Pseudomonas aeruginosa é um importante agente de pneumonia, particularmente em pacientes submetidos à ventilação mecânica, que pode evoluir para sepse, com elevadas taxas de letalidade. Na sepse, o processo inflamatório sistêmico exacerbado favorece o desequilíbrio entre as vias de coagulação e fibrinólise e a instalação de um estado pró-coagulante, com o aparecimento de trombose microvascular, coagulação intravascular disseminada e falência de múltiplos órgãos. Conhecendo a potente atividade pró-inflamatória da toxina ExoU produzida por P. aeruginosa, decorrente de sua atividade fosfolipásica A2, o objetivo desta tese foi investigar seu potencial de indução de alterações hemostáticas relacionadas à patogênese da sepse. Utilizando modelo de sepse em camundongos inoculados, por via intratraqueal, com suspensões de P. aeruginosa produtora de ExoU (PA103) ou de cepa com deleção do gene exoU, não produtora da toxina, foi mostrado que ExoU determinou maior gravidade da infecção, maior taxa de letalidade, leucopenia, trombocitose, hiperpermeabilidade vascular e transudação plasmática, evidenciadas, respectivamente, pela maior concentração de proteínas nos lavados broncoalveolares (LBAs) e acúmulo do corante Azul de Evans, previamente inoculado nos animais, por via endovenosa, no parênquima renal. ExoU favoreceu, também, a ativação plaquetária, confirmada pela maior concentração de plaquetas expressando P-selectina em sua superfície, maior número de micropartículas derivadas de plaquetas e maior concentração plasmática de tromboxano A2. A histopatologia dos pulmões e rins dos animais infectados com PA103 confirmou a formação de microtrombos, que não foram detectados nos animais controles ou infectados com a cepa mutante. Nos pulmões, a produção de ExoU determinou intensa resposta inflamatória com maior concentração de leucócitos totais e polimorfonucleados, interleucina-6 e fator de necrose tumoral-α nos LBAs. A análise imunohistoquímica mostrou intensa deposição de fibrina nos alvéolos e septos interalveolares. A atividade pró-coagulante dependente do fator tissular detectada nos LBAs dos camundongos infectados com PA103 foi independente da produção do inibidor da via de ativação do fator tissular (TFPI), mas associada ao aumento da produção do inibidor do ativador do plasminogênio-1 (PAI-1). Para investigar a participação do fator de ativação plaquetária (PAF) na liberação de PAI-1, foi pesquisada a atividade da enzima PAF-acetil-hidrolase (PAF-AH) nos LBAs dos camundongos. A atividade de PAF-AH apresentou-se significativamente elevada nos LBA dos camundongos infectados com PA103. O tratamento dos animais com um inibidor do PAF, antes da infecção, resultou na diminuição significativa das concentrações de PAI-1 e de leucócitos totais, bem como da atividade pró-coagulante dos LBAs. In vitro, ExoU induziu maior expressão do RNA mensageiro de PAI-1 e maior liberação da proteína PAI-1 nos sobrenadantes de células epiteliais respiratórias da linhagem A549. O tratamento das células A549 com um anticorpo anti-receptor de PAF, antes da infecção, reduziu significativamente a concentração de PAI-1 nos sobrenadantes de células infectadas com a cepa selvagem. Estes resultados demonstraram um novo mecanismo de virulência de P. aeruginosa através da atividade pró-trombótica de ExoU e a possibilidade de utilização da identificação de ExoU em isolados clínicos de pacientes graves como um marcador prognóstico para estes pacientes. / Pseudomonas aeruginosa is an important agent of pneumonia, mainly in patients undergoing mechanical ventilation, which can progress to sepsis with high mortality rates. In sepsis, the systemic inflammatory process favors exacerbated imbalance between the coagulation and fibrinolysis pathways and the installation of a procoagulant state, leading to microvascular thrombosis, disseminated intravascular coagulation and multiple organ failure. Knowing the powerful proinflammatory activity of the P. aeruginosa toxin ExoU, secondary to its phospholipase A2 activity, the goal of this study was to investigate the ExoU potential to induce hemostatic changes related to sepsis pathogenesis. By using a murine model of pneumosepsis, obtained by the intratracheal injection of suspensions of the ExoU-producing PA103 P. aeruginosa strain or of its isogenic mutant PA103ΔexoU, defective in the toxin synthesis, ExoU was shown to enhance the severity of the infection and to induce higher mice mortality rate as well as leukopenia, thrombocytosis, vascular hyperpermeability and plasma transudation, evidenced, respectively, by the higher protein concentration in the bronchoalveolar lavage fluids (BALF) and accumulation of Evans blue dye, previously intravenous injectioned, in mice renal parenchyma. ExoU also favored platelet activation, evidenced by the higher concentration of platelets expressing P-selectin on their surface, greater number of platelet-derived microparticles and increased plasma concentration of thromboxane A2. Histopathology of the lungs and kidneys of PA103-infected animals confirmed the formation of microthrombi, which were not detected in controls or in animals infected with the bacterial mutant. In lungs, ExoU induced an intense inflammatory response with high concentrations of total and polymorphonuclear leukocytes, interleukin-6 and tumor necrosis factor-α in mice BALF. Immunohistochemical analysis showed intense fibrin deposition in the alveoli and interalveolar septa. The tissue factor-dependent procoagulant activity detected in BALF from PA103-infected mice did not depend on decreased production of tissue factor pathway inhibitor (TFPI) production, but was associated with increased concentration of plasminogen activator inhibitor-1 (PAI-1). To investigate the role of platelet activating factor (PAF) in PAI-1 release, we compared the activity of the enzyme PAF-acetylhydrolase (PAF-AH) in BALF from control and infected mice, and we observed that PAF-AH activity was significantly elevated in BALF from PA103-infected animals. Mice treatment with a PAF inhibitor prior to infection resulted in a significant reduction of PAI-1 concentration, as well as of BALF total leukocytes and procoagulant activity. In vitro, ExoU induced higher expression of PAI-1 m RNA and increased release of PAI-1 protein in supernatants from A549 epithelial respiratory cell cultures. A549 cell treatment with an anti-PAF receptor prior to infection significantly reduced PAI-1 concentration in supernatants from cells infected with the wild type strain. These results show a novel mechanism by which a baterial product can favor a prothrombotic activity and ExoU production by infecting P. aeruginosa isolates may have prognostic implications for patients.

CoordenaÃÃo de AperfeiÃoamento de Pessoal de NÃvel Superior / This work as main objective to evaluate the eletrogenic effect in preparations of Ãleum of rabbit fixes in chambers of Ãssing, in presence of supernatant of macrophages (S.MfS), stimulated with microcistin-LR (MCLR), of Microcystis aeruginosa. S.MfS estimulated with MCLR (3,2.10-7M; 9,6.10-7M e 3,2.10-6M), produces effect secretion, of the form dose-dependent; being that short circuit current (Isc), the secular chain variation (t) can be described for an equation of the type Isc = a . ekt for a correlation coefficient r = 0,9988 and Iscmaximo = 128,16  14,54 ÂA . cm-2. Later, was observed that the metabolic processes associatesâ geneses of the FSI, from stimulated macrophages, require the participation of a protein G, sensible pertussis active toxin. It was also verified that inhibing of protÃic synthesis, proteases, phosfolipase A2, ciclooxigenases, lipoxigenases, synthesis TNF-a, and antagonists of the PAF, they had reduced the FSI synthesis. With the application of monoclonal antibodies, it was verified that interleukin-b (IL-1b), was the main FSI; as also, that macrophages stimulated with MCLR, in the concentrations above, produced IL-1b and TNF-a, of form dose-dependent. The pay-treatment of the ileum mucosal with bumetanide, indomethacin, tetrodotoxin and HOE, disclosed that the secretory effect, by means of stimulated action of the S.MfS with MCLR is dependent of the secretion of ions chloride, with the participation of PAF, prostaglandins and mediators of the enteric nervous system. With this effect, it associates reduction of the transepitelial resistance (Rte), also mediated for prostaglandins, TNF-a, and indirectly IL-1b. The analysis of the coefficient of Hurst, disclosed that these effect had not occurred of random form, but had involved significant alterations in the kinetic parameters of the eletrogÃnic effect, to the level of the ileum mucosal. Macrophages stimulated for MCLR, produces and liberate more TNF-a of that IL-1b, to the Constant taxes, being this a linked characteristic to the type of employed stimulation. It is concluded, therefore, that MCLR stimulates macrophages to produce substances that can act as intestinal secretion factor, to the level of the ileum mucosal, involving chloride canals, reduction of the Rte, requesting for this, the participation of pro-inflammatory mediators and the enteric nervous system. / Este trabalho teve-se como principal objetivo, avaliar os efeitos eletrogÃnicos em preparaÃÃes de Ãleo de coelho fixadas em cÃmaras de Ãssing, em presenÃa de sobrenadante de macrÃfagos (S.MfS) estimulados com microcistina-LR MCLR de Microcystis aeruginosa. S.MfS estimulados com MCLR (3,2.10-7M; 9,6.10-7M e 3,2.10-6M), produz, de forma dose-dependente; sendo que a variaÃÃo temporal (t) da corrente de curto-circuito (Isc), pode ser descrita por uma equaÃÃo do tipo Isc = a . ekt; para um coeficiente de correlaÃÃo r = 0,9988 e Iscmaximo = 128,16  14,54 ÂÂcm-2. Posteriormente, observou-se que os processos metabÃlicos associados à gÃnese do fator deâ secreÃÃo intestinalâ (FSI), a partir de macrÃfagos estimulados, requer a participaÃÃo de uma proteÃna G sensÃvel à toxina pertusis ativa. Verificou-se tambÃm que inibidores de sÃntese protÃica, proteases, fosfolipase A2, cicloxigenases, lipoxigenases,; sÃntese de TNF-a e antagonista do PAF, reduziram a sÃntese de FSI. Com o emprego de anticorpos monoclonais, verificou-se que IL-1b era o principal FSI; como tambÃm, que macrÃfagos estimulados com MCLR, nas concentraÃÃes acima, reduziu IL-1b e TNF-a, de forma dose-dependente. O prÃ-tratamento da mucosa ileal com bumetanida, indometacina, tetrodotoxina e HOE, revelou que o efeito secretÃrio mediante aÃÃo do S.MfS estimulados com MCLR, à dependente da secreÃÃo de Ãons cloreto, com a participaÃÃo de PAF, prostaglandinas e mediadores do sistema nervoso entÃrico. A este efeito associa-se a diminuiÃÃo da resistÃncia transepitelial (Rte), tambÃm mediada por, prostaglandinas, PAF, TNF-a e, indiretamente, IL-1b. A anÃlise do coeficiente de Hurst (H), revelou que estes efeitos nÃo ocorreram ao acaso, mas envolveram alteraÃÃes significativas nos parÃmetros cinÃticos dos efeitos eletrogÃnicos, ao nÃvel da mucosa ileal. MacrÃfagos estimulados com MCLR produz e libera mais TNFa do que IL-1b, à taxas constantes ; sendo esta uma caracterÃstica atrelada ao tipo de estÃmulo empregado. Conclui-se, portanto, que MCLR estimula macrÃfagos a produzir substÃncias que podem atuar como fator de âsecreÃÃo intestinalâ ao nÃvel da mucosa ileal, envolvendo canais de cloreto, diminuiÃÃo de Rte; requisitando para isto, a participaÃÃo de mediadores prÃ-inflamatÃrios e do sistema nervoso entÃrico.

O operon pst de P. aeruginosa codifica um transportador de fosfato de alta afinida-de e também a proteína PhoU que, em conjunto, atuam como repressores da ex-pressão do regulon Pho dessa espécie. A atividade de PhoU está também associada ao metabolismo de polifosfato (poliP), dado que mutantes phoU nulos apresentam um vasto acúmulo do biopolímero. Ensaios de β-galactosidase mostraram uma alteração na expressão dos genes ppk e ppx, envolvidos no metabolismo de poliP, no mutante phoU. Observou-se que na cepa selvagem, a transcrição de ppk e de ppx não responde às limitações de Pi ou de nitrogênio, sendo esses genes altamente expressos em condições normais de crescimento. Além disso, determinou-se que ppk é co-transcrito com o gene hemB, os quais formam, portanto, um operon. O operon pst também foi analisado. Foi identificado por ensaios de northern blot o transcrito do primeiro gene do operon, pstS, que codifica uma proteína periplasmática. Também, foi identificado um promotor imediatamente a montante de phoU, o gene mais distal do operon, que permitiria sua expressão em condições normais do crescimento bacteriano. Por fim, determinou-se por ensaios de EMSA que as duas sequências consenso Pho box presentes no operon pst são completamente funcionais. / The pst operon in P. aeruginosa encodes a high-affinity phosphate transporter and the PhoU protein, which together act as repressors of Pho regulon of this species. The PhoU activity is also related with polyphosphate (polyP) metabolism, since phoU null mutants have a large accumulation of the biopolymer. β-galactosidase assays allowed to confirm a change in the expression of ppk and ppx genes, in-volved in PolyP metabolism, in the phoU mutant. It was also evidenced that in the wild type strain, the ppk and ppx transcription does not respond to Pi or nitrogen starvation, and that these genes are highly expressed under conditions of normal growth. In addition, it was determined that ppk is co-transcribed with hemB, a gene involved in the synthesis of porphyrins, and they constitute therefore an operon. The pst operon was also examined. Was identified by northern blot the transcript of the first gene in the operon, pstS, which encodes a periplasmic protein. Also, a promoter was identified immediately upstream of phoU, the most distal gene in the operon, allowing its expression in normal conditions of bacterial growth. Finally, it was determined by EMSA that the two consensus sequences Pho box present in the pst operon are fully functional.

Les patients mucoviscidosiques sont prédisposés à une colonisation chronique de l’arbre bronchique par P. aeruginosa. Ce pathogène opportuniste se caractérise par sa capacité à adhérer à une surface et à y former un biofilm protecteur, hautement tolérant aux agents antimicrobiens. En routine, les antibiogrammes sont effectués sur des cultures bactériennes planctoniques. L’efficacité des antibiothérapies ainsi sélectionnées est donc peu probante pour l’éradication des biofilms bactériens. La réalisation d’Antibiofilmogrammes® sur des isolats cliniques mucoviscidosiques (nouvel outil évaluant la sensibilité des bactéries sessiles aux antibiotiques) a permis de mettre en évidence des phénomènes d’inhibition et d’induction de la formation du biofilm. Plus précisément, les aminosides sont capables de retarder l’adhérence bactérienne. À l’inverse, la famille des β-lactamines présente la capacité de stimuler l’adhésion précoce des micro-organismes. Ces différents effets de l’antibiothérapie générale sur le comportement microbien se vérifient par l’intermédiaire de techniques conventionnelles in vitro (Cristal Violet, traitement enzymatique à la DNase I) et cellulaires (modèle de co-culture statique cellules eucaryotes/bactéries). La pertinence clinique de l’Antibiofilmogramme® se confirme donc par sa capacité à détecter l’initiation précoce de l’adhésion bactérienne, à sélectionner les molécules l’inhibant et à écarter celles pouvant l’induire. Associée aux antibiogrammes traditionnels, son application peu permettre d’affiner les stratégies thérapeutiques pour le traitement des infections pulmonaires chroniques développées au cours de la mucoviscidose. / Cystic fibrosis (CF) patients are predisposed to chronic colonisation of the upper airways by P. aeruginosa. This opportunist pathogen is characterized by its ability to adhere to a surface and to form a protective biofilm, which is highly tolerant to antimicrobials. In routine, antibiograms are realised on planktonic bacterial cultures. The efficacy of the corresponding antimicrobial therapies appears low for the eradication of bacterial biofilms. The realisation of Antibiofilmograms® on CF clinical isolates (a new tool investigating the susceptibility of sessile bacteria to antibiotics) highlighted phenomena of biofilm formation inhibition and induction. More precisely, aminoglycosides are able to delay the bacterial adherence. Conversely, the β-lactam family shows the ability to stimulate the early adhesion of microorganisms. These different effects of antimicrobials on the bacterial behaviour are confirmed with more conventional in vitro methods (Crystal Violet, enzymatic treatment with DNase I) and a cell model (static co-culture of eukaryotic cells and bacteria). The clinical relevance of the Antibiofilmogram® is reinforced by its ability to detect the initiation of the early bacterial adhesion, to select inhibitor molecules and to avoid the inducer ones. Associated to traditional antibiograms, its application should be pertinent to optimise the CF therapies for the treatment of chronic lung infections.

Le typage bactérien est une mesure de contrôle essentielle pour lutter contre la diffusion des bactéries multirésistantes, mais les techniques actuelles sont longues et coûteuses. L'objectif de cette thèse était d'évaluer la capacité de la technique MALDI-TOF MS à typer les 3 principales espèces bactériennes responsables d'infections nosocomiales - Escherichia coli, Staphylococcus aureus et Pseudomonas aeruginosa. L'analyse par MALDI-TOF MS permet d'identifier les souches de E. coli appartenant au phylogroupe B2, souches les plus virulentes parmi les souches extra-intestinales, et au STI 31, clone très impliqué dans la dissémination des P-lactamases à spectre étendu. Chez S. aureus, cette technique reconnait les souches appartenant au CC398, impliquées dans une proportion importante d'infections graves chez des personnes fragiles. La technique MALDI-TOF MS identifie également cinq clones de P. aeruginosa à haut risque épidémique - STI 11, STI 75, ST235, ST253, ST395. Si nous avons confirmé des pics caractéristiques du phylogroupe B2 décrit également par d'autres auteurs, les pics biomarqueurs identifiant E. coli ST131 ou des clones épidémiques de S. aureus varient suivant les études. Différents paramètres peuvent influencer les résultats de typage par MALDI-TOF MS et doivent donc être standardisés. La technique MALDI-TOF MS permet d'identifier certains clones épidémiques. En gardant à l'esprit que le choix d'une méthode de typage doit être fait en fonction des objectifs mais aussi des performances des différents systèmes disponibles, la technique MALDI-TOF MS pourrait se positionner comme un outil de typage de première ligne. / Bacterial typing is crucial to tackle the spread of bacterial pathogens but current methods are time-consuming and costly. The objective of this study was to evaluate the ability of MALDI-TOF MS to type the 3 main bacterial species re.sponsible for nosocomial infections - Escherichia coti, Staphylococcus aureus and Pseudomonas aeruginosa. Analysis of MALDI-TOF mass spectra allow the identification (i) of E. coti isolates belonging to phylogroup B2, that fosters the most virulent extra-intestinal strains, and (ii) of E. coli STl 31, a clone involved in the dissemination of extended-spectrum β-lactamases. MALDI-TOF MS also recognizes S. aureus isolates belonging to CC398, a pathogen responsible for invasive infections in fragile patients and associated with a higher 30-day mortality. Furthermore the MALDI-TOF MS based typing method identifies the major high risk epidemic clones of P. aeruginosa STl 11, STl 75, ST235, ST253, and ST395. We confirmed phylogroup B2 specific peaks also described by other authors. However the identification of E. coli STl 31 or epidemic clones of S. aureus is based on biomarkers that differs between studies. Different parameters can influence the MALDI-TOF MS typing results and must therefore be standardized. MALDI-TOF-based typing methods allow the detection of epidemic pathogens. Keeping in mind that the choice of a method for routine bacterial typing should be made according to the objectives but also the performance of the different systems available, the MALDI-TOF MS technique could become a first-line typing method.

La bactérie Pseudomonas aeruginosa (PA) est un pathogène responsable de 20%-30% des infections nosocomiales en milieu hospitalier. Pour les individus sains, elle ne présente pas de réel danger, mais pour les personnes atteintes par la mucoviscidose et les patients immunodéprimés, elle est la cause principale de mortalité et des infections pulmonaires. PA a développé des souches multi-résistantes aux antibiotiques et des nouvelles approches thérapeutiques plus efficaces sont donc nécessaires. Elle se fixe à la surface des cellules-hôtes par une interaction entre des protéines (lectines) présentes sur sa membrane et des sucres présents sur la membrane cellulaire. L’interaction lectine-sucre joue un rôle important dans l’adhésion de la bactérie puis dans la fabrication d’un biofilm pathogène.Une nouvelle approche thérapeutique consiste à créer des molécules synthétiques (glycomimes) de plus grande affinité que les sucres présents sur les cellules. Pour cela, plus de 150 glycomimes ont été synthétisés et examinés afin de trouver le meilleur candidat pour empêche le processus d'infection de bactéries. Certains d'entre eux ont été choisis et étudiés par la Microscopie à Force Atomique (AFM). Cette thèse est consacrée à l’étude des interactions lectine-glycomime et aussi cellule-bactérie par AFM. L’imagerie combinée avec la modélisation permet de comprendre le rôle du glycomime sur la géométrie des complexes créés et la spectroscopie permet de mesurer les forces d’interaction présentes lors de l’adhésion, au niveau moléculaire et cellulaire. Une réduction de l’adhésion bactérienne a été observée après l’introduction du glycomime, confirmant son rôle d’inhibiteur et la validité de toute la démarche. L’objectif ultime est l’identification des meilleurs glycomimes à introduire afin de développer de nouveaux médicaments. / Pseudomonas aeruginosa (PA) is a human opportunistic pathogen responsible for 20% -30% of nosocomial infections in French hospitals. For healthy people, it presents no real danger, but for people with cystic fibrosis disease and immune-compromised patients, it is the leading cause of mortality and lung infections. PA has developed antibiotic multi-resistant strains and new and more effective therapeutic approaches are needed. It binds to the surface of the host cells by an interaction between proteins (lectins) present on the membrane and sugars of the host-cell membrane. The lectin-sugar interaction plays an important role in adherence of the bacteria and in the manufacture of a pathogenic biofilm.A new therapeutic approach is to create synthetic molecules (glycoclusters) of greater affinity than the natural sugars present on the cells. To this aim, more than 150 glycoclusters have been synthetized and screened to find the best candidate to inhibit the bacteria infection process. Some of them have been selected and studied by Atomic Force Microscopy (AFM). In particular, this thesis is devoted to study the lectin-glycocluster and cell-bacteria interactions by AFM. The combination of AFM imaging with molecular dynamic simulations let understanding the role of the geometry of the glycoclusters on the complex formation, while AFM spectroscopy accesses the lectin-glycocluster interaction forces at the molecular and cellular levels. The reduction of bacterial adhesion has been observed upon the addition of the glycocluster. This confirms the anti-adhesive properties of the glycocluster and validates the procedure. The ultimate goal is the identification of the best glycoclusters in order to develop new drugs.

La mucoviscidose est une pathologie pulmonaire causée par un dysfonctionnement du canal CFTR et caractérisée par un mucus visqueux, une susceptibilité accrue aux infections chroniques et une inflammation excessive. Une première partie de ma thèse a eu pour objectif d’étudier les mécanismes inflammatoires impliqués dans le développement de la pathologie. Nous avons plus particulièrement analysé le rôle de l’IL-1β et de l’IL-17 dans la réponse à l’infection par Pseudomonas aeruginosa, dans le modèle murin ΔF508 de mucoviscidose. La seconde partie de ma thèse a porté sur l’étude de la malaria pulmonaire et cérébrale, une complication létale de l’infection à P. falciparum. Nous avons mis en évidence l’importance de trois voies d’activation des lymphocytes T CD8+ cytotoxiques dans le développement de la neuropathologie induite par Plasmodium berghei ANKA chez la souris : la protéine PKC-θ, la sous-unité β2 du récepteur à l’IL-12 et le récepteur des IFN de type I, mais qui ne semblent pas impliquées dans l’inflammation pulmonaire associée. / Cystic fibrosis is a pulmonary pathology, caused by the CFTR channel dysfunction, and characterized by high mucus viscosity, increased sensitivity to chronic infections and excessive inflammation. The aim of my thesis was first to study the inflammatory mechanisms involved in this lung pathology. Indeed, we analyzed the role of IL-1β and IL-17 in response to Pseudomonas aeruginosa infection, in the ΔF508 mouse model of cystic fibrosis. In the second part of my thesis, I studied pulmonary and cerebral malaria, a lethal complication of P. falciparum infection. We showed the importance of three pathways implicated in cytotoxic CD8+ T lymphocytes activation during the Plasmodium berghei ANKA-induced neuropathology development in mice: PKC-θ protein, β2 subunit of IL-12 receptor and type I IFN receptor, which did not seem essential for the associated lung inflammation.

En santé publique, de nouveaux programmes de surveillance et de gestion sont à proposer notamment pour les masses d'eaux fortement affectées par l'urbanisation et les rejets urbains par temps de pluie. Les niveaux, les réservoirs et les sources de contamination microbiologique des milieux aquatiques doivent être évalués et identifiés, et leur incidence sur la dissémination des bactéries pathogènes et les risques d'exposition des populations humaines comprises. Parmi les agents pathogènes retrouvés dans les milieux hydriques, Pseudomonas aeruginosa représentent une préoccupation sanitaire majeure. A partir de deux sites expérimentaux, les objectifs de ce travail de thèse furent de définir la contribution des rejets d'eaux usées sur la prévalence de P. aeruginosa dans les cours d'eau récepteurs et d'étudier l'écologie des formes introduites dont ces habitats incluant leur dynamique spatiotemporelle. Les sédiments, les biofilms de surface (périphyton) et les végétaux aquatiques submergés, permettraient leur survie voire la multiplication de certains génotypes de Pseudomonas aeruginosa. La répartition des indicateurs de contaminations fécales et de la bactérie pathogène Aeromonas caviae ont également été étudiée. Il a été mis en évidence que les forces hydrauliques, le morpho-dynamisme de la rivière et les variations saisonnières étaient des facteurs structurants de la répartition des contaminants microbiens analysés. La dangerosité des souches isolées a été évaluée et montré que toutes les souches avaient un potentiel de virulence élevée. Ceci s'est confirmé par la détection de clones épidémiques majeurs au sein de la collection dont des souches apparentées aux clones PA14 ou C. Les capacités métaboliques de ces souches ont été étudiées dont leur antibio-résistance / In Public Health, new monitoring and management programs are needed, especially for the aquatic environments strongly affected by urbanization and urban wet weather discharges. The levels, reservoirs and sources of microbiological contamination of the aquatic environment should be assessed and identified, and their impact on the spread of pathogenic bacteria and the risk of exposure of human populations understood. Among the pathogens found in water environments, Pseudomonas aeruginosa is of major health concern. From two experimental sites, the objectives of this work were to define the contribution of wastewater discharges on the prevalence of P. aeruginosa in receiving watercourses and study the ecology of the introduced forms, including their spatiotemporal dynamic and preferential habitats. Sediments, surface biofilms (periphyton) and the submerged aquatic vegetations appeared to favour the survival or growth of some genotypes of Pseudomonas aeruginosa. The distribution of fecal indicator bacteria and of Aeromonas caviae were also studied. It was highlighted that hydraulic forces, the morpho-dynamics of the river and the seasonal vaiations were determinant factors in the distribution of the analyzed microbial contaminants. The health hazard of the clones found in these systems was estimated through indirect molecular approaches. It was shown that all Pseudomonas aeruginosa strains had a high virulence potential and that some were related to the PA14 and C clones which are spread worldwide and pathogenic

Staphylococcus aureus a été classé parmi les bactéries les plus pathogènes du genre Staphylococcus. Ce pathogène est responsable d'infections localisées (plaies chroniques, infections sur prothèses) voire de septicémies et d’infections nosocomiales. L’objectif principal de ce projet est d’élaborer des vecteurs colloïdaux biocompatibles à base de polysaccharides, chargés en principe actif antibactérien, et ciblant spécifiquement des biofilms de S. aureus. La méthode de complexation polyélectrolytes entre polysaccharides de charge opposée (chitosane/alginate et chitosane/dextrane sulfate) a été sélectionnée pour élaborer des particules de taille micrométrique. Ces microparticules n’étant pas stables, elles ont été stabilisées par réticulation chimique. Un antibiotique à large spectre d’activité de la famille des fluoroquinolones, la ciprofloxacine, a été séquestrée dans les microparticules. Des essais microbiologiques ont été réalisés en planctonique et sur biofilms, sur une souche de S. aureus et une souche de Pseudomonas aeruginosa. La ciprofloxacine encapsulée présente une activité antibactérienne (CMI, CMB et CMEB) plus importante que la ciprofloxacine libre. Par ailleurs, les MPs à base de chitosane/alginate sont plus actives que celles constituées de chitosane/dextrane sulfate. Enfin, un greffage d’un anticorps anti-protéine A a été réalisé sur les microparticules chitosane/alginate chargées en ciprofloxacine. Ces microparticules présentent une activité antibactérienne sur le biofilm de S. aureus légèrement améliorée par rapport aux microparticules dépourvues d’anticorps. / Staphylococcus aureus has been classified as one of the most pathogenic bacteria of the Staphylococcus genus. This bacterium is responsible for localized infections (chronic wounds, infections on artificial joints) or even septicemia and nosocomial infections. The main objective of this project is to develop biocompatible colloidal vectors based on polysaccharides, loaded with antibacterial active compound, and specifically targeting Staphylococcus aureus biofilms. The polyelectrolyte complexation between polysaccharide of opposite charge (chitosan / alginate and chitosan / dextran sulfate) has been selected to produce micrometric particles. By varying the total concentration of polysaccharide and the charge ratio between polyanion and polycation, it is possible to obtain variable sizes. As these microparticles were not stable, they were stabilized by chemical crosslinking. An antibiotic of the fluoroquinolone family, ciprofloxacin, with a large spectrum of activity, was entrapped in the micoparticles. Microbiological tests were carried out in planktonics and biofilms on different strains of Staphylococcus aureus and Pseudomonas aeruginosa. Loaded ciprofloxacin exhibits greater antibacterial activity (MIC, CMB and CMEB). Moreover, the chitosan / alginate-based MPs are more active than those consisting of chitosan / dextran sulfate. Finally, a grafting of an antiprotein A antibody was carried out on chitosan / alginate microparticles loaded with ciprofloxacin. These modified microparticles exhibit a slightly improved antibacterial activity compared to loaded ciprofloxaxin microparticles whitoutantibody.

Horizontal gene transfer enables acquisition and dissemination of novel traits including antibiotic resistance and virulence among bacteria. Frequently such traits are gained through the acquisition of clusters of functionally related genes, often referred to as genomic islands (GIs). Quantifying horizontal flow of GIs and assessing their contributions to the emergence and evolution of novel metabolic traits in bacterial organisms are central to understanding the evolution of bacteria in general and the evolution of pathogenicity and antibiotic resistance in particular, a focus of this dissertation study. Methods for GI detection have also evolved with advances in sequencing and bioinformatics, however, comprehensive assessment of these methods has been lacking. This motivated us to assess the performance of current methods for identifying islands on broad datasets of well-characterized bacterial genomes and synthetic genomes, and leverage this information to develop a novel approach that circumvents the limitations of the current state-of-the-art in GI detection. The main findings from our assessment studies were 1) the methods have complementary strengths, 2) a gene-clustering method utilizing codon usage bias as the discriminant criterion, namely, JS-CB, is most efficient in localizing genomic islands, specifically the well-studied SCCmec resistance island in methicillin resistant Staphylococcus aureus (MRSA) genomes, and 3) in general, the bottom up, gene by gene analysis methods, are inherently limited in their ability to decipher large structures such as GIs as single entities within bacterial genomes. We adapted a top-down approach based on recursive segmentation and agglomerative clustering and developed a GI prediction tool, GEMINI, which combined compositional features with segment context information to localize GIs in the Liverpool epidemic strain of Pseudomonas aeruginosa. Application of GEMINI to the genome of P. aeruginosa LESB58 demonstrated its ability to delineate experimentally verified GIs in the LESB58 genome. GEMINI identified several novel islands including pathogenicity islands and revealed the mosaic structure of several LESB58 harbored GIs. A new GI identification approach, CAFE, with broad applicability was developed. CAFE incorporates biological information encoded in a genome within the statistical framework of segmentation and clustering to more robustly localize GIs in the genome. CAFE identifies genomic islands lacking markers by virtue of their association with genomic islands with markers originating from the same source. This is made possible by performing marker enrichment and phyletic pattern analyses within the integrated framework of recursive segmentation and clustering. CAFE compared favorably with frequently used methods for genomic island detection on synthetic test datasets and on a test-set of known islands from 15 well-characterized bacterial species. These tools can be readily adapted for cataloging GIs in just sequenced, yet uncharacterized genomes.