Research Article: Performance of Xpert® MTB/RIF among tuberculosis outpatients in Lilongwe, Malawi

Date Published: March 31, 2017

Publisher: AOSIS

Author(s): Tarsizio Chikaonda, Nelson Nguluwe, Brian Barnett, Runa H. Gokhale, Robert Krysiak, Isaac Thengolose, Nora E. Rosenberg, Christopher Stanley, James Mpunga, Irving F. Hoffman, Mina Hosseinipour, Lesley Scott, Wendy Stevens.


Xpert® MTB/RIF is a molecular test for the detection of Mycobacterium tuberculosis and rifampicin resistance. It is considered to be a great advance over smear microscopy and culture. However, there is very little information regarding the performance characteristics of Xpert MTB/RIF in Malawi.

We aimed to evaluate the performance of Xpert MTB/RIF in a Malawian setting.

Stored sputum pellets were processed on Xpert MTB/RIF between June 2012 and May 2014. Results were compared to mycobacteria growth indicator tube and Löwenstein-Jensen cultures, LED fluorescent microscopy and GenoType® MTBDRplus assay. Rifampicin resistance was confirmed by DNA sequencing.

Of the 348 specimens with valid Xpert MTB/RIF results, 129/348 (37%) were smear-positive and 198/348 (57%) were culture-positive. Xpert MTB/RIF demonstrated a sensitivity of 93.8% (95% CI 89.4% – 96.8%) and specificity of 97.4% (95% CI 93.5% – 99.3%), with a positive predictive value of 97.8% (95% CI 94.6% – 99.4%) and a negative predictive value of 92.6% (95% CI 87.4% – 96.1%). Xpert MTB/RIF correctly identified 185/186 (99.5%) rifampicin-sensitive and 2/2 (100%) rifampicin-resistant M. tuberculosis strains. Mutations were not detected by sequencing in one isolate which was rifampicin resistant on Xpert MTB/RIF but sensitive on MTBDRplus. Four non-tuberculous mycobacteria grew from four smear-negative specimens, namely, M. avium (n = 1) and M. intracellulare (n = 3). No cross-reactivity was observed with any of the non-tuberculous mycobacteria when using Xpert MTB/RIF.

When fully implemented, Xpert MTB/RIF may have an impact on patient care in Malawi. The increased diagnostic yield of Xpert MTB/RIF over smear microscopy can increase laboratory-confirmed tuberculosis detection and ensure that treatment is given to appropriate individuals or groups.

Partial Text

Tuberculosis remains a major health challenge that has worsened with the emergence of multi-drug resistant (MDR) tuberculosis strains that are resistant to rifampicin and isoniazid. Globally, the impact of tuberculosis is significant, with an annual estimate of 9.6 million tuberculosis cases and over 1.5 million deaths due to tuberculosis in 2014.1 Preliminary data show that the prevalence of tuberculosis in Malawi is 286/100 000, which is higher than previous estimates by the World Health Organization.2 Diagnosis of tuberculosis continues to be a major challenge in Malawi due to the widespread use of diagnostics with poor sensitivity, such as sputum smear microscopy. Although more sensitive than smear microscopy, tuberculosis culture, when available, can take days to weeks before a result is available. Due to limitations of both smear and culture, pulmonary tuberculosis is often diagnosed late or presumptively. Low utilisation of laboratory confirmation and widespread use of empirical treatment can either lead to true tuberculosis cases being missed or to the initiation of tuberculosis treatment in people without the disease.1

A total of 351 sputum pellets were processed both on culture and Xpert MTB/RIF. However, only 348 sputum pellets had valid Xpert MTB/RIF results. The remaining three samples were not included in the final analysis due to an error (n = 1) and an invalid result (n = 2) on Xpert MTB/RIF. Of the 348 sputum pellets, 200 (57%) were from HIV-positive individuals, and 148 (43%) were HIV-negative. Among all samples, 219/348 (63%) were smear-negative and 129/348 (37%) were smear-positive. As shown in Table 1, 70/219 (32%) of smear-negative and 128/129 (99.2%) of smear-positive samples were culture positive.

In the present study, the Xpert MTB/RIF assay detected 58 more tuberculosis cases than smear microscopy. The paucibacillary nature of samples cultured from tuberculosis/HIV co-infected individuals revealed a more serious inability to detect tuberculosis using smear microscopy than was the case for Xpert MTB/RIF. Among HIV-positive individuals registering for tuberculosis treatment, a relatively larger percentage of those who were smear-negative, were also Xpert MTB/RIF and culture negative, and thus had no laboratory confirmation of disease. Overall analysis revealed expected results using the Xpert MTB/RIF assay, proving more sensitive and specific than fluorescent microscopy in detecting M. tuberculosis when using culture as the reference standard and there was no overlap of the confidence intervals. The sensitivity of Xpert MTB/RIF was lower in HIV-positive than in HIV-negative individuals. The Xpert MTB/RIF correctly distinguished M. tuberculosis from non-tuberculous mycobacteria. Among the non-tuberculous mycobacteria, three were isolated from HIV-positive individuals, and one was from an HIV-negative individual.




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