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Anaplasma phagocytophilum and A. marginale are the etiologic agents of bovine anaplasmosis and human granulocytic anaplasmosis, respectively. As obligate intracellular pathogens, binding and entry of host cells is a prerequisite for survival. The molecular events associated with these processes are poorly understood. Identifying the adhesins mediating binding, delineating their key functional domains, and determining the molecular determinants to which they bind not only benefits better understanding of Anaplasma spp. pathobiology, but could also benefit the development of novel approaches for protecting against infection. We previously demonstrated that A. phagocytophilum outer membrane protein A (ApOmpA) is critical for bacterial binding and entry host through recognition of α2,3-sialic acid and α1,3-fucose of its receptors, including 6-sulfo-sLex. In this study, we determined that two amino acids, G61 and K64, within its binding domain (ApOmpA59-74), are essential for ApOmpA function. We also confirmed the ability of ApOmpA to act as an adhesin and invasin as it conferred adhesiveness and invasiveness to inert beads. We next extended our studies to A. marginale as it also expresses OmpA (AmOmpA) and its role in infection has not been studied. Molecular models of ApOmpA and AmOmpA were nearly identical, especially in the ApOmpA binding domain and its counterpart in AmOmpA. Antisera raised against AmOmpA or its putative binding domain inhibit A. marginale infection. AmOmpA G55 and K58 are contributory and K59 is essential for AmOmpA to bind to host cells. AmOmpA binding is dependent on α2,3-sialic acid and α1,3-fucose. Coating inert beads with AmOmpA conferred the ability to bind to and be taken up by host cells, confirming that it acts as an adhesin and invasin. 6-sulfo-sLex is dispensable for AmOmpA binding and A. marginale infection. ApOmpA works cooperatively with Asp14 (14-kDa A. phagocytophilum surface protein) to promote optimal infection of host cells. We found that Asp14 is conserved across A. phagocytophilum strains and in A. marginale and confirmed the ability of Asp14 to act as an adhesin and invasin as it conferred adhesiveness and invasiveness to inert beads. Collectively, this work advances our understanding of A. phagocytophilum and A. marginale adhesion and invasion of host cells.

Les différents agents pathogènes ont développé de multiples stratégies pour contourner ou modifier les mécanismes de défense de l'hôte. La bactérie intracellulaire Brucella n'est pas une exception à la règle, car elle a développé des mécanismes qui lui permettent d'échapper à la surveillance immunitaire, persister pendant de longues périodes dans l'hôte et établir une infection chronique. En effet, Brucella responsable de la brucellose ou fièvre de Malte. La brucellose est une zoonose en réémergence ; dans cette maladie l'homme infecté représente une impasse épidémiologique. Il est indispensable de mieux connaître l'immunité développée contre Brucella qui est un excellent modèle d'étude d'autres maladies chroniques bactériennes. Le projet de thèse a été centré sur le développement et la modulation des réponses immunes par Brucella et les molécules bactériennes. Dans la première partie de cette thèse, nous avons analysé les réponses immunitaires innées et adaptatives lors de l'infection avec Brucella. D'une part, nous avons étudié l'influence des neutrophiles dans la réponse immunitaire lors de l'infection, en étudiant le cours de brucellose dans les modèles de souris neutropéniques. D'autre part, nous avons identifié et caractérisé in vivo une population des cellules CD4+ cytotoxiques au cours des infections avec Brucella. Dans la deuxième partie, nous nous sommes intéressés dans les modèles murins et humains aux propriétés immunomodulatrices des différentes molécules bactériennes telles que les glucans cycliques et des lipopolysaccharides (LPS). / Various successful pathogens have evolved multiple mechanisms to overcome or alter many normally very effective host defense mechanisms, including both innate and acquired immunity. The intracellular pathogen Brucella is not an exception to the rule as it displays mechanisms that allow it to evade immune surveillance and that are required to establish persistent infections in mammals. In this work, we studied the induction and modulation of immune responses by the intracellular bacteria Brucella and bacterial components. In the first part of this thesis, we have performed a systemic analysis of the innate and adaptive immune responses upon Brucella infection. On the one hand, we investigated the influence of polymorphonuclear neutrophils (PMNs) in the immune response during Brucella infection by exploring the course of brucellosis in antibody neutropenic mouse models. On the other hand, we identified and characterized in vivo a cytotoxic CD4+ T cell population upon Brucella abortus and Salmonella thyphimurium infections. In the second part, we focused on the immunomodulatory properties of various bacterial components such as cyclic glucans and lipopolysaccharides (LPS) both in mouse and human models.

Introdução: Embora a fisiopatogenia da rinossinusite crônica (RSC) ainda não esteja totalmente elucidada, em virtude da sua heterogeneidade e multifatorialidade, existe um crescente corpo de evidências apontando que as bactérias exerçam um papel significativo na gênese ou perpetuação da inflamação crônica. Uma das possíveis formas de atuação são os biofilmes bacterianos, comumente encontrados em pacientes com RSC e que estão relacionados com má evolução clínica. Ainda, existem evidências de que algumas espécies bacterianas, especialmente o Staphylococcus aureus (S. aureus), são capazes de invadir as células epiteliais e permanecerem viáveis em seu interior. Por fim, tem se demonstrado que pacientes RSC com pólipo nasal (RSCcPN) revelam alta associação com a presença de superantígenos estafilocócicos na mucosa respiratória, responsáveis pela estimulação acentuada de respostas inflamatórias locais. Apesar de essas diferentes formas bacterianas estarem bem descritas na RSC, não se sabe ainda com clareza como elas estão associadas nesses indivíduos. Objetivos: Avaliar a associação entre a presença de biofilmes, bactérias intracelulares e superantígenos estafilocócicos em pacientes com RSC (com e sem pólipo nasal), comparados com o grupo controle. Casuística e Métodos: Avaliou-se a prevalência de biofilmes bacterianos, bactérias intracelulares e presença de superantígenos bacterianos em indivíduos com RSCcPN, sem pólipo nasal (RSCsPN) e controles, analisando a associação de distribuição de prevalência desses diferentes grupos (teste exato de Fisher, nível de significância quando p<0,05). Os biofilmes foram definidos por características morfológicas à microscopia eletrônica de varredura (MEV), as bactérias intracelulares foram analisadas por microscopia eletrônica de transmissão (MET) e hibridização fluorescente in situ (FISH) para S. aureus, e superantígenos de S. aureus A-E foram quantificados pela técnica de ELISA (Enzime Linked Imunosorbent Assay). Foram incluídos 90 indivíduos, divididos em três grupos: 1) 38 pacientes com RSCcPN, 2) 26 com RSCsPN e 3) 26 controles. Resultados: Quarenta e dois por cento dos pacientes com RSCcPN (16/38), assim como os com RSCsPN (11/26) apresentaram amostras positivas para biofilmes bacterianos, mas não observou essa positividade no grupo controle (0/26). A análise para bactérias intracelulares demonstrou a presença em 31,5% de pacientes com RSCcPN (12/38), 19,2% em RSCsPN (5/26) e 0% nos controles (0/26). No estudo por FISH, 58% dos pacientes com RSCcPN (18/31) apresentaram positividade para S. aureus intracelular, seguido de 54% nos com RSCsPN (13/24) e em nenhum caso dos 24 analisados do grupo controle. Na avaliação por ELISA, apenas um paciente com RSCcPN foi positivo para a presença de superantígenos estafilocócicos. A avaliação da associação de biofilme bacteriano na superfície mucosa à MEV com bactéria intracelular à MET e com S. aureus intracelular por FISH nos dois diferentes grupos de RSC com e sem pólipo nasal, não mostrou diferença estatisticamente significativa. Conclusão: Foi observada uma maior prevalêcia de biofilmes e bactérias intracelulares em indivíduos com RSC com ou sem pólipo nasal, comparado a Resumo controles. Não houve diferença significativa dentre os grupos de RSC, com e sem pólipo nasal para a presença de biofilmes e bactérias intracelulares. Não houve associação entre a presença de biofilme e bactéria intracelular em pacientes com RSC. Os achados do presente estudo indicam que tanto biofilmes na superfície mucosa quanto microrganismos intracelulares podem estar envolvidos na fisiopatogenia da RSC. / Introduction: Although the pathophysiology of chronic rhinosinusitis (CRS) has not yet been fully elucidated, due to its heterogeneity and multifactorial etiology, there is a growing body of evidence that bacteria play a significant role in the genesis or perpetuation of chronic inflammation. One of the possible forms of acting are bacterial biofilms, which are commonly found in patients with CRS, and are associated with poor clinical outcomes in these patients. In addition to biofilms, there are some evidence pointing out that some bacterial species, especially Staphylococcus aureus (S. aureus), are able to invade into epithelial cells and remain viable intracellulary. Finally, it has been demonstrated that patients with CRS with nasal polyps (CRSwNP) have a high association with the presence of staphylococcal superantigens in the respiratory mucosa, responsible for the stimulation of marked local inflammatory responses. Although these different bacterial forms are well described in CRS, it is still unclear how they are associated in these individuals. Objectives: To evaluate the correlation between the presence of biofilms, intracellular bacteria expression and S. aureus superantigens in CRS patients (with and without nasal polyposis) compared to a control group. Casuistic and Methods: We evaluated the prevalence of bacterial biofilms, intracellular bacteria and the presence of bacterial superantigens in individuals with CRSwNP, without nasal polyp (CRSsNP) and controls, evaluating the association of prevalence distribution of these different groups (Fisher exact test, level of significance set at p<0.05). The biofilms were defined by morphological characteristics by scanning electron microscopy, intracellular bacteria were analyzed by transmission electron microscopy and fluorescence in situ hybridization (FISH) for S. aureus, and S. aureus A-E superantigens were quantified by ELISA. Ninety individuals were included, divided into 38 patients with CRSwNP, 26 patients with CRSsNP and 26 control patients. Results: 42% of patients with CRSwNP (16/38) as well as those with CRSsNP (11/26) presented positive samples for bacterial biofilms, while none of the control patients (0/26) had positive samples. The analysis for intracellular bacteria showed the presence in 31.5% of patients with CRSwNP (12/38), 19.2% in CRSsNP (5/26) and 0% in control patients (0/26). In the FISH study, 58% of patients with CRSwNP (18/31) presented intracellular S. aureus positivity, followed by 54% in patients with CRSsNP (13/24) and in none of the 24 analyzed in the control group. In the ELISA evaluation, only one patient with CRSwNP was positive for the presence of staphylococcal superantigens. The evaluation of the association of bacterial biofilm on the mucosal surface (SEM) with intracellular bacteria (MET) and with intracellular S. aureus by FISH in the two different groups of CRS (with and without nasal polyps) did not show a statistically significant difference. Conclusion: We found a higher prevalence of biofilms and intracellular bacteria in individuals with CRS, either with and without nasal polyps. There was no significant difference between the groups of CRS, with and without nasal polyp, for the presence of biofilms or intracellular bacteria. There was no significant diference on the association of biofilms and intracellular bacteria on pacientes with CRS. Our data indicate that both biofilms on the mucosal surface and intracellular microorganisms may be involved in the pathophysiology of CRS.

Les bactéries appartenant au complexe Burkholderia cepacia (Bcc) peuvent causer des infections pulmonaires dévastatrices chez les patients atteints de mucoviscidose. Les bactéries Bcc sont capables de survivre et se multiplier dans les macrophages in vitro. Des études cliniques ont confirmé que ces bactéries opportunistes se localisent au niveau des cellules phagocytaires et ne forment pas des biofilms dans les poumons des patients infectés comme on le croyait généralement. En utilisant le modèle d'infection zebrafish, nous avons établi précédemment que les macrophages constituent un site clé pour la réplication bactérienne et le développement de l'infection aiguë mortelle. Dans la présente étude, nous avons étudié le rôle des stades intracellulaires de B. cenocepacia en développant des nouvelles lignées transgéniques reportrices pour les études d’imagerie en temps réel, nous avons étudié le rôle de l'autophagie in vivo et analysé le profil « transcriptomique » des macrophages lors de l'infection par B. cenocepacia chez le poisson zèbre.En accord avec les études in vitro, nous avons constaté que la protéine « Microtubule-associated protein 1A/1B-light chain 3 » (Lc3), protéine clé dans l’autophagie, a été recrutée au niveau des vacuoles contenant B.cenocepacia K56-2. Nous avons observé en temps réel que les bactéries étaient capables de se répliquer dans ces organelles. Cependant la modulation de l'autophagie par voie génétique et pharmacologique n'a pas changé de manière significative le profil de réplication de B.cenocepacia K56-2 lors de l'infection. En dépit de la charge bactérienne inchangée, une baisse de l’autophagie était reliée avec une augmentation de la mortalité par rapport aux embryons de type sauvage. Ceci suggère une corrélation entre l'autophagie et l'inflammation, et nous proposons que la capacité de B. cenocepacia à arrêter la maturation des (auto) phagosomes et la présence de « cross-talk » entre l’autophagie d’une part et l’inflammasome de l’autre jouent un rôle important dans les réactions inflammatoires observées. Pour approfondir les connaissances sur le rôle des macrophages lors de l'infection aiguë, nous avons déterminé le profil transcriptomique des macrophages isolés à partir d'embryons de poisson zèbre infectés par B. cenocepacia après l'infection. Notre analyse bio-informatique a montré que la plupart des gènes surexprimés sont impliqués dans la signalisation de la réponse immunitaire, tandis que la plupart des gènes sous exprimés sont associés à la transcription et à la traduction. Nous avons confirmé l’activation de l’expression de tnfa dans les macrophages, et nous avons constaté que l'expression des cytokines cxcl8 et Il1b, induite par l'infection, ne dépendait pas de la signalisation par le récepteur TNFa, TNFRSF1A.Nos résultats contribuent à une meilleure compréhension de l'interaction entre B. cenocepacia et les macrophages in vivo, et peuvent contribuer à l’identification de nouvelles cibles pour le développement de thérapies anti-infectieuses pour lutter contre ces bactéries intracellulaires. / Opportunistic bacteria belonging to Burkholderia cepacia complex (Bcc) can cause devastating pulmonary infections in cystic fibrosis patients. These bacteria can survive and replicate in macrophages in vitro. Clinical evidence confirmed that the bacteria localize in phagocytic cells, and do not form biofilms in the lungs of infected patients as generally believed. Using a zebrafish infection model we established previously that macrophages are a critical site for bacterial replication and development of acute fatal infection. In the present study, we further explored the role of the intracellular stages of B. cenocepacia by developing new transgenic reporter lines for real time imaging of subcellular trafficking, studying in detail the role of autophagy in vivo, and performing host transcriptome analysis of FACS-sorted macrophages from zebrafish larvae infected with B. cenocepacia.In agreement with in vitro studies, we found that the autophagy related protein Microtubule-associated protein 1A/1B-light chain 3 (Lc3) was recruited to B. cenocepacia K56-2-containing vacuoles. Although not critical, using real time confocal microscopy, we observed that the bacteria were able to replicate in such organelles. Both genetic and pharmacological modulation of autophagy did not significantly change the replication profile of B. cenocepacia K56-2 during infection. However, reduction in autophagy resulted in more rapid embryo death compared to wild type embryos. This suggests an inverse correlation between autophagy and fatal inflammation, and we hypothesize that the ability of B. cenocepacia to arrest maturation of (auto)phagosomes, and cross talk between autophagy and inflammasome signaling pathways during B. cenocepacia infection play an important role in the observed inflammatory responses. This study further describes the host transcriptome profile of macrophages isolated from infected zebrafish embryos. Our bio-informatics analysis showed that most of the genes up-regulated during infection were involved in immune response signaling, while the major group of down-regulated genes was associated with transcription and translation. We experimentally confirmed rapidly increased expression of tnfa in macrophages, and found that infection-induced expression of the cytokines cxcl8 and il1b did not depend on signalling through the Tnfa receptor, Tnfrsf1a.Our results contribute to a better understanding of the interaction between B. cenocepacia and macrophages in vivo, and the zebrafish may help finding new targets for development of anti-infectious therapies to combat these intracellular bacteria.

Introdução: Embora a fisiopatogenia da rinossinusite crônica (RSC) ainda não esteja totalmente elucidada, em virtude da sua heterogeneidade e multifatorialidade, existe um crescente corpo de evidências apontando que as bactérias exerçam um papel significativo na gênese ou perpetuação da inflamação crônica. Uma das possíveis formas de atuação são os biofilmes bacterianos, comumente encontrados em pacientes com RSC e que estão relacionados com má evolução clínica. Ainda, existem evidências de que algumas espécies bacterianas, especialmente o Staphylococcus aureus (S. aureus), são capazes de invadir as células epiteliais e permanecerem viáveis em seu interior. Por fim, tem se demonstrado que pacientes RSC com pólipo nasal (RSCcPN) revelam alta associação com a presença de superantígenos estafilocócicos na mucosa respiratória, responsáveis pela estimulação acentuada de respostas inflamatórias locais. Apesar de essas diferentes formas bacterianas estarem bem descritas na RSC, não se sabe ainda com clareza como elas estão associadas nesses indivíduos. Objetivos: Avaliar a associação entre a presença de biofilmes, bactérias intracelulares e superantígenos estafilocócicos em pacientes com RSC (com e sem pólipo nasal), comparados com o grupo controle. Casuística e Métodos: Avaliou-se a prevalência de biofilmes bacterianos, bactérias intracelulares e presença de superantígenos bacterianos em indivíduos com RSCcPN, sem pólipo nasal (RSCsPN) e controles, analisando a associação de distribuição de prevalência desses diferentes grupos (teste exato de Fisher, nível de significância quando p<0,05). Os biofilmes foram definidos por características morfológicas à microscopia eletrônica de varredura (MEV), as bactérias intracelulares foram analisadas por microscopia eletrônica de transmissão (MET) e hibridização fluorescente in situ (FISH) para S. aureus, e superantígenos de S. aureus A-E foram quantificados pela técnica de ELISA (Enzime Linked Imunosorbent Assay). Foram incluídos 90 indivíduos, divididos em três grupos: 1) 38 pacientes com RSCcPN, 2) 26 com RSCsPN e 3) 26 controles. Resultados: Quarenta e dois por cento dos pacientes com RSCcPN (16/38), assim como os com RSCsPN (11/26) apresentaram amostras positivas para biofilmes bacterianos, mas não observou essa positividade no grupo controle (0/26). A análise para bactérias intracelulares demonstrou a presença em 31,5% de pacientes com RSCcPN (12/38), 19,2% em RSCsPN (5/26) e 0% nos controles (0/26). No estudo por FISH, 58% dos pacientes com RSCcPN (18/31) apresentaram positividade para S. aureus intracelular, seguido de 54% nos com RSCsPN (13/24) e em nenhum caso dos 24 analisados do grupo controle. Na avaliação por ELISA, apenas um paciente com RSCcPN foi positivo para a presença de superantígenos estafilocócicos. A avaliação da associação de biofilme bacteriano na superfície mucosa à MEV com bactéria intracelular à MET e com S. aureus intracelular por FISH nos dois diferentes grupos de RSC com e sem pólipo nasal, não mostrou diferença estatisticamente significativa. Conclusão: Foi observada uma maior prevalêcia de biofilmes e bactérias intracelulares em indivíduos com RSC com ou sem pólipo nasal, comparado a Resumo controles. Não houve diferença significativa dentre os grupos de RSC, com e sem pólipo nasal para a presença de biofilmes e bactérias intracelulares. Não houve associação entre a presença de biofilme e bactéria intracelular em pacientes com RSC. Os achados do presente estudo indicam que tanto biofilmes na superfície mucosa quanto microrganismos intracelulares podem estar envolvidos na fisiopatogenia da RSC. / Introduction: Although the pathophysiology of chronic rhinosinusitis (CRS) has not yet been fully elucidated, due to its heterogeneity and multifactorial etiology, there is a growing body of evidence that bacteria play a significant role in the genesis or perpetuation of chronic inflammation. One of the possible forms of acting are bacterial biofilms, which are commonly found in patients with CRS, and are associated with poor clinical outcomes in these patients. In addition to biofilms, there are some evidence pointing out that some bacterial species, especially Staphylococcus aureus (S. aureus), are able to invade into epithelial cells and remain viable intracellulary. Finally, it has been demonstrated that patients with CRS with nasal polyps (CRSwNP) have a high association with the presence of staphylococcal superantigens in the respiratory mucosa, responsible for the stimulation of marked local inflammatory responses. Although these different bacterial forms are well described in CRS, it is still unclear how they are associated in these individuals. Objectives: To evaluate the correlation between the presence of biofilms, intracellular bacteria expression and S. aureus superantigens in CRS patients (with and without nasal polyposis) compared to a control group. Casuistic and Methods: We evaluated the prevalence of bacterial biofilms, intracellular bacteria and the presence of bacterial superantigens in individuals with CRSwNP, without nasal polyp (CRSsNP) and controls, evaluating the association of prevalence distribution of these different groups (Fisher exact test, level of significance set at p<0.05). The biofilms were defined by morphological characteristics by scanning electron microscopy, intracellular bacteria were analyzed by transmission electron microscopy and fluorescence in situ hybridization (FISH) for S. aureus, and S. aureus A-E superantigens were quantified by ELISA. Ninety individuals were included, divided into 38 patients with CRSwNP, 26 patients with CRSsNP and 26 control patients. Results: 42% of patients with CRSwNP (16/38) as well as those with CRSsNP (11/26) presented positive samples for bacterial biofilms, while none of the control patients (0/26) had positive samples. The analysis for intracellular bacteria showed the presence in 31.5% of patients with CRSwNP (12/38), 19.2% in CRSsNP (5/26) and 0% in control patients (0/26). In the FISH study, 58% of patients with CRSwNP (18/31) presented intracellular S. aureus positivity, followed by 54% in patients with CRSsNP (13/24) and in none of the 24 analyzed in the control group. In the ELISA evaluation, only one patient with CRSwNP was positive for the presence of staphylococcal superantigens. The evaluation of the association of bacterial biofilm on the mucosal surface (SEM) with intracellular bacteria (MET) and with intracellular S. aureus by FISH in the two different groups of CRS (with and without nasal polyps) did not show a statistically significant difference. Conclusion: We found a higher prevalence of biofilms and intracellular bacteria in individuals with CRS, either with and without nasal polyps. There was no significant difference between the groups of CRS, with and without nasal polyp, for the presence of biofilms or intracellular bacteria. There was no significant diference on the association of biofilms and intracellular bacteria on pacientes with CRS. Our data indicate that both biofilms on the mucosal surface and intracellular microorganisms may be involved in the pathophysiology of CRS.

La première partie de ma thèse est une revue donnant un aperçu du répertoire génomique des bactéries intracellulaires et de leurs symbiotes. L'objectif de cette étude est d'explorer le processus permettant aux bactéries intracellulaires d'acquérir leur mode de vie spécifique. Nous avons commencé par examiner les données à propos de l'existence ancienne de bactéries intracellulaires, leur adaptation à leur hôte et les différences entre sympatrie et allopatrie. Une comparaison du contenu génomique de plusieurs bactéries avec différents modes de vie a révélé la capacité des bactéries à échanger des gènes à des degrés différents, en fonction de l'écosystème. La deuxième partie de ma thèse porte sur la séquence du génome de la souche Diplorickettsia massiliensis 20B qui est une bactérie intracellulaire obligatoire à Gram négatif isolée à partir des tiques de Slovaquie Ixodes ricinus. Dans ma troisième et dernière partie, nous exploré le répertoire du génome de Diplorickettsia massiliensis en le comparant aux génomes de bactéries phylogénétiquement très proches de Diplorickettsia massiliensis, issues de différentes niches. Ceci a permis de révélé son mode de vie allopatrique. Dans cette étude, nous avons comparé les caractéristiques du génome de Diplorickettsia massiliensis avec vingt-neuf espèces séquencées de Gammaproteobacteria (Legionella, Coxiella burnetii, Francisella tularensis et Rickettsiella grylli) en utilisant l'approche pangénomique multi-genre. Ce travail de thèse fournit des données originales et permet d’apporter plus de lumière sur la diversité des bactéries intracellulaires. / The initial purpose of my thesis is to understand with the help of comparative genomics, genomic variations based on coexistence, by examining data on the ancient existence of intracellular bacteria, their host adaptation and the differences between sympatry and allopatry. The first part of my thesis is a review giving insight into intracellular bacterial genome repertoire and symbionts. The goal of this review is to explore how intracellular microbes acquire their specific lifestyle. Due to their different evolutionary trajectories, these bacteria have different genomic compositions. We reviewed data on the ancient existence of intracellular bacteria, their host adaptation and the differences between sympatry and allopatry. A comparison of the genomic contents of bacteria with certain lifestyles revealed the bacterial capacity to exchange genes to different extents, depending on the ecosystem. The second part of my thesis present about the genome sequence of Diplorickettsia massiliensis strain 20B which is an obligate intracellular, gram negative bacterium isolated from Ixodes ricinus ticks collected from Slovak. In the third part, we investigated the genome repertoire of Diplorickettsia massiliensis compared to closely related bacteria according to its niche, revealing its allopatric lifestyle. In this study, we compared the genomic features of Diplorickettsia massiliensis with twenty-nine sequenced Gammaproteobacteria species (Legionella strains, Coxiella burnetii strains, Francisella tularensis strains and Rickettsiella grylli) using multi-genus pangenomic approach. This thesis work provides original data and sheds light on intracellular bacterial diversity.

Notre objectif est d’évaluer la sérologie, la biologie moléculaire et la culture pour le diagnostic des infections liées aux bactéries intracellulaires.La sérologie occupe une place importante dans le dépistage, le suivi et le monitoring des patients présentant une infection cardiovasculaire à C. burnetii ou Bartonella. Cependant, nous avons montré quelques limites aux seuils précédemment établis pour le diagnostic d’endocardite. Ce travail suggère que les faibles titres d’anticorps n'excluent pas le diagnostic de l'infection cardiovasculaire chez les patients ayant des facteurs prédisposant et qu'une valeur de seuil sérologique ne peut fournir une VPP de 100%.La qPCR réalisée sur des prélèvements cardiovasculaires pour le diagnostic d’endocardite à C. burnetii et Bartonella est plus sensible que la culture et l’immunohistochimie. Toutefois, des qPCR négatives ont été obtenues chez des patients présentant une endocardite avec de fort titre d’anticorps, par conséquent une qPCR négative ne doit pas définitivement exclure le diagnostic. Nous avons montré que l’ADN est capable de persister dans les prélèvements, malgré un traitement antibiotique préalable. Nous avons alors développé un nouvel outil pour évaluer la viabilité bactérienne en quantifiant la transcription de l'ARNr 16S de C. burnetii.La culture des bactéries intracellulaires reste nécessaire pour permettre la caractérisation des bactéries et faciliter le développement d'outils diagnostiques. Au cours de cette thèse, nous avons mis au point une technique innovante de plage de lyse pour mettre en évidence un effet délétère des antibiotiques sur les cellules infectées par R. conorii. / The aim of our study is to evaluate serology, molecular biology and culture for the diagnosis of intracellular bacteria.Serology plays an important role in the detection of Q fever and Bartonella infections and for the follow up and monitoring of patients with cardiovascular infection. However, we have shown some limits to the use of serological thresholds previously established for the diagnosis of endocarditis. In 2 series of Q fever and Bartonella endocarditis, we diagnosed patients with a definite cardiovascular infection associated with low antibody levels (<800). This work suggests that low antibody titers do not exclude the diagnosis of cardiovascular infection in patients with predisposing factors and a value of serological threshold cannot provide a positive predictive value of 100%.qPCR performed on cardiovascular samples for the diagnosis of C. burnetii and Bartonella endocarditis is more sensitive than the amplification of the 16S rRNA gene, culture and immunohistochemistry. Nevertheless, negative qPCR were obtained for patients presenting endocarditis with high antibody titer, therefore a negative qPCR should not definitively exclude the diagnosis. On the other hand, we have shown that DNA can persist in clinical specimens, despite previous antibiotic treatment. We developed a new tool to assess bacterial viability by quantifying the transcription of the 16S rRNA of C. burnetii.Culture of intracellular bacteria is necessary to enable the characterization of bacteria and facilitate the development of diagnostic tools. We developed an innovative technique of plaque assay to highlight a deleterious effect of antibiotics on infected cells by R. conorii.

Le traitement des infections intracellulaires est compliqué par la capacité des bactéries à «se cacher» à l’intérieur des cellules de l’hôte, en particulier celles du système immunitaire, entravant ainsi l’action de nombreux agents antimicrobiens. La diffusion croissante de souches résistantes est très inquiétante. Dans ce cadre, les nanoparticules (NPs) constituent une stratégie prometteuse pour administrer de manière optimisée des agents antimicrobiens.Ce travail de thèse, réalisé dans le cadre du projet européen ITN Cyclon Hit, visait à développer et caractériser des NPs biodégradables et biocompatibles chargées en antibiotiques, composés d’acide polylactique (PLA), d’acide poly (lactique-co-glycolique) (PLGA) et de polycaprolactone (PCL) ou de cyclodextrines polymérisées (pCD).Les deux premiers chapitres sont consacrés aux verrous technologiques liés à l'encapsulation de certains médicaments puissants dans les NPs polymériques. Tout d'abord, ces vecteurs ont été utilisés pour la délivrance simultanée d'une combinaison de molécules actives récemment découverte, l'éthionamide (ETH) et son Booster, pour le traitement de la tuberculose. Deuxièmement, ils ont été employés pour relever les défis liés à l'incorporation d'une quinolone de première génération, l'acide pipémidique (PIP), dans le but d'optimiser sa distribution intracellulaire dans des infections telles que la salmonellose.La co-incorporation efficace de l'ETH et du booster a dû surmonter de nombreuses difficultés liées à des problèmes de solubilité, de cristallisation et de biodisponibilité. Nos NPs en PLA et en pCD ont montré leur capacité de co-encapsuler efficacement les deux molécules et tout particulièrement celles en pCD. Elles incorporent les médicaments à la fois dans les cavités des CD et dans des microdomaines hydrophobes. Les NPs en pCD, non toxiques après administration pulmonaire répétée de fortes doses, ont été administrés in vivo par voie endotrachéale directement au site d'infection. Elles ont permis une diminution de 3-log de la charge bactérienne pulmonaire des animaux infectés après seulement 6 administrations. De même, l'incorporation de PIP a été confrontée à des défis liés à la cristallisation de PIP et à sa libération incontrôlée. Malheureusement, le PIP présentait une faible affinité pour tous les matériaux polymériques étudiés et son encapsulation physique était infructueuse. Ainsi, une approche alternative a été développée en couplant le PIP au PCL via une réaction sans catalyseur initiée par le médicament. Le conjugué PCL-PIP se auto-assemble en forme de NPs avec une charge en PIP de 27%. Cependant, le PCL-PIP n'a pas pu être dégradé in vitro, mais l’approche de synthèse de conjugués est séduisante pour obtenir de particules stables et avec un contenu important en PIP.La compréhension approfondie de la structure et de la composition du noyau et de la couronne des nanostructures contenant une ou deux molécules actives est cruciale pour leur optimisation. Les deux derniers chapitres sont donc consacrés à l'application innovante de l'AFM-IR, une méthode nanospectroscopique originale combinant la microscopie à force atomique (AFM) avec la spectroscopie infrarouge (IR), à l'analyse chimique des NPs en PLGA ou à leur détection sans marquage après internalisation dans les cellules.L’AFM-IR est capable de fournir une caractérisation chimique à l'échelle nanométrique (résolution ~10 nm). Une avancée majeure du travail est l'application du mode tapping permettant l'investigation individuelle de chaque NP. Le signal IR spécifique des composants des NPs a été utilisé pour appréhender la composition chimique de leur cœur et couronne ainsi que pour localiser précisément le médicament. De plus, l'AFM-IR en mode contact a permis pour la première fois la localisation sans marquage et l'identification chimique des NP à l'intérieur des cellules. Ce travail ouvre la voie à d'innombrables applications de cette technique dans le domaine de la nanomedecine. / The treatment of intracellular infections is very challenging given the ability of bacteria to “hide” inside the cells of the host, especially the ones of the immune system, thus hampering the action of many antimicrobial agents. The battle against these bacteria has been further exacerbated by the increasing diffusion of antimicrobial resistant strains. In this frame, nanoparticles (NPs) are a very promising strategy to overcome the limitations of free antimicrobial agents by administering them in an optimized manner.This PhD work, performed as part of the European Project ITN Cyclon Hit, aimed at the development and advanced characterisation of antibiotic-loaded biodegradable and biocompatible NPs made of poly (lactic acid) (PLA), poly (lactic-co-glycolic) (PLGA) and polycaprolactone (PCL) or of polymerised cyclodextrins (pCDs).The first two chapters are dedicated to the encapsulation of powerful but challenging drugs in polymeric NPs. Firstly, these carriers were employed for the simultaneous delivery of a potent drug combination recently discovered, ethionamide (ETH) and its booster, for tuberculosis therapy. Secondly, they were used to address the challenges related to the incorporation of a first-generation quinolone, pipemidic acid (PIP), with the aim of optimising its intracellular delivery in infections such as salmonellosis.The efficient co-incorporation of ETH and booster had to overcome several technological barriers. These drugs presented solubility, crystallisation and bioavailability-related problems which were overcome thanks to the developed NPs. Our engineered PLA and pCD NPs were both able to efficiently co-encapsulate the two molecules. Among the in depth-characterised formulations, pCDs NPs displayed the best physico-chemical properties and were shown to host the drugs both in the CD cavities and in confined spaces inside NPs crosslinked polymer. The pCD NPs were administered in vivo by endotracheal route directly to the infection site. Empty NPs were shown non-toxic after repeated pulmonary administration of high doses. Moreover, loaded pCD NPs led to a 3-log decrease in the pulmonary bacterial load of infected animals after only 6 administrations. Similarly, the incorporation of PIP faced challenges mainly related to PIP crystallization and burst release. Unfortunately, PIP displayed poor affinity for all the studied polymeric materials and its physical encapsulation was unsuccessful. Thus, an alternative approach was developed by coupling PIP to PCL by using an original catalyst-free drug-initiated reaction. The PCL-PIP conjugate self-assembled in NPs with up to 27 wt% PIP which were thoroughly characterised. However, the conjugate couldn’t be enzymatically degraded. With the design of novel PCL-PIP conjugates, this self-assembly approach could represent a promising strategy.The deep understanding of the structure and composition of complex core-corona nanocarriers containing one or two active molecules is crucial for their optimisation. The last two chapters are devoted to the innovative application of AFM-IR, an original nanospectroscopic method combining atomic force microscopy (AFM) with infrared (IR) spectroscopy, to the chemical analysis of PLGA NPs or to their label-free detection after cell internalisation.AFM-IR is able to provide chemical characterisation at the nanometer scale (resolution ~10nm). One main breakthrough here is the application of the recently developed tapping mode allowing the investigation of single polymeric NPs. The specific IR signal of NPs constituents was used to unravel the chemical composition of their core and corona as well as to precisely locate the drug. Moreover, the AFM-IR in contact mode enabled for the first time the label-free localisation and unambiguous chemical identification of NPs inside cells using the polymer IR specific response as a fingerprint. This work paves the way for countless application of this technique in the field of drug delivery.