Proof of Concept: MAGMA-MICK
The TORCH consortium, founded by Prof Van Rie at the University of Antwerp, developed MAGMA (Maximum Accessible Genome for Mtb Analysis), an easy-to-use bioinformatics pipeline specifically created for the analysis of Mtb sequencing data for clinical and public health applications (https://doi.org/10.1371/journal.pcbi.1011648). Even though MAGMA was developed with end-users in mind, the interpretation of resistance profiles and transmission clusters will remain challenging for doctors and public health workers who typically lack bioinformatics expertise. The MAGMA databases and software will also need regular updates and maintenance to remain up-to-date with the rapid scientific developments.
To meet these challenges and facilitate the clinical implementation of MAGMA technologies we are working with Sequentia Biotech, a commercial bioinformatics company with experience in clinical bioinformatics pipelines. Information obtained through surveys with end-users and stakeholders, Sequentia Biotech integrating MAGMA into their proprietary MICK data infrastructure, to create MAGMA-MICK, a web platform that generates automated, reliable, and actionable outputs. For doctors, we report and visualize the drug resistance profiles and translate these into the optimal treatment regimen for their patients, thus enabling the use of precision medicine for RR-TB. For regional and national DR-TB reference laboratories, we are working together with EPCON to create a dashboard that monitors resistance to ‘old’ TB drugs (such as rifampicin, isoniazid, pyrazinamide and fluoroquinolones) and emergence of resistance to new TB drugs (including bedaquiline, linezolid, delanamid and pretonamid). For contact tracing units, we translate the phylogenetic data generated by MAGMA into a dynamic and interactive display of transmission events with identification of superspreading and ‘high risk’ drug resistance profiles to target public health actions, thus enabling a precision public health approach to RR-TB control.