Loading...
Nanopore sequencing for Mycobacterium tuberculosis: a critical review of the literature, new developments and future opportunities
Dippenaar, A. Goossens, S.N. Grobbelaar, M. Oostvogels, S. Cuypers, B. Laukens, K. Meehan, Conor J. Warren, R.M. van Rie, A.
Dippenaar, A.
Goossens, S.N.
Grobbelaar, M.
Oostvogels, S.
Cuypers, B.
Laukens, K.
Meehan, Conor J.
Warren, R.M.
van Rie, A.
Publication Date
2021-06
End of Embargo
Supervisor
Rights
© 2021 Dippenaar et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.
Peer-Reviewed
Yes
Open Access status
openAccess
Accepted for publication
2021-06-16
Institution
Department
Awarded
Embargo end date
Collections
Additional title
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. Summary: 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 is 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.
Version
Accepted manuscript
Citation
Dippenaar A, Goossens SN, Grobbelaar M, Oostvogels S, Cuypers B, Laukens K, Meehan CJ, Warren RM and van Rie A (2021) Nanopore sequencing for Mycobacterium tuberculosis: a critical review of the literature, new developments and future opportunities. Journal of Clinical Microbiology. 60(1).
Link to publisher’s version
Link to published version
Link to Version of Record
Type
Article