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S. Gagneux · SciRah

Researcher profile · Semantic Scholar

S. Gagneux

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S. Gagneux — researcher profile on SciRah

h-index: 80
Works: 329
Citations: 25K

Most-cited papers

A sister lineage of the Mycobacterium tuberculosis complex discovered in the African Great Lakes region
J. Ngabonziza, C. Loiseau, M. Marceau, A. Jouet +21 more
2020Nature Communications182 citations Open access
Semantic Scholar
Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history
Mireia Coscollá, S. Gagneux, F. Menardo, C. Loiseau +25 more
2020bioRxiv170 citations Open access
Semantic Scholar
Mycobacterium tuberculosis associated with severe tuberculosis evades cytosolic surveillance systems and modulates IL-1β production
J. Sousa, Baltazar Cá, A. R. Maceiras, Luísa Simões-Costa +24 more
2020Nature Communications78 citations Open access
Semantic Scholar
Bedaquiline resistance in patients with drug-resistant tuberculosis in Cape Town, South Africa: a retrospective longitudinal cohort study
B. Derendinger, A. Dippenaar, M. de Vos, S. Huo +20 more
2023The Lancet Microbe77 citations Open access
Semantic Scholar
Evaluation of Nanopore sequencing for Mycobacterium tuberculosis drug susceptibility testing and outbreak investigation: a genomic analysis
M. Hall, M. Rabodoarivelo, A. Koch, A. Dippenaar +11 more
2022The Lancet Microbe75 citations Open access
Semantic Scholar
Clinical implications of molecular drug resistance testing for Mycobacterium tuberculosis: a 2023 TBnet/RESIST-TB consensus statement
J. Domínguez, M. Boeree, E. Cambau, D. Chesov +24 more
2023Lancet. Infectious Diseases (Print)71 citations Open access
Semantic Scholar
Ecology, global diversity and evolutionary mechanisms in the Mycobacterium tuberculosis complex
G. Goig, E. Windels, C. Loiseau, Christoph Stritt +4 more
2025Nature Reviews Microbiology67 citations
Semantic Scholar
Prisons as ecological drivers of fitness-compensated multidrug-resistant Mycobacterium tuberculosis
Sebastian M. Gygli, C. Loiseau, L. Jugheli, Natia Adamia +11 more
2021Nature Medicine63 citations Open access
Semantic Scholar
The relative transmission fitness of multidrug-resistant Mycobacterium tuberculosis in a drug resistance hotspot
C. Loiseau, E. Windels, Sebastian M. Gygli, L. Jugheli +16 more
2023Nature Communications61 citations Open access
Semantic Scholar
Interaction between host genes and Mycobacterium tuberculosis lineage can affect tuberculosis severity: Evidence for coevolution?
M. McHenry, Jacquelaine Bartlett, R. Igo, E. Wampande +12 more
2020PLoS Genetics60 citations Open access
Semantic Scholar
Transcontinental spread and evolution of Mycobacterium tuberculosis W148 European/Russian clade toward extensively drug resistant tuberculosis
M. Merker, Jean-Philippe Rasigade, M. Barbier, H. Cox +15 more
2022Nature Communications58 citations Open access
Semantic Scholar
The within-host evolution of antimicrobial resistance in Mycobacterium tuberculosis
Rhastin A. D. Castro, S. Borrell, S. Gagneux
2020FEMS Microbiology Reviews54 citations Open access
Semantic Scholar
Local adaptation in populations of Mycobacterium tuberculosis endemic to the Indian Ocean Rim
F. Menardo, L. Rutaihwa, M. Zwyer, S. Borrell +37 more
2020bioRxiv48 citations Open access
Semantic Scholar
A new nomenclature for the livestock-associated Mycobacterium tuberculosis complex based on phylogenomics [version 2; peer review: 2 approved]
M. Zwyer, C. Çavuşoğlu, G. Ghielmetti, M. Pacciarini +6 more
2021Open Research Europe46 citations Open access
Semantic Scholar
Genomic analyses of Mycobacterium tuberculosis from human lung resections reveal a high frequency of polyclonal infections
M. Moreno-Molina, N. Shubladze, I. Khurtsilava, Z. Avaliani +10 more
2021Nature Communications43 citations Open access
Semantic Scholar
Mortality from drug-resistant tuberculosis in high-burden countries comparing routine drug susceptibility testing with whole-genome sequencing: a multicentre cohort study
Kathrin Zürcher, Martina L. Reichmuth, M. Ballif, C. Loiseau +18 more
2021The Lancet Microbe37 citations Open access
Semantic Scholar
Effect of compensatory evolution in the emergence and transmission of rifampicin-resistant Mycobacterium tuberculosis in Cape Town, South Africa: a genomic epidemiology study
G. Goig, F. Menardo, Zubeida Salaam-Dreyer, A. Dippenaar +10 more
2023The Lancet Microbe32 citations Open access
Semantic Scholar
Impact of the diagnostic test Xpert MTB/RIF on patient outcomes for tuberculosis
F. Haraka, Mwaka A. Kakolwa, S. Schumacher, R. Nathavitharana +4 more
2021Cochrane Database of Systematic Reviews32 citations Open access
Semantic Scholar
Whole Genome Sequencing and Spatial Analysis Identifies Recent Tuberculosis Transmission Hotspots in Ghana
P. Asare, I. Otchere, Edmund Bedeley, D. Brites +11 more
2020Frontiers in Medicine25 citations Open access
Semantic Scholar
The Sputum Microbiome in Pulmonary Tuberculosis and Its Association With Disease Manifestations: A Cross-Sectional Study
M. Ticlla, J. Hella, H. Hiza, M. Sasamalo +11 more
2021Frontiers in Microbiology24 citations Open access
Semantic Scholar
Expression Dysregulation as a Mediator of Fitness Costs in Antibiotic Resistance
Andrej Trauner, Amir Banaei‐Esfahani, Sebastian M. Gygli, Philipp Warmer +7 more
2021Antimicrobial Agents and Chemotherapy23 citations Open access
Semantic Scholar
Quantifying transmission fitness costs of multi-drug resistant tuberculosis.
Jūlija Pečerska, D. Kühnert, C. Meehan, Mireia Coscollá +3 more
2021Epidemics22 citations Open access
Semantic Scholar
Transmission is a Key Driver of Resistance to the New Tuberculosis Drugs
G. Goig, C. Loiseau, N. Maghradze, K. Mchedlishvili +9 more
2025New England Journal of Medicine21 citations Open access
Semantic Scholar
Whole-Genome Sequencing Has the Potential To Improve Treatment for Rifampicin-Resistant Tuberculosis in High-Burden Settings: a Retrospective Cohort Study
H. Cox, G. Goig, Zubeida Salaam-Dreyer, A. Dippenaar +12 more
2022Journal of Clinical Microbiology21 citations Open access
Semantic Scholar
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
H. Cox, Zubeida Salaam-Dreyer, G. Goig, M. Nicol +13 more
2021The Lancet Microbe21 citations Open access
Semantic Scholar
Mycobacterium tuberculosis complex lineage 5 exhibits high levels of within-lineage genomic diversity and differing gene content compared to the type strain H37Rv
C. N. Sanoussi, Mireia Coscollá, Boatema Ofori-Anyinam, I. Otchere +10 more
2020bioRxiv21 citations Open access
Semantic Scholar
How do monomorphic bacteria evolve? The Mycobacterium tuberculosis complex and the awkward population genetics of extreme clonality
Christoph Stritt, S. Gagneux
2023Peer Community Journal20 citations Open access
Semantic Scholar
Case–control diagnostic accuracy study of a non-sputum CD38-based TAM-TB test from a single milliliter of blood
H. Hiza, J. Hella, A. Arbués, Beatrice Magani +4 more
2021Scientific Reports20 citations Open access
Semantic Scholar
Rifampicin-Monoresistant Tuberculosis Is Not the Same as Multidrug-Resistant Tuberculosis: a Descriptive Study from Khayelitsha, South Africa
Zubeida Salaam-Dreyer, E. Streicher, F. Sirgel, F. Menardo +11 more
2021medRxiv20 citations Open access
Semantic Scholar
Back-to-Africa introductions of Mycobacterium tuberculosis as the main cause of tuberculosis in Dar es Salaam, Tanzania
M. Zwyer, L. Rutaihwa, E. Windels, J. Hella +40 more
2023PLoS Pathogens19 citations Open access
Semantic Scholar
Balancing access to BPaLM regimens and risk of resistance.
A. Van Rie, T. Walker, B. D. de Jong, Praharshinie Rupasinghe +12 more
2022Lancet. Infectious Diseases (Print)17 citations Open access
Semantic Scholar
Natural Polymorphisms in Mycobacterium tuberculosis Conferring Resistance to Delamanid in Drug-Naive Patients
Martina L. Reichmuth, Rico Hömke, Kathrin Zürcher, P. Sander +12 more
2020Antimicrobial Agents and Chemotherapy15 citations Open access
Semantic Scholar
HIV co-infection is associated with reduced Mycobacterium tuberculosis transmissibility in sub-Saharan Africa
E. Windels, Eddie M. Wampande, M. Joloba, W. Boom +7 more
2023bioRxiv14 citations Open access
Semantic Scholar
Is the new WHO definition of extensively drug-resistant tuberculosis easy to apply in practice?
R. Alagna, A. Cabibbe, P. Miotto, F. Saluzzo +6 more
2021European Respiratory Journal14 citations Open access
Semantic Scholar
Gene conversion and duplication contribute to genetic variation in an outbreak of Mycobacterium tuberculosis
Christoph Stritt, Michelle Reitsma, Ana Maria Garcia Marin, G. Goig +6 more
2025Microbial Genomics13 citations Open access
Semantic Scholar
High burden of tuberculosis infection and disease among people receiving medication-assisted treatment for substance use disorder in Tanzania
Lillian T. Minja, J. Hella, J. Mbwambo, Cassian Nyandindi +8 more
2021PLoS ONE13 citations Open access
Semantic Scholar
Mycobacterium leprae Infection in a Wild Nine-Banded Armadillo, Nuevo León, Mexico
L. Vera-Cabrera, C. J. Ramos-Cavazos, N. A. Youssef, C. Pearce +10 more
2022Emerging Infectious Diseases12 citations Open access
Semantic Scholar
Soluble immune mediators orchestrate protective in vitro granulomatous responses across Mycobacterium tuberculosis complex lineages
Ainhoa Arbués, Sarah Schmidiger, M. Reinhard, S. Borrell +2 more
2025bioRxiv11 citations Open access
Semantic Scholar
HIV Coinfection Is Associated with Low-Fitness rpoB Variants in Rifampicin-Resistant Mycobacterium tuberculosis
C. Loiseau, D. Brites, M. Reinhard, Kathrin Zürcher +17 more
2020Antimicrobial Agents and Chemotherapy11 citations Open access
Semantic Scholar
Large-scale testing of antimicrobial lethality at single-cell resolution predicts mycobacterial infection outcomes
Alexander Jovanovic, Frederick K. Bright, A. Sadeghi, Basil Wicki +22 more
2026Nature Microbiology10 citations Open access
Semantic Scholar
Bacterial diversity dominates variable macrophage responses of tuberculosis patients in Tanzania
H. Hiza, M. Zwyer, J. Hella, A. Arbués +9 more
2023bioRxiv10 citations Open access
Semantic Scholar
Analysis of drug resistance among difficult-to-treat tuberculosis patients in Ghana identifies several pre-XDR TB cases
I. Otchere, P. Morgan, P. Asare, Stephen Osei-Wusu +12 more
2023Frontiers in Microbiology9 citations Open access
Semantic Scholar
High frequency of bedaquiline resistance in programmatically treated drug-resistant TB patients with sustained culture-positivity in Cape Town, South Africa
B. Derendinger, A. Dippenaar, M. De vos, S. Huo +19 more
2021medRxiv9 citations Open access
Semantic Scholar
A successful UN High-Level Meeting on antimicrobial resistance must build on the 2023 UN High-Level Meeting on tuberculosis
D. Cirillo, Richard Anthony, S. Gagneux, C. Horsburgh +24 more
2024Lancet Global Health7 citations Open access
Semantic Scholar
Genomic epidemiological analysis identifies high relapse among individuals with recurring tuberculosis and provides evidence of recent household-related transmission of tuberculosis in Ghana
P. Asare, Stephen Osei-Wusu, N. A. Baddoo, Edmund Bedeley +12 more
2021International Journal of Infectious Diseases7 citations Open access
Semantic Scholar
Genotypic and phenotypic diversity of Mycobacterium tuberculosis complex genotypes prevalent in West Africa
Stephen Osei-Wusu, I. Otchere, P. Morgan, A. Musah +8 more
2021PLoS ONE7 citations Open access
Semantic Scholar
Using population-specific add-on polymorphisms to improve genotype imputation in underrepresented populations
Zhi-Ming Xu, S. Rüeger, M. Zwyer, D. Brites +14 more
2021bioRxiv6 citations Open access
Semantic Scholar
Mycobacterium tuberculosis complex Lineage 1: A neglected cause of tuberculosis
Venus Marie R. Rojas, M. Zwyer, Selim Bouaouina, D. Brites +2 more
2025PLoS Neglected Tropical Diseases5 citations Open access
Semantic Scholar
Drug-induced differential culturability in diverse strains of Mycobacterium tuberculosis
Valerie F. A. March, N. Maghradze, K. Mchedlishvili, T. Avaliani +10 more
2025Scientific Reports5 citations Open access
Semantic Scholar
Granulysin Antimicrobial Activity Promotes Dormancy in Mycobacterium tuberculosis
Sarah Schmidiger, Erin F. McCaffrey, Jan M. Schmidt, O. Hameed +14 more
2024bioRxiv5 citations Open access
Semantic Scholar

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