The MAGMA platform for global and equitable WGS-guided management of drug resistant TB and TB control
V Rennie(2) T H Heupink(2) L Verboven(2) J Membrebe(3) A G Paytuví(1) R Malinverni(1) É M Martínez(1) W Sanseverino(1) A Van Rie(2)
1:Sequentia Biotech SL, Calle Comte d’Urgell 240, 08036 Barcelona, Spain; 2:Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, Wilrijk, Belgium; 3:Interuniversity Institute for Biostatistics and statistical Bioinformatics (I-BIOSTAT), Data Science Institute, Hasselt University, Hasselt, Belgium
Whole genome sequencing (WGS) holds great potential for the management and control of tuberculosis and is increasingly implemented in high income countries. In these settings, laboratories mostly use non-standardized in-house bioinformatics pipelines. Commonly used freely available bioinformatics pipelines (such as MTBSeq and UVP) were developed for retrospective rather than real-time analyses and struggle to accurately analyze clinical samples characterized by high contamination and low Mtb burden. The MAGMA (Maximum Accessible Genome for Mtb Analysis) pipeline was specifically developed for analysis of WGS data obtained from DNA extracted directly from sputum samples or from early positive primary liquid Mtb cultures. However, the interpretation of MAGMA pipeline outputs, such as drug resistance profile and phylogenetic information on clusters and recent transmission, requires a level of expertise that is often lacking in settings with high TB burden. To make WGS-guided care globally implementable, bioinformatics pipelines must produce outputs that are trustworthy, easily interpretable, and actionable by clinicians caring for TB patients, reference laboratories, and public health professionals working in TB control programs. The MAGMA platform aims to create standardized, user-friendly, actionable outputs. These outputs can be used for precision public health (targeted contact and source investigation), resistance surveillance (prevalence of resistance and emergence of new resistance conferring variants), and precision medicine (personalized treatment for drug resistant TB). Once developed and field-tested, the MAGMA platform could remove the current expertise and infrastructure bottlenecks and enable equitable global implementation of WGS-guided TB control and drug resistant TB management.