Publications

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