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Advances in tuberculosis diagnostics: the Xpert MTB/RIF assay and future prospects for a point-of-care test

https://doi.org/10.1016/S1473-3099(13)70008-2Get rights and content

Summary

Rapid progress has been made in the development of new diagnostic assays for tuberculosis in recent years. New technologies have been developed and assessed, and are now being implemented. The Xpert MTB/RIF assay, which enables simultaneous detection of Mycobacterium tuberculosis (MTB) and rifampicin (RIF) resistance, was endorsed by WHO in December, 2010. This assay was specifically recommended for use as the initial diagnostic test for suspected drug-resistant or HIV-associated pulmonary tuberculosis. By June, 2012, two-thirds of countries with a high tuberculosis burden and half of countries with a high multidrug-resistant tuberculosis burden had incorporated the assay into their national tuberculosis programme guidelines. Although the development of the Xpert MTB/RIF assay is undoubtedly a landmark event, clinical and programmatic effects and cost-effectiveness remain to be defined. We review the rapidly growing body of scientific literature and discuss the advantages and challenges of using the Xpert MTB/RIF assay in areas where tuberculosis is endemic. We also review other prospects within the developmental pipeline. A rapid, accurate point-of-care diagnostic test that is affordable and can be readily implemented is urgently needed. Investment in the tuberculosis diagnostics pipeline should remain a major priority for funders and researchers.

Introduction

The global burden of tuberculosis is unacceptably high (panel 1)1 and multidrug-resistant (MDR) tuberculosis is now a major health challenge worldwide. Of notified cases of pulmonary tuberculosis in 2011, an estimated 310 000 new cases were MDR, defined by active infection with Mycobacterium tuberculosis that is resistant to isoniazid and rifampicin.1 To eliminate tuberculosis as a public health problem by 2050, incidence will have to fall by an average of 16% per year for the next 40 years.2 Rates, however, are only declining at 2% per year.1 The scale of the disease burden is compounded by the intersection of the HIV and tuberculosis epidemics and by the global spread of MDR tuberculosis and extensively drug-resistant (XDR) tuberculosis (panel 1). Despite major efforts to increase case detection, an estimated third of new tuberculosis cases are still being missed each year, and the unavailability of a rapid, low-cost, accurate diagnostic assay that can be used at the point of care is a major hindrance.

Key messages

  • The Xpert MTB/RIF assay is a landmark development in tuberculosis diagnostics and yet it does not fulfil requirements as a point-of-care assay

  • One Xpert MTB/RIF test on sputum detects 90% of pulmonary tuberculosis (99% of smear-positive disease and about 75% of smear-negative disease)

  • High sensitivity of Xpert MTB/RIF for rifampicin resistance is accompanied by some false-positive results (which might be reduced by the new G4 version of the assay) and confirmatory drug sensitivity testing is needed

  • Despite substantial price discounting and relative simplicity of use, implementation of the Xpert MTB/RIF assay is hindered by several factors

  • Studies of clinical and programmatic effects and associated cost-effectiveness of the Xpert MTB/RIF assay are needed

  • Greater funding for research and development for a simple, low-cost, accurate point-of-care assay is needed

Low-income and middle-income countries, which bear most of the global burden of tuberculosis, rely heavily on outdated tuberculosis diagnostic tests, including sputum smear microscopy, solid culture, and chest radiography. These tests do not have sufficient sensitivity or specificity, are too slow, or are not available at the periphery of the health system where patients first seek care. Opportunities to intervene early in the disease are therefore lost. Global capacity for drug susceptibility testing (DST) is inadequate and only 9% of the estimated 630 000 prevalent cases of MDR tuberculosis worldwide in 2011 were diagnosed and notified.1, 3

For the past 5 years, the development of diagnostics for tuberculosis has progressed rapidly (figure).4 Old technologies have been reviewed and improved and new technologies have been developed, evaluated, and implemented. With a growing evidence base, WHO issued ten policy statements between 2007 and 2012 about tuberculosis diagnosis and diagnostic methods, which shows the progress that has been made. These policy statements address improvements in sputum smear microscopy,5, 6, 7, 8 use of commercial and non-commerical culture-based systems for diagnosis and DST,9, 10 and implementation of line-probe assays11 for rapid molecular diagnosis of drug resistance. Negative recommendations were issued about the use of serodiagnostic tests and interferon-gamma release assays for diagnosis of tuberculosis or latent M tuberculosis infection in low-income and middle-income countries.12, 13 After initial endorsement in December, 2010, WHO issued a policy statement in 2011, on the Xpert MTB/RIF automated molecular assay for rapid diagnosis of tuberculosis and detection of rifampicin resistance.14 Specifically, the assay was strongly recommended for use as the initial diagnostic test in individuals suspected of having MDR or HIV-associated tuberculosis.15 The assay was also conditionally recommended as a follow-on test to microscopy in settings where MDR tuberculosis and HIV-associated tuberculosis are less of a concern.

The development of the Xpert MTB/RIF assay is a landmark event in tuberculosis research, and this article summarises what is known about this assay, its assessment in different settings, and its implementation. Despite many compelling attributes of this new diagnostic test, the Xpert MTB/RIF assay is by no means the ideal test. We discuss the challenges associated with its use in resource-limited settings and review other important developments and future prospects within the diagnostics developmental pipeline.

Section snippets

Development of the Xpert MTB/RIF assay

The GeneXpert diagnostic system was originally developed by Cepheid (Sunnyvale, CA, USA) for rapid detection of anthrax,16 and was deployed for this purpose by the US Postal Service to permit rapid detection of mail contamination in sorting offices. It is a self-contained, fully integrated, automated platform that can be used with minimal technical skills. The cartridge-based system incorporates microfluidics technology and fully automated nucleic acid analysis to purify, concentrate, detect,

Preclinical laboratory-based assessment

A thorough preclinical assessment of analytic performance and biosafety of the Xpert MTB/RIF assay was done.17 By spiking defined numbers of M tuberculosis bacilli into clinical sputum samples from patients without tuberculosis, the limit of detection (95% reliability for detection) of the assay was 131 colony forming units (cfu)/mL (95% CI 106–176) of sputum.22 This result contrasts with the limit of detection of automated mycobacterial liquid culture, which is about 10–50 cfu/mL, and with

Diagnostic accuracy of the Xpert MTB/RIF assay for pulmonary tuberculosis

Many studies in both high-income and resource-limited settings of the diagnostic accuracy of the Xpert MTB/RIF assay for pulmonary tuberculosis have been published.17, 26 The multicountry assessment done by the Foundation for Innovative and New Diagnostics (FIND), published in 2010,27 enrolled 1730 patients suspected of having drug-sensitive or drug-resistant tuberculosis at five study sites in South Africa, Peru, Azerbaijan, and India. One direct test on sputum detected 551 (98·2%) of 561

Diagnostic accuracy for extrapulmonary tuberculosis

The Xpert MTB/RIF assay was developed, optimised, assessed, and endorsed specifically for the detection of pulmonary tuberculosis using sputum. More recently, however, assessments of the assay have extended to various non-respiratory clinical samples from patients with extrapulmonary tuberculosis. Investigation for use in extrapulmonary tuberculosis is far more complex because of the diversity of clinical sample types, difficulties in obtaining adequate tissue for analyses, the challenge of

Diagnostic accuracy in children

Microbiological confirmation of tuberculosis is possible only in a small minority of the children treated for the disease, and the time to diagnosis by culture is often prolonged. Table 2 summarises data from five studies on the use of the Xpert MTB/RIF assay to diagnose pulmonary and extrapulmonary tuberculosis in children. Using culture as the reference standard, four of these studies reported that the sensitivity of the Xpert MTB/RIF assay for pulmonary tuberculosis was about two to three

Diagnostic accuracy in people living with HIV

Diagnosis of HIV-associated tuberculosis is a huge challenge.47, 48 Table 3 summarises seven studies of patients infected with HIV, comparing the sensitivity of sputum microscopy and the Xpert MTB/RIF assay with culture as the reference standard. The median sensitivity of smear microscopy was 52·8% (range 22·2–68·9) compared with 84·0% (58·3–91·7) with the Xpert MTB/RIF assay. In all seven studies, the sensitivity of the Xpert MTB/RIF assay exceeded that of microscopy with a median increment of

Xpert MTB/RIF assay for active pulmonary tuberculosis case finding

In addition to screening for tuberculosis before antiretroviral therapy,51 use of the Xpert MTB/RIF assay for active case finding is being explored in other clinical populations. This assay might enable active tuberculosis screening to be done within antenatal clinics in high tuberculosis burden settings,56 for example, although data are awaited. If this assay was done at point-of-care, screening could be much more readily integrated into the antenatal care pathway. The Xpert MTB/RIF assay has

Rifampicin resistance

Despite the first large-scale multicountry assessment of the Xpert MTB/RIF assay by FIND reporting high specificity for detection of rifampicin resistance,27 several subsequent studies have reported cases of confirmed false-positive rifampicin resistance detected with the original version of the assay.50, 51, 59, 60, 61 Although absolute numbers of such cases have been quite small, this drawback is a substantial problem for clinical decision making in settings where the prevalence of rifampicin

Costs and cost-effectiveness

The high cost of this technology (similar to that of liquid culture, but far exceeding that of smear microscopy) is seen as a key hurdle to implementation.66, 67 FIND negotiated a discounted pricing structure applicable to 145 high burden and developing countries.68 A four module GeneXpert platform and linked computer costs about US$17 000 (more than 60% lower than elsewhere). Compared with cartridge costs of roughly $65 in the European Union, discounted costs were initially $18·68 per

Implementation and scale-up of the Xpert MTB/RIF assay

WHO policy guidance on the Xpert MTB/RIF assay has been incorporated into national guidelines by a third of reporting countries.1 Two-thirds of high tuberculosis burden countries and a half of high MDR tuberculosis burden countries have already incorporated the assay into their revised diagnostic policies. Up to the end of June, 2012, 1·1 million test cartridges were procured by 67 (46%) of the 145 countries eligible to purchase them at FIND-negotiated concessional prices.1, 4 Scale-up is

Challenges associated with implementation

Panel 2 summarises the key strengths and weaknesses of the Xpert MTB/RIF assay and panel 3 summarises the potential benefits as well as the challenges of Xpert MTB/RIF assay implementation for routine use in resource-limited settings.66, 75 Increased diagnosis of drug-sensitive tuberculosis and MDR tuberculosis should be matched by expanded capacity to effectively treat these cases, including a scale-up in quality MDR tuberculosis treatment facilities and trained staff. Rigorous quality

Other advances in tuberculosis diagnostic tests

Further developments in nucleic acid amplification test (NAAT) technology are promising.4 A simplified manual NAAT using loop-mediated isothermal amplification with a simple visual colorimetric read-out is being assessed for use in peripheral laboratory facilities in resource-limited settings.4, 79 However, fully automated systems that use isothermal amplification and operate at lower temperatures could potentially be used outside the laboratory environment.4, 80 Hand-held systems the size of a

Future prospects for point-of-care diagnosis

The ideal test for tuberculosis will be a true point-of-care assay that enables accurate diagnosis of tuberculosis and detection of drug resistance within the time of a clinic consultation, and one that can be implemented at all levels of the health system for adults and children, with and without HIV.93 Although the Xpert MTB/RIF assay undoubtedly represents an important breakthrough and step forward towards this ideal, its high relative cost, sophisticated hardware, and constraints for

Conclusions

The emergence of the Xpert MTB/RIF assay represents a major step forward in tuberculosis diagnostics. Although this assay is not perfect, the advantages offered in settings with high disease burdens and high rates of drug-resistant and HIV-associated tuberculosis convinced a country such as South Africa to adopt this technology as the initial diagnostic test for pulmonary tuberculosis. More wide-scale implementation of the Xpert MTB/RIF assay will provide data on clinical effect and

Search strategy and selection criteria

We searched PubMed and Google Scholar (Jan 1, 1995, to Dec 24, 2012), the Cochrane library (Jan 1, 2001, to Dec 24, 2012), and Embase (Jan 1, 2001, to Dec 24, 2012) for reports published in English with the terms “tuberculosis”, “Mycobacterium tuberculosis”, “TB diagnostic tests”, “TB diagnosis”, “clinical trials”, “Xpert MTB/RIF assay”, “GeneXpert”, “Cepheid”, “accuracy”, “sensitivity”, and “specificity”. We also searched the website of the STOP TB Partnership's New Diagnostic Working Group.

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