Dual transcriptomic analysis unraveling the immune landscape and host-pathogen interactions during Mycobacterium tuberculosis infection

Elucidating the host-pathogen interactions is critical for uncovering the mechanisms controlling <i>Mycobacterium tuberculosis</i> (<i>Mtb</i>) infection. Using dual RNA-seq with fluorescent <i>Mtb</i>, we simultaneously profiled macrophage and bacterial transcriptomes to resolve dynamic intracellular responses. Macrophages containing dead <i>Mtb</i> exhibited strong immune activation, including enhanced antigen presentation and lysosomal function, whereas macrophages harboring live <i>Mtb</i> showed persistent NF-κB signaling and metabolic reprogramming. <i>Mtb</i> counteracted host defenses through upregulation of DNA repair genes and manipulation of extracellular matrix signaling via SPP1 and integrins, alongside tryptophan catabolism and lipid binding pathways supporting adaptation. Cross-species correlation analysis revealed coordinated transcriptional programs, notably a strong inverse association between <i>Mtb</i> aromatic compound catabolism and host receptor tyrosine kinase signaling. Additional correlations linked bacterial metabolism with host lipid transport and steroid biosynthesis. Together, these results provide a high resolution view of macrophage and <i>Mtb</i> transcriptional interplay defining bacterial persistence versus immune clearance.