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Schwab TC, Perrig L, Göller PC, Guebely De la Hoz FF, Lahousse AP, Minder B, Günther G, Efthimiou O, Omar SV, Egger M, Fenner L. Targeted next-generation sequencing to diagnose drug-resistant tuberculosis: a systematic review and meta-analysis. THE LANCET. INFECTIOUS DISEASES 2024:S1473-3099(24)00263-9. [PMID: 38795712 DOI: 10.1016/s1473-3099(24)00263-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/05/2024] [Accepted: 04/12/2024] [Indexed: 05/28/2024]
Abstract
BACKGROUND Targeted next-generation sequencing (NGS) can rapidly and simultaneously detect mutations associated with resistance to tuberculosis drugs across multiple gene targets. The use of targeted NGS to diagnose drug-resistant tuberculosis, as described in publicly available data, has not been comprehensively reviewed. We aimed to identify targeted NGS assays that diagnose drug-resistant tuberculosis, determine how widely this technology has been used, and assess the diagnostic accuracy of these assays. METHODS In this systematic review and meta-analysis, we searched MEDLINE, Embase, Cochrane Library, Web of Science Core Collection, Global Index Medicus, Google Scholar, ClinicalTrials.gov, and the WHO International Clinical Trials Registry Platform for published and unpublished reports on targeted NGS for drug-resistant tuberculosis from Jan 1, 2005, to Oct 14, 2022, with updates to our search in Embase and Google Scholar until Feb 13, 2024. Studies eligible for the systematic review described targeted NGS approaches to predict drug resistance in Mycobacterium tuberculosis infections using primary samples, reference strain collections, or cultured isolates from individuals with presumed or confirmed tuberculosis. Our search had no limitations on study type or language, although only reports in English, German, and French were screened for eligibility. For the meta-analysis, we included test accuracy studies that used any reference standard, and we assessed risk of bias using the Quality Assessment of Diagnostic Accuracy Studies-2 tool. The primary outcomes for the meta-analysis were sensitivity and specificity of targeted NGS to diagnose drug-resistant tuberculosis compared to phenotypic and genotypic drug susceptibility testing. We used a Bayesian bivariate model to generate summary receiver operating characteristic plots and diagnostic accuracy measures, overall and stratified by drug and sample type. This study is registered with PROSPERO, CRD42022368707. FINDINGS We identified and screened 2920 reports, of which 124 were eligible for our systematic review, including 37 review articles and 87 reports of studies collecting samples for targeted NGS. Sequencing was mainly done in the USA (14 [16%] of 87), western Europe (ten [11%]), India (ten [11%]), and China (nine [10%]). We included 24 test accuracy studies in the meta-analysis, in which 23 different tuberculosis drugs or drug groups were assessed, covering first-line drugs, injectable drugs, and fluoroquinolones and predominantly comparing targeted NGS with phenotypic drug susceptibility testing. The combined sensitivity of targeted NGS across all drugs was 94·1% (95% credible interval [CrI] 90·9-96·3) and specificity was 98·1% (97·0-98·9). Sensitivity for individual drugs ranged from 76·5% (52·5-92·3) for capreomycin to 99·1% (98·3-99·7) for rifampicin; specificity ranged from 93·1% (88·0-96·3) for ethambutol to 99·4% (98·3-99·8) for amikacin. Diagnostic accuracy was similar for primary clinical samples and culture isolates overall and for rifampicin, isoniazid, ethambutol, streptomycin, and fluoroquinolones, and similar after excluding studies at high risk of bias (overall sensitivity 95·2% [95% CrI 91·7-97·1] and specificity 98·6% [97·4-99·3]). INTERPRETATION Targeted NGS is highly sensitive and specific for detecting drug resistance across panels of tuberculosis drugs and can be performed directly on clinical samples. There is a paucity of data on performance for some currently recommended drugs. The barriers preventing the use of targeted NGS to diagnose drug-resistant tuberculosis in high-burden countries need to be addressed. FUNDING National Institutes of Allergy and Infectious Diseases and Swiss National Science Foundation.
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Affiliation(s)
- Tiana Carina Schwab
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Lisa Perrig
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | | | | | | | - Beatrice Minder
- Public Health and Primary Care Library, University Library of Bern, University of Bern, Bern, Switzerland
| | - Gunar Günther
- Department of Pulmonology and Allergology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department of Medical Science, Faculty of Health Sciences, University of Namibia, Windhoek, Namibia
| | - Orestis Efthimiou
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland; Institute of Primary Health Care (BIHAM), University of Bern, Bern, Switzerland
| | - Shaheed Vally Omar
- Centre for Tuberculosis, National & WHO Supranational TB Reference Laboratory, National Institute for Communicable Diseases, a division of the National Health Laboratory Services, Johannesburg, South Africa
| | - Matthias Egger
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland; Centre for Infectious Disease Epidemiology & Research, School of Public Health & Family Medicine, University of Cape Town, Cape Town, South Africa; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Lukas Fenner
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.
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Rapid diagnosis of XDR and pre-XDR TB: a systematic review of available tools. Arch Bronconeumol 2022; 58:809-820. [DOI: 10.1016/j.arbres.2022.07.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/15/2022] [Accepted: 07/15/2022] [Indexed: 11/23/2022]
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Yadav RN, Bhalla M, Kumar G, Sah GC, Dewan RK, Singhal R. Diagnostic utility of GenoType MTBDR sl assay for the detection of moxifloxacin-resistant mycobacterium tuberculosis, as compared to phenotypic method and whole-genome sequencing. Int J Mycobacteriol 2022; 11:183-189. [PMID: 35775551 DOI: 10.4103/ijmy.ijmy_70_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Background Recently, moxifloxacin (MFX)-resistant results of Mycobacterium tuberculosis (Mtb) obtained by GenoType MTBDRsl (second-line line probe assay [SL-LPA]) have been stratified to determine their resistance level; however, its accuracy has not been well studied. Therefore, the study aimed to evaluate the diagnostic accuracy of SL-LPA, with phenotypic drug susceptibility testing (pDST) and whole-genome sequencing (WGS) for the detection of MFX-resistant Mtb and their resistance level. Methods A total of 111 sputum samples were subjected to SL-LPA according to the diagnostic algorithm of the National Tuberculosis Elimination Program. Results were compared with pDST of MFX (at critical concentration [CC, 0.25 μg/ml] and clinical breakpoint [CB, 1.0 μg/ml] using BACTEC mycobacterial growth indicator tube-960), and WGS. Results At CC, SL-LPA and pDST yielded concordant results of MFX for 104 of 111 (94%). However, at CB, 23 of 30 (77%) isolates carrying gyrA mutation known to confer low-level resistance to MFX were scored as susceptible by pDST. Among 46 Mtb isolates carrying gyrA mutations known to confer high-level resistance to MFX, 36 (78%) isolates yielded concordant results, while 10 (22%) isolates were scored as susceptible at CB by pDST. WGS identified gyrA mutations in all isolates suggested by SL-LPA. Conclusion It is concluded that the stratification of MFX-resistant results by SL-LPA/genotypic method is not very well correlated with pDST (at CB), and hence, pDST may not be completely replaced by SL-LPA. gyrA D94G and gyrAA90V are the most prevalent mutations in MFX-resistant Mtb.
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Affiliation(s)
- Raj Narayan Yadav
- Department of Microbiology, National Reference Laboratory and Canter of Excellence (TB) WHO, National Institute of Tuberculosis and Respiratory Diseases, New Delhi, India
| | - Manpreet Bhalla
- Department of Microbiology, National Reference Laboratory and Canter of Excellence (TB) WHO, National Institute of Tuberculosis and Respiratory Diseases, New Delhi, India
| | - Gavish Kumar
- Department of Microbiology, National Reference Laboratory and Canter of Excellence (TB) WHO, National Institute of Tuberculosis and Respiratory Diseases, New Delhi, India
| | - Grish C Sah
- Department of Microbiology, National Reference Laboratory and Canter of Excellence (TB) WHO, National Institute of Tuberculosis and Respiratory Diseases, New Delhi, India
| | - Ravindra Kumar Dewan
- Department of Thoracic Surgery and Surgical Anatomy, National Institute of Tuberculosis and Respiratory Diseases, New Delhi, India
| | - Ritu Singhal
- Department of Microbiology, National Reference Laboratory and Canter of Excellence (TB) WHO, National Institute of Tuberculosis and Respiratory Diseases, New Delhi, India
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Penn-Nicholson A, Georghiou SB, Ciobanu N, Kazi M, Bhalla M, David A, Conradie F, Ruhwald M, Crudu V, Rodrigues C, Myneedu VP, Scott L, Denkinger CM, Schumacher SG. Detection of isoniazid, fluoroquinolone, ethionamide, amikacin, kanamycin, and capreomycin resistance by the Xpert MTB/XDR assay: a cross-sectional multicentre diagnostic accuracy study. THE LANCET. INFECTIOUS DISEASES 2021; 22:242-249. [PMID: 34627496 DOI: 10.1016/s1473-3099(21)00452-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/30/2021] [Accepted: 07/19/2021] [Indexed: 11/17/2022]
Abstract
BACKGROUND The WHO End TB Strategy requires drug susceptibility testing and treatment of all people with tuberculosis, but second-line diagnostic testing with line-probe assays needs to be done in experienced laboratories with advanced infrastructure. Fewer than half of people with drug-resistant tuberculosis receive appropriate treatment. We assessed the diagnostic accuracy of the rapid Xpert MTB/XDR automated molecular assay (Cepheid, Sunnyvale, CA, USA) to overcome these limitations. METHODS We did a prospective study involving individuals presenting with pulmonary tuberculosis symptoms and at least one risk factor for drug resistance in four sites in India (New Delhi and Mumbai), Moldova, and South Africa between July 31, 2019, and March 21, 2020. The Xpert MTB/XDR assay was used as a reflex test to detect resistance to isoniazid, fluoroquinolones, ethionamide, amikacin, kanamycin, and capreomycin in adults with positive results for Mycobacterium tuberculosis complex on Xpert MTB/RIF or Ultra (Cepheid). Diagnostic performance was assessed against a composite reference standard of phenotypic drug-susceptibility testing and whole-genome sequencing. This study is registered with ClinicalTrials.gov, number NCT03728725. FINDINGS Of 710 participants, 611 (86%) had results from both Xpert MTB/XDR and the reference standard for any drug and were included in analysis. Sensitivity for Xpert MTB/XDR detection of resistance was 94% (460 of 488, 95% CI 92-96) for isoniazid, 94% (222 of 235, 90-96%) for fluoroquinolones, 54% (178 of 328, 50-61) for ethionamide, 73% (60 of 82, 62-81) for amikacin, 86% (181 of 210, 81-91) for kanamycin, and 61% (53 of 87, 49-70) for capreomycin. Specificity was 98-100% for all drugs. Performance was equivalent to that of line-probe assays. The non-determinate rate of Xpert MTB/XDR (ie, invalid M tuberculosis complex detection) was 2·96%. INTERPRETATION The Xpert MTB/XDR assay showed high diagnostic accuracy and met WHO's minimum target product profile criteria for a next-generation drug susceptibility test. The assay has the potential to diagnose drug-resistant tuberculosis rapidly and accurately and enable optimum treatment. FUNDING German Federal Ministry of Education and Research through KfW, Dutch Ministry of Foreign Affairs, and Australian Department of Foreign Affairs and Trade.
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Affiliation(s)
| | | | - Nelly Ciobanu
- Phthisiopneumology Institute "Chiril Draganiuc", Chișinău, Moldova
| | - Mubin Kazi
- PD Hinduja Hospital and Medical Research Centre, Mumbai, India
| | - Manpreet Bhalla
- National Institute of TB and Respiratory Diseases, New Delhi, India
| | - Anura David
- University of the Witwatersrand, School of Pathology, Johannesburg, South Africa
| | - Francesca Conradie
- University of the Witwatersrand, School of Pathology, Johannesburg, South Africa
| | | | - Valeriu Crudu
- Phthisiopneumology Institute "Chiril Draganiuc", Chișinău, Moldova
| | | | | | - Lesley Scott
- University of the Witwatersrand, School of Pathology, Johannesburg, South Africa
| | - Claudia M Denkinger
- FIND, Geneva, Switzerland; Heidelberg University Hospital, Center of Infectious Diseases, Heidelberg, Germany
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Fratter A, Biagi D, Giacomini I, Montopoli M, Cocetta V. Novel Adenosine Triphosphate-Based Nutraceutical Formulation to Prevent Non-Steroidal Anti-Inflammatory Drug Enteric Cell Toxicity: Preliminary In Vitro Evidence. J Med Food 2021; 24:1293-1303. [PMID: 34491844 DOI: 10.1089/jmf.2021.0019] [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] [Indexed: 12/18/2022] Open
Abstract
Nonsteroidal anti-inflammatory drugs (NSAIDs) are the most commonly prescribed and self-prescribed drugs to treat inflammation and pain associated with several conditions. Although their efficacy and overall safety have been recognized when used according to medical prescriptions and for a short period time, their acute impact on enteric physiology has rarely been studied. NSAIDs are known to cause gastrointestinal side effects due to their intrinsic mechanism of action, which involves prostaglandins synthesis, leading to impaired mucopolysaccharide layer production. Despite this well-known and investigated side effect, the short- and long-term influences of acute administration of these drugs on the biochemical environment of enteric cells are not well understood. This study investigates the rate of adenosine triphosphate (ATP) loss and permeability alterations occurring in a model of human enteric cells, as a consequence of acute administration of NSAIDs as major perpetrators of enteric toxicity. For the first time, we investigate the ability of a novel ATP-containing formulation to prevent ATP hydrolysis in the stomach and ensure its delivery at the proximal duodenal site.
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Affiliation(s)
- Andrea Fratter
- Labomar SPA, Nutraceutical Research and Innovation Department, Istrana, Treviso, Italy.,Italian Society of Nutraceutical Formulators (SIFNut), Castelfranco Veneto, Treviso, Italy
| | - Damiano Biagi
- Labomar SPA, Nutraceutical Research and Innovation Department, Istrana, Treviso, Italy
| | - Isabella Giacomini
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Monica Montopoli
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy.,Veneto Institute of Molecular Medicine, Padova, Italy
| | - Veronica Cocetta
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
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Getachew E, Adebeta T, Gebrie D, Charlie L, Said B, Assefa DG, Wanjiru CL, Zeleke ED, Tesfahunei HA, Abebe M, Joseph M, Manyazewal T. Pyrosequencing for diagnosis of multidrug and extensively drug-resistant tuberculosis: A systemic review and meta-analysis. J Clin Tuberc Other Mycobact Dis 2021; 24:100254. [PMID: 34278006 PMCID: PMC8267485 DOI: 10.1016/j.jctube.2021.100254] [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] [Indexed: 11/26/2022] Open
Abstract
Background Multidrug and extensively drug-resistant tuberculosis (M/XDR-TB) pose major threats to global health. Diagnosis accuracy and delay have been the major drivers for the upsurge of M/XDR-TB. Pyrosequencing (PSQ) is a novel, real-time DNA sequencing for rapid detection of mutations associated with M/XDR-TB. We aimed to systematically synthesize the evidence on the diagnostic accuracy of PSQ for M/XDR-TB. Methods We conducted an electronic search of PubMed, Embase, Biosis, Web of Science, and Google Scholar up to March 2020. We used the QUADAS‐2 (Quality Assessment of Diagnostic Accuracy Studies) tool to assess the quality of studies, the BRMA (bivariate random‐effects meta-analysis) model to synthesize diagnostic accuracies, and the Rev-Man 5.4 software to perform the meta-analyses. We analyzed dichotomous data using the risk ratio (RR) with a 95% confidence interval. PROSPERO Registration ID: CRD42020200817. Results The analysis included seven studies, with a total sample of 3,165. At 95% confidence interval, the pooled sensitivity and specificity of PSQ were 89.7 (CI: 83.5–93.8) and 97.8 (CI: 94.9–99.1) for Isoniazid, 94.6 (CI: 90.9–96.8) and 98.5 (CI: 96.5–99.3) for Rifampicin, 87.9 (CI: 81.2–92.4) and 98.8 (CI: 97.2–99.5) for Fluoroquinolone, 83.5 (CI: 72.8–90.5) and 99.4 (CI: 98.3–99.8) for Amikacin, 79 (CI: 67–8-87) and 97.9 (CI: 95.5–99) for Capreomycin, and 69.6 (CI: 57–79.8) and 98.2 (CI: 95.9–99.2) for Kanamycin. The overall pooled sensitivity and specificity were 85.8 (CI: 76.7–91.7) and 98.5 (CI: 96.5–99.3), respectively. Conclusion According to the pooled data, PSQ is highly sensitive and specific for detecting M/XDR-TB, both from clinical specimens and culture isolates, and within a shorter turnaround time. We suggest a continued synthesis of the evidence on the cost-effectiveness and technical feasibilities of PSQ in low-income countries context, including sub-Saharan Africa.
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Affiliation(s)
- Emnet Getachew
- Addis Ababa University, College of Health Sciences, Centre for Innovative Drug Development and Therapeutic Trials for Africa (CDT-Africa), Addis Ababa, Ethiopia.,Arsi University, College of Health Science, Department of Public Health, Asella, Ethiopia
| | | | - Desye Gebrie
- Addis Ababa University, College of Health Sciences, Centre for Innovative Drug Development and Therapeutic Trials for Africa (CDT-Africa), Addis Ababa, Ethiopia.,School of Pharmacy, College of Health Sciences, Mekelle University, Mekelle, Ethiopia
| | - Loveness Charlie
- Addis Ababa University, College of Health Sciences, Centre for Innovative Drug Development and Therapeutic Trials for Africa (CDT-Africa), Addis Ababa, Ethiopia
| | - Bibie Said
- Addis Ababa University, College of Health Sciences, Centre for Innovative Drug Development and Therapeutic Trials for Africa (CDT-Africa), Addis Ababa, Ethiopia.,Kibong'oto National Tuberculosis Hospital, Kilimanjaro, Tanzania
| | - Dawit Getachew Assefa
- Addis Ababa University, College of Health Sciences, Centre for Innovative Drug Development and Therapeutic Trials for Africa (CDT-Africa), Addis Ababa, Ethiopia.,Dilla University, College of Health Science and Medicine, Department of Nursing, Dilla, Ethiopia
| | - Cathrine Lydiah Wanjiru
- Addis Ababa University, College of Health Sciences, Centre for Innovative Drug Development and Therapeutic Trials for Africa (CDT-Africa), Addis Ababa, Ethiopia
| | - Eden Dagnachew Zeleke
- Addis Ababa University, College of Health Sciences, Centre for Innovative Drug Development and Therapeutic Trials for Africa (CDT-Africa), Addis Ababa, Ethiopia.,Bule-Hora University, College of Health Science, Department of Midwifery, Bule-Hora, Ethiopia
| | - Hanna Amanuel Tesfahunei
- Addis Ababa University, College of Health Sciences, Centre for Innovative Drug Development and Therapeutic Trials for Africa (CDT-Africa), Addis Ababa, Ethiopia.,Hager Biomedical Research Institute, Asmara, Eritrea
| | - Mekdelawit Abebe
- Addis Ababa University, College of Health Sciences, Centre for Innovative Drug Development and Therapeutic Trials for Africa (CDT-Africa), Addis Ababa, Ethiopia.,Saint Peter Tuberculosis Specialized Hospital, Addis Ababa, Ethiopia
| | - Michele Joseph
- Addis Ababa University, College of Health Sciences, Centre for Innovative Drug Development and Therapeutic Trials for Africa (CDT-Africa), Addis Ababa, Ethiopia
| | - Tsegahun Manyazewal
- Addis Ababa University, College of Health Sciences, Centre for Innovative Drug Development and Therapeutic Trials for Africa (CDT-Africa), Addis Ababa, Ethiopia
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Assessment of the GenoType MTBDRsl VER 2.0 compared to the phenotypic drug susceptibility testing and whole genome sequencing for the rapid detection of resistance to fluoroquinolone and second-line injectable drugs among rifampicin-resistant Mycobacterium tuberculosis isolates. Arch Microbiol 2021; 203:3989-3996. [PMID: 34032874 DOI: 10.1007/s00203-021-02387-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 04/23/2021] [Accepted: 05/18/2021] [Indexed: 10/21/2022]
Abstract
Molecular techniques have considerable advantages for rapid detection, a reduction of infectiousness, prevention of further resistance development and surveillance of drug-resistant TB. MTBDRsl VER 2.0 was used to detect resistance to second-line anti-tuberculosis drugs on 35 rifampicin-resistant M. tuberculosis (RR-MTB) isolates compared to the minimum inhibitory concentrations (MICs) and whole genome sequencing (WGS). The MTBDRsl VER 2.0 (Hain Life Science, Nehren, Germany) and WGS (San Diego, CA, USA) were performed for tracing mutations in resistant-related genes involved in resistance to fluoroquinolone (FLQ) and second-line injectable drugs. The broth microdilution method using 7H9 Middlebrook media supplemented with OADC was used to determine the MICs. The MTBDRsl VER 2.0 correctly detected 5/6 (83.3%) of FLQ-resistant strains. The MUT1 A1401G (seven strains) and MUT2 G1484T (one strain) mutations in rrs gene were detected in eight AMK/KAN/CAP-resistant strains. Four low-level KAN-resistant strains with the G-10A/C-12T (three strains) and eis C-14T (one strain) mutations in eis gene was diagnosed using MTBDRsl VER 2.0. Five errors were found in detecting resistance to kanamycin and capreomycin compared to the phenotypic drug susceptibility testing and WGS. Failling wild-type bands without improved mutant bands did not indicate a reliable resistance. WGS could efficiently resolve the discrepancies of the results. MTBDRsl showed better performance in detecting XDR strains than pre-XDR.
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Catanzaro DG, Colman RE, Linger Y, Georghiou SB, Kukhtin AV, Seifert M, Holmberg RC, Mshaiel H, Chiles P, Hillery N, Cooney CG, Rodwell TC. Laboratory Evaluation of a Lateral-Flow Cell for Molecular Detection of First-Line and Second-Line Antituberculosis Drug Resistance. J Clin Microbiol 2020; 58:e01417-20. [PMID: 32817085 PMCID: PMC7587100 DOI: 10.1128/jcm.01417-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 08/12/2020] [Indexed: 01/05/2023] Open
Abstract
Despite the WHO's call for universal drug susceptibility testing for all patients being evaluated for tuberculosis (TB), a lack of rapid diagnostic tests which can fully describe TB resistance patterns is a major challenge in ensuring that all persons diagnosed with drug-resistant TB are started on an appropriate treatment regime. We evaluated the accuracy of the Akonni Biosystems XDR-TB TruArray and lateral-flow cell (XDR-LFC), a novel multiplex assay to simultaneously detect mutations across seven genes that confer resistance to both first- and second-line anti-TB drugs. The XDR-LFC includes 271 discrete three-dimensional gel elements with target-specific probes for identifying mutations in katG, inhA promoter, and ahpC promoter (isoniazid), rpoB (rifampin), gyrA (fluoroquinolones), rrs and eis promoter (kanamycin), and rrs (capreomycin and amikacin). We evaluated XDR-LFC performance with 87 phenotypically and genotypically characterized clinical Mycobacterium tuberculosis isolates. The overall assay levels of accuracy for mutation detection in specific genes were 98.6% for eis promoter and 100.0% for the genes katG, inhA promoter, ahpC promoter, rpoB, gyrA, and rrs The sensitivity and specificity against phenotypic reference were 100% and 100% for isoniazid, 98.4% and 50% for rifampin (specificity increased to 100% once the strains with documented low-level resistance mutations in rpoB were excluded), 96.2% and 100% for fluoroquinolones, 92.6% and 100% for kanamycin, 93.9% and 97.4% for capreomycin, and 80% and 100% for amikacin. The XDR-LFC solution appears to be a promising new tool for accurate detection of resistance to both first- and second-line anti-TB drugs.
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Affiliation(s)
- Donald G Catanzaro
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA
| | - Rebecca E Colman
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | | | | | | | - Marva Seifert
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | | | - Haifa Mshaiel
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Peter Chiles
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Naomi Hillery
- Department of Family Medicine and Public Health, University of California, San Diego, La Jolla, California, USA
| | | | - Timothy C Rodwell
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
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9
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Kumar V, Jorwal P, Soneja M, Sinha S, Nischal N, Sethi P, Mondal S, Abdullah Z, Pandey RM. Evaluation of rapid diagnostic tests and assessment of risk factors in drug-resistant pulmonary tuberculosis. J Family Med Prim Care 2020; 9:1028-1034. [PMID: 32318462 PMCID: PMC7113933 DOI: 10.4103/jfmpc.jfmpc_883_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/10/2020] [Accepted: 01/29/2020] [Indexed: 11/05/2022] Open
Abstract
Background: Early diagnosis and treatment of drug-resistant tuberculosis (TB) is crucial to halt the spread of drug resistance in the community. Aim: The aim of the study was to compare rapid diagnostic tests (GeneXpert and line probe assay, LPA) with conventional liquid culture for the diagnosis of drug-resistant TB and to assess the risk factors for it. Method: This cross-sectional study recruited 229 multidrug-resistant TB suspects who were sputum smear positive. They were evaluated by the rapid diagnostic tests and sensitivity, specificity, positive predictive value and negative predictive value were calculated for drug resistance detection as compared to liquid culture drug susceptibility testing. The risk factors for the development of drug resistance were also assessed and the P value of < 0.05 was considered significant. Results: In the final comparison, 193 samples were included. The sensitivity and specificity of GeneXpert for detection of drug resistance (rifampicin) was 100% (95% confidence interval, CI: 88.8–100%) and 99.4% (95% CI: 96.6–99.9%), respectively. Whereas sensitivity and specificity of LPA was 94.3% (95% CI: 80.8–99.3%) and 100% (95% CI: 97.7–100%), respectively. Only three discordant samples were observed. Defaulting to antitubercular therapy, contact with resistant TB, and disseminated disease were found to be significant risk factors for the development of drug-resistant TB with high statistical significance (P value < 0.05). Conclusion: Both rapid diagnostic tests have very high sensitivity and specificity for detection of drug resistance in sputum smear positive with the advantage of short turn-around time. Defaulting to antitubercular therapy, contact with resistant TB, and disseminated disease are significant risk factors for drug resistance.
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Affiliation(s)
- Vimal Kumar
- Department of Medicine, All India Institute of Medical Sciences, 3rd Floor Teaching Block, New Delhi, India
| | - Pankaj Jorwal
- Department of Medicine, All India Institute of Medical Sciences, 3rd Floor Teaching Block, New Delhi, India
| | - Manish Soneja
- Department of Medicine, All India Institute of Medical Sciences, 3rd Floor Teaching Block, New Delhi, India
| | - Sanjeev Sinha
- Department of Medicine, All India Institute of Medical Sciences, 3rd Floor Teaching Block, New Delhi, India
| | - Neeraj Nischal
- Department of Medicine, All India Institute of Medical Sciences, 3rd Floor Teaching Block, New Delhi, India
| | - Prayas Sethi
- Department of Medicine, All India Institute of Medical Sciences, 3rd Floor Teaching Block, New Delhi, India
| | - Saikat Mondal
- Department of Emergency Medicine, JPN Trauma Centre, All India Institute of Medical Sciences, Ring Road, New Delhi, India
| | - Zia Abdullah
- Department of Cardiology, CN Centre, All India Institute of Medical Sciences, New Delhi, India
| | - R M Pandey
- Department of Biostatistics, All India Institute of Medical Sciences, New Delhi, India
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Tiberi S, Zumla A, Migliori GB. Multidrug and Extensively Drug-resistant Tuberculosis. Infect Dis Clin North Am 2019; 33:1063-1085. [DOI: 10.1016/j.idc.2019.09.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Kontsevaya I, Werngren J, Holicka Y, Klaos K, Tran A, Nikolayevskyy V. Non-commercial phenotypic assays for the detection of Mycobacterium tuberculosis drug resistance: a systematic review. Eur J Clin Microbiol Infect Dis 2019; 39:415-426. [PMID: 31667670 DOI: 10.1007/s10096-019-03723-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 09/24/2019] [Indexed: 10/25/2022]
Abstract
Several rapid non-commercial culture-based methods and assays for drug susceptibility testing (DST) of Mycobacterium tuberculosis have emerged over the last decades. The aim of the current review was to summarise evidence on the performance of microscopic observation of drug susceptibility (MODS), thin-layer agar (TLA) and colorimetric redox-indicator (CRI) assays for detection of resistance to first- and second-line anti-tuberculosis (TB) drugs. Forty-three publications satisfying selection criteria were selected for data extraction. MODS and CRI assays demonstrated pooled sensitivity and specificity of > 93% for the detection of resistance to rifampicin and isoniazid and confirmed their utility for an accurate detection of multidrug-resistant TB (MDR-TB) in various settings. Sensitivity and specificity values for indirect DST for ethambutol (EMB) using CRI assays were 94.0% and 82.0%, respectively, suggesting that CRIs could be used to rule out resistance to EMB. Performance for other drugs varied more substantially across the reports. There was no sufficient evidence on the performance of the TLA assay for making any conclusion on its utility for DST. Our data suggests that non-commercial assays could be used for a rapid and accurate DST in settings where the use of commercial World Health Organization-endorsed assays could be limited due to a variety of reasons including limited resources, laboratory facilities or trained personnel. While inexpensive and easy-to-perform MODS and TLA assays can be used in low-income settings, using CRI assays for determination of minimal inhibitory concentrations may be implemented in middle- and high-income countries with high MDR-TB burden to guide clinical management of TB patients.
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Affiliation(s)
- Irina Kontsevaya
- Imperial College London, Du Cane Road, London, W12 0NN, UK.,Research Center Borstel, Parkallee 1-40, D-23845, Borstel, Germany
| | - Jim Werngren
- Public Health Agency of Sweden, Nobels väg 18, 17165, Solna, Sweden
| | - Yen Holicka
- Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK
| | - Kadri Klaos
- Department of Pulmonary Medicine, University of Tartu, Puusepa 8, 50406, Tartu, Estonia.,Department of Mycobacteriology, United Laboratories, Tartu University Hospital, Puusepa 1A, 50406, Tartu, Estonia
| | - Anh Tran
- Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK
| | - Vladyslav Nikolayevskyy
- Imperial College London, Du Cane Road, London, W12 0NN, UK. .,Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK.
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12
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13
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Six versus 12 Months of Anti Tubercular Therapy in Patients With Biopsy Proven Spinal Tuberculosis: A Single Center, Open Labeled, Prospective Randomized Clinical Trial-A Pilot study. Spine (Phila Pa 1976) 2019; 44:E1-E6. [PMID: 30045346 DOI: 10.1097/brs.0000000000002811] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
STUDY DESIGN A single center pilot study, open labeled, prospective randomized clinical trial. OBJECTIVE To compare six versus 12 months of anti TB therapy in patients with biopsy proven spinal TB. SUMMARY OF BACKGROUND DATA There is no clear consensus or evidence based guidelines for the duration of treatment of spinal tuberculosis. We studied if 6 and 12 months of anti tubercular therapy (ATT) had equivalent outcomes at 24 months from completion of therapy. METHODS A prospective randomized open labeled clinical trial of 6 versus 12 months ATT in patients with biopsy proven spinal-vertebral tuberculosis. The primary end point was absence of recurrence 24 months after completing therapy. Secondary end points were clinical cure at the end of therapy, significant adverse effect of ATT, need for delayed surgery, and residual neurological dysfunction. RESULTS Hundred patients, randomized to 6 or 12 months ATT, were followed up for a minimum of 24 months from completion of therapy. All patients completed scheduled duration of ATT, with one crossover from 6 months ATT group to 12 months. There were no recurrences of disease on the 24 months follow up following completion of ATT. All 100 patients met criteria for cure at time of stopping medicines. One patient (12 months group) had residual neurological dysfunction at the time of stopping treatment, which completely resolved over the next 12 months.There were no patients with major drug induced hepatitis. One patient (12 months group) needed percutaneous drainage of an abscess. None needed surgical re-exploration for persistent infection of implant removal. CONCLUSION This pilot study concludes that, in patients with biopsy proven spinal-vertebral, TB, 6 and 12 months of ATT give similar clinical outcomes at 24 months of completion of therapy. LEVEL OF EVIDENCE 2.
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14
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Lowenthal P, Lin SYG, Desmond E, Shah N, Flood J, Barry PM. Evaluation of the Impact of a Sequencing Assay for Detection of Drug Resistance on the Clinical Management of Tuberculosis. Clin Infect Dis 2018; 69:668-675. [DOI: 10.1093/cid/ciy937] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 10/30/2018] [Indexed: 12/19/2022] Open
Abstract
AbstractBackgroundIn 2012, the California Department of Public Health began using pyrosequencing (PSQ) to detect mutations associated with resistance to isoniazid, rifampin, quinolones and injectable drugs in Mycobacterium tuberculosis complex. We evaluated the impact of the PSQ assay on the clinical management of tuberculosis (TB) in California.MethodsTB surveillance and laboratory data for specimens submitted 1 August 2012 through 31 December 2016 were analyzed to determine time to effective treatment initiation. A survey of clinicians was used to assess how PSQ results influenced clinical decision making.ResultsOf 1957 specimens tested with PSQ, 52% were sediments and 46% were culture isolates, submitted a median of 8 and 35 days, respectively, after collection. Among 36 patients with multidrug-resistant (MDR) TB who had a sediment specimen submitted for PSQ, median time from specimen collection to MDR-TB treatment initiation was 12 days vs 51 days when PSQ was not used. Completed surveys were returned for 303 patients, 177 of whom reported a treatment change; 75 (42%) of clinicians reported PSQ as a reason for change. Twenty-one patients either had an MDR-TB risk factor and a smear-positive sputum specimen, but had PSQ performed on a culture isolate (9/36 [25%]); or did not have PSQ used for MDR-TB diagnosis (12/38 [32%]) and thus had an opportunity for earlier MDR-TB diagnosis with PSQ on sediment.ConclusionsPatients with MDR-TB initiated effective treatment 5 weeks earlier when PSQ was used compared to those without PSQ. Survey data suggest clinicians use PSQ to devise effective TB drug regimens. To maximize the benefit of PSQ, earlier submission of specimens should be prioritized.
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Affiliation(s)
- Phil Lowenthal
- Tuberculosis Control Branch, Division of Communicable Disease, Center for Infectious Disease, California Department of Public Health, Richmond
| | - Shou-Yean Grace Lin
- Microbial Disease Laboratory, Division of Communicable Disease, Center for Infectious Disease, California Department of Public Health, Richmond
| | - Ed Desmond
- Microbial Disease Laboratory, Division of Communicable Disease, Center for Infectious Disease, California Department of Public Health, Richmond
| | - Neha Shah
- Tuberculosis Control Branch, Division of Communicable Disease, Center for Infectious Disease, California Department of Public Health, Richmond
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Jennifer Flood
- Tuberculosis Control Branch, Division of Communicable Disease, Center for Infectious Disease, California Department of Public Health, Richmond
| | - Pennan M Barry
- Tuberculosis Control Branch, Division of Communicable Disease, Center for Infectious Disease, California Department of Public Health, Richmond
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15
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Seifert M, Georghiou SB, Garfein RS, Catanzaro D, Rodwell TC. Impact of Fluoroquinolone Use on Mortality Among a Cohort of Patients With Suspected Drug-Resistant Tuberculosis. Clin Infect Dis 2018; 65:772-778. [PMID: 28475735 DOI: 10.1093/cid/cix422] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 04/28/2017] [Indexed: 11/13/2022] Open
Abstract
Background Previous retrospective and in vitro studies suggest that use of later-generation fluoroquinolones may reduce mortality risk and improve treatment outcomes for drug-resistant tuberculosis (TB) patients, including individuals resistant to a fluoroquinolone. Meta-analysis results are mixed and few studies have examined this relationship prospectively. Methods As part of a comparative diagnostic study, we conducted a prospective cohort study with 834 Mycobacterium tuberculosis-infected patients from selected hospitals and clinics with high prevalence of drug-resistant TB in India, Moldova, and South Africa. We used Cox proportional hazards regression models to assess the association between later-generation fluoroquinolone (moxifloxacin or levofloxacin) use and patient mortality, adjusting for risk factors typically associated with poor treatment outcomes. Results After adjusting for phenotypic resistance profile, low body mass index (<18.5 kg/m2), human immunodeficiency virus status, and study site, participants treated with a later-generation fluoroquinolone had half the risk of mortality compared with participants either not treated with any fluoroquinolone or treated only with an earlier-generation fluoroquinolone (adjusted hazard ratio, 0.46 [95% confidence interval, .26-.80]) during follow-up. Conclusions Use of later-generation fluoroquinolones significantly reduced patient mortality risk in our cohort, suggesting that removal of a later-generation fluoroquinolone from a treatment regimen because of demonstrated resistance to an earlier-generation fluoroquinolone might increase mortality risk. Further studies should evaluate the effectiveness of later-generation fluoroquinolones among patients with and without resistance to early-generation fluoroquinolones. Clinical Trials Registration NCT02170441.
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Affiliation(s)
- Marva Seifert
- Department of Medicine, University of California, San Diego, La Jolla
| | | | - Richard S Garfein
- Department of Medicine, University of California, San Diego, La Jolla
| | | | - Timothy C Rodwell
- Department of Medicine, University of California, San Diego, La Jolla
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16
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Nambiar R, Shah D, Ajbani K, Kazi M, Sadani M, Shetty A, Keskar P, Kamble S, van Belkum A, Rodrigues C. Evaluation of pyrosequencing for extensive drug resistance-defining anti-tuberculosis drugs for use in public healthcare. Tuberculosis (Edinb) 2018; 110:86-90. [PMID: 29779779 DOI: 10.1016/j.tube.2018.03.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 03/15/2018] [Accepted: 03/23/2018] [Indexed: 10/17/2022]
Abstract
MGIT 960 drug susceptibility testing (DST) for Mycobacterium tuberculosis was compared for performance and speed with pyrosequencing (PSQ). Pulmonary samples (n = 100), from GeneXpert/MTB/Rifampicin-resistant patients receiving second-line treatment for 1-3 months, were subjected to DST and PSQ for seven drugs (isoniazid, rifampicin, kanamycin, amikacin, capreomycin, moxifloxacin, and ofloxacin). The mean time-to-result was 35 and two days for DST and PSQ, respectively. Average concordancy was 92.7%. Theoretically, PSQ showed substantial incremental value over the commercial Genotype MTBDRplus/sl. Mutations not considered in commercial molecular tests were observed by PSQ. Our findings corroborated the association between S315T (katG region) and S531L (rpoB region) and phenotypic resistance. PSQ is more rapid, can be performed from the sample, provides information about all known mutations simultaneously, allows extensive post-processing analyses, and is open to the inclusion of new mutations. It indicates the exact mutation conferring resistance to the particular drug, unlike the qualitative DST.
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Affiliation(s)
- Remya Nambiar
- Department of Microbiology, PD Hinduja Hospital & MRC, Off Veer Savarkar Marg, Mahim West, Mumbai 400016, India.
| | - Daksha Shah
- Mumbai District TB Control Society MCGM, Dr. Babasaheb Ambedkar Road, Parel, Mumbai 400012, India.
| | - Kanchan Ajbani
- Department of Microbiology, PD Hinduja Hospital & MRC, Off Veer Savarkar Marg, Mahim West, Mumbai 400016, India.
| | - Mubin Kazi
- Department of Microbiology, PD Hinduja Hospital & MRC, Off Veer Savarkar Marg, Mahim West, Mumbai 400016, India.
| | - Meeta Sadani
- Department of Microbiology, PD Hinduja Hospital & MRC, Off Veer Savarkar Marg, Mahim West, Mumbai 400016, India.
| | - Anjali Shetty
- Department of Microbiology, PD Hinduja Hospital & MRC, Off Veer Savarkar Marg, Mahim West, Mumbai 400016, India.
| | - Padmaja Keskar
- Mumbai District TB Control Society MCGM, Dr. Babasaheb Ambedkar Road, Parel, Mumbai 400012, India.
| | - Sanjeev Kamble
- Mumbai District TB Control Society MCGM, Dr. Babasaheb Ambedkar Road, Parel, Mumbai 400012, India.
| | - Alex van Belkum
- bioMérieux SA Data Analytics Unit, La Balme Les Grottes, France.
| | - Camilla Rodrigues
- Department of Microbiology, PD Hinduja Hospital & MRC, Off Veer Savarkar Marg, Mahim West, Mumbai 400016, India.
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17
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Groessl EJ, Ganiats TG, Hillery N, Trollip A, Jackson RL, Catanzaro DG, Rodwell TC, Garfein RS, Rodrigues C, Crudu V, Victor TC, Catanzaro A. Cost analysis of rapid diagnostics for drug-resistant tuberculosis. BMC Infect Dis 2018; 18:102. [PMID: 29499645 PMCID: PMC5833048 DOI: 10.1186/s12879-018-3013-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 01/30/2018] [Indexed: 11/14/2022] Open
Abstract
Background Growth-based drug susceptibility testing (DST) is the reference standard for diagnosing drug-resistant tuberculosis (TB), but standard time to result (TTR) is typically ≥ 3 weeks. Rapid tests can reduce that TTR to days or hours, but accuracy may be lowered. In addition to the TTR and test accuracy, the cost of a diagnostic test may affect whether it is adopted in clinical settings. We examine the cost-effectiveness of rapid diagnostics for extremely drug-resistant TB (XDR-TB) in three different high-prevalence settings. Methods 1128 patients with confirmed TB were enrolled at clinics in Mumbai, India; Chisinau, Moldova; and Port Elizabeth, South Africa. Patient sputum samples underwent DST for first and second line TB drugs using 2 growth-based (MGIT, MODS) and 2 molecular (Pyrosequencing [PSQ], line-probe assays [LPA]) assays. TTR was the primary measure of effectiveness. Sensitivity and specificity were also evaluated. The cost to perform each test at each site was recorded and included test-specific materials, personnel, and equipment costs. Incremental cost-effectiveness ratios were calculated in terms of $/day saved. Sensitivity analyses examine the impact of batch size, equipment, and personnel costs. Results Our prior results indicated that the LPA and PSQ returned results in a little over 1 day. Mean cost per sample without equipment or overhead was $23, $28, $33, and $41 for the MODS, MGIT, PSQ, and LPA, respectively. For diagnosing XDR-TB, MODS was the most accurate, followed by PSQ, and LPA. MODS was quicker and less costly than MGIT. PSQ and LPA were considerably faster but cost more than MODS. Batch size and personnel costs were the main drivers of cost variation. Conclusions Multiple factors must be weighed when selecting a test for diagnosis of XDR-TB. Rapid tests can greatly improve the time required to diagnose drug-resistant TB, potentially improving treatment success, and preventing the spread of XDR-TB. Faster time to result must be weighed against the potential for reduced accuracy, and increased costs. Trial registration ClinicalTrials.gov Identifier: NCT02170441. Electronic supplementary material The online version of this article (10.1186/s12879-018-3013-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Erik J Groessl
- Department of Family Medicine and Public Health, University of California San Diego, 9500 Gilman Dr, #0994, San Diego, CA, USA. .,VA San Diego Healthcare System, San Diego, CA, USA.
| | - Theodore G Ganiats
- Department of Family Medicine and Public Health, University of California San Diego, 9500 Gilman Dr, #0994, San Diego, CA, USA
| | - Naomi Hillery
- Department of Family Medicine and Public Health, University of California San Diego, 9500 Gilman Dr, #0994, San Diego, CA, USA
| | - Andre Trollip
- Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa
| | - Roberta L Jackson
- Department of Medicine, University of California, San Diego, CA, USA
| | | | - Timothy C Rodwell
- Department of Medicine, University of California, San Diego, CA, USA
| | - Richard S Garfein
- Department of Medicine, University of California, San Diego, CA, USA
| | | | - Valeriu Crudu
- Microbiology and Morphology Laboratory, Institute of Phthisiopneumology, Chisinau, Moldova
| | - Thomas C Victor
- Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa
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Ramachandran R, Muniyandi M. Rapid molecular diagnostics for multi-drug resistant tuberculosis in India. Expert Rev Anti Infect Ther 2018; 16:197-204. [PMID: 29406800 DOI: 10.1080/14787210.2018.1438262] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
INTRODUCTION Rapid molecular diagnostic methods help in the detection of TB and Rifampicin resistance. These methods detect TB early, are accurate and play a crucial role in reducing the burden of drug resistant tuberculosis. Areas covered: This review analyses rapid molecular diagnostic tools used in the diagnosis of MDR-TB in India, such as the Line Probe Assay and GeneXpert. We have discussed the burden of MDR-TB and the impact of recent diagnostic tools on case detection and treatment outcomes. This review also discusses the costs involved in establishing these new techniques in India. Expert commentary: Molecular methods have considerable advantages for the programmatic management of drug resistant TB. These include speed, standardization of testing, potentially high throughput and reduced laboratory biosafety requirements. There is a desperate need for India to adopt modern, rapid, molecular tools with point-of-care tests being currently evaluated. New molecular diagnostic tests appear to be cost effective and also help in detecting missing cases. There is enough evidence to support the scaling up of these new tools in India.
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Affiliation(s)
| | - M Muniyandi
- b National Institute for Research in Tuberculosis (ICMR) , Chennai , India
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19
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Nurwidya F, Handayani D, Burhan E, Yunus F. Molecular Diagnosis of Tuberculosis. Chonnam Med J 2018; 54:1-9. [PMID: 29399559 PMCID: PMC5794472 DOI: 10.4068/cmj.2018.54.1.1] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 12/19/2017] [Accepted: 12/20/2017] [Indexed: 12/13/2022] Open
Abstract
Tuberculosis (TB) is one of the leading causes of adult death in the Asia-Pacific Region, including Indonesia. As an infectious disease caused by Mycobacterium tuberculosis (MTB), TB remains a major public health issue especially in developing nations due to the lack of adequate diagnostic testing facilities. Diagnosis of TB has entered an era of molecular detection that provides faster and more cost-effective methods to diagnose and confirm drug resistance in TB cases, meanwhile, diagnosis by conventional culture systems requires several weeks. New advances in the molecular detection of TB, including the faster and simpler nucleic acid amplification test (NAAT) and whole-genome sequencing (WGS), have resulted in a shorter time for diagnosis and, therefore, faster TB treatments. In this review, we explored the current findings on molecular diagnosis of TB and drug-resistant TB to see how this advancement could be integrated into public health systems in order to control TB.
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Affiliation(s)
- Fariz Nurwidya
- Department of Pulmonology and Respiratory Medicine, Universitas Indonesia Faculty of Medicine, Persahabatan Hospital, Jakarta, Indonesia
| | - Diah Handayani
- Department of Pulmonology and Respiratory Medicine, Universitas Indonesia Faculty of Medicine, Persahabatan Hospital, Jakarta, Indonesia
| | - Erlina Burhan
- Department of Pulmonology and Respiratory Medicine, Universitas Indonesia Faculty of Medicine, Persahabatan Hospital, Jakarta, Indonesia
| | - Faisal Yunus
- Department of Pulmonology and Respiratory Medicine, Universitas Indonesia Faculty of Medicine, Persahabatan Hospital, Jakarta, Indonesia
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20
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Arranz-Trullén J, Lu L, Pulido D, Bhakta S, Boix E. Host Antimicrobial Peptides: The Promise of New Treatment Strategies against Tuberculosis. Front Immunol 2017; 8:1499. [PMID: 29163551 PMCID: PMC5681943 DOI: 10.3389/fimmu.2017.01499] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 10/24/2017] [Indexed: 12/11/2022] Open
Abstract
Tuberculosis (TB) continues to be a devastating infectious disease and remerges as a global health emergency due to an alarming rise of antimicrobial resistance to its treatment. Despite of the serious effort that has been applied to develop effective antitubercular chemotherapies, the potential of antimicrobial peptides (AMPs) remains underexploited. A large amount of literature is now accessible on the AMP mechanisms of action against a diversity of pathogens; nevertheless, research on their activity on mycobacteria is still scarce. In particular, there is an urgent need to integrate all available interdisciplinary strategies to eradicate extensively drug-resistant Mycobacterium tuberculosis strains. In this context, we should not underestimate our endogenous antimicrobial proteins and peptides as ancient players of the human host defense system. We are confident that novel antibiotics based on human AMPs displaying a rapid and multifaceted mechanism, with reduced toxicity, should significantly contribute to reverse the tide of antimycobacterial drug resistance. In this review, we have provided an up to date perspective of the current research on AMPs to be applied in the fight against TB. A better understanding on the mechanisms of action of human endogenous peptides should ensure the basis for the best guided design of novel antitubercular chemotherapeutics.
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Affiliation(s)
- Javier Arranz-Trullén
- Faculty of Biosciences, Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.,Mycobacteria Research Laboratory, Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck University of London, London, United Kingdom
| | - Lu Lu
- Faculty of Biosciences, Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - David Pulido
- Faculty of Biosciences, Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Sanjib Bhakta
- Mycobacteria Research Laboratory, Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck University of London, London, United Kingdom
| | - Ester Boix
- Faculty of Biosciences, Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
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21
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Increased Tuberculosis Patient Mortality Associated with Mycobacterium tuberculosis Mutations Conferring Resistance to Second-Line Antituberculous Drugs. J Clin Microbiol 2017; 55:1928-1937. [PMID: 28404672 DOI: 10.1128/jcm.00152-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 04/04/2017] [Indexed: 12/22/2022] Open
Abstract
Rapid molecular diagnostics have great potential to limit the spread of multidrug-resistant tuberculosis (MDR-TB) and extensively drug-resistant tuberculosis (XDR-TB) (M/XDR-TB). These technologies detect mutations in the Mycobacterium tuberculosis genome that confer phenotypic drug resistance. However, there have been few data published regarding the relationships between the detected M. tuberculosis resistance mutations and M/XDR-TB treatment outcomes, limiting our current ability to exploit the full potential of molecular diagnostics. We analyzed clinical, microbiological, and sequencing data for 451 patients and their clinical isolates collected in a multinational, observational cohort study to determine if there was an association between M. tuberculosis resistance mutations and patient mortality. The presence of an rrs 1401G mutation was associated with significantly higher odds of patient mortality (adjusted odds ratio [OR] = 5.72; 95% confidence interval [CI], 1.65 to 19.84]) after adjusting for relevant patient clinical characteristics and all other resistance mutations. Further analysis of mutations, categorized by the associated resistance level, indicated that the detection of mutations associated with high-level fluoroquinolone (OR, 3.99 [95% CI, 1.10 to 14.40]) and kanamycin (OR, 5.47 [95% CI, 1.64 to 18.24]) resistance was also significantly associated with higher odds of patient mortality, even after accounting for clinical site, patient age, reported smoking history, body mass index (BMI), diabetes, HIV, and all other resistance mutations. Specific gyrA and rrs resistance mutations, associated with high-level resistance, were associated with patient mortality as identified in clinical M. tuberculosis isolates from a diverse M/XDR-TB patient population at three high-burden clinical sites. These results have important implications for the interpretation of molecular diagnostics, including identifying patients at increased risk for mortality during treatment. (This study has been registered at ClinicalTrials.gov under registration no. NCT02170441.).
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22
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Catanzaro DG, Trollip AP, Seifert M, Georghiou SB, Garfein RS, Rodwell TC, Catanzaro A, Eisenach KD. Evaluation of the microscopic observation drug susceptibility assay for the detection of first- and second-line drug susceptibility for Mycobacterium tuberculosis. Eur Respir J 2017; 49:49/4/1602215. [PMID: 28381434 DOI: 10.1183/13993003.02215-2016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 12/16/2016] [Indexed: 12/31/2022]
Affiliation(s)
- Donald G Catanzaro
- Dept of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
| | - Andre P Trollip
- Foundation for Innovative New Diagnostics, Cape Town, South Africa
| | - Marva Seifert
- University of California San Diego School of Medicine, La Jolla, CA, USA
| | | | - Richard S Garfein
- University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Timothy C Rodwell
- University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Antonino Catanzaro
- University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Kathleen D Eisenach
- University of Arkansas for Medical Sciences, Dept of Pathology, Little Rock, AR, USA
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23
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Nathavitharana RR, Cudahy PGT, Schumacher SG, Steingart KR, Pai M, Denkinger CM. Accuracy of line probe assays for the diagnosis of pulmonary and multidrug-resistant tuberculosis: a systematic review and meta-analysis. Eur Respir J 2017; 49:49/1/1601075. [PMID: 28100546 PMCID: PMC5898952 DOI: 10.1183/13993003.01075-2016] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 10/11/2016] [Indexed: 12/22/2022]
Abstract
Only 25% of multidrug-resistant tuberculosis (MDR-TB) cases are currently diagnosed. Line probe assays (LPAs) enable rapid drug-susceptibility testing for rifampicin (RIF) and isoniazid (INH) resistance and Mycobacterium tuberculosis detection. Genotype MTBDRplusV1 was WHO-endorsed in 2008 but newer LPAs have since been developed. This systematic review evaluated three LPAs: Hain Genotype MTBDRplusV1, MTBDRplusV2 and Nipro NTM+MDRTB. Study quality was assessed with QUADAS-2. Bivariate random-effects meta-analyses were performed for direct and indirect testing. Results for RIF and INH resistance were compared to phenotypic and composite (incorporating sequencing) reference standards. M. tuberculosis detection results were compared to culture. 74 unique studies were included. For RIF resistance (21 225 samples), pooled sensitivity and specificity (with 95% confidence intervals) were 96.7% (95.6–97.5%) and 98.8% (98.2–99.2%). For INH resistance (20 954 samples), pooled sensitivity and specificity were 90.2% (88.2–91.9%) and 99.2% (98.7–99.5%). Results were similar for direct and indirect testing and across LPAs. Using a composite reference standard, specificity increased marginally. For M. tuberculosis detection (3451 samples), pooled sensitivity was 94% (89.4–99.4%) for smear-positive specimens and 44% (20.2–71.7%) for smear-negative specimens. In patients with pulmonary TB, LPAs have high sensitivity and specificity for RIF resistance and high specificity and good sensitivity for INH resistance. This meta-analysis provides evidence for policy and practice. Line probe assays have high accuracy for detection of RIF resistance and INH resistancehttp://ow.ly/USX5305tqFV
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Affiliation(s)
| | - Patrick G T Cudahy
- Division of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
| | | | - Karen R Steingart
- Cochrane Infectious Diseases Group, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Madhukar Pai
- McGill International TB Centre, McGill University, Montreal, QC, Canada
| | - Claudia M Denkinger
- Division of Infectious Diseases, Beth Israel Deaconess Medical Center, Boston, MA, USA.,FIND, Geneva, Switzerland
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Seifert M, Ajbani K, Georghiou SB, Catanzaro D, Rodrigues C, Crudu V, Victor TC, Garfein RS, Catanzaro A, Rodwell TC. A performance evaluation of MTBDRplus version 2 for the diagnosis of multidrug-resistant tuberculosis. Int J Tuberc Lung Dis 2017; 20:631-7. [PMID: 27084817 DOI: 10.5588/ijtld.15.0788] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
OBJECTIVE To evaluate the performance of a recently updated rapid molecular diagnostic test, GenoType® MTBDRplus version 2, designed to detect drug resistance in both acid-fast bacilli (AFB) smear-negative and -positive specimens. DESIGN Sputum samples from 1128 patients at risk for multidrug-resistant tuberculosis (MDR-TB) were tested using MTBDRplus v2 and compared with reference standard MGIT™ 960™ drug susceptibility testing. The relationship of participant human immunodeficiency virus (HIV) status, diabetic status, previous treatment, and smear gradation to the likelihood of obtaining an interpretable result was assessed using logistic regression. RESULTS The sensitivity and specificity of MTBDRplus v2 for detecting MDR-TB, when compared to a reference standard, were respectively 96.0% (95%CI 93.5-97.6) and 99.2% (95%CI 97.0-99.9) in AFB smear-positive specimens and 82.8% (95%CI 63.5-93.5) and 98.3% (95%CI 89.9-99.9) in AFB smear-negative specimens. A dose-response relationship was observed between the proportion of interpretable test results and AFB smear bacterial load after adjusting for age, sex, body mass index, HIV status, previous treatment and diabetic status. CONCLUSION While MTBDRplus v2 performs well among both AFB smear-positive and -negative specimens, smear gradation appears to influence both the probability of obtaining an interpretable result and test sensitivity, indicating a significant association between bacillary load and test performance.
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Affiliation(s)
- M Seifert
- University of California, San Diego, California, USA
| | - K Ajbani
- Hinduja National Hospital, Mumbai, India
| | - S B Georghiou
- University of California, San Diego, California, USA
| | - D Catanzaro
- University of Arkansas, Fayetteville, Arkansas, USA
| | | | - V Crudu
- Institute of Phthisiopneumology, Chisinau, Moldova
| | - T C Victor
- Stellenbosch University, Cape Town, South Africa
| | - R S Garfein
- University of California, San Diego, California, USA
| | - A Catanzaro
- University of California, San Diego, California, USA
| | - T C Rodwell
- University of California, San Diego, California, USA
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Abstract
Robert Heinrich Herman Koch, a German physician and microbiologist, received Nobel Prize in 1905 for identifying the specific causative agent of tuberculosis (TB). During his time it was believed that TB was an inherited disease. However he was convinced that the disease was caused by a bacterium and was infectious, tested his postulates using guinea pigs, and found the causative agent to be slow growing mycobacterium tuberculosis. TB is the second most common cause of death from infectious diseases after HIV/AIDS. Drug-resistant TB poses serious challenge to effective management of TB worldwide. Multidrug-resistant TB accounted for about half a million new cases and over 200,000 deaths in 2013. Whole-genome sequencing (first done in 1998) technologies have provided new insight into the mechanism of drug resistance. For the first time in 50 y, new anti TB drugs have been developed. The World Health Organization (WHO) has recently revised their treatment guidelines based on 32 studies. In United States, latent TB affects between 10 and 15 million people, 10% of whom may develop active TB disease. QuantiFERON TB Gold and T-SPOT.TB test are used for diagnosis. Further research will look into the importance of newly discovered gene mutations in causing drug resistance.
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Conners E, Garfein RS, Rodwell TC, Udwadia ZF, Catanzaro DG. Mobility patterns of persons at risk for drug-resistant tuberculosis in Mumbai, India. Int J Tuberc Lung Dis 2016; 20:1633-1638. [PMID: 27931339 PMCID: PMC10424886 DOI: 10.5588/ijtld.16.0187] [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] [Indexed: 11/10/2022] Open
Abstract
SETTING Tuberculosis (TB) hospital in Mumbai, India. OBJECTIVE To describe the mobility patterns of persons with suspected drug-resistant tuberculosis (DR-TB) and to assess whether there were significant differences in demographic or risk characteristics based on mobility. DESIGN Observational cohort study of TB clinic patients at risk for DR-TB. RESULTS Among 602 participants, 37% had ever moved from their place of birth; 14% were local movers (within state), and 23% were distant movers, between states or countries. Univariate multinomial logistic regression models showed that distant movers were more likely than non-movers to have lower income, less education, a greater number of previous TB episodes, and to have ever smoked. Compared to non-movers, local movers were more likely to have lower income and were more likely to have seen a doctor in the past 2 years. Clinical outcomes, including DR-TB, diabetes, and human immunodeficiency virus (HIV), did not differ between the three mobility groups. CONCLUSION Mobility was common among patients at risk for DR-TB in Mumbai. TB programs should consider the implications of mobility on the protracted treatment for DR-TB in India.
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Affiliation(s)
- E Conners
- Department of Medicine, University of California, San Diego, San Diego State University, San Diego, California, USA
| | - R S Garfein
- Department of Medicine, University of California, San Diego
| | - T C Rodwell
- Department of Medicine, University of California, San Diego
| | | | - D G Catanzaro
- University of Arkansas, Department of Biological Sciences, Fayetteville, Arkansas, USA
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Theron G, Peter J, Richardson M, Warren R, Dheda K, Steingart KR. GenoType ® MTBDRsl assay for resistance to second-line anti-tuberculosis drugs. Cochrane Database Syst Rev 2016; 9:CD010705. [PMID: 27605387 PMCID: PMC5034505 DOI: 10.1002/14651858.cd010705.pub3] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Genotype® MTBDRsl (MTBDRsl) is a rapid DNA-based test for detecting specific mutations associated with resistance to fluoroquinolones and second-line injectable drugs (SLIDs) in Mycobacterium tuberculosis complex. MTBDRsl version 2.0 (released in 2015) identifies the mutations detected by version 1.0, as well as additional mutations. The test may be performed on a culture isolate or a patient specimen, which eliminates delays associated with culture. Version 1.0 requires a smear-positive specimen, while version 2.0 may use a smear-positive or -negative specimen. We performed this updated review as part of a World Health Organization process to develop updated guidelines for using MTBDRsl. OBJECTIVES To assess and compare the diagnostic accuracy of MTBDRsl for: 1. fluoroquinolone resistance, 2. SLID resistance, and 3. extensively drug-resistant tuberculosis, indirectly on a M. tuberculosis isolate grown from culture or directly on a patient specimen. Participants were people with rifampicin-resistant or multidrug-resistant tuberculosis. The role of MTBDRsl would be as the initial test, replacing culture-based drug susceptibility testing (DST), for detecting second-line drug resistance. SEARCH METHODS We searched the following databases without language restrictions up to 21 September 2015: the Cochrane Infectious Diseases Group Specialized Register; MEDLINE; Embase OVID; Science Citation Index Expanded, Conference Proceedings Citation Index-Science, and BIOSIS Previews (all three from Web of Science); LILACS; and SCOPUS; registers for ongoing trials; and ProQuest Dissertations & Theses A&I. We reviewed references from included studies and contacted specialists in the field. SELECTION CRITERIA We included cross-sectional and case-control studies that determined MTBDRsl accuracy against a defined reference standard (culture-based DST, genetic sequencing, or both). DATA COLLECTION AND ANALYSIS Two review authors independently extracted data and assessed quality using the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) tool. We synthesized data for versions 1.0 and 2.0 separately. We estimated MTBDRsl sensitivity and specificity for fluoroquinolone resistance, SLID resistance, and extensively drug-resistant tuberculosis when the test was performed indirectly or directly (smear-positive specimen for version 1.0, smear-positive or -negative specimen for version 2.0). We explored the influence on accuracy estimates of individual drugs within a drug class and of different reference standards. We performed most analyses using a bivariate random-effects model with culture-based DST as reference standard. MAIN RESULTS We included 27 studies. Twenty-six studies evaluated version 1.0, and one study version 2.0. Of 26 studies stating specimen country origin, 15 studies (58%) evaluated patients from low- or middle-income countries. Overall, we considered the studies to be of high methodological quality. However, only three studies (11%) had low risk of bias for the reference standard; these studies used World Health Organization (WHO)-recommended critical concentrations for all drugs in the culture-based DST reference standard. MTBDRsl version 1.0 Fluoroquinolone resistance: indirect testing, MTBDRsl pooled sensitivity and specificity (95% confidence interval (CI)) were 85.6% (79.2% to 90.4%) and 98.5% (95.7% to 99.5%), (19 studies, 2223 participants); direct testing (smear-positive specimen), pooled sensitivity and specificity were 86.2% (74.6% to 93.0%) and 98.6% (96.9% to 99.4%), (nine studies, 1771 participants, moderate quality evidence). SLID resistance: indirect testing, MTBDRsl pooled sensitivity and specificity were 76.5% (63.3% to 86.0%) and 99.1% (97.3% to 99.7%), (16 studies, 1921 participants); direct testing (smear-positive specimen), pooled sensitivity and specificity were 87.0% (38.1% to 98.6%) and 99.5% (93.6% to 100.0%), (eight studies, 1639 participants, low quality evidence). Extensively drug-resistant tuberculosis: indirect testing, MTBDRsl pooled sensitivity and specificity were 70.9% (42.9% to 88.8%) and 98.8% (96.1% to 99.6%), (eight studies, 880 participants); direct testing (smear-positive specimen), pooled sensitivity and specificity were 69.4% (38.8% to 89.0%) and 99.4% (95.0% to 99.3%), (six studies, 1420 participants, low quality evidence).Similar to the original Cochrane review, we found no evidence of a significant difference in MTBDRsl version 1.0 accuracy between indirect and direct testing for fluoroquinolone resistance, SLID resistance, and extensively drug-resistant tuberculosis. MTBDRsl version 2.0 Fluoroquinolone resistance: direct testing, MTBDRsl sensitivity and specificity were 97% (83% to 100%) and 98% (93% to 100%), smear-positive specimen; 80% (28% to 99%) and 100% (40% to 100%), smear-negative specimen. SLID resistance: direct testing, MTBDRsl sensitivity and specificity were 89% (72% to 98%) and 90% (84% to 95%), smear-positive specimen; 80% (28% to 99%) and 100% (40% to 100%), smear-negative specimen. Extensively drug-resistant tuberculosis: direct testing, MTBDRsl sensitivity and specificity were 79% (49% to 95%) and 97% (93% to 99%), smear-positive specimen; 50% (1% to 99%) and 100% (59% to 100%), smear-negative specimen.We had insufficient data to estimate summary sensitivity and specificity of version 2.0 (smear-positive and -negative specimens) or to compare accuracy of the two versions.A limitation was that most included studies did not consistently use the World Health Organization (WHO)-recommended concentrations for drugs in the culture-based DST reference standard. AUTHORS' CONCLUSIONS In people with rifampicin-resistant or multidrug-resistant tuberculosis, MTBDRsl performed on a culture isolate or smear-positive specimen may be useful in detecting second-line drug resistance. MTBDRsl (smear-positive specimen) correctly classified around six in seven people as having fluoroquinolone or SLID resistance, although the sensitivity estimates for SLID resistance varied. The test rarely gave a positive result for people without drug resistance. However, when second-line drug resistance is not detected (MTBDRsl result is negative), conventional DST can still be used to evaluate patients for resistance to the fluoroquinolones or SLIDs.We recommend that future work evaluate MTBDRsl version 2.0, in particular on smear-negative specimens and in different settings to account for different resistance-causing mutations that may vary by strain. Researchers should also consider incorporating WHO-recommended critical concentrations into their culture-based reference standards.
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Affiliation(s)
- Grant Theron
- Stellenbosch UniversityDST/NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health SciencesTygerbergSouth Africa
| | - Jonny Peter
- University of Cape TownDivision of Clinical Immunology and Allergology, Department of MedicineCape TownSouth Africa
| | - Marty Richardson
- Liverpool School of Tropical MedicineCochrane Infectious Diseases GroupPembroke PlaceLiverpoolUKL3 5QA
| | - Rob Warren
- Stellenbosch UniversityDST/NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health SciencesMatielandSouth Africa
| | - Keertan Dheda
- University of Cape TownLung Infection and Immunity Unit, Department of MedicineCape TownSouth Africa
| | - Karen R Steingart
- Liverpool School of Tropical MedicineCochrane Infectious Diseases GroupPembroke PlaceLiverpoolUKL3 5QA
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Matteelli A, Centis R, D'Ambrosio L, Sotgiu G, Tadolini M, Pontali E, Spanevello A, Migliori GB. WHO strategies for the programmatic management of drug-resistant tuberculosis. Expert Rev Respir Med 2016; 10:991-1002. [PMID: 27276361 DOI: 10.1080/17476348.2016.1199278] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
INTRODUCTION Adequate management of drug-resistant tuberculosis (TB), including multidrug- (MDR) and extensively drug-resistant (XDR-) TB are within the priorities of the newly launched World Health Organization's End TB and Elimination Strategies. AREAS COVERED This manuscript presents the evidence on the MDR- /XDR-TB epidemiology and discusses how the five recommended priority actions can be applied at the programmatic level to tackle the epidemic: 1) prevent development of MDR-TB thorough high quality treatment of drug- susceptible TB; 2) expand rapid testing and detection of drug-resistant TB; 3) provide immediate access to effective treatment and proper care; 4) prevent transmission through infection control; 5) increase political commitment and financing. A non-systematic review using Pubmed was carried out in addition to additional relevant information taken from the abstracts of international scientific conferences. Expert commentary: Current and future control of MDR-TB significantly relies on the correct use of new diagnostics and new drugs from one side, and on the consistent application of the five core interventions at the programmatic level. In addition, it is mandatory to tackle the social determinants and socio-economic barriers favouring the MDR-TB, otherwise it will not be possible to reach the planned goals as well as TB Elimination.
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Affiliation(s)
- Alberto Matteelli
- a Clinic of Infectious and Tropical Diseases , University of Brescia and Brescia Spedali Civili General Hospital , Brescia , Italy
| | - Rosella Centis
- b World Health Organization Collaborating Centre for Tuberculosis and Lung Diseases , Fondazione S. Maugeri, Care and Research Institute , Tradate , Italy
| | - Lia D'Ambrosio
- b World Health Organization Collaborating Centre for Tuberculosis and Lung Diseases , Fondazione S. Maugeri, Care and Research Institute , Tradate , Italy
- c Public Health Consulting Group , Lugano , Switzerland
| | - Giovanni Sotgiu
- d Clinical Epidemiology and Medical Statistics Unit, Department of Biomedical Sciences , University of Sassari, Research, Medical Education and Professional Development Unit, AOU , Sassari , Italy
| | - Marina Tadolini
- e Section of Infectious Diseases, Department of Medical and Surgical Sciences , University of Bologna , Bologna , Italy
| | - Emanuele Pontali
- f Department of Infectious Diseases , Galliera Hospital , Genova , Italy
| | - Antonio Spanevello
- g Pneumology Unit , Fondazione Maugeri, IRCCS , Tradate , Italy
- h Department of Clinical and Experimental Medicine , University of Insubria , Varese , Italy
| | - Giovanni Battista Migliori
- b World Health Organization Collaborating Centre for Tuberculosis and Lung Diseases , Fondazione S. Maugeri, Care and Research Institute , Tradate , Italy
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Georghiou SB, Seifert M, Lin SY, Catanzaro D, Garfein RS, Jackson RL, Crudu V, Rodrigues C, Victor TC, Catanzaro A, Rodwell TC. Shedding light on the performance of a pyrosequencing assay for drug-resistant tuberculosis diagnosis. BMC Infect Dis 2016; 16:458. [PMID: 27576542 PMCID: PMC5006534 DOI: 10.1186/s12879-016-1781-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 08/15/2016] [Indexed: 12/29/2022] Open
Abstract
Background Rapid molecular diagnostics, with their ability to quickly identify genetic mutations associated with drug resistance in Mycobacterium tuberculosis clinical specimens, have great potential as tools to control multi- and extensively drug-resistant tuberculosis (M/XDR-TB). The Qiagen PyroMark Q96 ID system is a commercially available pyrosequencing (PSQ) platform that has been validated for rapid M/XDR-TB diagnosis. However, the details of the assay’s diagnostic and technical performance have yet to be thoroughly investigated in diverse clinical environments. Methods This study evaluates the diagnostic performance of the PSQ assay for 1128 clinical specimens from patients from three areas of high TB burden. We report on the diagnostic performance of the PSQ assay between the three sites and identify variables associated with poor PSQ technical performance. Results In India, the sensitivity of the PSQ assay ranged from 89 to 98 % for the detection of phenotypic resistance to isoniazid, rifampicin, fluoroquinolones, and the injectables. In Moldova, assay sensitivity ranged from 7 to 94 %, and in South Africa, assay sensitivity ranged from 71 to 92 %. Specificity was high (94–100 %) across all sites. The addition of eis promoter sequencing information greatly improved the sensitivity of kanamycin resistance detection in Moldova (7 % to 79 %). Nearly all (89.4 %) sequencing reactions conducted on smear-positive, culture-positive specimens and most (70.8 %) reactions conducted on smear-negative, culture-positive specimens yielded valid PSQ reads. An investigation into the variables influencing sequencing failures indicated smear negativity, culture negativity, site (Moldova), and sequencing of the rpoB, gyrA, and rrs genes were highly associated with poor PSQ technical performance (adj. OR > 2.0). Conclusions This study has important implications for the global implementation of PSQ as a molecular TB diagnostic, as it demonstrates how regional factors may impact PSQ diagnostic performance, while underscoring potential gene targets for optimization to improve overall PSQ assay technical performance. Trial registration ClinicalTrials.gov (#NCT02170441). Registered 12 June 2014. Electronic supplementary material The online version of this article (doi:10.1186/s12879-016-1781-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sophia B Georghiou
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.
| | - Marva Seifert
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Shou-Yean Lin
- California Department of Public Health, Richmond, CA, USA
| | | | - Richard S Garfein
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Roberta L Jackson
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Valeriu Crudu
- Microbiology and Morphology Laboratory, Institute of Phthisiopneumology, Chisinau, Moldova
| | - Camilla Rodrigues
- Department of Microbiology, P.D. Hinduja Hospital and Medical Research Centre, Mumbai, India
| | - Thomas C Victor
- Division of Molecular Biology and Human Genetics, Stellenbosch University, Stellenbosch, South Africa
| | - Antonino Catanzaro
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Timothy C Rodwell
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
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Frequency and Distribution of Tuberculosis Resistance-Associated Mutations between Mumbai, Moldova, and Eastern Cape. Antimicrob Agents Chemother 2016; 60:3994-4004. [PMID: 27090176 DOI: 10.1128/aac.00222-16] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 04/12/2016] [Indexed: 01/17/2023] Open
Abstract
Molecular diagnostic assays, with their ability to rapidly detect resistance-associated mutations in bacterial genes, are promising technologies to control the spread of drug-resistant tuberculosis (DR-TB). Sequencing assays provide detailed information for specific gene regions and can help diagnostic assay developers prioritize mutations for inclusion in their assays. We performed pyrosequencing of seven Mycobacterium tuberculosis gene regions (katG, inhA, ahpC, rpoB, gyrA, rrs, and eis) for 1,128 clinical specimens from India, Moldova, and South Africa. We determined the frequencies of each mutation among drug-resistant and -susceptible specimens based on phenotypic drug susceptibility testing results and examined mutation distributions by country. The most common mutation among isoniazid-resistant (INH(r)) specimens was the katG 315ACC mutation (87%). However, in the Eastern Cape, INH(r) specimens had a lower frequency of katG mutations (44%) and higher frequencies of inhA (47%) and ahpC (10%) promoter mutations. The most common mutation among rifampin-resistant (RIF(r)) specimens was the rpoB 531TTG mutation (80%). The mutation was common in RIF(r) specimens in Mumbai (83%) and Moldova (84%) but not the Eastern Cape (17%), where the 516GTC mutation appeared more frequently (57%). The most common mutation among fluoroquinolone-resistant specimens was the gyrA 94GGC mutation (44%). The rrs 1401G mutation was found in 84%, 84%, and 50% of amikacin-resistant, capreomycin-resistant, and kanamycin (KAN)-resistant (KAN(r)) specimens, respectively. The eis promoter mutation -12T was found in 26% of KAN(r) and 4% of KAN-susceptible (KAN(s)) specimens. Inclusion of the ahpC and eis promoter gene regions was critical for optimal test sensitivity for the detection of INH resistance in the Eastern Cape and KAN resistance in Moldova. (This study has been registered at ClinicalTrials.gov under registration number NCT02170441.).
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Rapid Drug Susceptibility Testing of Drug-Resistant Mycobacterium tuberculosis Isolates Directly from Clinical Samples by Use of Amplicon Sequencing: a Proof-of-Concept Study. J Clin Microbiol 2016; 54:2058-67. [PMID: 27225403 PMCID: PMC4963505 DOI: 10.1128/jcm.00535-16] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 05/19/2016] [Indexed: 11/20/2022] Open
Abstract
Increasingly complex drug-resistant tuberculosis (DR-TB) is a major global health concern and one of the primary reasons why TB is now the leading infectious cause of death worldwide. Rapid characterization of a DR-TB patient's complete drug resistance profile would facilitate individualized treatment in place of empirical treatment, improve treatment outcomes, prevent amplification of resistance, and reduce the transmission of DR-TB. The use of targeted next-generation sequencing (NGS) to obtain drug resistance profiles directly from patient sputum samples has the potential to enable comprehensive evidence-based treatment plans to be implemented quickly, rather than in weeks to months, which is currently needed for phenotypic drug susceptibility testing (DST) results. In this pilot study, we evaluated the performance of amplicon sequencing of Mycobacterium tuberculosis DNA from patient sputum samples using a tabletop NGS technology and automated data analysis to provide a rapid DST solution (the Next Gen-RDST assay). One hundred sixty-six out of 176 (94.3%) sputum samples from the Republic of Moldova yielded complete Next Gen-RDST assay profiles for 7 drugs of interest. We found a high level of concordance of our Next Gen-RDST assay results with phenotypic DST (97.0%) and pyrosequencing (97.8%) results from the same clinical samples. Our Next Gen-RDST assay was also able to estimate the proportion of resistant-to-wild-type alleles down to mixtures of ≤1%, which demonstrates the ability to detect very low levels of resistant variants not detected by pyrosequencing and possibly below the threshold for phenotypic growth methods. The assay as described here could be used as a clinical or surveillance tool.
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Darban-Sarokhalil D, Nasiri MJ, Fooladi AAI, Heidarieh P, Feizabadi MM. Rapid Detection of Rifampicin- and Isoniazid-Resistant Mycobacterium tuberculosis using TaqMan Allelic Discrimination. Osong Public Health Res Perspect 2016; 7:127-30. [PMID: 27169012 PMCID: PMC4850365 DOI: 10.1016/j.phrp.2016.01.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 12/27/2015] [Accepted: 01/06/2016] [Indexed: 11/04/2022] Open
Abstract
Objectives Multidrug-resistant tuberculosis (MDR-TB) is a global problem that many countries are challenged with. Rapid and accurate detection of MDR-TB is critical for appropriate treatment and controlling of TB. The aim of the present study was to evaluate the TaqMan allelic discrimination without minor groove binder (MGB) as a rapid, efficient, and low-cost method for detection of drug resistant strains of Mycobacterium tuberculosis. Methods A total of 112 M. tuberculosis isolates from cases with diagnosed TB were subjected to drug susceptibility testing (DST), using the proportion method. Resistant isolates were tested for characterization of mutations in the rpoB and KatG genes by TaqMan genotyping. Results Of 112 M. tuberculosis isolates for which DST was performed, three, one, and two isolates were MDR, rifampin (RIF) resistant, and isoniazid (INH) resistant, respectively. According to the threshold cycle (Ct) and curve pattern of mutants, TaqMan probes detect all of the mutations in the analyzed genes (katG 315, AGC→ACC, rpoB 531, TCG→TTG, and rpoB 531, TCG→TGG). Conclusion The present study suggests that drug-resistant strains of M. tuberculosis can be detected by pattern’s curve or Ct with TaqMan probes without MGB in real-time polymerase chain reaction (PCR).
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Affiliation(s)
- Davood Darban-Sarokhalil
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad J Nasiri
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abbas A I Fooladi
- Applied Microbiology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Parvin Heidarieh
- Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Mohammad M Feizabadi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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MTBDRplus and MTBDRsl Assays: Absence of Wild-Type Probe Hybridization and Implications for Detection of Drug-Resistant Tuberculosis. J Clin Microbiol 2016; 54:912-8. [PMID: 26763971 DOI: 10.1128/jcm.02505-15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 01/06/2016] [Indexed: 01/24/2023] Open
Abstract
Accurate identification of drug-resistantMycobacterium tuberculosisis imperative for effective treatment and subsequent reduction in disease transmission. Line probe assays rapidly detect mutations associated with resistance and wild-type sequences associated with susceptibility. Examination of molecular-level performance is necessary for improved assay result interpretation and for continued diagnostic development. Using data collected from a large, multisite diagnostic study, probe hybridization results from line probe assays, MTBDRplusand MTBDRsl, were compared to those of sequencing, and the diagnostic performance of each individual mutation and wild-type probe was assessed. Line probe assay results classified as resistant due to the absence of wild-type probe hybridization were compared to those of sequencing to determine if novel mutations were inhibiting wild-type probe hybridization. The contribution of absent wild-type probe hybridization to the detection of drug resistance was assessed via comparison to a phenotypic reference standard. In our study, mutation probes demonstrated significantly higher specificities than wild-type probes and wild-type probes demonstrated marginally higher sensitivities than mutation probes, an ideal combination for detecting the presence of resistance conferring mutations while yielding the fewest number of false-positive results. The absence of wild-type probe hybridization without mutation probe hybridization was determined to be primarily the result of failure of mutation probe hybridization and not the result of novel or rare mutations. Compared to phenotypic culture-based drug susceptibility testing, the absence of wild-type probe hybridization without mutation probe hybridization significantly contributed to the detection of phenotypic rifampin and fluoroquinolone resistance with negligible increases in false-positive results.
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