BackgroundSalmonella typhimurium is an important intracellular pathogen that poses a health threat to humans. The key to studying the pathogenesis of Salmonella is to clarify the mechanisms responsible for its survival and reproduction in macrophages. In this study, RNA was extracted from S. typhimurium reference strain (ATCC 14028) and S. typhimurium isolated from the spleen of infected mice for RNA high-throughput sequencing analysis, based on the BGISEQ-500 platform.ResultsA total of 1,340 significant differentially expressed genes (DEGs) were screened through quantitative gene analysis and various analyses based on gene expression. Of these, 16 genes were randomly selected for fluorescence quantitative PCR verification. Two pairs of primers, 16S and pyridoxol 5ʹ-phosphate synthase (pdxJ), were used as internal references. The coincidence rate was determined to be 93.75%, which was consistent with the RNA-seq data, proving the reliability of the RNA-seq data. Functional annotation revealed DEGs associated with regulation, metabolism, transport and binding, pathogenesis, and motility. Through data mining and literature retrieval, 26 of the 58 upregulated DEGs (FPKM >10) were not reported to be related to the adaptation to intracellular survival, and were classified as candidate key genes (CKGs) for survival and proliferation in vivo. Among the CKGs, five were biotin synthetic bio family proteins. BioF is one of the first enzymes in the protein synthesis pathway. To evaluate the potential role of bioF in survival and proliferation, bioF mutants of Salmonella were constructed, and the virulence/attenuation was evaluated in vivo. Through the infection of BALB/c mice, bioF deficiency was found to significantly reduce the bacterial load and the fatality rate of mice. ConclusionsOur results indicated that the bioF gene plays an important role in the survival and proliferation of S. typhimurium in vivo. These data contribute to our understanding of the mechanisms used by Salmonella to regulate virulence gene expression whilst replicating inside mammalian cells.