Thesis (Ph. D.)--West Virginia University, 2004. / Title from document title page. Document formatted into pages; contains xi, 157 p. : ill. (some col.). Includes abstract. Includes bibliographical references.

Coxiella burnetii, the etiologic agent of acute Q fever and chronic endocarditis, has a unique biphasic life cycle, which includes a metabolically active intracellular form that occupies a large lysosome-derived acidic vacuole. C. burnetii is the only bacterium known to thrive within such a hostile intracellular niche, and this ability is fundamental to its pathogenicity; however, very little is known about genes that facilitate Coxiella's intracellular growth. This lack of knowledge of Coxiella's basic biology and molecular pathogenesis is a critical barrier to developing more effective therapies. In this study, we aimed to understand both bacterial and host factors that have important roles during C. burnetii infections. Using an evolutionary genomics approach, we identified metabolic pathways that are critical to C. burnetii's ability to grow intracellularly. Among those found, the most promising are fatty acid, biotin, and heme biosyntheses pathways. Coxiella has horizontally acquired extra copies of genes that enhance these processes; when these genes were disrupted, Coxiella's growth was significantly inhibited. Also, by analyzing the host transcriptome, we identified human genes, including microRNA (miRNA) genes that are important during C. burnetii infections. Coxiella induces the expression of multiple anti-apoptotic miRNAs, which likely have a role in inhibiting apoptosis in order to sustain the intracellular replication of the pathogen. The biosynthetic pathways and miRNAs identified in this study are ideal targets for developing more effective therapeutic strategies against Q fever and its chronic and often fatal complications.

Acute Q fever is the disease manifestation of Coxiella burnetii infection. This obligate intracellular bacterium is phagocytosed by innate immune cells, where it replicates within the usually bactericidal environment of the phagolysosome. As the immune response is activated, the resultant pro-inflammatory cytokines aid in pathogen clearance but also trigger an acute sickness response in the host. This thesis describes the natural history of acute Q fever in a prospective cohort ??? the Dubbo Infection Outcomes Study (DIOS). In these subjects, the acute febrile illness was characterised by severe headache, drenching sweats and fatigue. In approximately 10% of subjects, symptomatic illness marked by fatigue remained present for months, or occasionally years, after the acute illness. Subjects with more severe acute illness were more likely to develop this post Q fever fatigue syndrome (QFS). The aim of this thesis was to determine whether ongoing infection or aberrant immune activation drive the prolonged symptoms of QFS. Sensitive real time PCR detection of Coxiella DNA revealed a significant minority of subjects had very low copy numbers in circulating monocytes, with an increased prevalence in those with QFS. However, the detection was not consistently found within individual subjects and the copy number was at the threshold of reliable detection. C. burnetii was shown here to stimulate cytokine production in monocytic cells via interaction with Toll-like receptor (TLR)-2 and not TLR-4. Functional polymorphisms in these TLRs were identified in subjects with Q fever, but were not associated with Q fever susceptibility, severity or duration. Phase I-specific responses are believed to be critical in the generation of protective immunity to C. burnetii, yet the phase II-specific responses of innate and adaptive immune components were consistently of higher magnitude. Whole C. burnetii organisms induced antigen-non-specific T cell activation, presumably via the indirect activation of monocytes by C. burnetii LPS. No significant differences were found in the magnitude or kinetics of the host response to infection, or in the carriage of genetic polymorphisms, when comparing subjects who developed QFS with subjects who had promptly resolving illness. It remains unclear what factors mediate the progression of acute Q fever to QFS.

No description available.

Orientador: Jane Megid / Resumo: Coxiella burnetii é uma bactéria intracelular obrigatória responsável por causar a febre Q em humanos, mas também é conhecida como coxielose em animais. No Brasil, pouco é sabido a respeito da epidemiologia da enfermidade. O presente estudo objetiva estabelecer a prevalência do patógeno em bovinos abatidos no estado de São Paulo, além da detecção molecular em soro e fetos de bovinos. A sorologia de 1515 amostras de bovinos coletadas em frigoríficos foi realizada por reação de imunofluorescência indireta (RIFI) para anticorpos anti-C. burnetii. Reação em cadeia da polimerase em tempo real (qPCR) visando detectar o gene IS1111, foi utilizada para o diagnóstico molecular de C. burnetii em amostras de soro e fetos de bovinos. A prevalência aparente para anticorpos anti-C. burnetii em bovinos foi de 23,8% [IC95%=21,7% – 25,9%] (n=360), e a prevalência real de 20,0% [IC95%=17,8 – 22,3%]. A qPCR foi realizada nas 360 amostras soropositivas e apresentou resultado positivo em 92 amostras (25,6% [IC95%=20,1% – 28,8%]), demonstrando a presença do micro-organismo na corrente sanguínea dos bovinos amostrados. Entre as 28 amostras de fetos bovinos analisados, 10,7% (n=3) foram positivas na qPCR, confirmado por sequenciamento. A análise por qPCR quantitativo das amostras de abortamentos indicaram concentração entre 500 – 104 células por grama de tecido. Análise de multilocus de repetições em tandem de número variável (MLVA) e Multispacer Sequence Typing (MST) das amostras de fetos e do cont... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Coxiella burnetii is an obligate intracellular bacterium responsible for causing Q fever in humans but is also known as coxiellosis in animals. In Brazil, little is known about the epidemiology of the disease. The present study aims to establish the prevalence of the pathogen in cattle slaughtered in the state of São Paulo, in addition to molecular detection in bovine serum and fetuses. The serology of 1515 bovine samples collected in slaughterhouses was performed by indirect immunofluorescence reaction (IFA) for anti-C. burnetii antibodies. Real-time polymerase chain reaction (qPCR) to detect the IS1111 gene was used for the molecular diagnosis of C. burnetii in bovine serum and fetal samples. The apparent prevalence of anti-C. burnetii antibodies in cattle was 23.8% [95% CI = 21.7% - 25.9%] (n = 360) and the true prevalence was 20.0% [95% = 17.8 - 22.3%]. The qPCR was performed in the 360 seropositive samples and presented a positive result in 92 samples (25.6% [95% CI = 20.1% - 28.8%]), demonstrating the presence of the microorganism in the blood stream of the sampled cattle. Among the 28 samples of bovine fetuses analyzed, 10.7% (n = 3) were positive in qPCR, confirmed by sequencing. Quantitative qPCR analysis of the abortion samples indicated concentration between 500-104 cells per gram of tissue. Multiple-Locus Variable number tandem repeat Analysis (MLVA) and Multispacer Sequence Typing (MST) from fetal samples and positive control revealed new strains of C. burnetii c... (Complete abstract click electronic access below) / Doutor

Thesis (Ph.D.)--Murdoch University, 2009. / Thesis submitted to the Faculty of Health Sciences. Includes bibliographical references (p. 246-272)

L’objectif de cette thèse a été d’enrichir nos connaissances sur les bactériesintracellulaires strictes et spécialement Coxiella burnetii, agent responsable de la fièvre Q.Pour ce faire, nous avons d’une part amélioré les techniques de préparation de l’ARN pourles études transcriptionnelles et d’autre part utilisé la technologie des puces à ADN pouranalyser le transcriptome ainsi que la diversité génomique de C. burnetii.L’utilisation d’échantillons cliniques dans les études transcriptionnelles est limitéepar la quantité de matériel disponible qui ne permet pas d’analyser simultanément les profilsdu pathogène et de son hôte au cours de l’infection. De ce fait, nous avons développé, sur unmodèle d’escarres obtenus à partir de malades de fièvre boutonneuse méditerranéenne, unestratégie basée sur l’hybridation soustractive pour séparer les ARN eucaryotes etprocaryotes dans le but d’entreprendre des hybridations de puces à ADN.C. burnetii est une bactérie hautement résistante aux stress environnementaux commele changement de pH, la dessiccation, mais aussi le changement de température. Nous avonsparticulièrement étudié la réponse précoce de C. burnetii lors d’une exposition à une hauteet faible température. L’analyse globale du profil transcriptionnel a montré que la réponsede C. burnetii était limitée et similaire pour les différents stress appliqués. Cependant,malgré cette faible réponse, il apparait clairement qu’une accumulation de ppGpp, un arrêtde la croissance et des modifications de la membrane et de la paroi cellulaire permettraient àC. burnetii de résister à ces stress. Toutes ces régulations géniques convergent vers unchangement d’état de la bactérie vers une forme pseudo-sporulée. De plus, nous avonsobservé une organisation spatiale des gènes différentiellement exprimés. Nos analyses bioinformatiquesont montré que ces clusters de régulation ne répondaient ni au paradigmepromoteur - facteur de transcription – opéron, ni à des réseaux biologiques. Ayant retrouvéce phénomène dans plusieurs autres études transcriptionnelles chez d’autres bactériesintracellulaires, nous spéculons que ces clusters de régulations pourraient être dus à unerégulation épigénétique qu’il reste à caractériser.Différentes méthodes de typage ont déjà été mises au point pour classer les isolats deC. burnetii dans le but d'explorer son pouvoir pathogène. Ici, nous présentons une méthodede génomotypage basée sur la présence ou l'absence de gènes à l'aide de puces à ADN.Nous avons testé notre stratégie de génomotypage sur 52 isolats provenant de différenteszones géographiques, de différents hôtes et de patients présentant différentes manifestationscliniques. L'analyse a révélé la présence de 10 génomotypes organisés en 3 groupes avecune topologie congruente à celle observée avec le Multi Spacer Typing. Nous avons aussidécouvert 4 génomotypes particulièrement associés à la fièvre Q aiguë, alors que tous lesgénomotypes étaient associés à la forme chronique. De plus, le génomotypage a révélé queles isolats retrouvés dans les tiques dures, y compris la souche de référence Nine Mileappartiennent au même genomotype.Globalement, les données que nous avons obtenues confirment le fait que les puces àADN sont un outil adapté pour l’analyse de la pathogénicité de C .burnetti mais aussi desautres bactéries intracellulaires strictes. Cependant, de nouvelles technologies plusrésolutives comme le DNA ou RNAseq semblent être plus prometteuses mais restent encoreà optimiser / The objective of this thesis was to increase knowledge of obligate intracellular bacteriaand specifically, the causative agent of Q fever C. burnetii. In this regard, we have improvedstrategies to purify RNA for the transcriptional studies. We also used the technologymicroarrays to analyze the transcriptome and genomic diversity of C. burnetii.The use of clinical samples in the transcriptional studies is limited by the amount ofmaterial available and thus the transcriptional profiles of the pathogen and its host duringinfection can not be simultaneously analyze. We developed, with a model of eschars obtainedfrom Mediterranean spotted fever patients, a strategy based on subtractive hybridization toseparate RNA eukaryotic and prokaryotic cells in order to perform microarray experiments.Analysis of the survival strategies used by this bacterium to adapt to new environmentalconditions is critical for our understanding of C. burnetii pathogenicity. Here, we report theearly transcriptional response of C. burnetii under temperature stresses. Our data show thatC. burnetii exhibited minor changes in gene regulation under short exposure to heat or coldshock. While small differences were observed, C. burnetii seemed to respond similarly to coldand heat shock. The expression profiles obtained using microarrays produced in-house wereconfirmed by quantitative RT-PCR. Under temperature stresses, 190 genes were differentiallyexpressed in at least one condition, with a fold change of up to 4. Globally, the differentiallyexpressed genes in C. burnetii were associated with bacterial division, (p)ppGpp synthesis,wall and membrane biogenesis and, especially, lipopolysaccharide and peptidoglycansynthesis. These findings could be associated with growth arrest and witnessed transformationof the bacteria to a spore-like form. Unexpectedly, clusters of neighboring genes weredifferentially expressed. These clusters do not belong to operons or genetic networks; theyhave no evident associated functions and are not under the control of the same promoters. Wealso found undescribed but comparable clusters of regulation in previously reportedtranscriptomic analyses of intracellular bacteria, including Rickettsia sp. and Listeriamonocytogenes. The transcriptomic patterns of C. burnetii observed under temperature stressespermits the recognition of unpredicted clusters of regulation for which the trigger mechanismremains unidentified but which may be the result of a new mechanism of epigenetic regulation.Different typing methods have been previously developed to classify C. burnetii isolatesin order to explore its pathogenicity. Here, we report a comprehensive genomotyping methodbased on presence or absence of genes using microarray. The genomotyping method was thentested on 52 isolates obtained from different geographic areas, different hosts and isolated frompatient with different clinical manifestations. The analysis reveals the presence of10 genomotypes organized in 3 groups with a topology congruent with that of Multi SpacerTyping. We also found out 4 genomotypes especially associated with acute Q fever whereas allthe genomotypes could be associated to chronic human infection. Serendipity, genomotypingreveals that hard ticks isolates including Nine Mile belong to the same genomotype.Overall, the data we obtained confirm that DNA microarrays are a suitable tool forexploring pathogenicity of C. Burnetti and other obligate intracellular bacteria. However newtechnologies such as DNAseq or RNAseq seem more promising but still need to optimize andalso are still expensive compared to microarray.

A travers l'évolution, les agents pathogènes ont développé des stratégies leur permettant de survivre au sein de leur hôte en interférant avec la biogénèse des phagolysosomes. Comme C. burnetii vit dans un phagosome acide incapable de fusionner avec les lysosomes et que sa virulence est associée à l'expression de son LPS, nous avons étudié le rôle du LPS de C. burnetii dans le détournement de la conversion phagosomale. En effet, nous avons montré que C. burnetii virulent ainsi que son LPS se localisent dans des compartiments Lamp-1+ qui n'acquièrent pas la CathepsineD et Rab7 n'est pas recruté à leur surface. Contrairement au LPS du variant avirulent de C. burnetii, qui est localisé dans les lysosomes, le LPS de C. burnetii virulent (vLPS) n'induit pas l'activation de la MAPKinase p38, empêche le recrutement de Rab7 à la surface des compartiments en déstabilisant le complexe HOPS. Finalement, nous avons démontré que la bactérie virulente exprimant le vLPS détourne la conversion phagosomale pour survivre et pour se multiplier dans les macrophages en évitant l'activation de l'axe MAPK-p38/Vps41-HOPS. Nous avons également étudié les mécanismes permettant à Tropheryma whipplei, l'agent de la maladie de Whipple, de se répliquer dans les macrophages puisque les macrophages sont la cible in vivo de cette bactérie. Nous avons montré que T. whipplei bloque la conversion de son phagosome. / Through evolution, pathogens have developed strategies to survive within their host by interfering with the biogenesis of phagolysosomes. As it is known that C. burnetii lives in acidic phagosome which is unable to fuse with the lysosomes and that its virulence is associated with the expression of LPS, we studied the role of C. burnetii LPS in hijacking of phagosomal conversion. Indeed, we showed that the virulent C. burnetii and its LPS are located in Lamp-1+ compartments which do not acquire CathepsineD and Rab7 is not recruited to their surface. Contrary to LPS of avirulent C. burnetii, which is located in the lysosomes, the LPS of virulent C. burnetii (vLPS) does not induce activation of the p38 MAPKinase and it prevents the recruitment of Rab7 to the surface of compartments by destabilizing the HOPS complex. Finally, we demonstrated that virulent bacteria expressing virulent LPS hijack phagosomal conversion to survive and multiply in macrophages by preventing activation of p38-MAPK/Vps41HOPS axis. We also studied the mechanisms by which Tropheryma whipplei, the agent of Whipple's disease, replicates in macrophages, which are its target in vivo. We have shown that T. whipplei blocks the conversion of its phagosome. Indeed, after purification of phagosomes containing-T. whipplei, we observed by Western blot and confocal microscopy that T. whipplei survives in an immature phagosome with characteristics of both early and late phagosomes (presence of Rab5 and Rab7) making it unable to fuse with lysosomes. As the IL-16 is known to induce replication of T. whipplei, we studied the effect of this cytokine on the phagosome biogenesis of T. whipplei.

Le nombre de nouvelles espèces bactériennes identifiées augmente constamment. L'un des facteurs les plus importants de cette situation est l'approche culturomique. Par conséquent, la nécessité de classifier et de décrire taxonomiquement ces microorganismes pour comprendre leur évolution, leurs caractéristiques et leurs relations avec d'autres organismes vivants a émergé. À ce jour, plus de 170000 génomes bactériens sont disponibles. Face à cette situation, la taxonomie bactérienne ne peut être éloignée des informations fournies par le génome entier. La stratégie taxonogénomique a été élaborée dans notre laboratoire pour inclure les séquences du génome dans le schéma taxonomique. Cette nouvelle stratégie consiste en la combinaison de diverses données phénotypiques, et l'analyse génomique et la comparaison, aboutissant à une description rationnelle et complète de nouveaux taxons bactériens. Un deuxième aspect de notre travail de thèse a été l'analyse pangénomique de Coxiella burnetii. Profitant de la disponibilité de 75 génomes de C. burnetii, nous avons montré que ce pangénome est ouvert, ce qui s’oppose à ceux des autres bactéries intracellulaires. Aucun contenu génique spécifique à une maladie, ou à un géovar spécifique n'a pu être identifié. En revanche, l'analyse phylogénétique basée sur le core génome correspondait à celle obtenue à partir du typage. Ainsi, nous démontrons ici que le séquençage du génome peut être bien adapté à la description officielle ainsi que l'analyse pangénomique des bactéries associées à l'homme, et permettre de répondre à de nombreuses questions microbiologiques telles que l'évolution, la résistance aux antibiotiques et la pathogénicité. / The number of new identified bacterial species is constantly increasing. One of the most important contributors to this situation is the microbial culturomics approach. Consequently, the need to classify and taxonomically describe those microorganisms to understand their evolution, characteristics and relationships with other living organisms has emerged. To date, more than 170000 bacterial genomes are available. Facing this situation, bacterial taxonomy cannot be disconnected from the information provided from the whole genome. The taxono-genomics strategy was elaborated in our laboratory to include genome sequences in the taxonomic scheme. This new strategy consists in the combination of various phenotypic data and genomic analysis and comparison, resulting in a rational and comprehensive description of new bacterial taxa. A second aspect of our thesis work was the pangenomic analysis of Coxiella burnetii. Taking advantage of the availability of 75 C. burnetii genomes, we showed that this pangenome is open, which contrasts with those of other intracellular bacteria. No disease-specific, or geovar-specific gene content could be identified. In contrast, the core gene-based phylogenetic analysis matched that obtained from multi-spacer typing. Thus, we herein demonstrate that genome sequencing may, among its many applications, be well suited for the official description as well as pangenome analysis of human-associated bacteria, including pathogens, and may allow addressing many microbiological questions, such as evolution, outbreaks, antibiotic resistance, and pathogenicity.

Coxiella burnetii é a bactéria intracelular causadora da Febre Q, capaz de subverter funções celulares e evadir o reconhecimento do sistema imune da célula hospedeira permitindo o estabelecimento do seu nicho replicativo nas células-alvo: macrófagos e monócitos. É um patógeno altamente virulento, sendo necessário poucos organismos para desencadear a doença, e é considerado como um potencial agente de bioterrorismo da categoria B. Entre os danos econômicos causados por C. burnetii destaca-se a infecção de animais de gado, seu reservatório natural, pois causa aborto espontâneo dos filhotes e, consequentemente, prejuízo aos produtores. Seres humanos também adquirem a infecção, por inalação de partículas contaminadas. Hospedeiros imunocompetentes são capazes de restringir a infecção por C. burnetii apesar dos diversos mecanismos de evasão da resposta imune do hospedeiro, como interação com vias de sinalização celular e utilização de efetores bacterianos. No entanto, em hospedeiros não competentes a infecção pode evoluir para casos de Febre Q crônica e levá-los à morte. Modelos murinos são frequentemente utilizados para entender as interações patógeno-hospedeiro nas infecções por essa bactéria. A diferença na suscetibilidade de macrófagos de diferentes linhagens murinas e de diferentes tipos celulares à infecção por C. burnetii ainda é pouco conhecida. No entanto, sabe-se que C. burnetii fase II sucumbe a macrófagos derivados da medula óssea (BMDMs) de camundongos C57BL/6, enquanto células das linhagens BALB/c e A/J são suscetíveis à infecção. Nesse contexto, considerando a relevância biomédica de C. burnetii, faz-se necessário a determinação de um modelo relevante para melhor compreender as relações patógeno-hospedeiro nas infecções por essa bactéria. Neste trabalho, caracterizamos um novo modelo de estudo com macrófagos primários que permite avaliar a infecção com C. burnetii fase II in vitro, além de elucidar os mecanismos relacionados à suscetibilidade das células à bactéria. Por meio de quantificação do DNA genômico bacteriano por qPCR verificamos que macrófagos alveolares (AMs) murinos são altamente suscetíveis à replicação da bactéria, mesmo no fundo gênico restritivo C57BL/6. Caracterizamos a replicação da bactéria em AMs por microscopia de fluorescência e microscopia eletrônica de transmissão e demonstramos que essa replicação ocorre dentro dos vacúolos parasitóforos típicos. Pela análise de expressão gênica por RT-PCR efenotipagem de marcadores de superfície por FACS identificamos que a alta suscetibilidade dos AMs se deve a uma polarização dessas células para um padrão M2. Por fim, validamos a relevância desse modelo pela análise da suscetibilidade de AMs murinos deficientes para NOS2, IFN-? e IL-4 como prova de princípio. Verificamos que a suscetibilidade de AMs é comparável à de células Vero e células THP-1, modelos celulares imortalizados descritos como altamente suscetíveis à replicação de C. burnetii, e que AMs podem ser utilizados para estudos utilizando células derivadas de camundongos com fundo gênico C57BL/6. Dessa forma, nosso trabalho caracterizou os AMs murinos como um relevante modelo celular primário altamente suscetível para o estudo das interações patógeno-hospedeiro frente à infecção in vitro por C. burnetii fase II, além de elucidar os mecanismos por trás dessa suscetiblidade / Coxiella burnetii is the intracellular bacterium that causes Q fever, capable of subverting cellular functions and evading recognition by the host cell immune system, thus allowing the establishment of its replicative niche in its the target cells: macrophages and monocytes. It\'as a highly virulent pathogen, with few organisms being sufficient to cause the disease, and considered a potential class B bioterrorism agent. Among the economic damages caused by C. burnetii are infection of cattle animals, its natural reservoir, that leads to spontaneous abortion of the offspring and financial loss to the producers. Human beings also acquire the infection, through inhalation of contaminated air particles. Immunocompetent hosts are able to restrict infection by C. burnetii despite the several evasion mechanisms from the host immune system, which includes interaction with cell signaling pathways and utilization of bacterial effectors. However, in non-competent hosts the infection can evolve to chronic Q Fever and lead to death. Murine models are frequently used to understand the host-pathogen interactions during infections by this bacterium. The difference in the susceptibility among macrophages from different murine strains, as well as different cell types, still poorly known. However, it is known that C. burnetii phase II succumbs to bone-marrow derived macrophages (BMDMs) from C57BL/6 mice, whereas cells from BALB/c and A/J strains are susceptible to infection. In this context, considering the biomedical relevance of C. burnetii, it\'s necessary to establish a relevant study model to better understand the host-pathogen relations in infections by C. burnetii. In this work, we characterized a new study model with primary macrophages to assess the infection by C. burnetii phase II in vitro and elucidated the mechanisms underlying the susceptibility to C. burnetii. By using qPCR for quantification of bacterial genomic DNA, we saw that murine alveolar macrophages (AMs) are highly susceptible to C. burnetii replication, even in the usually restrictive C57BL/6 backgound. We characterized the bacterium replication in murine AMs by florescence microscopy and transmission electron microscopy, showing that this replication occurred inside the typical C. burnetii-containing vacuole. We also identified, through the gene expression by RT-PCR and the phenotypic profile of surface markers by FACS, that the increased susceptibility of murine AMs were due to a polarization of these cells into a M2 profile. To finish, we validated the relevance of thismodel through the analysis of the susceptibility of murine AMs deficient to NOS2, IFN-? and IL-4 as a proof of principle. We verified that the susceptibility of AMs is comparable to Vero cells and THP-1 cells, immortalized cell models described as highly susceptible to C. burnetii replication, and that AMs can be used to studies using cells derived from mice with the C57BL/6 background. In this way, our work characterized murine AMs as a relevant primary cell model highly susceptible to studies among the host-pathogen interactions in infections with C. burnetii phase II in vitro, and we also elucidate the mechanisms underlying this susceptibility