Publications

Hiza H, Zwyer M, Hella J, Arbués A, Sasamalo M, Borrell S, Xu Z.M, Ross A, Brites D, Fellay J, Reither K, Gagneux S, Portevin D. Bacterial diversity dominates variable macrophage responses of tuberculosis patients in Tanzania. Sci Rep. 2024;14(1):9287. DOI: 10.1038/s41598-024-60001-0

Windels E.M, Wampande E.M, Joloba M.L, Boom W.H, Goig G.A, Cox H, Hella J, Borrell S, Gagneux S, Brites D, Stadler T. HIV co-infection is associated with reduced Mycobacterium tuberculosis transmissibility in sub-Saharan Africa. PLoS Pathog. 2024;20(5):e1011675. DOI: 10.1371/journal.ppat.1011675

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

Maghradze N, Jugheli L, Borrell S, Tukvadze N, Kempker R.R, Blumberg H.M, Gagneux S. Developing customized stepwise MIRU-VNTR typing for tuberculosis surveillance in Georgia. PLoS One. 2022;17(3):e0264472. DOI: 10.1371/journal.pone.0264472

Merker M, Rasigade J.P, Barbier M, Cox H, Feuerriegel S, Kohl T.A, Shitikov E, Klaos K, Gaudin C, Antoine R, Diel R, Borrell S, Gagneux S, Nikolayevskyy V, Andres S, Crudu V, Supply P, Niemann S, Wirth T. Transcontinental spread and evolution of Mycobacterium tuberculosis W148 European/Russian clade toward extensively drug resistant tuberculosis. Nat Commun. 2022;13:5105. DOI: 10.1038/s41467-022-32455-1

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

Castro R.A.D, Borrell S, Gagneux S. The within-host evolution of antimicrobial resistance in Mycobacterium tuberculosis. FEMS Microbiol Rev. 2021;45(4):fuaa071. DOI: 10.1093/femsre/fuaa071

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

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

Trauner A, Banaei-Esfahani A, Gygli S.M, Warmer P, Feldmann J, Zampieri M, Borrell S, Collins B.C, Beisel C, Aebersold R, Gagneux S. Expression dysregulation as a mediator of fitness costs in antibiotic resistance. Antimicrob Agents Chemother. 2021;65(9):e0050421. DOI: 10.1128/AAC.00504-21

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

Oyas O, Borrell S, Trauner A, Zimmermann M, Feldmann J, Liphardt T, Gagneux S, Stelling J, Sauer U, Zampieri M. Model-based integration of genomics and metabolomics reveals SNP functionality in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A. 2020;117(15):8494-8502. DOI: 10.1073/pnas.1915551117

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

Maghradze N, Jugheli L, Borrell S, Tukvadze N, Aspindzelashvili R, Avaliani Z, Reither K, Gagneux S. Classifying recurrent Mycobacterium tuberculosis cases in Georgia using MIRU-VNTR typing. PLoS One. 2019;14(10):e0223610. DOI: 10.1371/journal.pone.0223610

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

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

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

Asare P, Asante-Poku A, Ahu Prah D, Borrell S, Osei-Wusu S, Otchere I.D, Forson A, Adjapong G, Koram K.A, Gagneux S, Yeboah-Manu D. Reduced transmission of Mycobacterium africanum compared to Mycobacterium tuberculosis in urban West Africa. Int J Infect Dis. 2018;73:30-42. DOI: 10.1016/j.ijid.2018.05.014

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

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. Compensatory evolution drives multidrug-resistant tuberculosis in Central Asia. eLife. 2018;7:e38200. DOI: 10.7554/eLife.38200

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

Zampieri M, Szappanos B, Buchieri M.V, Trauner A, Piazza I, Picotti P, Gagneux S, Borrell S, Gicquel B, Lelievre J, Papp B, Sauer U. High-throughput metabolomic analysis predicts mode of action of uncharacterized antimicrobial compounds. Sci Transl Med. 2018;10(429):eaal3973. DOI: 10.1126/scitranslmed.aal3973

Borrell S, Trauner A. Strain diversity and the evolution of antibiotic resistance. In: Gagneux S, ed. Advances in Experimental Medicine and Biology. 1019, 263-279. Cham: Springer, 2017. DOI: 10.1007/978-3-319-64371-7_14

Gygli S.M, Borrell S, Trauner A, Gagneux S. Antimicrobial resistance in Mycobacterium tuberculosis: mechanistic and evolutionary perspectives. FEMS Microbiol Rev. 2017;41(3):354-373. DOI: 10.1093/femsre/fux011