Helminth infections induce systemic changes to host immunity and can impact unrelated infections, even those occurring at anatomical sites not normally colonised by the helminths. A few studies have shown that helminths can increase the risk of infection and pathology resulting from sexually transmitted viral infections in the female reproductive tract, however the evidence is limited and the scope of helminth infection on immunity and infection in the female reproductive tract has not been fully elucidated. In this thesis the impact of hookworm infection on immunity in the female reproductive tract and risk of Human Papillomavirus infection in humans was investigated. The influence of helminth infection on B and T cell responses in the female reproductive tract and how this impacts vaccine mediated responses to another viral infection of the female reproductive tract, Herpes Simplex Virus, Type 2 was also assessed in a mouse model. To determine the risk of Human Papillomavirus among hookworm infected participants, we compared the prevalence of Human Papillomavirus infection among hookworm infected and uninfected women. Hookworm infected women were two times more likely to be Human Papillomavirus positive than women with no hookworm infection. Furthermore, hookworm infection was positively associated with the intensity of Human Papillomavirus infection. To determine whether hookworm infection induced changes in vaginal immunity we employed multiplex assays to measure chemokine, cytokine and antibody levels in the vaginal flushes of our study participants. Hookworm infected women displayed an elevated mixed Type 1 (TNF-a, IL-2 and IL-12) and Type 2 (IL-4, IL-5, IL-13, eotaxin and elevated IgG4/ IgE ratio) immune response in the female reproductive tract in xvi comparison to uninfected women. Type 2 immunity was pronounced in hookworm and Human Papillomavirus co-infected women who maintained an elevated Type 2 signature (IL-4, IL-5, IL-13, eotaxin and elevated IgG4/ IgE ratio) and an increased Th2/Th1 ratio in comparison to uninfected women. We then investigated the impact of primary helminth infection on B and T cell immunity in the female reproductive tract using the mouse model of hookworm infection, Nippostrongylus brasiliensis. Nippostrongylus brasiliensis infection of wild type BALB/c mice resulted in increased B cells, IgG1+ B cells and IgG1+ follicular B cells as well as increased effector memory T cells and T follicular helper cells in iliac lymph nodes, which drain the female reproductive tract. We then infected wild type BALB/c mice with Nippostrongylus brasiliensis and immunised them with formalin inactivated Herpes Simplex Virus, Type 2 then challenged them intravaginally with lethal dose Herpes Simplex Virus, Type 2. Nippostrongylus brasiliensis infection did not significantly impact B cell responses to vaccination and subsequent challenge though there was a trend towards lower B cell responses in mice that received Nippostrongylus brasiliensis treatment prior to vaccination. Mice that had prior Nippostrongylus brasiliensis infection, however, had significantly lower effector memory CD4+ T cells than mice that did not have helminth infection before vaccination. In summary, this thesis demonstrates that helminth infection induces Type 2 associated immune changes in the female reproductive tract in humans and alters B and T cell populations in lymph nodes draining the female reproductive tract of mice. Furthermore, in humans, an increased risk of Human Papillomavirus infection and increased intensity of Human Papillomavirus infection was associated with hookworm infection. In mice, a dampening of Herpes Simplex Virus, Type 2 vaccine mediated xvii effector CD4 T cells responses and increased pathology following viral challenge was observed in mice previously infected with Nippostrongylus brasiliensis. The findings in this thesis highlight helminth infection as a significant risk factor for sexually transmitted viral infections and have implications for control of these infections among women living in helminth endemic areas.

<p> Bacterial strains from the <i>Mycobacterium tuberculosis</i> complex (MTBC) are functionally diverse and vary in both geographic distribution and potential to cause tuberculosis (TB) disease. <i>Mycobacterium africanum </i>&mdash;a lineage of the MTBC&mdash;is restricted to West Africa and causes slower progression to active tuberculosis (TB) after initial infection than other MTBC lineages. We hypothesized that this may be partly due to how bacterial strains from these lineages interact with the host immune response. Specifically, we predicted that <i>M. africanum</i> would induce less of the innate cytokine type I interferon because type I interferon has been shown to contribute to TB disease. Our studies focused on (1) whether diverse MTBC strains induce distinct levels of type I interferon in host cells, (2) the mechanism underlying differential type I interferon induction by diverse MTBC strains, and (3) the consequences of the type I interferon response during infection with diverse MTBC strains. We found that <i>M. africanum</i> induced less mitochondrial stress, less release of mitochondrial DNA and less cGAS- and STING-dependent type I interferon in macrophages than other <i> M. tuberculosis</i> strains. Furthermore, we found that <i> M. africanum</i> contained a polymorphism in the Esx-1 gene locus and was unable to secrete the virulence factor EspB through the Esx-1 secretion system, which may contribute to the reduced type I interferon induction by this strain. Finally, we found that type I interferon signaling was pathogenic during chronic <i>M. africanum</i> infection in mice, and thus that the ability to induce pathogenic levels of type I interferon is likely widespread in MTBC strains. Our data suggest that reduced mitochondrial stress and reduced type I interferon induction may contribute to the attenuation of <i> M. africanum</i>. Moreover, our data show that treatments that limit type I interferon induction could be effective in treating diverse mycobacterial infections. Therefore our studies provide insight into a mycobacterial virulence mechanism and highlight the importance of studying diverse clinical isolates of <i>M. tuberculosis</i>.</p><p>

<p> <i>Clostridium difficile</i> is an anaerobic, gram-positive bacterium that is responsible for the majority of hospital-associated gastrointestinal infections. It has been recognized as a pathogen since the 1970s but more recently has become an urgent threat to public health. <i>C. difficile </i> produces two powerful toxins that disrupt the integrity of the colonic epithelium and induce a strong inflammatory response. Susceptible individuals experience symptoms that range from mild, self-limiting diarrhea to fulminant pseudomembranous colitis and even death. However, most healthy individuals are protected from <i>C. difficile</i> infections so long as they are able to maintain a diverse population of commensal bacteria in their gut. Disruptions to these commensals, often from antibiotic therapy, provide the niche <i>C. difficile</i> spores need to germinate, produce toxins, and cause disease. Current first-line therapy for infections is additional antibiotics that lead to a high risk of relapse. In fact, we found that short course antibiotic therapy leaves mice susceptible to additional infections in the days and weeks that the commensal microbiota spends recovering to pre-antibiotic levels. Beyond requiring disruptions to the microbiota before colonization, <i>C. difficile</i> is composed of hundreds of different strain subtypes. The variability in disease severity induced by each of these different subtypes has been hampered by diverse sources of human patient data and has confused the literature for years. We found that the mouse model could be used successfully to quantify the differences in disease burden of phylogenetically diverse <i>C. difficile</i> clinical isolates. Our results demonstrate that differences in observed virulence have less to do with the amount of toxin each isolate produces and more to do with its tolerance to secondary bile acids like lithocholic acid. In addition, whole genome sequencing allows us to identify groups of genes that are associated with highly lethal strains. This work emphasizes the need to evaluate the impact of antibiotic therapy and infecting strain when assessing and treating <i>C. difficile</i> infections.</p><p>

Asthma is the most common chronic respiratory disease affecting young children and adults all over the world. An estimated 34.1 million Americans have reported asthma in their lifetime and the disease costs ∼US $56 billion dollars to treat each year. Current treatment is based on a paradigm of asthma as a non-infectious atopic condition whose root cause is inflammation. Chronically administered anti-inflammatory medications, primarily inhaled corticosteroids (ICS), ameliorate asthma symptoms in many patients. However, up to 50% of asthmatics, characterized by neutrophil infiltration, IL-17 secretion and increased risk of fatality are refractory to ICS treatment. Chlamydia pneumoniae , a ubiquitous, obligate intracellular pathogen with an innate propensity to persist and cause chronic infections, along with Mycoplasma pneumoniae have been implicated in the development of chronic, refractory asthma. C. pneumoniae infections are common in infants and young children, often coinciding with the development of early onset asthma in the population. These facts lead the Webley lab to evaluate the carriage of Chlamydia in pediatric respiratory disease patients and the work confirmed that respiratory infections caused by Chlamydia is a significant risk factor in asthma development and live Chlamydia was isolated from the lungs of children with chronic asthma. However, the exact mechanism underlying chlamydial involvement in the disease remained unknown and we believed that a better understanding could shed important light on expanded treatment options and mechanisms of this infectious asthma phenotype. The work presented here provides new insight into how (1) early life chlamydial infection can lead to asthma initiation and exacerbation (2) respiratory chlamydial infection induces cellular and chemical immune responses that support asthmatic inflammation (3) other respiratory pathogens (eg. Mycoplasma) can drive similar immunological responses resulting in significant lung pathology.

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 <en>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.