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Bangarwa M, Dhingra D, Mittal M, Saigal K, Ghosh A. Role of line probe assay in detection of Mycobacterium tuberculosis in children with pulmonary tuberculosis. Indian J Tuberc 2023; 70 Suppl 1:S100-S103. [PMID: 38110251 DOI: 10.1016/j.ijtb.2023.04.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 04/11/2023] [Accepted: 04/25/2023] [Indexed: 12/20/2023]
Abstract
BACKGROUND India is the highest TB burden country in the world with almost 27 lakh cases reported in 2019. Pediatric tuberculosis in India accounts for almost 31% of global TB burden. Despite such high mortality and morbidity in children, diagnosis of pulmonary TB in children still remains very challenging. MATERIAL AND METHODS This cross-sectional study was conducted in a tertiary care hospital in Delhi, India. Children between 1 and 12 months with clinical suspicion of pulmonary tuberculosis who had not previously taken ATT were included. Early morning gastric aspirate samples were collected after overnight fasting, on two days. Both days sputum sample were subjected to sputum smear microscopy and one of the two samples was subjected to line probe assay (LPA), cartridge based nucleic acid amplification (CBNAAT) and mycobacterium growth in tube (MGIT-960). RESULTS 84 children with pulmonary tuberculosis were enrolled. The most common presenting complaint was fever seen in 83 patients (98.8%). Only 17 (20.24%) were sputum smear positive by Ziehl- Neelsen (ZN) staining. LPA was positive in 47 (55.95%) samples and among these positive samples both INH and RIF resistance was detected in 2 (4.26%) samples. CBNAAT was positive in 53 patients (63%). Growth in liquid culture media (MGIT 960) was observed in 44 (52.38%) samples. Among 17 smear positive samples, LPA was detected in 14 (82.35%) samples and among 67 smear negative sample LPA was detected in 33 (49.25%) samples. LPA had 63.46% sensitivity, 100% specificity in detecting mycobacterium tuberculosis. DISCUSSION WHO's recommendation for using LPAs has been limited to culture isolates or smear-positive sputum specimens. New data has since been generated on the use of LPAs as newer versions of LPA have been developed over past few years. Previous studies conducted using LPA version 1.0 reported much lower detection rate of mycobacterium tuberculosis in smear negative specimens. With the availability of newer versions such as Hain GenoTypeMTBDRplusversion 2 and Nipro NTM + MDRTB detection kit 2, the diagnostic utility of LPA may be enhanced.
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Affiliation(s)
- Manisha Bangarwa
- Department of Paediatrics, Chacha Nehru Bal Chikitsalya, New Delhi, 110031, Delhi
| | - Dhulika Dhingra
- Department of Paediatrics, Chacha Nehru Bal Chikitsalya, New Delhi, 110031, Delhi.
| | - Medha Mittal
- Department of Paediatrics, Chacha Nehru Bal Chikitsalya, New Delhi, 110031, Delhi
| | - Karnika Saigal
- Department of Microbiology, Chacha Nehru Bal Chikitsalya
| | - Arnab Ghosh
- Department of Microbiology, Post Graduate Institute of Medical Education & Research, Chandigarh, Delhi
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Kia P, Ruman U, Pratiwi AR, Hussein MZ. Innovative Therapeutic Approaches Based on Nanotechnology for the Treatment and Management of Tuberculosis. Int J Nanomedicine 2023; 18:1159-1191. [PMID: 36919095 PMCID: PMC10008450 DOI: 10.2147/ijn.s364634] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 02/06/2023] [Indexed: 03/11/2023] Open
Abstract
Tuberculosis (TB), derived from bacterium named Mycobacterium tuberculosis, has become one of the worst infectious and contagious illnesses in the world after HIV/AIDS. Long-term therapy, a high pill burden, lack of compliance, and strict management regimens are disadvantages which resulted in the extensively drug-resistant (XDR) along with multidrug-resistant (MDR) in the treatment of TB. One of the main thrust areas for the current scenario is the development of innovative intervention tools for early diagnosis and therapeutics towards Mycobacterium tuberculosis (MTB). This review discusses various nanotherapeutic agents that have been developed for MTB diagnostics, anti-TB drugs and vaccine. Undoubtedly, the concept of employing nanoparticles (NPs) has strong potential in this therapy and offers impressive outcomes to conquer the disease. Nanocarriers with different types were designed for drug delivery applications via various administration methods. Controlling and maintaining the drug release might be an example of the benefits of utilizing a drug-loaded NP in TB therapy over conventional drug therapy. Furthermore, the drug-encapsulated NP is able to lessen dosage regimen and can resolve the problems of insufficient compliance. Over the past decade, NPs were developed in both diagnostic and therapeutic methods, while on the other hand, the therapeutic system has increased. These "theranostic" NPs were designed for nuclear imaging, optical imaging, ultrasound, imaging with magnetic resonance and the computed tomography, which includes both single-photon computed tomography and positron emission tomography. More specifically, the current manuscript focuses on the status of therapeutic and diagnostic approaches in the treatment of TB.
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Affiliation(s)
- Pooneh Kia
- Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Umme Ruman
- Nanomaterials Synthesis and Characterization Laboratory (NSCL), Institute of Nanoscience and Nanotechnology (ION2), Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | - Ariyati Retno Pratiwi
- Department of Oral Biology, Faculty of Dentistry, Universitas Brawijaya, Malang, Indonesia
| | - Mohd Zobir Hussein
- Nanomaterials Synthesis and Characterization Laboratory (NSCL), Institute of Nanoscience and Nanotechnology (ION2), Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
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3
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Comparative Performance of Line Probe Assay and GeneXpert in the Detection of Rifampicin Monoresistance in a TB-Endemic African Country. Antibiotics (Basel) 2022; 11:antibiotics11111489. [PMID: 36358145 PMCID: PMC9686643 DOI: 10.3390/antibiotics11111489] [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: 09/13/2022] [Revised: 10/17/2022] [Accepted: 10/20/2022] [Indexed: 11/17/2022] Open
Abstract
Rapid, accurate and reliable assays are required for timely detection of drug-resistant tuberculosis and early initiation of second-line TB treatment as well as to minimize transmission of resistant strains. This study assessed diagnostic performance characteristics of two rapid molecular assays, line probe assay (LPA) and GeneXpert (MTB/RIF), in the detection rifampicin monoresistance using the phenotypic proportion method on Lowenstein−Jensen media as the gold standard. This study involved a total of 357 isolates, 74 rifampicin-resistant and 283 rifampicin-susceptible, collected at the Central Tuberculosis Reference Laboratory (CTRL) in Dar es Salaam, Tanzania, between 2016 and 2019. Sensitivity, specificity and positive and negative predictive values were used to assess the performance characteristics of the two assays while kappa coefficient was used to determine agreement of test results. The receiver operating curve (ROC) was used to determine the discriminatory ability of the test in distinguishing resistant and susceptible TB isolates. Our results showed that GeneXpert had sensitivity, specificity and positive and negative predictive values of 93.2, 82.7, 58.5 and 97.9%, respectively; the corresponding performance for LPA was 86.5, 97.5, 90.1 and 96.5%, respectively. Compared with conventional phenotypic DST results, GeneXpert had a moderate agreement (kappa 0.621, p < 0.001), while LPA had high agreement (0.853, p < 0.001). LPA showed an accuracy of 95.2% compared to GeneXpert’s 84.9%. ROC curve depicted the ability of the tests to distinguish rifampicin-sensitive and rifampicin-resistant strains to be 87.9% for GeneXpert and 92.0% for LPA. Our results indicate the superiority of LPA over GeneXpert regarding detection of rifampicin monoresistance. However, logistic challenges such as longer turnaround time and need for skilled laboratory personnel may limit its use.
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4
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Mariner-Llicer C, Goig GA, Zaragoza-Infante L, Torres-Puente M, Villamayor L, Navarro D, Borras R, Chiner-Oms Á, Comas I. Accuracy of an amplicon-sequencing nanopore approach to identify variants in tuberculosis drug-resistance-associated genes. Microb Genom 2021; 7:000740. [PMID: 34919513 PMCID: PMC8767343 DOI: 10.1099/mgen.0.000740] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
A rapid and accurate diagnostic assay represents an important means to detect Mycobacterium tuberculosis, identify drug-resistant strains and ensure treatment success. Currently employed techniques to diagnose drug-resistant tuberculosis include slow phenotypic tests or more rapid molecular assays that evaluate a limited range of drugs. Whole-genome-sequencing-based approaches can detect known drug-resistance-conferring mutations and novel variations; however, the dependence on growing samples in culture, and the associated delays in achieving results, represents a significant limitation. As an alternative, targeted sequencing strategies can be directly performed on clinical samples at high throughput. This study proposes a targeted sequencing assay to rapidly detect drug-resistant strains of M. tuberculosis using the Nanopore MinION sequencing platform. We designed a single-tube assay that targets nine genes associated with drug resistance to seven drugs and two phylogenetic-determining regions to determine strain lineage and tested it in nine clinical isolates and six sputa. The study's main aim is to calibrate MinNION variant calling to detect drug-resistance-associated mutations with different frequencies to match the accuracy of Illumina (the current gold-standard sequencing technology) from both culture and sputum samples. After calibrating Nanopore MinION variant calling, we demonstrated 100% agreement between Illumina WGS and our MinION set up to detect known drug resistance and phylogenetic variants in our dataset. Importantly, other variants in the amplicons are also detected, decreasing the recall. We identify minority variants and insertions/deletions as crucial bioinformatics challenges to fully reproduce Illumina WGS results.
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Affiliation(s)
| | - Galo A. Goig
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland,University of Basel, Basel, Switzerland
| | - Laura Zaragoza-Infante
- Institute of Applied Biosciences Centre for Research and Technology Hellas, Thessaloniki, Greece
| | | | | | - David Navarro
- Hospital Clínico Universitario de València, València, Spain,Department of Microbiology and Ecology, School of Medicine, University of València, València, Spain
| | - Rafael Borras
- Hospital Clínico Universitario de València, València, Spain,Department of Microbiology and Ecology, School of Medicine, University of València, València, Spain
| | | | - Iñaki Comas
- Instituto de Biomedicina de València (CSIC), València, Spain,CIBER in Epidemiology and Public Health, València, Spain,*Correspondence: Iñaki Comas,
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Tamilzhalagan S, Shanmugam S, Selvaraj A, Suba S, Suganthi C, Moonan PK, Surie D, Sathyanarayanan MK, Gomathi NS, Jayabal L, Sachdeva KS, Selvaraju S, Swaminathan S, Tripathy SP, Hall PJ, Ranganathan UD. Whole-Genome Sequencing to Identify Missed Rifampicin and Isoniazid Resistance Among Tuberculosis Isolates-Chennai, India, 2013-2016. Front Microbiol 2021; 12:720436. [PMID: 34880835 PMCID: PMC8645853 DOI: 10.3389/fmicb.2021.720436] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/12/2021] [Indexed: 11/15/2022] Open
Abstract
India has a high burden of drug-resistant tuberculosis (DR TB) and many cases go undetected by current drug susceptibility tests (DSTs). This study was conducted to identify rifampicin (RIF) and isoniazid (INH) resistance associated genetic mutations undetected by current clinical diagnostics amongst persons with DR TB in Chennai, India. Retrospectively stored 166 DR TB isolates during 2013–2016 were retrieved and cultured in Löwenstein-Jensen medium. Whole genome sequencing (WGS) and MGIT DST for RIF and INH were performed. Discordant genotypic and phenotypic sensitivity results were repeated for confirmation and the discrepant results considered final. Further, drug resistance-conferring mutations identified through WGS were analyzed for their presence as targets in current WHO-recommended molecular diagnostics. WGS detected additional mutations for rifampicin and isoniazid resistance than WHO-endorsed line probe assays. For RIF, WGS was able to identify an additional 10% (15/146) of rpoB mutant isolates associated with borderline rifampicin resistance compared to MGIT DST. WGS could detect additional DR TB cases than commercially available and WHO-endorsed molecular DST tests. WGS results reiterate the importance of the recent WHO revised critical concentrations of current MGIT DST to detect low-level resistance to rifampicin. WGS may help inform effective treatment selection for persons at risk of, or diagnosed with, DR TB.
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Affiliation(s)
| | | | - Ashok Selvaraj
- ICMR-National Institute for Research in Tuberculosis, Chennai, India
| | - Sakthi Suba
- ICMR-National Institute for Research in Tuberculosis, Chennai, India
| | | | - Patrick K Moonan
- U.S. Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Diya Surie
- U.S. Centers for Disease Control and Prevention, Atlanta, GA, United States
| | | | | | | | | | - Sriram Selvaraju
- ICMR-National Institute for Research in Tuberculosis, Chennai, India
| | - Soumya Swaminathan
- ICMR-National Institute for Research in Tuberculosis, Chennai, India.,World Health Organization, Geneva, Switzerland
| | | | - Patricia J Hall
- U.S. Centers for Disease Control and Prevention, Atlanta, GA, United States
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Martin DR, Sibuyi NR, Dube P, Fadaka AO, Cloete R, Onani M, Madiehe AM, Meyer M. Aptamer-Based Diagnostic Systems for the Rapid Screening of TB at the Point-of-Care. Diagnostics (Basel) 2021; 11:1352. [PMID: 34441287 PMCID: PMC8391981 DOI: 10.3390/diagnostics11081352] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/07/2021] [Accepted: 07/12/2021] [Indexed: 12/17/2022] Open
Abstract
The transmission of Tuberculosis (TB) is very rapid and the burden it places on health care systems is felt globally. The effective management and prevention of this disease requires that it is detected early. Current TB diagnostic approaches, such as the culture, sputum smear, skin tuberculin, and molecular tests are time-consuming, and some are unaffordable for low-income countries. Rapid tests for disease biomarker detection are mostly based on immunological assays that use antibodies which are costly to produce, have low sensitivity and stability. Aptamers can replace antibodies in these diagnostic tests for the development of new rapid tests that are more cost effective; more stable at high temperatures and therefore have a better shelf life; do not have batch-to-batch variations, and thus more consistently bind to a specific target with similar or higher specificity and selectivity and are therefore more reliable. Advancements in TB research, in particular the application of proteomics to identify TB specific biomarkers, led to the identification of a number of biomarker proteins, that can be used to develop aptamer-based diagnostic assays able to screen individuals at the point-of-care (POC) more efficiently in resource-limited settings.
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Affiliation(s)
- Darius Riziki Martin
- DSI/Mintek Nanotechnology Innovation Centre-Biolabels Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa; (D.R.M.); (N.R.S.); (P.D.); (A.O.F.); (A.M.M.)
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa;
| | - Nicole Remaliah Sibuyi
- DSI/Mintek Nanotechnology Innovation Centre-Biolabels Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa; (D.R.M.); (N.R.S.); (P.D.); (A.O.F.); (A.M.M.)
| | - Phumuzile Dube
- DSI/Mintek Nanotechnology Innovation Centre-Biolabels Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa; (D.R.M.); (N.R.S.); (P.D.); (A.O.F.); (A.M.M.)
| | - Adewale Oluwaseun Fadaka
- DSI/Mintek Nanotechnology Innovation Centre-Biolabels Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa; (D.R.M.); (N.R.S.); (P.D.); (A.O.F.); (A.M.M.)
| | - Ruben Cloete
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa;
| | - Martin Onani
- Department of Chemistry, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa;
| | - Abram Madimabe Madiehe
- DSI/Mintek Nanotechnology Innovation Centre-Biolabels Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa; (D.R.M.); (N.R.S.); (P.D.); (A.O.F.); (A.M.M.)
| | - Mervin Meyer
- DSI/Mintek Nanotechnology Innovation Centre-Biolabels Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa; (D.R.M.); (N.R.S.); (P.D.); (A.O.F.); (A.M.M.)
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Zifodya JS, Kreniske JS, Schiller I, Kohli M, Dendukuri N, Schumacher SG, Ochodo EA, Haraka F, Zwerling AA, Pai M, Steingart KR, Horne DJ. Xpert Ultra versus Xpert MTB/RIF for pulmonary tuberculosis and rifampicin resistance in adults with presumptive pulmonary tuberculosis. Cochrane Database Syst Rev 2021; 2:CD009593. [PMID: 33616229 DOI: 10.1002/14651858.cd009593.pub5] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Xpert MTB/RIF and Xpert MTB/RIF Ultra (Xpert Ultra) are World Health Organization (WHO)-recommended rapid tests that simultaneously detect tuberculosis and rifampicin resistance in people with signs and symptoms of tuberculosis. This review builds on our recent extensive Cochrane Review of Xpert MTB/RIF accuracy. OBJECTIVES To compare the diagnostic accuracy of Xpert Ultra and Xpert MTB/RIF for the detection of pulmonary tuberculosis and detection of rifampicin resistance in adults with presumptive pulmonary tuberculosis. For pulmonary tuberculosis and rifampicin resistance, we also investigated potential sources of heterogeneity. We also summarized the frequency of Xpert Ultra trace-positive results, and estimated the accuracy of Xpert Ultra after repeat testing in those with trace-positive results. SEARCH METHODS We searched the Cochrane Infectious Diseases Group Specialized Register, MEDLINE, Embase, Science Citation Index, Web of Science, LILACS, Scopus, the WHO ICTRP, the ISRCTN registry, and ProQuest to 28 January 2020 with no language restriction. SELECTION CRITERIA We included diagnostic accuracy studies using respiratory specimens in adults with presumptive pulmonary tuberculosis that directly compared the index tests. For pulmonary tuberculosis detection, the reference standards were culture and a composite reference standard. For rifampicin resistance, the reference standards were culture-based drug susceptibility testing and line probe assays. DATA COLLECTION AND ANALYSIS Two review authors independently extracted data using a standardized form, including data by smear and HIV status. We assessed risk of bias using QUADAS-2 and QUADAS-C. We performed meta-analyses comparing pooled sensitivities and specificities, separately for pulmonary tuberculosis detection and rifampicin resistance detection, and separately by reference standard. Most analyses used a bivariate random-effects model. For tuberculosis detection, we estimated accuracy in studies in participants who were not selected based on prior microscopy testing or history of tuberculosis. We performed subgroup analyses by smear status, HIV status, and history of tuberculosis. We summarized Xpert Ultra trace results. MAIN RESULTS We identified nine studies (3500 participants): seven had unselected participants (2834 participants). All compared Xpert Ultra and Xpert MTB/RIF for pulmonary tuberculosis detection; seven studies used a paired comparative accuracy design, and two studies used a randomized design. Five studies compared Xpert Ultra and Xpert MTB/RIF for rifampicin resistance detection; four studies used a paired design, and one study used a randomized design. Of the nine included studies, seven (78%) were mainly or exclusively in high tuberculosis burden countries. For pulmonary tuberculosis detection, most studies had low risk of bias in all domains. Pulmonary tuberculosis detection Xpert Ultra pooled sensitivity and specificity (95% credible interval) against culture were 90.9% (86.2 to 94.7) and 95.6% (93.0 to 97.4) (7 studies, 2834 participants; high-certainty evidence) versus Xpert MTB/RIF pooled sensitivity and specificity of 84.7% (78.6 to 89.9) and 98.4% (97.0 to 99.3) (7 studies, 2835 participants; high-certainty evidence). The difference in the accuracy of Xpert Ultra minus Xpert MTB/RIF was estimated at 6.3% (0.1 to 12.8) for sensitivity and -2.7% (-5.7 to -0.5) for specificity. If the point estimates for Xpert Ultra and Xpert MTB/RIF are applied to a hypothetical cohort of 1000 patients, where 10% of those presenting with symptoms have pulmonary tuberculosis, Xpert Ultra will miss 9 cases, and Xpert MTB/RIF will miss 15 cases. The number of people wrongly diagnosed with pulmonary tuberculosis would be 40 with Xpert Ultra and 14 with Xpert MTB/RIF. In smear-negative, culture-positive participants, pooled sensitivity was 77.5% (67.6 to 85.6) for Xpert Ultra versus 60.6% (48.4 to 71.7) for Xpert MTB/RIF; pooled specificity was 95.8% (92.9 to 97.7) for Xpert Ultra versus 98.8% (97.7 to 99.5) for Xpert MTB/RIF (6 studies). In people living with HIV, pooled sensitivity was 87.6% (75.4 to 94.1) for Xpert Ultra versus 74.9% (58.7 to 86.2) for Xpert MTB/RIF; pooled specificity was 92.8% (82.3 to 97.0) for Xpert Ultra versus 99.7% (98.6 to 100.0) for Xpert MTB/RIF (3 studies). In participants with a history of tuberculosis, pooled sensitivity was 84.2% (72.5 to 91.7) for Xpert Ultra versus 81.8% (68.7 to 90.0) for Xpert MTB/RIF; pooled specificity was 88.2% (70.5 to 96.6) for Xpert Ultra versus 97.4% (91.7 to 99.5) for Xpert MTB/RIF (4 studies). The proportion of Ultra trace-positive results ranged from 3.0% to 30.4%. Data were insufficient to estimate the accuracy of Xpert Ultra repeat testing in individuals with initial trace-positive results. Rifampicin resistance detection Pooled sensitivity and specificity were 94.9% (88.9 to 97.9) and 99.1% (97.7 to 99.8) (5 studies, 921 participants; high-certainty evidence) for Xpert Ultra versus 95.3% (90.0 to 98.1) and 98.8% (97.2 to 99.6) (5 studies, 930 participants; high-certainty evidence) for Xpert MTB/RIF. The difference in the accuracy of Xpert Ultra minus Xpert MTB/RIF was estimated at -0.3% (-6.9 to 5.7) for sensitivity and 0.3% (-1.2 to 2.0) for specificity. If the point estimates for Xpert Ultra and Xpert MTB/RIF are applied to a hypothetical cohort of 1000 patients, where 10% of those presenting with symptoms have rifampicin resistance, Xpert Ultra will miss 5 cases, and Xpert MTB/RIF will miss 5 cases. The number of people wrongly diagnosed with rifampicin resistance would be 8 with Xpert Ultra and 11 with Xpert MTB/RIF. We identified a higher number of rifampicin resistance indeterminate results with Xpert Ultra, pooled proportion 7.6% (2.4 to 21.0) compared to Xpert MTB/RIF pooled proportion 0.8% (0.2 to 2.4). The estimated difference in the pooled proportion of indeterminate rifampicin resistance results for Xpert Ultra versus Xpert MTB/RIF was 6.7% (1.4 to 20.1). AUTHORS' CONCLUSIONS Xpert Ultra has higher sensitivity and lower specificity than Xpert MTB/RIF for pulmonary tuberculosis, especially in smear-negative participants and people living with HIV. Xpert Ultra specificity was lower than that of Xpert MTB/RIF in participants with a history of tuberculosis. The sensitivity and specificity trade-off would be expected to vary by setting. For detection of rifampicin resistance, Xpert Ultra and Xpert MTB/RIF had similar sensitivity and specificity. Ultra trace-positive results were common. Xpert Ultra and Xpert MTB/RIF provide accurate results and can allow rapid initiation of treatment for rifampicin-resistant and multidrug-resistant tuberculosis.
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Affiliation(s)
- Jerry S Zifodya
- Department of Medicine, Section of Pulmonary, Critical Care, & Environmental Medicine , Tulane University, New Orleans, LA, USA
| | - Jonah S Kreniske
- Department of Internal Medicine, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Ian Schiller
- Centre for Outcomes Research, McGill University Health Centre - Research Institute, Montreal, Canada
| | - Mikashmi Kohli
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Canada
| | - Nandini Dendukuri
- Centre for Outcomes Research, McGill University Health Centre - Research Institute, Montreal, Canada
| | | | - Eleanor A Ochodo
- Centre for Evidence-based Health Care, Department of Global Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Frederick Haraka
- Elizabeth Glaser Pediatric AIDS Foundation, Dar es Salaam, Tanzania
- Ifakara Health Institute, Bagamoyo, Tanzania
| | - Alice A Zwerling
- School of Epidemiology & Public Health, University of Ottawa, Ottawa, Canada
| | - Madhukar Pai
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Canada
| | - Karen R Steingart
- Honorary Research Fellow, Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - David J Horne
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, and Firland Northwest TB Center, University of Washington, Seattle, WA, USA
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Dhar BC, Reed AJ, Mitra S, Rodriguez Sanchez P, Nedorezova DD, Connelly RP, Rohde KH, Gerasimova YV. Cascade of deoxyribozymes for the colorimetric analysis of drug resistance in Mycobacterium tuberculosis. Biosens Bioelectron 2020; 165:112385. [PMID: 32729510 DOI: 10.1016/j.bios.2020.112385] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 06/06/2020] [Accepted: 06/09/2020] [Indexed: 02/01/2023]
Abstract
A visual cascade detection system has been applied to the detection and analysis of drug-resistance profile of Mycobacterium tuberculosis complex (MTC), a causative agent of tuberculosis. The cascade system utilizes highly selective split RNA-cleaving deoxyribozyme (sDz) sensors. When activated by a complementary nucleic acid, sDz releases the peroxidase-like deoxyribozyme apoenzyme, which, in complex with a hemin cofactor, catalyzes the color change of the sample's solution. The excellent selectivity of the cascade has allowed for the detection of point mutations in the sequences of the MTC rpoB, katG, and gyrA genes, which are responsible for resistance to rifampin, isoniazid, and fluoroquinolone, respectively. When combined with isothermal nucleic acid sequence based amplification (NASBA), the assay was able to detect amplicons of 16S rRNA and katG mRNA generated from 0.1 pg and 10 pg total RNA taken for NASBA, respectively, in less than 2 h, producing a signal detectable with the naked eye. The proposed assay may become a prototype for point-of-care diagnosis of drug resistant bacteria with visual signal output.
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Affiliation(s)
- Bidhan C Dhar
- Chemistry Department, University of Central Florida, 4111 Libra Dr., Orlando, FL, 32816, USA
| | - Adam J Reed
- Chemistry Department, University of Central Florida, 4111 Libra Dr., Orlando, FL, 32816, USA
| | - Suvra Mitra
- Chemistry Department, University of Central Florida, 4111 Libra Dr., Orlando, FL, 32816, USA
| | | | - Daria D Nedorezova
- Chemistry Department, University of Central Florida, 4111 Libra Dr., Orlando, FL, 32816, USA
| | - Ryan P Connelly
- Chemistry Department, University of Central Florida, 4111 Libra Dr., Orlando, FL, 32816, USA
| | - Kyle H Rohde
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 6900 Lake Nona Blvd, Orlando, FL, 32827, USA
| | - Yulia V Gerasimova
- Chemistry Department, University of Central Florida, 4111 Libra Dr., Orlando, FL, 32816, USA.
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9
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Kazemian H, Kardan-Yamchi J, Bahador A, Khonsari S, Nasehi M, Hamzehloo G, Vaziri F, Salehi MR, Feizabadi MM. Efficacy Of Line Probe Assay In Detection Of Drug-Resistant Pulmonary Tuberculosis In Comparison With GeneXpert And Phenotypic Methods In Iran And Genetic Analysis Of Isolates By MIRU-VNTR. Infect Drug Resist 2019; 12:3585-3593. [PMID: 31814746 PMCID: PMC6863623 DOI: 10.2147/idr.s222905] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 10/30/2019] [Indexed: 11/23/2022] Open
Abstract
Background Successful treatment of tuberculosis depends on early diagnosis and use of appropriate drug susceptibility testing in a timely manner. In the present study, LPA efficacy was assayed in detection and drug susceptibility testing of pulmonary tuberculosis in comparison to available methods in Iran and phylogenetic analyses of isolated cases carried out by MIRU-VNTR. Methods This study was conducted at the Tehran Regional Reference Laboratory for Tuberculosis. All sputum specimens were subjected to smear, culture, and drug susceptibility testing (DST), GeneXpert, and LPA. Finally, 15-locus-based MIRU-VNTR was used for molecular genotyping. Results From a total of 920 sputum specimens, 6.08% (n=56) were identified as MTBC by culture, 6.8% (n=63) by GeneXpert, and 6.5% (n=60) by LPA. Phenotype DST and LPA methods confirmed the resistance of 4 and 14 specimens to rifampin (RIF) and isoniazid (INH); two cases were considered as multidrug-resistant (MDR). Using GeneXpert, four cases were identified as RIF-resistant. Based on LPA results, inhA and katG mutations were detected in 100% and 21.4% of INH-resistant cases, respectively. All 56 culture positive Mycobacterium tuberculosis isolates were placed in 29 different clusters using MIRU-VNTR genotyping. Two MDR-TB, 2 RIF mono-resistant, and 12 INH mono-resistant cases were placed in different clusters. Conclusion LPA is an appropriate method for early detection and accurate diagnosis of TB and drug-resistant cases that makes it possible to distinguish INH mono-resistant cases from MDR cases in Iran.
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Affiliation(s)
- Hossein Kazemian
- Department of Medical Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Jalil Kardan-Yamchi
- Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Abbas Bahador
- Department of Medical Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Shadi Khonsari
- Natural Science Department, School of Science and Technology, Middlesex University, London, UK
| | - Mahshid Nasehi
- Department of Epidemiology and Biostatistics, Iran University of Medical Sciences, Tehran, Iran
| | | | - Farzam Vaziri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Mohammad Reza Salehi
- Department of Infectious Disease, Imam Khomeini Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Mehdi Feizabadi
- Department of Medical Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Thoracic Research Center, Imam Khomeini Hospital, Tehran University of Medical Sciences, Tehran, Iran
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10
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Osei Sekyere J, Maphalala N, Malinga LA, Mbelle NM, Maningi NE. A Comparative Evaluation of the New Genexpert MTB/RIF Ultra and other Rapid Diagnostic Assays for Detecting Tuberculosis in Pulmonary and Extra Pulmonary Specimens. Sci Rep 2019; 9:16587. [PMID: 31719625 PMCID: PMC6851384 DOI: 10.1038/s41598-019-53086-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 10/28/2019] [Indexed: 12/13/2022] Open
Abstract
Studies evaluating the new GeneXpert Ultra with other rapid diagnostic assays are limited, particularly in different geographical settings. The performance of the GeneXpert Ultra, the GeneXpert G4, the Line probe assays (LPA) and auramine smear microscopy in detecting TB in pulmonary and extra-pulmonary samples were thus evaluated. Remnants (n = 205 samples) of pulmonary (n = 125 samples) and extra-pulmonary (n = 80 samples) specimens from TB suspects were prospectively collected. Each sample was divided for diagnosis using microscopy, GeneXpert MTB/RIF assays, and LPA; these were all comparatively evaluated, using the MGIT 960 culture as a gold standard. The sensitivity and specificity of microscopy, Xpert Ultra, Xpert G4 and MTBDRplus (ver 2) in pulmonary samples were respectively: 82.00% and 90.28%; 88.00% and 58.57%; 79.59% and 90.28%; 80.00% and 11.11%. For extra-pulmonary specimen, the sensitivity and specificity were respectively: 53.85% and 98.51%; 69.23% and 49.25%; 50.00% and 97.01%; 69.23% and 25.37%. The new and improved GeneXpert Ultra assay was more sensitive than GeneXpert G4 and LPA in both pulmonary and extra pulmonary samples, albeit with lower specificity than the GeneXpert G4. The auramine and LPA tests were also highly sensitive, although the LPA was less specific.
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Affiliation(s)
- John Osei Sekyere
- Department of Medical Microbiology, University of Pretoria, 0084, Pretoria, South Africa
| | - Nontobeko Maphalala
- Department of Medical Microbiology, University of Pretoria, 0084, Pretoria, South Africa
| | - Lesibana A Malinga
- South African Medical Research Council, TB Platform Unit, 0084, Pretoria, South Africa.,Department of Internal Medicine, University of Pretoria, 0084, Pretoria, South Africa
| | - Nontombi M Mbelle
- Department of Medical Microbiology, University of Pretoria, 0084, Pretoria, South Africa.,National Health Laboratory Services, Tshwane Academic Division, 0084, Pretoria, South Africa
| | - Nontuthuko E Maningi
- Department of Medical Microbiology, University of Pretoria, 0084, Pretoria, South Africa.
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11
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Horne DJ, Kohli M, Zifodya JS, Schiller I, Dendukuri N, Tollefson D, Schumacher SG, Ochodo EA, Pai M, Steingart KR. Xpert MTB/RIF and Xpert MTB/RIF Ultra for pulmonary tuberculosis and rifampicin resistance in adults. Cochrane Database Syst Rev 2019; 6:CD009593. [PMID: 31173647 PMCID: PMC6555588 DOI: 10.1002/14651858.cd009593.pub4] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
BACKGROUND Xpert MTB/RIF (Xpert MTB/RIF) and Xpert MTB/RIF Ultra (Xpert Ultra), the newest version, are the only World Health Organization (WHO)-recommended rapid tests that simultaneously detect tuberculosis and rifampicin resistance in persons with signs and symptoms of tuberculosis, at lower health system levels. A previous Cochrane Review found Xpert MTB/RIF sensitive and specific for tuberculosis (Steingart 2014). Since the previous review, new studies have been published. We performed a review update for an upcoming WHO policy review. OBJECTIVES To determine diagnostic accuracy of Xpert MTB/RIF and Xpert Ultra for tuberculosis in adults with presumptive pulmonary tuberculosis (PTB) and for rifampicin resistance in adults with presumptive rifampicin-resistant tuberculosis. SEARCH METHODS We searched the Cochrane Infectious Diseases Group Specialized Register, MEDLINE, Embase, Science Citation Index, Web of Science, Latin American Caribbean Health Sciences Literature, Scopus, the WHO International Clinical Trials Registry Platform, the International Standard Randomized Controlled Trial Number Registry, and ProQuest, to 11 October 2018, without language restriction. SELECTION CRITERIA Randomized trials, cross-sectional, and cohort studies using respiratory specimens that evaluated Xpert MTB/RIF, Xpert Ultra, or both against the reference standard, culture for tuberculosis and culture-based drug susceptibility testing or MTBDRplus for rifampicin resistance. DATA COLLECTION AND ANALYSIS Four review authors independently extracted data using a standardized form. When possible, we also extracted data by smear and HIV status. We assessed study quality using QUADAS-2 and performed meta-analyses to estimate pooled sensitivity and specificity separately for tuberculosis and rifampicin resistance. We investigated potential sources of heterogeneity. Most analyses used a bivariate random-effects model. For tuberculosis detection, we first estimated accuracy using all included studies and then only the subset of studies where participants were unselected, i.e. not selected based on prior microscopy testing. MAIN RESULTS We identified in total 95 studies (77 new studies since the previous review): 86 studies (42,091 participants) evaluated Xpert MTB/RIF for tuberculosis and 57 studies (8287 participants) for rifampicin resistance. One study compared Xpert MTB/RIF and Xpert Ultra on the same participant specimen.Tuberculosis detectionOf the total 86 studies, 45 took place in high tuberculosis burden and 50 in high TB/HIV burden countries. Most studies had low risk of bias.Xpert MTB/RIF pooled sensitivity and specificity (95% credible Interval (CrI)) were 85% (82% to 88%) and 98% (97% to 98%), (70 studies, 37,237 unselected participants; high-certainty evidence). We found similar accuracy when we included all studies.For a population of 1000 people where 100 have tuberculosis on culture, 103 would be Xpert MTB/RIF-positive and 18 (17%) would not have tuberculosis (false-positives); 897 would be Xpert MTB/RIF-negative and 15 (2%) would have tuberculosis (false-negatives).Xpert Ultra sensitivity (95% confidence interval (CI)) was 88% (85% to 91%) versus Xpert MTB/RIF 83% (79% to 86%); Xpert Ultra specificity was 96% (94% to 97%) versus Xpert MTB/RIF 98% (97% to 99%), (1 study, 1439 participants; moderate-certainty evidence).Xpert MTB/RIF pooled sensitivity was 98% (97% to 98%) in smear-positive and 67% (62% to 72%) in smear-negative, culture-positive participants, (45 studies). Xpert MTB/RIF pooled sensitivity was 88% (83% to 92%) in HIV-negative and 81% (75% to 86%) in HIV-positive participants; specificities were similar 98% (97% to 99%), (14 studies).Rifampicin resistance detectionXpert MTB/RIF pooled sensitivity and specificity (95% Crl) were 96% (94% to 97%) and 98% (98% to 99%), (48 studies, 8020 participants; high-certainty evidence).For a population of 1000 people where 100 have rifampicin-resistant tuberculosis, 114 would be positive for rifampicin-resistant tuberculosis and 18 (16%) would not have rifampicin resistance (false-positives); 886 would be would be negative for rifampicin-resistant tuberculosis and four (0.4%) would have rifampicin resistance (false-negatives).Xpert Ultra sensitivity (95% CI) was 95% (90% to 98%) versus Xpert MTB/RIF 95% (91% to 98%); Xpert Ultra specificity was 98% (97% to 99%) versus Xpert MTB/RIF 98% (96% to 99%), (1 study, 551 participants; moderate-certainty evidence). AUTHORS' CONCLUSIONS We found Xpert MTB/RIF to be sensitive and specific for diagnosing PTB and rifampicin resistance, consistent with findings reported previously. Xpert MTB/RIF was more sensitive for tuberculosis in smear-positive than smear-negative participants and HIV-negative than HIV-positive participants. Compared with Xpert MTB/RIF, Xpert Ultra had higher sensitivity and lower specificity for tuberculosis and similar sensitivity and specificity for rifampicin resistance (1 study). Xpert MTB/RIF and Xpert Ultra provide accurate results and can allow rapid initiation of treatment for multidrug-resistant tuberculosis.
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Affiliation(s)
- David J Horne
- University of WashingtonDepartment of Medicine, Division of Pulmonary and Critical Care Medicine, and Firland Northwest TB CenterSeattleUSA
| | - Mikashmi Kohli
- McGill UniversityDepartment of Epidemiology, Biostatistics and Occupational HealthMontrealCanada
| | - Jerry S Zifodya
- University of WashingtonPulmonary and Critical Care Medicine325 9th Avenue – Campus Box 359762SeattleUSA98104
| | - Ian Schiller
- McGill University Health Centre ‐ Research InstituteDivision of Clinical EpidemiologyMontrealCanada
| | - Nandini Dendukuri
- McGill University Health Centre ‐ Research InstituteDivision of Clinical EpidemiologyMontrealCanada
| | | | | | - Eleanor A Ochodo
- Stellenbosch UniversityCentre for Evidence‐based Health Care, Faculty of Medicine and Health SciencesPO Box 241Cape TownSouth Africa8000
| | - Madhukar Pai
- McGill UniversityDepartment of Epidemiology, Biostatistics and Occupational HealthMontrealCanada
| | - Karen R Steingart
- Department of Clinical Sciences, Liverpool School of Tropical MedicineHonorary Research FellowPembroke PlaceLiverpoolUK
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12
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Diagnostic utility of a line probe assay for multidrug resistant-TB in smear-negative pulmonary tuberculosis. PLoS One 2017; 12:e0182988. [PMID: 28829779 PMCID: PMC5568731 DOI: 10.1371/journal.pone.0182988] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 07/27/2017] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE To evaluate the performance of Genotype MTBDRplus VER 2.0 in the diagnosis of Mycobacterium tuberculosis (MTB) in sputum smear-negative pulmonary TB cases. METHODS A total of 572 Ziehl-Neelsen sputum smear-negative samples were selected and subjected to line probe assay (Genotype MTBDRplus VER 2.0), and culture in mycobacterial growth indicator tube (MGIT-960). Immunochromatographic test was used to confirm the MTB-complex (MTBC) in culture-positive samples and phenotypic drug-susceptibility testing was done using MGIT-960. RESULTS The line probe assay was able to diagnose MTBC in 38.2% (213/558) of specimens after excluding 14 nontuberculous mycobacteria. Sensitivity and specificity of the assay were 68.4% and 89.3% respectively, considering MGIT-960 culture as gold standard after excluding contaminated and invalid results. On comparing with composite reference standard, the assay had 71.5% sensitivity and 100% specificity in the diagnosis of tuberculosis. The sensitivity and specificity for detecting resistance to rifampicin (RMP) were 100% and 99.24% respectively and for resistance to isoniazid (INH) were 97.62% and 98.55%, respectively. CONCLUSION Genotype MTBDRplus VER 2.0 is a rapid and precise diagnostic tool for detection of MTB in sputum smear-negative samples. It also facilitates accurate diagnosis of RMP and INH resistance within turn around-time.
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