Bunyaviridae is one of the biggest known viral families, and includes many viruses of clinical and economic importance. The major virulence factor of most bunyaviruses is the non-structural protein (NSs). NSs is expressed early in infection and inhibits the innate immune response of the host by blocking several steps in the interferon induction and signalling pathways. Hence, NSs significantly contributes to the establishment of a successful viral infection and replication, persistent infection and the zoonotic capacity of bunyaviruses. Although functions and structures of many viral interferon antagonists are known, no structure of a bunyavirus NSs protein has been solved to date. This strongly limits our understanding of the role and the mechanism of interferon antagonism in this large virus family. In this work the first structure for a bunyavirus interferon antagonist, the core domain crystal structure of NSs from the Rift Valley fever virus (RVFV) is presented. RVFV is one of the most clinically significant members of the Bunyaviridae family, causing recurrent epidemics in Africa and Arabia, often featuring high-mortality haemorrhagic fevers. The structure shows a novel all-helical fold. The unique molecular packing of NSs in the crystal creates stable fibrillar networks, which could correspond to the characteristic fibrillation of NSs observed in vivo in the nuclei of RVFV infected cells. This first NSs structure might be a useful template for future structure-aided design of drugs that target the RVFV interferon antagonism. Attempts at characterising other bunyavirus NSs proteins of other genera were made, but were hampered by problems with obtaining sufficient amounts of soluble and folded protein. The approaches that proved unsuccessful for the solubilisation of these NSs proteins, however, should inform future experiments aimed at obtaining recombinant NSs for structural studies.

La fièvre Q est une zoonose de répartition mondiale due à une bactérie intracellulaire stricte, Coxiella burnetii. Les ruminants domestiques contaminent l’environnement en excrétant la bactérie principalement dans les produits de parturition, le mucus vaginal et les fèces. L’Homme et l’animal s’infectent ensuite par inhalation de pseudo-spores circulantes dans l’environnement. Des enjeux de santé publique et vétérinaires ont ainsi motivés la mise en place de ce projet de thèse afin de mieux maîtriser les infections par C. burnetii dans les élevages. Les objectifs de ce travail étaient de produire des connaissances épidémiologiques descriptives sur : (a) la dynamique de circulation de C. burnetii en élevage ovin naturellement infecté ; (b) la diversité génotypique des souches de C. burnetii circulantes dans les élevages de ruminants domestiques en France ; (c) la diversité phénotypique de ces souches via l’utilisation de deux modèles de virulence, un in vivo et un in vitro ; et (d) l’implication du cheval dans l’épidémiologie de la fièvre Q, en étudiant son exposition à C. burnetii ainsi qu’une potentielle symptomatologie.Le suivi longitudinal réalisé en élevage ovin a permis de fournir des indicateurs pertinents à utiliser pour évaluer rapidement le risque de transmission de C. burnetii en contexte infectieux, en termes de lots d’animaux, d’outils diagnostics ou encore de périodes d’échantillonnage à privilégier. Par ailleurs, nous avons également identifié trois grands clusters génotypiques de souches circulantes dans les élevages de ruminants domestiques en contexte d’avortement fièvre Q en France. Deux clusters génotypiques regroupent majoritairement les petits ruminants, dont un principalement les ovins et l’autre les caprins. Le troisième cluster génotypique est composé quasi-exclusivement de bovins. Nous avons montré que le gène IS1111 impacte significativement la diversité génotypique MLVA observée. Nous avons également montré qu’en plus d’une spécificité d’espèce, les génotypes circulants en France sont stables d’un point de vue spatio-temporel. Pour l’étude phénotypique, nous avons mis au point deux modèles d’infection, l’un in vivo par inoculation dans le coussinet plantaire de souris mâle CD1 et l’autre in vitro par infection de deux lignées cellulaires macrophagiques : l’une bovine (SV40) et l’autre ovine (MoCl4). Ces modèles nous ont permis d’identifier 4 clusters phénotypiques, qui n’étaient pas systématiquement corrélés aux trois clusters génotypiques, identifiés in vivo à partir de l’analyse de la charge bactérienne dans la rate de souris, ni aux cinétiques de multiplication de C. burnetii observés in vitro. Enfin, les séroprévalences obtenues chez le cheval dans une zone considérée hyperendémique pour l’Homme (Camargue et Plaine de La Crau) suggèrent que les chevaux sont exposés à la fièvre Q dans cette région et pourrait éventuellement être utilisés comme des indicateurs pertinents du risque zoonotique. Néanmoins, nos résultats ne nous permettent pas de conclure sur les formes cliniques potentiellement associées à la fièvre Q chez le cheval. À l’avenir, les résultats obtenus dans ce travail de thèse permettront une meilleure compréhension de la dynamique de circulation et des conséquences de l’infection par C. burnetii en élevages de ruminants domestiques et de chevaux. Ces données permettront in fine d’améliorer la surveillance, le diagnostic ainsi que la mise en œuvre de mesures de gestion sanitaire de la fièvre Q en santé publique et vétérinaire. / Q fever is a worldwide zoonosis, due to a strict intracellular bacterium: Coxiella burnetii. Domestic ruminants mainly shed the bacteria in parturition products, vaginal mucus and feces. Humans and animals infect by inhalation of circulating pseudo-spores into the environment.Public and veterinary health issues therefore motivated the implementation of this PhD project in order to better control C. burnetii infections on farms. The objectives of this thesis were to provide descriptive epidemiological findings about: (a) circulation dynamics of C. burnetii in a naturally infected flock of sheep; (b) the genotypic diversity of circulating C. burnetii strains on domestic ruminant farms in France; (c) the phenotypic diversity of these strains as demonstrated by the use of two virulence models, one in vivo and one in vitro; and (d) the involvement of horses in the epidemiology of C. burnetii, by studying their exposure and a potential symptomatology.Longitudinal follow-up in a flock of sheep provided relevant tools to rapidly assess the risk of C. burnetii transmission when a flock was identified as infected, in terms of animal pens, diagnostic tools, or sampling periods to be preferred. We also identified three main genotypic groups of circulating strains in domestic ruminant farms in France where Q fever abortion were recorded. Two genotypic groups mainly included small ruminants, with one group mainly composed of sheep and the other mainly composed of goats. The third genotypic group was comprised almost exclusively of cattle. We have shown that the IS1111 gene significantly impacts the genotypic MLVA diversity observed. In addition to this species specificity, we have shown that the circulating genotypes in France were also spatiotemporally stable. We then developed two models of infection, one in vivo by inoculating CD1 male mice in the footpad of and one in vitro by infecting two macrophage cell lines: one bovine (SV40) and one ovine (MoCl4). These two models allowed us to show that the genotypic clusters were not systematically correlated with both the four phenotypic clusters identified in vivo from the analysis of the bacterial load in the mouse spleens and the analysis in vitro of the C. burnetii multiplication kinetics.Finally, the seroprevalence observed in horses within hyperendemic areas for Q fever in humans (Camargue and Plain of La Crau) suggests that horses are exposed to the bacteria in the area and that they may be a relevant indicator of the zoonotic risk. Nevertheless, our results were inconclusive on the clinical forms associated with Q fever in horses.In the future, the findings found in our work will allow a global understanding of the circulation dynamics of C. burnetii on domestic ruminant farms as well as in others animal species. Thus, all these data will ultimately improve surveillance, diagnosis and management of Q fever in public and veterinary health.

Enteric (or typhoid) fever is a systemic infection mainly caused by Salmonella Typhi and Salmonella Paratyphi A. The disease is common in areas with poor water quality and insufficient sanitation. Humans are the only reservoir for transmission of the disease. The presence of asymptomatic chronic carriers is a complicating factor for the transmission. There are major limitations regarding the current diagnostic methods both for acute infection and chronic carriage. Metabolomics is a methodology studying metabolites in biological systems under influence of environmental or physiological perturbations. It has been applied to study several infectious diseases, with the goal of detecting diagnostic biomarkers. In this thesis, a mass spectrometry-based metabolomics approach, including chemometric bioinformatics techniques for data analysis, has been used to evaluate the potential of metabolite biomarker patterns for diagnosis of enteric fever at different stages of the disease. In Paper I, metabolite patterns related to acute enteric fever were investigated. Human plasma samples from patients in Nepal with culture-confirmed S. Typhi or S. Paratyphi A infection were compared to afebrile controls. A metabolite pattern discriminating between acute enteric fever and afebrile controls, as well as between the two causative agents of enteric fever was detected. The strength of using a panel of metabolites instead of single metabolites as biomarkers was also highlighted. In Paper II, metabolite patterns for acute enteric fever, this time focusing only on S. Typhi infections, were investigated. Human plasma from patients in Bangladesh with culture-positive or -negative but clinically suspected S. Typhi infection were compared to febrile controls. Differences were found in metabolite patterns between the culture-positive S. Typhi group and the febrile controls with a heterogeneity among the suspected S. Typhi samples. Consistencies in metabolite patterns were found to the results from Paper I. In addition, a validation cohort with culture-positive S. Typhi samples and a control group including patients with malaria and infections caused by other pathogens was analysed. Differences in metabolite patterns were detected between S. Typhi samples and all controls as well as between S. Typhi and malaria. Consistencies in metabolite patterns were found to the primary Bangladeshi cohort and the Nepali cohort from Paper I. Paper III focused on chronic Salmonella carriers. Human plasma samples from patients in Nepal undergoing cholecystectomy with confirmed S. Typhi or S. Paratyphi A gallbladder carriage were compared to non-carriage controls. The Salmonella carriage samples were distinguished from the non-carriage controls and differential signatures were also found between the S. Typhi and S. Paratyphi A carriage samples. Comparing metabolites found during chronic carriage and acute enteric fever (in Paper I) resulted in a panel of metabolites significant only during chronic carriage. This work has contributed to highlight the potential of using metabolomics as a tool to find diagnostic biomarker patterns associated with different stages of enteric fever.

This is a study of the creation and negotiation of different forms of knowledge about dengue fever. I explore how anthropology, in collaboration with ideas and practices drawn from science and art, may transform public understandings of dengue. Dengue is a vector-borne disease transmitted to humans by the bite of a mosquito which is infected with the dengue virus. Mosquito-borne diseases have normally been treated through vector control and the elimination of breeding sites. Until 1960, the use of the pesticide DDT allowed the virtual eradication of Aedes aegypti (Ae. aegypti) in many places of the world. DDT was banned in most of the world by 1970 and by 1980 the focus on vector-control was replaced by a discourse of sanitation, in which health authorities tried to ‘educate’ populations and ‘teach’ proper hygienic habits to avoid mosquito-human contact. At present, these practices are changing again. The World Health Organisation (WHO) suggests that dengue incidence could be reduced at least 50% by 2020 through applying health campaigns and social interventions that involve having people participating in the control of dengue outbreaks. In this thesis I explore how WHO guidelines are applied in the control of dengue in Medellín, and how we can think about the concepts of ‘knowledge’, ‘education’ and public health campaigns through ethnographic methods. My project has been about looking at how different understandings – or different forms of knowledge – are part of interactions of different ‘publics’, non-expert citizens, virologists, entomologists and artists. My argument is that health campaigns should be re-designed – privileging relations and stimulating debate – by focusing on experience and moving towards managing the disease and living with the mosquito. Contrary to the different models enacted in health campaigns – which neglect the value of everyday experiences – I advocate for interdisciplinary collaboration as a relational art strategy that can generate an intersubjective exchange of experiences.

Les maladies fébriles y compris les maladies bactériennes sont mal connues en Côte d’Ivoire et en Guinée. Tout d’abord, nous avons recherché par biologie moléculaire des bactéries pathogènes transmises par les tiques en Côte d’Ivoire. Nous avons analysé différentes espèces de tiques prélevées chez des bovins et mis en évidence des bactéries pathogènes responsables de nombreuses maladies infectieuses comme Rickettsia, Borrelia, Anaplasma, Ehrlichia, Coxiella burnetii (fièvre Q) et aussi vingt nouvelles espèces potentielles.Ensuite, notre objectif était de détecter par biologie moléculaire des micro-organismes pathogènes chez l’homme. Concernant l’étude des plaies et des peaux saines en Guinée, la plupart des patients étaient infectés par Pseudomonas aeruginosa, Staphylococcus aureus et plusieurs espèces d'Acinetobacter.Parmi les patients fébriles et les sujets apyrétiques recrutés en Guinée et en Côte d’Ivoire, Plasmodium falciparum reste le micro-organisme le plus fréquent surtout dans les échantillons de sang des patients fébriles bien que plusieurs bactéries aient été aussi identifiées. En Guinée, il s’agissait de Staphylococcus aureus, Streptococcus pyogenes, Streptococcus pneumoniae, Salmonella enterica Non Typhi et Non Paratyphi et R. felis. Ces bactéries ont été également identifiées ainsi que Salmonella enterica Typhi, Salmonella enterica Paratyphi, Tropheryma whipplei et une nouvelle espèce potentielle de Wolbachia en Côte d’Ivoire. Nos travaux ont permis d’établir le répertoire des bactéries transmises par les tiques en Côte d’Ivoire, celles impliquées dans les bactériémies en Côte d’Ivoire et en Guinée (Conakry). / Febrile illnesses including bacterial diseases are poorly known in Côte d'Ivoire and Guinea.In the first part of our work, we researched by molecular biology bacteria transmitted by ticks in Côte d’Ivoire. We analyzed different species of ticks collected from cattle and highlighted pathogenic bacteria responsible for many infectious diseases such as Rickettsia, Borrelia, Anaplasma, Ehrlichia, Coxiella burnetii (Q fever) and twenty potential new species. In the second part, our goal was to detect using molecular biology several microorganisms in humans in Guinea (Conakry) and Côte d'Ivoire. As regards the study of wounds and healthy skin in Guinea, most patients were infected with Pseudomonas aeruginosa, Staphylococcus aureus, several species of Acinetobacter.Among the febrile patients and healthy controls afebrile recruited in Guinea and Côte d'Ivoire, Plasmodium falciparum is the most common detected microorganism especially in blood samples from febrile patients although several bacteria were also identified. In Guinea, it was Staphylococcus aureus, Streptococcus pyogenes, Streptococcus pneumoniae, non-typhoidal Salmonella spp., and R. felis. These bacteria were also identified as well as Salmonella enterica Typhi, Salmonella enterica Paratyphi, Tropheryma whipplei and a potential new species of Wolbachia in Côte d’Ivoire.This work allowed establishing the repertory of bacteria transmitted by ticks in Côte d’Ivoire, as well as those involved in bacteremia in Côte d’Ivoire and Guinea (Conakry).

Magister Public Health - MPH / Aim: The aim of this study was to assess the prescribing practices and availability of antimalarial drugs to children under five years of age in primary health care facilities in Bondo district.

The aim of this study was to investigate the epidemiology of Rift Valley fever (RVF) in South Africa. The first part of the study consisted of the compilation of a full history of RVF in South Africa. This was done by compiling all references to outbreaks of the disease in South Africa from all available literature, annual reports, disease reports and animal disease databases. The geographic location and temporal occurrence of each outbreak was recorded as accurately as allowed by the available records. The result was a better and more complete picture than has hitherto been available of the spatial and temporal distribution of RVF for the period 1950, when the disease was first recognised in South Africa, to 2010. Several smaller outbreaks not mentioned in the literature were found. It emerged that large outbreaks occur in the Free State Province, Eastern Cape Province and Northern Cape Province with long periods of absence and smaller outbreaks occur in KwaZulu-Natal, Mpumalanga and Gauteng at more frequent intervals.The second part of the study used the data collected during the first part of the study to determine which climatic and other environmental factors could have played a role in the occurrence of RVF in South Africa. Multiple logistic regression analysis was used to estimate associations between the various potential risk factors and the occurrence of Rift Valley fever.The study found that the El Niño/Southern Oscillation influence on rainfall in South Africa has an effect on the occurrence of RVF in South Africa which is opposite to the effect that has been described for Kenya. A positive Southern Oscillation Index (La Niña) increases the likelihood of a RVF outbreak in South Africa.The study also found that very high rainfall during the summer months (December to February) is an important risk factor for the occurrence of RVF and it confirmed the increased risk of an outbreak where pans and wetlands are present as reported in several articles and disease reports on past outbreaks. Several other factors, such as minimum and maximum temperature were also found to have a statistically significant effect on the occurrence of Rift Valley fever. Copyright / Dissertation (MSc)--University of Pretoria, 2011. / Production Animal Studies / unrestricted

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.

L'objectif de cette thèse est d'explorer l'inflammation et l'infection au niveau du transcriptome, à l'aide de la technologie des puces à ADN. Pour cela, nous avons dans un premier temps travaillé sur des données publiques. Nous avons construit une base de données de signatures transcriptionnelles annotées, et développé un logiciel modulaire d'analyse. Ce logiciel permet d'explorer aisément les données publiques en effectuant des recherches par nom de gène ou par mots-clés. Nous avons ensuite exploré la modulation temporelle de l'expression des gènes du parenchyme pulmonaire dans un modèle murin d'inflammation aiguë par injection d'acide oléique. Dans un second modèle murin d'infection par Coxiella burnetii, nous avons analysé le rôle du sexe dans la modulation de la réponse transcriptionnelle hépatique, et identifié des voies métaboliques impliquées dans le contrôle de l'infection. Dans un troisième modèle in-vitro d'infection par différentes souches du virus de la grippe, nous avons identifié une signature transcriptionnelle commune de réponse à l'infection. Par une approche bio-informatique originale, cette signature a conduit à l'identification de nouveaux anti-viraux à large spectre, dont l'efficacité a été démontrée in-vitro sur les souches utilisées pour l'analyse, et sur la souche H1N1, responsable de la dernière pandémie grippale. Enfin, nous avons analysé les modulations du transcriptome lors de pneumonies associées à la ventilation mécanique compliquant l'évolution de sujets traumatisés graves admis en réanimation. / The goal of this PhD is to explore inflammation and infection at the transcriptome level, using DNA microarrays. In order to do so, we first analyzed public data. We built a database with annotated transcriptional signatures and developed a modular analysis software to query this database. This software allows to easily explore public data with requests based on gene names or annotation keywords. We then explored the temporal modulation of lung gene expression following oleic acid injection in a murine model. In a second murine model of infection with Coxiella burnetii, we analyzed the influence of sex-related modulation in the hepatic transcriptional response after infection and identified several pathways implicated in the control of infection. In a third model of in-vitro infection with various Influenza virus strains, we identified a shared transcriptional signature in response to cell infection. Using an original in-silico methodology, this signature allowed us to identify new broad-spectrum antivirals. Efficacy of these molecules was demonstrated in-vitro against the strains used to define the signature, and also against the new pandemic H1N1 SOIV strain. Finally, we analyzed the transcriptional modulation occurring in whole blood samples from trauma patients hospitalized in intensive care unit, and whose evolution was complicated with ventilator-associated pneumonia.

Rickettsia rickettsii é o agente etiológico da febre maculosa das Montanhas Rochosas, a mais letal dentre as riquetsioses que acometem o homem. A principal espécie de carrapato-vetor de R. rickettsii na área metropolitana da cidade de São Paulo é Amblyomma aureolatum. Quando um carrapato em jejum no solo encontra um hospedeiro vertebrado e inicia a alimentação sanguínea, R. rickettsii é exposta a uma elevação da temperatura e aos componentes da refeição sanguínea. Ambos os estímulos foram previamente associados à reativação da virulência da bactéria em carrapatos, porém, os fatores responsáveis por essa conversão do fenótipo avirulento em virulento não foram completamente elucidados até o momento. Dessa forma, o presente trabalho teve como objetivo determinar os efeitos desses dois estímulos ambientais sobre o perfil de expressão gênica dessa bactéria durante a infecção de A. aureolatum. Inicialmente, estabelecemos um sistema de propagação de riquétsias para obter material genético suficiente para a padronização dos procedimentos de preparação de amostras para os experimentos de microarranjos. Para tal, estabelecemos, pela primeira vez, a infecção de uma cepa patogênica brasileira de R. rickettsii em células embrionárias do carrapato Rhipicephalus (Boophilus) microplus (BME26). Através da utilização de microarranjos de oligonucleotídeos customizados, analisamos os efeitos da elevação da temperatura em 10°C e da alimentação sanguínea sobre o perfil transcricional da bactéria infectando o conjunto de órgãos de fêmeas de A. aureolatum. Esse é o primeiro estudo da expressão gênica global de uma bactéria do gênero Rickettsia infectando um carrapato-vetor natural. Apesar de ambos os estímulos terem promovido um aumento da carga bacteriana, a alimentação sanguínea teve um efeito maior, também modulando cinco vezes mais genes que a elevação da temperatura. Dentre os genes induzidos, alguns codificam fatores de virulência, tais como componentes do sistema de secreção do tipo IV (T4SS), sugerindo que esse importante sistema de secreção bacteriano seja utilizado para secretar efetores durante a ingestão de sangue pelo carrapato. Através de análises in silico de domínios conservados das proteínas hipotéticas, identificamos outros componentes do T4SS de R. rickettsii ainda não descritos na literatura. A alimentação sanguínea também induziu a expressão de genes codificadores de enzimas antioxidantes, o que pode corresponder a uma tentativa de R. rickettsii de se proteger contra os efeitos deletérios de radicais livres produzidos pelos carrapatos alimentados. Por fim, analisamos a transcrição de uma seleção de genes de R. rickettsii em glândulas salivares e intestinos de carrapatos machos e fêmeas através de RT-qPCR microfluídica. Os resultados mostraram que a elevação da temperatura e a alimentação modulam um conjunto específico de genes em cada tecido analisado, tendo sido possível definirem-se assinaturas transcricionais tecido-específicas. Os genes diferencialmente expressos identificados neste estudo devem ser caracterizados funcionalmente, podendo ser considerados como futuros alvos para o desenvolvimento de vacinas. / Rickettsia rickettsii is the causative agent of Rocky Mountain Spotted Fever, which is the most lethal spotted fever rickettsiosis that affects humans. The main tick species that transmits R. rickettsii in the metropolitan area of São Paulos city is Amblyomma aureolatum. When an infected and starving tick begins blood feeding from a vertebrate host, R. rickettsii is exposed to a temperature elevation and to components in the blood meal. These two environmental stimuli have been previously associated with the reactivation of rickettsial virulence in ticks, but the factors responsible for this phenotype conversion have not been completely elucidated. The main aim of the present work was to determine the effects of these two environmental stimuli on the R. rickettsii transcriptional profile during A. aureolatum infection. We initially established an effective system for rickettsia propagation to generate a substantial quantity of genetic material for microarray standardization. For that, for the first time, we established an in vitro infection of the virulent Brazilian R. rickettsii strain in the BME26 tick embryonic cell line from Rhipicephalus (Boophilus) microplus. Using customized oligonucleotide microarrays, we analyzed the effects of a 10°C temperature elevation and a blood meal on the transcriptional profile of R. rickettsii infecting whole organs of Amblyomma aureolatum female ticks. This is the first bacterial transcriptome study of the Rickettsia genus when infecting a natural tick vector. Although both stimuli significantly increased the bacterial load, blood feeding had a greater effect, also modulating five-fold more genes than the temperature upshift. Among the genes induced by blood-feeding, some encode virulence factors, such as Type IV Secretion System (T4SS) components, suggesting that this important bacterial transport system is used to secrete effectors during the acquisition of the blood meal by the tick. Using an in silico conserved domain analysis of hypothetical proteins, we identified additional T4SS components of R. rickettsii that were never previously described. Blood-feeding also up-regulated the expression of antioxidant enzymes, which might correspond to an attempt by R. rickettsii to protect itself against the deleterious effects of free radicals produced by fed ticks. Finally, we studied the transcriptional profile of selected genes of R. rickettsii on the salivary glands and midguts of male and female ticks by microfluidic RT-qPCR. Results showed that temperature upshift and blood feeding modulate specific sets of genes in each tissue, allowing for the establishment of a tissue-specific transcriptional signature. The modulated genes identified in this study require further functional analysis and may have potential as future targets for vaccine development.