Publications

Loiseau C, Windels E.M, Gygli S.M, Jugheli L, Maghradze N, Brites D, Ross A, Goig G, Reinhard M, Borrell S, Trauner A, Dötsch A, Aspindzelashvili R, Denes R, Reither K, Beisel C, Tukvadze N, Avaliani Z, Stadler T, Gagneux S. The relative transmission fitness of multidrug-resistant Mycobacterium tuberculosis in a drug resistance hotspot. Nat Commun. 2023;14:1988. DOI: 10.1038/s41467-023-37719-y

Asare P, Osei-Wusu S, Baddoo N.A, Bedeley E, Otchere I.D, Brites D, Loiseau C, Asante-Poku A, Prah D.A, Borrell S, Reinhard M, Omari M.A, Forson A, Koram K.A, Gagneux S, Yeboah-Manu D. Genomic epidemiological analysis identifies high relapse among individuals with recurring tuberculosis and provides evidence of household recent TB transmission in Ghana. Int J Infect Dis. 2021;106:13-22. DOI: 10.1016/j.ijid.2021.02.110

Coscolla M, Gagneux S, Menardo F, Loiseau C, Ruiz-Rodriguez P, Borrell S, Otchere I.D, Asante-Poku A, Asare P, Sanchez-Buso L, Gehre F, Sanoussi C.N, Antonio M, Affolabi D, Fyfe J, Beckert P, Niemann S, Alabi A.S, Grobusch M.P, Kobbe R, Parkhill J, Beisel C, Fenner L, Bottger E.C, Meehan C.J, Harris S.R, de Jong B.C, Yeboah-Manu D, Brites D. Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history. Microb Genom. 2021;7(2):000477. DOI: 10.1099/mgen.0.000477

Gygli S.M, Loiseau C, Jugheli L, Adamia N, Trauner A, Reinhard M, Ross A, Borrell S, Aspindzelashvili R, Maghradze N, Reither K, Beisel C, Tukvadze N, Avaliani Z, Gagneux S. Prisons as ecological drivers of fitness-compensated multidrug-resistant Mycobacterium tuberculosis. Nat Med. 2021;27:1171–1177. DOI: 10.1038/s41591-021-01358-x

Gygli S.M, Loiseau C, Jugheli L, Adamia N, Trauner A, Reinhard M, Ross A, Borrell S, Aspindzelashvili R, Maghradze N, Reither K, Beisel C, Tukvadze N, Avaliani Z, Gagneux S. Publisher Correction: Prisons as ecological drivers of fitness-compensated multidrug-resistant Mycobacterium tuberculosis. Nat Med. 2021;27(7):1308. DOI: 10.1038/s41591-021-01417-3

Menardo F, Rutaihwa L.K, Zwyer M, Borrell S, Comas I, Conceicao E.C, Coscolla M, Cox H, Joloba M, Dou H.Y, Feldmann J, Fenner L, Fyfe J, Gao Q, Garcia de Viedma D, Garcia-Basteiro A.L, Gygli S.M, Hella J, Hiza H, Jugheli L, Kamwela L, Kato-Maeda M, Liu Q, Ley S.D, Loiseau C, Mahasirimongkol S, Malla B, Palittapongarnpim P, Rakotosamimanana N, Rasolofo V, Reinhard M, Reither K, Sasamalo M, Silva Duarte R, Sola C, Suffys P, Batista Lima K.V, Yeboah-Manu D, Beisel C, Brites D, Gagneux S. Local adaptation in populations of Mycobacterium tuberculosis endemic to the Indian Ocean Rim. F1000Res. 2021;10:60. DOI: 10.12688/f1000research.28318.1

Röösli M, Hahad O, Dongus S, Loizeau N, Daiber A, Munzel T, Eeftens M. Gesundheitsrisiko Mobilfunkstrahlung? Was ändert sich mit 5G?. Aktuelle Kardiologie. 2021;10(6):531-536. DOI: 10.1055/a-1545-0875

Zürcher K, Reichmuth M.L, Ballif M, Loiseau C, Borrell S, Reinhard M, Skrivankova V, Hömke R, Sander P, Avihingsanon A, Abimiku A.G, Marcy O, Collantes J, Carter E.J, Wilkinson R.J, Cox H, Yotebieng M, Huebner R, Fenner L, Böttger E.C, Gagneux S, Egger M. Mortality from drug-resistant tuberculosis in high-burden countries comparing routine drug susceptibility testing with whole-genome sequencing: a multicentre cohort study. Lancet Microbe. 2021;2:e320–30. DOI: 10.1016/S2666-5247(21)00044-6

Asare P, Otchere I.D, Bedeley E, Brites D, Loiseau C, Baddoo N.A, Asante-Poku A, Osei-Wusu S, Prah D.A, Borrell S, Reinhard M, Forson A, Koram K.A, Gagneux S, Yeboah-Manu D. Whole genome sequencing and spatial analysis identifies recent tuberculosis transmission hotspots in Ghana. Front Med (Lausanne). 2020;7:161. DOI: 10.3389/fmed.2020.00161

Castro R.A.D, Ross A, Kamwela L, Reinhard M, Loiseau C, Feldmann J, Borrell S, Trauner A, Gagneux S. The genetic background modulates the evolution of fluoroquinolone-resistance in Mycobacterium tuberculosis. Mol Biol Evol. 2020;37(1):195-207. DOI: 10.1093/molbev/msz214

Loiseau C, Brites D, Reinhard M, Zurcher K, Borrell S, Ballif M, Fenner L, Cox H, Rutaihwa L.K, Wilkinson R.J, Yotebieng M, Carter E.J, Abimiku A, Marcy O, Gotuzzo E, Avihingsanon A, Zetola N, Doulla B, Bottger E.C, Egger M, Gagneux S. HIV coinfection is associated with low fitness rpoB variants in rifampicin-resistant Mycobacterium tuberculosis. Antimicrob Agents Chemother. 2020;64(10):e00782-20. DOI: 10.1128/AAC.00782-20

Loiseau C, Menardo F, Aseffa A, Hailu E, Gumi B, Ameni G, Berg S, Rigouts L, Robbe-Austerman S, Zinsstag J, Gagneux S, Brites D. An African origin for Mycobacterium bovis. Evol Med Public Health. 2020;2020:49-59. DOI: 10.1093/emph/eoaa005

Loiseau C. Evolutionary epidemiology of the Mycobacterium tuberculosis complex. Basel: Univ. Basel, 2020. Doctoral Thesis, University of Basel, Faculty of Science DOI: 10.5451/unibas-ep90906

Ngabonziza J.C.S, Loiseau C, Marceau M, Jouet A, Menardo F, Tzfadia O, Antoine R, Niyigena E.B, Mulders W, Fissette K, Diels M, Gaudin C, Duthoy S, Ssengooba W, Andre E, Kaswa M.K, Habimana Y.M, Brites D, Affolabi D, Mazarati J.B, de Jong B.C, Rigouts L, Gagneux S, Meehan C.J, Supply P. A sister lineage of the Mycobacterium tuberculosis complex discovered in the African Great Lakes region. Nat Commun. 2020;11:2917. DOI: 10.1038/s41467-020-16626-6

Reichmuth M.L, Homke R, Zürcher K, Sander P, Avihingsanon A, Collantes J, Loiseau C, Borrell S, Reinhard M, Wilkinson R.J, Yotebieng M, Fenner L, Böttger E.C, Gagneux S, Egger M, Keller P.M, International epidemiology Databases to Evaluate AIDS (IeDEA). Natural polymorphisms in Mycobacterium tuberculosis conferring resistance to delamanid in drug-naïve patients. Antimicrob Agents Chemother. 2020;64(11):e00513-20. DOI: 10.1128/AAC.00513-20

Borrell S, Trauner A, Brites D, Rigouts L, Loiseau C, Coscolla M, Niemann S, De Jong B, Yeboah-Manu D, Kato-Maeda M, Feldmann J, Reinhard M, Beisel C, Gagneux S. Reference set of Mycobacterium tuberculosis clinical strains: a tool for research and product development. PLoS One. 2019;14(3):e0214088. DOI: 10.1371/journal.pone.0214088

Gygli S.M, Keller P.M, Ballif M, Blöchliger N, Hömke R, Reinhard M, Loiseau C, Ritter C, Sander P, Borrell S, Loo J.C, Avihingsanon A, Gnokoro J, Yotebieng M, Egger M, Gagneux S, Böttger E.C. Whole genome sequencing for drug resistance profile prediction in Mycobacterium tuberculosis. Antimicrob Agents Chemother. 2019;63(4):e02175-18. DOI: 10.1128/AAC.02175-18

Loiseau C, Brites D, Moser I, Coll F, Pourcel C, Robbe-Austerman S, Escuyer V, Musser K.A, Peacock S.J, Feuerriegel S, Kohl T.A, Niemann S, Gagneux S, Köser C.U. Revised interpretation of the Hain Lifescience GenoType MTBC to differentiate Mycobacterium canettii and members of the M. tuberculosis complex. Antimicrob Agents Chemother. 2019;63(6):e00159-19. DOI: 10.1128/AAC.00159-19

Meehan C.J, Goig G.A, Kohl T.A, Verboven L, Dippenaar A, Ezewudo M, Farhat M.R, Guthrie J.L, Laukens K, Miotto P, Ofori-Anyinam B, Dreyer V, Supply P, Suresh A, Utpatel C, van Soolingen D, Zhou Y, Ashton P.M, Brites D, Cabibbe A.M, de Jong B.C, de Vos M, Menardo F, Gagneux S, Gao Q, Heupink T.H, Liu Q, Loiseau C, Rigouts L, Rodwell T.C, Tagliani E, Walker T.M, Warren R.M, Zhao Y, Zignol M, Schito M, Gardy J, Cirillo D.M, Niemann S, Comas I, Van Rie A. Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues. Nat Rev Microbiol. 2019;17:533-545. DOI: 10.1038/s41579-019-0214-5

Payne J.L, Menardo F, Trauner A, Borrell S, Gygli S.M, Loiseau C, Gagneux S, Hall A.R. Transition bias influences the evolution of antibiotic resistance in Mycobacterium tuberculosis. PLoS Biol. 2019;17(5):e3000265. DOI: 10.1371/journal.pbio.3000265

Benjak A, Avanzi C, Singh P, Loiseau C, Girma S, Busso P, Fontes A.N.B, Miyamoto Y, Namisato M, Bobosha K, Salgado C.G, da Silva M.B, Bouth R.C, Frade M.A.C, Filho F.B, Barreto J.G, Nery J.A.C, Buhrer-Sekula S, Lupien A, Al-Samie A.R, Al-Qubati Y, Alkubati A.S, Bretzel G, Vera-Cabrera L, Sakho F, Johnson C.R, Kodio M, Fomba A, Sow S.O, Gado M, Konate O, Stefani M.M.A, Penna G.O, Suffys P.N, Sarno E.N, Moraes M.O, Rosa P.S, Baptista Imfd, Spencer J.S, Aseffa A, Matsuoka M, Kai M, Cole S.T. Phylogenomics and antimicrobial resistance of the leprosy bacillus Mycobacterium leprae. Nat Commun. 2018;9:352. DOI: 10.1038/s41467-017-02576-z

Brites D, Loiseau C, Menardo F, Borrell S, Boniotti B, Warren R, Dippenaar A, Parsons S.D.C, Beisel C, Behr M.A, Fyfe J.A, Coscolla M, Gagneux S. A new phylogenetic framework for the animal-adapted Mycobacterium tuberculosis complex. Front Microbiol. 2018;9:2820. DOI: 10.3389/fmicb.2018.02820

Menardo F, Loiseau C, Brites D, Coscolla M, Gygli S.M, Rutaihwa L.K, Trauner A, Beisel C, Borrell S, Gagneux S. Treemmer: a tool to reduce large phylogenetic datasets with minimal loss of diversity. BMC Bioinformatics. 2018;19:164. DOI: 10.1186/s12859-018-2164-8

Otchere I.D, Coscolla M, Sanchez-Buso L, Asante-Poku A, Brites D, Loiseau C, Meehan C, Osei-Wusu S, Forson A, Laryea C, Yahayah A.I, Baddoo A, Ansa G.A, Aboagye S.Y, Asare P, Borrell S, Gehre F, Beckert P, Kohl T.A, N'Dira S, Beisel C, Antonio M, Niemann S, de Jong B.C, Parkhill J, Harris S.R, Gagneux S, Yeboah-Manu D. Comparative genomics of Mycobacterium africanum lineage 5 and lineage 6 from Ghana suggests distinct ecological niches. Sci Rep. 2018;8:11269. DOI: 10.1038/s41598-018-29620-2

Ghielmetti G, Coscolla M, Ruetten M, Friedel U, Loiseau C, Feldmann J, Steinmetz H.W, Stucki D, Gagneux S. Tuberculosis in Swiss captive Asian elephants: microevolution of Mycobacterium tuberculosis characterized by multilocus variable-number tandem-repeat analysis and whole-genome sequencing. Sci Rep. 2017;7:14647. DOI: 10.1038/s41598-017-15278-9

Stefani M.M.A, Avanzi C, Bührer-Sekula S, Benjak A, Loiseau C, Singh P, Pontes M.A.A, Goncalves H.S, Hungria E.M, Busso P, Piton J, Silveira M.I.S, Cruz R, Schetinni A, Costa M.B, Virmond M.C.L, Diorio S.M, Dias-Baptista I.M.F, Rosa P.S, Matsuoka M, Penna M.L.F, Cole S.T, Penna G.O. Whole genome sequencing distinguishes between relapse and reinfection in recurrent leprosy cases. PLoS Negl Trop Dis. 2017;11(6):e0005598. DOI: 10.1371/journal.pntd.0005598