Tuberculosis in Swiss captive Asian elephants: microevolution of Mycobacterium tuberculosis characterized by multilocus variable-number tandem-repeat analysis and whole-genome sequ...

by Ghielmetti, Giovanni, Coscolla, Mireia, Ruetten, Maja, Friedel, Ute, Loiseau, Chloé, Feldmann, Julia, Steinmetz, Hanspeter W., Stucki, David, Gagneux, Sebastien
Published in Sci Rep (2017)

Transition bias influences the evolution of antibiotic resistance in Mycobacterium tuberculosis

by Payne, Joshua L., Menardo, Fabrizio, Trauner, Andrej, Borrell, Sonia, Gygli, Sebastian M., Loiseau, Chloe, Gagneux, Sebastien, Hall, Alex R.
Published in PLoS Biol (2019)

The Genetic Background Modulates the Evolution of Fluoroquinolone-Resistance in Mycobacterium tuberculosis

by Castro, Rhastin A D, Ross, Amanda, Kamwela, Lujeko, Reinhard, Miriam, Loiseau, Chloé, Feldmann, Julia, Borrell, Sonia, Trauner, Andrej, Gagneux, Sebastien
Published in Mol Biol Evol (2020)

Treemmer: a tool to reduce large phylogenetic datasets with minimal loss of diversity

by Menardo, Fabrizio, Loiseau, Chloé, Brites, Daniela, Coscolla, Mireia, Gygli, Sebastian M., Rutaihwa, Liliana K., Trauner, Andrej, Beisel, Christian, Borrell, Sonia, Gagneux, Sebastien
Published in BMC Bioinformatics (2018)

An African origin for Mycobacterium bovis

by Loiseau, Chloé, Menardo, Fabrizio, Aseffa, Abraham, Hailu, Elena, Gumi, Balako, Ameni, Gobena, Berg, Stefan, Rigouts, Leen, Robbe-Austerman, Suelee, Zinsstag, Jakob, Gagneux, Sebastien, Brites, Daniela
Published in Evol Med Public Health (2020)

A New Phylogenetic Framework for the Animal-Adapted Mycobacterium tuberculosis Complex

by Brites, Daniela, Loiseau, Chloé, Menardo, Fabrizio, Borrell, Sonia, Boniotti, Maria Beatrice, Warren, Robin, Dippenaar, Anzaan, Parsons, Sven David Charles, Beisel, Christian, Behr, Marcel A., Fyfe, Janet A., Coscolla, Mireia, Gagneux, Sebastien
Published in Front Microbiol (2018)

Reference set of Mycobacterium tuberculosis clinical strains: A tool for research and product development

by Borrell, Sònia, Trauner, Andrej, Brites, Daniela, Rigouts, Leen, Loiseau, Chloe, Coscolla, Mireia, Niemann, Stefan, De Jong, Bouke, Yeboah-Manu, Dorothy, Kato-Maeda, Midori, Feldmann, Julia, Reinhard, Miriam, Beisel, Christian, Gagneux, Sebastien
Published in PLoS One (2019)

Revised Interpretation of the Hain Lifescience GenoType MTBC To Differentiate Mycobacterium canettii and Members of the Mycobacterium tuberculosis Complex

by Loiseau, Chloé, Brites, Daniela, Moser, Irmgard, Coll, Francesc, Pourcel, Christine, Robbe-Austerman, Suelee, Escuyer, Vincent, Musser, Kimberlee A., Peacock, Sharon J., Feuerriegel, Silke, Kohl, Thomas A., Niemann, Stefan, Gagneux, Sebastien, Köser, Claudio U.
Published in Antimicrob Agents Chemother (2019)

Natural Polymorphisms in Mycobacterium tuberculosis Conferring Resistance to Delamanid in Drug-Naive Patients

by Reichmuth, Martina L., Hömke, Rico, Zürcher, Kathrin, Sander, Peter, Avihingsanon, Anchalee, Collantes, Jimena, Loiseau, Chloé, Borrell, Sonia, Reinhard, Miriam, Wilkinson, Robert J., Yotebieng, Marcel, Fenner, Lukas, Böttger, Erik C., Gagneux, Sebastien, Egger, Matthias, Keller, Peter M.
Published in Antimicrob Agents Chemother (2020)

Whole Genome Sequencing and Spatial Analysis Identifies Recent Tuberculosis Transmission Hotspots in Ghana

by Asare, Prince, Otchere, Isaac Darko, Bedeley, Edmund, Brites, Daniela, Loiseau, Chloé, Baddoo, Nyonuku Akosua, Asante-Poku, Adwoa, Osei-Wusu, Stephen, Prah, Diana Ahu, Borrell, Sonia, Reinhard, Miriam, Forson, Audrey, Koram, Kwadwo Ansah, Gagneux, Sebastien, Yeboah-Manu, Dorothy
Published in Front Med (Lausanne) (2020)

Whole-Genome Sequencing for Drug Resistance Profile Prediction in Mycobacterium tuberculosis

by Gygli, Sebastian M., Keller, Peter M., Ballif, Marie, Blöchliger, Nicolas, Hömke, Rico, Reinhard, Miriam, Loiseau, Chloé, Ritter, Claudia, Sander, Peter, Borrell, Sonia, Collantes Loo, Jimena, Avihingsanon, Anchalee, Gnokoro, Joachim, Yotebieng, Marcel, Egger, Matthias, Gagneux, Sebastien, Böttger, Erik C.
Published in Antimicrob Agents Chemother (2019)

Genomic epidemiological analysis identifies high relapse among individuals with recurring tuberculosis and provides evidence of recent household-related transmission of tuberculosi...

by Asare, Prince, Osei-Wusu, Stephen, Baddoo, Nyonuku Akosua, Bedeley, Edmund, Otchere, Isaac Darko, Brites, Daniela, Loiseau, Chloé, Asante-Poku, Adwoa, Prah, Diana Ahu, Borrell, Sonia, Reinhard, Miriam, Omari, Michael Amo, Forson, Audrey, Koram, Kwadwo Ansah, Gagneux, Sebastien, Yeboah-Manu, Dorothy
Published in Int J Infect Dis (2021)

Oral Phage Therapy of Acute Bacterial Diarrhea With Two Coliphage Preparations: A Randomized Trial in Children From Bangladesh

by Sarker, Shafiqul Alam, Sultana, Shamima, Reuteler, Gloria, Moine, Deborah, Descombes, Patrick, Charton, Florence, Bourdin, Gilles, McCallin, Shawna, Ngom-Bru, Catherine, Neville, Tara, Akter, Mahmuda, Huq, Sayeeda, Qadri, Firdausi, Talukdar, Kaisar, Kassam, Mohamed, Delley, Michèle, Loiseau, Chloe, Deng, Ying, El Aidy, Sahar, Berger, Bernard, Brüssow, Harald
Published in EBioMedicine (2016)

HIV Coinfection Is Associated with Low-Fitness rpoB Variants in Rifampicin-Resistant Mycobacterium tuberculosis

by Loiseau, Chloé, Brites, Daniela, Reinhard, Miriam, Zürcher, Kathrin, Borrell, Sonia, Ballif, Marie, Fenner, Lukas, Cox, Helen, Rutaihwa, Liliana K., Wilkinson, Robert J., Yotebieng, Marcel, Carter, E. Jane, Abimiku, Alash'le, Marcy, Olivier, Gotuzzo, Eduardo, Avihingsanon, Anchalee, Zetola, Nicola, Doulla, Basra, Böttger, Erik C., Egger, Matthias, Gagneux, Sebastien
Published in Antimicrob Agents Chemother (2020)

A sister lineage of the Mycobacterium tuberculosis complex discovered in the African Great Lakes region

by Ngabonziza, Jean Claude Semuto, Loiseau, Chloé, Marceau, Michael, Jouet, Agathe, Menardo, Fabrizio, Tzfadia, Oren, Antoine, Rudy, Niyigena, Esdras Belamo, Mulders, Wim, Fissette, Kristina, Diels, Maren, Gaudin, Cyril, Duthoy, Stéphanie, Ssengooba, Willy, André, Emmanuel, Kaswa, Michel K., Habimana, Yves Mucyo, Brites, Daniela, Affolabi, Dissou, Mazarati, Jean Baptiste, de Jong, Bouke Catherine, Rigouts, Leen, Gagneux, Sebastien, Meehan, Conor Joseph, Supply, Philip
Published in Nat Commun (2020)

Whole genome sequencing distinguishes between relapse and reinfection in recurrent leprosy cases

by Stefani, Mariane M. A., Avanzi, Charlotte, Bührer-Sékula, Samira, Benjak, Andrej, Loiseau, Chloé, Singh, Pushpendra, Pontes, Maria A. A., Gonçalves, Heitor S., Hungria, Emerith M., Busso, Philippe, Piton, Jérémie, Silveira, Maria I. S., Cruz, Rossilene, Schetinni, Antônio, Costa, Maurício B., Virmond, Marcos C. L., Diorio, Suzana M., Dias-Baptista, Ida M. F., Rosa, Patricia S., Matsuoka, Masanori, Penna, Maria L. F., Cole, Stewart T., Penna, Gerson O.
Published in PLoS Negl Trop Dis (2017)

Comparative genomics of Mycobacterium africanum Lineage 5 and Lineage 6 from Ghana suggests distinct ecological niches

by Otchere, Isaac Darko, Coscollá, Mireia, Sánchez-Busó, Leonor, Asante-Poku, Adwoa, Brites, Daniela, Loiseau, Chloe, Meehan, Conor, Osei-Wusu, Stephen, Forson, Audrey, Laryea, Clement, Yahayah, Abdallah Iddrisu, Baddoo, Akosua, Ansa, Gloria Akosua, Aboagye, Samuel Yaw, Asare, Prince, Borrell, Sonia, Gehre, Florian, Beckert, Patrick, Kohl, Thomas A., N’dira, Sanoussi, Beisel, Christian, Antonio, Martin, Niemann, Stefan, de Jong, Bouke C., Parkhill, Julian, Harris, Simon R., Gagneux, Sebastien, Yeboah-Manu, Dorothy
Published in Sci Rep (2018)

Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history

by Coscolla, Mireia, Gagneux, Sebastien, Menardo, Fabrizio, Loiseau, Chloé, Ruiz-Rodriguez, Paula, Borrell, Sonia, Otchere, Isaac Darko, Asante-Poku, Adwoa, Asare, Prince, Sánchez-Busó, Leonor, Gehre, Florian, Sanoussi, C. N’Dira, Antonio, Martin, Affolabi, Dissou, Fyfe, Janet, Beckert, Patrick, Niemann, Stefan, Alabi, Abraham S., Grobusch, Martin P., Kobbe, Robin, Parkhill, Julian, Beisel, Christian, Fenner, Lukas, Böttger, Erik C., Meehan, Conor J., Harris, Simon R., de Jong, Bouke C., Yeboah-Manu, Dorothy, Brites, Daniela
Published in Microb Genom (2021)

The Genome of the Toluene-Degrading Pseudomonas veronii Strain 1YdBTEX2 and Its Differential Gene Expression in Contaminated Sand

by Morales, Marian, Sentchilo, Vladimir, Bertelli, Claire, Komljenovic, Andrea, Kryuchkova-Mostacci, Nadezda, Bourdilloud, Audrey, Linke, Burkhard, Goesmann, Alexander, Harshman, Keith, Segers, Francisca, Delapierre, Fabien, Fiorucci, Damien, Seppey, Mathieu, Trofimenco, Evgeniya, Berra, Pauline, El Taher, Athimed, Loiseau, Chloé, Roggero, Dejan, Sulfiotti, Madeleine, Etienne, Angela, Ruiz Buendia, Gustavo, Pillard, Loïc, Escoriza, Angelique, Moritz, Roxane, Schneider, Cedric, Alfonso, Esteban, Ben Jeddou, Fatma, Selmoni, Oliver, Resch, Gregory, Greub, Gilbert, Emery, Olivier, Dubey, Manupriyam, Pillonel, Trestan, Robinson-Rechavi, Marc, van der Meer, Jan Roelof
Published in PLoS One (2016)

Local adaptation in populations of Mycobacterium tuberculosis endemic to the Indian Ocean Rim

by Menardo, Fabrizio, Rutaihwa, Liliana K., Zwyer, Michaela, Borrell, Sonia, Comas, Iñaki, Conceição, Emilyn Costa, Coscolla, Mireia, Cox, Helen, Joloba, Moses, Dou, Horng-Yunn, Feldmann, Julia, Fenner, Lukas, Fyfe, Janet, Gao, Qian, García de Viedma, Darío, Garcia-Basteiro, Alberto L., Gygli, Sebastian M., Hella, Jerry, Hiza, Hellen, Jugheli, Levan, Kamwela, Lujeko, Kato-Maeda, Midori, Liu, Qingyun, Ley, Serej D., Loiseau, Chloe, Mahasirimongkol, Surakameth, Malla, Bijaya, Palittapongarnpim, Prasit, Rakotosamimanana, Niaina, Rasolofo, Voahangy, Reinhard, Miriam, Reither, Klaus, Sasamalo, Mohamed, Silva Duarte, Rafael, Sola, Christophe, Suffys, Philip, Batista Lima, Karla Valeria, Yeboah-Manu, Dorothy, Beisel, Christian, Brites, Daniela, Gagneux, Sebastien
Published in F1000Res (2021)