Nanopore Sequencing for Tuberculosis: Promise and Gaps in Current Evidence
A systematic review found only eight published studies applying Oxford Nanopore sequencing to M. tuberculosis, highlighting the technology's low uptake despite its portable, low-cost hardware and long-read capability. While promising for resource-limited TB-endemic settings, significant research investment is needed in software, accuracy validation, and clinical workflows before nanopore sequencing can be routinely deployed for TB diagnosis and resistance profiling.
The original study
Nanopore Sequencing for Mycobacterium tuberculosis: a Critical Review of the Literature, New Developments, and Future Opportunities.
- Authors
- Dippenaar A, Goossens SN, Grobbelaar M, Oostvogels S, Cuypers B, Laukens K, et al.
- Journal
- Journal of clinical microbiology
- Type
- Journal Article, Research Support, Non-U.S. Gov't, Systematic Review
- PMID
- 34133895
Original abstract
The next-generation, short-read sequencing technologies that generate comprehensive, whole-genome data with single nucleotide resolution have already advanced tuberculosis diagnosis, treatment, surveillance, and source investigation. Their high costs, tedious and lengthy processes, and large equipment remain major hurdles for research use in high tuberculosis burden countries and implementation into routine care. The portable next-generation sequencing devices developed by Oxford Nanopore Technologies (ONT) are attractive alternatives due to their long-read sequence capability, compact low-cost hardware, and continued improvements in accuracy and throughput. A systematic review of the published literature demonstrated limited uptake of ONT sequencing in tuberculosis research and clinical care. Of the 12 eligible articles presenting ONT sequencing data on at least one Mycobacterium tuberculosis sample, four addressed software development for long-read ONT sequencing data with potential applications for M. tuberculosis. Only eight studies presented results of ONT sequencing of M. tuberculosis, of which five performed whole-genome and three did targeted sequencing. Based on these findings, we summarize the standard processes, reflect on the current limitations of ONT sequencing technology, and the research needed to overcome the main hurdles. The low capital cost, portable nature and continued improvement in the performance of ONT sequencing make it an attractive option for sequencing for research and clinical care, but limited data are available on its application in the tuberculosis field. Important research investment is needed to unleash the full potential of ONT sequencing for tuberculosis research and care.