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2022

  • Ginex T, Marco-Marín C, Wieczór M, Mata CP, Krieger J, Ruiz-Rodriguez P, López-Redondo ML, Francés-Gómez C, Melero R, Sánchez-Sorzano CÓ, Martínez M, Gougeard N, Forcada-Nadal A, Zamora-Caballero S, Gozalbo-Rovira R, Sanz-Frasquet C, Arranz R, Bravo J, Rubio V, Marina A; IBV-Covid19-Pipeline, Geller R, Comas I, Gil C, Coscolla M, Orozco M, Llácer JL, Carazo JM. The structural role of SARS-CoV-2 genetic background in the emergence and success of spike mutations: The case of the spike A222V mutation. PLoS Pathog. 2022 Jul 11;18(7):e1010631. doi: 10.1371/journal.ppat.1010631. PMID: 35816514; PMCID: PMC9302720.
  • Santamaria G, Ruiz-Rodriguez P, Renau-Mínguez C, Pinto FR, Coscollá M. In Silico Exploration of Mycobacterium tuberculosis Metabolic Networks Shows Host-Associated Convergent Fluxomic Phenotypes. Biomolecules. 2022 Feb 28;12(3):376. doi: 10.3390/biom12030376. PMID: 35327567; PMCID: PMC8945471.

2021

  • Ruiz-Rodriguez P, Francés-Gómez C, Chiner-Oms Á, López MG, Jiménez-Serrano S, Cancino-Muñoz I, Ruiz-Hueso P, Torres-Puente M, Bracho MA, D'Auria G, Martinez-Priego L, Guerreiro M, Montero-Alonso M, Gómez MD, Piñana JL; SeqCOVID-SPAIN Consortium, González-Candelas F, Comas I, Marina A, Geller R, Coscolla M. Evolutionary and Phenotypic Characterization of Two Spike Mutations in European Lineage 20E of SARS-CoV-2. mBio. 2021 Dec 21;12(6):e0231521. doi: 10.1128/mBio.02315-21. Epub 2021 Nov 16. PMID: 34781748; PMCID: PMC8593680.
  • Cabañero-Navalon MD, Garcia-Bustos V, Ruiz-Rodriguez P, Comas I, Coscollá M, Martinez-Priego L, Todolí J, Moral Moral P. Persistent SARS-CoV-2 infection with repeated clinical recurrence in a patient with common variable immunodeficiency. Clin Microbiol Infect. 2021 Nov 10:S1198-743X(21)00623-6. doi: 10.1016/j.cmi.2021.10.021. Epub ahead of print. PMID: 34774757; PMCID: PMC8579735.
  • López MG, Chiner-Oms Á, García de Viedma D, Ruiz-Rodriguez P, Bracho MA, Cancino-Muñoz I, D'Auria G, de Marco G, García-González N, Goig GA, Gómez-Navarro I, Jiménez-Serrano S, Martinez-Priego L, Ruiz-Hueso P, Ruiz-Roldán L, Torres-Puente M, Alberola J, Albert E, Aranzamendi Zaldumbide M, Bea-Escudero MP, Boga JA, Bordoy AE, Canut-Blasco A, Carvajal A, Cilla Eguiluz G, Cordón Rodríguez ML, Costa-Alcalde JJ, de Toro M, de Toro Peinado I, Del Pozo JL, Duchêne S, Fernández-Pinero J, Fuster Escrivá B, Gimeno Cardona C, González Galán V, Gonzalo Jiménez N, Hernáez Crespo S, Herranz M, Lepe JA, López-Causapé C, López-Hontangas JL, Martín V, Martró E, Milagro Beamonte A, Montes Ros M, Moreno-Muñoz R, Navarro D, Navarro-Marí JM, Not A, Oliver A, Palop-Borrás B, Parra Grande M, Pedrosa-Corral I, Pérez González MC, Pérez-Lago L, Pérez-Ruiz M, Piñeiro Vázquez L, Rabella N, Rezusta A, Robles Fonseca L, Rodríguez-Villodres Á, Sanbonmatsu-Gámez S, Sicilia J, Soriano A, Tirado Balaguer MD, Torres I, Tristancho A, Marimón JM; SeqCOVID-Spain consortium, Coscolla M, González-Candelas F, Comas I. The first wave of the COVID-19 epidemic in Spain was associated with early introductions and fast spread of a dominating genetic variant. Nat Genet. 2021 Oct;53(10):1405-1414. doi: 10.1038/s41588-021-00936-6. Epub 2021 Sep 30. PMID: 34594042; PMCID: PMC8481935.
  • Pečerska J, Kühnert D, Meehan CJ, Coscollá M, de Jong BC, Gagneux S, Stadler T. Quantifying transmission fitness costs of multi-drug resistant tuberculosis. Epidemics. 2021 Sep;36:100471. doi: 10.1016/j.epidem.2021.100471. Epub 2021 May 21. PMID: 34256273.
  • Sanoussi CN, Coscolla M, Ofori-Anyinam B, Otchere ID, Antonio M, Niemann S, Parkhill J, Harris S, Yeboah-Manu D, Gagneux S, Rigouts L, Affolabi D, de Jong BC, Meehan CJ. 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 Jul;7(7):000437. doi: 10.1099/mgen.0.000437. PMID: 34241588; PMCID: PMC8477398.
  • Hodcroft EB, Zuber M, Nadeau S, Vaughan TG, Crawford KHD, Althaus CL, Reichmuth ML, Bowen JE, Walls AC, Corti D, Bloom JD, Veesler D, Mateo D, Hernando A, Comas I, González-Candelas F; SeqCOVID-SPAIN consortium, Stadler T, Neher RA. Spread of a SARS-CoV-2 variant through Europe in the summer of 2020. Nature. 2021 Jul;595(7869):707-712. doi: 10.1038/s41586-021-03677-y. Epub 2021 Jun 7. PMID: 34098568.
  • Menardo F, Rutaihwa LK, Zwyer M, Borrell S, Comas I, Conceição EC, Coscolla M, Cox H, Joloba M, Dou HY, Feldmann J, Fenner L, Fyfe J, Gao Q, García de Viedma D, Garcia-Basteiro AL, Gygli SM, Hella J, Hiza H, Jugheli L, Kamwela L, Kato-Maeda M, Liu Q, Ley SD, 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 KV, Yeboah-Manu D, Beisel C, Brites D, Gagneux S. Local adaptation in populations of Mycobacterium tuberculosis endemic to the Indian Ocean Rim. F1000Res. 2021 Feb 1;10:60. doi: 10.12688/f1000research.28318.2. PMID: 33732436; PMCID: PMC7921886.
  • Coscolla M, Gagneux S, Menardo F, Loiseau C, Ruiz-Rodriguez P, Borrell S, Otchere ID, Asante-Poku A, Asare P, Sánchez-Busó L, Gehre F, Sanoussi CN, Antonio M, Affolabi D, Fyfe J, Beckert P, Niemann S, Alabi AS, Grobusch MP, Kobbe R, Parkhill J, Beisel C, Fenner L, Böttger EC, Meehan CJ, Harris SR, de Jong BC, Yeboah-Manu D, Brites D. Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history. Microb Genom. 2021 Feb 8. doi: 10.1099/mgen.0.000477. Online ahead of print. PMID: 33555243 Free article.

2020

  • Alm E, Broberg EK, Connor T, Hodcroft EB, Komissarov AB, Maurer-Stroh S, Melidou A, Neher RA, O'Toole Á, Pereyaslov D; WHO European Region sequencing laboratories and GISAID EpiCoV group; WHO European Region sequencing laboratories and GISAID EpiCoV group*. Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020. Euro Surveill. 2020 Aug;25(32):2001410. doi: 10.2807/1560-7917.ES.2020.25.32.2001410. PMID: 32794443 Free PMC article.

2019

  • Brites D, Loiseau C, Menardo F, Borrell S, Boniotti MB, Warren R, Dippenaar A, Parsons SDC, Beisel C, Behr MA, Fyfe JA, Coscolla M, Gagneux S. A New Phylogenetic Framework for the Animal-Adapted Mycobacterium tuberculosis Complex. Front Microbiol. 2018 Nov 27;9:2820. doi: 10.3389/fmicb.2018.02820. eCollection 2018. PMID: 30538680 Free PMC article.
  • 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 Mar 25;14(3):e0214088.
  • Otchere ID, van Tonder AJ, Asante-Poku A, Sánchez-Busó L, Coscollá M, Osei-Wusu S, Asare P, Aboagye SY, Ekuban SA, Yahayah AI, Forson A, Baddoo A, Laryea C, Parkhill J, Harris SR, Gagneux S, Yeboah-Manu D. Molecular epidemiology and whole genome sequencing analysis of clinical Mycobacterium bovis from Ghana.  PLoS One. 2019 Mar 4;14(3):e0209395.

2018

  • Brites D, Loiseau C, Menardo F, Borrell S, Boniotti MB, Warren R, Dippenaar A, Parsons SDC, Beisel C, Behr MA, Fyfe JA, Coscolla M, Gagneux S. A New Phylogenetic Framework for the Animal-Adapted Mycobacterium tuberculosis Complex. Front Microbiol. 2018 Nov 27;9:2820.
  • Sanoussi CN, de Jong BC, Odoun M, Arekpa K, Ali Ligali M, Bodi O, Harris S, Ofori-Anyinam B, Yeboah-Manu D, Otchere ID, Asante-Poku A, Anagonou S, Gagneux S, Coscolla M, Rigouts L, Affolabi D. Low sensitivity of the MPT64 identification test to detect lineage 5 of the Mycobacterium tuberculosis complex. J Med Microbiol. 2018 Dec;67(12):1718-1727
  • Otchere ID, Coscollá M, Sánchez-Busó L, Asante-Poku A, Brites D, et al.. Comparative genomics of Mycobacterium africanum Lineage 5 and Lineage 6 from Ghana suggests distinct ecological niches. Sci Rep. 2018 Jul 26;8(1):11269
  • Kühnert D, Coscolla M, Brites D, Stucki D, Metcalfe J, Fenner L, Gagneux S, Stadler T. Tuberculosis outbreak investigation using phylodynamic analysis. Epidemics. 2018 Dec;25:47-53.
  • Menardo F, Loiseau C, Brites D, Coscolla M, Gygli SM, Rutaihwa LK, Trauner A, Beisel C, Borrell S, Gagneux S. Treemmer: a tool to reduce large phylogenetic datasets with minimal loss of diversity. BMC Bioinformatics. 2018 May 2;19(1):164.

2017

  • Coscolla M. Biological and Epidemiological Consequences of MTBC Diversity. Adv Exp Med Biol. 2017;1019:95-116.
  • Ghielmetti G, Coscolla M, Ruetten M, Friedel U, Loiseau C, Feldmann J, Steinmetz HW, Stucki D, Gagneux S. Tuberculosis in Swiss captive Asian elephants: microevolution of Mycobacterium tuberculosis characterized by multilocus variable-number tandem-repeat analysis and whole-genome sequencing. Sci Rep. 2017 Nov 7;7(1):14647
  • Ofori-Anyinam B, Dolganov G, Van T, Davis JL, Walter ND, Garcia BJ, Voskuil M, Fissette K, Diels M, Driesen M, Meehan CJ, Yeboah-Manu D, Coscolla M, Gagneux  S, Antonio M, Schoolnik G, Gehre F, de Jong BC. Significant under expression of the DosR regulon in M. tuberculosis complex lineage 6 in sputum. Tuberculosis (Edinb). 2017 May;104:58-64.
  • Blondiaux N, Moune M, Desroses M, Frita R, Flipo M, Mathys V, Soetaert K, Et al. Reversion of antibiotic resistance in Mycobacterium tuberculosis by spiroisoxazoline SMARt-420. Science. 2017 Mar17;355(6330):1206-1211.

2016

  • Copin R, Wang X, Louie E, Escuyer V, Coscolla M, Gagneux S, Palmer GH, Ernst JD. Within Host Evolution Selects for a Dominant Genotype of Mycobacterium tuberculosis while T Cells Increase Pathogen Genetic Diversity. PLoS Pathog. 2016 Dec 14;12(12):e1006111.
  • Stucki D, Brites D, Jeljeli L, Coscolla M, Liu Q, Trauner A, et al.Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages. Nat Genet. 2016 Dec;48(12):1535-1543.
  • Stucki D, Ballif M, Egger M, Furrer H, Altpeter E, Battegay M, et al. Standard Genotyping Overestimates Transmission of Mycobacterium tuberculosis among Immigrants in a Low-Incidence Country. J Clin Microbiol. 2016 Jul;54(7):1862-1870.

2015

  • Coscolla M, Copin R, Sutherland J, Gehre F, de Jong B, Owolabi O, Mbayo G, Giardina F, Ernst JD, Gagneux S. M. tuberculosis T Cell Epitope Analysis Reveals  Paucity of Antigenic Variation and Identifies Rare Variable TB Antigens. Cell Host Microbe. 2015 Nov 11;18(5):538-48.
  • Bloemberg GV, Keller PM, Stucki D, Trauner A, Borrell S, Latshang T, Coscolla M, Rothe T, Hömke R, Ritter C, Feldmann J, Schulthess B, Gagneux S, Böttger EC. Acquired Resistance to Bedaquiline and Delamanid in Therapy for Tuberculosis. N Engl J Med. 2015 Nov 12;373(20):1986-8.
  • Sánchez-Busó L, Coscollà M, Palero F, Camaró ML, Gimeno A, Moreno P, Escribano I, López Perezagua MM, Colomina J, Vanaclocha H, González-Candelas F. Geographical and Temporal Structures of Legionella pneumophila Sequence Types in  Comunitat Valenciana (Spain), 1998 to 2013. Appl Environ Microbiol. 2015 Oct;81(20):7106-13.
  • Young DC, Layre E, Pan SJ, Tapley A, Adamson J, Seshadri C, Wu Z, Buter J, Minnaard AJ, Coscolla M, Gagneux S, Copin R, Ernst JD, Bishai WR, Snider BB, Moody DB. In vivo biosynthesis of terpene nucleosides provides unique chemical markers of Mycobacterium tuberculosis infection. Chem Biol. 2015 Apr 23;22(4):516-526.
  • Rock JM, Lang UF, Chase MR, Ford CB, Gerrick ER, Gawande R, Coscolla M, Gagneux S, Fortune SM, Lamers MH. DNA replication fidelity in Mycobacterium tuberculosis is mediated by an ancestral prokaryotic proofreader. Nat Genet. 2015 Jun;47(6):677-81.
  • Coscolla M, Barry PM, Oeltmann JE, Koshinsky H, Shaw T, Cilnis M, Posey J, Rose J, Weber T, Fofanov VY, Gagneux S, Kato-Maeda M, Metcalfe JZ. Genomic epidemiology of multidrug-resistant Mycobacterium tuberculosis during transcontinental spread. J Infect Dis. 2015 Jul 15;212(2):302-10.

2014

  • Coscolla M, Gagneux S. Consequences of genomic diversity in Mycobacterium tuberculosis. Semin Immunol. 2014 Dec;26(6):431-44
  • Stucki D, Ballif M, Bodmer T, Coscolla M, Maurer AM, Droz S, Butz C, Borrell S, Längle C, Feldmann J, Furrer H, Mordasini C, Helbling P, Rieder HL, Egger M, Gagneux S, Fenner L. Tracking a tuberculosis outbreak over 21 years: strain-specific single-nucleotide polymorphism typing combined with targeted whole-genome sequencing. J Infect Dis. 2015 Apr 15;211(8):1306-16
  • Steiner A, Stucki D, Coscolla M, Borrell S, Gagneux S. KvarQ: targeted and direct variant calling from fastq reads of bacterial genomes. BMC Genomics. 2014  Oct 9;15:881.
  • Portevin D, Sukumar S, Coscolla M, Shui G, Li B, Guan XL, Bendt AK, Young D, Gagneux S, Wenk MR. Lipidomics and genomics of Mycobacterium tuberculosis reveal  lineage-specific trends in mycolic acid biosynthesis. Microbiologyopen. 2014 Dec;3(6):823-35. doi: 10.1002/mbo3.193
  • Copin R, Coscollá M, Efstathiadis E, Gagneux S, Ernst JD. Impact of in vitro evolution on antigenic diversity of Mycobacterium bovis bacillus Calmette-Guerin  (BCG). Vaccine. 2014 Oct 14;32(45):5998-6004.
  • Bos KI, Harkins KM, Herbig A, Coscolla M, Weber N, Comas I, Forrest SA, et al. Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis. Nature. 2014 Oct 23;514(7523):494-7.
  • Copin R, Coscollá M, Seiffert SN, Bothamley G, Sutherland J, Mbayo G, Gagneux S, Ernst JD. Sequence diversity in the pe_pgrs genes of Mycobacterium tuberculosis is independent of human T cell recognition. MBio. 2014 Jan 14;5(1):e00960-13.
  • Coscollá M, Fernández C, Colomina J, Sánchez-Busó L, González-Candelas F. Mixed infection by Legionella pneumophila in outbreak patients. Int J Med Microbiol. 2014 May;304(3-4):307-13.

2013

  • Rose G, Cortes T, Comas I, Coscolla M, Gagneux S, Young DB. Mapping of genotype-phenotype diversity among clinical isolates of mycobacterium tuberculosis by sequence-based transcriptional profiling. Genome Biol Evol. 2013;5(10):1849-62.
  • Garcia-Garcerà M, Garcia-Etxebarria K, Coscollà M, Latorre A, Calafell F. A new method for extracting skin microbes allows metagenomic analysis of whole-deep skin. PLoS One. 2013 Sep 20;8(9):e74914.
  • Comas I, Coscolla M, Luo T, Borrell S, Holt KE, Kato-Maeda M, Parkhill J, Malla B, Berg S, Thwaites G, Yeboah-Manu D, Bothamley G, Mei J, Wei L, Bentley S, Harris SR, Niemann S, Diel R, Aseffa A, Gao Q, Young D, Gagneux S. Out-of-Africa  migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans. Nat Genet. 2013 Oct;45(10):1176-82.
  • Coscolla M, Lewin A, Metzger S, Maetz-Rennsing K, Calvignac-Spencer S, Nitsche A, Dabrowski PW, Radonic A, Niemann S, Parkhill J, Couacy-Hymann E, Feldman J, Comas I, Boesch C, Gagneux S, Leendertz FH. Novel Mycobacterium tuberculosis complex isolate from a wild chimpanzee. Emerg Infect Dis. 2013 Jun;19(6):969-76.
  • Sánchez-Busó L, Coscollá M, Pinto-Carbó M, Catalán V, González-Candelas F. Genetic Characterization of Legionella pneumophila Isolated from a Common Watershed in Comunidad Valenciana, Spain. PLoS One. 2013 Apr 25;8(4):e61564.

2012

  • Ballif M, Harino P, Ley S, Coscolla M, Niemann S, Carter R, Coulter C, Borrell S, Siba P, Phuanukoonnon S, Gagneux S, Beck HP. Drug resistance-conferring mutations in Mycobacterium tuberculosis from Madang, Papua  New Guinea. BMC Microbiol. 2012 Sep 4;12:191.
  • Stucki D, Malla B, Hostettler S, Huna T, Feldmann J, Yeboah-Manu D, Borrell S, Fenner L, Comas I, Coscollà M, Gagneux S. Two new rapid SNP-typing methods for classifying Mycobacterium tuberculosis complex into the main phylogenetic lineages. PLoS One. 2012;7(7):e41253.
  • Kato-Maeda M, Shanley CA, Ackart D, Jarlsberg LG, Shang S, Obregon-Henao A, Harton M, Basaraba RJ, Henao-Tamayo M, Barrozo JC, Rose J, Kawamura LM, Coscolla  M, Fofanov VY, Koshinsky H, Gagneux S, Hopewell PC, Ordway DJ, Orme IM. Beijing sublineages of Mycobacterium tuberculosis differ in pathogenicity in the guinea pig. Clin Vaccine Immunol. 2012 Aug;19(8):1227-37.
  • Garcia-Garcerà M, Coscollà M, Garcia-Etxebarria K, Martín-Caballero J, González-Candelas F, Latorre A, Calafell F. Staphylococcus prevails in the skin microbiota of long-term immunodeficient mice. Environ Microbiol. 2012 Aug;14(8):2087-98.

2011

  • Coscollá M, Comas I, González-Candelas F. Quantifying nonvertical inheritance in the evolution of Legionella pneumophila. Mol Biol Evol. 2011 Feb;28(2):985-1001.

2010

  • Coscolla M, Gagneux S. Does M. tuberculosis genomic diversity explain disease diversity? Drug Discov Today Dis Mech. 2010 Spring;7(1):e43-e59.
  • Coscollá M, Fenollar J, Escribano I, González-Candelas F. Legionellosis outbreak associated with asphalt paving machine, Spain, 2009. Emerg Infect Dis. 2010 Sep;16(9):1381-7.

2009

  • Coscollá M, González-Candelas F. Direct sequencing of Legionella pneumophila from respiratory samples for sequence-based typing analysis. J Clin Microbiol. 2009 Sep;47(9):2901-5.
  • Coscollá M, González-Candelas F. Comparison of clinical and environmental samples of Legionella pneumophila at the nucleotide sequence level. Infect Genet  Evol. 2009 Sep;9(5):882-8.

2007

  • Coscollá M, González-Candelas F. Population structure and recombination in environmental isolates of Legionella pneumophila. Environ Microbiol. 2007 Mar;9(3):643-56.

2006

  • Coscollá M, Gosalbes MJ, Catalán V, González-Candelas F. Genetic variability in environmental isolates of Legionella pneumophila from Comunidad Valenciana (Spain). Environ Microbiol. 2006 Jun;8(6):1056-63.
  • López-Labrador FX, Bracho MA, Berenguer M, Coscollà M, Rayón JM, Prieto M, Carrasco D, Gómez MD, Moya A, González-Candelas F. Genetic similarity of hepatitis C virus and fibrosis progression in chronic and recurrent infection after liver transplantation. J Viral Hepat. 2006 Feb;13(2):104-15.