Alors que la pandémie de COVID-19 affecte le monde depuis presque deux ans, il va sans dire qu'une meilleure compréhension des processus de contagion, de leur évolution et des effets des mesures de contrôle est essentielle pour réduire leur impact sur la société. Le cadre théorique pour la modélisation des processus de contagion est très général et permet, bien entendu, de décrire la propagation des maladies infectieuses causées par des agents pathogènes (virus, bactéries, parasites, etc.), mais aussi la propagation des rumeurs et de la désinformation. Peu importe la nature du processus, la transmission s'effectue de proche en proche grâce aux interactions entre les individus. Par conséquent, la structure sociale complexe des populations, qui n'est ni parfaitement ordonnée, ni complètement aléatoire, joue un rôle de premier plan. Dans cette thèse, nous étudions les processus de contagion sur réseaux, où les individus et les interactions entre ces individus sont représentés par des nœuds et des liens respectivement. Nous utilisons une approche théorique principalement basée sur la physique statistique et la dynamique non linéaire. Nous nous concentrons plus spécifiquement sur les réseaux d'ordre supérieur, lesquels mettent les interactions de groupe à l'avant-plan. Notre analyse va donc au-delà des interactions dyadiques. Bien plus qu'une reformulation mathématique de la structure, cette perspective est primordiale pour obtenir une compréhension plus complète de la phénoménologie des processus de contagion. Nous démontrons l'importance des interactions de groupe à l'aide de trois résultats principaux. D'abord, nous caractérisons un phénomène de localisation mésoscopique : pour certaines structures hétérogènes, la propagation persiste uniquement dans les groupes de grande taille. Ce phénomène a notamment une incidence sur l'effet des mesures de contrôle visant à prohiber les regroupements au-delà d'une certaine taille, à l'instar de ce qui fut instauré pour endiguer la pandémie de COVID-19. Ensuite, nous étudions un modèle où les individus doivent accumuler une dose infectieuse minimale pour devenir infectés. Nous montrons qu'une structure d'ordre supérieur et des temps d'exposition hétérogènes induisent une probabilité d'infection non linéaire universelle. L'épidémie résultante peut alors croître de manière super-exponentielle en fonction du temps. Finalement, nous poussons plus en profondeur l'analyse des processus de contagion non linéaire. Dans ce contexte, nous montrons que les groupes peuvent avoir plus d'importance que les individus ultra-connectés pour qu'une épidémie ou un phénomène social envahissent le plus rapidement possible une population. / After almost two years into the COVID-19 pandemic, it is clear that a better understanding of contagion processes, their evolution, and the impact of control measures is essential to reduce their burden on society. The theoretical framework for the modeling of contagion is quite general. It can describe the spread of pathogens causing diseases (viruses, bacteria, parasites, etc.), but also the spread of rumors and disinformation. Irrespective of the nature of the underlying process, the contagion evolves through local interactions between the individuals. Consequently, the complex social structure of populations, which is neither perfectly ordered nor completely random, plays a fundamental role in shaping spreading. In this thesis, we study contagion processes on networks where individuals and the interaction between them are represented by nodes and edges respectively. We use a theoretical approach based on statistical physics and nonlinear dynamics. We focus on higher-order networks, putting group interactions beyond pairwise interactions at the forefront. More than a mere mathematical generalization, we find this perspective is paramount to obtain a complete picture of the phenomenology of contagion dynamics. We demonstrate the importance of group interactions through three principal results. First, we characterize a mesoscopic localization phenomenon where the contagion thrives only in large groups for certain types of heterogeneous structure. This phenomenon significantly affects the results of interventions like the cancelation of events larger than a critical size, similar to the measures being used to limit the spreading of COVID-19. Second, we study a model where individuals must accumulate a minimal infective dose to become infected. We show that a higher-order structure and heterogeneous exposure induce a universal nonlinear infection probability. The epidemic size can then grow super-exponentially with time. Finally, with a more in-depth analysis of nonlinear contagions, we show that groups can be more influential than hubs (super-connected individuals) to maximize the early spread of an epidemic.

CD8 T cells play a critical role in the clearance of pathogenic bacteria, viruses, and protozoan parasites. Upon encountering their cognate antigen through either infection or vaccination, naïve CD8 T cells undergo robust proliferative expansion, which is followed by contraction and the formation of a memory population. Memory CD8 T cells are long-lived, and because they persist in increased numbers and possess enhanced functional abilities compared to naïve CD8 T cells, they are able to provide the host with increased protection following re-infection. Because of these properties, vaccines designed to elicit memory CD8 T cells have the potential to reduce health care burdens related to infection with pathogens including human immuno deficiency virus (HIV), malaria, influenza, and hepatitis virus. However, stimulating protective CD8 T cell responses against these pathogens through vaccination has proven challenging. Therefore, a better understanding of the properties of memory CD8 T cells generated following vaccination, and the characteristics of memory CD8 T cells best suited for providing protection against diverse pathogens is needed. While memory CD8 T cells can be maintained for as long as the life of the host, evidence suggests that their properties change with time after infection. Because CD8 T cell-mediated protection is based upon both the numbers and quality or functional abilities of memory cells present at the time of re-infection, changes in memory CD8 T cell function over time could impact their ability to provide protection upon re-infection. Therefore, a better understanding of how memory CD8 T cells change with time after infection is needed. As part of the studies presented in this thesis, I found that the phenotype and function of memory CD8 T cells including localization, interleukin (IL)-2 cytokine production, responsiveness to homeostatic cytokines, metabolic capabilities, and proliferation and secondary memory generation potential change with time after infection. Interestingly functional changes could not be completely explained by changes in subset composition that occur with time, as changes over time were also seen in defined CD62Lhi subsets. Importantly, functional changes of memory CD8 T cells that occurred with time led to an increased ability to provide protection against a chronic viral infection. These data improve our knowledge of the capabilities of memory CD8 T cells generated following infection, and suggests that the outcome of vaccination strategies designed to elicit protective memory CD8 T cells using single or prime-boost immunizations will depend upon the timing between antigen encounters. Following re-infection, memory CD8 T cells become activated and produce effector cytokines and cytolytic molecules that aid the host in clearing invading microbes. Activation can be triggered not only through cognate antigen recognition, but also by antigen-independent cytokine driven signals. However, our knowledge of how antigen-dependent and –independent signals contribute to CD8 T cell activation and protection following infection is incomplete. In the second part of my thesis, I show that the ability of memory CD8 T cells to become activated in response to inflammation decreases with time after infection, that antigen and inflammation act synergistically to induce activation of memory CD8 T cells, that the presence of cognate antigen enhances activation of memory CD8 T cells that contribute to clearance of infection, and that bystander memory CD8 T cell responses following unrelated bacterial infection do not provide the host with a protective benefit. Together, the data in this thesis further our understanding of memory CD8 T cells generated following infection and/or vaccination, and the properties of memory CD8 T cells important for providing protection upon re-infection with invading pathogens.

Neonatal septicaemia and nosocomial infection are major causes of morbidity in neonatal intensive care units (NICU) in both developed and developing countries. This study documents infective episodes at two resource disparate NICUs; the Grantley Stable Neonatal Unit (GSNU), Royal Brisbane and Women’s Hospital (RBWH), Australia 1997-2006 and Danang NICU, Vietnam. The specific aims are: 1. To compare the incidence of neonatal septicaemia at RBWH and Danang NICU. 2. To compare of the epidemiological characteristics of nosocomial infections in the two NICUs. 3. To study risk factors associated with nosocomial infection in the two NICUs (including staff numbers, infant numbers and nursing workload). 4. To review published guidelines on healthcare physical environments and staffing levels and to survey the GSNU & Danang NICU in relation to these. 5. To develop a prospective surveillance system to monitor infection episodes in Danang NICU 6. To recommend strategies for the control of neonatal sepsis in Danang NICU. The GSNU at the RBWH, Australia is a 71 bed neonatal care facility with an established infection surveillance system in a well resource environment. Danang NICU, Vietnam provides care to a high risk neonatal population with no established infection surveillance system in a developing country with more limited resources. This study found the GSNU had a low rate of neonatal septicaemia, during the ten year period from 1997 to 2006 with 253 babies (2.1%) diagnosed with septicaemia. In Danang NICU, in the year 2007 alone, there were 52 cases (2.9%) of septicaemia documented but the incidence of neonatal infection is likely to have underestimated due to (i) the failure to collect blood culture before commencing antibiotic treatment. (ii) Difficulties associated with data retrieval from maternal and neonatal records and (iii) lack of a systematic surveillance system with prospectively collected data. The organisms causing early onset and late onset septicaemia were substantially different in the two NICUs. Group B streptococcus (GBS) and Escherichia coli were the major organisms causing early onset sepsis (EOS) at the GSNU, accounting for 37.8% and 29.7% respectively, whilst coagulase-negative staphylococcus (CONS) was the commonest organism (25.7%) for late onset sepsis (LOS). In Danang NICU, Klebsiella spp was the major pathogen and was responsible for 75% of neonatal septicaemia in both early and late onset sepsis. The isolation of Klebsiella spp in a high proportion of infants at less than 48 hours may suggest nosocomial or maternal route of acquisition. The rate of GBS infections in Danang Hospital, Vietnam, is hard to estimate and interpret due to limited microbiologic data. The anti-serum used to classify the Streptococcal types is not readily available in Danang Hospital. In some cases, organisms that are isolated are suspected to be GBS however, this is not confirmed microbiologically. The study identifies a high prevalence of neonatal septicaemia in Danang NICU. It identifies a close relationship between rates of infection and poor nursing care practices and limited resources. The standard care system used at the GSNU as well as the international literature was studied in relation to infection control practices. This was then used to develop the following recommendations that specifically target a reduction in infection rates in Danang NICU: 1. Implement an infection surveillance system 2. Report regularly from the database and embed discussion of the data into unit management policy 3. Revise neonatal and pathology practice in relation to blood cultures 4. Use shorter duration of antibiotics course based on culture results 5. Modify care practices that expose infants to cross infection 6. Identify specific staff with particular responsibilities in maintenance of standards

Le développement de maladies d'origine tellurique relève de mécanismes épidémiologiques particuliers, propres au cycle biologique et aux traits d'histoire de vie des agents pathogènes incriminés. La caractérisation des processus qui déterminent le développement des épidémies est une étape clé dans la conception et l'optimisation de méthodes de protection contre ces maladies. Les cultures légumières de plein champ constituent des agrosystèmes particulièrement sensibles aux attaques parasitaires. Les Pythium sont responsables du cavity spot de la carotte, une maladie racinaire qui affecte la qualité des récoltes dans plusieurs bassins de production en France et dans le monde. L'objectif des recherches présentées ici est d'identifier, comprendre et hiérarchiser les processus déterminant la dynamique spatio-temporelle de cette maladie, essentiellement due à Pythium violae, en association avec d'autres espèces du complexe parasitaire. L'analyse de la composition d'un de ces complexes, complétée par la caractérisation biologique des principales espèces pathogènes, suggère que par souci de simplification, il est raisonnable de négliger les interactions entre espèces au cours de la phase infectieuse. L'existence d'infections secondaires (auto- et allo-infections) chez P. violae, et donc la nature polycyclique d'une épidémie de cavity spot, sont démontrées expérimentalement. Cette hypothèse est initialement étayée par deux étapes de l'analyse, l'une portant sur l'examen de relations pathométriques, et l'autre sur les ajustements de modèles aux données illustrant des cinétiques de la maladie. L'ensemble des résultats obtenus permet de concevoir un modèle épidémiologique exploratoire, basé sur l'occurrence des infections primaires et secondaires. Les effets de différents facteurs sur ces processus, comme l'application d'un fongicide, l'humidité du sol et la densité de semis, sont testés expérimentalement et discutés. Ils permettent d'envisager l'association de moyens de lutte complémentaires dans le cadre de stratégies de protection intégrée.

Despite the advances made since the advent of germ theory, infectious diseases still wreak havoc on human societies, not only affecting us directly but impacting the crops and livestock upon which we rely. Infectious diseases also have dramatic effects on wildlife ecology. Therefore research into infectious diseases could not only directly lead to the improvement and saving of human lives, but aid in food security and the conservation of many wildlife species. Of vital importance in understanding the ecology of infectious diseases are the mechanisms by which they persist in host populations. One possible mechanism is vertical transmission: the transmission of a pathogen from a parent to its offspring as a result of the process of host reproduction. Another possible mechanism is inapparant infections, where an infected host does not display symptoms. Focusing on dengue fever and the Plodia interpunctella granulovirus laboratory system, this PhD thesis looks at the role these two mechanisms play on the persistence of two viral infections and their ecology. Regarding the Plodia interpunctella granulovirus (PiGV) low host food quality led to greater detection of vertically transmitted inapparant PiGV, but did not lead to its activation to an apparent form. Host inbreeding did not lead to vertically transmitted inapparant PiGV’s activation, nor had an effect on its vertical transmission. The vertical infection rate of PiGV was very low. I would therefore suggest that it may be better to use an insect virus system with a higher rate of vertical infection in future research into vertically transmitting inapparent infections. Regarding dengue virus I conclude that vertical transmission is not likely to play a role in the persistence of this virus. However modelling work found that inapparent infections could provide dengue viruses with a means of persistence and should be subject to further research.

Thesis (MPH.) --University of Limpopo, 2019. / Background: The purpose of this study was to investigate the extent of adherence to Infection Prevention and Control (IP&C) practices and programs amongst healthcare workers (HCWs) in the neonatal ward at Charlotte Maxeke Central Hospital (CMCH). Methods: Quantitative research was conducted on 57 Clinicians directly providing care to the patients and 5 Health Care Workers indirectly providing care to the patients by means of supporting the environment and logistics where patients are being taken care. Data collection was done using structured questionnaires. Because the population was so small, all available HCWs, who were willing to participate in the study were selected to participate in the study. Furthermore, the SAS statistical software was used to describe and analyse data received from the data collection tools. Results: Two groups of respondents participated in the study which were (n=57) who in the neonatal ward at CMCH and Health Care Workers (n=5), most of the clinicians were having 1 – 4 years’ experience working in the neonatal unit at 54.6% followed by 5 – 9 years at 21.8%. Participants were in the age group ≤ 30 years at 39.3% followed by 31 – 40 years (32.1%) and least being at ≥ 51 years (5.4%). Clinicians included 46% of professional nurses, 28.6% Auxiliary Nursing Assistant, 16.1% student nurses and 8.9% medical doctors. The findings revealed that there are some areas where there’s inconsistent in using gloves when anticipating exposure to blood or body fluids, drying of hands after washing and removing jewellery during clinical care among clinicians particularly doctors, professional nurses and student nurses about IPC practices during clinical care. In Conclusion: There was inadequate compliance with IPC standards and there’s a need for regular trainings to improve the knowledge about IPCs and awareness of its importance among clinicians and health care workers in the neonatal unit. The IPC committee need to be revitalized by the hospital management to be able to undertake its mandate. Furthermore, the Hospital administration should provide copies of IPPC policy Guidelines in all wards/units and ensure effective implementation through vi constant supervision and adequate supplies and conduct regular audits to enhance compliance and implementation of IPPC policy. The study concluded that there was inadequate compliance with IPC and there’s a need for regular trainings to improve the knowledge about IPCs and awareness of its importance among clinicians and health care workers in the neonatal unit.

The objectives of the study are to explore the effectiveness of the ABC HIV prevention strategy in South Africa with the purpose of establishing problem areas of the ABC HIV prevention strategy in South Africa. A systematic review design was followed. Electronic databases; Google scholar, Medline and PubMed were searched using broad combination of keywords to obtain all relevant articles. Studies written in English, published between 2000 and 2010, were selected if they met the inclusion criteria. In order to be included the study had to discuss the ABC HIV prevention strategy with the focus on effectiveness of the strategy. The Critical appraisal instrument for qualitative research studies (CASP, 2006) and Quality Assessment Tool for Quantitative studies (Effective Public Health Practice Project, 2005) were used to critically appraise the 9 studies that met the inclusion criteria. Thematic analysis was used for the analysis process. The findings regarding each objective were combined in a summary of findings. The findings revealed that the South African population engages in sexual activities at an early age. Males and females have concurrent sexual partnerships, which mean they are not faithful to their primary sexual partners and lastly, women are unable to use or negotiate condom use. Identified problem areas of the ABC HIV prevention strategy in South Africa were that the age gap between sexual partners is a problem as women cannot negotiate condom use with their seniors. The notion of love and romance that influences the use of condoms, has a negative impact whereby condom use is unacceptable in a long term relationship, irrespective of the level of faithfulness. Low socio-economic status of women that makes women to be dependent on men and also prone to engage in transactional sex. Lastly, local norms about sexuality that men subscribe to, to prove masculinity. / Thesis (M.Cur) North-West University, Mafikeng Campus, 2011

Blood pressure has previously been associated with decline in memory over time, though the exact mechanism behind this effect is uncertain. Infections, which can lead to systemic inflammation have also been linked to some cardiovascular damage to the brain, known as microbleeds, which have themselves been linked to greater declines in cognition in old age. The present study investigates whether blood pressure, a self-reported history of infection, and an indirect measure of inflammation known as the erythrocyte sedimentation rate have any association with on episodic and semantic memory and visuospatial skills in the Betula study, a Swedish longitudinal population study. The effect of elevated blood pressure (over 140 mm Hg systolic and/or 90 mm Hg diastolic), high blood sedimentation (top 33% against bottom 33% of participants), and self-reported infection were all found to not have any significant effect on episodic memory, semantic memory or visuospatial skills. Some of the possible explanations are elaborated in the discussion. / Högt blodtryck har associerats med minnesnedsättning men den exakta mekanismen hur ett samband kan förstås är dock oklar. Infektioner har visat sig ge systematiska inflammationer och har också satts i samband med vissa kardiovaskulära förändringar i hjärnan, så kallade mikroblödningar, vilka i sig har associerats med ökad risk för kognitive nedsättning i hög ålder. Denna uppsats syftar till att undersöka om blodtryck och infektion (självrapporterad infektion samt infektion indirekt mätt genom sänkereaktion) kan relateras till episodiskt och semantisk minne samt visuospatial förmåga i Betula studien, som är en svensk longitudinell populationsbaserad studie. Resultatet visade att varken högt blodtryck (över 140 mm Hg systoliskt eller 90 mm Hg diastoliskt), hög sänkereaktion (de 33 % med högst värde jämfört med de 33 % med lägst värde) eller självrapporterad infektion hade någon signifikant effekt för episodiskt minne, semantiskt minne eller visuospatial förmåga. Några möjliga förklaringar till detta resultat utvecklas i diskussionen. / The Betula Study

Introduction: Despite management advances worldwide, tuberculosis still remains a serious uncontrolled disease. The absence of either a ‘gold’ standard diagnostic test, or a conventional rapid ‘reference’ laboratory test for asymptomatic Mycobacterium tuberculosis (MTB) carriers complicates disease control. Through mandatory screening of high-risk groups, early diagnosis of latent tuberculosis infection (LTBI) cases allows recognition and better control of the tuberculosis pandemic. Materials and Methods: The current tuberculosis screening guidelines as recommended by the World Health Organization, chest X-ray and tuberculin skin test were assessed and revealed rises in TB morbidity and fatality trends in the Kuwait population (low incidence country). In order to evaluate options for LTBI diagnosis, the current work implemented a 4-month prospective, observational, repeated-measure and randomly implemented survey on 180 new immigrants to Kuwait using a structured risk factor questionnaire whilst, simultaneously evaluating the performance of the two standard diagnostics (chest X-ray and tuberculin skin test) with the new biomarker interferon gamma release assays (T-SPOT .TB test and QuantiFERON Gold In-Tube test (QNF-GIT)); which detect the release of interferon gamma (INF-γ) released from sensitization to specific MTB antigens. Results: Associations between various epidemiological risk factors - such as socio-demographic status, smoking and environmental exposure-contact - were associated in the laboratory diagnosed LTBI participants. Positive identification of LTBI prevalence detected by two radiologists was 10.1% having ‘moderate’ inter-reader agreement (Kappa = 0.505), compared to no positives being detected by three pulmonologists. TST results were negative (less than 10-mm ‘cut-off’) even in the 86.1% Bacillus Calmette-Guérin vaccinated expatriates. Estimated LTBI using QNFGIT was 28.3% compared to 41.1% positive T-SPOT .TB test. Both interferon gamma assays revealed concordant ‘abnormal’ results in 26.1% with ‘good’ agreement (kappa = 0.627). Conclusion: Detection of latent tuberculosis infection can be facilitated by introducing evidence-based diagnostic classification depending on history taking of epidemiological-related risk factors and chest X-ray plus either interferon gamma assays.

published_or_final_version / abstract / Medicine / Doctoral / Doctor of Philosophy