Additional file 1: Table S1. of Use of whole-genome sequencing to distinguish relapse from reinfection in a completed tuberculosis clinical trial

Spoligotype and sub-lineage information for isolates. (DOCX 23 kb

Additional file 3: Figure S2. of Blood and sputum eosinophils in COPD; relationship with bacterial load

A summary of the number of patients with blood / sputum eosinophil counts and qPCR data at exacerbation alone, or coupled to baseline measurements. PPM=potentially pathogenic microorganisms. (PPTX 51.6 kb

Additional file 1: of Blood and sputum eosinophils in COPD; relationship with bacterial load

Additional methods supplement. (DOCX 38.7 kb

Additional file 5: of Profiling persistent tubercule bacilli from patient sputa during therapy predicts early drug efficacy

Figure S1. An illustration of the computation process to test associations between transcriptional signatures and patient variables. Figure S2. Venn diagrams describing the overlapping transcriptional signatures of bacilli in sputum relative to aerobic log phase growth. Figure S3. Box and whisker plots mapping the differential expression of gene families. Figure S4. Hierarchical clustering of the mean M.tb transcriptional profiles derived from sputa. Figure S5. Venn diagram highlighting genes significantly induced 3 days after the start of drug therapy. Figure S6. Contrasting patient trajectories as defined by principle component analysis plotting day 0 and day 3 timepoints only. (PDF 526 kb

Additional file 2: Figure S1. of Blood and sputum eosinophils in COPD; relationship with bacterial load

Outline of the methods used for the processing of sputum qPCR and differential cell count samples. (PPTX 64.1 kb

Additional file 4: Figure S3. of Blood and sputum eosinophils in COPD; relationship with bacterial load

The blood eosinophil count at baseline and exacerbation in patients defined as PPM positive or PPM negative at exacerbation (PPM threshold value of 1x10 ). PPM=potentially pathogenic microorganisms. Dotted lines represent median values. (PPTX 274 kb

Additional file 6: Figure S4. of Blood and sputum eosinophils in COPD; relationship with bacterial load

The sputum neutrophil % at baseline and exacerbation in patients defined as PPM positive or PPM negative at exacerbation. PPM=potentially pathogenic microorganisms. Dotted lines represent median values. (PPTX 189 kb

Additional file 1: of Spot sputum samples are at least as good as early morning samples for identifying Mycobacterium tuberculosis

List of ethics committee approving the REMoxTB study. (DOCX 893 kb

Additional file 1: of Liver toxicity associated with tuberculosis chemotherapy in the REMoxTB study

Table S1. Daily dosing of TB medications for patients randomised into REMoxTB based on weight at screening. Table S2. The Roussel–Uclaf causality assessment method (RUCAM) for causality assessment of adverse drug reactions. Table S3. Child–Pugh scoring system for grading the prognosis of chronic liver disease. Figure S1. Graphs showing the median ALT and AST values for all patients at scheduled blood draws in all three treatment arms. (DOCX 318 kb

Additional file 2: of The use of digital PCR to improve the application of quantitative molecular diagnostic methods for tuberculosis

Protocol for gDNA extraction and dPCR quantification of materials. (PDF 394 kb