PharmD, qualification in clinical biology.
PhD in infectious diseases.

2021-today: Full Professor at the University Paris Cité and the bacteriology laboratory of the Bichat-Claude Bernard hospital.

2017-2021: Associate Professor at the University of Paris 7 and the bacteriology laboratory of the Bichat-Claude Bernard hospital.

2009-2013: Assistant Professor at the University Paris 7 faculty of Medicine and the bacteriology laboratory of the Bichat-Claude Bernard hospital.

2021-today: co-head of the team « EVRest » UMR1137 IAME.

2015-2017: Post-doctoral fellowship at the Geneva University Hospitals (Switzerland)

2013-2015: Post-doctoral fellowship at INRAe Jouy-en-Josas (France).

Gschwind R, Ugarcina Perovic S, Weiss M, Petitjean M, Lao J, Coelho LP, Ruppé E
ResFinderFG v2.0: a database of antibiotic resistance genes obtained by functional metagenomics.
Nucleic Acids Research 2023, 51, W493-W500.

Patrier J, Villageois-Tran K, Szychowiak P, Ruckly S, Gschwind R, Wicky PH, Gueye S, Armand-Lefevre L, Marzouk M, Sonneville R, Bouadma L, Petitjean M, Lamara F, de Montmollin E, Timsit JF, Ruppé E, French COVID Cohort Study Group
Oropharyngeal and intestinal concentrations of opportunistic pathogens are independently associated with death of SARS-CoV-2 critically ill adults.
Critical Care (London, England) 2022, 26, 300.

Habib A, Lo S, Villageois-Tran K, Petitjean M, Malik SA, Armand-Lefèvre L, Ruppé E, Zahra R
Dissemination of carbapenemase-producing Enterobacterales in the community of Rawalpindi, Pakistan.
PloS One 2022, 17, e0270707.

Petitjean M, Condamine B, Burdet C, Denamur E, Ruppé E
Phylum barrier and Escherichia coli intra-species phylogeny drive the acquisition of antibiotic-resistance genes.
Microbial Genomics 2021

Ruppé E, Cherkaoui A, Charretier Y, Girard M, Schicklin S, Lazarevic V, Schrenzel J
From genotype to antibiotic susceptibility phenotype in the order Enterobacterales: a clinical perspective.
Clinical Microbiology and Infection: The Official Publication of the European Society of Clinical Microbiology and Infectious Diseases 2020, 26, 643.e1-643.e7.

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
ResFinder 4.0 for predictions of phenotypes from genotypes.
The Journal of Antimicrobial Chemotherapy 2020, 75, 3491-3500.

Fontaine C, Armand-Lefèvre L, Magnan M, Nazimoudine A, Timsit JF, Ruppé E
Relationship between the composition of the intestinal microbiota and the tracheal and intestinal colonization by opportunistic pathogens in intensive care patients.
PloS One 2020, 15, e0237260.

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
Prediction of the intestinal resistome by a three-dimensional structure-based method.
Nature Microbiology 2019, 4, 112-123.

Leo S, Lazarevic V, Gaïa N, Estellat C, Girard M, Matheron S, Armand-Lefèvre L, Andremont A, Schrenzel J, Ruppé E
The intestinal microbiota predisposes to traveler's diarrhea and to the carriage of multidrug-resistant Enterobacteriaceae after traveling to tropical regions.
Gut Microbes 2019, 10, 631-641.

Ruppé E, Olearo F, Pires D, Baud D, Renzi G, Cherkaoui A, Goldenberger D, Huttner A, François P, Harbarth S, Schrenzel J
Clonal or not clonal? Investigating hospital outbreaks of KPC-producing Klebsiella pneumoniae with whole-genome sequencing.
Clinical Microbiology and Infection: The Official Publication of the European Society of Clinical Microbiology and Infectious Diseases 2017, 23, 470-475.

Ruppé E, Lazarevic V, Girard M, Mouton W, Ferry T, Laurent F, Schrenzel J
Clinical metagenomics of bone and joint infections: a proof of concept study.
Scientific Reports 2017, 7, 7718.

Ruppé E, Armand-Lefèvre L, Estellat C, Consigny PH, El Mniai A, Boussadia Y, Goujon C, Ralaimazava P, Campa P, Girard PM, Wyplosz B, Vittecoq D, Bouchaud O, Le Loup G, Pialoux G, Perrier M, Wieder I, Moussa N, Esposito-Farèse M, Hoffmann I, Coignard B, Lucet JC, Andremont A, Matheron S
High Rate of Acquisition but Short Duration of Carriage of Multidrug-Resistant Enterobacteriaceae After Travel to the Tropics.
Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America 2015, 61, 593-600.

Ruppé É, Woerther PL, Barbier F
Mechanisms of antimicrobial resistance in Gram-negative bacilli..
Annals of intensive care 2015, 5, 61.

Ruppé E, Lixandru B, Cojocaru R, Büke C, Paramythiotou E, Angebault C, Visseaux C, Djuikoue I, Erdem E, Burduniuc O, El Mniai A, Marcel C, Perrier M, Kesteman T, Clermont O, Denamur E, Armand-Lefèvre L, Andremont A
Relative fecal abundance of extended-spectrum-β-lactamase-producing Escherichia coli strains and their occurrence in urinary tract infections in women.
Antimicrobial Agents and Chemotherapy 2013, 57, 4512-4517.

Ruppé E, Barbier F, Mesli Y, Maiga A, Cojocaru R, Benkhalfat M, Benchouk S, Hassaine H, Maiga I, Diallo A, Koumaré AK, Ouattara K, Soumaré S, Dufourcq JB, Nareth C, Sarthou JL, Andremont A, Ruimy R
Diversity of staphylococcal cassette chromosome mec structures in methicillin-resistant Staphylococcus epidermidis and Staphylococcus haemolyticus strains among outpatients from four countries..
Antimicrobial agents and chemotherapy 2009, 53, 442-449.

Ruimy R, Armand-Lefevre L, Barbier F, Ruppé E, Cocojaru R, Mesli Y, Maiga A, Benkalfat M, Benchouk S, Hassaine H, Dufourcq JB, Nareth C, Sarthou JL, Andremont A, Feil EJ
Comparisons between geographically diverse samples of carried Staphylococcus aureus..
Journal of bacteriology 2009, 191, 5577-5583.

Ruppé E, Hem S, Lath S, Gautier V, Ariey F, Sarthou JL, Monchy D, Arlet G
CTX-M beta-lactamases in Escherichia coli from community-acquired urinary tract infections, Cambodia..
Emerging infectious diseases 2009, 15, 741-748.

2024

d'Humières C, Delavy M, Alla L, Ichou F, Gauliard E, Ghozlane A, Levenez F, Galleron N, Quinquis B, Pons N, Mullaert J, Bridier-Nahmias A, Condamine B, Touchon M, Rainteau D, Lamazière A, Lesnik P, Ponnaiah M, Lhomme M, Sertour N, Devente S, Docquier JD, Bougnoux ME, Tenaillon O, Magnan M, Ruppé E, Grall N, Duval X, Ehrlich D, Mentré F, Denamur E, Rocha EPC, Le Chatelier E, Burdet C, PrediRes study group
Perturbation and resilience of the gut microbiome up to 3 months after β-lactams exposure in healthy volunteers suggest an important role of microbial β-lactamases.
Microbiome 2024, 12, 50.

2023

Bengtsson-Palme J, Abramova A, Berendonk TU, Coelho LP, Forslund SK, Gschwind R, Heikinheimo A, Jarquín-Díaz VH, Khan AA, Klümper U, Löber U, Nekoro M, Osińska AD, Ugarcina Perovic S, Pitkänen T, Rødland EK, Ruppé E, Wasteson Y, Wester AL, Zahra R
Towards monitoring of antimicrobial resistance in the environment: For what reasons, how to implement it, and what are the data needs?.
Environment International 2023, 178, 108089.

Cotto O, Armand-Lefèvre L, Matheron S, Ruppé E, Blanquart F
Within-Host Dynamics and Duration of Colonization of Travel-Acquired Multidrug-Resistant Enterobacterales in Untreated Individuals.
Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America 2023, 77, 934-936.

Rondinaud E, Clermont O, Petitjean M, Ruppé E, Esposito-Farèse M, Nazimoudine A, VOYAG-R Study Group, Coignard B, Matheron S, Andremont A, Denamur E, Armand-Lefevre L
Acquisition of Enterobacterales carrying the colistin resistance gene mcr following travel to the tropics.
Journal of Travel Medicine 2023, 30, taac141.

Gschwind R, Ugarcina Perovic S, Weiss M, Petitjean M, Lao J, Coelho LP, Ruppé E
ResFinderFG v2.0: a database of antibiotic resistance genes obtained by functional metagenomics.
Nucleic Acids Research 2023, 51, W493-W500.

Hauser S, Lazarevic V, Tournoud M, Ruppé E, Santiago Allexant E, Guigon G, Schicklin S, Lanet V, Girard M, Mirande C, Gervasi G, Schrenzel J
A metagenomics method for the quantitative detection of bacterial pathogens causing hospital-associated and ventilator-associated pneumonia.
Microbiology Spectrum 2023, e0129423.

Dalmasso G, Beyrouthy R, Brugiroux S, Ruppé E, Guillouard L, Bonnin V, Saint-Sardos P, Ghozlane A, Gaumet V, Barnich N, Delmas J, Bonnet R
Genes mcr improve the intestinal fitness of pathogenic E. coli and balance their lifestyle to commensalism.
Microbiome 2023, 11, 12.

Dalmasso G, Beyrouthy R, Brugiroux S, Ruppé E, Guillouard L, Bonnin V, Saint-Sardos P, Ghozlane A, Gaumet V, Barnich N, Delmas J, Bonnet R
Correction: Genes mcr improve the intestinal fitness of pathogenic E. coli and balance their lifestyle to commensalism.
Microbiome 2023, 11, 23.

Ruppé E, Network for Enhancing Tricycle ESBL Surveillance Efficiency (NETESE) group
Lessons from a global antimicrobial resistance surveillance network.
Bulletin of the World Health Organization 2023, 101, 672-678.

Rezzoug I, Visseaux B, Bertine M, Parisey M, Bonnal C, Ruppe E, Descamps D, Timsit JF, Yazdanpanah Y, Armand-Lefevre L, Houze S, Argy N
Faecal Viral Excretion and Gastrointestinal Co-Infection Do Not Explain Digestive Presentation in COVID-19 Patients.
Microorganisms 2023, 11, 1780.

2022

Guk J, Bridier-Nahmias A, Magnan M, Grall N, Duval X, Clermont O, Ruppé E, d'Humières C, Tenaillon O, Denamur E, Mentré F, Guedj J, Burdet C, CEREMI study group
Modeling the bacterial dynamics in the gut microbiota following an antibiotic-induced perturbation.
CPT: pharmacometrics & systems pharmacology 2022, 11, 906-918.

Ruppé E, d'Humières C, Armand-Lefèvre L
Inferring antibiotic susceptibility from metagenomic data: dream or reality?.
Clinical Microbiology and Infection: The Official Publication of the European Society of Clinical Microbiology and Infectious Diseases 2022, 28, 1225-1229.

Blot S, Ruppé E, Harbarth S, Asehnoune K, Poulakou G, Luyt CE, Rello J, Klompas M, Depuydt P, Eckmann C, Martin-Loeches I, Povoa P, Bouadma L, Timsit JF, Zahar JR
Healthcare-associated infections in adult intensive care unit patients: Changes in epidemiology, diagnosis, prevention and contributions of new technologies.
Intensive & Critical Care Nursing 2022, 70, 103227.

Vigué L, Croce G, Petitjean M, Ruppé E, Tenaillon O, Weigt M
Deciphering polymorphism in 61,157 Escherichia coli genomes via epistatic sequence landscapes.
Nature Communications 2022, 13, 4030.

Lo S, Lolom I, Goldstein V, Petitjean M, Rondinaud E, Bunel-Gourdy V, Tran Dinh A, Wicky PH, Ruppé E, d'Humières C, Lucet JC, Armand-Lefèvre L
Simultaneous Hospital Outbreaks of New Delhi Metallo-β-Lactamase-Producing Enterobacterales Unraveled Using Whole-Genome Sequencing.
Microbiology Spectrum 2022, 10, e0228721.

Patrier J, Villageois-Tran K, Szychowiak P, Ruckly S, Gschwind R, Wicky PH, Gueye S, Armand-Lefevre L, Marzouk M, Sonneville R, Bouadma L, Petitjean M, Lamara F, de Montmollin E, Timsit JF, Ruppé E, French COVID Cohort Study Group
Oropharyngeal and intestinal concentrations of opportunistic pathogens are independently associated with death of SARS-CoV-2 critically ill adults.
Critical Care (London, England) 2022, 26, 300.

Habib A, Lo S, Villageois-Tran K, Petitjean M, Malik SA, Armand-Lefèvre L, Ruppé E, Zahra R
Dissemination of carbapenemase-producing Enterobacterales in the community of Rawalpindi, Pakistan.
PloS One 2022, 17, e0270707.

d'Humières C, Gaïa N, Gueye S, de Lastours V, Leflon-Guibout V, Maataoui N, Duprilot M, Lecronier M, Rousseau MA, Gamany N, Lescure FX, Senard O, Deconinck L, Dollat M, Isernia V, Le Hur AC, Petitjean M, Nazimoudine A, Le Gac S, Chalal S, Ferreira S, Lazarevic V, Guigon G, Gervasi G, Armand-Lefèvre L, Schrenzel J, Ruppé E
Contribution of Clinical Metagenomics to the Diagnosis of Bone and Joint Infections.
Frontiers in Microbiology 2022, 13, 863777.

2021

Maataoui N, Chemali L, Patrier J, Tran Dinh A, Le Fèvre L, Lortat-Jacob B, Marzouk M, d'Humières C, Rondinaud E, Ruppé E, Montravers P, Timsit JF, Armand-Lefèvre L
Impact of rapid multiplex PCR on management of antibiotic therapy in COVID-19-positive patients hospitalized in intensive care unit.
European Journal of Clinical Microbiology & Infectious Diseases: Official Publication of the European Society of Clinical Microbiology 2021, 40, 2227-2234.

d'Humières C, Salmona M, Dellière S, Leo S, Rodriguez C, Angebault C, Alanio A, Fourati S, Lazarevic V, Woerther PL, Schrenzel J, Ruppé E
The Potential Role of Clinical Metagenomics in Infectious Diseases: Therapeutic Perspectives.
Drugs 2021, 81, 1453-1466.

Deconinck L, Gschwind R, Petitjean M, Gueye S, Leflon-Guibout V, Maataoui N, Rondinaud E, Suard A, Gallais K, Richaud R, Fuchs A, Iung B, Alkhoder S, Ismaël S, Herrou J, Prié H, Armand-Lefèvre L, d'Humières C, Ruppé E
Endocarditis caused by Thalassospira sp.
IDCases 2021, 24, e01109.

Woerther PL, d'Humières C, Lescure X, Dubreuil L, Rodriguez C, Barbier F, Fihman V, Ruppé E
Is the term "anti-anaerobic" still relevant?.
International journal of infectious diseases: IJID: official publication of the International Society for Infectious Diseases 2021, 102, 178-180.

Sadek M, Ruppé E, Habib A, Zahra R, Poirel L, Nordmann P
International circulation of aztreonam/avibactam-resistant NDM-5-producing Escherichia coli isolates: successful epidemic clones.
Journal of Global Antimicrobial Resistance 2021, 27, 326-328.

Petitjean M, Condamine B, Burdet C, Denamur E, Ruppé E
Phylum barrier and Escherichia coli intra-species phylogeny drive the acquisition of antibiotic-resistance genes.
Microbial Genomics 2021

Armand-Lefèvre L, Rondinaud E, Desvillechabrol D, Mullaert J, Clermont O, Petitjean M, Ruppe E, Cokelaer T, Bouchier C, Tenaillon O, Ma L, Nooroya Y, Matheron S, The Voyag-R Study Group , Andremont A, Denamur E, Kennedy SP
Dynamics of extended-spectrum beta-lactamase-producing Enterobacterales colonization in long-term carriers following travel abroad.
Microbial Genomics 2021, 7, 000576.

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
A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing..
F1000Research 2021, 10, 80.

d'Humières C, Patrier J, Lortat-Jacob B, Tran-Dinh A, Chemali L, Maataoui N, Rondinaud E, Ruppé E, Burdet C, Ruckly S, Montravers P, Timsit JF, Armand-Lefevre L
Two original observations concerning bacterial infections in COVID-19 patients hospitalized in intensive care units during the first wave of the epidemic in France.
PloS One 2021, 16, e0250728.

Delaroche L, Bertine M, Oger P, Descamps D, Damond F, Genauzeau E, Meicler P, Le Hingrat Q, Lamazou F, Gschwind R, Ruppé E, Visseaux B
Evaluation of SARS-CoV-2 in semen, seminal plasma, and spermatozoa pellet of COVID-19 patients in the acute stage of infection.
PloS One 2021, 16, e0260187.

2020

Birgand G, Schouten J, Ruppé E
Less contact isolation is more in the ICU: con.
Intensive Care Medicine 2020, 46, 1732-1734.

Timsit JF, Ruppé E, Barbier F, Tabah A, Bassetti M
Bloodstream infections in critically ill patients: an expert statement.
Intensive Care Medicine 2020, 46, 266-284.

Andremont O, Armand-Lefevre L, Dupuis C, de Montmollin E, Ruckly S, Lucet JC, Smonig R, Magalhaes E, Ruppé E, Mourvillier B, Lebut J, Lermuzeaux M, Sonneville R, Bouadma L, Timsit JF, COMBACTE net consortium
Semi-quantitative cultures of throat and rectal swabs are efficient tests to predict ESBL-Enterobacterales ventilator-associated pneumonia in mechanically ventilated ESBL carriers.
Intensive Care Medicine 2020, 46, 1232-1242.

Ruppé E, Cherkaoui A, Charretier Y, Girard M, Schicklin S, Lazarevic V, Schrenzel J
From genotype to antibiotic susceptibility phenotype in the order Enterobacterales: a clinical perspective.
Clinical Microbiology and Infection: The Official Publication of the European Society of Clinical Microbiology and Infectious Diseases 2020, 26, 643.e1-643.e7.

Peiffer-Smadja N, Dellière S, Rodriguez C, Birgand G, Lescure FX, Fourati S, Ruppé E
Machine learning in the clinical microbiology laboratory: has the time come for routine practice?.
Clinical Microbiology and Infection: The Official Publication of the European Society of Clinical Microbiology and Infectious Diseases 2020, 26, 1300-1309.

Rondinaud E, Ruppé E, Matheron S, Lucet JC, Armand-Lefevre L, VOYAG-R study group
Screening methods for intestinal carriage of multidrug-resistant Enterobacterales: interest of enrichment broth.
Diagnostic Microbiology and Infectious Disease 2020, 97, 115079.

Charretier Y, Lazarevic V, Schrenzel J, Ruppé E
Messages from the Fourth International Conference on Clinical Metagenomics.
Microbes and Infection 2020, 22, 635-641.

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
ResFinder 4.0 for predictions of phenotypes from genotypes.
The Journal of Antimicrobial Chemotherapy 2020, 75, 3491-3500.

Rodrigues C, d'Humières C, Papin G, Passet V, Ruppé E, Brisse S
Community-acquired infection caused by the uncommon hypervirulent Klebsiella pneumoniae ST66-K2 lineage.
Microbial Genomics 2020

Fontaine C, Armand-Lefèvre L, Magnan M, Nazimoudine A, Timsit JF, Ruppé E
Relationship between the composition of the intestinal microbiota and the tracheal and intestinal colonization by opportunistic pathogens in intensive care patients.
PloS One 2020, 15, e0237260.

2019

Timsit JF, Bassetti M, Cremer O, Daikos G, de Waele J, Kallil A, Kipnis E, Kollef M, Laupland K, Paiva JA, Rodríguez-Baño J, Ruppé É, Salluh J, Taccone FS, Weiss E, Barbier F
Rationalizing antimicrobial therapy in the ICU: a narrative review.
Intensive Care Medicine 2019, 45, 172-189.

Ruppé E, Schrenzel J
Messages from the third International Conference on Clinical Metagenomics (ICCMg3).
Microbes and Infection 2019

Philippon A, Jacquier H, Ruppé E, Labia R
Structure-based classification of class A beta-lactamases, an update.
Current Research in Translational Medicine 2019, 67, 115-122.

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
Prediction of the intestinal resistome by a three-dimensional structure-based method.
Nature Microbiology 2019, 4, 112-123.

Leo S, Lazarevic V, Gaïa N, Estellat C, Girard M, Matheron S, Armand-Lefèvre L, Andremont A, Schrenzel J, Ruppé E
The intestinal microbiota predisposes to traveler's diarrhea and to the carriage of multidrug-resistant Enterobacteriaceae after traveling to tropical regions.
Gut Microbes 2019, 10, 631-641.

2018

Timsit JF, Rupp M, Bouza E, Chopra V, Kärpänen T, Laupland K, Lisboa T, Mermel L, Mimoz O, Parienti JJ, Poulakou G, Souweine B, Zingg W
A state of the art review on optimal practices to prevent, recognize, and manage complications associated with intravascular devices in the critically ill.
Intensive Care Medicine 2018, 44, 742-759.

Timsit JF, Ruppe E, Ferrer R
Focus on sepsis: new concepts and findings in sepsis care.
Intensive Care Medicine 2018, 44, 1997-1999.

Cherkaoui A, Gaïa N, Baud D, Leo S, Fischer A, Ruppe E, François P, Schrenzel J
Molecular characterization of fluoroquinolones, macrolides, and imipenem resistance in Haemophilus influenzae: analysis of the mutations in QRDRs and assessment of the extent of the AcrAB-TolC-mediated resistance.
European Journal of Clinical Microbiology & Infectious Diseases: Official Publication of the European Society of Clinical Microbiology 2018, 37, 2201-2210.

Ruppe E, Burdet C, Grall N, de Lastours V, Lescure FX, Andremont A, Armand-Lefevre L
Impact of antibiotics on the intestinal microbiota needs to be re-defined to optimize antibiotic usage.
Clin Microbiol Infect 2018, 24, 3-5.

Ruppé E, Martin-Loeches I, Rouzé A, Levast B, Ferry T, Timsit JF
What's new in restoring the gut microbiota in ICU patients? Potential role of faecal microbiota transplantation.
Clinical Microbiology and Infection: The Official Publication of the European Society of Clinical Microbiology and Infectious Diseases 2018, 24, 803-805.

Armand-Lefèvre L, Andremont A, Ruppé E
Travel and acquisition of multidrug-resistant Enterobacteriaceae.
Medecine Et Maladies Infectieuses 2018, 48, 431-441.

Ruppé E, Schrenzel J
Messages from the second International Conference on Clinical Metagenomics (ICCMg2)..
Microbes and infection 2018, 20, 222-227.

Ruppé E, Cherkaoui A, Wagner N, La Scala GC, Beaulieu JY, Girard M, Frey J, Lazarevic V, Schrenzel J
In vivo selection of a multidrug-resistant Aeromonas salmonicida during medicinal leech therapy.
New Microbes and New Infections 2018, 21, 23-27.

Ruppé E, Andremont A, Armand-Lefèvre L
Digestive tract colonization by multidrug-resistant Enterobacteriaceae in travellers: An update.
Travel Medicine and Infectious Disease 2018, 21, 28-35.

Munk P, Knudsen BE, Lukjancenko O, Duarte ASR, Van Gompel L, Luiken REC, Smit LAM, Schmitt H, Garcia AD, Hansen RB, Petersen TN, Bossers A, Ruppé E, EFFORT Group, Lund O, Hald T, Pamp SJ, Vigre H, Heederik D, Wagenaar JA, Mevius D, Aarestrup FM
Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries.
Nature Microbiology 2018, 3, 898-908.

Munk P, Knudsen BE, Lukjancenko O, Duarte ASR, Van Gompel L, Luiken REC, Smit LAM, Schmitt H, Garcia AD, Hansen RB, Petersen TN, Bossers A, Ruppé E, Lund O, Hald T, Pamp SJ, Vigre H, Heederik D, Wagenaar JA, Mevius D, Aarestrup FM
Author Correction: Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries..
Nature microbiology 2018, 3, 1186.

de Gunzburg J, Ghozlane A, Ducher A, Le Chatelier E, Duval X, Ruppe E, Armand-Lefevre L, Sablier-Gallis F, Burdet C, Alavoine L, Chachaty E, Augustin V, Varastet M, Levenez F, Kennedy S, Pons N, Mentre F, Andremont A
Protection of the Human Gut Microbiome From Antibiotics.
J Infect Dis 2018, 217, 628-636.

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
In-depth resistome analysis by targeted metagenomics.
Microbiome 2018, 6, 11.

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
The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies.
F1000Research 2018

Lorme F, Maataoui N, Rondinaud E, Esposito-Farèse M, Clermont O, Ruppe E, Arlet G, Genel N, VOYAG-R study group, Matheron S, Andremont A, Armand-Lefevre L
Acquisition of plasmid-mediated cephalosporinase producing Enterobacteriaceae after a travel to the tropics.
PloS One 2018, 13, e0206909.

Lazarevic V, Gaïa N, Girard M, Leo S, Cherkaoui A, Renzi G, Emonet S, Jamme S, Ruppé E, Vijgen S, Rubbia-Brandt L, Toso C, Schrenzel J
When Bacterial Culture Fails, Metagenomics Can Help: A Case of Chronic Hepatic Brucelloma Assessed by Next-Generation Sequencing.
Frontiers in Microbiology 2018, 9, 1566.

2017

Bassetti M, Poulakou G, Ruppe E, Bouza E, Van Hal SJ, Brink A
Antimicrobial resistance in the next 30 years, humankind, bugs and drugs: a visionary approach.
Intensive Care Medicine 2017, 43, 1464-1475.

Ruppé E, Olearo F, Pires D, Baud D, Renzi G, Cherkaoui A, Goldenberger D, Huttner A, François P, Harbarth S, Schrenzel J
Clonal or not clonal? Investigating hospital outbreaks of KPC-producing Klebsiella pneumoniae with whole-genome sequencing.
Clinical Microbiology and Infection: The Official Publication of the European Society of Clinical Microbiology and Infectious Diseases 2017, 23, 470-475.

Ruppé E, Greub G, Schrenzel J
Messages from the first International Conference on Clinical Metagenomics (ICCMg).
Microbes and Infection 2017, 19, 223-228.

Armand-Lefevre L, Ruppé E, Andremont A
ESBL-producing Enterobacteriaceae in travellers: doctors beware.
The Lancet. Infectious Diseases 2017, 17, 8-9.

Ruppé E, Lazarevic V, Girard M, Mouton W, Ferry T, Laurent F, Schrenzel J
Clinical metagenomics of bone and joint infections: a proof of concept study.
Scientific Reports 2017, 7, 7718.

Ruppé E, Chappuis F
What and how should we tell travellers about antimicrobial resistance?.
Journal of Travel Medicine 2017, 24,

Kardaś-Słoma L, Lucet JC, Perozziello A, Pelat C, Birgand G, Ruppé E, Boëlle PY, Andremont A, Yazdanpanah Y
Universal or targeted approach to prevent the transmission of extended-spectrum beta-lactamase-producing Enterobacteriaceae in intensive care units: a cost-effectiveness analysis.
BMJ open 2017, 7, e017402.

Emonet S, Lazarevic V, Pugin J, Schrenzel J, Ruppé E
Clinical Metagenomics for the Diagnosis of Hospital-acquired Infections: Promises and Hurdles.
American Journal of Respiratory and Critical Care Medicine 2017, 196, 1617-1618.

Ruppé E, Cherkaoui A, Lazarevic V, Emonet S, Schrenzel J
Establishing Genotype-to-Phenotype Relationships in Bacteria Causing Hospital-Acquired Pneumonia: A Prelude to the Application of Clinical Metagenomics.
Antibiotics (Basel, Switzerland) 2017

Leo S, Gaïa N, Ruppé E, Emonet S, Girard M, Lazarevic V, Schrenzel J
Detection of Bacterial Pathogens from Broncho-Alveolar Lavage by Next-Generation Sequencing.
International Journal of Molecular Sciences 2017, 18,

2016

Laupland KB, Ruppé E, Harbarth S
In 2035, will all bacteria be multidrug resistant? We are not sure.
Intensive Care Medicine 2016, 42, 2021-2023.

Bernard J, Armand-Lefèvre L, Luce E, El Mniai A, Chau F, Casalino E, Andremont A, Ruppé E
Impact of a short exposure to levofloxacin on faecal densities and relative abundance of total and quinolone-resistant Enterobacteriaceae.
Clinical Microbiology and Infection: The Official Publication of the European Society of Clinical Microbiology and Infectious Diseases 2016, 22, 646.e1-4.

Ruppé E, Chatelier EL, Pons N, Andremont A, Ehrlich SD
Dissemination of the mcr-1 colistin resistance gene.
The Lancet. Infectious Diseases 2016, 16, 290-291.

Pelat C, Kardaś-Słoma L, Birgand G, Ruppé E, Schwarzinger M, Andremont A, Lucet JC, Yazdanpanah Y
Hand Hygiene, Cohorting, or Antibiotic Restriction to Control Outbreaks of Multidrug-Resistant Enterobacteriaceae.
Infection Control and Hospital Epidemiology 2016, 37, 272-280.

Mercat M, Clermont O, Massot M, Ruppe E, de Garine-Wichatitsky M, Miguel E, Valls Fox H, Cornelis D, Andremont A, Denamur E, Caron A
Escherichia coli Population Structure and Antibiotic Resistance at a Buffalo/Cattle Interface in Southern Africa.
Applied and Environmental Microbiology 2016, 82, 1459-1467.

Sartelli M, Weber DG, Ruppé E, Bassetti M, Wright BJ, Ansaloni L, Catena F, Coccolini F, Abu-Zidan FM, Coimbra R, Moore EE, Moore FA, Maier RV, De Waele JJ, Kirkpatrick AW, Griffiths EA, Eckmann C, Brink AJ, Mazuski JE, May AK, Sawyer RG, Mertz D, Montravers P, Kumar A, Roberts JA, Vincent JL, Watkins RR, Lowman W, Spellberg B, Abbott IJ, Adesunkanmi AK, Al-Dahir S, Al-Hasan MN, Agresta F, Althani AA, Ansari S, Ansumana R, Augustin G, Bala M, Balogh ZJ, Baraket O, Bhangu A, Beltrán MA, Bernhard M, Biffl WL, Boermeester MA, Brecher SM, Cherry-Bukowiec JR, Buyne OR, Cainzos MA, Cairns KA, Camacho-Ortiz A, Chandy SJ, Che Jusoh A, Chichom-Mefire A, Colijn C, Corcione F, Cui Y, Curcio D, Delibegovic S, Demetrashvili Z, De Simone B, Dhingra S, Diaz JJ, Di Carlo I, Dillip A, Di Saverio S, Doyle MP, Dorj G, Dogjani A, Dupont H, Eachempati SR, Enani MA, Egiev VN, Elmangory MM, Ferrada P, Fitchett JR, Fraga GP, Guessennd N, Giamarellou H, Ghnnam W, Gkiokas G, Goldberg SR, Gomes CA, Gomi H, Guzmán-Blanco M, Haque M, Hansen S, Hecker A, Heizmann WR, Herzog T, Hodonou AM, Hong SK, Kafka-Ritsch R, Kaplan LJ, Kapoor G, Karamarkovic A, Kees MG, Kenig J, Kiguba R, Kim PK, Kluger Y, Khokha V, Koike K, Kok KYY, Kong V, Knox MC, Inaba K, Isik A, Iskandar K, Ivatury RR, Labbate M, Labricciosa FM, Laterre PF, Latifi R, Lee JG, Lee YR, Leone M, Leppaniemi A, Li Y, Liang SY, Loho T, Maegele M, Malama S, Marei HE, Martin-Loeches I, Marwah S, Massele A, McFarlane M, Melo RB, Negoi I, Nicolau DP, Nord CE, Ofori-Asenso R, Omari AH, Ordonez CA, Ouadii M, Pereira Júnior GA, Piazza D, Pupelis G, Rawson TM, Rems M, Rizoli S, Rocha C, Sakakhushev B, Sanchez-Garcia M, Sato N, Segovia Lohse HA, Sganga G, Siribumrungwong B, Shelat VG, Soreide K, Soto R, Talving P, Tilsed JV, Timsit JF, Trueba G, Trung NT, Ulrych J, van Goor H, Vereczkei A, Vohra RS, Wani I, Uhl W, Xiao Y, Yuan KC, Zachariah SK, Zahar JR, Zakrison TL, Corcione A, Melotti RM, Viscoli C, Viale P
Antimicrobials: a global alliance for optimizing their rational use in intra-abdominal infections (AGORA).
World journal of emergency surgery: WJES 2016, 11,

Ruppé E, Baud D, Schicklin S, Guigon G, Schrenzel J
Clinical metagenomics for the management of hospital- and healthcare-acquired pneumonia..
Future microbiology 2016, 11, 427-439.

Djuikoue IC, Woerther PL, Toukam M, Burdet C, Ruppe E, Gonsu KH, Fokunang C, El Mniai A, Larissa K, Pieme AC, Mboupaing MG, Kakam CM, Fogang HK, Andremont A, Ngogang J
Intestinal carriage of Extended Spectrum Beta-Lactamase producing E. coli in women with urinary tract infections, Cameroon.
J Infect Dev Ctries 2016, 10, 1135-1139.

2015

Le Dorze M, Gault N, Foucrier A, Ruppé E, Mourvillier B, Woerther PL, Birgand G, Montravers P, Dilly MP, Tubach F, Andremont A, Timsit JF, Wolff M, Armand-Lefèvre L
Performance and impact of a rapid method combining mass spectrometry and direct antimicrobial susceptibility testing on treatment adequacy of patients with ventilator-associated pneumonia.
Clinical Microbiology and Infection: The Official Publication of the European Society of Clinical Microbiology and Infectious Diseases 2015, 21, 468.e1-6.

Weiss E, Zahar JR, Lesprit P, Ruppe E, Leone M, Chastre J, Lucet JC, Paugam-Burtz C, Brun-Buisson C, Timsit JF, De-escalation Study Group
Elaboration of a consensual definition of de-escalation allowing a ranking of β-lactams.
Clinical Microbiology and Infection: The Official Publication of the European Society of Clinical Microbiology and Infectious Diseases 2015, 21, 649.e1-10.

Ruppé E, Armand-Lefèvre L, Estellat C, Consigny PH, El Mniai A, Boussadia Y, Goujon C, Ralaimazava P, Campa P, Girard PM, Wyplosz B, Vittecoq D, Bouchaud O, Le Loup G, Pialoux G, Perrier M, Wieder I, Moussa N, Esposito-Farèse M, Hoffmann I, Coignard B, Lucet JC, Andremont A, Matheron S
High Rate of Acquisition but Short Duration of Carriage of Multidrug-Resistant Enterobacteriaceae After Travel to the Tropics.
Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America 2015, 61, 593-600.

Ruppé E, Armand-Lefèvre L, Estellat C, Coignard B, Lucet JC, Andremont A, Matheron S
Reply to Collignon and Kennedy..
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2015, 61, 1767.

Soubirou JF, Rossi B, Couffignal C, Ruppé E, Chau F, Massias L, Lepeule R, Mentre F, Fantin B
Activity of temocillin in a murine model of urinary tract infection due to Escherichia coli producing or not producing the ESBL CTX-M-15.
The Journal of Antimicrobial Chemotherapy 2015, 70, 1466–1472.

Gosalbes MJ, Vázquez-Castellanos JF, Angebault C, Woerther PL, Ruppé E, Ferrús ML, Latorre A, Andremont A, Moya A
Carriage of enterobacteria producing extended spectrum beta-lactamases and composition of the gut microbiota in an Amerindian community.
Antimicrobial Agents and Chemotherapy 2015

2014

Neulier C, Birgand G, Ruppé E, Armand-Lefèvre L, Lolom I, Yazdanpanah Y, Lucet JC, Andremont A
Enterobacteriaceae bacteremia: Risk factors for ESBLPE.
Médecine et maladies infectieuses 2014, 44, 32-38.

Ruppe E, Armand-Lefevre L, Estellat C, El-Mniai A, Boussadia Y, Consigny P, Girard P, Vittecoq D, Bouchaud O, Pialoux G, Esposito-Farese M, Coignard B, Lucet J, Andremont A, Matheron S
Acquisition of carbapenemase-producing Enterobacteriaceae by healthy travellers to India, France, February 2012 to March 2013.
Euro surveillance: bulletin Européen sur les maladies transmissibles = European communicable disease bulletin 2014, 19,

2013

Birgand G, Armand-Lefevre L, Lolom I, Ruppe E, Andremont A, Lucet JC
Duration of colonization by extended-spectrum β-lactamase-producing Enterobacteriaceae after hospital discharge.
American Journal of Infection Control 2013, 41, 443-447.

Defrance G, Birgand G, Ruppé E, Billard M, Ruimy R, Bonnal C, Andremont A, Armand-Lefèvre L
Time-to-positivity-based discrimination between Enterobacteriaceae, Pseudomonas aeruginosa and strictly anaerobic Gram-negative bacilli in aerobic and anaerobic blood culture vials.
Journal of Microbiological Methods 2013, 93, 77-79.

Ruppé E, Lixandru B, Cojocaru R, Büke C, Paramythiotou E, Angebault C, Visseaux C, Djuikoue I, Erdem E, Burduniuc O, El Mniai A, Marcel C, Perrier M, Kesteman T, Clermont O, Denamur E, Armand-Lefèvre L, Andremont A
Relative fecal abundance of extended-spectrum-β-lactamase-producing Escherichia coli strains and their occurrence in urinary tract infections in women.
Antimicrobial Agents and Chemotherapy 2013, 57, 4512-4517.

Armand-Lefevre L, Angebault C, Barbier F, Hamelet E, Defrance G, Ruppe E, Bronchard R, Lepeule R, Lucet JC, El Mniai A, Wolff M, Montravers P, Plesiat P, Andremont A
Emergence of Imipenem-Resistant Gram-Negative Bacilli in Intestinal Flora of Intensive Care Patients.
Antimicrobial Agents and Chemotherapy 2013, 57, 1488-1495.

Ruppé E, Andremont A
Causes, consequences, and perspectives in the variations of intestinal density of colonization of multidrug-resistant enterobacteria.
Frontiers in Microbiology 2013, 4, 129.

2012

Ruppe E, Pitsch A, Tubach F, de Lastours V, Chau F, Pasquet B, Lucet JC, Andremont A, Fantin B
Clinical predictive values of extended-spectrum beta-lactamase carriage in patients admitted to medical wards.
European Journal of Clinical Microbiology & Infectious Diseases 2012, 31, 319-325.

Lebeaux D, Barbier F, Angebault C, Benmahdi L, Ruppé E, Felix B, Gaillard K, Djossou F, Epelboin L, Dupont C, Renard M, Peroz G, Vandenesch F, Wolff M, Andremont A, Ruimy R
Evolution of nasal carriage of methicillin-resistant coagulase-negative staphylococci in a remote population.
Antimicrobial Agents and Chemotherapy 2012, 56, 315-323.

Lepeule R, Ruppé E, Le P, Massias L, Chau F, Nucci A, Lefort A, Fantin B
Cefoxitin as an alternative to carbapenems in a murine model of urinary tract infection due to Escherichia coli harboring CTX-M-15-type extended-spectrum β-lactamase.
Antimicrobial Agents and Chemotherapy 2012, 56, 1376-1381.

2011

Woerther PL, Angebault C, Jacquier H, Hugede HC, Janssens AC, Sayadi S, El Mniai A, Armand-Lefèvre L, Ruppé E, Barbier F, Raskine L, Page AL, de Rekeneire N, Andremont A
Massive increase, spread, and exchange of extended spectrum β-lactamase-encoding genes among intestinal Enterobacteriaceae in hospitalized children with severe acute malnutrition in Niger.
Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America 2011, 53, 677-685.

Barbier F, Lebeaux D, Hernandez D, Delannoy AS, Caro V, François P, Schrenzel J, Ruppé E, Gaillard K, Wolff M, Brisse S, Andremont A, Ruimy R
High prevalence of the arginine catabolic mobile element in carriage isolates of methicillin-resistant Staphylococcus epidermidis..
The Journal of antimicrobial chemotherapy 2011, 66, 29-36.

Ruppé E, Armand-Lefèvre L, Lolom I, El Mniai A, Muller-Serieys C, Ruimy R, Woerther PL, Bilariki K, Marre M, Massin P, Andremont A, Lucet JC
Development of a phenotypic method for detection of fecal carriage of OXA-48-producing enterobacteriaceae after incidental detection from clinical specimen..
Journal of clinical microbiology 2011, 49, 2761-2762.

2010

Barbier F, Ruppé E, Hernandez D, Lebeaux D, Francois P, Felix B, Desprez A, Maiga A, Woerther PL, Gaillard K, Jeanrot C, Wolff M, Schrenzel J, Andremont A, Ruimy R
Methicillin-resistant coagulase-negative staphylococci in the community: high homology of SCCmec IVa between Staphylococcus epidermidis and major clones of methicillin-resistant Staphylococcus aureus..
The Journal of infectious diseases 2010, 202, 270-281.

Woerther PL, Angebault C, Lescat M, Ruppé E, Skurnik D, Mniai AE, Clermont O, Jacquier H, Costa AD, Renard M, Bettinger RM, Epelboin L, Dupont C, Guillemot D, Rousset F, Arlet G, Denamur E, Djossou F, Andremont A
Emergence and dissemination of extended-spectrum beta-lactamase-producing Escherichia coli in the community: lessons from the study of a remote and controlled population.
The Journal of Infectious Diseases 2010, 202, 515-523.

Skurnik D, Ruimy R, Ready D, Ruppe E, Bernède-Bauduin C, Djossou F, Guillemot D, Pier GB, Andremont A
Is exposure to mercury a driving force for the carriage of antibiotic resistance genes?.
Journal of medical microbiology 2010, 59, 804-807.

de Lastours V, Chau F, Tubach F, Pasquet B, Ruppé E, Fantin B
Independent behavior of commensal flora for carriage of fluoroquinolone-resistant bacteria in patients at admission..
Antimicrobial agents and chemotherapy 2010, 54, 5193-5200.

2009

Clermont O, Dhanji H, Upton M, Gibreel T, Fox A, Boyd D, Mulvey MR, Nordmann P, Ruppé E, Sarthou JL, Frank T, Vimont S, Arlet G, Branger C, Woodford N, Denamur E
Rapid detection of the O25b-ST131 clone of Escherichia coli encompassing the CTX-M-15-producing strains.
The Journal of Antimicrobial Chemotherapy 2009, 64, 274-277.

Ruppé E, Woerther PL, Diop A, Sene AM, Da Costa A, Arlet G, Andremont A, Rouveix B
Carriage of CTX-M-15-producing Escherichia coli isolates among children living in a remote village in Senegal..
Antimicrobial agents and chemotherapy 2009, 53, 3135-3137.

Ruppé E, Barbier F, Mesli Y, Maiga A, Cojocaru R, Benkhalfat M, Benchouk S, Hassaine H, Maiga I, Diallo A, Koumaré AK, Ouattara K, Soumaré S, Dufourcq JB, Nareth C, Sarthou JL, Andremont A, Ruimy R
Diversity of staphylococcal cassette chromosome mec structures in methicillin-resistant Staphylococcus epidermidis and Staphylococcus haemolyticus strains among outpatients from four countries..
Antimicrobial agents and chemotherapy 2009, 53, 442-449.

Ruimy R, Armand-Lefevre L, Barbier F, Ruppé E, Cocojaru R, Mesli Y, Maiga A, Benkalfat M, Benchouk S, Hassaine H, Dufourcq JB, Nareth C, Sarthou JL, Andremont A, Feil EJ
Comparisons between geographically diverse samples of carried Staphylococcus aureus..
Journal of bacteriology 2009, 191, 5577-5583.

Ruppé E, Hem S, Lath S, Gautier V, Ariey F, Sarthou JL, Monchy D, Arlet G
CTX-M beta-lactamases in Escherichia coli from community-acquired urinary tract infections, Cambodia..
Emerging infectious diseases 2009, 15, 741-748.

2006

Ruppé E, Bidet P, Verdet C, Arlet G, Bingen E
First detection of the Ambler class C 1 AmpC beta-lactamase in Citrobacter freundii by a new, simple double-disk synergy test..
Journal of clinical microbiology 2006, 44, 4204-4207.