Performance of Xpert MTB/RIF Ultra: a matter of dead or alive
Authors: Sandra M Arend, Dick van Soolingen
Journal: The Lancet Infectious Diseases (2017)

In our opinion, the implementation of the Xpert MTB/RIF assay (Cepheid, Sunnyvale, CA, USA) since 2010 has revolutionised molecular diagnosis of (multidrug-resistant) tuberculosis. Xpert combines early diagnosis of tuberculosis with direct detection of rifampicin resistance, but the limitations of the assay are its suboptimal sensitivity and high rate of false positivity in low-prevalence settings. To overcome these limitations, the assay was re-engineered to increase diagnostic sensitivity and improve specificity in the detection of rifampicin resistance. The resulting Xpert MTP/RIF Ultra (Xpert Ultra) assay is run on the same device as Xpert and requires only a software upgrade.1Chakravorty S Simmons AM Rowneki M et al.The New Xpert MTB/RIF Ultra: Improving detection of Mycobacterium tuberculosis and resistance to rifampin in an assay suitable for point-of-care testing.Mbio. 2017; 8: e00812-e00817Crossref PubMed Scopus (314) Google Scholar In The Lancet Infectious Diseases, Susan Dorman and colleagues2Dorman SE Schumacher SG Alland D et al.Xpert MTB/RIF Ultra for detection of Mycobacterium tuberculosis and rifampin resistance: a multicentre diagnostic accuracy study.Lancet Infect Dis. 2017; (published online Nov 30.)http://dx.doi.org/10.1016/S1473-3099(17)30691-6Summary Full Text Full Text PDF PubMed Scopus (359) Google Scholar report the results of a comparison between Xpert Ultra with Xpert assay performance on sputum samples from 1753 patients tested at ten reference laboratories in eight tuberculosis high-endemic countries. Xpert and Xpert Ultra had roughly similar performance in the detection of rifampicin resistance, but Xpert Ultra had a higher overall sensitivity than Xpert (88% [95% CI 85–91] with Xpert Ultra vs 83% [79–86] with Xpert)—the difference being more pronounced in smear-negative cases (63% [54–71] vs 46% [37–55]) and in HIV co-infected cases (90% [83–90] vs 77% [68–84]).2Dorman SE Schumacher SG Alland D et al.Xpert MTB/RIF Ultra for detection of Mycobacterium tuberculosis and rifampin resistance: a multicentre diagnostic accuracy study.Lancet Infect Dis. 2017; (published online Nov 30.)http://dx.doi.org/10.1016/S1473-3099(17)30691-6Summary Full Text Full Text PDF PubMed Scopus (359) Google Scholar Xpert Ultra's improved sensitivity was, however, associated with a 2% lower specificity than Xpert (96% [94–97] vs 98% [97–99]). The specificity of Xpert Ultra for detection of Mycobacterium tuberculosis was even lower in patients with previous tuberculosis or from high-incidence countries. The increased sensitivity and reduced specificity of Xpert Ultra compared with Xpert translates into a higher negative predictive value but a lower positive predictive value. These effects, which seem counterintuitive, are shown in the figure in terms of Bayes' theorem of conditional probabilities (figure). Compared with a useless test, a positive test result increases and a negative test result decreases the probability of tuberculosis, but to a different extent for Xpert and Xpert Ultra. In terms of percentage, the increase in sensitivity of Xpert Ultra exceeds the decrease in specificity.2Dorman SE Schumacher SG Alland D et al.Xpert MTB/RIF Ultra for detection of Mycobacterium tuberculosis and rifampin resistance: a multicentre diagnostic accuracy study.Lancet Infect Dis. 2017; (published online Nov 30.)http://dx.doi.org/10.1016/S1473-3099(17)30691-6Summary Full Text Full Text PDF PubMed Scopus (359) Google Scholar However, the number of participants with culture-negative sputum (n=977) was twice that of participants with culture-positive sputum (n=462). The observed percentages thus correspond to an additional 25 patients with positive-culture sputum diagnosed early by Xpert Ultra but not by Xpert, at a cost of 26 additional false-positive Xpert Ultra results that were culture-negative. We assume the observed excess of false-positive Xpert Ultra results can be explained by detection of DNA from non-viable M tuberculosis, a phenomenon previously shown for Xpert.3Theron G Venter R Calligaro G et al.Xpert MTB/RIF results in patients with previous tuberculosis: can we distinguish true from false positive results?.Clin Infect Dis. 2016; 62: 995-1001Crossref PubMed Scopus (85) Google Scholar The origin of M tuberculosis DNA in sputum in the absence of viable bacilli could be residual tuberculosis lesions after treatment, as prolonged excretion of M tuberculosis DNA has been demonstrated.4Malherbe ST Shenai S Ronacher K et al.Persisting positron emission tomography lesion activity and Mycobacterium tuberculosis mRNA after tuberculosis cure.Nat Med. 2016; 22: 1094-1100Crossref PubMed Scopus (29) Google Scholar Perhaps we should view tuberculosis as a spectrum of diseases,5Barry 3rd, CE Boshoff HI Dartois V et al.The spectrum of latent tuberculosis: rethinking the biology and intervention strategies.Nat Rev Microbiol. 2009; 7: 845-855Crossref PubMed Scopus (988) Google Scholar, 6Cadena AM Fortune SM Flynn JL Heterogeneity in tuberculosis.Nat Rev Immunol. 2017; 17: 691-702Crossref PubMed Scopus (243) Google Scholar with subclinical, self-contained tuberculosis or even a stage of latent tuberculosis as other possible sources of M tuberculosis DNA in sputum. In the study by Dorman and colleagues,2Dorman SE Schumacher SG Alland D et al.Xpert MTB/RIF Ultra for detection of Mycobacterium tuberculosis and rifampin resistance: a multicentre diagnostic accuracy study.Lancet Infect Dis. 2017; (published online Nov 30.)http://dx.doi.org/10.1016/S1473-3099(17)30691-6Summary Full Text Full Text PDF PubMed Scopus (359) Google Scholar positive results due to DNA from dead bacilli are only named false positive because the gold standard was culture. Although both Xpert and Xpert Ultra are designed to detect M tuberculosis DNA, dead or alive, the clinical question is whether viable M tuberculosis is present. Thus, the tests answer a different question. By contrast, a study by Bahr and colleagues7Bahr NC Nuwagira E Evans EE et al.Diagnostic accuracy of Xpert MTB/RIF Ultra for tuberculous meningitis in HIV-infected adults: a prospective cohort study.Lancet Infect Dis. 2017; (published online Sept 14.)http://dx.doi.org/10.1016/S1473-3099(17)30474-7Summary Full Text Full Text PDF PubMed Scopus (193) Google Scholar compared Xpert Ultra with Xpert for detection of M tuberculosis in cerebrospinal fluid, showing that Xpert Ultra's sensitivity was superior even compared with culture. The specificity of both tests was very high and comparable because the gold standard was a clinical case definition, and detection of M tuberculosis DNA was always considered significant. We show the unambiguous advantages of Xpert Ultra (figure), which was named a possible game changer in that setting.8Khonga M Nicol MP Xpert MTB/RIF Ultra: a gamechanger for tuberculous meningitis?.Lancet Infect Dis. 2017; (published online Sept 14.)http://dx.doi.org/10.1016/S1473-3099(17)30536-4Summary Full Text Full Text PDF PubMed Scopus (13) Google Scholar The ultimate cause of detection of DNA from dead bacilli is its high stability, which is just what palaeomicrobiology makes use of; M tuberculosis DNA has even been detected in millennia-old human remains.9Donoghue HD Spigelman M Greenblatt CL et al.Tuberculosis: from prehistory to Robert Koch, as revealed by ancient DNA.Lancet Infect Dis. 2004; 4: 584-592Summary Full Text Full Text PDF PubMed Scopus (136) Google Scholar Interestingly, the target region for such studies was IS6110, one of the two multicopy sequences for which additional primers were included in Xpert Ultra.1Chakravorty S Simmons AM Rowneki M et al.The New Xpert MTB/RIF Ultra: Improving detection of Mycobacterium tuberculosis and resistance to rifampin in an assay suitable for point-of-care testing.Mbio. 2017; 8: e00812-e00817Crossref PubMed Scopus (314) Google Scholar A test that exclusively identifies viable M tuberculosis would be the solution, for example by detection of M tuberculosis mRNA or analysis of exhaled breath for organic volatile compounds of M tuberculosis.4Malherbe ST Shenai S Ronacher K et al.Persisting positron emission tomography lesion activity and Mycobacterium tuberculosis mRNA after tuberculosis cure.Nat Med. 2016; 22: 1094-1100Crossref PubMed Scopus (29) Google Scholar, 10Coronel Teixeira R Rodriguez M Jimenez de Romero N et al.The potential of a portable, point-of-care electronic nose to diagnose tuberculosis.J Infect. 2017; 75: 441-447Summary Full Text Full Text PDF PubMed Scopus (42) Google Scholar However, these methods never passed the research stage of development. Based on a technical expert consultation, WHO states that Xpert Ultra can replace Xpert in all settings.11WHOFrequently asked questions about the WHO Technical Expert Consultation findings on Xpert MTB/RIF Ultra.http://www.who.int/tb/areas-of-work/laboratory/diagnostics/XpertUltraFAQs.pdfDate: March 24, 2017Google Scholar However, such replacement comes with pros, cons, and unknowns.12Garcia-Basteiro AL Saavedra B Cobelens F The good, the bad and the ugly of the next-generation Xpert Mtb/Rif Ultra test for tuberculosis diagnosis.Arch Bronconeumol. 2017; (published online July 10.)doi: 10.1016/j.arbres.2017.05.023PubMed Google Scholar Metaphorically speaking, if Xpert is a knife, Xpert Ultra is a sharper knife. However, the trade-off of the higher sensitivity is a lower specificity, as is customary for diagnostic tests. We eagerly await additional studies and algorithms that assess Xpert Ultra's improved sensitivity and solutions to avoid the trap of treating patients for dead bacilli. We declare no competing interests. Download .xlsx (.04 MB) Help with xlsx files Supplementary appendix Xpert MTB/RIF Ultra for detection of Mycobacterium tuberculosis and rifampicin resistance: a prospective multicentre diagnostic accuracy studyFor tuberculosis case detection, sensitivity of Xpert Ultra was superior to that of Xpert in patients with paucibacillary disease and in patients with HIV. However, this increase in sensitivity came at the expense of a decrease in specificity. Full-Text PDF Open Access