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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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Batuer M, Yuan Y, Yu M, Meng C. Establishment and evaluation of a new fluorescent probe method based on loop-mediated isothermal amplification for the detection of Mycobacterium tuberculosis complex. LUMINESCENCE 2024; 39:e4795. [PMID: 38899381 DOI: 10.1002/bio.4795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 05/07/2024] [Accepted: 05/19/2024] [Indexed: 06/21/2024]
Abstract
We aimed to develop a novel diagnostic method called multiplex fluorescence of loop primer upon self-dequenching loop-mediated isothermal amplification (mFLOS-LAMP) for the rapid detection of Mycobacterium tuberculosis complex (MTBC). A set of specific primers was designed to target the detection of IS1081 and IS6110 genes, which are insertion sequences within the MTBC. The 110 sputum specimens collected were assessed using the established mFLOS-LAMP method, multiplex polymerase chain reaction, Xpert MTB/RIF, and smear microscopy. The optimal reaction temperature and duration for mFLOS-LAMP were determined to be 65°C and 30 min, respectively, by optimizing the entire system. The detection sensitivity of mFLOS-LAMP was 6.0 × 101 CFU/mL, by Bacillus Calmette-Guerin, and the mFLOS-LAMP sensitivity of M. tuberculosis H37Rv genomic DNA was 500 fg, and the specificity was 100%. The sensitivity of mFLOS-LAMP was 94.2% and the specificity was 96.6%, when Xpert MTB/RIF was used as the reference method. There was no statistically significant difference in their detection rate (χ2 = 0, P = 1.000), and the consistency was good (kappa = 0.909, P < 0.001). The receiver operating characteristic analysis yielded the maximum area under the curve of 0.954. The mFLOS-LAMP method demonstrated high sensitivity and specificity, allowing for swift and accurate detection of MTBC.
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Affiliation(s)
- Mireguli Batuer
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Medical University, Urumqi, China
- Department of Clinical Laboratory, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Yue Yuan
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Medical University, Urumqi, China
- Department of Clinical Laboratory, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Mengsi Yu
- Department of Clinical Laboratory, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Cunren Meng
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Medical University, Urumqi, China
- Department of Clinical Laboratory, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
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Naidoo K, Perumal R, Ngema SL, Shunmugam L, Somboro AM. Rapid Diagnosis of Drug-Resistant Tuberculosis-Opportunities and Challenges. Pathogens 2023; 13:27. [PMID: 38251335 PMCID: PMC10819693 DOI: 10.3390/pathogens13010027] [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: 10/16/2023] [Revised: 12/08/2023] [Accepted: 12/20/2023] [Indexed: 01/23/2024] Open
Abstract
Global tuberculosis (TB) eradication is undermined by increasing prevalence of emerging resistance to available drugs, fuelling ongoing demand for more complex diagnostic and treatment strategies. Early detection of TB drug resistance coupled with therapeutic decision making guided by rapid characterisation of pre-treatment and treatment emergent resistance remains the most effective strategy for averting Drug-Resistant TB (DR-TB) transmission, reducing DR-TB associated mortality, and improving patient outcomes. Solid- and liquid-based mycobacterial culture methods remain the gold standard for Mycobacterium tuberculosis (MTB) detection and drug susceptibility testing (DST). Unfortunately, delays to result return, and associated technical challenges from requirements for specialised resource and capacity, have limited DST use and availability in many high TB burden resource-limited countries. There is increasing availability of a variety of rapid nucleic acid-based diagnostic assays with adequate sensitivity and specificity to detect gene mutations associated with resistance to one or more drugs. While a few of these assays produce comprehensive calls for resistance to several first- and second-line drugs, there is still no endorsed genotypic drug susceptibility test assay for bedaquiline, pretomanid, and delamanid. The global implementation of regimens comprising these novel drugs in the absence of rapid phenotypic drug resistance profiling has generated a new set of diagnostic challenges and heralded a return to culture-based phenotypic DST. In this review, we describe the available tools for rapid diagnosis of drug-resistant tuberculosis and discuss the associated opportunities and challenges.
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Affiliation(s)
- Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa (S.L.N.); (L.S.); (A.M.S.)
- SAMRC-CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Rubeshan Perumal
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa (S.L.N.); (L.S.); (A.M.S.)
- SAMRC-CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Senamile L. Ngema
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa (S.L.N.); (L.S.); (A.M.S.)
- SAMRC-CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Letitia Shunmugam
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa (S.L.N.); (L.S.); (A.M.S.)
- SAMRC-CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Anou M. Somboro
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa (S.L.N.); (L.S.); (A.M.S.)
- SAMRC-CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban 4001, South Africa
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David A, Scott LE, Da Silva P, Mayne E, Stevens WS. Storage of Mycobacterium tuberculosis culture isolates in Microbank TM beads at a South African laboratory. Afr J Lab Med 2023; 12:2172. [PMID: 38023785 PMCID: PMC10646387 DOI: 10.4102/ajlm.v12i1.2172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 08/23/2023] [Indexed: 12/01/2023] Open
Abstract
Background Mycobacterium tuberculosis complex (MTBC) isolates are typically stored at -70 °C in cryovials containing 1 mL aliquots of a liquid medium, with or without 50% glycerol. Multiple uses of the culture stock may decrease the strain viability while increasing the risk of culture contamination. Small culture aliquots may be more practical; however, storage capacity remains challenging. MicrobankTM beads (25 beads/vial) for the long-term storage of fungal cultures is well documented, but their use for storing MTBC isolates is uninvestigated. Objective The study aimed to determine the feasibility of using MicrobankTM beads for long-term storage of MTBC isolates at a laboratory in South Africa. Methods In February 2020, 20 isolates in liquid culture were stored in MicrobankTM beads, following an in-house developed protocol, at -70 °C. At defined time points (16 months [15 June 2021] and 21 months [18 November 2021]), two beads were retrieved from each storage vial and assessed for viability and level of contamination. Results Stored liquid isolates demonstrated MTBC growth within an average time-to-detection of 18 days following retrieval, even at 21 months post storage. Contaminating organisms were detected in 2 of 80 (2.5%) culture isolates. Conclusion MicrobankTM beads will allow for the reculture of up to 25 culture isolates using a reduced culture volume compared to current storage methods. MicrobankTM beads represent a storage solution for the medium-term storage of MTBC isolates. What this study adds This study evaluated the use of MicrobankTM beads as an alternate method for storing MTBC culture isolates at -70 °C and provided a suitable option for medium-term storage of MTBC.
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Affiliation(s)
- Anura David
- Wits Diagnostic Innovation Hub, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Lesley E. Scott
- Wits Diagnostic Innovation Hub, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Pedro Da Silva
- National Priority Program, National Health Laboratory Services, Johannesburg, South Africa
| | - Elizabeth Mayne
- National Priority Program, National Health Laboratory Services, Johannesburg, South Africa
- Division of Immunology, University of Cape Town, Cape Town, South Africa
| | - Wendy S. Stevens
- Wits Diagnostic Innovation Hub, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Priority Program, National Health Laboratory Services, Johannesburg, South Africa
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Nandlal L, Perumal R, Naidoo K. Rapid Molecular Assays for the Diagnosis of Drug-Resistant Tuberculosis. Infect Drug Resist 2022; 15:4971-4984. [PMID: 36060232 PMCID: PMC9438776 DOI: 10.2147/idr.s381643] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/20/2022] [Indexed: 11/23/2022] Open
Affiliation(s)
- Louansha Nandlal
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), South African Medical Research Council (SAMRC)-CAPRISA-TB-HIV Pathogenesis and Treatment Research Unit, University of KwaZulu-Natal Nelson R Mandela School of Medicine, Durban, South Africa
| | - Rubeshan Perumal
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), South African Medical Research Council (SAMRC)-CAPRISA-TB-HIV Pathogenesis and Treatment Research Unit, University of KwaZulu-Natal Nelson R Mandela School of Medicine, Durban, South Africa
- Correspondence: Rubeshan Perumal, Centre for the AIDS Programme of Research in South Africa (CAPRISA), South African Medical Research Council (SAMRC)-CAPRISA-TB-HIV Pathogenesis and Treatment Research Unit, University of KwaZulu-Natal Nelson R Mandela School of Medicine, Durban, South Africa, Email
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), South African Medical Research Council (SAMRC)-CAPRISA-TB-HIV Pathogenesis and Treatment Research Unit, University of KwaZulu-Natal Nelson R Mandela School of Medicine, Durban, South Africa
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Zabost A, Filipczak D, Kupis W, Szturmowicz M, Olendrzyński Ł, Winiarska A, Jagodziński J, Augustynowicz-Kopeć E. Use of a FluoroType® System for the Rapid Detection of Patients with Multidrug-Resistant Tuberculosis—State of the Art Case Presentations. Diagnostics (Basel) 2022; 12:diagnostics12030711. [PMID: 35328264 PMCID: PMC8947722 DOI: 10.3390/diagnostics12030711] [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: 02/02/2022] [Revised: 03/03/2022] [Accepted: 03/11/2022] [Indexed: 12/10/2022] Open
Abstract
According to the World Health Organization (WHO), there were 465,000 cases of tuberculosis caused by strains resistant to at least two first-line anti-tuberculosis drugs: rifampicin and isoniazid (MDR-TB). In light of the growing problem of drug resistance in Mycobacterium tuberculosis across laboratories worldwide, the rapid identification of drug-resistant strains of the Mycobacterium tuberculosis complex poses the greatest challenge. Progress in molecular biology and the development of nucleic acid amplification assays have paved the way for improvements to methods for the direct detection of Mycobacterium tuberculosis in specimens from patients. This paper presents two cases that illustrate the implementation of molecular tools in the recognition of drug-resistant tuberculosis.
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Affiliation(s)
- Anna Zabost
- Department of Microbiology, National Tuberculosis and Lung Diseases Research Institute, 01-138 Warsaw, Poland; (D.F.); (E.A.-K.)
- Correspondence:
| | - Dorota Filipczak
- Department of Microbiology, National Tuberculosis and Lung Diseases Research Institute, 01-138 Warsaw, Poland; (D.F.); (E.A.-K.)
| | - Włodzimierz Kupis
- Department of Thoracic Surgery, National Tuberculosis and Lung Diseases Research Institute, 01-138 Warsaw, Poland;
| | - Monika Szturmowicz
- 1st Department of Lung Diseases, National Tuberculosis and Lung Diseases Research Institute, 01-138 Warsaw, Poland;
| | - Łukasz Olendrzyński
- STOCER Mazovian Rehabilitation Center, Dr. Włodzimierz Roefler Memorial Hospital of the Polish Railroads, 05-800 Pruszków, Poland;
| | - Agnieszka Winiarska
- Department of Radiology, National Tuberculosis and Lung Diseases Research Institute, 01-138 Warsaw, Poland;
| | - Jacek Jagodziński
- X Department of Lung Diseases and Tuberculosis, Mazovian Centre of Lung Diseases and Tuberculosis, 05-400 Otwock, Poland;
| | - Ewa Augustynowicz-Kopeć
- Department of Microbiology, National Tuberculosis and Lung Diseases Research Institute, 01-138 Warsaw, Poland; (D.F.); (E.A.-K.)
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Dippenaar A, Derendinger B, Dolby T, Beylis N, van Helden PD, Theron G, Warren RM, de Vos M. Diagnostic accuracy of the FluoroType MTB and MTBDR VER 2.0 assays for the centralized high-throughput detection of Mycobacterium tuberculosis complex DNA and isoniazid and rifampicin resistance. Clin Microbiol Infect 2021; 27:1351.e1-1351.e4. [PMID: 33933566 DOI: 10.1016/j.cmi.2021.04.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 04/18/2021] [Accepted: 04/19/2021] [Indexed: 01/26/2023]
Abstract
OBJECTIVES To evaluate the accuracy of two new molecular diagnostic tests for the detection of drug-resistant tuberculosis, the FluoroType MTB and MTBDR VER 2.0 assays, in combination with manual and automated DNA extraction methods. METHODS Sputa from 360 Xpert Ultra Mycobacterium tuberculosis complex (MTBC)-positive patients and 250 Xpert Ultra MTBC-negative patients were tested. GenoType MTBDRplus served as reference for MTBC and drug resistance detection. Sanger sequencing was used to resolve discrepancies. RESULTS FluoroType MTB VER 2.0 showed similar MTBC sensitivity compared with FluoroType MTBDR VER 2.0 (manual DNA extraction: 91.6% (294/321) versus 89.8% (291/324); p 0.4); automated DNA extraction: 92.1% (305/331) versus 87.7% (291/332); p 0.05)). FluoroType MTBDR VER2.0 showed comparable diagnostic accuracy to FluoroType MTBDR VER1.0 as previously reported for the detection of MTBC and rifampicin and isoniazid resistance. CONCLUSIONS The FluoroType MTB and MTBDR VER 2.0 assays together with an automated DNA extraction and PCR set-up platform may improve laboratory operational efficiency for the diagnosis of MTBC and resistance to rifampicin and isoniazid and show promise for the implementation in a centralized molecular drug susceptibility testing model.
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Affiliation(s)
- Anzaan Dippenaar
- Department of Science and Innovation-National Research Foundation Centre for Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Brigitta Derendinger
- Department of Science and Innovation-National Research Foundation Centre for Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Tania Dolby
- National Health Laboratory Services, Green Point, Cape Town, South Africa
| | - Natalie Beylis
- National Health Laboratory Services, Green Point, Cape Town, South Africa; Division of Medical Microbiology, University of Cape Town, South Africa
| | - Paul D van Helden
- Department of Science and Innovation-National Research Foundation Centre for Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Grant Theron
- Department of Science and Innovation-National Research Foundation Centre for Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Robin M Warren
- Department of Science and Innovation-National Research Foundation Centre for Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Margaretha de Vos
- Department of Science and Innovation-National Research Foundation Centre for Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa.
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Rapid Molecular Diagnosis of Tuberculosis and Its Resistance to Rifampicin and Isoniazid with Automated MDR/MTB ELITe MGB ® Assay. Antibiotics (Basel) 2021; 10:antibiotics10070797. [PMID: 34208899 PMCID: PMC8300793 DOI: 10.3390/antibiotics10070797] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 11/22/2022] Open
Abstract
The MDR/MTB ELITe MGB® kit (ELITech) carried on the ELITe InGenius® platform is a new real-time PCR assay allowing automated extraction and detection of DNA of the Mycobacterium tuberculosis complex (MTB) and mutations in the rpoB and katG genes and inhA promoter region (pro-inhA) associated to resistance to rifampicin and isoniazid, the two markers of multidrug-resistant TB (MDR). We assessed the performances of the test on a collection of strains (n = 54) and a set of clinical samples (n = 242) from routine practice, comparatively to TB diagnosis and genotypic drug susceptibility testing (gDST) as references. Regarding the 242 clinical samples, the sensitivity and specificity of MTB detection by ELITe were 90.9% and 97.5%, respectively. For the detection of resistance-conferring mutations on positive clinical samples, we observed perfect agreement with gDST for katG and pro-inhA (κ = 1.0) and two discordant results for rpoB (κ = 0.82). Considering the 54 cultured strains, very good agreement with gDST was observed for the detection of the 25 distinct mutations in rpoB, katG, and pro-inhA, (κ = 0.95, 0.88, and 0.95, respectively). In conclusion, the automated MDR/MTB ELITe MGB® assay shows great promise and appears to be a valuable tool for rapid detection of pre-MDR- and MDR-TB directly from clinical specimens.
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Podlekareva DN, Folkvardsen DB, Skrahina A, Vassilenko A, Skrahin A, Hurevich H, Klimuk D, Karpov I, Lundgren JD, Kirk O, Lillebaek T. Tuberculosis Drug Susceptibility, Treatment, and Outcomes for Belarusian HIV-Positive Patients with Tuberculosis: Results from a National and International Laboratory. Tuberc Res Treat 2021; 2021:6646239. [PMID: 33868727 PMCID: PMC8035031 DOI: 10.1155/2021/6646239] [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: 10/27/2020] [Revised: 02/10/2021] [Accepted: 02/22/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND To cure drug-resistant (DR) tuberculosis (TB), the antituberculous treatment should be guided by Mycobacterium tuberculosis drug-susceptibility testing (DST). In this study, we compared conventional DST performed in Minsk, Belarus, a TB DR high-burden country, with extensive geno- and phenotypic analyses performed at the WHO TB Supranational Reference Laboratory in Copenhagen, Denmark, for TB/HIV coinfected patients. Subsequently, DST results were related to treatment regimen and outcome. METHODS Thirty TB/HIV coinfected patients from Minsk were included and descriptive statistics applied. RESULTS Based on results from Minsk, 10 (33%) TB/HIV patients had drug-sensitive TB. Two (7%) had isoniazid monoresistant TB, 8 (27%) had multidrug-resistant (MDR) TB, 5 (17%) preextensive drug-resistant (preXDR) TB, and 5 (17%) had extensive drug-resistant (XDR) TB. For the first-line drugs rifampicin and isoniazid, there was DST agreement between Minsk and Copenhagen for 90% patients. For the second-line anti-TB drugs, discrepancies were more pronounced. For 14 (47%) patients, there were disagreements for at least one drug, and 4 (13%) patients were classified as having MDR-TB in Minsk but were classified as having preXDR-TB based on DST results in Copenhagen. Initially, all patients received standard anti-TB treatment with rifampicin, isoniazid, pyrazinamide, and ethambutol. However, this was only suitable for 40% of the patients based on DST. On average, DR-TB patients were changed to 4 (IQR 3-5) active drugs after 1.5 months (IQR 1-2). After treatment adjustment, the treatment duration was 8 months (IQR 2-11). Four (22%) patients with DR-TB received treatment for >18 months. In total, sixteen (53%) patients died during 24 months of follow-up. CONCLUSIONS We found high concordance for rifampicin and isoniazid DST between the Minsk and Copenhagen laboratories, whereas discrepancies for second-line drugs were more pronounced. For patients with DR-TB, treatment was often insufficient and relevant adjustments delayed. This example from Minsk, Belarus, underlines two crucial points in the management of DR-TB: the urgent need for implementation of rapid molecular DSTs and availability of second-line drugs in all DR-TB high-burden settings. Carefully designed individualized treatment regimens in accordance with DST patterns will likely improve patients' outcome and reduce transmission with drug-resistant Mycobacterium tuberculosis strains.
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Affiliation(s)
| | - Dorte Bek Folkvardsen
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
| | - Alena Skrahina
- Republican Scientific and Practical Center for Pulmonology and TB, Minsk, Belarus
| | | | - Aliaksandr Skrahin
- Republican Scientific and Practical Center for Pulmonology and TB, Minsk, Belarus
- Belarusian State Medical University, Minsk, Belarus
| | - Henadz Hurevich
- Republican Scientific and Practical Center for Pulmonology and TB, Minsk, Belarus
| | - Dzmitry Klimuk
- Republican Scientific and Practical Center for Pulmonology and TB, Minsk, Belarus
| | - Igor Karpov
- Belarusian State Medical University, Minsk, Belarus
| | | | - Ole Kirk
- CHIP, Rigshospitalet, University of Copenhagen, Denmark
- Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Denmark
| | - Troels Lillebaek
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
- Global Health Section, Department of Public Health, University of Copenhagen, Denmark
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Kohli M, MacLean E, Pai M, Schumacher SG, Denkinger CM. Diagnostic accuracy of centralised assays for TB detection and detection of resistance to rifampicin and isoniazid: a systematic review and meta-analysis. Eur Respir J 2021; 57:13993003.00747-2020. [PMID: 32855226 DOI: 10.1183/13993003.00747-2020] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 07/30/2020] [Indexed: 11/05/2022]
Abstract
Various diagnostic companies have developed high throughput molecular assays for tuberculosis (TB) and resistance detection for rifampicin and isoniazid. We performed a systematic review and meta-analyses to assess the diagnostic accuracy of five of these tests for pulmonary specimens. The tests included were Abbott RealTime MTB, Abbott RealTime RIF/INH, FluoroType MTB, FluoroType MTDBR and BD Max MDR-TB assay.A comprehensive search of six databases for relevant citations was performed. Cross-sectional, case-control, cohort studies, and randomised controlled trials of any of the index tests were included. Respiratory specimens (such as sputum, bronchoalveolar lavage, tracheal aspirate, etc) or their culture isolates.A total of 21 included studies contributed 26 datasets. We could only meta-analyse data for three of the five assays identified, as data were limited for the remaining two. For TB detection, the included assays had a sensitivity of 91% or more and the specificity ranged from 97% to 100%. For rifampicin resistance detection, all the included assays had a sensitivity of more than 92%, with a specificity of 99-100%. Sensitivity for isoniazid resistance detection varied from 70 to 91%, with higher specificity of 99-100% across all index tests. Studies that included head-to-head comparisons of these assays with Xpert MTB/RIF for detection of TB and rifampicin resistance suggested comparable diagnostic accuracy.In people with symptoms of pulmonary TB, the centralised molecular assays demonstrate comparable diagnostic accuracy for detection of TB, rifampicin and isoniazid resistance to Xpert MTB/RIF assay, a WHO recommended molecular test.
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Affiliation(s)
- Mikashmi Kohli
- Dept of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada.,McGill International TB Centre, McGill University, Montreal, QC, Canada
| | - Emily MacLean
- Dept of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada.,McGill International TB Centre, McGill University, Montreal, QC, Canada
| | - Madhukar Pai
- Dept of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada.,McGill International TB Centre, McGill University, Montreal, QC, Canada
| | - Samuel G Schumacher
- Foundation for Innovative New Diagnostics, Geneva, Switzerland.,S.G. Schumacher and C.M. Denkinger are joint senior authors
| | - Claudia M Denkinger
- Foundation for Innovative New Diagnostics, Geneva, Switzerland.,Centre for Infectious Diseases, University Heidelberg, Heidelberg, Germany.,S.G. Schumacher and C.M. Denkinger are joint senior authors
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Svensson E, Folkvardsen DB, Rasmussen EM, Lillebaek T. Detection of Mycobacterium tuberculosis complex in pulmonary and extrapulmonary samples with the FluoroType MTBDR assay. Clin Microbiol Infect 2021; 27:1514.e1-1514.e4. [PMID: 33421581 DOI: 10.1016/j.cmi.2020.12.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 12/17/2020] [Accepted: 12/19/2020] [Indexed: 10/22/2022]
Abstract
OBJECTIVES Rifampicin (RIF) and isoniazid (INH) are the two most effective first-line antibiotic drugs for the treatment of tuberculosis (TB). The new FluoroType MTBDR (FT-MTBDR) real-time PCR is intended to detect INH and RIF resistance mutations as a second step following a primary Mycobacterium tuberculosis complex (MTBC) PCR. Here we evaluate the feasibility of the FT-MTBDR assay to detect simultaneously MTBC-specific DNA as well as to detect potential INH and RIF resistance through analysing inhA promotor, katG and rpoB sequences in one PCR reaction. METHODS We analysed 3885 consecutive primary samples with FT-MTBDR and compared the results with microscopy and culture: 978 were from sputum, 2007 from other respiratory tract locations plus gastric lavages, and 875 from extrapulmonary locations, respectively. RESULTS Overall, 176 samples were MTBC culture positive and 139 FT-MTBDR positive, providing a FT-MTBDR sensitivity of 0.714 (95% confidence interval 0.640-0.779) and specificity of 0.996 (0.994-0.998), respectively. For the 978 sputum, 96 were MTBC culture positive and 89 FT-MTBDR positive, sensitivity 0.854 (0.764-0.915) and specificity 0.992 (0.983-0.997). Of the 139 MTBC positive, 99 (71%) had interpretable genotypic resistance results for at least one drug, 92 (66%) for both drugs. DISCUSSION The ability of FT-MTBDR to detect MTBC is adequate with the significant added feature of simultaneous genotypic resistance detection of both INH and RIF in a single PCR reaction.
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Affiliation(s)
- Erik Svensson
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark.
| | - Dorte Bek Folkvardsen
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
| | - Erik Michael Rasmussen
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
| | - Troels Lillebaek
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark; Global Health Section, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
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12
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David A, Singh L, Da Silva P, Scott L, Stevens W. The Performance of the Abbott Real Time MTB RIF/INH Compared to the MTBDR plus V2 for the Identification of MDR-TB Among Isolates. Infect Drug Resist 2020; 13:3301-3308. [PMID: 33061477 PMCID: PMC7532077 DOI: 10.2147/idr.s247524] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 08/08/2020] [Indexed: 11/23/2022] Open
Abstract
Background The GenoType MTBDRplus V2 line-probe assay (LPA) is routinely used in clinical patient management to characterise the susceptibility of Mycobacterium tuberculosis complex to rifampicin (Rif) and isoniazid (INH) directly from sputum and cultured isolates. The laboratory workflow requires skill and three separate areas to minimize contamination and banding pattern interpretation requires experienced laboratory personnel. We explored the use of the RT MTB RIF/INH assay performed on the Abbott m2000 platform as an alternative laboratory platform. Methods Isolates (n=93) consisting of fully susceptible, Rif- or INH-mono-resistant and multi-drug resistant (MDR) strains were tested on both MTBDRplus v2 and RT MTB RIF/INH assays. Both assays target the rpoB, katG and inhA genes for resistance-detection mutations. Concordance was assessed using percent agreement and the kappa statistic. Those specimens with discordant results were further assessed using Sanger sequencing. Results A total of 89% (83/93) of cultured isolates generated successful results on the RT MTB/RIF-INH assay and MTBDRplus assays. Of the 10 discordant results, where sequencing was used as the reference method, the RT MTB RIF/INH assays misclassified six resistance isolates, while the LPA misclassified seven. Discussion Overall, the RT MTB RIF/INH demonstrated good agreement with the LPA, and a better correlation with sequencing on discrepant isolates specifically with mutations occurring in codon 511 of the rpoB gene. The RT MTB RIF/INH therefore can be used to complement existing laboratory algorithms determining Rif and INH resistance profiles, with less emphasis on manual laboratory processing.
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Affiliation(s)
- Anura David
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
| | - Lyndel Singh
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
| | - Pedro Da Silva
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa.,National Priority Program, National Health Laboratory Services, Johannesburg, South Africa
| | - Lesley Scott
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
| | - Wendy Stevens
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa.,National Priority Program, National Health Laboratory Services, Johannesburg, South Africa
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13
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Georghiou SB, Schumacher SG, Rodwell TC, Colman RE, Miotto P, Gilpin C, Ismail N, Rodrigues C, Warren R, Weyer K, Zignol M, Arafah S, Cirillo DM, Denkinger CM. Guidance for Studies Evaluating the Accuracy of Rapid Tuberculosis Drug-Susceptibility Tests. J Infect Dis 2020; 220:S126-S135. [PMID: 31593599 DOI: 10.1093/infdis/jiz106] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The development and implementation of rapid molecular diagnostics for tuberculosis (TB) drug-susceptibility testing is critical to inform treatment of patients and to prevent the emergence and spread of resistance. Optimal trial planning for existing tests and those in development will be critical to rapidly gather the evidence necessary to inform World Health Organization review and to support potential policy recommendations. The evidence necessary includes an assessment of the performance for TB and resistance detection as well as an assessment of the operational characteristics of these platforms. The performance assessment should include analytical studies to confirm the limit of detection and assay ability to detect mutations conferring resistance across globally representative strains. The analytical evaluation is typically followed by multisite clinical evaluation studies to confirm diagnostic performance in sites and populations of intended use. This paper summarizes the considerations for the design of these analytical and clinical studies.
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Affiliation(s)
| | | | | | | | - Paolo Miotto
- IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Nazir Ismail
- University of Pretoria, South Africa.,National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.,University Hospital Heidelberg, Division of Tropical Medicine, Centre of Infectious Diseases, Germany
| | | | - Rob Warren
- SAMRC Centre for Tuberculosis Research, Stellenbosch University, Tygerberg, South Africa
| | - Karin Weyer
- World Health Organization, Geneva, Switzerland
| | | | | | | | - Claudia M Denkinger
- FIND, Geneva, Switzerland.,University of Heidelberg, Centre of Infectious Diseases, Germany
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14
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Montiel Quezel-Guerraz N, Sánchez-Porto A, Ortega Torres M, Pérez Santos MJ, Acosta F, Guzman A, Correa Ruiz A, Bérmudez Ruiz P. Antituberculosis drug resistance in isolates of Mycobacterium tuberculosis complex in southeast Spain. J Glob Antimicrob Resist 2020; 20:183-186. [DOI: 10.1016/j.jgar.2019.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 05/29/2019] [Accepted: 08/02/2019] [Indexed: 11/15/2022] Open
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15
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Venter R, Minnies S, Derendinger B, Tshivhula H, de Vos M, Dolby T, Ruiters A, Warren RM, Theron G. Extract from used Xpert MTB/RIF Ultra cartridges is useful for accurate second-line drug-resistant tuberculosis diagnosis with minimal rpoB-amplicon cross-contamination risk. Sci Rep 2020; 10:2633. [PMID: 32060311 PMCID: PMC7021780 DOI: 10.1038/s41598-020-59164-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 01/24/2020] [Indexed: 12/01/2022] Open
Abstract
Xpert MTB/RIF Ultra (Ultra) detects Mycobacterium tuberculosis and rifampicin resistance. Follow-on drug susceptibility testing (DST) requires additional sputum. Extract from the diamond-shaped chamber of the cartridge (dCE) of Ultra's predecessor, Xpert MTB/RIF (Xpert), is useful for MTBDRsl-based DST but this is unexplored with Ultra. Furthermore, whether CE from non-diamond compartments is useful, the performance of FluoroType MTBDR (FT) on CE, and rpoB cross-contamination risk associated with the extraction procedure are unknown. We tested MTBDRsl, MTBDRplus, and FT on CEs from chambers from cartridges (Ultra, Xpert) tested on bacilli dilution series. MTBDRsl on Ultra dCE on TB-positive sputa (n = 40) was also evaluated and, separately, rpoB amplicon cross-contamination risk . MTBDRsl on Ultra dCE from dilutions ≥103 CFU/ml (CTmin <25, >"low semi-quantitation") detected fluoroquinolone (FQ) and second-line injectable (SLID) susceptibility and resistance correctly (some SLIDs-indeterminate). At the same threshold (at which ~85% of Ultra-positives in our setting would be eligible), 35/35 (100%) FQ and 34/35 (97%) SLID results from Ultra dCE were concordant with sputa results. Tests on other chambers were unfeasible. No tubes open during 20 batched extractions had FT-detected rpoB cross-contamination. False-positive Ultra rpoB results was observed when dCE dilutions ≤10-3 were re-tested. MTBDRsl on Ultra dCE is concordant with isolate results. rpoB amplicon cross-contamination is unlikely. These data mitigate additional specimen collection for second-line DST and cross-contamination concerns.
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MESH Headings
- Antibiotics, Antitubercular/pharmacology
- DNA, Bacterial/analysis
- DNA, Bacterial/genetics
- Drug Resistance, Bacterial
- Equipment Design
- Humans
- Microbial Sensitivity Tests/instrumentation
- Mycobacterium tuberculosis/drug effects
- Mycobacterium tuberculosis/genetics
- Mycobacterium tuberculosis/isolation & purification
- RNA, Ribosomal, 16S/analysis
- RNA, Ribosomal, 16S/genetics
- Rifampin/pharmacology
- Sputum/microbiology
- Tuberculosis, Multidrug-Resistant/diagnosis
- Tuberculosis, Multidrug-Resistant/drug therapy
- Tuberculosis, Multidrug-Resistant/microbiology
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Affiliation(s)
- Rouxjeane Venter
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, SA MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Stephanie Minnies
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, SA MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Brigitta Derendinger
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, SA MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Happy Tshivhula
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, SA MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Margaretha de Vos
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, SA MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Tania Dolby
- National Health Laboratory Services, Cape Town, South Africa
| | - Ashley Ruiters
- National Health Laboratory Services, Cape Town, South Africa
| | - Robin M Warren
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, SA MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Grant Theron
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, SA MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.
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16
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Stephen S, Muzhizhizhi D, Dhibi N, Chidemo T, Samaneka W, Matubu TA, Hakim JG, Chirenje ZM. Validation of the GenoType ® MTBDR plus Ver 2.0 assay for detection of rifampicin and isoniazid resistance in Mycobacterium tuberculosis complex isolates at UZCHS-CTRC TB research laboratory. Int J Mycobacteriol 2019; 8:83-88. [PMID: 30860184 DOI: 10.4103/ijmy.ijmy_170_18] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Background Multidrug-resistant tuberculosis (MDR-TB) is a public health concern globally. MDR-TB is defined as resistance to rifampicin (RIF) and isoniazid (INH), the two-major anti-TB first-line TB treatment drugs. Rapid identification of MDR-TB can contribute significantly to the control of TB. The GenoType® MTBDRplus Ver 2.0 assay is a molecular assay used to detect genetic mutations that result in RIF and INH resistance. The aim of this study was to validate the performance of the GenoType® MTBDRplus Ver 2.0 assay for the detection of INH and RIF resistance. Methods Fifty-five stored Mycobacterium tuberculosis isolates were tested using both the mycobacterial growth indicator tube (MGIT), antimicrobial susceptibility testing (AST), and the GenoType® MTBDRplus Ver 2.0 assay. The MGIT AST was done according to the BBL MGIT AST SIRE system with RIF and INH final critical concentrations of 1.0 μg/ml and 0.1 μg/ml, respectively. The GenoType® MTBDRplus assay (Hain Lifescience, Germany) was performed following the manufacturer's instructions. Results The GenoType® MTBDRplus Ver 2.0 assay had a sensitivity, specificity, positive predictive value, and negative predictive value of 100% for INH and RIF resistance. The intra-assay precision for the assay was 100%. Conclusion The GenoType® MTBDRplus Ver 2.0 assay's sensitivity and specificity show that the assay is highly accurate for the detection of RIF and INH resistance and thus can be used as an alternate platform due to its shorter results turnaround time.
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Affiliation(s)
- Stephen Stephen
- University of Zimbabwe College of Health Sciences-Clinical Trials Research Centre (UZCHS-CTRC), 15 Phillips Avenue, Belgravia, Harare, Zimbabwe
| | - Donhodzo Muzhizhizhi
- University of Zimbabwe College of Health Sciences-Clinical Trials Research Centre (UZCHS-CTRC), 15 Phillips Avenue, Belgravia, Harare, Zimbabwe
| | - Nicholas Dhibi
- University of Zimbabwe College of Health Sciences-Clinical Trials Research Centre (UZCHS-CTRC), 15 Phillips Avenue, Belgravia, Harare, Zimbabwe
| | - Tinashe Chidemo
- University of Zimbabwe College of Health Sciences-Clinical Trials Research Centre (UZCHS-CTRC), 15 Phillips Avenue, Belgravia, Harare, Zimbabwe
| | - Wadzanai Samaneka
- University of Zimbabwe College of Health Sciences-Clinical Trials Research Centre (UZCHS-CTRC), 15 Phillips Avenue, Belgravia, Harare, Zimbabwe
| | - Taguma Allen Matubu
- University of Zimbabwe College of Health Sciences-Clinical Trials Research Centre (UZCHS-CTRC), 15 Phillips Avenue, Belgravia, Harare, Zimbabwe
| | - James Gita Hakim
- University of Zimbabwe College of Health Sciences-Clinical Trials Research Centre (UZCHS-CTRC), 15 Phillips Avenue, Belgravia; Department of Medicine, College of Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - Zvavahera Mike Chirenje
- University of Zimbabwe College of Health Sciences-Clinical Trials Research Centre (UZCHS-CTRC), 15 Phillips Avenue, Belgravia; Department of Obstetrics, Gynaecology and Reproductive Sciences, College of Health Sciences, University of Zimbabwe, Mazowe Street, Avondale, Harare, Zimbabwe
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17
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Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues. Nat Rev Microbiol 2019; 17:533-545. [DOI: 10.1038/s41579-019-0214-5] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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18
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Nguyen TNA, Anton-Le Berre V, Bañuls AL, Nguyen TVA. Molecular Diagnosis of Drug-Resistant Tuberculosis; A Literature Review. Front Microbiol 2019; 10:794. [PMID: 31057511 PMCID: PMC6477542 DOI: 10.3389/fmicb.2019.00794] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 03/28/2019] [Indexed: 11/13/2022] Open
Abstract
Drug-resistant tuberculosis is a global health problem that hinders the progress of tuberculosis eradication programs. Accurate and early detection of drug-resistant tuberculosis is essential for effective patient care, for preventing tuberculosis spread, and for limiting the development of drug-resistant strains. Culture-based drug susceptibility tests are the gold standard method for the detection of drug-resistant tuberculosis, but they are time-consuming and technically challenging, especially in low- and middle-income countries. Nowadays, different nucleic acid-based assays that detect gene mutations associated with resistance to drugs used to treat tuberculosis are available. These tests vary in type and number of targets and in sensitivity and specificity. In this review, we will describe the available molecular tests for drug-resistant tuberculosis detection and discuss their advantages and limitations.
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Affiliation(s)
- Thi Ngoc Anh Nguyen
- UMR MIVEGEC, Institute of Research for Development, Centre National de la Recherche Scientifique, University of Montpellier, Montpellier, France.,Laboratory of Tuberculosis, Department of Bacteriology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam.,LMI Drug Resistance in South East Asia, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | | | - Anne-Laure Bañuls
- UMR MIVEGEC, Institute of Research for Development, Centre National de la Recherche Scientifique, University of Montpellier, Montpellier, France.,LMI Drug Resistance in South East Asia, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Thi Van Anh Nguyen
- Laboratory of Tuberculosis, Department of Bacteriology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam.,LMI Drug Resistance in South East Asia, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
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19
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Machado D, Couto I, Viveiros M. Advances in the molecular diagnosis of tuberculosis: From probes to genomes. INFECTION GENETICS AND EVOLUTION 2018; 72:93-112. [PMID: 30508687 DOI: 10.1016/j.meegid.2018.11.021] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 11/25/2018] [Accepted: 11/29/2018] [Indexed: 11/29/2022]
Abstract
Tuberculosis, disease caused by Mycobacterium tuberculosis, is currently the leading cause of death by a single infectious agent worldwide. Early, rapid and accurate identification of M. tuberculosis and the determination of drug susceptibility is essential for the treatment and management of this disease. Tuberculosis diagnosis is mainly based on chest radiography, smear microscopy and bacteriological culture. Smear microscopy has variable sensitivity, mainly in patients co-infected with the human immunodeficiency virus (HIV). Conventional culture for M. tuberculosis isolation, identification and drug susceptibility testing requires several weeks owning to the slow growth of M. tuberculosis. The delay in the time to results drives the prolongation of potentially inappropriate antituberculosis therapy contributing to the emergence of drug resistance, reducing treatment options and increasing treatment duration and associated costs, resulting in increased mortality and morbidity. For these reasons, novel diagnostic methods are need for timely identification of M. tuberculosis and determination of the antibiotic susceptibility profile of the infecting strain. Molecular methods offer enhanced sensitivity and specificity, early detection and the capacity to detect mixed infections. These technologies have improved turnaround time, cost effectiveness and are amenable for point-of-care testing. However, although these methods produce results within hours from sample collection, the phenotypic susceptibility testing is still needed for the determination of drug susceptibility and quantify the susceptibility levels of a given strain towards individual antibiotics. This review presents the history, advances and forthcoming promises in the molecular diagnosis of tuberculosis. An overview on the general principles, diagnostic value and the main advantages and disadvantages of the molecular methods used for the detection and identification of M. tuberculosis and its associated disease, is provided. It will be also discussed how the current phenotypic methods should be used in combination with the genotypic methods for rapid antituberculosis susceptibility testing.
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Affiliation(s)
- Diana Machado
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisboa, Portugal
| | - Isabel Couto
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisboa, Portugal
| | - Miguel Viveiros
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisboa, Portugal.
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20
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Tagliani E, Nikolayevskyy V, Tortoli E, Cirillo DM. Laboratory diagnosis of tuberculosis. Tuberculosis (Edinb) 2018. [DOI: 10.1183/2312508x.10021318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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21
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Mbelele PM, Mohamed SY, Sauli E, Mpolya EA, Mfinanga SG, Addo KK, Heysell SK, Mpagama SG. Meta-narrative review of molecular methods for diagnosis and monitoring of multidrug-resistant tuberculosis treatment in adults. Int J Mycobacteriol 2018; 7:299-309. [PMID: 30531026 PMCID: PMC6548176 DOI: 10.4103/ijmy.ijmy_135_18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Early and accurate diagnosis and rigorous clinical and microbiological monitoring of multidrug-resistant tuberculosis (MDR-TB) treatment can curb morbidity and mortality. While others are still under evaluation, the World Health Organization has recommended few novel molecular methods for MDR-TB diagnosis only. We present current molecular methods for diagnosis and monitoring of MDR-TB treatment in TB-endemic settings. A systematic meta-narrative review was conducted according to the RAMESES recommendations. Electronic databases were searched for relevant articles published in English language from January 2013 to June 2018. Based on predefined criteria, two independent reviewers extracted the key messages from relevant articles. Disagreement between them was resolved through discussion and the involvement of a third reviewer, if needed. Key messages were synthesized to create the meta-narratives for method's accuracy, drug-susceptibility capability, and laboratory infrastructure required. We included 33 articles out of 1213 records retrieved, of which 16 (48%) and 12 (36%) were conducted in high- and low-TB-endemic settings, respectively. Xpert® MTB/RIF, GenoType MTBDRplus, GenoType MTBDRsl, FlouroType™ MTBDR, TB TaqMan® array card, and DNA sequencers can accurately guide effective treatment regimens. Molecular bacterial load assay quantifies mycobactericidal impact of these regimens. Although they present inherent advantages compared to the current standard of care, they carry important limitations to implementation and/or scale-up. Therefore, considerable effort must now be directed to implementation and health systems research to maximize these forecasted benefits for individual patient's health outcomes.
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Affiliation(s)
- Peter M. Mbelele
- Kibong’oto Infectious Diseases Hospital, Sanya Juu,
Siha, Kilimanjaro
- Department of Global Health and Biomedical Sciences, School
of Life Science and Bioengineering, Nelson Mandela-African Institution for Science
and Technology, Arusha
| | - Sagal Y. Mohamed
- Division of Infectious Diseases and International Health,
University of Virginia, Charlottesville, Virginia, USA
| | - Elingarami Sauli
- Department of Global Health and Biomedical Sciences, School
of Life Science and Bioengineering, Nelson Mandela-African Institution for Science
and Technology, Arusha
| | - Emmanuel A. Mpolya
- Department of Global Health and Biomedical Sciences, School
of Life Science and Bioengineering, Nelson Mandela-African Institution for Science
and Technology, Arusha
| | - Sayoki G. Mfinanga
- Muhimbili Centre, National Institute for Medical Research,
Dar es Salaam, Tanzania
| | - Kennedy K. Addo
- Department of Bacteriology, Noguchi Memorial Institute for
Medical Research, University of Ghana, Accra, Ghana
| | - Scott K. Heysell
- Division of Infectious Diseases and International Health,
University of Virginia, Charlottesville, Virginia, USA
| | - Stellah G. Mpagama
- Kibong’oto Infectious Diseases Hospital, Sanya Juu,
Siha, Kilimanjaro
- Department of Global Health and Biomedical Sciences, School
of Life Science and Bioengineering, Nelson Mandela-African Institution for Science
and Technology, Arusha
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22
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Haasis C, Rupp J, Andres S, Schlüter B, Kernbach M, Hillemann D, Kranzer K. Validation of the FluoroType ® MTBDR assay using respiratory and lymph node samples. Tuberculosis (Edinb) 2018; 113:76-80. [PMID: 30514516 DOI: 10.1016/j.tube.2018.09.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 09/13/2018] [Accepted: 09/17/2018] [Indexed: 11/16/2022]
Abstract
BACKGROUND Tuberculosis (TB), especially drug-resistant TB, is a global public health problem. This study aimed to validate a new molecular diagnostic test, the FluoroType® MTBDR. METHOD Samples underwent routine diagnostic procedures (fluorescence microscopy, culture, species differentiation and phenotypic drug susceptibility testing). Left over samples stored at -20° underwent DNA extraction using the Fluorolyse® kit, followed by FluoroType® MTBDR and Genotype MTBDRplus testing. RESULTS A total of 350 respiratory and 59 lymph node samples were included in the study; 71 respiratory and 16 lymph node samples were culture positive for M. tuberculosis complex (MTBC). The sensitivity of the FluoroType® MTBDR to detect MTBC DNA was 91.4% (95%CI 82.3-96.8%), 68.4% (95%CI 43.4-87.4%) and 62.5%, (95%CI 35.4-84.8%) for respiratory, smear negative respiratory and lymph node samples respectively. The correlating sensitivities of the GenoType MTBDRplus were 85.9% (95%CI 75.6-93.0%), 52.6% (95%CI 28.9-75.6%) and 56.3% (29.9-80.2). Sensitivity of the FluoroType® MTBDR to detect RMP and INH resistance for respiratory samples was 96.5% (95%CI 82.2-99.9) and 70% (95%CI 45.7-88.1), respectively. The GenoType MTBDRplus revealed sensitivities of 97.1% (95% 85.1-99.9) 70.6% (95%CI 52.5-84.9) for detection of RMP and INH resistance. Indeterminate results were 13/64 (20.3%), 23/64 (35.9%) and 16/64 (25.0%) for rpoB, katG and inhA using the FluoroType® MTBDR. CONCLUSION The FluoroType® MTBDR has a high sensitivity to detect MTBC DNA. However, the high proportion of indeterminate results across all three genes needs to be addressed.
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Affiliation(s)
- Carsten Haasis
- Research Center Borstel, National Reference Center for Mycobacteria, Borstel, Germany
| | - Jan Rupp
- University Hospital Schleswig-Holstein, Department of Infectious Diseases and Microbiology, Lübeck, Germany
| | - Sönke Andres
- Research Center Borstel, National Reference Center for Mycobacteria, Borstel, Germany
| | - Birte Schlüter
- Research Center Borstel, National Reference Center for Mycobacteria, Borstel, Germany
| | - Margrit Kernbach
- Research Center Borstel, National Reference Center for Mycobacteria, Borstel, Germany
| | - Doris Hillemann
- Research Center Borstel, National Reference Center for Mycobacteria, Borstel, Germany
| | - Katharina Kranzer
- Research Center Borstel, National Reference Center for Mycobacteria, Borstel, Germany; London School of Hygiene and Tropical Medicine, London, United Kingdom.
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Diagnostic Accuracy and Utility of FluoroType MTBDR, a New Molecular Assay for Multidrug-Resistant Tuberculosis. J Clin Microbiol 2018; 56:JCM.00531-18. [PMID: 29976588 DOI: 10.1128/jcm.00531-18] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 06/23/2018] [Indexed: 11/20/2022] Open
Abstract
Most cases of multidrug-resistant (MDR) tuberculosis (TB) are never diagnosed (328,300 of the ∼490,000 cases in 2016 were missed). The Xpert MTB/RIF assay detects resistance only to rifampin, despite ∼20% of rifampin-resistant cases being susceptible to isoniazid (a critical first-line drug). Consequently, many countries require further testing with the GenoType MTBDRplus assay. However, MTBDRplus is not recommended for use on smear-negative specimens, and thus, many specimens require culture-based drug susceptibility testing. Furthermore, MTBDRplus requires specialized expertise, lengthy hands-on time, and significant laboratory infrastructure and interpretation is not automated. To address these gaps, we evaluated the accuracy of the FluoroType MTBDR (FluoroType) assay. Sputa from 244 smear-positive and 204 smear-negative patients with presumptive TB (Xpert MTB positive, n = 343) were tested. Culture and MTBDRplus on isolates served as reference standards (for active TB and MDR-TB, respectively). Sanger sequencing and MTBDRplus, both of which were performed on sputa, were used to resolve discrepancies. The sensitivity of FluoroType for the detection of M. tuberculosis complex was 98% (95% confidence interval [CI], 95 to 99%) and 92% (95% CI, 84 to 96%) for smear-positive and smear-negative specimens, respectively (232/237 versus 90/98 specimens; P < 0.009). The sensitivity and specificity for smear-negative specimens were 100% and 97%, respectively, for rifampin resistance; 100% and 98%, respectively, for isoniazid resistance; and 100% and 100%, respectively, for MDR-TB. FluoroType identified 98%, 97%, and 97% of the rpoB, katG, and inhA promoter mutations, respectively. FluoroType has excellent sensitivity with sputa equivalent to that of MTBDRplus with the isolates and can provide rapid drug susceptibility testing for rifampin and isoniazid. In addition, the capacity of FluoroType to simultaneously identify virtually all mutations in the rpoB, katG, and inhA promoter may be useful for individualized treatment regimens.
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