Un des enjeux majeurs dans la gestion de la plaie de pied diabétique est l’obtention d’informations permettant d’anticiper l’évolution de ces infections. Actuellement, il n’existe pas d’outils suffisamment efficaces qui permettent de distinguer une plaie colonisée d’une plaie infectée. L’approche proposée est basée sur discrimination de plusieurs bactéries fréquemment retrouvées dans les plaies chroniques de pied diabétique à partir de leur profil métabolique, et plus particulièrement des métabolites volatils qu’elles produisent. En effet, le dynamisme du métabolisme bactérien serait à même de mettre en évidence les changements qui s’opèrent dans la plaie. Dans un premier temps, une nouvelle méthodologie de concentration des métabolites volatils par Stir Bar Sorptive Extraction (SBSE) a été développée. Elle est basée sur l’utilisation de barreaux qui sont placés à la fois dans le milieu de culture et en espace de tête, suivie d’une analyse par GC-MS. La méthode a ensuite été comparée avec une autre méthode de concentration utilisant des fibres (la SPME) et a montré une meilleure capacité de concentration, permettant ainsi une détection plus sensible. Cette méthodologie a ensuite été utilisée pour suivre la production métabolique de six souches bactériennes cultivées dans des conditions mimant la plaie chronique. Grâce à leur profil métabolique, il a été possible de distinguer des espèces bactériennes. De plus, de manière plus surprenante, il a été possible de distinguer deux souches de Staphylococcus aureus présentant des profils de virulence différents. Enfin, une étude en co-culture a mis en évidence que 83% des métabolites produit en culture simple étaient retrouvés, prouvant l’intérêt de la méthodologie pour distinguer des souches bactériennes d’une même espèce au sein d’une plaie. / One of the major challenges in the management of diabetic foot wounds is to obtain information to anticipate the evolution of these infections. Currently, there are no sufficiently effective tools to distinguish a colonized wound to an infected wound. The proposed approach is based on the discrimination of several bacteria frequently found in chronic diabetic foot wounds from their metabolic profile, and more specifically the volatile metabolites they produce. Indeed, the dynamism of bacterial metabolism would be able to highlight the changes that are occurring in the wound. First, a new methodology for the concentration of volatile metabolites by Stir Bar Sorptive Extraction (SBSE) was developed. It is based on the use of stir bars that are placed both in the culture medium and in headspace, followed by GC-MS analysis. The method was then compared with another concentration method using the fibres (SPME) and we highlighted a better concentration capacity with a more sensitive detection. This methodology was then used to monitor the metabolic production of six bacterial strains grown under conditions mimicking the chronic wound. Their metabolic profile allowed us to distinguish bacterial species. Moreover, more surprisingly, it was possible to distinguish two strains of Staphylococcus aureus with different virulence profiles. Finally, a co-culture was performed and we showed that 83% of the metabolites produced in simple culture were found, proving the interest of the methodology to distinguish bacterial strains of the same species within a wound.

<p>The gastrointestinal mucus gel layer and blood flow are two important mechanisms for protection at the pre-epithelial and sub-epithelial levels, respectively. <i>Helicobacter pylori</i> might circumvent these mechanisms and elicit a chronic inflammatory response with consequent ulcers in the stomach and duodenum. In this thesis, the physical state and properties of the adherent mucus gel layer was studied from the stomach to colon. Furthermore, the acute and chronic effects of <i>H. pylori</i> on the integrity of the mucus gel layer and mucosal blood flow were studied in the anesthetized rat.</p><p>A translucent mucus gel covers all studied segments of the gastrointestinal tract during fasting conditions, with the thickest layers in the colon and ileum. Carefully applied suction revealed that the mucus gel was a multi-layered structure comprising a firmly adherent layer covering the mucosa, impossible to remove, and a loosely adherent upper layer. The firmly adherent layer was thick and continuous in the corpus (80μm), antrum (154μm) and colon (116μm), but thin (<20μm) and discontinuous in the small intestine.</p><p>Following mucus removal, a rapid renewal of the loosely adherent layer ensued. The highest rate was observed in the colon with intermediate values in the small intestine. Mucus renewal in the stomach was attenuated on acute luminal application of water extracts from <i>H. pylori</i> (HPE). In animals with a chronic <i>H. pylori</i> infection the mucus renewal rate was unaffected, but the total gastric mucus gel thickness was reduced and the mucus secretory response to luminal acid (pH1) attenuated in the antrum. </p><p>HPE from type I strains acutely reduced corporal mucosal blood flow, measured with laser-Doppler flowmetry, by approximately 15%. The reduction in blood flow was mediated by a heat stable factor other than VacA and CagA. Inhibition of endogenous nitric oxide production with Nω-nitro-l-arginine augmented the decrease. However, ketotifen, a mast cell stabilizer, completely attenuated the effect of the extract as did the platelet activating factor (PAF) receptor-antagonist, WEB2086, thus depicting a detrimental role for the microvascular actions of PAF.</p>

The gastrointestinal mucus gel layer and blood flow are two important mechanisms for protection at the pre-epithelial and sub-epithelial levels, respectively. Helicobacter pylori might circumvent these mechanisms and elicit a chronic inflammatory response with consequent ulcers in the stomach and duodenum. In this thesis, the physical state and properties of the adherent mucus gel layer was studied from the stomach to colon. Furthermore, the acute and chronic effects of H. pylori on the integrity of the mucus gel layer and mucosal blood flow were studied in the anesthetized rat. A translucent mucus gel covers all studied segments of the gastrointestinal tract during fasting conditions, with the thickest layers in the colon and ileum. Carefully applied suction revealed that the mucus gel was a multi-layered structure comprising a firmly adherent layer covering the mucosa, impossible to remove, and a loosely adherent upper layer. The firmly adherent layer was thick and continuous in the corpus (80μm), antrum (154μm) and colon (116μm), but thin (&lt;20μm) and discontinuous in the small intestine. Following mucus removal, a rapid renewal of the loosely adherent layer ensued. The highest rate was observed in the colon with intermediate values in the small intestine. Mucus renewal in the stomach was attenuated on acute luminal application of water extracts from H. pylori (HPE). In animals with a chronic H. pylori infection the mucus renewal rate was unaffected, but the total gastric mucus gel thickness was reduced and the mucus secretory response to luminal acid (pH1) attenuated in the antrum. HPE from type I strains acutely reduced corporal mucosal blood flow, measured with laser-Doppler flowmetry, by approximately 15%. The reduction in blood flow was mediated by a heat stable factor other than VacA and CagA. Inhibition of endogenous nitric oxide production with Nω-nitro-l-arginine augmented the decrease. However, ketotifen, a mast cell stabilizer, completely attenuated the effect of the extract as did the platelet activating factor (PAF) receptor-antagonist, WEB2086, thus depicting a detrimental role for the microvascular actions of PAF.

Le virus de l’hépatite C (VHC) est un problème mondial. La majorité des personnes infectées (70-85%) développent une infection chronique qui cause des complications hépatiques. Le seul régime thérapeutique approuvé pour le VHC est l'interféron alpha (IFN-α). Ce traitement a un taux de réussite de 50-80% selon le génotype de virus et le moment de l'initiation de la thérapie. Les facteurs régissant la réponse au traitement ne sont pas bien définis. Des études antérieures ont suggéré un rôle potentiel de la réponse immunitaire de l'hôte au succès de la thérapie, toutefois, ces résultats sont controversés. Nous avons émis l'hypothèse que la réponse immunitaire de l’hôte sera plus efficace chez les patients qui commencent la thérapie tôt pendant la phase aiguë de l'infection. En revanche, la réponse immunitaire sera épuisée lorsque le traitement est initié pendant la phase chronique. L'objectif principal de ce mémoire est d’étudier les facteurs immunologiques qui régissent la réponse à la thérapie, et de déterminer si la contribution de la réponse immunitaire de l'hôte peut être influencée par la période de l'infection. Nos résultats démontrent l'efficacité de la restauration de la réponse immunitaire spécifique au VHC lorsque la thérapie par l'interféron est initiée tôt. Ceci est démontré par le sauvetage des cellules T efficaces spécifiques au VHC efficace similaires à celles observées chez les individus qui ont résolu spontanément, suggérant ainsi qu'elles jouent un rôle actif dans la réponse au traitement. Toutefois, cette réponse n'a pas été restaurée chez les patients traités au cours de la phase chronique. Ces résultats ont des implications importantes dans la compréhension des mécanismes sous-jacents à la réponse aux traitements actuels et au développement des nouvelles thérapies. / Hepatitis C virus (HCV) is a major public health problem worldwide. Only 15-30% of infected individuals clear the virus spontaneously, while the majority develops chronic infection that causes liver complications. The only approved therapy for HCV is interferon alpha (IFN-α) based. This therapy has a 50-80% success rate depending on the infecting virus genotype and the timing of initiation of therapy. Factors governing the response to therapy are not well defined. Previous studies have suggested a role for the host immune response in the success of therapy. However, these results were controversial. We hypothesized that host immunity has an effective role in the success of IFN-α therapy when initiated early during the acute phase of HCV infection, while late initiation during the chronic phase minimizes this role. The main objective of this thesis was to dissect the immunological factors governing the differential response to IFN-α therapy, and to determine if the contribution of the immune response to success of therapy might be influenced by the period of infection. Our results demonstrate restoration of efficient HCV-specific immune responses when therapy is initiated early during the acute phase. This is demonstrated by the rescue of functional HCV-specific T cells similar to those observed in spontaneously resolved individuals, suggesting that they may play an active role in response to therapy. However, such responses were not restored following late therapy suggesting irreversible damage to the host’s defence system with chronicity. These findings have important implications in understanding the mechanisms underlying response to current treatments and development of novel therapies.

Toxoplasma gondii est un parasite intracellulaire responsable de la toxoplasmose. Lors de l’infection aiguë, le parasite se divise dans une vacuole parasitophore (VP), compartiment d’interactions avec la cellule hôte. La VP se modifie pour former un kyste qui persiste au cours de la phase chronique. Le rôle des protéines de granules denses (GRA) dans ce processus est suggéré par leur abondance dans la VP et la paroi kystique. Par des approches de génétique inverse et de protéomique, le but de ce travail visait à préciser au plan moléculaire, le rôle de la protéine GRA5. En utilisant un modèle de différenciation parasitaire in vitro, l’étude des phénotypes d’un mutant invalidé du gène gra5 a permis de découvrir son rôle clé dans la formation des kystes par le maintien 1/ de l’intégrité de la membrane délimitant la VP en cours de différenciation, 2/ de l’accumulation d’autres composants parasitaires dans la VP et 3/ de son interaction avec le reticulum endoplasmique de l’hôte. / Toxoplasmosis, which is caused by the intracellular parasite Toxoplasma gondii is characterized by a life-long chronic infection. The parasites replicate inside a parasitophorous vacuole (PV), which evolves into a persistent cyst. The molecular mechanisms governing the differentiation process are poorly characterized. It is known that the dense granules proteins (GRA) are major components of both the PV and the cyst wall, enabling their interaction with the host cells. Using a Prugniaud cystogenic type II strain in which the gra5 gene was invalidated and a combination of cellular and proteomic approaches, we discovered that GRA5 regulates i) the molecular content of the PV, ii) the PV interaction with the host endoplasmic reticulum and iii) host cell homeostasis,that is necessary to ensure the formation of a stable cyst wall.

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Human cytomegalovirus (HCMV) is a widespread human herpesvirus pathogen and prototypical member of the β-herpesvirus subfamily. Like all herpesviruses, the virus establishes a lifelong latent infection following host exposure, which has the potential to reactivate periodically and contribute to recurrent disease processes. In individuals with weak or compromised immune systems, such reactivation can lead to profound pathology. Understanding how latent infections are maintained is important for uncovering how HCMV causes disease. The study of viral genes that are expressed during latent infection grants insight into how latency is regulated and how it could be therapeutically targeted. To that end, this project has sought to evaluate the functional significance of one such viral gene termed LUNA in the context of latency. In models of experimental latent infection based on primary myeloid cells, levels of viral gene transcription were found to be significantly reduced following infection with LUNA deletion mutant viruses, consistent with corresponding observable changes in post-translational histone modifications over the viral promoters of latency-associated genes. Additionally, using luciferase reporter systems, latency-associated viral gene promoters became activated in response to the expression of wild-type LUNA. Together, these findings argue for a role of LUNA in regulating viral gene expression during latent HCMV infection. One possible mechanism by which LUNA may fulfil its role is by targeting cellular ND10 structures, known intrinsic inhibitors of herpesvirus gene expression, for disruption. In support of this, latently infected cells were found to be devoid of ND10, a phenotype that was recapitulated by the direct expression of wild-type LUNA. Furthermore, mutation studies confirmed the identification of a novel deSUMOylase activity encoded by LUNA that was responsible for mediating ND10 disruption. Use of a catalytically inactive LUNA mutant in transcriptional analyses of latent infection also generated similar results as with the LUNA deletion viruses. Overall, these data support the hypothesis that LUNA serves as an important regulator of viral gene expression during latency, which is likely linked to its ability to target ND10 structures for disruption, thus raising the possibility that inhibition of deSUMOylation may serve as a novel therapeutic strategy to target latent HCMV infection.

In Enterobacteriaceae, the transcriptional regulator AmpR, a member of the LysR family, regulates the expression of a chromosomal β-lactamase AmpC. The regulatory repertoire of AmpR is broader in Pseudomonas aeruginosa, an opportunistic pathogen responsible for numerous acute and chronic infections including cystic fibrosis. Previous studies showed that in addition to regulating ampC, P. aeruginosa AmpR regulates the sigma factor AlgT/U and production of some quorum sensing (QS)-regulated virulence factors. In order to better understand the ampR regulon, the transcriptional profiles generated using DNA microarrays and RNA-Seq of the prototypic P. aeruginosa PAO1 strain with its isogenic ampR deletion mutant, PAO∆ampR were analyzed. Transcriptome analysis demonstrates that the AmpR regulon is much more extensive than previously thought influencing the differential expression of over 500 genes. In addition to regulating resistance to β-lactam antibiotics via AmpC, AmpR also regulates non-β-lactam antibiotic resistance by modulating the MexEF-OprN efflux pump. Virulence mechanisms including biofilm formation, QS-regulated acute virulence, and diverse physiological processes such as oxidative stress response, heat-shock response and iron uptake are AmpR-regulated. Real-time PCR and phenotypic assays confirmed the transcriptome data. Further, Caenorhabditis elegans model demonstrates that a functional AmpR is required for full pathogenicity of P. aeruginosa. AmpR, a member of the core genome, also regulates genes in the regions of genome plasticity that are acquired by horizontal gene transfer. The extensive AmpR regulon included other transcriptional regulators and sigma factors, accounting for the extensive AmpR regulon. Gene expression studies demonstrate AmpR-dependent expression of the QS master regulator LasR that controls expression of many virulence factors. Using a chromosomally tagged AmpR, ChIP-Seq studies show direct AmpR binding to the lasR promoter. The data demonstrates that AmpR functions as a global regulator in P. aeruginosa and is a positive regulator of acute virulence while negatively regulating chronic infection phenotypes. In summary, my dissertation sheds light on the complex regulatory circuit in P. aeruginosa to provide a better understanding of the bacterial response to antibiotics and how the organism coordinately regulates a myriad of virulence factors.

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