Emergence of antibiotic-specificMycobacterium tuberculosisphenotypes during prolonged treatment of mice

Abstract

ABSTRACTA major challenge in tuberculosis (TB) therapeutics is that antibiotic exposure leads to changes in the physiologic state ofM. tuberculosis(Mtb) which may enable the pathogen to withstand treatment. While antibiotic-treatedMtbhave been evaluated in short-termin vitroexperiments, it is unclear if and how long-termin vivotreatment with diverse antibiotics with varying treatment-shortening activity (sterilizing activity) affectMtbphysiologic states differently. Here, we used SEARCH-TB, a pathogen-targeted RNA-sequencing platform, to characterize theMtbtranscriptome in the BALB/c high-dose aerosol infection mouse model following 4-week treatment with three sterilizing and three non-sterilizing antibiotics. Certain transcriptional changes were concordant among most antibiotics, including decreased expression of genes associated with protein synthesis and metabolism, and the induction of certain genes associated with stress responses. However, the magnitude of this concordant response differed between antibiotics. Sterilizing antibiotics rifampin, pyrazinamide, and bedaquiline generated a more quiescentMtbstate than did non-sterilizing antibiotics isoniazid, ethambutol, and streptomycin, as indicated by decreased expression of genes associated with translation, transcription, secretion of immunogenic proteins, metabolism, and cell wall synthesis. Additionally, we identified distinguishing transcriptional effects specific to each antibiotic, indicating that different mechanisms of action induce distinct patterns of cellular injury. In addition to elucidatingMtbphysiologic changes associated with antibiotic stress, this study demonstrates the value of SEARCH-TB as a highly granular pharmacodynamic assay that reveals antibiotic effects that are not apparent based on culture alone.