Prospective multicentre head-to-head validation of host blood transcriptomic biomarkers for pulmonary tuberculosis by real-time PCR

Abstract

Background Sensitive point-of-care screening tests are urgently needed to identify individuals at highest risk of tuberculosis. We prospectively tested performance of host-blood transcriptomic tuberculosis signatures. Methods Adults without suspicion of tuberculosis were recruited from five endemic South African communities. Eight parsimonious host-blood transcriptomic tuberculosis signatures were measured by microfluidic RT-qPCR at enrolment. Upper respiratory swab specimens were tested with a multiplex bacterial-viral RT-qPCR panel in a subset of participants. Diagnostic and prognostic performance for microbiologically confirmed prevalent and incident pulmonary tuberculosis was tested in all participants at baseline and during active surveillance through 15 months follow-up, respectively. Results Among 20,207 HIV-uninfected and 963 HIV-infected adults screened; 2923 and 861 were enroled. There were 61 HIV-uninfected (weighted prevalence 1.1%) and 10 HIV-infected (prevalence 1.2%) tuberculosis cases at baseline. Parsimonious signature diagnostic performance was superior among symptomatic (AUCs 0.85–0.98) as compared to asymptomatic (AUCs 0.61–0.78) HIV-uninfected participants. Thereafter, 24 HIV-uninfected and 9 HIV-infected participants progressed to incident tuberculosis (1.1 and 1.0 per 100 person-years, respectively). Among HIV-uninfected individuals, prognostic performance for incident tuberculosis occurring within 6–12 months was higher relative to 15 months. 1000 HIV-uninfected participants were tested for respiratory microorganisms and 413 HIV-infected for HIV plasma viral load; 7/8 signature scores were higher (p < 0.05) in participants with viral respiratory infections or detectable HIV viraemia than those without. Conclusions Several parsimonious tuberculosis transcriptomic signatures met triage test targets among symptomatic participants, and incipient test targets within 6 months. However, the signatures were upregulated with viral infection and offered poor specificity for diagnosing sub-clinical tuberculosis.

Are mRNA based transcriptomic signatures ready for diagnosing tuberculosis in the clinic? - A review of evidence and the technological landscape

“…A recent head-to-head qRT-PCR comparison of eight parsimonious signatures by Mendelsohn et al showed no signature met the minimal target for a triage test in whole blood specimens from over 3000 HIV-infected or uninfected South African adults, although 5 signatures (RISK11, RISK6, Roe1, Roe3 and Suliman4) met the optimal target in symptomatic HIV-uninfected participants, and four signatures (RISK11, Maertzdorf4, Suliman4, and Thompson5) in symptomatic HIV-infected participants. 45 Whether such signatures have any utility as a triage test only in symptomatic participants remains to be understood.…”

“…A recent prospective study similarly showed the prognostic performance of mRNA signatures could meet the target only in the short term. 49 …”

“… 43 In another prospective study, RISK11, RISK6, Roe1, Roe3 and Suliman4 met the optimal target in symptomatic HIV-uninfected participants, and RISK11, Maertzdorf4, Suliman4, and Thompson5 met the optimal target for PLHIV. 49 Yes Sweeney3 (Prototype GeneXpert PCR): achieved the minimal target when compared to Xpert MTB/RIF as a reference standard (Specificity of 86% at near 90% sensitivity) 56 No RT-PCR assays are typically in the range of 10-100 USD even for relatively simple qualitative assays so it would be unlikely that costs for RNA-based tests could be below this; and extremely unlikely that costs could be as low as those required for triage. Diagnosis Maybe BATF2, Kaforou25, Roe3, Sweeney3 showed specificities ranging between 86% and 94% at 65% sensitivity in a recent prospective study.…”

“…In PLHIV, Roe1 met the minimal target through 15 months. 49 Maybe None tested but Sweeney3 has been tested on the Gene Xpert platform Yes IPD: Individual participant data; PLHIV: people living with HIV; PCR: polymerase chain reaction. …”

“…In another prospective study, RISK11, RISK6, Roe1, Roe3 and Suliman4 met the optimal target in symptomatic HIV-uninfected participants, and RISK11, Maertzdorf4, Suliman4, and Thompson5 met the optimal target for PLHIV. 49 …”