Establishing Genotype-to-Phenotype Relationships in Bacteria Causing Hospital-Acquired Pneumonia: A Prelude to the Application of Clinical Metagenomics by Etienne Ruppé, Abdessalam Cherkaoui, Vladimir Lazarevic, Stéphane Emonet, Jacques Schrenzel

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Effect of bacterial DNA enrichment on detection and quantification of bacteria in an infected tissue model by metagenomic next-generation sequencing by Vladimir Lazarevic, Nadia Gaïa, Myriam Girard, Florian Mauffrey, Etienne Ruppé, Jacques Schrenzel

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International circulation of aztreonam/avibactam-resistant NDM-5-producing Escherichia coli isolates: successful epidemic clones by Mustafa Sadek, Etienne Ruppé, Amina Habib, Rabaab Zahra, Laurent Poirel, Patrice Nordmann

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Deciphering polymorphism in 61,157 Escherichia coli genomes via epistatic sequence landscapes by Lucile Vigué, Giancarlo Croce, Marie Petitjean, Etienne Ruppé, Olivier Tenaillon, Martin Weigt

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The role of the microbiota in the management of intensive care patients by Piotr Szychowiak, Khanh Villageois-Tran, Juliette Patrier, Jean-François Timsit, Étienne Ruppé

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Clinical metagenomics of bone and joint infections: a proof of concept study by Etienne Ruppé, Vladimir Lazarevic, Myriam Girard, William Mouton, Tristan Ferry, Frédéric Laurent, Jacques Schrenzel

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Detection of Bacterial Pathogens from Broncho-Alveolar Lavage by Next-Generation Sequencing by Stefano Leo, Nadia Gaïa, Etienne Ruppé, Stephane Emonet, Myriam Girard, Vladimir Lazarevic, Jacques Schrenzel

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Is the term “anti-anaerobic” still relevant? by Paul-Louis Woerther, Camille d’Humières, Xavier Lescure, Luc Dubreuil, Christophe Rodriguez, François Barbier, Vincent Fihman, Etienne Ruppé

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Dissemination of carbapenemase-producing Enterobacterales in the community of Rawalpindi, Pakistan. by Amina Habib, Stéphane Lo, Khanh Villageois-Tran, Marie Petitjean, Shaheen Akhtar Malik, Laurence Armand-Lefèvre, Etienne Ruppé, Rabaab Zahra

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Correction: Genes mcr improve the intestinal fitness of pathogenic E. coli and balance their lifestyle to commensalism by Guillaume Dalmasso, Racha Beyrouthy, Sandrine Brugiroux, Etienne Ruppé, Laurent Guillouard, Virginie Bonnin, Pierre Saint-Sardos, Amine Ghozlane, Vincent Gaumet, Nicolas Barnich, Julien Delmas, Richard Bonnet

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Faecal Viral Excretion and Gastrointestinal Co-Infection Do Not Explain Digestive Presentation in COVID-19 Patients by Inès Rezzoug, Benoit Visseaux, Mélanie Bertine, Marion Parisey, Christine Bonnal, Etienne Ruppe, Diane Descamps, Jean François Timsit, Yazdan Yazdanpanah, Laurence Armand-Lefevre, Sandrine Houze, Nicolas Argy

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Acquisition of plasmid-mediated cephalosporinase producing Enterobacteriaceae after a travel to the tropics. by Florian Lorme, Naouale Maataoui, Emilie Rondinaud, Marina Esposito-Farèse, Olivier Clermont, Etienne Ruppe, Guillaume Arlet, Nathalie Genel, VOYAG-R study group, Sophie Matheron, Antoine Andremont, Laurence Armand-Lefevre

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When Bacterial Culture Fails, Metagenomics Can Help: A Case of Chronic Hepatic Brucelloma Assessed by Next-Generation Sequencing by Vladimir Lazarevic, Nadia Gaïa, Myriam Girard, Stefano Leo, Abdessalam Cherkaoui, Gesuele Renzi, Stéphane Emonet, Sharon Jamme, Etienne Ruppé, Sandrine Vijgen, Laura Rubbia-Brandt, Christian Toso, Jacques Schrenzel, Jacques Schrenzel

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Simultaneous Hospital Outbreaks of New Delhi Metallo-β-Lactamase-Producing Enterobacterales Unraveled Using Whole-Genome Sequencing by Stéphane Lo, Isabelle Lolom, Valérie Goldstein, Marie Petitjean, Emilie Rondinaud, Vincent Bunel-Gourdy, Alexy Tran Dinh, Paul-Henri Wicky, Etienne Ruppé, Camille d’Humières, Jean-Christophe Lucet, Laurence Armand-Lefèvre

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Modeling the bacterial dynamics in the gut microbiota following an antibiotic‐induced perturbation by Jinju Guk, Antoine Bridier‐Nahmias, Mélanie Magnan, Nathalie Grall, Xavier Duval, Olivier Clermont, Etienne Ruppé, Camille d'Humières, Olivier Tenaillon, Erick Denamur, France Mentré, Jérémie Guedj, Charles Burdet, for the CEREMI study group

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Contribution of Clinical Metagenomics to the Diagnosis of Bone and Joint Infections by Camille d’Humières, Camille d’Humières, Nadia Gaïa, Signara Gueye, Victoire de Lastours, Victoire de Lastours, Véronique Leflon-Guibout, Naouale Maataoui, Marion Duprilot, Marie Lecronier, Marc-Antoine Rousseau, Naura Gamany, François-Xavier Lescure, François-Xavier Lescure, Olivia Senard, Laurène Deconinck, Marion Dollat, Valentina Isernia, Anne-Claire Le Hur, Marie Petitjean, Anissa Nazimoudine, Sylvie Le Gac, Solaya Chalal, Stéphanie Ferreira, Vladimir Lazarevic, Ghislaine Guigon, Gaspard Gervasi, Laurence Armand-Lefèvre, Laurence Armand-Lefèvre, Jacques Schrenzel, Etienne Ruppé, Etienne Ruppé

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In-depth resistome analysis by targeted metagenomics by Val F. Lanza, Fernando Baquero, José Luís Martínez, Ricardo Ramos-Ruíz, Bruno González-Zorn, Antoine Andremont, Antonio Sánchez-Valenzuela, Stanislav Dusko Ehrlich, Sean Kennedy, Etienne Ruppé, Willem van Schaik, Rob J. Willems, Fernando de la Cruz, Teresa M. Coque

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Endocarditis caused by Thalassospira sp. by Laurène Deconinck, Rémi Gschwind, Marie Petitjean, Signara Gueye, Véronique Leflon-Guibout, Naouale Maataoui, Emilie Rondinaud, Augustin Suard, Katell Gallais, Rainui Richaud, Adeline Fuchs, Bernard Iung, Soleiman Alkhoder, Sophie Ismaël, Julia Herrou, Héloïse Prié, Laurence Armand-Lefèvre, Camille d’Humières, Etienne Ruppé

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Oropharyngeal and intestinal concentrations of opportunistic pathogens are independently associated with death of SARS-CoV-2 critically ill adults by Juliette Patrier, Khanh Villageois-Tran, Piotr Szychowiak, Stéphane Ruckly, Rémi Gschwind, Paul-Henri Wicky, Signara Gueye, Laurence Armand-Lefevre, Mehdi Marzouk, Romain Sonneville, Lila Bouadma, Marie Petitjean, Fariza Lamara, Etienne de Montmollin, Jean-Francois Timsit, Etienne Ruppé, The French COVID Cohort Study Group

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Towards monitoring of antimicrobial resistance in the environment: For what reasons, how to implement it, and what are the data needs? by Johan Bengtsson-Palme, Anna Abramova, Thomas U. Berendonk, Luis Pedro Coelho, Sofia K. Forslund, Rémi Gschwind, Annamari Heikinheimo, Víctor Hugo Jarquín-Díaz, Ayaz Ali Khan, Uli Klümper, Ulrike Löber, Marmar Nekoro, Adriana D. Osińska, Svetlana Ugarcina Perovic, Tarja Pitkänen, Ernst Kristian Rødland, Etienne Ruppé, Yngvild Wasteson, Astrid Louise Wester, Rabaab Zahra

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