La thèse aborde le problème de l’évolution de la forme à travers l’exemple d’une différence de forme de branches ventrales mâles liée à l’isolement reproducteur chez deux espèces soeurs : Drosophila yakuba et Drosophila santomea. L’objectif de ce travail est d’identifier les gènes impliqués dans l’évolution de cette différence de forme ainsi que les causes évolutives de cette différence entre espèces. Dans une première partie, la thèse interroge la notion de “gène” et sa recherche. Puis sont caractérisées, dans un cadre formel, les questions de type "comment" et "pourquoi" et leur lien avec la distinction causes prochaines/causes ultimes ou évolutives. Ces réflexions philosophiques sont ensuite reliées à l’Evo-Devo et au projet expérimental. Dans la deuxième partie, par morphométrie géométrique et une nouvelle méthode de génotypage à haut débit, le MSG, nous identifions un locus de 2.7 méga-bases situé sur le chromosome 3L comme étant impliqué dans l’évolution de la forme des branches ventrales entre D. yakuba et D. santomea. Ces résultats sont mis en perspective avec notre analyse quantitative de la variation de forme dans plusieurs souches naturelles, souches de laboratoire et souches élevées à différentes températures qui apportent des indices sur les causes évolutives de cette différence de forme / The thesis tackles the problem of the evolution of shape through the example of a shape difference in the male ventral branches linked to reproductive isolation in two sister species: Drosophila yakuba and Drosophila santomea. The goal is to identify the genes involved in the evolution of this shape difference and the evolutionary causes of such difference. In a first part, the thesis interrogates the concept of “gene” and its search. Then are scientifically characterized the “how” and “why” questions and their link with the distinction of proximal/ultimate, or evolutionary, causes; these philosophical grounds are then linked to Evo-Devo and the experimental work presented in the thesis. In a second part, through geometric morphometrics and a new high-throughput genotyping method, MSG, we identify a loci of 2.7 mega-bases located on chromosome 3L as involved in the evolution of the shape of ventral branches between D. yakuba and D. santomea. These results are linked to our quantitative analysis of shape variation in multiple natural and laboratory strains and strains reared at different temperatures which bring light into the evolutionary causes of this shape difference

The broader purpose of the work is to find and interpret polymorphism in the genes of natural immunity of cattle to be used to improve disease resistance. The NGS method on the PacBio platform was applied for the resequencing of the gene for the key receptor of innate immunity TLR2 and two genes coding for the components of the downstream transcriptional factor NF-κB. In the population of 149 bulls of the Czech Simmental breed, 22 polymorphisms were found in the gene NFKB1 (5 new), while in the NFKB2 gene 13 SNP were found (10 new). 21 SNP were found in the TLR2 gene (3 new). Of the 56 found polymorphisms, 6 SNPs were nonsynonymous. One SNP leads to a change R474G in the NFKB1 product and five to changes E63D, R152Q, I211V, R563H and H665Q in the protein TLR2. Knowledge of the haplotypes facilitated the development of individual genotyping reactions. In TLR2, a high number of haplotypes was detected, both from the PacBio reads and the statistical reconstruction. In addition, two clusters of haplotypes were ditinguished inTLR2, possibly due to diversifying selection or introgression. The knowledge of genetic diversity in the population allows for the planned association studies with health data. Localization in functional domains allow to define the change with the greatest effect, in particular...

Le virus de l’hépatite E (VHE) est l’agent causal d’une partie des hépatites aigues ou fulminantes qui surviennent essentiellement dans les pays en voie de développement (Afrique, Asie) ou le VHE de génotype 1 semble présenter un profil endémique ponctué de bouffées épidémiques souvent liées à des déplacements de populations (catastrophe climatique ou conflits) (Lui et al., 2013). Récemment il a été montré que ce virus était largement distribué dans des réservoirs animaux (génotype 3 et 4) et la cause d’un grand nombre d’infections zoonotiques aussi bien dans les pays du nord que du sud. Dans la plupart des cas, il s'agit d'une infection spontanément résolutive avec une clairance virale rapide, mais il peut évoluer vers des formes plus sévères avec un niveau de mortalité variant de 1 à 4% dans la population générale et à près de 20% chez la femme enceinte lors des flambées épidémiques (OMS, 2014). Au Burkina Faso, très peu de données existent sur la prévalence chez l’homme, l'épidémiologie moléculaire du VHE ou la présence de ce virus dans le réservoir animal principal que constituent les porcs. De plus, l’ignorance de la population quant aux causes de cette infection d’origine alimentaire, est un facteur de risque qu’on ne peut pas ignorer. L’objectif de ce travail est donc d’améliorer notre connaissance sur cet agent des hépatites. La première partie de notre étude s’est consacrée à l’évaluation de la séroprévalence du VHE chez les donneurs de sang et les femmes venant en consultation prénatale à Ouagadougou. Au total plus de 1700 échantillons de sérums de volontaires ont été collectés dans les banques de sang et centres médicaux: entre 2010 et 2012, sur les 178 donneurs de sang et 189 femmes enceintes testés, 19,1% [IC95, 13,3-24,9%] et 11,6% [IC95, 7,1-16,2%] étaient respectivement positifs aux IgG anti-VHE. Ces taux élevés sont peut-être associé au faible statut socioéconomique et à l’absence de réseaux d’assainissement des eaux (Traoré et al., 2012). En 2014, 3,19% [IC95, 1,70-4,68%] des 533 donneurs de sang testé sont positifs pour des IgM anti-VHE. Ces résultats montrent un risque résiduel transfusionnel non négligeable associé à une transmission à bas bruit et confirme l’intérêt d’identifier la ou les sources de ce virus. La seconde partie de ce travail a été de vérifier le rôle d’une source zoonotique des infections à VHE, via l’évaluation du VHE (par sérologie et typage moléculaire après PCR) dans le réservoir potentiel que sont les porcs et la population à risques exposé à ce réservoir (bouchers et éleveurs). Pour cela nous avons réalisé un recensement des sites de ventes de porcs et évalué la consommation d’animaux. Un taux de séroprévalence de 76% [IC95, 67,6-84,4%] a été mesuré dans une cohorte de 100 bouchers de Ouagadougou avec un facteur de risque de séropositivité 3 fois plus élevé par rapport à la population générale (OR = 3,46 [95%CI 2,85 – 4,21] p <0.001). Les IgG anti-VHE chez les porcs abattus ont été estimés à 80% IC95 [72-87%]. Cette forte prévalence confirme une circulation silencieuse du VHE dans l’élevage porcin au Burkina Faso comme en témoigne l'échantillon positif de foie pour l’ARN VHE qui soutient fermement le risque de zoonose. L’analyse des séquences des produits de PCR des foies de porcs positifs pour VHE a révélé la présence de VHE génotype 3 et 99,8 % d'homologie avec les souches Yaounde et Madagascar. En conclusion, notre étude, la première caractérisation moléculaire des souches du VHE au Burkina, montre la présence de souches VHE génotype 3 dans des régions ou seul le génotype 1 avait été identifié jusqu’alors (Tchad, Maroc). L’évaluation du risque transfusionnel associé nécessite des études complémentaires afin d’évaluer le bénéfice/coût de l'ajout de dépistage du VHE dans les examens de routines des banques de sang, afin de garantir la sécurité du receveur de sang. / The hepatitis E virus (HEV) is causative agent several acute or fulminant hepatitis which mainly occur in developing countries where HEV genotype 1 or 2 appears to have a endemic profile punctuated with epidemic outbreaks (Africa, Asia) (Lui et al., 2013). Genotype 3 and 4 distributed widely in animal reservoirs, were the cause many zoonotic infection in northern and southern countries. In most cases, it is a self-limited infection with rapid viral clearance, but it can evolve into more severe forms with a mortality level ranging from 1 to 4% in the general population to nearly 20% in pregnancy during outbreaks (WHO, 2014). In Burkina Faso, very little epidemiological data are available on HEV. The objective of this work is to improve our understanding of this agent hepatitis. The first part of our study was devoted to the evaluation HEV seroprevalence among blood donors and women attending antenatal care in Ouagadougou. In total more than 1,700 volunteers serum samples were collected in blood banks and medical centers in Burkina Faso. Between 2010 and 2012 on 178 blood donors and 189 pregnant women tested, 19.1% [CI95, 13.3-24.9%] and 11.6% [CI95, 7.1-16.2%], were respectively positive for anti-HEV IgG. These high rates in the general population may be associated a low income and the poor hygienic status (Traoré et al., 2012). In 2014, 3.19% [CI95, 1.70-4.68%] on 525 blood donors tested, were positive for anti-HEV IgM. These results indicate a residual risk for transfusion, probably associated with silent infections and confirm the importance to identify the sources of the virus. The second part of this work was 1) to assess HEV infection among humans in Burkina Faso by exploring the HEV seroprevalence in a high risk population, i.e., butchers; 2) to explore a possible pig-to-human zoonotic transmission cycle by assessing the HEV seroprevalence in slaughter swine; and 3) to identify the genotype of HEV circulating in pigs. The global HEV prevalence among Ouagadougou butchers was estimated to 76%, CI95 [67, 63–84.37%] with a significant risk factor, 3 times higher compared with the general population (OR = 3.46 [95%CI 2.85 - 4.21] p <0.001). IgG anti-HEV in pigs older than 6 months of age were estimated at 80% CI95 [72-87%]. This high prevalence confirms the presence and active circulation HEV among domestic pigs in Burkina Faso as evidenced by the positive sample of liver for HEV RNA which strongly supports the risk of zoonosis. Phylogenetic analyses revealed that genotype 3 HEV is circulating among swine population in Burkina. A similarity >98% was found between swHEV-BF from Yaounde and Madagascar. This data showed for the first time the role of swine in introduction of new HEV in African population. In conclusion, these results latter sign a persistent introduction of HEV infection in the population and hence deserved to be taken in account in transfusion associated risk. Further assessments of the transfusion risk associated require an evaluation of the cost/benefit ratio for the addition of routine HEV RNA screening to the panel of tests on donated blood, to guarantee transfusion safety for the recipient.

Le botulisme est une maladie nerveuse, commune à l’homme et aux animaux, due à l’action de la toxine botulique produite par Clostridium botulinum. Il existe 8 types de toxines dénommées A à H. Les bactéries capables de produire cette toxine se différencient en six groupe sur la base de leurs caractéristiques phénotypiques et biologiques. Les souches de C. botulinum responsables du botulisme humain appartiennent aux groupes I et II selon qu’elles soient protéolytiques ou non. Elles produisent les toxines A, B, E et F, ainsi que le nouveau type H récemment découvert. C. butyricum et C. baratii sont également capables de produire les toxines botuliques de type F et E et appartiennent au groupe V et VI. C. argentinense appartient au groupe IV et est capable de synthétiser la toxine de type G. Elle a été soupçonnée d’être impliquée dans des cas de botulisme infantile en Argentine. Les souches de C. botulinum responsables du botulisme animal appartiennent au groupe III (C. novyi sensu lato) et produisent les toxines C, D et leurs formes mosaïques C/D et D/C. La toxine botulique est le poison le plus puissant connu à ce jour. La dose létale nécessaire pour tuer une personne en bonne santé par intoxication alimentaire est de 70 µg seulement. C’est pourquoi cette toxine a fait l’objet d’études particulièrement approfondies, notamment celles impliquées dans des cas de botulisme humain. Elle peut également être utilisée pour le traitement de certaine pathologie ou la chirurgie esthétique (Botox). Malheureusement, elle peut également être utilisée à mauvais escient, en tant qu’arme de guerre ou à des fins de bioterrorisme. C’est pourquoi l’emploi de la toxine botulique ou de sa bactérie productrice fait l’objet d’une législation particulièrement stricte. Mon projet de doctorat s’est organisé autour de plusieurs projets de recherche visant à développer des méthodes de détection et de typage de du germe et de sa toxine (projets Européens BIOTRACER et AniBioThreat ; projets NRBC-bio ; LNR botulisme aviaire en France). Lors de mes recherches j’ai concentré mon travail sur le développement de méthodes capable de suivre et remonter à la source d’une contamination, qu’elle soit délibérée, accidentelle ou naturelle. Afin d’y parvenir j’ai investigué les gènes des flagellines de C. botulinum groupe I à III, responsables du botulisme humain et animal. L’analyse des gènes flaA et flaB a mis en évidence 5 groupes majeurs et 15 sous-groupes, certain étant spécifiques de régions géographiques. FlaB s’est montré spécifique de C. botulinum type E. Les gènes flagellines fliC, spécifiques à C. botulinum du groupe III, se divisent 5 groupes, avec fliC-I et fliC-IV associés aux types mosaïques C/D et D/C. J’ai étudié la prévalence des souches productrices de toxine de type mosaïques chez les volailles et les bovins. Les résultats montrent que les types C/D et D/C sont majoritaires en Europe. Enfin, j’ai séquencé 17 génomes provenant de souches responsables de botulisme animal en France (14 types C/D et 3 types D/C). Leur analyse montre que ces souches sont très proche génétiquement, entre elles et avec les souches Européennes. Grâce à ces données j’ai mis en évidence un large contenu extra chromosomique dans les souches C/D, qui peut être utilisé pour créer une carte d’identité génétique. D’autre part, l’étude des séquences Crisps à des fins de typage ne s’est pas avérée suffisamment résolutive, du fait de système Crispr-Cas déficient chez les souches C/D. Enfin, un très haut degré de discrimination a été atteint par typage SNP, qui a permis de distinguer jusqu’à l’origine de chaque souche. L’ensemble de ces résultats est développé dans le présent manuscrit / Clostridium botulinum is the etiologic agent of botulism, a deadly paralytic disease that can affects both human and animals. Different bacteria, producing neurotoxins type A to H, are responsible for the disease. They are separated into different groups (I to VI) on the basis of their phenotypical and biological characteristics. Human botulism is mainly due to Groups I and II producing neurotoxins A, B, E and F, with type H recently discovered. Also C. butyricum and C. baratii species (Groups V and VI), producing toxins type F and E respectively, are scarcely reported. C. argentinense Group IV, producing toxin type G, which has been suspected to be associated with infant botulism in Argentina. Animal botulism is mainly due to Group III, which is constituted by C. novyi sensu lato species. They produce toxin types C, D and their mosaic variants. Botulinum neurotoxins are the most powerful toxin known to date with as little as 70 µg enough to kill a person by food poisoning. Therefore, it received a great deal of attention. Botulinum neurotoxins have been deeply studied, especially human related toxins compared to animal. The toxins found to be useful for medical or cosmetic (Botox) treatments, but it was also used as a biological warfare agent, and for bioterrorism. Its extreme potency is equal to its dangerousness. Therefore, governments show concerns of its potential misuse as a bioterrorism weapon; research programs are funded to study and raise awareness about both the toxins and the producing organisms. My PhD work was structured by the different projects I was involved in, which were related to C. botulinum detection and typing, like BIOTRACER and AniBioThreat European projects, the French national CBRN program, or the NRL for avian botulism. The main transversal objective I followed lead me to develop new methods to trace back the origin of C. botulinum contamination, in case of a deliberate, accidental or naturally occurring botulism outbreak. I investigated flagellin genes as potential genetic targets for typing C. botulinum Group I-II and III, responsible for human and animal botulism respectively. Flagellin genes flaA and flaB showed the investigated C. botulinum Group I and II strains to cluster into 5 major groups and up to 15 subgroups, some being specific for certain geographical areas, and flaB being specific to C. botulinum type E. Flagellin fliC gene investigated in C. botulinum Group III showed to cluster into five groups, with fliC-I and fliC-IV associated to type C/D and D/C respectively, being not discriminative enough to differentiate highly genetically related strains. I also studied the prevalence of mosaic toxin genes in C. botulinum Group III in animal botulism, mainly in poultry and bovine. The results brought out the mosaic toxin types C/D and D/C to be predominant in the samples investigated throughout Europe. Finally, I explored the full genome sequences of 14 types C/D and 3 types D/C C. botulinum Group III strains, mainly originating from French avian and bovine botulism outbreaks. Analyses of their genome sequences showed them to be closely related to other European strains from Group III. While studying their genetic content, I was able to point out that the extrachromosomal elements of strains type C/D could be used to generate a genetic ID card. Investigation of Crispr typing method showed to be irrelevant for type C/D, due to a deficient Crispr-Cas mechanism, but deserve more investigation for type D/C. The highest level of discrimination was achieved while using SNP core phylogeny, which allowed distinguishing up to the strain level. Here are the results I’m going to develop in this manuscript

Canine brucellosis is a zoonotic disease, caused by Brucella canis, which is the main cause of abortion and infertility in dogs. This study had the objective to investigate a B. canis outbreak in a breeding kennel, to describe a multistep approach to characterize the B. canis isolates obtained, and to identify B. canis proteins specifically reacting with antibodies from naturally infected dogs. The kennel was located in São Paulo, SP, Brazil. At the time of sampling, in 2014, the kennel comprised 17 adult Pug dogs. Blood samples were used both to isolate the bacteria and to detect Brucella spp. DNA by the polymerase chain reaction. Serum samples were used to detect antibodies against B. canis using an immunocromatographic test, the rapid slide agglutination test with or without 2-mercaptoethanol and two ELISA kits. The Brucella isolates were characterized through the classical bacteriological tests, mass spectrometry and whole genome sequencing. The total protein content of Brucella isolates was extracted and separated using one and two-dimension polyacrylamide gel electrophoresis (1D and 2D, respectively), and then tested against sera collected from bacteremic, non-bacteremic and non-B. canis infected dogs using western immunoblotting. The reacting protein spots were identified using matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS). Vaginal discharge, abortion, stillbirth, conception failure and general lymphadenopathy were the clinical signs found in the infected dogs. Gram-negative, coccoid rod-shaped bacteria were isolated from 24 blood samples. Antibodies against B. canis were detected in all dogs at least once by the performed serological tests. Mass spectrometry analysis assigned all isolates to the genus Brucella. The phenotypic data clearly identified the isolates as B. canis with only slight differences in phage typing patterns. The 2D separated protein spots were identified by MALDI-TOF MS as 93 different proteins, out of them, 19 were identified in infected dogs (during the bacteremic and non-bacteremic phases of the infection) and were not identified in non-infected dogs. These proteins have the potential to be used as antigens in serological tests in an attempt to improve the diagnosis of the infection, since a reliable diagnosis is an essential measure for the control and prevention of canine brucellosis. The multistep approach using classical microbiological methods, mass spectrometry and whole genome sequencing allowed the characterization of the B. canis with high discriminatory power, which may be useful for outbreak investigations. / A brucelose canina é uma doença zoonótica, causada pela Brucella canis, que é uma das principais causas de abortamentos e infertilidade em cães. O objetivo deste estudo foi investigar um surto de B. canis em um canil, caracterizar os isolados de Brucella obtidos e identificar proteínas de B. canis reagentes especificamente a anticorpos de cães naturalmente infectados. O canil é localizado em São Paulo, SP, Brasil e no momento da amostragem, em 2014, o canil era composto por 17 cães adultos da raça Pug. Amostras de sangue foram utilizadas tanto para isolar as bactérias quanto para detectar o DNA de Brucella spp. pela reação em cadeia pela polimerase. Amostras de soro foram utilizadas para detectar anticorpos contra B. canis nos soros dos cães, utilizando um teste imunocromatográfico, o teste de soroaglutinação rápida em placa com ou sem 2-mercaptoetanol e dois kits de ELISA. Os isolados foram caracterizados pelos métodos bacteriológicos clássicos, espectrometria de massa e pelo sequenciamento do genoma completo. O conteúdo proteico total dos isolados de B. canis foi extraído e as proteínas separadas por eletroforese em gel de poliacrilamida de uma e duas dimensões (1D e 2D, respeectivamente), sendo então testadas frente aos soros dos cães infectados (com ou sem bacteremia) e não infectados, utilizando Western Immunoblotting. Os spots proteicos reagentes foram identificados usando espectrometria de massa por ionização/dessorção a laser assistida por matriz (MALDI-TOF MS). Secreção vaginal, aborto, natimorto, falha na concepção e linfoadenopatia foram os sinais clínicos observados nos cães infectados. Coco-bacilos gram-negativos foram isolados em 24 amostras de sangue. Anticorpos contra B. canis foram observadas em todos os cães, em pelo menos uma amostragem, pelos testes sorológicos empregados. A MS atribuiu todos os isolados ao gênero Brucella. Os dados fenotípicos identificaram claramente B. canis com apenas pequenas diferenças nos padrões de lise por fagos. Os spots de proteínas, separados por 2D, foram identificados por MALDI-TOF MS como 93 diferentes proteínas, dentre elas, 19 foram identificadas em cães infectados (com ou sem bacteremia) e não foram identificadas nos cães não infectados. Tais proteínas são candidatas a serem utilizadas como antígenos para o aprimoramento do sorodiagnóstico, uma vez que a existência de um diagnóstico confiável constitui uma medida essencial para o controle e a prevenção da brucelose canina. A abordagem múltipla utilizada, envolvendo métodos microbiológicos clássicos, espectrometria de massa e sequenciamento completo do genoma bacteriano possibilitou a caracterização dos isolados de B. canis com elevado poder discriminatório, o que pode auxiliar em investigações de surtos.

Toxoplasma gondii é um protozoário formador de cistos capaz de infectar diversas espécies de aves e mamíferos domésticos e selvagens, incluindo o homem. Apesar de evidências sorológicas da infecção por T. gondii em animais selvagens, pouco se sabe sobre o papel da vida selvagem na cadeia epidemiológica e tampouco a susceptibilidade das variadas espécies a este parasito. O presente trabalho consistiu no isolamento e caracterização genotípica de T. gondii de tecidos de animais selvagens, de vida livre e de cativeiro, provenientes de diversas localidades do Brasil e na detecção sorológica de anticorpos contra o parasito nas amostras em que foi possível obter o soro. A sorologia foi realizada em 54 amostras de soros de aves e mamíferos de várias espécies por meio do Teste de Aglutinação Modificado (MAT). Deste total, 18 amostras (cinco de aves e 13 de mamíferos) foram positivas para anticorpos anti-T. gondii. Para o isolamento do parasito foi realizado o bioensaio em camundongos. Homogenados de coração e cérebro de cada um dos animais foram submetidos à digestão péptica e inoculados em grupos de cinco camundongos. Tecidos dos camundongos que vinham à óbito eram examinados para constatar a presença de formas de T. gondii. Seis semanas após inoculação, foi colhido sangue dos camundongos para a realização de testes sorológicos (MAT) para detecção de anticorpos anti-T. gondii e dois meses após a inoculação estes animais foram submetidos à eutanásia para a procura por cistos teciduais do parasito. Por meio desta prova biológica foi possível isolar T. gondii em 18 animais selvagens (16 de diversas espécies de mamíferos e duas de aves) provenientes de diferentes localidades. T. gondii foi isolado em uma coruja-buraqueira (Athene cunicularia), um pica-pau-de-banda-branca (Dryocopus lineatus), um gato-do-mato-pequeno (Leopardus tigrinus), um lobo-guará (Chrysocyon brachyurus), uma mucura (Didelphis marsupialis), uma paca (Cuniculus paca), três queixadas (Tayassu pecari), uma raposa-do-campo (Pseudalopex etulus), três tamanduás-mirim (Tamandua tetradactyla), três tatus-galinha (Dasypus novemcinctus) e dois tatuspeba (Eufractus sexcinctus). Dezesseis dos 18 isolados obtidos foram letais para 100% dos camundongos infectados. O isolado de um tatu-peba não causou mortalidade em camundongos e o isolado da coruja-buraqueira causou 50% de mortalidade. A caracterização genotípica dos isolados foi realizada pela técnica de PCR/RFLP utilizando 12 marcadores genotípicos. As amostras primárias dos tecidos provenientes dos animais selvagens que foram positivas na PCR de triagem também foram submetidas à caracterização genotípica. Por meio da PCR/RFLP foi possível obter o genótipo completo de 22 amostras, 15 delas provenientes de isolados e sete de amostras primárias de tecidos. Dos 18 isolados obtidos através do bioensaio, em três (tatu-peba, coruja-buraqueira e mucura) não foi possível obter a caracterização completa de todos os 12 marcadores utilizados. Pela análise das 22 amostras caracterizadas foram observados 17 genótipos diferentes, sendo que 13 deles são inéditos. A mortalidade de camundongos infectados foi comparada com a ocorrência dos diferentes alelos no marcador CS3 nos 15 genótipos provenientes de isolados, dos quais, sete apresentaram o alelo tipo I, seis o alelo tipo II e os alelos u-1 e u-3 foram encontrados em um isolado cada. Todos os isolados apresentaram 100% de mortalidade para os camundongos infectados. / Toxoplasma gondii is an intracellular protozoan parasite that infects almost all warmblooded animals, including humans. Although studies indicate that wild animals are frequently positive for antibodies anti-T. gondii, the role of wild life in the epidemiology of this parasite is not well understood nor the susceptibility of different wild species. The present study aimed to isolate T. gondii from free-living and captive wild birds and mammals from different locations from Brazil, to perform the genotipic characterization of T. gondii found in the analyzed tissue samples and to detect aintibodies anti-T. gondii in samples which were possible to obtain the serum. Serology was performed in 54 serum samples from different species of wild birds and mammals by the Modified Agglutination Test (MAT). From this total, 18 samples (five from birds and 13 from mammals) were seropositive for antibodies anti-T. gondii. For the isolation of the parasite, mice bioassay was performed. Brain and heart homogenates were submitted to peptic digestion and were inoculated in groups of five mice per animal sampled. Tissues of mice that died were examined for the presence of T. gondii. Mice were bled six weeks post-inoculation, and their sera were tested for anti-T. gondii antibodies by MAT. Surviving mice were euthanized two months after the inoculation and their brains were examined for the presence of T.gondii tissue cysts. T. gondii was isolated in 18 wild animals (16 from different species of mammals and two from birds) from different locations. T. gondii was isolated from one burrowing owl (Athene cunicularia), one lineated woodpecker (Dryocopus lienatus), three collared anteater (Tamandua tetradactyla), one hoary fox (Pseudalopex vetulus), one maned wolf (Chrysocyon brachyurus), one oncilla (Leopardus tigrinus), one opossum (Didelphis marsupialis), one paca (Cuniculus paca), three nine-banded armadillo (Dasypus novemcinctus), two six-banded armadillo (Euphractus sexcincticus) and three white-lipped peccary (Tayassu pecari). Sixteen of the 18 isolates were lethal to 100% of inoculated mice. The genotypic characterization was performed using 12 PCR-restriction fragment length polymorphism (RFLP) Primary tissue samples which were positive in a trial PCR were also submitted to genotypic characterization. It was possible, by PCR/RFLP, to obtain the complete genotype of 22 samples, 15 from isolates and seven from primary tissue samples. It was not possible to accomplish the complete genotypic characterization in three isolates; one burrowing owl, one opossum and one sixbanded armadillo. In this 22 samples characterized, a total of 17 different genotypes were found with 13 of them described for the first time. Mortality of infected mice was compared between the different alleles of the marker CS3 in the 15 genotypes originated from isolates, which seven were type I, six were type II and alleles u-1 and u-3 were found in one isolate each. All the isolates presented 100% of mortality in infected mice.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Sporothrix schenckii é um fungo dimórfico e agente etiológico da esporotricose, uma micose profunda que apresenta diferentes manifestações clínicas. As diversas manifestações clínicas desta e de outras doenças infecciosas podem ser relacionadas ao status imune do hospedeiro, a fatores de virulência do patógeno ou a diferentes genótipos. Dados anteriores do nosso grupo demonstram que diferenças na expressão de adesinas do S. schenckii para fibronectina estão diretamente relacionadas à virulência de diferentes cepas. Neste trabalho visamos avaliar caracteres morfológicos bioquímicos e genotípicos de doze isolados de geofílicos, zoofílicos e antropofílicos de S. schenckii, de diferentes origens geográficas, que apresentam diferentes graus de virulência. Foi analisada a morfologia das formas de micélio e levedura de cada isolado. Foi observado que a fase de micélio dos isolados estudados apresentaram morfologia típica com hifas finas e septadas, com conídios obovóides ou ovóides alongados. As leveduras apresentaram pleomorfismo típico da espécie, com células variando do formato ovóide ao alongado. Verificamos ainda a expressão de adesinas para fibronectina e laminina, do antígeno gp70 e, o padrão de bandas antigênicas reconhecidas por anticorpos IgG presentes em soro de pacientes com esporotricose ou de camundongos infectados. Para isso, foram extraídas proteínas de superfície da forma de levedura de cada isolada, sendo os extratos ensaiados por Western blot. Nestes ensaios observamos que os isolados mais virulentos de S. schenckii expressavam mais adesinas para fibronectina e laminina. A presença da gp70 foi detectada em dez dos doze isolados, sendo que apenas os isolados zoofílicos não expressam esta glicoproteína. O padrão antigênico foi variável entre os isolados, não havendo clara relação com a origem e/ou distribuição geográfica. Os dados fenotípicos foram confrontados com dados genotípicos. Para isso, sequenciamos os loci da calmodulina (CAL) e do Internal Transcribed Spacer 1/2 (ITS 1/2) a fim de averiguar se haviam diferenças genotípicas entre os isolados estudados. As análises do sequenciamento do loci CAL e ITS, contudo, apontam a divisão dos isolados em duas espécies filogenéticas, S. schenckii e S. brasiliensis não correlacionada com a distribuição geográfica dos mesmos. Nosso estudo reforça a hipótese de haver uma correlação entre virulência e expressão de adesinas, porém, sem qualquer relação entre a distribuição geográfica dos isolados zoofilicos, antropofílicos ou geofílicos, bem como dos genótipos encontrados. / The dimorphic fungus Sporothrix schenckii is the etiological agent of sporotrichosis, a deep mycosis that presents different clinical manifestations. The diverse manifestations of this and other infections can be related the host immunity, virulence factors or different genotypes of the pathogen. Previous data of our group demonstrated that differences in the expression of adhesins to fibronectin are directly related to the virulence of the different strains of S. schenckii. In the present work we have evaluated the morphological, biochemical and genotypic characteristics of twelve strains of S. schenckii (isolated from human and cat cases of sporotrichosis and from environment) from different geographic regions that present distinct virulence levels. The mycelium and yeast phases of each strain were morphologically analyzed. The strains has presented the typical morphology, with thin and septated hyphae. The conidia exhibited obovoidal or ovoidal elongated form. The yeast phase presented the ovoid or elongated cell form. Furthermore, we have verified the adhesins expression to fibronectin, to laminin, to gp70 antigen and to the antigenic bands pattern of all protein extracts, recognized by patients or infected mice sera antibodies. For this, the proteins were extracted from the surface of each strain yeast phase and assayed by Western blot technique. We have observed that the most virulent strains of S. schenckii expressed more adhesins to fibronectin and to laminina than less virulent strains. The presence of the gp70 was confirmed in ten isolates of twelve. Just strains isolated from infected cats did not present this glycoprotein. The antigenic bands pattern was variable between the different extracts, with no clear correlation with origin or geographical distribution of the isolates of S. schenckii. In order to cross phenotypic and genotypic data we have sequenced the calmodulin loci (CAL) and the Internal Transcribed Spacer 1/2 (ITS 1/2) in order to check if there was differences between the strains studied. In this analysis we found that this strains are divided in two species, S. schenckii and S. brasiliensis, again with no correlation with the geographical distribution. Our study reinforces the hypothesis on the correlation between adhesins expression pattern and virulence levels with no connection among geographical distribution or genotype of the different strains of S. schenckii.

Made available in DSpace on 2015-04-11T13:38:39Z (GMT). No. of bitstreams: 1 Dissertacao Final Luana Karen.pdf: 1636172 bytes, checksum: c9eb81400c0c198ae103082ad8f70318 (MD5) Previous issue date: 2007-11-16 / Fundação de Amparo à Pesquisa do Estado do Amazonas / The Human Immunodeficiency Virus (HIV) is characterized by a wide genetic diversity. Two types of HIV are recognized at present: HIV-1 and HIV-2. The HIV-1, responsible for most of the cases of AIDS in the world, is divided in three groups denominated M (Major), O (Outlier) and N (Non-M/Non-O), and until this moment nine subtypes of the group M (A-D, F-H, J-K) were already identified. Beyond of those subtypes, the HIV-1 also have been classified in circulating recombinant forms (CRFs) and unique recombinant forms (URFs). In Brazil, a pattern complex of distribution of those subtypes has been described in their different geographical areas. In search of elucidating the predominant subtypes of HIV-1 in the city of Manaus, this study had as objective to analyze blood samples of subjects that presented results positive or indeterminate for HIV, in the systematic selection of blood donors of the Fundação de Hematologia e Hemoterapia do Amazonas (HEMOAM). In the moment of the collect, the donors registered their authorization by the signature of the free consent and knowledge term and they answered a questionnaire used for epidemic data investigation. DNA proviral extracted of the samples with indeterminate/positive resulted in Western Blot was submitted a Polimerase Chain Reaction in two stages (Nested PCR) for the confirmation of the HIV-I infection. The amplified products (regions gag, pol and env) of the 31 samples reactivate for PCR were automatically sequencing and analyzed phylogenetically by the Phylip program. All of the indeterminate samples for the confirmatory test presented negative amplification pattern. Of the reactivates samples for HIV in the confirmatory test and PCR, it was observed male predominance (77,4%) and in the donors of first time (67,7%). Among the repetition donors, 60% presented seroconvertion in up to 20 months. Of the total of samples, was identified the predominance of the subtype B (87,1%), following by the subtype C (6,5%), F (3,2%) and recombinant BF (3,2%). The amino acids sequences of 19 isolated were analyzed for the genetic variability characterization of the region of the loop V3. Among the isolated of the subtype B, the tetrapeptide more prevalente was GPGR (68,4%), following by the Brazilian variant B" GWGR (15,8%). The Subtype C occurrence in the North Region still was not reported in the literature. The analyses of similarity of the isolated of the subtype C in this study demonstrated larger similarity of these with other isolated ones brazilian, in relation to isolated in other parts of the world. Our results can contribute to a better understanding of the characteristics of the lineages of the HIV-1 circulating in Brazil, information that can be used in benefit of the diagnosis, treatment, control of the disease and preparation of vaccines. / O Vírus da Imunodeficiência Humana (HIV) é caracterizado por uma ampla diversidade genética. Dois tipos de HIV são reconhecidos atualmente: HIV-1 e HIV-2. O HIV-1, responsável pela maioria dos casos de aids no mundo, é dividido em três grupos denominados M (Major), O (Outlier) e N (Non-M/Non-O). Para o grupo M, nove subtipos foram identificados até o momento: A-D, F-H, J, K. Além desses subtipos, o HIV-1 também tem sido classificado em formas recombinantes circulantes (CRFs) e formas recombinantes únicas (URFs). No Brasil, um complexo padrão de distribuição desses subtipos tem sido descrito em suas diferentes regiões geográficas. Buscando esclarecer a distribuição dos subtipos de HIV-1 predominantes na cidade de Manaus, este estudo teve como objetivo analisar amostras de sangue de indivíduos candidatos a doadores de sangue que apresentaram resultados positivo ou indeterminado para HIV-1, na triagem sistemática para doação de sangue da Fundação de Hematologia e Hemoterapia do Amazonas (HEMOAM). Na ocasião da coleta, os doadores registraram a sua autorização através da assinatura do termo de consentimento livre e esclarecido e responderam a um questionário utilizado para investigação de dados epidemiológicos. O DNA proviral extraído das amostras com resultados indeterminado/positivo no Wersten Blot foi submetido a uma Reação em Cadeia da Polimerase em duas etapas (Nested PCR) para a confirmação da infecção pelo HIV-1. Os produtos amplificados (regiões gag, pol e env) das 31 amostras reativas por PCR foram seqüenciados e analisados por métodos filogenéticos usando o programa Phylip. Todas as amostras indeterminadas para o teste confirmatório apresentaram padrão de amplificação negativo. Das amostras reativas para HIV-I no teste confirmatório e PCR, observou-se predominância do sexo masculino (77,4%) e de doadores de primeira vez (67,7%). Entre os doadores de repetição, 60 % apresentaram soroconversão em até 20 meses. Do total de amostras, identificou-se a predominância do subtipo B (87,1%), seguida do subtipo C (6,5%), F (3,2%) e recombinante BF (3,2%). As seqüências de aminoácidos de 19 isolados foram analisadas para a caracterização da variabilidade genética da região da alça V3. Dentre os isolados do subtipo B, o tetrapeptídeo mais prevalente foi o GPGR (68,4%), seguido pelo variante brasileiro B GWGR (15,8%). A ocorrência do Subtipo C na região Norte, ainda não foi relatada na literatura. As análises de similaridade dos isolados do subtipo C nesse estudo demonstraram maior semelhança destes com outros isolados brasileiros, em relação a isolados de outras partes do mundo. Nossos resultados contribuem para uma melhor compreensão das características dos isolados do HIV-1 circulantes no Brasil, informações que poderão ser utilizados em benefício do diagnóstico, tratamento, controle da doença e preparação de vacinas.

As manifestações bucais da AIDS têm sido relacionadas a diversas características clínicas da infecção pelo HIV como decréscimo de células T CD4+, aumento de carga viral e falha terapêutica, entre outras. Os avanços recentes da medicina mostram que a falha terapêutica, nesses pacientes, está diretamente vinculada a mutações na transcriptase reversa (TR) e na protease (PR). O objetivo deste estudo foi descrever, em pacientes HIV+ apresentando falha terapêutica, o perfil de mutações do vírus e o perfil de resistência a antirretrovirais, e correlacioná-los as manifestações bucais da imunodeficiência. Foram acessados prontuários, laudos de genotipagem e informações de bancos de dados digitais de pacientes com AIDS, que se submeteram a genotipagem no Centro de Referência e Treinamento em Doenças Sexualmente Transmissíveis e AIDS (CRT-DST/AIDS), entre 2003 e 2010. Os dados foram transferidos para o Epiinfo, onde foi construído um banco de dados informatizado para posterior análise estatística. O evento lesões orais foi escolhido como variável dependente. Calculou-se o odds ratio para cada variável independente, utilizando intervalo de confiança de 95%. Foram cruzados dados sobre mutações encontradas no vírus e resistência às medicações com a presença e tipo de manifestações bucais. O teste de Bartlett foi utilizado para testar a normalidade dos dados. Para variáveis sem distribuição normal foram aplicados os testes de Mann-Whitney ou Kruskal-Wallis. Para comparação entre frequências e proporções, foi utilizado o Teste de Exato de Fisher ou o Qui quadrado. O nível de significância foi estabelecido como 0,05 ou 5%. A análise de características sociocomportamentais e clínico laboratoriais permitiu verificar que a presença de lesões orais pode ser relacionada estatisticamente a baixas taxas de CD4 (p<0,05), faixa de carga viral (p=0,048) e ao uso prévio de mais de cinco esquemas antirretrovirais diferentes (p=0,021). Verificou-se maior prevalência de lesões virais (75%) e bacterianas (66,7%) do que de lesões fúngicas (37,3%) apenas em pacientes que apresentavam resistência a inibidores de protease (IP) (p=0,02). Foram encontradas 146 mutações diferentes nos pacientes que apresentavam lesões orais, dentre essas, quatro (101E, 20T, 188L, 93L) apresentaram correlação negativa com a presença de lesões orais (respectivamente, p=0,01, p=0,01, p=0,03, p=0,03) e oito (215Y, 118I, 20R, 44D, 71I, 82I E 84V) apresentaram correlação positiva (respectivamente p=0,04, p=0,05, p=0,03, p=0,01, p=0,01, p=0,04, p=0,0004). Subsequentemente, as mutações que apresentaram correlação positiva com a presença de lesões orais foram avaliadas para verificar se sua presença estaria realmente associada a resistência aos ARVs (aos quais seriam supostamente resistentes). Foram excluídas dessa avaliação as mutações 71I e 82I, por apresentarem uma quantidade extremamente pequena de ocorrências. Todas as mutações apresentaram correlação estatística positiva para a resistência aos respectivos antirretrovirais (p<0,05). Em pacientes HIV+, que apresentavam falha terapêutica e manifestações bucais, foram identificadas as mutações 84V e 20R na PR e as mutações 215Y, 44D e 118I na TR e a presença dessas mutações foi associada a resistência a inibidores de protease e inibidores de transcriptase reversa nucleosídeos, respectivamente. / Oral manifestation of AIDS have been associated with several clinical characteristics of HIV infection such as reduction in T CD4+ cells, increase in viral load and treatment failure, among others. Recent advances have shown that treatment failure in these patients is directly linked to mutations in reverse transcriptases (RT) and in proteases (PR). The objective of the present study was to describe the profile of virus mutations and of resistance to antiretroviral drugs in HIV+ patients in treatment failure, and to correlate mutations to the oral manifestations of the immunodeficiency. Patient charts, genotyping results and information from digital databases of AIDS patients, who underwent genotyping at the Sexually Transmissible Diseases and AIDS Training and Reference Center (CRT-DST/AIDS) between 2003 and 2010, were accessed. Data were transferred to the Epiinfo program, in which a computerized database was built for statistical analysis. The event oral lesions was chosen as a dependent variable. Odds ratio for each independent variable was calculated, using a 95% confidence interval. Data found on virus mutations and drug resistance was analyzed to check for correlation with presence and type of oral manifestations. The Bartlett test was used to test normality of data. Mann-Whitney or Kruskal-Wallis tests were used for variables without a normal distribution. The Fisher Exact or Chi-square Tests were used to compare frequencies and proportions. A 0.05 or 5% significance level was established. The analysis of socio-behavioral and clinical-laboratorial characteristics allowed concluding that the presence of oral lesions may be related to statistically low CD4 rates (p<0.05), viral load range (p=0.048) and previous use of more than five different antiretroviral regimens (p=0.021). A higher prevalence of viral (75%) and bacterial (66.7%) lesions in relation to fungal lesions (37.3%) was observed only in patients who were resistant to protease inhibitors (PI) (p=0.02). We found 146 different mutations in patients with oral lesions, among which, four (101E, 20T, 188L, 93L) with a negative correlation with the presence of oral lesions (p=0.01, p=0.01, p=0.03, p=0.03, respectively) and eight (215Y, 118I, 20R, 44D, 71I, 82I E 84V) with a positive correlation (p=0.04, p=0.05, p=0.03, p=0.01, p=0.01, p=0.04, p=0.0004, respectively). Subsequently, mutations with a positive correlation with the presence of oral lesions were assessed to check if their presence would really be associated with resistance to ARVs (to which they supposedly would be resistant to). Mutations 71I and 82I were excluded from this assessment because they had an extremely low frequency. All mutations had a statistically positive correlation for resistance to their respective antiretroviral drugs (p<0.05). Mutations 84V and 20R were identified in PR, and mutations 215Y, 44D and 118I in TR of HIV+ in patients undergoing treatment failure and presenting oral manifestations. Moreover, the presence of these mutations was associated with resistance to protease inhibitors and to nucleoside reverse transcriptase inhibitors, respectively.

As doenças causadas por patógenos emergentes e oportunistas são uma grande preocupação para os profissionais de Saúde Pública. A criptosporidiose é uma doença cosmopolita, cujo agente etiológico é o protozoário coccídia Cryptosporidium. Este parasita emergiu como um importante patógeno de veiculação hídrica, responsável por surtos em diferentes países e atualmente é considerado um problema para indivíduos imunocomprometidos e imunocompetentes. A taxonomia do gênero, baseada em aspectos morfológicos, é de difícil realização devido ao reduzido tamanho dos oocistos e também devido à perda de suas características morfológicas, principalmente em amostras ambientais. Essa limitação estimulou a aplicação de métodos moleculares na identificação das espécies destes microrganismos. Neste estudo, amostras de águas superficiais foram submetidas à ested-PCR para detecção de Cryptosporidium. No total 30 amostras de águas de 10 pontos de coleta situados no estado de São Paulo foram analisadas. Cryptosporidium foi detectado em 30% das amostras analisadas e a genotipagem permitiu a identificação de C. hominis, C. meleagridis e C. andersoni. Embora a identificação de Cryptosporidium em amostras ambientais seja uma tarefa complexa, os métodos moleculares são essenciais para determinação de espécies, ajudando a elucidar a epidemiologia deste protozoário em nosso país. / The illnesses caused by emerging and opportunist pathogens are a great concern for Public Health professionals. Criptosporidiosis is a cosmopolitan disease, whose etiologic agent is the coccidian protozoan Cryptosporidium. This parasite has emerged as an important waterborne pathogen, responsible for outbreaks in different countries, and it is currently considered a problem for immunocompromised and immunocompetent patients. The taxonomy of the genus, based on morphologic aspects, is of difficult accomplishment due to the small size of the oocysts, and also due to loss of its characteristics, mainly in environmental samples. This limitation has estimulated the application of molecular methods for species identification of these microorganisms. In this study, superficial water samples were submitted to nested-PCR to detect the presence of Cryptosporidium. A total of 30 water samples, from 10 points located in the state of São Paulo, were analyzed. Cryptosporidium was detected in 30% of the studied samples and genotyping allowed the identification of C. hominis, C. meleagridis and C. andersoni. Although the identification of Cryptosporidium in environmental samples is a complex task, molecular methods are essential for the species determination, helping to elucidate the epidemiology of this protozoan in our country.