List of publications

Atavliyeva Sabina, Auganova Dana, Gharbi Nour, Zholdybayeva Elena, Skiba Yuri, Akisheva Akmaral, Tsepke Anna, Wirth Thierry, Sola Christophe, and Tarlykov Pavel. 2026. “Molecular Epidemiology of Mycobacterium Tuberculosis Lineage 2 in Kazakhstan”. The International Journal of Mycobacteriology 15 (January): S52–S52. doi:10.4103/ijmy.ijmy_277_25.

Auganova Dana, Atavliyeva Sabina, Gharbi Nour, Zholdybayeva Elena, Skiba Yuri, Akisheva Akmaral, Tsepke Anna, et al. 2025. “Genomic Characterization and Epidemiology of Mycobacterium Tuberculosis Lineage 2 Isolates from Kazakhstan”. Scientific Reports 15 (January): 37715. doi:10.1038/s41598-025-22485-2.

Barilar Ivan, Fernando Tatiana, Utpatel Christian, Abujate Cláudio, Madeira Carla Maria, José Benedita, Mutaquiha Claudia, et al. 2024. “Emergence of Bedaquiline-Resistant Tuberculosis and of Multidrug-Resistant and Extensively Drug-Resistant Mycobacterium Tuberculosis Strains With RpoB Ile491Phe Mutation Not Detected by Xpert MTB RIF in Mozambique: A Retrospective Observational Study”. The Lancet Infectious Diseases 24 (January): 297–307. doi:10.1016/S1473-3099(23)00498-X.

Wirth Thierry. 2023. “Evolutionary History and Phylogeography of the MTBC Complex”. Bulletin de L’Académie Nationale de Médecine 207 (January): 1034–1043. doi:10.1016/j.banm.2023.05.003.

Merker Matthias, Rasigade Jean-Philippe, Barbier Maxime, Cox Helen, Feuerriegel Silke, Kohl Thomas A., Shitikov Egor, et al. 2022. “Transcontinental Spread and Evolution of Mycobacterium Tuberculosis W148 European Russian Clade Toward Extensively Drug Resistant Tuberculosis”. Nature Communications 13 (January): 5105. doi:10.1038/s41467-022-32455-1.

Sassi Mohamed, Bronsard Julie, Pascreau Gaetan, Emily Mathieu, Donnio Pierre-Yves, Revest Matthieu, Felden Brice, Wirth Thierry, and Augagneur Yoann. 2022. “Forecasting Staphylococcus Aureus Infections Using Genome-Wide Association Studies, Machine Learning, and Transcriptomic Approaches”. MSystems, January, e00378–22. doi:10.1128/msystems.00378-22.

Dreyer Viola, Mandal Ayan, Dev Prachi, Merker Matthias, Barilar Ivan, Utpatel Christian, Nilgiriwala Kayzad, et al. 2022. “High Fluoroquinolone Resistance Proportions Among Multidrug-Resistant Tuberculosis Driven by Dominant L2 Mycobacterium Tuberculosis Clones in the Mumbai Metropolitan Region”. Genome Medicine 14 (January): 95. doi:10.1186/s13073-022-01076-0.

Wirth Thierry. 2021. “When Specialized Clones Go Global”. Nature Microbiology 6 (October): 1215–1216. doi:10.1038/s41564-021-00967-z.

Alili Rohia, Belda Eugeni, Le Phuong, Wirth Thierry, Zucker Jean-Daniel, Prifti Edi, and Clément Karine. 2021. “Exploring Semi-Quantitative Metagenomic Studies Using Oxford Nanopore Sequencing: A Computational and Experimental Protocol”. Genes 12 (January): 1496. doi:10.3390/genes12101496.

Moura Alexandra, Lefrancq Noémie, Leclercq Alexandre, Wirth Thierry, Borges Vítor, Gilpin Brent, Dallman Timothy, et al. 2020. Emergence and Global Spread of Listeria Monocytogenes Main Clinical Clonal Complex. Science Advances. Vol. 7. doi:10.1126/sciadv.abj9805.

Wirth Thierry. 2020. “Applied Phyloepidemiology: Detecting Drivers of Pathogen Transmission from Genomic Signatures Using Density Measures”. Evolutionary Applications 13 (July): 1513–1525. doi:10.1111/eva.12991.

Wirth Thierry, Bergot Marine, Rasigade Jean-Philippe, Pichon Bruno, Barbier Maxime, Martins-Simoes Patricia, Jacob Laurent, et al. 2020. “Niche Specialization and Spread of Staphylococcus Capitis Involved in Neonatal Sepsis”. Nature Microbiology 5 (May): 735–745. doi:10.1038/s41564-020-0676-2.

Franssen Susanne U, Durrant Caroline, Stark Olivia, Moser Bettina, Downing Tim, Imamura Hideo, Dujardin Jean-Claude, et al. 2020. “Global Genome Diversity of the Leishmania Donovani Complex”. ELife 9 (January): e51243. doi:10.7554/eLife.51243.

Kohl Thomas A., Kranzer Katharina, Andres Sönke, Wirth Thierry, Niemann Stefan, and Moser Irmgard. 2020. “Population Structure of Mycobacterium Bovis in Germany: A Long-Term Study Using Whole-Genome Sequencing Combined With Conventional Molecular Typing Methods”. Journal of Clinical Microbiology 58 (January): e01573–20, /jcm/58/11/JCM.01573–20.atom. doi:10.1128/JCM.01573-20.

Tevell Staffan, Baig Sharmin, Hellmark Bengt, Martins Simoes Patricia, Wirth Thierry, Butin Marine, Nilsdotter-Augustinsson Åsa, Söderquist Bo, and Stegger Marc. 2020. “Presence of the Neonatal Staphylococcus Capitis Outbreak Clone (NRCS-A) in Prosthetic Joint Infections”. Scientific Reports 10 (January): 22389. doi:10.1038/s41598-020-79225-x.

Arandjelović Irena, Merker Matthias, Richter Elvira, Kohl Thomas A., Savić Branislava, Soldatović Ivan, Wirth Thierry, Vuković Dragana, and Niemann Stefan. 2019. “Longitudinal Outbreak of Multidrug-Resistant Tuberculosis in a Hospital Setting, Serbia”. Emerging Infectious Diseases 25 (March): 555–558. doi:10.3201/eid2503.181220.

Bal A., Sabatier M., Wirth T., Coste-Burel M., Lazrek M., Stefic K., Brengel-Pesce K., et al. 2019. “Emergence of Enterovirus D68 Clade D1, France, August to November 2018”. Euro Surveillance : Bulletin Europeen Sur les Maladies Transmissibles = European Communicable Disease Bulletin 24 (January). doi:10.2807/1560-7917.ES.2019.24.3.1800699.

Merker M., Barbier M., Cox H., Rasigade J. P., Feuerriegel S., Kohl T. A., Diel R., et al. 2018. “Compensatory Evolution Drives Multidrug-Resistant Tuberculosis in Central Asia”. ELife 7 (October). doi:10.7554/eLife.38200.

Lalis Aude, and Wirth Thierry. 2018. “Mice and Men: An Evolutionary History of Lassa Fever”. In Biodiversity and Evolution, 189–212. Elsevier; Elsevier. doi:10.1016/B978-1-78548-277-9.50011-5.

Barbier M., Dumitrescu O., Pichat C., Carret G., Ronnaux-Baron A. S., Blasquez G., Godin-Benhaim C., et al. 2018. “Changing Patterns of Human Migrations Shaped the Global Population Structure of Mycobacterium Tuberculosis in France”. Scientific Reports 8 (January): 5855. doi:10.1038/s41598-018-24034-6.