Antimicrobial drugs constitute a fundamental part of modern medicine. The global rise in antimicrobial resistance poses a major threat to global health. Optimising antimicrobial treatment... Show moreAntimicrobial drugs constitute a fundamental part of modern medicine. The global rise in antimicrobial resistance poses a major threat to global health. Optimising antimicrobial treatment strategies in patients offers an important direction to address this challenge. In this thesis, we describe how quantitative characterisation of the drug, the pathogen, and the patients, and how these three factors interact, can help to achieve this goal. To this end, we used a combination of state-of-the-art in silico model-based approaches to analyse and integrate experimental data from in vitro models, and clinical data from healthy volunteers and patients. We developed models describing infection site drug exposure, antimicrobial resistance evolution, and host response biomarker dynamics. We explored the impact of infection on pulmonary pharmacokinetics, evolutionary-based treatment strategies, and the utility host response biomarker for treatment monitoring. The work in this thesis builds towards developing novel strategies to optimise antimicrobial treatments and showcases the importance on interdisciplinary collaborations. Show less
The research described in this thesis has, using the zebrafish as a model system, shed new light on the intricate relationship between TB and DM2, in particular on the role of leptin, SHP-1 and... Show moreThe research described in this thesis has, using the zebrafish as a model system, shed new light on the intricate relationship between TB and DM2, in particular on the role of leptin, SHP-1 and glucocorticoids.Leptin plays an important role during TB infection and has a huge impact on insulin sensitivity in zebrafish larvae. Similarly to what has been observed in the murine model, leptin deficiency in zebrafish increased the bacterial burden and mortality during the infection, leading to hyperglycemia and the development of insulin resistance. In addition, a novel SHP-1/SHP-2 inhibitor, NSC-87877, was shown to represent a promising anti-diabetic drug that can be used for further DM2 research, as it is able to rescue the phenotype of the leptin-deficient zebrafish and to restore glucose transport to the tissues. In contrast to metformin, NSC-87877 can act at very early developmental stages and inhibits the function of SHP-1 and factors that underlay impaired glucose metabolism, whereas metformin is mostly known to improve insulin sensitivity. Additionally, treatment with the glucocorticoid beclomethasone attenuates the metabolic changes associated with the infection, and transcriptional alterations induced by beclomethasone treatment suggest that genes involved in glucose metabolism, insulin and leptin signaling all play an important role in the modulation of the metabolism.Our data show that zebrafish larvae represent an interesting model system to investigate the complex pathology of TB, and the studies described in this thesis in which this model has been used have provided novel insights into the molecular mechanisms underlying wasting syndrome and the possibilities for adjunctive glucocorticoid therapy to alleviate this metabolic state. Show less
Upon infection or vaccination, naïve CD8+ T cells clonally expand and differentiate into antigen-specific effector cell populations, which turn into phenotypically diverse memory CD8+ T cell... Show moreUpon infection or vaccination, naïve CD8+ T cells clonally expand and differentiate into antigen-specific effector cell populations, which turn into phenotypically diverse memory CD8+ T cell subsets that differ in their cytokine polyfunctionality, cytolytic capacity and homing properties. The circulating memory CD8+ T cell pool can be largely classified in two major subsets: effector memory T (TEM) and central memory T (TCM) cells. Contrary to the classical view that lymphocytes continuously recirculate, tissue-resident memory T (TRM) cells have been discovered as cells with the unique ability to reside in tissues with limited recirculation through the blood. Antigen-specific CD8+ TRM cells are induced upon antigen encounter and localize to many different tissues, including barrier tissues, where they play a crucial role in protection against infectious and malignant disease. Within these major circulating and resident T cell subsets a variety of phenotypes and functions exists. However, the development of the heterogeneous populations of memory T cells is not fully understood. In this thesis we dissect the development and heterogeneity of antigen-specific circulating and tissue-resident CD8+ T cells upon vaccination and infection, study their protective capacity in infectious and malignant disease and use this information to improve vaccination and immunotherapeutic strategies. Show less
Preface: The content of this thesis is based on research that was conducted at the travel and vaccination clinic at Leiden University Medical Centre (LUMC). This clinic provides pre-travel care to... Show morePreface: The content of this thesis is based on research that was conducted at the travel and vaccination clinic at Leiden University Medical Centre (LUMC). This clinic provides pre-travel care to the general population, and to special groups of travellers, such as patients who use immunosuppressants or who have chronic diseases. The clinic is closely connected to the department of Infectious Diseases at LUMC. The setting of a travel clinic within an academic medical hospital, provides unique circumstances for medical research, like an experienced team of nurses, expertise regarding immunization, a constant flux of travellers and the knowledge and infrastructure that is required for research into microbiology, virology and parasitology. Examples of research that stem from this clinic are projects on immunization against malaria, yellow fever, travellers' diarrhea, poliomyelitis and hepatitis B, vaccination of immunocompromised patients, and projects on travel related acquisition of extended spectrum ß-lactamase producing Enterobacteriacae and on the utility of post-travel screening of asymptomatic travellers for parasites. Show less
Until a few years ago, only two human polyomaviruses (JC and BK) were known to infect humans and cause severe illness in immunocompromised hosts. Since 2007, at least eleven new polyomaviruses... Show moreUntil a few years ago, only two human polyomaviruses (JC and BK) were known to infect humans and cause severe illness in immunocompromised hosts. Since 2007, at least eleven new polyomaviruses became known that infect humans. Among them is the polyomavirus associated with trichodysplasia spinulosa (TSPyV). In Chapter 1 of this dissertation, the main focus is on the recent developments in studying the newly identified human polyomaviruses until mid-2014. This introductory chapter sets the stage for further investigation into TSPyV infection, pathogenesis, evolution and host adaptation, which is detailed in Chapter 2. To study causality between TSPyV infection and TS disease, in Chapter 3, the prevalence, load and localization of this virus is described. In Chapter 4, the cellular mechanisms behind disruption of cellular proliferation and TS spicule formation by TSPyV Large T-antigen is investigated. By In-silico analysis, in Chapter 5, the identification of a polyomavirus evolution and adaptation mechanism called COCO-VA is highlighted. Subsequently, in Chapter 6, TSPyV genome sequences are tested to gain more insight into this COCO-VA mechanism. Finally, in Chapter 7, the findings described in this dissertation are discussed with regard to several TSPyV aspects, and compared to existing knowledge about polyomaviruses in a broader context. Show less
Insects are the most diverse group of animals on earth. They inhabit nearly all terrestrial habitats. One of the factors underlying this success is the ability of insect eggs to survive in adverse... Show moreInsects are the most diverse group of animals on earth. They inhabit nearly all terrestrial habitats. One of the factors underlying this success is the ability of insect eggs to survive in adverse conditions. For a long time the ability to survive these adverse conditions has been attributed to maternal investment in the form of a protective eggshell. In this thesis, I show that contrary to common belief, insect eggs are far from helpless. The insect egg itself develops a cellular layer around the egg called the serosa. This serosa protects the developing embryo from dehydration which enables it to survive in dry habitats. The serosa furthermore protects against infection, mounting an impressive immune response upon the entry of bacteria in the egg. The data presented in this thesis show the importance of the serosa in the survival of the insect egg. I propose that this multifunctional serosa contributed to the great success of insects. Show less
This thesis is focused on the innate immune defence mechanisms responsible for controlling mycobacterial growth after infection. To provide a detailed description of the host__s innate immune... Show moreThis thesis is focused on the innate immune defence mechanisms responsible for controlling mycobacterial growth after infection. To provide a detailed description of the host__s innate immune response to M. marinum infection, zebrafish gene expression levels were analysed by RNA sequencing at various time points during infection and correlated with imaging data of the process of pathogenesis. We demonstrate that the scavenger receptor Marco (macrophage receptor with collagenous structure) is a key player in the rapid phagocytosis of M. marinum and we use gene expression analysis in combination with gene knockdown studies to show that it is also essential in the establishment of an initial transient pro-inflammatory response to M. marinum infection. Once phagocytosed, M. marinum is capable of avoiding killing mechanisms of the host cell and can continue to grow within macrophages. This is the period when Membrane Attack Complex/Perforin proteins are involved in killing intracellular bacteria by their pore-forming activities. We reveal the regulatory mechanisms and function of two macrophage specific genes, mpeg1 and mpeg1.2 (macrophage expressed gene 1.2). The results from this thesis complement knowledge obtained from other model organisms by providing new insights into both counteracting and supporting mechanisms underlying the innate immune response. Show less
The work presented in this thesis has provided new insights into the mechanisms involved in the regulation of innate immune responses in zebrafish embryos. Furthermore, cell-specific transcriptome... Show moreThe work presented in this thesis has provided new insights into the mechanisms involved in the regulation of innate immune responses in zebrafish embryos. Furthermore, cell-specific transcriptome profiling studies identified novel marker genes for distinguishing immune cell types, which is highly useful information to fulfill the demand for new fluorescent reporter lines and lineage-specific antibodies in the zebrafish model. We have shown that Ptpn6, a protein tyrosine phosphatase homolog of human SHP1, functions as a critical negative regulator, required for a properly balanced innate immune response and for controlling infections with bacterial pathogens. In Salmonella typhimurium infection, ptpn6 deficiency caused a general hyperinduction of pro-inflammatory genes, which was contraproductive as it impaired the infection control. In Mycobacterium marinum infection, a more specific effect of ptpn6 deficiency on matrix metalloproteinase gene expression was found as a major underlying cause of increased bacterial burden. We further concluded that Ptpn6 functions as a much stronger negative regulator than infection-inducible miRNAs of the miR-146 family, which may be involved in more subtle fine-tuning of the innate immune response. Knowledge about the distinct roles of Ptpn6 and miR-146 miRNAs has practical applicability in regard to their potential as therapeutic targets for inflammatory diseases and cancer. Show less
In a world where bacterial infections are becoming harder and harder to fight due to rising antibiotic resistance, disease models that allow high throughput screening are needed more than ever. An... Show moreIn a world where bacterial infections are becoming harder and harder to fight due to rising antibiotic resistance, disease models that allow high throughput screening are needed more than ever. An ideal model organism for high throughput screening is the zebrafish embryo. However, models for high throughput screening of infection are still wanted. In this thesis the fish pathogen Edwardsiella tarda was tested for use in high throughput studies of infectious disease in zebrafish. First the genome of Edwardsiella tarda was sequenced to determine the virulence factors of this bacterium. Next different types of exposure of zebrafish to Edwardsiella tarda were tested. This showed an absence of detectable infection after static immersion, but a reproducible infection on the level of single embryos after caudal vein injection. Finally, using the caudal vein injection method, the zebrafish knock-out mutant in the gene Myd88 was characterized. This is the first zebrafish knock-out mutant in a gene central in the innate immune system. Show less
Following antigen encounter, activated T cells can give rise to functionally distinct T cell subsets. Understanding how different T cell subsets arise requires technologies that can monitor the... Show moreFollowing antigen encounter, activated T cells can give rise to functionally distinct T cell subsets. Understanding how different T cell subsets arise requires technologies that can monitor the developmental potential of single precursor cells (chapter 2). This thesis describes the development and use of two novel genetic tagging strategies aimed at following cell differentiation in vivo. These strategies are based on the marking of precursor cells with unique DNA sequences (barcodes), following which cell fate is analyzed by barcode comparison of different daughter populations. The first technology, termed cellular barcoding, makes use of a retroviral barcode library to provide T cells with unique genetic tags via in vitro transduction. Cellular barcoding was used to analyze the kinship of diverse T cell populations (chapter 3-5) as well as to measure the clonality of antigen-specific T cell responses under varying conditions of infection (chapter 6). The second technology, termed in vivo barcoding, makes use of a transgenic mouse model in which unique DNA sequences are introduced via inducible VDJ recombination. The feasibility of in vivo barcoding was demonstrated by conditionally labeling lung and liver cells with different barcodes (chapter 7). Together, these studies have yielded important new insights for vaccine optimization. Show less
In the last decade the study of the innate immune system has gained renewed scientific momentum as a result of the discovery of essential receptor families, such as the Toll-like receptor (TLR)... Show moreIn the last decade the study of the innate immune system has gained renewed scientific momentum as a result of the discovery of essential receptor families, such as the Toll-like receptor (TLR) family, that are required for pathogen recognition. These receptors detect specific molecular structures of microorganisms and in turn are able to trigger host immune responses. The work described in this thesis focuses on the use of the zebrafish embryo as a model to study the vertebrate immune system in order to gain new insights into the mechanisms of innate immune defence against bacterial infections and TLR signalling. Making use of a Salmonella infection model in combination with microarray technology and gene knock-down studies we were able to thoroughly characterize the embryonic host transcriptome response to a bacterial infection. Furthermore, we have demonstrated important functions for key signalling molecules in the innate immune response, including Tlr5, MyD88 and Traf6 and discovered new downstream targets of the TLR signalling pathway. The data presented here will enable in-depth functional follow-up studies that will provide new insights into the mechanisms of innate immune defence systems. This, in combination with future applications of zebrafish embryo infection models in high-throughput compound screens, holds much promise for the discovery of novel anti-microbial and anti-inflammatory drugs. Show less
Congenital Human Parvovirus B19 (B19V) infection can lead to life threatening fetal complications as hydrops, fetal demise or severe fetal anaemia and thrombocytopenia. Maternal symptoms frequently... Show moreCongenital Human Parvovirus B19 (B19V) infection can lead to life threatening fetal complications as hydrops, fetal demise or severe fetal anaemia and thrombocytopenia. Maternal symptoms frequently pass unnoticed at the time of maternal infection and there was little information on the mechanism and time course of vertical transmission of B19V during gestation. Treatment consists of intrauterine fetal red blood cell and/ or platelet transfusion (IUT). The indication for treatment with IUT is set by performing fetal ultrasound screening for fetal anaemia and signs of fetal hydrops. The fetal middle cerebral artery peak systolic flow correlates well with the severity of fetal anaemia. The first two chapters of this thesis give an overview of the existing literature concerning fetal hydrops and congenital B19V infection. In the ensuing chapters we describe the course of maternal and fetal B19V infection by the B19V viral load and maternal immune response. We did not find a correlation between the fetal or maternal B19V viral load and the severity of fetal anaemia or thrombocytopenia. Thrombocytopenia is frequently encountered in congenital B19V infection, but fetal bleeding complications are not. The use of fetal platelet transfusion is therefore a matter of debate. The long- term neurodevelopment of affected fetus can be significantly delayed at a later age despite a technically correct IUT procedure. The possibility of cerebral damage due to congenital B19V infection is discussed. Parents should be counselled of these risks before the IUT procedure and long term follow -up following congenital B19V infection is advised Show less
T cells recognize pathogen-derived antigens and are crucial for fighting pathogens such as viruses and bacteria. In addition, T cells are able to recognize and attack certain types of tumors, in... Show moreT cells recognize pathogen-derived antigens and are crucial for fighting pathogens such as viruses and bacteria. In addition, T cells are able to recognize and attack certain types of tumors, in particular virally induced tumors. In this thesis we aimed 1) to obtain more insight into antigen-specific T cell responses and 2) to study how antigen-specific T cell responses can be improved. For the first aim we generated new tools that by enabling the visualization of antigen-specific CD4+ and CD8+ T cells allow the study of the dynamics of antigen-specific T cell responses in time throughout an ongoing immune response (chapter 2). In addition, we developed a novel technique that enables the study of family relationships between different T cell populations. This technique for instance allows us to determine whether two different types of effector T cell populations arise from the same or different pool(s) of na_ve T cells (chapter 5). For the second aim, we analyzed whether antigen-specific T cell responses can be manipulated by providing increased costimulation in the form of constitutive triggering of CD27 (chapter 3) or by generating CD4+ T cells that are modified by the introduction of MHC class I restricted TCRs (chapter 4). Show less
Venous thrombosis is a well-known complication of central vein catheters (CVCs), which may cause serious morbidity and may result in potentially lethal complications such as pulmonary embolism. In... Show moreVenous thrombosis is a well-known complication of central vein catheters (CVCs), which may cause serious morbidity and may result in potentially lethal complications such as pulmonary embolism. In this thesis the general risk of CVC related thrombosis has been assessed, i.e., what is the overall risk of developing CVC related thrombosis? Which patients are prone to develop thrombosis with its associated morbidity? Are we able to predict this risk by routine surveillance in "high-risk" patients? Better knowledge of the incidence of CVC related thrombosis and identification of high-risk groups will assist clinicians in decision making about CVC use in the various patient-groups and in whom anticoagulant prophylaxis may be warranted. In summary, the a priori determination of common inherited and acquired risk factors may form a basis to guide (prophylactic) treatment decisions. Vulnerable patients may benefit the most, i.e. those who have a high risk of clinically manifest thrombosis, and who are at risk of hemorrhage, such as patients who undergo intensive chemotherapy. Besides, surveillance of these patients with screening by ultrasound, or alternatively surveillances cultures, may be useful to identify patients at high or low risk for clinically manifest CVC related thrombosis, and focused early intervention may be initiated. Show less
