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Mycobacteriology and Aerobic Actinomycetes

How Well Do Routine Molecular Diagnostics Detect Rifampin Heteroresistance in Mycobacterium tuberculosis?

Kamela C. S. Ng, Philip Supply, Frank G. J. Cobelens, Cyril Gaudin, Julian Gonzalez-Martin, Bouke C. de Jong, Leen Rigouts
Geoffrey A. Land, Editor
Kamela C. S. Ng
aMycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
bDepartment of Global Health and Amsterdam Institute for Global Health and Development, Amsterdam UMC, Location Academic Medical Center, Amsterdam, The Netherlands
cServei de Microbiologia, Centre de Diagnòstic Biomèdic, Hospital Clínic, Institut de Salut Global de Barcelona, Universitat de Barcelona, Barcelona, Spain
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  • ORCID record for Kamela C. S. Ng
Philip Supply
dUniversity Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019, UMR 8204, Center for Infection and Immunity of Lille (CIIL), Lille, France
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Frank G. J. Cobelens
bDepartment of Global Health and Amsterdam Institute for Global Health and Development, Amsterdam UMC, Location Academic Medical Center, Amsterdam, The Netherlands
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Cyril Gaudin
eGenoscreen, Lille, France
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Julian Gonzalez-Martin
cServei de Microbiologia, Centre de Diagnòstic Biomèdic, Hospital Clínic, Institut de Salut Global de Barcelona, Universitat de Barcelona, Barcelona, Spain
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Bouke C. de Jong
aMycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
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Leen Rigouts
aMycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
fDepartment of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
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Geoffrey A. Land
Carter BloodCare and Baylor University Medical Center
Roles: Editor
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DOI: 10.1128/JCM.00717-19
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    FIG 1

    Presence/absence of Xpert Ultra wild-type and mutant melt probes detected for the rifampin-resistant (RR):rifampin-susceptible (RS) mixtures per mutation type at various proportions of the minority resistant variants at the limit of detection (LOD) reported as heteroresistant (shaded in yellow), below LOD reported as RS (shaded in pink), and at full RR reported as resistant (shaded in green).

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  • TABLE 1

    Proportions of minority resistant variants detected among the rifampin-resistant:rifampin-susceptible mixtures by targeted deep sequencinga

    TABLE 1
    • ↵a The values represent the percentage of sequence reads bearing the indicated rpoB mutation. Gray boxes represent proportions below the nominal threshold of 3% for calling minority resistant variants used in the Deeplex-MycTB application.

  • TABLE 2

    Limits of detection for rifampin heteroresistance among triplicatesa

    Strain IDRifampin resistance-conferring mutationsValues by RDT quantified by Deeplex
    LPA-Hain (%LOD)1Deeplex (%QP)1LPA-Nipro (%LOD)1Deeplex (%QP)1Xpert (%LOD)1Deeplex (%QP)1Ultra (%LOD)2Deeplex (%QP)2
    TB-TDR-0036H445DbH526Dc5–107.557.540–6055.940–60
    TB-TDR-0090S450LbS531Lc551–5520–4021.720–3021.7
    TB-TDR-0100D435VbD516Vc5–1065–10670–8069.640–50
    TB-TDR-0131H445YbH526Yc5–104.3108.770–8066.760–70
    • ↵a With quantification of the respective lowest proportion by targeted deep sequencing (Deeplex-MycTB). ID, identifier; Deeplex-MycTB, targeted deep sequencing; RDT, rapid diagnostic test; LPA-Hain, GenoTypeMTDBRplusv2.0; LPA-Nipro, GenoscholarNTM+MTBII; Xpert, classic XpertMTB/RIF; Ultra, Xpert MTB/RIF Ultra; 1, batch 1; 2, batch 2; %LOD, limit of detection (range) among triplicates for the RDTs; %QP, quantified proportion of minority resistant variants determined by Deeplex on replicate 3.

    • ↵b In M. tuberculosis numbering.

    • ↵c In E. coli numbering.

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      Tables S1 to S3 and Fig. S1 to S5

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How Well Do Routine Molecular Diagnostics Detect Rifampin Heteroresistance in Mycobacterium tuberculosis?
Kamela C. S. Ng, Philip Supply, Frank G. J. Cobelens, Cyril Gaudin, Julian Gonzalez-Martin, Bouke C. de Jong, Leen Rigouts
Journal of Clinical Microbiology Oct 2019, 57 (11) e00717-19; DOI: 10.1128/JCM.00717-19

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How Well Do Routine Molecular Diagnostics Detect Rifampin Heteroresistance in Mycobacterium tuberculosis?
Kamela C. S. Ng, Philip Supply, Frank G. J. Cobelens, Cyril Gaudin, Julian Gonzalez-Martin, Bouke C. de Jong, Leen Rigouts
Journal of Clinical Microbiology Oct 2019, 57 (11) e00717-19; DOI: 10.1128/JCM.00717-19
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KEYWORDS

Deeplex-MycTB
GenoscholarNTM+MDRTBII
GenoTypeMTBDRplusv2.0
Mycobacterium tuberculosis
XpertMTB/RIF
XpertMTB/RIF Ultra
limit of detection
rifampin heteroresistance
rifampin-resistant tuberculosis

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