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.

Rice blast disease is caused by the ascomycete fungus Magnaporthe oryzae and is of economic importance worldwide, due to its wide geographical distribution and the severe yield losses it causes on cultivated rice. Understanding the population structure of M. oryzae is key to sustainable management of blast disease. In this study, a total of 290 M. oryzae isolates were collected from rice growing regions in Kenya including Central Kenya (Mwea irrigation scheme), Western Kenya (Ahero and Maugo irrigation schemes in Ahero and Homa-Bay respectively) and Coastal Kenya (Kwale). Initially, I undertook genotyping of a subset of Kenyan isolates by DNA sequence analysis of the internal transcribed spacer regions (ITS 1 and ITS 2) of the rRNA-encoding gene unit and by DNA fingerprinting using the Pot2 repetitive DNA element. Phylogenetic analyses based on ITS sequences clustered together isolates from Western and Coastal Kenya which were distinct from Central Kenya isolates. Cluster analysis based on 80% DNA fingerprint similarity, identified five clonal lineages designated KL1, KL2, KL3, KL4 and KL5 with most isolates belonging to lineages KL2, KL3, KL4. The clustering of isolates was region specific with Western and Coastal isolates closely related to each other and distinct from Central Kenya isolates. Distribution of mating type gene loci (MAT1.1 and MAT1.2) was determined using mating type gene specific primers. My results indicate that MAT1.1 is the predominant mating type and is distributed in all the rice growing regions of Kenya. MAT1.2 isolates were identified only in Coastal Kenya. I further undertook high throughput next-generation DNA sequencing of the genomes of 27 M. oryzae isolates from sub-Saharan Africa (SSA), including Kenya, Uganda, Tanzania, Benin, Togo, Nigeria and Burkina Faso and compared them to other sequenced strains from China, India, USA, Philippines, Thailand, Korea, Japan, France and French Guiana. Single nucleotide polymorphisms (SNPs) indicated that majority of East African isolates of M. oryzae clustered separately from West African isolates. African isolates clustered with isolates from India and China, indicating that rice blast in SSA may have originated from Asia. Pathotype analysis of Kenyan isolates was undertaken using a set of monogenic differential rice varieties, collectively harbouring 24 disease resistance genes. Rice blast resistance gene Pi-z5 conferred resistance to all the isolates tested. Other resistance genes that conferred resistance to majority of isolates tested include Pi-9, Pi-12(t), Pi-ta, Pi-ta2 and Pi-z. These resistance genes are suitable candidates for introgressing into commercially grown varieties in Kenya in combinations. I also investigated the population of M. oryzae isolates to identify cognate avirulence gene loci, including novel genes not yet reported. Finally, I evaluated rice varieties grown in Kenya for resistance to indigenous rice blast isolates under laboratory conditions. Rice variety Basmati 370 was susceptible to rice blast with varieties IR2793-80-1, BW 196, NERICA 1, NERICA 4, NERICA 10, and NERICA 11 showing some disease resistance. Varieties ITA 310 and Duorado Precoce were moderately tolerant to rice blast. This information is being used to develop a durable blast resistance strategy in sub-Saharan Africa.

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Einleitung Streptococcus (S.) suis verursacht bei Schweinen unter anderem Meningitis, Arthritis, Serositis und Endokarditis und ist eine der größten Herausforderungen für die Schweineindustrie. Von 29 beschriebenen Serotypen sind die Serotypen 2, 7 und 9 unter invasiven Isolaten weltweit besonders prävalent, vor allem in Europa. Bis heute gibt es keinen zugelassenen Impfstoff zur Prävention von S. suis-Erkrankungen in Europa, daher ist im Feld die Anwendung stallspezifischer Impfstoffe verbreitet. Diese bieten jedoch höchstens homologen Schutz und ihre Wirkung kann durch prädisponierende Faktoren wie eine Infektion mit dem porcine reproductive and respiratory syndrome Virus (PRRSV) beeinträchtigt werden. Daher hat sich die Forschung auf Antigene fokussiert, die potentiell heterologen Schutz vermitteln. Zielstellung Ziele der Studie waren die Charakterisierung vernachlässigter invasiver S. suis Pathotypen der wichtigen Serotypen 7 und 9 und die Etablierung neuer Infektionsmodelle im Schwein. Des Weiteren sollte die immunogene und protektive Wirkung des Immunoglobulin (Ig) M-degradierenden Enzyms von S. suis, IdeSsuis, im Serotyp 9 Infektionsversuch untersucht werden. Material und Methoden In dieser Arbeit wurden in vitro Versuche und experimentelle Infektionen im Schwein durchgeführt. Dazu gehörte die Geno- und Phänotypisierung von 22 S. suis Serotyp 7 Stämmen und vier Serotyp 9 Stämmen. Die Genotypisierung erfolgte mittels multiplex (MP) Polymerase-Kettenreaktion (PCR), einer PCR zur Differenzierung verschiedener Genvarianten des muramidase-release protein (MRP) sowie mittels multilocus sequence typing (MLST). Zur Phänotypisierung der S. suis Stämme wurden bactericidal assays eingesetzt, die als Bakteriämiemodell fungierten. Auf diese Weise konnten die Empfänglichkeit gegenüber S. suis Stämmen sowie deren Virulenz beurteilt werden. Durch Zugabe von rekombinantem (r) IdeSsuis wurde die Rolle adaptiven IgMs in der Begrenzung der Bakteriämie untersucht. Anhand von Western Blot Analysen erfolgte die Untersuchung der Expression und Funktionalität von IdeSsuis sowie die Expression von MRP in S. suis Serotyp 7 Stämmen. Enzyme-linked immunosorbent assays (ELISA) kamen zum Einsatz, um die Entwicklung von IgM und IgG Spiegeln in Ferkeln im zeitlichen Verlauf und die IgG Spiegel nach rIdeSsuis Immunisierung zu messen. Durch rIdeSsuis Immunisierung induzierte Antigen-spezifische T-Helferzellen (Th-Zellen) wurden mithilfe der Durchflusszytometrie untersucht. Schließlich erfolgte die Durchführung zweier S. suis Serotyp 7 Etablierungsversuche mit je 18 bzw. 5 Ferkeln sowie zwei S. suis Serotyp 9 Impf- und Infektionsversuche mit je 18 Ferkeln. Sektionsproben wurden histologisch untersucht. In einem Fall wurde eine Endokarditis mittels fluorescence in situ hybridization (FISH) charakterisiert. Ergebnisse Die meisten untersuchten Serotyp 7 Stämme gehörten dem Sequenztyp (ST) 29 an, einem emerging pathotype in Europa. Trotz der engen phylogenetischen Verwandtschaft, war mrp in den Stämmen sehr variabel. Phänotypisch bildeten alle Stämme gleichermaßen eine kleine MRP Variante, MRPs. Für vier ausgewählte Serotyp 7 Stämme wurde die Expression von IdeSsuis gezeigt, jedoch mit Unterschieden in Größe und Funktionalität. Bactericidal assays dieser vier Stämme zeigten starke Proliferation im Blut von Absatzferkeln, aber Abtöten im Blut von Läuferschweinen aus zwei Herden mit unterschiedlichem S. suis Status. Dieses Überlebensmuster unterschied sich deutlich von dem eines Serotyp 9 Stammes. Durch Zugabe von rIdeSsuis, konnte gezeigt werden, dass das Abtöten der Serotyp 7 Stämme im Blut von Läuferschweinen des infizierten Bestandes IgM-vermittelt war. Unabhängig von der Herkunft entwickelten sich die IgM Spiegel in den Ferkeln im zeitlichen Verlauf fast synchron. Schließlich konnte die Virulenz eines Serotyp 7 Stammes in einem intravenösen Infektionsversuch mit 5 Ferkeln gezeigt werden. Alle Tiere entwickelten schwere Symptome einer S. suis Erkrankung. In einem Impf- und Infektionsversuch mit einem hoch virulenten Serotyp 9 Stamm wurde die immunogene und protektive Wirkung einer rIdeSsuis Immunisierung untersucht. Neun Ferkel wurden mit rIdeSsuis oder einem Placebo prime-boost-boost immunisiert und zwei Wochen später infiziert. Neunzig Prozent der Placebotiere entwickelten schwere Symptome einer S. suis Erkrankung und starben oder mussten aus Tierschutzgründen euthanasiert werden. Alle geimpften Tiere überlebten den Versuch, fielen jedoch mit Fieber und Lahmheiten auf. Es konnte also gezeigt werden, dass eine rIdeSsuis Immunisierung vor Mortalität, nicht aber Morbidität durch den Infektionsstamm schützt. Alle immunisierten Ferkel serokonvertierten und Antigen-spezifische Th-Zellen wurden nachgewiesen. Weder die IgG Antwort noch die Th-Zell Antwort wurde jedoch durch die Infektion verstärkt. In einem weiteren Impf- und Infektionsversuch mit einem anderen Serotyp 9 Stamm fiel ein Tier am 11. Tag nach der Infektion mit Zeichen einer akuten Leptomeningitis auf, nachdem es zuvor klinisch völlig unauffällig war. In der Sektion des Tieres wurde eine Endokarditis der Mitralklappe diagnostiziert, die mit Biofilm-Bildung assoziiert war, was mithilfe von Histologie und FISH gezeigt werden konnte. Zusätzlich wurde eine fibrinopurulente Leptomeningitis diagnostiziert. Das Ferkel hatte Antikörper gegen rIdeSsuis und tötete den Infektionsstamm ex vivo im Blut ab. Schlussfolgerungen In dieser Arbeit habe ich zwei wichtige S. suis Pathotypen charakterisiert: S. suis Serotyp 7 Stämme des ST29 und einen hoch virulenten Serotyp 9 Stamm vom ST94. Die Serotyp 7 Stämme stellten einen besonderen Pathotypen dar, bei dessen Bekämpfung IgM eine wichtige Rolle spielt. Bei einer Serotyp 9 Infektion konnten trotz des Abtötens der Bakterien im Blut und opsonisierender Antikörper Biofilmbildung und eine folgende akute Leptomeningitis nicht verhindert werden. Letztlich wurde Schutz vor einem hoch virulenten Serotyp 9 Stamm durch rIdeSsuis Immunisierung und damit zum ersten Mal für ein Antigen Protektion vor den wichtigen Serotypen 2 und 9 aufgezeigt. Dies ist ein vielversprechendes Ergebnis hinsichtlich der Entwicklung eines Impfstoffes gegen S. suis. / Introduction Streptococcus (S.) suis causes meningitis, arthritis, serositis and endocarditis and is one of the biggest challenges for the swine industry. Of 29 described serotypes, the serotypes 2, 7 and 9 are highly prevalent amongst invasive S. suis isolates worldwide, especially in European countries. To date, no commercially produced vaccine is available in Europe for prevention of S. suis disease, thus the use of autogenous vaccines in the field is common. However, bacterins may at most confer homologous protection and their efficacy may be influenced by predisposing factors such as an infection with the porcine reproductive and respiratory syndrome virus (PRRSV). Research has therefore focused on subunit vaccines with the potential to elicit cross-protection against various serotypes. Aim of the study The objective of this study was to characterize neglected invasive S. suis pathotypes of the important serotypes 7 and 9 and to establish infection models in the main host of S. suis, the pig. A further aim was to investigate immunogenicities and protective efficacies of the immunoglobulin (Ig) M-degrading enzyme of S. suis, IdeSsuis, in a serotype 9 challenge experiment. Materials and methods In vitro experiments and experimental challenges in swine were conducted as part of this thesis. This included the geno- and phenotyping of 22 S. suis serotype 7 strains and four serotype 9 strains. Genotyping was conducted using a multiplex (MP) polymerase chain reaction (PCR), a PCR for differentiation of variants of the muramidase-released protein (MRP) gene and multilocus sequence typing (MLST). For phenotyping of the S. suis strains, bactericidal assays were carried out which served as a model for bacteraemia. This way, susceptibility to S. suis strains and virulence of different strains was assessed. Further, through addition of recombinant (r) IdeSsuis, the role of adaptive IgM in limiting bacteraemia was elucidated. Western blot analyses were conducted to investigate expression and functionality of IdeSsuis as well as expression of MRP in S. suis serotype 7 strains. Enzyme-linked immunosorbent assays (ELISA) were used to determine the development of IgM and IgG levels in piglets over time and to assess IgG levels following rIdeSsuis immunization. Antigen-reactive T-helper (h) cells induced by rIdeSsuis immunization were investigated using flow cytometry. Finally, two experiments to establish a serotype 7 infection model with 18 and 5 piglets each and two vaccination and challenge experiments using different S. suis serotype 9 strains (n=18 piglets/ experiment) were conducted. Samples of dissected animals were examined histologically. In one case, an endocarditis was analysed using fluorescence in situ hybridization (FISH). Results Most of the investigated serotype 7 strains belonged to sequence type (ST) 29 which was thus shown to be an emerging pathotype in Europe. Despite the close phylogenetic relation of the strains, mrp was highly variable. Phenotypically, all strains expressed a small variant of MRP, MRPs. Four selected serotype 7 strains were shown to express IdeSsuis with differences in size and functionality. Bactericidal assays of these four strains revealed high proliferation in blood of weaning piglets but killing in blood of growing piglets of two herds which differed in their S. suis infection status. This survival pattern was distinct from a serotype 9 strain. Addition of rIdeSsuis revealed that killing of the serotype 7 strains in blood of growing piglets of the infected herd was IgM-mediated. Independent of the originating herd, IgM levels of the piglets rose almost synchronous over time. Finally, the virulence of a serotype 7 strain was proven in an intravenous challenge experiment with five pigs which all developed severe clinical signs of S. suis disease. In a vaccination and challenge experiment using a highly virulent serotype 9 strain, immunogenicities and protective efficacies of rIdeSsuis immunization were investigated. Nine piglets were prime-boost-boost vaccinated with rIdeSsuis or placebo-treated and challenged two weeks later. Ninety per cent of the placebo-treated piglets developed severe clinical signs of S. suis disease and died or had to be euthanized due to animal welfare reasons. All vaccinated piglets survived the experiment, however elevated body temperatures and lameness were also noted in this group. Accordingly, rIdeSsuis vaccination protected from mortality but not morbidity caused by the challenge strain. Seroconversion of the immunized piglets and antigen-reactive Th cells were detected. Neither the IgG response nor the Th cell response was boosted through the challenge. In a further vaccination and challenge experiment with a different serotype 9 strain, one animal was clinically unobtrusive following infection and then developed an acute leptomeningitis on the 11th day post infection and had to be euthanized. Dissection of the animal revealed an endocarditis on the mitral valve which was proven to be associated with biofilm formation by histology and FISH. In addition, a fibrinosuppurative leptomeningitis was diagnosed. The piglet had specific antibodies against rIdeSsuis and mediated killing of the challenge strain in a bactericidal assay. Conclusions In this thesis, I characterized two important pathotypes: S. suis serotype 7 strains of ST29 and a highly virulent serotype 9 strain of ST94. The serotype 7 strains represent a distinct pathotype and IgM plays a significant role in their control. Following a serotype 9 infection, biofilm formation and a subsequent acute leptomeningitis could not be prevented despite blood bactericidal activity and opsonizing antibodies. Finally, protection against challenge with a highly virulent serotype 9 strain through rIdeSsuis immunization was demonstrated. Thereby, for the first time an antigen was shown to confer cross-protection against the important serotypes 2 and 9, which is highly encouraging regarding the development of a vaccine against S. suis.