Publications

Jovanovic A, Bright F. K, Sadeghi A, Wicki B, Caño Muñiz S. E, Giannini G. C, Toprak S, Sauteur L, Rodoni A, Wüst A, Lupien A, Borrell S, Grogono D. M, Wheeler N. E, Dehio P, Nemeth J, Pargger H, Thomson R, Bell S. C, Gagneux S, Bryant J. M, Peng T, Diacon A. H, Floto R. A, Abanto M, Boeck L. Large-scale testing of antimicrobial lethality at single-cell resolution predicts mycobacterial infection outcomes. Nat Microbiol. 2026(in press). DOI: 10.1038/s41564-025-02217-y

Arbués A, Schmidiger S, Reinhard M, Borrell S, Gagneux S, Portevin D. Soluble immune mediators orchestrate protective in vitro granulomatous responses across Mycobacterium tuberculosis complex lineages. Elife. 2025;13:RP99062. DOI: 10.7554/eLife.99062

Goig G.A, Loiseau C, Maghradze N, McHedlishvili K, Avaliani T, Brites D, Borrell S, Aspindzelashvili R, Avaliani Z, Kipiani M, Tukvadze N, Jugheli L, Gagneux S. Transmission as a key driver of resistance to the new tuberculosis drugs. N Engl J Med. 2025;392(1):97-99. DOI: 10.1056/NEJMc2404644

Goig G.A, Loiseau C, Maghradze N, McHedlishvili K, Avaliani T, Tsutsunava A, Brites D, Kalkan S, Borrell S, Aspindzelashvili R, Avaliani Z, Kipiani M, Tukvadze N, Jugheli L, Gagneux S. Clinical and bacterial determinants of unfavorable tuberculosis treatment outcomes: an observational study in Georgia. Genome Med. 2025;17:143. DOI: 10.1186/s13073-025-01555-0

Goig G.A, Windels E.M, Loiseau C, Stritt C, Biru L, Borrell S, Brites D, Gagneux S. Ecology, global diversity and evolutionary mechanisms in the Mycobacterium tuberculosis complex. Nat Rev Microbiol. 2025;23(9):602-614. DOI: 10.1038/s41579-025-01159-w

Maghradze N, Loiseau C, Goig G.A, Bablishvili N, Jugheli L, Borrell S, Tukvadze N, Kempker R.R, Avaliani Z, Gagneux S. Linking genetic and phenotypic bedaquiline resistance in Mycobacterium tuberculosis strains from Georgia. PLoS One. 2025;20(7):e0326794. DOI: 10.1371/journal.pone.0326794

March V.F.A, Maghradze N, McHedlishvili K, Avaliani T, Aspindzelashvili R, Avaliani Z, Kipiani M, Tukvadze N, Jugheli L, Bouaouina S, Doetsch A, Goig G.A, Gagneux S, Borrell S. Drug-induced differential culturability in diverse strains of Mycobacterium tuberculosis. Sci Rep. 2025;15:3588. DOI: 10.1038/s41598-024-85092-7

March V.F.A, Zwyer M, Loiseau C, Brites D, Goig G.A, Bouaouina S, Doetsch A, Reinhard M, Kalkan S, Gagneux S, Borrell S. Variability in intrinsic drug tolerance in Mycobacterium tuberculosis corresponds with phylogenetic lineage. Antimicrob Agents Chemother. 2025;69(12):e0099625. DOI: 10.1128/aac.00996-25

Rojas V.M.R, Zwyer M, Bouaouina S, Brites D, Borrell S, Gagneux S. Mycobacterium tuberculosis complex Lineage 1: A neglected cause of tuberculosis. PLoS Negl Trop Dis. 2025;19(10):e0013513. DOI: 10.1371/journal.pntd.0013513

Schmidiger S, McCaffrey E.F, Schmidt J.M, Hameed O.A, Mpina M, Tumbo A, Mfinanga E, Haraka F, Hiza H, Sasamalo M, Hella J, Walch M, Fellay J, Gagneux S, Reither K, Carballido J.M, Arbués A, Portevin D. Granulysin antimicrobial activity promotes dormancy in Mycobacterium tuberculosis. Eur J Immunol. 2025;55(8):e70004. DOI: 10.1002/eji.70004

Stritt C, Reitsma M, Marin A.M.G, Goig G, Dötsch A, Borrell S, Beisel C, Comas I, Brites D, Gagneux S. Gene conversion and duplication contribute to genetic variation in an outbreak of Mycobacterium tuberculosis. Microb Genom. 2025;11(5):001396. DOI: 10.1099/mgen.0.001396

Tutumlu T.K, Dollé C, Kusejko K, Gagneux S, Brugger S.D, Günthard H.F, Nemeth J. Mycobacteria beyond disease. Trends Microbiol. 2025;33(9):930-933. DOI: 10.1016/j.tim.2025.04.008

Windels E.M, Valenzuela Agüí C, de Jong B.C, Meehan C.J, Loiseau C, Goig G.A, Zwyer M, Borrell S, Brites D, Gagneux S, Stadler T. Onset of infectiousness explains differences in transmissibility across Mycobacterium tuberculosis lineages. Epidemics. 2025;51:100821. DOI: 10.1016/j.epidem.2025.100821

Xu Z.M, Zwyer M, Hiza H, Schmidiger S, Sasamalo M, Reinhard M, Doetsch A, Borrell S, Naret O, Rüeger S, Lawless D, Tang S, Isihaka F, Temba H, Maroa T, Naftari R, Beisel C, Hella J, Reither K, Brites D, Portevin D, Gagneux S, Fellay J. Genome-to-genome analysis reveals associations between human and mycobacterial genetic variation in tuberculosis patients from Tanzania. BMC Med Genomics. 2025;18:99. DOI: 10.1186/s12920-025-02164-x

Cirillo D, Anthony R, Gagneux S, Horsburgh C.R. Jr, Hasan R, Darboe S, Laniado-Laborin R, Probandari A, Tukvadze N, Arcêncio R.A, Bimba J.S, Brighenti S, Chesov D, Chiang C.Y, Kalmambetova G, Knight G, Konstantynovska O, Kruse A, Lange C, Mayanja-Kizza H, McBryde E, Min J, Sanchez-Montalva A, Sulis G, Tsogt B, van der Walt M, Yeboah-Manu D, Hauser J. A successful UN High-Level Meeting on antimicrobial resistance must build on the 2023 UN High-Level Meeting on tuberculosis. Lancet Glob Health. 2024;12(8):e1225-e1226. DOI: 10.1016/s2214-109x(24)00229-8

Conceição E.C, Loubser J, Guimarães Aeds, Sharma A, Rutaihwa L.K, Dippenaar A, Salvato R.S, de Paula Souza E.Guimarães R.J, da Silva Lourenço M.C, Barros W.A, Cardoso N.C, Warren R.M, Gagneux S, Grinsztejn B.G.J, Suffys P.N, Lima K.V.B. A genome-focused investigation reveals the emergence of a Mycobacterium tuberculosis strain related to multidrug-resistant tuberculosis in the Amazon region of Brazil. Microorganisms. 2024;12(9):1817. DOI: 10.3390/microorganisms12091817

Esteves L.S, Gomes L.L, Brites D, Fandinho F.C.O, Bhering M, Pereira M.A.D.S, Conceição E.C, Salvato R, Costa B.P.D, Medeiros R.F.D.M, Caldas P.C.D.S, Redner P, Dalcolmo M.P, Eldholm V, Gagneux S, Rossetti M.L, Kritski A.L, Suffys P.N. Genetic characterization and population structure of drug-resistant Mycobacterium tuberculosis isolated from Brazilian patients using whole-genome sequencing. Antibiotics (Basel). 2024;13(6):496. DOI: 10.3390/antibiotics13060496

Hailu E, Cantillon D, Madrazo C, Rose G, Wheeler P.R, Golby P, Adnew B, Gagneux S, Aseffa A, Gordon S.V, Comas I, Young D.B, Waddell S.J, Larrouy-Maumus G, Berg S. Corrigendum: Lack of methoxy-mycolates characterizes the geographically restricted lineage 7 of Mycobacterium tuberculosis complex. Microb Genom. 2024;10(3). DOI: 10.1099/mgen.0.001226

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;14:9287. DOI: 10.1038/s41598-024-60001-0

Tschan Y, Sasamalo M, Hiza H, Fellay J, Gagneux S, Reither K, Hella J, Portevin D. Diagnostic accuracy of a sequence-specific Mtb-DNA hybridization assay in urine: a case-control study including subclinical TB cases. Microbiol Spectr. 2024;12(6):e0042624. DOI: 10.1128/spectrum.00426-24

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

Derendinger B, Dippenaar A, de Vos M, Huo S, Alberts R, Tadokera R, Limberis J, Sirgel F, Dolby T, Spies C, Reuter A, Folkerts M, Allender C, Lemmer D, Van Rie A, Gagneux S, Rigouts L, Te Riele J, Dheda K, Engelthaler D.M, Warren R, Metcalfe J, Cox H, Theron G. Bedaquiline resistance in patients with drug-resistant tuberculosis in Cape Town, South Africa: a retrospective longitudinal cohort study. Lancet Microbe. 2023;4(12):e972-e982. DOI: 10.1016/s2666-5247(23)00172-6

Domínguez J, Boeree M.J, Cambau E, Chesov D, Conradie F, Cox V, Dheda K, Dudnyk A, Farhat M.R, Gagneux S, Grobusch M.P, Gröschel M.I, Guglielmetti L, Kontsevaya I, Lange B, van Leth F, Lienhardt C, Mandalakas A.M, Maurer F.P, Merker M, Miotto P, Molina-Moya B, Morel F, Niemann S, Veziris N, Whitelaw A, Horsburgh C.R. Jr, Lange C, TBnet and RESIST-TB networks. Clinical implications of molecular drug resistance testing for Mycobacterium tuberculosis: a 2023 TBnet/RESIST-TB consensus statement. Lancet Infect Dis. 2023;23(4):e122-e137. DOI: 10.1016/S1473-3099(22)00875-1

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

Hailu E, Cantillon D, Madrazo C, Rose G, Wheeler P.R, Golby P, Adnew B, Gagneux S, Aseffa A, Gordon S.V, Comas I, Young D.B, Waddell S.J, Larrouy-Maumus G, Berg S. Lack of methoxy-mycolates characterizes the geographically restricted lineage 7 of Mycobacterium tuberculosis complex. Microb Genom. 2023;9(5):001011. DOI: 10.1099/mgen.0.001011

Hall M.B, Rabodoarivelo M.S, Koch A, Dippenaar A, George S, Grobbelaar M, Warren R, Walker T.M, Cox H, Gagneux S, Crook D, Peto T, Rakotosamimanana N, Grandjean Lapierre S, Iqbal Z. Evaluation of nanopore sequencing for Mycobacterium tuberculosis drug susceptibility testing and outbreak investigation: a genomic analysis. Lancet Microbe. 2023;4(2):e84-e92. DOI: 10.1016/S2666-5247(22)00301-9

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

Mäser P, Bernhard S, Brun R, Burri C, Gagneux S, Hetzel M.W, Kaiser M, Lengeler C, Pluschke G, Reus E, Rottmann M, Utzinger J, Warryn L, Wittlin S, Keiser J. Key contributions by the Swiss Tropical and Public Health Institute towards new and better drugs for tropical diseases. Chimia (Aarau). 2023;77(9):593-606. DOI: 10.2533/chimia.2023.593

Osei-Wusu S, Tetteh J.K.A, Musah A.B, Ntiamoah D.O, Arthur N, Adjei A, Arbues A, Ofori E.A, Mensah K.A, Galevo S.E.A, Frempong A.F, Asare P, Asante-Poku A, Otchere I.D, Kusi K.A, Lenz T.L, Gagneux S, Portevin D, Yeboah-Manu D. Macrophage susceptibility to infection by Ghanaian Mycobacterium tuberculosis complex lineages 4 and 5 varies with self-reported ethnicity. Front Cell Infect Microbiol. 2023;13:1163993. DOI: 10.3389/fcimb.2023.1163993

Otchere I.D, Morgan P.A, Asare P, Osei-Wusu S, Aboagye S.Y, Yirenkyi S.O, Musah A.B, Danso E.K, Tetteh-Ocloo G, Afum T, Asante-Poku A, Laryea C, Poku Y.A, Bonsu F, Gagneux S, Yeboah-Manu D. Analysis of drug resistance among difficult-to-treat tuberculosis patients in Ghana identifies several pre-XDR TB cases. Front Microbiol. 2023;13:1069292. DOI: 10.3389/fmicb.2022.1069292

Stritt C, Gagneux S. How do monomorphic bacteria evolve? The Mycobacterium tuberculosis complex and the awkward population genetics of extreme clonality. Peer Community J. 2023;3:e92. DOI: 10.24072/pcjournal.322

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

Hiza H, Hella J, Arbués A, Sasamalo M, Misana V, Fellay J, Gagneux S, Reither K, Portevin D. CD38 expression by antigen-specific CD4 t cells is significantly restored 5 months after treatment initiation independently of sputum bacterial load at the time of tuberculosis diagnosis. Front Med. 2022;9:821776. DOI: 10.3389/fmed.2022.821776

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

Van Rie A, Walker T, de Jong B, Rupasinghe P, Riviere E, Dartois V, Sonnenkalb L, Machado D, Gagneux S, Supply P, Dreyer V, Niemann S, Goig G, Meehan C, Tagliani E, Cirillo D.M. Balancing access to BPaLM regimens and risk of resistance. Lancet Infect Dis. 2022;S1473-3099(22):00543-6. DOI: 10.1016/S1473-3099(22)00543-6

Vera-Cabrera L, Ramos-Cavazos C.J, Youssef N.A, Pearce C.M, Molina-Torres C.A, Avalos-Ramirez R, Gagneux S, Ocampo-Candiani J, Gonzalez-Juarrero M, Mayorga-Rodriguez J.A, Mayorga-Garibaldi L, Spencer J.S, Jackson M, Avanzi C. Mycobacterium leprae infection in a wild nine-banded armadillo, Nuevo León, Mexico. Emerg Infect Dis. 2022;28(3):747-749. DOI: 10.3201/eid2803.211295

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

Alagna R, Cabibbe A.M, Miotto P, Saluzzo F, Köser C.U, Niemann S, Gagneux S, Rodrigues C, Rancoita P.V.M, Cirillo D.M. Is the new WHO definition of extensively drug-resistant tuberculosis easy to apply in practice?. Eur Respir J. 2021;58:2100959. DOI: 10.1183/13993003.00959-2021

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

Guimarães A.E.D.S, Sharma A, Furlaneto I.P, Rutaihwa L, Cardoso J.F, da Conceição M.L, Spinassé L.B, Machado E, Lopes M.L, Duarte R.S, Gagneux S, Suffys P.N, Lima K.V.B, Conceição E.C. Evaluation of drug susceptibility profile of Mycobacterium tuberculosis lineage 1 from Brazil based on whole genome sequencing and phenotypic methods. Mem Inst Oswaldo Cruz. 2021;115:e200520. DOI: 10.1590/0074-02760200520

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

Haraka F, Kakolwa M, Schumacher S.G, Nathavitharana R.R, Denkinger C.M, Gagneux S, Reither K, Ross A. Impact of the diagnostic test Xpert MTB/RIF on patient outcomes for tuberculosis (Review). Cochrane Database Syst Rev. 2021;2021(4):CD012972. DOI: 10.1002/14651858.CD012972.pub2

Hiza H, Hella J, Arbués A, Magani B, Sasamalo M, Gagneux S, Reither K, Portevin D. Case-control diagnostic accuracy study of a non-sputum CD38-based TAM-TB test from a single milliliter of blood. Sci Rep. 2021;11(1):13190. DOI: 10.1101/2021.03.10.21253246

Hockings K.J, Mubemba B, Avanzi C, Pleh K, Dux A, Bersacola E, Bessa J, Ramon M, Metzger S, Patrono L.V, Jaffe J.E, Benjak A, Bonneaud C, Busso P, Couacy-Hymann E, Gado M, Gagneux S, Johnson R.C, Kodio M, Lynton-Jenkins J, Morozova I, Mätz-Rensing K, Regalla A, Said A.R, Schuenemann V.J, Sow S.O, Spencer J.S, Ulrich M, Zoubi H, Cole S.T, Wittig R.M, Calvignac-Spencer S, Leendertz F.H. Leprosy in wild chimpanzees. Nature. 2021;598(7882):652-656. DOI: 10.1038/s41586-021-03968-4

Ley S.D, Pillay S, Streicher E.M, van der Heijden Y.F, Sirgel F, Derendinger B, de Kock M, Gagneux S, Warren R.M, Theron G, de Vos M. Melting the eis: non-detection of kanamycin resistance markers by routine diagnostic tests and identification of new eis-promoter variants. Antimicrob Agents Chemother. 2021;65(7):e0250220. DOI: 10.1128/AAC.02502-20

Menardo F, Gagneux S, Freund F. Multiple merger genealogies in outbreaks of Mycobacterium tuberculosis. Mol Biol Evol. 2021;38(1):290-306. DOI: 10.1093/molbev/msaa179

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

Minja L.T, Hella J, Mbwambo J, Nyandindi C, Omary U.S, Levira F, Mpagama S, Shimwela M, Okuma J, Gagneux S, Bruce R.D, Reither K. High burden of tuberculosis infection and disease among people receiving medication-assisted treatment for substance use disorder in Tanzania. PLoS One. 2021;16(4):e0250038. DOI: 10.1371/journal.pone.0250038

Moreno-Molina M, Shubladze N, Khurtsilava I, Avaliani Z, Bablishvili N, Torres-Puente M, Villamayor L, Gabrielian A, Rosenthal A, Vilaplana C, Gagneux S, Kempker R.R, Vashakidze S, Comas I. Genomic analyses of Mycobacterium tuberculosis from human lung resections reveal a high frequency of polyclonal infections. Nat Commun. 2021;12:2716. DOI: 10.1038/s41467-021-22705-z

Osei-Wusu S, Otchere I.D, Morgan P, Musah A.B, Siam I.M, Asandem D, Afum T, Asare P, Asante-Poku A, Kusi K.A, Gagneux S, Yeboah-Manu D. Genotypic and phenotypic diversity of Mycobacterium tuberculosis complex genotypes prevalent in West Africa. PLoS One. 2021;16(8):e0255433. DOI: 10.1371/journal.pone.0255433

Pečerska J, Kuhnert D, Meehan C.J, Coscolla M, de Jong B.C, Gagneux S, Stadler T. Quantifying transmission fitness costs of multi-drug resistant tuberculosis. Epidemics. 2021;36:100471. DOI: 10.1016/j.epidem.2021.100471

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

Sanoussi C.N, Coscolla M, Ofori-Anyinam B, Otchere I.D, Antonio M, Niemann S, Parkhill J, Harris S, Yeboah-Manu D, Gagneux S, Rigouts L, Affolabi D, de Jong B.C, Meehan C.J. Mycobacterium tuberculosis complex lineage 5 exhibits high levels of within-lineage genomic diversity and differing gene content compared to the type strain H37Rv. Microb Genom. 2021;7(7):000437. DOI: 10.1099/mgen.0.000437

Ticlla M.R, Hella J, Hiza H, Sasamalo M, Mhimbira F, Rutaihwa L.K, Droz S, Schaller S, Reither K, Hilty M, Comas I, Beisel C, Schmid C.D, Fenner L, Gagneux S. The sputum microbiome in pulmonary tuberculosis and its association with disease manifestations: a cross-sectional study. Front Microbiol. 2021;12:633396. DOI: 10.3389/fmicb.2021.633396

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

Ezewudo M, Borens A, Chiner-Oms A, Miotto P, Chindelevitch L, Starks A.M, Hanna D, Liwski R, Zignol M, Gilpin C, Niemann S, Kohl T.A, Warren R.M, Crook D, Gagneux S, Hoffner S, Rodrigues C, Comas I, Engelthaler D.M, Alland D, Rigouts L, Lange C, Dheda K, Hasan R, McNerney R, Cirillo D.M, Schito M, Rodwell T.C, Posey J. Author correction: Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase. Sci Rep. 2020;10(1):3531. DOI: 10.1038/s41598-020-58955-y

Haraka F, Schumacher S.G, Ross A, Mantsoki A, Gagneux S, Reither K, Denkinger C.M. Effect of history of tuberculosis on specificity of Xpert MTB/RIF. Eur Respir J. 2020;56(3):2000343. DOI: 10.1183/13993003.00343-2020

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

McHenry M.L, Bartlett J, Igo R.P. Jr, Wampande E.M, Benchek P, Mayanja-Kizza H, Fluegge K, Hall N.B, Gagneux S, Tishkoff S.A, Wejse C, Sirugo G, Boom W.H, Joloba M, Williams S.M, Stein C.M. Interaction between host genes and Mycobacterium tuberculosis lineage can affect tuberculosis severity: evidence for coevolution?. PLoS Genet. 2020;16(4):e1008728. DOI: 10.1371/journal.pgen.1008728

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

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

Sousa J, Cá B, Maceiras A.R, Simões-Costa L, Fonseca K.L, Fernandes A.I, Ramos A, Carvalho T, Barros L, Magalhães C, Chiner-Oms A, Machado H, Veiga M.I, Singh A, Pereira R, Amorim A, Vieira J, Vieira C.P, Bhatt A, Rodrigues F, Rodrigues P.N.S, Gagneux S, Castro A.G, Guimarães J.T, Bastos H.N, Osorio N.S, Comas I, Saraiva M. Mycobacterium tuberculosis associated with severe tuberculosis evades cytosolic surveillance systems and modulates IL-1beta production. Nat Commun. 2020;11:1949. DOI: 10.1038/s41467-020-15832-6

Asante-Poku A, Asare P, Baddoo N.A, Forson A, Klevor P, Otchere I.D, Aboagye S.Y, Osei-Wusu S, Danso E.K, Koram K, Gagneux S, Yeboah-Manu D. TB-diabetes co-morbidity in Ghana: the importance of Mycobacterium africanum infection. PLoS One. 2019;14(2):e0211822. DOI: 10.1371/journal.pone.0211822

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

Chiner-Oms A, Berney M, Boinett C, Gonzalez-Candelas F, Young D.B, Gagneux S, Jacobs W.R. Jr, Parkhill J, Cortes T, Comas I. Genome-wide mutational biases fuel transcriptional diversity in the Mycobacterium tuberculosis complex. Nat Commun. 2019;10(1):3994. DOI: 10.1038/s41467-019-11948-6

Chiner-Oms A, Sánchez-Busó L, Corander J, Gagneux S, Harris S.R, Young D, González-Candelas F, Comas I. Genomic determinants of speciation and spread of the Mycobacterium tuberculosis complex. Sci Adv. 2019;5(6):eaaw3307. DOI: 10.1126/sciadv.aaw3307

Conceicao E.C, Refregier G, Gomes H.M, Olessa-Daragon X, Coll F, Ratovonirina N.H, Rasolofo-Razanamparany V, Lopes M.L, van Soolingen D, Rutaihwa L, Gagneux S, Bollela V.R, Suffys P.N, Duarte R.S, Lima K.V.B, Sola C.N. Mycobacterium tuberculosis lineage 1 genetic diversity in Para, Brazil, suggests common ancestry with east-African isolates potentially linked to historical slave trade. Infect Genet Evol. 2019;73:337-341. DOI: 10.1016/j.meegid.2019.06.001

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

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