Determinants of PCR performance (Xpert MTB/RIF), including bacterial load and inhibition, for TB diagnosis using specimens from different body compartments

Grant Theron, Jonny Peter, Greg Calligaro, Richard Meldau, Colleen Hanrahan, Hoosain Khalfey, Brian Matinyenya, Tapuwa Muchinga, Liezel Smith, Shaheen Pandie, Laura Lenders, Vinod Patel, Bongani M. Mayosi, Keertan Dheda

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Abstract

The determinants of Xpert MTB/RIF sensitivity, a widely used PCR test for the diagnosis of tuberculosis (TB) are poorly understood. We compared culture time-to-positivity (TTP; a surrogate of bacterial load), MTB/RIF TB-specific and internal positive control (IPC)-specific C T values, and clinical characteristics in patients with suspected TB who provided expectorated (n = 438) or induced sputum (n = 128), tracheal aspirates (n = 71), bronchoalveolar lavage fluid (n = 152), pleural fluid (n = 76), cerebral spinal fluid (CSF; n = 152), pericardial fluid (n = 131), or urine (n = 173) specimens. Median bacterial load (TTP in days) was the strongest associate of MTB/RIF positivity in each fluid. TTP correlated with C T values in pulmonary specimens but not extrapulmonary specimens (Spearman's coefficient 0.5043 versus 0.1437; p = 0.030). Inhibition affected a greater proportion of pulmonary specimens than extrapulmonary specimens (IPC C T > 34: 6% (47/731) versus 1% (4/381; p < 0.0001). Pulmonary specimens had greater load than extrapulmonary specimens [TTPs (interquartile range) of 11 (7-16) versus 22 (18-33.5) days; p < 0.0001]. HIV-infection was associated with a decreased likelihood of MTB/RIF-positivity in pulmonary specimens but an increased likelihood in extrapulmonary specimens. Mycobacterial load, which displays significant variation across different body compartments, is the main determinant of MTB/RIF-positivity rather than PCR inhibition. MTB/RIF C T is a poor surrogate of load in extrapulmonary specimens.

Original languageEnglish (US)
Article number5658
JournalScientific reports
Volume4
DOIs
StatePublished - Jul 11 2014

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    Theron, G., Peter, J., Calligaro, G., Meldau, R., Hanrahan, C., Khalfey, H., Matinyenya, B., Muchinga, T., Smith, L., Pandie, S., Lenders, L., Patel, V., Mayosi, B. M., & Dheda, K. (2014). Determinants of PCR performance (Xpert MTB/RIF), including bacterial load and inhibition, for TB diagnosis using specimens from different body compartments. Scientific reports, 4, [5658]. https://doi.org/10.1038/srep05658