Integrating genomics, epidemiology and evolution to accelerate tuberculosis eradication

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

Auteurs: 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
Publié dans: Nature Communications, Numéro 11/1, 2020, ISSN 2041-1723
Éditeur: 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

Auteurs: Galo A. Goig; Manuela Torres-Puente; Carla Mariner-Llicer; Luis M. Villamayor; Álvaro Chiner-Oms; Ana Gil-Brusola; Rafa Borrás; Iñaki Comas
Publié dans: Bioinformatics, Numéro 3, 2019, ISSN 1759-6653
Éditeur: Oxford University Press
DOI: 10.1101/569384

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

Auteurs: Mariana G. López, John B. Dogba, Manuela Torres-Puente, Galo A. Goig, Miguel Moreno-Molina, Luis M. Villamayor, Simeon Cadmus, Iñaki Comas
Publié dans: Microbial Genomics, Numéro 6/1, 2020, ISSN 2057-5858
Éditeur: Microbiology Society
DOI: 10.1099/mgen.0.000325

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

Auteurs: 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
Publié dans: Nature Reviews Microbiology, Numéro 17/9, 2019, Page(s) 533-545, ISSN 1740-1526
Éditeur: Nature Publishing Group
DOI: 10.1038/s41579-019-0214-5

Genomic determinants of speciation and spread of the Mycobacterium tuberculosis complex

Auteurs: Á. Chiner-Oms, L. Sánchez-Busó, J. Corander, S. Gagneux, S. R. Harris, D. Young, F. González-Candelas, I. Comas
Publié dans: Science Advances, Numéro 5/6, 2019, Page(s) eaaw3307, ISSN 2375-2548
Éditeur: 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

Auteurs: 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
Publié dans: Eurosurveillance, Numéro 24/4, 2019, ISSN 1560-7917
Éditeur: ECDC
DOI: 10.2807/1560-7917.es.2019.24.4.1800005

Cryptic Resistance Mutations Associated With Misdiagnoses of Multidrug-Resistant Tuberculosis

Auteurs: 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
Publié dans: The Journal of Infectious Diseases, Numéro 220/2, 2019, Page(s) 316-320, ISSN 0022-1899
Éditeur: 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

Auteurs: 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
Publié dans: Scientific Reports, Numéro 9/1, 2019, ISSN 2045-2322
Éditeur: 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

Auteurs: A. Castañeda-García, I. Martín-Blecua, E. Cebrián-Sastre, A. Chiner-Oms, M. Torres-Puente, I. Comas, J. Blázquez
Publié dans: Science Advances, Numéro 6/7, 2020, Page(s) eaay4453, ISSN 2375-2548
Éditeur: 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

Auteurs: 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
Publié dans: Current Biology, Numéro 25/24, 2015, Page(s) 3260-3266, ISSN 0960-9822
Éditeur: Cell Press
DOI: 10.1016/j.cub.2015.10.061

Draft Genome Sequence of Mycobacterium brumae ATCC 51384

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

Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages

Auteurs: 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
Publié dans: Nature Genetics, Numéro 48/12, 2016, Page(s) 1535-1543, ISSN 1061-4036
Éditeur: 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

Auteurs: Laura Pérez-Lago, Miguel Martínez-Lirola, Sergio García, Marta Herranz, Igor Mokrousov, Iñaki Comas, Llúcia Martínez-Priego, Emilio Bouza, Darío García-de-Viedma
Publié dans: Journal of Clinical Microbiology, Numéro 54/12, 2016, Page(s) 2969-2974, ISSN 0095-1137
Éditeur: 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

Auteurs: 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
Publié dans: European Respiratory Journal, Numéro 50/6, 2017, Page(s) 1701354, ISSN 0903-1936
Éditeur: 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

Auteurs: 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
Publié dans: Clinical Microbiology and Infection, Numéro 23/2, 2017, Page(s) 92-97, ISSN 1198-743X
Éditeur: Blackwell Publishing Inc.
DOI: 10.1016/j.cmi.2016.10.006

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

Auteurs: Helder Novais Bastos, Nuno S. Osório, Sebastien Gagneux, Iñaki Comas, Margarida Saraiva
Publié dans: Frontiers in Immunology, Numéro 8, 2018, ISSN 1664-3224
Éditeur: Frontiers
DOI: 10.3389/fimmu.2017.01948

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

Auteurs: 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
Publié dans: New England Journal of Medicine, Numéro 379/15, 2018, Page(s) 1403-1415, ISSN 0028-4793
Éditeur: Massachusetts Medical Society
DOI: 10.1056/NEJMoa1800474

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

Auteurs: 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
Publié dans: Frontiers in Microbiology, Numéro 8, 2018, ISSN 1664-302X
Éditeur: 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

Auteurs: Álvaro Chiner-Oms, Fernando González-Candelas, Iñaki Comas
Publié dans: Scientific Reports, Numéro 8/1, 2018, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-018-22237-5

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

Auteurs: 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,
Publié dans: Scientific Reports, Numéro 8/1, 2018, ISSN 2045-2322
Éditeur: 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

Auteurs: Yurena Navarro, Laura Pérez-Lago, Marta Herranz, Olalla Sierra, Iñaki Comas, Javier Sicilia, Emilio Bouza, Darío García de Viedma
Publié dans: Frontiers in Microbiology, Numéro 8, 2017, ISSN 1664-302X
Éditeur: 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

Auteurs: 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
Publié dans: Scientific Reports, Numéro 6/1, 2016, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/srep37793

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

Auteurs: Galo A. Goig, Silvia Blanco, Alberto L. Garcia-Basteiro, Iñaki Comas
Publié dans: BMC Biology, Numéro 18/1, 2020, ISSN 1741-7007
Éditeur: BioMed Central
DOI: 10.1186/s12915-020-0748-z

Mycobacterium tuberculosis clinical isolates carry mutational signatures of host immune environments

Auteurs: 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
Publié dans: Science Advances, Numéro 6/22, 2020, Page(s) eaba4901, ISSN 2375-2548
Éditeur: 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

Auteurs: 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,
Publié dans: PLOS Medicine, Numéro 16/10, 2019, Page(s) e1002961, ISSN 1549-1676
Éditeur: Public Library of Sciences
DOI: 10.1371/journal.pmed.1002961

Genomic epidemiology of tuberculosis

Auteurs: Iñaki Comas
Publié dans: 2017, Page(s) 79-93
Éditeur: Springer International Publishing
DOI: 10.1007/978-3-319-64371-7_4

Evolutionary Biology

Auteurs: Pierre Pontarotti
Publié dans: 2016, ISBN 978-3-319-41324-2
Éditeur: Springer International Publishing
DOI: 10.1007/978-3-319-41324-2

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