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Bisimwa BC, Nachega JB, Warren RM, Theron G, Metcalfe JZ, Shah M, Diacon AH, Sam-Agudu NA, Yotebieng M, Bulabula ANH, Katoto PDMC, Chirambiza JP, Nyota R, Birembano FM, Musafiri EM, Byadunia S, Bahizire E, Kaswa MK, Callens S, Kashongwe ZM. Xpert Mycobacterium tuberculosis/Rifampicin-Detected Rifampicin Resistance is a Suboptimal Surrogate for Multidrug-resistant Tuberculosis in Eastern Democratic Republic of the Congo: Diagnostic and Clinical Implications. Clin Infect Dis 2021; 73:e362-e370. [PMID: 32590841 DOI: 10.1093/cid/ciaa873] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 06/19/2020] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Rifampicin (RIF) resistance is highly correlated with isoniazid (INH) resistance and used as proxy for multidrug-resistant tuberculosis (MDR-TB). Using MTBDRplus as a comparator, we evaluated the predictive value of Xpert MTB/RIF (Xpert)-detected RIF resistance for MDR-TB in eastern Democratic Republic of the Congo (DRC). METHODS We conducted a cross-sectional study involving data from new or retreatment pulmonary adult TB cases evaluated between July 2013 and December 2016. Separate, paired sputa for smear microscopy and MTBDRplus were collected. Xpert testing was performed subject to the availability of Xpert cartridges on sample remnants after microscopy. RESULTS Among 353 patients, 193 (54.7%) were previously treated and 224 (63.5%) were MTBDRplus TB positive. Of the 224, 43 (19.2%) were RIF monoresistant, 11 (4.9%) were INH monoresistant, 53 (23.7%) had MDR-TB, and 117 (52.2%) were RIF and INH susceptible. Overall, among the 96 samples detected by MTBDRplus as RIF resistant, 53 (55.2%) had MDR-TB. Xpert testing was performed in 179 (50.7%) specimens; among these, 163 (91.1%) were TB positive and 73 (44.8%) RIF resistant. Only 45/73 (61.6%) Xpert-identified RIF-resistant isolates had concomitant MTBDRplus-detected INH resistance. Xpert had a sensitivity of 100.0% (95% CI, 92.1-100.0) for detecting RIF resistance but a positive-predictive value of only 61.6% (95% CI, 49.5-72.8) for MDR-TB. The most frequent mutations associated with RIF and INH resistance were S531L and S315T1, respectively. CONCLUSIONS In this high-risk MDR-TB study population, Xpert had low positive-predictive value for the presence of MDR-TB. Comprehensive resistance testing for both INH and RIF should be performed in this setting.
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Affiliation(s)
- Bertin C Bisimwa
- Laboratoire de Recherche Biomédicale Professeur André Lurhuma, Université Catholique de Bukavu, Bukavu, Democratic Republic of Congo.,Institut Supérieur des Techniques Médicales, Bukavu, Democratic Republic of Congo
| | - Jean B Nachega
- Departments of Epidemiology, Infectious Diseases, and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, USA.,Department of Medicine and Center for Infectious Diseases, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,Departments of Epidemiology and International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Robin M Warren
- Division of Science and Technology (DST) Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Grant Theron
- Division of Science and Technology (DST) Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - John Z Metcalfe
- Division of Pulmonary and Critical Care Medicine, Zuckerberg San Francisco General Hospital and Trauma Center, University of California, San Francisco, San Francisco, California, USA
| | - Maunank Shah
- Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Andreas H Diacon
- Task Foundation and Department of Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Nadia A Sam-Agudu
- International Research Center of Excellence, Institute of Human Virology Nigeria, Abuja, Nigeria.,Division of Epidemiology and Prevention, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Marcel Yotebieng
- Department of Medicine, Albert Einstein College of Medicine, New York, New York, USA
| | - André N H Bulabula
- Department of Pediatrics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,Infection Control Africa Network, Cape Town, South Africa
| | - Patrick D M C Katoto
- Centre for Environment and Health, Department of Public Health and Primary Care, Laboratory of Pneumology, Katholieke Universiteit Leuven, Leuven, Belgium.,Department of Internal Medicine, Faculty of Medicine, Université Catholique de Bukavu, Bukavu, Democratic Republic of Congo
| | - Jean-Paul Chirambiza
- National TB Program, Provincial Anti-Leprosy and TB Coordination, Bukavu, Democratic Republic of Congo
| | - Rosette Nyota
- National TB Program, Provincial Anti-Leprosy and TB Coordination, Bukavu, Democratic Republic of Congo
| | - Freddy M Birembano
- National TB Program, Provincial Anti-Leprosy and TB Coordination, Bukavu, Democratic Republic of Congo
| | - Eric M Musafiri
- National TB Program, Provincial Anti-Leprosy and TB Coordination, Bukavu, Democratic Republic of Congo
| | - Sifa Byadunia
- Institut Supérieur des Techniques Médicales, Bukavu, Democratic Republic of Congo
| | - Esto Bahizire
- Center for Tropical Diseases and Global Health, Catholic University of Bukavu, Bukavu, Democratic Republic of the Congo.,Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya.,Centre of Research in Epidemiology, Biostatistics, and Clinical Research, Université Libre de Bruxelles, Brussels, Belgium
| | - Michel K Kaswa
- National Tuberculosis Program, Ministry of Health, Kinshasa, Democratic Republic of Congo
| | - Steven Callens
- Department of Internal Medicine, Ghent University Hospital, Ghent, Belgium
| | - Zacharie M Kashongwe
- Laboratoire de Recherche Biomédicale Professeur André Lurhuma, Université Catholique de Bukavu, Bukavu, Democratic Republic of Congo.,Institut Supérieur des Techniques Médicales, Bukavu, Democratic Republic of Congo.,Cliniques Universitaire de Kinshasa, Université Nationale de Kinshasa, Kinshasa, Democratic Republic of Congo
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2
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Jouet A, Gaudin C, Badalato N, Allix-Béguec C, Duthoy S, Ferré A, Diels M, Laurent Y, Contreras S, Feuerriegel S, Niemann S, André E, Kaswa MK, Tagliani E, Cabibbe A, Mathys V, Cirillo D, de Jong BC, Rigouts L, Supply P. Deep amplicon sequencing for culture-free prediction of susceptibility or resistance to 13 anti-tuberculous drugs. Eur Respir J 2021; 57:13993003.02338-2020. [PMID: 32943401 PMCID: PMC8174722 DOI: 10.1183/13993003.02338-2020] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/03/2020] [Indexed: 02/06/2023]
Abstract
Conventional molecular tests for detecting Mycobacterium tuberculosis complex (MTBC) drug resistance on clinical samples cover a limited set of mutations. Whole-genome sequencing (WGS) typically requires culture. Here, we evaluated the Deeplex Myc-TB targeted deep-sequencing assay for prediction of resistance to 13 anti-tuberculous drugs/drug classes, directly applicable on sputum. With MTBC DNA tests, the limit of detection was 100–1000 genome copies for fixed resistance mutations. Deeplex Myc-TB captured in silico 97.1–99.3% of resistance phenotypes correctly predicted by WGS from 3651 MTBC genomes. On 429 isolates, the assay predicted 92.2% of 2369 first- and second-line phenotypes, with a sensitivity of 95.3% and a specificity of 97.4%. 56 out of 69 (81.2%) residual discrepancies with phenotypic results involved pyrazinamide, ethambutol and ethionamide, and low-level rifampicin or isoniazid resistance mutations, all notoriously prone to phenotypic testing variability. Only two out of 91 (2.2%) resistance phenotypes undetected by Deeplex Myc-TB had known resistance-associated mutations by WGS analysis outside Deeplex Myc-TB targets. Phenotype predictions from Deeplex Myc-TB analysis directly on 109 sputa from a Djibouti survey matched those of MTBSeq/PhyResSE/Mykrobe, fed with WGS data from subsequent cultures, with a sensitivity of 93.5/98.5/93.1% and a specificity of 98.5/97.2/95.3%, respectively. Most residual discordances involved gene deletions/indels and 3–12% heteroresistant calls undetected by WGS analysis or natural pyrazinamide resistance of globally rare “Mycobacterium canettii” strains then unreported by Deeplex Myc-TB. On 1494 arduous sputa from a Democratic Republic of the Congo survey, 14 902 out of 19 422 (76.7%) possible susceptible or resistance phenotypes could be predicted culture-free. Deeplex Myc-TB may enable fast, tailored tuberculosis treatment. The novel Deeplex Myc-TB molecular assay shows a high degree of accuracy for extensive prediction of susceptibility and resistance to 13 anti-tuberculous drugs, directly achievable without culture, which may enable fast, tailored tuberculosis treatmenthttps://bit.ly/3bAvcAt
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Affiliation(s)
- Agathe Jouet
- GenoScreen, Lille, France.,These authors contributed equally to this work
| | - Cyril Gaudin
- GenoScreen, Lille, France.,These authors contributed equally to this work
| | | | | | | | | | - Maren Diels
- BCCM/ITM, Mycobacteria Collection, Institute of Tropical Medicine, Antwerp, Belgium
| | | | | | - Silke Feuerriegel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel, Borstel, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel, Borstel, Germany
| | - Emmanuel André
- Laboratory of Clinical Bacteriology and Mycology, Dept of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Michel K Kaswa
- National Tuberculosis Program, Kinshasa, Democratic Republic of the Congo
| | - Elisa Tagliani
- Emerging Bacterial Pathogens, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Andrea Cabibbe
- Emerging Bacterial Pathogens, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Vanessa Mathys
- Unit Bacterial Diseases Service, Infectious Diseases in Humans, Sciensano, Brussels, Belgium
| | - Daniela Cirillo
- Emerging Bacterial Pathogens, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Bouke C de Jong
- Mycobacteriology Unit, Dept of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Leen Rigouts
- Mycobacteriology Unit, Dept of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,Dept of Biomedical Sciences, Antwerp University, Antwerp, Belgium
| | - Philip Supply
- Université de Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL (Center for Infection and Immunity of Lille), Lille, France
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3
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Bulabula ANH, Nelson JA, Musafiri EM, Machekano R, Sam-Agudu NA, Diacon AH, Shah M, Creswell J, Theron G, Warren RM, Jacobson KR, Chirambiza JP, Kalumuna D, Bisimwa BC, Katoto PDMC, Kaswa MK, Birembano FM, Kitete L, Grobusch MP, Kashongwe ZM, Nachega JB. Prevalence, Predictors, and Successful Treatment Outcomes of Xpert MTB/RIF-identified Rifampicin-resistant Tuberculosis in Post-conflict Eastern Democratic Republic of the Congo, 2012-2017: A Retrospective Province-Wide Cohort Study. Clin Infect Dis 2020; 69:1278-1287. [PMID: 30759187 PMCID: PMC6763636 DOI: 10.1093/cid/ciy1105] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 12/20/2018] [Indexed: 11/19/2022] Open
Abstract
Background Multidrug-resistant tuberculosis (MDR-TB) jeopardizes global TB control. The prevalence and predictors of Rifampicin-resistant (RR) TB, a proxy for MDR-TB, and the treatment outcomes with standard and shortened regimens have not been assessed in post-conflict regions, such as the South Kivu province in the eastern Democratic Republic of the Congo (DRC). We aimed to fill this knowledge gap and to inform the DRC National TB Program. Methods of adults and children evaluated for pulmonary TB by sputum smear microscopy and Xpert MTB/RIF (Xpert) from February 2012 to June 2017. Multivariable logistic regression, Kaplan–Meier estimates, and multivariable Cox regression were used to assess independent predictors of RR-TB and treatment failure/death. Results Of 1535 patients Xpert-positive for TB, 11% had RR-TB. Independent predictors of RR-TB were a positive sputum smear (adjusted odds ratio [aOR] 2.42, 95% confidence interval [CI] 1.63–3.59), retreatment of TB (aOR 4.92, 95% CI 2.31–10.45), and one or more prior TB episodes (aOR 1.77 per episode, 95% CI 1.01–3.10). Over 45% of RR-TB patients had no prior TB history or treatment. The median time from Xpert diagnosis to RR-TB treatment initiation was 12 days (interquartile range 3–60.2). Cures were achieved in 30/36 (83%) and 84/114 (74%) of patients on 9- vs 20/24-month MDR-TB regimens, respectively (P = .06). Predictors of treatment failure/death were the absence of directly observed therapy (DOT; adjusted hazard ratio [aHR] 2.77, 95% CI 1.2–6.66) and any serious adverse drug event (aHR 4.28, 95% CI 1.88–9.71). Conclusions Favorable RR-TB cure rates are achievable in this post-conflict setting with a high RR-TB prevalence. An expanded Xpert scale-up; the prompt initiation of shorter, safer, highly effective MDR-TB regimens; and treatment adherence support are critically needed to optimize outcomes.
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Affiliation(s)
- André N H Bulabula
- Department of Global Health, Division of Health Systems and Public Health, Unit for Infection Prevention and Control, Faculty of Medicine and Health Sciences, Stellenbosch University.,Infection Control Africa Network, Cape Town, South Africa
| | - Jenna A Nelson
- Department of Epidemiology, University of Pittsburgh Graduate School of Public Health, Pennsylvania
| | - Eric M Musafiri
- National Tuberculosis Program, Provincial Leprosy and Tuberculosis Coordination, South Kivu Branch, Bukavu, Democratic Republic of the Congo
| | - Rhoderick Machekano
- Department of Global Health, Center for Evidence-Based Health Care, Biostatistics Unit, Faculty of Medicine and Health Sciences, Cape Town, South Africa
| | - Nadia A Sam-Agudu
- International Research Center of Excellence and Pediatric and Adolescent Human Immunodeficiency Virus Unit, Institute of Human Virology Nigeria, Abuja.,Division of Epidemiology and Prevention, Institute of Human Virology, University of Maryland School of Medicine, Baltimore
| | - Andreas H Diacon
- Division of Medical Physiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Maunank Shah
- Center for Tuberculosis Research & Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Jacob Creswell
- Stop TB Partnership, TB REACH Initiative, Geneva, Switzerland
| | - Grant Theron
- South African Department of Science and Technology and the National Research Foundation, Centre of Excellence for Biomedical Tuberculosis Research and South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Robin M Warren
- South African Department of Science and Technology and the National Research Foundation, Centre of Excellence for Biomedical Tuberculosis Research and South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Karen R Jacobson
- Department of Medicine, Division of Infectious Diseases, Boston University School of Medicine, Massachusetts
| | - Jean-Paul Chirambiza
- National Tuberculosis Program, Provincial Leprosy and Tuberculosis Coordination, South Kivu Branch, Bukavu, Democratic Republic of the Congo
| | - Dieudonné Kalumuna
- National Tuberculosis Program, Provincial Leprosy and Tuberculosis Coordination, South Kivu Branch, Bukavu, Democratic Republic of the Congo
| | - Bertin C Bisimwa
- Biomedical Laboratory Professor A. Z. Lurhuma, Mycobacterium Unit, Université Catholique de Bukavu, Democratic Republic of the Congo
| | - Patrick D M C Katoto
- Centre for Environment and Health, Department of Public Health and Primary Care, Laboratory of Pulmonology, The Katholieke Universiteit Leuven, Belgium.,Department of Internal Medicine, Faculty of Medicine, Catholic University of Bukavu
| | - Michel K Kaswa
- National Tuberculosis Program, Provincial Leprosy and Tuberculosis Coordination, South Kivu Branch, Bukavu, Democratic Republic of the Congo
| | - Freddy M Birembano
- National Tuberculosis Program, Provincial Leprosy and Tuberculosis Coordination, South Kivu Branch, Bukavu, Democratic Republic of the Congo
| | - Liliane Kitete
- The Union Against Tuberculosis and Lung Diseases, Challenge Tuberculosis Initiative, Bukavu, Democratic Republic of the Congo
| | - Martin P Grobusch
- Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases, Amsterdam University Medical Centers, The Academic Medical Center, The Netherlands
| | - Zacharie M Kashongwe
- Department of Medicine, University Hospital of Kinshasa, Democratic Republic of the Congo
| | - Jean B Nachega
- Department of Epidemiology, University of Pittsburgh Graduate School of Public Health, Pennsylvania.,Department of Medicine and Center for Infectious Diseases, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,Departments of Epidemiology and International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.,International Centre for Advanced Research and Training, Panzi, Bukavu, Democratic Republic of the Congo
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4
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Meehan CJ, Moris P, Kohl TA, Pečerska J, Akter S, Merker M, Utpatel C, Beckert P, Gehre F, Lempens P, Stadler T, Kaswa MK, Kühnert D, Niemann S, de Jong BC. The relationship between transmission time and clustering methods in Mycobacterium tuberculosis epidemiology. EBioMedicine 2018; 37:410-416. [PMID: 30341041 PMCID: PMC6284411 DOI: 10.1016/j.ebiom.2018.10.013] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/17/2018] [Accepted: 10/03/2018] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Tracking recent transmission is a vital part of controlling widespread pathogens such as Mycobacterium tuberculosis. Multiple methods with specific performance characteristics exist for detecting recent transmission chains, usually by clustering strains based on genotype similarities. With such a large variety of methods available, informed selection of an appropriate approach for determining transmissions within a given setting/time period is difficult. METHODS This study combines whole genome sequence (WGS) data derived from 324 isolates collected 2005-2010 in Kinshasa, Democratic Republic of Congo (DRC), a high endemic setting, with phylodynamics to unveil the timing of transmission events posited by a variety of standard genotyping methods. Clustering data based on Spoligotyping, 24-loci MIRU-VNTR typing, WGS based SNP (Single Nucleotide Polymorphism) and core genome multi locus sequence typing (cgMLST) typing were evaluated. FINDINGS Our results suggest that clusters based on Spoligotyping could encompass transmission events that occurred almost 200 years prior to sampling while 24-loci-MIRU-VNTR often represented three decades of transmission. Instead, WGS based genotyping applying low SNP or cgMLST allele thresholds allows for determination of recent transmission events, e.g. in timespans of up to 10 years for a 5 SNP/allele cut-off. INTERPRETATION With the rapid uptake of WGS methods in surveillance and outbreak tracking, the findings obtained in this study can guide the selection of appropriate clustering methods for uncovering relevant transmission chains within a given time-period. For high resolution cluster analyses, WGS-SNP and cgMLST based analyses have similar clustering/timing characteristics even for data obtained from a high incidence setting.
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Affiliation(s)
- Conor J Meehan
- Unit of Mycobacteriology, Biomedical Sciences, Institute of Tropical Medicine, Antwerp 2000, Belgium.
| | - Pieter Moris
- Unit of Mycobacteriology, Biomedical Sciences, Institute of Tropical Medicine, Antwerp 2000, Belgium; Adrem Data Lab (Adrem), Department of Mathematics and Computer Science, University of Antwerp, Antwerp 2020, Belgium; Biomedical Informatics Research Network Antwerp (biomina), University of Antwerp, Antwerp 2020, Belgium
| | - Thomas A Kohl
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, D-23845 Borstel, Germany; Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, D-23845 Borstel, Germany
| | - Jūlija Pečerska
- Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
| | - Suriya Akter
- Unit of Mycobacteriology, Biomedical Sciences, Institute of Tropical Medicine, Antwerp 2000, Belgium
| | - Matthias Merker
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, D-23845 Borstel, Germany; Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, D-23845 Borstel, Germany
| | - Christian Utpatel
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, D-23845 Borstel, Germany; Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, D-23845 Borstel, Germany
| | - Patrick Beckert
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, D-23845 Borstel, Germany; Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, D-23845 Borstel, Germany
| | - Florian Gehre
- Unit of Mycobacteriology, Biomedical Sciences, Institute of Tropical Medicine, Antwerp 2000, Belgium; Vaccines and Immunity Theme, Medical Research Council Unit The Gambia, Serekunda, Gambia; Department Infectious Diseases Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg 20359, Germany
| | - Pauline Lempens
- Unit of Mycobacteriology, Biomedical Sciences, Institute of Tropical Medicine, Antwerp 2000, Belgium
| | - Tanja Stadler
- Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
| | - Michel K Kaswa
- Unit of Mycobacteriology, Biomedical Sciences, Institute of Tropical Medicine, Antwerp 2000, Belgium; National Tuberculosis Program, Kinshasa, DR Congo
| | - Denise Kühnert
- Max Planck Institute for the Science of Human History, 07745 JENA, Germany
| | - Stefan Niemann
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, D-23845 Borstel, Germany; Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, D-23845 Borstel, Germany
| | - Bouke C de Jong
- Unit of Mycobacteriology, Biomedical Sciences, Institute of Tropical Medicine, Antwerp 2000, Belgium
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