Fig. 1

The transcriptional signature of M.tb bacilli in sputa relative to aerobic log phase growth before chemotherapy (D0) and 3 days (D3), 7 days (D7) and 14 days (D14) after beginning standard regimen drug therapy. a The 1337 genes significantly differentially expressed at any sputum timepoint compared to axenic log phase bacilli are displayed as rows; each patient/timepoint as columns. Colouring details fold change relative to log phase bacilli; red denoting up-regulation, blue repression. Adaptations to mycobacterial respiratory and metabolic state are summarized as text, listing key indicator genes that were significantly regulated at D0. Grey columns (A-D) mark in which comparison each gene was identified. Clear boxes signpost clusters of genes that were differentially expressed over time. b Quantitative RT-PCR verification of 10 genes as key indicators of M.tb physiological state measured in patient samples before treatment (day 0) and after 3, 7 and 14 days drug therapy. Genes induced in sputum icl, hspX, sigG, tgs1 and prpC and genes repressed in sputum atpE, kasA, nuoA, qcrC and ctaD. Log2 expression ratios are plotted; the y-axis detailing fold change relative to log phase bacilli. Error bars mark the standard error of the mean