Publications

Duwor S, Brites D, Mäser P. Phylogenetic analysis of pyruvate-ferredoxin oxidoreductase, a redox enzyme involved in the pharmacological activation of nitro-based prodrugs in bacteria and protozoa. Biology (Basel). 2024;13(3):178. DOI: 10.3390/biology13030178

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

Zwyer M, Rutaihwa L.K, Windels E, Hella J, Menardo F, Sasamalo M, Sommer G, Schmülling L, Borrell S, Reinhard M, Dötsch A, Hiza H, Stritt C, Sikalengo G, Fenner L, De Jong B.C, Kato-Maeda M, Jugheli L, Ernst J.D, Niemann S, Jeljeli L, Ballif M, Egger M, Rakotosamimanana N, Yeboah-Manu D, Asare P, Malla B, Dou H.Y, Zetola N, Wilkinson R.J, Cox H, Carter E.J, Gnokoro J, Yotebieng M, Gotuzzo E, Abimiku A, Avihingsanon A, Xu Z.M, Fellay J, Portevin D, Reither K, Stadler T, Gagneux S, Brites D. Back-to-Africa introductions of Mycobacterium tuberculosis as the main cause of tuberculosis in Dar es Salaam, Tanzania. PLoS Pathog. 2023;19(4):e1010893. DOI: 10.1371/journal.ppat.1010893

Xu Z.M, Rüeger S, Zwyer M, Brites D, Hiza H, Reinhard M, Rutaihwa L, Borrell S, Isihaka F, Temba H, Maroa T, Naftari R, Hella J, Sasamalo M, Reither K, Portevin D, Gagneux S, Fellay J. Using population-specific add-on polymorphisms to improve genotype imputation in underrepresented populations. PLoS Comput Biol. 2022;18(1):e1009628. DOI: 10.1371/journal.pcbi.1009628

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

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

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

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

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

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

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

Menardo F, Duchene S, Brites D, Gagneux S. The molecular clock of Mycobacterium tuberculosis. PLoS Pathog. 2019;15(9):e1008067. DOI: 10.1371/journal.ppat.1008067

Mulholland C.V, Shockey A.C, Aung H.L, Cursons R.T, O'Toole R.F, Gautam S.S, Brites D, Gagneux S, Roberts A.R, Karalus N, Cook G.M, Pepperell C.S, Arcus V.L. Dispersal of Mycobacterium tuberculosis driven by historical European trade in the South Pacific. Front Microbiol. 2019;10(4):2778. DOI: 10.3389/fmicb.2019.02778

Rutaihwa L, Menardo F, Stucki D, Gygli S.M, Ley S.D, Malla B, Feldmann J, Borrell S, Beisel C, Middelkoop K, Carter J.E, Diero L, Ballif M, Jugheli L, Reither K, Fenner L, Brites D, Gagneux S. Multiple introductions of Mycobacterium tuberculosis lineage 2-Beijing into Africa over centuries. Front Ecol Evol. 2019;7:112. DOI: 10.3389/fevo.2019.00112

Rutaihwa L.K, Sasamalo M, Jaleco A, Hella J, Kingazi A, Kamwela L, Kingalu A, Malewo B, Shirima R, Dötsch A, Feldmann J, Reinhard M, Borrell S, Brites D, Reither K, Doulla B, Fenner L, Gagneux S. Insights into the genetic diversity of Mycobacterium tuberculosis in Tanzania. PLoS One. 2019;14(4):e0206334. DOI: 10.1371/journal.pone.0206334

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

Kuhnert D, Coscolla M, Brites D, Stucki D, Metcalfe J, Fenner L, Gagneux S, Stadler T. Tuberculosis outbreak investigation using phylodynamic analysis. Epidemics. 2018;25:47-53. DOI: 10.1016/j.epidem.2018.05.004

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

Armitage S.A.O, Kurtz J, Brites D, Dong Y, Du Pasquier L, Wang H.C. Dscam1 in pancrustacean immunity: current status and a look to the future. Front Immunol. 2017;8:662. DOI: 10.3389/fimmu.2017.00662

Brites D, Gagneux S. The nature and evolution of genomic diversity in the Mycobacterium tuberculosis complex. In: Gagneux S, ed. Advances in Experimental Medicine and Biology. 1019, 1-26. Cham: Springer, 2017. DOI: 10.1007/978-3-319-64371-7_1

Koch A, Brites D, Stucki D, Evans J.C, Seldon R, Heekes A, Mulder N, Nicol M, Oni T, Warner D.F, Mizrahi V, Parkhill J, Gagneux S, Martin D.P, Wilkinson R.J. The influence of HIV on the evolution of Mycobacterium tuberculosis. Mol Biol Evol. 2017;34(7):1654-1668. DOI: 10.1093/molbev/msx107

Trauner A, Liu Q, Via L.E, Liu X, Ruan X, Liang L, Shi H, Chen Y, Wang Z, Liang R, Zhang W, Wei W, Gao J, Sun G, Brites D, England K, Zhang G, Gagneux S, Barry C.E, Gao Q. The within-host population dynamics of Mycobacterium tuberculosis vary with treatment efficacy. Genome Biol. 2017;18:71. DOI: 10.1186/s13059-017-1196-0

Stucki D, Brites D, Jeljeli L, Coscolla M, Liu Q, Trauner A, Fenner L, Rutaihwa L, Borrell S, Luo T, Gao Q, Kato-Maeda M, Ballif M, Egger M, Macedo R, Mardassi H, Moreno M, Vilanova G.T, Fyfe J, Globan M, Thomas J, Jamieson F, Guthrie J.L, Asante-Poku A, Yeboah-Manu D, Wampande E, Ssengooba W, Joloba M, Boom W.H, Basu I, Bower J, Saraiva M, Vasconcellos S.E, Suffys P, Koch A, Wilkinson R, Gail-Bekker L, Malla B, Ley S.D, Beck H.P, de Jong B.C, Toit K, Sanchez-Padilla E, Bonnet M, Gil-Brusola A, Frank M, Penlap Beng V.N, Eisenach K, Alani I, Ndung'u P.W, Revathi G, Gehre F, Akter S, Ntoumi F, Stewart-Isherwood L, Ntinginya N.E, Rachow A, Hoelscher M, Cirillo D.M, Skenders G, Hoffner S, Bakonyte D, Stakenas P, Diel R, Crudu V, Moldovan O, Al-Hajoj S, Otero L, Barletta F, Carter E.J, Diero L, Supply P, Comas I, Niemann S, Gagneux S. Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages. Nat Genet. 2016;48(12):1535-1543. DOI: 10.1038/ng.3704

Bolz M, Bratschi M.W, Kerber S, Minyem J.C, Um Boock A, Vogel M, Bayi P.F, Junghanss T, Brites D, Harris S.R, Parkhill J, Pluschke G, Lamelas Cabello A. Locally confined clonal complexes of Mycobacterium ulcerans in two Buruli ulcer endemic regions of Cameroon. PLoS Negl Trop Dis. 2015;9(6):e0003802. DOI: 10.1371/journal.pntd.0003802

Brites D, Du Pasquier L. Somatic and germline diversification of a putative immunoreceptor within one phylum: dscam in arthropods. In: Hsu E,Du Pasquier L, eds. Pathogen-host interactions: antigenic variation v. somatic adaptations, 131-158. Cham: Springer, 2015. DOI: 10.1007/978-3-319-20819-0_6

Brites D, Gagneux S. Co-evolution of Mycobacterium tuberculosis and Homo sapiens. Immunol Rev. 2015;264:6-24. DOI: 10.1111/imr.12264

Chipman A.D, Ferrier D.E, Brena C, Qu J, Hughes D.S, Schroder R, Torres-Oliva M, Znassi N, Jiang H, Almeida F.C, Alonso C.R, Apostolou Z, Aqrawi P, Arthur W, Barna J.C, Blankenburg K.P, Brites D, Capella-Gutierrez S, Coyle M, Dearden P.K, Du Pasquier L, Duncan E.J, Ebert D, Eibner C, Erikson G, Evans P.D, Extavour C.G, Francisco L, Gabaldon T, Gillis W.J, Goodwin-Horn E.A, Green J.E, Griffiths-Jones S, Grimmelikhuijzen C.J, Gubbala S, Guigo R, Han Y, Hauser F, Havlak P, Hayden L, Helbing S, Holder M, Hui J.H, Hunn J.P, Hunnekuhl V.S, Jackson L, Javaid M, Jhangiani S.N, Jiggins F.M, Jones T.E, Kaiser T.S, Kalra D, Kenny N.J, Korchina V, Kovar C.L, Kraus F.B, Lapraz F, Lee S.L, Lv J, Mandapat C, Manning G, Mariotti M, Mata R, Mathew T, Neumann T, Newsham I, Ngo D.N, Ninova M, Okwuonu G, Ongeri F, Palmer W.J, Patil S, Patraquim P, Pham C, Pu L.L, Putman N.H, Rabouille C, Ramos O.M, Rhodes A.C, Robertson H.E, Robertson H.M, Ronshaugen M, Rozas J, Saada N, Sánchez-Gracia A, Scherer S.E, Schurko A.M, Siggens K.W, Simmons D, Stief A, Stolle E, Telford M.J, Tessmar-Raible K, Thornton R, van der Zee M, von Haeseler A, Williams J.M, Willis J.H, Wu Y, Zou X, Lawson D, Muzny D.M, Worley K.C, Gibbs R.A, Akam M, Richards S. The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede strigamia maritima. PLoS Biol. 2014;12(11):e1002005. DOI: 10.1371/journal.pbio.1002005

Brites D, Brena C, Ebert D, Du Pasquier L. More than one way to produce protein diversity: duplication and limited alternative splicing of an adhesion molecule gene in basal arthropods. Evolution. 2013;67(10):2999-3011. DOI: 10.1111/evo.12179

Brites D, Gagneux S. Old and new selective pressures on Mycobacterium tuberculosis. Infect Genet Evol. 2012;12(4):678-685. DOI: 10.1016/j.meegid.2011.08.010