. In the second experiment, there was a 0.6 log10 and a 0.8 log10 reduction in cecal SENAR by supplementation of FOS at 0.5 and 1.0%, respectively. Fecal shedding was significantly lower in 1.0% FOS supplemented groups compared to SENAR challenge 0.0% FOS. There was no significant difference among the 3 treatments on SENAR recovery in liver with gall bladder and ovaries. However, the frequency of positive SENAR in the ovaries (10 to 40%) in SENAR challenge 0.0% FOS was significantly lower than liver with gall bladder (60 to 80%) in both experiments. There was a significant upregulation of toll-like receptor-4 in 1.0% FOS and interferon gamma in both 0.5 and 1.0% FOS. Histologic measurements of ileal villi height and crypt depth were similar across all treatments. Immunohistochemistry analyses of ileal samples showed that immunoglobulin A positive cells increased as FOS concentration increased reaching significance at 1.0% as well as altered cytokine gene expression in the ileum. Further, FOS supplementation also reduced cecal SENAR and feces SENAR levels. Collectively, the results suggest that dietary supplementation with FOS may impair SE pathogenesis while modulating humoral immunity within the gut-associated lymphoid tissue.