Transcriptional Approach for Decoding the Mechanism of Compensatory Mutations for the Fitness Cost in Rifampicin-Resistant .

Multidrug-resistant tuberculosis (TB), defined as TB resistant to the two first-line drugs, isoniazid and rifampin, is a serious challenge to global TB eradication efforts. Although mutations in or have been proposed to compensate for this fitness cost due to mutation in rifampicin-resistant mutants, whether the compensatory effect exists and the underlying mechanisms of compensation remain unclear. Here, we used RNA sequencing to investigate the global transcriptional profiles of 6 rifampin-resistant clinical isolates with either single mutation in or dual mutations in /, as well as 3 rifampin-susceptible clinical isolates, trying to prove the potential compensatory effect of by transcriptomic alteration. In rifampin-free conditions, mutation was associated with upregulation of ribosomal protein-coding genes, dysregulation of growth-related essential genes and balancing the expression of arginine and glutamate synthesis-associated genes. Upon rifampin exposure of isolates, mutations were associated with the upregulation of the oxidative phosphorylation machinery, which was inhibited in the single mutants, as well as stabilization of the expression of rifampin-regulated essential genes and balancing the expression of genes involved in metabolism of sulfur-containing amino acids. Taken together, our data suggest that mutation may compensate for the fitness defect of rifampicin-resistant by altering gene expression in response to rifampin exposure.