biostudies-literatureUnknown3(1)Lamont EIBacterial gene expression from sites of infection are poorly studied due to low levels of bacterial mRNA present in clinical samples. Here, we develop Transcript-Capture Seq, which uses customizable biotinylated probes generated in-house to enrich bacteria-specific RNA from host samples before Next Generation Sequencing (NGS). This method results in a >200-fold increase in bacterial mRNA reads from mixed samples and allows analysis of the complete bacterial transcriptome from clinical samples. We apply Transcript-Capture to models of tuberculosis (TB) infection as well as sputum samples from TB patients. TB patients exhibit unexplained heterogeneity in disease progression, and the activity of <i>Mycobacterium tuberculosis</i> (Mtb) has been proposed to affect treatment response. By applyinNAR molecular medicineugaf045https://www.ebi.ac.uk/biostudies/studies/S-EPMC12783040biostudies-literatureTranscript-Capture sequencing enriches mRNA of &lt;i&gt;Mycobacterium tuberculosis&lt;/i&gt; from host samples.PMC12783040Ma SJones RMWilkinson RJLamont EIAssadi JWinter JSherman DRWeiner DMMorrison RSong TBarry CEYu XVia LEfalseTranscript-Capture sequencing enriches mRNA of &lt;i&gt;Mycobacterium tuberculosis&lt;/i&gt; from host samples.Bacterial gene expression from sites of infection are poorly studied due to low levels of bacterial mRNA present in clinical samples. Here, we develop Transcript-Capture Seq, which uses customizable biotinylated probes generated in-house to enrich bacteria-specific RNA from host samples before Next Generation Sequencing (NGS). This method results in a >200-fold increase in bacterial mRNA reads from mixed samples and allows analysis of the complete bacterial transcriptome from clinical samples. We apply Transcript-Capture to models of tuberculosis (TB) infection as well as sputum samples from TB patients. TB patients exhibit unexplained heterogeneity in disease progression, and the activity of <i>Mycobacterium tuberculosis</i> (Mtb) has been proposed to affect treatment response. By applyin2026-01-01T00:00:00Z2026 Jan2026-05-30T03:13:05.375Z2026-05-30T03:07:25.84ZS-EPMC127830404152288010.1093/narmme/ugaf045