Assessing transcriptomic responses of Salmonella Infantis in the presence of poultry litter.

UNLABELLED: Litter is a major source for harboring and transmitting Salmonella from one flock to another flock. The objective of this experiment was to elucidate the persistence mechanism of S. Infantis by analyzing transcriptomic changes in the presence of litter. To achieve this, four treatments were arranged: (1) BHI, (2) BHI+Litter, (3) PBS, and (4) PBS+Litter. Each treatment was inoculated with S. Infantis, and RNA was extracted. Quality, quantity, and integrity of RNA were assessed and then subjected to Illumina sequencing. HISAT2 was used to align reads to the reference genome, HTSeq to obtain read counts, and DESeq to study differential gene expression. The compared treatments were BHI vs BHI+Litter, PBS vs PBS+Litter, and PBS vs BHI. Starvation stress was pronounced in bacteria with upregulated expression of rpoS and dksA genes in nutrient-poor media, like PBS, in comparison to BHI and litter treatments. Additionally, the genes fad, eutS, and pduF, associated with alternative carbon utilization, were upregulated in PBS compared to PBS+Litter and BHI. Compared to non-litter media, alternative respiration system genes dmsA, dmsB, dmsC, ttrB, ttrC, fdnH, and fdnG upregulation in litter highlights S. Infantis' ability for metabolic adaptation to oxygen-limited environments. Furthermore, virulent genes such as invA and sopD were found to be upregulated in BHI in comparison to BHI+Litter. In contrast, genes associated with amino acid-dependent acid resistance mechanisms including adiA, cadA, and cadB were downregulated in BHI in comparison to BHI+Litter. In conclusion, S. Infantis upregulated stress response and metabolic genes to survive in challenging environments.

IMPORTANCE

Poultry litter plays a pivotal role in the persistence, proliferation, and transmission of Salmonella. Recent studies have reported the increased prevalence of Salmonella Infantis in the broiler houses and chicken meat in the United States and Europe. Moreover, Salmonella strains could persist in the recycled litter despite undergoing several treatment methods. In commercial production systems, it is a common practice to reuse poultry litter for raising multiple broiler flocks in the United States. Therefore, it is crucial to understand the mechanism of the survival of bacteria in reused litter to curb the prevalence of Salmonella. The objective of this study was to determine the transcriptional variations in S. Infantis in the presence and absence of litter. The findings from this study will provide insights into the potential persistence mechanism of S. Infantis within the litter environments.