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Botella JR. Point-of-Care DNA Amplification for Disease Diagnosis and Management. ANNUAL REVIEW OF PHYTOPATHOLOGY 2022; 60:1-20. [PMID: 36027938 DOI: 10.1146/annurev-phyto-021621-115027] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Early detection of pests and pathogens is of paramount importance in reducing agricultural losses. One approach to early detection is point-of-care (POC) diagnostics, which can provide early warning and therefore allow fast deployment of preventive measures to slow down the establishment of crop diseases. Among the available diagnostic technologies, nucleic acid amplification-based diagnostics provide the highest sensitivity and specificity, and those technologies that forego the requirement for thermocycling show the most potential for use at POC. In this review, I discuss the progress, advantages, and disadvantages of the established and most promising POC amplification technologies. The success and usefulness of POC amplification are ultimately dependent on the availability of POC-friendly nucleic acid extraction methods and amplification readouts, which are also briefly discussed in the review.
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Affiliation(s)
- José R Botella
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, University of Queensland, Brisbane, Australia;
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2
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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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3
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Pragmatic accuracy of an in-house loop-mediated isothermal amplification (LAMP) for diagnosis of pulmonary tuberculosis in a Thai community hospital. PLoS One 2020; 15:e0236496. [PMID: 32702008 PMCID: PMC7377475 DOI: 10.1371/journal.pone.0236496] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 07/07/2020] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND To improve the quality of diagnosing pulmonary tuberculosis (TB), WHO recommends the use of rapid molecular testing as an alternative to conventional microscopic methods. Loop-mediated isothermal amplification assay (LAMP test) is a practical and cost-effective nucleic amplification technique. We evaluated the pragmatic accuracy of an in-house LAMP assay for the diagnosis of TB in a remote health care setting where an advanced rapid molecular test is not available. METHODS A prospective diagnostic accuracy study was conducted. Patients with clinical symptoms suggestive of TB were consecutively enrolled from April to August 2016. Sputum samples were collected from each patient and were sent for microscopic examination (both acid-fast stain and fluorescence stain), in-house LAMP test, and TB culture. RESULTS One hundred and seven patients with TB symptoms were used in the final analysis. This included 50 (46.7%) culture-positive TB patients and 57 (53.3%) culture-negative patients. The overall sensitivity of the in-house LAMP based on culture positivity was 88.8% (95/107) with a 95%CI of 81.2-94.1. The sensitivity was 90.9% (40/44) with a 95%CI of 78.3-97.5 for smear-positive, culture-positive patients, and was 16.7% (1/6) with a 95%CI of 0.4-64.1 for smear-negative, culture-positive patients. The overall sensitivity of the in-house LAMP test compared to smear microscopy methods were not significantly different (p = 0.375). The specificity of the in-house LAMP based on non-TB patients (smear-negative, culture-negative) was 94.7% (54/57) with a 95%CI of 85.4-98.9. CONCLUSIONS The diagnostic accuracy of the in-house LAMP test in a community hospital was comparable to other previous reports in terms of specificity. The sensitivity of the in-house assay could be improved with better sputum processing and DNA extraction method.
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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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5
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Kumari S, Kumar RR, Mendiratta SK, Kumar D, Rana P, Kumar D, Jawla J. Species-specific loop-mediated isothermal amplification (LAMP) assay for identification of tissue of cattle origin by targeting mitochondrial gene sequences. 3 Biotech 2019; 9:69. [PMID: 30729093 PMCID: PMC6363609 DOI: 10.1007/s13205-019-1595-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 01/24/2019] [Indexed: 01/15/2023] Open
Abstract
The present study was carried out with the objective of development of species-specific loop-mediated isothermal amplification (LAMP) assay for identification of tissue of cattle origin. The cattle-specific LAMP primer set was designed by targeting mitochondrial D-loop gene. The conditions for LAMP reaction for amplification of template DNA from cattle using designed cattle-specific primer set were optimized for the components of mixture and temperature of reaction. Amplified products were analysed using SYBR Green I dye and by agarose gel electrophoresis. The developed species-specific LAMP assay was evaluated for its specificity, sensitivity and validated in laboratory on samples from known, coded, binary meat admixture with other than cattle at relative percentage of 20%, 10%, 5% and 1%, Phire tissue direct PCR master mix treated tissues of cattle and on species-specific polymerase chain reaction assay positive samples. The developed LAMP assay using self-designed primer set was highly specific, amplifying the DNA template exclusively from cattle tissue under the optimized LAMP reaction conditions. The sensitivity assay using serially diluted DNA templates revealed lowest level of detection as 0.01 ng of absolute DNA from target species. Laboratory validation substantiated the accuracy of assay in known/unknown (coded) samples and up to the 1% level of admixture in binary meat sample. DNA present in supernatant of Phire Animal tissue kit treated samples were also amplified successfully eliminating the extra step of extraction of genomic DNA. The developed assays exhibited comparable results with previously established species-specific PCR assay taken as gold standards. Thus, it was concluded that developed species-specific loop-mediated isothermal amplification assay was effective in identification of tissue of cattle origin.
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Affiliation(s)
- Sarita Kumari
- Department of Livestock Products Technology, PGIVER, RAJUVAS, Jaipur, India
| | - Rajiv Ranjan Kumar
- Division of Livestock Products Technology, Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122 India
| | - Sanjod Kumar Mendiratta
- Division of Livestock Products Technology, Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122 India
| | - Deepak Kumar
- Division of Veterinary Biotechnology, IVRI, Izatnagar, India
| | - Preeti Rana
- Department of Livestock Products Technology, CVASc, DUVASU, Mathura, India
| | - Dhananjay Kumar
- Division of Livestock Products Technology, Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122 India
| | - Jyoti Jawla
- Division of Livestock Products Technology, Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122 India
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Ramya M, Kayalvizhi M, Haripriya G, Rathinasabapathi P. Detection of microcystin-producing cyanobacteria in water samples using loop-mediated isothermal amplification targeting mcyB gene. 3 Biotech 2018; 8:378. [PMID: 30148028 DOI: 10.1007/s13205-018-1402-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 08/10/2018] [Indexed: 12/30/2022] Open
Abstract
Microcystin toxin-producing cyanobacteria are known to have harmful effects on humans and animals. We have developed a loop-mediated isothermal amplification (LAMP)-based detection method by targeting the microcystin synthetase B gene (mcyB), the gene responsible for the production of microcystin. The sensitivity of the method was found to be 1 fg per reaction, and it was 1000-fold higher than the conventional PCR. The LAMP method was able to amplify the target gene with a minimum amount of dNTP (0.4 mM), which further reduces the cost of reaction. The improved LAMP assay could detect the presence of the toxin-producing cyanobacteria in water samples within 2 h of time, which demonstrates the rapidness of the method. Freshwater samples were screened using the developed LAMP, and seven water samples collected from lakes and a bird sanctuary tested positive for mcyB gene harboring cyanobacteria, and negative in all other drinking waters. Hence, the developed LAMP could be a possible alternative to the existing molecular methods for screening for microcystin in environmental samples with greater sensitivity.
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Kim CK, Cho EA, Shin DM, Choi SW, Shin SY. Comparative Evaluation of the Loop-Mediated Isothermal Amplification Assay for Detecting Pulmonary Tuberculosis. Ann Lab Med 2018; 38:119-124. [PMID: 29214755 PMCID: PMC5736670 DOI: 10.3343/alm.2018.38.2.119] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 07/07/2017] [Accepted: 10/10/2017] [Indexed: 11/19/2022] Open
Abstract
Background Early detection of tuberculosis (TB) is challenging in resource-poor settings because of limited accessibility to molecular diagnostics. The aim of this study was to evaluate the performance of the loop-mediated isothermal amplification kit (TB-LAMP) for TB diagnosis compared with conventional and molecular tests. Methods A total of 290 consecutive sputum samples were collected from May till September, 2015. All samples were processed using the N-Acetyl-L-cysteine (NALC) NaOH method and tested by smear microscopy, solid and liquid culture, real-time PCR, and TB-LAMP. Results The sensitivity of TB-LAMP for smear-positive and smear-negative samples with culture positivity was 92.0% and 58.8%, respectively. TB-LAMP was positive in 14.9% of TB culture-negative samples; however, all those samples were also positive by real-time PCR. In addition, none of the samples positive for nontuberculous mycobacteria by culture were positive by TB-LAMP. The overall agreement between TB-LAMP and real-time PCR was good; however, the concordance rate was significantly lower for real-time PCR positive samples with Ct values of 30–35. Conclusions TB-LAMP could replace smear microscopy and increase TB diagnostic capacity when Xpert MTB/RIF is not feasible because of poor infrastructure.
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Affiliation(s)
- Chang Ki Kim
- Department of Laboratory Medicine, Hanyang University Guri Hospital, Guri, Korea.
| | - Eun A Cho
- Korean Institute of Tuberculosis, Cheongju, Korea
| | - Dong Mi Shin
- Korean Institute of Tuberculosis, Cheongju, Korea
| | | | - So Youn Shin
- Korean Institute of Tuberculosis, Cheongju, Korea
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Smear Microscopy for Diagnosis of Pulmonary Tuberculosis in Eastern Sudan. Tuberc Res Treat 2018; 2018:8038137. [PMID: 30013800 PMCID: PMC6022320 DOI: 10.1155/2018/8038137] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/19/2018] [Indexed: 11/24/2022] Open
Abstract
Background In Sudan, tuberculosis diagnosis largely relies on clinical symptoms and smear microscopy as in many other low- and middle-income countries. The aim of this study was to investigate the positive predictive value of a positive sputum smear in patients investigated for pulmonary tuberculosis in Eastern Sudan. Methods Two sputum samples from patients presenting with symptoms suggestive of tuberculosis were investigated using direct Ziehl-Neelsen (ZN) staining and light microscopy between June to October 2014 and January to July 2016. If one of the samples was smear positive, both samples were pooled, stored at −20°C, and sent to the National Reference Laboratory (NRL), Germany. Following decontamination, samples underwent repeat microscopy and culture. Culture negative/contaminated samples were investigated using polymerase chain reaction (PCR). Results A total of 383 samples were investigated. Repeat microscopy categorized 123 (32.1%) as negative, among which 31 were culture positive. This increased to 80 when PCR and culture results were considered together. A total of 196 samples were culture positive, of which 171 (87.3%), 14 (7.1%), and 11 (5.6%) were M. tuberculosis, M. intracellulare, and mixed species. Overall, 15.6% (57/365) of the samples had no evidence of M. tuberculosis, resulting in a positive predictive value of 84.4%. Conclusions There was a discordance between the results of smear microscopy performed at local laboratories in the Sudan and at the NRL, Germany; besides, a considerable number of samples had no evidence of M. tuberculosis. Improved quality control for smear microscopy and more specific diagnostics are crucial to avoid possible overtreatment.
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Lee HB, Cong A, Leopold H, Currie M, Boersma AJ, Sheets ED, Heikal AA. Rotational and translational diffusion of size-dependent fluorescent probes in homogeneous and heterogeneous environments. Phys Chem Chem Phys 2018; 20:24045-24057. [DOI: 10.1039/c8cp03873b] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Macromolecular crowding effects on diffusion depend on the fluorophore structure, the concentration of crowding agents, and the technique employed.
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Affiliation(s)
- Hong Bok Lee
- Department of Chemistry and Biochemistry
- Swenson College of Science and Engineering
- University of Minnesota Duluth
- Duluth
- USA
| | - Anh Cong
- Department of Chemistry and Biochemistry
- Swenson College of Science and Engineering
- University of Minnesota Duluth
- Duluth
- USA
| | - Hannah Leopold
- Department of Chemistry and Biochemistry
- Swenson College of Science and Engineering
- University of Minnesota Duluth
- Duluth
- USA
| | - Megan Currie
- Department of Chemistry and Biochemistry
- Swenson College of Science and Engineering
- University of Minnesota Duluth
- Duluth
- USA
| | | | - Erin D. Sheets
- Department of Chemistry and Biochemistry
- Swenson College of Science and Engineering
- University of Minnesota Duluth
- Duluth
- USA
| | - Ahmed A. Heikal
- Department of Chemistry and Biochemistry
- Swenson College of Science and Engineering
- University of Minnesota Duluth
- Duluth
- USA
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Theron A, Roth RL, Hoppe H, Parkinson C, van der Westhuyzen CW, Stoychev S, Wiid I, Pietersen RD, Baker B, Kenyon CP. Differential inhibition of adenylylated and deadenylylated forms of M. tuberculosis glutamine synthetase as a drug discovery platform. PLoS One 2017; 12:e0185068. [PMID: 28972974 PMCID: PMC5626031 DOI: 10.1371/journal.pone.0185068] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 09/06/2017] [Indexed: 11/29/2022] Open
Abstract
Glutamine synthetase is a ubiquitous central enzyme in nitrogen metabolism that is controlled by up to four regulatory mechanisms, including adenylylation of some or all of the twelve subunits by adenylyl transferase. It is considered a potential therapeutic target for the treatment of tuberculosis, being essential for the growth of Mycobacterium tuberculosis, and is found extracellularly only in the pathogenic Mycobacterium strains. Human glutamine synthetase is not regulated by the adenylylation mechanism, so the adenylylated form of bacterial glutamine synthetase is of particular interest. Previously published reports show that, when M. tuberculosis glutamine synthetase is expressed in Escherichia coli, the E. coli adenylyl transferase does not optimally adenylylate the M. tuberculosis glutamine synthetase. Here, we demonstrate the production of soluble adenylylated M. tuberulosis glutamine synthetase in E. coli by the co-expression of M. tuberculosis glutamine synthetase and M. tuberculosis adenylyl transferase. The differential inhibition of adenylylated M. tuberulosis glutamine synthetase and deadenylylated M. tuberulosis glutamine synthetase by ATP based scaffold inhibitors are reported. Compounds selected on the basis of their enzyme inhibition were also shown to inhibit M. tuberculosis in the BACTEC 460TB™ assay as well as the intracellular inhibition of M. tuberculosis in a mouse bone-marrow derived macrophage assay.
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Affiliation(s)
- A. Theron
- CSIR Biosciences, Pretoria, South Africa
| | - R. L. Roth
- CSIR Biosciences, Pretoria, South Africa
| | - H. Hoppe
- CSIR Biosciences, Pretoria, South Africa
| | - C. Parkinson
- School of Biomedical Sciences, Charles Sturt University, Orange NSW, Australia
| | | | | | - I. Wiid
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - R. D. Pietersen
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - B. Baker
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - C. P. Kenyon
- CSIR Biosciences, Pretoria, South Africa
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- * E-mail:
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Sethi S, Dhaliwal L, Dey P, Kaur H, Yadav R, Sethi S. Loop-mediated isothermal amplification assay for detection of Mycobacterium tuberculosis complex in infertile women. Indian J Med Microbiol 2017; 34:322-7. [PMID: 27514954 DOI: 10.4103/0255-0857.188323] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Female genital tuberculosis (FGTB) has a profound impact on the reproductive health of patients including infertility. Conventional diagnostic techniques have low sensitivity and specificity as well as long turnaround time. There is a need of developing newer, rapid and practically adaptable technique, especially in low-income countries. OBJECTIVE To standardize and evaluate loop-mediated isothermal amplification (LAMP) technique for diagnosis of FGTB. METHODS A total of 300 endometrial biopsy samples from infertile females were subjected to Ziehl-Neelsen (ZN) staining, Lowenstein-Jensen culture, automated culture (BACTEC mycobacterial growth indicator tube), histopathological examination (HPE), nucleic acid amplification by polymerase chain reaction (PCR) and LAMP technique. Composite gold standard (either smear/culture/HPE/PCR positive) was considered for calculation of outcome parameters. RESULTS The observed sensitivities of ZN smear, culture, HPE, PCR and LAMP were 2.94%, 10.29%, 8.82%, 95.59% and 66.18%, respectively. Overall concordance between PCR and LAMP was 63%, which shows a good agreement. CONCLUSION This study is the first to evaluate LAMP in the diagnosis of FGTB and found it to be a rapid and convenient technique, especially in low resource endemic settings.
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Affiliation(s)
- S Sethi
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - L Dhaliwal
- Department of Obstetrics and Gynaecology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - P Dey
- Department of Cytology and Gynaecological Pathology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - H Kaur
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - R Yadav
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - S Sethi
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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12
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Wang F, Li R, Shang Y, Wang C, Wang GQ, Zhou DX, Yang DH, Xi W, Wang KQ, Bao J, Kang Y, Gao ZC. A Pilot Study of Quantitative Loop-mediated Isothermal Amplification-guided Target Therapies for Hospital-acquired Pneumonia. Chin Med J (Engl) 2017; 129:181-6. [PMID: 26830989 PMCID: PMC4799545 DOI: 10.4103/0366-6999.173484] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Background: It is important to achieve the definitive pathogen identification in hospital-acquired pneumonia (HAP), but the traditional culture results always delay the target antibiotic therapy. We assessed the method called quantitative loop-mediated isothermal amplification (qLAMP) as a new implement for steering of the antibiotic decision-making in HAP. Methods: Totally, 76 respiratory tract aspiration samples were prospectively collected from 60 HAP patients. DNA was isolated from these samples. Specific DNA fragments for identifying 11 pneumonia-related bacteria were amplified by qLAMP assay. Culture results of these patients were compared with the qLAMP results. Clinical data and treatment strategies were analyzed to evaluate the effects of qLAMP results on clinical data. McNemar test and Fisher's exact test were used for statistical analysis. Results: The detection of Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumonia, Stenotrophomonas maltophilia, Streptococcus pneumonia, and Acinetobacter baumannii by qLAMP was consistent with sputum culture (P > 0.05). The qLAMP results of 4 samples for Haemophilus influenzae, Legionella pneumophila, or Mycoplasma pneumonia (MP) were inconsistent with culture results; however, clinical data revealed that the qLAMP results were all reliable except 1 MP positive sample due to the lack of specific species identified in the final diagnosis. The improvement of clinical condition was more significant (P < 0.001) in patients with pathogen target-driven therapy based on qLAMP results than those with empirical therapy. Conclusion: qLAMP is a more promising method for detection of pathogens in an early, rapid, sensitive, and specific manner than culture.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Zhan-Cheng Gao
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China
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Gelaw B, Shiferaw Y, Alemayehu M, Bashaw AA. Comparison of loop-mediated isothermal amplification assay and smear microscopy with culture for the diagnostic accuracy of tuberculosis. BMC Infect Dis 2017; 17:79. [PMID: 28095790 PMCID: PMC5240421 DOI: 10.1186/s12879-016-2140-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 12/20/2016] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Tuberculosis (TB) caused by Mycobacterium tuberculosis is one of the leading causes of death from infectious diseases worldwide. Sputum smear microscopy remains the most widely available pulmonary TB diagnostic tool particularly in resource limited settings. A highly sensitive diagnostic with minimal infrastructure, cost and training is required. Hence, we assessed the diagnostic performance of Loop-mediated isothermal amplification (LAMP) assay in detecting M.tuberculosis infection in sputum sample compared to LED fluorescent smear microscopy and culture. METHOD A cross-sectional study was conducted at the University of Gondar Hospital from June 01, 2015 to August 30, 2015. Pulmonary TB diagnosis using sputum LED fluorescence smear microscopy, TB-LAMP assay and culture were done. A descriptive analysis was used to determine demographic characteristics of the study participants. Analysis of sensitivity and specificity for smear microscopy and TB-LAMP compared with culture as a reference test was performed. Cohen's kappa was calculated as a measure of agreement between the tests. RESULTS A total of 78 pulmonary presumptive TB patients sputum sample were analyzed. The overall sensitivity and specificity of LAMP were 75 and 98%, respectively. Among smear negative sputum samples, 33.3% sensitivity and 100% specificity of LAMP were observed. Smear microscopy showed 78.6% sensitivity and 98% specificity. LAMP and smear in series had sensitivity of 67.8% and specificity of 100%. LAMP and smear in parallel had sensitivity of 85.7% and specificity of 96%. The agreement between LAMP and fluorescent smear microscopy tests was very good (κ = 0.83, P-value ≤0.0001). CONCLUSIONS TB-LAMP showed similar specificity but a slightly lower sensitivity with LED fluorescence microscopy. The specificity of LAMP and smear microscopy in series was high. The sensitivity of LAMP was insufficient for smear negative sputum samples.
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Affiliation(s)
- Baye Gelaw
- Department of Medical Microbiology, School of Biomedical and Laboratory sciences, CMHS, University of Gondar, P.O. box 196, Gondar, Ethiopia
| | - Yitayal Shiferaw
- Department of Microbiology, Parasitology and Immunology, Faculty of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
- School of Medicine, Flinders University, Bedford Park, SA 5042 Adelaide, Australia
| | - Marta Alemayehu
- Department of Medical Microbiology, School of Biomedical and Laboratory sciences, CMHS, University of Gondar, P.O. box 196, Gondar, Ethiopia
| | - Abate Assefa Bashaw
- Department of Medical Microbiology, School of Biomedical and Laboratory sciences, CMHS, University of Gondar, P.O. box 196, Gondar, Ethiopia
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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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Minakawa S, Kaneko T, Hagiwara C, Takahata T, Sawamura D. A diagnostically challenging case of tuberculous lymphadenitis. DERMATOL SIN 2016. [DOI: 10.1016/j.dsi.2016.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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16
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Abstract
BACKGROUND Tuberculosis (TB) remains a major contributor to morbidity and mortality in HIV-positive individuals, causing 1.1 million incident cases and 0.32 million deaths in 2012. Diagnosis of TB is particularly challenging in HIV-coinfected individuals, due to a high frequency of smear-negative disease, atypical presentations, and extrapulmonary TB. OBJECTIVE The aim of this article was to review the current literature on molecular diagnostics for TB with an emphasis on the performance of these diagnostic tests in the HIV-positive population. METHODS We searched the PubMed database using at least one of the terms TB, HIV, diagnostics, Xpert MTB/RIF, nucleic acid amplification tests, drug susceptibility testing, RNA transcription, and drew on World Health Organization publications. FINDINGS With increased focus on reducing TB prevalence worldwide, a new set of tools for diagnosing the disease have emerged. Molecular tools such as Xpert MTB/RIF and line-probe assays are now in use or are being rolled out in many regions. The diagnostic performance of these and other molecular assays are discussed here as they pertain to the HIV-positive population. CONCLUSIONS Molecular diagnostics offer a useful addition and at times, alternative, to traditional culture methods for the diagnosis of TB. However, most of these tests suffer from decreased accuracy in the HIV-positive population.
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17
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Bentaleb EM, Abid M, El Messaoudi MD, Lakssir B, Ressami EM, Amzazi S, Sefrioui H, Ait Benhassou H. Development and evaluation of an in-house single step loop-mediated isothermal amplification (SS-LAMP) assay for the detection of Mycobacterium tuberculosis complex in sputum samples from Moroccan patients. BMC Infect Dis 2016; 16:517. [PMID: 27677540 PMCID: PMC5039794 DOI: 10.1186/s12879-016-1864-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 09/22/2016] [Indexed: 11/16/2022] Open
Abstract
Background Tuberculosis (TB) is a major global health problem and remains the leading cause of morbidity and mortality in developing countries. Routinely used TB diagnostic methods, in most endemic areas, are time-consuming, often less-sensitive, expensive and inaccessible to most patients. Therefore, there is an urgent need for the development of early, easy to use and effective diagnosis tools of TB, which can be effectively integrated into resource limited settings, to anticipate the early treatment and limit further spread of the disease. Over the last decade, Loop-mediated isothermal amplification (LAMP) assays have become a powerful tool for rapid diagnosis of infectious diseases because of the simplicity of device requirements. Indeed, LAMP is a simple, quick and cost effective Isothermal Nucleic Acid Amplification diagnostic test (INAAT) that has the potential to be used in TB endemic settings of resource-poor countries. Methods In the present study, we have developed a simple and rapid TB molecular diagnostic test using a Single-Step Loop-mediated isothermal DNA amplification (SS-LAMP) method for the detection of Mycobacterium tuberculosis complex (MTBC) strains, with a simplified sample preparation procedure, eliminating DNA extraction prior to LAMP amplification, DNA initial denaturation and enzymatic inactivation steps during the amplification process. To perform our in-house SS-LAMP assay, a set of six specific primers was specifically designed to recognize eight distinct regions on the MTBC species-specific repetitive insertion sequence 6110 (IS6110). The amplification of the targeted DNA was carried out under isothermal conditions at 65 °C within 1 h. Our protocol was firstly optimized using 60 of confirmed MTBC isolates and a recombinant pGEMeasy-IS6110 vector for sensitivity testing. Thereafter, the assay was evaluated on liquefied sputum specimens collected from 157 Moroccan patients suspected of having TB. Results Our SS-LAMP developed assay was able to detect MTBC DNA directly from liquefied sputum samples without any prior DNA extraction, denaturation nor the final enzymatic inactivation step. When compared to routinely used Löwenstein Jensen (LJ) Culture method, our SS-LAMP assay is rapid and showed specificity and sensitivity of 99.14 % and 82.93 % respectively which are within the international standards. In addition, the limit of detection of our assay was found to be as little as 10 copies of bacterial DNA. Conclusion To our knowledge, this is the first study using a single step LAMP (SS-LAMP) procedure as a rapid, easy to perform and cost effective testing for TB early detection. This innovative assay could be suitable for low-income countries with restricted health equipment facilities.
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Affiliation(s)
- El Mehdi Bentaleb
- Moroccan Foundation for Advanced Science, Innovation and Research (MAScIR), Rabat Design Center, Avenue Mohamed El Jazouli - Madinat Al Irfane, 10100, Rabat, Morocco.,Laboratory of Biochemistry and Immunology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Mohammed Abid
- Laboratory of Mycobacteria Genetics, Pasteur Institute of Morocco, Tangier, Morocco
| | | | - Brahim Lakssir
- Moroccan Foundation for Advanced Science, Innovation and Research (MAScIR), Rabat Design Center, Avenue Mohamed El Jazouli - Madinat Al Irfane, 10100, Rabat, Morocco
| | - El Mostafa Ressami
- Moroccan Foundation for Advanced Science, Innovation and Research (MAScIR), Rabat Design Center, Avenue Mohamed El Jazouli - Madinat Al Irfane, 10100, Rabat, Morocco
| | - Saaïd Amzazi
- Laboratory of Biochemistry and Immunology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Hassan Sefrioui
- Moroccan Foundation for Advanced Science, Innovation and Research (MAScIR), Rabat Design Center, Avenue Mohamed El Jazouli - Madinat Al Irfane, 10100, Rabat, Morocco
| | - Hassan Ait Benhassou
- 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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18
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A novel visual loop-mediated isothermal amplification assay targeting gene62181533 for the detection of Salmonella spp. in foods. Food Control 2016. [DOI: 10.1016/j.foodcont.2015.07.036] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Yan L, Xiao H, Zhang Q. Systematic review: Comparison of Xpert MTB/RIF, LAMP and SAT methods for the diagnosis of pulmonary tuberculosis. Tuberculosis (Edinb) 2015; 96:75-86. [PMID: 26786658 DOI: 10.1016/j.tube.2015.11.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 09/29/2015] [Accepted: 11/17/2015] [Indexed: 11/17/2022]
Abstract
Technological advances in nucleic acid amplification have led to breakthroughs in the early detection of PTB compared to traditional sputum smear tests. The sensitivity and specificity of loop-mediated isothermal amplification (LAMP), simultaneous amplification testing (SAT), and Xpert MTB/RIF for the diagnosis of pulmonary tuberculosis were evaluated. A critical review of previous studies of LAMP, SAT, and Xpert MTB/RIF for the diagnosis of pulmonary tuberculosis that used laboratory culturing as the reference method was carried out together with a meta-analysis. In 25 previous studies, the pooled sensitivity and specificity of the diagnosis of tuberculosis were 93% and 94% for LAMP, 96% and 88% for SAT, and 89% and 98% for Xpert MTB/RIF. The I(2) values for the pooled data were >80%, indicating significant heterogeneity. In the smear-positive subgroup analysis of LAMP, the sensitivity increased from 93% to 98% (I(2) = 2.6%), and specificity was 68% (I(2) = 38.4%). In the HIV-infected subgroup analysis of Xpert MTB/RIF, the pooled sensitivity and specificity were 79% (I(2) = 72.9%) and 99% (I(2) = 64.4%). In the HIV-negative subgroup analysis for Xpert MTB/RIF, the pooled sensitivity and specificity were 72% (I(2) = 49.6%) and 99% (I(2) = 64.5%). LAMP, SAT and Xpert MTB/RIF had comparably high levels of sensitivity and specificity for the diagnosis of tuberculosis. The diagnostic sensitivity and specificity of three methods were similar, with LAMP being highly sensitive for the diagnosis of smear-positive PTB. The cost effectiveness of LAMP and SAT make them particularly suitable tests for diagnosing PTB in developing countries.
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Affiliation(s)
- Liping Yan
- Tuberculosis Clinic and Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, No. 507, Zhengmin Road, Shanghai 200433, China
| | - Heping Xiao
- Tuberculosis Clinic and Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, No. 507, Zhengmin Road, Shanghai 200433, China
| | - Qing Zhang
- Tuberculosis Clinic and Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, No. 507, Zhengmin Road, Shanghai 200433, China.
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20
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Bamogo W, Mugherli L, Banyasz A, Novelli-Rousseau A, Mallard F, Tran-Thi TH. Assessment of terbium (III) as a luminescent probe for the detection of tuberculosis biomarkers. Anal Chim Acta 2015; 896:143-51. [PMID: 26481998 DOI: 10.1016/j.aca.2015.09.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 09/07/2015] [Accepted: 09/09/2015] [Indexed: 10/23/2022]
Abstract
A detection method for nicotinic acid, a specific metabolite marker of Mycobacterium tuberculosis present in cultures and patients' breath, is studied in complex solutions containing other metabolites and in biological media such as urine, saliva and breath condensate. The method is based on the analysis of the luminescence increase of Tb(3+) complexes in the presence of nicotinic acid due to the energy transfer from the excited ligand to the lanthanide ion. It is shown that other potential markers found in M. tuberculosis culture supernatant, such as methyl phenylacetate, p-methyl anisate, methyl nicotinate and 2-methoxy biphenyl, can interfere with nicotinic acid via a competitive absorption of the excitation photons. A new strategy to circumvent these interferences is proposed with an upstream trapping of volatile markers preceding the detection of nicotinic acid in the liquid phase via the luminescence of Tb(3+) complexes. The cost of the method is evaluated and compared with the Xpert MTB/RIF test endorsed by the World Health Organization.
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Affiliation(s)
- W Bamogo
- CNRS, IRAMIS, UMR 3685 NIMBE/LEDNA, F-91191 Gif-sur-Yvette, France
| | - L Mugherli
- CEA, IRAMIS, UMR 3685 NIMBE/LEDNA, F-91191 Gif-sur-Yvette, France
| | - A Banyasz
- CNRS, IRAMIS, LIDyL/Laboratoire Francis Perrin, URA 2453, F-91191 Gif-sur-Yvette, France
| | | | - F Mallard
- BioMérieux SA, F-38000 Grenoble, France
| | - T-H Tran-Thi
- CNRS, IRAMIS, UMR 3685 NIMBE/LEDNA, F-91191 Gif-sur-Yvette, France.
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21
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Moon SH, Kim EJ, Tomono J, Miyamoto S, Mitarai S, Kim DW, Seki M. Detection of Mycobacterium tuberculosis complex in sputum specimens using a loop-mediated isothermal amplification assay in Korea. J Med Microbiol 2015; 64:1335-1340. [PMID: 26338293 DOI: 10.1099/jmm.0.000164] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Tuberculosis (TB), an infectious disease caused by Mycobacterium tuberculosis complex (MTC), remains one of the leading causes of death in the world. In Korea, the current prevalence of multidrug-resistant TB (MDR-TB) poses a major problem. The most common method for diagnosing TB in developing countries is sputum smear microscopy; however, the sensitivity of this test is relatively low and it usually requires well-trained laboratory staff. Cultures of MTC require up to several weeks in sophisticated facilities, such as Biosafety Level 3. Effective diagnostic techniques are necessary to control TB. In Korea, we evaluated a loop-mediated isothermal amplification (LAMP) assay targeting the hspX gene (TB-hspX-LAMP) of MTC. For clinical evaluation, culture confirmation, smear microscopy and TB-hspX-LAMP were performed on 303 sputum specimens obtained from suspected TB patients in Korea. The sensitivity, specificity, positive predictive value and negative predictive value of TB-hspX-LAMP were 71.1, 98.8, 91.4 and 95.1%, respectively, compared with TB culture, which is the gold standard for diagnosis of TB. In contrast, the comparable values of smear microscopy were 24.4, 98.1, 68.8 and 88.2%, respectively. Therefore, we concluded that TB-hspX-LAMP was superior to the use of smear microscopy for the detection of MTC in sputum specimens in clinical settings in Korea.
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Affiliation(s)
- Se Hoon Moon
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Republic of Korea.,Institute of Pharmacological Research, Hanyang University, Ansan, Republic of Korea.,Korea University Medical Center Ansan Hospital, Ansan, Republic of Korea
| | - Eun Jin Kim
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Republic of Korea.,Institute of Pharmacological Research, Hanyang University, Ansan, Republic of Korea
| | | | | | - Satoshi Mitarai
- Department of Mycobacterium Reference and Research, Bacteriology Division, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Dong Wook Kim
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Republic of Korea.,Institute of Pharmacological Research, Hanyang University, Ansan, Republic of Korea
| | - Mitsuko Seki
- Dental Research Center, Nihon University School of Dentistry, Tokyo, Japan.,Department of Oral Health Sciences, Nihon University School of Dentistry, Tokyo, Japan
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Abstract
Approximately one-third of the global burden of tuberculosis (TB) remains undiagnosed each year and the vast majority of cases of multidrug-resistant TB remain undetected. Many countries still place heavy reliance on outdated technologies that are blunt and ineffective tools for controlling this epidemic. However, during the past 10 years, there has been substantial progress within the TB diagnostics developmental pipeline. Old technologies have been reviewed and improved and new technologies have been developed and evaluated and are now being implemented. This review summarizes these developments and describes the currently available diagnostic tools. Consideration is given to the requirements of future diagnostic tests and how these should be evaluated not only with regard to their diagnostic accuracy and operational feasibility, but ultimately in terms of whether they impact clinical outcomes cost effectively, especially for those most in need.
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Affiliation(s)
- Stephen D Lawn
- Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom The Desmond Tutu HIV Centre, Institute for Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
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23
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Cao D, Hu L, Lin M, Li M, Ye Z, Sun H, Huang J, Yang H, Tian J. Real-time fluorescence Loop-Mediated Isothermal Amplification (LAMP) for rapid and reliable diagnosis of pulmonary tuberculosis. J Microbiol Methods 2015; 109:74-8. [DOI: 10.1016/j.mimet.2014.12.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 12/18/2014] [Accepted: 12/18/2014] [Indexed: 11/27/2022]
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Kumar P, Pandya D, Singh N, Behera D, Aggarwal P, Singh S. Loop-mediated isothermal amplification assay for rapid and sensitive diagnosis of tuberculosis. J Infect 2014; 69:607-15. [PMID: 25218428 DOI: 10.1016/j.jinf.2014.08.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 08/11/2014] [Accepted: 08/12/2014] [Indexed: 02/07/2023]
Abstract
OBJECTIVES Loop-mediated isothermal amplification (LAMP) is a newly developed molecular method that can be performed isothermally. We developed and evaluated a LAMP assay using novel primers to diagnose tuberculosis directly from clinical samples. MATERIALS Primers were designed to amplify the specific novel esat-6 gene target of Mycobacterium tuberculosis (MTB). Quantitated DNA was used to determine analytical sensitivity and specificity was evaluated by testing 29 NTM and 37 other bacterial species. After standardization, its sensitivity and specificity were evaluated on samples from 118 TB suspected and 31 non-TB patients and compared it with smear, culture and mPCR methods. RESULTS LAMP was able to detect 5 fg DNA (one MTB) within 21 min and found to be 10 times more sensitive than mPCR and showed 100% specificity against NTM and other bacterial species. In clinical samples, LAMP showed highest MTB detection rate (52.5%) as compared to mPCR (44%) and culture (30.5%). On culture positive and mPCR positive samples, the sensitivity of LAMP was found to be 100% (95% CI 90.2-100) and 96.1% (95% CI 86.7-99.5) respectively with 93.5% (95% CI 78.5-99.2) of overall specificity. CONCLUSION LAMP was found to be more sensitive than culture and mPCR for the detection of MTB. It showed specificity comparable to mPCR but was rapid and cost effective.
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Affiliation(s)
- Parveen Kumar
- Division of Clinical Microbiology and Molecular Medicine, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Deepal Pandya
- AmpliGene India Biotech Pvt. Ltd., Ahmedabad, Gujarat, India
| | - Niti Singh
- National Institute of Tuberculosis and Respiratory Diseases, New Delhi, India
| | - Digambar Behera
- National Institute of Tuberculosis and Respiratory Diseases, New Delhi, India
| | - Praveen Aggarwal
- Department of Emergency Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Sarman Singh
- Division of Clinical Microbiology and Molecular Medicine, All India Institute of Medical Sciences, New Delhi 110029, India.
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Kawano S, Maeda T, Watanabe J, Fujikura Y, Mikita K, Hara Y, Kanoh S, Kimura F, Miyahira Y, Kawana A. Successful diagnosis of tuberculous lymphadenitis by loop-mediated isothermal amplification of cutaneous samples from an ulcerated surface lesion: a case report. J Med Case Rep 2014; 8:254. [PMID: 25030753 PMCID: PMC4108240 DOI: 10.1186/1752-1947-8-254] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Accepted: 06/11/2014] [Indexed: 11/10/2022] Open
Abstract
INTRODUCTION Tuberculous lymphadenitis is the most frequent form of extrapulmonary tuberculous. Although nucleic acid amplification assays such as polymerase chain reaction have recently become mainstream techniques for diagnosing tuberculous lymphadenitis, they are still not routinely performed in developing countries because of their high costs and complicated procedures. CASE PRESENTATION We describe a case of tuberculous lymphadenitis in a 79-year-old Japanese man who had been on continuous hemodialysis for end-stage renal disease. We employed loop-mediated isothermal amplification and the procedure for ultrarapid extraction to develop a fast and easy-to-perform procedure for diagnosing tuberculous lymphadenitis. CONCLUSIONS The commercially available loop-mediated isothermal amplification assay kit and a rapid purification procedure enabled us to identify and amplify a Mycobacterium tuberculosis-specific gene within just 1.5 hours.
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Affiliation(s)
| | - Takuya Maeda
- Division of Infectious Diseases and Pulmonary Medicine, Department of Internal Medicine, National Defense Medical College, 3-2, Namiki, Tokorozawa, Saitama 359-8513, Japan.
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26
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Li Y, Shi L, Pan A, Cao W, Chen X, Meng H, Yan H, Miyoshi SI, Ye L. Evaluation of real-time loop-mediated isothermal amplification (RealAmp) for rapid detection of Mycobacterium tuberculosis from sputum samples. J Microbiol Methods 2014; 104:55-8. [PMID: 24968954 DOI: 10.1016/j.mimet.2014.06.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 06/12/2014] [Accepted: 06/13/2014] [Indexed: 11/29/2022]
Abstract
Tuberculosis (TB) caused by Mycobacterium tuberculosis (MTB) leads to serious health problems as a chronic respiratory infectious disease. Here we established a real-time fluorescence loop-mediated isothermal amplification assay (RealAmp) using a portable ESE Quant tube scanner as a convenient rapid detection method for MTB. The method efficacy from sputum samples was further investigated, and the reaction time was only 20min with the detection limit low to 10(2)CFU/ml concentration of MTB. We assessed a total of 1067 samples by the RealAmp assay, comparing the results with smear microscopy and conventional culture methods. To examine whether the failure to detect TB by culturing is due to low sensitivity or true absence, we examined the culture negative samples by commercial real time PCR MTB detection kit, and the results were compared with RealAmp. The data showed that RealAmp assay had a higher positive rate than that of sputum smear and culture methods. RealAmp had a sensitivity of 96.70% and a specificity of 91.55% when compared with culture. In addition, its sensitivity and specificity were 95.29% and 86.88% respectively compared with examination of smear samples using light microscopy. The sensitivity of RealAmp in comparison to real time PCR was 98.25% and specificity was 99.11% in validation of culture negative samples. The present study revealed the newly established RealAmp assay as a convenient, efficient, sensitive and specific method that could be an alternative for rapid detection of MTB and a tool to validate culture and smear negative samples. Furthermore, the portability of the ESE Quant tube scanner also contributed to the promising application for grassroots and field detection of MTB.
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Affiliation(s)
- Yiming Li
- College of Light Industry and Food Sciences, South China University of Technology, 510640 Guangzhou, PR China
| | - Lei Shi
- College of Light Industry and Food Sciences, South China University of Technology, 510640 Guangzhou, PR China
| | - Anqi Pan
- College of Light Industry and Food Sciences, South China University of Technology, 510640 Guangzhou, PR China
| | - Weiwei Cao
- Guangzhou DE AOU Biotechnology Technology Co., Ltd., Innovation Building, Science Road, Guangzhou Science City, 510663 Guangzhou, PR China
| | - Xun Chen
- Guangzhou DE AOU Biotechnology Technology Co., Ltd., Innovation Building, Science Road, Guangzhou Science City, 510663 Guangzhou, PR China
| | - Hecheng Meng
- College of Light Industry and Food Sciences, South China University of Technology, 510640 Guangzhou, PR China
| | - He Yan
- College of Light Industry and Food Sciences, South China University of Technology, 510640 Guangzhou, PR China
| | - Shin-ichi Miyoshi
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Lei Ye
- College of Light Industry and Food Sciences, South China University of Technology, 510640 Guangzhou, PR China.
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27
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Zhou D, Guo J, Xu L, Gao S, Lin Q, Wu Q, Wu L, Que Y. Establishment and application of a loop-mediated isothermal amplification (LAMP) system for detection of cry1Ac transgenic sugarcane. Sci Rep 2014; 4:4912. [PMID: 24810230 PMCID: PMC4014978 DOI: 10.1038/srep04912] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 04/14/2014] [Indexed: 11/22/2022] Open
Abstract
To meet the demand for detection of foreign genes in genetically modified (GM) sugarcane necessary for regulation of gene technology, an efficient method with high specificity and rapidity was developed for the cry1Ac gene, based on loop-mediated isothermal amplification (LAMP). A set of four primers was designed using the sequence of cry1Ac along with optimized reaction conditions: 5.25 mM of Mg(2+), 4:1 ratio of inner primer to outer primer, 2.0 U of Bst DNA polymerase in a reaction volume of 25.0 μL. Three post-LAMP detection methods (precipitation, calcein (0.60 mM) with Mn(2+) (0.05 mM) complex and SYBR Green I visualization), were shown to be effective. The sensitivity of the LAMP method was tenfold higher than that of conventional PCR when using templates of the recombinant cry1Ac plasmid or genomic DNA from cry1Ac transgenic sugarcane plants. More importantly, this system allowed detection of the foreign gene on-site when screening GM sugarcane without complex and expensive instruments, using the naked eye. This method can not only provide technological support for detection of cry1Ac, but can also further facilitate the use of this detection technique for other transgenes in GM sugarcane.
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Affiliation(s)
- Dinggang Zhou
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou 350002, China
| | - Jinlong Guo
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou 350002, China
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou 350002, China
| | - Shiwu Gao
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou 350002, China
| | - Qingliang Lin
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou 350002, China
| | - Qibin Wu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou 350002, China
| | - Luguang Wu
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane 4072, Australia
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou 350002, China
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Yoshikawa T, Matsuo T, Kawamura Y, Ohashi M, Yonekawa T, Kanda H, Notomi T, Ihira M. Direct detection of human herpesvirus 6B by the LAMP method using newly developed dry-reagents. J Virol Methods 2014; 201:65-7. [PMID: 24589515 DOI: 10.1016/j.jviromet.2014.02.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 01/24/2014] [Accepted: 02/04/2014] [Indexed: 10/25/2022]
Abstract
The reliability of the HHV-6B LAMP using the dry-reagent method was evaluated using serum samples obtained from febrile children. The sensitivity of the original and dry-reagent methods was 10 copies/reaction and 100 copies/reaction, respectively. The dry-reagent LAMP method was highly sensitive (94.0%) and specific (96.0%) for the detection of HHV-6B.
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Affiliation(s)
- Tetsushi Yoshikawa
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan.
| | - Takahiro Matsuo
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Yoshiki Kawamura
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Masahiro Ohashi
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | | | - Hidetoshi Kanda
- Eiken Chemical Co. Ltd., Shimoishigami, Ohtawara, Tochigi, Japan
| | - Tsugunori Notomi
- Eiken Chemical Co. Ltd., Shimoishigami, Ohtawara, Tochigi, Japan
| | - Masaru Ihira
- Faculty of Clinical Engineering, Fujita Health University School of Health Sciences, Toyoake, Aichi, Japan
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Yuan LY, Li Y, Wang M, Ke ZQ, Xu WZ. Rapid and effective diagnosis of pulmonary tuberculosis with novel and sensitive loop-mediated isothermal amplification (LAMP) assay in clinical samples: A meta-analysis. J Infect Chemother 2014; 20:86-92. [DOI: 10.1016/j.jiac.2013.07.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 06/24/2013] [Accepted: 07/25/2013] [Indexed: 11/29/2022]
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Sethi S, Sethi SK, Singh S, Dhatwalia SK, Yadav R, Mewara A, Singh M, Tewari R, Sharma M. Evaluation of in-house loop-mediated isothermal amplification (LAMP) assay for rapid diagnosis of M. tuberculosis in pulmonary specimens. J Clin Lab Anal 2014; 27:272-6. [PMID: 23852783 DOI: 10.1002/jcla.21596] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 02/04/2013] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Loop-mediated isothermal amplification (LAMP) assay has come forward as a rapid, cost-effective molecular technique for diagnosis of tuberculosis (TB) in developing countries. This study evaluated Mycobacterium tuberculosis-specific in-house LAMP assay targeting 16s rRNA and compared it with other conventional tests and nucleic acid amplification assay (IS6110 PCR). METHODS A total of 133 sputum specimens (103 from suspected pulmonary TB cases and 30 from non-TB controls) were subjected to conventional tests, IS6110 PCR and 16s rRNA LAMP assay. RESULTS Of the 103 patients, the maximum number of cases were found to be positive by LAMP assay, that is, in 87 (84.5%) patients, followed by culture positive in 78 (75.7%), IS6110 PCR in 74 (71.8%), and smear positive in 70 (67.9%) patients. Of the 83 smear positive and/or culture positive cases, LAMP detected 77 (92.77%) cases, and was found to be superior to IS6110 PCR, which could detect 69 (83.1%) cases; a concordance of 0.6 was obtained between the two tests using kappa statistics. CONCLUSION Overall, LAMP was simple and efficacious for early diagnosis of smear positive, culture positive cases as well as for confirmation of smear negative, culture negative cases, and was found to be superior to IS6110 PCR.
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Affiliation(s)
- Sunil Sethi
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India.
| | - Sunil Kumar Sethi
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India.
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Abstract
PURPOSE OF REVIEW This review summarizes the recent literature on the developments in diagnostics for pulmonary tuberculosis (TB). RECENT FINDINGS A growing body of literature regarding the Xpert MTB/RIF assay confirms the high diagnostic accuracy in a range of clinical settings, including amongst inpatients, those with HIV coinfection and in children with culture-positive disease. Early experiences with operational implementation are now being reported from South Africa. Initial small-scale evaluations suggest that newer versions of line-probe assays have diagnostic accuracy similar to that of the Xpert MTB/RIF assay. Next-generation fully automated molecular assays that use isothermal amplification may in the future be more readily implemented at the point of care. The first low-cost, lateral-flow (strip-test) assay for lipoarabinomannan in urine shows promise as a rapid point-of-care test for TB amongst HIV-infected patients who have advanced immunodeficiency. A range of other diagnostic tools are also at various stages of development. SUMMARY There is continued momentum and optimism regarding the developments in TB diagnostics. However, studies of clinical and programmatic impact and operational research are needed to guide implementation and scale-up of new assays in resource-limited settings. Further concerted efforts are needed to develop point-of-care assays which are desperately needed to accelerate progress in TB control.
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Wang Q, Zhou Y, Li S, Zhuo C, Xu S, Huang L, Yang L, Liao K. Real-time fluorescence loop mediated isothermal amplification for the detection of Acinetobacter baumannii. PLoS One 2013; 8:e66406. [PMID: 23843955 PMCID: PMC3699609 DOI: 10.1371/journal.pone.0066406] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 05/06/2013] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Detection of Acinetobacter baumannii has been relying primarily on bacterial culture that often fails to return useful results in time. Although DNA-based assays are more sensitive than bacterial culture in detecting the pathogen, the molecular results are often inconsistent and challenged by doubts on false positives, such as those due to system- and environment-derived contaminations. In addition, these molecular tools require expensive laboratory instruments. Therefore, establishing molecular tools for field use require simpler molecular platforms. The loop-mediated isothermal amplification method is relatively simple and can be improved for better use in a routine clinical bacteriology laboratory. A simple and portable device capable of performing both the amplification and detection (by fluorescence) of LAMP in the same platform has been developed in recent years. This method is referred to as real-time loop-mediated isothermal amplification. In this study, we attempted to utilize this method for rapid detection of A. baumannii. METHODOLOGY AND SIGNIFICANT FINDINGS Species-specific primers were designed to test the utility of this method. Clinical samples of A. baumannii were used to determine the sensitivity and specificity of this system compared to bacterial culture and a polymerase chain reaction method. All positive samples isolated from sputum were confirmed to be the species of Acinetobacter by 16S rRNA gene sequencing. The RealAmp method was found to be simpler and allowed real-time detection of DNA amplification, and could distinguish A. baumannii from Acinetobacter calcoaceticus and Acinetobacter genomic species 3. DNA was extracted by simple boiling method. Compared to bacterial culture, the sensitivity and specificity of RealAmp in detecting A. baumannii was 98.9% and 75.0%, respectively. CONCLUSION The RealAmp assay only requires a single unit, and the assay positivity can be verified by visual inspection. Therefore, this assay has great potential of field use as a molecular tool for detection of A. baumannii.
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Affiliation(s)
- Qinqin Wang
- Department of Respiratory Medicine, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
- Institute of Respiratory Diseases, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yanbin Zhou
- Department of Respiratory Medicine, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
- Institute of Respiratory Diseases, Sun Yat-sen University, Guangzhou, Guangdong, China
- * E-mail:
| | - Shaoli Li
- Department of Respiratory Medicine, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
- Institute of Respiratory Diseases, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Chao Zhuo
- State Key Laboratory of Respiratory Diseases, Guangzhou Medical College, Guangzhou, Guangdong, China
| | - Siqi Xu
- Department of Respiratory Medicine, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
- Institute of Respiratory Diseases, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Lixia Huang
- Department of Respiratory Medicine, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
- Institute of Respiratory Diseases, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Ling Yang
- State Key Laboratory of Respiratory Diseases, Guangzhou Medical College, Guangzhou, Guangdong, China
| | - Kang Liao
- Department of Clinical Laboratory, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
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Application of hyperbranched rolling circle amplification for direct detection of mycobacterium tuberculosis in clinical sputum specimens. PLoS One 2013; 8:e64583. [PMID: 23750210 PMCID: PMC3672175 DOI: 10.1371/journal.pone.0064583] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2012] [Accepted: 04/16/2013] [Indexed: 11/24/2022] Open
Abstract
Background Global tuberculosis (TB) control is encumbered by the lack of a rapid and simple detection method for diagnosis, especially in low-resource areas. An isothermal amplification method, hyperbranched rolling circle amplification (HRCA), was optimized to detect Mycobacterium tuberculosis (Mtb) in clinical sputum specimens. Methods A clinical validation study was performed to assess the diagnostic accuracy of HRCA. In order to analyze the detection limit of HRCA under optimal conditions, the method was initially used to detect purified H37Rv strain DNA and culture suspensions. Next, three strains of Mycobacterium tuberculosis complex (MTC) and eight strains of non-tuberculosis mycobacterium (NTM) were analyzed in order to evaluate specificity. Sputum specimens from 136 patients with diagnosed pulmonary TB, 38 lung cancer patients, and 34 healthy donors were tested by HRCA to validate the clinical application of HRCA for the rapid detection of Mtb. Results The detection limit of HRCA for purified H37Rv DNA and culture suspensions was 740 aM and 200cfu/ml, respectively. The results of all MTC strains were positive in contrast to the NTM specimens which were all negative. The detection sensitivity for the 136 sputum specimens from TB patients was 77.2% (105/136), which was slightly lower than that of quantitative real-time PCR(79.4%, 108/136) and culture (80.9%,110/136). The sensitivity of all three methods was statistically higher than smear microscopy (44.9%, 61/136). The overall specificity of HRCA was 98.6% (71/72) which was similar to that of quantitative real-time PCR (qRT-PCR) and smear/culture methods (100%, 72/72). Conclusions Use of the HRCA assay for detection of Mtb within clinical sputum specimens was demonstrated to be highly sensitive and specific. Moreover, the performance of HRCA is simple and cost-effective compared with qRT-PCR and is less time consuming than culture. Therefore, HRCA is a promising TB diagnostic tool that can be used routinely in low-resource clinical settings.
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Aryan E, Makvandi M, Farajzadeh A, Huygen K, Alvandi AH, Gouya MM, Sadrizadeh A, Romano M. Clinical value of IS6110-based loop-mediated isothermal amplification for detection of Mycobacterium tuberculosis complex in respiratory specimens. J Infect 2013; 66:487-93. [DOI: 10.1016/j.jinf.2013.02.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 02/08/2013] [Accepted: 02/16/2013] [Indexed: 12/01/2022]
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Desikan P. Sputum smear microscopy in tuberculosis: is it still relevant? Indian J Med Res 2013; 137:442-4. [PMID: 23640550 PMCID: PMC3705651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Affiliation(s)
- Prabha Desikan
- Department of Microbiology, Bhopal Memorial Hospital & Research Centre, Raisen Bypass Road, Karond, Bhopal 462 038, India
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Jo A, Ishibashi Y, Hirohama D, Takara Y, Kume H, Fujita T. Early surgical intervention may prevent peritonitis in cases with Tenckhoff catheter infection by nontuberculous mycobacterium. Perit Dial Int 2012; 32:227-9. [PMID: 22383730 DOI: 10.3747/pdi.2011.00080] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Novel real-time simultaneous amplification and testing method to accurately and rapidly detect Mycobacterium tuberculosis complex. J Clin Microbiol 2012; 50:646-50. [PMID: 22205804 DOI: 10.1128/jcm.05853-11] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The aim of this study was to establish and evaluate a simultaneous amplification and testing method for detection of the Mycobacterium tuberculosis complex (SAT-TB assay) in clinical specimens by using isothermal RNA amplification and real-time fluorescence detection. In the SAT-TB assay, a 170-bp M. tuberculosis 16S rRNA fragment is reverse transcribed to DNA by use of Moloney murine leukemia virus (M-MLV) reverse transcriptase, using specific primers incorporating the T7 promoter sequence, and undergoes successive cycles of amplification using T7 RNA polymerase. Using a real-time PCR instrument, hybridization of an internal 6-carboxyfluorescein-4-[4-(dimethylamino)phenylazo] benzoic acid N-succinimidyl ester (FAM-DABCYL)-labeled fluorescent probe can be used to detect RNA amplification. The SAT-TB assay takes less than 1.5 h to perform, and the sensitivity of the assay for detection of M. tuberculosis H37Rv is 100 CFU/ml. The TB probe has no cross-reactivity with nontuberculous mycobacteria or other common respiratory tract pathogens. For 253 pulmonary tuberculosis (PTB) specimens and 134 non-TB specimens, the SAT-TB results correlated with 95.6% (370/387 specimens) of the Bactec MGIT 960 culture assay results. The sensitivity, specificity, and positive and negative predictive values of the SAT-TB test for the diagnosis of PTB were 67.6%, 100%, 100%, and 62.0%, respectively, compared to 61.7%, 100%, 100%, and 58.0% for Bactec MGIT 960 culture. For PTB diagnosis, the sensitivities of the SAT-TB and Bactec MGIT 960 culture methods were 97.6% and 95.9%, respectively, for smear-positive specimens and 39.2% and 30.2%, respectively, for smear-negative specimens. In conclusion, the SAT-TB assay is a novel, simple test with a high specificity which may enhance the detection rate of TB. It is therefore a promising tool for rapid diagnosis of M. tuberculosis infection in clinical microbiology laboratories.
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