Drug-resistance is a major barrier to global efforts to reduce incidence of TB, which was the second leading infectious killer after COVID-191 in 2020. The lack of rapid, accurate and information-rich tests for DR-TB is exacerbating its spread; major healthcare organisations and Non-Governmental Organisations (NGOs) have identified sequencing-based drug resistance testing as a priority. In 2019 the Seq&Treat programme was launched to investigate improved DR-TB detection by introducing and accelerating the uptake of sequencing in clinical settings.
Oxford Nanopore, together with QIB have successfully completed phase I of a DR-TB targeted next-generation sequencing (NGS) study as part of Seq&Treat, grant funded by Unitaid and led by the Foundation for Innovative New Diagnostics (FIND). This involved the development of a rapid end-to-end sequencing workflow to identify mutations associated with drug-resistance across the TB genome, directly from clinical samples as part of a research study.
The nanopore targeted sequencing solution succeeded in the Phase I analytical evaluation by reaching or surpassing the main World Health Organisation (WHO) performance targets including genotypic sensitivity (>98%), genotypic specificity (>98%), limit-of-detection (<1000 cells) failure rates (0%), turnaround time (target <24 hours, we achieved 8 hours) and ability to detect mixed resistance (≥10% heteroresistance detection).
Oxford Nanopore has now advanced to Phase II where the performance of the solution will be evaluated in a prospective clinical study in India, South Africa and Georgia from April 2022. Success in this and the final stage is anticipated to result in confirmation that the Oxford Nanopore sequencing solution meets the diagnostic performance criteria outlined in the NGS Target Product Profile (TPP) established by FIND/WHO for clinical diagnosis of drug resistant TB. The Oxford Nanopore sequencing solution is available today only as a life science research tool.
“We were really pleased to see that our nanopore sequencing-based targeted analysis has been so successful in phase I of this important research to tackle a major global killer with rapidly increasing drug resistance. Once validated, this has potential to be routinely used in resource-limited settings, where our MinION device can be used in distributed networks, as well as in more developed markets.” commented Gordon Sanghera, CEO Oxford Nanopore Technologies
“Tackling the biggest challenges to global health, like drug resistant TB, requires innovative solutions that deliver their benefits where and when they are needed. It’s therefore really exciting to see how the Quadram Institute has supported the development of this new tool to combat TB. We look forward to seeing its performance in clinical trials, and subsequently its deployment in those areas of the world where it will deliver real life-saving impact” Low cost, portable nanopore sequencing for DR-TB.” commented Dr Graeme Brown, Chief Business Officer, the Quadram Institute
Low cost, portable nanopore sequencing for Drug Resistant TB profiling
Today, TB remains one of the deadliest diseases in the world, with an estimated 10 million reported new cases in 2020, 1.5 million deaths and three million undiagnosed patients. Multi-drug resistant TB (MDR-TB) and extensively drug resistant TB (XDR-TB) are a major threat to TB control as they represent roughly 10% of diagnosed cases and treating affected patients is 50 to 200 times more expensive than patients with drug sensitive TB. Only about one in three people with drug DR-TB accessed treatment in 20201 leaving the majority of DR-TB patients without access to appropriate care.
Rapid and comprehensive detection of resistance, directly from patient samples (sputum or decontaminated sputum), is required to initiate appropriate therapy for DR-TB. Nanopore targeted sequencing can provide faster and more comprehensive data that has the potential to be used by clinicians to identify drug resistance better than current culture and molecular methods.
This is not the first time nanopore technology has been used in research to show the potential to tackle DR-TB. In a 2018 study, a research team investigated the possibility of point-of-care TB whole genome nanopore sequencing in rural Madagascar using the portable MinION device. This involved capacity building by training 20 local scientists to use nanopore technology for DR-TB DNA sequencing. The MinION’s portability, versatility, and low capital costs made this ideal for targeted next generation sequencing for DR-TB surveillance and has the potential to become a drug susceptibility testing (DST) solution. The team concluded that the research demonstrated this is a promising DST solution and found it provided rapid, clinically relevant data to help manage complex DR-TB. Full study presentation here.
- World Health Organization TB Factsheet 2021: https://www.who.int/news-room/fact-sheets/detail/tuberculosis