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    Nanopore sequencing for Mycobacterium tuberculosis: a critical review of the literature, new developments and future opportunities

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    Publication date
    2021-06
    Author
    Dippenaar, A.
    Goossens, S.N.
    Grobbelaar, M.
    Oostvogels, S.
    Cuypers, B.
    Laukens, K.
    Meehan, Conor J.
    Warren, R.M.
    van Rie, A.
    Keyword
    Mycobacterium tuberculosis sequencing
    Nanopore sequencing
    Oxford Nanopore Technologies (ONT)
    ONT sequencing
    Tuberculosis research
    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
    Gold
    
    Metadata
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    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.
    URI
    http://hdl.handle.net/10454/18521
    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
    https://doi.org/10.1128/JCM.00646-21
    Type
    Article
    Collections
    Life Sciences Publications

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