Travail en codirection avec M. Frédéric Raymond / Avec la présente augmentation de la résistance aux antibiotiques et l’inquiétude des consommateurs, de nouvelles alternatives sont nécessaires afin de contrôler l’entérite nécrotique (EN), une maladie causant des millions de dollars en pertes économiques pour l’industrie de la volaille mondialement. Les bactériocines sont des peptides antimicrobiens produits par une bactérie pour tuer ou inhiber la croissance d’autres compétiteurs bactériens. La perfrine est la seule bactériocine reportée associée aux souches pathogènes de Clostridium perfringens, l’agent causal de l’EN. Les objectifs de cette étude étaient de détecter les souches commensales de Clostridium perfringens possédant une activité antimicrobienne contre des souches pathogènes de C. perfringens et d’identifier et caractériser les bactériocines produites. Les souches commensales de C. perfringens ont été sélectionnées à partir de notre banque de souches. L’activité antimicrobienne de ces souches a été testée contre des souches pathogènes de C. perfringens en utilisant la méthode d’inhibition sur gélose. Une souche commensale active démontrant une activité antimicrobienne a été cultivée et ses bactériocines ont été partiellement purifiées grâce à la précipitation au sulfate d’ammonium et par chromatographie (HPLC). À la suite de chaque chromatographie, l’activité antimicrobienne des fractions a été vérifiée en utilisant la méthode décrite précédemment afin de choisir les fractions contenant les bactériocines. La susceptibilité enzymatique, la stabilité à la chaleur et au pH et le poids moléculaire estimé des bactériocines ont été caractérisés. Les bactériocines étudiées étaient sensibles à la protéinase K, thermolabiles, stables à pH entre 4 et 8 et leur poids moléculaire étaient supérieur à 30 kDa. Le génome de la souche CP1676 a été séquencé et des analyses bio-informatiques ont été réalisées. Nous avons trouvé 28 séquences de bactériocines potentielles, mais seulement 4 d’entre elles semblaient être prometteuses. Dans cette étude, des souches commensales de C. perfringens produisant des bactériocines actives contre des souches pathogènes ont été identifiées. Ces bactériocines pourraient devenir une alternative intéressante aux antibiotiques afin de contrôler l’entérite nécrotique, mais davantage d’information est nécessaire. / With the current increase in antimicrobial resistance and consumers’ concern, new alternatives are needed to control necrotic enteritis (NE), a disease that causes billions of dollars in economic losses to the poultry industry worldwide. Bacteriocins are antimicrobial peptides produced by bacteria to kill or inhibit the growth of other bacterial competitors. Perfrin is the only reported bacteriocin associated with pathogenic strains of Clostridium perfringens, the causal agent of NE. The aims of this study were to screen for commensal Clostridium perfringens strains with an antimicrobial activity against C. perfringens pathogenic strains and to identify and characterize the produced bacteriocins. Commensal C. perfringens strains were selected from our bacterial collection. Antimicrobial activity of those selected strains was tested against C. perfringens pathogenic strains using the agar spot test method. An active commensal strain showing antimicrobial activity was cultured and its bacteriocins were partially purified using the ammonium sulfate precipitation method and HPLC. After each chromatography, antimicrobial activity of fractions was tested using the method described above to choose fractions containing bacteriocins. Enzyme susceptibility, heat and pH stability and the estimated molecular weight of the bacteriocins were characterized. The studied bacteriocins were sensitive to proteinase K, thermolabile, stable at pH between 4 and 8 and their molecular weight higher than 30 kDa. CP1676 strain genome was sequenced and bioinformatics were performed. We found 28 potential bacteriocin sequences, but 4 of them seemed to be promising. In this study, commensal C. perfringens strains producing bacteriocins active against pathogenic strains have been identified. These bacteriocins could be an interesting alternative to antibiotics for the control of necrotic enteritis but further data is still needed.

Das MMS stellt eine lebensbedrohliche Erkrankung großwüchsiger Hunde dar. Die ansteigenden Inzidenzzahlen der letzten Jahre, die ungeklärte Ätiologie sowie die hohe Mortalitätsrate rechtfertigen weitere Untersuchungen zu diesem Krankheitskomplex. Daher wurden in der vorliegenden Arbeit Mageninhalte (30 Tiere mit MMS / 13 Kontrolltiere) und Blutproben (102 Tiere mit MMS / 116 Kontrolltiere) mikrobiologisch, biochemisch (kurz-kettige Fettsäuren, Amylase, Lipase, Laktat, pH) und immunologisch (BotNt, CRP, Gesamt-immunglobuline, IgA-, IgG- und IgM-Spiegel ausgewählter mikrobieller Antigene) untersucht. Die Untersuchung des Mageninhaltes der Tiere mit MMS erbrachte signifikant gesteigerte Nachweishäufigkeiten für Hefen, hier v.a. von Rhodotorula mucilaginosa. Des Weiteren konnten in der Gruppe der Tiere mit MMS signifikant gesteigerte pH-Werte sowie signifikant erhöhte Mengen an Acetat, Butyrat und Gesamtfettsäuren im Vergleich zu den Kontrolltieren festgestellt werden. Die gesteigerte bakterielle Fermentation, die ursächlich mit der Entstehung des MMS zusammenhängen dürfte, ist vermutlich auf ein gesteigertes Vorkommen gasbildender Kokken zurückzuführen. Ein Einfluss von Clostridium perfringens an der Entstehung des MMS lässt sich anhand der ermittelten bakteriologischen Ergebnisse nicht belegen. BotNt haben nach den in der vorliegenden Arbeit gewonnenen Daten keinen Einfluss auf die Entstehung des MMS. Serologisch konnten in der Gruppe der Tiere mit MMS signifikant erhöhte CRP-Spiegel gemessen werden. Das CRP ließ aber keine prognostische Aussage über die Überlebenschancen der Tiere zu. Der erhöhte Gesamtimmunglobulin A-Spiegel, bei signifikant erniedrigtem Gesamtimmunglobulin G-Titer weist auf eine vermehrte Auseinandersetzung mit Antigenen hin, die über die geschädigten Schleimhäute eindringen können. Während der Serumlaktatspiegel eine prognostische Aussage über das Outcome der Tiere erlaubt, erscheint eine Bestimmung der Amylase und Lipase beim MMS nicht sinnvoll. Über einen Fragebogen konnte ein gesteigertes Risiko mit zunehmendem Alter, steigender Futtermenge pro Mahlzeit und niedriger Fütterungsfrequenz ermittelt werden. Eine gesteigerte Freßgeschwindigkeit übt einen tendenziellen Einfluss auf die Ausbildung des MMS aus. Keinen Einfluss dahingegen haben das Geschlecht und der Charakter der Tiere, bestehende gastrointestinale Störungen sowie vorangegangene Antibiotikumgaben.

Avian pathogenic Escherichia coli and Clostridium perfringens cause economic and welfare concerns to the broiler industry. The recent shift to no antibiotics ever (NAE) production has increased disease incidence. The objectives of this study were to determine the influence of season, age of flock, and sample type on E. coli prevalence and virulence and to identify C. perfringens prevalence and toxinotypes in NAE farms. Results indicated high prevalence of virulent E. coli; prevalence of virulent E. coli decreased from Spring to Summer. Virulent E. coli showed high resistance to antimicrobials. Serogroups O8 and O78 were most prevalent in virulent E. coli. C. perfringens prevalence was very low and all recovered isolates were toxinotype A with variation in netB, cpb2, and tpeL presence. In conclusion, NAE farms should have measures to control E. coli infections, especially in spring season. Further studies are required to confirm the lower prevalence of C. perfringens.

Clostridium perfringens is the most common cause of gas gangrene (clostridial myonecrosis), a disease that begins when ischemic tissues become contaminated with C. perfringens. C. perfringens quickly multiplies in ischemic tissues and spreads to healthy areas, leading to high levels of morbidity and mortality. As a species, the bacterium can synthesize thirteen different toxins. The alpha toxin (PLC) and perfringolysin O (PFO) are thought to be important virulence factors in gangrene. We wished to understand how C. perfringens is capable of avoiding killing by the host immune system, and determine if PLC and PFO play a role in this avoidance. We found C. perfringens was not killed by J774-33 cells or mouse peritoneal macrophages under aerobic or anaerobic conditions. Using electron microscopy, we showed that C. perfringens could escape the phagosome of J774-33 and mouse peritoneal macrophages. We believe the ability of C. perfringens to survive in the presence of macrophages is due to its ability to escape the phagosome. Using a variety of inhibitors of specific receptors, we identified those used by J774-33 cells to phagocytose C. perfringens. The scavenger receptor, mannose receptor(s), and complement receptor (CR3) were involved in the phagocytosis of C. perfringens. To determine if PFO or PLC were involved in the ability of C. perfringens to survive in the presence of macrophages, we constructed C. perfringens strains lacking these toxins. The ability of C. perfringens to survive in the presence of J774-33 cells is dependent on PFO, while survival in mouse peritoneal macrophages is dependent on PFO and PLC. The ability of C. perfringens to escape the phagosome of J774-33 cells and mouse peritoneal macrophages is mediated by either PFO or PLC. Using a mouse model, we found that PFO and PLC were necessary for C. perfringens to survive in vivo using infectious doses 1000 times lower than those required to initiate a gangrene infection. We propose that PFO and PLC play a critical role in the survival of C. perfringens during the early stages of gangrene infections, when phagocytic cells are present and bacterial numbers are low. / Ph. D.

The ƒÑ-toxin of Clostridium perfringens is a toxin involved in numerous diseases of humans and agriculturally important animals. One of these diseases is necrotic enteritis (NE), a sporadic enteric disease which affects avian species world-wide. This study involved the inactivation of alpha-toxin (ƒÑ-toxin) for use as a potential vaccine candidate to combat NE in chickens, and other diseases caused by C. perfringens type A. During the course of this research a number of ƒÑ-toxin recombinant proteins were developed through molecular inactivation of the ƒÑ-toxin gene, plc. Proteins plc316 and plc204 were developed by the deletion of the first three and seven ƒÑ-helices of the N-terminal domain respectively. These deletions resulted in proteins which were unstable in solution, constantly aggregated into insoluble masses and elicited lower overall antibody responses when administered to mice. A third protein, plcInv3 was developed from the deletion of part of the catalytic domain of the ƒÑ-toxin. PlcInv3 was highly soluble and upon immunisation of mice elicited a significant antibody response which was also capable of protecting mice against a live challenge of C. perfringens. The fourth and final protein developed was plc104. The smallest of the recombinant ƒÑ-toxin proteins, it consisted entirely of the C-terminal domain of ƒÑ-toxin. Its small size did not affect its ability to induce a strong antibody response when administered to mice, the antibodies of which were also protective during a challenge with C. perfringens. STM1, an attenuated strain of S. Typhimurium was used in the development of a vectored vaccine for the expression and oral delivery of plcInv3 and plc104 within the mouse host. The proteins were expressed within STM1 from expression plasmids containing the in vivo inducible promoters PhtrA and PpagC. A measurable humoral immune response against ƒÑ-toxin was absent following three oral vaccinations with the vectored vaccines, although, cytokine profiling of splenocytes from vaccinated mice revealed an increase in the number of interleukin-4 (IL-4)secreting cells and the lack of interferon-gamma (IFN-ƒ×) secreting cells. This indicated the stimulation of a T-helper type 2 (TH2) immune response which also lead to partial protection against a live C. perfringens challenge. This study demonstrates the feasibility of using STM1 as a carrier for the in vivo expression of the C. perfringens ƒÑ-toxin recombinant proteins plcInv3 and plc104. It is the first study to express C. perfringens antigens within an attenuated strain of S. Typhimurium, STM1.The partial protection of mice immunised with these vaccines indicates there is potential for this vectored vaccine system to be used in the protection of diseases caused by the ƒÑ-toxin of C. perfringens.

Proteins modularity enhances the multi-functionality and versatility of proteins by providing such properties as multiple and various ligand-binding sites, increased ligand affinity through the avidity effect, and the juxtaposition of ligand-binding modules near catalytic domains. An NMR-based "dissect-and-build" approach to studying modular protein structure and function has proven very successful, whereby modules are initially characterized individually and then correlated with the overall function of a protein. We have used the dissect-and-build approach and NMR to study two modular protein systems. Chapter 2 details the NMR solution structure of the weak-lysine-binding kringle IV type 8 (KIV8) module from the apolipoprotein(a) (apo(a)) component of lipoprotein(a) was determined and its ligand-binding properties assessed. In vitro studies have demonstrated the importance of the apo(a) KIV7 and KIV8 modules in mediating specific lysine-dependent interactions with the apolipoproteinB-100 (apoB-100) component of LDL in the initial non-covalent step of lipoprotein assembly. Notable differences identified in the lysine binding site (LBS) of the KIV8 were deemed responsible for the differential modes of apoB-100 recognition by KIV7 and KIV8. In addition, the KIV8 structure has brought to light the importance of an RGD sequence at the N-terminus of the apo(a) KIV8 module, which may mediate important apo(a)-integrin interactions. In Chapters 3-6, structure-function studies of the CpGH84C X82 and the CpGH84A dockerin-containing modular pair were conducted to understand how the varying modularity unique to the C-terminal regions of the secreted multi-modular family 84 glycoside hydrolases influences the spreading of Clostridium perfringens. Identification of a CpGH84C cohesin module (X82), and the structural characterization of a dockerin-containing modular pair provides the first evidence for multi-enzyme complex formation mediated by non-cellulosomal cohesin-dockerin interactions. The formation of large hydrolytic enzyme complexes introduces a novel mechanism by which C. perfringens may enhance its role in pathogenesis. / Thesis (Ph.D, Biochemistry) -- Queen's University, 2007-09-27 11:46:38.753

Clostridium perfringens is a gram positive spore forming anaerobe and a causative agent of gas gangrene, necrotic enteritis (pig-bel) and food poisoning in humans and other animals. This organism secretes a battery of exotoxins during the course of infection as well as a variety of virulence factors which may help to potentiate the activities of the toxins. Among these virulence factors is the μ-toxin, a family 84 glycoside hydrolase which acts to degrade hyaluronan, a component of human connective tissue. C. perfringens has 53 open reading frames encoding glycoside hydrolases. About half of these glycoside hydrolases are predicted to be secreted. Among these are CpGH84C, a paralogue of the μ-toxin, and CpGH89. CpGH89 shares sequence similarity to the human α-N-acetylglucosaminidase, NAGLU, in which mutations can cause a devastating genetic disease called mucopolysaccharidosis IIIB. One striking feature of the secreted glycoside hydrolase enzymes of C. perfringens is their modularity, with modules predicted to be dedicated to catalysis, carbohydrate-binding, protein-protein interactions and cell wall attachment. The extent of the modularity is remarkable, with some enzymes containing up to eight ancillary modules. In order to help understand the role of carbohydrate-active enzymes produced by bacterial pathogens, this thesis will focus on the structure and function of the modular extracellular glycoside hydrolase enzymes secreted by the disease causing bacterium, C. perfringens. These structure function studies examine two family 32 CBMs (carbohydrate-binding modules), one from the μ-toxin and the other from CpGH84C. As well we examine the complete structure of CpGH84C in order to help further our understanding of the structure of carbohydrate-active enzymes as a whole. Finally, the catalytic module of CpGH89 is characterized and its relationship to the human NAGLU enzyme is discussed.

Thesis addresses the physiological role of formyl tetrahydrofolate synthetase (Fhs) and bifunctional folate dehydrogenase (FolD) in folate mediated one carbon metabolism in bacteria. Thesis consists of 5 chapters. First chapter provides the details of the literature on folate metabolism, enzymes involved the synthesis and physiological roles various folate co-factors. Second chapter discusses the study of Clostridium perfringens Fhs generation of folD deletion in the support of fhs. Third chapter explores the characterization of the folD deletion strain. Fourth chapter presents the characterization of monofunctional versions of FolD from Clostridium perfringens. Fifth chapters talks about anti-correlation existence of Fhs and PurT (phosphoribosyl glycinamide formyl transferase II) The detailed experimental study is discussed below i. Characterization of Clostridium perfringens Formyl Tetrahydrofolate Synthetase (Fhs) In this chapter we have characterized Fhs from pathogenic Clostridium perfringens. Fhs catalyzes the formation of N10-formyl THF from THF and formate. Previously Fhs has been characterized from various non-pathogenic species of Clostridium. In addition, the detailed kinetic parameters are not known. In this report we have characterized the Fhs Clostridium perfringens and detailed kinetic parameters were determined. We have also shown the biological function by rescue of UV photorepair sensitive strain. ii. One-carbon metabolic pathway rewiring in Escherichia coli reveals an evolutionary advantage of 10-formyltetrahydrofolate synthetase (Fhs) in survival under hypoxia In cells, N10-formyltetrahydrofolate (N10-formyl THF) required for formylation of eubacterial/organeller initiator tRNA and purine biosynthesis is produced by methylene- tetrahydrofolate dehydrogenase/cyclohydrolase (FolD) and/or 10-formyltetrahydrofolate synthetase (Fhs). folD is present in all organisms, where as fhs shows mixed distribution. We show that in E. coli, which naturally lacks fhs, essential function of folD could be replaced with fhs of Clostridium perfringens when provided on a medium copy plasmid or integrated as single copy gene in the chromosome of the ∆folD strains, for their growth in a complex medium. However, these strains require purines and glycine as supplements for growth in M9 minimal medium. The in vivo levels of N10-formyl THF in the ∆folD strains (harboring fhs) were limiting despite their high enzymatic capacity to synthesize the same. Auxotrophy for purines could be alleviated by adding formate to the medium, and that for glycine by engineering THF import into the cells. The ∆folD strains showed high NADP+/NADPH ratio and were hypersensitive to trimethoprim (TMP). Further, the presence of fhs was disadvantageous to E. coli under aerobic growth. However, under hypoxia, E. coli strains harboring fhs outcompeted those lacking it. And, the computational analysis revealed a predominant natural occurrence of fhs in anaerobic and facultative anaerobic bacteria. We also propose that inhibitors aimed at folD could potentiate the effect TMP drugs. iii. 5, 10-methylene-THF dehydrogenase (DH) and 5, 10-methenyl-THF cyclohydrolase (CH) activities of FolD are essential to maintain folate homeostasis and anti-folate resistance While E. coli and many other organisms have folD alone or folD and fhs, Clostridium species possess an annotated bi-functional FolD and an annotated methenyl tetrahydrofolate cyclohydrolase (FchA). Simultaneous presence of 3 enzymes for the synthesis of N10-formyl THF was intriguing. To understand this unusual feature we have cloned Clostridium perfringens CpeFolD and CpeFchA, over expressed and purified to near homogeneity. Biochemical analyses revealed that CpeFolD possess only dehydrogenase activity as opposed to in silico prediction, while CpeFchA possess cyclohydrolase activity as expected. We also show that expression of both proteins together allowed folD deletion in E. coli. From this study we found that presence of dehydrogenase and cyclohydrolase functions are very important in the maintenance of folate homeostasis and anti-folate resistance. iv. Analysis of distribution of fhs and purT genes in the organisms While analysing distribution of fhs across genomes, serendipitously we also found that large number of organism which have fhs lack purT(phosphoribosyl glycinamide formyl transferase II), in short where ever purT was present fhs was absent. This kind of anti-correlation was strictly conserved in Bacillus genes as well. Growth competition experiments were done to address anti-correlation between fhs and purT. Growth competition experiments revealed that simultaneous presence of both purT and fhs is disadvantageous, when compared to presence of either one gene.

L’entérite nécrotique aviaire causée par Clostridium perfringens est une maladie économiquement dévastatrice et celle-ci est en émergence dans les troupeaux de poulets de chair éliminant l’usage des antibiotiques. À ce jour, aucune alternative en élevage ne permet de prévenir efficacement la maladie et un contrôle par une stratégie vaccinale serait des plus prisé. Une approche par génomique comparative jumelée à la vaccinologie réverse soustractive et comparative identifiant des protéines bactériennes de surface immunogènes figure parmi les approches méthodologiques des plus prometteuses pour le développement rapide d’un vaccin efficace. Une étude génomique comparative réalisée sur 48 souches de C. perfringens provenant de poulets de chair en santé ou affectés par l’entérite nécrotique a permis d’établir que les génomes analysés étaient composés de 155 700 protéines distinctes, où 13% étaient extracellulaires, 65% cytoplasmiques et 22% membranaires. L’évaluation du pouvoir immunogène de ces protéines à l’aide de l’outil de prédiction VaxiJen v.2.0 a permis d’identifier 4 catégories de scores pour les protéines identifiées, allant de 0,5 (seuil minimal recommandé) à 1,5. Les protéines présentant les scores les plus élevés ont été majoritairement associées à des localisations extracellulaires. La combinaison du score d’immunogénicité et de la localisation cellulaire des protéines analysées a mené à la sélection de 12 protéines candidates vaccinales, la plupart d’entre elles étant de fonction hypothétique. Une description plus approfondie de ces protéines permettra de mieux définir leur fonction, d’évaluer leur potentiel antigénique réel en caractérisant leur interaction avec le système immunitaire de la volaille et ultimement, d’évaluer leur rôle probable dans la pathogénie de l’entérite nécrotique. / Avian necrotic enteritis caused by Clostridium perfringens is a disease with a major economical impact, generating losses up to 6 billion dollars for the poultry industry worldwide. This disease appears in broiler chicken flocks that no longer employ the use of antibiotics. To date, no alternative method allows for the efficient prevention of necrotic enteritis (NE) and a control by a vaccinal strategy would be mostly prized. A comparative genomics approach as well as comparative and subtractive reverse vaccinology identifying immunogenic bacterial surface proteins is one of the most promising methodologies for the rapid development of an efficient vaccine. A comparative genomic study was performed on 48 C. perfringens strains isolated from healthy broiler chickens and from broilers affected by necrotic enteritis. From this study, it was established that the genomes analyzed were composed of 155 700 distinct proteins where 13% were predicted to have an extracellular expression, 65% at the cytoplasma level and 22% within the plasma membrane. The evaluation of the immunogenic potential of these proteins was established with the prediction software VaxiJen v2.0 for which a 0.5 threshold score allowed for the identification of four score categories among the identified proteins, from 0.5 to 1.5. For the most part, proteins with the highest scores were associated with an extracellular localisation. The combination of the immunogenicity score and localisation of the analysed proteins led to the selection of 12 vaccinal candidate proteins that were mostly identified as hypothetical. A more in-depth description of these proteins would allow the assessment of their function, the evaluation of their true immunogenic potential by characterizing their interaction with the avian immune system and ultimately, evaluate their probable role in the pathogenesis of necrotic enteritis.

No description available.