Search Results - "Niemann, Stefan"

Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes by Comas, Iñaki, Borrell, Sonia, Roetzer, Andreas, Rose, Graham, Malla, Bijaya, Kato-Maeda, Midori, Galagan, James, Niemann, Stefan, Gagneux, Sebastien

“…Sebastien Gagneux and colleagues identify a set of compensatory mutations in the RNA polymerase of rifampicin-resistant M. tuberculosis by comparing the…”
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Genotyping of genetically monomorphic bacteria: DNA sequencing in Mycobacterium tuberculosis highlights the limitations of current methodologies by Comas, Iñaki, Homolka, Susanne, Niemann, Stefan, Gagneux, Sebastien

“…Because genetically monomorphic bacterial pathogens harbour little DNA sequence diversity, most current genotyping techniques used to study the epidemiology of…”
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PhyResSE: a Web Tool Delineating Mycobacterium tuberculosis Antibiotic Resistance and Lineage from Whole-Genome Sequencing Data by Feuerriegel, Silke, Schleusener, Viola, Beckert, Patrick, Kohl, Thomas A, Miotto, Paolo, Cirillo, Daniela M, Cabibbe, Andrea M, Niemann, Stefan, Fellenberg, Kurt

“…Antibiotic-resistant tuberculosis poses a global threat, causing the deaths of hundreds of thousands of people annually. While whole-genome sequencing (WGS),…”
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Mycobacterium tuberculosis resistance prediction and lineage classification from genome sequencing: comparison of automated analysis tools by Schleusener, Viola, Köser, Claudio U., Beckert, Patrick, Niemann, Stefan, Feuerriegel, Silke

“…Whole-genome sequencing (WGS) has the potential to accelerate drug-susceptibility testing (DST) to design appropriate regimens for drug-resistant tuberculosis…”
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Whole genome sequencing of Mycobacterium tuberculosis for detection of recent transmission and tracing outbreaks: A systematic review by Nikolayevskyy, Vlad, Kranzer, Katharina, Niemann, Stefan, Drobniewski, Francis

“…Contact tracing complemented with genotyping is considered an important means of understanding person-to-person transmission of tuberculosis (TB). It still…”
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MTBseq: a comprehensive pipeline for whole genome sequence analysis of Mycobacterium tuberculosis complex isolates by Kohl, Thomas Andreas, Utpatel, Christian, Schleusener, Viola, De Filippo, Maria Rosaria, Beckert, Patrick, Cirillo, Daniela Maria, Niemann, Stefan

“…Analyzing whole-genome sequencing data of complex (MTBC) isolates in a standardized workflow enables both comprehensive antibiotic resistance profiling and…”
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Evaluation and Strategy for Use of MIRU-VNTRplus, a Multifunctional Database for Online Analysis of Genotyping Data and Phylogenetic Identification of Mycobacterium tuberculosis Complex Isolates by Allix-Béguec, Caroline, Harmsen, Dag, Weniger, Thomas, Supply, Philip, Niemann, Stefan

“…Because of its portable data, discriminatory power, and recently proposed standardization, mycobacterial interspersed repetitive-unit-variable-number…”
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Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages by Stucki, David, Brites, Daniela, Jeljeli, Leïla, Coscolla, Mireia, Liu, Qingyun, Trauner, Andrej, Fenner, Lukas, Rutaihwa, Liliana, Borrell, Sonia, Luo, Tao, Gao, Qian, Kato-Maeda, Midori, Ballif, Marie, Egger, Matthias, Macedo, Rita, Mardassi, Helmi, Moreno, Milagros, Vilanova, Griselda Tudo, Fyfe, Janet, Globan, Maria, Thomas, Jackson, Jamieson, Frances, Guthrie, Jennifer L, Asante-Poku, Adwoa, Yeboah-Manu, Dorothy, Wampande, Eddie, Ssengooba, Willy, Joloba, Moses, Boom, W Henry, Basu, Indira, Bower, James, Saraiva, Margarida, Vasconcellos, Sidra E G, Suffys, Philip, Koch, Anastasia, Wilkinson, Robert, Gail-Bekker, Linda, Malla, Bijaya, Ley, Serej D, Beck, Hans-Peter, de Jong, Bouke C, Toit, Kadri, Sanchez-Padilla, Elisabeth, Bonnet, Maryline, Gil-Brusola, Ana, Frank, Matthias, Penlap Beng, Veronique N, Eisenach, Kathleen, Alani, Issam, Ndung'u, Perpetual Wangui, Revathi, Gunturu, Gehre, Florian, Akter, Suriya, Ntoumi, Francine, Stewart-Isherwood, Lynsey, Ntinginya, Nyanda E, Rachow, Andrea, Hoelscher, Michael, Cirillo, Daniela Maria, Skenders, Girts, Hoffner, Sven, Bakonyte, Daiva, Stakenas, Petras, Diel, Roland, Crudu, Valeriu, Moldovan, Olga, Al-Hajoj, Sahal, Otero, Larissa, Barletta, Francesca, Carter, E Jane, Diero, Lameck, Supply, Philip, Comas, Iñaki, Niemann, Stefan, Gagneux, Sebastien

“…Sebastien Gagneux and colleagues analyze a global collection of Mycobacterium tuberculosis clinical isolates to classify sublineages by phylogeography. They…”
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Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study by Roetzer, Andreas, Diel, Roland, Kohl, Thomas A, Rückert, Christian, Nübel, Ulrich, Blom, Jochen, Wirth, Thierry, Jaenicke, Sebastian, Schuback, Sieglinde, Rüsch-Gerdes, Sabine, Supply, Philip, Kalinowski, Jörn, Niemann, Stefan

“…Understanding Mycobacterium tuberculosis (Mtb) transmission is essential to guide efficient tuberculosis control strategies. Traditional strain typing lacks…”
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Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage by Merker, Matthias, Blin, Camille, Mona, Stefano, Duforet-Frebourg, Nicolas, Lecher, Sophie, Willery, Eve, Blum, Michael G B, Rüsch-Gerdes, Sabine, Mokrousov, Igor, Aleksic, Eman, Allix-Béguec, Caroline, Antierens, Annick, Augustynowicz-Kopeć, Ewa, Ballif, Marie, Barletta, Francesca, Beck, Hans Peter, Barry, Clifton E, Bonnet, Maryline, Borroni, Emanuele, Campos-Herrero, Isolina, Cirillo, Daniela, Cox, Helen, Crowe, Suzanne, Crudu, Valeriu, Diel, Roland, Drobniewski, Francis, Fauville-Dufaux, Maryse, Gagneux, Sébastien, Ghebremichael, Solomon, Hanekom, Madeleine, Hoffner, Sven, Jiao, Wei-wei, Kalon, Stobdan, Kohl, Thomas A, Kontsevaya, Irina, Lillebæk, Troels, Maeda, Shinji, Nikolayevskyy, Vladyslav, Rasmussen, Michael, Rastogi, Nalin, Samper, Sofia, Sanchez-Padilla, Elisabeth, Savic, Branislava, Shamputa, Isdore Chola, Shen, Adong, Sng, Li-Hwei, Stakenas, Petras, Toit, Kadri, Varaine, Francis, Vukovic, Dragana, Wahl, Céline, Warren, Robin, Supply, Philip, Niemann, Stefan, Wirth, Thierry

“…Thierry Wirth, Philip Supply, Stefan Niemann and colleagues analyze 4,987 Mycobacterium tuberculosis strains of the Beijing lineage isolated from 99 countries…”
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Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis by Bos, Kirsten I., Harkins, Kelly M., Herbig, Alexander, Coscolla, Mireia, Weber, Nico, Comas, Iñaki, Forrest, Stephen A., Bryant, Josephine M., Harris, Simon R., Schuenemann, Verena J., Campbell, Tessa J., Majander, Kerttu, Wilbur, Alicia K., Guichon, Ricardo A., Wolfe Steadman, Dawnie L., Cook, Della Collins, Niemann, Stefan, Behr, Marcel A., Zumarraga, Martin, Bastida, Ricardo, Huson, Daniel, Nieselt, Kay, Young, Douglas, Parkhill, Julian, Buikstra, Jane E., Gagneux, Sebastien, Stone, Anne C., Krause, Johannes

“…Three 1,000-year-old mycobacterial genomes from Peruvian human skeletons reveal that a member of the Mycobacterium tuberculosis complex derived from seals…”
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Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study by Walker, Timothy M, Dr, Kohl, Thomas A, PhD, Omar, Shaheed V, MSc, Hedge, Jessica, PhD, Del Ojo Elias, Carlos, MSc, Bradley, Phelim, MPhil, Iqbal, Zamin, DPhil, Feuerriegel, Silke, PhD, Niehaus, Katherine E, MS, Wilson, Daniel J, DPhil, Clifton, David A, DPhil, Kapatai, Georgia, PhD, Ip, Camilla L C, PhD, Bowden, Rory, PhD, Drobniewski, Francis A, PhD, Allix-Béguec, Caroline, PhD, Gaudin, Cyril, PhD, Parkhill, Julian, PhD, Diel, Roland, PhD, Supply, Philip, PhD, Crook, Derrick W, FRCPath, Smith, E Grace, FRCPath, Walker, A Sarah, PhD, Ismail, Nazir, FCPath, Niemann, Stefan, PhD, Peto, Tim E A, FRCP

“…Summary Background Diagnosing drug-resistance remains an obstacle to the elimination of tuberculosis. Phenotypic drug-susceptibility testing is slow and…”
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Delamanid and Bedaquiline Resistance in Mycobacterium tuberculosis Ancestral Beijing Genotype Causing Extensively Drug-Resistant Tuberculosis in a Tibetan Refugee by Hoffmann, Harald, Kohl, Thomas A, Hofmann-Thiel, Sabine, Merker, Matthias, Beckert, Patrick, Jaton, Katia, Nedialkova, Lubov, Sahalchyk, Evgeni, Rothe, Thomas, Keller, Peter M, Niemann, Stefan

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Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis by Bradley, Phelim, Gordon, N. Claire, Walker, Timothy M., Dunn, Laura, Heys, Simon, Huang, Bill, Earle, Sarah, Pankhurst, Louise J., Anson, Luke, de Cesare, Mariateresa, Piazza, Paolo, Votintseva, Antonina A., Golubchik, Tanya, Wilson, Daniel J., Wyllie, David H., Diel, Roland, Niemann, Stefan, Feuerriegel, Silke, Kohl, Thomas A., Ismail, Nazir, Omar, Shaheed V., Smith, E. Grace, Buck, David, McVean, Gil, Walker, A. Sarah, Peto, Tim E. A., Crook, Derrick W., Iqbal, Zamin

“…The rise of antibiotic-resistant bacteria has led to an urgent need for rapid detection of drug resistance in clinical samples, and improvements in global…”
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Deep amplicon sequencing for culture-free prediction of susceptibility or resistance to 13 anti-tuberculous drugs by Jouet, Agathe, Gaudin, Cyril, Badalato, Nelly, Allix-Béguec, Caroline, Duthoy, Stéphanie, Ferré, Alice, Diels, Maren, Laurent, Yannick, Contreras, Sandy, Feuerriegel, Silke, Niemann, Stefan, André, Emmanuel, Kaswa, Michel K, Tagliani, Elisa, Cabibbe, Andrea, Mathys, Vanessa, Cirillo, Daniela, de Jong, Bouke C, Rigouts, Leen, Supply, Philip

“…Conventional molecular tests for detecting complex (MTBC) drug resistance on clinical samples cover a limited set of mutations. Whole-genome sequencing (WGS)…”
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Population structure, biogeography and transmissibility of Mycobacterium tuberculosis by Freschi, Luca, Vargas, Roger, Husain, Ashaque, Kamal, S. M. Mostofa, Skrahina, Alena, Tahseen, Sabira, Ismail, Nazir, Barbova, Anna, Niemann, Stefan, Cirillo, Daniela Maria, Dean, Anna S., Zignol, Matteo, Farhat, Maha Reda

“…Mycobacterium tuberculosis is a clonal pathogen proposed to have co-evolved with its human host for millennia, yet our understanding of its genomic diversity…”
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Detection of Drug-Resistant Tuberculosis by Xpert MTB/RIF in Swaziland by Sanchez-Padilla, Elisabeth, Merker, Matthias, Beckert, Patrick, Jochims, Frauke, Dlamini, Themba, Kahn, Patricia, Bonnet, Maryline, Niemann, Stefan

“…Rapid diagnosis of drug-resistant tuberculosis is important in determining proper management. This letter reports on limitations of the Xpert MTB/RIF assay in…”
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Whole-genome-based Mycobacterium tuberculosis surveillance: a standardized, portable, and expandable approach by Kohl, Thomas A, Diel, Roland, Harmsen, Dag, Rothgänger, Jörg, Walter, Karen Meywald, Merker, Matthias, Weniger, Thomas, Niemann, Stefan

“…Whole-genome sequencing (WGS) allows for effective tracing of Mycobacterium tuberculosis complex (MTBC) (tuberculosis pathogens) transmission. However, it is…”
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High Sequence Variability of the ppE18 Gene of Clinical Mycobacterium tuberculosis Complex Strains Potentially Impacts Effectivity of Vaccine Candidate M72/AS01E by Homolka, Susanne, Ubben, Tanja, Niemann, Stefan

“…The development of an effective vaccine is urgently needed to fight tuberculosis (TB) which is still the leading cause of death from a single infectious agent…”
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Rapid genomic first- and second-line drug resistance prediction from clinical Mycobacterium tuberculosis specimens using Deeplex-MycTB by Feuerriegel, Silke, Kohl, Thomas A, Utpatel, Christian, Andres, Sönke, Maurer, Florian P, Heyckendorf, Jan, Jouet, Agathe, Badalato, Nelly, Foray, Lynda, Fouad Kamara, Rashidatu, Conteh, Osman S, Supply, Philip, Niemann, Stefan

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