117 The transcriptional activity of <i>Mycobacterium tuberculosis</i> in vivo and its influence on treatment outcome

Objectives/Goals: The overall goal of this project is to determine bacterial transcriptional signatures from clinical sputum and assess their potential to monitor treatment response and predict the outcome of drug therapy in patients with tuberculosis (TB). Methods/Study Population: We are developing a novel transcript capture sequencing (TC-Seq) approach to sequence the mRNA of Mycobacterium tuberculosis (Mtb) and analyze transcriptomes from clinical samples containing minimal amounts of bacterial RNA. This protocol generates single-stranded biotinylated probes from Mtb DNA. Probes are hybridized to and allow enrichment of Mtb-specific mRNA within next-generation RNA sequencing libraries. We will apply TC-Seq to sputum samples collected throughout an 18-month Phase II clinical trial investigating response to TB treatment to compare the transcriptome of Mtb between patients whose treatment results in cure or relapse. Results/Anticipated Results: We have refined a technique to generate biotinylated probes starting from DNA of lab grown Mtb. This protocol achieves robust and unbiased sampling of the Mtb transcriptome from mixed samples containing both human and Mtb RNA. Preliminary sequencing of clinical sputum collected pretreatment has generated 1–4 million Mtb-specific reads, a sequencing depth that allows examination of the entire bacterial transcriptome. We will measure differential gene expression before and during treatment as well as between cure and relapse cases. These results will allow us to characterize bacterial response to treatment and identify bacterial markers that correlate with relapse. Discussion/Significance of Impact: Understanding Mtb activity during treatment will offer new ways to assess the efficacy of different treatment regimens. Crucially, identifying clear bacterial markers that demarcate a cure or relapse outcome will have a significant impact on determining patient eligibility for shorter drug therapy.