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Sun C, Wang C, Xiao F, Jia N, Huang X, Fu J, Zhang Y, Zhou J, Wang G, Wang Y. Development and clinical evaluation of a real-time multiple cross displacement amplification assay for rapid and sensitive detection of Mycobacterium tuberculosis. Heliyon 2024; 10:e31901. [PMID: 38845879 PMCID: PMC11154602 DOI: 10.1016/j.heliyon.2024.e31901] [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] [Received: 01/02/2024] [Revised: 05/16/2024] [Accepted: 05/23/2024] [Indexed: 06/09/2024] Open
Abstract
Molecular techniques of nucleic acid testing recommended by the World Health Organization (WHO) for the Mycobacterium tuberculosis (MTB) detection were considered to have the potential access to the accurate tuberculosis (TB) notifications. In this study, a new method, which coupled real-time (rt) fluorescence technique with multiple cross displacement amplification (MCDA), was developed for the rapid, sensitive and specific detection of MTB (termed MTB-rt-MCDA). According to the principle of the rt-MCDA test, a set of ten primers were designed for the MCDA reaction, of which one was engineered with a restrictive endonuclease recognition site, a fluorophore and a quencher for achieving the real-time fluorescence detection. MTB-rt-MCDA test was conducted under the optimized conditions (67 °C, 40 min) on the real-time fluorescence platform. The MTB-rt-MCDA assay accurately identified the MTB strains with no cross reaction with other bacteria. The lowest detectable genomic DNA concentration of the MTB-rt-MCDA assay was 25 fg/μl. We employed the genomic DNA templates extracted from sputum of clinical cases for validating the practical applicability of this assay, and the detection power of the MTB-rt-MCDA assay was comparable to that of the Xpert method and MCDA-based biosensor detection and superior to smear microscope method. The complete process of the MTB-rt-MCDA assay, including rapid extraction of DNA and rt-MCDA test, takes less than 1 h. In conclusion, the presented MTB-rt-MCDA assay provided an effective and simple option for the rapid screening of MTB infection.
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Affiliation(s)
- Chunrong Sun
- Experiment Research Center, Capital Institute of Pediatrics, Beijing, 100020, PR China
| | - Chaohong Wang
- Department of Clinical Laboratory, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, 101125, PR China
| | - Fei Xiao
- Experiment Research Center, Capital Institute of Pediatrics, Beijing, 100020, PR China
| | - Nan Jia
- Experiment Research Center, Capital Institute of Pediatrics, Beijing, 100020, PR China
| | - Xiaolan Huang
- Experiment Research Center, Capital Institute of Pediatrics, Beijing, 100020, PR China
| | - Jin Fu
- Experiment Research Center, Capital Institute of Pediatrics, Beijing, 100020, PR China
| | - Yu Zhang
- Experiment Research Center, Capital Institute of Pediatrics, Beijing, 100020, PR China
| | - Juan Zhou
- Experiment Research Center, Capital Institute of Pediatrics, Beijing, 100020, PR China
| | - Guirong Wang
- Department of Clinical Laboratory, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, 101125, PR China
| | - Yi Wang
- Experiment Research Center, Capital Institute of Pediatrics, Beijing, 100020, PR China
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Yadav B, Sharma M, Singla N, Shree R, Goyal M, Modi T, Sharma A, Sharma A, Sharma N, Ray P, Modi M, Sharma K. Molecular diagnosis of Tuberculous meningitis: sdaA-based multi-targeted LAMP and GeneXpert Ultra. Tuberculosis (Edinb) 2023; 140:102339. [PMID: 37011559 DOI: 10.1016/j.tube.2023.102339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 03/05/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023]
Abstract
SETTING Nucleic acid amplification techniques like GeneXpert and GeneXpert Ultra (Xpert Ultra), the first-line tests for diagnosing Tuberculous meningitis (TBM), are expensive and depend on sophisticated equipment. OBJECTIVE The diagnostic potential of multitargeted loop-mediated isothermal assay (MLAMP), a low-cost simple test using novel gene combination, was evaluated for TBM. DESIGN 300 CSF specimen (200 TBM patients, 100 controls) processed between January 2017 and December 2021 were subjected to MLAMP (using sdaA, IS1081 and IS6110 gene targets), sdaA PCR and Xpert Ultra. The performance was evaluated against uniform case definition as per Marais criteria, and against culture. RESULTS Uniform case definition classified 50 as definite TBM and 150 as probable or definite TBM. Against this uniform case definition, the sensitivity and specificity of MLAMP was 88% and 100%, respectively. The sensitivity was 96% against culture-positive cases and 85.3% against culture-negative cases. The sensitivity of sdaA-LAMP, IS1081-LAMP, IS6110-LAMP, Xpert Ultra and sdaA-PCR was 82.5%, 80.5%, 85.3%, 67% and 71%, respectively against uniform case definition. sdaA-LAMP detected additional two cases and IS1081-LAMP detected nine. 11 of 134 (8.2%) cases were reported rifampicin resistant by Xpert Ultra. CONCLUSION MLAMP, incorporating sdaA and IS1081, is a cheap, easy and accurate first-line diagnostic test for TBM.
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Detection of Mycobacterium tuberculosis Complex in Sputum Samples Using Droplet Digital PCR Targeting mpt64. Pathogens 2023; 12:pathogens12020345. [PMID: 36839617 PMCID: PMC9966028 DOI: 10.3390/pathogens12020345] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
Tuberculosis (TB) is one of the top 10 causes of death worldwide. It is challenging to find methods of diagnosis of active pulmonary TB that are sensitive enough to detect cases for proper treatment before unintentional transmission. Droplet digital PCR (ddPCR) is a highly sensitive method to detect genetic material of pathogens, but it has rarely been used for diagnosis of TB. This study compared the sensitivity of ddPCR with that of GeneXpert and AFB smear microscopy in 180 leftover sputum samples from patients suspected of having TB on the basis of clinical symptoms and radiography. Absolute quantification of copy numbers of MTB-specific genes was possible using ddPCR targeting the mpt64 gene. Among the 180 samples, 41.1% were diagnosed as having TB using ddPCR. The sensitivities of AFB smear microscopy, GeneXpert and ddPCR were 41.9%, 82.4% and 100%, respectively. AFB smear microscopy and GeneXpert both had a specificity of 100%, and the specificity of ddPCR was 95.3%. The accuracy of ddPCR (97.2%) is higher than that of GeneXpert (92.7%). This robust ddPCR system could potentially be used as a method for early diagnosis of TB.
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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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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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Kakhki RK, Neshani A, Sankian M, Ghazvini K, Hooshyar A, Sayadi M. The short-chain dehydrogenases/reductases (SDR) gene: A new specific target for rapid detection of Mycobacterium tuberculosis complex by modified comparative genomic analysis. INFECTION GENETICS AND EVOLUTION 2019; 70:158-164. [DOI: 10.1016/j.meegid.2019.01.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 01/07/2019] [Accepted: 01/11/2019] [Indexed: 01/23/2023]
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Neshani A, Kamali Kakhki R, Sankian M, Zare H, Hooshyar Chichaklu A, Sayyadi M, Ghazvini K. Modified genome comparison method: a new approach for identification of specific targets in molecular diagnostic tests using Mycobacterium tuberculosis complex as an example. BMC Infect Dis 2018; 18:517. [PMID: 30314460 PMCID: PMC6186143 DOI: 10.1186/s12879-018-3417-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 09/26/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The first step of designing any genome-based molecular diagnostic test is to find a specific target sequence. The modified genome comparison method is one of the easiest and most comprehensive ways to achieve this goal. In this study, we aimed to explain this method with the example of Mycobacterium tuberculosis complex and investigate its efficacy in a diagnostic test. METHODS A specific target was identified using modified genome comparison method and an in-house PCR test was designed. To determine the analytical sensitivity and specificity, 10 standard specimens were used. Also, 230 specimens were used to determine the clinical sensitivity and specificity. RESULTS The identity and query cover of our new diagnostic target (5KST) were ≥ 90% with M. tuberculosis complex. The 5KST-PCR sensitivity was 100% for smear-positive, culture-positive and 85.7% for smear-negative, culture-positive specimens. All of 100 smear-negative, culture-negative specimens were negative in 5KST-PCR (100% clinical specificity). Analytical sensitivity of 5KST-PCR was approximately 1 copy of genomic DNA per microliter. CONCLUSIONS Modified genome comparison method is a confident way to find specific targets for use in diagnostic tests. Accordingly, the 5KST-PCR designed in this study has high sensitivity and specificity and can be replaced for conventional TB PCR tests.
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Affiliation(s)
- Alireza Neshani
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Reza Kamali Kakhki
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mojtaba Sankian
- Immunology Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hosna Zare
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amin Hooshyar Chichaklu
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahsa Sayyadi
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Kiarash Ghazvini
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Microbiology and Virology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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Shrivastava K, Garima K, Narang A, Bhattacharyya K, Vishnoi E, Singh RK, Chaudhry A, Prasad R, Bose M, Varma-Basil M. Rv1458c: a new diagnostic marker for identification of Mycobacterium tuberculosis complex in a novel duplex PCR assay. J Med Microbiol 2017; 66:371-376. [PMID: 28126044 DOI: 10.1099/jmm.0.000440] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Kamal Shrivastava
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Kushal Garima
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Anshika Narang
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Kausik Bhattacharyya
- Dr B R Ambedkar Centre for Biomedical Research (ACBR), University of Delhi, Delhi, India
| | - Ekta Vishnoi
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Roshan Kumar Singh
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Anil Chaudhry
- Department of Pulmonary Medicine, Rajan Babu Institute of Pulmonary Medicine and Tuberculosis, Delhi, India
| | - Rajendra Prasad
- Department of Pulmonary Medicine, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Mridula Bose
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Mandira Varma-Basil
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
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Gallo JF, Pinhata JMW, Chimara E, Gonçalves MG, Fukasawa LO, Oliveira RSD. Performance of an in-house real-time polymerase chain reaction for identification of Mycobacterium tuberculosis isolates in laboratory routine diagnosis from a high burden setting. Mem Inst Oswaldo Cruz 2016; 111:545-50. [PMID: 27598243 PMCID: PMC5027861 DOI: 10.1590/0074-02760160048] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 06/30/2016] [Indexed: 01/15/2023] Open
Abstract
Brazil is one of the high burden countries for tuberculosis, and a rapid diagnosis is essential for effective control of the disease. In the present study, an in-house real-time polymerase chain reaction (PCR) assay targeting the mpt64 gene for identification of Mycobacterium tuberculosis complex isolates was evaluated under routine diagnosis conditions in a reference laboratory. From May 2011 to July 2012, 1,520 isolates of mycobacteria were prospectively submitted for phenotypic and/or PRA-hsp65 identification and to real-time PCR. The mpt64 real-time PCR showed 99.7% sensitivity and 96% specificity and detected 79.4% of the cases missed by phenotypic and PRA-hsp65 identification. The in-house real-time PCR assay showed high sensitivity and specificity and was successfully implemented in the routine diagnosis of tuberculosis in a reference laboratory from a high burden setting.
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Affiliation(s)
- Juliana Failde Gallo
- Instituto Adolfo Lutz, Centro de Bacteriologia, Núcleo de Tuberculose e Micobacterioses, São Paulo, SP, Brasil
| | | | - Erica Chimara
- Instituto Adolfo Lutz, Centro de Bacteriologia, Núcleo de Tuberculose e Micobacterioses, São Paulo, SP, Brasil
| | - Maria Gisele Gonçalves
- Instituto Adolfo Lutz, Centro de Imunologia, Laboratório de Diagnóstico Molecular de Infecções Bacterianas, São Paulo, SP, Brasil
| | - Lucila Okuyama Fukasawa
- Instituto Adolfo Lutz, Centro de Imunologia, Laboratório de Diagnóstico Molecular de Infecções Bacterianas, São Paulo, SP, Brasil
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Rapid detection of Mycobacterium tuberculosis complex by real-time PCR in sputum samples and its use in the routine diagnosis in a reference laboratory. J Med Microbiol 2015; 64:1040-1045. [DOI: 10.1099/jmm.0.000121] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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11
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Development and clinical evaluation of sdaA loop-mediated isothermal amplification assay for detection of Mycobacterium tuberculosis with an approach to prevent carryover contamination. J Clin Microbiol 2014; 52:2662-4. [PMID: 24789191 DOI: 10.1128/jcm.00907-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A rapid and sensitive loop-mediated isothermal amplification assay for the sdaA gene of Mycobacterium tuberculosis was developed using a dUTP-uracil-N-glycosylase (dUTP-UNG) strategy to prevent carryover contamination. Evaluation of the assay using clinical specimens (n = 648) showed high specificity (97.2%) and sensitivity (100%), demonstrating its potential as a diagnostic test for tuberculosis, especially in resource-limited settings.
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