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

2021
Journal Article
PubMed (33667696)
Link

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

2021
Journal Article
PubMed (33555243)
Link

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

2021
Journal Article
PubMed (34766068)
Link

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(in press). DOI: 10.1038/s41591-021-01358-x

2021
Journal Item
PubMed (34031604)

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(in press). DOI: 10.1038/s41591-021-01417-3

2021
Journal Item
PubMed (34075249)

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

2021
Journal Article
PubMed (33732436)
Link

Salaam-Dreyer Z, Streicher E.M, Sirgel F.A, Menardo F, Borrell S, Reinhard M, Doetsch 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(in press). DOI: 10.1128/AAC.00364-21

2021
Journal Article
PubMed (34460307)

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(in press). DOI: 10.1128/AAC.00504-21

2021
Journal Article
PubMed (34228548)
Link

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

2021
Journal Article
Link

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

2020
Journal Article
PubMed (32509791)
Link

Castro R.A.D, Borrell S, Gagneux S. The within-host evolution of antimicrobial resistance in Mycobacterium tuberculosis. FEMS Microbiol Rev. 2020(in press). DOI: 10.1093/femsre/fuaa071

2020
Journal Article
PubMed (33320947)

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

2020
Journal Article
PubMed (31532481)
Link

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

2020
Journal Article
PubMed (32718966)
Link

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

2020
Journal Article
PubMed (32229570)

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

2020
Journal Article
PubMed (32868333)

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

2019
Journal Article
PubMed (30908506)
Link

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

2019
Journal Article
PubMed (30718257)
Link

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

2019
Journal Article
PubMed (31626647)
Link

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

2019
Journal Article
PubMed (31083647)
Link

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

2019
Journal Article
Link

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

2019
Journal Article
PubMed (30978186)
Link

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

2019
Journal Article
PubMed (30671031)
Link

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

2019
Journal Article
PubMed (30744962)

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

2018
Journal Article
PubMed (29879521)
Link

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

2018
Journal Article
PubMed (30538680)
Link

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(1):164. DOI: 10.1186/s12859-018-2164-8

2018
Journal Article
PubMed (29716518)
Link

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

2018
Journal Article
PubMed (30373719)
Link

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

2018
Journal Article
PubMed (30050166)
Link

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

2018
Journal Article
PubMed (29467300)

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

2017
Book Section
PubMed (29116640)

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

2017
Journal Article
PubMed (28369307)

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

2017
Journal Article
PubMed (28841870)
Link

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

2016
Journal Article
PubMed (27506391)
Link

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

2016
Journal Article
PubMed (27194683)

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

2016
Journal Article
PubMed (27798628)

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

2015
Journal Article
PubMed (25569290)
Link

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

2015
Journal Article
PubMed (26559594)

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

2015
Conference Paper

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

2015
Conference Paper

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

2015
Journal Article
PubMed (25362193)

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

2014
Journal Article
PubMed (24667333)
Link

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

2014
Conference Paper

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

2014
Journal Article
PubMed (25297886)
Link

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

2014
Journal Article
PubMed (24962424)

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

2013
Journal Article

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

2013
Journal Article
PubMed (23995134)

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

2013
Journal Article
PubMed (23208709)

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

2013
Journal Article
PubMed (23505379)
Link

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

2013
Journal Article
PubMed (23245857)

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

2012
Journal Article
PubMed (22710686)

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

2012
Journal Article
PubMed (22943573)
Link

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

2012
Journal Article
PubMed (22953005)
Link

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

2012
Journal Article
PubMed (22179134)

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

2012
Journal Article
PubMed (22470121)

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

2012
Journal Article
PubMed (23300635)
Link

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

2012
Journal Article
PubMed (22911768)
Link

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

2011
Journal Article
PubMed (21682802)

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

2011
Conference Paper

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

2011
Journal Article
PubMed (21935448)
Link

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

2011
Journal Article
PubMed (21791442)

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

2011
Journal Article
PubMed (20920607)

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

2009
Journal Article
PubMed (19919762)