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Epidémiologie Et Régulation Des Intégrons De Classe 1 Chez Thèse de doctorat Université de Limoges École Doctorale Bio-Santé (ED 524) INSERM UMR 1092 : Anti-Infectieux supports moléculaires des résistances et innovations thérapeutiques (RESINFIT) Thèse pour obtenir le grade de Docteur de l’Université de Limoges Spécialité : Immunologie, oncologie et infectiologie Présentée et soutenue par Élodie Couvé-Deacon Le 14 décembre 2017 Épidémiologie et régulation des intégrons de classe 1 chez Acinetobacter baumannii Thèse dirigée par M. le Dr Fabien GARNIER et Mme le Pr Marie-Cécile PLOY JURY : Rapporteurs Mme le Pr Marie KEMPF, PU-PH, Equipe 06 ATOMycA, Université d’Angers M. le Pr Didier HOCQUET, PU-PH, UMR 6249 Chrono-environnement, université de Besançon Examinateur M. le Pr Christophe BURUCOA, PU-PH, LITEC EA 4331, Université de Poitiers Invités Mme le Pr Marie-Cécile PLOY, PU-PH, UMR 1092, université de Limoges M. le Dr Fabien GARNIER, PH, UMR 1092, université de Limoges Elodie Couvé-Deacon | Thèse de doctorat | Université de Limoges | 2017 2 A Mike, à Éléa, à Éva Julia Elodie Couvé-Deacon | Thèse de doctorat | Université de Limoges | 2017 3 Elodie Couvé-Deacon | Thèse de doctorat | Université de Limoges | 2017 4 REMERCIEMENTS A Monsieur le Professeur Christophe Burucoa, Professeur des Universités, Praticien hospitalier, Chef du service de Bactériologie et Hygiène du CHU de Poitiers, je vous remercie d’avoir accepté de présider ce jury et de m’avoir fait l’honneur d’être examinateur de ce travail de thèse. Veuillez trouver ici l’expression de mon profond respect pour votre travail. A Madame le Professeur Marie Kempf, Professeur des Universités, Praticien hospitalier, Responsable médical - Unité fonctionnelle de Bactériologie – Hygiène du CHU d’Angers, et Monsieur le Professeur Didier Hocquet, Professeur des Universités, Praticien hospitalier dans le service d’Hygiène Hospitalière du CHU de Besançon, je vous remercie de m’avoir fait l’honneur d’être rapporteurs de ce travail de thèse. Veuillez trouver ici l’expression de mon profond respect pour votre travail à tous les deux. A Madame le Professeur Marie-Cécile Ploy, Professeur des Universités, Praticien hospitalier, Chef du laboratoire de Bactériologie-Virologie-Hygiène du CHU de Limoges, je vous remercie de m’avoir transmis un peu de votre immense passion pour la science ainsi que pour vos conseils scientifiques toujours constructifs. Je vous remercie pour vos encouragements, de croire en mon potentiel depuis toutes ces années et pour ces mots qui remettent le monde à l’endroit quand je suis « au fond du fait-tout ». Veuillez trouver ici l’expression de ma sincère reconnaissance et de mon profond respect. A Monsieur le Docteur Fabien Garnier, Praticien hospitalier au laboratoire de Bactériologie- Virologie-Hygiène du CHU de Limoges, je te remercie de m’avoir accompagnée et surtout supportée toutes ces années. Merci d’avoir été un guide pour ce long travail, d’avoir apporté tes conseils scientifiques et stratégiques, de m’avoir orientée, aidée et d’avoir toujours été disponible. Notre parcours commun avait commencé avec un M2R, c’est une joie de le voir aboutir avec cette thèse. Je te prie de bien vouloir trouver ici l’expression de toute ma gratitude et de mon profond respect. Elodie Couvé-Deacon | Thèse de doctorat | Université de Limoges | 2017 5 Je tiens à remercier l’équipe de l’UMR 1092 pour ces années de travail à vos côtés, tout particulièrement Marie-Cécile et Fabien pour votre accompagnement dans les bons moments et aussi dans les plus difficiles de cette thèse qui, je l’espère, marque le début d’une encore plus grande aventure. Un grand merci à Thomas, Emilie G, Emilie S, Valentin, Pierrette, qui m’ont aussi accompagnée et ont apporté leur pavé à ce long chemin, vos conseils et aides m’ont été précieux. Je n’oublie pas les autres membres de l’équipe Olivier, Christian, Sandra, Christophe, Sophie A, Sophie R, Sébastien, Bruno, Pierre-Yves, Thibault, Anthony, Romain, Margaux, Melissa, Nicolas, Martine, Laetitia, Emmanuelle, Isabelle, car sans une équipe solide le travail n’avance pas ! Je remercie tout particulièrement mes co-doctorants, Murielle (Lamu) pour ton soutien « spychologique » sans faille et ta princessitude, Yohann (mon Yo), mon coach technique, pour ta gentillesse sans limites, Déborah (Deyby) pour tous les à-côtés et projets communs (couture, japan expo, Sharel…), Claire (Clairounette) pour tes discussions hautement intéressantes, Chloé (^ㅅ^) pour ta motivation toujours au rendez-vous (Claire et Chloé : see you on the other side !), Florence (la Flo) pour en un mot : LICORNE, sans oublier Elena for the right words at the right time et mes stagiaires la douce et brillante Paméla et Mathilde. Merci aussi à Erwan, sidekick de Lamu et aux autres doctorants qui ont marqué la route, Maxime, Chloé et Clothilde. Tout cela n’aurait pas été possible sans l’aide du Laboratoire de Bactériologie-Virologie- Hygiène et en premier lieu le soutien et la patience de l’unité d’Hygiène, merci à Nathalie car je sais que mon absence a pesé, mais que tu as tenu bon, et merci à vous Marie-Christine, Annick, Marie-Claire, Hélène, Sylvie, Laurence, Hervé, Isabelle, Stéphanie, Camille et Audrey. Merci aussi à Laure, Jérôme, Sylvie, Nadia et tous les autres membres du laboratoire. A mes parents, Pierre-Yves et Marie-Christine, je sais que vous trouvez que la voie que j’ai choisie est difficile, mais tout en essayant de me protéger, vous m’avez toujours soutenu et je peux voir qu’aujourd’hui vous êtes fiers de ce que j’ai accompli. Allez pour un millon un, un millon deux, bon un millon c’est grâce à vous tout ça ! A mes frères et soeurs, PO et Maud, Gwen et Jo, Perrine et Mat et les marmailles qui sont nées pendant ces années de dur labeur (Enoa, Galy et Ayun, Arnaud, Clément, Hanivai et Maiana), merci d’avoir été les pilliers de ma santé mentale, de m’avoir fait rire et penser à autre chose. A mes grands-parents, Mamico et Grand Père Roland, Mimie et Nounou, je sais que vous êtes fiers de moi, ici ou là-bas, merci pour votre amour et votre soutien inconditionnel. Merci aussi aux autres membres de ma grande famille. Badette, Olivier, Félix et Diane, ma famille canado-bretonne, merci à vous qui m’avez suivie de près comme une grande fille et cousine. A Catou, Laetitia, Christophe, Fanny, merci d’être toujours là avec votre bonne humeur et votre soleil ! Alain, Caro, Lucie, Alix, Florian, merci pour votre soutien et votre accueil en toute circonstance. Thierry et Mauricette, merci aussi à vous deux pour votre Elodie Couvé-Deacon | Thèse de doctorat | Université de Limoges | 2017 6 amour et soutien. A special thanks to my English family, Sandra and Phil, Alan and Karen, Erin and Finley, Lawrence and Rachel, Bob and Mo, Lucy, Elsie and Derrick, even far away you always had a supportive thought for me and always understood my choices. Merci aussi aux amis qui sont devenus famille, Evelyne, Alain, Flora et Paul, famille de la bonne fée ! Valérie, Clémentine et Nicolas, François et Cécile, chez qui grandir a été doux, Christelle, Pierre, Auriane et Maëlle les habitants du Peyroux, Matoum, mon jumeau de signe astral et de mangeage d’œuf au plat. Merci aux Amis de l’ASABB DD et Béa, Miguel, Cyril et Murielle, Waldé, Philippe, j’ai l’extrême honneur de vous avoir pour grand frères et en tant que tel vous avez fait un travail exceptionnel. Nastya et tatie Delphine, merci à vous qui avez pris soins de mes Doudoues pendant que je travaillais, et merci à toi Martin, mon répétiteur officiel. Merci à tous les autres pour votre soutien Clélia, Sandrine, Delphine et Greg, Céleste, Charline et Niels, la petite famille de Valentin : Amélie, Simon et Aurore. De près ou de loin vous avez été présent et m’avez donné de la force. Merci à mes amis Drédré et Julien B, Mika, Kiki (Maître Kitus, je suis à jamais ta padawan), Aude, Sandra et Tom, Marie-Claire, Malvina et David, Marie la ptite, Nico, Jo Q et Marlène, Saket, Dub, Stéphane, MatizZz et Julien G vous qui m’avez supportée pendant toutes ces années d’études pendant lesquelles je vous ai vu commencer et terminer les vôtres. Je vous Kiffe. A mes amis du basket, merci d’avoir été ma soupape de sécurité, Thomas M, Aurélie, Olivier, Marie-Brique, Baptiste, Doudou, Jo, Sophie, Margaux, Fanny, Mégane, Marie, Ilana. Merci aux membres d’ADN de m’avoir permi de retrouver mes ailes (à roulettes) Thomas S, Laurent, Bastien, Emmanuel, Thomas V, Sébastien. Mes derniers remerciements vont à Mike mon mari et mes filles Éléa et Éva Julia, car je sais que c’est vous qui avez fait les plus gros sacrifices pour me permettre d’aller au bout de ma thèse. You make me live. You’re my sunshine and I want you to know that my feeling are true, I really love you! You’re my best friends. In rain or shine you’ve stood by me guys, I’m happy at home. You’re my best friends! Elodie Couvé-Deacon | Thèse de doctorat | Université de Limoges | 2017 7 Droits d’auteurs Cette création est mise à disposition selon le Contrat : « Attribution-Pas d'Utilisation Commerciale-Pas de modification 3.0 France » disponible en ligne : http://creativecommons.org/licenses/by-nc-nd/3.0/fr/ Elodie Couvé-Deacon | Thèse de doctorat | Université de Limoges | 2017 8 SOMMAIRE Sommaire ................................................................................................................................... 1 Glossaire ..................................................................................................................................... 4 Index des tableaux.....................................................................................................................
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