A New Phylogenetic Framework for the Animal-Adapted Mycobacterium tuberculosis Complex by Daniela Brites, Daniela Brites, Chloé Loiseau, Chloé Loiseau, Fabrizio Menardo, Fabrizio Menardo, Sonia Borrell, Sonia Borrell, Maria Beatrice Boniotti, Robin Warren, Anzaan Dippenaar, Sven David Charles Parsons, Christian Beisel, Marcel A. Behr, Janet A. Fyfe, Mireia Coscolla, Sebastien Gagneux, Sebastien Gagneux

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Treemmer: a tool to reduce large phylogenetic datasets with minimal loss of diversity by Fabrizio Menardo, Chloé Loiseau, Daniela Brites, Mireia Coscolla, Sebastian M. Gygli, Liliana K. Rutaihwa, Andrej Trauner, Christian Beisel, Sonia Borrell, Sebastien Gagneux

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Whole Genome Sequencing and Spatial Analysis Identifies Recent Tuberculosis Transmission Hotspots in Ghana by Prince Asare, Prince Asare, Prince Asare, Isaac Darko Otchere, Edmund Bedeley, Daniela Brites, Daniela Brites, Chloé Loiseau, Chloé Loiseau, Nyonuku Akosua Baddoo, Adwoa Asante-Poku, Stephen Osei-Wusu, Diana Ahu Prah, Sonia Borrell, Sonia Borrell, Miriam Reinhard, Miriam Reinhard, Audrey Forson, Kwadwo Ansah Koram, Sebastien Gagneux, Sebastien Gagneux, Dorothy Yeboah-Manu, Dorothy Yeboah-Manu

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Reference set of Mycobacterium tuberculosis clinical strains: A tool for research and product development. by Sònia Borrell, Andrej Trauner, Daniela Brites, Leen Rigouts, Chloe Loiseau, Mireia Coscolla, Stefan Niemann, Bouke De Jong, Dorothy Yeboah-Manu, Midori Kato-Maeda, Julia Feldmann, Miriam Reinhard, Christian Beisel, Sebastien Gagneux

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Genomic epidemiological analysis identifies high relapse among individuals with recurring tuberculosis and provides evidence of recent household-related transmission of tuberculosi... by Prince Asare, Stephen Osei-Wusu, Nyonuku Akosua Baddoo, Edmund Bedeley, Isaac Darko Otchere, Daniela Brites, Chloé Loiseau, Adwoa Asante-Poku, Diana Ahu Prah, Sonia Borrell, Miriam Reinhard, Michael Amo Omari, Audrey Forson, Kwadwo Ansah Koram, Sebastien Gagneux, Dorothy Yeboah-Manu

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The relative transmission fitness of multidrug-resistant Mycobacterium tuberculosis in a drug resistance hotspot by Chloé Loiseau, Etthel M. Windels, Sebastian M. Gygli, Levan Jugheli, Nino Maghradze, Daniela Brites, Amanda Ross, Galo Goig, Miriam Reinhard, Sonia Borrell, Andrej Trauner, Anna Dötsch, Rusudan Aspindzelashvili, Rebecca Denes, Klaus Reither, Christian Beisel, Nestani Tukvadze, Zaza Avaliani, Tanja Stadler, Sebastien Gagneux

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Oral Phage Therapy of Acute Bacterial Diarrhea With Two Coliphage Preparations: A Randomized Trial in Children From Bangladesh by Shafiqul Alam Sarker, Shamima Sultana, Gloria Reuteler, Deborah Moine, Patrick Descombes, Florence Charton, Gilles Bourdin, Shawna McCallin, Catherine Ngom-Bru, Tara Neville, Mahmuda Akter, Sayeeda Huq, Firdausi Qadri, Kaisar Talukdar, Mohamed Kassam, Michèle Delley, Chloe Loiseau, Ying Deng, Sahar El Aidy, Bernard Berger, Harald Brüssow

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Whole genome sequencing distinguishes between relapse and reinfection in recurrent leprosy cases. by Mariane M A Stefani, Charlotte Avanzi, Samira Bührer-Sékula, Andrej Benjak, Chloé Loiseau, Pushpendra Singh, Maria A A Pontes, Heitor S Gonçalves, Emerith M Hungria, Philippe Busso, Jérémie Piton, Maria I S Silveira, Rossilene Cruz, Antônio Schetinni, Maurício B Costa, Marcos C L Virmond, Suzana M Diorio, Ida M F Dias-Baptista, Patricia S Rosa, Masanori Matsuoka, Maria L F Penna, Stewart T Cole, Gerson O Penna

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The Genome of the Toluene-Degrading Pseudomonas veronii Strain 1YdBTEX2 and Its Differential Gene Expression in Contaminated Sand. by Marian Morales, Vladimir Sentchilo, Claire Bertelli, Andrea Komljenovic, Nadezda Kryuchkova-Mostacci, Audrey Bourdilloud, Burkhard Linke, Alexander Goesmann, Keith Harshman, Francisca Segers, Fabien Delapierre, Damien Fiorucci, Mathieu Seppey, Evgeniya Trofimenco, Pauline Berra, Athimed El Taher, Chloé Loiseau, Dejan Roggero, Madeleine Sulfiotti, Angela Etienne, Gustavo Ruiz Buendia, Loïc Pillard, Angelique Escoriza, Roxane Moritz, Cedric Schneider, Esteban Alfonso, Fatma Ben Jeddou, Oliver Selmoni, Gregory Resch, Gilbert Greub, Olivier Emery, Manupriyam Dubey, Trestan Pillonel, Marc Robinson-Rechavi, Jan Roelof van der Meer

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Mortality from drug-resistant tuberculosis in high-burden countries comparing routine drug susceptibility testing with whole-genome sequencing: a multicentre cohort study by Kathrin Zürcher, MSc, Martina L Reichmuth, MSc, Marie Ballif, PhD, Chloé Loiseau, PhD, Sonia Borrell, PhD, Miriam Reinhard, Veronika Skrivankova, PhD, Rico Hömke, Peter Sander, MD, Anchalee Avihingsanon, MD, Alash'le G Abimiku, ProfPhD, Olivier Marcy, MD, Jimena Collantes, MSc, E Jane Carter, MD, Robert J Wilkinson, ProfPhD, Helen Cox, ProfPhD, Marcel Yotebieng, ProfMD, Robin Huebner, PhD, Lukas Fenner, ProfMD, Erik C Böttger, ProfMD, Sebastien Gagneux, ProfPhD, Matthias Egger, ProfMD

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Local adaptation in populations of Mycobacterium tuberculosis endemic to the Indian Ocean Rim [version 1; peer review: 2 approved] by Fabrizio Menardo, Liliana K. Rutaihwa, Michaela Zwyer, Sonia Borrell, Iñaki Comas, Emilyn Costa Conceição, Mireia Coscolla, Helen Cox, Moses Joloba, Horng-Yunn Dou, Julia Feldmann, Lukas Fenner, Janet Fyfe, Qian Gao, Darío García de Viedma, Alberto L. Garcia-Basteiro, Sebastian M. Gygli, Jerry Hella, Hellen Hiza, Levan Jugheli, Lujeko Kamwela, Midori Kato-Maeda, Qingyun Liu, Serej D. Ley, Chloe Loiseau, Surakameth Mahasirimongkol, Bijaya Malla, Prasit Palittapongarnpim, Niaina Rakotosamimanana, Voahangy Rasolofo, Miriam Reinhard, Klaus Reither, Mohamed Sasamalo, Rafael Silva Duarte, Christophe Sola, Philip Suffys, Karla Valeria Batista Lima, Dorothy Yeboah-Manu, Christian Beisel, Daniela Brites, Sebastien Gagneux

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Local adaptation in populations of Mycobacterium tuberculosis endemic to the Indian Ocean Rim [version 2; peer review: 3 approved] by Fabrizio Menardo, Liliana K. Rutaihwa, Michaela Zwyer, Sonia Borrell, Iñaki Comas, Emilyn Costa Conceição, Mireia Coscolla, Helen Cox, Moses Joloba, Horng-Yunn Dou, Julia Feldmann, Lukas Fenner, Janet Fyfe, Qian Gao, Darío García de Viedma, Alberto L. Garcia-Basteiro, Sebastian M. Gygli, Jerry Hella, Hellen Hiza, Levan Jugheli, Lujeko Kamwela, Midori Kato-Maeda, Qingyun Liu, Serej D. Ley, Chloe Loiseau, Surakameth Mahasirimongkol, Bijaya Malla, Prasit Palittapongarnpim, Niaina Rakotosamimanana, Voahangy Rasolofo, Miriam Reinhard, Klaus Reither, Mohamed Sasamalo, Rafael Silva Duarte, Christophe Sola, Philip Suffys, Karla Valeria Batista Lima, Dorothy Yeboah-Manu, Christian Beisel, Daniela Brites, Sebastien Gagneux

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Phylogenomics and antimicrobial resistance of the leprosy bacillus Mycobacterium leprae by Andrej Benjak, Charlotte Avanzi, Pushpendra Singh, Chloé Loiseau, Selfu Girma, Philippe Busso, Amanda N. Brum Fontes, Yuji Miyamoto, Masako Namisato, Kidist Bobosha, Claudio G. Salgado, Moisés B. da Silva, Raquel C. Bouth, Marco A. C. Frade, Fred Bernardes Filho, Josafá G. Barreto, José A. C. Nery, Samira Bührer-Sékula, Andréanne Lupien, Abdul R. Al-Samie, Yasin Al-Qubati, Abdul S. Alkubati, Gisela Bretzel, Lucio Vera-Cabrera, Fatoumata Sakho, Christian R. Johnson, Mamoudou Kodio, Abdoulaye Fomba, Samba O. Sow, Moussa Gado, Ousmane Konaté, Mariane M. A. Stefani, Gerson O. Penna, Philip N. Suffys, Euzenir Nunes Sarno, Milton O. Moraes, Patricia S. Rosa, Ida M. F. Dias Baptista, John S. Spencer, Abraham Aseffa, Masanori Matsuoka, Masanori Kai, Stewart T. Cole

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