title: Determinants of PCR performance (Xpert MTB/RIF), including bacterial load and inhibition, for TB diagnosis using specimens from different body compartments.
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.
authors.affiliation: Lung Infection and Immunity Unit, Division of Pulmonology & UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa.
authors.forename: Grant
authors.initials: G
authors.lastname: Theron
authors.affiliation: Lung Infection and Immunity Unit, Division of Pulmonology & UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa.
authors.forename: Jonny
authors.initials: J
authors.lastname: Peter
authors.affiliation: Lung Infection and Immunity Unit, Division of Pulmonology & UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa.
authors.forename: Greg
authors.initials: G
authors.lastname: Calligaro
authors.affiliation: Lung Infection and Immunity Unit, Division of Pulmonology & UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa.
authors.forename: Richard
authors.initials: R
authors.lastname: Meldau
authors.affiliation: Johns Hopkins Bloomberg School of Public Health, Department of Epidemiology, Baltimore, MD, USA.
authors.forename: Colleen
authors.initials: C
authors.lastname: Hanrahan
authors.affiliation: Lung Infection and Immunity Unit, Division of Pulmonology & UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa.
authors.forename: Hoosain
authors.initials: H
authors.lastname: Khalfey
authors.affiliation: Lung Infection and Immunity Unit, Division of Pulmonology & UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa.
authors.forename: Brian
authors.initials: B
authors.lastname: Matinyenya
authors.affiliation: Lung Infection and Immunity Unit, Division of Pulmonology & UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa.
authors.forename: Tapuwa
authors.initials: T
authors.lastname: Muchinga
authors.affiliation: Lung Infection and Immunity Unit, Division of Pulmonology & UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa.
authors.forename: Liezel
authors.initials: L
authors.lastname: Smith
authors.affiliation: Division of Cardiology, Department of Medicine, Groote Schuur Hospital and University of Cape Town, South Africa.
authors.forename: Shaheen
authors.initials: S
authors.lastname: Pandie
authors.affiliation: Lung Infection and Immunity Unit, Division of Pulmonology & UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa.
authors.forename: Laura
authors.initials: L
authors.lastname: Lenders
authors.affiliation: Department of Neurology, University of KwaZulu Natal, South Africa.
authors.forename: Vinod
authors.initials: V
authors.lastname: Patel
authors.affiliation: Division of Cardiology, Department of Medicine, Groote Schuur Hospital and University of Cape Town, South Africa.
authors.forename: Bongani M
authors.initials: BM
authors.lastname: Mayosi
authors.affiliation: 1] Lung Infection and Immunity Unit, Division of Pulmonology & UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa [2] Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
authors.forename: Keertan
authors.initials: K
authors.lastname: Dheda
mesh_terms: D000328:Adult; D000368:Aged; D000904:Antibiotics, Antitubercular / Q000494:pharmacology*; D058491:Bacterial Load / Q000187:drug effects*; D001992:Bronchoalveolar Lavage Fluid / Q000737:chemistry / Q000382:microbiology; D024881:Drug Resistance, Bacterial; D005260:Female; D015658:HIV Infections / Q000175:diagnosis* / Q000453:epidemiology; D006801:Humans; D008168:Lung / Q000378:metabolism / Q000382:microbiology; D008297:Male; D008875:Middle Aged; D009169:Mycobacterium tuberculosis / Q000187:drug effects* / Q000302:isolation & purification; D011237:Predictive Value of Tests; D015995:Prevalence; D060888:Real-Time Polymerase Chain Reaction / Q000592:standards*; D013019:South Africa / Q000453:epidemiology; D013183:Sputum / Q000382:microbiology; D014376:Tuberculosis / Q000175:diagnosis* / Q000453:epidemiology
chemical_list: D000904:Antibiotics, Antitubercular