Detection of isoniazid, fluoroquinolone, ethionamide, amikacin, kanamycin, and capreomycin resistance by the Xpert MTB/XDR assay: a cross-sectional multicentre diagnostic accuracy study


The WHO End TB Strategy requires drug susceptibility testing and treatment of all
people with tuberculosis, but second-line diagnostic testing with line-probe assays
needs to be done in experienced laboratories with advanced infrastructure. Fewer than
half of people with drug-resistant tuberculosis receive appropriate treatment. We
assessed the diagnostic accuracy of the rapid Xpert MTB/XDR automated molecular assay
(Cepheid, Sunnyvale, CA, USA) to overcome these limitations.


We did a prospective study involving individuals presenting with pulmonary tuberculosis
symptoms and at least one risk factor for drug resistance in four sites in India (New
Delhi and Mumbai), Moldova, and South Africa between July 31, 2019, and March 21,
2020. The Xpert MTB/XDR assay was used as a reflex test to detect resistance to isoniazid,
fluoroquinolones, ethionamide, amikacin, kanamycin, and capreomycin in adults with
positive results for Mycobacterium tuberculosis complex on Xpert MTB/RIF or Ultra (Cepheid). Diagnostic performance was assessed
against a composite reference standard of phenotypic drug-susceptibility testing and
whole-genome sequencing. This study is registered with, number NCT03728725.


Of 710 participants, 611 (86%) had results from both Xpert MTB/XDR and the reference
standard for any drug and were included in analysis. Sensitivity for Xpert MTB/XDR
detection of resistance was 94% (460 of 488, 95% CI 92–96) for isoniazid, 94% (222
of 235, 90–96%) for fluoroquinolones, 54% (178 of 328, 50–61) for ethionamide, 73%
(60 of 82, 62–81) for amikacin, 86% (181 of 210, 81–91) for kanamycin, and 61% (53
of 87, 49–70) for capreomycin. Specificity was 98–100% for all drugs. Performance
was equivalent to that of line-probe assays. The non-determinate rate of Xpert MTB/XDR
(ie, invalid M tuberculosis complex detection) was 2·96%.


The Xpert MTB/XDR assay showed high diagnostic accuracy and met WHO’s minimum target
product profile criteria for a next-generation drug susceptibility test. The assay
has the potential to diagnose drug-resistant tuberculosis rapidly and accurately and
enable optimum treatment.


German Federal Ministry of Education and Research through KfW, Dutch Ministry of Foreign
Affairs, and Australian Department of Foreign Affairs and Trade.

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