This thesis focuses on the use of a genomic approach to identify novel molecular markers to differentiate Streptococcus suis (S. suis) isolates into two populations, i) disease-associated and ii) non-disease associated. S. suis is a Gram-positive coccus that is considered one of the most important zoonotic bacterial pathogens of swine responsible for significant economic losses to swine production worldwide. Importantly, S. suis is not only an invasive pathogen but also a very successful coloniser of mucosal surfaces; often endemic in swine populations sampled. The widescale use of antibiotics to control and prevent the various clinical manifestations caused by S.suis has become unsustainable, due to increases in antibiotic resistance and government pressures. Other popular control strategies, such as the development of efficacious vaccines, are hindered by differences in virulence not only between but also within S. suis serotypes, as well as, the lack of a detailed understanding of the role in pathogenesis of many proposed virulence-factors. As a result, the detection of S. suis in asymptomatic swine herds is of little practical value in predicting the likelihood of future clinical relevance. This thesis aims to further understanding of the role the S. suis genome has in pathogenesis. The value of future surveillance and preventative health management lies in the detection of strains that genetically have increased potential to cause disease in presently healthy animals. The first results chapter of this thesis (chapter 3) describes the use of genome-wide associations studies, a so-far unexploited method for S. suis, to identify genetic markers associated with the observed clinical phenotype i) invasive disease or ii) asymptomatic carriage on the palatine tonsils of swine. Chapter 4 then describes the analyses used to select three genetic markers to pathotype S. suis - differentiate isolates of the same species based on their ability to cause disease; going on to describe the design and evaluation of a multiplex-PCR tool targeting the three newly defined "pathotyping markers" in comparison to existing methods used to characterise S. suis. These findings were taken further by using the pathotyping markers to screen material scrapped from the palatine tonsils of swine with no obvious signs of streptococcal disease. This produced an interesting result - the production of both invasive disease-associated and non- disease associated multiplex-PCR amplicons from the same experimental sample. Unsurprising in itself, what was surprising is the frequency with which this observation was found. Picking single colonies from solid agar plates is a crippling bottleneck of existing S. suis diagnostics, and its removal has the potential to improve the sensitivity of surveillance and preventive health management programs. Chapter 5 describes investigation of this surprising observation and indicates that classic culture-based methods of detection are not sensitive enough to confidently report the presence (or absence) of invasive disease-associated S. suis strains. This thesis concludes with the description of efforts to address the lack of a comprehensive understanding of S. suis virulence/'virulence-associated' factors. Chapter 6 describes the design of an isogenic mutant knocking out the invasive disease-associated pathotyping marker, SSU1589 (also known as virA). That is then evaluated in simple in vitro and in vivo experimental models in order to understand the role Type I restriction modification proteins have in S. suis pathogenesis. In conclusion, this thesis furthers our understanding that differences in the S. suis genome are an important factor in S. suis pathogenesis, and describes the identification and evaluation of novel genetic markers for the detection and control of invasive disease-associated S. suis strains in intensive pig production systems.

Tierärztl. Hochsch., Diss., 2004--Hannover.

Les cas d'infections à Streptococcus suis sont très répandus dans tous les pays producteurs de porcs. Cet organisme est également reconnu comme un agent de zoonose pour les personnes en contact étroit avec les porcs ou leurs produits dérivés. De nombreux rapports indiquent que depuis le début des années soixante-dix, le nombre de cas d'infections ainsi que la gravité des infections à S. suis ont considérablement augmenté. Un temps d'incubation plus court, une progression plus rapide de la maladie, un taux plus élevé de mortalité soulignent la nécessité urgente de mieux comprendre les facteurs associés à la pathogenèse de l'infection par S. suis. Des 35 serotypes décrits, le serotype 2 demeure le plus fréquemment associé à un phénomène de septicémie et à des cas de maladies telles que les méningites, endocardites et pneumonies. C'est également le serotype le plus souvent retrouvé chez l'humain et le porc. La pathogenèse de l'infection causée par S. suis est encore relativement mal connue. La présence d'une capsule riche en acide sialique est classiquement considérée comme un facteur de virulence essentiel, mais récemment d'autres facteurs ont également été cités. Cette étude avait pour but d'identifier et de caractériser de nouveaux déterminants de virulence chez S. suis. Dans un premier temps, la capacité de S. suis à former un biofilm a été étudiée. Il a été démontré que la présence de fibrinogène pouvait induire la formation d'un biofilm chez S. suis. Un mutant déficient pour l'expression de la capsule de même que des souches non-sérotypables de S. suis dépourvues de capsule ont montré une capacité de former un biofilm sans apport de fibrinogène. Il a été suggéré que la capsule chez S. suis pourait cacher des adhésines de surface et ainsi interférer avec la formation du biofilm et les capacités d'adhésion. Dans un second temps, l'utilisation d'un mutant de S. suis déficient pour une pseudo-subtilisine a permis de démontrer le rôle critique de cette protease pour le développement d'une infection dans un modèle de souris. La pseudo-subtilisine de S. suis a été clonée, purifiée et caractérisée. Certaines protéines de l'hôte comme le fibrinogène se sont révélées susceptibles à la protease. Une stimulation de macrophages par la pseudo-subtilisine recombinante a induit à une forte sécrétion de cytokines pro-inflammatoires. Lors d'infections expérimentales à S. suis chez le porc, les animaux ont développé des anticorps dirigés contre la pseudo-subtilisine, suggérant ainsi que cette protease représente un immunogène d'intérêt pour la vaccination. Enfin, un nouveau modèle pour l'analyse de la virulence de S. suis a été mis au point utilisant l'amibe Dictyostelium discoideum. Ce modèle a mis en évidence des différences majeures entre des souches sauvages virulentes de S. suis et des mutants ayant une virulence atténuée dans des modèles animaux classiques. En conclusion, ce projet a permis d'améliorer nos connaissances des mécanismes étiopathogéniques des infections à S. suis et a ouvert de nouvelles perspectives de prévention et traitement de ces infections.

Les progrès technologiques dans l'industrie de la viande ont des répercussions considérables sur les agents pathogènes de ces environnements. Parmi ceux-ci, Streptococcus suis occupe une place prédominante dans l’industrie porcine. En effet, S. suis, colonisateur naturel des voies respiratoires et digestives du porc, peut infecter son hôte en provoquant des méningites, septicémies, endocardites, arthrites ou pneumonies. De surcroît, S. suis peut également infecter l’humain en provoquant majoritairement des méningites et septicémies, et a notamment été la cause de deux épidémies en Chine en 1998 et 2005. La pathogenèse des infections à S. suis demeure partiellement connue à l’heure actuelle, rendant difficile le contrôle des infections. Il est par conséquent essentiel de caractériser les facteurs de virulence chez S. suis puisqu'ils pourraient représenter des cibles d’intérêt pour des applications préventives ou thérapeutiques. Ce projet de doctorat consiste donc en la caractérisation fonctionnelle de facteurs de virulence chez S. suis. Dans un premier temps, la capacité de S. suis à moduler son potentiel pro-inflammatoire en présence de concentrations sous-inhibitrices d'amoxicilline a été mise en évidence. Dans un second temps, la caractérisation plus avancée de la hyaluronate lyase de S. suis a permis de démontrer que son activité ne contribue pas à la virulence de la bactérie étant donné son absence au sein de souches les plus virulentes, mais que les interactions avec l'acide hyaluronique pourraient moduler la virulence de S. suis. Par la suite, l'étude fonctionnelle d’une DNase de S. suis a permis de démontrer son implication comme facteur de virulence et suggère son intérêt dans le développement de vaccins. Finalement, le dernier objectif du projet a permis la mise en évidence de la production de microvésicules fortement immunogéniques par S. suis. La présence de facteurs de virulence dans leur contenu protéique représente un élément encourageant dans le développement de vaccins contre l'agent pathogène. Ce projet a donc permis d'élargir les connaissances sur le potentiel néfaste de l'utilisation des antibiotiques à faible concentration dans l'industrie porcine, sur le rôle des activités hyaluronate lyase et DNase dans la virulence de S. suis, et de découvrir un nouveau mécanisme impliqué dans la virulence de la bactérie par le biais des microvésicules. / Technological progress in the meat industry has a substantial impact on pathogens within these environments. Among these pathogens, Streptococcus suis is of utmost importance in the swine industry. S. suis, natural colonizer of the respiratory and digestive tracts of porks, can infect its host causing mainly meningitis and septicemia as well as endocarditis, arthritis and pneumonia. Furthermore, S. suis can infect humans causing mainly meningitis and septicemia, and was the cause of two major outbreaks in China in 1998 and 2005. The pathogenesis of S. suis infections remains partially understood, making the control of infections challenging. Consequently, it is of utmost importance to characterize virulence factors that could represent targets of interest for preventive or therapeutic applications. This project focused on the functional charaterization of virulence factors produced by S. suis. First, the ability of S. suis to modulate its pro-inflammatory potential in the presence of sub-inhibitory concentrations of amoxicillin was demonstrated. Then, a further characterization of S. suis hyaluronate lyase brought evidence that this activity does not contribute to the bacterium's virulence since it is absent in most virulent strains. However, interactions with hyaluronic acid could modulate S. suis virulence. The functional study of S. suis DNase showed its implication as a virulence factor and suggested its interest in vaccine development. Finally, the last objective of this project lead to the discovery of the production of highly immunogenic microvesicles by S. suis. The presence of major virulence factors associated with these structures also represents an exciting fact for the development of vaccines against S. suis. This project allowed to expand the knowledge on the noxious potential of the use of low concentrations of antibiotics in the swine industry, on the role of hyaluronate lyase and DNase activities in S. suis virulence as well as on the production of microvesicles by S. suis that represents a new virulence mechanism.

Streptococcus suis est un agent pathogène porcin causant des pneumonies, des septicémies et des méningites. Il est aussi un agent de zoonose responsable de plusieurs éclosions en Asie. Les souches de S. suis sont classifiées en 35 sérotypes basés sur la composition de leur capsule polysaccharidique. S. suis sérotype 2 cause la majorité des infections sévères et est sous-divisé en séquence types (ST). Le ST1 est associé avec des souches hautement virulentes. En Amérique du Nord, les souches communément isolées appartiennent aux ST25 et ST28, respectivement modérément et faiblement virulentes dans un modèle animal. La présence de S. suis sous forme de bioaérosols dans l’air des bâtiments porcins a été démontré. Le but de ce projet est d’étudier l’aérosolisation préférentielle de différentes souches de S. suis en utilisant une chambre expérimentale et un nébuliseur développés pour ce projet. Bien qu’un nombre supérieur de souches doivent être étudiées, les résultats du projet suggèrent que les souches hautement virulentes du sérotype 2 de ST1 semblent être préférentiellement aérosolisées et que l’aérosolisation préférentielle de S. suis semble être un processus souche dépendant. Cette étude est une preuve de concept et améliore nos connaissances sur la potentielle transmission de S. suis via les bioaérosols. / Streptococcus suis is a swine pathogen that causes pneumonia, septicaemia and meningitis. It is also a zoonotic agent responsible for outbreaks in Asia. S. suis strains are classified into 35 serotypes based on the composition of their polysaccharide capsule. S. suis serotype 2 causes the majority of severe infections and it is subdivided into sequence types (STs). The ST1 is associated with highly virulent strains. In North America, the strains most commonly isolated belong to ST25 and ST28, which are respectively moderately and weakly virulent in animal model. The presence of S. suis bioaerosols in the air of swine confinement buildings has been demonstrated. The aim of this study was to better understand the aerosolization behaviour of S. suis by investigating preferential aerosolization of different S. suis strains using in-house developed environmental chamber and nebulizer. Although more strains should be studied, the results suggest that the highly virulent serotype 2 ST1 strains seem to be preferentially aerosolized and that the S. suis preferential aerosolization is a strain-dependant process. This study is a proof of concept and increases our knowledge on the potential aerosol transmission of S. suis.

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

Submitted by Nathália Faria da Silva (nathaliafsilva.ufv@gmail.com) on 2017-07-13T13:35:59Z No. of bitstreams: 1 texto completo.PDF: 380446 bytes, checksum: 7e55c93cd23967dc3c52fb63f4b4ab1f (MD5) / Made available in DSpace on 2017-07-13T13:35:59Z (GMT). No. of bitstreams: 1 texto completo.PDF: 380446 bytes, checksum: 7e55c93cd23967dc3c52fb63f4b4ab1f (MD5) Previous issue date: 2001-10-17 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / No presente trabalho, estudaram-se aspectos epidemiológicos das infecções causadas por Streptococcus suis, enfocando, principalmente, a ocorrência dos seus diversos sorotipos. Analisaram-se 323 amostras de S. suis, isoladas de animais clinicamente doentes, as quais foram sorotipadas, de acordo com a técnica de coaglutinação, utilizando soro hiperimune produzido para este trabalho. Um questionário foi elaborado e enviado aos proprietários das granjas questionários recebidos, positivas para observou-se que S. todas suis. as Analisando granjas os possuem sistema de criação de ciclo completo, 40,5% possuem entre 10 e 20 anos de existência e 38,1% possuem entre 100 e 500 matrizes. Pela sorotipagem das amostras, constatou-se que o S. suis está presente em vários estados brasileiros, sendo o maior número de isolados correspondente ao Estado de Minas Gerais (60,1%), seguido de São Paulo (10,4%) e Paraná (8,9%). O sorotipo 2 foi o mais freqüente (61,9%), seguido dos sorotipos 1, 3, 4, 7 e 8. O maior número de isolamentos foi obtido de cérebro (56,0%), seguido do pulmão (9,8%) e casos de septicemia (9,2%). Em relação à sensibilidade a antibióticos, as amostras de S. suis foram mais sensíveis a amoxicilina (96,4%), seguida de lincomicina-espectinomicina (90,9%), ampicilina (87,2%), cloranfenicol (79,1%) e penicilina (71,0%). / In the present work, epidemiological features of Streptococcus infections were studied, mainly focalizing the serotypes suis occurrence. It was analyzed 323 S. suis isolated samples, of clinically sick pigs. These samples were serotyped following the coaglutination method, using hyperimmune sera, specially produced for this work. A questionnaire was developed and then sent to farmers that had S. suis positives pigs. Analyzing the received questionnaires, it was observed that all farms have farrow-to-finish production system, 40,5% have 10 to 20 years of production and 38,1% had between 100 and 500 sows. Serotyping these samples, it was noticed that S. suis is present in several Brazilian states, and the greater number of them belong to Minas Gerais, followed by São Paulo (10,4%) and Paraná (8,9%).The serotype 2 was the most frequent one (61,9%), followed by the serotypes 1, 3, 4, 7 and 8. The greater number of isolations occurred in brain (56,0%), followed by lung (9,8%) and septicemic cases (9,2%). Regarding to drugs’ sensitivity, the S. suis isolated samples were more sensitive to amoxicillin (96,4%), followed by lincomycin-spectinomycin (90,9%), ampicillin (87,2%), chloranphenicol (79,1%) and penicillin (71,0%).

Le but de cette étude était d'évaluer le potentiel antimicrobien de bactériocines pour le contrôle du pathogène porcin Streptococcus suis sérotype 2. Pour répondre au premier objectif de ce projet, la susceptibilité de S. suis à la nisine, une bactériocine produite par Lactococcus lactis, seule ainsi qu'en combinaison avec différents antibiotiques, a été démontré. Pour réaliser le second objectif, la purification et la caractérisation d'une bactériocine produite par une souche non-virulente de S. suis sérotype 2 ont été effectuées. La bactériocine a d'abord été purifiée par HPLC pour ensuite être caractérisée au niveau biochimique, ainsi que génique. Des études plus approfondies permettront d'évaluer la capacité de la nisine, de la suicine 90-1330 ou de leur souche productrice respective à prévenir des infections expérimentales à S. suis chez le porc en vue d'une potentielle application thérapeutique et préventive.

Métodos microbiológicos tradicionais como isolamento, coloração de Gram e testes bioquímicos auxiliam na identificação do gênero Streptococcus, no entanto, as espécies apresentam ampla variação fenotípica, tornando difícil a identificação ou diferenciação das mesmas apenas por estes métodos. Uma das espécies mais importantes em suínos, Streptococcus suis, tem provocado grandes prejuízos em todo o mundo e tem sido descrito como uma importante zoonose em alguns países. S. suis está presente nas vias respiratórias superiores, colonizando principalmente tonsilas, cavidades oral e nasal facilitando a alta disseminação por contato direto, principalmente em leitões entre 4 e 12 semanas de vida. Os quadros clínicos mais frequentes em suínos infectados pelo S. suis são meningite, artrite e pneumonia. O objetivo do presente estudo foi identificar estirpes do gênero Streptococcus mediante as técnicas de reação em cadeia pela polimerase (PCR), sequenciamento parcial do gene 16S rRNA e espectrometria de massa MALDI-TOF (MALDI-TOF MS). As análises por PCR e por MALDI-TOF MS resultaram na identificação de 215 estirpes como S. suis e 35 como diferentes espécies pertencentes ao gênero Streptococcus. Os resultados da identificação das 35 estirpes pertencentes a outras espécies do gênero Streptococcus pelo MALDI-TOF MS foram confirmados pelo sequenciamento parcial do gene 16S rRNA, sendo que as duas técnicas apresentaram 100% de concordância. Os resultados obtidos indicam grande eficácia na utilização das técnicas avaliadas para a identificação de S suis e de outras espécies do gênero Streptococcus. A técnica de MALDI-TOF MS, apesar do custo elevado do equipamento, apresentou a vantagem de ser rápida, apresentar baixo custo por análise e reduzida utilização de material / Traditional microbiological methods such as isolation, Gram staining and biochemical tests help to identify the Streptococcus genus, however, the species present broad phenotypic variation, making it difficult for their identification or even differentiation just by these methods. One of the most important species in swine, Streptococcus suis, has led to great losses worldwide and has been described as an important zoonosis in some countries. S. suis is present in the upper airways, especially colonizing tonsils, oral and nasal cavities facilitating the high dissemination by direct contact, especially among piglets between 4 to 12 weeks of age. The most common clinical manifestations in pigs infected by S. suis are meningitis, arthritis and pneumonia. The aim of this study was to identify Streptococcus strains by polymerase chain reaction (PCR), 16S rRNA gene partial sequencing and MALDI-TOF mass spectrometry (MALDI-TOF MS). PCR and MALDI-TOF MS analysis resulted in the identification of 215 strains as S. suis and 35 as different species of the Streptococcus genus. The identification of the 35 strains belonging to other species of the genus by MALDI-TOF MS was confirmed by 16S rRNA gene partial sequencing, and both techniques presented 100% concordance. These results demonstrate the high efficiency in the use of the evaluated techniques for the identification of S. suis and the other species of the Streptococcus genus. The MALDI-TOF MS technique, despite the equipment high cost, presented the advantage of being fast, have low cost per analysis and reduced material usage

Métodos microbiológicos tradicionais como isolamento, coloração de Gram e testes bioquímicos auxiliam na identificação do gênero Streptococcus, no entanto, as espécies apresentam ampla variação fenotípica, tornando difícil a identificação ou diferenciação das mesmas apenas por estes métodos. Uma das espécies mais importantes em suínos, Streptococcus suis, tem provocado grandes prejuízos em todo o mundo e tem sido descrito como uma importante zoonose em alguns países. S. suis está presente nas vias respiratórias superiores, colonizando principalmente tonsilas, cavidades oral e nasal facilitando a alta disseminação por contato direto, principalmente em leitões entre 4 e 12 semanas de vida. Os quadros clínicos mais frequentes em suínos infectados pelo S. suis são meningite, artrite e pneumonia. O objetivo do presente estudo foi identificar estirpes do gênero Streptococcus mediante as técnicas de reação em cadeia pela polimerase (PCR), sequenciamento parcial do gene 16S rRNA e espectrometria de massa MALDI-TOF (MALDI-TOF MS). As análises por PCR e por MALDI-TOF MS resultaram na identificação de 215 estirpes como S. suis e 35 como diferentes espécies pertencentes ao gênero Streptococcus. Os resultados da identificação das 35 estirpes pertencentes a outras espécies do gênero Streptococcus pelo MALDI-TOF MS foram confirmados pelo sequenciamento parcial do gene 16S rRNA, sendo que as duas técnicas apresentaram 100% de concordância. Os resultados obtidos indicam grande eficácia na utilização das técnicas avaliadas para a identificação de S suis e de outras espécies do gênero Streptococcus. A técnica de MALDI-TOF MS, apesar do custo elevado do equipamento, apresentou a vantagem de ser rápida, apresentar baixo custo por análise e reduzida utilização de material / Traditional microbiological methods such as isolation, Gram staining and biochemical tests help to identify the Streptococcus genus, however, the species present broad phenotypic variation, making it difficult for their identification or even differentiation just by these methods. One of the most important species in swine, Streptococcus suis, has led to great losses worldwide and has been described as an important zoonosis in some countries. S. suis is present in the upper airways, especially colonizing tonsils, oral and nasal cavities facilitating the high dissemination by direct contact, especially among piglets between 4 to 12 weeks of age. The most common clinical manifestations in pigs infected by S. suis are meningitis, arthritis and pneumonia. The aim of this study was to identify Streptococcus strains by polymerase chain reaction (PCR), 16S rRNA gene partial sequencing and MALDI-TOF mass spectrometry (MALDI-TOF MS). PCR and MALDI-TOF MS analysis resulted in the identification of 215 strains as S. suis and 35 as different species of the Streptococcus genus. The identification of the 35 strains belonging to other species of the genus by MALDI-TOF MS was confirmed by 16S rRNA gene partial sequencing, and both techniques presented 100% concordance. These results demonstrate the high efficiency in the use of the evaluated techniques for the identification of S. suis and the other species of the Streptococcus genus. The MALDI-TOF MS technique, despite the equipment high cost, presented the advantage of being fast, have low cost per analysis and reduced material usage