Temporal dynamics of macrophage activation during Salmonella enterica serovar Typhi infection: An integrated transcriptomic and metabolomic analysis

Salmonella enterica serovar Typhi (S. Typhi) is a major bacteria responsible for foodborne illnesses. Understanding the temporal dynamics of the host immune response and associated metabolic reprogramming is crucial for identifying potential therapeutic targets. This study employed an integrated transcriptomic and metabolomic approach to investigate the response of macrophages infected with S. Typhi over a defined stage (0 h, 2 h, 4 h, 8 h, and 24 h). RNA sequencing (RNA-seq) was used to profile gene expression changes, while untargeted metabolomics characterized metabolic shifts. Gene set enrichment and pathway analyses were conducted to identify key immune and metabolic pathways. Additionally, Convergent Cross-Mapping (CCM) analysis was applied to uncover causal relationships between gene expression and metabolite fluctuations. Transcriptomic revealed distinct temporal phases of immune activation. Early responses were dominated by interferon signaling, cytokine production, and inflammatory responses, whereas later stages involved sustained immune signaling and metabolic adaptation. Key pathways, including NF-κB, TNF, and cytokine-cytokine receptor interactions, were significantly enriched. Metabolomic profiling demonstrated a transition from glycolysis and amino acid metabolism in early infection stages to fatty acid oxidation and mitochondrial function in later stages, with glutathione metabolism playing a central role in oxidative stress regulation. CCM analysis identified critical genes (e.g. RGS4, KIF18A, RSPO1) exhibiting strong causal relationships with metabolic alterations, underscoring the tight integration between immune and metabolic responses. This study provides a comprehensive, time-resolved view of S. Typhi infection, highlighting dynamic immune activation and metabolic reprogramming in macrophages. These findings advance our understanding of host-pathogen interactions.