Barilar Ivan, Fernando Tatiana, Utpatel Christian, Abujate Cláudio, Madeira Carla Maria, José Benedita, Mutaquiha Claudia, Kranzer Katharina, Niemann Tanja, Ismael Nalia, De Araujo Leonardo, Wirth Thierry, Niemann Stefan & Viegas Sofia, 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 vol. 24, n° 3, p. 297-307
ISSN
14733099
https://dx.doi.org/10.1016/S1473-3099(23)00498-X
Merker Matthias, Rasigade Jean-Philippe, Barbier Maxime, Cox Helen, Feuerriegel Silke, Kohl Thomas A., Shitikov Egor, Klaos Kadri, Gaudin Cyril, Antoine Rudy, Diel Roland, Borrell Sonia, Gagneux Sebastien, Nikolayevskyy Vladyslav, Andres Sönke et al., 2022 — Transcontinental spread and evolution of Mycobacterium tuberculosis W148 European/Russian clade toward extensively drug resistant tuberculosis. Nature Communications vol. 13, n° 1, p. 5105
ISSN
2041-1723
https://dx.doi.org/10.1038/s41467-022-32455-1
Sassi Mohamed, Bronsard Julie, Pascreau Gaetan, Emily Mathieu, Donnio Pierre-Yves, Revest Matthieu, Felden Brice, Wirth Thierry & Augagneur Yoann, 2022 — Forecasting Staphylococcus aureus Infections Using Genome-Wide Association Studies, Machine Learning, and Transcriptomic Approaches. mSystems , , e00378–22
ISSN
2379-5077
https://dx.doi.org/10.1128/msystems.00378-22
Dreyer Viola, Mandal Ayan, Dev Prachi, Merker Matthias, Barilar Ivan, Utpatel Christian, Nilgiriwala Kayzad, Rodrigues Camilla, Crook Derrick W., the CRyPTIC Consortium and Crook Derrick W., Peto Timothy E. A., Walker A. Sarah, Hoosdally Sarah J., Gibertoni Cruz Ana L., Carter Joshua 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 vol. 14, n° 1, p. 95
ISSN
1756-994X
https://dx.doi.org/10.1186/s13073-022-01076-0
Alili Rohia, Belda Eugeni, Le Phuong, Wirth Thierry, Zucker Jean-Daniel, Prifti Edi & Clément Karine, 2021 — Exploring Semi-Quantitative Metagenomic Studies Using Oxford Nanopore Sequencing: A Computational and Experimental Protocol. Genes vol. 12, n° 10, p. 1496
ISSN
2073-4425
https://dx.doi.org/10.3390/genes12101496
Moura Alexandra, Lefrancq Noémie, Leclercq Alexandre, Wirth Thierry, Borges Vítor, Gilpin Brent, Dallman Timothy, Frey Joachim, Franz Eelco, Nielsen Eva, Thomas Juno, Pightling Arthur, Howden Benjamin, Tarr Cheryl, Gerner-Smidt Peter et al., December 2020 — Emergence and global spread of Listeria monocytogenes main clinical clonal complex. Retracing microbial emergence and spread is essential to understanding the evolution and dynamics of pathogens. The bacterial… Science Advances vol. 7, n° 49, eabj9805 Type: 10.1101/2020.12.18.423387
ISSN
2375-2548
https://dx.doi.org/10.1126/sciadv.abj9805
Wirth Thierry, July 2020 — Applied phyloepidemiology: Detecting drivers of pathogen transmission from genomic signatures using density measures. AbstractUnderstanding the driving forces of an epidemic is key to inform intervention strat- egies against it. Correlating… Evolutionary Applications vol. 13, n° 6, p. 1513-1525 ISBN: 1752-4563 Publisher: Blackwell Type: 10.1111/eva.12991
ISSN
1752-4571, 1752-4571
https://dx.doi.org/10.1111/eva.12991
Wirth Thierry, Bergot Marine, Rasigade Jean-Philippe, Pichon Bruno, Barbier Maxime, Martins-Simoes Patricia, Jacob Laurent, Pike Rachel, Tissieres Pierre, Picaud Jean-Charles, Kearns Angela, Supply Philip, Butin Marine & Laurent Frédéric, May 2020 — Niche specialization and spread of Staphylococcus capitis involved in neonatal sepsis. Nature Microbiology vol. 5, n° 5, p. 735-745
ISSN
2058-5276
https://dx.doi.org/10.1038/s41564-020-0676-2
Franssen Susanne U, Durrant Caroline, Stark Olivia, Moser Bettina, Downing Tim, Imamura Hideo, Dujardin Jean-Claude, Sanders Mandy J, Mauricio Isabel, Miles Michael A, Schnur Lionel F, Jaffe Charles L, Nasereddin Abdelmajeed, Schallig Henk, Yeo Matthew et al., 2020 — Global genome diversity of the Leishmania donovani complex. eLife vol. 9, , e51243
ISSN
2050-084X
https://dx.doi.org/10.7554/eLife.51243
Kohl Thomas A., Kranzer Katharina, Andres Sönke, Wirth Thierry, Niemann Stefan & 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 vol. 58, n° 11, e01573–20, /jcm/58/11/JCM.01573–20.atom
ISSN
0095-1137, 1098-660X
https://dx.doi.org/10.1128/JCM.01573-20
Tevell Staffan, Baig Sharmin, Hellmark Bengt, Martins Simoes Patricia, Wirth Thierry, Butin Marine, Nilsdotter-Augustinsson Åsa, Söderquist Bo & Stegger Marc, 2020 — Presence of the neonatal Staphylococcus capitis outbreak clone (NRCS-A) in prosthetic joint infections. Scientific Reports vol. 10, n° 1, p. 22389
ISSN
2045-2322
https://dx.doi.org/10.1038/s41598-020-79225-x
Arandjelović Irena, Merker Matthias, Richter Elvira, Kohl Thomas A., Savić Branislava, Soldatović Ivan, Wirth Thierry, Vuković Dragana & Niemann Stefan, March 2019 — Longitudinal Outbreak of Multidrug-Resistant Tuberculosis in a Hospital Setting, Serbia. Emerging Infectious Diseases vol. 25, n° 3, p. 555-558
ISSN
1080-6040, 1080-6059
https://dx.doi.org/10.3201/eid2503.181220
Bal A., Sabatier M., Wirth T., Coste-Burel M., Lazrek M., Stefic K., Brengel-Pesce K., Morfin F., Lina B., Schuffenecker I. & Josset L., January 2019 — Emergence of enterovirus D68 clade D1, France, August to November 2018. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin vol. 24, n° 3, Citation Key Alias: bal\_emergence\_2019-1
ISSN
1560-7917 (Electronic) 1025-496X (Linking)
https://dx.doi.org/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., Borrell S., Gagneux S., Nikolayevskyy V., Andres S., Nubel U., Supply P., Wirth T. & Niemann S., October 2018 — Compensatory evolution drives multidrug-resistant tuberculosis in Central Asia. eLife vol. 7, ,
ISSN
2050-084X (Electronic) 2050-084X (Linking)
https://dx.doi.org/10.7554/eLife.38200
Barbier M., Dumitrescu O., Pichat C., Carret G., Ronnaux-Baron A. S., Blasquez G., Godin-Benhaim C., Boisset S., Carricajo A., Jacomo V., Fredenucci I., Perouse de Montclos M., Genestet C., Flandrois J. P., Ader F. et al., 2018 — Changing patterns of human migrations shaped the global population structure of Mycobacterium tuberculosis in France. Scientific reports vol. 8, n° 1, p. 5855
ISSN
2045-2322 (Electronic) 2045-2322 (Linking)
https://dx.doi.org/10.1038/s41598-018-24034-6
Gustave C. A., Tristan A., Martins-Simoes P., Stegger M., Benito Y., Andersen P. S., Bes M., Le Hir T., Diep B. A., Uhlemann A. C., Glaser P., Laurent F., Wirth T. & Vandenesch F., 2018 — Demographic fluctuation of community-acquired antibiotic-resistant Staphylococcus aureus lineages: potential role of flimsy antibiotic exposure. Isme Journal vol. 12, n° 8, p. 1879-1894
ISSN
1751-7370 (Electronic) 1751-7362 (Linking)
https://dx.doi.org/10.1038/s41396-018-0110-4
Kramer R., Sabatier M., Wirth T., Pichon M., Lina B., Schuffenecker I. & Josset L., 2018 — Molecular diversity and biennial circulation of enterovirus D68: a systematic screening study in Lyon, France, 2010 to 2016. Eurosurveillance vol. 23, n° 37,
ISSN
1560-7917 (Electronic) 1025-496X (Linking)
https://dx.doi.org/10.2807/1560-7917.ES.2018.23.37.1700711