Clinical evaluation of the Xpert MTB/XDR assay for rapid detection of isoniazid, fluoroquinolone, ethionamide and second-line drug resistance: A cross-sectional multicentre diagnostic accuracy study
Authors: Penn-Nicholson Adam , Georghiou Sophia B. , Ciobanu Nelly , Kazi Mubin , Bhalla Manpreet , David Anura , Conradie Francesca , Ruhwald Morten , Crudu Valeriu , Rodrigues Camilla , Myneedu Vithal Prasad , Scott Lesley , Denkinger Claudia M , Schumacher Samuel G ,   Xpert XDR Trial Consortium
Published: May 2021

Background

The WHO End TB Strategy requires universal drug susceptibility testing and treatment of all people with tuberculosis. However, available second-line diagnostic tools are cumbersome and require sophisticated laboratory infrastructure, and ultimately less than half of those with drug-resistant tuberculosis receive appropriate treatment. Xpert MTB/XDR was developed to help overcome these limitations.

Methods

We assessed the diagnostic accuracy of sputum-based Xpert MTB/XDR for isoniazid, fluoroquinolone, ethionamide and second-line injectable resistance detection in adults with an Xpert MTB/RIF or Ultra Mycobacterium tuberculosis-positive result against a composite reference standard of phenotypic drug-susceptibility testing and whole genome sequencing (NCT03728725). Participants with pulmonary tuberculosis symptoms and ≥1 risk factor for drug resistance were consecutively enrolled between four clinical sites in India, Moldova and South Africa.

Findings

Between 31 July 2019 and 21 March 2020, we enrolled 710 patients, of which 611 (86.1%) had results from index and composite reference standard tests and were included in analysis. The sensitivity of Xpert MTB/XDR was 94% for isoniazid, 95% for fluoroquinolones, 54% for ethionamide, 73% for amikacin, 86% for kanamycin, and 61% for capreomycin resistance detection. Specificity was 98-100% for all drugs. Performance was equivalent to line-probe assays. The non-determinate rate of Xpert MTB/XDR was 2·96%.

Interpretation

This first prospective, multicentre clinical study of the Xpert MTB/XDR assay demonstrated high diagnostic test accuracy, meeting target product profile criteria for a next-generation drug susceptibility test.

Funding

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

Research in context

Evidence before this study

The World Health Organization (WHO) has highlighted the development of expanded, rapid molecular drug susceptibility tests as a key priority to tackle drug-resistant tuberculosis (TB). Prior to the Cepheid Xpert MTB/XDR assay, the only WHO-recommended rapid molecular assay for second-line resistance detection was the Bruker-Hain GenoType MTBDRsl line probe assay. However, the high complexity of DNA-based hybridization assays limits their use to central reference or regional-level laboratories where the appropriate infrastructure and user expertise can be ensured. In this context, the Xpert MTB/XDR assay is the only lower complexity, automated molecular assay for broader resistance detection suitable for use at lower levels of the laboratory network. We searched PubMed databases for articles evaluating the performance of the sputum-based assay using search terms (tuberculosis or TB) AND (Xpert OR GeneXpert OR cartridge) AND (second-line OR XDR OR “extensively drug-resistant”) AND (sputum OR sputa) AND (test OR assay OR diagnostic OR “point of care”) AND (performance OR accuracy OR sensitivity OR specificity OR diagnos*). The search was done on 8 Feb 2021 with no search date or language restrictions. Our search yielded 51 studies, of which only three reported on a sputum-based cartridge for expanded resistance detection. The first two studies described the assay design approach and reported initial performance metrics for a prototype version of the Xpert MTB/XDR assay. In the third study, the manufacturer demonstrated high performance for the final assay (sensitivity of 94–100% and a specificity of 100% for all drugs except for ethionamide) when compared with sequencing for 314 sputum specimens and sediments. This study was the first assessment of Xpert MTB/XDR assay diagnostic accuracy in a prospective patient cohort.

Added value of this study

This is the first clinical study of the diagnostic performance of the Xpert MTB/XDR assay for expanded drug resistance detection. This study was performed independent of the manufacturer in settings of intended use utilizing prospectively collected primary clinical samples. The study employed a comprehensive reference standard using both phenotypic drug susceptibility testing and whole genome sequencing separately, as well as in combination, which allowed a differentiated view of performance of the assay for resistance detection. Moreover, we compared the performance of the assay on direct sputum samples with the performance of the WHO-recommended Bruker-Hain MTBDRplus and MTBDRsl line probe assays on culture.

Implications of all the available evidence

The WHO End TB Strategy calls for early diagnosis and universal access to drug susceptibility testing. With a 10-color calibration to GeneXpert instruments, the Xpert MTB/XDR assay expands upon the drug detection landscape of the Xpert MTB/RIF and Ultra assays and overcomes the limitations of the Bruker-Hain line probe assays to offer an option for lower-level health care centres to conduct rapid, expanded drug susceptibility testing in follow-up to a TB-positive result using existing laboratory infrastructure. Data from this study demonstrates that the Xpert MTB/XDR assay has high performance for a diverse clinical population in the intended setting of use, providing national TB programmes with a valuable tool for expanded drug susceptibility testing for all persons with signs and symptoms of TB.