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Editorial
. 2021 Mar 18;57(3):2004077.
doi: 10.1183/13993003.04077-2020. Print 2021 Mar.

Targeted next-generation sequencing: a Swiss army knife for mycobacterial diagnostics?

Sagal Mohamed  1 , Claudio U Köser  2 , Max Salfinger  3 , Wladimir Sougakoff  4 , Scott K Heysell  1
Affiliations
Editorial

Targeted next-generation sequencing: a Swiss army knife for mycobacterial diagnostics?

Sagal Mohamed et al. Eur Respir J. .
No abstract available

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Conflict of interest statement

Conflict of interest: S. Mohamed has nothing to disclose. Conflict of interest: C.U. Köser reports personal fees for consultancy from World Health Organization, TB Alliance, Becton Dickinson, QuantuMDx and Foundation for Innovative New Diagnostics (including work for Cepheid Inc. and Hain Lifescience), other (travel and accommodation support to attend meetings) from Hain Lifescience, other (collaboration) from YD Diagnostics, outside the submitted work; is an unpaid advisor to GenoScreen. Conflict of interest: M. Salfinger has nothing to disclose. Conflict of interest: W. Sougakoff has nothing to disclose. Conflict of interest: S.K. Heysell has nothing to disclose.

Figures

FIGURE 1
FIGURE 1
Functionality of selected first-generation nucleic acid amplification tests (NAATs) for Mycobacterium tuberculosis complex (MTBC) diagnostics compared with targeted next-generation sequencing (NGS) and whole genome sequencing (WGS). All currently World Health Organization-endorsed NAATs are listed and underlined [10]. Additional assays are included but many more exist. Unless otherwise marked (#), the assays are only capable of identifying MTBC rather than differentiating nontuberculous mycobacteria. Cluster analysis is not currently a feature of Spit Seq but could be integrated and the resolution of Deeplex is considerably lower than WGS in this context. AMK: amikacin; AST: antimicrobial susceptibility testing; BDQ: bedaquiline; CAP: capreomycin; CFZ: clofazimine; EMB: ethambutol; ETH: ethionamide; FQs: fluoroquinolones; INH: isoniazid; KAN: kanamycin; LZD: linezolid; PZA: pyrazinamide; RIF: rifampicin; RUO: research use only; STR: streptomycin.
See this image and copyright information in PMC

Comment on

References

    1. Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH. List of Prokaryotic Names with Standing in Nomenclature. Genus Mycobacterium. https://lpsn.dsmz.de/genus/mycobacterium Date last accessed: 29 Oct 2020.
    1. Daley CL, Iaccarino JM, Lange C, et al. Treatment of nontuberculous mycobacterial pulmonary disease: an official ATS/ERS/ESCMID/IDSA clinical practice guideline. Eur Respir J 2020; 56: 2000535. - PMC - PubMed
    1. Banaei N, Musser KA, Salfinger M, et al. Novel assays/applications for patients suspected of mycobacterial diseases. Clin Lab Med 2020; 40: 535–552. - PubMed
    1. Adjemian J, Daniel-Wayman S, Ricotta E, et al. Epidemiology of nontuberculous mycobacteriosis. Semin Respir Crit Care Med 2018; 39: 325–335. - PMC - PubMed
    1. Köser CU, Ellington MJ, Cartwright EJ, et al. Routine use of microbial whole genome sequencing in diagnostic and public health microbiology. PLoS Pathog 2012; 8: e1002824. - PMC - PubMed

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