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T H È S E Rita Abou Abdallah

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81,9(56,7e D’AIX0$56(,//( )$&8/7e'(0e'(&,1('(0$56(,//( 7+Ê6( 6RXWHQXHSXEOLTXHPHQWOH-XLOOHW en vue de l’obtention du titre de Docteur de l’Université d’Aix0DUVHLOOH 6SpFLDOLWp0DODGLHV,QIHFWLHXVHV SDU 5LWD$ERX$EGDOODK /D*pQRPLTXH 8Q2XWLO5REXVWHHW(PHUJHQW8WLOLVp GDQVOD7D[RQRPLH%DFWpULHQQHHW O’analyse Comparative &RPSRVLWLRQGXMXU\ 3URIHVVHXU%/$6&2/$ 8QLYHUVLWp$L[0DUVHLOOH 3UpVLGHQWGX-XU\ 3URIHVVHXU00$85,1 8QLYHUVLWpGH*UHQREOH 5DSSRUWHXU 3URIHVVHXU35(1(672 8QLYHUVLWpGH*UHQREOH 5DSSRUWHXU 3URIHVVHXU3()2851,(5 Université d’Aix0DUVHLOOH 'LUHFWHXUGH7KqVH 8059,7520( $L[0DUVHLOOH8QLYHUVLWp,QVWLWXWGH5HFKHUFKHSRXUOH'pYHORSSHPHQW $VVLVWDQFH3XEOLTXH–+{SLWDX[GH0DUVHLOOH $3+0 6HUYLFHGH6DQWp GHV$UPpHV,QVWLWXW+RVSLWDOR8QLYHUVLWDLUH0pGLWHUUDQpH,QIHFWLRQ 5HPHUFLHPHQWV Je tiens à remercier Professeur Pierre-Edourad Fournier, pour son encadrement et enseignement au cours de ces dernières années. Ses conseils et encouragements ont été des éléments moteurs pour moi et déterminants pour le déroulement de cette thèse. Votre calme, respect, humanité et gentillesse envers vos étudiants sont gravés dans mon cœur. Finalement, je vous remercie pour votre support et confiance tout au long de ces trois années. Vous aurez toujours une place dans mon esprit et mon cœur. Je remercie Professeur Didier Raoult pour m’avoir accueillie au sein de l’Institut Hospitalo-Universitaire, Méditerranée-Infection. C’est dans un environnement stimulant intellectuellement que mon goût pour la recherche est né. Je remercie Professeur Bernard La Scola, d’avoir accepté de présider au sein du jury de cette Thèse. Je remercie Professeur Max Maurin et Patricia Renesto d’avoir accepté de siéger au sein du jury de cette Thèse et pour l’intérêt porté à ce travail. Je remercie ma mère et ma sœur, pour leurs supports et conseils quotidiens. Vous êtes deux femmes exceptionnelles, sans vous rien n’aurait été pareil. Vous êtes le reflet de l’amour, du sacrifice et de la force. Vos appels tous les jours me réchauffait le cœur. Merci d’être là. Je remercie mon père et mon frère, vous êtes le soutien que chaque fille souhaite recevoir de la part de ses parents. Avec vous je peux conquérir le monde ! Je remercie mes neveux et ma nièce, vous êtes une source de joie. Surtout toi Ryan, tu es mon trésor et le plus beau cadeau. Je remercie Jacques Bou Khalil et Michel Hosny, pour leurs présences, soutiens et confiances. Vous étiez plus qu’une famille, grâce à vous je ne me suis jamais senti seule. On a partagé énormément de bons moments, dont je me souviendrai pour le reste de ma vie. Je suis très reconnaissante pour votre aide. Vous me manquerez ! Je remercie tous les membres de notre équipe pour l’entraide et les conseils, surtout Awa et Mamadou, merci pour toute l’aide que vous m’avez donné. Les mots, et la place, ne suffiraient pas à exprimer toute ma reconnaissance envers tous ceux qui m’ont permis d’en arriver là, à travers les bons moments comme les mauvais. Merci à ceux et celles qui par leurs encouragements et leur présence me permettent aujourd’hui d’écrire ces lignes ; merci Michelle Dib, Marianne Samaha, Docteur Fadi Bittar, Jeremy Delerce, Docteur Ahmad Yassine, Souheil Hallit, Dory Tannoury et Rania Francis. A mes parents, Gabriel et Elhame qui m’ont comblé de bonheur par leur affection. Que Dieu leurs préserve une longue vie et bonne santé. 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    Immunoproteomic identification of biomarkers for diagnosis of legionellosis Submitted in total fulfilment of the requirements for the degree of Doctor of philosophy by Kaylass Poorun Department of Chemistry and Biotechnology Faculty of Science, Engineering and Technology Swinburne University of Technology Australia 2014 Abstract Abstract Legionellosis, a disease with significant mortality and morbidity rates, is considered to be the second most frequent cause of severe community-acquired pneumonia. It is difficult to distinguish from other types of pneumonia due to similar clinical manifestations. Several studies have demonstrated the inadequacies of current diagnostic tests for confirming Legionella infections. This study was aimed at identifying biomarkers that can be used in an improved test. A comparative proteomic analysis, using DIGE, was carried out between L. pneumophila ATCC33152 and L. longbeachae NSW150 and D4968 isolates. While many homologous proteins were found to be commonly expressed, numerous others were identified to be differentially expressed under similar in vitro conditions suggesting that the two species have different lifestyles and infection strategies. The bacterial immunoglobulin domain containing protein, found to share sequence homology to Type V secretion proteins intimin and invasin, is not known to be present in Legionella. Human sera containing antibodies against Legionella from a set of blind samples were identified by ELISA. Downstream analyses revealed that diverse immunogens may be responsible for eliciting immune response in different Legionella species which in turn show little to no congeneric cross-reactivity. To the best of our knowledge, this is a unique finding not previously reported. Several serological diagnostic tests currently in use do not include many Legionella species in their testing panel, which may be a reason for many Legionella species being under-reported.
  • Emergence of Carbapenem-Resistant Pseudomonas Aeruginosa and Acinetobacter Baumannii Clinical Isolates Collected from Some Libyan Hospitals

    Emergence of Carbapenem-Resistant Pseudomonas Aeruginosa and Acinetobacter Baumannii Clinical Isolates Collected from Some Libyan Hospitals

    UNIVERSITE DE TUNIS EL MANAR Ecole Doctorale des Sciences Biologiques et AIX-MARSEILLE UNIVERSITE Ecole Doctorale des Sciences de la Vie et de la Santé THESE DE DOCTORAT EN COTUTELLE En Vue de l’obtention de grade de Docteur de l’Université de Tunis et d’Aix-Marseille Université Spécialités: Microbiologie / Pathologie humaine et maladies infectieuses Déterminisme du support moléculaire et de l’épidémiologie de la résistance aux ȕ-lactamines chez des bacilles à Gram négatif isolés dans des hôpitaux tunisiens et libyens Présentée par: Najla MATHLOUTHI Composition du Jury: Pr. Imane ZOUARI Université Tunis el Manar Président de Jury Dr. Marie KEMPF Université d’Angers Rapporteur Dr. Taoufik GHRAIRI Université Tunis el Manar Rapporteur Pr. Philippe COLSON Université d’Aix-Marseille Examinateur Pr. Mr. Jean-Marc ROLAIN Université d’Aix-Marseille Directeur de Thèse Dr. Chedly CHOUCHANI Université de Carthage Directeur de Thèse (8 Avril 2017) SOMMAIRE AVANT PROPOS ...................................................................... 3 RESUME .................................................................................... 4 SUMMARY ................................................................................ 5 INTRODUCTION ..................................................................... 7 CHAPITRE I: Revue: L’émergence et la dissémination des carbapénèmases produites par les bacilles à Gram négatifs dans les pays du bassin méditerranéen ............................................... 15 Article 1: Prevalence and emergence of
  • Thermolongibacillus Cihan Et Al

    Thermolongibacillus Cihan Et Al

    Genus Firmicutes/Bacilli/Bacillales/Bacillaceae/ Thermolongibacillus Cihan et al. (2014)VP .......................................................................................................................................................................................... Arzu Coleri Cihan, Department of Biology, Faculty of Science, Ankara University, Ankara, Turkey Kivanc Bilecen and Cumhur Cokmus, Department of Molecular Biology & Genetics, Faculty of Agriculture & Natural Sciences, Konya Food & Agriculture University, Konya, Turkey Ther.mo.lon.gi.ba.cil’lus. Gr. adj. thermos hot; L. adj. Type species: Thermolongibacillus altinsuensis E265T, longus long; L. dim. n. bacillus small rod; N.L. masc. n. DSM 24979T, NCIMB 14850T Cihan et al. (2014)VP. .................................................................................. Thermolongibacillus long thermophilic rod. Thermolongibacillus is a genus in the phylum Fir- Gram-positive, motile rods, occurring singly, in pairs, or micutes,classBacilli, order Bacillales, and the family in long straight or slightly curved chains. Moderate alka- Bacillaceae. There are two species in the genus Thermo- lophile, growing in a pH range of 5.0–11.0; thermophile, longibacillus, T. altinsuensis and T. kozakliensis, isolated growing in a temperature range of 40–70∘C; halophile, from sediment and soil samples in different ther- tolerating up to 5.0% (w/v) NaCl. Catalase-weakly positive, mal hot springs, respectively. Members of this genus chemoorganotroph, grow aerobically, but not under anaer- are thermophilic (40–70∘C), halophilic (0–5.0% obic conditions. Young cells are 0.6–1.1 μm in width and NaCl), alkalophilic (pH 5.0–11.0), endospore form- 3.0–8.0 μm in length; cells in stationary and death phases ing, Gram-positive, aerobic, motile, straight rods. are 0.6–1.2 μm in width and 9.0–35.0 μm in length.
  • THE LAKE VOSTOK Ferran Romero Blanch

    THE LAKE VOSTOK Ferran Romero Blanch

    MICROBIOLOGY OF A SUBGLACIAL LAKE: THE LAKE VOSTOK Ferran Romero Blanch OBJECTIVES INTRODUCTION: Lake Vostok is the largest and deepest The aim of the present review is to describe subglacial body of water in Antarctica. It has the communities present in a subglacial lake an area of 14000Km2 and a volume of (the Lake Vostok). 5600Km3. Nowadays, it is accepted that it has been buried under glacial ice for 14-15 millions It is also objective of this review to describe of years (Figure 1). Discovered between 1950 the use of ice-binding proteins as a and 1960, it has been recently reported that it method to survive in extremely cold forms a complex ecosystem with both environments. prokaryotic and eukaryotic microorganisms1,2. The living forms here have evolved to survive in an extremely oligotrophic, Main characteristics of Lake Vostok hyperbaric, cold and dark Temperature: -2°C environment. Pressure: 350atm (as it is covered by a 4- kilometer-thick layer of glacial ice) Nutrient availability: very slow Figure 1. Location of lake Vostok under Antarctic glacial ice1. Light: absent The ice above Lake Vostok freezes forming a 220m layer of accreted ice. It is generally accepted that this 220m layer of accreted ice reflects the contents into the lake and, because of this, it has been under study during the last 30 years. Ice accreting near the embayment has higher concentrations of ions, biomass and solid inclusions and it is known as type I accretion ice. The ice that forms over open water contains lower concentrations of biomass and ions and has been termed type II accretion ice3 (Figure 2).
  • Clinical Infectious Diseases Emerging Concepts and Strategies in Clinical

    Clinical Infectious Diseases Emerging Concepts and Strategies in Clinical

    Clinical Infectious Diseases Emerging Concepts and Strategies in Clinical Microbiology and Infectious Diseases Guest Editors: Didier Raoult, MD, PhD Fernando Baquero, MD, PhD This supplement was sponsored by the Fondation Méditerranée Infection (FMI). Cover Image: View of the new Méditerranée Infection building in Marseille, France. Photograph by Oleg Mediannikov © Oleg Mediannikov. The opinions expressed in this publication are those of the authors and are not attributable to the sponsors or to the publisher, editor, or editorial board of Clinical Infectious Diseases. Articles may refer to uses of drugs or dosages for periods of time, for indication, or in combinations not included in the current prescribing information. The reader is therefore urged to check the full prescribing information for each drug for the recommended indications, dosage, and precautions and to use clinical judgment in weighing benefits against risk of toxicity. MARCH20176513 15 August 2017 Volume 65 Clinical Infectious Diseases Supplement 1 The title Clinical Infectious Diseases is a registered trademark of the IDSA EMERGING CONCEPTS AND STRATEGIES IN CLINICAL MICROBIOLOGY AND INFECTIOUS DISEASES S1 Rewiring Microbiology and Infection S55 A Hospital-Based Committee of Moral Philosophy Didier Raoult and Fernando Baquero to Revive Ethics Margaux Illy, Pierre Le Coz, and Jean-Louis Mege S4 Building an Intelligent Hospital to Fight Contagion S58 Evaluating the Clinical Burden and Mortality Jérôme Bataille and Philippe Brouqui Attributable to Antibiotic Resistance:
  • Downloaded from the NCBI Database

    Downloaded from the NCBI Database

    marine drugs Article Isolation, Phylogenetic and Gephyromycin Metabolites Characterization of New Exopolysaccharides-Bearing Antarctic Actinobacterium from Feces of Emperor Penguin Hui-Min Gao 1, Peng-Fei Xie 1,2, Xiao-Ling Zhang 1,2,* and Qiao Yang 1,2,3,* 1 College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316022, China; [email protected] (H.-M.G.); [email protected] (P.-F.X.) 2 ABI Group, Zhejiang Ocean University, Zhoushan 316022, China 3 Department of Environment Science and Engineering, Zhejiang Ocean University, Zhoushan 316022, China * Correspondence: [email protected] (X.-L.Z.); [email protected] (Q.Y.) Abstract: A new versatile actinobacterium designated as strain NJES-13 was isolated from the feces of the Antarctic emperor penguin. This new isolate was found to produce two active gephyromycin analogues and bioflocculanting exopolysaccharides (EPS) metabolites. Phylogenetic analysis based on pairwise comparison of 16S rRNA gene sequences showed that strain NJES-13 was closely related to Mobilicoccus pelagius Aji5-31T with a gene similarity of 95.9%, which was lower than the threshold value (98.65%) for novel species delineation. Additional phylogenomic calculations of the average Citation: Gao, H.-M.; Xie, P.-F.; nucleotide identity (ANI, 75.9–79.1%), average amino acid identity (AAI, 52.4–66.9%) and digital Zhang, X.-L.; Yang, Q. Isolation, DNA–DNA hybridization (dDDH, 18.6–21.9%), along with the constructed phylogenomic tree based Phylogenetic and Gephyromycin on the up-to-date bacterial core gene (UBCG) set from the bacterial genomes, unequivocally separated Metabolites Characterization of New strain NJES-13 from its close relatives within the family Dermatophilaceae.