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Role of Klebsiella pneumoniae Type VI secretion system (T6SS) in long-term gastrointestinal colonization

 Thomas Merciecca , Stéphanie Bornes , Laurence Nakusi , Sébastien Theil , Olaya Rendueles , et al.
Scientific Reports, 2022, 12 (1), pp.16968. ⟨10.1038/s41598-022-21396-w⟩
Article dans une revue pasteur-03809977v1
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Atypical organizations and epistatic interactions of CRISPRs and cas clusters in genomes and their mobile genetic elements

 Aude Bernheim , David Bikard , Marie Touchon , Eduardo Rocha
Nucleic Acids Research, 2020, 48, pp.748 - 760. ⟨10.1093/nar/gkz1091⟩
Article dans une revue pasteur-02626502v1
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Phage-Plasmids Spread Antibiotic Resistance Genes through Infection and Lysogenic Conversion

 Eugen Pfeifer , Rémy A. Bonnin , Eduardo Rocha
mBio, 2022, Ahead of print. ⟨10.1128/mbio.01851-22⟩
Article dans une revue pasteur-03818031v1
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Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes

 Alexandra Moura , Alexis Criscuolo , Hannes Pouseele , Mylène M. Maury , Alexandre Leclercq , et al.
Nature Microbiology, 2016, 2, pp.16185. ⟨10.1038/nmicrobiol.2016.185⟩
Article dans une revue pasteur-01415883v1
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How capsules protect the cell, shape genetic exchanges and drive bacterial evolution

 Matthieu Haudiquet
Human health and pathology. Université Paris Cité, 2022. English. ⟨NNT : 2022UNIP7137⟩
Thèse tel-04076297v2
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Phage-inducible chromosomal minimalist islands (PICMIs), a novel family of small marine satellites of virulent phages

 Rubén Barcia-Cruz , David Goudenège , Jorge Moura de Sousa , Damien Piel , Martial Marbouty , et al.
Nature Communications, 2024, 15 (1), pp.664. ⟨10.1038/s41467-024-44965-1⟩
Article dans une revue hal-04413133v1
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In-vivo loss of carbapenem resistance by extensively drug-resistant Klebsiella pneumoniae during treatment via porin expression modification

 Suzanne Bialek-Davenet , Noémie Mayer , Julia Vergalli , Marion Duprilot , Sylvain Brisse , et al.
Scientific Reports, 2017, 7 (1), ⟨10.1038/s41598-017-06503-6⟩
Article dans une revue hal-01831725v1
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TLR9 Activation Is Triggered by the Excess of Stimulatory versus Inhibitory Motifs Present in Trypanosomatidae DNA

 Melissa Erin Khan , Chloé Borde , Eduardo P C Rocha , Véronique Mériaux , Vincent Maréchal , et al.
PLoS Neglected Tropical Diseases, 2014, 8 (11), pp.e3308. ⟨10.1371/journal.pntd.0003308⟩
Article dans une revue hal-01342968v1
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Impact of antibiotics on the human gut phageome : from method to application

 Camille d'Humières
Life Sciences [q-bio]. Université Paris Cité, 2020. English. ⟨NNT : 2020UNIP7014⟩
Thèse tel-04076281v1
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MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes

 Bertrand Néron , Rémi Denise , Charles Coluzzi , Marie Touchon , Eduardo P.C. Rocha , et al.
Peer Community Journal, 2023, 3, pp.e28. ⟨10.24072/pcjournal.250⟩
Article dans une revue pasteur-04060331v2
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Identification and characterization of thousands of bacteriophage satellites across bacteria

 Jorge A Moura de Sousa , Alfred Fillol-Salom , José Penadés , Eduardo P.C. Rocha
Nucleic Acids Research, 2023, 51 (6), pp.2759-2777. ⟨10.1093/nar/gkad123⟩
Article dans une revue hal-03838678v2
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Adaptation to novel spatially-structured environments is driven by the capsule and alters virulence-associated traits

 Amandine Nucci , Eduardo Rocha , Olaya Rendueles
Nature Communications, 2022, 13 (1), pp.4751. ⟨10.1038/s41467-022-32504-9⟩
Article dans une revue pasteur-03794548v1
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Evo‐Scope : Fully automated assessment of correlated evolution on phylogenetic trees

 Maxime Godfroid , Charles Coluzzi , Amaury Lambert , Philippe Glaser , Eduardo P C Rocha , et al.
Methods in Ecology and Evolution, 2024, 15 (2), pp.282 - 289. ⟨10.1111/2041-210x.14190⟩
Article dans une revue pasteur-04778723v1
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Phages and their satellites encode hotspots of antiviral systems

 François Rousset , Florence Depardieu , Solange Miele , Julien Dowding , Anne-Laure Laval , et al.
Cell Host & Microbe, 2022, 30 (5), pp.740 - 753.e5. ⟨10.1016/j.chom.2022.02.018⟩
Article dans une revue pasteur-04075930v1
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Horizontal gene transfer among host-associated microbes

 Jorge Moura de Sousa , Marta Lourenço , Isabel Gordo
Cell Host & Microbe, 2023, 31 (4), pp.513 - 527. ⟨10.1016/j.chom.2023.03.017⟩
Article dans une revue hal-04604566v1
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A widespread family of phage-inducible chromosomal islands only steals bacteriophage tails to spread in nature

 Nasser Alqurainy , Laura Miguel-Romero , Jorge Moura de Sousa , John Chen , Eduardo P.C. Rocha , et al.
Cell Host & Microbe, 2023, 31 (1), pp.69-82.e5. ⟨10.1016/j.chom.2022.12.001⟩
Article dans une revue pasteur-03952543v2
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Latent evolution of biofilm formation depends on life-history and genetic background

 Amandine Nucci , Eduardo P C Rocha , Olaya Rendueles
npj Biofilms and Microbiomes, 2023, 9 (1), pp.53. ⟨10.1038/s41522-023-00422-3⟩
Article dans une revue pasteur-04177373v1
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Structural and Genomic Evolution of RRNPPA Systems and Their Pheromone Signaling

 Alonso Felipe-Ruiz , Alberto Marina , Eduardo P C Rocha
mBio, 2022, 13 (6), pp.e0251422. ⟨10.1128/mbio.02514-22⟩
Article dans une revue pasteur-03952614v1
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BioConvert: a comprehensive format converter for life sciences

 Hugo Caro , Sulyvan Dollin , Anne Biton , Bryan Brancotte , Dimitri Desvillechabrol , et al.
NAR Genomics and Bioinformatics, 2023, 5 (3), ⟨10.1093/nargab/lqad074⟩
Article dans une revue pasteur-04279554v2
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Tail assembly interference is a common strategy in bacterial antiviral defenses

 Lingchen He , Laura Miguel-Romero , Jonasz B Patkowski , Nasser Alqurainy , Eduardo P C Rocha , et al.
Nature Communications, 2024, 15, pp.7539. ⟨10.1038/s41467-024-51915-4⟩
Article dans une revue pasteur-04778725v1

Sedentary chromosomal integrons as biobanks of bacterial anti-phage defence systems

 Baptiste Darracq , Eloi Littner , Manon Brunie , Julia Bos , Pierre Alexandre Kaminski , et al.
2024
Pré-publication, Document de travail hal-04783441v1
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IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella

 Bertrand Néron , Eloi Littner , Matthieu Haudiquet , Amandine Perrin , Jean Cury , et al.
Microorganisms, 2022, 10 (4), pp.700. ⟨10.3390/microorganisms10040700⟩
Article dans une revue hal-03655020v1
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Differences in Integron Cassette Excision Dynamics Shape a Trade-Off between Evolvability and Genetic Capacitance

 Céline Loot , Aleksandra Nivina , Jean Cury , José Antonio Escudero , Magaly Ducos-Galand , et al.
mBio, 2017, 8 (2), pp.e02296-16. ⟨10.1128/mBio.02296-16⟩
Article dans une revue pasteur-01689524v1
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Development of a multiplex PCR assay for identification of Klebsiella pneumoniae hypervirulent clones of capsular serotype K2

 Suzanne Bialek-Davenet , Alexis Criscuolo , Florent Ailloud , Virginie Passet , Marie-Hélène Nicolas-Chanoine , et al.
Journal of Medical Microbiology, 2014, 63 (12), pp.1608-1614. ⟨10.1099/jmm.0.081448-0⟩
Article dans une revue hal-04575045v1
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Restriction-modification systems have shaped the evolution and distribution of plasmids across bacteria

 Liam Shaw , Eduardo Rocha , R Craig Maclean
Nucleic Acids Research, 2023, 51 (13), pp.6806-6818. ⟨10.1093/nar/gkad452⟩
Article dans une revue pasteur-04236062v1
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Ongoing shuffling of protein fragments diversifies core viral functions linked to interactions with bacterial hosts

 Bogna J Smug , Krzysztof Szczepaniak , Eduardo P. C. Rocha , Stanislaw Dunin-Horkawicz , Rafał J Mostowy
Nature Communications, 2023, 14 (1), pp.7460. ⟨10.1038/s41467-023-43236-9⟩
Article dans une revue pasteur-04778709v1
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Antimicrobial resistance level and conjugation permissiveness shape plasmid distribution in clinical enterobacteria

 Aida Alonso-del Valle , Laura Toricelestino , Anna Quirant , Carles Tardio Pi , Javier Delafuente , et al.
Proceedings of the National Academy of Sciences of the United States of America, 2023, 120 (51), pp.e2314135120. ⟨https://doi.org/10.1073/pnas.2314135120⟩
Article dans une revue pasteur-04778706v1
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Evolution of Plasmid Mobility: Origin and Fate of Conjugative and Nonconjugative Plasmids

 Charles Coluzzi , Maria Pilar Garcillán-Barcia , Fernando de la Cruz , Eduardo P.C. Rocha
Molecular Biology and Evolution, 2022, 39 (6), pp.msac115. ⟨10.1093/molbev/msac115⟩
Article dans une revue pasteur-03818036v1

Integron_Finder

 Bertrand Néron , Jean Cury , Eduardo Rocha , Amandine Perrin
2024, ⟨swh:1:dir:6cc5d36f34974f2264a2ea9e195edb1981b2f9ba;origin=https://github.com/gem-pasteur/Integron_Finder;visit=swh:1:snp:f5d82d096a64d390358869946048ca7f801b2ded;anchor=swh:1:rev:0388197211bd9b232082a2dd9275623b62c5599a⟩
Logiciel hal-04603009v1
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Listeria monocytogenes sequence type 1 is predominant in ruminant rhombencephalitis

 Margaux Dreyer , Lisandra Aguilar-Bultet , Sebastian Rupp , Claudia Guldimann , Roger Stephan , et al.
Scientific Reports, 2016, 6 (1), pp.36419. ⟨10.1038/srep36419⟩
Article dans une revue pasteur-02185472v1
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