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Chlamydia, caused by the bacterium Chlamydia trachomatis, is one of the most important sexually-transmitted infections globally. In addition to accounting for millions of cases every year, the disease causes numerous irreversible complications such as chronic pelvic pain, infertility in females and pelvic inflammatory disease. This thesis presents a number of mathematical models, of the form of deterministic systems of non-linear differential equations, for gaining qualitative insight into the transmission dynamics and control of Chlamydia within an infected host (in vivo) and in a population. The models designed address numerous important issues relating to the transmission dynamics of Chlamydia trachomatis, such as the roles of immune response, sex structure, time delay (in modelling the latency period) and risk structure (i.e., risk of acquiring or transmitting infection). The in-host model is shown to have a globally-asymptotically stable Chlamydia-free equilibrium whenever a certain biological threshold is less than unity. It has a unique Chlamydia-present equilibrium when the threshold exceeds unity. Unlike the in-host model, the two-group (males and females) population-level model undergoes a backward bifurcation, where a stable disease-free equilibrium co-exists with one or more stable endemic equilibria when the associated reproduction number is less than unity. This phenomenon, which is shown to be caused by the re-infection of recovered individuals, makes the effort to eliminate the disease from the population more difficult. Extending the two-group model to incorporate risk structure shows that the backward bifurcation phenomenon persists even when recovered individuals do not acquire re-infection. In other words, it is shown that stratifying the sexually-active population in terms of risk of acquiring or transmitting infection guarantees the presence of backward bifurcation in the transmission dynamics of Chlamydia in a population. Finally, it is shown (via numerical simulations) that a future Chlamydia vaccine that boosts cell-mediated immune response will be more effective in curtailing Chlamydia burden in vivo than a vaccine that enhances humoral immune response. The population-level impact of various targeted treatment strategies, in controlling the spread of Chlamydia in a population, are compared. In particular, it is shown that the use of treatment could have positive or negative population-level impact (depending on the sign of a certain epidemiological threshold).

La chlamydiose génitale est une infection transmise sexuellement causée par la bactérie intracellulaire obligatoire Chlamydia trachomatis. Avec une incidence en constante augmentation depuis 1997, la chlamydiose génitale représente aujourd’hui la maladie à déclaration obligatoire la plus rapportée au Canada et correspond à 80% de l'ensemble des ITS diagnostiquées. Par contre, environ 15% des patients traités pour la chlamydiose génitale sont toujours infectés après la fin du traitement. Au-delà des réinfections possibles à la suite de contacts sexuels non-protégés avec un partenaire infecté, nous avons émis l’hypothèse que des causes bactériennes puissent être responsables des cas d'échec de traitement et d'infection persistante. Les travaux de recherches présentés dans ce mémoire ont donc eu pour objectifs de déterminer si la résistance à l’azithromycine, la charge bactérienne de l’infection ou un génotype particulier de la bactérie, pourraient être associés aux cas d'échec de traitement et d’infection persistante. Pour ce faire, une étude rétrospective de type cas-témoins composée de 204 patients ayant eu deux épisodes de chlamydiose génitale ou plus entre 2002 et 2012 (506 spécimens cliniques analysés au total) a été mise sur pied. En se servant de Campylobacter jejuni comme organisme modèle, il a été possible de développer une nouvelle méthode de détection moléculaire des mutations ponctuelles basée sur la PCR en temps réel, que nous avons nommée TaqTm Probing. Cette méthode a par la suite été exploitée pour chercher des mutations pouvant conférer une résistance à l’azithromycine chez C. trachomatis. Toujours par PCR en temps réel, une méthode d’évaluation semi-quantitative de la charge bactérienne des spécimens cliniques a aussi été mise au point et les spécimens ont été caractérisés par le typage de la protéine majeur de la membrane externe. Aucun cas de résistance n'a été observé, ni d’ailleurs de lien entre la charge bactérienne et l’évolution de l'infection vers un état de persistance ou d'échec de traitement. Par contre, il s'est avéré qu'une infection par le génotype E était significativement associée aux cas d'échec de traitement et d'infection persistante et augmentait le risque de survenue. Il sera important d'identifier subséquemment les mécanismes moléculaires impliqués.

Contexte : L'infection génitale à Chlamydia trachomatis (C. trachomatis ) est un important problème de santé publique car elle peut entraîner de graves séquelles en matière de reproduction, y compris l'atteinte inflammatoire pelvienne, l'infertilité tubaire et la grossesse ectopique. On retrouve une absence de symptômes de l'infection à C. trachomatis chez 70% des femmes infectées ce qui apporte une morbidité élevée car, même si l'infection est facilement curable, elle doit d'abord être dépistée. Objectif : L'objectif principal de la recherche est d'établir le risque de développer un problème de fertilité féminine après une infection à C. trachomatis et sa récidive. Méthode : L'étude de cohorte rétrospective, qui a eu lieu entre les années 1996 et 2011, a permis l'observation de deux groupes de femmes, âgées entre 15 et 24 ans, selon leur exposition à une infection à C. trachomatis . Avec une médiane de 7 ans pour le temps de suivi, les analyses de régressions se sont portées principalement sur les issues de reproduction telles que la naissance et le diagnostic d'infertilité tubaire. L'échantillon est constitué de 5,057 femmes qui ont effectué 12,301 examens de C. trachomatis avec seulement 8,6% de tests positifs. Résultat : Les analyses semblent démontrer que le potentiel d'accoucher est significativement moindre chez les femmes qui ont été exposées à une infection à C. trachomatis , pour un rapport de cote brut de 0,82 (IC à 95% : 0,67-0,99) et un RC ajusté, pour l'âge et d'autres infections vaginales, de 0,84 (0,69-1,02). Lorsqu'on stratifie selon l'âge, le RC ajusté indique 0,71; IC 95% (0,53-0,94) pour le groupe des 20-24 ans alors qu'il est sans effet chez les 15-19 ans. En ce qui concerne l'infertilité, on constate un risque significatif 3 fois plus élevé de développer une infertilité tubaire, RC brut de 2,81 (1,04-7,56), après avoir obtenu au moins une infection à C. trachomatis . Lorsqu'on ajuste pour l'âge, la tendance indique un RC ajusté de 1,52 (0,41-2,75). Conclusion : Les résultats de cette étude suggèrent qu'une infection à C. trachomatis contribue à l'infertilité tubaire et diminue le taux de natalité chez une femme. L'impact de l'infection se manifeste principalement chez les femmes âgées entre 20 et 24 ans lorsque la durée de suivi est minimalement de 4 ans suite au premier test à C. trachomatis . La détection et le traitement de l'infection doit se faire, particulièrement chez les femmes asymptomatiques, avant le développement de séquelles. La fréquence du dépistage doit être suffisante pour permettre une détection précoce.

Chlamydia, caused by the bacterium Chlamydia trachomatis, is one of the most important sexually-transmitted infections globally. In addition to accounting for millions of cases every year, the disease causes numerous irreversible complications such as chronic pelvic pain, infertility in females and pelvic inflammatory disease. This thesis presents a number of mathematical models, of the form of deterministic systems of non-linear differential equations, for gaining qualitative insight into the transmission dynamics and control of Chlamydia within an infected host (in vivo) and in a population. The models designed address numerous important issues relating to the transmission dynamics of Chlamydia trachomatis, such as the roles of immune response, sex structure, time delay (in modelling the latency period) and risk structure (i.e., risk of acquiring or transmitting infection). The in-host model is shown to have a globally-asymptotically stable Chlamydia-free equilibrium whenever a certain biological threshold is less than unity. It has a unique Chlamydia-present equilibrium when the threshold exceeds unity. Unlike the in-host model, the two-group (males and females) population-level model undergoes a backward bifurcation, where a stable disease-free equilibrium co-exists with one or more stable endemic equilibria when the associated reproduction number is less than unity. This phenomenon, which is shown to be caused by the re-infection of recovered individuals, makes the effort to eliminate the disease from the population more difficult. Extending the two-group model to incorporate risk structure shows that the backward bifurcation phenomenon persists even when recovered individuals do not acquire re-infection. In other words, it is shown that stratifying the sexually-active population in terms of risk of acquiring or transmitting infection guarantees the presence of backward bifurcation in the transmission dynamics of Chlamydia in a population. Finally, it is shown (via numerical simulations) that a future Chlamydia vaccine that boosts cell-mediated immune response will be more effective in curtailing Chlamydia burden in vivo than a vaccine that enhances humoral immune response. The population-level impact of various targeted treatment strategies, in controlling the spread of Chlamydia in a population, are compared. In particular, it is shown that the use of treatment could have positive or negative population-level impact (depending on the sign of a certain epidemiological threshold).

Chlamydia trachomatis infections are among the most frequently reported causes of human sexually transmitted infection. In Australia, the reported rate of infection in 2004 reached 175 per 100,000 population, the highest rate since surveillance of the condition began in 1991. Severe adverse sequelae that commonly occur following progression of the infection from the lower to the upper genital tract include pelvic inflammatory disease, infertility and ectopic pregnancy. However the frequent prevalance of asymptomatic infection makes diagnosis and treatment often late and therefore ineffective against upper genital tract complications. Hence there is a great need to develop a vaccine to protect against the sexual transmission of C.trachomatis. Despite many years of research investigating potential vaccine strategies to prevent sexually transmitted C.trachomatis infections, there remains no commercially available C.trachomatis vaccine. Early research showed that the use of live, attenuated or inactivated whole Chlamydia as a vaccine was not a viable option due to adverse effects caused by immunopathogenic cellular components. The early human vaccine trials that utilized whole chlamydial cells and resulted in exacerbated disease when immunized individuals were re-exposed to Chlamydia have led to the investigation of chlamydial subunit components as potential vaccine antigens. The most widely investigated vaccine candidate antigen is the major outer membrane protein (MOMP) as it is known to be immunogenic and surface exposed. Much research using this antigen has been undertaken with the antigen being delivered as a protein, peptide or DNA, via many mucosal and systemic routes of immunization, and in combination with various vaccine adjuvants. However, at best only partial protection against a chlamydial genital tract infection has been achieved. Only a few alternative candidate antigens have been investigated as potential vaccine targets to protect against chlamydial infections. These include the outer membrane porin PorB, the large cysteine rich outer membrane protein Omp2 and the heat shock proteins DnaK and GroEL. Although other candidate antigens have been predicted in various models of chlamydial infection (Finco et al., 2005; Stemke-Hale et al., 2005; Li et al., 2006), few have been tested for their protective efficacy. The aim of this study was to use expression library immunization to screen the whole C.muridarum genome for novel vaccine candidates capable of protecting against a chlamydial genital tract infection. C.muridarum was selected as the disease model for chlamydial genital tract infection as it has similarities to C.trachomatis in pathogenesis, immune response to infection and gene content and order. Once protective antigens had been isolated from an expression library, these were screened individually for immunogenicity and protective efficacy in the C.muridarum model of infection. An expression library containing over 21,000 recombinant C.muridarum clones was constructed and divided into pools of clones. DNA was extracted from these pools and used to immunize mice through gene gun technology, delivering 1μg of DNA to the abdomen of mice. Following the immunization regime, mice were challenged intra-vaginally with live C.muridarum as this route of infection best resembles the natural route of infection that is responsible for the sexual transmission of C.trachomatis in humans. Four in vivo screens of the C.muridarum expression library, each time using reduced numbers of clones, resulted in the identification of seven novel vaccine antigens that conferred protection against a genital tract challenge infection in mice. These warrant further investigation as vaccine antigens in the development of a vaccine against C.trachomatis infection. The identified antigens include antigens not conventionally believed to be potential vaccine candidates such as hypothetical proteins and housekeeping genes, including a DNA gyrase subunit, TC0462, and the ATP-dependent Clp protease, ATP-binding subunit ClpC, TC0559. Other antigens identified were more traditional, surface exposed vaccine targets that have not been previously investigated as vaccine targets, including a novel outer membrane protein, TC0512, a polymorphic membrane protein, TC0693, and TC0850, a protein of the type three secretion system, a family of proteins that allow gram-negative bacteria to inject virulence related proteins into the cytoplasm of a host cell. All antigens were shown to be partially protective with the putative outer membrane protein TC0512 showing an overall reduction in chlamydial burden of 55% and other antigens showing overall reductions in chlamydial burden of 26 - 44%. These antigens were also either capable of stimulating an immune response, or predicted to contain epitopes that may stimulate strong immune responses and so warrant further investigation as vaccine antigens to protect against chlamydial genital tract infections. The results of this research demonstrate that it is possible to identify novel vaccine targets through screening an expression library in a disease model. This study has identified several novel vaccine targets that are partially-protective against a C.muridarum infection and that are thought to be capable of stimulating strong immune responses. These antigens have high homology with C.trachomatis sequences, indicating that they have potential as vaccine candidates capable of protecting against the serovars of C.trachomatis that cause sexually transmitted infections in humans. Although the protection observed in this study was only partial, the immunization strategy utilised only fragments of the genes, an immunization mechanism known to elicit Th2 type immune responses, and no adjuvant to enhance the immunogenicity of the antigens. Through different immunization routes and in conjunction with adjuvants that stimulate Th1 type immune responses, complete protection against chlamydial genital tract infections may be achieved.

Chlamydia trachomatis is a human pathogen of the genital tract and ocular epithelium. It is an obligate intracellular parasite with a unique biphasic development cycle. C.trachomatis infection is the most common bacterial sexually transmitted disease in industrialized nations. Its ability to cause chronic disease makes it a serious economic burden and health threat to developed and developing countries. Although treatable, approximately 70% of C.trachomatis infections are asymptomatic, potentially leading to the development of chronic sequelae. Furthermore, chlamydial genital tract infection has been associated with an increased risk of cervical cancer and human immunodeficiency virus infection. Consequently, the development of an efficacious vaccine is the most convenient, potentially reliable and cost effective option to control chlamydial infection and disease complications. Anti-chlamydial protective immunity is essentially mediated by a T helper, type 1 (Th1), response that is dependent upon the presentation of antigen via major histocompatibility (MHC) class II molecules. While antibody secreting cells are not critical components of the primary effector response, they have been shown to be important for clearance of re-infection. Thus an ideal vaccine would be one capable of inducing both a strong Th1 T cell response and a strong mucosal antibody response. Currently there are very few efficacious vaccine candidates that have been identified and characterized. More specifically, there is only a limited number of known T cell antigens processed and presented by the human leukocyte antigen (HLA) class II molecules. This type of antigen is going to be essential to the development of an efficacious chlamydial vaccine. In this study we have identified a number of unique vaccine candidates using a novel in silico approach. In an attempt to overcome HLA polymorphism the whole chlamydial genome was screened for proteins containing epitopes predicted to bind multiple HLA class II molecules (i.e. predicted ‘promiscuous’ T cell epitopes). A wide range of HLA class II molecules were used in this screen to identify vaccine antigens that could potentially offer broad and ethnically balanced population coverage. This analysis identified a number of novel targets and was validated by the identification of a known chlamydial T cell epitope. A selection of these target proteins was cloned, expressed and purified. Recombinant protein was screened against serum samples from patients with both acute and chronic chlamydial infections. Two novel targets, hypothetical protein CT425 and ribonucleotide reductase small chain protein (NrdB) were identified as being immunoreactive. The in vivo protective efficacy of NrdB was analyzed using a mouse model. CD4+ T cells were harvested from NrdB immunized mice and adoptively transferred to naïve mice, which were subsequently infected at the genital site. NrdB immunization was found to confer a CD4+ T cell driven degree of protection similar to that seen with CD4+ T cells primed from a live challenge. The adjuvants and route of immunization used ensured immunological responses were initiated at both the systemic and local sites of infection. Immunization elicited a predominant Th1 response with primed T cells producing high levels of interferon gamma, an essential requirement for the development of an efficacious chlamydial vaccine. Furthermore, high titres of antigen specific IgG and IgA were produced following immunization, with sera derived antibodies demonstrating neutralization properties. NrdB is a highly conserved chlamydial protein with an essential role in the replication of chlamydiae and could play a central role in a multi-subunit vaccine against chlamydial genital tract infections.

The asymptomatic nature of chlamydial infection renders the differential diagnosis of acute and chronic infection difficult. An untreated Chlamydia trachomatis infection can become chronic, result in disease sequelae such as salpingitis and pelvic inflammatory disease (PID), and ultimately culminate in tubal occlusion and infertility. Diagnostic tests for C. trachomatis such as nucleic acid amplification testing (PCR), antigen detection and serological methods have variable performance capabilities with respect to sensitivity, specificity and stage of infection. The use of PCR as a diagnostic tool is somewhat limited, as specimen collection is routinely sampled from the lower genital tract; hence, infections in the fallopian tube where inflammatory damage is most significant, escape detection. Furthermore, PCR can only detect selected Chlamydia DNA sequences from readily accessible sites of the genital tract, and therefore cannot differentiate between acute and chronic infection. Other serological assays aim to discriminate the various stages of C. trachomatis infection through identification of key antigens. The efficacy of these assays however is impeded due to cross-reactivity between chlamydial species and the subsequent antibody response against the target antigen is not restricted to patients with a specific stage of infection. To identify antibody responses capable of differentiating various states of chlamydial infection, samples were collected from both men and women given the variability of immune responses between the two genders. Samples were assigned to a patient group according to infection status and then probed against protein extracts of HEp-2 cells infected with C. trachomatis serovar L2 and HEp-2 cells pre-treated with IFN-γ and infected with C. trachomatis serovar L2. (persistence cell culture) Serological analysis revealed the presence of five antigens (denoted bands A, B, C, D and M) which were shown to be differential between patient groups. Identification of bands B and C by N-terminal sequencing provided two possible candidates for each antigen, ie. CT727 and CT396 (band B) and CT157 and CT423 (band C). In contrast, band M which was unique to males was a PmpB (probable outer membrane protein B) fragment. The four target antigens (CT157, CT423, CT727 and CT396) were expressed as recombinant proteins using autoinduction media and were subsequently probed by both male and female sera to evaluate their diagnostic potential. Results showed that two chlamydial antigenic targets (CT157 and CT727) have the potential to discriminate between acute and chronic C. trachomatis infection. However, since only a small number of samples (n = 3) were used for this aspect of the study, the findings should simply be viewed as preliminary. In females, sensitivity and specificity values were derived using various combinations of the four target antigens into a panel format for the purpose of detecting chronic C. trachomatis infections. The preferred format was B + C with a sensitivity and specificity of 80% and 84% respectively. Using the IFN-γ-mediated persistence model, only two of the five antigenic targets were shown to be differentially expressed. PmpB in males and CT157 (the most likely band C candidate) in females were shown to be up-regulated to varying degrees in samples across the patient groups. We also demonstrated that no other chlamydial antigens are up-regulated during a persistent C. trachomatis infection. In conclusion, although combinations of bands A, B, C, D and M differentiate between male and female patient groups under normal chlamydial growth conditions, during IFN-γ-induced persistence, only bands C (CT157) and M (CT413 - PmpB) are up-regulated thus suggesting a potential role in chronic C. trachomatis infection.

This thesis presents data on two separate areas relevant to the prevention of HIV and sexually transmitted infection (STI) transmission in homosexual men. These data arise from the community-based Health in Men (HIM) cohort of HIV-negative homosexual men in Sydney. First, the association of circumcision status with HIV and STIs was examined. Older age, ethnicity and country of birth were demographic factors independently associated with circumcision status. Self-report was a valid measure of circumcision status in this population. Overall, being circumcised was associated with a non-significant reduced risk of HIV seroconversion in the HIM cohort (HR 0.76, 95% CI 0.41-1.41, p=0.381). Among the one-third of participants predominantly practising the insertive role in anal intercourse (AI), being circumcised was associated with a significantly reduced risk of HIV infection (HR 0.15, 95% CI 0.03-0.80, p=0.026). Circumcised HIM participants also had a lower risk of incident syphilis (HR 0.35, 95% CI 0.15-0.84, p=0.019), however circumcision status had no significant effect on the remainder of prevalent and incident STIs examined. Second, risk factors for pharyngeal gonorrhoea and chlamydia were investigated. The BD ProbeTec nucleic acid amplification test (NAAT) had a positive predictive value (PPV) for pharyngeal gonorrhoea diagnosis of only 30.4% (95% CI 25.2-36.1%) when compared to a previously validated NAAT targeting the gonococcal porA pseudogene. Pharyngeal gonorrhoea was common in HIM, mostly occurred without concurrent anogenital infection and may frequently spontaneously resolve. Infection was independently associated with younger age (p-trend=0.001), higher number of male partners (p-trend=0.002), contact with gonorrhoea (p<0.001) and insertive oro-anal sex with casual partners (p-trend=0.044). Pharyngeal chlamydia was less common but a high prevalence/incidence ratio suggested that infection may persist in the pharynx for long periods. Pharyngeal chlamydia was independently associated with receptive penile-oral sex with casual partners (p-trend=0.009). In conclusion, circumcision may have a role as an HIV prevention intervention among the subgroup of homosexual men who predominantly practise insertive rather than receptive AI. Regular screening of the pharynx including a validated supplemental NAAT for gonorrhoea diagnosis may prevent much transmission to anogenital sites, whereas chlamydia occurs too infrequently in the pharynx to recommend routine screening in homosexual men.

Good sexual and reproductive health is fundamental to the overall health status of Māori communities. In 2001, the Ministry of Health reported that New Zealand was facing a Chlamydia epidemic. This epidemic has not abated as rates of Chlamydia have increased significantly in the past five years, with disproportionately high rates in young Māori women compared to non-Māori women. Despite significant sexual health disparities, young Māori have had limited opportunities to participate in research focussed on sexual health and voice their opinions and concerns on sexual health issues. This qualitative descriptive study has used a Māori inquiry paradigm and approached the research from a Kaupapa Māori perspective. The primary research question asked what the knowledge, attitudes and reported behaviours of young urban Māori women were in regards to sexual health and in particular, the sexually transmitted infection Chlamydia. Secondary aims were to ascertain the sources of information used and accessibility of sexual health services, as well as identifying resilience factors associated with protection against Chlamydia infection. The data was collected from semi-structured interviews with 16 young Māori women living in the Auckland region. Data analysis involved the inductive approach of categorical content analysis to identify major categorical themes to answer the specific questions posed. The main conclusion was that there are a number of barriers to accessing quality sexual health information and services for young Māori women. Participants’ level of knowledge varied reflecting their personal experiences and many were unaware that Chlamydia is asymptomatic and that delayed diagnosis can lead to fertility problems. The main sources of sexual health information accessed were whānau, peers, school, and contact with health professionals. Racism was identified as one of the barriers to sexual healthcare services. The young women expressed a clear preference for sexual health services to be delivered by Māori. Most importantly, for sexual health interventions to be successful it is essential that Māori communities, including young people and their whānau, are an integral part of creating positive solutions. Resilience factors that may help protect young women from contracting chlamydia characteristic of this group were having a strong connection with a caring adult or friend and parents who viewed sexuality as a normal part of adolescent development. In addition, having a positive Māori cultural identity with an ability to understand bicultural differences was strongly associated with participants accessing sexual healthcare services despite identified barriers.