Florfenicol Enhances Colonization of Salmonella enterica serovar Enteritidis floR mutant with Major Alterations to the Intestinal Microbiota and Metabolome in Neonatal Chickens.

Florfenicol is an important antibiotic commonly used in poultry production to prevent and treat Salmonella infection. However, oral administration of florfenicol may alter the animals' natural microbiota and metabolome, thereby reducing the intestinal colonization resistance and increasing the susceptibility to Salmonella infection. In this study, we determined the effect of florfenicol (30 mg/kg) on gut colonization of neonatal chickens challenged with Salmonella enterica subsp. enterica serovar Enteritidis (S. Enteritidis). We then analyzed the microbial community structure and metabolic profiling of cecal contents using microbial 16S amplicon sequencing and LC-MS untargeted metabolomics, respectively. We also screened the marker metabolites using a multi-omics technique and assessed the effect of these markers on the intestinal colonization S. Enteritidis. Florfenicol administration significantly increased the loads of S. Enteritidis in cecal contents, spleen, and liver, and prolonged the residence of S. Enteritidis. Moreover, florfenicol significantly affected the cecal colony structures, with reduced the abundance of Lactobacillus and Bacteroidetes, and increased the levels of Clostridia, Clostridium and Dorea. The metabolome was greatly influenced by florfenicol administration, and perturbation in metabolic pathways related to linoleic acid metabolism (linoleic acid, conjugated linoleic acid, 12,13-EpOME and 12,13-diHOME) was most prominently detected. We screened conjugated linoleic acid (CLA) and 12,13-diHOME as the marker metabolites, which were highly associated with Lactobacillus, Clostridium and Dorea. Supplementation with CLA maintained intestinal integrity, reduced intestinal inflammation, and accelerated Salmonella clearance from the gut and remission of enteropathy. Whereas, treatment with 12,13-diHOME promoted intestinal inflammation and disrupted the intestinal barrier function to sustain Salmonella infection. Thus, these results highlight that florfenicol alters the intestinal microbiota and metabolism of neonatal chickens, and promotes Salmonella infection mainly by affecting linoleic acid metabolism.