Publications

Goig G.A, Menardo F, Salaam-Dreyer Z, Dippenaar A, Streicher E.M, Daniels J, Reuter A, Borrell S, Reinhard M, Dötsch A, Beisel C, Warren R.M, Cox H, Gagneux S. Effect of compensatory evolution in the emergence and transmission of rifampicin-resistant Mycobacterium tuberculosis in Cape Town, South Africa: a genomic epidemiology study. Lancet Microbe. 2023;4(7):e506-e515. DOI: 10.1016/S2666-5247(23)00110-6

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

Cox H, Goig G.A, Salaam-Dreyer Z, Dippenaar A, Reuter A, Mohr-Holland E, Daniels J, Cudahy P.G.T, Nicol M.P, Borrell S, Reinhard M, Dötsch A, Beisel C, Gagneux S, Warren R.M, Furin J. Whole genome sequencing has the potential to improve treatment for rifampicin-resistant tuberculosis in high burden settings: a retrospective cohort study. J Clin Microbiol. 2022;60(3):e0236221. DOI: 10.1128/jcm.02362-21

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

Cox H, Salaam-Dreyer Z, Goig G.A, Nicol M.P, Menardo F, Dippenaar A, Mohr-Holland E, Daniels J, Cudahy P.G.T, Borrell S, Reinhard M, Dötsch A, Beisel C, Reuter A, Furin J, Gagneux S, Warren R.M. Potential contribution of HIV during first-line tuberculosis treatment to subsequent rifampicin-monoresistant tuberculosis and acquired tuberculosis drug resistance in South Africa: a retrospective molecular epidemiology study. Lancet Microbe. 2021;2(11):e584-e593. DOI: 10.1016/S2666-5247(21)00144-0

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

Salaam-Dreyer Z, Streicher E.M, Sirgel F.A, Menardo F, Borrell S, Reinhard M, Dötsch A, Cudahy P.G.T, Mohr-Holland E, Daniels J, Dippenaar A, Nicol M.P, Gagneux S, Warren R.M, Cox H. Rifampicin mono-resistant tuberculosis is not the same as multidrug-resistant tuberculosis: a descriptive study from Khayelitsha, South Africa. Antimicrob Agents Chemother. 2021;65(11):e0036421. DOI: 10.1128/AAC.00364-21

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

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

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

Seth-Smith H.M.B, Imkamp F, Tagini F, Cuénod A, Hömke R, Jahn K, Tschacher A, Grendelmeier P, Bättig V, Erb S, Reinhard M, Rütimann G, Borrell S, Gagneux S, Casanova C, Droz S, Osthoff M, Tamm M, Nübel U, Greub G, Keller P.M, Egli A. Discovery and characterization of Mycobacterium basiliense sp. nov., a nontuberculous Mycobacterium isolated from human lungs. Front Microbiol. 2019;9:3184. DOI: 10.3389/fmicb.2018.03184

Zürcher K, Ballif M, Fenner L, Borrell S, Keller P.M, Gnokoro J, Marcy O, Yotebieng M, Diero L, Carter E.J, Rockwood N, Wilkinson R.J, Cox H, Ezati N, Abimiku A.G, Collantes J, Avihingsanon A, Kawkitinarong K, Reinhard M, Hömke R, Huebner R, Gagneux S, Böttger E.C, Egger M, International Epidemiology Databases to Evaluate Aids Consortium. Drug susceptibility testing and mortality in patients treated for tuberculosis in high-burden countries: a multicentre cohort study. Lancet Infect Dis. 2019;19(3):298-307. DOI: 10.1016/S1473-3099(18)30673-X

Yahyaoui-Azami H, Aboukhassib H, Bouslikhane M, Berrada J, Rami S, Reinhard M, Gagneux S, Feldmann J, Borrell S, Zinsstag J. Molecular characterization of bovine tuberculosis strains in two slaughterhouses in Morocco. BMC Vet Res. 2017;13:272. DOI: 10.1186/s12917-017-1165-6