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

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Genotyping of genetically monomorphic bacteria: DNA sequencing in Mycobacterium tuberculosis highlights the limitations of current methodologies von Comas, Iñaki, Homolka, Susanne, Niemann, Stefan, Gagneux, Sebastien

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Whole genome sequencing of Mycobacterium tuberculosis for detection of recent transmission and tracing outbreaks: A systematic review von Nikolayevskyy, Vlad, Kranzer, Katharina, Niemann, Stefan, Drobniewski, Francis

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Common patterns and disease-related signatures in tuberculosis and sarcoidosis von Maertzdorf, Jeroen, Weiner, January, Mollenkopf, Hans-Joachim, Bauer, Torsten, Prasse, Antje, Müller-Quernheim, Joachim, Kaufmann, Stefan H. E.

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PhyResSE: a Web Tool Delineating Mycobacterium tuberculosis Antibiotic Resistance and Lineage from Whole-Genome Sequencing Data von Feuerriegel, Silke, Schleusener, Viola, Beckert, Patrick, Kohl, Thomas A, Miotto, Paolo, Cirillo, Daniela M, Cabibbe, Andrea M, Niemann, Stefan, Fellenberg, Kurt

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Mycobacterium tuberculosis resistance prediction and lineage classification from genome sequencing: comparison of automated analysis tools von Schleusener, Viola, Köser, Claudio U., Beckert, Patrick, Niemann, Stefan, Feuerriegel, Silke

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MTBseq: a comprehensive pipeline for whole genome sequence analysis of Mycobacterium tuberculosis complex isolates von Kohl, Thomas Andreas, Utpatel, Christian, Schleusener, Viola, De Filippo, Maria Rosaria, Beckert, Patrick, Cirillo, Daniela Maria, Niemann, Stefan

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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 Co... von Allix-Béguec, Caroline, Harmsen, Dag, Weniger, Thomas, Supply, Philip, Niemann, Stefan

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Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages von 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

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Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study von 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

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Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage von 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

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Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis von 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

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Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study von 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

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Delamanid and Bedaquiline Resistance in Mycobacterium tuberculosis Ancestral Beijing Genotype Causing Extensively Drug-Resistant Tuberculosis in a Tibetan Refugee von 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 von 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

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Deep amplicon sequencing for culture-free prediction of susceptibility or resistance to 13 anti-tuberculous drugs von Jouet, Agathe, Gaudin, Cyril, Badalato, Nelly, Allix-Beguec, Caroline, Duthoy, Stephanie, Ferre, Alice, Diels, Maren, Laurent, Yannick, Contreras, Sandy, Feuerriegel, Silke, Niemann, Stefan, Andre, Emmanuel, Kaswa, Michel K., Tagliani, Elisa, Cabibbe, Andrea, Mathys, Vanessa, Cirillo, Daniela, de Jong, Bouke C., Rigouts, Leen, Supply, Philip

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Population structure, biogeography and transmissibility of Mycobacterium tuberculosis von 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

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Detection of Drug-Resistant Tuberculosis by Xpert MTB/RIF in Swaziland von Sanchez-Padilla, Elisabeth, Merker, Matthias, Beckert, Patrick, Jochims, Frauke, Dlamini, Themba, Kahn, Patricia, Bonnet, Maryline, Niemann, Stefan

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Whole-genome-based Mycobacterium tuberculosis surveillance: a standardized, portable, and expandable approach von Kohl, Thomas A, Diel, Roland, Harmsen, Dag, Rothgänger, Jörg, Walter, Karen Meywald, Merker, Matthias, Weniger, Thomas, Niemann, Stefan

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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 von Homolka, Susanne, Ubben, Tanja, Niemann, Stefan

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