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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Google Scholar, ClinicalTrials.gov, and the WHO International Clinical Trials Registry Platform for published and unpublished reports on targeted NGS for drug-resistant tuberculosis from Jan 1, 2005, to Oct 14, 2022, with updates to our search in Embase and Google Scholar until Feb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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2
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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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3
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Molina-Moya B, Abdurrahman ST, Madukaji LI, Gomgnimbou MK, Spinasse L, Gomes-Fernandes M, Gomes HM, Kacimi S, Dacombe R, Bimba JS, Lawson L, Sola C, Cuevas LE, Dominguez J. Genetic characterization of Mycobacterium tuberculosis complex isolates circulating in Abuja, Nigeria. Infect Drug Resist 2018; 11:1617-1625. [PMID: 30319278 PMCID: PMC6171509 DOI: 10.2147/idr.s166986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Objective Nigeria ranks fourth among the high tuberculosis (TB) burden countries. This study describes the prevalence of drug resistance and the genetic diversity of Mycobacterium tuberculosis in Abuja’s Federal Capital Territory. Materials and methods Two hundred and seventy-eight consecutive sputum samples were collected from adults with presumptive TB during 2013–2014. DNA was extracted from Löwenstein–Jensen cultures and analyzed for the identification of nontuberculous mycobacteria species, detection of drug resistance with line probe assays, and high-throughput spacer oligonucleotide typing (spoligotyping) using microbead-based hybridization. Results Two hundred and two cultures were positive for M. tuberculosis complex, 24 negative, 38 contaminated, and 15 positive for nontuberculous mycobacteria. Five (2.5%) M. tuberculosis complex isolates were resistant to rifampicin (RIF) and isoniazid (multidrug resistant), nine (4.5%) to RIF alone, and 15 (7.4%) to isoniazid alone; two RIF-resistant isolates were also resistant to fluoroquinolones and ethambutol, and one multidrug resistant isolate was also resistant to ethambutol. Among the 180 isolates with spoligotyping results, 164 (91.1%) were classified as lineage 4 (Euro-American), 13 (7.2%) as lineage 5 (West African 1), two (1.1%) as lineage 2 (East Asia), and one (0.6%) as lineage 6 (West African 2). One hundred and fifty-six (86.7%) isolates were grouped in 17 clusters (2–108 isolates/cluster), of which 108 (60.0%) were grouped as L4.6.2/Cameroon (spoligotype international type 61). Conclusion The description of drug resistance prevalence and genetic diversity of M. tuberculosis in this study may be useful for improving TB control in Nigeria.
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Affiliation(s)
- Barbara Molina-Moya
- Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Barcelona, Spain, .,CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain,
| | | | | | - Michel Kiréopori Gomgnimbou
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France.,Centre Muraz, Bobo-Dioulasso, Burkina Faso
| | - Lizania Spinasse
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| | - Meissiner Gomes-Fernandes
- Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Barcelona, Spain, .,CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain, .,CAPES Foundation, Ministry of Education of Brazil, Brasília, Brazil
| | - Harrison Magdinier Gomes
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| | - Sarah Kacimi
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| | | | | | | | - Christophe Sola
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| | - Luis E Cuevas
- Liverpool School of Tropical Medicine, Liverpool, UK
| | - Jose Dominguez
- Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Barcelona, Spain, .,CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain,
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4
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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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Molina-Moya B, Lacoma A, García-Sierra N, Blanco S, Haba L, Samper S, Ruiz-Manzano J, Prat C, Arnold C, Domínguez J. PyroTyping, a novel pyrosequencing-based assay for Mycobacterium tuberculosis genotyping. Sci Rep 2017; 7:6777. [PMID: 28754991 PMCID: PMC5533701 DOI: 10.1038/s41598-017-06760-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 06/19/2017] [Indexed: 11/09/2022] Open
Abstract
We developed a novel method, PyroTyping, for discrimination of Mycobacterium tuberculosis isolates combining pyrosequencing and IS6110 polymorphism. A total of 100 isolates were analysed with IS6110-restriction fragment length polymorphism (RFLP), spoligotyping, mycobacterial interspersed repetitive units - variable number tandem repeats (MIRU-VNTR), and PyroTyping. PyroTyping results regarding clustering or discrimination of the isolates were highly concordant with the other typing methods performed. PyroTyping is more rapid than RFLP and presents the same discriminatory power, thus, it may be useful for taking timely decisions for tuberculosis control.
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Affiliation(s)
- B Molina-Moya
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Carretera del Canyet s/n, 08916, Badalona, Spain.,CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, 28029, Spain
| | - A Lacoma
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Carretera del Canyet s/n, 08916, Badalona, Spain.,CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, 28029, Spain
| | - N García-Sierra
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Carretera del Canyet s/n, 08916, Badalona, Spain
| | - S Blanco
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Carretera del Canyet s/n, 08916, Badalona, Spain.,CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, 28029, Spain
| | - L Haba
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Carretera del Canyet s/n, 08916, Badalona, Spain
| | - S Samper
- CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, 28029, Spain.,Instituto Aragonés de Ciencias de la Salud, Zaragoza, 50009, Spain.,Fundación Instituto de Investigación Sanitaria de Aragón, Zaragoza, 50009, Spain
| | - J Ruiz-Manzano
- Servei de Pneumologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Carretera del Canyet s/n, 08916, Badalona, Spain.,CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, 28029, Spain
| | - C Prat
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Carretera del Canyet s/n, 08916, Badalona, Spain.,CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, 28029, Spain
| | - C Arnold
- Genomic Services and Development Unit, Public Health England, 61 Colindale Avenue, London, United Kingdom
| | - J Domínguez
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Carretera del Canyet s/n, 08916, Badalona, Spain. .,CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, 28029, Spain.
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6
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Molina-Moya B, Gomgnimbou MK, Lafoz C, Lacoma A, Prat C, Refrégier G, Samper S, Dominguez J, Sola C. Molecular Characterization of Mycobacterium tuberculosis Strains with TB-SPRINT. Am J Trop Med Hyg 2017; 97:806-809. [PMID: 28722603 DOI: 10.4269/ajtmh.16-0782] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
We evaluated Tuberculosis-Spoligo-Rifampicin-Isoniazid Typing (TB-SPRINT), a microbead-based method for spoligotyping and detection of rifampicin and isoniazid resistance in Mycobacterium tuberculosis. For that, 67 M. tuberculosis complex strains were retrospectively selected. Membrane-based spoligotyping, restriction fragment length polymorphism, DNA sequencing/pyrosequencing of rpoB, katG, and inhA promoter, TB-SPRINT, and SNP typing were performed. Concordance between spoligotyping methods was 99.6% (2,785/2,795 spoligotype data points). For most of the discordant cases, the same lineage was assigned with both methods. Concordance between phenotypic drug susceptibility testing and TB-SPRINT for detecting rifampicin and isoniazid resistance was 98.4% (63/64) and 93.8% (60/64), respectively. Concordance between DNA sequencing/pyrosequencing and TB-SPRINT for detecting mutations in rpoB, katG, and inhA were 98.4% (60/61), 100% (64/64), and 96.9% (62/64), respectively. In conclusion, TB-SPRINT is a rapid and easy-to-perform assay for genotyping and detecting drug resistance in a single tube; therefore, it may be a useful tool to improve epidemiological surveillance.
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Affiliation(s)
- Barbara Molina-Moya
- CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain.,Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Michel Kiréopori Gomgnimbou
- Centre Muraz, Bobo-Dioulasso, Burkina Faso.,Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Carmen Lafoz
- Instituto Aragonés de Ciencias de la Salud, Fundación Instituto de Investigación Sanitaria de Aragón, Hospital Universitario Miguel Servet, Zaragoza, Spain.,CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Alicia Lacoma
- CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain.,Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Cristina Prat
- CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain.,Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Guislaine Refrégier
- Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Sofia Samper
- Instituto Aragonés de Ciencias de la Salud, Fundación Instituto de Investigación Sanitaria de Aragón, Hospital Universitario Miguel Servet, Zaragoza, Spain.,CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Jose Dominguez
- CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain.,Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Christophe Sola
- Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
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7
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Shea J, Halse TA, Lapierre P, Shudt M, Kohlerschmidt D, Van Roey P, Limberger R, Taylor J, Escuyer V, Musser KA. Comprehensive Whole-Genome Sequencing and Reporting of Drug Resistance Profiles on Clinical Cases of Mycobacterium tuberculosis in New York State. J Clin Microbiol 2017; 55:1871-1882. [PMID: 28381603 PMCID: PMC5442544 DOI: 10.1128/jcm.00298-17] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 03/28/2017] [Indexed: 12/19/2022] Open
Abstract
Whole-genome sequencing (WGS) is a newer alternative for tuberculosis (TB) diagnostics and is capable of providing rapid drug resistance profiles while performing species identification and capturing the data necessary for genotyping. Our laboratory developed and validated a comprehensive and sensitive WGS assay to characterize Mycobacterium tuberculosis and other M. tuberculosis complex (MTBC) strains, composed of a novel DNA extraction, optimized library preparation, paired-end WGS, and an in-house-developed bioinformatics pipeline. This new assay was assessed using 608 MTBC isolates, with 146 isolates during the validation portion of this study and 462 samples received prospectively. In February 2016, this assay was implemented to test all clinical cases of MTBC in New York State, including isolates and early positive Bactec mycobacterial growth indicator tube (MGIT) 960 cultures from primary specimens. Since the inception of the assay, we have assessed the accuracy of identification of MTBC strains to the species level, concordance with culture-based drug susceptibility testing (DST), and turnaround time. Species identification by WGS was determined to be 99% accurate. Concordance between drug resistance profiles generated by WGS and culture-based DST methods was 96% for eight drugs, with an average resistance-predictive value of 93% and susceptible-predictive value of 96%. This single comprehensive WGS assay has replaced seven molecular assays and has resulted in resistance profiles being reported to physicians an average of 9 days sooner than with culture-based DST for first-line drugs and 32 days sooner for second-line drugs.
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Affiliation(s)
- Joseph Shea
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Tanya A Halse
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Pascal Lapierre
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Matthew Shudt
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Donna Kohlerschmidt
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Patrick Van Roey
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Ronald Limberger
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Jill Taylor
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Vincent Escuyer
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Kimberlee A Musser
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
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8
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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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9
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Evaluation of GenoFlow DR-MTB Array Test for Detection of Rifampin and Isoniazid Resistance in Mycobacterium tuberculosis. J Clin Microbiol 2016; 54:1160-3. [PMID: 26865688 DOI: 10.1128/jcm.03341-15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 02/03/2016] [Indexed: 11/20/2022] Open
Abstract
The aim of this study was to evaluate the GenoFlow DR-MTB array test (DiagCor Bioscience, Hong Kong) on 70 cultured isolates and 50 sputum specimens. The GenoFlow array test showed good sensitivity and specificity compared to the phenotypic Bactec 460TB. This array accurately detected mutations inrpoB,katG, andinhAassociated with resistance to rifampin and isoniazid.
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10
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Drobniewski F, Cooke M, Jordan J, Casali N, Mugwagwa T, Broda A, Townsend C, Sivaramakrishnan A, Green N, Jit M, Lipman M, Lord J, White PJ, Abubakar I. Systematic review, meta-analysis and economic modelling of molecular diagnostic tests for antibiotic resistance in tuberculosis. Health Technol Assess 2016; 19:1-188, vii-viii. [PMID: 25952553 DOI: 10.3310/hta19340] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Drug-resistant tuberculosis (TB), especially multidrug-resistant (MDR, resistance to rifampicin and isoniazid) disease, is associated with a worse patient outcome. Drug resistance diagnosed using microbiological culture takes days to weeks, as TB bacteria grow slowly. Rapid molecular tests for drug resistance detection (1 day) are commercially available and may promote faster initiation of appropriate treatment. OBJECTIVES To (1) conduct a systematic review of evidence regarding diagnostic accuracy of molecular genetic tests for drug resistance, (2) conduct a health-economic evaluation of screening and diagnostic strategies, including comparison of alternative models of service provision and assessment of the value of targeting rapid testing at high-risk subgroups, and (3) construct a transmission-dynamic mathematical model that translates the estimates of diagnostic accuracy into estimates of clinical impact. REVIEW METHODS AND DATA SOURCES A standardised search strategy identified relevant studies from EMBASE, PubMed, MEDLINE, Bioscience Information Service (BIOSIS), System for Information on Grey Literature in Europe Social Policy & Practice (SIGLE) and Web of Science, published between 1 January 2000 and 15 August 2013. Additional 'grey' sources were included. Quality was assessed using quality assessment of diagnostic accuracy studies version 2 (QUADAS-2). For each diagnostic strategy and population subgroup, a care pathway was constructed to specify which medical treatments and health services that individuals would receive from presentation to the point where they either did or did not complete TB treatment successfully. A total cost was estimated from a health service perspective for each care pathway, and the health impact was estimated in terms of the mean discounted quality-adjusted life-years (QALYs) lost as a result of disease and treatment. Costs and QALYs were both discounted at 3.5% per year. An integrated transmission-dynamic and economic model was used to evaluate the cost-effectiveness of introducing rapid molecular testing (in addition to culture and drug sensitivity testing). Probabilistic sensitivity analysis was performed to evaluate the impact on cost-effectiveness of diagnostic and treatment time delays, diagnosis and treatment costs, and associated QALYs. RESULTS A total of 8922 titles and abstracts were identified, with 557 papers being potentially eligible. Of these, 56 studies contained sufficient test information for analysis. All three commercial tests performed well when detecting drug resistance in clinical samples, although with evidence of heterogeneity between studies. Pooled sensitivity for GenoType® MTBDRplus (Hain Lifescience, Nehren, Germany) (isoniazid and rifampicin resistance), INNO-LiPA Rif.TB® (Fujirebio Europe, Ghent, Belgium) (rifampicin resistance) and Xpert® MTB/RIF (Cepheid Inc., Sunnyvale, CA, USA) (rifampicin resistance) was 83.4%, 94.6%, 95.4% and 96.8%, respectively; equivalent pooled specificity was 99.6%, 98.2%, 99.7% and 98.4%, respectively. Results of the transmission model suggest that all of the rapid assays considered here, if added to the current diagnostic pathway, would be cost-saving and achieve a reduction in expected QALY loss compared with current practice. GenoType MTBDRplus appeared to be the most cost-effective of the rapid tests in the South Asian population, although results were similar for GeneXpert. In all other scenarios GeneXpert appeared to be the most cost-effective strategy. CONCLUSIONS Rapid molecular tests for rifampicin and isoniazid resistance were sensitive and specific. They may also be cost-effective when added to culture drug susceptibility testing in the UK. There is global interest in point-of-care testing and further work is needed to review the performance of emerging tests and the wider health-economic impact of decentralised testing in clinics and primary care, as well as non-health-care settings, such as shelters and prisons. STUDY REGISTRATION This study is registered as PROSPERO CRD42011001537. FUNDING The National Institute for Health Research Health Technology Assessment programme.
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Affiliation(s)
- Francis Drobniewski
- Public Health England National Mycobacterium Reference Laboratory, London, UK
| | - Mary Cooke
- Centre for Infectious Disease Epidemiology, Research Department of Infection and Population Health, University College London, London, UK
| | - Jake Jordan
- Health Economics Research Group, Brunel University, Uxbridge, UK
| | - Nicola Casali
- Department of Infectious Diseases and Immunity, Imperial College London, London, UK
| | - Tendai Mugwagwa
- Modelling and Economics Unit, Centre for Infectious Disease Surveillance and Control, Public Health England, London, UK
| | - Agnieszka Broda
- Department of Infectious Diseases and Immunity, Imperial College London, London, UK
| | | | | | - Nathan Green
- Modelling and Economics Unit, Centre for Infectious Disease Surveillance and Control, Public Health England, London, UK
| | - Mark Jit
- Modelling and Economics Unit, Centre for Infectious Disease Surveillance and Control, Public Health England, London, UK
| | - Marc Lipman
- Division of Medicine, University College London, London, UK
| | - Joanne Lord
- Health Economics Research Group, Brunel University, Uxbridge, UK
| | - Peter J White
- Modelling and Economics Unit, Centre for Infectious Disease Surveillance and Control, Public Health England, London, UK
| | - Ibrahim Abubakar
- Centre for Infectious Disease Epidemiology, Research Department of Infection and Population Health, University College London, London, UK
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11
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Luo W, Qu ZL, Xie Y, Xiang J, Zhang XL. Identification of a novel immunodominant antigen Rv2645 from RD13 with potential as a cell-mediated immunity-based TB diagnostic agent. J Infect 2015; 71:534-43. [DOI: 10.1016/j.jinf.2015.07.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 07/13/2015] [Accepted: 07/14/2015] [Indexed: 12/31/2022]
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12
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Novel katG mutations causing isoniazid resistance in clinical M. tuberculosis isolates. Emerg Microbes Infect 2015; 4:e42. [PMID: 26251830 PMCID: PMC4522615 DOI: 10.1038/emi.2015.42] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 04/08/2015] [Accepted: 05/19/2015] [Indexed: 12/16/2022]
Abstract
We report the discovery and confirmation of 23 novel mutations with previously undocumented role in isoniazid (INH) drug resistance, in catalase-peroxidase (katG) gene of Mycobacterium tuberculosis (Mtb) isolates. With these mutations, a synonymous mutation in fabG1g609a, and two canonical mutations, we were able to explain 98% of the phenotypic resistance observed in 366 clinical Mtb isolates collected from four high tuberculosis (TB)-burden countries: India, Moldova, Philippines, and South Africa. We conducted overlapping targeted and whole-genome sequencing for variant discovery in all clinical isolates with a variety of INH-resistant phenotypes. Our analysis showed that just two canonical mutations (katG 315AGC-ACC and inhA promoter-15C-T) identified 89.5% of resistance phenotypes in our collection. Inclusion of the 23 novel mutations reported here, and the previously documented point mutation in fabG1, increased the sensitivity of these mutations as markers of INH resistance to 98%. Only six (2%) of the 332 resistant isolates in our collection did not harbor one or more of these mutations. The third most prevalent substitution, at inhA promoter position -8, present in 39 resistant isolates, was of no diagnostic significance since it always co-occurred with katG 315. 79% of our isolates harboring novel mutations belong to genetic group 1 indicating a higher tendency for this group to go down an uncommon evolutionary path and evade molecular diagnostics. The results of this study contribute to our understanding of the mechanisms of INH resistance in Mtb isolates that lack the canonical mutations and could improve the sensitivity of next generation molecular diagnostics.
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13
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Lacoma A, Molina-Moya B, Prat C, Pimkina E, Diaz J, Dudnyk A, García-Sierra N, Haba L, Maldonado J, Samper S, Ruiz-Manzano J, Ausina V, Dominguez J. Pyrosequencing for rapid detection of Mycobacterium tuberculosis second-line drugs and ethambutol resistance. Diagn Microbiol Infect Dis 2015; 83:263-9. [PMID: 26256417 DOI: 10.1016/j.diagmicrobio.2015.07.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 07/06/2015] [Accepted: 07/07/2015] [Indexed: 01/08/2023]
Abstract
The aim of this work was to study the diagnostic accuracy of pyrosequencing to detect resistance to fluoroquinolones, kanamycin, amikacin, capreomycin, and ethambutol (EMB) in Mycobacterium tuberculosis clinical strains. One hundred four clinical isolates previously characterized by BACTEC 460TB/MGIT 960 were included. Specific mutations were targeted in gyrA, rrs, eis promoter, and embB. When there was a discordant result between BACTEC and pyrosequencing, Genotype MTBDRsl (Hain Lifescience, Nehren, Germany) was performed. Sensitivity and specificity of pyrosequencing were 70.6% and 100%, respectively, for fluoroquinolones; 93.3% and 81.7%, respectively, for kanamycin; 94.1% and 95.9%, respectively, for amikacin; 90.0% and 100%, respectively, for capreomycin; and 64.8% and 87.8%, respectively, for EMB. This study shows that pyrosequencing may be a useful tool for making early decisions regarding second-line drugs and EMB resistance. However, for a correct management of patients with suspected extensively drug-resistant tuberculosis, susceptibility results obtained by molecular methods should be confirmed by a phenotypic method.
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Affiliation(s)
- Alicia Lacoma
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Carretera del Canyet s/n, 08916, Badalona, Spain; CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Spain
| | - Barbara Molina-Moya
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Carretera del Canyet s/n, 08916, Badalona, Spain; CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Spain
| | - Cristina Prat
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Carretera del Canyet s/n, 08916, Badalona, Spain; CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Spain
| | - Edita Pimkina
- Infectious Diseases and Tuberculosis Hospital, Affiliate of Vilnius University Hospital Santariskiu Klinikos, Vilnius, Lithuania
| | - Jessica Diaz
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Carretera del Canyet s/n, 08916, Badalona, Spain; CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Spain
| | - Andriy Dudnyk
- Department of Tuberculosis, Clinical Immunology and Allergology, Vinnitsa National Pirogov Memorial Medical University, Vinnitsa, Ukraine
| | - Nerea García-Sierra
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Carretera del Canyet s/n, 08916, Badalona, Spain
| | - Lucía Haba
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Carretera del Canyet s/n, 08916, Badalona, Spain
| | | | - Sofia Samper
- CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Spain; Instituto Aragonés de Ciencias de la Salud, Hospital Universitario Miguel Servet, Zaragoza, Spain
| | - Juan Ruiz-Manzano
- Servei de Pneumologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Carretera del Canyet s/n, 08916, Badalona, Spain; CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Spain
| | - Vicente Ausina
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Carretera del Canyet s/n, 08916, Badalona, Spain; CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Spain
| | - Jose Dominguez
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Carretera del Canyet s/n, 08916, Badalona, Spain; CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Spain.
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14
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Molina-Moya B, Lacoma A, Prat C, Pimkina E, Diaz J, García-Sierra N, Haba L, Maldonado J, Samper S, Ruiz-Manzano J, Ausina V, Dominguez J. Diagnostic accuracy study of multiplex PCR for detecting tuberculosis drug resistance. J Infect 2015; 71:220-30. [PMID: 25936742 DOI: 10.1016/j.jinf.2015.03.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 03/05/2015] [Accepted: 03/09/2015] [Indexed: 10/23/2022]
Abstract
OBJECTIVE To study the diagnostic accuracy of a multiplex real-time PCR (Anyplex II MTB/MDR/XDR, Seegene, Corea) that detects Mycobacterium tuberculosis resistant to isoniazid (INH), rifampicin (RIF), fluoroquinolones (FLQ) and injectable drugs (kanamycin [KAN], amikacin [AMK] and capreomycin [CAP]) in isolates and specimens. METHODS One hundred fourteen cultured isolates and 73 sputum specimens were retrospectively selected. Results obtained with multiplex PCR were compared with those obtained with BACTEC. Discordant results between multiplex PCR and BACTEC were tested by alternative molecular methods. RESULTS Sensitivity and specificity of multiplex PCR for detecting drug resistance in isolates were 76.5% and 100%, respectively, for INH; 97.2% and 96.0%, respectively, for RIF; 70.4% and 87.9%, respectively, for FLQ; 81.5% and 84.8%, respectively, for KAN; 100% and 60%, respectively, for AMK, and 100% and 72.3%, respectively, for CAP. Sensitivity and specificity of Anyplex for detecting drug resistance in specimens were 93.3% and 100%, respectively, for INH; 100% and 100%, respectively, for RIF; 50.0% and 100%, respectively, for FLQ; and 100% and 94.4%, respectively, for both KAN and CAP. Among the discordant results, 87.7% (71/81) of results obtained with the multiplex PCR were concordant with at least one of the alternative molecular methods. CONCLUSIONS This multiplex PCR may be a useful tool for the rapid identification of drug resistant tuberculosis in isolates and specimens, thus allowing an initial therapeutic approach. Nevertheless, for a correct management of patients, results should be confirmed by a phenotypic method.
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Affiliation(s)
- B Molina-Moya
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Carretera del Canyet s/n, 08916 Badalona, Spain; CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Spain
| | - A Lacoma
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Carretera del Canyet s/n, 08916 Badalona, Spain; CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Spain
| | - C Prat
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Carretera del Canyet s/n, 08916 Badalona, Spain; CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Spain
| | - E Pimkina
- Infectious Diseases and Tuberculosis Hospital, Affiliate of Vilnius University Hospital Santariskiu klinikos, Vilnius, Lithuania
| | - J Diaz
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Carretera del Canyet s/n, 08916 Badalona, Spain; CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Spain
| | - N García-Sierra
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Carretera del Canyet s/n, 08916 Badalona, Spain
| | - L Haba
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Carretera del Canyet s/n, 08916 Badalona, Spain
| | | | - S Samper
- CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Spain; Instituto Aragonés de Ciencias de la Salud, Zaragoza, Spain; Hospital Universitario Miguel Servet, Zaragoza, Spain
| | - J Ruiz-Manzano
- Servei de Pneumologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Carretera del Canyet s/n, 08916 Badalona, Spain; CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Spain
| | - V Ausina
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Carretera del Canyet s/n, 08916 Badalona, Spain; CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Spain
| | - J Dominguez
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Carretera del Canyet s/n, 08916 Badalona, Spain; CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Spain.
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15
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Amoako KK. Application of Pyrosequencing® in Food Biodefense. Methods Mol Biol 2015; 1315:363-375. [PMID: 26103911 DOI: 10.1007/978-1-4939-2715-9_25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The perpetration of a bioterrorism attack poses a significant risk for public health with potential socioeconomic consequences. It is imperative that we possess reliable assays for the rapid and accurate identification of biothreat agents to make rapid risk-informed decisions on emergency response. The development of advanced methodologies for the detection of biothreat agents has been evolving rapidly since the release of the anthrax spores in the mail in 2001, and recent advances in detection and identification techniques could prove to be an essential component in the defense against biological attacks. Sequence-based approaches such as Pyrosequencing(®), which has the capability to determine short DNA stretches in real time using biotinylated PCR amplicons, have potential biodefense applications. Using markers from the virulence plasmids and chromosomal regions, my laboratory has demonstrated the power of this technology in the rapid, specific, and sensitive detection of B. anthracis spores and Yersinia pestis in food. These are the first applications for the detection of the two organisms in food. Furthermore, my lab has developed a rapid assay to characterize the antimicrobial resistance (AMR) gene profiles for Y. pestis using Pyrosequencing. Pyrosequencing is completed in about 60 min (following PCR amplification) and yields accurate and reliable results with an added layer of confidence, thus enabling rapid risk-informed decisions to be made. A typical run yields 40-84 bp reads with 94-100 % identity to the expected sequence. It also provides a rapid method for determining the AMR profile as compared to the conventional plate method which takes several days. The method described is proposed as a novel detection system for potential application in food biodefense.
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Affiliation(s)
- Kingsley Kwaku Amoako
- National Centers for Animal Disease, Lethbridge Laboratory, Canadian Food Inspection Agency, P.O. Box 640, Township Road 9-1, Lethbridge, AB, Canada, T1J 3Z4,
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16
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Ajbani K, Lin SYG, Rodrigues C, Nguyen D, Arroyo F, Kaping J, Jackson L, Garfein RS, Catanzaro D, Eisenach K, Victor TC, Crudu V, Gler MT, Ismail N, Desmond E, Catanzaro A, Rodwell TC. Evaluation of pyrosequencing for detecting extensively drug-resistant Mycobacterium tuberculosis among clinical isolates from four high-burden countries. Antimicrob Agents Chemother 2015; 59:414-20. [PMID: 25367911 PMCID: PMC4291380 DOI: 10.1128/aac.03614-14] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Accepted: 10/28/2014] [Indexed: 12/15/2022] Open
Abstract
Reliable molecular diagnostics, which detect specific mutations associated with drug resistance, are promising technologies for the rapid identification and monitoring of drug resistance in Mycobacterium tuberculosis isolates. Pyrosequencing (PSQ) has the ability to detect mutations associated with first- and second-line anti-tuberculosis (TB) drugs, with the additional advantage of being rapidly adaptable for the identification of new mutations. The aim of this project was to evaluate the performance of PSQ in predicting phenotypic drug resistance in multidrug- and extensively drug-resistant tuberculosis (M/XDR-TB) clinical isolates from India, South Africa, Moldova, and the Philippines. A total of 187 archived isolates were run through a PSQ assay in order to identify M. tuberculosis (via the IS6110 marker), and to detect mutations associated with M/XDR-TB within small stretches of nucleotides in selected loci. The molecular targets included katG, the inhA promoter and the ahpC-oxyR intergenic region for isoniazid (INH) resistance; the rpoB core region for rifampin (RIF) resistance; gyrA for fluoroquinolone (FQ) resistance; and rrs for amikacin (AMK), capreomycin (CAP), and kanamycin (KAN) resistance. PSQ data were compared to phenotypic mycobacterial growth indicator tube (MGIT) 960 drug susceptibility testing results for performance analysis. The PSQ assay illustrated good sensitivity for the detection of resistance to INH (94%), RIF (96%), FQ (93%), AMK (84%), CAP (88%), and KAN (68%). The specificities of the assay were 96% for INH, 100% for RIF, FQ, AMK, and KAN, and 97% for CAP. PSQ is a highly efficient diagnostic tool that reveals specific nucleotide changes associated with resistance to the first- and second-line anti-TB drug medications. This methodology has the potential to be linked to mutation-specific clinical interpretation algorithms for rapid treatment decisions.
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Affiliation(s)
- Kanchan Ajbani
- P. D. Hinduja National Hospital & Medical Research Centre, Department of Microbiology, Veer Sarvarkar Marg, Mahim, Mumbai, India
| | - Shou-Yean Grace Lin
- California Department of Public Health, Microbial Diseases Laboratory, Richmond, California, USA
| | - Camilla Rodrigues
- P. D. Hinduja National Hospital & Medical Research Centre, Department of Microbiology, Veer Sarvarkar Marg, Mahim, Mumbai, India
| | - Duylinh Nguyen
- California Department of Public Health, Microbial Diseases Laboratory, Richmond, California, USA
| | - Francine Arroyo
- California Department of Public Health, Microbial Diseases Laboratory, Richmond, California, USA
| | - Janice Kaping
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Lynn Jackson
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Richard S Garfein
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Donald Catanzaro
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Kathleen Eisenach
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Thomas C Victor
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Valeru Crudu
- Microbiology and Morphology Laboratory, Institute of Phthisiopneumology, Chisinau, Moldova
| | - Maria Tarcela Gler
- Tropical Disease Foundation/Makati Medical Center, Makati City, Philippines
| | - Nazir Ismail
- National Tuberculosis Reference Laboratory, Johannesburg, South Africa
| | - Edward Desmond
- California Department of Public Health, Microbial Diseases Laboratory, Richmond, California, USA
| | - Antonino Catanzaro
- Department of Medicine, 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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Recent Advances in Tuberculosis Diagnosis: IGRAs and Molecular Biology. CURRENT TREATMENT OPTIONS IN INFECTIOUS DISEASES 2014. [DOI: 10.1007/s40506-014-0034-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Molina-Moya B, Lacoma A, Prat C, Diaz J, Dudnyk A, Haba L, Maldonado J, Samper S, Ruiz-Manzano J, Ausina V, Dominguez J. AID TB resistance line probe assay for rapid detection of resistant Mycobacterium tuberculosis in clinical samples. J Infect 2014; 70:400-8. [PMID: 25305498 DOI: 10.1016/j.jinf.2014.09.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 08/25/2014] [Accepted: 09/17/2014] [Indexed: 10/24/2022]
Abstract
OBJECTIVES To determine the sensitivity and specificity of AID TB Resistance line probe assay (AID Diagnostika, Germany) to detect Mycobacterium tuberculosis and its resistance to first- and second-line drugs in clinical samples using BACTEC 460TB as the reference standard. METHODS The test consists on three strips to detect resistance to isoniazid/rifampicin, fluoroquinolones/ethambutol, and kanamycin/amikacin/capreomycin/streptomycin, respectively. This test was performed on 65 retrospectively selected clinical samples corresponding to 32 patients. RESULTS A valid result was obtained for 92.3% (60/65), 90.8% (59/65) and 78.5% (51/65) of the samples tested, considering the three strips, respectively. Global concordance rates between AID and BACTEC for detecting resistance to isoniazid, rifampicin, fluoroquinolones, ethambutol, kanamycin/capreomycin and streptomycin were 98.3% (59/60), 100% (60/60), 91.5% (54/59), 72.9% (43/59), 100% (51/51) and 98.0% (50/51), respectively. Regarding the discordant results obtained between AID and BACTEC, the alternative molecular methods performed (GenoType MTBDRplus, GenoType MTBDRsl [Hain Lifescience, Germany] and/or pyrosequencing) confirmed the genotypic result in 90.9% (20/22) of the cases. CONCLUSIONS AID line probe assay is a useful tool for the rapid detection of drug resistance in clinical samples enabling an initial therapeutic approach. Nevertheless, for a correct management of drug resistant tuberculosis patients, molecular results should be confirmed by a phenotypic method.
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Affiliation(s)
- B Molina-Moya
- Servei de Microbiologia Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Carretera del Canyet s/n, 08916 Badalona, Spain; CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Spain
| | - A Lacoma
- Servei de Microbiologia Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Carretera del Canyet s/n, 08916 Badalona, Spain; CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Spain
| | - C Prat
- Servei de Microbiologia Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Carretera del Canyet s/n, 08916 Badalona, Spain; CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Spain
| | - J Diaz
- Servei de Microbiologia Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Carretera del Canyet s/n, 08916 Badalona, Spain
| | - A Dudnyk
- Department of Tuberculosis, Clinical Immunology and Allergology, Vinnitsa National Pirogov Memorial Medical University, Vinnitsa, Ukraine
| | - L Haba
- Servei de Microbiologia Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Carretera del Canyet s/n, 08916 Badalona, Spain
| | | | - S Samper
- CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Spain; Instituto Aragonés de Ciencias de la Salud, Zaragoza, Spain; Hospital Universitario Miguel Servet, Zaragoza, Spain
| | - J Ruiz-Manzano
- Servei de Pneumologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain; CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Spain
| | - V Ausina
- Servei de Microbiologia Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Carretera del Canyet s/n, 08916 Badalona, Spain; CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Spain
| | - J Dominguez
- Servei de Microbiologia Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Carretera del Canyet s/n, 08916 Badalona, Spain; CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Spain.
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Zheng R, Zhu C, Guo Q, Qin L, Wang J, Lu J, Cui H, Cui Z, Ge B, Liu J, Hu Z. Pyrosequencing for rapid detection of tuberculosis resistance in clinical isolates and sputum samples from re-treatment pulmonary tuberculosis patients. BMC Infect Dis 2014; 14:200. [PMID: 24725975 PMCID: PMC4021344 DOI: 10.1186/1471-2334-14-200] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 04/09/2014] [Indexed: 12/02/2022] Open
Abstract
Background Multidrug-resistant tuberculosis (MDR-TB) is a major public health problem. Early diagnosis of MDR-TB patients is essential for minimizing the risk of Mycobacterium tuberculosis (MTB) transmission. The conventional drug susceptibility testing (DST) methods for detection of drug-resistant M.tuberculosis are laborious and cannot provide the rapid detection for clinical practice. Methods The aim of this study was to develop a pyrosequencing approach for the simultaneous detection of resistance to rifampin (RIF), isoniazid (INH), ethambutol (EMB), streptomycin (SM), ofloxacin (OFL) and amikacin (AMK) in M. tuberculosis clinical isolates and sputum samples from re-treatment pulmonary tuberculosis (PTB) patients. We identified the optimum conditions for detection mutation of rpoB, katG, rpsl, embB, gyrA and rrs gene by pyrosequencing. Then this approach was applied to detect 205 clinical isolates and 24 sputum samples of M. tuberculosis from re-treatment PTB patients. Results The mutations of rpoB and gyrA gene were detected by pyrosequencig with the SQA mode, and the mutations of katG, rpsl, embB, gyrA and rrs gene were detected by pyrosequencing with SNP mode. Compared with the Bactec MGIT 960 mycobacterial detection system, the accuracy of pyrosequencing for the detection of RIF, INH, EMB, SM, AMK and OFL resistance in clinical isolates was 95.0%, 79.2%, 70.3%, 84.5%, 96.5% and 91.1%, respectively. In sputum samples the accuracy was 83.3%, 83.3%, 60.9%, 83.3%, 87.5% and 91.7%, respectively. Conclusions The newly established pyrosequencing assay is a rapid and high-throughput method for the detection of resistance to RIF, INH, SM, EMB, OFL and AMK in M.tuberculosis. Pyrosequencing can be used as a practical molecular diagnostic tool for screening and predicting the resistance of re-treatment pulmonary tuberculosis patients.
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Affiliation(s)
| | - Changtai Zhu
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, No, 507 Zhengmin Rd, Shanghai 200433, People's Republic of China.
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Rodwell TC, Valafar F, Douglas J, Qian L, Garfein RS, Chawla A, Torres J, Zadorozhny V, Kim MS, Hoshide M, Catanzaro D, Jackson L, Lin G, Desmond E, Rodrigues C, Eisenach K, Victor TC, Ismail N, Crudu V, Gler MT, Catanzaro A. Predicting extensively drug-resistant Mycobacterium tuberculosis phenotypes with genetic mutations. J Clin Microbiol 2014; 52:781-9. [PMID: 24353002 PMCID: PMC3957771 DOI: 10.1128/jcm.02701-13] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 12/12/2013] [Indexed: 01/20/2023] Open
Abstract
Molecular diagnostic methods based on the detection of mutations conferring drug resistance are promising technologies for rapidly detecting multidrug-/extensively drug-resistant tuberculosis (M/XDR TB), but large studies of mutations as markers of resistance are rare. The Global Consortium for Drug-Resistant TB Diagnostics analyzed 417 Mycobacterium tuberculosis isolates from multinational sites with a high prevalence of drug resistance to determine the sensitivities and specificities of mutations associated with M/XDR TB to inform the development of rapid diagnostic methods. We collected M/XDR TB isolates from regions of high TB burden in India, Moldova, the Philippines, and South Africa. The isolates underwent standardized phenotypic drug susceptibility testing (DST) to isoniazid (INH), rifampin (RIF), moxifloxacin (MOX), ofloxacin (OFX), amikacin (AMK), kanamycin (KAN), and capreomycin (CAP) using MGIT 960 and WHO-recommended critical concentrations. Eight genes (katG, inhA, rpoB, gyrA, gyrB, rrs, eis, and tlyA) were sequenced using Sanger sequencing. Three hundred seventy isolates were INHr, 356 were RIFr, 292 were MOXr/OFXr, 230 were AMKr, 219 were CAPr, and 286 were KANr. Four single nucleotide polymorphisms (SNPs) in katG/inhA had a combined sensitivity of 96% and specificities of 97 to 100% for the detection of INHr. Eleven SNPs in rpoB had a combined sensitivity of 98% for RIFr. Eight SNPs in gyrA codons 88 to 94 had sensitivities of 90% for MOXr/OFXr. The rrs 1401/1484 SNPs had 89 to 90% sensitivity for detecting AMKr/CAPr but 71% sensitivity for KANr. Adding eis promoter SNPs increased the sensitivity to 93% for detecting AMKr and to 91% for detecting KANr. Approximately 30 SNPs in six genes predicted clinically relevant XDR-TB phenotypes with 90 to 98% sensitivity and almost 100% specificity.
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Affiliation(s)
- Timothy C. Rodwell
- Department of Medicine, University of California San Diego, San Diego, California, USA
| | - Faramarz Valafar
- Department of Bioinformatics and Medical Informatics, San Diego State University, San Diego, California, USA
| | - James Douglas
- Department of Microbiology, University of Hawaii Manoa, Honolulu, Hawaii, USA
| | - Lishi Qian
- Department of Microbiology, University of Hawaii Manoa, Honolulu, Hawaii, USA
| | - Richard S. Garfein
- Department of Medicine, University of California San Diego, San Diego, California, USA
| | - Ashu Chawla
- Department of Bioinformatics and Medical Informatics, San Diego State University, San Diego, California, USA
| | - Jessica Torres
- Department of Bioinformatics and Medical Informatics, San Diego State University, San Diego, California, USA
| | - Victoria Zadorozhny
- Department of Bioinformatics and Medical Informatics, San Diego State University, San Diego, California, USA
| | - Min Soo Kim
- Department of Bioinformatics and Medical Informatics, San Diego State University, San Diego, California, USA
| | - Matt Hoshide
- Department of Microbiology, University of Hawaii Manoa, Honolulu, Hawaii, USA
| | - Donald Catanzaro
- Department of Bioinformatics and Medical Informatics, San Diego State University, San Diego, California, USA
| | - Lynn Jackson
- Department of Medicine, University of California San Diego, San Diego, California, USA
| | - Grace Lin
- California Department of Public Health, Microbial Diseases Laboratory, Richmond, California, USA
| | - Edward Desmond
- California Department of Public Health, Microbial Diseases Laboratory, Richmond, California, USA
| | | | - Kathy Eisenach
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Thomas C. Victor
- Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa
| | - Nazir Ismail
- National Tuberculosis Reference Laboratory, Johannesburg, South Africa
| | - Valeru Crudu
- Microbiology and Morphology Laboratory, Institute of Phthisiopneumology, Chisinau, Moldova
| | | | - Antonino Catanzaro
- Department of Medicine, University of California San Diego, San Diego, California, USA
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Matrix-assisted laser desorption ionization-time of flight mass spectrometry: a fundamental shift in the routine practice of clinical microbiology. Clin Microbiol Rev 2014; 26:547-603. [PMID: 23824373 DOI: 10.1128/cmr.00072-12] [Citation(s) in RCA: 511] [Impact Index Per Article: 51.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Within the past decade, clinical microbiology laboratories experienced revolutionary changes in the way in which microorganisms are identified, moving away from slow, traditional microbial identification algorithms toward rapid molecular methods and mass spectrometry (MS). Historically, MS was clinically utilized as a high-complexity method adapted for protein-centered analysis of samples in chemistry and hematology laboratories. Today, matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) MS is adapted for use in microbiology laboratories, where it serves as a paradigm-shifting, rapid, and robust method for accurate microbial identification. Multiple instrument platforms, marketed by well-established manufacturers, are beginning to displace automated phenotypic identification instruments and in some cases genetic sequence-based identification practices. This review summarizes the current position of MALDI-TOF MS in clinical research and in diagnostic clinical microbiology laboratories and serves as a primer to examine the "nuts and bolts" of MALDI-TOF MS, highlighting research associated with sample preparation, spectral analysis, and accuracy. Currently available MALDI-TOF MS hardware and software platforms that support the use of MALDI-TOF with direct and precultured specimens and integration of the technology into the laboratory workflow are also discussed. Finally, this review closes with a prospective view of the future of MALDI-TOF MS in the clinical microbiology laboratory to accelerate diagnosis and microbial identification to improve patient care.
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Pyrosequencing for rapid detection of extensively drug-resistant Mycobacterium tuberculosis in clinical isolates and clinical specimens. J Clin Microbiol 2013; 52:475-82. [PMID: 24478476 DOI: 10.1128/jcm.01821-13] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Treating extensively drug-resistant (XDR) tuberculosis (TB) is a serious challenge. Culture-based drug susceptibility testing (DST) may take 4 weeks or longer from specimen collection to the availability of results. We developed a pyrosequencing (PSQ) assay including eight subassays for the rapid identification of Mycobacterium tuberculosis complex (MTBC) and concurrent detection of mutations associated with resistance to drugs defining XDR TB. The entire procedure, from DNA extraction to the availability of results, was accomplished within 6 h. The assay was validated for testing clinical isolates and clinical specimens, which improves the turnaround time for molecular DST and maximizes the benefit of using molecular testing. A total of 130 clinical isolates and 129 clinical specimens were studied. The correlations between the PSQ results and the phenotypic DST results were 94.3% for isoniazid, 98.7% for rifampin, 97.6% for quinolones (ofloxacin, levofloxacin, or moxifloxacin), 99.2% for amikacin, 99.2% for capreomycin, and 96.4% for kanamycin. For testing clinical specimens, the PSQ assay yielded a 98.4% sensitivity for detecting MTBC and a 95.8% sensitivity for generating complete sequencing results from all subassays. The PSQ assay was able to rapidly and accurately detect drug resistance mutations with the sequence information provided, which allows further study of the association of drug resistance or susceptibility with each mutation and the accumulation of such knowledge for future interpretation of results. Thus, reporting of false resistance for mutations known not to confer resistance can be prevented, which is a significant benefit of the assay over existing molecular diagnostic methods endorsed by the World Health Organization.
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França RFO, da Silva CC, De Paula SO. Recent advances in molecular medicine techniques for the diagnosis, prevention, and control of infectious diseases. Eur J Clin Microbiol Infect Dis 2013; 32:723-8. [PMID: 23339016 PMCID: PMC7087945 DOI: 10.1007/s10096-013-1813-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 01/01/2013] [Indexed: 11/24/2022]
Abstract
In recent years we have observed great advances in our ability to combat infectious diseases. Through the development of novel genetic methodologies, including a better understanding of pathogen biology, pathogenic mechanisms, advances in vaccine development, designing new therapeutic drugs, and optimization of diagnostic tools, significant infectious diseases are now better controlled. Here, we briefly describe recent reports in the literature concentrating on infectious disease control. The focus of this review is to describe the molecular methods widely used in the diagnosis, prevention, and control of infectious diseases with regard to the innovation of molecular techniques. Since the list of pathogenic microorganisms is extensive, we emphasize some of the major human infectious diseases (AIDS, tuberculosis, malaria, rotavirus, herpes virus, viral hepatitis, and dengue fever). As a consequence of these developments, infectious diseases will be more accurately and effectively treated; safe and effective vaccines are being developed and rapid detection of infectious agents now permits countermeasures to avoid potential outbreaks and epidemics. But, despite considerable progress, infectious diseases remain a strong challenge to human survival.
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Affiliation(s)
- R F O França
- Department of Pharmacology, School of Medicine of Ribeirão Preto, University of São Paulo, Avenida dos Bandeirantes 3900, Ribeirão Preto, SP, 14049-900, Brazil
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Amoako KK, Thomas MC, Kong F, Janzen TW, Hahn KR, Shields MJ, Goji N. Rapid detection and antimicrobial resistance gene profiling of Yersinia pestis using pyrosequencing technology. J Microbiol Methods 2012; 90:228-34. [DOI: 10.1016/j.mimet.2012.05.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 05/18/2012] [Accepted: 05/18/2012] [Indexed: 10/28/2022]
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Rapid, high-throughput detection of rifampin resistance and heteroresistance in Mycobacterium tuberculosis by use of sloppy molecular beacon melting temperature coding. J Clin Microbiol 2012; 50:2194-202. [PMID: 22535987 DOI: 10.1128/jcm.00143-12] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Rifampin resistance in Mycobacterium tuberculosis is largely determined by mutations in an 80-bp rifampin resistance determining region (RRDR) of the rpoB gene. We developed a rapid single-well PCR assay to identify RRDR mutations. The assay uses sloppy molecular beacons to probe an asymmetric PCR of the M. tuberculosis RRDR by melting temperature (T(m)) analysis. A three-point T(m) code is generated which distinguishes wild-type from mutant RRDR DNA sequences in approximately 2 h. The assay was validated on synthetic oligonucleotide targets containing the 44 most common RRDR mutations. It was then tested on a panel of DNA extracted from 589 geographically diverse clinical M. tuberculosis cultures, including isolates with wild-type RRDR sequences and 25 different RRDR mutations. The assay detected 236/236 RRDR mutant sequences as mutant (sensitivity, 100%; 95% confidence interval [CI], 98 to 100%) and 353/353 RRDR wild-type sequences as wild type (specificity, 100%; 95% CI, 98.7 to 100%). The assay identified 222/225 rifampin-resistant isolates as rifampin resistant (sensitivity, 98.7%; 95% CI, 95.8 to 99.6%) and 335/336 rifampin-susceptible isolates as rifampin susceptible (specificity, 99.7%; 95% CI, 95.8 to 99.6%). All mutations were either individually identified or clustered into small mutation groups using the triple T(m) code. The assay accurately identified mixed (heteroresistant) samples and was shown analytically to detect RRDR mutations when present in at least 40% of the total M. tuberculosis DNA. This was at least as accurate as Sanger DNA sequencing. The assay was easy to use and well suited for high-throughput applications. This new sloppy molecular beacon assay should greatly simplify rifampin resistance testing in clinical laboratories.
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GenoType MTBDRsl for molecular detection of second-line-drug and ethambutol resistance in Mycobacterium tuberculosis strains and clinical samples. J Clin Microbiol 2011; 50:30-6. [PMID: 22075597 DOI: 10.1128/jcm.05274-11] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The purpose of this study was to evaluate the GenoType MTBDRsl assay (Hain Lifescience GmbH, Nehren, Germany) for its ability to detect resistance to fluoroquinolones (FLQ), injectable second-line antibiotics [kanamycin (KM) and capreomycin (CM)], and ethambutol (EMB) in Mycobacterium tuberculosis clinical strains and directly in clinical samples. A total of 34 clinical strains were characterized with the Bactec 460 TB system. Fifty-four clinical samples from 16 patients (5 were smear negative and 49 were smear positive) were also tested directly. The corresponding isolates of the clinical specimens were also analyzed with the Bactec 460TB. When there was a discrepancy between assays, pyrosequencing was performed. The overall rates of concordance of the MTBDRsl and the Bactec 460TB for the detection of FLQ, KM/CM, and EMB susceptibility in clinical strains were 72.4% (21/29), 88.8% (24/27), and 67.6% (23/34), whereas for clinical samples, rates were 86.5% (45/52), 92.3% (48/52), and 56% (28/50), respectively. In conclusion, the GenoType MTBDRsl assay may be a useful tool for making early decisions regarding KM/CM susceptibility and to a lesser extent regarding FLQ and EMB susceptibility. The test is able to detect mutations in both clinical strains and samples with a short turnaround time. However, for correct management of patients with extensively drug-resistant tuberculosis, results must be confirmed by a phenotypical method.
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