Investigating the quality of expectorated sputum for tuberculosis diagnosis in Bolivia

Transcriptional profiles predict treatment outcome in patients with tuberculosis and diabetes at diagnosis and at two weeks after initiation of anti-tuberculosis treatment

BACKGROUND

Globally, the tuberculosis (TB) treatment success rate is approximately 85%, with treatment failure, relapse and death occurring in a significant proportion of pulmonary TB patients. Treatment success is lower among people with diabetes mellitus (DM). Predicting treatment outcome early after diagnosis, especially in TB-DM patients, would allow early treatment adaptation for individuals and may improve global TB control.

METHODS

Samples were collected in a longitudinal cohort study of adult TB patients from South Africa (n  =  94) and Indonesia (n  =  81), who had concomitant DM (n  =  59), intermediate hyperglycaemia (n  =  79) or normal glycaemia/no DM (n  =  37). Treatment outcome was monitored, and patients were categorized as having a good (cured) or poor (failed, recurrence, died) outcome during treatment and 12 months follow-up. Whole blood transcriptional profiles before, during and at the end of TB treatment were characterized using unbiased RNA-Seq and targeted gene dcRT-MLPA.

FINDINGS

We report differences in whole blood transcriptome profiles, which were observed before initiation of treatment and throughout treatment, between patients with a good versus poor TB treatment outcome. An eight-gene and a 22-gene blood transcriptional signature distinguished patients with a good TB treatment outcome from patients with a poor TB treatment outcome at diagnosis (AUC = 0·815) or two weeks (AUC = 0·834) after initiation of TB treatment, respectively. High accuracy was obtained by cross-validating this signature in an external cohort (AUC = 0·749).

INTERPRETATION

These findings suggest that transcriptional profiles can be used as a prognostic biomarker for treatment failure and success, even in patients with concomitant DM.

FUNDING

The research leading to these results, as part of the TANDEM Consortium, received funding from the European Community's Seventh Framework Programme (FP7/2007-2013 Grant Agreement No. 305279) and the Netherlands Organization for Scientific Research (NWO-TOP Grant Agreement No. 91214038). The research leading to the results presented in the Indian validation cohort was supported by Research Council of Norway Global Health and Vaccination Research (GLOBVAC) projects: RCN 179342, 192534, and 248042, the University of Bergen (Norway).

Application of Next Generation Sequencing for Diagnosis and Clinical Management of Drug-Resistant Tuberculosis: Updates on Recent Developments in the Field

The World Health Organization’s End TB Strategy prioritizes universal access to an early diagnosis and comprehensive drug susceptibility testing (DST) for all individuals with tuberculosis (TB) as a key component of integrated, patient-centered TB care. Next generation whole genome sequencing (WGS) and its associated technology has demonstrated exceptional potential for reliable and comprehensive resistance prediction for Mycobacterium tuberculosis isolates, allowing for accurate clinical decisions. This review presents a descriptive analysis of research describing the potential of WGS to accelerate delivery of individualized care, recent advances in sputum-based WGS technology and the role of targeted sequencing for resistance detection. We provide an update on recent research describing the mechanisms of resistance to new and repurposed drugs and the dynamics of mixed infections and its potential implication on TB diagnosis and treatment. Whilst the studies reviewed here have greatly improved our understanding of recent advances in this arena, it highlights significant challenges that remain. The wide-spread introduction of new drugs in the absence of standardized DST has led to rapid emergence of drug resistance. This review highlights apparent gaps in our knowledge of the mechanisms contributing to resistance for these new drugs and challenges that limit the clinical utility of next generation sequencing techniques. It is recommended that a combination of genotypic and phenotypic techniques is warranted to monitor treatment response, curb emerging resistance and further dissemination of drug resistance.

Whole-genome sequencing and Mycobacterium tuberculosis: Challenges in sample preparation and sequencing data analysis

The numbers of patients with tuberculosis (TB) caused by resistant strains are still alarming. Therefore, it is necessary to determine resistance more quickly and precisely, than it is with the currently used phenotypic and genotypic methods. In recent years, technological advances have been made and the whole-genome sequencing (WGS) method has been introduced as a part of routine diagnostics in clinical laboratories. Comparing a wide range of mycobacterial genomic variations with a reference genome leads to a consistent evaluation of molecular-epidemiology and resistance of Mycobacterium tuberculosis (M. tuberculosis) to a wide range of anti-TB drugs. The quality of the obtained sequencing data is closely related to the type of sample and the method used for DNA extraction and sequencing library preparation. Moreover, the correct interpretation of results is also influenced by a bioinformatic data processing. A large number of bioinformatics pipelines are currently available, the sensitivity of which varies due to the different sizes of databases containing relevant mutations. This review focuses on the individual steps included in the sequencing workflow and factors that may affect the interpretation of final results.

Does mobile phone instructional video demonstrating sputum expectoration improve the sputum sample quality and quantity in presumptive pulmonary TB cases? Protocol for a prospective pragmatic non-randomised controlled trial in Karnataka state, India

INTRODUCTION

Sputum smear microscopy is the cornerstone of tuberculosis (TB) diagnosis under the Revised National Tuberculosis Control Programme (RNTCP) in India. Instructions on how to produce a good sputum sample are a part of RNTCP training manuals, but its assessment is not emphasised. Healthcare provider's instruction to expectorate a good sputum sample has limitations. Presumptive TB patients often submit inadequate (in quantity and/or quality) sputum samples, which may result in false-negative results. Objectives of the study are, among the selected RNTCP designated microscopy centres in Dakshina Kannada district, Karnataka, India, (a) to assess the effectiveness of mobile phone instructional video demonstrating sputum expectoration on sputum quality and quantity and (b) to explore the mobile phone video implementation challenges as perceived by the healthcare providers.

METHODS AND ANALYSIS

This is a pragmatic, prospective, non-randomised controlled trial in two pairs of RNTCP Designated Microscopy Centres (located at secondary and primary healthcare facilities) of Dakshina Kannada district, India. Presumptive pulmonary TB patients aged ≥18 years will be included. We will exclude who are severely ill, blind, hearing impaired, patients who have already brought their sputum for examination, and transported sputum. In the intervention group, participants will watch a mobile phone instructional video demonstrating submission of an adequate sputum sample. The control group will follow the usual ongoing procedure for sputum submission. This study would require 406 participants for each group to achieve a power of 90% for detecting a difference of 15% between the two groups. The participant enrolment started in December 2019.

ETHICS AND DISSEMINATION

Yenepoya University Ethics Committee, Mangaluru, India, has approved the study protocol (YEC-1/158/2019). It complies with the Declaration of Helsinki, local laws, and the International Council for Harmonization-good clinical practices. Investigators will present the results in scientific forums, publish in a scientific journal, and share with RNTCP officers.

TRIAL REGISTRATION NUMBER

Clinical Trial Registry of India (CTRI/2019/06/019887).

Removing the bottleneck in whole genome sequencing of Mycobacterium tuberculosis for rapid drug resistance analysis: a call to action

Whole genome sequencing (WGS) can provide a comprehensive analysis of Mycobacterium tuberculosis mutations that cause resistance to anti-tuberculosis drugs. With the deployment of bench-top sequencers and rapid analytical software, WGS is poised to become a useful tool to guide treatment. However, direct sequencing from clinical specimens to provide a full drug resistance profile remains a serious challenge. This article reviews current practices for extracting M. tuberculosis DNA and possible solutions for sampling sputum. Techniques under consideration include enzymatic digestion, physical disruption, chemical degradation, detergent solubilization, solvent extraction, ligand-coated magnetic beads, silica columns, and oligonucleotide pull-down baits. Selective amplification of genomic bacterial DNA in sputum prior to WGS may provide a solution, and differential lysis to reduce the levels of contaminating human DNA is also being explored. To remove this bottleneck and accelerate access to WGS for patients with suspected drug-resistant tuberculosis, it is suggested that a coordinated and collaborative approach be taken to more rapidly optimize, compare, and validate methodologies for sequencing from patient samples.