Dissertations / Theses on the topic 'Typhoid fever'

Typhoid disease, caused by infection with S. Typhi, is a significant cause of mortality and morbidity in resource–poor countries. Efforts have been made to generate a new generation of vaccines that are efficacious and can be given to infants, but have been hindered by a poor understanding of the protective immune response to S. Typhi infection, and in particular by the absence of a correlate of protection. Controlled human infection studies (‘challenge studies’) provide a model for investigating infectious diseases and appraising novel vaccines, including in typhoid disease. This DPhil described the development of a human challenge model of typhoid fever using S. Typhi Quailes strain administered to healthy adults in a sodium bicarbonate buffer. The careful characterisation and manufactured of the strain is described. Following ingestion of 10³ CFU of S. Typhi 55% of participants developed typhoid disease, whilst ingestion of 10⁴ CFU gave a higher attack rate of 65%. At this attack rate vaccine efficacy against human challenge should be demonstrable with a modest sample size. Validity of the model in the appraisal of vaccines was demonstrated using Ty21a, a live, oral, attenuated vaccine. Protective efficacy of Ty21a compared to placebo against challenge was 35%, comparable to that observed in some endemic settings, and the estimated protection in the first year after vaccination in Cochrane meta-analysis. Clinical, microbiological and humoral immune responses were investigated in participants challenged during model development. Typhoid disease was associated with a high fever in most, but not all participants, and a range of symptoms. Severity of disease was variable, and included asymptomatic bacteraemia, as well as fever and symptoms in participants in whom bacteraemia could not be demonstrated. Typhoid disease was associated with a strong humoral immune response to the flagellin and lipopolysaccharide antigens of S. Typhi but not the Vi polysaccharide capsule. Humoral immune responses were not demonstrated in participants without typhoid fever. There was a dose-response relationship to the clinical, microbiological and humoral responses with participants challenged with 10⁴ CFU having more marked responses than those challenged with 10³ CFU. Future success of challenge studies relies on the willing participation of healthy adult volunteers. The motivations for participation, and experiences of participants, were appraised by questionnaire. Whilst financial compensation was an important motivator, it was not the sole motivator. Participants were positive about their experiences, and most would participate again.

Typhoid fever is a forgotten disease in today's society, but for the people of nineteenth century Australia it was part of their every day lives. This thesis examines the role that the Queensland colonial government, the medical profession, and the communities of Toowoomba and Brisbane played in the fight against the disease. At separation from New South Wales the Queensland government officials were new and inexperienced and had inherited a financial debt. These circumstances resulted in cautionary governance when it came to public health policy and issues, but determination and single-mindedness when it came to development of roads and railway lines. The government’s view at the time was if the colony was to prosper then this type of infrastructure must be developed at all costs. What the government failed to realise was that the infrastructure of drainage and sewerage, associated with good public health policies, needed to go side by side with other types of infrastructure. The prosperity of the colony rested on the health of its people. Because of the failure of the government to recognise the value of strong public health legislation it was up to the medical profession and the community to be vigilant and take the challenge to the government. This study has found that throughout the second half of the nineteenth century the medical profession and the community with the support of various newspapers had to challenge the government on public health issues consistently in relation to typhoid fever. This political pressure was more successful in Toowoomba where William Groom’s leadership achieved some important engineering solutions whereas campaigns in the capital, Brisbane, were marked by diversity and divisions. Intransigent colonial government policy condemned both cities to inadequate sanitation infrastructure until the twentieth century.

Typhoid fever remains an important public health problem globally. Cluster randomized effectiveness trials with typhoid Vi polysaccharide vaccine were conducted in Kolkata, India and Karachi, Pakistan, to provide evidence for vaccine introduction. While efficacy trials are limited to estimate vaccine's performance on the vaccine recipients, effectiveness trials consider the public health impact, notably the herd protection, or indirect effect, which can only be seen when vaccines are administered to groups rather than to individuals. The observed total protection by the Vi polysaccharide vaccine in school-aged children was consistent in Kolkata and Karachi (61% and 56%, respectively), and was associated with minimal side-effects. The total protection in young children, however, was different (80% in Kolkata and no protection in Karachi). The Kolkata trial demonstrated significant herd protective effects, as demonstrated by indirect protection of non-vaccinees (45%), which was not shown in the Karachi trial. The difference in the effectiveness estimates between the trials may be due to the difference in study design and the population characteristics. Immunogenicity studies were undertaken for randomly selected persons from both sites at pre-vaccination, 6 weeks, and 2 years post-vaccination. Serum Vi antibody titres (IgG) were measured through ELISA. At baseline, the GMTs were below the protective level for both sites. At six weeks after vaccination, though there is a significant increase in the GMTs in children from both site, the level of GMTs were significantly lower from those in Karachi (2,307.0 ELU vs. 1,189.1 ELU). GMT declined from 6 week to 2 year testing points for both sites but maintained the protective level. These effectiveness trials gave a conclusive evidence of the protection conferred by the Vi polysaccharide vaccine in children older than 5 years of age. Targeted vaccination programme in high endemic areas, as stipulated in the WHO Position Paper, suggest the potential for effective control of typhoid fever in places like India and Pakistan with the school-based Vi vaccination.

Thesis (Ph. D.)--Georgia State University, 2007.
Title from file title page. Wendy H. Venet, committee chair; Stuart Galishoff, Charles G. Steffen, committee members. Electronic text (338 p.) : digital, PDF file. Description based on contents viewed Feb. 4, 2008. Includes bibliographical references (p. 308-338).

Улучшение социально-экономических условий жизни привели к резкому снижению заболеваемости брюшным тифом, что вдохновило некоторых исследователей на позитивные прогнозы в отношении возможности его ликвидации. Теоретической основой для научного обоснования такой возможности является учение Л.В. Громашевского о движущих силах эпидемического процесса. При цитировании документа, используйте ссылку http://essuir.sumdu.edu.ua/handle/123456789/32131

This dissertation examines the experience of those involved in the typhoid fever outbreak at Camp Thomas, Chickamauga National Military Park, Georgia between April and August 1898. Among American volunteer soliders in the Spanish-American War, those stationed at this camp suffered the highest number of typhoid cases and deaths from typhoid. Treatments of the war have referred to the outbreak and some studies have examined it as part of wider subjects, but none from the standpoint of those involved, commanders, doctors, civilians, officers and enlisted men. The mobilized soldiers represented numerous states and reflected the disease experience of civilian society. The study considers the mobilization process, the disease outbreak and the aftermath.

Enteric fever continues to affect people living in endemic settings substantially causing at least 20 million cases of febrile illnesses every year with 1% mortality. Over the last decade there has been considerable debate surrounding the burden and disease profile of enteric fever in the paediatric population. This is partially due to the similarity of the clinical features of paediatric enteric fever to most other febrile illness seen in endemic settings. The treatment of enteric fever is proving to be a challenge with the emergence of antimicrobial resistant strains, particularly the 4.3.1 genotype (H58 haplotype), which is spreading rapidly. Multi-drug resistant (MDR) enteric fever, defined as infection with typhoidal Salmonellae that exhibit a combined resistance to ampicillin, cotrimoxazole and chloramphenicol emerged in the 1990s and was mediated primarily via the 4.3.1 genotype population through the horizontal acquisition of antimicrobial resistance determinants. Subsequently, fluoroquinolones became the drug of choice and the treatment of enteric fever following which fluoroquinolone resistance emerged, again through the 4.3.1 genotype. However, these antimicrobial trends may not be uniform across endemic regions and an understanding of these differing patterns as well the temporal changes in these trends are important in planning treatment strategies. In the short and medium term work needs to be focused on achieving the greatest benefits from the prudent use of the recently WHO pre-qualified Vi-TT conjugate vaccine candidate. Whilst the long term vision towards eradicating enteric fever needs to focus on better understanding the underlying the biology of this disease through the use of contemporary technologies while simultaneously improving infrastructure for the provision of clean water, adequate sanitation and hygiene. This thesis aims to age-characterise the disease burden of typhoid fever in endemic regions of South and South-East Asia as well as the African continent. Following this, the molecular epidemiology of enteric fever in two endemic settings in the Indian subcontinent is delineated with a keen focus on the 4.3.1 genotype (H58) population as well the phenotypic patterns and molecular determinants of antimicrobial resistance. This thesis finally systematically reviews the global trends of antimicrobial resistance of S. Typhi isolates over time both from a phenotypic and molecular perspective. The key results from this thesis include; the age stratification of disease occurrence in endemic regions which showed a substantial proportion occurs in the youngest age group in both Africa and Asia, the uniform dominance of 4.3.1 genotypes conferring a high degree of fluoroquinolone resistance contrary to earlier suggestions of younger children being more susceptible to a broader range of infecting genotypes, the dissimilarities between the antimicrobial resistance carrying capabilities of lineage I and lineage II strains of the 4.3.1 genotype as well as novel AMR gene arrangements and finally the temporal trends of AMR in S. Typhi which were different between Asia an Africa. The high prevalence of lineage I strains in Africa and South-East Asia in contrast to the high prevalence of lineage II strains in the Indian subcontinent reflect the antimicrobial selection pressures as well the evolutionary characteristics of circulating pathogen populations in these regions. The implications of the data reported in this thesis have implications for treatment and prevention strategies. For the first time in history an opportunity has risen to effectively vaccinate the youngest age group (0-4 years) from typhoid through the Vi-TT conjugate vaccine. As highlighted in this thesis the youngest age group (0-4 years) have a high disease occurrence in endemic areas as seen in a meta-analysis as well as through data from two endemic sites collated and reported in this thesis. The older age groups also suffer greatly from this disease calling for a broad based vaccine strategy. The implications for treatment of enteric fever are however more relevant in the immediate term which suggest that in endemic regions in Asia, fluoroquinolones have little role to play in treatment protocols while fluoroquinolones are still relevant in the African setting. In Asia, reverting back to former first-line antimicrobials might be an option but the possibility of re-emergence of widespread resistance to these currently sensitive antimicrobials is very high exemplifying the ability of S. Typhi to adapt to changing antimicrobial pressures.

Nontyphoidal \(Salmonella\) is strongly associated with HIV infection, whereas there is a negative association between HIV and typhoid fever. To investigate this phenomenon, we explored humoral and cytokine responses in HIV-infected and uninfected blood and sera against \(S.\) Typhimurium and \(S.\) Typhi, finding that HIV-infected sera had significantly impaired bactericidal and opsonic activity against \(S.\) Typhi compared with HIV-uninfected sera. We observed dysregulated cytokine responses in blood from HIV-infected individuals after Salmonella stimulation, with RANTES levels being modulated by HIV status and \(Salmonella\) serovar. Most \(S.\) Typhi isolates express Vi capsule and O:9 O-antigen. The roles played by the Vi capsule and by anti- \(S.\) Typhi antibody in infection are unclear. Effective vaccines against typhoid exist, but the mechanisms of protection afforded by the antibody they elicit is poorly characterised. We investigated the role of Vi capsule and anti-S. Typhi antibody in the killing of \(Salmonella\). Using isogenic Vi+/- \(Salmonella\) we show that Vi-expression is associated with reduced antibody and complement deposition on \(Salmonella\) and increased resistance to serum and phagocyte killing. We characterised the bactericidal and opsonic activity of purified human anti-Vi and anti-O:9 antibodies against \(S.\) Typhi, finding that both antibodies kill \(Salmonella\) but anti-O:9 antibody has poor opsonic activity. Collectively our data suggest cytokine, but not antibody, dysregulation may underlie the dichotomy of \(Salmonella\) infection in the context of HIV. We demonstrate that both anti-capsular and anti-O-antigen antibodies elicit bactericidal activity against \(S.\) Typhi but anti-O:9 antibody is a poor opsonin. This has implications in the development of O:9 vaccines against O:9 –expressing \(Salmonellae\).

Before the consolidation of the germ theory of human diseases at the end of the nineteenth century, medical explanations about disease causation were dominated by the environmental notions of medical geography. This dissertation explores how nineteenth-century Colombian physicians transformed the medical geographical approach using the early concepts and technologies of the emerging Pasteurian germ theory. I follow this transformation in the cases of periodic fevers (yellow fever and malaria), continuous fevers (typhoid fever and typhus) and leprosy. The analysis reveals that by mid century physicians had incorporated neo-Hippocratic versions of disease causation and French medical geographical ideas in order to make sense of disease of the warm, temperate and cold lands. Their conceptual network revolved around the specific, predisposing and occasional causes in which climate and geography played a determinant role. Evidence indicates that this was the case of periodic fevers of the warm lands (yellow fever and malaria). I argue that the “parasitic” hypothesis of yellow fever was accepted during the controversy around the prophylactic inoculations inspired by Pasteurism that were applied in Colombia in 1887. However, doctors struggled to reconcile the medical geographical and the bacteriological perspective of both yellow fever and malaria. Continuous fevers, on the other hand, were also framed within the medical geography scheme of disease causation. I show how during the debates about typhoid fever and typhus happening in the Colombian highlands during the 70s, 80s and 90s, doctors used medical geographical notions and developed anti-pasteurian arguments, while the international scientific community had identified the specific bacilli for typhoid fever. Finally, I argue that the strong interest of Colombian doctors on leprosy –also understood in neo-Hippocratic terms- that foster the search for local treatments based on Pasteurism (antiseptics in the 1880s and serotherapy in the 1890s) also prompted the extension of the bacteriological model and techniques to other diseases in those decades.

I performed two randomised controlled trials (RCTs) to determine the best treatments for enteric fever in Kathmandu, Nepal, an area with a high proportion of nalidixic acid resistant S. Typhi and S. Paratyphi A isolates. I recruited 844 patients with suspected enteric fever to compare chloramphenicol versus gatifloxacin. 352 patients were culture confirmed. 14/175 patients treated with chloramphenicol and 12/177 patients treated with gatifloxacin experienced treatment failure (HR=0.86 (95% CI 0.40 to 1.86), p=0.70). The median times to fever clearance were 3.95 and 3.90 days, respectively (HR=1.06 [CI 0.86 to 1.32], p=0.59). The second RCT compared ofloxacin versus gatifloxacin and recruited 627 patients. Of the 170 patients infected with nalidixic acid resistant strains, the number of patients with treatment failure was 6/83 in the ofloxacin group and 5/87 in the gatifloxacin group (Hazard Ratio, HR=0.81, 95% CI 0.25 to 2.65; p=0.73); the median times to fever clearance were 4.7 and 3.3 days respectively (HR=1.59 [CI 1.16 to 2.18], p=0.004). I compared conventional blood culture against an electricity free culture approach. 66 of 304 patients with suspected enteric fever were positive for S. Typhi or S. Paratyphi A, 55 (85%) isolates were identified by the conventional blood culture and 60 (92%) isolates were identified by the experimental method. The percentages of positive and negative agreement for diagnosis of enteric fever were 90.9% and 96.0%, respectively. This electricity free blood culture system may have utility in resource-limited settings or potentially in disaster relief and refugee camps. I performed a literature review of RCTs of enteric fever which showed that trial design varied greatly. I was interested in the perspective of patients and what they regarded as cure. 1,481 patients were interviewed at the start of treatment, 860 (58%) reported that the resolution of fever would mean cure to them. At the completion of treatment, 877/1,448 (60.6%) reported that they felt cured when fever was completely gone. We suggest that fever clearance time is the best surrogate for clinical cure in patients with enteric fever and should be used as the primary outcome in future RCTs for the treatment of enteric fever.

Many current disease threats involve interactions within and between nested subsystems of biological organisation. Typhoid fever is a serious disease threat in the South Pacific region, with Fiji reporting the highest annual number of cases, yet risk factors in this setting have been poorly studied. While localised behaviours have dominated perspectives on typhoid transmission, interactions between distal ecological conditions, conditions of the residential environment and localised behaviour deserve greater attention for their potential to influence transmission. This thesis demonstrates a nested approach to typhoid epidemiology using a fivefold methodology to explore how regional, river basin, residential, socio-cultural and behavioural subsystems influence the risk of typhoid transmission in Central Division, Fiji, whereby I: (1) provide a regionally specific literature review examining health consequences of wetland ecosystem service interruption associated with common natural disasters; (2) use quantitative geospatial analysis to evaluate relationships between sub-catchment environmental characteristics and typhoid incidence and recurrence; (3) use a case-control design at a residential level to investigate bacterial contamination and chemical composition of water and soil as vehicles of exposure, complemented with observational analysis of living conditions, spatial analysis of household position and factor analysis to explore multivariate relationships influencing typhoid risk; (4) question 160 typhoid fever cases and 319 control subjects to reveal risky socio-cultural and behavioural practices and; (5) synthesize significant risk factors within and across nested subsystems and test several intervention scenarios using a Bayesian Network approach. Regional typhoid burden is influenced by climate change induced warming, altered rainfall patterns, increased storm severity and rising seas, coupled with population growth, slow economic growth, urbanisation, environmental change and limited capacity for adaptive management. The most parsimonious models for incidence and recurrence at the sub-catchment scale included total high soil-erosion risk area, percentage area that was highly erodible, connectivity between road and river networks and riparian forest fragmentation as predictor variables. In the residential setting, five factors, related to drainage, housing and condition of water and sanitation were significant in predicting typhoid. Multivariate analysis of household questionnaires indicated the following significant risk factors for typhoid fever: using an unimproved pit latrine, not washing produce (i.e. fruit or vegetables) or hands before eating, bathing outside, water not always accessible, having sand/wood plank floors and attending mass gatherings. The above results suggest that anthropogenic alteration of land cover and hydrology in river basin and residential systems increases risk of exposure where sediment increases following runoff. Localised socio-cultural and behavioural subsystems interact with residential and river basin subsystems to enhance risk of typhoid transmission. Bayesian network analysis suggests combined interventions within a subsystem provides greater exposure reduction than the sum of individual interventions and simultaneous interventions on select risk factors, across multiple nested subsystems, provides greater exposure reduction than elimination of risk factors in any one subsystem. A nested epidemiological approach to studying and interrupting waterborne disease transmission extends the testing of causal assumptions beyond the domestic domain, enhances traditional case-control approaches and provides evidence for multi-scale interventions on both distal and proximal drivers of disease and environmental degradation.

Typhoid fever is a potentially-life threatening systemic disease caused by Salmonella Typhi, a human-restricted bacterium, spread through the faecal-oral route. Following a sustained rise in observed incidence in Fiji from 2004, in 2013, I undertook a nationally-representative cross-sectional serological survey of 1,531 participants to determine infection by age, assess putative risk factors, and quantify social contact patterns. These data were utilised in the development of a transmission dynamic model. The literature indicated that typhoid transmission models are relatively under-utilised, particularly in economic evaluation, with little to guide use of vaccination in place of or alongside water, sanitation and hygiene (WASH). The serosurvey found that iTaukei and non-iTaukei Fijians have similar risk of raised IgG antibodies to the Vi antigen expressed by S. Typhi. Seroprevalence increased with age, suggestive of endemic transmission or declining incidence. Unimproved sanitation may increase risk of seropositivity. Geospatial analysis suggested rainfall, proximity to major rivers and creeks, or flood-prone areas were risk factors for acquisition of anti-Vi IgG antibodies. Social mixing was assortative by ethnicity and age when assessed by mealtime contacts and highest in school-age children. Increasing number of age-adjusted contacts increases the odds ratio for being seropositive, though substantial uncertainties remain around the specificity and sensitivity of serological thresholds as indicators of past typhoid infection. An age- and ethnicity-structured transmission dynamic model fitted the serology and case surveillance data well when including a substantially reduced force of infection for high-dose infection being passed to non-iTaukei Fijians, and high generation of asymptomatic non-infectious cases per new infectious case. Surveillance reporting of infectious cases was estimated as one in five infectious adult cases and one in twelve infectious child cases. The fit to the data suggested endemic rather than declining transmission, and there was better fit with age-ethnic assortative mixing than with ethnically-assortative or homogeneous mixing. Vaccine scenarios suggested that of single dose routine programmes, school entry could be more effective than school leaver vaccination, reflecting age-contact transmission probabilities in the model. Modest reduction (10%) in per-case infectious transmission through effective WASH programmes offered substantial incidence reductions of around 25%, comparable to two-dose (school entry and exit) ViPS vaccination programmes. Potential benefits of conjugate vaccines were projected to be similar to more effective WASH programmes, with administration alongside other vaccines in the second year of life projected to offer approximately 50% incidence reduction, the most benefit of any single dose regimen; with the impact being greater if typhoid carrier daily infectious risk is lower than the daily infectiousness of acute typhoid fever cases.

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A febre tifóide (FT) é uma doença de distribuição universal, associada às precárias condições higiênico-sanitárias. Nas regiões Norte e Nordeste do Brasil a doença é endêmica, com ocorrência freqüente de surtos. A vigilância epidemiológica (VE) da FT representa importante ferramenta para detecção oportuna de surtos visando impedir ou dificultar a sua propagação. Objetivos: Avaliar o sistema de vigilância da febre tifóide no Brasil, entre os anos de 2001 a 2003. Métodos: Um estudo descritivo foi realizado baseado nas Diretrizes dos Centers for Disease Control and Prevention (CDC, EUA) publicado em 1988. A fonte de dados incluiu informações do Sistema de Informação de Agravos de Notificação (Sinan) e o Sistema de Informação sobre Mortalidade (SIM). Os atributos avaliados foram qualitativos (simplicidade, flexibilidade, aceitabilidade) e quantitativos (sensibilidade, valor preditivo positivo- VPP, representatividade, oportunidade). Resultados: O sistema de vigilância é complexo envolvendo vários níveis de gestão para transferência dos dados, com mais de 30 mil unidades notificadoras vários formulários para notificação de caso ou surto. A ficha individual de investigação apresenta mais de 70 campos. A aceitabilidade é baixa pela ausência de preenchimento de campos importantes para a VE: 54% das variáveis estavam incompletas em mais de 50% dos dados. A flexibilidade do sistema não foi possível avaliar pela ausência de informações. A sensibilidade do Sinan para óbitos foi baixa (19%) e ambos os sistemas detectaram apenas 54% dos óbitos estimados (N=52). O VPP dos casos encerrados pelo critério laboratorial foi abaixo: 29% em 2001, 44% em 2002 e 41% em 2003. O sistema foi oportuno, com uma mediana de 07 dias para a notificação após o início dos sintomas, < de 01 dia para a investigação e 25 dias para o encerramento dos casos. O sistema é representativo pela alta cobertura do Sinan e SIM no país, no entanto, há limitações quanto ao subregistro de casos. Conclusão: Apesar do baixo desempenho, o sistema de vigilância da FT é útil para análise das informações de morbidade e mortalidade e o efeito das medidas de controle e prevenção. Porém, o sistema precisa melhorar a sensibilidade e aceitabilidade para alcançar seus objetivos mais eficientemente. Desta forma, recomendamos capacitação dos profissionais de saúde na detecção, notificação e investigação de FT.
Salvador

Polysaccharide antigens are T cell-independent antigens, and do not induce immune B cell memory. Consequently, vaccines based on polysaccharides have limited clinical usefulness and induce short-lasting antibody responses in adults. Their immunogenicity can be enhanced by conjugation to an immunogenic carrier protein, generating T cell-dependent glycoconjugate antigens able to induce immunological memory. However, these glycoconjugates suffer from some problems. Recent investigations have found a group of structurally distinct bacterial polysaccharides able to activate T cells in vivo and in vitro. They present a zwitterionic charge motif distributed along the chain and, for this reason, they are called zwitterionic polysaccharides (ZPSs). This zwitterionic charge motif is believed to be responsible for their particular immunological behavior. The integrity of the zwitterionic motif is essential for the biological activity of ZPS. However, it must be clarified if the introduction of the zwitterionic motif into a naturally non-zwitterionic polysaccharide confers to the resulting ZPS the ability to activate T cells without protein conjugation. To this end, zwitterionic oligomers must be obtained by chemical modification of fully synthetic, non-zwitterionic polysaccharide fragments. With these compounds in hand it would be possible to correlate structural and conformational properties of the ZPS with their biological activity, in terms of charge pattern and minimum molecular weight required for immunogenicity. For this purpose the capsular polysaccharide (CPS) of Salmonella typhi was chosen as a suitable model for our investigation. S. typhi is an encapsulated Gram-negative bacterium that causes typhoid fever. Its CPS, commonly named Vi antigen, is an anionic polymer composed of alpha-(1-4)-linked N-acetylgalactosaminuronic acid repeating units predominantly O-acetylated at position 3. Recent studies indicated the importance of the acetylation for the immunogenicity. The structure of the Vi antigen makes it an ideal candidate for our investigation, since its fragments can be easily converted into zwitterionic derivatives by formal N-deacetylation, without introducing huge structural modifications. We designed a flexible synthetic strategy in order to obtain, from common building blocks, two distinct series of oligomers: the ones corresponding to the natural structure and their zwitterionic derivatives. Moreover, the role of 3-O-acetylation will be investigated by the synthesis of both fully 3-O-acetylated and fully 3-non-O-acetylated oligosaccharides. We selected N-phenyltrifluoroacetimidate moieties as the best leaving group in the glycosyl donors. Moreover, all the oligomers were endowed with a suitable linker at the anomeric position of the reducing end in order to facilitate subsequent conjugation to multivalent scaffolds. In the first part of the work the synthesis of oligomers non acetylated at position 3 is described. The glycosyl donor and acceptor were obtained from commercially available D-galactosamine hydrochloride. Their glycosylation was performed by a slow addition of a diluted solution of the Lewis acid via a syringe pump, and complete alpha stereoselectivity was obtained. We also successfully applied a more efficient elongation strategy based on disaccharide donors to the synthesis of the Vi trisaccharide and its zwitterionic derivative. Evaluation of the biological behavior of the target compounds was also performed by ELISA competitive assay. The second part of the work was focused on the synthesis of oligomers acetylated at C-3. In particular, a different approach based on pre-oxidized galacturonate building blocks obtained via inversion of C-4 configuration of commercially available D-glucosamine hydrochloride is described.

Enteric fever caused by Salmonella enterica serovars Typhi and Paratyphi A are a major public health concern in Kathmandu. The aim of this thesis was to identify and assess the population most at risk by investigating epidemiologic trends of enteric fever within a subset population of Kathmandu. Therefore,the burden and incidence of enteric fever within the study population and the seasonal and gender distribution of enteric fever was assessed. Considerable burden of enteric fever, unrelated to population density, correlating with the seasonal fluctuations in rainfall was observed. This thesis also aimed to improve the understanding of enteric fever transmission by identifying probable transmission routes,hence various water and food samples were analysed and the extent of faecal contamination in them was determined. S. Typhi isolates were sequenced and genotyped and combined with GPS data to longitudinally study the local distribution and infer transmission of this human restricted bacterial pathogen. Extensive clustering of typhoid independent of population size and density and existence of an extensive range of genotypes within typhoid clusters including individual households with multiple cases was observed. These observations predict that indirect transmission had an overwhelming contribution for disease persistence, potentially through contaminated water. Consistent with this hypothesis, S. Typhi and S. Paratyphi A were detected in water supplies and it was observed that typhoid was spatially associated with public water sources and low elevation. A concurrent case-control study was also conducted which allowed for the determination of risk factors in the population at risk. These studies imply that resources should be allocated toward controlling the most important vectors of enteric fever, including food sold by vendors, chlorination of drinking water, construction of proper water distribution and sewage networks,vaccination campaigns and hygiene education.

Enteric fever remains the most common febrile illness in urban Nepal. Some individuals may have recurrent infection and some may even progress to become long term chronic carriers. The aim of this thesis was to investigate the rate and factors leading to relapse with typhoid fever in patients who were enrolled in clinical treatment trials for acute enteric fever. The results show that relapses in enteric fever is a common complication and is more likely to be associated with the treatment antimicrobial, cefixime. Gallbladder carriage of invasive Salmonella is considered fundamental in sustaining enteric fever transmission as humans are the only known natural host. This thesis, therefore, also aimed to investigate the prevalence, characteristics, immunological responses, and mechanism of carriage of invasive Salmonella in the gallbladder by examining bile and tissue obtained from individuals who underwent cholecystectomy in Kathmandu. Data presented here demonstrate that S. Paratyphi A is almost as prevalent as S. Typhi in the gallbladder and that carriage may not be driven by antimicrobial resistance. Gallbladders that contained Salmonella were more likely to show evidence of acute inflammation with extensive neutrophil infiltrate. Chronic carriers were found to have dramatically elevated levels of IgG to O:2 and Vi antigens with high bactericidal activity yet low pro-inflammatory cytokine levels suggesting that Salmonella are stimulating a constant immunological response, in the form of antibody. S. Typhi may be controlling the inflammatory process through the expression of the Vi capsule in the gallbladder. Genome sequencing of S. Typhi isolated from chronic carriers were different from those S. Typhi causing acute disease. These data question the current dogmas surrounding the carriage of S. Typhi in gallbladder and predict a pivotal role of Vi capsule and gallstones in maintaining carriage. Therefore, prospectively identifying these individuals is paramount for rapid local and regional elimination. Furthermore, combining cytokine profiles and antibody levels may be a method of prospectively detecting carriers in the general population.

Dissertation presented as the partial requirement for obtaining a Master's degree in Statistics and Information Management, specialization in Information Analysis and Management
Malaria and typhoid fever are major causes of death in Sub-Saharan African countries. Due to the high risk of these two diseases in Sub-Saharan African countries and Nigeria in particular, this dissertation investigate the incidence of malaria and typhoid fever in Nigeria from January 2003 to December 2017 with the aim of identifying an appropriate statistical model that can be used to describe the trend of malaria and typhoid fever and make future projections of the two diseases in Nigeria which will serve as guide to policy makers in reducing the incidence of the two diseases. Several statistical methods were used in this research work. The Least Square Estimation was used to estimate the trend of both malaria and typhoid fever and the trend line equation obtained shows a gradual downward trend movement for both diseases. Arima modeling was used to describe the general behavior and pattern of occurrence of both diseases over the period under study and forecasts of future occurrence were made. SARIMA model was identified as the appropriate model for both malaria and typhoid fever. This result shows that the incidence of both diseases is influenced by seasonal factor. High occurrence of both diseases is expected around May to August according to the forecasts obtained in this study. The Chi-square test of association was used to ascertain if any form of association exists between gender and the diseases and the result obtained shows that there is no significant association between gender and the diseases. Correlation analysis conducted shows that there is a strong relationship between the two diseases.

This thesis represents the first anthropological perspective to be offered on the nature of the Klondike Gold Rush population. In order to better understand the experience of the average gold rusher, morbidity and mortality patterns are examined for the residents of the Yukon Territory following the discovery of gold in the region (1898-1904). Infectious diseases such as measles, pneumonia, smallpox and typhoid fever are the primary focus of this study, however local factors such as the severe climate and the seclusion of the gold fields from the outside world also offers an interesting opportunity to examine the consequences of leading a particularly harsh and physically demanding lifestyle in an inhospitable environment.
October 2008

Salmonella genus encompasses Gram-negative, rod-shaped, facultative anaerobic, non-sporulating, and predominantly motile enteric bacteria. It causes pathogenesis in a wide array of hosts, from cold-blooded animals to humans and diseases ranging from occasionally fatal systemic fever (Typhoid) to self-limiting diarrhea (gastroenteritis) in humans. Regardless of current medical advancements, Salmonella remains a significant cause of morbidity and mortality in developing countries. Salmonella remains enclosed in a vacuole inside the host cells, and these modified vacuoles are called Salmonella-containing vacuoles (SCV). In general, intracellular pathogens are subjected to the various host defense mechanisms, among which avoiding fusion with lysosomes is a prime challenge. Several intracellular bacteria have employed strategies to escape lysosomal degradation, such as Listeria spp., Shigella spp., E. coli K12, and Mycobacterium tuberculosis. Similarly, during the intracellular life of Salmonella, the SCVs are also targets for the lysosomes. Hence, Salmonella substantially alters host endo-lysosomal pathways to thrive inside the host cell. In our study, we have tried to decipher a novel molecular mechanism employed by Salmonella to modulate the host endo-lysosomal machinery to establish its replicative niche in otherwise hostile host cells. We found that Salmonella pathogenicity island 1 (SPI-1) effector SopB subverts host xenophagy by altering the phosphatidylinositol phosphate dynamics on the SCV membrane. It also mediates the downregulation of host lysosomal number, which is one of the prime strategies for establishing a replicative niche inside the host cell. Several of these fusion events of endo-lysosomal pathways are with the help of host syntaxin proteins. We further identified a crucial interaction of host Syntaxin 3 (STX3) with SCVs and observed that this interaction is SPI-2 dependent. Furthermore, this interaction with STX3 facilitates the division of the bacterium along with SCV and maintains a single bacterium per vacuole status, thus, facilitating a hospitable niche inside the host cells. Part I: To unravel the mechanisms employed by Salmonella SopB to subvert host cell xenophagy in macrophages. Salmonella survives and utilizes macrophages for effective dissemination throughout the host, causing systemic infection. One of the central host defense mechanisms in macrophages is xenophagy, or macro-autophagy where invading pathogens are targeted for degradation by fusion with lysosomes. The process of autophagy depends on the dynamics of phosphatidyl-inositol phosphates (PIPs) species present on the vesicular membranes. Salmonella, when inside intact SCV, escapes autophagy. However, the exact mechanism remains unknown. Interestingly, we observed that Salmonella SPI-1 effector SopB, which plays a crucial role in inducing uptake of bacteria inside non-phagocytic cells, inhibits the recruitment of various autophagic adaptor proteins such as Syntaxin 17 (STX17), microtubule-associated proteins 1A/1B light chain 3B (MAP1LC3B or LC3B), p62/SQSTM (sequestosome 1) onto the SCV membrane. Notably, we also found that SopB downregulates the transcript levels of these adaptor proteins and the overall autophagy flux inside host cells. We further demonstrate that SopB alters the PIP dynamics (PI3P and PI4P) of the SCV membrane. This activity of SopB helps the bacterium escape autophagy by inhibiting the fusion of SCVs with both lysosomes and autophagosomes. Part II: To decipher the mechanism behind the reduction in lysosomal number in Salmonella-infected cells. Previous work from our laboratory has shown that Salmonella infection causes a reduction in the overall lysosomal number inside the cell. This downregulation of lysosomal number facilitates survival of Salmonella inside host cells, as there are not enough lysosomes for the SCVs to fuse with and mediate clearance of the pathogen. While performing infection experiments with SopB mutants, we observed that the levels of LAMP1 and the number of lysosomes were significantly higher in SopB mutant infected cells than in STM WT. SopB has also been shown to activate Akt by phosphorylating Ser437 residue. In an independent study, it has been reported that Akt can further phosphorylate transcription factor EB (TFEB), which is a master regulator of the CLEAR (Coordinated Lysosomal Expression and Regulation) gene network. The phosphorylated TFEB is inactive and cannot translocate into the nucleus and hence cannot initiate the transcription of genes responsible for lysosomal biogenesis and autophagy. Therefore, we hypothesized that Salmonella SopB might also mediate overall downregulation through the Akt-TFEB axis in infected cells. We observed that SopB indeed reduced the number of acidic lysosomes inside the infected cells via the Akt-TFEB axis and thus facilitates the survival of Salmonella in host macrophages. These results were also validated in the mice model of Salmonella infection. Part III: To elucidate the role of host Syntaxins in Salmonella pathogenesis and its virulence. Intracellular membrane fusion is mediated by membrane-bridging complexes of soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs). SNARE proteins are one of the key players in the endosomal trafficking pathways. Recent reports shed light on intracellular bacteria modulating host syntaxin to establish infection successfully. Salmonella actively modulates its vacuole to escape lysosomal fusion. One of the critical SNAREs in macrophages responsible for phagosome maturation is Syntaxin 3 and Syntaxin 4. Also, there is a report which suggests that SCV harbors Syntaxin 12. Therefore, in the third part of the study, based on the literature available, we have screened a few Syntaxins in SCV biogenesis and found that STX3 could play a role in SCV biogenesis. Upon knockdown of STX 3, we have observed that the bacterial proliferation is hindered and is restored upon the overexpression of STX3. We observed using live-cell imaging that during infection, SCV interacts with STX3 and thus might help in fusion and fission events of SCV with other vesicles to acquire membrane for facilitating the division of SCV. We also found this interaction abrogated when we infected with SPI-2 encoded T3SS apparatus mutant (STM ∆ssaV) but not with SPI-1 encoded T3SS (STM ∆invC). Together, these results indicated that the effector molecule secreted through SPI-2 encoded T3SS is involved in interaction with host STX3, which is essential to maintain Salmonella division along with SCV and maintenance of a single bacterium per vacuole. Significant Findings and Conclusions: This study concludes that Salmonella modulates host endo-lysosomal machinery to establish replicative niches inside host cells. Mainly, SopB plays a dual role in subverting the host cell xenophagy in macrophages; (1) by modulating the phosphatidylinositol phosphates dynamics on the SCV membrane to inhibit fusion of SCV with autophagosomes or lysosomes and (2) it downregulates the overall lysosomal biogenesis through Akt-TFEB axis inside infected host macrophages. This study also elucidates one of the critical interactions with host STX3, which helps the bacteria inside the host cell to divide along with SCV and is essential for maintaining a single bacterium per vacuole. Overall, we have deciphered that through the involvement of various effector molecules, Salmonella substantially modulates the host endo-lysosomal machinery to cause pathogenesis in the host.
CSIR

Salmonella enterica sérovar Typhi (Typhi) est une bactérie pathogène spécifique à l’homme. Typhi est l’agent étiologique de la fièvre typhoïde chez l’humain, causant plus de 16 millions de nouveaux cas par année et plus de 600 000 morts. Il a été démontré que pour causer une infection systémique, Salmonella doit nécessairement survivre dans les macrophages de l'hôte. Paradoxalement, S. enterica sérovar Typhimurium, très apparenté à Typhi (près de 90 % d’homologie), n’a pas la capacité de se disséminer dans l’organisme humain et peut infecter plusieurs espèces animales. Nous avons antérieurement identifié 36 gènes uniques à Typhi (absents chez Typhimurium) situés sur 15 régions différentes et exprimés sélectivement lors de l’infection de macrophages humains. Ainsi, l’une de ces régions a suscité notre attention, soit la région sty4217-4222 et plus particulièrement le produit du gène sty4221, une aminotransférase hypothétique. Ce dernier gène est d’intérêt dû à l’homologie qu’il détient avec une hémolysine connue (Hly) produite par Treponema denticola, possédant elle-même une activité d’aminotransférase. Chez T. denticola, Hly dégrade la cystéine et produit du H2S qui est toxique pour l’hôte. Notre hypothèse est que la spécificité d’hôte et la capacité de produire une infection systémique de Typhi sont dues à l’expression de gènes qui ne se retrouvent pas chez d’autres salmonelles. Le but de cette étude était donc de caractériser le gène sty4221 quant à son activité hémolytique, cytotoxique et tenter de déterminer son rôle dans la virulence de cette bactérie. Le gène sty4221 a été cloné sous le contrôle d’un promoteur inductible à l’arabinose et exprimé par E. coli. L’activité hémolytique du clone a été déterminée par simple observation sur gélose sang. Ce clone a également permis d’observer l’effet cytotoxique du surnageant de culture sur différentes lignées cellulaires, par quantification de la relâche de LDH. Le gène sty4221 a été muté chez la souche sauvage de Typhi, ISP1820, l’implication pathogénique du gène a ainsi pu être étudiée. Des tests de phagocytose, d’invasion et de survie dans des macrophages humains ont été effectués, ainsi que des tests d’adhésion et d’invasion sur des cellules HeLa. Par ailleurs, une première tentative de purification de la protéine a été entreprise. En somme, nous savons maintenant que STY4221 a des propriétés hémolytiques, augmentées par la présence de cystéine. De plus, STY4221 a un effet cytotoxique sur les macrophages THP-I, mais aucun effet sur les HeLa. Or, sty4221 ne semble pas impliqué dans les étapes d’adhésion, d’invasion, de phagocytose ou de survie. La caractérisation de sty4221 permettra sans doute d’approfondir nos connaissances sur les toxines trouvées uniquement chez Typhi.
Salmonella enterica serovar Typhi (Typhi) is a human restricted pathogen causing typhoid fever, a systemic infection. Annually, at least 16 million new cases with 600, 000 associated deaths are reported. It has been demonstrated that Salmonella has to survive in the macrophages of its host, in order to produce a systemic disease. This ability to cause a disseminated infection in human is unique to Typhi. Our laboratory had isolated 36 genes that were unique to Typhi (absent from Typhimurium’s genome), and that were expressed during human macrophages infection. One of these genes, sty4221, a putative aminotransferase, was of high interest since it shares sequence similarities with a known hemolysin (Hly), which also possesses an aminotransferase activity. That hemolysin is produced by Treponema denticola, it catabolizes cysteine and produces H2S, a toxic metabolite for the host. Our hypothesis is that host specificity and the ability to cause a systemic infection might be explained by the expression of genes that are not found in other salmonellas. The goal of this study was to characterize the gene sty4221, in terms of hemolytic and cytotoxic activity and to determine its role in virulence. The sty4221gene has been cloned in a vector under an arabinose inducible promoter and transformed in a strain of E. coli. The hemolytic activity has been investigated on blood-agar medium. To evaluate the cytotoxicity of the STY4221 protein on human cultured cells, direct observation by photonic microscopy was done. The cytotoxicity activity on human cultured cells has been quantitatively measured with a lactate dehydrogenase release assay. Moreover, the sty4221 gene has been deleted in order to study its implication in the infection and the survival within human macrophages and for adhesion/invasion on epithelial. Protein purification was also attempted. We now know that protein STY4221 has a hemolytic activity that is enhanced by cysteine. Also, we proved that the expression of sty4221 has a cytotoxic effect on THP-I macrophages, but not on epithelial HeLa cells. Meanwhile, sty4221 does not seem to be important during adhesion, invasion, infection nor survival. The characterization of protein STY4221 might extend the list of known exotoxin of Typhi.

Le genre bactérien Salmonella regroupe plus de 2500 sérovars, mais peu sont responsables de pathologies humaines. Salmonella enterica sérovar Typhi (S. Typhi) est reconnu pour son importance médicale à travers le globe. S. Typhi cause la fièvre typhoïde chez l’Homme, une maladie infectieuse létale caractérisée par la dissémination systémique de la bactérie vers des organes du système réticulo-endothélial. La fièvre typhoïde représente un fardeau pour la santé mondiale, notamment auprès des pays en développement où les conditions sanitaires sont désuètes. La situation se complique davantage par l’apparition de souches résistantes aux antibiotiques. De plus, les deux vaccins licenciés sont d’efficacité modérée, présentent certaines contraintes techniques et ne sont pas appropriés pour les jeunes enfants et nourrissons. La phase systémique de l’infection par Salmonella repose sur sa survie dans les macrophages du système immunitaire. Dans ce compartiment intracellulaire, la bactérie module les défenses antimicrobiennes grâce à de multiples facteurs de virulence encodés dans son génome. Les mécanismes moléculaires sollicités sont complexes et finement régulés. Malgré les progrès scientifiques réalisés précédemment, plusieurs incompréhensions persistent au sujet de l’adaptation de ce pathogène dans les macrophages de l’hôte. Pour mieux concevoir les déterminants génétiques de S. Typhi impliqués dans l’interaction avec ces cellules, une stratégie de sélection négative a été appliquée afin de vérifier systématiquement l’effet direct des gènes pendant l’infection. En premier temps, une librairie de mutants par transposon chez S. Typhi a été créée pour l’infection de macrophages humains en culture. Après 24 heures d’infection, la présence des mutants fut évaluée simultanément par analyse sur des biopuces de Salmonella. Au total, 130 gènes ont été sélectionnés pour leur contribution potentielle auprès des macrophages infectés. Ces gènes comptaient des composantes d’enveloppe bactérienne, des éléments fimbriaires, des portions du flagelle, des régulateurs, des facteurs de pathogenèse et plusieurs protéines sans fonction connue. En deuxième temps, cette collection de gènes a dirigé la création de 28 mutants de délétion définie chez S. Typhi. Les capacités d’entrée et de réplication intracellulaire de ces mutants au sein des macrophages humains ont été caractérisées. D’abord, les macrophages ont été co-infectés avec les mutants en présence de la souche sauvage, pour vérifier la compétitivité de chacun d’eux envers cette dernière. Ensuite, les mutants ont été inoculés individuellement chez les macrophages et leur infectivité fut mesurée comparativement à celle de la souche sauvage. Sommairement, 26 mutants ont présenté des défauts lorsqu’en compétition, tandis que 14 mutants se sont montrés défectueux lorsque testés seuls. Par ailleurs, 12 mutants ont exposé une déficience lors de l’infection mixte et individuelle, incluant les mutants acrA, exbDB, flhCD, fliC, gppA, mlc, pgtE, typA, waaQGP, STY1867-68, STY2346 et SPI-4. Notamment, 35 nouveaux phénotypes défectueux d’entrée ou de survie intracellulaire chez Salmonella ont été révélés par cette étude. Les données générées ici offrent plusieurs nouvelles pistes pour élucider comment S. Typhi manipule sa niche intracellulaire, menant à l’infection systémique. Les gènes décrits représentent des cibles potentielles pour atténuer la bactérie chez l’humain et pourraient contribuer au développement de meilleures souches vaccinales pour immuniser contre la fièvre typhoïde.
The bacterial genus Salmonella holds over 2500 serovars, but few are responsible for human pathologies. Salmonella enterica serovar Typhi (S. Typhi) is recognized across the globe for its medical importance. S. Typhi causes typhoid fever in humans, a lethal infectious disease characterized by systemic dissemination of the bacteria to organs of the reticulo-endothelial system. Typhoid fever represents a burden for public health, notably in developing countries where sanitary conditions are obsolete. The situation is further complicated by the appearance of strains resistant to antibiotics. Moreover, both of the licensed vaccines are of moderate efficiency, present certain technical constraints and are not appropriate for young children and newborns. The systemic phase of infection by Salmonella relies on its survival within macrophages of the immune system. In this intracellular compartment, the bacterium modulates antimicrobial defenses thanks to multiple virulence factors encoded within its genome. Molecular mechanisms taking place are complex and finely regulated. Despite scientific advances made previously, many misunderstandings persist concerning the adaptation of this pathogen within host macrophages. To better conceive the genetic determinants of S. Typhi involved in interaction with these cells, a negative selection strategy was applied to systematically verify the direct effect of genes during infection. Firstly, a library of transposon insertion mutants in S. Typhi was created for infection of cultured human macrophages. After 24 hours of infection, the presence of mutants was evaluated simultaneously by analysis on Salmonella microarrays. In total, 130 genes were selected for their potential contribution within infected macrophages. These genes included bacterial envelope components, fimbrial elements, portions of the flagellum, regulators, pathogenesis factors, and many proteins of unknown function. Secondly, this collection of genes led to the creation of 28 defined deletion mutants in S. Typhi. The ability of entry and intracellular replication of these mutants within human macrophages were characterized. To start, macrophages were coinfected with mutants in the presence of the wild-type strain, in order to verify the competitiveness of each of them against the latter. Then, mutants were inoculated individually into macrophages and their infectiveness was measured in comparison with the wild-type strain. In summary, 26 mutants presented defects when in competition, whereas 14 mutants were shown defective when tested alone. Furthermore, 12 mutants exposed a deficiency during mixed and individual infection experiments, including mutants acrA, exbDB, flhCD, fliC, gppA, mlc, pgtE, typA, waaQGP, STY1867-68, STY2346, and SPI-4. In particular, 35 new defective phenotypes of Salmonella entry or intracellular survival were revealed in this study. Data generated here provides significant novel insight for elucidating how S. Typhi manipulates its intracellular niche, leading to systemic infection. Genes described represent potential targets for attenuating the bacteria in the human host and could contribute to the development of better vaccine strains to immunize against typhoid fever.