Exploring alternative biomaterials for diagnosis of pulmonary tuberculosis in HIV-negative patients by use of the GeneXpert MTB/RIF assay

Abstract

The utility of the GeneXpert MTB/RIF (Xpert) assay for detection of Mycobacterium tuberculosis in sputum samples has been extensively studied. However, the performance of the Xpert assay as applied to other readily accessible body fluids such as exhaled breath condensate (EBC), saliva, urine, and blood has not been established. We used the Xpert assay to test EBC, saliva, urine, and blood samples from HIV-negative, smear- and culture-positive pulmonary tuberculosis (TB) patients for the presence of M. tuberculosis. To compare the ability of the assay to perform bacterial load measurements on sputum samples with versus without sample processing, the assay was also performed on paired direct and processed sputum samples from each patient. The Xpert assay detected M. tuberculosis in none of the 26 EBC samples (sensitivity, 0.0%; 95% confidence interval [95% CI], 0.0%, 12.9%), 10 of the 26 saliva samples (sensitivity, 38.5%; 95% CI, 22.4%, 57.5%), 1 of 26 urine samples (sensitivity, 3.8%; 95% CI, 0.7%, 18.9%), and 2 of 24 blood samples (sensitivity, 8.3%; 95% CI, 2.3%, 25.8%). For bacterial load measurements in the different types of sputum samples, the cycle thresholds of the two M. tuberculosis-positive sputum types were well correlated (Spearman correlation of 0.834). This study demonstrates that the Xpert assay should not be routinely used to detect M. tuberculosis in EBC, saliva, urine, or blood samples from HIV-negative patients suspected of having pulmonary tuberculosis. As a test of bacterial load, the assay produced similar results when used to test direct versus processed sputum samples. Sputum remains the optimal sample type for diagnosing pulmonary tuberculosis in HIV-negative patients with the Xpert assay.

Fig 1

Detection of TB in different body fluids collected from culture-proven pulmonary TB cases. The Xpert assay was used to test each body fluid, EBC, saliva, urine, and blood, for TB. The assay cycle threshold (C_T) (Ct in the figure) values for each body fluid are compared to the C_T value of the direct sputum sample collected from the same patient on the same day. Samples where TB was not detected have been plotted at a C_T value of 40, which is above the highest C_T value used to identify TB in the Xpert assay.

Fig 2

Correlation between direct and processed sputum specimens collected from confirmed pulmonary TB cases at the baseline and during treatment. The Xpert assay was performed on paired samples. The cycle threshold (C_T) (Ct in the figure) value for each direct sputum sample is plotted in comparison to the C_T value of the processed sputum sample obtained from the same patient on the same day. Samples where TB was not detected have been plotted at a C_T value of 40, which is above the highest observed C_T value.