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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Google Scholar, ClinicalTrials.gov, and the WHO International Clinical Trials Registry Platform for published and unpublished reports on targeted NGS for drug-resistant tuberculosis from Jan 1, 2005, to Oct 14, 2022, with updates to our search in Embase and Google Scholar until Feb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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Tram TTB, Trieu LPT, Nhat LTH, Thu DDA, Quang NL, Bang ND, Chau TTH, Thwaites GE, Walker TM, Ha VTN, Thuong NTT. Targeted sequencing from cerebrospinal fluid for rapid identification of drug-resistant tuberculous meningitis. J Clin Microbiol 2024; 62:e0128723. [PMID: 38466092 PMCID: PMC11005362 DOI: 10.1128/jcm.01287-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 02/03/2024] [Indexed: 03/12/2024] Open
Abstract
Mortality from tuberculous meningitis (TBM) remains around 30%, with most deaths occurring within 2 months of starting treatment. Mortality from drug-resistant strains is higher still, making early detection of drug resistance (DR) essential. Targeted next-generation sequencing (tNGS) produces high read depths, allowing the detection of DR-associated alleles with low frequencies. We applied Deeplex Myc-TB-a tNGS assay-to cerebrospinal fluid (CSF) samples from 72 adults with microbiologically confirmed TBM and compared its genomic drug susceptibility predictions to a composite reference standard of phenotypic susceptibility testing (pDST) and whole genome sequencing, as well as to clinical outcomes. Deeplex detected Mycobacterium tuberculosis complex DNA in 24/72 (33.3%) CSF samples and generated full DR reports for 22/24 (91.7%). The read depth generated by Deeplex correlated with semi-quantitative results from MTB/RIF Xpert. Alleles with <20% frequency were seen at canonical loci associated with first-line DR. Disregarding these low-frequency alleles, Deeplex had 100% concordance with the composite reference standard for all drugs except pyrazinamide and streptomycin. Three patients had positive CSF cultures after 30 days of treatment; reference tests and Deeplex identified isoniazid resistance in two, and Deeplex alone identified low-frequency rifampin resistance alleles in one. Five patients died, of whom one had pDST-identified pyrazinamide resistance. tNGS on CSF can rapidly and accurately detect drug-resistant TBM, but its application is limited to those with higher bacterial loads. In those with lower bacterial burdens, alternative approaches need to be developed for both diagnosis and resistance detection.
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Affiliation(s)
| | | | | | - Do Dang Anh Thu
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nguyen Le Quang
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nguyen Duc Bang
- Pham Ngoc Thach Hospital for Tuberculosis and Lung Disease, Ho Chi Minh City, Vietnam
| | | | - Guy E. Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Timothy M. Walker
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Vu Thi Ngoc Ha
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nguyen Thuy Thuong Thuong
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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Naidoo K, Perumal R, Ngema SL, Shunmugam L, Somboro AM. Rapid Diagnosis of Drug-Resistant Tuberculosis-Opportunities and Challenges. Pathogens 2023; 13:27. [PMID: 38251335 PMCID: PMC10819693 DOI: 10.3390/pathogens13010027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/08/2023] [Accepted: 12/20/2023] [Indexed: 01/23/2024] Open
Abstract
Global tuberculosis (TB) eradication is undermined by increasing prevalence of emerging resistance to available drugs, fuelling ongoing demand for more complex diagnostic and treatment strategies. Early detection of TB drug resistance coupled with therapeutic decision making guided by rapid characterisation of pre-treatment and treatment emergent resistance remains the most effective strategy for averting Drug-Resistant TB (DR-TB) transmission, reducing DR-TB associated mortality, and improving patient outcomes. Solid- and liquid-based mycobacterial culture methods remain the gold standard for Mycobacterium tuberculosis (MTB) detection and drug susceptibility testing (DST). Unfortunately, delays to result return, and associated technical challenges from requirements for specialised resource and capacity, have limited DST use and availability in many high TB burden resource-limited countries. There is increasing availability of a variety of rapid nucleic acid-based diagnostic assays with adequate sensitivity and specificity to detect gene mutations associated with resistance to one or more drugs. While a few of these assays produce comprehensive calls for resistance to several first- and second-line drugs, there is still no endorsed genotypic drug susceptibility test assay for bedaquiline, pretomanid, and delamanid. The global implementation of regimens comprising these novel drugs in the absence of rapid phenotypic drug resistance profiling has generated a new set of diagnostic challenges and heralded a return to culture-based phenotypic DST. In this review, we describe the available tools for rapid diagnosis of drug-resistant tuberculosis and discuss the associated opportunities and challenges.
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Affiliation(s)
- Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa (S.L.N.); (L.S.); (A.M.S.)
- SAMRC-CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Rubeshan Perumal
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa (S.L.N.); (L.S.); (A.M.S.)
- SAMRC-CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Senamile L. Ngema
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa (S.L.N.); (L.S.); (A.M.S.)
- SAMRC-CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Letitia Shunmugam
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa (S.L.N.); (L.S.); (A.M.S.)
- SAMRC-CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Anou M. Somboro
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa (S.L.N.); (L.S.); (A.M.S.)
- SAMRC-CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban 4001, South Africa
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Dohál M, Porvazník I, Solovič I, Mokrý J. Advancing tuberculosis management: the role of predictive, preventive, and personalized medicine. Front Microbiol 2023; 14:1225438. [PMID: 37860132 PMCID: PMC10582268 DOI: 10.3389/fmicb.2023.1225438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 09/22/2023] [Indexed: 10/21/2023] Open
Abstract
Tuberculosis is a major global health issue, with approximately 10 million people falling ill and 1.4 million dying yearly. One of the most significant challenges to public health is the emergence of drug-resistant tuberculosis. For the last half-century, treating tuberculosis has adhered to a uniform management strategy in most patients. However, treatment ineffectiveness in some individuals with pulmonary tuberculosis presents a major challenge to the global tuberculosis control initiative. Unfavorable outcomes of tuberculosis treatment (including mortality, treatment failure, loss of follow-up, and unevaluated cases) may result in increased transmission of tuberculosis and the emergence of drug-resistant strains. Treatment failure may occur due to drug-resistant strains, non-adherence to medication, inadequate absorption of drugs, or low-quality healthcare. Identifying the underlying cause and adjusting the treatment accordingly to address treatment failure is important. This is where approaches such as artificial intelligence, genetic screening, and whole genome sequencing can play a critical role. In this review, we suggest a set of particular clinical applications of these approaches, which might have the potential to influence decisions regarding the clinical management of tuberculosis patients.
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Affiliation(s)
- Matúš Dohál
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Igor Porvazník
- National Institute of Tuberculosis, Lung Diseases and Thoracic Surgery, Vyšné Hágy, Slovakia
- Faculty of Health, Catholic University in Ružomberok, Ružomberok, Slovakia
| | - Ivan Solovič
- National Institute of Tuberculosis, Lung Diseases and Thoracic Surgery, Vyšné Hágy, Slovakia
- Faculty of Health, Catholic University in Ružomberok, Ružomberok, Slovakia
| | - Juraj Mokrý
- Department of Pharmacology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
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Ismail N, Dippenaar A, Morgan G, Grobbelaar M, Wells F, Caffry J, Morais C, Gizynski K, McGurk D, Boada E, Murton H, Warren RM, Van Rie A. Microfluidic Capture of Mycobacterium tuberculosis from Clinical Samples for Culture-Free Whole-Genome Sequencing. Microbiol Spectr 2023; 11:e0111423. [PMID: 37358439 PMCID: PMC10433858 DOI: 10.1128/spectrum.01114-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 05/25/2023] [Indexed: 06/27/2023] Open
Abstract
Mycobacterium tuberculosis whole-genome sequencing (WGS) is a powerful tool as it can provide data on population diversity, drug resistance, disease transmission, and mixed infections. Successful WGS is still reliant on high concentrations of DNA obtained through M. tuberculosis culture. Microfluidics technology plays a valuable role in single-cell research but has not yet been assessed as a bacterial enrichment strategy for culture-free WGS of M. tuberculosis. In a proof-of-principle study, we evaluated the use of Capture-XT, a microfluidic lab-on-chip cleanup and pathogen concentration platform to enrich M. tuberculosis bacilli from clinical sputum specimens for downstream DNA extraction and WGS. Three of the four (75%) samples processed by the microfluidics application passed the library preparation quality control, compared to only one of the four (25%) samples not enriched by the microfluidics M. tuberculosis capture application. WGS data were of sufficient quality, with mapping depth of ≥25× and 9 to 27% of reads mapping to the reference genome. These results suggest that microfluidics-based M. tuberculosis cell capture might be a promising method for M. tuberculosis enrichment in clinical sputum samples, which could facilitate culture-free M. tuberculosis WGS. IMPORTANCE Diagnosis of tuberculosis is effective using molecular methods; however, a comprehensive characterization of the resistance profile of Mycobacterium tuberculosis often requires culturing and phenotypic drug susceptibility testing or culturing followed by whole-genome sequencing (WGS). The phenotypic route can take anywhere from 1 to >3 months to result, by which point the patient may have acquired additional drug resistance. The WGS route is a very attractive option; however, culturing is the rate-limiting step. In this original article, we provide proof-of-principle evidence that microfluidics-based cell capture can be used on high-bacillary-load clinical samples for culture-free WGS.
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Affiliation(s)
- Nabila Ismail
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Anzaan Dippenaar
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Tuberculosis Omics Research Consortium, Family Medicine and Population Health, Institute of Global Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | | | - Melanie Grobbelaar
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Felicia Wells
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | | | | | | | - David McGurk
- QuantuMDx Ltd., Newcastle upon Tyne, United Kingdom
| | | | | | - Robin M. Warren
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Annelies Van Rie
- Tuberculosis Omics Research Consortium, Family Medicine and Population Health, Institute of Global Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
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Comín J, Viñuelas J, Lafoz C, Cebollada A, Ibarz D, Iglesias MJ, Samper S. Rapid Identification of Lineage and Drug Resistance in Clinical Samples of Mycobacterium tuberculosis. Microorganisms 2023; 11:1467. [PMID: 37374968 DOI: 10.3390/microorganisms11061467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/25/2023] [Accepted: 05/27/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND Mycobacterium tuberculosis is a slow-growing bacterium, which could delay its diagnosis and, therefore, promote the spread of the disease. Whole-genome sequencing allows us to obtain the complete drug-resistance profile of the strain; however, bacterial cultivation of clinical samples, along with complex processing, is required. METHODS In this work, we explore AmpliSeq, an amplicon-based enrichment method for preparing libraries for targeted next-generation sequencing, to identify lineage and drug resistance directly from clinical samples. RESULTS In our study, 111 clinical samples were tested. The lineage was identified in 100% of the culture-derived samples (52/52), in 95% of the smear (BK)-positive clinical samples (38/40) and in 42.1% of the BK-negative clinical samples (8/19). The drug-resistance profile was accurately identified in all but 11 samples, in which some phenotypic and genotypic discrepancies were found. In this respect, our panels were not exact in the detection of streptomycin resistance for isolates derived from clinical samples, as an extremely high number of SNPs in the rrs and rrl genes were detected due to cross-contamination. CONCLUSION This technique has demonstrated high sensitivity in obtaining the drug-resistance profile of the isolates, as even those samples with DNA concentrations below the detection limit of Qubit produced a result. AmpliSeq technology is cheaper than whole-genome sequencing, easy to perform by laboratory technicians and applicable to any microorganism using the Ion Torrent platform.
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Affiliation(s)
- Jéssica Comín
- Instituto Aragonés de Ciencias de la Salud, C/de San Juan Bosco 13, 50009 Zaragoza, Spain
| | - Jesús Viñuelas
- Servicio de Microbiología, Hospital Universitario Miguel Servet, Paseo Isabel la Católica 1-3, 50009 Zaragoza, Spain
- Grupo de Estudio de Infecciones por Micobacterias (GEIM), Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica, C/Agustín de Bentacourt, No. 13, 28003 Madrid, Spain
| | - Carmen Lafoz
- Servicio General de Apoyo a la Investigación, Servicio de Análisis Microbiológico, Universidad de Zaragoza, C/Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - Alberto Cebollada
- Unidad de Biocomputación, Instituto Aragonés de Ciencias de la Salud, C/de San Juan Bosco 13, 50009 Zaragoza, Spain
| | - Daniel Ibarz
- Grupo de Genética de Micobacterias, Facultad de Medicina, Universidad de Zaragoza, C/Domingo Miral S/N, 50009 Zaragoza, Spain
| | - María-José Iglesias
- Grupo de Genética de Micobacterias, Facultad de Medicina, Universidad de Zaragoza, C/Domingo Miral S/N, 50009 Zaragoza, Spain
- Fundación IIS Aragón, C/de San Juan Bosco 13, 50009 Zaragoza, Spain
- CIBER de Enfermedades Respiratorias, Av. Monforte de Lemos 3-5, Pabellón 11, Planta 0, 28029 Madrid, Spain
| | - Sofía Samper
- Instituto Aragonés de Ciencias de la Salud, C/de San Juan Bosco 13, 50009 Zaragoza, Spain
- Grupo de Genética de Micobacterias, Facultad de Medicina, Universidad de Zaragoza, C/Domingo Miral S/N, 50009 Zaragoza, Spain
- Fundación IIS Aragón, C/de San Juan Bosco 13, 50009 Zaragoza, Spain
- CIBER de Enfermedades Respiratorias, Av. Monforte de Lemos 3-5, Pabellón 11, Planta 0, 28029 Madrid, Spain
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Schaberg T, Brinkmann F, Feiterna-Sperling C, Geerdes-Fenge H, Hartmann P, Häcker B, Hauer B, Haas W, Heyckendorf J, Lange C, Maurer FP, Nienhaus A, Otto-Knapp R, Priwitzer M, Richter E, Salzer HJ, Schoch O, Schönfeld N, Stahlmann R, Bauer T. Tuberkulose im Erwachsenenalter. Pneumologie 2022; 76:727-819. [DOI: 10.1055/a-1934-8303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
ZusammenfassungDie Tuberkulose ist in Deutschland eine seltene, überwiegend gut behandelbare Erkrankung. Weltweit ist sie eine der häufigsten Infektionserkrankungen mit ca. 10 Millionen Neuerkrankungen/Jahr. Auch bei einer niedrigen Inzidenz in Deutschland bleibt Tuberkulose insbesondere aufgrund der internationalen Entwicklungen und Migrationsbewegungen eine wichtige Differenzialdiagnose. In Deutschland besteht, aufgrund der niedrigen Prävalenz der Erkrankung und der damit verbundenen abnehmenden klinischen Erfahrung, ein Informationsbedarf zu allen Aspekten der Tuberkulose und ihrer Kontrolle. Diese Leitlinie umfasst die mikrobiologische Diagnostik, die Grundprinzipien der Standardtherapie, die Behandlung verschiedener Organmanifestationen, den Umgang mit typischen unerwünschten Arzneimittelwirkungen, die Besonderheiten in der Diagnostik und Therapie resistenter Tuberkulose sowie die Behandlung bei TB-HIV-Koinfektion. Sie geht darüber hinaus auf Versorgungsaspekte und gesetzliche Regelungen wie auch auf die Diagnosestellung und präventive Therapie einer latenten tuberkulösen Infektion ein. Es wird ausgeführt, wann es der Behandlung durch spezialisierte Zentren bedarf.Die Aktualisierung der S2k-Leitlinie „Tuberkulose im Erwachsenenalter“ soll allen in der Tuberkuloseversorgung Tätigen als Richtschnur für die Prävention, die Diagnose und die Therapie der Tuberkulose dienen und helfen, den heutigen Herausforderungen im Umgang mit Tuberkulose in Deutschland gewachsen zu sein.
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Affiliation(s)
- Tom Schaberg
- Deutsches Zentralkomitee zur Bekämpfung der Tuberkulose e. V. (DZK), Berlin
| | - Folke Brinkmann
- Abteilung für pädiatrische Pneumologie/CF-Zentrum, Universitätskinderklinik der Ruhr-Universität Bochum, Bochum
| | - Cornelia Feiterna-Sperling
- Klinik für Pädiatrie mit Schwerpunkt Pneumologie, Immunologie und Intensivmedizin, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin und Humboldt-Universität zu Berlin, Berlin
| | | | - Pia Hartmann
- Labor Dr. Wisplinghoff Köln, Klinische Infektiologie, Köln
- Department für Klinische Infektiologie, St. Vinzenz-Hospital, Köln
| | - Brit Häcker
- Deutsches Zentralkomitee zur Bekämpfung der Tuberkulose e. V. (DZK), Berlin
| | | | | | - Jan Heyckendorf
- Klinik für Innere Medizin I, Universitätsklinikum Schleswig-Holstein, Campus Kiel
| | - Christoph Lange
- Klinische Infektiologie, Forschungszentrum Borstel
- Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hamburg-Lübeck-Borstel-Riems
- Respiratory Medicine and International Health, Universität zu Lübeck, Lübeck
- Baylor College of Medicine and Texas Childrenʼs Hospital, Global TB Program, Houston, TX, USA
| | - Florian P. Maurer
- Nationales Referenzzentrum für Mykobakterien, Forschungszentrum Borstel, Borstel
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Hamburg
| | - Albert Nienhaus
- Institut für Versorgungsforschung in der Dermatologie und bei Pflegeberufen (IVDP), Universitätsklinikum Hamburg Eppendorf (UKE), Hamburg
| | - Ralf Otto-Knapp
- Deutsches Zentralkomitee zur Bekämpfung der Tuberkulose e. V. (DZK), Berlin
| | | | | | | | | | | | - Ralf Stahlmann
- Institut für klinische Pharmakologie und Toxikologie, Charité Universitätsmedizin, Berlin
| | - Torsten Bauer
- Deutsches Zentralkomitee zur Bekämpfung der Tuberkulose e. V. (DZK), Berlin
- Lungenklinik Heckeshorn, Helios Klinikum Emil von Behring, Berlin
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Abstract
The current diagnostic abilities for the detection of pediatric tuberculosis are suboptimal. Multiple factors contribute to the under-diagnosis of intrathoracic tuberculosis in children, namely the absence of pathognomonic features of the disease, low bacillary loads in respiratory specimens, challenges in sample collection, and inadequate access to diagnostic tools in high-burden settings. Nonetheless, the 2020s have witnessed encouraging progress in the area of novel diagnostics. Recent WHO-endorsed rapid molecular assays hold promise for use in service decentralization strategies, and new policy recommendations include stools as an alternative, child-friendly specimen for testing with the GeneXpert assay. The pipeline of promising assays in mid/late-stage development is expanding, and novel pediatric candidate biomarkers based on the host immune response are being identified for use in diagnostic and triage tests. For a new test to meet the pediatric target product profiles prioritized by the WHO, it is key that the peculiarities and needs of the hard-to-reach pediatric population are considered in the early planning phases of discovery, validation, and implementation studies.
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Affiliation(s)
| | - Pamela Nabeta
- FIND, the global alliance for diagnostics, Chemin des Mines 9, 1202 Geneva, Switzerland
| | - Morten Ruhwald
- FIND, the global alliance for diagnostics, Chemin des Mines 9, 1202 Geneva, Switzerland
| | - Rinn Song
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
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Genestet C, Baffert Y, Vallée M, Bernard A, Benito Y, Lina G, Hodille E, Dumitrescu O. Development, Evaluation, and Implementation of a House-Made Targeted Next-Generation Sequencing Spoligotyping in a French Laboratory. Int J Mol Sci 2022; 23:ijms231911302. [PMID: 36232601 PMCID: PMC9569608 DOI: 10.3390/ijms231911302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/16/2022] [Accepted: 09/20/2022] [Indexed: 11/26/2022] Open
Abstract
Epidemiological studies investigating transmission chains of tuberculosis are undertaken worldwide to tackle its spread. CRISPR locus diversity, called spoligotyping, is a widely used genotyping assay for Mycobacterium tuberculosis complex (MTBC) characterization. Herein, we developed a house-made targeted next-generation sequencing (tNGS) spoligotyping, and compared its outputs with those of membrane-based spoligotyping. A total of 144 clinical MTBC strains were retrospectively selected to be representative of the local epidemiology. Data analysis of a training set allowed for the setting of “presence”/“absence” thresholds for each spacer to maximize the sensibility and specificity related to the membrane-based spoligotyping. The thresholds above, in which the spacer was considered present, were 50 read per millions for spacers 10 and 14, 20,000 for spacers 20, 21, and 31, and 1000 for the other spacers. The confirmation of these thresholds was performed using a validation set. The overall agreement on the training and validation sets was 97.5% and 93.8%, respectively. The discrepancies concerned six strains: Two for spacer 14, two for spacer 31, and two for spacer 32. The tNGS spoligotyping, whose thresholds were finely-tuned during a careful bioinformatics pipeline development process, appears be a technique that is reliable, inexpensive, free of handling errors, and automatable through automatic transfer into the laboratory computer system.
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Affiliation(s)
- Charlotte Genestet
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, 69007 Lyon, France
- Laboratoire de Bactériologie, Institut des Agents Infectieux, Hospices Civils de Lyon, CEDEX 04, 69317 Lyon, France
| | - Yannick Baffert
- Laboratoire de Bactériologie, Institut des Agents Infectieux, Hospices Civils de Lyon, CEDEX 04, 69317 Lyon, France
| | - Maxime Vallée
- Laboratoire de Bactériologie, Institut des Agents Infectieux, Hospices Civils de Lyon, CEDEX 04, 69317 Lyon, France
| | - Albin Bernard
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, 69007 Lyon, France
| | - Yvonne Benito
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, 69007 Lyon, France
| | - Gérard Lina
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, 69007 Lyon, France
- Laboratoire de Bactériologie, Institut des Agents Infectieux, Hospices Civils de Lyon, CEDEX 04, 69317 Lyon, France
| | - Elisabeth Hodille
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, 69007 Lyon, France
- Laboratoire de Bactériologie, Institut des Agents Infectieux, Hospices Civils de Lyon, CEDEX 04, 69317 Lyon, France
- Correspondence:
| | - Oana Dumitrescu
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, 69007 Lyon, France
- Laboratoire de Bactériologie, Institut des Agents Infectieux, Hospices Civils de Lyon, CEDEX 04, 69317 Lyon, France
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Leung KSS, Tam KKG, Ng TTL, Lao HY, Shek RCM, Ma OCK, Yu SH, Chen JX, Han Q, Siu GKH, Yam WC. Clinical utility of target amplicon sequencing test for rapid diagnosis of drug-resistant Mycobacterium tuberculosis from respiratory specimens. Front Microbiol 2022; 13:974428. [PMID: 36160212 PMCID: PMC9505518 DOI: 10.3389/fmicb.2022.974428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/02/2022] [Indexed: 12/02/2022] Open
Abstract
An in-house-developed target amplicon sequencing by next-generation sequencing technology (TB-NGS) enables simultaneous detection of resistance-related mutations in Mycobacterium tuberculosis (MTB) against 8 anti-tuberculosis drug classes. In this multi-center study, we investigated the clinical utility of incorporating TB-NGS for rapid drug-resistant MTB detection in high endemic regions in southeast China. From January 2018 to November 2019, 4,047 respiratory specimens were available from patients suffering lower respiratory tract infections in Hong Kong and Guangzhou, among which 501 were TB-positive as detected by in-house IS6110-qPCR assay with diagnostic sensitivity and specificity of 97.9 and 99.2%, respectively. Preliminary resistance screening by GenoType MTBDRplus and MTBDRsl identified 25 drug-resistant specimens including 10 multidrug-resistant TB. TB-NGS was performed using MiSeq on all drug-resistant specimens alongside 67 pan-susceptible specimens, and demonstrated 100% concordance to phenotypic drug susceptibility test. All phenotypically resistant specimens with dominating resistance-related mutations exhibited a mutation frequency of over 60%. Three quasispecies were identified with mutation frequency of less than 35% among phenotypically susceptible specimens. They were well distinguished from phenotypically resistant cases and thus would not complicate TB-NGS results interpretations. This is the first large-scale study that explored the use of laboratory-developed NGS platforms for rapid TB diagnosis. By incorporating TB-NGS with our proposed diagnostic algorithm, the workflow would provide a user-friendly, cost-effective routine diagnostic solution for complicated TB cases with an average turnaround time of 6 working days. This is critical for timely management of drug resistant TB patients and expediting public health control on the emergence of drug-resistant TB.
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Affiliation(s)
- Kenneth Siu-Sing Leung
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Kingsley King-Gee Tam
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Timothy Ting-Leung Ng
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Hiu-Yin Lao
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Raymond Chiu-Man Shek
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | | | - Shi-Hui Yu
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Guangzhou, China
| | | | - Qi Han
- Guangzhou KingMed Diagnostics Group, Guangzhou, China
| | - Gilman Kit-Hang Siu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Wing-Cheong Yam
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- *Correspondence: Wing-Cheong Yam,
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