A research report submitted to the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg in partial fulfillment of the requirements for the degree of Master of Science in Nursing Johannesburg, 2017 / The Hajj is widely recognized as the world’s largest and globally most diverse kind of mass gathering. This annual five day gathering takes place in the city of Mecca and includes between 2.5 and 3.5 million participants. This poses a great concern by the organizers as the risk for the spread of infectious disease due to overcrowding is greatly increased. These diseases are increasingly being recognized as a potential threat to both local and international public health systems. The lack of understanding of the infectious diseases that originate and disseminate during the Hajj was raised in the Jeddah declaration. Furthermore, despite the protective measures put in place, poor health practices from selective use of the measures by the participants contributes to the increased risks. Exploring the health information needs of the pilgrims attending Hajj, would help in knowing what is required to reduce poor health practices and simplify and improve compliance with protective measures against infectious diseases before, during and after Hajj, and this will help in minimising the spread of infectious diseases in the Hajj. The aim of this study was to explore the health information needs of the pilgrims attending Hajj in order to know what was required to reduce poor health practices and simplify and improve compliance with protective measures against infectious diseases before, during and after Hajj, and this would help in minimizing the spread of infectious diseases in the Hajj. In this study, a qualitative research design was used and focus group discussion using semi-structured questions was conducted. The members were purposely recruited and divided into four groups, two groups of males and two of females. The division of participants into focus groups was in part done in compliance with the Muslim beliefs. Data were collected using a focus group discussion with semistructured questions that was recorded using a tape recorder. These discussions were transcribed verbatim before being analyzed using thematic analysis. The findings of the study showed that pilgrims need a holistic health educational program that addresses their experiences of illnesses and chosen format as educational pamphlets are no longer effective. The findings also revealed that collaboration, surveillance and screening of pilgrims for diseases prior to departure are useful as they help in spreading messages of health and diseases issues with simplicity and yield effective result as well as identifying those at risk of contracting infectious diseases, spreading infectious diseases and exacerbating their diseased conditions. The study recommends the use of digital technology such as an app for phone to send health information to participants and promptly identify and manage individuals who develop illness during mass gathering events like Hajj. It also recommends the incorporation of mass gathering medicine into the curriculum of Nursing program in order to effectively train and equip nurses with better preparation measures against infectious diseases during mass gatherings like Hajj / MT 2019

Cytomegalovirus (CMV) is the most common congenitally acquired infection. It is of major concern due to the long-term neurodevelopmental morbidity in both symptomatic and asymptomatic newborns. While CMV infection is less commonly diagnosed in infancy to adulthood, mostly due to its asymptomatic presentation, it is still an important differential to consider. A missed diagnosis could lead to visual impairments and neurological complications. Infants can acquire CMV by encountering bodily secretions from those who have an active infection. Symptoms of infection include fever, fatigue, pharyngitis, and hepatitis. Laboratory abnormalities include thrombocytopenia, elevated transaminases, and abnormal lymphocyte count. We investigated a clinical case of a previously healthy 5-month-old whose only symptoms were petechial rash and thrombocytopenia. They presented to the ED with a worsening petechial rash for 11 days. The patient’s mother had prenatal care and an uncomplicated pregnancy. In the ED IgM for CMV was positive and platelet count on admission was 35K. The patient was discharged without intervention because platelet count remained above 20K. Outpatient hematology workup ruled out other potential causes of thrombocytopenia. There is no family history of bleeding disorders. The patient was prescribed valganciclovir for 2 months and urine CMV PCR was ordered for the patient and the patient’s mother. The patient’s urine CMV was positive, but the mother’s urine CMV was negative. The patient’s petechiae and thrombocytopenia improved while on valganciclovir treatment. In this case, since the patient’s mother was negative for CMV, it is unlikely that the infection was maternally acquired. Our case illustrates that CMV infection in infancy can be acquired through horizontal transmission and its only presentation can be thrombocytopenia. Since the CMV infection was diagnosed early the patient did not have any neurological symptoms, such as sensorineural hearing loss or delayed developmental milestones.

<b>Background</b>: The world is at risk of epidemics of novel and reemerging infectious diseases. These may be national, regional or international as in the case of Nipah, African Viral Haemorrhagic Fevers, SARS and H1N1 respectively. It is crucial that public health and clinical research is conducted in such epidemics. Yet the conduct of heath research during rapidly evolving epidemics or disasters represents an enormous challenge. In addition to the large number of practical challenges to undertaking such research there are also major ethical issues to consider. However, there is very little understanding of these ethical issues and very little empirical evidence of the views of patients, their families, society and key stakeholders. <b>Objective</b>: To collect and analyse data on ethical considerations arising in the setting of research on rapidly evolving epidemics posed by the urgent and unpredictable nature of epidemics. <b>Design</b>: The study was conducted in Oxford University Clinical Research Unit (OUCRU), Viet Nam and 3 other hospitals in Viet Nam with experience of epidemics. Data were collected by semi-structured interviews with key stakeholders representing research staff, IRB members, patients/family members and study sponsors/funders who have participated in or reviewed research projects on infectious diseases including SARS, H5N1, H1N1, dengue and Hand, Foot, Mouth disease. <b>Result</b>: A total of 64 interviews with all key stakeholders were conducted. Analysis of the ethical problems/challenges discussed in the interviews led to the identification of three themes 1) International research collaboration, 2) IRB review and 3) Consent. These tended to arise at three levels of relationship: macro (between institutions internationally), meso (within and between institutions nationally) and micro (within institutions and between health professionals and patients). <b>Conclusion</b>: The issues and types of considerations and their relative importance were raised and/or valued differently by the members of different key stakeholder groups due to their role and experience in research participation. Some of the issues raised also related to health research in other settings. However, many were unique to the setting of rapidly evolving epidemics. Addressing these issues is crucial for successful and appropriate research in the context of epidemics. It is inevitable that epidemics of emerging and reemerging infectious diseases will occur in the future and there is a clear need to undertake crucial scientific research in such settings. It is therefore imperative that we understand the challenges and ethical issues surrounding such research. It is desirable that further research into the ethical challenges identified in this thesis takes place in the inter-epidemic period in order to better prepare for the next epidemic.

This thesis is about analyzing genetic differences among isolates of Francisella tularensis – the tularemia-causing bacterium. To elucidate how these bacterial isolates are related, and their geographical and genetic origins, I have developed typing assays for Francisella and used them to study the epidemiology of tularemia. Tularemia is an infectious disease of humans and other mammals found throughout the Northern Hemisphere. The severity of the disease depends on the type of F. tularensis causing the infection. In Sweden, as in other countries of Europe and Eurasia, tularemia is caused by F. tularensis subsp. holarctica, while other varieties of the bacterium occur in Middle Asia and North America. It is important to identify a tularemia infection promptly in order to initiate the correct antibiotic treatment. A rapid identification of the causative F. tularensis variety gives additional clinical information. In recent years, several genomes of various Francisella strains have been sequenced, and in this thesis, I have utilized these genomes to identify genetic markers. In studies reported in the first paper (I) appended to the thesis, we identified and analyzed insertion/deletion mutations (INDELs) inferred to have resulted from a sequence repeat-mediated excision mechanism. We found eight new Regions of Difference (RDs) among Francisella strains. Using RDs together with single nucleotide polymorphisms (SNPs), we were able to predict an evolutionary scenario for F. tularensis in which Francisella novicida was the oldest variety while F. tularensis subsp. holarctica was the youngest. We also found that all virulence-attenuated isolates analyzed had deletions at two specific genetic regions - denoted RD18 and RD19 – suggesting that repeat-mediated excision is a mechanism of attenuation in F. tularensis. In subsequent studies (presented in paper II), we developed a combined analysis of INDELs lacking flanking repeats and variable number of tandem repeats (VNTRs). Both markers could be assayed using the same analytical equipment. The inclusion of INDELs provided increased phylogenetic robustness compared with the use of VNTRs alone, while still maintaining a high level of genetic resolution. In analyses described in the next paper (III), we selected INDELs from paper (II) and discovered novel SNPs by DNA comparisons of multiple Francisella strains. Thirty-four phylogenetically informative genetic markers were included in a hierarchical real-time PCR array for rapid and robust characterization of Francisella. We successfully used the assay to genotype 14 F. tularensis isolates from tularemia patients and DNA in six clinical ulcer specimens. Finally, in paper (IV) we demonstrated a strategy to enhance epidemiological investigations of tularemia by combining GIS-mapping of disease-transmission place collected from patient interviews, with high-resolution genotyping of F. tularensis subsp. holarctica isolates recovered from tularemia patients. We found the geographic distributions of specific F. tularensis subsp. holarctica sub-populations to be highly localized during outbreaks (infections by some genotypes being restricted to areas as small as 2 km2), indicative of a landscape epidemiology of tularemia with distinct point sources of infection. In conclusion, the results acquired during the studies underlying this thesis contribute to our understanding of the genetic genealogy of tularemia at both global and local outbreak scales.

No description available.

New and emerging diseases in human and animal populations appear to be predominately associated with generalist pathogens that are able to infect multiple hosts. Carnivores are susceptible to a wide range of these pathogens and can act as effective samplers of their vertebrate prey, which are important reservoirs of many emerging diseases. This thesis evaluates the utility of carnivores as sentinels for pathogens present in their prey by exploration of four selected pathogen-prey-sentinel combinations in three rural study sites of varying habitat in northern England and Scotland over a twenty-two month period (2007-2009). Selected pathogens were Coxiella burnetii, Leptospira spp., Encephalitozoon cuniculi, and rabbit haemorrhagic disease virus (RHDV), selected prey species were wild rodents and rabbits, and selected carnivores were foxes, domestic cats and corvids. Seroprevalence to C.burnetii, Leptospira spp and E.cuniculi was assessed using adapted or novel test methodologies to enable their use for multiple mammalian species, however these were not applicable to corvids. RHDV seroprevalence was not assessed due to low acquisition of rabbit samples. Overall, seroprevalence to all three pathogens was significantly higher in predators than prey, at 24.2% and 12.4 % for C.burnetii, 22.73% and 1.95% for Leptospira spp and 39.06% and 5.31% for E.cuniculi in predator and prey species respectively. A similar pattern was found in all study areas and was consistent irrespective of individual prey or predator species, although serological evidence of exposure to E.cuniculi was not detected in domestic cats in any area. A semi-quantitative assessment of the time and financial costs of the study approach and application to hypothetical examples indicates that sampling carnivores is a much more costeffective approach to pathogen detection than sampling prey. The results indicate that carnivores can act as useful sentinels for broad-scale detection of pathogen presence and relative levels of prevalence in prey and predator populations. Careful selection of predator species and methods of sample acquisition are necessary to maximise their utility, and issues associated with diagnostic test performance and validation must also be acknowledged. Suggestions are made as to how this principle might be applied to future surveillance programmes. In addition, the study is the first report on the seroprevalence of C.burnetii, Leptospira spp and E.cuniculi in multiple wildlife species (field voles, bank voles, wood mice, foxes), the first detection of antibodies to C. burnetii in wildlife and cats, the first detection of antibodies to L mini, L hardjo prajitno and L hardjo bovis in wild rodents, and to L mini in cats, and the first detection of antibodies to E.cuniculi in wild rodents and foxes in the UK.

In this thesis, I examined the expression of CD1d on respiratory epithelial cells (REC) in human and explored its potential role in mucosal immunity in the lungs. Hitherto, there have been no published reports of CD1d expression on REC though it has been observed on other epithelial surface (notably intestinal epithelial cells). This observation, and work in my supervisor’s laboratory demonstrating CD1d-restricted natural killer T cells (iNKT) cells as early players in the lungs of influenza A virus (IAV)–infected mice prompted my interest in this area. I hypothesized that CD1d is expressed on REC and that it contributes to activation of iNKT cells in the lungs via presentation of endogenous or pathogenic glycolipids. I asked following questions – i) is CD1d expressed on REC ii) can this expression be regulated and iii) does CD1d expression on REC have a function. This thesis provides the first evidence for CD1d expression on human RECs (in cell lines and primary RECs) and also presence of alternatively spliced variants. CD1d expression was inducible by viral-associated signals in vitro and despite being non-professional antigen presenting cells, RECs can present glycolipid (α–GC) to, and activate iNKT cells in a CD1d-dependent process resulting in production of both Th1 and Th2 cytokines. Using whole genome expression profiling, I then showed that iNKT cells expressed a distinct profile of genes while in direct contact with α–GC-bound CD1d on RECs compared to cells separated by transwell membrane. Here early biological pathways were dominated by cytokine and chemokine related genes (JAK-STAT signaling pathways, cytokine-responsive elements and cytokine/chemokine genes) and apoptosis-related genes. This suggested that glycolipid-bound CD1d on REC was capable of inducing a programme of immune activation in iNKT cells. I concluded my work by examining if CD1d expression on RECs influenced its active role in immunity. Using wild type and CD1d-deficient transgenic mice challenged with IAV, I showed that CD1d expression is induced on REC in vivo after viral challenge, and in the absence of CD1d, mice showed worse outcome. RECs isolated from CD1d-deficient mice had a much stronger gene expression profile for pro-inflammatory genes. This suggested that CD1d expression on REC could have a bi-directional effect – on the RECs that expressed CD1d (preventing excessive immune-related genes activation) and on the iNKT cells that it engaged (activation, with pro-immunity effects). The thesis concludes with discussion of the potential implications of these findings and future work to examine hypotheses generated from this work.

The development of an efficacious P. falciparum malaria vaccine remains a top priority. Pre-erythrocytic vaccine efforts have traditionally focussed on two well- known antigens, CSP and TRAP, yet thousands of antigens are expressed throughout the liver-stage. The work described in this thesis aimed to assess the ability of other pre-erythrocytic antigens to induce an immune response and provide protective efficacy against transgenic parasites in a mouse model. Research undertaken in our laboratory has demonstrated the ability of prime-boost viral vectored sub-unit vaccination regimens to elicit high levels of antigen-specific T cells. Eight candidate antigens were therefore expressed individually in the viral vectors ChAd63 and MVA. Two antigens, PfLSA1 and PfLSAP2, were identified that confer greater protective efficacy in inbred mice than either CSP or TRAP. PfLSA1 was also able to induce almost complete sterile efficacy in outbred mice, suggesting this vaccine should be assessed in a clinical trial. Immune responses to the candidate antigens were also assessed in human volunteers following their first exposure to controlled malaria infection. The antigen TRAP was further characterised by epitope mapping in volunteers vaccinated with ChAd63-MVA ME-TRAP. However, no functional T cell assay exists to measure inhibition of P. falciparum liver-stage parasites. An improved murine in vitro T cell killing assay was developed, and preliminary experiments were conducted that demonstrate the potential and promise of a P. falciparum T cell killing assay. Such assays will not only allow mechanistic studies to be undertaken, but could also change the way we screen pre-clinical liver-stage vaccines.

No description available.

M.tuberculosis, the causative agent of human tuberculosis, is able to achieve long-term persistence within host organism macrophages. This persistence is achieved via the ability of the mycobacterium to prevent phagosomal-lysosomal fusion. The mechanisms by which fusion is inhibited remain incompletely understood. Here we provide evidence supporting a mechanistic link between infection with pathogenic mycobacteria and the cellular pathway defective in the rare lysosomal storage disorder Niemann-Pick disease type C (NPC). We observed that NPC phenotypes, including lipid storage and reduced lysosomal calcium release, can be induced in wild-type murine and human macrophages by infection with pathogenic mycobacteria. This phenotype induction did not occur following infection with the non-pathogenic M.smegmatis. Phenotype induction could be achieved in the absence of the mycobacteria using lipids from the mycobacterial cell walls. The importance of mycobacterial cell wall lipids to mycobacterial virulence has been well-documented. This lipid-mediated inhibition likely occurs through the NPC1 protein. Susceptibility to phenotype induction was inversely proportional to levels of functional NPC1, whilst a pre-existing dysfunction in the NPC pathway (either stemming from mutation or pharmacological inhibition) rendered cells less able to clear non-pathogenic mycobacteria. Finally, we demonstrate that therapies for NPC, particularly curcumin, are able to promote clearance of mycobacteria from infected macrophages. NPC therapies may hold promise for a new approach to the treatment of tuberculosis.