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Leo S, Narasimhan M, Rathinam S, Banerjee A. Biomarkers in diagnosing and therapeutic monitoring of tuberculosis: a review. Ann Med 2024; 56:2386030. [PMID: 39097795 PMCID: PMC11299445 DOI: 10.1080/07853890.2024.2386030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 03/06/2024] [Accepted: 06/12/2024] [Indexed: 08/05/2024] Open
Abstract
Tuberculosis (TB) continues to pose a significant health challenge worldwide, emphasizing the importance of prompt diagnosis and efficient monitoring of treatment outcomes for effective disease control. Biomarkers have become increasingly important in the realm of TB diagnoses and treatment. The objective of this comprehensive review is to examine the present state of biomarkers employed in the diagnosis of TB, monitoring the response to treatment, and predicting treatment outcomes. In this study, we undertake a comprehensive examination of the diverse biomarkers utilized in TB diagnoses, spanning molecular, immunological, and other novel methodologies. Furthermore, we examine the potential of biomarkers in the context of therapeutic monitoring, assessment of treatment effectiveness, and anticipation of drug resistance. Additionally, this paper presents future prospects regarding the utilization of biomarkers in the therapy of tuberculosis.
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Affiliation(s)
- Sneha Leo
- Department of Respiratory Medicine, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, Tamil Nadu, India
| | - Meenakshi Narasimhan
- Department of Respiratory Medicine, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, Tamil Nadu, India
| | - Sridhar Rathinam
- Department of Respiratory Medicine, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, Tamil Nadu, India
| | - Antara Banerjee
- Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, Tamil Nadu, India
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Derseh NM, Agimas MC, Tesfie TK. Risk score prediction for bacteriologically confirmed tuberculosis among adults with HIV on antiretroviral therapy in northwest Ethiopia: prognostic model development. AIDS 2024; 38:1333-1341. [PMID: 38691024 DOI: 10.1097/qad.0000000000003917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
OBJECTIVE This study was aimed at developing a risk score prediction model for bacteriologically confirmed tuberculosis (TB) among adults with HIV receiving antiretroviral therapy in Ethiopia. METHODS An institutional-based retrospective follow-up study was conducted among 569 adults with HIV on ART. We used demographic and clinical prognostic factors to develop a risk prediction model. Model performance was evaluated by discrimination and calibration using the area under the receiver operating characteristic (AUROC) curve and calibration plot. Bootstrapping was used for internal validation. A decision curve analysis was used to evaluate the clinical utility. RESULTS Opportunistic infection, functional status, anemia, isoniazid preventive therapy, and WHO clinical stages were used to develop risk prediction. The AUROC curve of the original model was 87.53% [95% confidence interval (CI): 83.88-91.25] and the calibration plot ( P -value = 0.51). After internal validation, the AUROC curve of 86.61% (95% CI: 82.92-90.29%) was comparable with the original model, with an optimism coefficient of 0.0096 and good calibration ( P -value = 0.10). Our model revealed excellent sensitivity (92.65%) and negative predictive value (NPV) (98.60%) with very good specificity (70.06%) and accuracy (72.76%). After validation, accuracy (74.85%) and specificity (76.27%) were improved, but sensitivity (86.76%) and NPV (97.66%) were relatively reduced. The risk prediction model had a net benefit up to 7.5 threshold probabilities. CONCLUSION This prognostic model had very good performance. Moreover, it had very good sensitivity and excellent NPV. The model could help clinicians use risk estimation and stratification for early diagnosis and treatment to improve patient outcomes and quality of life.
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Affiliation(s)
- Nebiyu Mekonnen Derseh
- Department of Epidemiology and Biostatistics, Institute of Public Health, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
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Huang Z, Xiong C, Luo Q, Zhu J, Guo Y, Fu P, Zhu H, Xu J, Guo Y, Peng Y, Qing C, Li J, Le A. tRF-Glu-TTC-026 as novel diagnostic biomarkers for active tuberculosis and regulates intracellular survival of Mycobacterium tuberculosis in macrophages by regulating macrophage polarization. Clin Transl Med 2024; 14:e1781. [PMID: 39043626 PMCID: PMC11265989 DOI: 10.1002/ctm2.1781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 07/09/2024] [Accepted: 07/11/2024] [Indexed: 07/25/2024] Open
Affiliation(s)
- Zikun Huang
- Department of Clinical LaboratoryThe First Affiliated HospitalJiangxi Medical CollegeNanchang UniversityNanchangJiangxiChina
- Nanchang Key Laboratory of Diagnosis of Infectious DiseasesGaoxin Branch Of The First Affiliated Hospital, Jiangxi Medical College, Nanchang UniversityNanchangJiangxiChina
| | - Cuifen Xiong
- Department of Clinical LaboratoryThe First Affiliated HospitalJiangxi Medical CollegeNanchang UniversityNanchangJiangxiChina
| | - Qing Luo
- Department of Clinical LaboratoryThe First Affiliated HospitalJiangxi Medical CollegeNanchang UniversityNanchangJiangxiChina
- Nanchang Key Laboratory of Diagnosis of Infectious DiseasesGaoxin Branch Of The First Affiliated Hospital, Jiangxi Medical College, Nanchang UniversityNanchangJiangxiChina
| | - Juxiang Zhu
- Department of Clinical LaboratoryThe First Affiliated HospitalJiangxi Medical CollegeNanchang UniversityNanchangJiangxiChina
| | - Yongqin Guo
- Department of Clinical LaboratoryThe First Affiliated HospitalJiangxi Medical CollegeNanchang UniversityNanchangJiangxiChina
| | - Peng Fu
- Department of Clinical LaboratoryThe First Affiliated HospitalJiangxi Medical CollegeNanchang UniversityNanchangJiangxiChina
| | - Haiyan Zhu
- Department of Clinical LaboratoryThe First Affiliated HospitalJiangxi Medical CollegeNanchang UniversityNanchangJiangxiChina
| | - Jianqing Xu
- Department of Clinical LaboratoryThe First Affiliated HospitalJiangxi Medical CollegeNanchang UniversityNanchangJiangxiChina
| | - Yang Guo
- Department of Clinical LaboratoryThe First Affiliated HospitalJiangxi Medical CollegeNanchang UniversityNanchangJiangxiChina
| | - Yiping Peng
- Department of TuberculosisJiangxi Chest HospitalNanchangJiangxiChina
| | - Cheng Qing
- Nanchang Key Laboratory of Diagnosis of Infectious DiseasesGaoxin Branch Of The First Affiliated Hospital, Jiangxi Medical College, Nanchang UniversityNanchangJiangxiChina
- Department of Intensive Care MedicineMedical Center of Anesthesiology and PainThe First Affiliated HospitalJiangxi Medical CollegeNanchang UniversityNanchangJiangxiChina
| | - Junming Li
- Department of Clinical LaboratoryThe First Affiliated HospitalJiangxi Medical CollegeNanchang UniversityNanchangJiangxiChina
| | - Aiping Le
- Department of Blood TransfusionKey Laboratory of Jiangxi Province for Transfusion MedicineThe First Affiliated HospitalJiangxi Medical CollegeNanchang UniversityNanchangJiangxiChina
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Mann T, Gupta RK, Reeve BWP, Ndlangalavu G, Chandran A, Krishna AP, Calderwood CJ, Tshivhula H, Palmer Z, Naidoo S, Mbu DL, Theron G, Noursadeghi M. Blood RNA biomarkers for tuberculosis screening in people living with HIV before antiretroviral therapy initiation: a diagnostic accuracy study. Lancet Glob Health 2024; 12:e783-e792. [PMID: 38583459 DOI: 10.1016/s2214-109x(24)00029-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/06/2023] [Accepted: 01/11/2024] [Indexed: 04/09/2024]
Abstract
BACKGROUND Undiagnosed tuberculosis remains a major threat for people living with HIV. Multiple blood transcriptomic biomarkers have shown promise for tuberculosis diagnosis. We sought to evaluate their diagnostic accuracy and clinical utility for systematic pre-antiretroviral therapy (ART) tuberculosis screening. METHODS We enrolled consecutive adults (age ≥18 years) referred to start ART at a community health centre in Cape Town, South Africa, irrespective of symptoms. Sputa were obtained (using induction if required) for two liquid cultures. Whole-blood RNA samples underwent transcriptional profiling using a custom Nanostring gene panel. We measured the diagnostic accuracy of seven candidate RNA signatures (one single gene biomarker [BATF2] and six multigene biomarkers) for the reference standard of Mycobacterium tuberculosis culture status, using area under the receiver-operating characteristic curve (AUROC) analysis, and sensitivity and specificity at prespecified thresholds (two standard scores above the mean of healthy controls; Z2). Clinical utility was assessed by calculating net benefit in decision curve analysis. We compared performance with C-reactive protein (CRP; threshold ≥5 mg/L), WHO four-symptom screen (W4SS), and the WHO target product profile for tuberculosis triage tests. FINDINGS A total of 707 people living with HIV (407 [58%] female and 300 [42%] male) were included, with median CD4 count 306 cells per mm3 (IQR 184-486). Of 676 participants with available sputum culture results, 89 (13%) had culture-confirmed tuberculosis. The seven RNA signatures were moderately to highly correlated (Spearman rank coefficients 0·42-0·93) and discriminated tuberculosis culture positivity with similar AUROCs (0·73-0·80), but none statistically better than CRP (AUROC 0·78, 95% CI 0·72-0·83). Diagnostic accuracy was similar across CD4 count strata, but lower among participants with negative W4SS (AUROCs 0·56-0·65) compared with positive (AUROCs 0·75-0·84). The RNA biomarker with the highest AUROC point estimate was a four-gene signature (Suliman4; AUROC 0·80, 95% CI 0·75-0·86), with sensitivity 83% (95% CI 74-90) and specificity 59% (55-63) at the Z2 threshold. In decision curve analysis, Suliman4 and CRP had similar clinical utility to guide confirmatory tuberculosis testing, but both had higher net benefit than W4SS. In exploratory analyses, an approach combining CRP (≥5 mg/L) and Suliman4 (≥Z2) had sensitivity of 80% (70-87), specificity of 70% (66-74), and higher net benefit than either biomarker alone. INTERPRETATION RNA biomarkers showed better clinical utility to guide confirmatory tuberculosis testing for people living with HIV before ART initiation than symptom-based screening, but their performance did not exceed that of CRP and fell short of WHO recommended targets. Interferon-independent approaches might be required to improve accuracy of host-response biomarkers to support tuberculosis screening before ART initiation. FUNDING South African Medical Research Council, European and Developing Countries Clinical Trials Partnership 2, National Institutes of Health National Institute of Allergy and Infectious Diseases, The Wellcome Trust, National Institute for Health and Care Research, Royal College of Physicians London.
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Affiliation(s)
- Tiffeney Mann
- Division of Infection and Immunity, University College London, London, UK
| | - Rishi K Gupta
- Institute of Health Informatics, University College London, London, UK
| | - Byron W P Reeve
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Gcobisa Ndlangalavu
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Aneesh Chandran
- Division of Infection and Immunity, University College London, London, UK
| | - Amirtha P Krishna
- Division of Infection and Immunity, University College London, London, UK
| | - Claire J Calderwood
- Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Happy Tshivhula
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Zaida Palmer
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Selisha Naidoo
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Desiree L Mbu
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Grant Theron
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, London, UK.
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Alonzi T, Repele F, Goletti D. Research tests for the diagnosis of tuberculosis infection. Expert Rev Mol Diagn 2023; 23:783-795. [PMID: 37561602 DOI: 10.1080/14737159.2023.2240230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 07/20/2023] [Indexed: 08/12/2023]
Abstract
INTRODUCTION Despite huge efforts, tuberculosis (TB) is still a major public health threat worldwide, it is estimated that a quarter of the global population is infected by Mycobacterium tuberculosis (Mtb). For controlling TB and reducing Mtb transmission it is fundamental to diagnose TB infection (TBI) as well as the progressors from TBI to disease to identify those requiring preventive therapy. At present, there is no gold standard test for TBI diagnosis although several new methodologies have been attempted. AREAS COVERED This review provides an update on the most recent approaches to develop reliable tests to diagnose TBI and progressors from infection to disease. Experimental tests are based on either the direct identification of Mtb (i.e., Mtb DNA upon host cells isolation; Mtb proteins or peptides) or host response (i.e., levels and quality of specific anti-Mtb antibodies; host blood transcriptome signatures). EXPERT OPINION The experimental tests described are very interesting. However, further investigation and randomized clinical trials are needed to improve the sensitivity and specificity of these new research-based tests. More reliable proofs-of-concept and simplification of technical procedures are necessary to develop new diagnostic tools for identifying TBI patients and those that will progress from infection to TB disease.
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Affiliation(s)
- Tonino Alonzi
- Translational Research Unit, Department of Epidemiology and Preclinical Research National Institute for Infectious Diseases L. Spallanzani-IRCCS, Rome, Italy
| | - Federica Repele
- Translational Research Unit, Department of Epidemiology and Preclinical Research National Institute for Infectious Diseases L. Spallanzani-IRCCS, Rome, Italy
| | - Delia Goletti
- Translational Research Unit, Department of Epidemiology and Preclinical Research National Institute for Infectious Diseases L. Spallanzani-IRCCS, Rome, Italy
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Ortiz-Brizuela E, Apriani L, Mukherjee T, Lachapelle-Chisholm S, Miedy M, Lan Z, Korobitsyn A, Ismail N, Menzies D. Assessing the Diagnostic Performance of New Commercial Interferon-γ Release Assays for Mycobacterium tuberculosis Infection: A Systematic Review and Meta-Analysis. Clin Infect Dis 2023; 76:1989-1999. [PMID: 36688489 PMCID: PMC10249994 DOI: 10.1093/cid/ciad030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 01/05/2023] [Accepted: 01/13/2023] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND We compared 6 new interferon-γ release assays (IGRAs; hereafter index tests: QFT-Plus, QFT-Plus CLIA, QIAreach, Wantai TB-IGRA, Standard E TB-Feron, and T-SPOT.TB/T-Cell Select) with World Health Organization (WHO)-endorsed tests for tuberculosis infection (hereafter reference tests). METHODS Data sources (1 January 2007-18 August 2021) were Medline, Embase, Web of Science, Cochrane Database of Systematic Reviews, and manufacturers' data. Cross-sectional and cohort studies comparing the diagnostic performance of index and reference tests were selected. The primary outcomes of interest were the pooled differences in sensitivity and specificity between index and reference tests. The certainty of evidence (CoE) was summarized using the GRADE approach. RESULTS Eighty-seven studies were included (44 evaluated the QFT-Plus, 4 QFT-Plus CLIA, 3 QIAreach, 26 TB-IGRA, 10 TB-Feron [1 assessing the QFT-Plus], and 1 T-SPOT.TB/T-Cell Select). Compared to the QFT-GIT, QFT Plus's sensitivity was 0.1 percentage points lower (95% confidence interval [CI], -2.8 to 2.6; CoE: moderate), and its specificity 0.9 percentage points lower (95% CI, -1.0 to -.9; CoE: moderate). Compared to QFT-GIT, TB-IGRA's sensitivity was 3.0 percentage points higher (95% CI, -.2 to 6.2; CoE: very low), and its specificity 2.6 percentage points lower (95% CI, -4.2 to -1.0; CoE: low). Agreement between the QFT-Plus CLIA and QIAreach with QFT-Plus was excellent (pooled κ statistics of 0.86 [95% CI, .78 to .94; CoE: low]; and 0.96 [95% CI, .92 to 1.00; CoE: low], respectively). The pooled κ statistic comparing the TB-Feron and the QFT-Plus or QFT-GIT was 0.85 (95% CI, .79 to .92; CoE: low). CONCLUSIONS The QFT-Plus and the TB-IGRA have very similar sensitivity and specificity as WHO-approved IGRAs.
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Affiliation(s)
- Edgar Ortiz-Brizuela
- McGill International Tuberculosis Centre, Department of Medicine, McGill University, Montreal, Quebec, Canada
- Department of Medicine, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Lika Apriani
- Tuberculosis Working Group, Research Centre for Care and Control of Infectious Diseases, Universitas Padjadjaran, Bandung, Indonesia
- Department of Public Health, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Tania Mukherjee
- Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Sophie Lachapelle-Chisholm
- McGill International Tuberculosis Centre, Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Michele Miedy
- McGill University Health Center, Department of Intensive Care Unit, McGill University, Montreal, Quebec, Canada
| | - Zhiyi Lan
- McGill International Tuberculosis Centre, Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Alexei Korobitsyn
- Global Tuberculosis Programme, World Health Organization, Geneva, Switzerland
| | - Nazir Ismail
- Global Tuberculosis Programme, World Health Organization, Geneva, Switzerland
| | - Dick Menzies
- McGill International Tuberculosis Centre, Department of Medicine, McGill University, Montreal, Quebec, Canada
- Respiratory Epidemiology and Clinical Research Unit, Research Institute of the McGill University Health Centre, Montreal Chest Institute, McGill University, Montreal, Quebec, Canada
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Mann T, Gupta RK, Reeve BWP, Ndlangalavu G, Chandran A, Krishna AP, Calderwood CJ, Tshivhula H, Palmer Z, Naidoo S, Mbu DL, Theron G, Noursadeghi M. Blood RNA biomarkers for tuberculosis screening in people living with HIV prior to anti-retroviral therapy initiation: A diagnostic accuracy study. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.01.23290783. [PMID: 37397982 PMCID: PMC10312886 DOI: 10.1101/2023.06.01.23290783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Background Undiagnosed tuberculosis (TB) remains a major threat for people living with HIV (PLHIV). Multiple blood transcriptomic biomarkers have shown promise for TB diagnosis. We sought to evaluate their diagnostic accuracy and clinical utility for systematic pre-antiretroviral therapy (ART) TB screening. Methods We enrolled consecutive adults referred to start ART at a community health centre in Cape Town, South Africa, irrespective of symptoms. Sputa were obtained (using induction if required) for two liquid cultures. Whole-blood RNA samples underwent transcriptional profiling using a custom Nanostring gene-panel. We measured the diagnostic accuracy of seven candidate RNA biomarkers for the reference standard of Mycobacterium tuberculosis culture status, using area under the receiver-operating characteristic curve (AUROC) analysis, and sensitivity/specificity at pre-specified thresholds (two standard scores above the mean of healthy controls; Z2). Clinical utility was assessed using decision curve analysis. We compared performance to CRP (threshold ≥5mg/L), World Health Organisation (WHO) four-symptom screen (W4SS) and the WHO target product profile for TB triage tests. Results A total of 707 PLHIV were included, with median CD4 count 306 cells/mm3. Of 676 with available sputum culture results, 89 (13%) had culture-confirmed TB. The seven RNA biomarkers were moderately to highly correlated (Spearman rank coefficients 0.42-0.93) and discriminated TB culture-positivity with similar AUROCs (0.73-0.80), but none statistically better than CRP (AUROC 0.78; 95% CI 0.72-0.83). Diagnostic accuracy was similar across CD4 count strata, but lower among W4SS-negative (AUROCs 0.56-0.65) compared to W4SS-positive participants (AUROCs 0.75-0.84). The RNA biomarker with highest AUROC point estimate was a 4-gene signature (Suliman4; AUROC 0.80; 95% CI 0.75-0.86), with sensitivity 0.83 (0.74-0.90) and specificity 0.59 (0.55-0.63) at Z2 threshold. In decision curve analysis, Suliman4 and CRP had similar clinical utility to guide confirmatory TB testing, but both had higher net benefit than W4SS. In exploratory analyses, an approach combining CRP (≥5mg/L) and Suliman4 (≥Z2) had sensitivity of 0.80 (0.70-0.87), specificity of 0.70 (0.66-0.74) and higher net benefit than either biomarker alone. Interpretation RNA biomarkers showed better clinical utility to guide confirmatory TB testing for PLHIV prior to ART initiation than symptom-based screening, but their performance did not exceed that of CRP, and fell short of WHO recommended targets. Interferon-independent approaches may be required to improve accuracy of host-response biomarkers to support TB screening pre-ART initiation. Funding South African MRC, EDCTP2, NIH/NIAID, Wellcome Trust, NIHR, Royal College of Physicians London.
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Affiliation(s)
- Tiffeney Mann
- Division of Infection and Immunity, University College London, London, UK
| | - Rishi K Gupta
- Institute of Health Informatics, University College London, London, UK
| | - Byron WP Reeve
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town
| | - Gcobisa Ndlangalavu
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town
| | - Aneesh Chandran
- Division of Infection and Immunity, University College London, London, UK
| | - Amirtha P Krishna
- Division of Infection and Immunity, University College London, London, UK
| | - Claire J Calderwood
- Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Happy Tshivhula
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town
| | - Zaida Palmer
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town
| | - Selisha Naidoo
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town
| | - Desiree L Mbu
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town
| | | | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, London, UK
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Mendelsohn SC, Verhage S, Mulenga H, Scriba TJ, Hatherill M. Systematic review of diagnostic and prognostic host blood transcriptomic signatures of tuberculosis disease in people living with HIV. Gates Open Res 2023; 7:27. [PMID: 37123047 PMCID: PMC10133453 DOI: 10.12688/gatesopenres.14327.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2023] [Indexed: 02/05/2023] Open
Abstract
Background HIV-associated tuberculosis (TB) has high mortality; however, current triage and prognostic tools offer poor sensitivity and specificity, respectively. We conducted a systematic review of diagnostic and prognostic host-blood transcriptomic signatures of TB in people living with HIV (PLHIV). Methods We systematically searched online databases for studies published in English between 1990-2020. Eligible studies included PLHIV of any age in test or validation cohorts, and used microbiological or composite reference standards for TB diagnosis. Inclusion was not restricted by setting or participant age. Study selection, quality appraisal using the QUADAS-2 tool, and data extraction were conducted independently by two reviewers. Thereafter, narrative synthesis of included studies, and comparison of signatures performance, was performed. Results We screened 1,580 records and included 12 studies evaluating 31 host-blood transcriptomic signatures in 10 test or validation cohorts of PLHIV that differentiated individuals with TB from those with HIV alone, latent Mycobacterium tuberculosis infection, or other diseases (OD). Two (2/10; 20%) cohorts were prospective (29 TB cases; 51 OD) and 8 (80%) case-control (353 TB cases; 606 controls) design. All cohorts (10/10) were recruited in Sub-Saharan Africa and 9/10 (90%) had a high risk of bias. Ten signatures (10/31; 32%) met minimum WHO Target Product Profile (TPP) criteria for TB triage tests. Only one study (1/12; 8%) evaluated prognostic performance of a transcriptomic signature for progression to TB in PLHIV, which did not meet the minimum WHO prognostic TPP. Conclusions Generalisability of reported findings is limited by few studies enrolling PLHIV, limited geographical diversity, and predominantly case-control design, which also introduces spectrum bias. New prospective cohort studies are needed that include PLHIV and are conducted in diverse settings. Further research exploring the effect of HIV clinical, virological, and immunological factors on diagnostic performance is necessary for development and implementation of TB transcriptomic signatures in PLHIV.
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Affiliation(s)
- Simon C Mendelsohn
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, Western Cape, 7935, South Africa
| | - Savannah Verhage
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, Western Cape, 7935, South Africa
| | - Humphrey Mulenga
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, Western Cape, 7935, South Africa
| | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, Western Cape, 7935, South Africa
| | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, Western Cape, 7935, South Africa
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Sivakumaran D, Jenum S, Srivastava A, Steen VM, Vaz M, Doherty TM, Ritz C, Grewal HMS. Host blood-based biosignatures for subclinical TB and incipient TB: A prospective study of adult TB household contacts in Southern India. Front Immunol 2023; 13:1051963. [PMID: 36713386 PMCID: PMC9876034 DOI: 10.3389/fimmu.2022.1051963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 12/21/2022] [Indexed: 01/13/2023] Open
Abstract
A large proportion of the global tuberculosis (TB) burden is asymptomatic and not detectable by symptom-based screening, driving the TB epidemic through continued M. tuberculosis transmission. Currently, no validated tools exist to diagnose incipient and subclinical TB. Nested within a large prospective study in household contacts of pulmonary TB cases in Southern India, we assessed 35 incipient TB and 12 subclinical TB cases, along with corresponding household active TB cases (n=11), and household controls (n=39) using high throughput methods for transcriptional and protein profiling. We split the data into training and test sets and applied a support vector machine classifier followed by a Lasso regression model to identify signatures. The Lasso regression model identified an 11-gene signature (ABLIM2, C20orf197, CTC-543D15.3, CTD-2503O16.3, HLADRB3, METRNL, RAB11B-AS1, RP4-614C10.2, RNA5SP345, RSU1P1, and UACA) that distinguished subclinical TB from incipient TB with a very good discriminatory power by AUCs in both training and test sets. Further, we identified an 8-protein signature comprising b-FGF, IFNγ, IL1RA, IL7, IL12p70, IL13, PDGF-BB, and VEGF that differentiated subclinical TB from incipient TB with good and moderate discriminatory power by AUCs in the training and test sets, respectively. The identified 11-gene signature discriminated well between the distinct stages of the TB disease spectrum, with very good discriminatory power, suggesting it could be useful for predicting TB progression in household contacts. However, the high discriminatory power could partly be due to over-fitting, and validation in other studies is warranted to confirm the potential of the immune biosignatures for identifying subclinical TB.
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Affiliation(s)
- Dhanasekaran Sivakumaran
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, Faculty of Medicine, University of Bergen, Bergen, Norway
- Department of Microbiology, Haukeland University Hospital, University of Bergen, Bergen, Norway
| | - Synne Jenum
- Department of Infectious Diseases, Oslo University Hospital, Oslo, Norway
| | - Aashish Srivastava
- Genome Core Facility, Clinical Laboratory (K2), Haukeland University Hospital, University of Bergen, Bergen, Norway
| | - Vidar M. Steen
- Genome Core Facility, Clinical Laboratory (K2), Haukeland University Hospital, University of Bergen, Bergen, Norway
| | - Mario Vaz
- Department of Physiology, St. John’s Medical College and Division of Health and Humanities, St. John’s Research Institute, Koramangala, Bangalore, India
| | | | - Christian Ritz
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, Faculty of Medicine, University of Bergen, Bergen, Norway
- National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark
| | - Harleen M. S. Grewal
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, Faculty of Medicine, University of Bergen, Bergen, Norway
- Department of Microbiology, Haukeland University Hospital, University of Bergen, Bergen, Norway
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10
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Nick JA, Malcolm KC, Hisert KB, Wheeler EA, Rysavy NM, Poch K, Caceres S, Lovell VK, Armantrout E, Saavedra MT, Calhoun K, Chatterjee D, Aboellail I, De P, Martiniano SL, Jia F, Davidson RM. Culture independent markers of nontuberculous mycobacterial (NTM) lung infection and disease in the cystic fibrosis airway. Tuberculosis (Edinb) 2023; 138:102276. [PMID: 36417800 PMCID: PMC10965158 DOI: 10.1016/j.tube.2022.102276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/12/2022] [Accepted: 11/15/2022] [Indexed: 11/18/2022]
Abstract
Nontuberculous mycobacteria (NTM) are opportunistic pathogens that affect a relatively small but significant portion of the people with cystic fibrosis (CF), and may cause increased morbidity and mortality in this population. Cultures from the airway are the only test currently in clinical use for detecting NTM. Culture techniques used in clinical laboratories are insensitive and poorly suited for population screening or to follow progression of disease or treatment response. The lack of sensitive and quantitative markers of NTM in the airway impedes patient care and clinical trial design, and has limited our understanding of patterns of acquisition, latency and pathogenesis of disease. Culture-independent markers of NTM infection have the potential to overcome many of the limitations of standard NTM cultures, especially the very slow growth, inability to quantitate bacterial burden, and low sensitivity due to required decontamination procedures. A range of markers have been identified in sputum, saliva, breath, blood, urine, as well as radiographic studies. Proposed markers to detect presence of NTM or transition to NTM disease include bacterial cell wall products and DNA, as well as markers of host immune response such as immunoglobulins and the gene expression of circulating leukocytes. In all cases the sensitivity of culture-independent markers is greater than standard cultures; however, most do not discriminate between various NTM species. Thus, each marker may be best suited for a specific clinical application, or combined with other markers and traditional cultures to improve diagnosis and monitoring of treatment response.
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Affiliation(s)
- Jerry A Nick
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA; Department of Medicine, University of Colorado School of Medicine, Aurora, CO, 80045, USA.
| | - Kenneth C Malcolm
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Katherine B Hisert
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA; Department of Medicine, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Emily A Wheeler
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Noel M Rysavy
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Katie Poch
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Silvia Caceres
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Valerie K Lovell
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Emily Armantrout
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Milene T Saavedra
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA; Department of Medicine, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Kara Calhoun
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Delphi Chatterjee
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, 1682 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Ibrahim Aboellail
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, 1682 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Prithwiraj De
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, 1682 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Stacey L Martiniano
- Department of Pediatrics, Children's Hospital Colorado, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Fan Jia
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, 80206, USA
| | - Rebecca M Davidson
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, 80206, USA
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11
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Mendelsohn SC, Verhage S, Mulenga H, Scriba TJ, Hatherill M. Systematic review of diagnostic and prognostic host blood transcriptomic signatures of tuberculosis disease in people living with HIV. Gates Open Res 2023; 7:27. [PMID: 37123047 PMCID: PMC10133453.2 DOI: 10.12688/gatesopenres.14327.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2023] [Indexed: 05/09/2023] Open
Abstract
Background HIV-associated tuberculosis (TB) has high mortality; however, current triage and prognostic tools offer poor sensitivity and specificity, respectively. We conducted a systematic review of diagnostic and prognostic host-blood transcriptomic signatures of TB in people living with HIV (PLHIV). Methods We systematically searched online databases for studies published in English between 1990-2020. Eligible studies included PLHIV of any age in test or validation cohorts, and used microbiological or composite reference standards for TB diagnosis. Inclusion was not restricted by setting or participant age. Study selection, quality appraisal using the QUADAS-2 tool, and data extraction were conducted independently by two reviewers. Thereafter, narrative synthesis of included studies, and comparison of signatures performance, was performed. Results We screened 1,580 records and included 12 studies evaluating 31 host-blood transcriptomic signatures in 10 test or validation cohorts of PLHIV that differentiated individuals with TB from those with HIV alone, latent Mycobacterium tuberculosis infection, or other diseases (OD). Two (2/10; 20%) cohorts were prospective (29 TB cases; 51 OD) and 8 (80%) case-control (353 TB cases; 606 controls) design. All cohorts (10/10) were recruited in Sub-Saharan Africa and 9/10 (90%) had a high risk of bias. Ten signatures (10/31; 32%) met minimum WHO Target Product Profile (TPP) criteria for TB triage tests. Only one study (1/12; 8%) evaluated prognostic performance of a transcriptomic signature for progression to TB in PLHIV, which did not meet the minimum WHO prognostic TPP. Conclusions Generalisability of reported findings is limited by few studies enrolling PLHIV, limited geographical diversity, and predominantly case-control design, which also introduces spectrum bias. New prospective cohort studies are needed that include PLHIV and are conducted in diverse settings. Further research exploring the effect of HIV clinical, virological, and immunological factors on diagnostic performance is necessary for development and implementation of TB transcriptomic signatures in PLHIV.
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Affiliation(s)
- Simon C Mendelsohn
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, Western Cape, 7935, South Africa
| | - Savannah Verhage
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, Western Cape, 7935, South Africa
| | - Humphrey Mulenga
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, Western Cape, 7935, South Africa
| | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, Western Cape, 7935, South Africa
| | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, Western Cape, 7935, South Africa
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12
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The role of IGRA in the diagnosis of tuberculosis infection, differentiating from active tuberculosis, and decision making for initiating treatment or preventive therapy of tuberculosis infection. Int J Infect Dis 2022; 124 Suppl 1:S12-S19. [PMID: 35257904 DOI: 10.1016/j.ijid.2022.02.047] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 02/19/2022] [Accepted: 02/21/2022] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVES The World Health Organization estimated that a quarter of the global population is infected by Mycobacterium tuberculosis (Mtb). A better control of tuberculosis (TB) is based on the ability to detect Mtb infection, identifying the progressors to TB disease, undergoing to preventive therapy and implementing strategies to register the infections and treatment completion. DESIGN we reviewed the literature regarding the tests available for TB infection diagnosis, the preventive therapies options and the cascade of care for controlling TB at a public health level. RESULTS current tests for TB infection diagnosis as IFN-γ release assays or tuberculin skin tests are based on the detection of an immune response to Mtb in the absence of clinical disease. The main limit is their low accuracy to detect progressors to disease. New preventive treatments are available with short duration that are associated with better adherence. Options to register TB infections are presented. CONCLUSIONS Tests to diagnose TB infection are available but they lack accuracy to identify the progressors from infection to TB disease. Shorter preventive TB therapy are available but need to be implemented worldwide. A TB infection registry is crucial for improving the cascade of care leading to a better TB control.
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13
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Nogueira BMF, Krishnan S, Barreto‐Duarte B, Araújo‐Pereira M, Queiroz ATL, Ellner JJ, Salgame P, Scriba TJ, Sterling TR, Gupta A, Andrade BB. Diagnostic biomarkers for active tuberculosis: progress and challenges. EMBO Mol Med 2022; 14:e14088. [PMID: 36314872 PMCID: PMC9728055 DOI: 10.15252/emmm.202114088] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/05/2022] [Accepted: 09/05/2022] [Indexed: 12/14/2022] Open
Abstract
Tuberculosis (TB) is a leading cause of morbidity and mortality from a single infectious agent, despite being preventable and curable. Early and accurate diagnosis of active TB is critical to both enhance patient care, improve patient outcomes, and break Mycobacterium tuberculosis (Mtb) transmission cycles. In 2020 an estimated 9.9 million people fell ill from Mtb, but only a little over half (5.8 million) received an active TB diagnosis and treatment. The World Health Organization has proposed target product profiles for biomarker- or biosignature-based diagnostics using point-of-care tests from easily accessible specimens such as urine or blood. Here we review and summarize progress made in the development of pathogen- and host-based biomarkers for active TB diagnosis. We describe several unique patient populations that have posed challenges to development of a universal diagnostic TB biomarker, such as people living with HIV, extrapulmonary TB, and children. We also review additional limitations to widespread validation and utilization of published biomarkers. We conclude with proposed solutions to enhance TB diagnostic biomarker validation and uptake.
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Affiliation(s)
- Betânia M F Nogueira
- Programa de Pós‐graduação em Ciências da SaúdeUniversidade Federal da BahiaSalvadorBrazil,Instituto Couto MaiaSalvadorBrazil,Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) InitiativeSalvadorBrazil
| | - Sonya Krishnan
- Division of Infectious Diseases, Department of MedicineJohns Hopkins University School of MedicineBaltimoreMDUSA
| | - Beatriz Barreto‐Duarte
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) InitiativeSalvadorBrazil,Curso de MedicinaUniversidade Salvador (UNIFACS)SalvadorBrazil,Programa de Pós‐Graduação em Clínica MédicaUniversidade Federal do Rio de JaneiroRio de JaneiroBrazil,Laboratório de Inflamação e Biomarcadores, Instituto Gonçalo MonizFundação Oswaldo CruzSalvadorBrazil
| | - Mariana Araújo‐Pereira
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) InitiativeSalvadorBrazil,Laboratório de Inflamação e Biomarcadores, Instituto Gonçalo MonizFundação Oswaldo CruzSalvadorBrazil,Faculdade de MedicinaUniversidade Federal da BahiaSalvadorBrazil
| | - Artur T L Queiroz
- Instituto Couto MaiaSalvadorBrazil,Center of Data and Knowledge Integration for Health (CIDACS), Instituto Gonçalo MonizFundação Oswaldo CruzSalvadorBrazil
| | - Jerrold J Ellner
- Department of Medicine, Centre for Emerging PathogensRutgers‐New Jersey Medical SchoolNewarkNJUSA
| | - Padmini Salgame
- Department of Medicine, Centre for Emerging PathogensRutgers‐New Jersey Medical SchoolNewarkNJUSA
| | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative and Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of PathologyUniversity of Cape TownCape TownSouth Africa
| | - Timothy R Sterling
- Division of Infectious Diseases, Department of MedicineVanderbilt University Medical CenterNashvilleTNUSA
| | - Amita Gupta
- Division of Infectious Diseases, Department of MedicineJohns Hopkins University School of MedicineBaltimoreMDUSA
| | - Bruno B Andrade
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) InitiativeSalvadorBrazil,Curso de MedicinaUniversidade Salvador (UNIFACS)SalvadorBrazil,Laboratório de Inflamação e Biomarcadores, Instituto Gonçalo MonizFundação Oswaldo CruzSalvadorBrazil,Faculdade de MedicinaUniversidade Federal da BahiaSalvadorBrazil,Curso de MedicinaFaculdade de Tecnologia e Ciências (FTC)SalvadorBrazil,Curso de MedicinaEscola Bahiana de Medicina e Saúde Pública (EBMSP)SalvadorBrazil
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14
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Preventive Treatment for Household Contacts of Drug-Susceptible Tuberculosis Patients. Pathogens 2022; 11:pathogens11111258. [DOI: 10.3390/pathogens11111258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 10/25/2022] [Accepted: 10/26/2022] [Indexed: 11/16/2022] Open
Abstract
People who live in the household of someone with infectious pulmonary tuberculosis are at a high risk of tuberculosis infection and subsequent progression to tuberculosis disease. These individuals are prioritized for contact investigation and tuberculosis preventive treatment (TPT). The treatment of TB infection is critical to prevent the progression of infection to disease and is prioritized in household contacts. Despite the availability of TPT, uptake in household contacts is poor. Multiple barriers prevent the optimal implementation of these policies. This manuscript lays out potential next steps for closing the policy-to-implementation gap in household contacts of all ages.
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15
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Valinetz ED, Matemo D, Gersh JK, Joudeh LL, Mendelsohn SC, Scriba TJ, Hatherill M, Kinuthia J, Wald A, Cangelosi GA, Barnabas RV, Hawn TR, Horne DJ. Isoniazid preventive therapy and tuberculosis transcriptional signatures in people with HIV. AIDS 2022; 36:1363-1371. [PMID: 35608118 PMCID: PMC9329226 DOI: 10.1097/qad.0000000000003262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVES To examine the association between isoniazid preventive therapy (IPT) or nontuberculous mycobacteria (NTM) sputum culture positivity and tuberculosis (TB) transcriptional signatures in people with HIV. DESIGN Cross-sectional study. METHODS We enrolled adults living with HIV who were IPT-naive or had completed IPT more than 6 months prior at HIV care clinics in western Kenya. We calculated TB signatures using gene expression data from qRT-PCR. We used multivariable linear regression to analyze the association between prior receipt of IPT or NTM sputum culture positivity with a transcriptional TB risk score, RISK6 (range 0-1). In secondary analyses, we explored the association between IPT or NTM positivity and four other TB transcriptional signatures. RESULTS Among 381 participants, 99.7% were receiving antiretroviral therapy and 86.6% had received IPT (completed median of 1.1 years prior). RISK6 scores were lower (mean difference 0.10; 95% confidence interval (CI): 0.06-0.15; P < 0.001) among participants who received IPT than those who did not. In a model that adjusted for age, sex, duration of ART, and plasma HIV RNA, the RISK6 score was 52.8% lower in those with a history of IPT ( P < 0.001). No significant association between year of IPT receipt and RISK6 scores was detected. There was no association between NTM sputum culture positivity and RISK6 scores. CONCLUSION In people with HIV, IPT was associated with significantly lower RISK6 scores compared with persons who did not receive IPT. These data support investigations of its performance as a TB preventive therapy response biomarker.
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Affiliation(s)
- Ethan D Valinetz
- Department of Medicine, University of Washington, Seattle, Washington
- Division of Infectious Disease, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Daniel Matemo
- Department of Research and Programs, Kenyatta National Hospital, Nairobi
- School of Public Health and Community Development Maseno University, Kisumu, Kenya
| | - Jill K Gersh
- Department of Medicine, University of Washington, Seattle, Washington
| | - Lara L Joudeh
- Department of Medicine, University of Washington, Seattle, Washington
| | - Simon C Mendelsohn
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, South Africa
| | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, South Africa
| | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, South Africa
| | - John Kinuthia
- Department of Research and Programs, Kenyatta National Hospital, Nairobi
- Department of Global Health
| | - Anna Wald
- Department of Medicine, University of Washington, Seattle, Washington
- Department of Epidemiology
- Department of Lab Medicine & Pathology, University of Washington
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | | | - Ruanne V Barnabas
- Department of Medicine, University of Washington, Seattle, Washington
- Department of Global Health
- Department of Epidemiology
| | - Thomas R Hawn
- Department of Medicine, University of Washington, Seattle, Washington
| | - David J Horne
- Department of Medicine, University of Washington, Seattle, Washington
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16
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Are mRNA based transcriptomic signatures ready for diagnosing tuberculosis in the clinic? - A review of evidence and the technological landscape. EBioMedicine 2022; 82:104174. [PMID: 35850011 PMCID: PMC9294474 DOI: 10.1016/j.ebiom.2022.104174] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 05/11/2022] [Accepted: 07/01/2022] [Indexed: 11/20/2022] Open
Abstract
Funding
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17
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Kelly E, Whelan SO, Harriss E, Murphy S, Pollard AJ, O' Connor D. Systematic review of host genomic biomarkers of invasive bacterial disease: Distinguishing bacterial from non-bacterial causes of acute febrile illness. EBioMedicine 2022; 81:104110. [PMID: 35792524 PMCID: PMC9256842 DOI: 10.1016/j.ebiom.2022.104110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 05/27/2022] [Accepted: 05/28/2022] [Indexed: 12/03/2022] Open
Abstract
Background Infectious diseases play a significant role in the global burden of disease. The gold standard for the diagnosis of bacterial infection, bacterial culture, can lead to diagnostic delays and inappropriate antibiotic use. The advent of high- throughput technologies has led to the discovery of host-based genomic biomarkers of infection, capable of differentiating bacterial from other causes of infection, but few have achieved validation for use in a clinical setting. Methods A systematic review was performed. PubMed/Ovid Medline, Ovid Embase and Scopus databases were searched for relevant studies from inception up to 30/03/2022 with forward and backward citation searching of key references. Studies assessing the diagnostic performance of human host genomic biomarkers of bacterial infection were included. Study selection and assessment of quality were conducted by two independent reviewers. A meta-analysis was undertaken using a diagnostic random-effects model. The review was registered with PROSPERO (ID: CRD42021208462). Findings Seventy-two studies evaluating the performance of 116 biomarkers in 16,216 patients were included. Forty-six studies examined TB-specific biomarker performance and twenty-four studies assessed biomarker performance in a paediatric population. The results of pooled sensitivity, specificity, negative and positive likelihood ratio, and diagnostic odds ratio of genomic biomarkers of bacterial infection were 0.80 (95% CI 0.78 to 0.82), 0.86 (95% CI 0.84 to 0.88), 0.18 (95% CI 0.16 to 0.21), 5.5 (95% CI 4.9 to 6.3), 30.1 (95% CI 24 to 37), respectively. Significant between-study heterogeneity (I2 77%) was present. Interpretation Host derived genomic biomarkers show significant potential for clinical use as diagnostic tests of bacterial infection however, further validation and attention to test platform is warranted before clinical implementation can be achieved. Funding No funding received.
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Affiliation(s)
- Eimear Kelly
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford. UK; NIHR Oxford Biomedical Research Centre, Oxford, UK.
| | - Seán Olann Whelan
- Department of Clinical Microbiology, Galway University Hospital, Galway, Ireland
| | - Eli Harriss
- Bodleian Health Care Libraries, University of Oxford
| | - Sarah Murphy
- Department of Paediatrics, Cork University Maternity Hospital, Wilton, Cork, Ireland
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford. UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Daniel O' Connor
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford. UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
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18
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Garcia-Basteiro AL, White RG, Tait D, Schmidt AC, Rangaka MX, Quaife M, Nemes E, Mogg R, Hill PC, Harris RC, Hanekom WA, Frick M, Fiore-Gartland A, Evans T, Dagnew AF, Churchyard G, Cobelens F, Behr MA, Hatherill M. End-point definition and trial design to advance tuberculosis vaccine development. Eur Respir Rev 2022; 31:220044. [PMID: 35675923 PMCID: PMC9488660 DOI: 10.1183/16000617.0044-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/04/2022] [Indexed: 11/05/2022] Open
Abstract
Tuberculosis (TB) remains a leading infectious cause of death worldwide and the coronavirus disease 2019 pandemic has negatively impacted the global TB burden of disease indicators. If the targets of TB mortality and incidence reduction set by the international community are to be met, new more effective adult and adolescent TB vaccines are urgently needed. There are several new vaccine candidates at different stages of clinical development. Given the limited funding for vaccine development, it is crucial that trial designs are as efficient as possible. Prevention of infection (POI) approaches offer an attractive opportunity to accelerate new candidate vaccines to advance into large and expensive prevention of disease (POD) efficacy trials. However, POI approaches are limited by imperfect current tools to measure Mycobacterium tuberculosis infection end-points. POD trials need to carefully consider the type and number of microbiological tests that define TB disease and, if efficacy against subclinical (asymptomatic) TB disease is to be tested, POD trials need to explore how best to define and measure this form of TB. Prevention of recurrence trials are an alternative approach to generate proof of concept for efficacy, but optimal timing of vaccination relative to treatment must still be explored. Novel and efficient approaches to efficacy trial design, in addition to an increasing number of candidates entering phase 2-3 trials, would accelerate the long-standing quest for a new TB vaccine.
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Affiliation(s)
- Alberto L Garcia-Basteiro
- Centro de Investigação em Sade de Manhiça (CISM), Maputo, Mozambique
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFECT), Barcelona, Spain
| | | | - Dereck Tait
- International AIDS Vaccine Initiative (IAVI) NPC, Cape Town, South Africa
| | | | - Molebogeng X Rangaka
- Institute for Global Health and MRC Clinical Trials Unit at University College London, London, UK
- CIDRI-AFRICA, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Matthew Quaife
- London School of Hygiene and Tropical Medicine, London, UK
| | - Elisa Nemes
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Dept of Pathology, University of Cape Town, Cape Town, South Africa
| | - Robin Mogg
- Takeda Pharmaceutical Company Limited, Cambridge, MA, USA
| | - Philip C Hill
- Centre for International Health, University of Otago, Dunedin, New Zealand
| | - Rebecca C Harris
- London School of Hygiene and Tropical Medicine, London, UK
- Sanofi Pasteur, Singapore
| | - Willem A Hanekom
- Africa Health Research Institute, KwaZulu-Natal, South Africa
- Division of Infection and Immunity, University College London, London, UK
| | - Mike Frick
- Treatment Action Group, New York, NY, USA
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Alemnew F Dagnew
- Bill and Melinda Gates Medical Research Institute, Cambridge, MA, USA
| | - Gavin Churchyard
- The Aurum Institute, Parktown, South Africa
- Vanderbilt University, Nashville, TN, USA
- University of the Witwatersrand, Johannesburg, South Africa
| | - Frank Cobelens
- Dept of Global Health and Amsterdam Institute for Global health and development, Amsterdam University Medical Centres, Amsterdam, The Netherlands
| | - Marcel A Behr
- Dept of Medicine, McGill University; McGill International TB Centre, Montreal, QC, Canada
| | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Dept of Pathology, University of Cape Town, Cape Town, South Africa
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Mulenga H, Fiore-Gartland A, Mendelsohn SC, Penn-Nicholson A, Mbandi SK, Nemes E, Borate B, Musvosvi M, Tameris M, Walzl G, Naidoo K, Churchyard G, Scriba TJ, Hatherill M. Evaluation of a transcriptomic signature of tuberculosis risk in combination with an interferon gamma release assay: A diagnostic test accuracy study. EClinicalMedicine 2022; 47:101396. [PMID: 35497063 PMCID: PMC9046130 DOI: 10.1016/j.eclinm.2022.101396] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/25/2022] [Accepted: 03/29/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND We evaluated the diagnostic and prognostic performance of a transcriptomic signature of tuberculosis (TB) risk (RISK11) and QuantiFERON-TB Gold-plus (QFTPlus) as combination biomarkers of TB risk. METHODS Healthy South Africans who were HIV-negative aged 18-60 years with baseline RISK11 and QFTPlus results were evaluated in a prospective cohort study conducted between Sept 20, 2016 and Dec 20, 2019. Prevalence and incidence-rate ratios were used to evaluate risk of TB. Positive (LR+) and negative (LR-) likelihood ratios were used to compare individual tests versus Both-Positive (RISK11+/QFTPlus+) and Either-Positive (RISK11+ or QFTPlus+) combinations. FINDINGS Among 2912 participants, prevalent TB in RISK11+/QFTPlus+ participants was 13·3-fold (95% CI 4·2-42·7) higher than RISK11-/QFTPlus-; 2·4-fold (95% CI 1·2-4·8) higher than RISK11+/QFTPlus-; and 4·5-fold (95% CI 2·5-8·0) higher than RISK11-/QFTPlus+ participants. Risk of incident TB in RISK11+/QFTPlus+ participants was 8·3-fold (95% CI 2·5-27·0) higher than RISK11-/QFTPlus-; 2·5-fold (95% CI 1·0-6·6) higher than RISK11+/QFTPlus-; and 2·1-fold (95% CI 1·2-3·4) higher than RISK11-/QFTPlus+ participants, respectively. Compared to QFTPlus, the Both-Positive test combination increased diagnostic LR+ from 1·3 (95% CI 1·2-1·5) to 4·7 (95% CI 3·2-7·0), and prognostic LR+ from 1·4 (95% CI 1·2-1·5) to 2·8 (95% CI 1·5-5·1), but did not improve upon RISK11 alone. Compared with RISK11, the Either-Positive test combination decreased diagnostic LR- from 0·7 (95% CI 0·6-0·9) to 0·3 (95% CI 0·2-0·6), and prognostic LR- from 0·9 (95% CI 0·8-1·0) to 0·3 (0·1-0·7), but did not improve upon QFTPlus alone. INTERPRETATION Combining two tests such as RISK11 and QFTPlus, with discordant individual performance characteristics does not improve overall discriminatory performance, relative to the individual tests. FUNDING Bill and Melinda Gates Foundation, South African Medical Research Council.
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Affiliation(s)
- Humphrey Mulenga
- South African Tuberculosis Vaccine Initiative, Department of Pathology, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, University of Cape Town, Anzio Road, Observatory 7925, South Africa
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Fairview Ave. N., Seattle, WA 98109-1024, USA
| | - Simon C. Mendelsohn
- South African Tuberculosis Vaccine Initiative, Department of Pathology, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, University of Cape Town, Anzio Road, Observatory 7925, South Africa
| | - Adam Penn-Nicholson
- South African Tuberculosis Vaccine Initiative, Department of Pathology, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, University of Cape Town, Anzio Road, Observatory 7925, South Africa
| | - Stanley Kimbung Mbandi
- South African Tuberculosis Vaccine Initiative, Department of Pathology, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, University of Cape Town, Anzio Road, Observatory 7925, South Africa
| | - Elisa Nemes
- South African Tuberculosis Vaccine Initiative, Department of Pathology, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, University of Cape Town, Anzio Road, Observatory 7925, South Africa
| | - Bhavesh Borate
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Fairview Ave. N., Seattle, WA 98109-1024, USA
| | - Munyaradzi Musvosvi
- South African Tuberculosis Vaccine Initiative, Department of Pathology, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, University of Cape Town, Anzio Road, Observatory 7925, South Africa
| | - Michèle Tameris
- South African Tuberculosis Vaccine Initiative, Department of Pathology, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, University of Cape Town, Anzio Road, Observatory 7925, South Africa
| | - Gerhard Walzl
- DST/NRF Centre of Excellence for Biomedical TB Research and SAMRC Centre for TB Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Francie Van Zijl Drive, Parow 7505, South Africa
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa
- MRC-CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Doris Duke Medical Research Institute, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa
| | - Gavin Churchyard
- The Aurum Institute, 29 Queens Rd, Parktown, Johannesburg, Gauteng 2194, South Africa
- School of Public Health, University of Witwatersrand, 27 St Andrews Road, Parktown, Johannesburg 2193, South Africa
- Department of Medicine, Vanderbilt University, Nashville, TN, USA
| | - Thomas J. Scriba
- South African Tuberculosis Vaccine Initiative, Department of Pathology, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, University of Cape Town, Anzio Road, Observatory 7925, South Africa
| | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative, Department of Pathology, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, University of Cape Town, Anzio Road, Observatory 7925, South Africa
- Corresponding author.
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20
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Mendelsohn SC, Mbandi SK, Fiore-Gartland A, Penn-Nicholson A, Musvosvi M, Mulenga H, Fisher M, Hadley K, Erasmus M, Nombida O, Tameris M, Walzl G, Naidoo K, Churchyard G, Hatherill M, Scriba TJ. Prospective multicentre head-to-head validation of host blood transcriptomic biomarkers for pulmonary tuberculosis by real-time PCR. COMMUNICATIONS MEDICINE 2022; 2:26. [PMID: 35342900 PMCID: PMC8954216 DOI: 10.1038/s43856-022-00086-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 02/10/2022] [Indexed: 01/31/2023] Open
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.
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Affiliation(s)
- Simon C. Mendelsohn
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, 7925 Cape Town, South Africa
| | - Stanley Kimbung Mbandi
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, 7925 Cape Town, South Africa
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
| | - Adam Penn-Nicholson
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, 7925 Cape Town, South Africa
| | - Munyaradzi Musvosvi
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, 7925 Cape Town, South Africa
| | - Humphrey Mulenga
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, 7925 Cape Town, South Africa
| | - Michelle Fisher
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, 7925 Cape Town, South Africa
| | - Katie Hadley
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, 7925 Cape Town, South Africa
| | - Mzwandile Erasmus
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, 7925 Cape Town, South Africa
| | - Onke Nombida
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, 7925 Cape Town, South Africa
| | - Michèle Tameris
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, 7925 Cape Town, South Africa
| | - Gerhard Walzl
- DST/NRF Centre of Excellence for Biomedical TB Research; South African Medical Research Council Centre for TB Research; Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, 7505 Cape Town, South Africa
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), 4001 Durban, South Africa
- MRC-CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Doris Duke Medical Research Institute, University of KwaZulu-Natal, 4001 Durban, South Africa
| | - Gavin Churchyard
- The Aurum Institute, 2194 Johannesburg, South Africa
- School of Public Health, University of Witwatersrand, 2193 Johannesburg, South Africa
- Department of Medicine, Vanderbilt University, Nashville, TN 37232 USA
| | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, 7925 Cape Town, South Africa
| | - Thomas J. Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, 7925 Cape Town, South Africa
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21
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Mulenga H, Fiore-Gartland A, Mendelsohn SC, Penn-Nicholson A, Mbandi SK, Borate B, Musvosvi M, Tameris M, Walzl G, Naidoo K, Churchyard G, Scriba TJ, Hatherill M. The effect of host factors on discriminatory performance of a transcriptomic signature of tuberculosis risk. EBioMedicine 2022; 77:103886. [PMID: 35183869 PMCID: PMC8861653 DOI: 10.1016/j.ebiom.2022.103886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 01/19/2022] [Accepted: 02/01/2022] [Indexed: 01/28/2023] Open
Abstract
Background We aimed to understand host factors that affect discriminatory performance of a transcriptomic signature of tuberculosis risk (RISK11). Methods HIV-negative adults aged 18–60 years were evaluated in a prospective study of RISK11 and surveilled for tuberculosis through 15 months. Generalised linear models and receiver-operating characteristic (ROC) regression were used to estimate effect of host factors on RISK11 score (%marginal effect) and on discriminatory performance for tuberculosis disease (area under the curve, AUC), respectively. Findings Among 2923 participants including 74 prevalent and 56 incident tuberculosis cases, percentage marginal effects on RISK11 score were increased among those with prevalent tuberculosis (+18·90%, 95%CI 12·66−25·13), night sweats (+14·65%, 95%CI 5·39−23·91), incident tuberculosis (+7·29%, 95%CI 1·46−13·11), flu-like symptoms (+5·13%, 95%CI 1·58−8·68), and smoking history (+2·41%, 95%CI 0·89−3·93) than those without; and reduced in males (−6·68%, 95%CI −8·31−5·04) and with every unit increase in BMI (−0·13%, −95%CI −0·25−0·01). Adjustment for host factors affecting controls did not change RISK11 discriminatory performance. Cough was associated with 72·55% higher RISK11 score in prevalent tuberculosis cases. Stratification by cough improved diagnostic performance from AUC = 0·74 (95%CI 0·67−0·82) overall, to 0·97 (95%CI 0·90−1·00, p < 0·001) in cough-positive participants. Combining host factors with RISK11 improved prognostic performance, compared to RISK11 alone, (AUC = 0·76, 95%CI 0·69−0·83 versus 0·56, 95%CI 0·46−0·68, p < 0·001) over a 15-month predictive horizon. Interpretation Several host factors affected RISK11 score, but only adjustment for cough affected diagnostic performance. Combining host factors with RISK11 should be considered to improve prognostic performance. Funding Bill and Melinda Gates Foundation, South African Medical Research Council.
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Affiliation(s)
- Humphrey Mulenga
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Anzio Road, Observatory, 7925, South Africa
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Fairview Ave. N., Seattle, WA 98109-1024, USA
| | - Simon C Mendelsohn
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Anzio Road, Observatory, 7925, South Africa
| | - Adam Penn-Nicholson
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Anzio Road, Observatory, 7925, South Africa
| | - Stanley Kimbung Mbandi
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Anzio Road, Observatory, 7925, South Africa
| | - Bhavesh Borate
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Fairview Ave. N., Seattle, WA 98109-1024, USA
| | - Munyaradzi Musvosvi
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Anzio Road, Observatory, 7925, South Africa
| | - Michèle Tameris
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Anzio Road, Observatory, 7925, South Africa
| | - Gerhard Walzl
- DST/NRF Centre of Excellence for Biomedical TB Research and SAMRC Centre for TB Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Francie Van Zijl Dr, Parow, 7505, South Africa
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, Doris Duke Medical Research Institute, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa; MRC-CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Doris Duke Medical Research Institute, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa
| | - Gavin Churchyard
- The Aurum Institute, 29 Queens Rd, Parktown, Johannesburg, Gauteng 2194, South Africa; School of Public Health, University of Witwatersrand, 27 St Andrews Road, Parktown, Johannesburg 2193, South Africa; Department of Medicine, Vanderbilt University, Nashville, TN, USA
| | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Anzio Road, Observatory, 7925, South Africa
| | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Anzio Road, Observatory, 7925, South Africa.
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Mendelsohn SC, Fiore-Gartland A, Awany D, Mulenga H, Mbandi SK, Tameris M, Walzl G, Naidoo K, Churchyard G, Scriba TJ, Hatherill M. Clinical predictors of pulmonary tuberculosis among South African adults with HIV. EClinicalMedicine 2022; 45:101328. [PMID: 35274090 PMCID: PMC8902614 DOI: 10.1016/j.eclinm.2022.101328] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 02/04/2022] [Accepted: 02/14/2022] [Indexed: 11/17/2022] Open
Abstract
Background Tuberculosis (TB) clinical prediction rules rely on presence of symptoms, however many undiagnosed cases in the community are asymptomatic. This study aimed to explore the utility of clinical factors in predicting TB among people with HIV not seeking care. Methods Baseline data were analysed from an observational cohort of ambulant adults with HIV in South Africa. Participants were tested for Mycobacterium tuberculosis (Mtb) sensitisation (interferon-γ release assay, IGRA) and microbiologically-confirmed prevalent pulmonary TB disease at baseline, and actively surveilled for incident TB through 15 months. Multivariable LASSO regression with post-selection inference was used to test associations with Mtb sensitisation and TB disease. Findings Between March 22, 2017, and May 15, 2018, 861 participants were enrolled; Among 851 participants included in the analysis, 94·5% were asymptomatic and 45·9% sensitised to Mtb. TB prevalence was 2·0% at baseline and incidence 2·3/100 person-years through 15 months follow-up. Study site was associated with baseline Mtb sensitisation (p < 0·001), prevalent (p < 0·001), and incident TB disease (p = 0·037). Independent of site, higher CD4 counts (per 50 cells/mm3, aOR 1·48, 95%CI 1·12-1·77, p = 0·006) were associated with increased IGRA positivity, and participants without TB disease (aOR 0·80, 95%CI 0·69-0·94, p = 0·006) had reduced IGRA positivity; no variables were independently associated with prevalent TB. Mixed ancestry (aHR 1·49, 95%CI 1·30->1000, p = 0·005) and antiretroviral initiation (aHR 1·48, 95%CI 1·01-929·93, p = 0·023) were independently associated with incident TB. Models incorporating clinical features alone performed poorly in diagnosing prevalent (AUC 0·65, 95%CI 0·44-0·85) or predicting progression to incident (0·67, 0·46-0·88) TB. Interpretation CD4 count and antiretroviral initiation, proxies for immune status and HIV stage, were associated with Mtb sensitisation and TB disease. Inadequate performance of clinical prediction models may reflect predominantly subclinical disease diagnosed in this setting and unmeasured local site factors affecting transmission and progression. Funding The CORTIS-HR study was funded by the Bill & Melinda Gates Foundation (OPP1151915) and by the Strategic Health Innovation Partnerships Unit of the South African Medical Research Council with funds received from the South African Department of Science and Technology. The regulatory sponsor was the University of Cape Town.
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Affiliation(s)
- Simon C. Mendelsohn
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Denis Awany
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa
| | - Humphrey Mulenga
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa
| | - Stanley Kimbung Mbandi
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa
| | - Michèle Tameris
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa
| | - Gerhard Walzl
- DST/NRF Centre of Excellence for Biomedical TB Research, South African Medical Research Council Centre for TB Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4001, South Africa
- MRC-CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Gavin Churchyard
- The Aurum Institute, Johannesburg 2194, South Africa
- School of Public Health, University of Witwatersrand, Johannesburg 2193, South Africa
- Department of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | - Thomas J. Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa
| | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa
| | - the CORTIS-HR Study Team
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- DST/NRF Centre of Excellence for Biomedical TB Research, South African Medical Research Council Centre for TB Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4001, South Africa
- MRC-CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban 4001, South Africa
- The Aurum Institute, Johannesburg 2194, South Africa
- School of Public Health, University of Witwatersrand, Johannesburg 2193, South Africa
- Department of Medicine, Vanderbilt University, Nashville, TN 37232, USA
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23
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Migliori GB, Ong CWM, Petrone L, D'Ambrosio L, Centis R, Goletti D. The definition of tuberculosis infection based on the spectrum of tuberculosis disease. Breathe (Sheff) 2022; 17:210079. [PMID: 35035549 PMCID: PMC8753649 DOI: 10.1183/20734735.0079-2021] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/19/2021] [Indexed: 11/11/2022] Open
Abstract
Latent tuberculosis infection was the term traditionally used to indicate tuberculosis (TB) infection. This term was used to define “a state of persistent immune response to stimulation by Mycobacterium tuberculosis antigens through tests such as the tuberculin skin test (TST) or an interferon-γ release assay (IGRA) without clinically active TB”. Recent evidence indicates that the spectrum from TB infection to TB disease is much more complex, including a “continuum” of situations didactically reported as uninfected individual, TB infection, incipient TB, subclinical TB without signs/symptoms, subclinical TB with unrecognised signs/symptoms, and TB disease with signs/symptoms. Recent evidence suggests that subclinical TB is responsible for important M. tuberculosis transmission. This review describes the different stages described above and their relationships. It also summarises the new developments in prevention, diagnosis and treatment of TB infection as well as their public health and policy implications. The evolution from TB infection to disease is now described as a “continuum process”. Understanding of this is important to appreciate what is new on prevention, diagnosis and treatment of TB infection.https://bit.ly/3jauRKA
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Affiliation(s)
- Giovanni Battista Migliori
- Servizio di Epidemiologia Clinica delle Malattie Respiratorie, Istituti Clinici Scientifici Maugeri IRCCS, Tradate, Italy
| | - Catherine W M Ong
- Dept of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Institute for Health Innovation and Technology (iHealthtech), National University of Singapore, Singapore
| | - Linda Petrone
- Translational Research Unit, National Institute for Infectious Diseases "Lazzaro Spallanzani"-IRCCS, Rome, Italy
| | | | - Rosella Centis
- Servizio di Epidemiologia Clinica delle Malattie Respiratorie, Istituti Clinici Scientifici Maugeri IRCCS, Tradate, Italy
| | - Delia Goletti
- Translational Research Unit, National Institute for Infectious Diseases "Lazzaro Spallanzani"-IRCCS, Rome, Italy
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24
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Noursadeghi M, Gupta RK. New Insights into the Limitations of Host Transcriptional Biomarkers of Tuberculosis. Am J Respir Crit Care Med 2021; 204:1363-1365. [PMID: 34705613 PMCID: PMC8865719 DOI: 10.1164/rccm.202109-2146ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Mahdad Noursadeghi
- Division of Infection and Immunity University College London London, United Kingdom
| | - Rishi K Gupta
- Institute for Global Health University College London London, United Kingdom
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25
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Wykowski JH, Phillips C, Ngo T, Drain PK. A systematic review of potential screening biomarkers for active TB disease. J Clin Tuberc Other Mycobact Dis 2021; 25:100284. [PMID: 34805557 PMCID: PMC8590066 DOI: 10.1016/j.jctube.2021.100284] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
INTRODUCTION The standard TB Four Symptom Screen does not meet the World Health Organization (WHO) ideal screening criteria for having greater than 90% sensitivity to identify active TB disease, regardless of HIV status. To identify novel screening biomarkers for active TB, we performed a systematic review of any cohort or case-control study reporting associations between screening biomarkers and active TB disease. METHODS We searched PubMed and Embase for articles published before October 10, 2021. We included studies from high or medium tuberculosis burden countries. We excluded articles focusing on C-reactive protein and lipoarabinomannan. For all included biomarkers, we calculated sensitivity, specificity and 95% confidence intervals, and assessed study quality using a tool adapted from the QUADAS-2 risk of bias. RESULTS From 8,062 abstracts screened, we included 79 articles. The articles described 302 unique biomarkers, including host antibodies, host proteins, TB antigens, microRNAs, whole blood gene PCRs, and combinations of biomarkers. Of these, 23 biomarkers had sensitivity greater than 90% and specificity greater than 70%, meeting WHO criteria for an ideal screening test. Among the eleven biomarkers described in people living with HIV, only one had a sensitivity greater than 90% and specificity greater than 70% for active TB. CONCLUSION Further evaluation of biomarkers of active TB should be pursued to accelerate identification of TB disease.
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Affiliation(s)
- James H. Wykowski
- Department of Medicine, 925 9 Ave Seattle, WA 98104, University of Washington, Seattle, USA
| | - Chris Phillips
- Department of Global Health, 925 9 Ave Seattle, WA 98104, University of Washington, Seattle, USA
| | - Thao Ngo
- Department of Global Health, 925 9 Ave Seattle, WA 98104, University of Washington, Seattle, USA
| | - Paul K. Drain
- Department of Medicine, 925 9 Ave Seattle, WA 98104, University of Washington, Seattle, USA
- Department of Global Health, 925 9 Ave Seattle, WA 98104, University of Washington, Seattle, USA
- Department of Epidemiology, 925 9 Ave Seattle, WA 98104, University of Washington, Seattle, USA
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26
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A 10-gene biosignature of tuberculosis treatment monitoring and treatment outcome prediction. Tuberculosis (Edinb) 2021; 131:102138. [PMID: 34801869 DOI: 10.1016/j.tube.2021.102138] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/30/2021] [Accepted: 10/07/2021] [Indexed: 11/23/2022]
Abstract
The clinical utility of blood transcriptomic biosignatures for the treatment monitoring and outcome prediction of tuberculosis (TB) remains limited. In this study, we aimed to discover and validate biomarkers for pulmonary TB treatment monitoring and outcome prediction based on kinetic responses of gene expression during treatment. In particular, differentially expressed genes (DEGs) were identified by time-series comparison. Subsequently, DEGs with the monotonic expression alterations during the treatment were selected. Ten consistently down-regulated genes (CD274, KIF1B, IL15, TLR1, TLR5, FCGR1A, GBP1, NOD2, GBP2, EGF) exhibited significant potential in treatment monitoring, demonstrated via biological and technical validation. Additionally, the biosignature showed potential in predicting the cured versus relapsed patients. Furthermore, the biosignature could be utilized for TB diagnosis, latent tuberculosis infection/active TB differential diagnosis, and risk of progression to active TB. Benchmarking analysis of the 10-gene biosignature with other biosignatures showed equivalent performance in tested data sets. In conclusion, we established a 10-gene transcriptomic biosignature that represents the kinetic responses of TB treatment. Subsequent studies are warranted to validate, refine and translate the biosignature into a precise assay to assist clinical decisions in a broad spectrum of TB management.
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Sumner T, Mendelsohn SC, Scriba TJ, Hatherill M, White RG. The impact of blood transcriptomic biomarker targeted tuberculosis preventive therapy in people living with HIV: a mathematical modelling study. BMC Med 2021; 19:252. [PMID: 34711213 PMCID: PMC8555196 DOI: 10.1186/s12916-021-02127-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 09/14/2021] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Tuberculosis (TB) preventive therapy is recommended for all people living with HIV (PLHIV). Despite the elevated risk of TB amongst PLHIV, most of those eligible for preventive therapy would never develop TB. Tests which can identify individuals at greatest risk of disease would allow more efficient targeting of preventive therapy. METHODS We used mathematical modelling to estimate the potential impact of using a blood transcriptomic biomarker (RISK11) to target preventive therapy amongst PLHIV. We compared universal treatment to RISK11 targeted treatment and explored the effect of repeat screening of the population with RISK11. RESULTS Annual RISK11 screening, with preventive therapy provided to those testing positive, could avert 26% (95% CI 13-34) more cases over 10 years compared to one round of universal treatment. For the cost per case averted to be lower than universal treatment, the maximum cost of the RISK11 test was approximately 10% of the cost of preventive therapy. The benefit of RISK11 screening may be greatest amongst PLHIV on ART (compared to ART naïve individuals) due to the increased specificity of the test in this group. CONCLUSIONS Biomarker targeted preventive therapy may be more effective than universal treatment amongst PLHIV in high incidence settings but would require repeat screening.
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Affiliation(s)
- Tom Sumner
- TB Modelling Group, TB Centre, Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK.
| | - Simon C Mendelsohn
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Richard G White
- TB Modelling Group, TB Centre, Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
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28
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Mulenga H, Musvosvi M, Mendelsohn SC, Penn-Nicholson A, Kimbung Mbandi S, Gartland AF, Tameris M, Mabwe S, Africa H, Bilek N, Kafaar F, Khader SA, Carstens B, Hadley K, Hikuam C, Erasmus M, Jaxa L, Raphela R, Nombida O, Kaskar M, Nicol MP, Mbhele S, Van Heerden J, Innes C, Brumskine W, Hiemstra A, Malherbe ST, Hassan-Moosa R, Walzl G, Naidoo K, Churchyard G, Hatherill M, Scriba TJ. Longitudinal Dynamics of a Blood Transcriptomic Signature of Tuberculosis. Am J Respir Crit Care Med 2021; 204:1463-1472. [PMID: 34520313 PMCID: PMC8865716 DOI: 10.1164/rccm.202103-0548oc] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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.
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Affiliation(s)
- Humphrey Mulenga
- University of Cape Town Faculty of Health Sciences, 63726, Pathology, Observatory, South Africa
| | - Munyaradzi Musvosvi
- University of Cape Town, Institute of Infectious Diseases and Molecular Medicine, Observatory, South Africa
| | - Simon C Mendelsohn
- University of Cape Town, 37716, South African Tuberculosis Vaccine Initiative, Cape Town, South Africa
| | - Adam Penn-Nicholson
- University of Cape Town Faculty of Health Sciences, 63726, South Africa Tuberculosis Vaccines Initiative (SATVI), Cape Town, South Africa
| | - Stanley Kimbung Mbandi
- University of Cape Town Faculty of Health Sciences, 63726, South Africa Tuberculosis Vaccines Initiative (SATVI), Cape Town, South Africa
| | - Andrew-Fiore Gartland
- Fred Hutchinson Cancer Research Center, 7286, Vaccine and Infectious Disease Division, Seattle, Washington, United States
| | | | - Simbarashe Mabwe
- University of Cape Town Faculty of Health Sciences, 63726, South African Tuberculosis Vaccine Initiative, Observatory, Cape Town, South Africa
| | - Hadn Africa
- University of Cape Town, South African Tuberculosis Vaccine Initiative, Cape Town, South Africa
| | - Nicole Bilek
- University of Cape Town Faculty of Health Sciences, 63726, South African Tuberculosis Vaccine Initiative, Observatory, Cape Town, South Africa
| | - Fazlin Kafaar
- University of Cape Town Faculty of Health Sciences, 63726, South Africa Tuberculosis Vaccines Initiative (SATVI), Cape Town, South Africa
| | | | - Balie Carstens
- University of Cape Town Faculty of Health Sciences, 63726, South Africa Tuberculosis Vaccines Initiative (SATVI), Cape Town, South Africa
| | - Katie Hadley
- University of Cape Town Faculty of Health Sciences, 63726, South Africa Tuberculosis Vaccines Initiative (SATVI), Cape Town, South Africa
| | - Chris Hikuam
- University of Cape Town Faculty of Health Sciences, 63726, South Africa Tuberculosis Vaccines Initiative (SATVI), Cape Town, South Africa
| | - Mzwandile Erasmus
- University of Cape Town Faculty of Health Sciences, 63726, South African Tuberculosis Vaccine Initiative, Observatory, Cape Town, South Africa
| | - Lungisa Jaxa
- University of Cape Town Faculty of Health Sciences, 63726, South Africa Tuberculosis Vaccines Initiative (SATVI), Cape Town, South Africa
| | - Rodney Raphela
- University of Cape Town Faculty of Health Sciences, 63726, South Africa Tuberculosis Vaccines Initiative (SATVI), Cape Town, South Africa
| | - Onke Nombida
- University of Cape Town Faculty of Health Sciences, 63726, South Africa Tuberculosis Vaccines Initiative (SATVI), Cape Town, South Africa
| | - Masooda Kaskar
- University of Cape Town Faculty of Health Sciences, 63726, South Africa Tuberculosis Vaccines Initiative (SATVI), Cape Town, South Africa
| | - Mark P Nicol
- University of Capetown, Pediatrics & Child Health, Cape Town, South Africa
| | - Slindile Mbhele
- University of Capetown, Pediatrics & Child Health, Cape Town, South Africa
| | - Judi Van Heerden
- University of Capetown, Pediatrics & Child Health, Cape Town, South Africa
| | - Craig Innes
- The Aurum Institute for Health Research, 72030, Parktown, South Africa
| | - William Brumskine
- The Aurum Institute for Health Research, 72030, Parktown, South Africa
| | - Andriëtte Hiemstra
- 7DST/NRF Centre of Excellence for Biomedical TB Research and SAMRC Centre for TB Research, Division of Molecular Biology and Human Genetics, Stellenbosch, South Africa
| | | | | | | | | | | | | | - Thomas J Scriba
- University of Cape Town, Institute of Infectious Diseases and Molecular Medicine, Observatory, South Africa;
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29
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Kerkhoff AD, Cattamanchi A, Muyoyeta M, Denkinger CM, Dowdy DW. Validating novel diagnostic assays for tuberculosis in the context of existing tools. LANCET GLOBAL HEALTH 2021; 9:e1209. [PMID: 34416206 PMCID: PMC9541186 DOI: 10.1016/s2214-109x(21)00306-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 06/24/2021] [Indexed: 11/13/2022]
Affiliation(s)
- Andrew D Kerkhoff
- Division of HIV, Infectious Diseases and Global Medicine, Zuckerberg San Francisco General Hospital and Trauma Center, University of California San Francisco, San Francisco, CA 94110, USA.
| | - Adithya Cattamanchi
- Center for Tuberculosis and Division of Pulmonary and Critical Care Medicine, Zuckerberg San Francisco General Hospital and Trauma Center, University of California San Francisco, San Francisco, CA 94110, USA; Uganda Tuberculosis Implementation Research Consortium, Makerere University, Kampala, Uganda
| | - Monde Muyoyeta
- TB Department, Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
| | - Claudia M Denkinger
- Division of Tropical Medicine, Center of Infectious Diseases, University of Heidelberg, Heidelberg, Germany
| | - David W Dowdy
- Uganda Tuberculosis Implementation Research Consortium, Makerere University, Kampala, Uganda; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
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30
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Kumar Gupta R, Noursadeghi M. Blood transcriptomic biomarkers for tuberculosis screening: time to redefine our target populations? Lancet Glob Health 2021; 9:e736-e737. [PMID: 33862011 DOI: 10.1016/s2214-109x(21)00088-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 02/18/2021] [Indexed: 01/14/2023]
Affiliation(s)
- Rishi Kumar Gupta
- Institute for Global Health, University College London, London WC1E 6JB, UK.
| | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, London WC1E 6JB, UK
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