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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. Angers-Loustau A, et al. Among authors: ruppe e. F1000Res. 2018 Apr 13;7:ISCB Comm J-459. doi: 10.12688/f1000research.14509.2. eCollection 2018. F1000Res. 2018. PMID: 30026930 Free PMC article. Review.
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. Lanza VF, et al. Among authors: ruppe e. Microbiome. 2018 Jan 15;6(1):11. doi: 10.1186/s40168-017-0387-y. Microbiome. 2018. PMID: 29335005 Free PMC article.
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. Ruppé E, et al. Nat Microbiol. 2019 Jan;4(1):112-123. doi: 10.1038/s41564-018-0292-6. Epub 2018 Nov 26. Nat Microbiol. 2019. PMID: 30478291
A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing.
Petrillo M, Fabbri M, Kagkli DM, Querci M, Van den Eede G, Alm E, Aytan-Aktug D, Capella-Gutierrez S, Carrillo C, Cestaro A, Chan KG, Coque T, Endrullat C, Gut I, Hammer P, Kay GL, Madec JY, Mather AE, McHardy AC, Naas T, Paracchini V, Peter S, Pightling A, Raffael B, Rossen J, Ruppé E, Schlaberg R, Vanneste K, Weber LM, Westh H, Angers-Loustau A. Petrillo M, et al. Among authors: ruppe e. F1000Res. 2021 Feb 8;10:80. doi: 10.12688/f1000research.39214.2. eCollection 2021. F1000Res. 2021. PMID: 35847383 Free PMC article.
ResFinder 4.0 for predictions of phenotypes from genotypes.
Bortolaia V, Kaas RS, Ruppe E, Roberts MC, Schwarz S, Cattoir V, Philippon A, Allesoe RL, Rebelo AR, Florensa AF, Fagelhauer L, Chakraborty T, Neumann B, Werner G, Bender JK, Stingl K, Nguyen M, Coppens J, Xavier BB, Malhotra-Kumar S, Westh H, Pinholt M, Anjum MF, Duggett NA, Kempf I, Nykäsenoja S, Olkkola S, Wieczorek K, Amaro A, Clemente L, Mossong J, Losch S, Ragimbeau C, Lund O, Aarestrup FM. Bortolaia V, et al. Among authors: ruppe e. J Antimicrob Chemother. 2020 Dec 1;75(12):3491-3500. doi: 10.1093/jac/dkaa345. J Antimicrob Chemother. 2020. PMID: 32780112 Free PMC article.
Lessons from a global antimicrobial resistance surveillance network.
Ruppé E; Network for Enhancing Tricycle ESBL Surveillance Efficiency (NETESE) group. Ruppé E, et al. Bull World Health Organ. 2023 Oct 1;101(10):672-678. doi: 10.2471/BLT.22.289520. Epub 2023 Sep 6. Bull World Health Organ. 2023. PMID: 37772195 Free PMC article.
128 results