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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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2
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Zhang H, Tang M, Li D, Xu M, Ao Y, Lin L. Applications and advances in molecular diagnostics: revolutionizing non-tuberculous mycobacteria species and subspecies identification. Front Public Health 2024; 12:1410672. [PMID: 38962772 PMCID: PMC11220129 DOI: 10.3389/fpubh.2024.1410672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 06/10/2024] [Indexed: 07/05/2024] Open
Abstract
Non-tuberculous mycobacteria (NTM) infections pose a significant public health challenge worldwide, affecting individuals across a wide spectrum of immune statuses. Recent epidemiological studies indicate rising incidence rates in both immunocompromised and immunocompetent populations, underscoring the need for enhanced diagnostic and therapeutic approaches. NTM infections often present with symptoms similar to those of tuberculosis, yet with less specificity, increasing the risk of misdiagnosis and potentially adverse outcomes for patients. Consequently, rapid and accurate identification of the pathogen is crucial for precise diagnosis and treatment. Traditional detection methods, notably microbiological culture, are hampered by lengthy incubation periods and a limited capacity to differentiate closely related NTM subtypes, thereby delaying diagnosis and the initiation of targeted therapies. Emerging diagnostic technologies offer new possibilities for the swift detection and accurate identification of NTM infections, playing a critical role in early diagnosis and providing more accurate and comprehensive information. This review delineates the current molecular methodologies for NTM species and subspecies identification. We critically assess the limitations and challenges inherent in these technologies for diagnosing NTM and explore potential future directions for their advancement. It aims to provide valuable insights into advancing the application of molecular diagnostic techniques in NTM infection identification.
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Affiliation(s)
- Haiyang Zhang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Maoting Tang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Deyuan Li
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Min Xu
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Yusen Ao
- Department of Pediatrics, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Liangkang Lin
- Department of Pediatrics, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
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Dahiya B, Mehta N, Soni A, Mehta PK. Diagnosis of extrapulmonary tuberculosis by GeneXpert MTB/RIF Ultra assay. Expert Rev Mol Diagn 2023; 23:561-582. [PMID: 37318829 DOI: 10.1080/14737159.2023.2223980] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 06/06/2023] [Indexed: 06/17/2023]
Abstract
INTRODUCTION Diagnosis of extrapulmonary tuberculosis (EPTB) is an arduous task owing to different anatomical locations, unusual clinical presentations, and sparse bacillary load in clinical specimens. Although GeneXpert® MTB/RIF is a windfall in TB diagnostics including EPTB, it yields low sensitivities but high specificities in many EPTB specimens. To further improve the sensitivity of GeneXpert®, GeneXpert® Ultra, a fully nested real-time PCR targeting IS6110, IS1081 and rpoB (Rv0664) has been endorsed by the WHO (2017), wherein melt curve analysis is utilized to detect rifampicin-resistance (RIF-R). AREA COVERED We described the assay chemistry/work design of Xpert Ultra and evaluated its performance in several EPTB types, that is, TB lymphadenitis, TB pleuritis, TB meningitis, and so on, against the microbiological reference standard or composite reference standard. Notably, Xpert Ultra exhibited better sensitivities than Xpert, but mostly at the compensation of specificity values. Moreover, Xpert Ultra exhibited low false-negative and false-positive RIF-R results, compared with Xpert. We also detailed other molecular tests, that is, Truenat MTBTM/TruPlus, commercial real-time PCR, line probe assay, and so on, for EPTB diagnosis. EXPERT OPINION A combination of clinical features, imaging, histopathological findings, and Xpert Ultra are adequate for definite EPTB diagnosis so as to initiate an early anti-tubercular therapy.
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Affiliation(s)
- Bhawna Dahiya
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, India
| | - Neeru Mehta
- Department of Medical Electronics, Ambedkar Delhi Skill & Entrepreneurship University, Shakarpur, New Delhi, India
| | - Aishwarya Soni
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, India
- Department of Biotechnology, Deenbandhu Chhotu Ram University of Science and Technology, Murthal, Sonipat, India
| | - Promod K Mehta
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, India
- Microbiology Department, Faculty of Allied Health Sciences, SGT University, Budhera, Gurgaon, India
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Kaswabuli S, Musisi E, Byanyima P, Sessolo A, Sanyu I, Zawedde J, Worodria W, Huang L, Okeng A, Bwanga F. Accuracy of GenoQuick MTB test in detection of Mycobacterium tuberculosis in sputum from TB presumptive patients in Uganda. SAGE Open Med 2022; 10:20503121221116861. [PMID: 35993094 PMCID: PMC9386833 DOI: 10.1177/20503121221116861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 07/13/2022] [Indexed: 11/29/2022] Open
Abstract
Objective: The objective of the study was to determine the diagnostic performance of the GenoQuick MTB test on heated sputum against the conventional Lowenstein–Jensen Mycobacterium tuberculosis culture as the reference method for tuberculosis diagnosis. Introduction: Fast, reliable, and easy-to-use tests for tuberculosis diagnosis are essential to achieving the Sustainable Development Goal of diagnosing and treating 90% of tuberculosis patients by 2030. We evaluated the diagnostic performance of the GenoQuick MTB, a polymerase chain reaction–lateral flow test, in Uganda, a resource-constrained, high tuberculosis- and HIV-burden setting. Methods: Fresh sputum samples from presumptive tuberculosis patients at Mulago Hospital were tested for M. tuberculosis using smear microscopy, GenoQuick MTB test, and Lowenstein–Jensen culture. For the GenoQuick MTB test, mycobacterial DNA was extracted by heating sputum at 95°C for 30 min while DNA amplification and detection were done following the manufacturer’s protocol (Hain Lifescience, Nehren, Germany). Sensitivity, specificity, and kappa agreements were calculated against Lowenstein–Jensen M. tuberculosis culture as a reference test using STATA V12. Results: Of the 86 tested samples, 30.2% had culture-confirmed pulmonary tuberculosis. Overall, sensitivity was higher for GenoQuick MTB (81%, 95% confidence interval: 60%−93%) than for smear microscopy (69%, 95% confidence interval: 48%−86%). Among people living with HIV, sensitivity was identical for GenoQuick MTB and smear tests (75%, 95% confidence interval: 42%−95%). Contrastingly, smear had a higher overall specificity (98%, 95% confidence interval: 91%−100%) than for GenoQuick MTB (92%, 95% confidence interval: 81%−97%). A similar trend of specificity was observed among the people living with HIV for smear microscopy (100%, 95% CI: 87%−100%) and for GenoQuick MTB (96%, 95% confidence interval: 81%−100%). Conclusion: The GenoQuick MTB test could be a potential tuberculosis diagnostic test given its higher sensitivity. Evaluation of this test in larger studies is recommended.
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Affiliation(s)
| | - Emmanuel Musisi
- Division of Infection and Global Health, School of Medicine, University of St Andrews, St Andrews, UK
| | | | - Abdul Sessolo
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Ingvar Sanyu
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | | | | | - Laurence Huang
- Infectious Diseases Research Collaboration, Kampala, Uganda.,Division of HIV, Infectious Diseases & Global Medicine, University of California San Francisco, San Francisco, CA, USA.,Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, CA, USA
| | | | - Freddie Bwanga
- Department of Medical Microbiology, Makerere University College of Health Sciences, Kampala, Uganda
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Kamra E, Sharma S, Sheoran A, Singh V, Chauhan M, Pawar DS, Yadav A, Mehta PK. Identification of mycobacterial MPT-64 and ESAT-6 proteins in urogenital tuberculosis patients by real-time immuno-PCR. Future Microbiol 2022; 17:829-842. [PMID: 35704296 DOI: 10.2217/fmb-2022-0037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: Diagnosis of urogenital tuberculosis (UGTB) is difficult and there is an immediate need to develop a reliable diagnostic test. Methods: A real-time immuno-PCR (RT-I-PCR) was developed to identify a cocktail of MPT-64 + ESAT-6 in both male/female UGTB patients comprising five confirmed cases, 40 clinically suspected cases and 37 non-TB controls, from whom mid-stream urine specimens were collected, while endometrial biopsies of female patients were obtained on day 1 of their menstrual cycle. Results obtained by RT-I-PCR were compared with I-PCR/ELISA and GeneXpert. Results: A wide range (500 fg/ml-10 ng/ml) of MPT-64 + ESAT-6 was detected in UGTB specimens by RT-I-PCR, although ELISA showed a narrow range (2.5-11 ng/ml). Sensitivities of 80% and 82.2% were obtained by RT-I-PCR in clinically suspected and total UGTB cases, respectively, whereas 94.6% specificity was obtained. Concurrently, RT-I-PCR revealed significantly higher (p < 0.05-0.001) sensitivity than I-PCR/ELISA and GeneXpert. Conclusion: After improving the specificity, the authors may develop RT-I-PCR into a diagnostic kit.
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Affiliation(s)
- Ekta Kamra
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, 124001, India
| | - Suman Sharma
- Department of Microbiology, Pt. B. D. Sharma University of Health Sciences (UHS), Rohtak, 124001, India
| | - Abhishek Sheoran
- Department of Statistics, Ramanujan College, University of Delhi, Delhi, 110019, India
| | - Vishwajeet Singh
- Department of Geriatric Medicine, All India Institute of Medical Sciences, New Delhi, 110029, India
| | | | | | - Aparna Yadav
- Department of Microbiology, Pt. B. D. Sharma University of Health Sciences (UHS), Rohtak, 124001, India
| | - Promod K Mehta
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, 124001, India
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Huang WC, Lin CB, Chien ST, Wang JY, Lin CJ, Feng JY, Lee CH, Shu CC, Yu MC, Lee JJ, Chiang CY. Performance of Nucleic Acid Amplification Tests in Patients with Presumptive Pulmonary Tuberculosis in Taiwan. Infect Dis Ther 2022; 11:871-885. [PMID: 35254635 PMCID: PMC8900096 DOI: 10.1007/s40121-022-00610-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 02/14/2022] [Indexed: 11/24/2022] Open
Abstract
INTRODUCTION Several nucleic acid amplification tests (NAATs) for detection of Mycobacterium tuberculosis (TB) complex (MTBC) are available in Taiwan; however, their performances may differ and have not been extensively evaluated. Therefore, we aimed to explore the accuracy of NAATs overall followed by comparison between platforms commonly used in Taiwan. METHODS This study enrolled presumptive pulmonary TB patients with NAATs throughout Taiwan. The diagnostic performance of smear microscopy and NAATs was assessed using sputum culture as a reference standard. To investigate the performance of NAATs in excluding non-tuberculous mycobacteria (NTM), we quantified the false-positive proportion of NAATs in patients infected with NTM. RESULTS Of the 4126 enrollees, 860 (20.8%) had positive NAATs. The sensitivity and specificity of NAATs were 83.2% and 96.7%, respectively, compared to 81.5% and 55.3% for smear. There was no significant difference in sensitivity between the NAATs and smear; however, the specificity of smear was significantly lower than that of the NAATs [difference 41.4%, 95% confidence interval (CI) 39.6-43.2%]. There was no significant difference in sensitivity among Roche Cobas Amplicor Mycobacterium tuberculosis assay (Amplicor), Xpert MTB/RIF assay (Xpert) and in-house polymerase chain reaction (in-house PCR) (82.2% versus 83.8% versus 82.4%); however, in-house PCR was significantly less specific than Amplicor (difference 5.3%, 95% CI 2.4-8.2%) and Xpert (difference 5.8%, 95% CI 3.1-8.5%). The sensitivity of NAATs among smear-negative cases was 33.1% (95% CI 26.0-40.3%). In-house PCR had a significantly higher false-positive rate among specimens that were culture positive for NTM than Amplicor (7.7% versus 0.3%; difference 7.4%, 95% CI 3.4-11.5%) and Xpert (7.7% versus 0.7%; difference 7.0%, 95% CI 2.9-11.0%). CONCLUSION The NAATs overall had a relatively high sensitivity and specificity in detecting MTBC while Amplicor and Xpert performed better than in-house PCR in excluding NTM. Our findings will be useful for the development of national policy.
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Affiliation(s)
- Wei-Chang Huang
- Division of Chest Medicine, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, 407, Taiwan.,Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, 402, Taiwan.,Department of Translational Medicine, National Chung Hsing University, Taichung, 402, Taiwan.,School of Medicine, Chung Shan Medical University, Taichung, 402, Taiwan.,Department of Industrial Engineering and Enterprise Information, Tunghai University, Taichung, 407, Taiwan.,Department of Medical Technology, Jen-Teh Junior College of Medicine, Nursing and Management, Miaoli, 350, Taiwan
| | - Chih-Bin Lin
- Division of Chest Medicine, Department of Internal Medicine, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien, 970, Taiwan.,School of Medicine, Tzu Chi University, Hualien, 970, Taiwan
| | - Shun-Tien Chien
- Chest Hospital, Ministry of Health and Welfare, Tainan, 701, Taiwan
| | - Jann-Yuan Wang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, 100, Taiwan.,School of Medicine, College of Medicine, National Taiwan University, Taipei, 100, Taiwan
| | - Chou-Jui Lin
- Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, 330, Taiwan
| | - Jia-Yih Feng
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei, 112, Taiwan.,School of Medicine, National Yang Ming Chiao Tung University, Taipei, 112, Taiwan.,Institute of Emergency and Critical Care Medicine, National Yang Ming Chiao Tung University, Taipei, 112, Taiwan
| | - Chih-Hsin Lee
- Division of Pulmonary Medicine & Pulmonary Research Center, Department of Internal Medicine, Wan Fang Hospital, Taipei Medical University, 111 Xing-Long Road, Section 3, Taipei, 116, Taiwan.,Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, 110, Taiwan
| | - Chin-Chung Shu
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, 100, Taiwan.,School of Medicine, College of Medicine, National Taiwan University, Taipei, 100, Taiwan
| | - Ming-Chih Yu
- Division of Pulmonary Medicine & Pulmonary Research Center, Department of Internal Medicine, Wan Fang Hospital, Taipei Medical University, 111 Xing-Long Road, Section 3, Taipei, 116, Taiwan.,School of Respiratory Therapy, College of Medicine, Taipei Medical University, Taipei, 110, Taiwan
| | - Jen-Jyh Lee
- Division of Chest Medicine, Department of Internal Medicine, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien, 970, Taiwan.,School of Medicine, Tzu Chi University, Hualien, 970, Taiwan
| | - Chen-Yuan Chiang
- Division of Pulmonary Medicine & Pulmonary Research Center, Department of Internal Medicine, Wan Fang Hospital, Taipei Medical University, 111 Xing-Long Road, Section 3, Taipei, 116, Taiwan. .,Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, 110, Taiwan. .,International Union Against Tuberculosis and Lung Disease, Paris, France.
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Innovations in Molecular Identification of Mycobacterium tuberculosis. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2022. [DOI: 10.22207/jpam.16.1.76] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tuberculosis (TB) continues to be a significant public health concern on a global scale. Quick and precise identification of Mycobacterium tuberculosis (MTB) in symptomatic patients is pivotal for worldwide TB eradication initiatives. As an infectious disorder induced by MTB, it remains a critical threat to public health, particularly in poor countries, due to an inadequate diagnostic research laboratory. There is a need for a persistent incentive to reduce response time for effective diagnosis and control of TB infection, which is a benefit that molecular techniques provide over traditional methods. Although there is a tremendous overall prevalence of TB and a relatively poor probability of case identification worldwide. Common screening techniques have focused on tests that have many fundamental shortcomings. Due to the development of antibiotic-resistant Mycobacterium strains, TB is one of the leading contributors to fatalities. It is now possible to examine TB using molecular detection techniques, which are faster and more cost-effective than previous methods, such as standard culture procedures to test and verify antibiotic resistance in patients with TB. Whole genome sequencing (WGS), faster nucleic acid amplification tests, has made it easier to diagnose and treat TB more quickly. This article addresses the genetic approaches for detecting Mycobacterium tuberculosis complex (MTBC) in clinical specimens as well as antibiotic resistance in mycobacterium and discusses the practical limitations of using these methods.
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Jung T, Kim SH, Kim S, Choi JS, Kim YK. Comparison of Quantitative Relationship between Real-Time PCR and Acid Fast Bacilli Staining for Diagnosis of Pulmonary Tuberculosis. KOREAN JOURNAL OF CLINICAL LABORATORY SCIENCE 2020. [DOI: 10.15324/kjcls.2020.52.4.335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Taewon Jung
- Department of Laboratory Medicine, Samsung Medical Center, Seoul, Korea
| | - Sang-Ha Kim
- Department of Laboratory Medicine, Konyang University Hospital, Daejeon, Korea
| | - Sunghyun Kim
- Department of Clinical Laboratory Science, College of Health Sciences, Catholic University of Pusan, Busan, Korea
| | - Jae-Sun Choi
- Department of Biomedical Laboratory Science, Far East University, Eumseong, Korea
| | - Young-Kwon Kim
- Department of Health Sciences, The Graduate School of Konyang University, Daejeon, Korea
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Porter BW, Venkatappa TK. Uncloaking an ancient adversary: Can pathogen biomarker elicitors play a role in confirming extrapulmonary TB and latent TB infection? Tuberculosis (Edinb) 2018; 113:30-37. [PMID: 30514511 DOI: 10.1016/j.tube.2018.08.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 07/07/2018] [Accepted: 08/29/2018] [Indexed: 10/28/2022]
Abstract
Latent tuberculosis infection (LTBI) is diagnosed immunologically using the Mantoux tuberculin skin test (TST) or interferon-gamma release assays (IGRAs). While widely used, immunodiagnostics can produce false negative or false positive results. Pathogen biomarkers provide an alternative, but direct detection in LTBI and extrapulmonary TB cases is challenging. Mycobacterium tuberculosis grows slowly, has limited hematogenous movement, is protected by a lipid rich cell wall, and produces low levels of secreted factors. Here we discuss the potential of elicitors by first considering pathogen markers that may be released following the administration of isoniazid. Isoniazid targets the cell wall of mycobacteria found in extracellular compartments and within monocytes, macrophages, dendritic cells, and lymphatic endothelial cells. Isoniazid's dual-purpose potential as an antibiotic and elicitor is supported by knowledge of latent infection dynamics, time-kill kinetics, and new detection techniques. Within hours, the bactericidal action of isoniazid likely enriches plasma with M. tuberculosis DNA, RNA, proteins/peptides, and lipids. Undoubtedly a portion of these biomarkers are eliminated as some bacilli undergo phagocytosis and lysosomal destruction. However, advances in immunoprecipitation and nucleic acid amplification, combined with the use of larger blood volumes during assay development, may overcome these losses. Other anticipated challenges include determining optimal sample collection times and designing diagnostic workflows that minimize processing-associated marker loss and degradation. Conventional, commercial, and emerging technologies that address these variables are discussed. If realized, isoniazid associated markers could provide proof of concept for novel elicitor-based diagnostic approaches capable of confirming LTBI and empirically treated extrapulmonary TB.
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Affiliation(s)
- Brad W Porter
- Independent Researcher; P.O. Box 56224, Atlanta, GA 30343, USA.
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Carnevale GG, Vargas FS, Caiaffa-Filho HH, Acencio MMP, Marçal LJ, Sales RKB, Teixeira LR, Antonangelo L. Preanalytical conditions can interfere with M. tuberculosis detection by PCR in respiratory samples. Clinics (Sao Paulo) 2018; 73:e410. [PMID: 30517280 PMCID: PMC6238817 DOI: 10.6061/clinics/2017/e410] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 08/09/2018] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVES Tuberculosis is one of the most prevalent infections in humans. Although culture is the reference for diagnosis, its sensitivity is compromised, especially in paucibacillary samples. Because polymerase chain reaction (PCR) amplifies mycobacterial DNA, it is more sensitive than culture for the diagnosis of Mycobacterium tuberculosis (Mtb). However, its performance can be affected by intrinsic sample inhibitors and by the extraction/detection techniques used. METHODS We evaluated the influence of preanalytical conditions on Mtb detection in samples of sputum (SPU), bronchoalveolar lavage (BAL), and pleural fluid (PF) using combinations of extraction/detection methods. Respiratory samples were prepared to contain different concentrations of red blood cells and nucleated cells to which increasing amounts of Mtb colonies were inoculated and submitted to PCR. RESULTS Up to 102 CFU/ml of Mtb were detected in the SPU in all methods, except for the Roche extraction/detection method, regardless of the preanalytical sample condition. In BAL samples, medium and high concentrations of cells and high concentrations of red blood cells contributed to a lower Mtb detection, regardless of the extraction method used. In PF, red blood cells were the variable that most interfered with Mtb detection, with better recovery (102 CFU/ml) observed with the Qiagen/Nanogen combination. CONCLUSION The choice of Mtb extraction and detection method is of fundamental importance for PCR analytical sensitivity, especially when paucibacillary samples and/or samples containing potential PCR inhibitors are analyzed.
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Affiliation(s)
- Gabriela Gaspar Carnevale
- Divisao Pulmonar, Instituto do Coracao (InCor), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, BR
- Laboratorio de Investigacao Medica (LIM 03), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Francisco Suso Vargas
- Divisao Pulmonar, Instituto do Coracao (InCor), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Hélio Hehl Caiaffa-Filho
- Laboratorio de Investigacao Medica (LIM 03), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Milena Marques Pagliarelli Acencio
- Divisao Pulmonar, Instituto do Coracao (InCor), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Lia Junqueira Marçal
- Divisao Pulmonar, Instituto do Coracao (InCor), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Roberta Karla Barbosa Sales
- Divisao Pulmonar, Instituto do Coracao (InCor), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Lisete Ribeiro Teixeira
- Divisao Pulmonar, Instituto do Coracao (InCor), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Leila Antonangelo
- Divisao Pulmonar, Instituto do Coracao (InCor), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, BR
- Laboratorio de Investigacao Medica (LIM 03), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, BR
- Corresponding author. E-mail: /
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11
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Baron EJ, Tenover FC, Gnanashanmugam D. Direct Detection of Mycobacterium tuberculosis in Clinical Specimens Using Nucleic Acid Amplification Tests. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.clinmicnews.2018.06.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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12
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Eddabra R, Ait Benhassou H. Rapid molecular assays for detection of tuberculosis. Pneumonia (Nathan) 2018; 10:4. [PMID: 29876241 PMCID: PMC5968606 DOI: 10.1186/s41479-018-0049-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 05/14/2018] [Indexed: 01/01/2023] Open
Abstract
Tuberculosis (TB) is an infectious disease that remains an important public health problem at the global level. It is one of the main causes of morbidity and mortality, due to the emergence of antibiotic resistant Mycobacterium strains and HIV co-infection. Over the past decade, important progress has been made for better control of the disease. While microscopy and culture continue to be indispensible for laboratory diagnosis of tuberculosis, the range of several molecular diagnostic tests, including the nucleic acid amplification test (NAAT) and whole-genome sequencing (WGS), have expanded tremendously. They are becoming more accessible not only for detection and identification of Mycobacterium tuberculosis complex in clinical specimens, but now extend to diagnosing multi-drug resistant strains. Molecular diagnostic tests provide timely results useful for high-quality patient care, low contamination risk, and ease of performance and speed. This review focuses on the current diagnostic tests in use, including emerging technologies used for detection of tuberculosis in clinical specimens. The sensitivity and specificity of these tests have also been taken into consideration.
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Affiliation(s)
- Rkia Eddabra
- Higher Institute of Nursing Professions and Health Techniques, Avenue Colonnel Major Habbouha Oueld Laâbid. Madinat Al Wahda I, Laayoune, Morocco
| | - Hassan Ait Benhassou
- Medical Biotechnology Center, Moroccan Foundation for Advanced Science, Innovation and Research (MAScIR), Rabat Design Center, Avenue Mohamed El Jazouli - Madinat Al Irfane, 10100 Rabat, Morocco
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Improved performance of the artus Mycobacterium tuberculosis RG PCR kit in a low incidence setting: a retrospective monocentric study. Sci Rep 2017; 7:14127. [PMID: 29074852 PMCID: PMC5658397 DOI: 10.1038/s41598-017-14367-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 10/09/2017] [Indexed: 11/12/2022] Open
Abstract
Tuberculosis (TB) and the spread of Mycobacterium tuberculosis complex (MTBC) strains resistant against rifampin (RIF) and isoniazid (INH) pose a serious threat to global health. However, rapid and reliable MTBC detection along with RIF/INH susceptibility testing are challenging in low prevalence countries due to the higher rate of false positives. Here, we provide the first performance data for the artus MTBC PCR assay in a low prevalence setting. We analyze 1323 respiratory and 311 non-respiratory samples with the artus MTBC PCR assay as well as by mycobacterial culture and microscopy. We propose retesting of specimens in duplicate and consideration of a determined cycle-threshold value cut-off greater than 34, as this significantly increases accuracy, specificity, and negative predictive value without affecting sensitivity. Furthermore, we tested fourteen MTBC positive samples with the GenoType MTBDRplus test and demonstrate that using an identical DNA extraction protocol for both assays does not impair downstream genotypic testing for RIF and INH susceptibility. In conclusion, our procedure optimizes the use of the artus MTB assay with workload efficient methods in a low incidence setting. Combining the modified artus MTB with the GenoType MTBDRplus assays allows rapid and accurate detection of MTBC and RIF/INH resistance.
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14
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Babafemi EO, Cherian BP, Banting L, Mills GA, Ngianga K. Effectiveness of real-time polymerase chain reaction assay for the detection of Mycobacterium tuberculosis in pathological samples: a systematic review and meta-analysis. Syst Rev 2017; 6:215. [PMID: 29070061 PMCID: PMC5657121 DOI: 10.1186/s13643-017-0608-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 10/12/2017] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Rapid and accurate diagnosis of tuberculosis (TB) is key to manage the disease and to control and prevent its transmission. Many established diagnostic methods suffer from low sensitivity or delay of timely results and are inadequate for rapid detection of Mycobacterium tuberculosis (MTB) in pulmonary and extra-pulmonary clinical samples. This study examined whether a real-time polymerase chain reaction (RT-PCR) assay, with a turn-a-round time of 2 h, would prove effective for routine detection of MTB by clinical microbiology laboratories. METHODS A systematic literature search was performed for publications in any language on the detection of MTB in pathological samples by RT-PCR assay. The following sources were used MEDLINE via PubMed, EMBASE, BIOSIS Citation Index, Web of Science, SCOPUS, ISI Web of Knowledge and Cochrane Infectious Diseases Group Specialised Register, grey literature, World Health Organization and Centres for Disease Control and Prevention websites. Forty-six studies met set inclusion criteria. Generated pooled summary estimates (95% CIs) were calculated for overall accuracy and bivariate meta-regression model was used for meta-analysis. RESULTS Summary estimates for pulmonary TB (31 studies) were as follows: sensitivity 0.82 (95% CI 0.81-0.83), specificity 0.99 (95% CI 0.99-0.99), positive likelihood ratio 43.00 (28.23-64.81), negative likelihood ratio 0.16 (0.12-0.20), diagnostic odds ratio 324.26 (95% CI 189.08-556.09) and area under curve 0.99. Summary estimates for extra-pulmonary TB (25 studies) were as follows: sensitivity 0.70 (95% CI 0.67-0.72), specificity 0.99 (95% CI 0.99-0.99), positive likelihood ratio 29.82 (17.86-49.78), negative likelihood ratio 0.33 (0.26-0.42), diagnostic odds ratio 125.20 (95% CI 65.75-238.36) and area under curve 0.96. CONCLUSIONS RT-PCR assay demonstrated a high degree of sensitivity for pulmonary TB and good sensitivity for extra-pulmonary TB. It indicated a high degree of specificity for ruling in TB infection from sampling regimes. This was acceptable, but may better as a rule out add-on diagnostic test. RT-PCR assays demonstrate both a high degree of sensitivity in pulmonary samples and rapidity of detection of TB which is an important factor in achieving effective global control and for patient management in terms of initiating early and appropriate anti-tubercular therapy. SYSTEMATIC REVIEW REGISTRATION PROSPERO CRD42015027534 .
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Affiliation(s)
- Emmanuel O. Babafemi
- Microbiology Department, Pathology Division, Sandwell and West Birmingham Hospitals NHS Trust, Birmingham, UK
| | | | - Lee Banting
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, UK
| | - Graham A. Mills
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, UK
| | - Kandala Ngianga
- School of Health Sciences and Social Work, University of Portsmouth, Portsmouth, UK
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15
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Park JE, Huh HJ, Koh WJ, Song DJ, Ki CS, Lee NY. Performance evaluation of the Cobas TaqMan MTB assay on respiratory specimens according to clinical application. Int J Infect Dis 2017; 64:42-46. [PMID: 28882668 DOI: 10.1016/j.ijid.2017.08.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 08/10/2017] [Accepted: 08/26/2017] [Indexed: 11/16/2022] Open
Abstract
OBJECTIVE To evaluate the performance of the Cobas TaqMan MTB assay (Cobas assay) with respect to its clinical application. METHODS This was a retrospective analysis of 1154 results from 1034 patients for whom mycobacterial cultures and the Cobas assay were performed simultaneously. Based on the patient medical records, two categories of clinical application were defined: (1) the diagnosis of patients with a high probability of pulmonary tuberculosis according to clinical and radiological features (n=128), and (2) the exclusion of tuberculosis in clinically indeterminate patients (n=1026). Standard culture was used as the reference method. RESULTS The sensitivity of the Cobas assay for the detection of Mycobacterium tuberculosis was 70.4% (95% confidence interval (CI) 49.7-85.5%) for category 1, but only 25.0% (95% CI 4.5-64.4%) for category 2. The specificity was ≥95.0% for both categories. The positive predictive value was 79.2% (95% CI 57.3-92.1%) for category 1 and 33.3% (95% CI 6.0-75.9%) for category 2, while the negative predictive value was 92.3% (95% CI 85.0-96.4%) for category 1 and 99.4% (95% CI 98.7-99.8%) for category 2. CONCLUSIONS The results of this study indicate that Cobas assay results must be interpreted carefully according to the clinical purpose of the assay.
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Affiliation(s)
- Jong Eun Park
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Won-Jung Koh
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Dong Joon Song
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Chang-Seok Ki
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
| | - Nam Yong Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
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Gkaravela L, Papadimitriou-Olivgeris M, Foka A, Kolonitsiou F, Spiliopoulou A, Charokopos N, Voulgaridis A, Tsiamita M, Marangos M, Anastassiou ED, Spiliopoulou I. Combination of commercially available molecular assays and culture based methods in diagnosis of tuberculosis and drug resistant tuberculosis. Braz J Microbiol 2017; 48:785-790. [PMID: 28689813 PMCID: PMC5628296 DOI: 10.1016/j.bjm.2017.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 01/16/2017] [Accepted: 04/27/2017] [Indexed: 01/09/2023] Open
Abstract
Early diagnosis of tuberculosis is of major clinical importance. Among 4733 clinical specimens collected from 3363 patients and subjected to Ziehl–Neelsen microscopy, 4109 were inoculated onto Löwenstein–Jensen slants and 3139 in Bactec/9000MB. Polymerase Chain Reaction (PCR) was performed in 3139 specimens, whereas, a genotypic assay was directly applied in 93 Mycobacterium tuberculosis complex PCR-positive for isoniazid and rifampicin resistance detection specimens (GenoType MTBDRplus). Recovered M. tuberculosis isolates (64) as well as, 21 more sent from Regional Hospitals were tested for antimycobacterial resistance with a phenotypic (manual MGIT-SIRE) and a genotypic assay (GenoType MTBDRplus). PCR in the clinical specimens showed excellent specificity (97.4%) and accuracy (96.8%), good sensitivity (70.4%), but low positive predictive value (40.3%). MGIT-SIRE performed to M. tuberculosis did not confer a reliable result in 16 isolates. Of the remaining 69 isolates, 15 were resistant to streptomycin, seven to isoniazid, seven to ethambutol and five to rifampicin. GenoType MTBDRplus correctly detected isoniazid (seven) and rifampicin-resistant M. tuberculosis strains (five), showing an excellent performance overall (100%). Susceptibility results by the molecular assay applied directly to clinical specimens were identical to those obtained from recovered isolates of the corresponding patients. Combining molecular and conventional methods greatly contribute to early diagnosis and accurate susceptibility testing of tuberculosis.
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Affiliation(s)
- Lamprini Gkaravela
- Department of Microbiology, School of Medicine, University of Patras, Rion, Patras, Greece
| | | | - Antigoni Foka
- Department of Microbiology, School of Medicine, University of Patras, Rion, Patras, Greece
| | - Fevronia Kolonitsiou
- Department of Microbiology, School of Medicine, University of Patras, Rion, Patras, Greece
| | - Anastasia Spiliopoulou
- Department of Microbiology, School of Medicine, University of Patras, Rion, Patras, Greece
| | - Nikolaos Charokopos
- Department of Pulmonology, Regional General Hospital of Pirgos, Pirgos, Greece
| | - Apostolos Voulgaridis
- Department of Pulmonology, University General Hospital of Patras, Rion, Patras, Greece
| | - Maria Tsiamita
- Department of Pulmonology, University General Hospital of Patras, Rion, Patras, Greece
| | - Markos Marangos
- Division of Infectious Diseases, School of Medicine, University of Patras, Rion, Patras, Greece
| | | | - Iris Spiliopoulou
- Department of Microbiology, School of Medicine, University of Patras, Rion, Patras, Greece.
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17
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Wang HY, Uh Y, Kim S, Lee H. Performance of the Quantamatrix Multiplexed Assay Platform system for the differentiation and identification of Mycobacterium species. J Med Microbiol 2017; 66:777-787. [PMID: 28604333 DOI: 10.1099/jmm.0.000495] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
PURPOSE The purpose of this study was to evaluate the usefulness of a new diagnostic multiplexed bead-based bioassay (Quantamatrix Multiplexed Assay Platform; QMAP) system with shape-encoded silica microparticles for the rapid and accurate detection and identification of 23 mycobacterial species/groups, including Mycobacterium tuberculosis complex (MTBC). METHODOLOGY A total of 295 mycobacterial clinical isolates cultured from respiratory specimens were used for identification of MTBC and non-tuberculous mycobacteria (NTM) using the QMAP system and the results were confirmed with PCR-restriction fragment length polymorphism (RFLP) analysis of the rpoB gene, rpoB sequence analysis and PCR-reverse blot hybridization assay (REBA).Results/Key findings. The Mycobacterium genus-specific probe of the QMAP system was positive for all 46 Mycobacterium reference strains and negative for 59 non-Mycobacterium strains. Based on 295 liquid culture-positive samples, both the culture-based conventional identification method and the QMAP system identified each 212 and 81 isolates as MTB and NTM species. The concordance rates for the identification of NTM species between the QMAP system and molecular assays were 92.8 % (77/83), 97.6 % (81/83) and 100 % (83/83) for PCR-RFLP, the rpoB sequence analysis and PCR-REBA, respectively. CONCLUSION The QMAP system yielded rapid, highly sensitive and specific results for the identification of MTBC and NTM and accurately discriminated between NTM species within 3 h.
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Affiliation(s)
- Hye-Young Wang
- Optipharm, Inc., Wonju Eco Environmental Technology Center, Wonju, Gangwon, 26493, Republic of Korea
| | - Young Uh
- Department of Laboratory Medicine, Yonsei University Wonju College of Medicine, 20 Ilsan-ro, Wonju, Gangwon, 26426, Republic of Korea
| | - Seoyong Kim
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, Gangwon, 26493, Republic of Korea
| | - Hyeyoung Lee
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, Gangwon, 26493, Republic of Korea
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18
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Wang HY, Uh Y, Kim S, Shim TS, Lee H. Evaluation of the Quantamatrix Multiplexed Assay Platform system for simultaneous detection of Mycobacterium tuberculosis and the rifampicin resistance gene using cultured mycobacteria. Int J Infect Dis 2017. [PMID: 28627431 DOI: 10.1016/j.ijid.2017.06.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The differentiation of Mycobacterium tuberculosis complex (MTBC) from non-tuberculous mycobacteria (NTM) is of primary importance for infection control and the selection of anti-tuberculosis drugs. Up to date data on rifampicin (RIF)-resistant tuberculosis (TB) is essential for the early management of multidrug-resistant TB. The aim of this study was to evaluate the usefulness of a newly developed multiplexed, bead-based bioassay (Quantamatrix Multiplexed Assay Platform, QMAP) for the rapid differentiation of 23 Mycobacterium species including MTBC and RIF-resistant strains. METHODS A total of 314 clinical Mycobacterium isolates cultured from respiratory specimens were used in this study. RESULTS The sensitivity and specificity of the QMAP system for Mycobacterium species were 100% (95% CI 99.15-100%, p<0.0001) and 97.8% (95% CI 91.86-99.87%, p<0.0001), respectively. The results of conventional drug susceptibility testing and the QMAP Dual-ID assay were completely concordant for all clinical isolates (100%, 95% CI 98.56-100%). Out of 223 M. tuberculosis (MTB) isolates, 196 were pan-susceptible and 27 were resistant to RIF according to QMAP results. All of the mutations in the RIF resistance-determining region detected by the QMAP system were confirmed by rpoB sequence analysis and a REBA MTB-Rifa reverse blot hybridization assay. The majority of the mutations (n=26, 96.3%), including those missing wild-type probe signals, were located in three codons (529-534, 524-529, and 514-520), and 17 (65.4%) of these mutations were detected by three mutation probes (531TTG, 526TAC, and 516GTC). CONCLUSIONS The entire QMAP system assay takes about 3h to complete, while results from the culture-based conventional method can take up to 48-72h. Although improvements to the QMAP system are needed for direct respiratory specimens, it may be useful for rapid screening, not only to identify and accurately discriminate MTBC from NTM, but also to identify RIF-resistant MTB strains in positive culture samples.
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Affiliation(s)
- Hye-Young Wang
- Optipharm, Inc., Wonju Eco Environmental Technology Center, Wonju, Gangwon, 26493, Republic of Korea
| | - Young Uh
- Department of Laboratory Medicine, Yonsei University Wonju College of Medicine, 20 Ilsan-ro, Wonju, Gangwon, 26426, Republic of Korea.
| | - Seoyong Kim
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, Gangwon, 26493, Republic of Korea
| | - Tae-Sun Shim
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05535, Republic of Korea
| | - Hyeyoung Lee
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, Gangwon, 26493, Republic of Korea.
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Hinić V, Feuz K, Turan S, Berini A, Frei R, Pfeifer K, Goldenberger D. Clinical evaluation of the Abbott RealTime MTB Assay for direct detection of Mycobacterium tuberculosis-complex from respiratory and non-respiratory samples. Tuberculosis (Edinb) 2017; 104:65-69. [PMID: 28454651 DOI: 10.1016/j.tube.2017.03.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 02/27/2017] [Accepted: 03/02/2017] [Indexed: 10/20/2022]
Abstract
Rapid and reliable diagnosis is crucial for correct management of tuberculosis. The Abbott RealTime MTB Assay represents a novel qualitative real-time PCR assay for direct detection of M. tuberculosis-complex (MTB) DNA from respiratory samples. The test targets two highly conserved sequences, the multi-copy insertion element IS6110 and the protein antigen B (PAB) gene of MTB, allowing even the detection of IS6610-deficient strains. We evaluated this commercial diagnostic test by analyzing 200 respiratory and, for the first time, 87 non-respiratory clinical specimens from our tertiary care institution and compared its results to our IS6110-based in-house real-time PCR for MTB as well as MTB culture. Overall sensitivity for Abbott RealTime MTB was 100% (19/19) in smear positive and 87.5% (7/8) in smear negative specimens, while the specificity of the assay was 100% (260/260). For both non-respiratory smear positive and smear negative specimens Abbott RealTime MTB tests showed 100% (8/8) sensitivity and 100% (8/8) specificity. Cycle threshold (Ct) value analysis of 16 MTB positive samples showed a slightly higher Ct value of the Abbott RealTime MTB test compared to our in-house MTB assay (mean delta Ct = 2.55). In conclusion, the performance of the new Abbott RealTime MTB Assay was highly similar to culture and in-house MTB PCR. We document successful analysis of 87 non-respiratory samples with the highly automated Abbott RealTime MTB test with no inhibition observed.
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Affiliation(s)
- Vladimira Hinić
- Division of Clinical Microbiology, University Hospital Basel, Petersgraben 4, 4031 Basel, Switzerland.
| | - Kinga Feuz
- Division of Clinical Microbiology, University Hospital Basel, Petersgraben 4, 4031 Basel, Switzerland.
| | - Selda Turan
- Division of Clinical Microbiology, University Hospital Basel, Petersgraben 4, 4031 Basel, Switzerland.
| | - Andrea Berini
- Division of Clinical Microbiology, University Hospital Basel, Petersgraben 4, 4031 Basel, Switzerland.
| | - Reno Frei
- Division of Clinical Microbiology, University Hospital Basel, Petersgraben 4, 4031 Basel, Switzerland.
| | - Karin Pfeifer
- Abbott Molecular, Max-Planck-Ring 2, 65205 Wiesbaden, Germany.
| | - Daniel Goldenberger
- Division of Clinical Microbiology, University Hospital Basel, Petersgraben 4, 4031 Basel, Switzerland.
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20
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Su KY, Yan BS, Chiu HC, Yu CJ, Chang SY, Jou R, Liu JL, Hsueh PR, Yu SL. Rapid Sputum Multiplex Detection of the M. tuberculosis Complex (MTBC) and Resistance Mutations for Eight Antibiotics by Nucleotide MALDI-TOF MS. Sci Rep 2017; 7:41486. [PMID: 28134321 PMCID: PMC5278408 DOI: 10.1038/srep41486] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 12/21/2016] [Indexed: 01/29/2023] Open
Abstract
The increasing incidence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) Mycobacterium tuberculosis (MTB) adds further urgency for rapid and multiplex molecular testing to identify the MTB complex and drug susceptibility directly from sputum for disease control. A nucleotide matrix-assisted-laser-desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS)-based assay was developed to identify MTB (MTBID panel) and 45 chromosomal mutations for resistance to eight antibiotics (MTBDR panel). We conducted a 300 case trial from outpatients to evaluate this platform. An MTBID panel specifically identified MTB with as few as 10 chromosome DNA copies. The panel was 100% consistent with an acid-fast stain and culture for MTB, nontuberculous mycobacteria, and non-mycobacteria bacteria. The MTBDR panel was validated using 20 known MDR-MTB isolates. In a 64-case double-blind clinical isolates test, the sensitivity and specificity were 83% and 100%, respectively. In a 300-case raw sputum trial, the MTB identification sensitivity in smear-negative cases using MALDI-TOF MS was better than the COBAS assay (61.9% vs. 46.6%). Importantly, the failure rate of MALDI-TOF MS was better than COBAS (11.3% vs. 26.3%). To the best of our knowledge, the test described herein is the only multiplex test that predicts resistance for up to eight antibiotics with both sensitivity and flexibility.
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Affiliation(s)
- Kang-Yi Su
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan.,Department of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Bo-Shiun Yan
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hao-Chieh Chiu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan.,Department of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chong-Jen Yu
- Department of Internal Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - So-Yi Chang
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ruwen Jou
- Centers for Disease Control, Taipei, Taiwan
| | - Jia-Long Liu
- Department of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Po-Ren Hsueh
- Department of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan.,Department of Internal Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Sung-Liang Yu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan.,Department of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan.,Department of Pathology and Graduate Institute of Pathology, College of Medicine, National Taiwan University, Taipei, Taiwan.,Center for Optoelectronic Biomedicine, College of Medicine, National Taiwan University, Taipei, Taiwan.,Institute of Medical Device and Imaging, College of Medicine, National Taiwan University, Taipei, Taiwan
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Methodological and Clinical Aspects of the Molecular Epidemiology of Mycobacterium tuberculosis and Other Mycobacteria. Clin Microbiol Rev 2016; 29:239-90. [PMID: 26912567 DOI: 10.1128/cmr.00055-15] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Molecular typing has revolutionized epidemiological studies of infectious diseases, including those of a mycobacterial etiology. With the advent of fingerprinting techniques, many traditional concepts regarding transmission, infectivity, or pathogenicity of mycobacterial bacilli have been revisited, and their conventional interpretations have been challenged. Since the mid-1990s, when the first typing methods were introduced, a plethora of other modalities have been proposed. So-called molecular epidemiology has become an essential subdiscipline of modern mycobacteriology. It serves as a resource for understanding the key issues in the epidemiology of tuberculosis and other mycobacterial diseases. Among these issues are disclosing sources of infection, quantifying recent transmission, identifying transmission links, discerning reinfection from relapse, tracking the geographic distribution and clonal expansion of specific strains, and exploring the genetic mechanisms underlying specific phenotypic traits, including virulence, organ tropism, transmissibility, or drug resistance. Since genotyping continues to unravel the biology of mycobacteria, it offers enormous promise in the fight against and prevention of the diseases caused by these pathogens. In this review, molecular typing methods for Mycobacterium tuberculosis and nontuberculous mycobacteria elaborated over the last 2 decades are summarized. The relevance of these methods to the epidemiological investigation, diagnosis, evolution, and control of mycobacterial diseases is discussed.
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Leylabadlo HE, Kafil HS, Yousefi M, Aghazadeh M, Asgharzadeh M. Pulmonary Tuberculosis Diagnosis: Where We Are? Tuberc Respir Dis (Seoul) 2016; 79:134-42. [PMID: 27433173 PMCID: PMC4943897 DOI: 10.4046/trd.2016.79.3.134] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Revised: 11/01/2015] [Accepted: 01/19/2016] [Indexed: 11/24/2022] Open
Abstract
In recent years, in spite of medical advancement, tuberculosis (TB) remains a worldwide health problem. Although many laboratory methods have been developed to expedite the diagnosis of TB, delays in diagnosis remain a major problem in the clinical practice. Because of the slow growth rate of the causative agent Mycobacterium tuberculosis, isolation, identification, and drug susceptibility testing of this organism and other clinically important mycobacteria can take several weeks or longer. During the past several years, many methods have been developed for direct detection, species identification, and drug susceptibility testing of TB. A good understanding of the effectiveness and practical limitations of these methods is important to improve diagnosis. This review summarizes the currently-used advances in nonmolecular and molecular diagnostics.
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Affiliation(s)
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehdi Yousefi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Aghazadeh
- Infectious Disease and Tropical Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Asgharzadeh
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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Diagnostic Molecular Mycobacteriology in Regions With Low Tuberculosis Endemicity: Combining Real-time PCR Assays for Detection of Multiple Mycobacterial Pathogens With Line Probe Assays for Identification of Resistance Mutations. EBioMedicine 2016; 9:228-237. [PMID: 27333026 PMCID: PMC4972562 DOI: 10.1016/j.ebiom.2016.06.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 06/10/2016] [Accepted: 06/12/2016] [Indexed: 11/25/2022] Open
Abstract
Molecular assays have not yet been able to replace time-consuming culture-based methods in clinical mycobacteriology. Using 6875 clinical samples and a study period of 35 months we evaluated the use of PCR-based assays to establish a diagnostic workflow with a fast time-to-result of 1–2 days, for 1. detection of Mycobacterium tuberculosis complex (MTB), 2. detection and identification of nontuberculous mycobacteria (NTM), and 3. identification of drug susceptible MTB. MTB molecular-based detection and culture gave concordant results for 97.7% of the specimens. NTM PCR-based detection and culture gave concordant results for 97.0% of the specimens. Defining specimens on the basis of combined laboratory data as true positives or negatives with discrepant results resolved by clinical chart reviews, we calculated sensitivity, specificity, PPV and NPV for PCR-based MTB detection as 84.7%, 100%, 100%, and 98.7%; the corresponding values for culture-based MTB detection were 86.3%, 100%, 100%, and 98.8%. PCR-based detection of NTM had a sensitivity of 84.7% compared to 78.0% of that of culture-based NTM detection. Molecular drug susceptibility testing (DST) by line-probe assay was found to predict phenotypic DST results in MTB with excellent accuracy. Our findings suggest a diagnostic algorithm to largely replace lengthy culture-based techniques by rapid molecular-based methods. Molecular assays have not yet been able to replace time-consuming culture-based methods in the mycobacteriology laboratory. We have evaluated genetic tests for: i) detection of MTB, ii) detection of NTM, and iii) identification of susceptible MTB. Our findings suggest a diagnostic algorithm to replace lengthy culture-based techniques by rapid molecular-based methods.
There are > 700 reports on molecular detection of tuberculosis in respiratory and non-respiratory specimens. Limited published data exist on molecular tests for detection of nontuberculous mycobacteria (NTM) and tuberculosis drug susceptibility in clinical samples. We demonstrate an excellent accuracy of molecular-based detection of tuberculosis and NTM in conjunction with molecular-based rapid recognition of drug-susceptible and drug-resistant tuberculosis. The diagnostic algorithm developed in this work allows the rapid recognition of clinically relevant mycobacterial infections and tuberculosis drug resistance.
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Early detection of Mycobacterium tuberculosis complex in BACTEC MGIT cultures using nucleic acid amplification. Eur J Clin Microbiol Infect Dis 2016; 35:977-84. [PMID: 27039339 DOI: 10.1007/s10096-016-2625-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Accepted: 03/10/2016] [Indexed: 10/22/2022]
Abstract
We evaluated the application of nucleic acid amplification (NAA) in liquid cultures for the early detection of Mycobacterium tuberculosis. The Cobas TaqMan MTB test, IS6110 real-time PCR, and hsp65 PCR-restriction fragment length polymorphism (RFLP) analysis were used to detect BACTEC MGIT 960 (MGIT) cultures on days 3, 5, 7, and 14. The procedure was initially tested with a reference strain, H37Rv (ATCC 27294). Subsequently, 200 clinical specimens, including 150 Acid Fast bacillus (AFB) smear-positive and 50 AFB smear-negative samples, were examined. The Cobas TaqMan MTB test and IS6110-based PCR analysis were able to detect M. tuberculosis after 1 day when the inoculum of H37Rv was >3 x 10(-2) CFU/ml. After a 5-day incubation in the MGIT system, all three NAA assays had a positive detection regardless of the inoculum size. After a 1-day incubation of the clinical specimens in the MGIT system, the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) for the Cobas TaqMan MTB assay were 70.2%, 100%, 100%, and 82.3% respectively. For IS6110-based PCR analysis, these values were 63.1%, 100%, 100%, and 78.9%, and were 88.1%, 100%, 100%, and 92.1% respectively for hsp65 PCR-RFLP analysis. After a 3-day incubation, the specificity and PPV were 100% for all three NAA tests; the Cobas TaqMan MTB assay had the best sensitivity (97.6%) and NPV (98.3%). The sensitivity, specificity, PPV, and NPV for conventional culture analysis were 98.8%, 100%, 100%, and 99.1%. Thus, NAA may be useful for the early detection of M. tuberculosis after 3 days in MGIT.
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Performance characteristics of the new Abbott Real Time MTB assay for detection of Mycobacterium tuberculosis complex in respiratory specimens. Diagn Microbiol Infect Dis 2016; 84:212-4. [DOI: 10.1016/j.diagmicrobio.2015.11.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 10/19/2015] [Accepted: 11/03/2015] [Indexed: 11/22/2022]
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Shetty P, Ghosh D, Singh M, Tripathi A, Paul D. Rapid amplification of Mycobacterium tuberculosis DNA on a paper substrate. RSC Adv 2016. [DOI: 10.1039/c6ra07529k] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We have amplified DNA from Mycobacterium tuberculosis on a paper substrate in 10 minutes using helicase dependent amplification technique.
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Affiliation(s)
- Prasad Shetty
- Department of Biosciences and Bioengineering
- Indian Institute of Technology Bombay
- Mumbai 400076
- India
| | - Dipayan Ghosh
- Department of Biosciences and Bioengineering
- Indian Institute of Technology Bombay
- Mumbai 400076
- India
| | - Minakshi Singh
- Department of Biosciences and Bioengineering
- Indian Institute of Technology Bombay
- Mumbai 400076
- India
| | - Aparna Tripathi
- Department of Biosciences and Bioengineering
- Indian Institute of Technology Bombay
- Mumbai 400076
- India
| | - Debjani Paul
- Department of Biosciences and Bioengineering
- Indian Institute of Technology Bombay
- Mumbai 400076
- India
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Raizada N, Sachdeva KS, Swaminathan S, Kulsange S, Khaparde SD, Nair SA, Khanna A, Chopra KK, Hanif M, Sethi GR, Umadevi KR, Keshav Chander G, Saha B, Shah A, Parmar M, Ghediya M, Jaju J, Boehme C, Paramasivan CN. Piloting Upfront Xpert MTB/RIF Testing on Various Specimens under Programmatic Conditions for Diagnosis of TB & DR-TB in Paediatric Population. PLoS One 2015; 10:e0140375. [PMID: 26469691 PMCID: PMC4607299 DOI: 10.1371/journal.pone.0140375] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 09/24/2015] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND India accounts for one-fifth of the global TB incidence. While the exact burden of childhood TB is not known, TB remains one of the leading causes of childhood mortality in India. Bacteriological confirmation of TB in children is challenging due to difficulty in obtaining quality specimens, in the absence of which diagnosis is largely based on clinical judgement. While testing multiple specimens can potentially contribute to higher proportion of laboratory confirmed paediatric TB cases, lack of high sensitivity tests adds to the diagnostic challenge. We describe here our experiences in piloting upfront Xpert MTB/RIF testing, for diagnosis of TB in paediatric population in respiratory and extra pulmonary specimens, as recently recommended by WHO. METHOD Xpert MTB/RIF testing was offered to all paediatric (0-14 years) presumptive TB cases (both pulmonary and extra-pulmonary) seeking care at public and private health facilities in the project areas covering 4 cities of India. RESULTS Under this pilot project, 8,370 paediatric presumptive TB & presumptive DR-TB cases were tested between April and-November 2014. Overall, 9,149 specimens were tested, of which 4,445 (48.6%) were non-sputum specimens. Xpert MTB/RIF gave 9,083 (99.2%, CI 99.0-99.4) valid results. Of the 8,143 presumptive TB cases enrolled, 517 (6.3%, CI 5.8-6.9) were bacteriologically confirmed. TB detection rates were two fold higher with Xpert MTB/RIF as compared to smear microscopy. Further, a total of 60 rifampicin resistant TB cases were detected, of which 38 were detected among 512 presumptive TB cases while 22 were detected amongst 227 presumptive DR-TB cases tested under the project. CONCLUSION Xpert MTB/RIF with advantages of quick turnaround testing-time, high proportion of interpretable results and feasibility of rapid rollout, substantially improved the diagnosis of bacteriologically confirmed TB in children, while simultaneously detecting rifampicin resistance.
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Affiliation(s)
- Neeraj Raizada
- Foundation for Innovative New Diagnostics, New Delhi, India
- * E-mail:
| | | | | | | | | | | | | | | | | | | | - K. R. Umadevi
- National Institute of research in Tuberculosis, Chennai, India
| | | | | | - Amar Shah
- Central TB Division, Government of India, New Delhi, India
| | - Malik Parmar
- World Health Organization, Country Office for India, New Delhi, India
| | - Mayank Ghediya
- Central TB Division, Government of India, New Delhi, India
| | - Jyoti Jaju
- Central TB Division, Government of India, New Delhi, India
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Chen JHK, She KKK, Kwong TC, Wong OY, Siu GKH, Leung CC, Chang KC, Tam CM, Ho PL, Cheng VCC, Yuen KY, Yam WC. Performance of the new automated Abbott RealTime MTB assay for rapid detection of Mycobacterium tuberculosis complex in respiratory specimens. Eur J Clin Microbiol Infect Dis 2015; 34:1827-32. [PMID: 26071001 DOI: 10.1007/s10096-015-2419-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 06/01/2015] [Indexed: 11/29/2022]
Abstract
The automated high-throughput Abbott RealTime MTB real-time PCR assay has been recently launched for Mycobacterium tuberculosis complex (MTBC) clinical diagnosis. This study would like to evaluate its performance. We first compared its diagnostic performance with the Roche Cobas TaqMan MTB assay on 214 clinical respiratory specimens. Prospective analysis of a total 520 specimens was then performed to further evaluate the Abbott assay. The Abbott assay showed a lower limit of detection at 22.5 AFB/ml, which was more sensitive than the Cobas assay (167.5 AFB/ml). The two assays demonstrated a significant difference in diagnostic performance (McNemar's test; P = 0.0034), in which the Abbott assay presented significantly higher area under curve (AUC) than the Cobas assay (1.000 vs 0.880; P = 0.0002). The Abbott assay demonstrated extremely low PCR inhibition on clinical respiratory specimens. The automated Abbott assay required only very short manual handling time (0.5 h), which could help to improve the laboratory management. In the prospective analysis, the overall estimates for sensitivity and specificity of the Abbott assay were both 100 % among smear-positive specimens, whereas the smear-negative specimens were 96.7 and 96.1 %, respectively. No cross-reactivity with non-tuberculosis mycobacterial species was observed. The superiority in sensitivity of the Abbott assay for detecting MTBC in smear-negative specimens could further minimize the risk in MTBC false-negative detection. The new Abbott RealTime MTB assay has good diagnostic performance which can be a useful diagnostic tool for rapid MTBC detection in clinical laboratories.
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Affiliation(s)
- J H K Chen
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Queen, Pokfulam, Hong Kong Special Administrative Region, China
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Cho WH, Won EJ, Choi HJ, Kee SJ, Shin JH, Ryang DW, Suh SP. Comparison of AdvanSure TB/NTM PCR and COBAS TaqMan MTB PCR for Detection of Mycobacterium tuberculosis Complex in Routine Clinical Practice. Ann Lab Med 2015; 35:356-61. [PMID: 25932446 PMCID: PMC4390706 DOI: 10.3343/alm.2015.35.3.356] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/05/2014] [Accepted: 01/12/2015] [Indexed: 11/19/2022] Open
Abstract
The AdvanSure tuberculosis/non-tuberculous mycobacterium (TB/NTM) PCR (LG Life Science, Korea) and COBAS TaqMan Mycobacterium tuberculosis (MTB) PCR (Roche Diagnostics, USA) are commonly used in clinical microbiology laboratories. We aimed to evaluate these two commercial real-time PCR assays for detection of MTB in a large set of clinical samples over a two-year period. AdvanSure TB/NTM PCR and COBAS TaqMan MTB PCR were performed on 9,119 (75.2%) and 3,010 (24.8%) of 12,129 (9,728 respiratory and 2,401 non-respiratory) MTB specimens, with 361 (4.0%) and 102 (3.4%) acid-fast bacilli (AFB)-positive results, respectively. In MTB culture, 788 (6.5%) MTB and 514 (4.2%) NTM were identified. The total sensitivity and specificity of the AdvanSure assay were 67.8% (95% confidence interval [CI], 63.9-71.6) and 98.3% (95% CI, 98.0-98.6), while those of the COBAS TaqMan assay were 67.2% (95% CI, 60.0-73.8) and 98.4% (95% CI, 97.9-98.9), respectively. The sensitivities and specificities of the AdvanSure and COBAS TaqMan assays for AFB-positive and AFB-negative samples were comparable. Furthermore, the AdvanSure assay showed fewer invalid results compared with the COBAS TaqMan assay (5.0 vs. 20.4 invalid results/1,000 tests, P<0.001). AdvanSure assay represents a comparable yet more reliable method than COBAS TaqMan for the identification of mycobacteria in routine clinical microbiology.
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Affiliation(s)
- Won-Hyung Cho
- Department of Surgery, Gwangju Veterans Hospital, Gwangju, Korea
| | - Eun-Jeong Won
- Department of Laboratory Medicine, Chonnam National University Medical School and Hospital, Gwangju, Korea
| | - Hyun-Jung Choi
- Department of Laboratory Medicine, Chonnam National University Medical School and Hospital, Gwangju, Korea
| | - Seung-Jung Kee
- Department of Laboratory Medicine, Chonnam National University Medical School and Hospital, Gwangju, Korea
| | - Jong-Hee Shin
- Department of Laboratory Medicine, Chonnam National University Medical School and Hospital, Gwangju, Korea
| | - Dong-Wook Ryang
- Department of Laboratory Medicine, Chonnam National University Medical School and Hospital, Gwangju, Korea
| | - Soon-Pal Suh
- Department of Laboratory Medicine, Chonnam National University Medical School and Hospital, Gwangju, Korea
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Jönsson B, Lönnermark E, Ridell M. Evaluation of the Cobas TaqMan MTB test for detection ofMycobacterium tuberculosiscomplex. Infect Dis (Lond) 2015; 47:231-6. [DOI: 10.3109/00365548.2014.987162] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Diagnostic challenges of tuberculous lymphadenitis using polymerase chain reaction analysis: a case study. Case Rep Infect Dis 2015; 2015:723726. [PMID: 25685567 PMCID: PMC4320933 DOI: 10.1155/2015/723726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Revised: 01/03/2015] [Accepted: 01/07/2015] [Indexed: 11/30/2022] Open
Abstract
This report presents a case of tuberculous lymphadenitis that was difficult to diagnose using polymerase chain reaction analysis. An 80-year-old Japanese female was hospitalized due to swollen cervical lymph nodes. Her lymph node tests revealed paradoxical polymerase chain reaction results. Polymerase chain reaction analysis of two biopsy tissues using the Cobas TaqMan revealed a positive result for Mycobacterium avium and a negative result for Mycobacterium tuberculosis. However, polymerase chain reaction analysis of a cultured colony of acid-fast bacteria from biopsy tissue using the Cobas TaqMan and an alternative polymerase chain reaction analysis of biopsy tissue yielded discordant results. The patient was diagnosed as having tuberculous lymphadenitis. She was treated with antitubercular drugs and subsequently had a reduction in cervical lymph node swelling. Polymerase chain reaction analysis is not 100% accurate; hence, its use as a diagnostic tool for mycobacterial infection requires increased attention.
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Comparison of the genedia MTB detection kit and the cobas TaqMan MTB assay for detection of Mycobacterium tuberculosis in respiratory specimens. J Clin Microbiol 2015; 53:1012-4. [PMID: 25568443 DOI: 10.1128/jcm.03163-14] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The performance of the Genedia MTB detection kit was compared with that of the Cobas TaqMan MTB test using respiratory specimens. The Genedia and Cobas assays showed comparable sensitivities (81.8% and 78.8%, respectively) and specificities (99.8% and 99.5%, respectively), while the Genedia assay produced fewer invalid results and required less turnaround time and labor.
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Hu X, Shang M, Chen X, Xie Y, Ye Y, Zhou J, Song X, Lu X, Ying B, Wang L. Evaluation of three rapid assays for Mycobacterium tuberculosis complex detection in a comprehensive hospital from West China. Clin Biochem 2014; 48:79-84. [PMID: 25444951 DOI: 10.1016/j.clinbiochem.2014.10.003] [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: 07/24/2014] [Revised: 09/26/2014] [Accepted: 10/01/2014] [Indexed: 02/05/2023]
Abstract
OBJECTIVES To assess the capacity of rapid and accurate confirmation of the Mycobacterium tuberculosis complex (MTBC) in a Chinese clinical laboratory. DESIGN AND METHODS This prospective study investigated three rapid assays, the Amplified Mycobacterium Tuberculosis Direct (MTD) test, real-time PCR, and acid-fast bacilli (AFB) smear, for direct detection of MTBC in a large consecutive series of different clinical specimens. Performance parameters were estimated and compared overall and for separate specimen categories using a combined reference gold standard. RESULTS The overall sensitivities were similar for MTD and real-time PCR (62.26% vs. 58.49%), significantly higher than those of AFB smear (31.13%). Among three assays, MTD had a satisfactory sensitivity in respiratory specimen (73.33%) and a nearly perfect detection for smear-positive samples (96.97%). Real-time PCR showed a high positive rate (58.97%) in regard to nonrespiratory specimen. A combination of molecular assays with conventional methods reached marked additive diagnostic values (sensitivity up to 76.42%), higher than each method individually. All detection systems showed excellent specificities (>96.00%). CONCLUSIONS The present study indicated that our lab had a moderate diagnostic performance for tuberculosis. Quality guarantee for specimen pretreatment, as well as combination analysis, will enable these assays to better incorporate into the routine laboratory workflow in China.
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Affiliation(s)
- Xuejiao Hu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Mengqiao Shang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Xuerong Chen
- Division of Pulmonary Disease, Department of Respiratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Yi Xie
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Yuanxin Ye
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Juan Zhou
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Xingbo Song
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Xiaojun Lu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, PR China.
| | - Lanlan Wang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, PR China.
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Wang HY, Kim H, Kim S, Bang H, Kim DK, Lee H. Evaluation of PCR-reverse blot hybridization assay for the differentiation and identification of Mycobacterium
species in liquid cultures. J Appl Microbiol 2014; 118:142-51. [DOI: 10.1111/jam.12670] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 10/07/2014] [Accepted: 10/15/2014] [Indexed: 11/29/2022]
Affiliation(s)
- H.-Y. Wang
- M&D, Inc.; Wonju Eco Environmental Technology Center; Wonju Gangwon Korea
| | - H. Kim
- Department of Biomedical Laboratory Science; College of Health Sciences; Yonsei University; Wonju Gangwon Korea
| | - S. Kim
- Department of Biomedical Laboratory Science; College of Health Sciences; Yonsei University; Wonju Gangwon Korea
- Institute for Life Science and Biotechnology; Yonsei University; Seoul Korea
| | - H. Bang
- Department of Biomedical Laboratory Science; College of Health Sciences; Yonsei University; Wonju Gangwon Korea
| | - D.-K. Kim
- Department of Laboratory Medicine; St. Vincent's Hospital; The Catholic University of Korea; Suwon Gyeonggi Korea
| | - H. Lee
- Department of Biomedical Laboratory Science; College of Health Sciences; Yonsei University; Wonju Gangwon Korea
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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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