selected papers

Published: 2021 Feb 5

Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era

Pöntinen, A.K., Top, J., Arredondo-Alonso, S. et al. Nat Commun 12, 1523 (2021). https://doi.org/10.1038/s41467-021-21749-5

Published: 2020 Aug 28

Antibiotic Resistance: Moving From Individual Health Norms to Social Norms in One Health and Global Health.

Hernando-Amado S, Coque TM, Baquero F, Martínez JL.

Front Microbiol. 2020 Aug 28;11:1914. doi: 10.3389/fmicb.2020.01914. eCollection 2020.

PMID: 32983000 Free PMC article. Review.

Published: 2018 Jan 15

In-depth resistome analysis by targeted metagenomics.

Lanza VF, Baquero F, Martínez JL, Ramos-Ruíz R, González-Zorn B, Andremont A, Sánchez-Valenzuela A, Ehrlich SD, Kennedy S, Ruppé E, van Schaik W, Willems RJ, de la Cruz F, Coque TM.

Microbiome. 2018 Jan 15;6(1):11. doi: 10.1186/s40168-017-0387-y.

PMID: 29335005 Free PMC article.

Published: 2018

The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies.

Angers-Loustau A, Petrillo M, Bengtsson-Palme J, Berendonk T, Blais B, Chan KG, Coque TM, Hammer P, Heß S, Kagkli DM, Krumbiegel C, Lanza VF, Madec JY, Naas T, O'Grady J, Paracchini V, Rossen JWA, Ruppé E, Vamathevan J, Venturi V, Van den Eede G.

F1000Res. 2018 Apr 13;7:ISCB Comm J-459. doi: 10.12688/f1000research.14509.2. eCollection 2018.

PMID: 30026930 Free PMC article. Review.

Published: 2019 Jun 21

Transfer dynamics of Tn6648, a composite integrative conjugative element generated by tandem accretion of Tn5801 and Tn6647 in Enterococcus faecalis.

León-Sampedro R, Fernández-de-Bobadilla MD, San Millán Á, Baquero F, Coque TM*. J Antimicrob Chemother. doi: 10.1093/jac/dkz239. PMID: 31225883.

Published: 2017 Dec 7

Multilevel population genetic analysis of vanA and vanB Enterococcus faecium causing nosocomial outbreaks in 27 countries (1986-2012).

Freitas AR, Tedim AP, Francia MV, Jensen LB, Novais C, Peixe L, Sánchez-Valenzuela A, Sundsfjord A, Hegstad K, Werner G, Sadowy E, Hammerum AM, Garcia-Migura L, Willems RJ, Baquero F, Coque TM.

J Antimicrob Chemother. 2016 Dec;71(12):3351-3366. doi: 10.1093/jac/dkw312. Epub 2016 Aug 15.

PMID: 27530756

Published: 201

The Plasmidome of Firmicutes: Impact on the Emergence and the Spread of Resistance to Antimicrobials.

Lanza VF, Tedim AP, Martínez JL, Baquero F, Coque TM.

Microbiol Spectr. 2015 Apr;3(2):PLAS-0039-2014. doi: 10.1128/microbiolspec.PLAS-0039-2014.

PMID: 26104702 Review.

Published: 2015 Mar 30

Polymorphic variation in susceptibility and metabolism of triclosan-resistant mutants of Escherichia coli and Klebsiella pneumoniae clinical strains obtained after exposure to biocides and antibiotics.

Curiao T, Marchi E, Viti C, Oggioni MR, Baquero F, Martinez JL, Coque TM.

Antimicrob Agents Chemother. 2015;59(6):3413-23. doi: 10.1128/AAC.00187-15. Epub 2015 Mar 30.

PMID: 25824225 Free PMC article.

Published: 2014 Dec 15

What is a resistance gene? Ranking risk in resistomes.

Martínez JL, Coque TM, Baquero F.

Nat Rev Microbiol. 2015 Feb;13(2):116-23. doi: 10.1038/nrmicro3399. Epub 2014 Dec 15.

PMID: 25534811 Review.

Published: 2016 Sep 23

AcCNET (Accessory Genome Constellation Network): comparative genomics software for accessory genome analysis using bipartite networks.

Lanza VF, Baquero F, de la Cruz F, Coque TM.

Bioinformatics. 2017 Jan 15;33(2):283-285. doi: 10.1093/bioinformatics/btw601. Epub 2016 Sep 23.

PMID: 27663497

Published: 2021

PATO: Pangenome Analysis Toolkit

Miguel D. Fernández-de-Bobadilla, Alba Talavera-Rodríguez, Lucía Chacón, Fernando Baquero, Teresa M. Coque, Val F. Lanza

bioRxiv 2021.01.30.428878; doi: https://doi.org/10.1101/2021.01.30.428878

Published: 2021

A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing

Petrillo M, Fabbri M, Kagkli DM et al. A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing [version 1; peer review: awaiting peer review]. F1000Research 2021, 10:80 (https://doi.org/10.12688/f1000research.39214.1)

Published 2019 Sep 4

Defining and combating antibiotic resistance from One Health and Global Health perspectives.

Hernando-Amado S, Coque TM, Baquero F, Martínez JL.

Nat Microbiol. 2019 Sep;4(9):1432-1442. doi: 10.1038/s41564-019-0503-9. Epub 2019 Aug 22.

PMID: 31439928 Review.

Published: 2019 Aug 21

Phylogenomics of Enterococcus faecalis from wild birds: new insights into host-associated differences in core and accessory genomes of the species.

León-Sampedro R, Del Campo R, Rodriguez-Baños M, Lanza VF, Pozuelo MJ, Francés-Cuesta C, Tedim AP, Freitas AR, Novais C, Peixe L, Willems RJL, Corander J, González Candelas F, Baquero F, Coque TM.

Environ Microbiol. 2019 Aug;21(8):3046-3062. doi: 10.1111/1462-2920.14702. Epub 2019 Jul 4.

PMID: 31162871

Published: 2019 Jan 4

Prediction of the intestinal resistome by a three-dimensional structure-based method.

Ruppé E, Ghozlane A, Tap J, Pons N, Alvarez AS, Maziers N, Cuesta T, Hernando-Amado S, Clares I, Martínez JL, Coque TM, Baquero F, Lanza VF, Máiz L, Goulenok T, de Lastours V, Amor N, Fantin B, Wieder I, Andremont A, van Schaik W, Rogers M, Zhang X, Willems RJL, de Brevern AG, Batto JM, Blottière HM, Léonard P, Léjard V, Letur A, Levenez F, Weiszer K, Haimet F, Doré J, Kennedy SP, Ehrlich SD.

Nat Microbiol. 2019 Jan;4(1):112-123. doi: 10.1038/s41564-018-0292-6. Epub 2018 Nov 26.

PMID: 30478291

Published: 2017 Jan

Long-term clonal dynamics of Enterococcus faecium strains causing bloodstream infections (1995-2015) in Spain.

Tedim AP, Ruíz-Garbajosa P, Rodríguez MC, Rodríguez-Baños M, Lanza VF, Derdoy L, Cárdenas Zurita G, Loza E, Cantón R, Baquero F, Coque TM.

J Antimicrob Chemother. 2017 Jan;72(1):48-55. doi: 10.1093/jac/dkw366. Epub 2016 Sep 21.

PMID: 27655856

Published: 2016 Jan 13

Multiple adaptive routes of Salmonella enterica Typhimurium to biocide and antibiotic exposure.

Curiao T, Marchi E, Grandgirard D, León-Sampedro R, Viti C, Leib SL, Baquero F, Oggioni MR, Martinez JL, Coque TM.

BMC Genomics. 2016 Jul 13;17:491. doi: 10.1186/s12864-016-2778-z.

PMID: 27411385 Free PMC article.

Published: 2015

Public health evolutionary biology of antimicrobial resistance: priorities for intervention.

Baquero F, Lanza VF, Cantón R, Coque TM.

Evol Appl. 2015 Mar;8(3):223-39. doi: 10.1111/eva.12235. Epub 2014 Dec 11.

PMID: 25861381 Free PMC article.

Published: 2014 Dec 29

Population biology of intestinal enterococcus isolates from hospitalized and nonhospitalized individuals in different age groups.

Tedim AP, Ruiz-Garbajosa P, Corander J, Rodríguez CM, Cantón R, Willems RJ, Baquero F, Coque TM.

Appl Environ Microbiol. 2015 Mar;81(5):1820-31. doi: 10.1128/AEM.03661-14. Epub 2014 Dec 29.

PMID: 25548052 Free PMC article.

Published: 2011 Jul 19

Multilevel population genetics in antibiotic resistance.

Baquero F, Coque TM.

FEMS Microbiol Rev. 2011 Sep;35(5):705-6. doi: 10.1111/j.1574-6976.2011.00293.x. Epub 2011 Jul 19.

PMID: 21714793 No abstract available.

Published: 2017

Genomic and metagenomic technologies to explore the antibiotic resistance mobilome.

Martínez JL, Coque TM, Lanza VF, de la Cruz F, Baquero F.

Ann N Y Acad Sci. 2017 Jan;1388(1):26-41. doi: 10.1111/nyas.13282. Epub 2016 Nov 10.

PMID: 27861983 Review.

Conference and Workshop Reports

2021. Angers-Loustau A, Petrillo M, Bengtsson-Palme J, Berendonk T, Blais B, Chan KG, Coque TM, Hammer P, Heß S, Kagkli DM, Krumbiegel C, Lanza VF, Madec J-Y, Naas T, O’Grady J, Paracchini V, Rossen JWA, Ruppé E, Vamathevan J, Venturi V, Van den Eede G: The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies. F1000Research, 7, 459 (2018). doi: 10.12688/f1000research.14509.2

2019. Scientific Research Agenda on Antimicrobial Resistance of the Joint Programming Initiative on Antimicrobial Resistance. https://www.jpiamr.eu/wp-content/uploads/2019/05/JPIAMR_SRIA_final.pdf

2018. FAO/WHO Scientific advice report on foodborne antimicrobial resistance resulting from the FAO/WHO expert meeting on foodborne antimicrobial resistance: Role of environment, crops and biocides Rome, 11-15 June 2018. https://www.who.int/foodsafety/publications/Environment-Crops-and-Biocides/en/

2017. European Comission. Joint Research Centre (JRC) Conference and Workshop Reports. The Role and Implementation of Next-Generation Sequencing Technologies in the Coordinated Action Plan against Antimicrobial Resistance. March 21th - 22nd, 2017 Villa Borghi, Italy. JRC Conference and Workshop Report, EUR 28619 (2017). doi: 10.2760/745099

TECHNOLOGICAL TRANSFERENCE

Bioinformatic freetware. Available at https://github.com/irycisBioinfo/PATO/wiki

ResCap. Transference to Roche-Nimblegene. Application of SeqCapE