Single-cell RNA sequencing delineates compositional and transcriptional changes of porcine peripheral blood mononuclear cell populations following Salmonella I 4,[5],12:i:- inoculation

A major contributor to foodborne illnesses worldwide is non-typhoidal Salmonella enterica . Consumption of contaminated pork products is a leading cause of salmonellosis, and understanding porcine cell type-specific immune response to Salmonella may provide information to reduce the Salmonella burden in pigs and conversely reduce the risk of salmonellosis in humans. Five young pigs were inoculated with Salmonella enterica subsp. enterica serovar I 4,[5],12:i:-. Blood was collected at 0, 2, and 8 days post-inoculation (DPI) to assess leukocyte populations in whole blood and isolate peripheral blood mononuclear cells (PBMCs). Single-cell RNA sequencing (scRNA-seq) was performed on PBMCs to interrogate gene expression and compositional changes through the acute stage following inoculation. Eight major immune cell types were identified, and differences in gene expression and cell abundance were assessed for each cell type. A whole-blood flow cytometry assay was performed to determine the proportion and concentration of specific immune cell types. Our findings indicated an increase in circulating monocytes at 2 DPI, including a distinct cluster of intermediate monocytes with increased expression of genes in inflammatory and antibacterial pathways. Major differences in natural killer cell gene expression were detected at 8 DPI compared to 0 DPI. Further, natural killer cells had distinct subsets representing effector and migratory cell states. Collectively, these discoveries unveil the acute, circulating cell type-specific immune response following Salmonella inoculation of pigs.