Transcriptomic Analysis of Immune Evasion Mechanisms in Mycobacterium tuberculosis Isolates from Treatment-Relapsed Patients in Plateau State

Treatment relapse in tuberculosis represents a clinically challenging scenario associated with persistent bacterial populations and inadequate immune clearance. Transcriptomic profiling of M. tuberculosis under host-mimicking stress conditions can reveal gene expression patterns that mediate immune evasion and bacterial persistence. This study performed RNA sequencing (RNA-seq)-based transcriptomic analysis of M. tuberculosis isolates from treatment-relapsed pulmonary TB patients attending Plateau State Specialist Hospital, Jos, North Central Nigeria. Nine isolates were cultured under standard laboratory conditions and then subjected to macrophage infection models to simulate in vivo conditions. Total bacterial RNA was extracted using the TRIzol-based protocol, and rRNA depleted. Libraries were sequenced on the Illumina HiSeq platform, and differential gene expression analysis was performed using DESeq2 in R. Relapse-associated isolates demonstrated significant upregulation (log2FC greater than 2, adjusted p less than 0.05) of genes in the DosR dormancy regulon, including dosR, hspX, and acg, under macrophage infection conditions. Additionally, PE/PPE family genes with roles in antigenic variation were overexpressed in 7 of 9 isolates. Genes encoding lipid metabolism pathways (mmpL3, fadD26) were differentially expressed, suggesting altered cell wall composition as an immune evasion mechanism. These data provide transcriptomic evidence for distinct immune evasion strategies in relapse M. tuberculosis clinical strains in North Central Nigeria. Keywords: Mycobacterium tuberculosis, transcriptomics, RNA-seq, treatment relapse, immune evasion.