Longitudinal Dynamics of a Blood Transcriptomic Signature of Tuberculosis

Abstract

Rationale: Performance of blood transcriptomic tuberculosis (TB) signatures in longitudinal studies and effects of TB-preventive therapy and coinfection with HIV or respiratory organisms on transcriptomic signatures has not been systematically studied. Objectives: We evaluated longitudinal kinetics of an 11-gene blood transcriptomic TB signature, RISK11, and effects of TB-preventive therapy (TPT) and respiratory organisms on RISK11 signature score, in HIV-uninfected and HIV-infected individuals. Methods: RISK11 was measured in a longitudinal study of RISK11-guided TPT in HIV-uninfected adults, a cross-sectional respiratory organisms cohort, or a longitudinal study in people living with HIV (PLHIV). HIV-uninfected RISK11⁺ participants were randomized to TPT or no TPT; RISK11^- participants received no TPT. PLHIV received standard-of-care antiretroviral therapy and TPT. In the cross-sectional respiratory organisms cohort, viruses and bacteria in nasopharyngeal and oropharyngeal swabs were quantified by real-time quantitative PCR. Measurements and Main Results: RISK11⁺ status was transient in most of the 128 HIV-negative participants with longitudinal samples; more than 70% of RISK11⁺ participants reverted to RISK11^- by 3 months, irrespective of TPT. By comparison, reversion from a RISK11⁺ state was less common in 645 PLHIV (42.1%). Non-HIV viral and nontuberculous bacterial organisms were detected in 7.2% and 38.9% of the 1,000 respiratory organisms cohort participants, respectively, and among those investigated for TB, 3.8% had prevalent disease. Median RISK11 scores (%) were higher in participants with viral organisms alone (46.7%), viral and bacterial organisms (42.8%), or prevalent TB (85.7%) than those with bacterial organisms other than TB (13.4%) or no organisms (14.2%). RISK11 could not discriminate between prevalent TB and viral organisms. Conclusions: Positive RISK11 signature status is often transient, possibly due to intercurrent viral infection, highlighting potentially important challenges for implementation of these biomarkers as new tools for TB control.

Keywords: HIV; Mycobacterium tuberculosis; biomarkers; mRNA; respiratory tract infections.

Figure 1.

Study flow diagram. HIV-uninfected participants were recruited from the CORTIS (Correlate of Risk Targeted Intervention Study) parent study and coenrolled into the (A) HIV-uninfected longitudinal cohort and (B) respiratory organisms cohort. All participants living with HIV (PLHIV) enrolled in the CORTIS-HR (Validation of Correlates of Risk of TB Disease in High Risk Populations) parent study with a baseline RISK11 score and without prevalent tuberculosis (TB) were eligible for inclusion in the (C) PLHIV longitudinal cohort. ^†Out of 999 participants enrolled in the respiratory organisms cohort, only 286 (28.6%) participants were coenrolled in the CORTIS parent study and investigated for TB at enrollment (Figure E1); 11/286 (3.8%) had prevalent TB confirmed by MTB liquid culture and/or Xpert MTB/RIF (Cepheid). 3HP = 3 months’ rifapentine and isoniazid preventive therapy; MTB = Mycobacterium tuberculosis.

Figure 2.

RISK11 positivity is transient among most adults in the HIV-uninfected longitudinal cohort. RISK11 scores at enrollment (M0), and 3 months (M3) and 12 months (M12) after enrollment in (A) baseline RISK11⁻ participants in the observational arm (n = 59), (B) baseline RISK11⁺ participants in the 3 months’ rifapentine and isoniazid preventive therapy–positive treatment arm (n = 43), and (C) baseline RISK11⁺ participants in the observational arm (n = 26). All prevalent and incident cases were excluded. Boxes represent the interquartile range, and horizontal lines represent medians. The whiskers represent the lowest and highest RISK11⁺ score within 1.5 times the interquartile range from the lower quantile and upper quantile, respectively. The proportions of RISK11⁺ participants at each time point are indicated above each plot. The Wilcoxon signed-rank test was used to compare RISK11 scores between time points.

Figure 3.

RISK11 reversion is less common among participants of the people living with HIV (PLHIV) longitudinal cohort. (A) RISK11 scores at enrollment (M0) and 3 months (M3) for all participants in the PLHIV longitudinal cohort, excluding all prevalent and incident cases. Participants have been stratified by baseline RISK11 status, and the proportions of RISK11-positive (RISK11⁺) participants at each time point are indicated above each plot. (B) RISK11 scores at enrollment (M0) and 3 months (M3) for all participants in the PLHIV longitudinal cohort, excluding all prevalent and incident tuberculosis (TB) cases, stratified by antiretroviral therapy (ART) status. The proportions of RISK11⁺ participants at each time point are indicated above each plot. (C–E) RISK11 scores at M0 and M3 for ART-experienced participants (C), participants who initiated ART after enrollment (D), and ART-naive participants (E), excluding all prevalent and incident TB cases. Boxes represent the interquartile range, and horizontal lines represent medians. The whiskers represent the lowest and highest RISK11⁺ score within 1.5 times the interquartile range from the lower quantile and upper quantile, respectively. Participants have been stratified by baseline RISK11 status, and the proportions of RISK11⁺ participants at each time point are indicated above each plot. The Wilcoxon signed-rank test was used to compare RISK11 scores between time points.

Figure 4.

RISK11 performance for differentiating between participants with tuberculosis (TB), viral or bacterial upper respiratory tract organisms, and uninfected individuals. (A and B) Distributions of RISK11 scores in participants investigated for TB (n = 286) (A) and participants not investigated for TB (n = 713) (B). Only P values below 0.1 are shown. Boxes represent the interquartile range, and horizontal lines represent medians. The whiskers represent the lowest and highest RISK11⁺ score within 1.5 times the interquartile range from the lower quantile and upper quantile, respectively. The proportions of RISK11⁺ participants at each time point are indicated above each plot. (C–H) Performance of RISK11 in differentiating between participants with TB and participants with a bacterial upper respiratory organism (C), between participants with TB and uninfected participants (D), between participants with TB and participants with a viral upper respiratory organism (E), between participants with a viral upper respiratory organism and participants with a bacterial upper respiratory organism (F), between participants with a viral upper respiratory organism and uninfected participants (G), and between participants with a bacterial organism and uninfected participants (H). Shaded areas represent the 95% confidence interval (CI). AUC = area under the curve.