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Mahmoudi S, García MJ, Drain PK. Current approaches for diagnosis of subclinical pulmonary tuberculosis, clinical implications and future perspectives: a scoping review. Expert Rev Clin Immunol 2024; 20:715-726. [PMID: 38879875 DOI: 10.1080/1744666x.2024.2326032] [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: 11/12/2023] [Accepted: 02/28/2024] [Indexed: 06/18/2024]
Abstract
INTRODUCTION Subclinical tuberculosis (TB) is the presence of TB disease among people who are either asymptomatic or have minimal symptoms. AREAS COVERED Currently, there are no accurate diagnostic tools and clear treatment approaches for subclinical TB. In this study, a comprehensive literature search was conducted across major databases. This review aimed to uncover the latest advancements in diagnostic approaches, explore their clinical implications, and outline potential future perspectives. While innovative technologies are in development to enable sputum-free TB tests, there remains a critical need for precise diagnostic tools tailored to the unique characteristics of subclinical TB. Given the complexity of subclinical TB, a multidisciplinary approach involving clinicians, microbiologists, epidemiologists, and public health experts is essential. Further research is needed to establish standardized diagnostic criteria and treatment guidelines specifically tailored for subclinical TB, acknowledging the unique challenges posed by this elusive stage of the disease. EXPERT OPINION Efforts are needed for the detection, diagnosis, and treatment of subclinical TB. In this review, we describe the importance of subclinical TB, both from a clinical and public health perspective and highlight the diagnostic and treatment gaps of this stage.
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Affiliation(s)
- Shima Mahmoudi
- Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Maria J García
- Department of Preventive Medicine and Public Health and Microbiology, Autonoma University of Madrid, Madrid, Spain
| | - Paul K Drain
- International Clinical Research Center, Department of Global Health, Schools of Medicine and Public Health, University of Washington, Seattle, WA, USA
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA
- Division of Allergy and Infectious Diseases, Department of Medicine, School of Medicine, University of Washington, Seattle, WA, USA
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Rajendran P, Jayabal L, Venkatesan M, Kumar MP, Ramalingam R, Sivaraman P, Fredrick A, Shanmugam S. Assessing the utility of Truenat in extrapulmonary tuberculosis diagnosis - A NRL's experience. J Clin Tuberc Other Mycobact Dis 2024; 35:100420. [PMID: 38440213 PMCID: PMC10909875 DOI: 10.1016/j.jctube.2024.100420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024] Open
Abstract
Background Diagnosis of extra pulmonary TB (EPTB) remains a big challenge. While data on utility of Xpert testing in EPTB diagnosis is enormous, there is limited data on Truenat MTB testing. Aim In this study we aimed to evaluate the usefulness of Truenat in EPTB diagnosis. Materials and methods The study included patients suspected and/or treated for EPTB located from Chennai district during the year 2021-2022. All processed EPTB samples were subjected to smear microscopy, culture and Truenat MTB testing. Results Of the 195 samples tested, 38 (19.4%) samples were positive for EPTB by any one of the diagnostic methods (smear, culture, microscopy). Out of these 38, 16 (42.1 %) were positive for MTB by Truenat and negative by Culture, 12 (31.5%) were positive by culture but negative by Truenat and 8 (21%) were positive by both Truenat and/or smear and culture. The sensitivity and specificity of the test was calculated with the composite reference standard (Culture (exclusion of colonies as positives), clinical conditions, and smear) and was found to be 60% and 100% respectively. Conclusion Truenat MTB test is a cost-effective rapid molecular test that can be used only for the diagnosis of presumptive EPTB and not on follow-up samples.
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Affiliation(s)
- Priya Rajendran
- ICMR -National Institute for Research in Tuberculosis, Chennai, India
| | - Lavanya Jayabal
- District Tuberculosis Office, National Tuberculosis Elimination Programme, Chennai, India
| | | | - Michel Prem Kumar
- ICMR -National Institute for Research in Tuberculosis, Chennai, India
| | | | - P Sivaraman
- ICMR -National Institute for Research in Tuberculosis, Chennai, India
| | - Asha Fredrick
- State Tuberculosis Office, National Tuberculosis Elimination Programme, Chennai, India
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Ssengooba W, Katamba A, Sserubiri J, Semugenze D, Nyombi A, Byaruhanga R, Turyahabwe S, Joloba ML. Performance evaluation of Truenat MTB and Truenat MTB-RIF DX assays in comparison to gene XPERT MTB/RIF ultra for the diagnosis of pulmonary tuberculosis in Uganda. BMC Infect Dis 2024; 24:190. [PMID: 38350885 PMCID: PMC10863216 DOI: 10.1186/s12879-024-09063-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 01/26/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND The World Health Organization endorsed Truenat MTB rapid molecular assay in 2020 and recommended additional in-country evaluation studies before uptake. We evaluated the accuracy and operational feasibility of Truenat MTB assay (Truenat) in comparison with GeneXpert Ultra and culture. METHODS In a cross-sectional study of 250 presumptive TB patients, participants were requested to provide a sputum sample on the day of their visit to the clinic. The sputum sample was homogenized and a portion was tested using GeneXpert Ultra as per the routine standard procedure and the other portion was tested using Truenat assay at the clinic laboratory. The second sample portion was processed for Concentrated Fluorescent smear Microscopy (CFM), LJ, and MGIT cultures. Truenat sensitivity and specificity were compared to GeneXpert Ultra and culture. Test performance characteristics and operational feasibility assessment data through interview of the study laboratory staff were also collected and summarized as proportions and percentages. RESULTS Of the 250 participants recruited in the study, the sensitivity and specificity of Truenat was n/N (%, 95%CI); 66/82 (80.5, 70.2-88.4) and 156/159 (98.1, 94.5-99.6) when compared with Ultra, 50/64 (89.3, 66.0-87.4) and 166/180 (92.2, 87.2-95.6) when compared with LJ, 58/71 (81.7,70.7-89.8) and 131/138 (94.9, 89.8-97.9) when compared to MGIT culture and 59/73 (80.8, 69.9-89.1) and 159/169 (94.1,89.3-97.1) when compared to LJ and/or MGIT culture. The sensitivity of Truenat was lower, 14/23 (60.9, 40.6-82.8) among smear-negative compared to 45/50 (90.0, 78.1-96.6) among smear-positive participants but not different by HIV status. There were no special training needs especially among laboratory personnel with previous GeneXpert /molecular test experience, 19/242 (7.8%) error/invalid, and 12 (17,4%) uninterpretable/indeterminate results mainly for rifampicin resistance determination. However, there were 3 (3.5%) of GeneXpert Ultra indeterminate results. CONCLUSION Among presumptive TB patients in Uganda, the Truenat assay has high sensitivity and specificity. The Truenat assay has acceptable operational feasibility attributes when compared with the GeneXpert Assay.
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Affiliation(s)
- Willy Ssengooba
- Department of Medical Microbiology, Makerere University, Kampala, Uganda.
- Makerere University Lung Institute, Kampala, Uganda.
- Biomedical Research Center, Makerere University, Kampala, Uganda.
| | - Achilles Katamba
- Department of Medicine, School of Medicine, Clinical Epidemiology and Biostatistics Unit, Makerere University, Kampala, Uganda
- Uganda TB Implementation Research Consortium, Kampala, Uganda
| | - James Sserubiri
- Department of Medical Microbiology, Makerere University, Kampala, Uganda
- Makerere University Lung Institute, Kampala, Uganda
| | - Derrick Semugenze
- Department of Medical Microbiology, Makerere University, Kampala, Uganda
- Makerere University Lung Institute, Kampala, Uganda
| | - Abdunoor Nyombi
- Ministry of Health, National Tuberculosis, and Leprosy Programme, Kampala, Uganda
| | - Raymond Byaruhanga
- Ministry of Health, National Tuberculosis, and Leprosy Programme, Kampala, Uganda
| | - Stavia Turyahabwe
- Ministry of Health, National Tuberculosis, and Leprosy Programme, Kampala, Uganda
| | - Moses L Joloba
- Department of Medical Microbiology, Makerere University, Kampala, Uganda
- Biomedical Research Center, Makerere University, Kampala, Uganda
- Ministry of Health, National Tuberculosis, and Leprosy Programme, Kampala, Uganda
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Vijayan S, Jondhale V, Pande T, Khan A, Brouwer M, Hegde A, Gandhi R, Roddawar V, Jichkar S, Kadu A, Bharaswadkar S, Sharma M, Vasquez NA, Richardson L, Robert D, Pawar S. Implementing a chest X-ray artificial intelligence tool to enhance tuberculosis screening in India: Lessons learned. PLOS DIGITAL HEALTH 2023; 2:e0000404. [PMID: 38060461 PMCID: PMC10703224 DOI: 10.1371/journal.pdig.0000404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 11/06/2023] [Indexed: 02/12/2024]
Abstract
Artificial Intelligence (AI) based chest X-ray (CXR) screening for tuberculosis (TB) is becoming increasingly popular. Still, deploying such AI tools can be challenging due to multiple real-life barriers like software installation, workflow integration, network connectivity constraints, limited human resources available to interpret findings, etc. To understand these challenges, PATH implemented a TB REACH active case-finding program in a resource-limited setting of Nagpur in India, where an AI software device (qXR) intended for TB screening using CXR images was used. Eight private CXR laboratories that fulfilled prerequisites for AI software installation were engaged for this program. Key lessons about operational feasibility and accessibility, along with the strategies adopted to overcome these challenges, were learned during this program. This program also helped to screen 10,481 presumptive TB individuals using informal providers based on clinical history. Among them, 2,303 individuals were flagged as presumptive for TB by a radiologist or by AI based on their CXR interpretation. Approximately 15.8% increase in overall TB yield could be attributed to the presence of AI alone because these additional cases were not deemed presumptive for TB by radiologists, but AI was able to identify them. Successful implementation of AI tools like qXR in resource-limited settings in India will require solving real-life implementation challenges for seamless deployment and workflow integration.
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Affiliation(s)
| | | | - Tripti Pande
- External consultant, Washington DC, United States of America
| | - Amera Khan
- STOP TB Partnership, Geneva, Switzerland
| | | | | | | | | | - Shilpa Jichkar
- Department of Health Services, Nagpur Municipal Corporation, Nagpur, India
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Katamba A, Ssengooba W, Sserubiri J, Semugenze D, Kasule GW, Nyombi A, Byaruhanga R, Turyahabwe S, Joloba ML. Evaluation of Xpert MTB/XDR test for susceptibility testing of Mycobacterium tuberculosis to first and second-line drugs in Uganda. PLoS One 2023; 18:e0284545. [PMID: 37590288 PMCID: PMC10434885 DOI: 10.1371/journal.pone.0284545] [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: 03/31/2023] [Accepted: 07/31/2023] [Indexed: 08/19/2023] Open
Abstract
BACKGROUND Drug-Resistant Tuberculosis (DR-TB) is one of the major challenges to TB control. DESIGN AND METHODS This was a blinded, laboratory-based cross-sectional study using sputum samples or culture isolates. Samples were from patients with rifampicin-resistant-TB and/or with high risk for isoniazid (INH) resistance and/or 2nd line fluoroquinolones (FQ) and injectable agents (IAs). The diagnostic accuracy of the Xpert® MTB/XDR test was compared to MGIT960 and the Hain Genotype® MTBDRplus and MDRsl assays (LPA) as reference DST methods. Factors for laboratory uptake of the Xpert® MTB/XDR test were also evaluated. RESULTS Of the 100 stored sputum samples included in this study, 65/99 (65.6%) were resistant to INH, 5/100 (5.0%) were resistant to FQ and none were resistant to IAs using MGIT960. The sensitivity and specificity, n (%; 95% Confidence Interval, CI) of Xpert® MTB/XDR test for; INH was 58 (89.2; 79.1-95.5) and 30 (88.2; 72.5-96.6) and for FQ; 4 (80.0; 28.3-99.4) and 95 (100; 96.2-100), respectively. Using LPA as a reference standard, a total of 52/98 (53.1%) were resistant to INH, 3/100 (3.0%) to FQ, and none to IA. The sensitivity and specificity, n (%; 95%CI) of Xpert® MTB/XDR test compared to LPA for; INH was 50 (96.1; 86.7-99.5) and 34 (74.0; 58.8-85.7) for FQ 3 (100; 29.2-100) and 96 (99.0; 94.3-99.9) respectively. The factors for laboratory uptake and roll-out of the Xpert® MTB/XDR test included: no training needed for technicians with, and one day for those without, previous Xpert-ultra experience, recording and reporting needs were not different from those of Xpert-ultra, the error rate was 4/100 (4%), one (1%) indeterminate rate and test turn-around-time were 1hr/45 minutes. CONCLUSION There is high sensitivity and specificity of Xpert® MTB/XDR test for isoniazid and fluoroquinolones. There are acceptable Xpert® MTB/XDR test attributes for the test uptake and roll-out.
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Affiliation(s)
- Achilles Katamba
- Department of Medicine, School of Medicine, Clinical Epidemiology and Biostatistics Unit and Uganda Implementation Research Consortium, Makerere University, Kampala, Uganda
| | - Willy Ssengooba
- Department of Medical Microbiology, Makerere University, Kampala, Uganda
- Lung Institute, Makerere University, Kampala, Uganda
- Biomedical Research Center, Makerere University, Kampala, Uganda
| | - James Sserubiri
- Department of Medical Microbiology, Makerere University, Kampala, Uganda
- Biomedical Research Center, Makerere University, Kampala, Uganda
| | - Derrick Semugenze
- Department of Medical Microbiology, Makerere University, Kampala, Uganda
- Biomedical Research Center, Makerere University, Kampala, Uganda
| | | | - Abdunoor Nyombi
- Ministry of Health, National Tuberculosis, and Leprosy Programme, Kampala, Uganda
| | - Raymond Byaruhanga
- Ministry of Health, National Tuberculosis, and Leprosy Programme, Kampala, Uganda
| | - Stavia Turyahabwe
- Ministry of Health, National Tuberculosis, and Leprosy Programme, Kampala, Uganda
| | - Moses L. Joloba
- Department of Medical Microbiology, Makerere University, Kampala, Uganda
- Biomedical Research Center, Makerere University, Kampala, Uganda
- Ministry of Health, National Tuberculosis, and Leprosy Programme, Kampala, Uganda
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Rajendran P, Padmapriyadarsini C, Nair S, Sivakumar S. Newer TB diagnostics: An update. Indian J Tuberc 2023; 70:372-375. [PMID: 37562916 DOI: 10.1016/j.ijtb.2023.04.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 04/06/2023] [Accepted: 04/20/2023] [Indexed: 08/12/2023]
Abstract
In recent years, nucleic-acid amplification tests (NAATs), which are highly specific and sensitive, have helped to transform the TB diagnostic landscape. According to the WHO 2021 Guidelines on Diagnostics, the NAATs used in TB diagnosis at the point of care (POC) include Xpert MTB/RIF a cartridge-based test manufactured by Cepheid, and Truenat a chip-based test manufactured by Molbio. Other POC tests that are expected to be implemented in near future include Xpert Omni and Xpert MTB/XDR. The use of line probe assay is involved at the level of reference labs for the detection of MTB and its resistance to first-line (Isoniazid and Rifampicin) and second-line (fluoroquinolones and second-line injectables) drugs. When the currently available NAATs detect mutations for drug resistance at a particular region of MTB sequence, the Whole genome sequencing (WGS) platform demonstrates the exceptional potential for reliable and comprehensive resistance prediction for MTB isolates, by multiple gene regions or whole genome sequence analysis allowing for accurate clinical decisions.
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Affiliation(s)
- Priya Rajendran
- ICMR-National Institute for Research in Tuberculosis, Chetpet, Chennai, India
| | - C Padmapriyadarsini
- ICMR-National Institute for Research in Tuberculosis, Chetpet, Chennai, India.
| | | | - S Sivakumar
- ICMR-National Institute for Research in Tuberculosis, Chetpet, Chennai, India
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Graciaa DS, Schechter MC, Fetalvero KB, Cranmer LM, Kempker RR, Castro KG. Updated considerations in the diagnosis and management of tuberculosis infection and disease: integrating the latest evidence-based strategies. Expert Rev Anti Infect Ther 2023; 21:595-616. [PMID: 37128947 PMCID: PMC10227769 DOI: 10.1080/14787210.2023.2207820] [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: 02/28/2023] [Accepted: 04/24/2023] [Indexed: 05/03/2023]
Abstract
INTRODUCTION Tuberculosis (TB) is a leading infectious cause of global morbidity and mortality, affecting nearly a quarter of the human population and accounting for over 10 million deaths each year. Over the past several decades, TB incidence and mortality have gradually declined, but 2021 marked a threatening reversal of this trend highlighting the importance of accurate diagnosis and effective treatment of all forms of TB. AREAS COVERED This review summarizes advances in TB diagnostics, addresses the treatment of people with TB infection and TB disease including recent evidence for treatment regimens for drug-susceptible and drug-resistant TB, and draws attention to special considerations in children and during pregnancy. EXPERT OPINION Improvements in diagnosis and management of TB have expanded the available options for TB control. Molecular testing has enhanced the detection of TB disease, but better diagnostics are still needed, particularly for certain populations such as children. Novel treatment regimens have shortened treatment and improved outcomes for people with TB. However, important questions remain regarding the optimal management of TB. Work must continue to ensure the potential of the latest developments is realized for all people affected by TB.
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Affiliation(s)
- Daniel S. Graciaa
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Marcos Coutinho Schechter
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Krystle B. Fetalvero
- Angelo King Medical Research Center-De La Salle Medical and Health Science Institute, Cavite, Philippines
- Department of Family and Community Medicine, Calamba Medical Center, Laguna, Philippines
| | - Lisa Marie Cranmer
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
- Children’s Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Russell R. Kempker
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Kenneth G. Castro
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
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Katamba A, Ssengooba W, Sserubiri J, Semugenze D, William KG, Abdunoor N, Byaruhanga R, Turyahabwe S, Joloba ML. Evaluation of Xpert ® MTB/XDR test for susceptibility testing of Mycobacterium tuberculosis to first and second-line drugs in Uganda. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.04.03.23288099. [PMID: 37066316 PMCID: PMC10104194 DOI: 10.1101/2023.04.03.23288099] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Background Drug-Resistant Tuberculosis (DR-TB) is one of the key challenges toward TB control. There is an urgent need for rapid and accurate drug susceptibility tests (DST) for the most commonly used 1 st and 2 nd line TB drugs. Design and Methods In a blinded, laboratory-based cross-sectional study, we set out to validate the performance of the Xpert ® MTB/XDR test for DST of M. tuberculosis . Sputum samples or culture isolates collected between January 2020 and December 2021 from patients with rifampicin resistance -TB and/or with higher suspicion index for isoniazid (INH) resistance and/or 2 nd line fluoroquinolones (FQ) and injectable agents (IAs) were tested using the Xpert ® MTB/XDR test from 11/September 2021 to 26/May /2022. Diagnostic accuracy and factors for laboratory uptake of Xpert ® MTB/XDR test were compared to MGIT960 and the Hain Genotype® MTBDR plus and MDRsl assays (LPA) as reference DST methods. Results A total of 100 stored sputum samples were included in this study. Of the samples tested using MGIT960, 65/99 (65.6%) were resistant to INH, 5/100 (5.0%) resistant to FQ and none were resistant to IAs. The sensitivity and specificity, n (%; 95%Confidence Interval, CI) of Xpert ® MTB/XDR test for; INH were 58 (89.2; 79.1-95.5) and 30 (88.2; 72.5-96.6), FQ; 4 (80.0; 28.3-99.4) and 95 (100; 96.2-100), respectively. The specificity for AIs was 100 (100; 96.3-100). Using LPA as a reference standard, a total of 52/98 (53.1%) were resistant to INH, 3/100 (3.0%) to FQ, and none to IA. The sensitivity and specificity, n (%; 95%CI) of Xpert ® MTB/XDR test compared to LPA for; INH was 50 (96.1; 86.7-99.5) and 34 (74.0; 58.8-85.7) and FQ 3 (100; 29.2-100) and 96 (99.0; 94.3-99.9) respectively. The specificity of IAs was 96 (100; 96.2-100). The factors for laboratory uptake and roll-out included; no training needed for technicians with previous Xpert-ultra experience and one day for those without, recording and reporting needs were not different from those of Xpert ultra, the error rate was 4/100 (4%), no uninterpretable results reported, test turn-around-time was 1hr/45 minutes and workflow similar to that of the Xpert-ultra test. Conclusion There is high sensitivity and specificity of Xpert ® MTB/XDR test for isoniazid, fluoroquinolones, and Injectable agents. There are acceptable Xpert ® MTB/XDR test attributes for test uptake and roll-out.
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Affiliation(s)
- Achilles Katamba
- Makerere University, Department of Medicine, school of Medicine, Clinical Epidemiology and Biostatistics Unit, Uganda Implementation Research Consortium, Kampala, Uganda
| | - Willy Ssengooba
- Makerere University, Department of Medical Microbiology
- Makerere University Lung Institute
- Makerere University, Biomedical Research Center
| | - James Sserubiri
- Makerere University, Department of Medical Microbiology
- Makerere University, Biomedical Research Center
| | - Derrick Semugenze
- Makerere University, Department of Medical Microbiology
- Makerere University, Biomedical Research Center
| | | | - Nyombi Abdunoor
- Ministry of Health, National Tuberculosis and Leprosy Programme
| | | | | | - Moses L Joloba
- Makerere University, Department of Medical Microbiology
- Makerere University, Biomedical Research Center
- Ministry of Health, National Tuberculosis and Leprosy Programme
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Inbaraj LR, Daniel J, Rajendran P, Bhaskar A, Srinivasalu VA, Narayanan MKS, Shewade HD, Kirubakaran R, Scandrett K, Malaisamy M, Takwoingi Y, Padmapriyadarsini C. Truenat MTB assays for pulmonary tuberculosis and rifampicin resistance in adults. THE COCHRANE DATABASE OF SYSTEMATIC REVIEWS 2023; 2023:CD015543. [PMCID: PMC9837843 DOI: 10.1002/14651858.cd015543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
This is a protocol for a Cochrane Review (diagnostic). The objectives are as follows: To determine the diagnostic accuracy of Truenat assays (MTB, MTB Plus, and MTB RIF Dx) for detecting pulmonary tuberculosis and rifampicin resistance in adults with presumptive pulmonary tuberculosis.
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Affiliation(s)
| | - Leeberk Raja Inbaraj
- Department of Clinical ResearchICMR – National Institute for Research in TuberculosisChennaiIndia
| | - Jefferson Daniel
- Department of Pulmonary MedicineChristian Medical CollegeVelloreIndia
| | - Priya Rajendran
- Department of BacteriologyICMR – National Institute for Research in TuberculosisChennaiIndia
| | - Adhin Bhaskar
- Department of BiostatisticsICMR – National Institute for Research in TuberculosisChennaiIndia
| | - Vignes Anand Srinivasalu
- Department of Clinical ResearchICMR - National Institute for Research in TuberculosisChennaiIndia
| | - Mukesh KS Narayanan
- Department of EpidemiologyICMR – National Institute for Research in TuberculosisChennaiIndia
| | - Hemant D Shewade
- Division of Health System ResearchICMR – National Institute of EpidemiologyChennaiIndia
| | - Richard Kirubakaran
- Prof. BV Moses Center for Evidence-Informed Health Care and Health PolicyChristian Medical CollegeVelloreIndia
| | - Katie Scandrett
- Test Evaluation Research Group, Institute of Applied Health ResearchUniversity of BirminghamBirminghamUK
| | - Muniyandi Malaisamy
- Department of Health EconomicsICMR – National Institute for Research in TuberculosisChennaiIndia
| | - Yemisi Takwoingi
- Test Evaluation Research Group, Institute of Applied Health ResearchUniversity of BirminghamBirminghamUK
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Wu SH, Xiao YX, Hsiao HC, Jou R. Development and Assessment of a Novel Whole-Gene-Based Targeted Next-Generation Sequencing Assay for Detecting the Susceptibility of Mycobacterium tuberculosis to 14 Drugs. Microbiol Spectr 2022; 10:e0260522. [PMID: 36255328 PMCID: PMC9769975 DOI: 10.1128/spectrum.02605-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/23/2022] [Indexed: 01/07/2023] Open
Abstract
Targeted next-generation sequencing (tNGS) has emerged as an alternative method for detecting drug-resistant tuberculosis (DR-TB). To provide comprehensive drug susceptibility information and to address mutations missed by available commercial molecular diagnostics, we developed and evaluated a tNGS panel with 22 whole-gene targets using the Ion Torrent platform to predict drug resistance to 14 drugs, namely, rifampicin (RIF), isoniazid (INH), ethambutol (EMB), pyrazinamide (PZA), moxifloxacin (MFX), levofloxacin (LFX), amikacin (AMK), capreomycin (CM), kanamycin (KM), streptomycin (SM), bedaquiline (BDQ), clofazimine (CFZ), linezolid (LZD), and delamanid (DLM). We selected 50 and 35 Mycobacterium tuberculosis isolates with various DR profiles as the training set and the challenge set, respectively. Comparative variant analyses of the DR genes were performed using Sanger sequencing and whole-genome sequencing (WGS). Phenotypic drug susceptibility testing (pDST) results were used as gold standards. Regarding the limit of detection, the tNGS assay detected 2.9 to 3.8% minority variants in 4% mutant mixtures. The sensitivity and specificity of tNGS were 97.0% (95% confidence interval [CI] = 93.1 to 98.7%) and 99.1% (95% CI = 97.7 to 99.7%), respectively. The concordance of tNGS with pDST was 98.5% (95% CI = 97.2 to 99.2%), which was comparable to that of WGS (98.7%, 95% CI = 97.4 to 99.3%) and better than that of Sanger sequencing (96.9%, 95% CI = 95.3 to 98.0%). The agreement between tNGS and pDST was almost perfect for RIF, INH, EMB, MFX, LFX, AMK, CM, KM, SM, BDQ, and LZD (kappa value = 0.807 to 1.000) and substantial for PZA (kappa value = 0.791). Our customized novel whole-gene-based tNGS panel is highly consistent with pDST and WGS for comprehensive and accurate prediction of drug resistance in a strengthened and streamlined DR-TB laboratory program. IMPORTANCE We developed and validated a tNGS assay that was the first to target 22 whole genes instead of regions of drug resistance genes and comprehensively detected susceptibility to 14 anti-TB drugs, with great flexibility to include new or repurposed drugs. Notably, we demonstrated that our custom-designed Ion AmpliSeq TB research panel platform had high concordance with pDST and could significantly reduce turnaround time (by approximately 70%) to meet a clinically actionable time frame. Our tNGS assay is a promising DST solution for providing needed clinical information for precision medicine-guided therapies for DR-TB and allows the rollout of active pharmacovigilance.
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Affiliation(s)
- Sheng-Han Wu
- Tuberculosis Research Center, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
- Reference Laboratory of Mycobacteriology, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Yu-Xin Xiao
- Tuberculosis Research Center, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
- Reference Laboratory of Mycobacteriology, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Hseuh-Chien Hsiao
- Tuberculosis Research Center, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
- Reference Laboratory of Mycobacteriology, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Ruwen Jou
- Tuberculosis Research Center, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
- Reference Laboratory of Mycobacteriology, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
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11
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Markandan K, Tiong YW, Sankaran R, Subramanian S, Markandan UD, Chaudhary V, Numan A, Khalid M, Walvekar R. Emergence of infectious diseases and role of advanced nanomaterials in point-of-care diagnostics: a review. Biotechnol Genet Eng Rev 2022:1-89. [PMID: 36243900 DOI: 10.1080/02648725.2022.2127070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 09/12/2022] [Indexed: 11/09/2022]
Abstract
Infectious outbreaks are the foremost global public health concern, challenging the current healthcare system, which claims millions of lives annually. The most crucial way to control an infectious outbreak is by early detection through point-of-care (POC) diagnostics. POC diagnostics are highly advantageous owing to the prompt diagnosis, which is economical, simple and highly efficient with remote access capabilities. In particular, utilization of nanomaterials to architect POC devices has enabled highly integrated and portable (compact) devices with enhanced efficiency. As such, this review will detail the factors influencing the emergence of infectious diseases and methods for fast and accurate detection, thus elucidating the underlying factors of these infections. Furthermore, it comprehensively highlights the importance of different nanomaterials in POCs to detect nucleic acid, whole pathogens, proteins and antibody detection systems. Finally, we summarize findings reported on nanomaterials based on advanced POCs such as lab-on-chip, lab-on-disc-devices, point-of-action and hospital-on-chip. To this end, we discuss the challenges, potential solutions, prospects of integrating internet-of-things, artificial intelligence, 5G communications and data clouding to achieve intelligent POCs.
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Affiliation(s)
- Kalaimani Markandan
- Temasek Laboratories, Nanyang Technological University, Nanyang Drive, Singapore
- Faculty of Engineering, Technology and Built Environment, UCSI University, Kuala Lumpur, Malaysia
| | - Yong Wei Tiong
- NUS Environmental Research Institute, National University of Singapore, Engineering Drive, Singapore
| | - Revathy Sankaran
- Graduate School, University of Nottingham Malaysia Campus, Semenyih, Selangor, Malaysia
| | - Sakthinathan Subramanian
- Department of Materials & Mineral Resources Engineering, National Taipei University of Technology (NTUT), Taipei, Taiwan
| | | | - Vishal Chaudhary
- Research Cell & Department of Physics, Bhagini Nivedita College, University of Delhi, New Delhi, India
| | - Arshid Numan
- Graphene & Advanced 2D Materials Research Group (GAMRG), School of Engineering and Technology, Sunway University, Petaling Jaya, Selangor, Malaysia
- Sunway Materials Smart Science & Engineering (SMS2E) Research Cluster School of Engineering and Technology, Sunway University, Selangor, Malaysia
| | - Mohammad Khalid
- Graphene & Advanced 2D Materials Research Group (GAMRG), School of Engineering and Technology, Sunway University, Petaling Jaya, Selangor, Malaysia
- Sunway Materials Smart Science & Engineering (SMS2E) Research Cluster School of Engineering and Technology, Sunway University, Selangor, Malaysia
| | - Rashmi Walvekar
- Department of Chemical Engineering, School of Energy and Chemical Engineering, Xiamen University Malaysia, Sepang, Selangor, Malaysia
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12
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Huang Y, Ai L, Wang X, Sun Z, Wang F. Review and Updates on the Diagnosis of Tuberculosis. J Clin Med 2022; 11:jcm11195826. [PMID: 36233689 PMCID: PMC9570811 DOI: 10.3390/jcm11195826] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/27/2022] [Accepted: 09/27/2022] [Indexed: 11/05/2022] Open
Abstract
Diagnosis of tuberculosis, and especially the diagnosis of extrapulmonary tuberculosis, still faces challenges in clinical practice. There are several reasons for this. Methods based on the detection of Mycobacterium tuberculosis (Mtb) are insufficiently sensitive, methods based on the detection of Mtb-specific immune responses cannot always differentiate active disease from latent infection, and some of the serological markers of infection with Mtb are insufficiently specific to differentiate tuberculosis from other inflammatory diseases. New tools based on technologies such as flow cytometry, mass spectrometry, high-throughput sequencing, and artificial intelligence have the potential to solve this dilemma. The aim of this review was to provide an updated overview of current efforts to optimize classical diagnostic methods, as well as new molecular and other methodologies, for accurate diagnosis of patients with Mtb infection.
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13
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Sharma K, Sharma M, Sharma V, Sharma M, Samanta J, Sharma A, Kochhar R, Sinha SK. Evaluating diagnostic performance of Truenat MTB Plus for gastrointestinal tuberculosis. J Gastroenterol Hepatol 2022; 37:1571-1578. [PMID: 35501293 DOI: 10.1111/jgh.15878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/24/2022] [Accepted: 04/28/2022] [Indexed: 12/09/2022]
Abstract
BACKGROUND AND AIM Prompt and accurate diagnosis of gastrointestinal tuberculosis (GITB) along with simultaneous detection of drug resistance is inevitable for tuberculosis elimination. Truenat MTB Plus (TruPlus), a chip-based real-time polymerase chain reaction assay, was evaluated for the first time for diagnosing GITB and detecting rifampicin resistance. METHODS Fifty ileocecal biopsy specimens (5 microbiologically confirmed GITB [culture-positive], 25 clinically confirmed GITB [culture-negative], and 20 control patients) processed in the Department of Microbiology between 2011 and 2021 were subjected to TruPlus assay, Xpert MTB RIF assay multiplex polymerase chain reaction. Their performance was evaluated against both culture and composite reference standard. RESULTS The overall sensitivity and specificity of TruPlus in diagnosing GITB was 70% (21/30) and 100%, respectively. The sensitivity was 60% (3/5) for microbiologically confirmed cases and 72% (18/25) for clinically confirmed cases. Performance of TruPlus was superior to Xpert (sensitivity = 30%; P = 0.001) and comparable with MPCR (sensitivity = 83.33%; P = 0.13). Both TruPlus and MPCR had moderate agreement with reference standards, and MPCR detected additional three cases. Both TruPlus and Xpert correctly reported Rifampicin resistance in three cases. CONCLUSIONS TruPlus, with its greater portability and higher sensitivity than Xpert, could serve as an important tool for diagnosing GITB and rifampicin resistance at outreach endemic areas.
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Affiliation(s)
- Kusum Sharma
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Megha Sharma
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India.,Department of Microbiology, All India Institute of Medical Sciences, Bilaspur, India
| | - Vishal Sharma
- Department of Gastroenterology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Megha Sharma
- Department of Gastroenterology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Jayanta Samanta
- Department of Gastroenterology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Aman Sharma
- Department of Internal Medicine, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Rakesh Kochhar
- Department of Gastroenterology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Saroj Kant Sinha
- Department of Gastroenterology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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14
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Diagnostic Accuracy of the Truenat MTB Plus Assay and Comparison with the Xpert MTB/RIF Assay to Detect Tuberculosis among Hospital Outpatients in Cameroon. J Clin Microbiol 2022; 60:e0015522. [PMID: 35861529 PMCID: PMC9383115 DOI: 10.1128/jcm.00155-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The Truenat MTB Plus assay is a rapid molecular test that has been recommended by the World Health Organization since 2020 as an initial test to detect tuberculosis (TB). The WHO highlighted the need to further evaluate assay performance to inform future recommendations, including in people living with HIV and compared to the Xpert MTB/RIF assay. We conducted a prospective evaluation of the diagnostic accuracy of the Truenat assay in Cameroon, a country with a high burden of HIV/TB. Adult outpatients were recruited at four hospitals; demographic information and medical history were collected, and participants produced two sputum specimens. Truenat and Xpert testing was performed on the same specimen, and performance was compared to TB culture as the reference standard. From November 2019 to December 2020, 945 participants were enrolled and included in the analysis. Among 251 participants with culture-positive TB, the sensitivity of Truenat MTB Plus was 91% (95% confidence interval [CI], 86 to 94%), similar to Xpert (90%; 95% CI, 86 to 93%). Among 74 HIV-positive participants with culture-positive TB, the sensitivity of Truenat MTB Plus was 85% (95% CI, 75 to 92%) compared to 81% for Xpert (95% CI, 70 to 89%). Among 47 participants with smear-negative TB, the sensitivity of Truenat MTB Plus was 55% (95% CI, 40 to 70%), similar to Xpert (53%; 95% CI, 38 to 68%). The specificity of Truenat MTB Plus was 96% (95% CI, 94 to 97%) compared to 99% (95% CI, 97 to 99%) for Xpert. For TB detection compared to the reference standard of TB culture, the performance of the Truenat MTB Plus assay was similar to that of Xpert in this population, including among people living with HIV.
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15
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Soni A, Guliani A, Nehra K, Mehta PK. Insight into diagnosis of pleural tuberculosis with special focus on nucleic acid amplification tests. Expert Rev Respir Med 2022; 16:887-906. [PMID: 35728039 DOI: 10.1080/17476348.2022.2093189] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Pleural tuberculosis (TB) is the archetype of extrapulmonary TB (EPTB), which mainly affects the pleural space and leads to exudative pleural effusion. Diagnosis of pleural TB is a difficult task predominantly due to atypical clinical presentations and sparse bacillary load in clinical specimens. AREA COVERED We reviewed the current literature on the globally existing conventional/latest modalities for diagnosing pleural TB. Bacteriological examination (smear/culture), tuberculin skin testing/interferon-γ release assays, biochemical testing, imaging and histopathological/cytological examination are the main modalities. Moreover, nucleic acid amplification tests (NAATs), i.e. loop-mediated isothermal amplification, PCR/multiplex-PCR, nested-PCR, real-time PCR and GeneXpert® MTB/RIF are being utilized. Currently, GeneXpert Ultra, Truenat MTBTM, detection of circulating Mycobacterium tuberculosis (Mtb) cell-free DNA by NAATs, aptamer-linked immobilized sorbent assay and immuno-PCR (I-PCR) have also been exploited. EXPERT OPINION Routine tests are not adequate for effective pleural TB diagnosis. The latest molecular/immunological tests as discussed above, and the other tools, i.e. real-time I-PCR/nanoparticle-based I-PCR and identification of Mtb biomarkers within urinary/serum extracellular vesicles being utilized for pulmonary TB and other EPTB types may also be exploited to diagnose pleural TB. Reliable diagnosis and early therapy would reduce the serious complications associated with pleural TB, i.e. TB empyema, pleural fibrosis, etc.
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Affiliation(s)
- Aishwarya Soni
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak-124001, India.,Department of Biotechnology, Deenbandhu Chhotu Ram University of Science and Technology, Murthal, Sonipat-131039, India
| | - Astha Guliani
- Department of TB & Respiratory Medicine, Pt. BD Postgraduate Institute of Medical Sciences, Rohtak-124001, India
| | - Kiran Nehra
- Department of Biotechnology, Deenbandhu Chhotu Ram University of Science and Technology, Murthal, Sonipat-131039, India
| | - Promod K Mehta
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak-124001, India
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16
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Hong JM, Lee H, Menon NV, Lim CT, Lee LP, Ong CWM. Point-of-care diagnostic tests for tuberculosis disease. Sci Transl Med 2022; 14:eabj4124. [PMID: 35385338 DOI: 10.1126/scitranslmed.abj4124] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Rapid diagnosis is one key pillar to end tuberculosis (TB). Point-of-care tests (POCTs) facilitate early detection, immediate treatment, and reduced transmission of TB disease. This Review evaluates current diagnostic assays endorsed by the World Health Organization and identifies the gaps between existing conventional tests and the ideal POCT. We discuss the commercial development of new rapid tests and research studies on nonsputum-based diagnostic biomarkers from both pathogen and host. Last, we highlight advances in integrated microfluidics technology that may aid the development of new POCTs.
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Affiliation(s)
- Jia Mei Hong
- Infectious Diseases Translational Research Programme, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
| | - Hyeyoung Lee
- Infectious Diseases Translational Research Programme, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
| | - Nishanth V Menon
- Department of Biomedical Engineering, National University of Singapore, Singapore 117583, Singapore
| | - Chwee Teck Lim
- Department of Biomedical Engineering, National University of Singapore, Singapore 117583, Singapore.,Institute for Health Innovation & Technology (iHealthtech), National University of Singapore, Singapore 117599, Singapore.,Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore
| | - Luke P Lee
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA.,Berkeley Sensor and Actuator Center, University of California, Berkeley, Berkeley, CA 94720-1764, USA.,Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA 94720, USA.,Biophysics Graduate Program, University of California, Berkeley, Berkeley, CA 94720, USA.,Harvard Medical School, Brigham and Women's Hospital, Harvard Institute of Medicine, Harvard University, Boston, MA 02115, USA.,Institute of Quantum Biophysics, Department of Biophysics, Sungkyunkwan University, Suwon, Korea
| | - Catherine W M Ong
- Infectious Diseases Translational Research Programme, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore.,Institute for Health Innovation & Technology (iHealthtech), National University of Singapore, Singapore 117599, Singapore
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17
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Innovations in Molecular Identification of Mycobacterium tuberculosis. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2022. [DOI: 10.22207/jpam.16.1.76] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tuberculosis (TB) continues to be a significant public health concern on a global scale. Quick and precise identification of Mycobacterium tuberculosis (MTB) in symptomatic patients is pivotal for worldwide TB eradication initiatives. As an infectious disorder induced by MTB, it remains a critical threat to public health, particularly in poor countries, due to an inadequate diagnostic research laboratory. There is a need for a persistent incentive to reduce response time for effective diagnosis and control of TB infection, which is a benefit that molecular techniques provide over traditional methods. Although there is a tremendous overall prevalence of TB and a relatively poor probability of case identification worldwide. Common screening techniques have focused on tests that have many fundamental shortcomings. Due to the development of antibiotic-resistant Mycobacterium strains, TB is one of the leading contributors to fatalities. It is now possible to examine TB using molecular detection techniques, which are faster and more cost-effective than previous methods, such as standard culture procedures to test and verify antibiotic resistance in patients with TB. Whole genome sequencing (WGS), faster nucleic acid amplification tests, has made it easier to diagnose and treat TB more quickly. This article addresses the genetic approaches for detecting Mycobacterium tuberculosis complex (MTBC) in clinical specimens as well as antibiotic resistance in mycobacterium and discusses the practical limitations of using these methods.
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18
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Allam U, Polu VP, Kota NK, Karumanchi D, Basireddy S, Munagapati S, Mugudalabetta S, Ganta V. Evaluation of detection of severe acute respiratory syndrome coronavirus-2 by chip-based real-time polymerase chain reaction test (truenat™ beta CoV) in multi-sample pools. INTERNATIONAL JOURNAL OF ACADEMIC MEDICINE 2022. [DOI: 10.4103/ijam.ijam_14_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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19
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Meaza A, Tesfaye E, Mohamed Z, Zerihun B, Seid G, Eshetu K, Amare M, Sinshaw W, Dagne B, Mollalign H, Diriba G, Getu M, Yenew B, Tadesse M, Fikadu D, Abebaw Y, Moga S, Kebede A, Tola HH, Alemu A, Getahun M, Gumi B. Diagnostic accuracy of Truenat Tuberculosis and Rifampicin-Resistance assays in Addis Ababa, Ethiopia. PLoS One 2021; 16:e0261084. [PMID: 34962949 PMCID: PMC8714111 DOI: 10.1371/journal.pone.0261084] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 11/23/2021] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Rapid and sensitive Tuberculosis (TB) diagnosis closer to patients is a key global TB control priority. Truenat assays (MTB, MTB Plus, and MTB-RIF Dx) are new TB molecular diagnostic tools for the detection of TB and Rifampicin (RIF)-resistance from sputum samples. The diagnostic accuracy of the assays is needed prior to implementation in clinical use in Ethiopia. This study aimed to determine the sensitivity and specificity of Truenat assays; and aimed to compare the assays to the Xpert MTB/RIF assay. METHODS A prospective evaluation study was conducted among 200 presumptive TB patients in microscopy centers in Addis Ababa, Ethiopia from May 2019 to December 2020. Culture (Solid and Liquid methods) and phenotypic (liquid method) drug susceptibility testing (DST) were used as a reference standard. RESULTS Of 200 adult participants, culture confirmed TB cases were 25 (12.5%), and only one isolate was resistant to RIF by phenotypic DST. The sensitivity of Truenat MTB was 88.0% [95% CI 70.1, 95.8], while 91.7 [95% CI 74.2, 97.7] for Truenat MTB Plus at the microscopy centers. The specificity of Truenat MTB was 97.2% [95% CI 93.1, 98.9], while for Truenat MTB Plus was 97.2% [95% CI 93.0, 99.0]. The sensitivity of Truenat MTB was 90.5% while for MTB Plus, 100% compared to the Xpert MTB/RIF assay. CONCLUSION Truenat assays were found to have high diagnostic accuracy. The assays have the potential to be used as a point of care (POC) TB diagnostic tests.
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Affiliation(s)
- Abyot Meaza
- Ethiopian Public Health Institute (EPHI), Addis Ababa, Ethiopia
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Ephrem Tesfaye
- Ethiopian Public Health Institute (EPHI), Addis Ababa, Ethiopia
| | - Zemedu Mohamed
- Ethiopian Public Health Institute (EPHI), Addis Ababa, Ethiopia
| | | | - Getachew Seid
- Ethiopian Public Health Institute (EPHI), Addis Ababa, Ethiopia
| | - Kirubel Eshetu
- Ethiopian Public Health Institute (EPHI), Addis Ababa, Ethiopia
| | - Miskir Amare
- Ethiopian Public Health Institute (EPHI), Addis Ababa, Ethiopia
| | - Waganeh Sinshaw
- Ethiopian Public Health Institute (EPHI), Addis Ababa, Ethiopia
| | - Biniyam Dagne
- Ethiopian Public Health Institute (EPHI), Addis Ababa, Ethiopia
| | | | - Getu Diriba
- Ethiopian Public Health Institute (EPHI), Addis Ababa, Ethiopia
| | - Melak Getu
- Ethiopian Public Health Institute (EPHI), Addis Ababa, Ethiopia
| | - Bazezew Yenew
- Ethiopian Public Health Institute (EPHI), Addis Ababa, Ethiopia
| | | | - Dinka Fikadu
- Ethiopian Public Health Institute (EPHI), Addis Ababa, Ethiopia
| | | | - Shewki Moga
- Ethiopian Public Health Institute (EPHI), Addis Ababa, Ethiopia
| | - Abebaw Kebede
- Ethiopian Public Health Institute (EPHI), Addis Ababa, Ethiopia
| | | | - Ayinalem Alemu
- Ethiopian Public Health Institute (EPHI), Addis Ababa, Ethiopia
| | | | - Balako Gumi
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
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20
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Datta B, Ford D, Goyal P, Prakash A, Tripathy JP, Gnanashanmugam D, Mishra S, Aggarwal A, Kotalwar SG, Mittal S, Mangla A, Jaiswal A, Trehan N. Mobile digital x-ray and portable cartridge based nucleic acid amplification test machines for point-of-care diagnosis of TB in rural India. Trans R Soc Trop Med Hyg 2021; 115:937-939. [PMID: 33347591 DOI: 10.1093/trstmh/traa152] [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: 07/26/2020] [Revised: 10/25/2020] [Accepted: 11/19/2020] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND There is no experience of point-of-care (POC) microbiological confirmation for TB in India in field settings. METHODS Under the TB-Free Haryana project, a mobile van-mounted digital x-ray and portable GeneXpert system screened all presumptive TB patients with strong clinic-radiological suspicion for TB. RESULTS Of 1673 x-rays, 215 (13%) had findings suggestive of TB, 109 had strong clinical suspicion and were eligible for POC GeneXpert, in whom a test was performed in 82 (75%) cases; 59 (72%) tested positive and were initiated on treatment within 24 h. CONCLUSIONS A mobile van equipped with digital x-ray and POC GeneXpert is feasible and has a good success rate with potential for replication.
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Affiliation(s)
- Bornali Datta
- Department of Respiratory Medicine, Medanta the Medicity, Gurgaon, Haryana, India
| | - David Ford
- Department of Respiratory Medicine, Scarborough General Hospital, Scarborough, UK
| | - Pinky Goyal
- Department of Respiratory Medicine, Medanta the Medicity, Gurgaon, Haryana, India
| | - Ashish Prakash
- Department of Respiratory Medicine, Medanta the Medicity, Gurgaon, Haryana, India
| | - Jaya Prasad Tripathy
- Department of Community Medicine, All India Institute of Medical Sciences, Nagpur, India
| | | | - Sunil Mishra
- Department of Respiratory Medicine, Medanta the Medicity, Gurgaon, Haryana, India
| | - Ankit Aggarwal
- Department of Respiratory Medicine, Medanta the Medicity, Gurgaon, Haryana, India
| | | | - Sandeep Mittal
- Department of Respiratory Medicine, Medanta the Medicity, Gurgaon, Haryana, India
| | - Anshul Mangla
- Department of Pulmonary, Critical care and Sleep Medicine, VMMC and Safdarjung Hospital, New Delhi, India
| | - Anand Jaiswal
- Department of Respiratory Medicine, Medanta the Medicity, Gurgaon, Haryana, India
| | - Naresh Trehan
- Department of Respiratory Medicine, Medanta the Medicity, Gurgaon, Haryana, India
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21
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Bajaj AO, Saraswat S, Knuuttila JEA, Freeke J, Stielow JB, Barker AP. Accurate Identification of Closely Related Mycobacterium tuberculosis Complex Species by High Resolution Tandem Mass Spectrometry. Front Cell Infect Microbiol 2021; 11:656880. [PMID: 34239815 PMCID: PMC8259740 DOI: 10.3389/fcimb.2021.656880] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 05/07/2021] [Indexed: 11/22/2022] Open
Abstract
Rapid and accurate differentiation of Mycobacterium tuberculosis complex (MTBC) species from other mycobacterium is essential for appropriate therapeutic management, timely intervention for infection control and initiation of appropriate health care measures. However, routine clinical characterization methods for Mycobacterium tuberculosis (Mtb) species remain both, time consuming and labor intensive. In the present study, an innovative liquid Chromatography-Mass Spectrometry method for the identification of clinically most relevant Mycobacterium tuberculosis complex species is tested using a model set of mycobacterium strains. The methodology is based on protein profiling of Mycobacterium tuberculosis complex isolates, which are used as markers of differentiation. To test the resolving power, speed, and accuracy of the method, four ATCC type strains and 37 recent clinical isolates of closely related species were analyzed using this new approach. Using different deconvolution algorithms, we detected hundreds of individual protein masses, with a subpopulation of these functioning as species-specific markers. This assay identified 216, 260, 222, and 201 proteoforms for M. tuberculosis ATCC 27294™, M. microti ATCC 19422™, M. africanum ATCC 25420™, and M. bovis ATCC 19210™ respectively. All clinical strains were identified to the correct species with a mean of 95% accuracy. Our study successfully demonstrates applicability of this novel mass spectrometric approach to identify clinically relevant Mycobacterium tuberculosis complex species that are very closely related and difficult to differentiate with currently existing methods. Here, we present the first proof-of-principle study employing a fast mass spectrometry-based method to identify the clinically most prevalent species within the Mycobacterium tuberculosis species complex.
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Affiliation(s)
- Amol O Bajaj
- Research & Development, Associated Regional and University Pathologists, Inc. (ARUP) Institute for Clinical and Experimental Pathology, Salt Lake City, UT, United States
| | - Suraj Saraswat
- Research & Development, Associated Regional and University Pathologists, Inc. (ARUP) Institute for Clinical and Experimental Pathology, Salt Lake City, UT, United States
| | - Juha E A Knuuttila
- Research & Development, Thermo Fisher Scientific, Helsinki-Vantaa, Finland
| | - Joanna Freeke
- Centre for Infectious Diseases, Radboud University Medical Center (UMC), Nijmegen, Netherlands.,Research & Development, Thermo Fisher Scientific, Landsmeer, Netherlands
| | - J Benjamin Stielow
- Centre for Infectious Diseases, Radboud University Medical Center (UMC), Nijmegen, Netherlands.,Research & Development, Thermo Fisher Scientific, Landsmeer, Netherlands
| | - Adam P Barker
- Research & Development, Associated Regional and University Pathologists, Inc. (ARUP) Institute for Clinical and Experimental Pathology, Salt Lake City, UT, United States
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22
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A prospective multicentre diagnostic accuracy study for the Truenat tuberculosis assays. Eur Respir J 2021; 58:13993003.00526-2021. [PMID: 34049948 PMCID: PMC8607906 DOI: 10.1183/13993003.00526-2021] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 03/29/2021] [Indexed: 11/26/2022]
Abstract
Background Bringing reliable and accurate tuberculosis (TB) diagnosis closer to patients is a key priority for global TB control. Molbio Diagnostics have developed the Truenat point-of-care molecular assays for detection of TB and rifampicin (RIF) resistance. Methods We conducted a prospective multicentre diagnostic accuracy study at 19 primary healthcare centres and seven reference laboratories in Peru, India, Ethiopia and Papua New Guinea to estimate the diagnostic accuracy of the point-of-care Truenat MTB, MTB Plus and MTB-RIF Dx assays for pulmonary TB using culture and phenotypic drug susceptibility testing as the reference standard, compared with Xpert MTB/RIF or Ultra. Results Of 1807 enrolled participants with TB signs/symptoms, 24% were culture-positive for Mycobacterium tuberculosis, of which 15% were RIF-resistant. In microscopy centres, the pooled sensitivity of Truenat MTB and Truenat MTB Plus was 73% (95% CI 67–78%) and 80% (95% CI 75–84%), respectively. Among smear-negative specimens, sensitivities were 36% (95% CI 27–47%) and 47% (95% CI 37–58%), respectively. Sensitivity of Truenat MTB-RIF was 84% (95% CI 62–95%). Truenat assays showed high specificity. Head-to-head comparison in the central reference laboratories suggested that the Truenat assays have similar performance to Xpert MTB/RIF. Conclusion We found the performance of Molbio's Truenat MTB, MTB Plus and MTB-RIF Dx assays to be comparable to that of the Xpert MTB/RIF assay. Performing the Truenat tests in primary healthcare centres with very limited infrastructure was feasible. These data supported the development of a World Health Organization policy recommendation of the Molbio assays. Diagnostic performance of point-of-care Truenat assays in primary healthcare centres is comparable to that of Xpert MTB/RIF placed in reference laboratories. The WHO now recommends Truenat as an initial test for detection of TB and RIF resistance.https://bit.ly/31Wj3S6
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23
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Kamra E, Mehta PK. Current updates in diagnosis of male urogenital tuberculosis. Expert Rev Anti Infect Ther 2021; 19:1175-1190. [PMID: 33688791 DOI: 10.1080/14787210.2021.1902305] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: Urogenital tuberculosis (UGTB) is a common manifestation of extrapulmonary TB (EPTB), which affects both men and women in a ratio of 2:1. Similar to other EPTB types, diagnosis of UGTB is quite challenging owing to atypical clinical presentation and paucibacillary nature of specimens. This review is primarily focused on the current updates developed in the diagnosis of male UGTB.Area covered: Smear/culture, imaging, histopathology, and interferon-γ release assays are the main modalities employed for detecting male UGTB cases. Moreover, we described the utility of nucleic acid amplification tests (NAATs), including loop-mediated isothermal amplification, PCR, nested-PCR, and GeneXpert (MTB/RIF) assays. The possibility of using other novel modalities, such as immuno-PCR (I-PCR), aptamer-linked immobilized sorbent assay (ALISA), and identification of circulating cell-free DNA (cfDNA) by NAATs were also discussed.Expert opinion: The current methods used for the diagnosis of male UGTB are not adequate. Therefore, the latest molecular/immunological tools, i.e. Xpert Ultra, Truenat MTBTM, I-PCR, ALISA, and cfDNA detection employed for the diagnosis of other EPTB forms and pulmonary TB may also be exploited for UGTB diagnosis. Reliable and timely diagnosis of male UGTB may initiate an early start of anti-tubercular therapy that would reduce infertility and other complications associated with disease.
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Affiliation(s)
- Ekta Kamra
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, India
| | - Promod K Mehta
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, India
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Gomathi NS, Singh M, Singh UB, Myneedu VP, Chauhan DS, Sarin R, Mohan A, Bhatnagar A, Khangembam JS, Kannan T, Rao MVV, Logani J, Dey B, Gangakhedkar RR, Swaminathan S, Tripathy S. Multicentric validation of indigenous molecular test Truenat™ MTB for detection of Mycobacterium tuberculosis in sputum samples from presumptive pulmonary tuberculosis patients in comparison with reference standards. Indian J Med Res 2021; 152:378-385. [PMID: 33380702 PMCID: PMC8061602 DOI: 10.4103/ijmr.ijmr_2539_19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Background & objectives: Early case detection is essential to interrupt transmission and to prevent further spread of tuberculosis (TB) in high endemic settings. Nucleic acid amplification tests (NAATs) with visual read-outs are ideal as point-of-care tests. Truenat™ MTB is an indigenous chip-based NAAT for detection of Mycobacterium tuberculosis, which involves extraction of DNA and real-time polymerase chain reaction (PCR) using portable, automated, battery-operated instruments. The current multicentric study was aimed to evaluate Truenat for detection of MTB in sputum samples obtained from patients with presumptive pulmonary TB with reference to culture as gold standard and Xpert as a comparator. Methods: The study was conducted at four sites, namely ICMR-National Institute for Research in Tuberculosis, Chennai; All India Institute of Medical Sciences, New Delhi; ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra; and National Institute of TB and Respiratory Diseases, New Delhi. Patients suspected to have TB were screened for eligibility. Two sputum samples were collected from each patient. Tests included smear, Xpert and Truenat directly from the sputum sample and culture by Lowenstein-Jensen (L-J) medium and MGIT960 from decontaminated pellets. Sample used for Truenat assay was coded. Resolution of Truenat false positives was done using an in-house PCR with TRC4 primers. Results: The study enrolled 2419 presumptive TB patients after screening 2465 patients, and 3541 sputum samples were collected from the enrolled patients. Results of 2623 samples were available for analysis. Truenat showed a positivity rate of 48.5 per cent as compared to 37.0 per cent by Xpert. The sensitivities of Truenat and Xpert were was 88.3 and 79.7 per cent, respectively in comparison with culture. Interpretation & conclusions: Truenat MTB identified more positives among culture-confirmed samples than Xpert and had higher sensitivity. In addition, other advantageous operational features of Truenat MTB were identified which would be useful in field settings.
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Affiliation(s)
- N S Gomathi
- Department of Bacteriology, ICMR-National Institute for Research in Tuberculosis, Chennai, Tamil Nadu, India
| | - Manjula Singh
- Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Urvashi B Singh
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - V P Myneedu
- Department of Microbiology, National Institute of Tuberculosis & Other Respiratory Diseases, New Delhi, India
| | - D S Chauhan
- Department of Microbiology & Molecular Biology, ICMR-National JALMA Institute of Leprosy & Other Mycobacterial Diseases, Agra, Uttar Pradesh, India
| | - Rohit Sarin
- National Institute of Tuberculosis & Other Respiratory Diseases, New Delhi, India
| | - Anant Mohan
- Department of Pulmonary Medicine & Sleep Disorders, All India Institute of Medical Sciences, New Delhi, India
| | - Anuj Bhatnagar
- Department of Chest & TB, National Institute of Tuberculosis & Other Respiratory Diseases, New Delhi, India
| | - Jiten Singh Khangembam
- Department of Pulmonary Medicine & Sleep Disorders, All India Institute of Medical Sciences, New Delhi, India
| | - T Kannan
- Statistics Section, Epidemiology Unit, ICMR-National Institute for Research in Tuberculosis, Chennai, Tamil Nadu, India
| | - M V V Rao
- ICMR-National Institute of Medical Statistics, New Delhi, India
| | - Jyoti Logani
- Department of Biotechnology, Ministry of Science & Technology, Government of India, New Delhi, India
| | - Bindu Dey
- Department of Biotechnology, Ministry of Science & Technology, Government of India, New Delhi, India
| | - Raman R Gangakhedkar
- Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | | | - Srikanth Tripathy
- ICMR-National Institute for Research in Tuberculosis, Chennai, Tamil Nadu, India
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25
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Gomathi NS, Singh M, Myneedu VP, Chauhan DS, Tripathy S, Sarin R, Mohan A, Bhatnagar A, Khangembam JS, Kannan T, V Rao MV, Logani J, Dey B, Gangakhedkar RR, Swaminathan S, Singh UB. Validation of an indigenous assay for rapid molecular detection of rifampicin resistance in presumptive multidrug-resistant pulmonary tuberculosis patients. Indian J Med Res 2021; 152:482-489. [PMID: 33707390 PMCID: PMC8157890 DOI: 10.4103/ijmr.ijmr_2557_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background & objectives: There is a need for an affordable, easy, high-sensitivity test usable at the peripheral health facility for diagnosis of drug-resistant (DR) tuberculosis (TB) to interrupt disease transmission. Nucleic acid amplification tests (NAATs) for early detection of DR-TB are ideal to bring testing near to the patient. Truenat™ MTB (Mycobacterium tuberculosis) and Truenat™ MTB-RIF (rifampicin) is an indigenous chip-based real-time polymerase chain reaction (PCR) based test for detection of multidrug-resistant (MDR) TB. The test involves extraction of DNA using automated, battery operated Trueprep instrument and real-time PCR performed on the Truelab analyzer. We report here multicentric validation of Truenat MTB-RIF for detection of DR-TB in suspected DR-TB patients. Methods: Consecutive patients aged 18-65 yr, with symptoms suggestive of TB and with a history of previous treatment, reporting to the National TB Elimination Programme (NTEP) clinics under four national institutes, namely AIIMS (All India Institute of Medical Sciences, New Delhi), NITRD (National Institute of Tuberculosis and Respiratory Diseases, New Delhi), NIRT (National Institute for Research in Tuberculosis, Chennai) and ICMR-National JALMA Institute for Leprosy and other Mycobacterial Diseases, Agra, were included in the study. Two sputum samples (one spot and one morning) were collected from each patient, after obtaining informed written consent. The samples were subjected to smear, GeneXpert and MGIT 960 culture (and drug susceptibility testing to RIF) (surrogate for MDR-TB) to serve as reference tests. The samples were coded to ensure blinding and subjected to Truenat MTB-RIF. Truenat MTB-RIF Version 1.5 was used for testing 1084 samples for RIF resistance, while Version 2.0 was used to test another 1201 samples. Results: Truenat MTB-RIF Version 1.5 in comparison with comprehensive laboratory reference standards yielded sensitivity and specificity of 76.2 and 94.7 per cent, respectively for the detection of RIF resistance in 1084 samples, collected across four sites. Based on the analysis of discordant samples, Version 2.0 of Truenat was developed by the manufacturer and this was further tested on additional 1201 samples, yielding a sensitivity of 87.5 per cent and specificity of 99.5 per cent. Interpretation & conclusions: Multicentric trial of Truenat™ MTB-RIF demonstrated a great potential of this point of care NAAT for detection of MDR-TB. The test would be useful in limited resource settings and inaccessible areas without need for any additional infrastructure.
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Affiliation(s)
- N S Gomathi
- Department of Bacteriology, Epidemiology Unit, Chennai, Tamil Nadu, India
| | - Manjula Singh
- Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - V P Myneedu
- Department of Microbiology, National Institute of Tuberculosis & Other Respiratory Diseases, New Delhi, India
| | - D S Chauhan
- Department of Microbiology & Molecular Biology, ICMR-National JALMA Institute for Leprosy & Other Mycobacterial Diseases, Agra, Uttar Pradesh, India
| | - Srikanth Tripathy
- ICMR-National Institute of Research in Tuberculosis, Chennai, Tamil Nadu, India
| | - Rohit Sarin
- National Institute of Tuberculosis & Other Respiratory Diseases, New Delhi, India
| | - Anant Mohan
- Department of Pulmonary Medicine & Sleep Disorders, All India Institute of Medical Sciences, New Delhi, India
| | - Anuj Bhatnagar
- Department of Chest & TB, Rajan Babu Institute of Pulmonary Medicine and Tuberculosis, New Delhi, India
| | | | - T Kannan
- Statistics Section, Epidemiology Unit, ICMR-National Institute of Research in Tuberculosis, Chennai, Tamil Nadu, India
| | - M V V Rao
- ICMR-National Institute of Medical Statistics, New Delhi, India
| | - Jyoti Logani
- Department of Biotechnology, Ministry of Science & Technology, New Delhi, India
| | - Bindu Dey
- Department of Biotechnology, Ministry of Science & Technology, New Delhi, India
| | - R R Gangakhedkar
- Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | | | - Urvashi B Singh
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
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26
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Guinn KM, Rubin EJ. Implementing New Approaches to Tuberculosis Control. China CDC Wkly 2021; 3:256-259. [PMID: 34594861 PMCID: PMC8392953 DOI: 10.46234/ccdcw2021.053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 02/19/2021] [Indexed: 11/17/2022] Open
Affiliation(s)
- Kristine M Guinn
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Eric J Rubin
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
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27
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Lin CR, Wang HY, Lin TW, Lu JJ, Hsieh JCH, Wu MH. Development of a two-step nucleic acid amplification test for accurate diagnosis of the Mycobacterium tuberculosis complex. Sci Rep 2021; 11:5750. [PMID: 33707640 PMCID: PMC7952592 DOI: 10.1038/s41598-021-85160-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 02/02/2021] [Indexed: 12/28/2022] Open
Abstract
The Mycobacterium tuberculosis complex (MTBC) remains one of the top 10 leading causes of death globally. The early diagnosis of MTBC can reduce mortality and mitigate disease transmission. However, current nucleic acid amplification diagnostic test methods are generally time-consuming and show suboptimal diagnostic performance, especially in extrapulmonary MTBC samples or acid-fast stain (AFS)-negative cases. Thus, development of an accurate assay for the diagnosis of MTBC is necessary, particularly under the above mentioned conditions. In this study, a single-tube nested real-time PCR assay (N-RTP) was developed and compared with a newly in-house-developed high-sensitivity real-time PCR assay (HS-RTP) using 134 clinical specimens (including 73 pulmonary and 61 extrapulmonary specimens). The amplification efficiency of HS-RTP and N-RTP was 99.8% and 100.7%, respectively. The sensitivity and specificity of HS-RTP and N-RTP for the diagnosis of MTBC in these specimens were 97.5% (77/79) versus 94.9% (75/79) and 80.0% (44/55) versus 89.1% (49/55), respectively. The sensitivity and specificity of HS-RTP and N-RTP for the diagnosis of MTBC in pulmonary specimens were 96.3% (52/54) versus 96.3% (52/54) and 73.7.0% (14/19) versus 89.5% (17/19), respectively; in extrapulmonary specimens, the sensitivity and specificity of HS-RTP and N-RTP were 100% (25/25) versus 92% (23/25) and 83.3% (30/36) versus 88.9% (32/36), respectively. Among the AFS-negative cases, the sensitivity and specificity of HS-RTP and N-RTP were 97.0% (32/33) versus 90.9% (30/33) and 88.0% (44/50) versus 92.0% (46/50), respectively. Overall, the sensitivity of HS-RTP was higher than that of N-RTP, and the performance was not compromised in extrapulmonary specimens and under AFS-negative conditions. In contrast, the specificity of the N-RTP assay was higher than that of the HS-RTP assay in all types of specimens. In conclusion, the HS-RTP assay would be useful for screening patients suspected of exhibiting an MTBC infection due to its higher sensitivity, while the N-RTP assay could be used for confirmation because of its higher specificity. Our results provide a two-step method (screen to confirm) that simultaneously achieves high sensitivity and specificity in the diagnosis of MTBC.
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Affiliation(s)
- Chien-Ru Lin
- Graduate Institute of Biomedical Engineering, Chang Gung University, Taoyuan, Taiwan
| | - Hsin-Yao Wang
- Department of Laboratory Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan City, Taiwan.,Ph.D. Program in Biomedical Engineering, Chang Gung University, Taoyuan City, Taiwan
| | - Ting-Wei Lin
- Department of Laboratory Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan City, Taiwan
| | - Jang-Jih Lu
- School of Medicine, Chang Gung University, Taoyuan City, Taiwan.,Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan City, Taiwan
| | - Jason Chia-Hsun Hsieh
- Division of Haematology/Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan City, Taiwan.,Division of Haematology/Oncology, Department of Internal Medicine, New Taipei Municipal Hospital, New Taipei City, Taiwan
| | - Min-Hsien Wu
- Graduate Institute of Biomedical Engineering, Chang Gung University, Taoyuan, Taiwan. .,Division of Haematology/Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan City, Taiwan. .,Department of Chemical Engineering, Ming Chi University of Technology, New Taipei City, Taiwan.
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28
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Cilloni L, Kranzer K, Stagg HR, Arinaminpathy N. Trade-offs between cost and accuracy in active case finding for tuberculosis: A dynamic modelling analysis. PLoS Med 2020; 17:e1003456. [PMID: 33264288 PMCID: PMC7710036 DOI: 10.1371/journal.pmed.1003456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 11/02/2020] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Active case finding (ACF) may be valuable in tuberculosis (TB) control, but questions remain about its optimum implementation in different settings. For example, smear microscopy misses up to half of TB cases, yet is cheap and detects the most infectious TB cases. What, then, is the incremental value of using more sensitive and specific, yet more costly, tests such as Xpert MTB/RIF in ACF in a high-burden setting? METHODS AND FINDINGS We constructed a dynamic transmission model of TB, calibrated to be consistent with an urban slum population in India. We applied this model to compare the potential cost and impact of 2 hypothetical approaches following initial symptom screening: (i) 'moderate accuracy' testing employing a microscopy-like test (i.e., lower cost but also lower accuracy) for bacteriological confirmation and (ii) 'high accuracy' testing employing an Xpert-like test (higher cost but also higher accuracy, while also detecting rifampicin resistance). Results suggest that ACF using a moderate-accuracy test could in fact cost more overall than using a high-accuracy test. Under an illustrative budget of US$20 million in a slum population of 2 million, high-accuracy testing would avert 1.14 (95% credible interval 0.75-1.99, with p = 0.28) cases relative to each case averted by moderate-accuracy testing. Test specificity is a key driver: High-accuracy testing would be significantly more impactful at the 5% significance level, as long as the high-accuracy test has specificity at least 3 percentage points greater than the moderate-accuracy test. Additional factors promoting the impact of high-accuracy testing are that (i) its ability to detect rifampicin resistance can lead to long-term cost savings in second-line treatment and (ii) its higher sensitivity contributes to the overall cases averted by ACF. Amongst the limitations of this study, our cost model has a narrow focus on the commodity costs of testing and treatment; our estimates should not be taken as indicative of the overall cost of ACF. There remains uncertainty about the true specificity of tests such as smear and Xpert-like tests in ACF, relating to the accuracy of the reference standard under such conditions. CONCLUSIONS Our results suggest that cheaper diagnostics do not necessarily translate to less costly ACF, as any savings from the test cost can be strongly outweighed by factors including false-positive TB treatment, reduced sensitivity, and foregone savings in second-line treatment. In resource-limited settings, it is therefore important to take all of these factors into account when designing cost-effective strategies for ACF.
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Affiliation(s)
- Lucia Cilloni
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
- * E-mail:
| | - Katharina Kranzer
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Biomedical Research and Training Institute, Harare, Zimbabwe
- Research Centre Borstel, Sülfeld, Germany
| | - Helen R. Stagg
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Nimalan Arinaminpathy
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
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29
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Lu HW, Sakamuri R, Kumar P, Ferguson TM, Doebler RW, Herrington KD, Talbot RP, Weigel KM, Nguyen FK, Cangelosi GA, Narita M, Boyle DS, Niemz A. Integrated nucleic acid testing system to enable TB diagnosis in peripheral settings. LAB ON A CHIP 2020; 20:4071-4081. [PMID: 33021611 PMCID: PMC7787164 DOI: 10.1039/d0lc00445f] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
To facilitate treatment and limit transmission of tuberculosis (TB), new methods are needed to enable rapid and affordable diagnosis of the disease in high-burden low-resource settings. We have developed a prototype integrated nucleic acid testing device to detect Mycobacterium tuberculosis (M.tb) in sputum. The device consists of a disposable cartridge and compact, inexpensive instrument that automates pathogen lysis, nucleic acid extraction, isothermal DNA amplification and lateral flow detection. A liquefied and disinfected sputum sample is manually injected into the cartridge, and all other steps are automated, with a result provided in <1.5 h. Cell disruption and DNA extraction is executed within a four-port active valve containing a miniature bead blender (based on PureLyse® technology, Claremont BioSolutions LLC). The DNA-containing eluate is combined with dry master-mix reagents and target DNA is isothermally amplified. Amplified master-mix is then pumped into a lateral flow strip chamber for detection. The entire process is performed in a single-use closed-system cartridge to prevent amplicon carryover. For testing of M.tb-spiked sputum the system provided a limit of detection of 5 × 103 colony forming units (CFU) per mL. None of the negative sputum-only controls yielded a false-positive result. Testing of 45 clinical sputum specimens from TB cases and controls relative to a validated manual qPCR-based comparator method revealed a preliminary sensitivity of 90% and specificity of 96%. With further development, the herein described integrated nucleic acid testing device can enable TB diagnosis and treatment initiation in the same clinical encounter in near-patient low-resource settings of high TB burden countries.
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Affiliation(s)
- Hsiang-Wei Lu
- Riggs School of Applied Life Sciences, Keck Graduate Institute, 535 Watson Drive, Claremont, CA 91711, USA.
| | - Rama Sakamuri
- Riggs School of Applied Life Sciences, Keck Graduate Institute, 535 Watson Drive, Claremont, CA 91711, USA.
| | - Pranav Kumar
- Riggs School of Applied Life Sciences, Keck Graduate Institute, 535 Watson Drive, Claremont, CA 91711, USA.
| | - Tanya M Ferguson
- Claremont BioSolutions, 1182 Monte Vista Ave # 11, Upland, CA 91786, USA
| | - Robert W Doebler
- Claremont BioSolutions, 1182 Monte Vista Ave # 11, Upland, CA 91786, USA
| | - Keith D Herrington
- Claremont BioSolutions, 1182 Monte Vista Ave # 11, Upland, CA 91786, USA
| | - Ryan P Talbot
- Claremont BioSolutions, 1182 Monte Vista Ave # 11, Upland, CA 91786, USA
| | - Kris M Weigel
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA 98195, USA
| | - Felicia K Nguyen
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA 98195, USA
| | - Gerard A Cangelosi
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA 98195, USA
| | - Masahiro Narita
- Seattle & King County Tuberculosis Control Clinic, Harborview Medical Center, 325 9th Ave, Seattle, WA 98104, USA
| | | | - Angelika Niemz
- Riggs School of Applied Life Sciences, Keck Graduate Institute, 535 Watson Drive, Claremont, CA 91711, USA.
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30
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Agarwal N, Raheja A, Suri A. Guidelines for Preoperative Testing for Neurosurgery in Coronavirus Disease 2019 (COVID-19) Era: Indian Viewpoint Amidst Global Practice. World Neurosurg 2020; 146:103-112. [PMID: 33283759 PMCID: PMC7584495 DOI: 10.1016/j.wneu.2020.10.086] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 10/15/2020] [Accepted: 10/17/2020] [Indexed: 12/18/2022]
Abstract
Preoperative testing and evaluation for coronavirus disease 2019 (COVID-19) have been an enigmatic challenge for the neurosurgical community during the pandemic. Since the beginning of the pandemic, laboratory diagnostic methods have evolved substantially, and with them has been the necessity for readily available, fast, and accurate preoperative testing methods. In this article, we provide an overview of the various laboratory testing methods that are presently available and a comprehensive literature review how various institutes and neurosurgical communities across the globe are employing them to ensure safe and effective delivery of surgical care to patients. Through this review, we highlight the guiding principles for preoperative testing, which may serve as a road map for other medical institutions to follow. In addition, we provide an Indian perspective of preoperative testing and share our experience in this regard.
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Affiliation(s)
- Nitish Agarwal
- Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India
| | - Amol Raheja
- Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India
| | - Ashish Suri
- Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India.
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31
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Abstract
Molecular tests for tuberculosis (TB) have the potential to help reach the three million people with TB who are undiagnosed or not reported each year and to improve the quality of care TB patients receive by providing accurate, quick results, including rapid drug-susceptibility testing. The World Health Organization (WHO) has recommended the use of molecular nucleic acid amplification tests (NAATs) tests for TB detection instead of smear microscopy, as they are able to detect TB more accurately, particularly in patients with paucibacillary disease and in people living with HIV. Importantly, some of these WHO-endorsed tests can detect mycobacterial gene mutations associated with anti-TB drug resistance, allowing clinicians to tailor effective TB treatment. Currently, a wide array of molecular tests for TB detection is being developed and evaluated, and while some tests are intended for reference laboratory use, others are being aimed at the point-of-care and peripheral health care settings. Notably, there is an emergence of molecular tests designed, manufactured, and rolled out in countries with high TB burden, of which some are explicitly aimed for near-patient placement. These developments should increase access to molecular TB testing for larger patient populations. With respect to drug susceptibility testing, NAATs and next-generation sequencing can provide results substantially faster than traditional phenotypic culture. Here, we review recent advances and developments in molecular tests for detecting TB as well as anti-TB drug resistance.
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32
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Jeyashree K, Shanmugasundaram D, Rade K, Gangakhedkar RR, Murhekar MV. Impact and operational feasibility of TrueNat ™ MTB/Rif under India's RNTCP. Public Health Action 2020; 10:87-91. [PMID: 33134121 PMCID: PMC7577004 DOI: 10.5588/pha.20.0004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 05/02/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Revised National Tuberculosis Control Programme (RNTCP) in Andhra Pradesh, India, introduced TrueNat™ MTB/Rif, a rapid molecular test for detecting Mycobacterium tuberculosis (MTB) and rifampicin (RIF) resistance at 193 TB units (TUs) in October 2018. We evaluated its impact on TB diagnosis and assessed the operational feasibility of its deployment at point-of-care (POC) settings. METHODS We compared the number of presumptive TB cases tested and the number (proportion) of microbiologically positive before (January-August 2018) and after (January-August 2019) the deployment of TrueNat. We interviewed laboratory technicians and Senior TB Laboratory Supervisor from 25 randomly selected TUs to assess operational feasibility. RESULTS In 2018, 10.5% (range 8.9-13.1) of 245,989 presumptive cases tested were positive. In 2019, of the 185,435 presumptive cases tested, 13.7% (range 9.6-18.9) were positive. The proportion of presumptive TB cases in whom MTB was detected using TrueNat was 14.4% (range 10.0-21.2). TrueNat significantly increased case detection (incidence rate ratio [IRR] 1.30; 95%CI 1.15-1.46), yielding an additional 18 TB cases per 100 000 population. Laboratory technicians became comfortable in performing TrueNat after a median of 10 tests (interquartile range 5-17.5). Invalid reports declined from 6.8% to 3.6%. CONCLUSION The deployment of TrueNat as POC diagnostic test improved case detection and was operationally feasible under RNTCP.
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Affiliation(s)
- K Jeyashree
- Indian Council of Medical Research (ICMR)-National Institute of Epidemiology, Chennai, India
| | - D Shanmugasundaram
- Indian Council of Medical Research (ICMR)-National Institute of Epidemiology, Chennai, India
| | - K Rade
- World Health Organization India Country Office, New Delhi, India
| | | | - M V Murhekar
- Indian Council of Medical Research (ICMR)-National Institute of Epidemiology, Chennai, India
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Georghiou SB, Schumacher SG, Rodwell TC, Colman RE, Miotto P, Gilpin C, Ismail N, Rodrigues C, Warren R, Weyer K, Zignol M, Arafah S, Cirillo DM, Denkinger CM. Guidance for Studies Evaluating the Accuracy of Rapid Tuberculosis Drug-Susceptibility Tests. J Infect Dis 2020; 220:S126-S135. [PMID: 31593599 DOI: 10.1093/infdis/jiz106] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The development and implementation of rapid molecular diagnostics for tuberculosis (TB) drug-susceptibility testing is critical to inform treatment of patients and to prevent the emergence and spread of resistance. Optimal trial planning for existing tests and those in development will be critical to rapidly gather the evidence necessary to inform World Health Organization review and to support potential policy recommendations. The evidence necessary includes an assessment of the performance for TB and resistance detection as well as an assessment of the operational characteristics of these platforms. The performance assessment should include analytical studies to confirm the limit of detection and assay ability to detect mutations conferring resistance across globally representative strains. The analytical evaluation is typically followed by multisite clinical evaluation studies to confirm diagnostic performance in sites and populations of intended use. This paper summarizes the considerations for the design of these analytical and clinical studies.
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Affiliation(s)
| | | | | | | | - Paolo Miotto
- IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Nazir Ismail
- University of Pretoria, South Africa.,National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.,University Hospital Heidelberg, Division of Tropical Medicine, Centre of Infectious Diseases, Germany
| | | | - Rob Warren
- SAMRC Centre for Tuberculosis Research, Stellenbosch University, Tygerberg, South Africa
| | - Karin Weyer
- World Health Organization, Geneva, Switzerland
| | | | | | | | - Claudia M Denkinger
- FIND, Geneva, Switzerland.,University of Heidelberg, Centre of Infectious Diseases, Germany
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Acharya B, Acharya A, Gautam S, Ghimire SP, Mishra G, Parajuli N, Sapkota B. Advances in diagnosis of Tuberculosis: an update into molecular diagnosis of Mycobacterium tuberculosis. Mol Biol Rep 2020; 47:4065-4075. [DOI: 10.1007/s11033-020-05413-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 03/28/2020] [Indexed: 01/02/2023]
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Arinaminpathy N, Gomez GB, Sachdeva KS, Rao R, Parmar M, Nair SA, Rade K, Kumta S, Hermann D, Hanson C, Chin DP, Dewan P. The potential deployment of a pan-tuberculosis drug regimen in India: A modelling analysis. PLoS One 2020; 15:e0230808. [PMID: 32218585 PMCID: PMC7100958 DOI: 10.1371/journal.pone.0230808] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 03/09/2020] [Indexed: 11/24/2022] Open
Abstract
There is increasing interest in future, highly-potent ‘pan-TB’ regimens against tuberculosis (TB), that may be equally effective in both drug-susceptible and rifampicin-resistant (RR) forms of TB. Taking the example of India, the country with the world’s largest burden of TB, we show that adoption of these regimens could be: (i) epidemiologically impactful, and (ii) cost-saving to the national TB programme, even if the regimen itself is more costly than current TB treatment. Mathematical modelling suggests that deployment of a pan-TB regimen in 2022 would reduce the annual incidence of TB in 2030 by 23.9% [95% Bayesian credible intervals [CrI] 17.6–30.8%] if used to treat all TB cases, and by 2.30% [95% CrI 1.57–3.48%] if used to treat only RR-TB. Notably, with a regimen costing less than USD 359 (95% CrI 287–441), treating all diagnosed TB cases with the pan-TB regimen yielded greater cost-savings than treating just those diagnosed with RR-TB. One limitation of our approach is that it does not capture the risk of resistance to the new regimen. We discuss ways in which this risk could be mitigated using modern adherence support mechanisms, as well as drug sensitivity testing at the point of TB diagnosis, to prevent new resistant forms from becoming established. A combination of such approaches would be important for maximising the useful lifetime of any future regimen.
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Affiliation(s)
- Nimalan Arinaminpathy
- MRC Centre for Global Infectious Disease Analysis, Faculty of Medicine, Imperial College London, United Kingdom
- * E-mail:
| | - Gabriela B. Gomez
- Department of Global Health and Development, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - Raghuram Rao
- Central TB Division, Government of India, New Delhi, India
| | - Malik Parmar
- India Country Office, World Health Organization, New Delhi, India
| | | | - Kiran Rade
- India Country Office, World Health Organization, New Delhi, India
| | - Sameer Kumta
- Bill and Melinda Gates Foundation, India Country Office, New Delhi, India
| | - David Hermann
- Bill and Melinda Gates Foundation, Seattle, WA, United States of America
| | - Christy Hanson
- Bill and Melinda Gates Foundation, Seattle, WA, United States of America
| | - Daniel P. Chin
- Bill and Melinda Gates Foundation, Seattle, WA, United States of America
| | - Puneet Dewan
- Global Good, Intellectual Ventures, Seattle, WA, United States of America
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SeeTB: A novel alternative to sputum smear microscopy to diagnose tuberculosis in high burden countries. Sci Rep 2019; 9:16371. [PMID: 31719539 PMCID: PMC6851358 DOI: 10.1038/s41598-019-52739-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 10/10/2019] [Indexed: 01/22/2023] Open
Abstract
Microscopy-based tuberculosis (TB) diagnosis i.e. Ziehl-Neelsen screening still remains the primary diagnostic method in resource poor and high TB burden countries, however this method has poor sensitivity (~60%). Bringing three million TB patients who are left undiagnosed under the treatment has been a major focus as part of END-TB strategy across the world. We have developed a portable set-up called ‘SeeTB’ that converts a bright-field microscope into fluorescence microscope (FM) with minimal interventions. SeeTB, a total internal reflection-based fluorescence excitation system allows visualization of auramine-O stained bacilli efficiently with high signal-to-noise ratio. Along with the device, we have developed a sputum-processing reagent called ‘CLR’ that homogenizes and digests the viscous polymer matrix of sputum. We have compared the performance of SeeTB system in 237 clinical sputum samples along with FM, GeneXpert and liquid culture. In comparison with culture as gold standard, FM has sensitivity of 63.77% and SeeTB has improved sensitivity to 76.06%. In comparison with GeneXpert, FM has sensitivity of 73.91% while SeeTB has improved sensitivity to 85.51%. However, there is no significant change in the specificity between FM and SeeTB system. In short, SeeTB system offers the most realistic option for improved TB case identification in resource-limited settings.
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Sharma S, Singhal R, Sarin R, Myneedu VP. Emerging trends in microbiological diagnostics in children. Indian J Tuberc 2019; 66:549-554. [PMID: 31813447 DOI: 10.1016/j.ijtb.2019.11.007] [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] [Indexed: 06/10/2023]
Abstract
The targets of the WHO's End TB Strategy and the United Nations' (UN) Sustainable Development Goals (SDGs) have been expanded to"Find. Treat. All #EndTB" with universal access to TB diagnosis, treatment and care by 2022 in an effort to end the global TB epidemic. Trends to achieve the above targets in children have led to greater emphasis on the newer diagnostics paving way to microbiological confirmation and universal drug sensitivity in children.
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Affiliation(s)
| | | | - Rohit Sarin
- National Institute of Tuberculosis and Respiratory Diseases, India
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Babafemi EO, Cherian BP, Ouma B, Mogoko G. Paediatric tuberculosis diagnosis using Mycobacterium tuberculosis real-time polymerase chain reaction assay: protocol for systematic review and meta-analysis. Syst Rev 2019; 8:225. [PMID: 31470893 PMCID: PMC6716920 DOI: 10.1186/s13643-019-1137-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 08/13/2019] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Tuberculosis (TB) diagnosis in children is a major challenge with up to 94% of children with TB treated empirically in TB high-burden countries. Paediatric tuberculosis (PTB) remains a major cause of morbidity and mortality globally, particularly in developing countries. Most deaths/morbidity from TB in paediatrics could be prevented with early diagnosis and appropriate treatment. The main objective of this systematic review is to examine the evidence whether real-time polymerase chain reaction assay could be the most accurate clinical laboratory diagnostic methodology for the Mycobacterium tuberculosis (MTB) detection in paediatrics. METHODS We will search MEDLINE/PubMed, EMBASE, BIOSIS, LILACS, Cochrane Infectious Diseases Group Specialised Register (CIDG SR), Global Health, and CINAHL for published studies that recruited children less than 16 years of age being investigated for Mycobacterium tuberculosis (MTB) infection using real-time polymerase chain reaction assay accompanied by mycobacteriological culture investigation as the reference standard. There will be no restriction regarding the language, date of publication, and publication status. We will include randomised controlled trials and observational studies (cohort, cross-sectional) in the review. Selection of studies, data extraction and management, assessment of risk of bias, and quality of evidence will be performed by two independent reviewers (EB and BC). A third researcher will be consulted in case of discrepancies. Depending on the availability and quality of the data, a meta-analysis will be performed. Otherwise, findings will be qualitatively reported. DISCUSSION To our knowledge, this is the first systematic review and meta-analysis assessing the detection of MTB from all clinical sample types using real-time polymerase chain reaction assay in paediatric population. This review will make available evidence on the accuracy, approach, and interpretation of results of this assay in the context of MTB diagnosis which will meet an urgent need, considering the challenges of MTB diagnosis in paediatrics. SYSTEMATIC REVIEW REGISTRATION PROSPERO CRD42018104052.
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Affiliation(s)
- Emmanuel O. Babafemi
- Microbiology Department, Paediatrics Laboratory Medicine, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham, UK
| | - Benny P. Cherian
- Barts Health NHS Trust, Room MICR324, 3rd floor Pathology & Pharmacy Building, 80 Newark Street, London, E1 2ES UK
| | - Betty Ouma
- Chelsea & Westminster Hospital, 369 Fulham Road, London, Greater London SW10 9NH UK
| | - Gilbert Mogoko
- Microbiology Department, IPP Pathology First, Dobson House, Bentalls, Basildon, SS14 3BY UK
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Anthwal D, Lavania S, Gupta RK, Verma A, Myneedu VP, Sharma PP, Verma H, Malhotra V, Gupta A, Gupta NK, Sarin R, Haldar S, Tyagi JS. Development and evaluation of novel bio-safe filter paper-based kits for sputum microscopy and transport to directly detect Mycobacterium tuberculosis and associated drug resistance. PLoS One 2019; 14:e0220967. [PMID: 31408508 PMCID: PMC6692035 DOI: 10.1371/journal.pone.0220967] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 07/26/2019] [Indexed: 11/18/2022] Open
Abstract
India has the highest burden of Tuberculosis (TB) and multidrug-resistant TB (MDR-TB) worldwide. Innovative technology is the need of the hour to identify these cases that remain either undiagnosed or inadequately diagnosed due to the unavailability of appropriate tools at primary healthcare settings. We developed and evaluated 3 kits, namely ‘TB Detect’ (containing BioFM-Filter device), ‘TB Concentration and Transport’ (containing Trans-Filter device) and ‘TB DNA Extraction’ kits. These kits enable bio-safe equipment-free concentration of sputum on filters and improved fluorescence microscopy at primary healthcare centres, ambient temperature transport of dried inactivated sputum filters to central laboratories and molecular detection of drug resistance by PCR and DNA sequencing (Mol-DST). In a 2-site evaluation (n = 1190 sputum specimens) on presumptive TB patients, BioFM-Filter smear exhibited a significant increase in positivity of 7% and 4% over ZN smear and LED-FM smear (p<0.05), respectively and an increment in smear grade status (1+ or 2+ to 3+) of 16% over ZN smear and 20% over LED-FM smear. The sensitivity of Mol-DST in presumptive MDR-TB and XDR-TB cases (n = 148) was 90% for Rifampicin (95% confidence interval [CI], 78–96%), 84% for Isoniazid (95% CI, 72–92%), 83% for Fluoroquinolones (95% CI, 66–93%) and 75% for Aminoglycosides (95% CI, 35–97%), using phenotypic DST as the reference standard. Test specificity was 88–93% and concordance was ~89–92% (κ value 0.8–0.9). The patient-friendly kits described here address several of the existing challenges and are designed to provide ‘Universal Access’ to rapid TB diagnosis, including drug-resistant disease. Their utility was demonstrated by application to sputum at 2 sites in India. Our findings pave the way for larger studies in different point-of-care settings, including high-density urban areas and remote geographical locations.
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Affiliation(s)
- Divya Anthwal
- Center for Bio-design and Diagnostics, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad–Gurgaon Expressway, Faridabad, India
| | - Surabhi Lavania
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | - Rakesh Kumar Gupta
- Center for Bio-design and Diagnostics, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad–Gurgaon Expressway, Faridabad, India
| | - Ajoy Verma
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, Mehrauli, New Delhi, India
| | - Vithal Prasad Myneedu
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, Mehrauli, New Delhi, India
| | - Prem Prakash Sharma
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, Mehrauli, New Delhi, India
| | | | | | - Ashawant Gupta
- Advanced Microdevices Pvt Ltd, Industrial Area, Ambala Cantt, India
| | | | - Rohit Sarin
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, Mehrauli, New Delhi, India
- * E-mail: (JST); (SH); (RS)
| | - Sagarika Haldar
- Center for Bio-design and Diagnostics, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad–Gurgaon Expressway, Faridabad, India
- * E-mail: (JST); (SH); (RS)
| | - Jaya Sivaswami Tyagi
- Center for Bio-design and Diagnostics, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad–Gurgaon Expressway, Faridabad, India
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
- * E-mail: (JST); (SH); (RS)
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Lee DJ, Kumarasamy N, Resch SC, Sivaramakrishnan GN, Mayer KH, Tripathy S, Paltiel AD, Freedberg KA, Reddy KP. Rapid, point-of-care diagnosis of tuberculosis with novel Truenat assay: Cost-effectiveness analysis for India's public sector. PLoS One 2019; 14:e0218890. [PMID: 31265470 PMCID: PMC6605662 DOI: 10.1371/journal.pone.0218890] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 06/11/2019] [Indexed: 11/19/2022] Open
Abstract
Background Truenat is a novel molecular assay that rapidly detects tuberculosis (TB) and rifampicin-resistance. Due to the portability of its battery-powered testing platform, it may be valuable in peripheral healthcare settings in India. Methods Using a microsimulation model, we compared four TB diagnostic strategies for HIV-negative adults with presumptive TB: (1) sputum smear microscopy in designated microscopy centers (DMCs) (SSM); (2) Xpert MTB/RIF in DMCs (Xpert); (3) Truenat in DMCs (Truenat DMC); and (4) Truenat for point-of-care testing in primary healthcare facilities (Truenat POC). We projected life expectancy, costs, incremental cost-effectiveness ratios (ICERs), and 5-year budget impact of deploying Truenat POC in India’s public sector. We defined a strategy “cost-effective” if its ICER was <US$990/year-of-life saved (YLS). Model inputs included: TB prevalence, 15% (among those not previously treated for TB) and 27% (among those previously treated for TB); sensitivity for TB detection, 89% (Xpert) and 86% (Truenat); per test cost, $12.63 (Xpert) and $13.20 (Truenat); and linkage-to-care after diagnosis, 84% (DMC) and 95% (POC). We varied these parameters in sensitivity analyses. Results Compared to SSM, Truenat POC increased life expectancy by 0.39 years and was cost-effective (ICER $210/YLS). Compared to Xpert, Truenat POC increased life expectancy by 0.08 years due to improved linkage-to-care and was cost-effective (ICER $120/YLS). In sensitivity analysis, the cost-effectiveness of Truenat POC, relative to Xpert, depended on the diagnostic sensitivity of Truenat and linkage-to-care with Truenat. Deploying Truenat POC instead of Xpert increased 5-year expenditures by $270 million, due mostly to treatment costs. Limitations of our study include uncertainty in Truenat’s sensitivity for TB and not accounting for the “start-up” costs of implementing Truenat in the field. Conclusions Used at the point-of-care in India, Truenat for TB diagnosis should improve linkage-to-care, increase life expectancy, and be cost-effective compared with smear microscopy or Xpert.
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Affiliation(s)
- David J. Lee
- Harvard Medical School, Boston, Massachusetts, United States of America
- Medical Practice Evaluation Center, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- * E-mail: (DJL); (KPR)
| | - Nagalingeswaran Kumarasamy
- Chennai Antiviral Research and Treatment Clinical Research Site, Voluntary Health Services, Chennai, India
| | - Stephen C. Resch
- Center for Health Decision Science, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Department of Health Policy and Management, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | | | - Kenneth H. Mayer
- Harvard Medical School, Boston, Massachusetts, United States of America
- The Fenway Institute, Fenway Health, Boston, Massachusetts, United States of America
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | | | - A. David Paltiel
- Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Kenneth A. Freedberg
- Harvard Medical School, Boston, Massachusetts, United States of America
- Medical Practice Evaluation Center, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Health Policy and Management, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Krishna P. Reddy
- Harvard Medical School, Boston, Massachusetts, United States of America
- Medical Practice Evaluation Center, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- * E-mail: (DJL); (KPR)
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Ergonomic Diagnostic Tool based on Chip Mini RT-PCR for Diagnosis of Pulmonary and Extra Pulmonary Tuberculosis. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2019. [DOI: 10.22207/jpam.13.2.58] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Beall SG, Cantera J, Diaz MH, Winchell JM, Lillis L, White H, Kalnoky M, Gallarda J, Boyle DS. Performance and workflow assessment of six nucleic acid extraction technologies for use in resource limited settings. PLoS One 2019; 14:e0215753. [PMID: 30998749 PMCID: PMC6472818 DOI: 10.1371/journal.pone.0215753] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 02/16/2019] [Indexed: 01/20/2023] Open
Abstract
Infectious disease nucleic acid amplification technologies (NAAT) have superior sensitivity, specificity, and rapid time to result compared to traditional microbiological methods. Recovery of concentrated, high quality pathogen nucleic acid (NA) from complex specimen matrices is required for optimal performance of several NA amplification/detection technologies such as polymerase chain reaction (PCR). Fully integrated NAAT platforms that enable rapid sample-to-result workflows with minimal user input are generally restricted to larger reference lab settings, and their complexity and cost are prohibitive to widespread implementation in resource limited settings (RLS). Identification of component technologies for incorporation of reliable and affordable sample preparation with pathogen NA amplification/detection into an integrated platform suitable for RLS, is a necessary first step toward achieving the overarching goal of reducing infectious disease-associated morbidity and mortality globally. In the current study, we evaluate the performance of six novel NA extraction technologies from different developers using blinded panels of stool, sputum and blood spiked with variable amounts of quality-controlled DNA- and/or RNA-based microbes. The extraction efficiencies were semi-quantitatively assessed using validated real-time reverse transcription (RT)-PCR assays specific for each microbe and comparing target-specific RT-PCR results to those obtained with reference NA extraction methods. The technologies were ranked based on overall diagnostic accuracy (analytical sensitivity and specificity). Sample input and output volumes, total processing time, user-required manual steps and cost estimates were also examined for suitability in RLS. Together with the performance analysis, these metrics were used to select the more suitable candidate technologies for further optimization of integrated NA amplification and detection technologies for RLS.
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Affiliation(s)
- Shivani G. Beall
- Centers for Disease Control and Prevention, Division of Bacterial Diseases, Respiratory Diseases Branch, Atlanta, Georgia, United States of America
| | | | - Maureen H. Diaz
- Centers for Disease Control and Prevention, Division of Bacterial Diseases, Respiratory Diseases Branch, Atlanta, Georgia, United States of America
| | - Jonas M. Winchell
- Centers for Disease Control and Prevention, Division of Bacterial Diseases, Respiratory Diseases Branch, Atlanta, Georgia, United States of America
| | | | | | | | - James Gallarda
- Bill and Melinda Gates Foundation, Seattle, Washington, United States of America
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Poeta P, Silva V, Guedes A, Eduardo Pereira J, Cláudia Coelho A, Igrejas G. Tuberculosis in the 21th century: Current status of diagnostic methods. Exp Lung Res 2019; 44:352-360. [PMID: 30663432 DOI: 10.1080/01902148.2018.1545880] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Tuberculosis is an infectious bacterial disease with a high mortality rate worldwide constituting a serious public health problem. The diagnostic methods commonly used by health professionals are slow and expensive and the results may take about sixty days which will cause a delay in administrating the most proper treatment to the patient, as well as increase health care costs and infection transmission possibility. Patients infected simultaneously with human immunodeficiency virus and Mycobacterium tuberculosis are a constant and worrying challenge for the scientific community which will research and develop new methods of diagnosis, new drugs and new therapies. Nowadays there are new tuberculosis diagnosis methods and some of which are already in clinical trial phases. These methods have high sensitivity, but do not replace the microbiological examination for isolation and culture of Mycobacterium spp. However, in clinical practice, microbiological, imaging, clinical and epidemiological data integration provide the best diagnosis and treatment possible. Consequently, throughout this paper, the different methods of diagnosis of human tuberculosis with its advantages and disadvantages will be covered, describing new omics and ultra-fast methods to increase knowledge and obtain a rapid diagnosis of tuberculosis.
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Affiliation(s)
- Patrícia Poeta
- a Department of Veterinary Sciences , University of Trás-os-Montes and Alto Douro (UTAD) , Vila Real , Portugal.,b Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro , Vila Real , Portugal
| | - Vanessa Silva
- a Department of Veterinary Sciences , University of Trás-os-Montes and Alto Douro (UTAD) , Vila Real , Portugal.,b Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro , Vila Real , Portugal.,c Functional Genomics and Proteomics Unit , University of Tras-os-Montes and Alto Douro (UTAD) , Vila Real , Portugal.,d Associated Laboratory for Green Chemistry (LAQV-REQUIMTE) , University NOVA of Lisboa , Lisboa , Caparica, Portugal
| | - Andreia Guedes
- a Department of Veterinary Sciences , University of Trás-os-Montes and Alto Douro (UTAD) , Vila Real , Portugal
| | - José Eduardo Pereira
- a Department of Veterinary Sciences , University of Trás-os-Montes and Alto Douro (UTAD) , Vila Real , Portugal.,e CECAV, Centro de Ciência Animal e Veterinária , Universidade de Trás-os-Montes e Alto Douro , Vila Real , Portugal
| | - Ana Cláudia Coelho
- a Department of Veterinary Sciences , University of Trás-os-Montes and Alto Douro (UTAD) , Vila Real , Portugal.,e CECAV, Centro de Ciência Animal e Veterinária , Universidade de Trás-os-Montes e Alto Douro , Vila Real , Portugal
| | - Gilberto Igrejas
- b Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro , Vila Real , Portugal.,c Functional Genomics and Proteomics Unit , University of Tras-os-Montes and Alto Douro (UTAD) , Vila Real , Portugal.,d Associated Laboratory for Green Chemistry (LAQV-REQUIMTE) , University NOVA of Lisboa , Lisboa , Caparica, Portugal
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Baron EJ, Tenover FC, Gnanashanmugam D. Direct Detection of Mycobacterium tuberculosis in Clinical Specimens Using Nucleic Acid Amplification Tests. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.clinmicnews.2018.06.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Gupta S, Kakkar V. Recent technological advancements in tuberculosis diagnostics - A review. Biosens Bioelectron 2018; 115:14-29. [PMID: 29783081 DOI: 10.1016/j.bios.2018.05.017] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 04/26/2018] [Accepted: 05/09/2018] [Indexed: 01/14/2023]
Abstract
Early diagnosis and on-time effective treatment are indispensable for Tuberculosis (TB) control - a life threatening infectious communicable disease. The conventional techniques for diagnosing TB normally take two to three weeks. This delay in diagnosis and further increase in detection complexity due to the emerging risks of XDR-TB (Extensively drug Resistant-TB) and MDR-TB (Multidrug Resistant-TB) are evoking interest of researchers in the field of developing rapid TB detection techniques such as biosensing and other point-of-care (POC) techniques. Biosensing technologies along with the collaboration with nanotechnology have enormous potential to boost the MTB detection and for overall management in clinical diagnosis. A diverse range of portable, sensitive and rapid biosensors based on different signal transducer principles and with different biomarkers detection capabilities have been developed for TB detection in the early stages. Further, a lot of progress has been achieved over the years in developing various point-of-care diagnostic tools including non-molecular methods and molecular techniques. The objective of this study is to present a succinct review of the available TB detection techniques that are either in use or under development. The focus of this review is on the current developments occurred in nano-biosensing technologies. A synopsis of ameliorations in different non-molecular diagnostic tools and progress in the field of molecular techniques along with the role of emerging Lab-on-Chip technology for diagnosing and mitigating the TB consequences have also been presented.
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Affiliation(s)
- Shagun Gupta
- School of Electronics and Communication Engineering, Shri Mata Vaishno Devi University, Katra 182320, India.
| | - Vipan Kakkar
- School of Electronics and Communication Engineering, Shri Mata Vaishno Devi University, Katra 182320, India.
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Babafemi EO, Cherian BP, Banting L, Mills GA, Ngianga K. Effectiveness of real-time polymerase chain reaction assay for the detection of Mycobacterium tuberculosis in pathological samples: a systematic review and meta-analysis. Syst Rev 2017; 6:215. [PMID: 29070061 PMCID: PMC5657121 DOI: 10.1186/s13643-017-0608-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 10/12/2017] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Rapid and accurate diagnosis of tuberculosis (TB) is key to manage the disease and to control and prevent its transmission. Many established diagnostic methods suffer from low sensitivity or delay of timely results and are inadequate for rapid detection of Mycobacterium tuberculosis (MTB) in pulmonary and extra-pulmonary clinical samples. This study examined whether a real-time polymerase chain reaction (RT-PCR) assay, with a turn-a-round time of 2 h, would prove effective for routine detection of MTB by clinical microbiology laboratories. METHODS A systematic literature search was performed for publications in any language on the detection of MTB in pathological samples by RT-PCR assay. The following sources were used MEDLINE via PubMed, EMBASE, BIOSIS Citation Index, Web of Science, SCOPUS, ISI Web of Knowledge and Cochrane Infectious Diseases Group Specialised Register, grey literature, World Health Organization and Centres for Disease Control and Prevention websites. Forty-six studies met set inclusion criteria. Generated pooled summary estimates (95% CIs) were calculated for overall accuracy and bivariate meta-regression model was used for meta-analysis. RESULTS Summary estimates for pulmonary TB (31 studies) were as follows: sensitivity 0.82 (95% CI 0.81-0.83), specificity 0.99 (95% CI 0.99-0.99), positive likelihood ratio 43.00 (28.23-64.81), negative likelihood ratio 0.16 (0.12-0.20), diagnostic odds ratio 324.26 (95% CI 189.08-556.09) and area under curve 0.99. Summary estimates for extra-pulmonary TB (25 studies) were as follows: sensitivity 0.70 (95% CI 0.67-0.72), specificity 0.99 (95% CI 0.99-0.99), positive likelihood ratio 29.82 (17.86-49.78), negative likelihood ratio 0.33 (0.26-0.42), diagnostic odds ratio 125.20 (95% CI 65.75-238.36) and area under curve 0.96. CONCLUSIONS RT-PCR assay demonstrated a high degree of sensitivity for pulmonary TB and good sensitivity for extra-pulmonary TB. It indicated a high degree of specificity for ruling in TB infection from sampling regimes. This was acceptable, but may better as a rule out add-on diagnostic test. RT-PCR assays demonstrate both a high degree of sensitivity in pulmonary samples and rapidity of detection of TB which is an important factor in achieving effective global control and for patient management in terms of initiating early and appropriate anti-tubercular therapy. SYSTEMATIC REVIEW REGISTRATION PROSPERO CRD42015027534 .
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Affiliation(s)
- Emmanuel O. Babafemi
- Microbiology Department, Pathology Division, Sandwell and West Birmingham Hospitals NHS Trust, Birmingham, UK
| | | | - Lee Banting
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, UK
| | - Graham A. Mills
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, UK
| | - Kandala Ngianga
- School of Health Sciences and Social Work, University of Portsmouth, Portsmouth, UK
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Vergara Gómez A, González-Martín J, García-Basteiro AL. Xpert® MTB/RIF: Usefulness for the diagnosis of tuberculosis and resistance to rifampicin. Med Clin (Barc) 2017; 149:399-405. [PMID: 28739268 DOI: 10.1016/j.medcli.2017.06.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 06/05/2017] [Accepted: 06/06/2017] [Indexed: 11/19/2022]
Abstract
The advent of the Xpert® MTB/RIF technique was a revolution in the diagnosis of tuberculosis, especially in areas with high incidence and low resources. It allows the detection of Mycobacterium tuberculosis complex and simultaneously the most common resistance mutations to rifampicin in less than 2h. For respiratory samples the sensitivity is very high, but it decreases for extrapulmonary samples and children. Although it is faster and simpler than conventional methods, it presents some limitations and new and better techniques are needed to reduce the number of cases and deaths caused by tuberculosis. This review aims to assess the scientific evidence around the diagnostic performance of Xpert® MTB/RIF in different types of samples and populations, as well as analyse its strengths and limitations for TB diagnosis.
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Affiliation(s)
- Andrea Vergara Gómez
- Servicio de Microbiología, CDB, Hospital Clínic de Barcelona, Universitat de Barcelona, Barcelona, España
| | - Julià González-Martín
- Servicio de Microbiología, CDB, Hospital Clínic de Barcelona, Universitat de Barcelona, Barcelona, España; Institut de Salut Global de Barcelona (ISGlobal), Barcelona, España
| | - Alberto L García-Basteiro
- Institut de Salut Global de Barcelona (ISGlobal), Barcelona, España; Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique; Amsterdam Institute for Global Health and Development (AIGHD), Ámsterdam, Países Bajos.
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Schito M, Migliori GB, Fletcher HA, McNerney R, Centis R, D'Ambrosio L, Bates M, Kibiki G, Kapata N, Corrah T, Bomanji J, Vilaplana C, Johnson D, Mwaba P, Maeurer M, Zumla A. Perspectives on Advances in Tuberculosis Diagnostics, Drugs, and Vaccines. Clin Infect Dis 2016; 61Suppl 3:S102-18. [PMID: 26409271 DOI: 10.1093/cid/civ609] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Despite concerted efforts over the past 2 decades at developing new diagnostics, drugs, and vaccines with expanding pipelines, tuberculosis remains a global emergency. Several novel diagnostic technologies show promise of better point-of-care rapid tests for tuberculosis including nucleic acid-based amplification tests, imaging, and breath analysis of volatile organic compounds. Advances in new and repurposed drugs for use in multidrug-resistant (MDR) or extensively drug-resistant (XDR) tuberculosis have focused on development of several new drug regimens and their evaluation in clinical trials and now influence World Health Organization guidelines. Since the failure of the MVA85A vaccine 2 years ago, there have been no new tuberculosis vaccine candidates entering clinical testing. The current status quo of the lengthy treatment duration and poor treatment outcomes associated with MDR/XDR tuberculosis and with comorbidity of tuberculosis with human immunodeficiency virus and noncommunicable diseases is unacceptable. New innovations and political and funder commitment for early rapid diagnosis, shortening duration of therapy, improving treatment outcomes, and prevention are urgently required.
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Affiliation(s)
- Marco Schito
- Critical Path to TB Drug Regimens, Critical Path Institute, Tucson, Arizona
| | - Giovanni Battista Migliori
- World Health Organization Collaborating Centre for Tuberculosis and Lung Diseases, Fondazione S. Maugeri, Care and Research Institute, Tradate, Italy
| | - Helen A Fletcher
- Department of Immunology and Infection, London School of Hygiene and Tropical Medicine
| | | | - Rosella Centis
- World Health Organization Collaborating Centre for Tuberculosis and Lung Diseases, Fondazione S. Maugeri, Care and Research Institute, Tradate, Italy
| | - Lia D'Ambrosio
- World Health Organization Collaborating Centre for Tuberculosis and Lung Diseases, Fondazione S. Maugeri, Care and Research Institute, Tradate, Italy
| | - Matthew Bates
- University of Zambia-University College London Medical School Research and Training Project, University Teaching Hospital, Lusaka, Zambia
| | - Gibson Kibiki
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
| | - Nathan Kapata
- University of Zambia-University College London Medical School Research and Training Project, University Teaching Hospital, Lusaka, Zambia
| | - Tumena Corrah
- Department of Infectious Diseases and Tropical Medicine, Northwick Park Hospital
| | - Jamshed Bomanji
- Department of Nuclear Imaging, University College London Hospitals NHS Foundation Trust, United Kingdom
| | - Cris Vilaplana
- Unitat de Tuberculosi Experimental, Fundació Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Ctra. de Can Ruti, Camí de les Escoles, Barcelona, Spain
| | - Daniel Johnson
- Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Peter Mwaba
- University of Zambia-University College London Medical School Research and Training Project, University Teaching Hospital, Lusaka, Zambia
| | - Markus Maeurer
- Therapeutic Immunology, Departments of Laboratory Medicine and Microbiology, Tumour and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Alimuddin Zumla
- Division of Infection and Immunity, University College London and National Institute for Health Research Biomedical Research Centre, UCL Hospitals NHS Foundation Trust, United Kingdom
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Datta S, Budhauliya R, Chatterjee S, Veer V, Chakravarty R. Enhancement of PCR Detection Limit by Single-Tube Restriction Endonuclease-PCR (RE-PCR). Mol Diagn Ther 2016; 20:297-305. [PMID: 26993322 DOI: 10.1007/s40291-016-0195-2] [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: 11/26/2022]
Abstract
BACKGROUND Polymerase chain reaction (PCR) is widely used in biological research and diagnostics because of its high sensitivity and specificity. However, the sensitivity of PCR is strongly influenced by topological characteristics of the template. Supercoiled templates are known to inhibit PCR, whereas linearized forms of the same supercoiled templates facilitate PCR. OBJECTIVES This study was conducted to compare the PCR efficiency of circular supercoiled DNA templates to their restriction endonuclease (RE)-mediated linearized forms. Additionally, we also evaluated the possibility of RE digestion of the circular supercoiled templates within the complete PCR buffer. METHODS Following a systematic approach, we demonstrated that circular supercoiled templates could be efficiently linearized by RE in the complete PCR buffer itself. This allowed linearization of circular supercoiled templates and their subsequent amplification in the PCR buffer in a single-tube format. RESULTS Using this extremely simple RE-PCR approach, we documented up to tenfold increases in detection efficiency of PCR with two different circular supercoiled templates of clinical origin, including an international calibration standard. CONCLUSIONS This inexpensive and easy approach to increasing PCR sensitivity can be easily adapted to any standard PCR protocol aimed at amplifying circular supercoiled genomes. Apart from its application in the development of sensitive clinical diagnostic PCR assays for a large number of organisms, this method could also prove to be very useful in simplifying the existing protocols for other applications where pre-PCR restriction digestion is required, such as mutation detection, genotyping, and selective template amplification.
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Affiliation(s)
- Sibnarayan Datta
- Molecular Virology Laboratory, Defence Research Laboratory (DRDO), Tezpur, Assam, 784001, India.
| | - Raghvendra Budhauliya
- Molecular Virology Laboratory, Defence Research Laboratory (DRDO), Tezpur, Assam, 784001, India
| | - Soumya Chatterjee
- Molecular Virology Laboratory, Defence Research Laboratory (DRDO), Tezpur, Assam, 784001, India
| | - Vijay Veer
- Molecular Virology Laboratory, Defence Research Laboratory (DRDO), Tezpur, Assam, 784001, India
| | - Runu Chakravarty
- Hepatitis Research Laboratory, ICMR Virus Unit, Kolkata (ICMR), Kolkata, 700010, West Bengal, India
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Sinha P, Gupta A, Prakash P, Anupurba S, Tripathi R, Srivastava GN. Differentiation of Mycobacterium tuberculosis complex from non-tubercular mycobacteria by nested multiplex PCR targeting IS6110, MTP40 and 32kD alpha antigen encoding gene fragments. BMC Infect Dis 2016; 16:123. [PMID: 26968508 PMCID: PMC4788904 DOI: 10.1186/s12879-016-1450-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 03/01/2016] [Indexed: 11/30/2022] Open
Abstract
Background Control of the global burden of tuberculosis is obstructed due to lack of simple, rapid and cost effective diagnostic techniques that can be used in resource poor-settings. To facilitate the early diagnosis of TB directly from clinical specimens, we have standardized and validated the use of nested multiplex PCR, targeting gene fragments IS6110, MTP40 and 32kD α-antigen encoding genes specific for Mycobacterium tuberculosis complex and non-tubercular mycobacteria (NTM), in comparison to smear microscopy, solid culture and single step multiplex PCR. The results were evaluated in comparison to a composite reference standard (CRS) comprising of microbiological results (smear and culture), clinical, radiological and cytopathological findings, clinical treatment and response to anti-tubercular therapy. Methods The nested multiplex PCR (nMPCR) assay was evaluated to test its utility in 600 (535 pulmonary and 65 extra-pulmonary specimens) clinically suspected TB cases. All specimens were processed for smear, culture, single step multiplex PCR and nested multiplex PCR testing. Results Out of 535 screened pulmonary and 65 extra-pulmonary specimens, 329 (61.5 %) and 19 (29.2 %) cases were culture positive for M. tuberculosis. Based on CRS, 450 patients had “clinical TB” (definitive-TB, probable-TB and possible-TB). Remaining 150 were confirmed “non-TB” cases. For culture, the sensitivity was low, 79.3 % for pulmonary and 54.3 % for extra-pulmonary cases. The sensitivity and specificity results for nMPCR test were evaluated taken composite reference standard as a gold standard. The sensitivity of the nMPCR assay was 97.1 % for pulmonary and 91.4 % for extra-pulmonary TB cases with specificity of 100 % and 93.3 % respectively. Conclusion Nested multiplex PCR using three gene primers is a rapid, reliable and highly sensitive and specific diagnostic technique for the detection and differentiation of M. tuberculosis complex from NTM genome and will be useful in diagnosing paucibacillary samples. Nested multiplex PCR assay was found to be better than single step multiplex PCR for assessing the diagnosis of TB. Electronic supplementary material The online version of this article (doi:10.1186/s12879-016-1450-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pallavi Sinha
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, 221 005, Varanasi, India
| | - Anamika Gupta
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, 221 005, Varanasi, India
| | - Pradyot Prakash
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, 221 005, Varanasi, India
| | - Shampa Anupurba
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, 221 005, Varanasi, India.
| | - Rajneesh Tripathi
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, 221 005, Varanasi, India
| | - G N Srivastava
- Departmrnt of TB and Respiratory Diseases, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
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