Fighting Drug-Resistant Tuberculosis with Mykrobe Atlas
Turning the tide in Tuberculosis. Using whole-genome sequencing and mutation analysis to identify drug resistance at the point of care
Revolutionising the process of detecting anti-microbial resistance with Mykrobe Atlas
Tuberculosis (TB) is a bacterial infection. It’s spread by inhaling tiny droplets from the coughs or sneezes of an infected person.
It is the second leading infectious killer after COVID-19 (above HIV/AIDS). And it occurs in every part of the world. But almost 90% of new cases occur in 30 high-burden countries.
It is a serious condition but it’s curable with proper treatment using antibiotics. Antibiotic resistance, however, is a threat to TB care and prevention globally. It makes TB harder to treat and longer to treat. And the outcomes for patients are significantly poorer.
Comprehensive drug-susceptibility testing (DST)
Providing clinicians with information on drug resistance at the point of care. And public health programmes with real-time data to track outbreaks and improve control.
Over a seven-year engagement, we collaborated with expert Bioinformaticians from the Univesity of Oxford the European Bioinformatics Institute
to address these challenges using Whole Genome Sequencing, creating Mykrobe Atlas.
Mykrobe Predictor - Drug resistance prediction
Mykrobe analyses the whole genome of a bacterial sample. Using it to identify the species and antibiotic resistance profiles of Tuberculosis bacteria. And it does this in minutes. Which means it can be used effectively at the point of care.
Predictor supports the output of multiple sequencing machines. But importantly from the Oxford nanopore (https://nanoporetech.com/products/minion), a USB stick-sized sequencer that can be used in the field.
These two innovations together mean prediction is mobile. In high-burden locations - this is critical for treatment but also for surveillance.
Mykrobe Atlas adds scale to Predictor. A platform containing a secure library of sequence data. Containing drug resistance information for point-of-care treatment. But supporting analysis of outbreaks, surveillance, and anonymous collaboration between labs operating globally.
India has the highest number of tuberculosis cases in the world. With 300 million people affected, that’s 21% of the global total. We were fortunate enough to be part of a research trip to Mumbai supported by the Foundation for Medical Research and Hinduja Hospital. Understanding the issues faced at a local and national level informed the design and implementation of the platform.
Atlas is comprised of
- A rich sequence library and search containing 70000 sequence samples
- Upload and resistance prediction of new samples
- Indexing and analysis against the existing library to identify outbreaks. Tracking mutations over time and geographically
- Surveillance dashboards built to meet the needs of state and national eradication programmes
- Organisation management and secure controls