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Jain R, Gupta G, Mitra DK, Guleria R. Diagnosis of extra pulmonary tuberculosis: An update on novel diagnostic approaches. Respir Med 2024; 225:107601. [PMID: 38513873 DOI: 10.1016/j.rmed.2024.107601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 02/29/2024] [Accepted: 03/12/2024] [Indexed: 03/23/2024]
Abstract
Tuberculosis (TB) remains a major global public health problem worldwide. Though Pulmonary TB (PTB) is mostly discussed, one in five cases of TB present are extrapulmonary TB (EPTB) that manifests conspicuous diagnostic and management challenges with respect to the site of infection. The diagnosis of EPTB is often delayed or even missed due to insidious clinical presentation, pauci-bacillary nature of the disease, and lack of laboratory facilities in the resource limited settings. Culture, the classical gold standard for the diagnosis of tuberculosis, suffers from increased technical and logistical constraints in EPTB cases. Other than culture, several other tests are available but their feasibility and effciacy for the detection of EPTB is still the matter of interest. We need more specific and precise test/s for the various forms of EPTB diagnosis which can easily be applied in the routine TB control program is required. A test that can contribute remarkably towards improving EPTB case detection reducing the morbidity and mortality is the utmost requirement. In this review we described the scenario of molecular and other noval methods available for laboratory diagnosis of EPTB, and also discussed the challenges linked with each diagnostic method. This review will make the readers aware of new emerging diagnostic techniques in the field of EPTB diagnosis. They can make an informed decision to choose the appropriate one according to the test availability, their clinical settings and financial considerations.
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Affiliation(s)
- Rashi Jain
- Department of Pulmonary Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, 110029, India; Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Gopika Gupta
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - D K Mitra
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Randeep Guleria
- Department of Pulmonary Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, 110029, India; Institute of Internal Medicine & Respiratory and Sleep Medicine, Medanta-The Medicity, Gurugram, Haryana, 122033, India.
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2
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Soni A, Dahiya B, Sheoran A, Kumar V, Guliani A, Kumar N, Hooda V, Yadav A, Nehra K, Mehta PK. Diagnosis of pleural tuberculosis by multi-targeted loop-mediated isothermal amplification assay based on SYBR Green I reaction: comparison with GeneXpert® MTB/RIF assay. Expert Rev Respir Med 2023; 17:1079-1089. [PMID: 38058175 DOI: 10.1080/17476348.2023.2292738] [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: 09/23/2023] [Accepted: 12/05/2023] [Indexed: 12/08/2023]
Abstract
BACKGROUND Diagnosis of pleural tuberculosis (TB) is tedious owing to its close resemblance with malignant pleural effusion and sparse bacterial load in clinical specimens. There is an immediate need to design a rapid and dependable diagnostic test to prevent unnecessary morbidity/mortality. RESEARCH DESIGN AND METHODS A multi-targeted loop-mediated isothermal amplification (MT-LAMP) was deliberated using mpt64 and IS6110 to diagnose pleural TB within pleural fluids/biopsies. MT-LAMP products were analyzed by gel-based and visual detection methods, viz. SYBR Green I, SYBR Green I+deoxyuridine triphosphate uracil-N-glycosylase (dUTP-UNG), and dry methyl green reactions. RESULTS In a pilot study, while assessing pleural TB/non-TB control subjects (n = 40), both SYBR Green I+dUTP-UNG/gel-based MT-LAMP assays exhibited better sensitivity/specificity than SYBR Green I and dry methyl green MT-LAMP. Since it is facile to work with SYBR Green I+dUTP-UNG than gel-based MT-LAMP, we validated the performance of SYBR Green I+dUTP-UNG in a higher number of specimens (n = 97), which revealed somewhat higher sensitivity (85.2 vs. 81.5%) and specificity (97.7 vs. 90.7%) than SYBR Green I MT-LAMP. Furthermore, the sensitivity attained by SYBR Green I+dUTP-UNG MT-LAMP was significantly higher (p < 0.001) than GeneXpert. CONCLUSIONS Our SYBR Green I+dUTP-UNG MT-LAMP is a simple and reliable method to diagnose pleural TB, which may translate into a point-of-care test.
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Affiliation(s)
- Aishwarya Soni
- Centre for Biotechnology, Maharshi Dayanand University (MDU), Rohtak, India
- Department of Biotechnology, Deenbandhu Chhotu Ram University of Science and Technology (DCRUST), Murthal, Sonipat, India
| | - Bhawna Dahiya
- Centre for Biotechnology, Maharshi Dayanand University (MDU), Rohtak, India
- Microbiology Department, Faculty of Allied Health Sciences, Shree Guru Gobind Singh Tricentenary (SGT) University, Gurugram, India
| | - Abhishek Sheoran
- Department of Statistics, Ramanujan College, University of Delhi, New Delhi, India
| | - Vipul Kumar
- Department of TB & Respiratory Medicine, University of Health Sciences (UHS), Rohtak, India
| | - Astha Guliani
- Department of TB & Respiratory Medicine, University of Health Sciences (UHS), Rohtak, India
| | - Nitin Kumar
- Centre for Medical Biotechnology, MDU, Rohtak, India
| | - Vikas Hooda
- Centre for Biotechnology, Maharshi Dayanand University (MDU), Rohtak, India
| | | | - Kiran Nehra
- Department of Biotechnology, Deenbandhu Chhotu Ram University of Science and Technology (DCRUST), Murthal, Sonipat, India
| | - Promod K Mehta
- Centre for Biotechnology, Maharshi Dayanand University (MDU), Rohtak, India
- Microbiology Department, Faculty of Allied Health Sciences, Shree Guru Gobind Singh Tricentenary (SGT) University, Gurugram, India
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3
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Kamra E, Singh N, Khan A, Singh J, Chauhan M, Kamal H, Mehta PK. Diagnosis of genitourinary tuberculosis by loop-mediated isothermal amplification based on SYBR Green I dye reaction. Biotechniques 2022; 73:47-57. [PMID: 35787144 DOI: 10.2144/btn-2022-0027] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
A multitargeted loop-mediated isothermal amplification (MT-LAMP) assay targeting mpt64 (Rv1980c) and IS6110 was designed to diagnose genitourinary tuberculosis (GUTB) cases. While assessing gel-based, hydroxynaphthol blue (HNB) and SYBR Green I MT-LAMP assays on GUTB specimens (n = 28) in a pilot study, both gel-based/SYBR Green I assays exhibited better sensitivity than HNB LAMP. Since SYBR Green MT-LAMP is easier to perform compared with a gel-based assay, a higher number of GUTB specimens (n = 55) were evaluated by SYBR Green MT-LAMP, wherein 85.5% sensitivity and 94.4% specificity (n = 36) were obtained. Moreover, the sensitivity attained by MT-LAMP was significantly higher (p < 0.05) than with multiplex-PCR (mpt64 + IS6110). After further validating these MT-LAMP data in different epidemiological settings, this assay may be developed as a diagnostic kit.
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Affiliation(s)
- Ekta Kamra
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, 124001, India
| | - Netrapal Singh
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, 124001, India
| | - Anish Khan
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, 124001, India
| | - Jaideep Singh
- Noor Medical Centre, Sector-6, Karnal, 132001, India
| | - Meenakshi Chauhan
- Department of Obstetrics & Gynaecology, Pt. B.D. Sharma University of Health Sciences (UHS), Rohtak, 124001, India
| | - Hemant Kamal
- Department Of Urology, UHS, Rohtak, 124001, India
| | - Promod K Mehta
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, 124001, India
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Zhang C, Zheng T, Wang H, Chen W, Huang X, Liang J, Qiu L, Han D, Tan W. Rapid One-Pot Detection of SARS-CoV-2 Based on a Lateral Flow Assay in Clinical Samples. Anal Chem 2021; 93:3325-3330. [PMID: 33570399 PMCID: PMC7885334 DOI: 10.1021/acs.analchem.0c05059] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/05/2021] [Indexed: 01/01/2023]
Abstract
Rapid tests for pathogen identification and spread assessment are critical for infectious disease control and prevention. The control of viral outbreaks requires a nucleic acid diagnostic test that is sensitive and simple and delivers fast and reliable results. Here, we report a one-pot direct reverse transcript loop-mediated isothermal amplification (RT-LAMP) assay of SARS-CoV-2 based on a lateral flow assay in clinical samples. The entire contiguous sample-to-answer workflow takes less than 40 min from a clinical swab sample to a diagnostic result without professional instruments and technicians. The assay achieved an accuracy of 100% in 12 synthetic and 12 clinical samples compared to the data from PCR-based assays. We anticipate that our method will provide a universal platform for rapid and point-of-care detection of emerging infectious diseases.
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Affiliation(s)
- Chao Zhang
- Institute
of Molecular Medicine (IMM), Shanghai Key Laboratory for Nucleic Acid
Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and
Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Tingting Zheng
- Institute
of Molecular Medicine (IMM), Shanghai Key Laboratory for Nucleic Acid
Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and
Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Hua Wang
- Department
of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Wei Chen
- Clinical
Laboratory, Central Hospital of Loudi, Loudi, Hunan 417099, China
| | - Xiaoye Huang
- Clinical
Laboratory, Central Hospital of Loudi, Loudi, Hunan 417099, China
| | - Jianqi Liang
- Clinical
Laboratory, Central Hospital of Loudi, Loudi, Hunan 417099, China
| | - Liping Qiu
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Bio- Sensing and Chemometrics, College of Chemistry and Chemical
Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Da Han
- Institute
of Molecular Medicine (IMM), Shanghai Key Laboratory for Nucleic Acid
Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and
Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Weihong Tan
- Institute
of Molecular Medicine (IMM), Shanghai Key Laboratory for Nucleic Acid
Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and
Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Bio- Sensing and Chemometrics, College of Chemistry and Chemical
Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Institute
of Cancer and Basic Medicine (ICBM), Chinese Academy of Sciences, The Cancer Hospital of the University of Chinese Academy
of Sciences, Hangzhou, Zhejiang 310018, China
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Wu X, Wang Y, Yin Q, Jiao W, Sun L, Qi H, Li J, Quan S, Xu B, Shen A. A diagnostic test that uses isothermal amplification and lateral flow detection sdaA can detect tuberculosis in 60 min. J Appl Microbiol 2020; 130:2102-2110. [PMID: 33070404 DOI: 10.1111/jam.14902] [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: 07/27/2020] [Revised: 09/29/2020] [Accepted: 10/13/2020] [Indexed: 11/28/2022]
Abstract
AIMS Tuberculosis (TB), caused by Mycobacterium tuberculosis (MTB), is now the leading cause of death from infectious disease, thus rapid diagnostic and screening techniques for TB are urgently needed. METHODS AND RESULTS Here, a detection of MTB using multiple cross displacement amplification coupling with nanoparticles-based lateral flow device (MCDA-LFD) was developed and validated, targeting the specific sdaA gene. The whole detection procedure, including rapid genomic DNA extraction (15 min), amplification (30 min) and result reporting (2 min), was completed within 50 min. No cross-reaction with non-mycobacteria and non-tuberculous mycobacteria (NTM) strains was observed. The sensitivity of sdaA-MCDA-LFD, Xpert MTB/RIF assay and culture results was 81·6, 48·3 and 37·9%, respectively, in TB patients. Among positive culture samples, the sensitivity of sdaA-MCDA-LFD and Xpert MTB/RIF assay was 93·9% (31/33) and 81·8% (27/33), respectively. Among culture-negative samples, the sensitivity of sdaA-MCDA-LFD and Xpert MTB/RIF assay was 74·1% (40/54) and 27·8% (15/54), respectively. The specificity of sdaA-MCDA-LFD and Xpert MTB/RIF was 95·4% (62/65) and 100% (65/65) in clinical samples from non-TB patients. CONCLUSION The sdaA-MCDA-LFD assay was a rapid, simple, specific and sensitive TB diagnostic test. SIGNIFICANCE AND IMPACT OF THE STUDY The sdaA-MCDA-LFD assay holds promise for application as a useful point-of-care test to detect MTB, and will play an important role in controlling and preventing TB.
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Affiliation(s)
- X Wu
- Department of Respiratory Diseases, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Y Wang
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Q Yin
- Department of Respiratory Diseases, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - W Jiao
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - L Sun
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - H Qi
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - J Li
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - S Quan
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - B Xu
- Department of Respiratory Diseases, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - A Shen
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
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Sreedeep K, Sethi S, Yadav R, Vaidya PC, Angurana SK, Saini A, Mehra N, Singh M. Loop-mediated isothermal amplification (LAMP) in the respiratory specimens for the diagnosis of pediatric pulmonary tuberculosis: A pilot study. J Infect Chemother 2020; 26:823-830. [DOI: 10.1016/j.jiac.2020.03.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 03/19/2020] [Accepted: 03/24/2020] [Indexed: 11/28/2022]
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7
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Lee JW, Nguyen VD, Seo TS. Paper-based Molecular Diagnostics for the Amplification and Detection of Pathogenic Bacteria from Human Whole Blood and Milk Without a Sample Preparation Step. BIOCHIP JOURNAL 2019. [DOI: 10.1007/s13206-019-3310-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Joon D, Nimesh M, Gupta S, Kumar C, Varma-Basil M, Saluja D. Development and evaluation of rapid and specific sdaA LAMP-LFD assay with Xpert MTB/RIF assay for diagnosis of tuberculosis. J Microbiol Methods 2019; 159:161-166. [PMID: 30858005 DOI: 10.1016/j.mimet.2019.03.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 03/04/2019] [Accepted: 03/06/2019] [Indexed: 11/19/2022]
Abstract
There is need for rapid and cost-effective diagnostic test for tuberculosis. The present study was carried out to design a Loop-mediated isothermal amplification (LAMP) assay combined with lateral flow dipstick (LFD) as a point-of-care method for diagnosis of TB. LAMP assay targeting sdaA gene combined with LFD for sequence specific detection was standardized in user friendly and rapid format. It does not require sophisticated instruments and shows visual results instantly. The LAMP-LFD assay was validated using culture confirmed specimens. The assay was evaluated in a cross-sectional study using respiratory specimens collected from patients in Delhi, India and it showed high concordance with GeneXpert MTB/RIF assay. Lateral flow dipstick method has provided an excellent detection format with LAMP method. The LAMP-LFD assay showed high diagnostic accuracy in comparison to other methods and can be used as a point-of-care test in cost-effective manner.
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Affiliation(s)
- Deepali Joon
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110 007, India; Shri Guru Tegh Bahadur Khalsa College, University of Delhi, Delhi 110 007, India
| | - Manoj Nimesh
- Shri Guru Tegh Bahadur Khalsa College, University of Delhi, Delhi 110 007, India
| | - Shraddha Gupta
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi 11007, India
| | - Chanchal Kumar
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi 11007, India
| | - Mandira Varma-Basil
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi 11007, India
| | - Daman Saluja
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110 007, India.
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Eddabra R, Ait Benhassou H. Rapid molecular assays for detection of tuberculosis. Pneumonia (Nathan) 2018; 10:4. [PMID: 29876241 PMCID: PMC5968606 DOI: 10.1186/s41479-018-0049-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 05/14/2018] [Indexed: 01/01/2023] Open
Abstract
Tuberculosis (TB) is an infectious disease that remains an important public health problem at the global level. It is one of the main causes of morbidity and mortality, due to the emergence of antibiotic resistant Mycobacterium strains and HIV co-infection. Over the past decade, important progress has been made for better control of the disease. While microscopy and culture continue to be indispensible for laboratory diagnosis of tuberculosis, the range of several molecular diagnostic tests, including the nucleic acid amplification test (NAAT) and whole-genome sequencing (WGS), have expanded tremendously. They are becoming more accessible not only for detection and identification of Mycobacterium tuberculosis complex in clinical specimens, but now extend to diagnosing multi-drug resistant strains. Molecular diagnostic tests provide timely results useful for high-quality patient care, low contamination risk, and ease of performance and speed. This review focuses on the current diagnostic tests in use, including emerging technologies used for detection of tuberculosis in clinical specimens. The sensitivity and specificity of these tests have also been taken into consideration.
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Affiliation(s)
- Rkia Eddabra
- Higher Institute of Nursing Professions and Health Techniques, Avenue Colonnel Major Habbouha Oueld Laâbid. Madinat Al Wahda I, Laayoune, Morocco
| | - Hassan Ait Benhassou
- Medical Biotechnology Center, Moroccan Foundation for Advanced Science, Innovation and Research (MAScIR), Rabat Design Center, Avenue Mohamed El Jazouli - Madinat Al Irfane, 10100 Rabat, Morocco
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Wang Y, Liu D, Deng J, Wang Y, Xu J, Ye C. Loop-mediated isothermal amplification using self-avoiding molecular recognition systems and antarctic thermal sensitive uracil-DNA-glycosylase for detection of nucleic acid with prevention of carryover contamination. Anal Chim Acta 2017; 996:74-87. [PMID: 29137710 DOI: 10.1016/j.aca.2017.10.022] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Revised: 10/11/2017] [Accepted: 10/21/2017] [Indexed: 02/05/2023]
Abstract
Loop-mediated isothermal amplification (LAMP) is the most popular technique to amplify nucleic acid sequence without the use of temperature cycling. However, LAMP is often confounded by false-positive results, arising from interactions between (hetero-dimer) or within (self-dimerization) primers, off-target hybrids and carryover contaminants. Here, we devised a new LAMP technique that is self-avoiding molecular recognition system (SAMRS) components and antarctic thermal sensitive uracil-DNA-glycosylase (AUDG) enzyme-assisted, termed AUDG-SAMRS-LAMP. Incorporating SAMRS components into 3'-ends of LAMP primers can improve assay's specificity, which completely prevents the non-specific amplification yielding from off-target hybrids and undesired interactions between or within primers. Adding AUDG into reaction mixtures can effectively eliminate the false-positive results arising from carryover contamination, thus the genuine positive reactions are generated from the amplification of target templates. Furthermore, AUDG-SAMRS-LAMP results are confirmed using a new analysis strategy, which is developed for detecting LAMP amplicons by lateral flow biosensor (LFB). Only a single labeled primer is required in the analysis system, thus the false positive results arising from hybridization (the labeled primer and probe, or between two labeled primers) are avoided. Hence, the SAMRS components, AUDG and LFB convert traditional LAMP from a technique suited for the research laboratory into one that has practical value in the field of diagnosis. Human Tuberculosis (TB) is caused by infection with members of Mycobacterium tuberculosis complex (MTC), which are detected by the AUDG-SAMRS-LAMP technique to demonstrate the availability of target analysis. The proof-of-concept method can be reconfigured to detect various nucleic acids by redesigning the specific primers.
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Affiliation(s)
- Yi Wang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Dongxin Liu
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Jianping Deng
- Zigong Center for Disease Control and Prevention, Zigong 643000, Sichuan Province, PR China
| | - Yan Wang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Changyun Ye
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China.
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11
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Kanitkar YH, Stedtfeld RD, Hatzinger PB, Hashsham SA, Cupples AM. Most probable number with visual based LAMP for the quantification of reductive dehalogenase genes in groundwater samples. J Microbiol Methods 2017; 143:44-49. [PMID: 29031631 DOI: 10.1016/j.mimet.2017.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 10/11/2017] [Accepted: 10/11/2017] [Indexed: 01/26/2023]
Abstract
The remediation of chlorinated solvent contaminated sites frequently involves bioaugmentation with mixed cultures containing Dehalococcoides mccartyi. Their activity is then examined by quantifying reductive dehalogenase (RDase) genes. Recently, we described a rapid, low cost approach, based on loop mediated isothermal amplification (LAMP), which allowed for the visual detection of RDase genes from groundwater. In that study, samples were concentrated (without DNA extraction), incubated in a water bath (avoiding the use of a thermal cycler) and amplification was visualized by the addition of SYBR green (post incubation). Despite having a detection limit less than the threshold recommended for effective remediation, the application of the assay was limited because of the semi-quantitative nature of the data. Moreover, the assay was prone to false positives due to the aerosolization of amplicons. In this study, deoxyuridine triphosphate (dUTP) and uracil DNA glycosylase (UNG) were incorporated into the assay to reduce the probability of false positives. Optimization experiments revealed a UNG concentration of 0.2units per reaction was adequate for degrading trace levels of AUGC based contamination (~1.4×104 gene copies/reaction) without significant changes to the detection limit (~100 gene copies/reaction). Additionally, the optimized assay was used with the most probable number (MPN) method to quantify RDase genes (vcrA and tceA) in multiple groundwater samples from a chlorinated solvent contaminated site. Using this approach, gene concentrations were significantly correlated to concentrations obtained using traditional methods (qPCR and DNA templates). Although the assay underestimated RDase genes concentrations, a strong correlation (R2=0.78 and 0.94) was observed between the two data sets. The regression equations obtained will be valuable to determine gene copies in groundwater using the newly developed, low cost and time saving method.
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Affiliation(s)
- Yogendra H Kanitkar
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA
| | - Robert D Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA
| | - Paul B Hatzinger
- APTIM Federal Services, 17 Princess Road, Lawrenceville, NJ 08648, USA
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA; Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
| | - Alison M Cupples
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA.
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Joon D, Nimesh M, Varma-Basil M, Saluja D. Evaluation of improved IS 6110 LAMP assay for diagnosis of pulmonary and extra pulmonary tuberculosis. J Microbiol Methods 2017; 139:87-91. [DOI: 10.1016/j.mimet.2017.05.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/11/2017] [Accepted: 05/12/2017] [Indexed: 11/16/2022]
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Diagnostic test accuracy of loop-mediated isothermal amplification assay for Mycobacterium tuberculosis: systematic review and meta-analysis. Sci Rep 2016; 6:39090. [PMID: 27958360 PMCID: PMC5153623 DOI: 10.1038/srep39090] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 11/17/2016] [Indexed: 11/08/2022] Open
Abstract
Diagnostic test accuracy of the loop-mediated isothermal amplification (LAMP) assay for culture proven tuberculosis is unclear. We searched electronic databases for both cohort and case-control studies that provided data to calculate sensitivity and specificity. The index test was any LAMP assay including both commercialized kits and in-house assays. Culture-proven M. tuberculosis was considered a positive reference test. We included 26 studies on 9330 sputum samples and one study on 315 extra-pulmonary specimens. For sputum samples, 26 studies yielded the summary estimates of sensitivity of 89.6% (95% CI 85.6–92.6%), specificity of 94.0% (95% CI 91.0–96.1%), and a diagnostic odds ratio of 145 (95% CI 93–226). Nine studies focusing on Loopamp MTBC yielded the summary estimates of sensitivity of 80.9% (95% CI 76.0–85.1%) and specificity of 96.5% (95% CI 94.7–97.7%). Loopamp MTBC had higher sensitivity and lower specificity for smear-positive sputa compared to smear-negative sputa. In-house assays showed higher sensitivity and lower specificity compared to Loopamp MTBC. LAMP promises to be a useful test for the diagnosis of TB, however there is still need to improve the assay to make it simpler, cheaper and more efficient to make it competitive against other PCR methods already available.
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Nliwasa M, MacPherson P, Chisala P, Kamdolozi M, Khundi M, Kaswaswa K, Mwapasa M, Msefula C, Sohn H, Flach C, Corbett EL. The Sensitivity and Specificity of Loop-Mediated Isothermal Amplification (LAMP) Assay for Tuberculosis Diagnosis in Adults with Chronic Cough in Malawi. PLoS One 2016; 11:e0155101. [PMID: 27171380 PMCID: PMC4865214 DOI: 10.1371/journal.pone.0155101] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 04/25/2016] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Current tuberculosis diagnostics lack sensitivity, and are expensive. Highly accurate, rapid and cheaper diagnostic tests are required for point of care use in low resource settings with high HIV prevalence. OBJECTIVE To investigate the sensitivity and specificity, and cost of loop-mediated isothermal amplification (LAMP) assay for tuberculosis diagnosis in adults with chronic cough compared to Xpert® MTB/RIF, fluorescence smear microscopy. METHODS Between October 2013 and March 2014, consecutive adults at a primary care clinic were screened for cough, offered HIV testing and assessed for tuberculosis using LAMP, Xpert® MTB/RIF and fluorescence smear microscopy. Sensitivity and specificity (with culture as reference standard), and costs were estimated. RESULTS Of 273 adults recruited, 44.3% (121/273) were HIV-positive and 19.4% (53/273) had bacteriogically confirmed tuberculosis. The sensitivity of LAMP compared to culture was 65.0% (95% CI: 48.3% to 79.4%) with 100% (95% CI: 98.0% to 100%) specificity. The sensitivity of Xpert® MTB/RIF (77.5%, 95% CI: 61.5% to 89.2%) was similar to that of LAMP, p = 0.132. The sensitivity of concentrated fluorescence smear microscopy with routine double reading (87.5%, 95% CI: 73.2% to 95.8%) was higher than that of LAMP, p = 0.020. All three tests had high specificity. The lowest cost per test of LAMP was at batch size of 14 samples (US$ 9.98); this was lower than Xpert® MTB/RIF (US$ 13.38) but higher than fluorescence smear microscopy (US$ 0.65). CONCLUSION The sensitivity of LAMP was similar to Xpert® MTB/RIF but lower than fluorescence smear microscopy; all three tests had high specificity. These findings support the Malawi policy that recommends a combination of fluorescence smear microscopy and Xpert® MTB/RIF prioritised for people living with HIV, already found to be smear-negative, or being considered for retreatment of tuberculosis.
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Affiliation(s)
- Marriott Nliwasa
- Helse Nord Tuberculosis Initiative, Department of Microbiology, College of Medicine, Blantyre, Malawi
- Malawi-Liverpool-Welcome Trust Clinical Research Programme, Blantyre, Malawi
- Clinical Research Department, London School of Hygiene & Tropical Medicine (LSHTM), London, United Kingdom
| | - Peter MacPherson
- Department of Public Health and Policy, University of Liverpool, Liverpool, United Kingdom
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Palesa Chisala
- Department of Surgery, College of Medicine, Blantyre, Malawi
| | - Mercy Kamdolozi
- Helse Nord Tuberculosis Initiative, Department of Microbiology, College of Medicine, Blantyre, Malawi
- Malawi-Liverpool-Welcome Trust Clinical Research Programme, Blantyre, Malawi
| | - McEwen Khundi
- Malawi-Liverpool-Welcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Kruger Kaswaswa
- Helse Nord Tuberculosis Initiative, Department of Microbiology, College of Medicine, Blantyre, Malawi
| | - Mphatso Mwapasa
- Helse Nord Tuberculosis Initiative, Department of Microbiology, College of Medicine, Blantyre, Malawi
| | - Chisomo Msefula
- Helse Nord Tuberculosis Initiative, Department of Microbiology, College of Medicine, Blantyre, Malawi
| | - Hojoon Sohn
- Department of Epidemiology, Biostatistics & Occupational Health, McGill University, Montreal, Canada
| | - Clare Flach
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine (LSHTM), London, United Kingdom
| | - Elizabeth L. Corbett
- Helse Nord Tuberculosis Initiative, Department of Microbiology, College of Medicine, Blantyre, Malawi
- Malawi-Liverpool-Welcome Trust Clinical Research Programme, Blantyre, Malawi
- Clinical Research Department, London School of Hygiene & Tropical Medicine (LSHTM), London, United Kingdom
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Livingstone DM, Rohatensky M, Mintchev P, Nakoneshny SC, Demetrick DJ, van Marle G, Dort JC. Loop mediated isothermal amplification (LAMP) for the detection and subtyping of human papillomaviruses (HPV) in oropharyngeal squamous cell carcinoma (OPSCC). J Clin Virol 2016; 75:37-41. [PMID: 26780110 DOI: 10.1016/j.jcv.2016.01.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 12/08/2015] [Accepted: 01/05/2016] [Indexed: 01/12/2023]
Abstract
BACKGROUND Human papillomavirus (HPV)-related oropharyngeal squamous cell carcinoma (OPSCC) is a growing problem that presents a significant challenge to Otolaryngologist-Head and Neck Surgeons. Knowledge of HPV status yields critical prognostic information, with potential for treatment selection based on tumour HPV status. The current gold standard of diagnosis, PCR, is expensive, demanding and time consuming. Alternatives such as p16 immunohistochemistry are subjective and potentially inaccurate. Loop-mediated isothermal amplification (LAMP) is a rapid, robust and inexpensive molecular diagnostic technique. OBJECTIVES Our aim was to verify LAMP as a potential bedside diagnostic assay for subtyping of HPV in OPSCC. STUDY DESIGN DNA from 72 formalin-fixed paraffin embedded (FFPE) OPSCC patient samples was tested. PCR and LAMP were then performed to specifically identify HPV 16, 18, 31, 33 and 35. RESULTS AND CONCLUSIONS For these high-risk subtypes, LAMP had an overall sensitivity of 99.4% and specificity of 93.2% relative to PCR. LAMP is a promising technology that can accurately diagnose high-risk HPV infection.
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Affiliation(s)
- D M Livingstone
- Section of Otolaryngology-Head and Neck Surgery, Department of Surgery, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.
| | - M Rohatensky
- Undergraduate Medical Education, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - P Mintchev
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - S C Nakoneshny
- Ohlson Research Initiative, Southern Alberta Cancer Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - D J Demetrick
- Department of Pathology and Laboratory Medicine, Cumming School of Medicine, University of Calgary and Calgary Laboratory Services, Calgary, Alberta, Canada
| | - G van Marle
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - J C Dort
- Section of Otolaryngology-Head and Neck Surgery, Department of Surgery, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Ohlson Research Initiative, Southern Alberta Cancer Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
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