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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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Jain B, Kulkarni S. Development of DNA Bio-chip for Detection of Mutations of rpoB, embB and inhA Genes in Drug-Resistant Mycobacterium Tuberculosis. Indian J Clin Biochem 2023; 38:242-250. [PMID: 37025431 PMCID: PMC10070561 DOI: 10.1007/s12291-022-01044-w] [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: 02/23/2022] [Accepted: 04/04/2022] [Indexed: 10/18/2022]
Abstract
Drug-resistant (DR) tuberculosis (TB) is a global threat to health security and TB control programs. Since conventional drug susceptibility testing (DST) takes several weeks, we have developed a molecular method for the rapid identification of DR strains of Mycobacterium Tuberculosis (M.tb) utilizing DNA bio-chips. DNA bio-chips were prepared by immobilizing oligonucleotides (probes) on highly microporous polycarbonate track-etched membranes (PC-TEM) as novel support. Bio-chip was designed to contain 15 specific probes to detect mutations in three genes (rpoB, embB, and inhA). A sensitive and specific chemiluminescence based bio-chip assay was developed based on multiplex PCR followed by hybridization on bio-chip. Fifty culture isolates were used to evaluate the ability of in-house developed bio-chip to detect the mutations. Bio-chip analysis shows that 37.7% of samples show wild type sequences, 53.3% of samples were monoresistance showing resistance to either rifampicin (RMP), isoniazid (INH), or ethambutol (EMB). 4.4% of samples were polydrug resistant showing mutations in both the rpoB gene and embB gene while 4.4% of samples were multidrug-resistant (MDR), harboring mutations in the rpoB and inhA genes. The results were compared with DST and sequencing. Compared to sequencing, bio-chip assay shows a sensitivity of 96.5% and specificity of 100% for RMP resistance. For EMB and INH, the results were in complete agreement with sequencing. This study demonstrates the first-time use of PC-TEMs for developing DNA bio-chip for the detection of mutations associated with drug resistance in M.tb. Developed DNA bio-chip accurately detected different mutations present in culture isolates and thus provides detailed and reliable data for clinical diagnosis.
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Affiliation(s)
- Bharti Jain
- Radiation Medicine Centre, Bhabha Atomic Research Centre, Parel, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Savita Kulkarni
- Radiation Medicine Centre, Bhabha Atomic Research Centre, Parel, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
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AYDIN E, TARHAN G, ŞAHİN F, EREN S. Molecular epidemiological typing of M. tuberculosis isolates isolated from Turkey's Eastern Anatolia with in house PCR method. CUKUROVA MEDICAL JOURNAL 2022. [DOI: 10.17826/cumj.997873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Campelo TA, Cardoso de Sousa PR, Nogueira LDL, Frota CC, Zuquim Antas PR. Revisiting the methods for detecting Mycobacterium tuberculosis: what has the new millennium brought thus far? Access Microbiol 2021; 3:000245. [PMID: 34595396 PMCID: PMC8479963 DOI: 10.1099/acmi.0.000245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 06/17/2021] [Indexed: 01/07/2023] Open
Abstract
Tuberculosis (TB) affects around 10 million people worldwide in 2019. Approximately 3.4 % of new TB cases are multidrug-resistant. The gold standard method for detecting Mycobacterium tuberculosis, which is the aetiological agent of TB, is still based on microbiological culture procedures, followed by species identification and drug sensitivity testing. Sputum is the most commonly obtained clinical specimen from patients with pulmonary TB. Although smear microscopy is a low-cost and widely used method, its sensitivity is 50-60 %. Thus, owing to the need to improve the performance of current microbiological tests to provide prompt treatment, different methods with varied sensitivity and specificity for TB diagnosis have been developed. Here we discuss the existing methods developed over the past 20 years, including their strengths and weaknesses. In-house and commercial methods have been shown to be promising to achieve rapid diagnosis. Combining methods for mycobacterial detection systems demonstrates a correlation of 100 %. Other assays are useful for the simultaneous detection of M. tuberculosis species and drug-related mutations. Novel approaches have also been employed to rapidly identify and quantify total mycobacteria RNA, including assessments of global gene expression measured in whole blood to identify the risk of TB. Spoligotyping, mass spectrometry and next-generation sequencing are also promising technologies; however, their cost needs to be reduced so that low- and middle-income countries can access them. Because of the large impact of M. tuberculosis infection on public health, the development of new methods in the context of well-designed and -controlled clinical trials might contribute to the improvement of TB infection control.
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Affiliation(s)
- Thales Alves Campelo
- Faculdade de Medicina, Departamento de Patologia e Medicina Legal, Federal University of Ceará, Fortaleza, Brazil
| | | | - Lucas de Lima Nogueira
- Faculdade de Medicina, Departamento de Patologia e Medicina Legal, Federal University of Ceará, Fortaleza, Brazil
| | - Cristiane Cunha Frota
- Faculdade de Medicina, Departamento de Patologia e Medicina Legal, Federal University of Ceará, Fortaleza, Brazil
| | - Paulo Renato Zuquim Antas
- Laboratório de Imunologia Clínica, Instituto Oswaldo Cruz, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
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Goud KI, Kavitha M, Mahalakshmi A, Vempati R, Alodhayani AA, Mohammed AA, Khan IA. Molecular detection of Mycobacterium tuberculosis in pulmonary and extrapulmonary samples in a hospital-based study. Afr Health Sci 2020; 20:1617-1623. [PMID: 34394222 PMCID: PMC8351870 DOI: 10.4314/ahs.v20i4.14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
OBJECTIVE Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains a deadly infectious disease. India contributes to one-third of the global TB burden. However, no studies have been carried out in the Telangana (Hyderabad) population using real-time polymerase chain reaction (RT-PCR). Therefore, the current study evaluated the role of RT-PCR as a rapid and non-invasive test to diagnose TB by testing for pulmonary tuberculosis (PTB) and extrapulmonary tuberculosis (EPTB). MATERIALS AND METHODS This hospital-based study examined 1670 samples (900 EPTB; 770 PTB) comprising tissue (n = 537), peritoneal fluid (n = 420), sputum (n = 166), bronchial fluid (n = 126), cerebrospinal fluid (n = 145), ascetic fluid (n = 76), sputum pus (n = 78), urine (n = 79), and bronchoalveolar fluid (n = 43) samples. DNA from samples was separated using specific isolation kits and subjected to RT-PCR. RESULTS In this study, we enrolled 1670 subjects and categorized 54.4% as females and 45.6% as males. The collected samples were categorized as 48.5% of fluid samples, followed by tissue (32.2%), sputum (9.9%), urine (4.7%), and pus-swab (4.6%). RT-PCR analysis revealed that 4.7% patients were positive for Mtb. Our results revealed that 61% of the affected patients were male and 39% were female. Among the specimen types, tissue samples gave the highest proportion of positive results (36.3%). CONCLUSION The results showed that RT-PCR should be implemented and given top priority in TB diagnosis to save time and facilitate a definitive diagnosis. Tissue samples are highly recommended to screen the Mtb through the technique RTPCR. Future studies should extend the technique to the global population and exome sequencing analysis should be performed to identify TB risk markers.
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Affiliation(s)
- Kalal Iravathy Goud
- Molecular Biology and Cytogenetics Department, Apollo Hospitals, Jubilee Hills Hyderabad-500096, Telangana, India
| | - Matam Kavitha
- Molecular Biology and Cytogenetics Department, Apollo Hospitals, Jubilee Hills Hyderabad-500096, Telangana, India
| | - Adi Mahalakshmi
- Molecular Biology and Cytogenetics Department, Apollo Hospitals, Jubilee Hills Hyderabad-500096, Telangana, India
| | - Ravi Vempati
- Molecular Biology and Cytogenetics Department, Apollo Hospitals, Jubilee Hills Hyderabad-500096, Telangana, India
| | - Abdulaziz A Alodhayani
- Family & Community Medicine Department, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Arif A Mohammed
- Center of Excellence in Biotechnology Research, King Saud University, PO Box-2455, Riyadh, Saudi Arabia
| | - Imran Ali Khan
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, P.O. Box-10219, Riyadh-11433, Saudi Arabia
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Wei Z, Zhang X, Wei C, Yao L, Li Y, Zhang X, Xu H, Jia Y, Guo R, Wu Y, Yang K, Gao X. Diagnostic accuracy of in-house real-time PCR assay for Mycobacterium tuberculosis: a systematic review and meta-analysis. BMC Infect Dis 2019; 19:701. [PMID: 31395014 PMCID: PMC6686366 DOI: 10.1186/s12879-019-4273-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 07/10/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In recent years, studies on the diagnostic accuracy of in-house real-time PCR (hRT-PCR) assay for the detection of Mycobacterium tuberculosis (Mtb) have been reported with unignorable discrepancies. To assess the overall accuracy of the hRT-PCR assay for Mtb diagnosis in different samples for individuals with active pulmonary and extra-pulmonary Mtb infection, a systematic review and meta-analysis were performed. METHODS The PUBMED, EMBASE, Web of Science, and Cochrane databases were searched up to June 2017 for eligible studies that estimated diagnostic sensitivity and specificity with the hRT-PCR assay in respiratory and non-respiratory samples in pulmonary and extra-pulmonary Mtb infection patients, with Mtb culture as the reference standard. Bivariate random effect models were used to provide pooled estimation of diagnostic accuracy. Further, subgroup and meta-regression analyses were performed to explore sources of heterogeneity. The risk of bias was assessed by the QUADAS-2 tool. RESULTS Of the 3589 candidate studies, 18 eligible studies met our inclusion criteria. Compared to Mtb culture data, the pooled sensitivity and specificity were 0.96 and 0.92, respectively. The diagnostic odds ratio (DOR) was 192.96 (95% CI 68.46, 543.90), and the area under the summary ROC curve (AUC) was 0.9791. There was significant heterogeneity in sensitivity and specificity among the enrolled studies (p < 0.001). The studies with high-quality assessment and application of respiratory specimen were associated with better accuracy. CONCLUSIONS In low-income/high-burden settings, our results suggested that the hRT-PCR assay could be a useful test for the diagnosis of TB with high sensitivity and specificity.
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Affiliation(s)
- Zhenhong Wei
- Blood Transfusion Department, Gansu Provincial Hospital, Lanzhou, 730000, Gansu, China
| | - Xiaoping Zhang
- Blood Transfusion Department, Gansu Provincial Hospital, Lanzhou, 730000, Gansu, China
| | - Chaojun Wei
- The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital, No. 204, Donggang street, Chengguan district, Lanzhou, 730000, Gansu, China
| | - Liang Yao
- The Institute of Clinical Study and Evidence-Based Medicine, Gansu Provincial Hospital, Lanzhou, 730000, Gansu, China.,Evidence-Based Medicine Center and Key Laboratory of Evidence-Based Medicine and Knowledge Translation of Gansu Province, College of Basic Medicine, Lanzhou University, No. 199, Donggang street, Chengguan district, Lanzhou, 73000, Gansu, China
| | - Yonghong Li
- The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital, No. 204, Donggang street, Chengguan district, Lanzhou, 730000, Gansu, China
| | - Xiaojing Zhang
- Blood Transfusion Department, Gansu Provincial Hospital, Lanzhou, 730000, Gansu, China
| | - Hui Xu
- The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital, No. 204, Donggang street, Chengguan district, Lanzhou, 730000, Gansu, China
| | - Yanjuan Jia
- The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital, No. 204, Donggang street, Chengguan district, Lanzhou, 730000, Gansu, China
| | - Rui Guo
- The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital, No. 204, Donggang street, Chengguan district, Lanzhou, 730000, Gansu, China
| | - Yu Wu
- The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital, No. 204, Donggang street, Chengguan district, Lanzhou, 730000, Gansu, China
| | - Kehu Yang
- The Institute of Clinical Study and Evidence-Based Medicine, Gansu Provincial Hospital, Lanzhou, 730000, Gansu, China. .,Evidence-Based Medicine Center and Key Laboratory of Evidence-Based Medicine and Knowledge Translation of Gansu Province, College of Basic Medicine, Lanzhou University, No. 199, Donggang street, Chengguan district, Lanzhou, 73000, Gansu, China.
| | - Xiaoling Gao
- The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital, No. 204, Donggang street, Chengguan district, Lanzhou, 730000, Gansu, China.
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