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Simulating Multilevel Dynamics of Antimicrobial Resistance in a Membrane Computing Model.

Campos M, Capilla R, Naya F, Futami R, Coque T, Moya A, Fernandez-Lanza V, Cantón R, Sempere JM, Llorens C, Baquero F.

MBio. 2019 Jan 29;10(1). pii: e02460-18. doi: 10.1128/mBio.02460-18.


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.

Version 2. F1000Res. 2018 Apr 13 [revised 2018 Jan 1];7. pii: ISCB Comm J-459. doi: 10.12688/f1000research.14509.2. eCollection 2018.


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.


Update on prevalence and mechanisms of resistance to linezolid, tigecycline and daptomycin in enterococci in Europe: Towards a common nomenclature.

Bender JK, Cattoir V, Hegstad K, Sadowy E, Coque TM, Westh H, Hammerum AM, Schaffer K, Burns K, Murchan S, Novais C, Freitas AR, Peixe L, Del Grosso M, Pantosti A, Werner G.

Drug Resist Updat. 2018 Sep;40:25-39. doi: 10.1016/j.drup.2018.10.002. Epub 2018 Nov 2.


First Report of an OXA-48- and CTX-M-213-Producing Kluyvera Species Clone Recovered from Patients Admitted in a University Hospital in Madrid, Spain.

Hernández-García M, León-Sampedro R, Pérez-Viso B, Morosini MI, López-Fresneña N, Díaz-Agero C, Coque TM, Ruiz-Garbajosa P, Cantón R.

Antimicrob Agents Chemother. 2018 Oct 24;62(11). pii: e01238-18. doi: 10.1128/AAC.01238-18. Print 2018 Nov.


Antimicrobial Resistance in Enterococcus spp. of animal origin.

Torres C, Alonso CA, Ruiz-Ripa L, León-Sampedro R, Del Campo R, Coque TM.

Microbiol Spectr. 2018 Jul;6(4). doi: 10.1128/microbiolspec.ARBA-0032-2018. Review.


Enterococcus spp. in Ragusano PDO and Pecorino Siciliano cheese types: A snapshot of their antibiotic resistance distribution.

Russo N, Caggia C, Pino A, Coque TM, Arioli S, Randazzo CL.

Food Chem Toxicol. 2018 Oct;120:277-286. doi: 10.1016/j.fct.2018.07.023. Epub 2018 Jul 20.


Water supply and feed as sources of antimicrobial-resistant Enterococcus spp. in aquacultures of rainbow trout (Oncorhyncus mykiss), Portugal.

Novais C, Campos J, Freitas AR, Barros M, Silveira E, Coque TM, Antunes P, Peixe L.

Sci Total Environ. 2018 Jun 1;625:1102-1112. doi: 10.1016/j.scitotenv.2017.12.265. Epub 2018 Jan 12.


Wild corvid birds colonized with vancomycin-resistant Enterococcus faecium of human origin harbor epidemic vanA plasmids.

Oravcová V, Peixe L, Coque TM, Novais C, Francia MV, Literák I, Freitas AR.

Environ Int. 2018 Sep;118:125-133. doi: 10.1016/j.envint.2018.05.039. Epub 2018 Jun 2.


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.


High rates of colonisation by ampicillin-resistant enterococci in residents of long-term care facilities in Porto, Portugal.

Freitas AR, Novais C, Duarte B, Pereira AP, Coque TM, Peixe L.

Int J Antimicrob Agents. 2018 Mar;51(3):503-507. doi: 10.1016/j.ijantimicag.2017.11.007. Epub 2017 Nov 23.


Distribution of putative virulence markers in Enterococcus faecium: towards a safety profile review.

Freitas AR, Tedim AP, Novais C, Coque TM, Peixe L.

J Antimicrob Chemother. 2018 Feb 1;73(2):306-319. doi: 10.1093/jac/dkx387.


Detection of optrA in the African continent (Tunisia) within a mosaic Enterococcus faecalis plasmid from urban wastewaters.

Freitas AR, Elghaieb H, León-Sampedro R, Abbassi MS, Novais C, Coque TM, Hassen A, Peixe L.

J Antimicrob Chemother. 2017 Dec 1;72(12):3245-3251. doi: 10.1093/jac/dkx321.


Complete Genome Sequences of Isolates of Enterococcus faecium Sequence Type 117, a Globally Disseminated Multidrug-Resistant Clone.

Tedim AP, Lanza VF, Manrique M, Pareja E, Ruiz-Garbajosa P, Cantón R, Baquero F, Coque TM, Tobes R.

Genome Announc. 2017 Mar 30;5(13). pii: e01553-16. doi: 10.1128/genomeA.01553-16.


Rapid detection of high-risk Enterococcus faecium clones by matrix-assisted laser desorption ionization time-of-flight mass spectrometry.

Freitas AR, Sousa C, Novais C, Silva L, Ramos H, Coque TM, Lopes J, Peixe L.

Diagn Microbiol Infect Dis. 2017 Apr;87(4):299-307. doi: 10.1016/j.diagmicrobio.2016.12.007. Epub 2016 Dec 14.


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. Review.


Elucidating constraints for differentiation of major human Klebsiella pneumoniae clones using MALDI-TOF MS.

Rodrigues C, Novais Â, Sousa C, Ramos H, Coque TM, Cantón R, Lopes JA, Peixe L.

Eur J Clin Microbiol Infect Dis. 2017 Feb;36(2):379-386. doi: 10.1007/s10096-016-2812-8. Epub 2016 Nov 3.


Co-diversification of Enterococcus faecium Core Genomes and PBP5: Evidences of pbp5 Horizontal Transfer.

Novais C, Tedim AP, Lanza VF, Freitas AR, Silveira E, Escada R, Roberts AP, Al-Haroni M, Baquero F, Peixe L, Coque TM.

Front Microbiol. 2016 Oct 6;7:1581. eCollection 2016.


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.


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. Epub 2016 Sep 21.


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. Epub 2016 Aug 15.


Dissemination of Novel Antimicrobial Resistance Mechanisms through the Insertion Sequence Mediated Spread of Metabolic Genes.

Furi L, Haigh R, Al Jabri ZJ, Morrissey I, Ou HY, León-Sampedro R, Martinez JL, Coque TM, Oggioni MR.

Front Microbiol. 2016 Jun 28;7:1008. doi: 10.3389/fmicb.2016.01008. eCollection 2016.


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.


Global Emergence and Dissemination of Enterococci as Nosocomial Pathogens: Attack of the Clones?

Guzman Prieto AM, van Schaik W, Rogers MR, Coque TM, Baquero F, Corander J, Willems RJ.

Front Microbiol. 2016 May 26;7:788. doi: 10.3389/fmicb.2016.00788. eCollection 2016. Review.


The impact of host metapopulation structure on the population genetics of colonizing bacteria.

Numminen E, Gutmann M, Shubin M, Marttinen P, Méric G, van Schaik W, Coque TM, Baquero F, Willems RJ, Sheppard SK, Feil EJ, Hanage WP, Corander J.

J Theor Biol. 2016 May 7;396:53-62. doi: 10.1016/j.jtbi.2016.02.019. Epub 2016 Feb 23.


Diversity and Evolution of the Tn5801-tet(M)-Like Integrative and Conjugative Elements among Enterococcus, Streptococcus, and Staphylococcus.

León-Sampedro R, Novais C, Peixe L, Baquero F, Coque TM.

Antimicrob Agents Chemother. 2016 Jan 4;60(3):1736-46. doi: 10.1128/AAC.01864-15.


Relevance of tcrYAZB operon acquisition for Enterococcus survival at high copper concentrations under anaerobic conditions.

Mourão J, Rae J, Silveira E, Freitas AR, Coque TM, Peixe L, Antunes P, Novais C.

J Antimicrob Chemother. 2016 Feb;71(2):560-3. doi: 10.1093/jac/dkv330. Epub 2015 Oct 19. No abstract available.


Erratum to: Investigating the mobilome in clinically important lineages of Enterococcus faecium and Enterococcus faecalis.

Mikalsen T, Pedersen T, Willems R, Coque TM, Werner G, Sadowy E, van Schaik W, Jensen LB, Francia MV, Sundsfjord A, Hegstad K.

BMC Genomics. 2015 Sep 15;16(1):689. doi: 10.1186/s12864-015-1722-y. No abstract available.


A membrane computing simulator of trans-hierarchical antibiotic resistance evolution dynamics in nested ecological compartments (ARES).

Campos M, Llorens C, Sempere JM, Futami R, Rodriguez I, Carrasco P, Capilla R, Latorre A, Coque TM, Moya A, Baquero F.

Biol Direct. 2015 Aug 5;10:41. doi: 10.1186/s13062-015-0070-9.


Sequencing of plasmids pAMBL1 and pAMBL2 from Pseudomonas aeruginosa reveals a blaVIM-1 amplification causing high-level carbapenem resistance.

San Millan A, Toll-Riera M, Escudero JA, Cantón R, Coque TM, MacLean RC.

J Antimicrob Chemother. 2015 Nov;70(11):3000-3. doi: 10.1093/jac/dkv222. Epub 2015 Jul 24.


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. Review.


Prioritizing risks of antibiotic resistance genes in all metagenomes.

Martínez JL, Coque TM, Baquero F.

Nat Rev Microbiol. 2015 Jun;13(6):396. doi: 10.1038/nrmicro3399-c2. Epub 2015 Apr 27. No abstract available.


Investigating the mobilome in clinically important lineages of Enterococcus faecium and Enterococcus faecalis.

Mikalsen T, Pedersen T, Willems R, Coque TM, Werner G, Sadowy E, van Schaik W, Jensen LB, Sundsfjord A, Hegstad K.

BMC Genomics. 2015 Apr 10;16:282. doi: 10.1186/s12864-015-1407-6. Erratum in: BMC Genomics. 2015;16(1):689.


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.


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.


Significant Differences Characterise the Correlation Coefficients between Biocide and Antibiotic Susceptibility Profiles in Staphylococcus aureus.

Oggioni MR, Coelho JR, Furi L, Knight DR, Viti C, Orefici G, Martinez JL, Freitas AT, Coque TM, Morrissey I; BIOHYPO consortium.

Curr Pharm Des. 2015;21(16):2054-7.


A hospital sewage ST17 Enterococcus faecium with a transferable Inc18-like plasmid carrying genes coding for resistance to antibiotics and quaternary ammonium compounds (qacZ).

Silveira E, Marques P, Freitas AR, Mourão J, Coque TM, Antunes P, Peixe L, Novais C.

J Glob Antimicrob Resist. 2015 Mar;3(1):49-51. doi: 10.1016/j.jgar.2014.11.005. Epub 2014 Dec 3. No abstract available.


Antibiotic-resistant Klebsiella pneumoniae and Escherichia coli high-risk clones and an IncFII(k) mosaic plasmid hosting Tn1 (blaTEM-4) in isolates from 1990 to 2004.

Rodríguez I, Novais Â, Lira F, Valverde A, Curião T, Martínez JL, Baquero F, Cantón R, Coque TM.

Antimicrob Agents Chemother. 2015 May;59(5):2904-8. doi: 10.1128/AAC.00296-15. Epub 2015 Feb 17.


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.


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. Review.


Plasmid flux in Escherichia coli ST131 sublineages, analyzed by plasmid constellation network (PLACNET), a new method for plasmid reconstruction from whole genome sequences.

Lanza VF, de Toro M, Garcillán-Barcia MP, Mora A, Blanco J, Coque TM, de la Cruz F.

PLoS Genet. 2014 Dec 18;10(12):e1004766. doi: 10.1371/journal.pgen.1004766. eCollection 2014 Dec.


Widening the spaces of selection: evolution along sublethal antimicrobial gradients.

Baquero F, Coque TM.

MBio. 2014 Dec 9;5(6):e02270. doi: 10.1128/mBio.02270-14.


Counteracting antibiotic resistance: breaking barriers among antibacterial strategies.

Baquero F, Coque TM, Cantón R.

Expert Opin Ther Targets. 2014 Aug;18(8):851-61. doi: 10.1517/14728222.2014.925881. Epub 2014 May 31. Review.


Extrachromosomal and Mobile Elements in Enterococci: Transmission, Maintenance, and Epidemiology.

Clewell DB, Weaver KE, Dunny GM, Coque TM, Francia MV, Hayes F.

In: Gilmore MS, Clewell DB, Ike Y, Shankar N, editors. Enterococci: From Commensals to Leading Causes of Drug Resistant Infection [Internet]. Boston: Massachusetts Eye and Ear Infirmary; 2014-.
2014 Feb 9.


MALDI-TOF mass spectrometry as a tool for the discrimination of high-risk Escherichia coli clones from phylogenetic groups B2 (ST131) and D (ST69, ST405, ST393).

Novais Â, Sousa C, de Dios Caballero J, Fernandez-Olmos A, Lopes J, Ramos H, Coque TM, Cantón R, Peixe L.

Eur J Clin Microbiol Infect Dis. 2014 Aug;33(8):1391-9. doi: 10.1007/s10096-014-2071-5. Epub 2014 Mar 7.


Evaluation of epidemiological cut-off values indicates that biocide resistant subpopulations are uncommon in natural isolates of clinically-relevant microorganisms.

Morrissey I, Oggioni MR, Knight D, Curiao T, Coque T, Kalkanci A, Martinez JL; BIOHYPO Consortium.

PLoS One. 2014 Jan 23;9(1):e86669. doi: 10.1371/journal.pone.0086669. eCollection 2014.


Co-transfer of resistance to high concentrations of copper and first-line antibiotics among Enterococcus from different origins (humans, animals, the environment and foods) and clonal lineages.

Silveira E, Freitas AR, Antunes P, Barros M, Campos J, Coque TM, Peixe L, Novais C.

J Antimicrob Chemother. 2014 Apr;69(4):899-906. doi: 10.1093/jac/dkt479. Epub 2013 Dec 15.


Spread of multidrug-resistant Enterococcus to animals and humans: an underestimated role for the pig farm environment.

Novais C, Freitas AR, Silveira E, Antunes P, Silva R, Coque TM, Peixe L.

J Antimicrob Chemother. 2013 Dec;68(12):2746-54. doi: 10.1093/jac/dkt289. Epub 2013 Jul 16.


Diversity and biofilm-production ability among isolates of Escherichia coli phylogroup D belonging to ST69, ST393 and ST405 clonal groups.

Novais Â, Vuotto C, Pires J, Montenegro C, Donelli G, Coque TM, Peixe L.

BMC Microbiol. 2013 Jun 21;13:144. doi: 10.1186/1471-2180-13-144.


Multiclonal dispersal of KPC genes following the emergence of non-ST258 KPC-producing Klebsiella pneumoniae clones in Madrid, Spain.

Ruiz-Garbajosa P, Curiao T, Tato M, Gijón D, Pintado V, Valverde A, Baquero F, Morosini MI, Coque TM, Cantón R.

J Antimicrob Chemother. 2013 Nov;68(11):2487-92. doi: 10.1093/jac/dkt237. Epub 2013 Jun 20.


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