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Integrating genomics, epidemiology and evolution to accelerate tuberculosis eradication

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Publications

Mycobacterium tuberculosis associated with severe tuberculosis evades cytosolic surveillance systems and modulates IL-1β production

Author(s): Jeremy Sousa, Baltazar Cá, Ana Raquel Maceiras, Luisa Simões-Costa, Kaori L. Fonseca, Ana Isabel Fernandes, Angélica Ramos, Teresa Carvalho, Leandro Barros, Carlos Magalhães, Álvaro Chiner-Oms, Henrique Machado, Maria Isabel Veiga, Albel Singh, Rui Pereira, António Amorim, Jorge Vieira, Cristina P. Vieira, Apoorva Bhatt, Fernando Rodrigues, Pedro N. S. Rodrigues, Sebastien Gagneux, António
Published in: Nature Communications, 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-15832-6

Towards next generation diagnostics for tuberculosis: identification of novel molecular targets by large-scale comparative genomics

Author(s): Galo A. Goig; Manuela Torres-Puente; Carla Mariner-Llicer; Luis M. Villamayor; Álvaro Chiner-Oms; Ana Gil-Brusola; Rafa Borrás; Iñaki Comas
Published in: Bioinformatics, 3, 2019, ISSN 1759-6653
Publisher: Oxford University Press
DOI: 10.1101/569384

Tuberculosis in Liberia: high multidrug-resistance burden, transmission and diversity modelled by multiple importation events

Author(s): Mariana G. López, John B. Dogba, Manuela Torres-Puente, Galo A. Goig, Miguel Moreno-Molina, Luis M. Villamayor, Simeon Cadmus, Iñaki Comas
Published in: Microbial Genomics, 6/1, 2020, ISSN 2057-5858
Publisher: Microbiology Society
DOI: 10.1099/mgen.0.000325

Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues

Author(s): Conor J. Meehan, Galo A. Goig, Thomas A. Kohl, Lennert Verboven, Anzaan Dippenaar, Matthew Ezewudo, Maha R. Farhat, Jennifer L. Guthrie, Kris Laukens, Paolo Miotto, Boatema Ofori-Anyinam, Viola Dreyer, Philip Supply, Anita Suresh, Christian Utpatel, Dick van Soolingen, Yang Zhou, Philip M. Ashton, Daniela Brites, Andrea M. Cabibbe, Bouke C. de Jong, Margaretha de Vos, Fabrizio Menardo, Sebastien G
Published in: Nature Reviews Microbiology, 17/9, 2019, Page(s) 533-545, ISSN 1740-1526
Publisher: Nature Publishing Group
DOI: 10.1038/s41579-019-0214-5

Genomic determinants of speciation and spread of the Mycobacterium tuberculosis complex

Author(s): Á. Chiner-Oms, L. Sánchez-Busó, J. Corander, S. Gagneux, S. R. Harris, D. Young, F. González-Candelas, I. Comas
Published in: Science Advances, 5/6, 2019, Page(s) eaaw3307, ISSN 2375-2548
Publisher: AAAS
DOI: 10.1126/sciadv.aaw3307

Whole genome sequencing–based analysis of tuberculosis (TB) in migrants: rapid tools for cross-border surveillance and to distinguish between recent transmission in the host country and new importations

Author(s): Estefanía Abascal, Laura Pérez-Lago, Miguel Martínez-Lirola, Álvaro Chiner-Oms, Marta Herranz, Imane Chaoui, Iñaki Comas, My Driss El Messaoudi, José Antonio Garrido Cárdenas, Sheila Santantón, Emilio Bouza, Darío García-de-Viedma
Published in: Eurosurveillance, 24/4, 2019, ISSN 1560-7917
Publisher: ECDC
DOI: 10.2807/1560-7917.es.2019.24.4.1800005

Cryptic Resistance Mutations Associated With Misdiagnoses of Multidrug-Resistant Tuberculosis

Author(s): Irving Cancino-Muñoz, Miguel Moreno-Molina, Victoria Furió, Galo A Goig, Manuela Torres-Puente, Álvaro Chiner-Oms, Luis M Villamayor, Francisco Sanz, María Remedio Guna-Serrano, Iñaki Comas
Published in: The Journal of Infectious Diseases, 220/2, 2019, Page(s) 316-320, ISSN 0022-1899
Publisher: University of Chicago Press
DOI: 10.1093/infdis/jiz104

Development and application of affordable SNP typing approaches to genotype Mycobacterium tuberculosis complex strains in low and high burden countries

Author(s): Irving Cancino-Muñoz, Ana Gil-Brusola, Manuela Torres-Puente, Carla Mariner-Llicer, John Dogba, Victor Akinseye, Kehinde Adesokan, Ayi Kwaghe, Francis Ejeh, Simeon Cadmus, Iñaki Comas
Published in: Scientific Reports, 9/1, 2019, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-019-51326-2

Specificity and mutagenesis bias of the mycobacterial alternative mismatch repair analyzed by mutation accumulation studies

Author(s): A. Castañeda-García, I. Martín-Blecua, E. Cebrián-Sastre, A. Chiner-Oms, M. Torres-Puente, I. Comas, J. Blázquez
Published in: Science Advances, 6/7, 2020, Page(s) eaay4453, ISSN 2375-2548
Publisher: Nature Publishing Group
DOI: 10.1126/sciadv.aay4453

Population Genomics of Mycobacterium tuberculosis in Ethiopia Contradicts the Virgin Soil Hypothesis for Human Tuberculosis in Sub-Saharan Africa

Author(s): Iñaki Comas, Elena Hailu, Teklu Kiros, Shiferaw Bekele, Wondale Mekonnen, Balako Gumi, Rea Tschopp, Gobena Ameni, R. Glyn Hewinson, Brian D. Robertson, Galo A. Goig, David Stucki, Sebastien Gagneux, Abraham Aseffa, Douglas Young, Stefan Berg
Published in: Current Biology, 25/24, 2015, Page(s) 3260-3266, ISSN 0960-9822
Publisher: Cell Press
DOI: 10.1016/j.cub.2015.10.061

Draft Genome Sequence of Mycobacterium brumae ATCC 51384

Author(s): Giuseppe D'Auria, Eduard Torrents, Marina Luquin, Iñaki Comas, Esther Julián
Published in: Genome Announcements, 4/2, 2016, Page(s) e00237-16, ISSN 2169-8287
Publisher: American Society for Microbiology
DOI: 10.1128/genomeA.00237-16

Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages

Author(s): David Stucki, Daniela Brites, Leïla Jeljeli, Mireia Coscolla, Qingyun Liu, Andrej Trauner, Lukas Fenner, Liliana Rutaihwa, Sonia Borrell, Tao Luo, Qian Gao, Midori Kato-Maeda, Marie Ballif, Matthias Egger, Rita Macedo, Helmi Mardassi, Milagros Moreno, Griselda Tudo Vilanova, Janet Fyfe, Maria Globan, Jackson Thomas, Frances Jamieson, Jennifer L Guthrie, Adwoa Asante-Poku, Dorothy Yeboah-Manu, Edd
Published in: Nature Genetics, 48/12, 2016, Page(s) 1535-1543, ISSN 1061-4036
Publisher: Nature Publishing Group
DOI: 10.1038/ng.3704

Urgent Implementation in a Hospital Setting of a Strategy To Rule Out Secondary Cases Caused by Imported Extensively Drug-Resistant Mycobacterium tuberculosis Strains at Diagnosis

Author(s): Laura Pérez-Lago, Miguel Martínez-Lirola, Sergio García, Marta Herranz, Igor Mokrousov, Iñaki Comas, Llúcia Martínez-Priego, Emilio Bouza, Darío García-de-Viedma
Published in: Journal of Clinical Microbiology, 54/12, 2016, Page(s) 2969-2974, ISSN 0095-1137
Publisher: American Society for Microbiology
DOI: 10.1128/JCM.01718-16

A standardised method for interpreting the association between mutations and phenotypic drug resistance in Mycobacterium tuberculosis

Author(s): Paolo Miotto, Belay Tessema, Elisa Tagliani, Leonid Chindelevitch, Angela M. Starks, Claudia Emerson, Debra Hanna, Peter S. Kim, Richard Liwski, Matteo Zignol, Christopher Gilpin, Stefan Niemann, Claudia M. Denkinger, Joy Fleming, Robin M. Warren, Derrick Crook, James Posey, Sebastien Gagneux, Sven Hoffner, Camilla Rodrigues, Iñaki Comas, David M. Engelthaler, Megan Murray, David Alland, Leen Ri
Published in: European Respiratory Journal, 50/6, 2017, Page(s) 1701354, ISSN 0903-1936
Publisher: European Respiratory Society
DOI: 10.1183/13993003.01354-2017

A novel strategy based on genomics and specific PCR reveals how a multidrug-resistant Mycobacterium tuberculosis strain became prevalent in Equatorial Guinea 15 years after its emergence

Author(s): L. Pérez-Lago, S. Izco, M. Herranz, G. Tudó, M. Carcelén, I. Comas, O. Sierra, J. González-Martín, M.J. Ruiz-Serrano, J. Eyene, E. Bouza, D. García de Viedma
Published in: Clinical Microbiology and Infection, 23/2, 2017, Page(s) 92-97, ISSN 1198-743X
Publisher: Blackwell Publishing Inc.
DOI: 10.1016/j.cmi.2016.10.006

The Troika Host–Pathogen–Extrinsic Factors in Tuberculosis: Modulating Inflammation and Clinical Outcomes

Author(s): Helder Novais Bastos, Nuno S. Osório, Sebastien Gagneux, Iñaki Comas, Margarida Saraiva
Published in: Frontiers in Immunology, 8, 2018, ISSN 1664-3224
Publisher: Frontiers
DOI: 10.3389/fimmu.2017.01948

Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing

Author(s): CRyPTIC Consortium and the 100,000 Genomes Project, Allix-Béguec C, Arandjelovic I, Bi L, Beckert P, Bonnet M, Bradley P, Cabibbe AM, Cancino-Muñoz I, Caulfield MJ, Chaiprasert A, Cirillo DM, Clifton DA, Comas I, Crook DW, De Filippo MR, de Neeling H, Diel R, Drobniewski FA, Faksri K, Farhat MR, Fleming J, Fowler P, Fowler TA, Gao Q, Gardy J, Gascoyne-Binzi D, Gibertoni-Cruz AL, Gil-Brusola A, G
Published in: New England Journal of Medicine, 379/15, 2018, Page(s) 1403-1415, ISSN 0028-4793
Publisher: Massachusetts Medical Society
DOI: 10.1056/NEJMoa1800474

Mycobacterium tuberculosis Acquires Limited Genetic Diversity in Prolonged Infections, Reactivations and Transmissions Involving Multiple Hosts

Author(s): Marta Herranz, Ilva Pole, Iveta Ozere, Álvaro Chiner-Oms, Miguel Martínez-Lirola, Felipe Pérez-García, Paloma Gijón, María Jesús Ruiz Serrano, Laura Clotet Romero, Oscar Cuevas, Iñaki Comas, Emilio Bouza, Laura Pérez-Lago, Darío García-de-Viedma
Published in: Frontiers in Microbiology, 8, 2018, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2017.02661

Gene expression models based on a reference laboratory strain are poor predictors of Mycobacterium tuberculosis complex transcriptional diversity

Author(s): Álvaro Chiner-Oms, Fernando González-Candelas, Iñaki Comas
Published in: Scientific Reports, 8/1, 2018, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-018-22237-5

Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase

Author(s): Matthew Ezewudo, Amanda Borens, Álvaro Chiner-Oms, Paolo Miotto, Leonid Chindelevitch, Angela M. Starks, Debra Hanna, Richard Liwski, Matteo Zignol, Christopher Gilpin, Stefan Niemann, Thomas Andreas Kohl, Robin M. Warren, Derrick Crook, Sebastien Gagneux, Sven Hoffner, Camilla Rodrigues, Iñaki Comas, David M. Engelthaler, David Alland, Leen Rigouts, Christoph Lange, Keertan Dheda, Rumina Hasan,
Published in: Scientific Reports, 8/1, 2018, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-018-33731-1

In-Depth Characterization and Functional Analysis of Clonal Variants in a Mycobacterium tuberculosis Strain Prone to Microevolution

Author(s): Yurena Navarro, Laura Pérez-Lago, Marta Herranz, Olalla Sierra, Iñaki Comas, Javier Sicilia, Emilio Bouza, Darío García de Viedma
Published in: Frontiers in Microbiology, 8, 2017, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2017.00694

New Genome-Wide Algorithm Identifies Novel In-Vivo Expressed Mycobacterium Tuberculosis Antigens Inducing Human T-Cell Responses with Classical and Unconventional Cytokine Profiles

Author(s): Mariateresa Coppola, Krista E. van Meijgaarden, Kees L. M. C. Franken, Susanna Commandeur, Gregory Dolganov, Igor Kramnik, Gary K. Schoolnik, Inaki Comas, Ole Lund, Corine Prins, Susan J. F. van den Eeden, Gro E. Korsvold, Fredrik Oftung, Annemieke Geluk, Tom H. M. Ottenhoff
Published in: Scientific Reports, 6/1, 2016, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/srep37793

Contaminant DNA in bacterial sequencing experiments is a major source of false genetic variability

Author(s): Galo A. Goig, Silvia Blanco, Alberto L. Garcia-Basteiro, Iñaki Comas
Published in: BMC Biology, 18/1, 2020, ISSN 1741-7007
Publisher: BioMed Central
DOI: 10.1186/s12915-020-0748-z

Mycobacterium tuberculosis clinical isolates carry mutational signatures of host immune environments

Author(s): Qingyun Liu, Jianhao Wei, Yawei Li, Mei Wang, Jun Su, Yonghui Lu, Mariana G. López, Xueqin Qian, Zhaoqin Zhu, Haiying Wang, Mingyun Gan, Qi Jiang, Yun-Xin Fu, Howard E. Takiff, Iñaki Comas, Feng Li, Xuemei Lu, Sarah M. Fortune, Qian Gao
Published in: Science Advances, 6/22, 2020, Page(s) eaba4901, ISSN 2375-2548
Publisher: Nature Pubclishing Group
DOI: 10.1126/sciadv.aba4901

High-resolution mapping of tuberculosis transmission: Whole genome sequencing and phylogenetic modelling of a cohort from Valencia Region, Spain

Author(s): Yuanwei Xu, Irving Cancino-Muñoz, Manuela Torres-Puente, Luis M. Villamayor, Rafael Borrás, María Borrás-Máñez, Montserrat Bosque, Juan J. Camarena, Ester Colomer-Roig, Javier Colomina, Isabel Escribano, Oscar Esparcia-Rodríguez, Ana Gil-Brusola, Concepción Gimeno, Adelina Gimeno-Gascón, Bárbara Gomila-Sard, Damiana González-Granda, Nieves Gonzalo-Jiménez, María Remedio Guna-Serrano,
Published in: PLOS Medicine, 16/10, 2019, Page(s) e1002961, ISSN 1549-1676
Publisher: Public Library of Sciences
DOI: 10.1371/journal.pmed.1002961

Genomic epidemiology of tuberculosis

Author(s): Iñaki Comas
Published in: 2017, Page(s) 79-93
Publisher: Springer International Publishing
DOI: 10.1007/978-3-319-64371-7_4

Evolutionary Biology

Author(s): Pierre Pontarotti
Published in: 2016, ISBN 978-3-319-41324-2
Publisher: Springer International Publishing
DOI: 10.1007/978-3-319-41324-2