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Mousavi-Sagharchi SMA, Afrazeh E, Seyyedian-Nikjeh SF, Meskini M, Doroud D, Siadat SD. New insight in molecular detection of Mycobacterium tuberculosis. AMB Express 2024; 14:74. [PMID: 38907086 PMCID: PMC11192714 DOI: 10.1186/s13568-024-01730-3] [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: 11/29/2023] [Accepted: 06/06/2024] [Indexed: 06/23/2024] Open
Abstract
Mycobacterium tuberculosis, the causative agent of tuberculosis, is a pathogenic bacterium that has claimed millions of lives since the Middle Ages. According to the World Health Organization's report, tuberculosis ranks among the ten deadliest diseases worldwide. The presence of an extensive array of genes and diverse proteins within the cellular structure of this bacterium has provided us with a potent tool for diagnosis. While the culture method remains the gold standard for tuberculosis diagnosis, it is possible that molecular diagnostic methods, emphasis on the identification of mutation genes (e.g., rpoB and gyrA) and single nucleotide polymorphisms, could offer a safe and reliable alternative. Over the past few decades, as our understanding of molecular genetics has expanded, methods have been developed based on gene expansion and detection. These methods typically commence with DNA amplification through nucleic acid targeted techniques such as polymerase chain reaction. Various molecular compounds and diverse approaches have been employed in molecular assays. In this review, we endeavor to provide an overview of molecular assays for the diagnosis of tuberculosis with their properties (utilization, challenges, and functions). The ultimate goal is to explore the potential of replacing traditional bacterial methods with these advanced molecular diagnostic techniques.
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Affiliation(s)
| | - Elina Afrazeh
- Department of Marine Biology, Faculty of Marine Science, Khorramshahr University of Marine Science and Technology, Khorramshahr, Iran
| | | | - Maryam Meskini
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
- Department of Genetics, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein, 9301, South Africa.
- Student Research Committee, Pasteur Institute of Iran, Tehran, Iran.
| | - Delaram Doroud
- Department of Immunotherapy and Leishmania Vaccine Research, Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
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Jabber Benellam YK, Ozkan O, Saadoon Aziz Z. Diagnosis of Mycobacterium tuberculosis using GeneXpert MTB / RIF and TB-LAMP techniques from pulmonary and extra-pulmonary TB patients in Iraq. BIONATURA 2022. [DOI: 10.21931/rb/2022.07.02.50] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Tuberculosis is considered one globally public health problem, particularly in unindustrialized countries. The disease has an increasing threat to public health, causing high morbidity and mortality rates. So, rapid diagnosis is critical to diminish the death and interfere with transmission. In this study, GeneXpert MTB/RIF and Loop-Mediated Isothermal Amplification (TB-LAMP) assays were utilized for the rapid molecular diagnosis of Mycobacterium tuberculosis bacteria and compared sensitivity and specificity of Mycobacterium tuberculosis bacteria; these tests with acid-fast bacilli staining in pulmonary and extra-pulmonary clinical specimens from Iraqi patients in Baghdad capital. 141 pulmonary and extra-pulmonary samples were collected and tested for tuberculosis detection. Acid-fast bacilli, TB-LAMP and GeneXpert MTB/RIF methods were used to diagnose tuberculosis. Of 141 tuberculosis specimens, 58 were acid-fast bacilli smear-positive, while 90 samples were positive for Mycobacterium tuberculosis by GeneXpert MTB/RIF assay and 78 by TB-LAMP assay. The results reported a high sensitivity rate of GeneXpert MTB/RIF assay compared to the TB-LAMP and bacilli staining method. The sensitivity of GeneXpert was 63.83%, specificity 50%; positive and negative predictive values were 58.36% to 68.96% and 42.73% to 57.27%, respectively. TB-LAMP sensitivity was 55.32%, specificity 50%; positive and negative predictive values were 49.61% to 60.89% and 43.70% to 56.30%, respectively, while the sensitivity of bacilli staining was 41.13%, specificity 50%; positive and negative predictive values were 35.26% to 47.27% and 44.88% to 55.12%, respectively, these values are dependent on disease prevalence. We concluded that the GeneXpert MTB/RIF test is more sensitive and specific than the TB-LAMP and both techniques are more sensitive and specific than the conventional acid-fast staining method for both pulmonary and extra-pulmonary specimens. Despite culture remaining the gold standard for laboratory confirmation of TB, GeneXpert MTB/RIF and TB-LAMP should become standard practice for patients with suspected TB, and all clinicians and public health programs for TB control should have access to molecular testing for TB to shorten diagnosis time.
Keywords. Mycobacterium tuberculosis; Pulmonary TB; Extrapulmonary TB; GeneXpert MTB/RIF; TB-LAMP; A.F.B
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Affiliation(s)
| | - Ozcan Ozkan
- Department of Biology, Faculty of Science, Cankiri Karatekin University, Cankiri, Turkey
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Comparison of LAMP, GeneXpert, Mycobacterial Culture, Smear Microscopy, TSPOT.TB, TBAg/PHA Ratio for Diagnosis of Pulmonary Tuberculosis. Curr Med Sci 2021; 41:1023-1028. [PMID: 34476662 PMCID: PMC8412392 DOI: 10.1007/s11596-021-2404-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 03/23/2021] [Indexed: 11/28/2022]
Abstract
Objective To investigate the application value of loop-mediated isothermal amplification (LAMP), GeneXpert, mycobacterial culture, smear microscopy, TSPOT.TB (TSPOT), ratio of TB-specific antigen to phytohemagglutinin (TBAg/PHA ratio) in the detection of mycobacterium tuberculosis in the bronchoalveolar lavage fluid. Methods A retrospective analysis was performed on the patients who underwent bronchoscopy from December 2018 to November 2019 in Tongji Hospital. The patients with positive tuberculosis culture or positive GeneXpert in bronchoalveolar lavage fluid were selected as the case group, and those without tuberculosis served as the control group. The receiver operating characteristic (ROC) curve was used to evaluate the diagnostic value of LAMP, GeneXpert, culture, smear microscopy, TSPOT, and TBAg/PHA ratio. Results For the patients with positive cultures as case, the sensitivity of LAMP, GeneXpert, smear microscopy, TSPOT and TBAg/PHA ratio was 73.49%, 89.16%, 25.30%, 80.00%, 33.85%, respectively, the specificity was 99.00%, 100.00%, 99.00%, 86.00%, 100.00%, respectively, the area under the ROC curve (AUC) was 0.849, 0.938, 0.633, 0.830, 0.669, respectively. For the patients with positive GeneXpert as case, the sensitivity of LAMP, mycobacterial culture, smear microscopy, TSPOT and TBAg/PHA ratio was 73.20%, 74.23%, 22.68%, 68.92%, 29.73%, respectively, the specificity was 99.00%, 100.00%, 99.00%, 86.00%, 100.00%, respectively, the AUC was 0.853, 0.878, 0.623, 0.775, 0.649, respectively. Conclusion The sensitivity of GeneXpert was best. The sensitivity and diagnostic value of LAMP were slightly lower than those of GeneXpert, and were similar to tuberculosis culture. The sensitivity of smear microscopy was low. The specificity of TSPOT was low. When TBAg/PHA ratio >0.2 was used as a diagnostic index, the specificity was improved, but the sensitivity was low.
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Wang Y, Ge G, Mao R, Wang Z, Sun YZ, Du YG, Gao XH, Qi RQ, Chen HD. Genotyping of 30 kinds of cutaneous human papillomaviruses by a multiplex microfluidic loop-mediated isothermal amplification and visual detection method. Virol J 2020; 17:99. [PMID: 32646520 PMCID: PMC7345449 DOI: 10.1186/s12985-020-01373-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 06/30/2020] [Indexed: 11/13/2022] Open
Abstract
Background Human papillomaviruses (HPVs), a group of non-enveloped small viruses with double-stranded circular DNA which lead to multiple skin diseases such as benign warts, are commonly seen in clinics. The current HPV detection systems aim mainly at mucosal HPVs, however, an efficient clinical approach for cutaneous HPVs detection is lacking. Objectives To establish a rapid detection system for cutaneous HPVs using a colorimetric loop-mediated isothermal amplification (LAMP) with hydroxynaphthol blue (HNB) dye in combination with microfluidic technology. Methods L1 DNA sequences of the 30 cutaneous HPVs were chemically synthesized, and LAMP primers against L1 DNA were designed with use of an online LAMP designing tool. Isothermal amplification was performed with use of a water bath and the amplification results were inspected with the naked eye. Using PCR sequencing as a control method, the specificity and sensitivity of the new detection system were obtained by detecting clinical samples. Results The lower detection limit of the LAMP assay was 107 viral DNA copies/μl when tested on synthesized L1 DNA sequences, which was better than the conventional PCR. Compared to PCR sequencing, the sensitivity of HPV27, HPV2, HPV1, HPV57, HPV3, HPV4, HPV7 and HPV75 genotypes detections were 100%, whereas the specificity was 34.55, 45.12, 95.83, 98.59 and 97.62% respectively, when tested on clinical samples. Conclusions The new cutaneous type HPV detection system is characterized by both a good sensitivity and specificity compared to conventional methods.
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Affiliation(s)
- Yining Wang
- Department of Dermatology, The First Hospital of China Medical University, No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China.,NHC Key Laboratory of Immunodermatology (China Medical University), No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China.,Key Laboratory of Immunodermatology (China Medical University), Ministry of Education, No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China.,Key Laboratory of Immunodermatology, Liaoning Province, No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China.,Key Laboratory of Immunodermatology (China Medical University), Department of education of Liaoning Province, No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China
| | - Ge Ge
- Department of Dermatology, The First Hospital of China Medical University, No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China.,NHC Key Laboratory of Immunodermatology (China Medical University), No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China.,Key Laboratory of Immunodermatology (China Medical University), Ministry of Education, No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China.,Key Laboratory of Immunodermatology, Liaoning Province, No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China.,Key Laboratory of Immunodermatology (China Medical University), Department of education of Liaoning Province, No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China.,Key Laboratory of Biopharmaceutical Production & Formulation Engineering, PLA and State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, PR China
| | - Rui Mao
- Key Laboratory of Biopharmaceutical Production & Formulation Engineering, PLA and State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, PR China
| | - Zhuo Wang
- Key Laboratory of Biopharmaceutical Production & Formulation Engineering, PLA and State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, PR China
| | - Yu-Zhe Sun
- Dermatology Hospital of Southern Medical University, No. 2 Lujing Road, Yuexiu District, Guangzhou, Guangdong Province, 510091, PR China.
| | - Yu-Guang Du
- Key Laboratory of Biopharmaceutical Production & Formulation Engineering, PLA and State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, PR China.
| | - Xing-Hua Gao
- Department of Dermatology, The First Hospital of China Medical University, No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China. .,NHC Key Laboratory of Immunodermatology (China Medical University), No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China. .,Key Laboratory of Immunodermatology (China Medical University), Ministry of Education, No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China. .,Key Laboratory of Immunodermatology, Liaoning Province, No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China. .,Key Laboratory of Immunodermatology (China Medical University), Department of education of Liaoning Province, No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China.
| | - Rui-Qun Qi
- Department of Dermatology, The First Hospital of China Medical University, No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China. .,NHC Key Laboratory of Immunodermatology (China Medical University), No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China. .,Key Laboratory of Immunodermatology (China Medical University), Ministry of Education, No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China. .,Key Laboratory of Immunodermatology, Liaoning Province, No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China. .,Key Laboratory of Immunodermatology (China Medical University), Department of education of Liaoning Province, No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China.
| | - Hong-Duo Chen
- Department of Dermatology, The First Hospital of China Medical University, No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China.,NHC Key Laboratory of Immunodermatology (China Medical University), No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China.,Key Laboratory of Immunodermatology (China Medical University), Ministry of Education, No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China.,Key Laboratory of Immunodermatology, Liaoning Province, No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China.,Key Laboratory of Immunodermatology (China Medical University), Department of education of Liaoning Province, No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China
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Loop Mediated Isothermal Amplification: A Promising Tool for Screening Genetic Mutations. Mol Diagn Ther 2020; 23:723-733. [PMID: 31396882 DOI: 10.1007/s40291-019-00422-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Mutation screening is elemental for clinical diagnosis and in determining therapeutic strategies. Nucleic acid-based techniques are considered to be the most accurate tools in genetic diagnosis. One such technique is loop-mediated isothermal amplification (LAMP) assay, which has seen tremendous applications in recent years. The advantages of the assay lie in its rapidity, efficiency, sensitivity, and cost. It works in isothermal conditions and amplifies the target gene using DNA polymerases that have strand displacement activity. To date, the assay has been widely used in different fields of research, including pathogen detection, crop development, and disease diagnosis. However, despite the potential, its application in mutation screening has been minimal. This review highlights the LAMP assay and its variants that have been developed for screening single-nucleotide polymorphisms and gene translocations in cancer.
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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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Poeta P, Silva V, Guedes A, Eduardo Pereira J, Cláudia Coelho A, Igrejas G. Tuberculosis in the 21th century: Current status of diagnostic methods. Exp Lung Res 2019; 44:352-360. [PMID: 30663432 DOI: 10.1080/01902148.2018.1545880] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Tuberculosis is an infectious bacterial disease with a high mortality rate worldwide constituting a serious public health problem. The diagnostic methods commonly used by health professionals are slow and expensive and the results may take about sixty days which will cause a delay in administrating the most proper treatment to the patient, as well as increase health care costs and infection transmission possibility. Patients infected simultaneously with human immunodeficiency virus and Mycobacterium tuberculosis are a constant and worrying challenge for the scientific community which will research and develop new methods of diagnosis, new drugs and new therapies. Nowadays there are new tuberculosis diagnosis methods and some of which are already in clinical trial phases. These methods have high sensitivity, but do not replace the microbiological examination for isolation and culture of Mycobacterium spp. However, in clinical practice, microbiological, imaging, clinical and epidemiological data integration provide the best diagnosis and treatment possible. Consequently, throughout this paper, the different methods of diagnosis of human tuberculosis with its advantages and disadvantages will be covered, describing new omics and ultra-fast methods to increase knowledge and obtain a rapid diagnosis of tuberculosis.
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Affiliation(s)
- Patrícia Poeta
- a Department of Veterinary Sciences , University of Trás-os-Montes and Alto Douro (UTAD) , Vila Real , Portugal.,b Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro , Vila Real , Portugal
| | - Vanessa Silva
- a Department of Veterinary Sciences , University of Trás-os-Montes and Alto Douro (UTAD) , Vila Real , Portugal.,b Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro , Vila Real , Portugal.,c Functional Genomics and Proteomics Unit , University of Tras-os-Montes and Alto Douro (UTAD) , Vila Real , Portugal.,d Associated Laboratory for Green Chemistry (LAQV-REQUIMTE) , University NOVA of Lisboa , Lisboa , Caparica, Portugal
| | - Andreia Guedes
- a Department of Veterinary Sciences , University of Trás-os-Montes and Alto Douro (UTAD) , Vila Real , Portugal
| | - José Eduardo Pereira
- a Department of Veterinary Sciences , University of Trás-os-Montes and Alto Douro (UTAD) , Vila Real , Portugal.,e CECAV, Centro de Ciência Animal e Veterinária , Universidade de Trás-os-Montes e Alto Douro , Vila Real , Portugal
| | - Ana Cláudia Coelho
- a Department of Veterinary Sciences , University of Trás-os-Montes and Alto Douro (UTAD) , Vila Real , Portugal.,e CECAV, Centro de Ciência Animal e Veterinária , Universidade de Trás-os-Montes e Alto Douro , Vila Real , Portugal
| | - Gilberto Igrejas
- b Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro , Vila Real , Portugal.,c Functional Genomics and Proteomics Unit , University of Tras-os-Montes and Alto Douro (UTAD) , Vila Real , Portugal.,d Associated Laboratory for Green Chemistry (LAQV-REQUIMTE) , University NOVA of Lisboa , Lisboa , Caparica, Portugal
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A Novel Design Combining Isothermal Exponential Amplification and Gold-Nanoparticles Visualization for Rapid Detection of miRNAs. Int J Mol Sci 2018; 19:ijms19113374. [PMID: 30373308 PMCID: PMC6275053 DOI: 10.3390/ijms19113374] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 10/22/2018] [Accepted: 10/25/2018] [Indexed: 11/17/2022] Open
Abstract
MicroRNAs (miRNAs) play important roles in a wide range of biological processes, and their aberrant expressions are associated with various diseases. The levels of miRNAs can be useful biomarkers for cellular events or disease diagnosis; thus, sensitive and selective detection of microRNAs is of great significance in understanding biological functions of miRNAs, early-phase diagnosis of cancers, and discovery of new targets for drugs. However, traditional approaches for the detection of miRNAs are usually laborious and time-consuming, with a low sensitivity. Here, we develop a simple, rapid, ultrasensitive colorimetric assay based on the combination of isothermal Exponential Amplification Reaction (EXPAR) and AuNP-labeled DNA probes for the detection of miRNAs (taking let-7a as a model analyte). In this assay, the presence of let-7a is converted to the reporter Y through EXPAR under isothermal conditions. The subsequent sandwich hybridization of the reporter Y with the AuNP-labeled DNA probes generates a red-to-purple color change. In other words, if the reporter Y is complementary to the AuNP-labeled DNA probes, the DNA-functionalized AuNPs will be aggregated, resulting in the change of solution color from red to purple/blue, while when the AuNP-labeled DNA probes are mismatched to the reporter Y, the solution remains red. This assay represents a simple, time-saving technique, and its results can be visually detected with the naked eye due to the colorimetric change. The method provides superior sensitivity, with a detection limit of 4.176 aM over a wide range from 1 nM to 1 aM under optimal conditions. The method also shows high selectivity for discriminating even single-nucleotide differences between let-7 miRNA family members. Notably, it is comparable to the most sensitive method reported to date, thus providing a promising alternative to standard approaches for the direct detection of let-7a miRNA. Importantly, through combination with specific templates, different miRNAs can be converted to the same reporter Y, which can hybridize with the same set of AuNP-labeled DNA probes to form sandwich hybrids. The color change of the solution can be observed in the presence of the target miRNA. This technique has potential as a routine method for assessing the levels of miRNAs, not only for let-7, but also for various miRNAs in the early phase of cancers. In addition, it can be a useful tool in biomedical research and clinical diagnosis, as well as diagnosis or surveillance programs in field conditions.
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Nurwidya F, Handayani D, Burhan E, Yunus F. Molecular Diagnosis of Tuberculosis. Chonnam Med J 2018; 54:1-9. [PMID: 29399559 PMCID: PMC5794472 DOI: 10.4068/cmj.2018.54.1.1] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 12/19/2017] [Accepted: 12/20/2017] [Indexed: 12/13/2022] Open
Abstract
Tuberculosis (TB) is one of the leading causes of adult death in the Asia-Pacific Region, including Indonesia. As an infectious disease caused by Mycobacterium tuberculosis (MTB), TB remains a major public health issue especially in developing nations due to the lack of adequate diagnostic testing facilities. Diagnosis of TB has entered an era of molecular detection that provides faster and more cost-effective methods to diagnose and confirm drug resistance in TB cases, meanwhile, diagnosis by conventional culture systems requires several weeks. New advances in the molecular detection of TB, including the faster and simpler nucleic acid amplification test (NAAT) and whole-genome sequencing (WGS), have resulted in a shorter time for diagnosis and, therefore, faster TB treatments. In this review, we explored the current findings on molecular diagnosis of TB and drug-resistant TB to see how this advancement could be integrated into public health systems in order to control TB.
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Affiliation(s)
- Fariz Nurwidya
- Department of Pulmonology and Respiratory Medicine, Universitas Indonesia Faculty of Medicine, Persahabatan Hospital, Jakarta, Indonesia
| | - Diah Handayani
- Department of Pulmonology and Respiratory Medicine, Universitas Indonesia Faculty of Medicine, Persahabatan Hospital, Jakarta, Indonesia
| | - Erlina Burhan
- Department of Pulmonology and Respiratory Medicine, Universitas Indonesia Faculty of Medicine, Persahabatan Hospital, Jakarta, Indonesia
| | - Faisal Yunus
- Department of Pulmonology and Respiratory Medicine, Universitas Indonesia Faculty of Medicine, Persahabatan Hospital, Jakarta, Indonesia
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Joon D, Nimesh M, Varma-Basil M, Saluja D. Evaluation of improved IS 6110 LAMP assay for diagnosis of pulmonary and extra pulmonary tuberculosis. J Microbiol Methods 2017; 139:87-91. [DOI: 10.1016/j.mimet.2017.05.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/11/2017] [Accepted: 05/12/2017] [Indexed: 11/16/2022]
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Canberk S, Longatto-Filho A, Schmitt F. Molecular diagnosis of infectious diseases using cytological specimens. Diagn Cytopathol 2015; 44:156-64. [PMID: 26620694 DOI: 10.1002/dc.23394] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 11/13/2015] [Indexed: 01/02/2023]
Abstract
Pathologists have an important role in the diagnosis of infectious disease (ID). In many cases, a definitive diagnosis can be made using cytopathology alone. However, several ancillary techniques can be used on cytological material to reach a specific diagnosis by identifying the causative agent and consequently defining the management of the patient. This review aims to present the effectiveness of the application of molecular studies on cytological material to diagnose IDs and discuss the advantages and disadvantages of the various molecular techniques according to the type of cytological specimen and the infectious agents.
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Affiliation(s)
- Sule Canberk
- Department of Pathology-Cytopathology, Haydarpasa Numune Education and Research Hospital, Istanbul, Turkey
| | - Adhemar Longatto-Filho
- Laboratory of Medical Investigation (LIM) 14, Faculty of Medicine, São Paulo University, FMUSP, São Paulo, Brazil.,Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal.,ICVS/3B's, PT Government Associate Laboratory, Braga, Portugal.,Molecular Oncology Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Fernando Schmitt
- Department of Pathology and Medicine, Laboratoire National De Sante, Dudelange, Luxembourg.,Instituto De Patologia E Imunologia Molecular Da Universidade Do Porto (IPATIMUP) E Faculdade De Medicina Do Porto, Porto, Portugal
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Beissner M, Phillips RO, Battke F, Bauer M, Badziklou K, Sarfo FS, Maman I, Rhomberg A, Piten E, Frimpong M, Huber KL, Symank D, Jansson M, Wiedemann FX, Banla Kere A, Herbinger KH, Löscher T, Bretzel G. Loop-Mediated Isothermal Amplification for Laboratory Confirmation of Buruli Ulcer Disease-Towards a Point-of-Care Test. PLoS Negl Trop Dis 2015; 9:e0004219. [PMID: 26566026 PMCID: PMC4643924 DOI: 10.1371/journal.pntd.0004219] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 10/17/2015] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND As the major burden of Buruli ulcer disease (BUD) occurs in remote rural areas, development of point-of-care (POC) tests is considered a research priority to bring diagnostic services closer to the patients. Loop-mediated isothermal amplification (LAMP), a simple, robust and cost-effective technology, has been selected as a promising POC test candidate. Three BUD-specific LAMP assays are available to date, but various technical challenges still hamper decentralized application. To overcome the requirement of cold-chains for transport and storage of reagents, the aim of this study was to establish a dry-reagent-based LAMP assay (DRB-LAMP) employing lyophilized reagents. METHODOLOGY/PRINCIPAL FINDINGS Following the design of an IS2404 based conventional LAMP (cLAMP) assay suitable to apply lyophilized reagents, a lyophylization protocol for the DRB-LAMP format was developed. Clinical performance of cLAMP was validated through testing of 140 clinical samples from 91 suspected BUD cases by routine assays, i.e. IS2404 dry-reagent-based (DRB) PCR, conventional IS2404 PCR (cPCR), IS2404 qPCR, compared to cLAMP. Whereas qPCR rendered an additional 10% of confirmed cases and samples respectively, case confirmation and positivity rates of DRB-PCR or cPCR (64.84% and 56.43%; 100% concordant results in both assays) and cLAMP (62.64% and 52.86%) were comparable and there was no significant difference between the sensitivity of the assays (DRB PCR and cPCR, 86.76%; cLAMP, 83.82%). Likewise, sensitivity of cLAMP (95.83%) and DRB-LAMP (91.67%) were comparable as determined on a set of 24 samples tested positive in all routine assays. CONCLUSIONS/SIGNIFICANCE Both LAMP formats constitute equivalent alternatives to conventional PCR techniques. Provided the envisaged availability of field friendly DNA extraction formats, both assays are suitable for decentralized laboratory confirmation of BUD, whereby DRB-LAMP scores with the additional advantage of not requiring cold-chains. As validation of the assays was conducted in a third-level laboratory environment, field based evaluation trials are necessary to determine the clinical performance at peripheral health care level.
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Affiliation(s)
- Marcus Beissner
- Department of Infectious Diseases and Tropical Medicine (DITM), University Hospital, Ludwig-Maximilians-University, Munich, Germany
| | - Richard Odame Phillips
- Komfo Anokye Teaching Hospital (KATH), Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | | | - Malkin Bauer
- Department of Infectious Diseases and Tropical Medicine (DITM), University Hospital, Ludwig-Maximilians-University, Munich, Germany
| | - Kossi Badziklou
- Institut National d’Hygiène (INH), Ministère de la Santé, Lomé, Togo
| | - Fred Stephen Sarfo
- Komfo Anokye Teaching Hospital (KATH), Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Issaka Maman
- Institut National d’Hygiène (INH), Ministère de la Santé, Lomé, Togo
| | - Agata Rhomberg
- Department of Infectious Diseases and Tropical Medicine (DITM), University Hospital, Ludwig-Maximilians-University, Munich, Germany
| | - Ebekalisai Piten
- Centre Hospitalier Régional Maritime (CHR-Maritime), Tsévié, Togo
| | - Michael Frimpong
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Komfo Anokye Teaching Hospital (KATH), Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Kristina Lydia Huber
- Department of Infectious Diseases and Tropical Medicine (DITM), University Hospital, Ludwig-Maximilians-University, Munich, Germany
| | - Dominik Symank
- Department of Infectious Diseases and Tropical Medicine (DITM), University Hospital, Ludwig-Maximilians-University, Munich, Germany
| | - Moritz Jansson
- Department of Infectious Diseases and Tropical Medicine (DITM), University Hospital, Ludwig-Maximilians-University, Munich, Germany
| | - Franz Xaver Wiedemann
- German Leprosy and Tuberculosis Relief Association, Togo office (DAHW-T), Lomé, Togo
| | - Abiba Banla Kere
- Institut National d’Hygiène (INH), Ministère de la Santé, Lomé, Togo
| | - Karl-Heinz Herbinger
- Department of Infectious Diseases and Tropical Medicine (DITM), University Hospital, Ludwig-Maximilians-University, Munich, Germany
| | - Thomas Löscher
- Department of Infectious Diseases and Tropical Medicine (DITM), University Hospital, Ludwig-Maximilians-University, Munich, Germany
| | - Gisela Bretzel
- Department of Infectious Diseases and Tropical Medicine (DITM), University Hospital, Ludwig-Maximilians-University, Munich, Germany
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Hoshino Y, Suzuki K. Differential diagnostic assays for discriminating mycobacteria, especially for nontuberculous mycobacteria: what does the future hold? Future Microbiol 2015; 10:205-16. [PMID: 25689533 DOI: 10.2217/fmb.14.120] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Mycobacteria infections are an important medical problem, and many are regarded as emerging and re-emerging diseases. Mycobacterium tuberculosis, the causative agent of tuberculosis, remains a leading cause of human morbidity and mortality worldwide, with approximately 8.6 million cases and 1.3 million deaths in 2012. In addition, the incidence of nontuberculous Mycobacterium infection has significantly increased, especially among developed countries. Although phenotypical appearances such as culture characteristics and/or susceptibility to anti-Mycobacterium drugs are variable between different mycobacterial species, early diagnosis is crucial in terms of patient treatment and clinical outcome. In this manuscript, we describe the development of diagnostic techniques, from the classical/conventional to the most recent advances, and provide an overview of the future direction of discrimination procedures.
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Affiliation(s)
- Yoshihiko Hoshino
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, 4-2-1 Aoba, Higashi-Murayama, Tokyo, Japan
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14
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Liu Z, Zhu J, Xia X, Wang L, Yang C, Li X. Development of a Loop-Mediated Isothermal Amplification Assay Based on lmo0460 Sequence for Detection of L
isteria monocytogenes. J Food Saf 2015. [DOI: 10.1111/jfs.12183] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Zhanmin Liu
- School of Life Sciences; Shanghai University; Shanghai 200444 China
| | - Jiachao Zhu
- School of Life Sciences; Shanghai University; Shanghai 200444 China
| | - Xueying Xia
- School of Life Sciences; Shanghai University; Shanghai 200444 China
| | - Lin Wang
- School of Life Sciences; Shanghai University; Shanghai 200444 China
| | - Cuiyun Yang
- Shanghai Entry-Exit Inspection and Quarantine Bureau; Shanghai China
| | - Xiaohong Li
- Shanghai Entry-Exit Inspection and Quarantine Bureau; Shanghai China
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15
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Gazi MA, Islam MR, Kibria MG, Mahmud Z. General and advanced diagnostic tools to detect Mycobacterium tuberculosis and their drug susceptibility: a review. Eur J Clin Microbiol Infect Dis 2015; 34:851-61. [DOI: 10.1007/s10096-014-2306-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 12/14/2014] [Indexed: 10/24/2022]
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16
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Zhang X, Lowe SB, Gooding JJ. Brief review of monitoring methods for loop-mediated isothermal amplification (LAMP). Biosens Bioelectron 2014; 61:491-9. [DOI: 10.1016/j.bios.2014.05.039] [Citation(s) in RCA: 194] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 05/14/2014] [Accepted: 05/15/2014] [Indexed: 01/20/2023]
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Ignatov KB, Barsova EV, Fradkov AF, Blagodatskikh KA, Kramarova TV, Kramarov VM. A strong strand displacement activity of thermostable DNA polymerase markedly improves the results of DNA amplification. Biotechniques 2014; 57:81-7. [PMID: 25109293 DOI: 10.2144/000114198] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 07/08/2014] [Indexed: 11/23/2022] Open
Abstract
The sensitivity and robustness of various DNA detection and amplification techniques are to a large extent determined by the properties of the DNA polymerase used. We have compared the performance of conventional Taq and Bst DNA polymerases to a novel Taq DNA polymerase mutant (SD DNA polymerase), which has a strong strand displacement activity, in PCR (including amplification of GC-rich and complex secondary structure templates), long-range PCR (LR PCR), loop-mediated amplification (LAMP), and polymerase chain displacement reaction (PCDR). Our results demonstrate that the strand displacement activity of SD DNA polymerase, in combination with the robust polymerase activity, provides a notable improvement in the sensitivity and efficiency of all these methods.
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Affiliation(s)
- Konstantin B Ignatov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia; All-Russia Institute of Agricultural Biotechnology, Moscow, Russia
| | - Ekaterina V Barsova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia; Evrogen JSC, Moscow, Russia
| | - Arkady F Fradkov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia; Evrogen JSC, Moscow, Russia
| | | | - Tatiana V Kramarova
- The Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Vladimir M Kramarov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia; All-Russia Institute of Agricultural Biotechnology, Moscow, Russia
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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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19
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Norbis L, Alagna R, Tortoli E, Codecasa LR, Migliori GB, Cirillo DM. Challenges and perspectives in the diagnosis of extrapulmonary tuberculosis. Expert Rev Anti Infect Ther 2014; 12:633-47. [PMID: 24717112 DOI: 10.1586/14787210.2014.899900] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Extrapulmonary tuberculosis (EPTB) accounts for a significant proportion of tuberculosis cases worldwide. Nevertheless, the diagnosis is often delayed or even missed due to insidious clinical presentation and poor performance of diagnostic tests. Culture, the classical gold standard for tuberculosis, suffers from increased technical and logistical constraints in EPTB cases. In this review the authors outline current diagnostic options for the main forms of EPTB. The authors also discuss the opportunities and challenges linked in particular to microbiological diagnostics and to the attempts to find a new gold standard test for EPTB. Finally, new biomarkers and tests currently under evaluation are hopefully on the way to introduce significant improvements in EPTB diagnosis, for which clinical suspicion will nevertheless be essential.
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Affiliation(s)
- Luca Norbis
- San Raffaele Scientific Institute, Via Olgettina 58, 20132, Milano, Italy
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20
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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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21
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Yurdakul P, Colakoglu S. Molecular methods for detection of invasive fungal infections and mycobacteria and their clinical significance in hematopoietic stem cell transplantation. Methods Mol Biol 2014; 1109:239-70. [PMID: 24473787 DOI: 10.1007/978-1-4614-9437-9_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Infection remains an important source of morbidity and mortality in patients who undergo hematopoietic stem cell transplantation (HSCT). In the immune reconstitution period after transplantation, HSCT recipients are most likely to have bacterial or fungal infections. Invasive fungal infections (IFIs) and mycobacterial infections (MBIs) are among the complications of HSCT, with high morbidity and mortality rates. Early diagnosis of both is crucial in order to manipulate the disease and to avoid fulminant outcomes. This chapter reviews the current knowledge on the molecular diagnosis of IFIs and MBIs in HSCT recipients, describing two different polymerase chain reaction (PCR)-based methods, one commercial (qPCR, Roche) and one in-house IS6110-based protocol.
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Affiliation(s)
- Pinar Yurdakul
- Ankara University Faculty of Medicine, Cord Blood Bank, Ankara, Turkey
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22
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Wilson ML. Rapid Diagnosis of Mycobacterium tuberculosis Infection and Drug Susceptibility Testing. Arch Pathol Lab Med 2013; 137:812-9. [DOI: 10.5858/arpa.2011-0578-ra] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Context.—The global control of tuberculosis remains a challenge from the standpoint of diagnosis, detection of drug resistance, and treatment. This is an area of special concern to the health of women and children, particularly in regions of the world with high infant mortality rates and where women have limited access to health care.
Objective.—Because treatment can only be initiated when infection is detected, and is guided by the results of antimicrobial susceptibility testing, there recently has been a marked increase in the development and testing of novel assays designed to detect Mycobacterium tuberculosis complex, with or without simultaneous detection of resistance to isoniazid and/or rifampin. Both nonmolecular and molecular assays have been developed. This review will summarize the current knowledge about the use of rapid tests to detect M tuberculosis and drug resistance.
Data Sources.—Review of the most recent World Health Organization Global Tuberculosis Report, as well as selected publications in the primary research literature, meta-analyses, and review articles.
Conclusions.—To a large extent, nonmolecular methods are refinements or modifications of conventional methods, with the primary goal of providing more rapid test results. In contrast, molecular methods use novel technologies to detect the presence of M tuberculosis complex and genes conferring drug resistance. Evaluations of molecular assays have generally shown that these assays are of variable sensitivity for detecting the presence of M tuberculosis complex, and in particular are insensitive when used with smear-negative specimens. As a group, molecular assays have been shown to be of high sensitivity for detecting resistance to rifampin, but of variable sensitivity for detecting resistance to isoniazid.
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Affiliation(s)
- Michael L. Wilson
- From the Department of Pathology and Laboratory Services, Denver Health, Denver, Colorado; and the Department of Pathology, University of Colorado School of Medicine, Aurora
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23
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Hamburger J, Abbasi I, Kariuki C, Wanjala A, Mzungu E, Mungai P, Muchiri E, King CH. Evaluation of loop-mediated isothermal amplification suitable for molecular monitoring of schistosome-infected snails in field laboratories. Am J Trop Med Hyg 2012. [PMID: 23208875 DOI: 10.4269/ajtmh.2012.12-0208] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
We previously described loop-mediated isothermal amplification (LAMP) for detection of Schistosoma haematobium and S. mansoni DNA in infected snails. In the present study, we adapted the LAMP assay for application in field laboratories in schistosomiasis-endemic areas. Isolation of DNA was simplified by blotting snail tissue (extracted in NaOH/sodium dodecyl sulfate) onto treated membranes, which enabled preservation at ambient temperatures. A ready-mix of LAMP reagents, suitable for shipment at ambient temperature and storage in minimal refrigeration, was used. Local survey teams without experience in molecular biology acquired operational expertise with this test within a few hours. Fifty-four field-caught snails were tested locally by LAMP and 59 were tested at similar conditions in Jerusalem. The LAMP results were consistent with those of a polymerase chain reaction; only four samples showed false-negative results. Results indicate that LAMP assays are suitable for detection of S. haematobium and S. mansoni in low-technology parasitology laboratories in which schistosomiasis elimination activities are undertaken.
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Affiliation(s)
- Joseph Hamburger
- Kuvin Center, Hebrew University, Hadassah Medical School, Jerusalem, Israel.
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Cuevas LE, Petrucci R, Swaminathan S. Tuberculosis diagnostics for children in high-burden countries: what is available and what is needed. Paediatr Int Child Health 2012; 32 Suppl 2:S30-7. [PMID: 23394756 DOI: 10.1179/2046904712z.00000000076] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
BACKGROUND The diagnosis of childhood tuberculosis (TB) is complex and most of the new diagnostics for TB are for adults. AIMS To review the performance of TB diagnostics and their suitability to its characteristics in young children. METHODS Expert opinion and review of the literature. MAIN FINDINGS The lack of a sufficient number of research studies on TB diagnostics for children hinders the preparation of systematic literature reviews. Information on test performance in children is often extrapolated from studies in adults and there is a dearth of evidence of test performance in children. Approaches to shorten the time required for diagnosis (by using a variety of specimens) are needed and there is preliminary evidence that such schemes are feasible. Diagnostics based on smear microscopy such as LED-FM, serological tests and IGRAS are unlikely to improve the diagnosis of active TB in children. Liquid and the MODS culture methods are more sensitive than solid culture, and new methods to detect mycobacterium nucleic acid or its components such as TrDNA fragments, LAMP assays and Xpert MTB/RIF have good potential to increase the number of cases confirmed. These tests should be evaluated in specimens which are easily accessible in children such as fine-needle aspiration biopsy, urine, blood and stools. INTERPRETATION The evaluation of new diagnostic tests for TB in children is overdue. The lack of suitable diagnostic tests hinders the proper management of children, the assessment of the real burden of childhood TB, evaluation of the efficacy of new treatments and vaccines and, ultimately, the development of effective control interventions.
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Affiliation(s)
- Luis E Cuevas
- UNICEF/UNDP/World Bank/WHO Special Programme for Research and Training in Tropical Diseases, Geneva, Switzerland.
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Craw P, Balachandran W. Isothermal nucleic acid amplification technologies for point-of-care diagnostics: a critical review. LAB ON A CHIP 2012; 12:2469-86. [PMID: 22592150 DOI: 10.1039/c2lc40100b] [Citation(s) in RCA: 483] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Nucleic Acid Testing (NAT) promises rapid, sensitive and specific diagnosis of infectious, inherited and genetic disease. The next generation of diagnostic devices will interrogate the genetic determinants of such conditions at the point-of-care, affording clinicians prompt reliable diagnosis from which to guide more effective treatment. The complex biochemical nature of clinical samples, the low abundance of nucleic acid targets in the majority of clinical samples and existing biosensor technology indicate that some form of nucleic acid amplification will be required to obtain clinically relevant sensitivities from the small samples used in point-of-care testing (POCT). This publication provides an overview and thorough review of existing technologies for nucleic acid amplification. The different methods are compared and their suitability for POCT adaptation are discussed. Current commercial products employing isothermal amplification strategies are also investigated. In conclusion we identify the factors impeding the integration of the methods discussed in fully automated, sample-to-answer POCT devices.
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Affiliation(s)
- Pascal Craw
- Department of Electronic & Computer Engineering, School of Engineering & Design, Brunel University, London, UK.
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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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Yang B, Wang X, Li H, Li G, Cao Z, Cheng X. Comparison of loop-mediated isothermal amplification and real-time PCR for the diagnosis of tuberculous pleurisy. Lett Appl Microbiol 2011; 53:525-31. [DOI: 10.1111/j.1472-765x.2011.03141.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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George G, Mony P, Kenneth J. Comparison of the efficacies of loop-mediated isothermal amplification, fluorescence smear microscopy and culture for the diagnosis of tuberculosis. PLoS One 2011; 6:e21007. [PMID: 21695047 PMCID: PMC3117872 DOI: 10.1371/journal.pone.0021007] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2011] [Accepted: 05/16/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Despite the advent of novel diagnostic techniques, smear microscopy remains as the most practical test available in resource-limited settings for tuberculosis (TB) diagnosis. Due to the low sensitivity of microscopy and the long time required for culture, feasible and accessible rapid diagnostic methods are urgently needed. Loop-mediated Isothermal Amplification (LAMP) is a promising nucleic-acid amplification assay, which could be accessible, cost-effective and more suited for use with unpurified samples. METHODOLOGY/PRINCIPAL FINDINGS In the current study, the objective was to assess the efficacy of a LAMP assay for tuberculosis compared with fluorescence smear microscopy as well as Löwenstein-Jensen (LJ) and Mycobacteria Growth Indicator Tube (MGIT) cultures for the diagnosis of pulmonary tuberculosis using sputum samples. Smear microscopy and culture were performed for decontaminated and concentrated sputum from TB suspects and the LAMP was also performed on these specimens. The LAMP and smear microscopy were compared, in series and in parallel, to culture. LAMP and smear microscopy showed sensitivities of 79.5% and 82.1% respectively and specificities of 93.8% and 96.9% respectively, compared to culture. LAMP and smear in series had sensitivity and specificity of 79.5% and 100.0% respectively. LAMP and smear in parallel had sensitivity and specificity of 82.1% and 90.6% respectively. CONCLUSIONS/SIGNIFICANCE The overall efficacies of LAMP and fluorescence smear microscopy in the current study were high and broadly similar. LAMP and smear in series had high specificity (100.0%) and can be used as a rule-in test combination. However, the performance of LAMP in smear negative samples was found to be insufficient.
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Affiliation(s)
- Geojith George
- Division of Infectious Disease, St. John's Research Institute, Bangalore, India
| | - Prem Mony
- Division of Epidemiology and Biostatistics, St. John's Research Institute, Bangalore, India
| | - John Kenneth
- Division of Infectious Disease, St. John's Research Institute, Bangalore, India
- * E-mail:
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