Research Article: Sputum quality and diagnostic performance of GeneXpert MTB/RIF among smear-negative adults with presumed tuberculosis in Uganda

Date Published: July 7, 2017

Publisher: Public Library of Science

Author(s): Amanda J. Meyer, Collins Atuheire, William Worodria, Samuel Kizito, Achilles Katamba, Ingvar Sanyu, Alfred Andama, Irene Ayakaka, Adithya Cattamanchi, Freddie Bwanga, Laurence Huang, J. Lucian Davis, Pere-Joan Cardona.


Introduction of GeneXpert MTB/RIF (Xpert) assay has constituted a major breakthrough for tuberculosis (TB) diagnostics. Several patient factors may influence diagnostic performance of Xpert including sputum quality.

We carried out a prospective, observational, cross-sectional study to determine the effect of sputum quality on diagnostic performance of Xpert among presumed TB patients in Uganda.

We collected clinical and demographic information and two sputum samples from participants. Staff recorded sputum quality and performed LED fluorescence microscopy and mycobacterial culture on each sample. If both smear examinations were negative, Xpert testing was performed. We calculated diagnostic yield, sensitivity, specificity, and other indicators for Xpert for each stratum of sputum quality in reference to a standard of mycobacterial culture.

Patients with salivary sputum showed a trend towards a substantially higher proportion of samples that were Xpert-positive (54/286, 19%, 95% CI 15–24) compared with those with all other sputum sample types (221/1496, 15%, 95% CI 13–17). Blood-stained sputum produced the lowest sensitivity (28%; 95% CI 12–49) and salivary sputum the highest (66%; 95% CI 53–77). Specificity didn’t vary meaningfully by sample types. Salivary sputum was significantly more sensitive than mucoid sputum (+13%, 95% CI +1 to +26), while blood-stained sputum was significantly less sensitive (-24%, 95% CI -42 to -5).

Our findings demonstrate the need to exercise caution in collecting sputum for Xpert and in interpreting results because sputum quality may impact test yield and sensitivity. In particular, it may be wise to pursue additional testing should blood-stained sputum test negative while salivary sputum should be readily accepted for Xpert testing given its higher sensitivity and potentially higher yield than other sample types. These findings challenge conventional recommendations against collecting salivary sputum for TB diagnosis and could inform new standards for sputum quality.

Partial Text

Introduction of the GeneXpert MTB/RIF (Xpert) assay has constituted a major breakthrough for tuberculosis (TB) diagnostics, providing a rapid and accurate way of identifying TB patients in high TB-burden, low-income countries [1, 2]. Nevertheless, post-implementation studies have identified several challenges [3–6], emphasizing the need for deeper understanding of clinical and operational factors affecting real-world performance [7]. Previous studies have shown that pauci-bacillary forms of TB are more commonly identified in patients who are HIV-seropositive [8–10] and in those who are sputum acid-fast bacilli (AFB) smear-negative, and may reduce the overall sensitivity of Xpert in reference to the standard of mycobacterial culture [11–13]. However, because microscopy is also less sensitive in these populations, these groups are also the ones most likely to benefit from Xpert, and in whom Xpert has been especially recommended [14, 15].

Specimen quality has long been assumed to be as an important predictor of the performance characteristics of microbiologic tests, particularly those used to diagnose lower respiratory-tract infections. Unfortunately, the amount and quality of evidence about how sputum quality affects the performance of TB diagnostic tests is limited. In this prospective cross-sectional study, we found no significant difference in diagnostic yield of Xpert testing between salivary and non-salivary specimens among adults with negative sputum AFB-smear examinations in a low-income country with high burdens of TB and HIV. In fact, we identified a strong trend towards a higher diagnostic yield in salivary than in non-salivary specimens. These differences were confirmed by a secondary comparison of diagnostic accuracy in reference to mycobacterial culture. This analysis showed significantly higher diagnostic sensitivity of Xpert on salivary samples as compared with the referent category, mucoid sputum samples, while blood-stained sputum was associated with significantly lower sensitivity.




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