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

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

Asante-Poku A, Otchere I.D, Osei-Wusu S, Sarpong E, Baddoo A, Forson A, Laryea C, Borrell S, Bonsu F, Hattendorf J, Ahorlu C, Koram K.A, Gagneux S, Yeboah-Manu D. Molecular epidemiology of Mycobacterium africanum in Ghana. BMC Infect Dis. 2016;16:385. DOI: 10.1186/s12879-016-1725-6

Stucki D, Ballif M, Egger M, Furrer H, Altpeter E, Battegay M, Droz S, Bruderer T, Coscolla M, Borrell S, Zurcher K, Janssens J.P, Calmy A, Mazza Stalder J, Jaton K, Rieder H.L, Pfyffer G.E, Siegrist H.H, Hoffmann M, Fehr J, Dolina M, Frei R, Schrenzel J, Bottger E.C, Gagneux S, Fenner L, Swiss H.I.V, Molecular Epidemiology of Tuberculosis Study Groups. Standard genotyping overestimates transmission of Mycobacterium tuberculosis among immigrants in a low incidence country. J Clin Microbiol. 2016;54(7):1862-1870. DOI: 10.1128/JCM.00126-16

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

Asante-Poku A, Yeboah-Manu D, Otchere I.D, Aboagye S.Y, Stucki D, Hattendorf J, Borrell S, Feldmann J, Danso E, Gagneux S. Mycobacterium africanum is associated with patient ethnicity in Ghana. PLoS Negl Trop Dis. 2015;9(1):e3370. DOI: 10.1371/journal.pntd.0003370

Bloemberg G.V, Keller P.M, Stucki D, Trauner A, Borrell S, Latshang T, Coscolla M, Rothe T, Hömke R, Ritter C, Feldmann J, Schulthess B, Gagneux S, Böttger E.C. Acquired resistance to bedaquiline and delamanid in therapy for tuberculosis. N Engl J Med. 2015;373(20):1986-1988. DOI: 10.1056/NEJMc1505196

Borrell S, Feldman J, Castro R, Trauner A, Gagneux S. Impact of the M. tuberculosis genetic background on the acquisition of drug resistance-conferring mutations. Trop Med Int Health, 2015;20(Suppl. 1):25. Abstracts of the 9th European Congress on Tropical Medicine and International Health, 6-10 September 2015, Basel, Switzerland

Rutaihwa L, Sasamalo M, Hella J, Borrell S, Feldmann J, Coscolla M, Fenner L, Gagneux S. Global genomic diversity and clinical consequences of Mycobacterium tuberculosis in a high-burden setting. Trop Med Int Health, 2015;20(Suppl. 1):190. Abstracts of the 9th European Congress on Tropical Medicine and International Health, 6-10 September 2015, Basel, Switzerland

Stucki D, Ballif M, Bodmer T, Coscolla M, Maurer A.M, Droz S, Butz C, Borrell S, Langle C, Feldmann J, Furrer H, Mordasini C, Helbling P, Rieder H.L, Egger M, Gagneux S, Fenner L. Tracking a tuberculosis outbreak over 21 years: strain-specific single nucleotide polymorphism-typing combined with targeted whole genome sequencing. J Infect Dis. 2015;211(8):1306-1016. DOI: 10.1093/infdis/jiu601

Asante-Poku A, Nyaho M.S, Borrell S, Comas I, Gagneux S, Yeboah-Manu D. Evaluation of customised lineage-specific sets of MIRU-VNTR loci for genotyping Mycobacterium tuberculosis complex isolates in Ghana. PLoS One. 2014;9(3):e92675. DOI: 10.1371/journal.pone.0092675

Merker M, Feuerriegel S, Cox H, Borrell S, Gagneux S, Rüsch-Gerdes S, Kohl T.A, Niemann S. Understanding Mycobacterium tuberculosis evolution in times of antibiotic treatment - a whole genome approach. Int J Mycobacteriol, 2014;4(Suppl. 1):2. DOI: 10.1016/j.ijmyco.2014.08.008

Steiner A, Stucki D, Coscolla M, Borrell S, Gagneux S. KvarQ: targeted and direct variant calling from fastq reads of bacterial genomes. BMC Genomics. 2014;15:881. DOI: 10.1186/1471-2164-15-881

Trauner A, Borrell S, Reither K, Gagneux S. Evolution of drug resistance in tuberculosis: recent progress and implications for diagnosis and therapy. Drugs. 2014;74(10):1063-1072. DOI: 10.1007/s40265-014-0248-y

Borrell S, Teo Y, Giardina F, Streicher E.M, Klopper M, Feldmann J, Müller B, Victor T.C, Gagneux S. Epistasis between antibiotic resistance mutations drives the evolution of extensively drug-resistant tuberculosis. Evol Med Public Health. 2013(1):65-74. DOI: 10.1093/emph/eot03

Comas I, Coscolla M, Luo T, Borrell S, Holt K.E, Kato-Maeda M, Parkhill J, Malla B, Berg S, Thwaites G, Yeboah-Manu D, Bothamley G, Mei J, Wei L, Bentley S, Harris S.R, Niemann S, Diel R, Aseffa A, Gao Q, Young D, Gagneux S. Out-of-Africa migration and neolithic coexpansion of Mycobacterium tuberculosis with modern humans. Nat Genet. 2013;45(10):1176-1182. DOI: 10.1038/ng.2744

de Vos M, Müller B, Borrell S, Black P, van Helden P, Warren R, Gagneux S, Victor T. Putative compensatory mutations in the rpoC gene of rifampicin-resistant Mycobacterium tuberculosis are associated with ongoing transmission. Antimicrob Agents Chemother. 2013;57(2):827-832. DOI: 10.1128/AAC.01541-12

Fenner L, Egger M, Bodmer T, Furrer H, Ballif M, Battegay M, Helbling P, Fehr J, Gsponer T, Rieder H.L, Zwahlen M, Hoffmann M, Bernasconi E, Cavassini M, Calmy A, Dolina M, Frei R, Janssens J.P, Borrell S, Stucki D, Schrenzel J, Böttger E.C, Gagneux S, Swiss HIV Cohort and Molecular Epidemiology of Tuberculosis Study Groups. HIV infection disrupts the sympatric host-pathogen relationship in human tuberculosis. PLoS Genet. 2013;9(3):e1003318. DOI: 10.1371/journal.pgen.1003318

Müller B, Borrell S, Rose G, Gagneux S. The heterogeneous evolution of multidrug-resistant Mycobacterium tuberculosis. Trends Genet. 2013;29(3):160-169. DOI: 10.1016/j.tig.2012.11.005

Ballif M, Harino P, Ley S, Carter R, Coulter C, Niemann S, Borrell S, Fenner L, Siba P, Phuanukoonnon S, Gagneux S, Beck H.P. Genetic diversity of Mycobacterium tuberculosis in Madang, Papua New Guinea. Int J Tuberc Lung Dis. 2012;16(8):1100-1107. DOI: 10.5588/ijtld.11.0779

Ballif M, Harino P, Ley S, Coscolla M, Niemann S, Carter R, Coulter C, Borrell S, Siba P, Phuanukoonnon S, Gagneux S, Beck H.P. Drug resistance-conferring mutations in Mycobacterium tuberculosis from Madang, Papua New Guinea. BMC Microbiol. 2012;12:191. DOI: 10.1186/1471-2180-12-191

Bratschi M.W, Njih Tabah E, Bolz M, Stucki D, Borrell S, Gagneux S, Noumen-Djeunga B, Junghanss T, Um Boock A, Pluschke G. A case of cutaneous tuberculosis in a Buruli ulcer-endemic area. PLoS Negl Trop Dis. 2012;6(8):e1751. DOI: 10.1371/journal.pntd.0001751

Comas I, Borrell S, Roetzer A, Rose G, Malla B, Kato-Maeda M, Galagan J, Niemann S, Gagneux S. Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes. Nat Genet. 2012;44(1):106-110. DOI: 10.1038/ng.1038

Fenner L, Egger M, Bodmer T, Altpeter E, Zwahlen M, Jaton K, Pfyffer G.E, Borrell S, Dubuis O, Bruderer T, Siegrist H.H, Furrer H, Calmy A, Fehr J, Stalder J.M, Ninet B, Bottger E.C, Gagneux S. Effect of mutation and genetic background on drug resistance in Mycobacterium tuberculosis. Antimicrob Agents Chemother. 2012;56(6):3047-3053. DOI: 10.1128/AAC.06460-11

Malla B, Stucki D, Borrell S, Feldmann J, Maharjan B, Shrestha B, Fenner L, Gagneux S. First insights into the phylogenetic diversity of Mycobacterium tuberculosis in Nepal. PLoS One. 2012;7(12):e52297. DOI: 10.1371/journal.pone.0052297

Stucki D, Malla B, Hostettler S, Huna T, Feldmann J, Yeboah-Manu D, Borrell S, Fenner L, Comas I, Coscolla M, Gagneux S. Two new rapid SNP-typing methods for classifying Mycobacterium tuberculosis complex into the main phylogenetic lineages. PLoS One. 2012;7(7):e41253. DOI: 10.1371/journal.pone.0041253

Borrell S, Gagneux S. Strain diversity, epistasis and the evolution of drug resistance in Mycobacterium tuberculosis. Clin Microbiol Infect. 2011;17(6):815-820. DOI: 10.1111/j.1469-0691.2011.03556.x

Borrell S. Advances in molecular epidemiology: tracking M. Tuberculosis strains. Trop Med Int Health, 2011;16(Suppl. 1):50-50

Fenner L, Gagneux S, Kabuya G, Stucki D, Kabuayi J.P, Borrell S, Frei R, Burri C, Kalemwa D, Egger M, Okiata J.P. Mycobacterium tuberculosis genetic diversity and drug resistance conferring mutations in the Democratic Republic of the Congo. East Afr Med J. 2011;88(12):409-415

Fenner L, Malla B, Ninet B, Dubuis O, Stucki D, Borrell S, Huna T, Bodmer T, Egger M, Gagneux S. "Pseudo-Beijing": evidence for convergent evolution in the direct repeat region of Mycobacterium tuberculosis. PLoS One. 2011;6(9):e24737. DOI: 10.1371/journal.pone.0024737

Rey-Jurado E, Tudo G, Borrell S, Alcaide F, Coll P, Espanol M, Martin-Casabona N, Mick V, Montemayor M, Moure R, Salvado M, Vicente E, Gonzalez-Martin J. Impaired fitness of Mycobacterium tuberculosis resistant isolates in a cell culture model of murine macrophages. J Antimicrob Chemother. 2011;66(10):2277-2280. DOI: 10.1093/jac/dkr288

Thorne N, Borrell S, Evans J, Magee J, García de Viedma D, Bishop C, Gonzalez-Martin J, Gharbia S, Arnold C. IS6110-based global phylogeny of Mycobacterium tuberculosis. Infect Genet Evol. 2011;11(1):132-138. DOI: 10.1016/j.meegid.2010.09.011

Borrell S, Gagneux S. Infectiousness, reproductive fitness and evolution of drug-resistant Mycobacterium tuberculosis. Int J Tuberc Lung Dis. 2009;13(12):1456-1466