Erreger des Leishmania donovani Komplexes (LDC) verursachen viszerale Leishmaniose (VL), eine der häufigsten durch Sandmücken übertragenen Infektionskrankheiten beim Menschen. Die vorliegende von der EU geförderte Dissertation untersucht die weltweite Populationsstruktur des LDC mit besonderem Schwerpunkt auf dem Indischen Subkontinent (ISC), wo das gehäufte Auftreten von Therapieversagen ein Problem für die geplante Eliminierung von VL darstellt. Zwei hoch diskriminierende molekulare Typisierungsverfahren wurden angewendet. 845 LDC-Isolate wurden mittels Multi-Lokus-Mikrosatelliten-Typisierung (MLMT) charakterisiert. Die Parasiten wurden in Gebieten mit endemischer VL aus unterschiedlichen Wirten isoliert und repräsentieren verschiedene klinische Formen der Leishmaniose. Eine 125 Parasiten umfassende Teilprobe wurde vollständig sequenziert und in einem next-generation Multi-Lokus-Sequenz-Ansatz (ng-MLSA) typisiert, welcher auf der Analyse von genomweiten Single-Nukleotid-Polymorphismen (SNP) beruht. Sowohl die MLMT- als auch die SNP-Daten wurden mit den gleichen populationsgenetischen Methoden ausgewertet. Der ng-MLSA Ansatz bestätigte weitgehend die Populationsstrukturen des mit dem MLMT analysierten größeren Datensatzes, die genetische Struktur korrelierte mit der geographischen Herkunft der Isolate. Die Unempfänglichkeit der Parasiten gegenüber Antimon- oder Miltefosin sowie die in vitro gemessene Resistenz der Isolate vom ISC konnten nicht auf einen spezifischen Genotyp zurückgeführt oder mit einem spezifischen genetischen Merkmal verknüpft werden. Die Gesamtgenomsequenzierung konnte bisher keine Mutationen im Parasitengenom nachweisen, die in Zusammenhang mit der Antimon- und Miltefosin-Unempfindlichkeit bzw. dem Therapieversagen gebracht werden könnten. Analysen basierend auf ausgewählten Sequenzen deuten auf eine variable chromosomale Ploidie und eine erhöhte Kopienzahl einiger Gene hin, die zur Entstehung von Arzneimittelresistenzen beitragen könnten. / Parasites of the Leishmania donovani species complex (LDC) cause most cases of visceral leishmaniasis (VL), one of the most fatal vector-borne parasitic human diseases. As part of an EU funded project, this dissertation has investigated the worldwide genetic population structure of parasites of the LDC, with special focus on the Indian subcontinent (ISC) where unresponsiveness to anti-leishmanial drugs has recently become an urgent problem for the containment of VL. Two types of highly discriminatory approaches have been used. Multi-locus microsatellite typing (MLMT) has been applied to 845 LDC isolates from numerous Old and New World foci of VL, from different clinical forms of the disease and from various hosts. A subset of 125 fully sequenced isolates, reflecting the worldwide distribution of the LDC, was analysed using a next-generation multi-locus sequence approach (ng-MLSA) including single nucleotide polymorphisms (SNP). Both microsatellite and SNP data sets were analysed using, in general, the same population genetic tools. The ng-MLSA approach has, in general, corroborated the population structures obtained with MLMT for the larger data set. With the exception of non MON-1 parasites, the genetic structure revealed was largely associated with the geographic origin of the isolates, but not with the clinical presentation, host specificity and the immune status of the host or year of parasite isolation. Unresponsiveness to antimony or miltefosine treatment as well as the respective resistances measured in vitro could not be linked to a specific genotype or genetic trait. Wg sequencing also failed, so far, to identify mutations, which could be related to the unresponsiveness of LDC isolates from the ISC to antimony and miltefosine therapy. Analyses of selected targets have revealed extensive variation in chromosomal ploidy in all wg sequenced isolates under study and copy number variations for some genes possibly involved in drug resistance.

Cette thèse concerne la combinaison du lambda-calcul et de la réécriture, dont nous étudions principalement deux propriétés : la confluence et la normalisation forte. Nous commençons par étudier sous quelles conditions la combinaison d'une relation de réécriture conditionnelle confluente au lambda-calcul donne une relation de réécriture confluente. Ensuite nous nous intéressons aux preuves de normalisation forte de lambda-calculs typés utilisant la technique de réductibilité. Notre contribution la plus importante est une comparaison de diverses variantes de cette technique, utilisant comme outil de comparaison la manière dont ces variantes s'étendent à la réécriture et dont elles prennent en compte les types unions et les types existentiels implicites. Enfin, nous présentons un critère, basé sur un système de types contraints, pour la normalisation forte de la réécriture conditionnelle combinée au lambda-calcul. Notre approche étend des critères de terminaison existants qui utilisent des annotations de taille. C'est à notre connaissance le premier critère de terminaison pour la réécriture conditionnelle avec membres droits d'ordre supérieur qui prenne en compte, dans l'argument de terminaison, de l'information issue de la satisfaction des conditions des règles de réécriture / This thesis is about the combination of lambda-calculus with rewriting. We mainly study two properties: confluence and strong normalization. We begin by studying under which conditions the combination of a confluent conditional rewrite relation to the lambda-calculus leads to a confluent relation. Next, we study strong normalization proofs of typed lambda-calculi that use the reducibility technique. Our main contribution is a comparison of variants of this technique, with respect to how they extend to rewriting and how they handle union and implicit existential types. Finally, we present a termination criterion for the combination of conditional rewriting and lambda-calculus based on a constrained type system. Our approach, which extends known criteria that use sized types, is to our knowledge the first termination criterion for conditional rewriting with higher-order right-hand sides that takes into account in the termination argument some information generated by the satisfaction of the conditions of the rewrite rules

L’objectif de mon travail fut de valider et d’optimiser la spectrométrie de masse de type MALDI-TOF pour l’identification et la classification d'un ensemble de bactéries pathogènes ou opportunistes chez l’homme, en enrichissant une base de données et en testant la robustesse de la méthode, afin d’obtenir une méthode rapide fixe et fiable d'acquisition de résultats. Les différents résultats obtenus ont permis la validation de la technique comme outil d’identification bactérienne fiable en routine. Elle permet désormais de caractériser les mélanges de deux bactéries voir même la différentiation d’espèces très proches comme les Shigella spp et E. coli. Nous avons montré que la technique sera encore améliorée par un outil supplémentaire de comparaison des souches pour une veille épidémiologique "en temps réel", sans investissement supplémentaire, en permettant plusieurs types d'économie. Elle apporte un gain réel dans la prise en charge du patient et le choix éclairé des antibiotiques testés pour l'antibiogramme. La technique peut aussi constituer un outil alternatif de sérotypage. / The aim of this work was to validate and optimize MALDI-TOF mass spectrometry for the identification and classification of a set of pathogens or opportunistic bacteria, by enriching a database and testing the robustness of the method, in order to obtain a quick and reliable fixed acquisition results. The different results obtained allowed the validation of the technique as a reliable tool for bacterial identification in hospital routine. In addition, we have shown that it can characterize mixtures of two bacteria and differentiate closely related species such as Shigella spp and E. coli. We demonstrate that MALDI-TOF/MS will be further enhanced by an additional tool for comparison of strains for epidemiological monitoring in "real time". The technique can also be an alternative tool for serotyping. MALDI-TOF/MS identification provides a real benefit in terms of patient care and the choice of antibiotics tested for sensitivity, without additional investment, which allows different types of economy.

A presente tese de doutorado insere-se na área de interação pelo olhar. A interação pelo olhar é uma forma de comunicação com o computador utilizando os movimentos oculares do usuário. Pessoas com deficiência física, que não conseguem usar dispositivos convencionais como um teclado e um mouse de computador, podem se beneficiar da interação pelo olhar para se comunicarem e se inserirem na sociedade. Para isso a entrada de texto ou digitação pelo olhar é um recurso importante e assunto principal dessa tese. O instrumento mais comum para entrada de texto pelo olhar consiste de um teclado virtual onde os caracteres são selecionados por tempo de latência. Essa forma de interação, embora simples, sofre de seleções involuntárias (problema conhecido como toque de Midas) se o tempo de latência for curto (menos de 500 ms). Já para tempos de latência mais longos, a interação se torna lenta. Alternativas para entrada de texto pelo olhar são os gestos discretos ou contínuos do olhar. O uso de gestos discretos permite reduzir o toque de Midas, porém o desempenho é inferior ao tempo de latência. Já nos métodos baseados em gestos contínuos, o olhar está sempre preso ao controle da interface. Uma técnica de interação proposta recentemente, chamada de \"alternância entre contextos\", permite reduzir o efeito do toque de Midas, utilizando apenas uma sacada para cada seleção. Além disso, essa técnica permite aos usuários manterem o ritmo de interação sem ajustar nenhum parâmetro na interface. A presente tese de doutorado visa melhorar a usabilidade e experiência dos usuários na interação pelo olhar com teclados virtuais. Os objetivos específicos são: investigar a relação entre a manipulação do contraste dos estímulos visuais e o tempo de reação sacádico para facilitar os movimentos oculares e tornar a interação mais rápida e agradável; propor e investigar novas extensões e aplicações da alternância entre contextos, visando reduzir o toque de Midas e ao mesmo tempo generalizar o método para outras tarefas de navegação e seleção de objetos pelo olhar; e desenvolver novos métodos de entrada de texto pelo olhar para melhorar a velocidade de digitação dos usuários, sem incrementar a carga de trabalho e mantendo a interação simples e fácil de aprender. A avaliação dos novos métodos e modelos propostos foi feita por meio de vários estudos com usuários. Os dados coletados nos estudos, tanto quantitativos quanto qualitativos, foram analisados com métodos estatísticos utilizados na área de interação homem-computador. As contribuições originais apresentadas na presente tese são: a proposta e a avaliação do efeito gap gradiente como feedback visual para facilitar a execução de movimentos sacádicos durante a interação pelo olhar; a proposta e investigação de contextos dinâmicos como extensão da alternância entre contextos, para permitir um melhor aproveitamento da área útil do monitor com uma baixa taxa de erros de seleção, assim como de meta-keys para navegação e execução de comandos de forma geral; e a proposta e a avaliação de AugFix, um novo modelo de feedback visual que melhora a velocidade e a experiência dos usuários na entrada de texto pelo olhar, com aplicação em teclados virtuais baseados nos paradigmas do tempo de latência e a alternância entre contextos. / This PhD thesis lays in the context of gaze-based interaction. Gaze-based interfaces allows the user to control a computer using his/her eye movements. Gaze interaction is specially useful for people with physical disabilities who cannot use conventional devices (such as a keyboard and/or mouse) to communicate. Entering text by gaze (also known as eye typing) is a very important activity and the main focus of this dissertation. The most common eye typing technique uses a virtual keyboard, where the letters are selected by dwell time. Though simple, this interaction technique suffers from involuntary activations (known as the Midas\' touch problem) for short dwell times (shorter than 500 ms). On the other hand, with longer dwell times the interaction becomes slow. Alternatives to dwell time are discrete and continuous gaze gestures. The use of discrete gaze gestures reduces the Midas\' touch problem, but its performance is slower compared to dwell time. When using continuous gaze gestures, the user gaze is always controlling the interface. A recently proposed technique called \"context switching\" avoids the Midas touch problem by mapping selection to a single saccade. Furthermore, with this technique the users can keep their rhythm of interaction without adjusting any parameter of the interface. This PhD thesis aims at improving the usability and user experience in gaze interaction with virtual keyboards. The objectives are: to investigate the relationship between contrast manipulation of visual stimuli and saccadic reaction time, to facilitate eye movements and make the interaction faster and more comfortable; to propose and investigate new extensions and applications of the context switching paradigm, in order to reduce the Midas touch problem and generalize the extensions to other tasks such as browsing and selection; and to develop new methods of eye typing that can improve typing performance without increasing the user workload, while keeping the interaction simple and easy to learn. Several user studies were designed and conducted to evaluate the methods and models proposed in this thesis. The data (both quantitative and qualitative) collected in the experiments is rigorously analysed using statistical methods. The original contributions of this thesis are: the proposal and investigation of the gradient gap effect as a visual feedback to facilitate the execution of saccadic movements during gaze interaction; the proposal and investigation of two extensions to the context switching paradigm: dynamic contexts that improve the utilization of the screen space while keeping a low selection error rate, and meta-keys for browsing and executing general-purpose commands; and the proposal and evaluation of AugFix, a new method that improves eye typing speed and user experience without increasing the cognitive load, that can be used with virtual keyboards controlled by both dwell time and context switching.

O Brasil consolidou-se como o principal produtor e exportador mundial de carne bovina. Estudos microbiológicos, geralmente realizados com amostras de carne coletadas no comércio e não na cadeia produtiva de carne, resultam numa insuficiência de dados a respeito das características fenotípicas e genotípicas das bactérias patogênicas de relevância nos produtos destinados à exportação. Objetivando determinar a prevalência e características de Salmonella spp em carne bovina para exportação, realizou-se a coleta de amostras de superfícies de 200 bovinos adultos, provenientes de 12 fazendas, abatidos em Frigorífico Exportador em São Paulo, Brasil, no ano de 2008. Foram coletadas amostras do couro do animal, logo após a realização da sangria (Co), da carcaça do mesmo animal, após a esfola (Ca I) e da carcaça do mesmo animal, após o toalete e antes da refrigeração (Ca II). O isolamento e a identificação de Salmonella spp foram realizados de acordo com o método - ISO 6579:2002, com algumas modificações. O patógeno foi detectado em 14 amostras de couro (7,0%), 5 de carcaça I (2,5%) e 4 de carcaça II (2,0%). Verificou-se a prevalência do sorovar S. Give (52,0%), seguido de S. Abaetetuba (16,0%), S. Typhimurium (8,0%), S. Agona (4,0%) e S. Dublin (4,0%), e quatro cepas (16,0%) não tipáveis. A tipagem molecular, feita por PFGE, mostrou que as salmonelas expressaram 12 perfis genéticos distintos, sendo 10 formados por apenas uma cepa, cada. As demais cepas (15) pertenceram a dois perfis genéticos apenas, que apresentaram 91,7% de similaridade. De acordo com o teste de infecção de células Caco-2, a maioria das cepas (92,0%) apresentou Eficiência de Invasão inferior a 1,0%, indicando baixo potencial de virulência. Quanto ao perfil de resistência a antibióticos, 68,0% das cepas analisadas foram multiresistentes, apresentando 12 perfis diferentes. Animais diferentes, provenientes de uma mesma fazenda, apresentaram salmonelas de um mesmo sorovar e com o mesmo perfil genético e de resistência a drogas, comprovando a ocorrência de contaminação cruzada durante o processamento da carne bovina. A multiresistência das salmonelas isoladas e a possibilidade de disseminação desses patógenos denotam a necessidade de se adotar medidas de higiene adequadas e maior prudência no emprego de antimicrobianos, na dieta alimentar e na terapêutica veterinária. / Brazil is an important bovine meat producer and exporter. Microbiological surveys are generally run with meat samples collected at retail level and not with meat for export, explaining the lack of data on the phenotypic and genotypic characteristics of pathogens of relevance in exported food products. This study aimed to evaluate the prevalence and characteristics of Salmonella spp in bovine meat destined for export, through surface sampling of hides and carcasses of 200 animals, from 12 farms, slaughtered in 2008 in an export slaughterhouse located in São Paulo, Brazil. Sampling was done from the hides right after bleeding (Co) and from carcasses of the same animal after removal of the hide (Ca I) and after cleaning but before chilling (Ca II). Isolation and identification of Salmonella spp were done according to ISO 6579:2002, with some modifications. The pathogen was detected in 14 samples of hides (7,0%), 5 of carcasses Ca I (2,5%) and 4 of carcasses Ca II (2,0%). The most prevalent serovars were S. Give (52,0%), followed by S. Abaetetuba (16,0%), S. Typhimurium (8,0%), S. Agona (4,0%) and S. Dublin (4,0%). Four isolates (16,0%) were not typable. Molecular typing using PFGE indicated that the isolates presented 12 molecular profiles, ten of them containing one single isolate. Fifteen isolates belonged to only two distinct profiles, with 91.7% similarity. Invasion Efficiency tests, run with Caco-2 cells, indicated that most isolates (92,0%) presented low virulence potential. 68,0% of the isolates were multiresistant to antimicrobial drugs, presenting 12 different resistance profiles. Different animals, coming from the same rearing farm, harbored salmonellae belonging to same serovar and presenting the same genetic and antimicrobial resistance profiles, indicating cross contamination in the slaughterhouse during production of meat. The occurrence of salmonellae that can disseminate in the slaughterhouse and the multiresistance presented by the strains strengthen the need for adoption of proper hygiene control measures and care in the use of antibiotics in human and veterinary therapeutics.

Infecções invasivas por Trichosporon spp. ocorrem com maior frequência em pacientes neutropênicos, principalmente portadores de doenças hematológicas malignas, e estão associadas a elevados índices de mortalidade devido às dificuldades na identificação do patógeno e à resistência aos fármacos mais empregados na terapêutica antifúngica. A identificação das espécies de Trichosporon é importante tanto para estudos epidemiológicos, como para associar aspectos clínicos com as espécies causadoras das infecções. Além disso, auxilia no tratamento da enfermidade, uma vez que a suscetibilidades aos fármacos antifúngicos pode variar de acordo com a espécie. Além disso, as leveduras do gênero Trichosporon sintetizam a glucuronoxilomanana (GXM) em sua parede celular, que pode estar envolvida no mecanismo de virulência do patógeno. Este estudo teve como objetivo determinar, por identificação fenotípica e molecular, espécies isoladas de pacientes internados em unidades hospitalares, comparando os resultados obtidos por ambos os métodos; avaliar diferenças na distribuição dessas espécies em relação às formas invasivas e não invasivas da infecção; determinar o perfil de suscetibilidade dessas leveduras aos antifúngicos, empregando um método de micro-diluição de referência e um método comercial; e avaliar a presença de GXM na parede celular dos isolados. Foram avaliados 74 isolados obtidos de amostras clínicas de pacientes do Hospital das Clinicas da FMUSP e de outras unidades hospitalares do Estado de São Paulo, no período de 2003 a 2011. Dezenove amostras foram isoladas de sítios estéreis do organismo (infecções invasivas) e 55 foram isoladas de urina e cateter (isolados não invasivos). Para a identificação das espécies, os isolados foram submetidos a análises fenotípicas, que incluíram estudo macro e micromorfológico, provas fisiológicas e avaliação do perfil bioquímico por sistema automatizado VITEK 2. A identificação molecular foi realizada pelo sequenciamento das regiões IGS e D1/D2 do DNA ribossomal. O perfil de suscetibilidade dos 74 isolados foi analisado pelo método de micro-diluição EUCAST (referência) com os fármacos fluconazol (FCZ), itraconazol (ITZ), voriconazol (VCZ), cetoconazol (CTZ), anfotericina B (AMB) e 5-fluocitosina (5FC); e pelo método de micro-diluição comercial Sensititre YeastOne, com os mesmos fármacos empregados no EUCAST, acrescidos do posaconazol (POS) e caspofungina (CAS). Os valores das concentrações inibitórias mínimas (CIM), erros categórico e essencial, bem como outros parâmetros foram comparados entre os dois métodos. A presença de GXM na parede celular dos 74 isolados foi determinada por citometria de fluxo, empregando anticorpo monoclonal anti-GXM. Os resultados dos estudos morfológicos e fisiológicos foram insuficientes para definir as espécies dos 74 isolados. Pela assimilação de carboidratos analisada pelo sistema VITEK 2, verificou-se que 71 isolados foram identificados como T. asahii (17 de infecção invasiva e 54 não invasivos), um isolado como T. mucoides (invasivo), e para dois isolados (um invasivo e um não invasivo), a identificação não foi conclusiva. Para estes últimos foi realizado o auxanograma (método manual), e a identificação permaneceu inconclusiva, pois pelo perfil de assimilação, os isolados poderiam ser identificados como T. asahii ou T. faecale. Pela técnica de sequenciamento, 62 dos 74 isolados foram identificados como T. asahii, demonstrando 82,4% de concordância com o sistema VITEK 2. Onze isolados com identificações discordantes pertenciam às espécies T. inkin (8), T. faecale (2) e T. dermatis (1), como determinado por sequenciamento. Dos dois isolados com identificação inconclusiva pelo VITEK 2, um foi identificado pela técnica molecular como T. asahii, enquanto para o outro isolado não foi possível definir a espécie. Portanto, dos 74 isolados do estudo, 62 foram identificados como T. asahii, 8 como T. inkin, 2 como T. faecale e 1 T. dermatis; dois isolados permaneceram sem identificação conclusiva. Os resultados dos testes de suscetibilidade in vitro mostraram que, em ambos os métodos, VCZ apresentou a melhor atividade antifúngica. Pelo método EUCAST, foram obtidos valores elevados de CIM para AMB, enquanto o mesmo não foi observado no teste comercial. Neste último, foram observados valores elevados de CIM para FCZ, POS e CAS. Em relação à 5FC, os valores de CIM 90% por ambos os testes foram elevados (16mg/L). Diferenças significantes foram observadas entre os valores de CIM obtidas pelos dois métodos, e percentuais relativamente elevados de erros categóricos graves quando o método comercial foi comparado ao de referência. Não houve diferença estatística significante de valores de CIM entre isolados de infecção invasiva e não invasiva, exceto para ITZ e 5FC. Cerca de 30% dos isolados obtidos de casos de infecção invasiva e não invasivos apresentaram resistência cruzada entre os azóis FCZ e VCZ, e uma pequena porcentagem apresentou multirresistência. Para a análise de GXM na parede celular dos 74 isolados do estudo, foi avaliada a intensidade de fluorescência emitida pela citometria de fluxo, não tendo sido observada diferença estatística significante entre isolados invasivos e não invasivos. O estudo permitiu concluir que T. asahii foi a espécie mais isolada das amostras clínicas obtidas de sítios estéreis e não estéreis. A metodologia clássica de identificação fenotípica não foi suficiente para definir as espécies do gênero Trichosporon, e o sistema VITEK 2 apresentou discordância quando comparado à técnica molecular para as espécies não T. asahii. Em relação aos testes de suscetibilidade in vitro, VCZ apresentou-se mais adequado para a inibição das leveduras, enquanto os fármacos AMB, FCZ e POS não foram eficazes para a maior parte dos isolados. As discordâncias encontradas entre o método de referência e o comercial sugerem que, para o segundo, são necessárias mais avaliações para seu emprego em rotina laboratorial para o gênero Trichosporon. A detecção de GXM não resultou em diferenças entre os isolados de ambos os grupos; no entanto, para se determinar o efeito protetor do polissacarídeo contra a ação de macrófagos, ensaios de fagocitose devem ser realizados / Invasive Trichosporon spp. infections occur more frequently in neutropenic patients, especially those with hematologic malignancies, and are associated with high mortality rates due to difficulties in identifying the pathogen and treating patients with drugs most currently employed in antifungal therapy. Trichosporon species identification is important for epidemiological studies and to better define eventual species-specific clinical association. Additionally, antifungal susceptibility may vary according to the species. Furthermore, glucuronoxylomannan (GXM) is a cell wall-associated polysaccharide produced by genus Trichosporon, which may be involved in virulence mechanisms of this pathogen. This study aimed (i) to identify Trichosporon species isolated from hospitalized patients by both phenotypic and molecular methods, comparing results; (ii) to verify the distribution of these species in invasive and non-invasive infection episodes; (iii) to determine the in vitro activities of various antifungals agents against the Trichosporon spp. isolates, employing a reference micro-dilution method and a commercial system; (iv) and to analyze the surface expression of GXM. Seventy-four Trichosporon spp. isolates obtained from clinical specimens of patients admitted to the Hospital das Clínicas-FMUSP and to other hospitals in the state of São Paulo, from 2003 to 2011, were included in the study. Nineteen samples were isolated from sterile deep sites (invasive infections) and 55 were isolated from catheter and urine samples (non-invasive isolates). All isolates were submitted to phenotypic analysis, which consisted in morphological features observation, physiological tests and determination of the biochemical profile by VITEK 2 system. Molecular identification was performed by sequencing of IGS1 and D1/D2 regions from the ribosomal DNA. The susceptibility antifungal profiles of the 74 isolates were analyzed by both the EUCAST micro-dilution method (reference) employing fluconazole (FCZ), itraconazole (ITZ), voriconazole (VCZ), ketoconazole (CTZ), amphotericin B (AMB) and 5 - flucytosine (5FC), and the commercial micro-dilution test Sensititre YeastOne, with the same drugs employed in EUCAST plus posaconazole (POS) and caspofungin (CAS). The minimum inhibitory concentration values (MIC), categorical and essential errors as well as other susceptibility parameters were compared between both methods. The cell wall expression of GXM of all isolates was measured by flow cytometry employing an anti-GXM monoclonal antibody. The morphological and physiological features of the Trichosporon spp. isolates were insufficientto define species. The carbohydrate assimilation analysis, performed by VITEK 2 system, has resulted in 71 isolates identified as T. asahii (17 from invasive infections and 54 non-invasive isolates) and one isolate as T. mucoides (invasive). The species identification for the two remaining isolates (one invasive and one non-invasive) was inconclusive. For this reason, a manual auxanogram was performed with these isolates, resulting again in non-conclusive species identification. By the automated sequencing method, 62 of the 74 isolates were identified as T. asahii, showing 82.4% of agreement with the VITEK 2 identification. Eleven isolates were identified by sequencing as T. inkin (8), T. faecale (2) and T. dermatis (1), showing disagreement identification with the VITEK 2 system. Regarding the two isolates with inconclusive results by the carbohydrate assimilation, the molecular technique identified one as T. asahii, whereas for the other isolate the sequencing was also unable to define species. Therefore, among the 74 studied isolates, 62 were identified as T. asahii, eight as T. inkin, two as T. faecale and one as T. dermatis; and two isolates remained with unconclusive identification. Almost all Trichosporon spp. isolates displayed susceptibility to VCZ with both methods. By the EUCAST method, high values of MIC were observed for AMB, while by the commercial test especially the invasive isolates showed susceptibility to this drug. Additionally, the Sensititre kit provided elevated MIC values for FCZ, POS and CAS. In regards to 5FC, the MIC 90% values were consistently high (16 mg/L) in both methodologies. The MIC values obtained by both EUCAST and commercial methods were compared, resulting in significant differences of MIC values for all tested antifungal drugs; major categorical errors occurred at relatively high percentage with the commercial method. No statistically significant differences in MIC values were verified when invasive and non-invasive isolates were compared. Around 30% of both invasive and non-invasive isolates showed cross-resistance to FCZ and VCZ, while a small number of isolates was multiresistant. The GXM analysis by cytometry demonstrated no significant differences between invasive and non- invasive isolates. This study demonstrated that T. asahii was the most frequently isolated species from both deep and non-sterile sites of the patients. The classical phenotypic methodology was not able to define Trichosporon species, and the VITEK 2 system identification showed disagreement with the sequencing technique for the non-T. asahii species. Regarding the in vitro susceptibility tests, VCZ was the most effective drug against the isolates, whereas most of them appear to be less susceptible to AMB, FCZ and POS. The discrepancies in the Trichosporon spp. susceptibility results between the reference and commercial methods suggest that the latter requires further evaluation tests before it can be used in routine laboratory. Although the GXM expression seemed to be equal in both invasive and non-invasive Trichosporon spp. isolates, phagocytic assays should be performed in order to determine the protective effect of the polysaccharide against phagocytosis

Le Staphylococcus aureus résistant à la méthicilline (SARM) est un pathogène important qui a été identifié comme agent d‟infection chez les animaux d‟élevage et les travailleurs exposés à ces animaux. Au Canada, très peu d‟informations sont disponibles concernant les SARMs d‟origine porcine. L‟objectif de cette étude était de déterminer la prévalence des SARMs provenant de porcs à l‟abattoir, de caractériser leur résistance aux antibiotiques ainsi que d‟évaluer le niveau de séroconversion des porcs envers le S. aureus chez les animaux porteurs ou non du SARM. Un total de 107 isolats ont été identifiés positifs aux SARMs sur 660 échantillons. La prévalence de SARMs à l‟abattoir A était de 30,8% et de 23,8% à l‟abattoir B. La susceptibilité aux antibiotiques a été déterminée en utilisant la méthode de micro-dilution de Sensititre. Tous les isolats ont démontré une sensibilité envers la ciprofloxacine, la gatifloxacine, la gentamicine, la lévofloxacine, le linézolide, la quinupristine/dalfopristine, la rifampicine, la streptomycine, le triméthoprime/sulfaméthoxazole et la vancomycine. De la résistance a été observée envers la daptomycine (0,93%), l‟érythromycine (29%), la clindamycine (29%), la tétracycline (98,1%). De plus, 30% des SARMs isolés étaient résistants à plus de deux antibiotiques autres que les β-lactamines. Par typage, deux clones prédominants ont été obtenus ainsi que deux types de SCCmec (type V et possiblement un nouveau type comprenant les cassettes III et IVb). 15 clones ont été identifiés par typage MLVA, comprenant les clones prédominants VI (40.1%; 43/107) et XI (17.7%; 19/107). Deux souches de SARMs ont été caractérisées par biopuce à ADN et des gènes d‟antibiorésistance, de typage (SCCmec et MLST) et de virulence ont été identifiés. Sans considération pour le site de colonisation, les porcs SA-/MRSA- (n=34) et les porcs SA+ (n=194) montrent, respectivement, des taux de séroconversion de 20.6% et 32.5%. Les porcs colonisés par un SARM à un site de iv prélèvement et non colonisés par un SA à l‟autre site (n=18) montrent une séroconversion (5.6%) significativement (P < 0.05) plus faible comparativement aux porcs colonisés par SA à un ou deux sites de prélèvement et n‟ayant pas de SARM. Nos résultats démontrent que les porcs provenant d‟abattoir peuvent être colonisés par des SARMs multi-résistants aux antibiotiques. De plus, ces SARMs sont possiblement capable de coloniser leurs hôtes sans stimuler la production d‟anticorps et ce par l‟atténuation de la réponse immunitaire ou par la colonisation de porcs qui sont moins immunocompétents. / Methicillin-resistant Staphylococcus aureus (MRSA) found in food producing animals is a major public health concern. Transmission to humans has been reported and MRSA represents a reservoir of antimicrobial resistance genes. Little is known on how MRSA successfully establishes colonization and how it is able to persist in the host. This study was conducted to determine the occurrence and the antimicrobial resistance profile of MRSA from abattoir pigs and their level of seroconversion toward S. aureus (SA). A total of 107 isolates were identified as MRSA from 660 samples. Antimicrobial susceptibilities were determined by broth microdilutions. Fifteen clones were identified by MLVA with clones VI (40.1%; 43/107) and XI (17.7%; 19/107) being the most predominant. All MRSA isolates were pvl-, tst-, eta- and etb-negative. Most isolates were SCCmec type V (70.1%; 75/107). All MRSA isolates were susceptible to ciprofloxacin, gatifloxacin, gentamicin, levofloxacin, linezolid, quinupristin/dalfopristin, rifampin, streptomycin, trimethroprim/sulfamethoxazole and vancomycin. However, resistance was observed toward clindamycin (29%), daptomycin (0.9%), erythromycin (29%) and tetracycline (98.1%). Multi-resistance was confirmed in MRSA since 28% of all isolates were resistant toward three antimicrobials other than β-lactams. The effect of MRSA carriage on seroconversion was examined to see whether the host responded differently to MRSA or SA colonization. The presence of SA-specific antibodies in pig serums was measured for each animal using indirect ELISA and a mixture of two widespread SA antigens (IsdH [HarA] and IsdB). Regardless of the colonization site, SA-/MRSA- pigs (n=34) and SA+ pigs (n=194) showed 20.6% and 32.5% seroconversion, respectively. Notably, pigs colonized by MRSA at one body site and no SA at the other sampling site (n=18) showed a significantly lower (5.6%) seroconversion (P < 0.05) compared to pigs colonized by SA at one or both vi sites without MRSA. The findings of the study show that the nares and axillae of abattoir pigs can harbor MRSA strains with multiple antimicrobial resistances. In addition, these MRSA were possibly able to colonize the host either without stimulating antibody production, by attenuating the immune response or by colonizing pigs that are less immunocompetent. This may explain the success of MRSA colonization and persistence in pigs. Further studies are required to better elucidate MRSA colonization in abattoir pigs and their public health risk.

Methicillin-resistant Staphylococcus aureus (MRSA) is an important human pathogen that is endemic in hospitals all over the world. It has more recently emerged as a serious threat to the general public in the form of community-acquired MRSA. MRSA has been implicated in a wide variety of diseases, ranging from skin infections and food poisoning to more severe and potentially fatal conditions, including; endocarditis, septicaemia and necrotising pneumonia. Treatment of MRSA disease is complicated and can be unsuccessful due to the bacterium's remarkable ability to develop antibiotic resistance. The considerable economic and public health burden imposed by MRSA has fuelled attempts by researchers to understand the evolution of virulent and antibiotic resistant strains and thereby improve epidemiological management strategies. Central to MRSA transmission management strategies is the implementation of active surveillance programs, via which unique genetic fingerprints, or genotypes, of each strain can be identified. Despite numerous advances in MRSA genotyping methodology, there remains a need for a rapid, reproducible, cost-effective method that is capable of producing a high level of genotype discrimination, whilst being suitable for high throughput use. Consequently, the fundamental aim of this thesis was to develop a novel MRSA genotyping strategy incorporating these benefits. This thesis explored the possibility that the development of more efficient genotyping strategies could be achieved through careful identification, and then simple interrogation, of multiple, unlinked DNA loci that exhibit progressively increasing mutation rates. The baseline component of the MRSA genotyping strategy described in this thesis is the allele-specific real-time PCR interrogation of slowly evolving core single nucleotide polymorphisms (SNPs). The genotyping SNP set was identified previously from the Multi-locus sequence typing (MLST) sequence database using an in-house software package named Minimum SNPs. As discussed in Chapter Three, the genotyping utility of the SNP set was validated on 107 diverse Australian MRSA isolates, which were largely clustered into groups of related strains as defined by MLST. To increase the resolution of the SNP genotyping method, a selection of binary virulence genes and antimicrobial resistance plasmids were tested that were successful at sub typing the SNP groups. A comprehensive MRSA genotyping strategy requires characterisation of the clonal background as well as interrogation of the hypervariable Staphylococcal Cassette Chromosome mec (SCCmec) that carries the β-lactam resistance gene, mecA. SCCmec genotyping defines the MRSA lineages; however, current SCCmec genotyping methods have struggled to handle the increasing number of SCCmec elements resulting from a recent explosion of comparative genomic analyses. Chapter Four of this thesis collates the known SCCmec binary marker diversity and demonstrates the ability of Minimum SNPs to identify systematically a minimal set of binary markers capable of generating maximum genotyping resolution. A number of binary targets were identified that indeed permit high resolution genotyping of the SCCmec element. Furthermore, the SCCmec genotyping targets are amenable for combinatorial use with the MLST genotyping SNPs and therefore are suitable as the second component of the MRSA genotyping strategy. To increase genotyping resolution of the slowly evolving MLST SNPs and the SCCmec binary markers, the analysis of a hypervariable repeat region was required. Sequence analysis of the Staphylococcal protein A (spa) repeat region has been conducted frequently with great success. Chapter Five describes the characterisation of the tandem repeats in the spa gene using real-time PCR and high resolution melting (HRM) analysis. Since the melting rate and precise point of dissociation of double stranded DNA is dependent on the size and sequence of the PCR amplicon, the HRM method was used successfully to identify 20 of 22 spa sequence types, without the need for DNA sequencing. The accumulation of comparative genomic information has allowed the systematic identification of key MRSA genomic polymorphisms to genotype MRSA efficiently. If implemented in its entirety, the strategy described in this thesis would produce efficient and deep-rooted genotypes. For example, an unknown MRSA isolate would be positioned within the MLST defined population structure, categorised based on its SCCmec lineage, then subtyped based on the polymorphic spa repeat region. Overall, by combining the genotyping methods described here, an integrated and novel MRSA genotyping strategy results that is efficacious for both long and short term investigations. Furthermore, an additional benefit is that each component can be performed easily and cost-effectively on a standard real-time PCR platform.

No description available.

Ehrlichia ruminantium est l'agent causal de la cowdriose, une maladie tropicale mortelle des ruminantstransmis par les tiques Amblyomma. Jusqu'à présent, il n'existe pas de vaccin efficace dû à la faible protection croisée des souches vaccinales vis-à-vis des isolats de terrain. Ceci est principalement lié àdiversité génétique d'E. ruminantium au sein les zones géographiques. Par conséquent, la caractérisation de lastructure génétique de la population d'E. ruminantium à l'échelle mondiale et régionale est importante pour définir les meilleures stratégies de contrôle et améliorer les stratégies de surveillance de la cowdriose. / Ehrlichia ruminantium is the causal agent of heartwater, a ruminant tropical fatal diseasetransmitted by Amblyomma ticks. Up to now, no effective vaccine is available due to a limitedcross protection of vaccinal strains on field isolates mainly associated to a high geneticdiversity of E. ruminantium within geographical locations. Thus, both characterization of E.ruminantium genetic population structure at worldwide and regional scale and estimation of E.ruminantium tick prevalence are important to delimitate better control strategies and improveheartwater monitoring strategies