Author

E. Ruppe

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Microbiology· 10 Evolutionary Biology· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 7 Organism:human· 5 Assay:metagenomics· 5 Approach:experimental assay· 4 Research Focus:host-pathogen & immune response· 4 Assay:whole-genome sequencing· 3 Organism:E. coli· 2 Research Focus:variant calling· 2

Frequent Co-Authors

M. Petitjean· 4 shared J. Schrenzel· 3 shared M. Girard· 3 shared V. Lazarevic· 3 shared A. Andremont· 2 shared B. Gonzalez-Zorn· 2 shared E. Denamur· 2 shared J. Lao· 2 shared

Activity by Year

2016-2023 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 17 mutual co-author links

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4 shared papersMicrobiology

M. Petitjean

Mutual co-authors in cluster

Author profile →

11 papers

Recent·Most cited

Inter-phylum circulation of a beta-lactamase - encoding gene: a rare but observable event

R. GSCHWIND, M. Petitjean, C. Fournier, J. Lao, O. Clermont, P. Nordmann, A. Mellmann, E. Denamur, L. Poirel, E. RUPPE

The paper reports the first inter-phylum transfer of an ESBL-encoding gene, blaMUN-1, between Bacteroidota and Pseudomonadota, highlighting rare but possible horizontal gene transfer events.

bioRxiv · Nov 10, 2023Microbiology

Within-host density and duration of colonization of multidrug-resistant Enterobacterales acquired during travel to the tropics

O. COTTO, L. Armand-Lefevre, S. MATHERON, E. RUPPE, F. Blanquart

The paper studies within-host dynamics of multidrug-resistant Enterobacterales in travelers, finding that resistant strains coexist with sensitive ones for months before abrupt clearance.

bioRxiv · Mar 3, 2023Microbiology

ResFinderFG v2.0: a database of antibiotic resistance genes obtained by functional metagenomics

R. Gschwind, S. Ugarcina Perovic, M. Weiss, M. Petitjean, J. Lao, L. P. Coelho, E. Ruppe

ResFinderFG v2.0 is a database of antibiotic resistance genes from functional metagenomics, improving resistome description by detecting ARGs not found in conventional databases.

bioRxiv · Oct 19, 2022Microbiology

Deciphering polymorphism in 61,157 Escherichia coli genomes via epistatic sequence landscapes

L. Vigue, G. Croce, M. Petitjean, E. Ruppe, O. Tenaillon, M. Weigt

The paper predicts polymorphisms in 61,157 Escherichia coli genomes using context-aware models, showing genetic context constrains amino-acid changes in 30-50% of sites.

bioRxiv · Jan 21, 2022Evolutionary Biology

Phylum barrier and Escherichia coli intra-species phylogeny drive the acquisition of resistome in E. coli

M. Petitjean, B. Condamine, E. Denamur, E. Ruppe

This study characterizes the resistome in 70,301 E. coli genomes, showing that phylogroup lineage and phylum barriers drive antibiotic resistance gene acquisition.

bioRxiv · Oct 26, 2020Microbiology

Relationship between the composition of the digestive microbiota and the concentrations of opportunistic pathogens in intensive care patients.

C. Fontaine, L. Armand-Lefèvre, M. Magnan, A. Nazimoudine, J.-F. Timsit, E. RUPPE

The study examines the relationship between intestinal and tracheal microbiota composition and colonization by multidrug-resistant Gram-negative bacilli in ICU patients, finding no link between microbiota diversity and MDR-GNB abundance but a negative link with Enterococcus spp.

bioRxiv · May 12, 2020 · PreprintMicrobiology

From genotype to antibiotic susceptibility phenotype in Enterobacteriaceae: a clinical perspective

E. Ruppe, A. Cherkaoui, M. Girard, S. Schicklin, V. Lazarevic, J. Schrenzel

This study evaluates the accuracy of predicting antibiotic susceptibility from whole-genomic sequencing in Enterobacteriaceae, finding high concordance rates but some errors due to chromosomal gene overexpression.

bioRxiv · Dec 22, 2018 · PreprintMicrobiology

The intestinal microbiota predisposes to traveller’s diarrhoea and to the carriage of multidrug-resistant Enterobacteriaceae after travelling to tropical regions

S. Leo, V. Lazarevic, N. Gaia, C. Estellat, M. Girard, S. Matheron, L. Armand-Lefevre, A. Andremont, The VOYAG-R Study Group, J. Schrenzel, E. Ruppe

The study examines how gut microbiota changes during and after travel to tropical regions and its association with traveller’s diarrhoea and multidrug-resistant Enterobacteriaceae (MRE) carriage.

bioRxiv · Feb 14, 2018Microbiology

Abundance and diversity of the fecal resistome in slaughter pigs and broilers in nine European countries

P. Munk, B. E. Knudsen, O. Lukjacenko, A. S. R. Duarte, R. E. C. Luiken, L. Van Gompel, L. A. M. Smit, H. Schmitt, A. D. Garcia, R. B. Hansen, T. N. Petersen, A. Bossers, E. Ruppe, H. Graveland, A. van Essen, , F. M. Aarestrup

The paper quantifies and compares the resistomes of slaughter pigs and broilers across nine European countries, finding differences in AMR gene abundance and diversity linked to country-specific antimicrobial usage.

bioRxiv · Sep 28, 2017Microbiology

In-Depth Resistome Analysis by Targeted Metagenomics

V. F. Lanza, F. Baquero, J. L. Martinez, R. Ramos-Ruiz, B. Gonzalez-Zorn, A. Andremont, A. Sanchez-Valenzuela, D. Ehrlich, S. Kennedy, E. Ruppe, W. van Schaik, R. J. Willems, F. de la Cruz, T. M. Coque

The paper introduces ResCap, a targeted metagenomics platform for analyzing resistomes, enhancing sensitivity and specificity in detecting antimicrobial resistance genes.

bioRxiv · Jan 30, 2017Microbiology

Clinical metagenomics of bone and joint infections: a proof of concept study

E. Ruppe, V. Lazarevic, M. Girard, W. Mouton, T. Ferry, F. Laurent, J. Schrenzel

This study evaluates clinical metagenomics for identifying pathogens and predicting antibiotic susceptibility in bone and joint infections, showing high accuracy in monomicrobial cases and partial success in polymicrobial cases.

bioRxiv · Nov 30, 2016Microbiology