Medicine (St Vincent's) - Theses
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ItemPredicting response to anti-TNF therapy in Crohn's disease: clinical and metabolic studies( 2018)Crohn’s disease is a chronic, disabling inflammatory condition that affects the gastrointestinal tract that is associated with significant morbidity. Up to 80 percent of patients require surgery at some point in their lives. A third of patients require surgery within five year of diagnosis even in the era of biologic therapy. Ant- Tumour Necrosis Factor alpha (Anti-TNF) therapies form the backbone of drug therapy in patients with moderate to severe Crohn’s disease and remain the most effective biologic drugs available. There are currently three classes of biological drugs available on the Pharmaceutical Benefits Scheme (PBS) for Australians with many more under development. Up to thirty percent of patients fail to have an adequate response to anti-TNF therapy and loss of response occurs at a rate of ten percent per year. There are at present no highly sensitive biomarkers of response to anti-TNF therapies. Without biomarkers to assist with selecting the most effective biologic for a particular patient, there is a risk of exposing patients to ineffective drug therapies with unnecessary side-effects and costs. This thesis comprises a range of clinical and scientific studies that seek to identify predictors of loss of response to anti-TNF therapies in Crohn’s disease. Two types of loss of response have been identified: Primary nonresponse (PNR), is defined as a lack of response to the initial drug therapy as determined at 12 weeks post induction, and Secondary Loss of Response (SLOR) is defined as the loss of response after the patient has had an initial response to the drug. Based on the clinical observation that patients with altered body composition and those with strictures have a variable to response to anti-TNF therapy, we sought to identify whether there were specific clinical, endoscopic, histologic and biochemical parameters that correlated with response to anti-TNF therapy amongst patients from whom longitudinal body composition and endoscopic data had been collected. A prospective cohort study of patients who had been newly started on anti-TNF therapies was also undertaken. In this cohort samples of urine, blood and faeces were taken prior to anti-TNF therapy delivery (baseline) and then at 3 monthly intervals thereafter. A combination of bioinformatic analyses and novel techniques evaluating the metabolome were applied to the cohort, in order to find clinical factors and biomarkers that might correlate with therapeutic response to anti-TNF therapy. This series of studies presented in this thesis on clinical and metabolic predictors of outcomes in patients receiving anti-TNF therapy for Crohn’s disease reveals new insights into the pathophysiology of Crohn’s disease and has identified biomarkers for the prediction of therapeutic response – thereby helping to come a step closer towards the ultimate goal of precision medicine.
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ItemInvestigating the natural history, serologic and genetic associations with disease outcomes, disability and cost of care in inflammatory bowel disease( 2018)Inflammatory bowel disease (IBD) is an emerging global health condition. In the second half of the 20th century, the incidence of Crohn’s disease (CD) and ulcerative colitis (UC) increased dramatically in the Western world. In the last two decades a corresponding rise has been observed in South East Asia(1) and Australia has one of the highest incidences of IBD in the world.(2) At this point in time there is no cure for IBD, and individuals with the condition usually receive lifelong treatment and a significant proportion will need intestinal surgery.(3) Early aggressive treatment with immunomodulator (IM) and biologic therapy can improve steroid free remission rates, reduce the need for surgery and hospitalisation, and reduce the rate of progression to a complex disease phenotype. (4-9) Medicare-subsidised biologic therapy for CD was first made available in Australia in late 2007, while infliximab was not available for use in UC in Australia until 2014. Although the rate of biologic prescription is steadily rising, the impact of increasing biologic use on the natural history and cost of care in the real-world is not clear. Furthermore, it is difficult to identify patients who would benefit from early biologic therapy, and it is uncertain if advancements in treatment are translating into improved patient function and reduced disability. Previous Australian researchers established a prospective community-based IBD inception registry in Barwon, Victoria in 2007 and collected cases to June 2013.(2, 10, 11) The initial aim of the registry was to establish the incidence and prevalence of IBD in Australia, to identify environmental exposures associated with disease aetiology, and to assess the course of disease and healthcare costs in the first 12 months from diagnosis. The aims of the work presented in this thesis were to use the community-based cohort from Barwon, in addition to a newly constructed tertiary IBD center hospital-cohort to determine the natural history of IBD in the first five years of disease, to identify clinical, serologic and genetic associations with disease course and outcomes in IBD, to determine the health care cost of IBD within the first four years of diagnosis from a health care system perspective and identify early clinical predictors of high cost of care, and to describe the burden of disability and identify determinants of disability in IBD. Incident cases diagnosed from July 2013 to April 2016 were identified through a multifaceted approach from Barwon and St Vincent’s Hospital Melbourne to ensure complete capture. Cases were enrolled into the IBD registry that was used as a basis to collect outcome data on disease course, healthcare costs, and disability. Serological analysis was performed for anti-Saccharomyces cerevisiae (ASCA) IgG and IgA antibodies in CD patients, as well as perinuclear anti-Neutrophil Cytoplasmic antibodies (p-ANCA) in CD and UC patients. DNA analysis was performed using 26 single nucleotide polymorphisms (SNPs) that were identified from the literature as potentially having a prognostic role. A total of 408 patients [243(59.6%) CD and 165(40.4%) UC] were included in the analysis of natural history, as well as the cost analysis. 56% of CD and 62% of UC patients were from the Community cohort. 20.8% of CD patients needed intestinal surgery at 5 years which is lower than older population-based studies from the pre-biologic era. 28.1% of CD patients progressed to complex disease phenotype and 8.9% of UC patients underwent colectomy by 5 years which is similar to population-based studies from the pre-biologic era. There was no significant difference in disease outcomes in CD or UC between the hospital and community cohorts. 38% of CD patients and 15% of UC patients were exposed to biologic therapy. Anti-Saccharomyces cerevisiae positivity was associated with progression to complex disease and surgery in CD. Anti-Neutrophil Cytoplasmic Antibody positivity was associated with the need for biologic therapy in UC. There were no significant genetic associations with disease outcomes in CD or UC. In both CD and UC, medication costs accounted for over 50% of total cost, of which biologics accounted for the majority of medication cost. In CD, the mean medication cost per patient per year increased by $3,144 between years 1 to 4 (<0.01), which was offset by a fall in medical and surgical hospitalisation costs of $1,547 (p <0.01) and $3,321 (p <0.01) respectively leading to a reduction in total cost of care over 4 years. There were no significant changes in cost over time in UC. In both CD and UC, surgery, biologic use, and hospitalisation use were associated with higher cost of care. Disability was measured using the newly developed and validated IBD Disability Index (IBD-DI). 334 patients completed the IBD-DI. 56% of all patients had no or only mild disability while 32% of patients in remission had moderate to severe disability. Patients who had previous surgery or current biologic therapy but were currently in remission were more likely to be disabled. Factors associated with greater disability on multivariate regression analysis were active disease, female gender, socioeconomic disadvantage, and biologic use. In summary, this thesis has shown a numerically lower rate of intestinal surgery in CD compared with studies from the true pre-biologic era. Colectomy rates in UC were stable compared with historical controls however biologic exposure rates in UC were modest. We have demonstrated for the first time the nature of changes in IBD-associated healthcare costs over 4 years. After the first year of diagnosis, the use of IM and biologics rose significantly in CD, while surgery and hospitalisation rates declined. Over this time, healthcare cost profiles shifted in a similar fashion, in that as biologic usage rates increased, so did the cost of medications. As hospitalisation and surgical rates fell, so too did their corresponding costs. Disability in IBD is prevalent, and although active disease is an important contributor to disability, a significant proportion of patients were disabled despite being in remission. This novel finding indicates that other factors such as mental health issues may be contributing to disability in IBD.
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ItemThe natural history of inflammatory bowel disease in an Australian community cohort: investigating the aetiology, clinical course, predictors of severe disease and health cost( 2015)Inflammatory Bowel Disease (IBD), including Crohn’s Disease (CD), Ulcerative colitis (UC) and IBD undifferentiated (IBDU), are chronic disorders of the gastrointestinal tract that exert a major impact on an individual’s quality of life and result in very high usage of health care resources. The aetiology of IBD remains unknown. Clinical course can vary from mild to severe and debilitating, and it remains unclear at diagnosis what disease progression will be. Identifying early clinical prognostic factors that predict a severe course is important, thereby enabling early medical therapy to minimize complications of disease. In recent years there has been greater emphasis on intensive therapy and disease monitoring. The greatest impact has been the introduction of biological therapy. However, it remains unclear if these advances are translating into better disease outcomes in the community and at what cost. A population based inception cohort study of patients with IBD was set up in Barwon, Victoria. The aims of the study were to validate the previously reported high incidence, to identify environmental exposures that are associated with disease aetiology, to assess the early course of disease as measured by objective markers such as surgery and hospitalization rates, to identify early clinical prognostic factors associated with severe disease and to determine the health care cost early in the course of IBD. Incident cases from 2007/2008 and 2010-2013 in a well-defined geographical area were prospectively identified through a multifaceted approach to ensure complete capture. Cases were subsequently enrolled into the IBD registry that was used as a basis to collect outcome data on the disease progression, environmental exposures and health care cost. A number of environmental exposures were found to be associated with increased risk of CD included smoking, frequent fast food intake and childhood events such as tonsillectomy and chicken pox infection. In UC, the risk factors included smoking, childhood chicken pox infection as well as frequent fast food. In UC, high caffeine intake was protective (a novel finding), while frequent fruit intake and pets as a child reduced the risk of UC. Objective clinical outcomes were measured for a median of 18 months from diagnosis (range 12-60 months) for 252 patients comprising 146 CD, 96 with Ulcerative colitis UC and 10 IBDU. Immunomodulators (IM) were prescribed in 57% of CD patients, and 19% with UC; biological therapy in 13% of CD patients. A third of all CD patients were hospitalised, the majority (77%) in the first 12 months. Risk factors for hospitalisation included penetrating, perianal and ileocolonic disease. A quarter of UC patients were hospitalized, most within the first 12 months. Resective surgery rates were 13% at 1 year in CD, and 26% at 5 years. Risk factors at diagnosis included penetrating, stricturing and ileal disease. Colectomy rates in UC were 2% and 13% at 1 and 5 years. High CRP at diagnosis was associated with colectomy. Health cost analysis in the first year of disease showed that per patient cost was higher in CD than UC; and that there has been a shift from inpatient to outpatient resources driving the majority of health cost in IBD compared to older studies. This was primarily due to the expense from medications. This first Australian population based study of an inception cohort confirms a high incidence of IBD in Barwon, Victoria that has remained stable over 6 years. A number of environmental risk factors associated with an increased risk of IBD were identified, as well as protective factors, of which high caffeine intake is a novel finding. Disease progress in this cohort was optimistic, compared to historical cohorts, with low rates of intestinal surgery. This was associated with high rates of IM and biological therapy. Early clinical predictors of severe disease were identified that can be used in clinical practice to tailor therapy. Health cost analysis in the first year shows a shift from inpatient to outpatient resources, with medications and investigations contributing the most.
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ItemInflammatory bowel disease in the East and West: clinical, serological and microbiological studies( 2013)The incidence of inflammatory bowel disease (IBD) in Australia is equal to the highest in the world, in contrast to the incidence in Asia which is low but rapidly increasing. The pathophysiology of IBD relates to the mucosal immune response to antigenicstimulation from the gut microbiota, on a background of genetic susceptibility. Immigrants from low to high incidence areas, have a high incidence of IBD, suggesting that exposure to new environmental factors is a key factor in the development of IBD. “Westernization” of lifestyle and industrialization in Asia likely also plays a role. Our gut microbiota is affected by our genes, our immune system, and environmental factors. Patients with IBD have altered gut microbiota. Little is known about the gut microbiota of IBD patients in the Asia, and in particular whether it is changing to Western patterns, especially after migration. Initially the clinical characteristics and management of IBD patients in Australia and Asia were compared. Then gut microbiota was assessed and compared, using state-of-the-art metagenomic techniques, within and between China and Australia (countries with different IBD incidence) both in the healthy, and IBD populations in subjects of Caucasian and Asian (Chinese) ethnicity. Serological antibodies to microbial antigens, and environmental factors were also assessed. Studying clinical characteristics of disease, the gut microbiota and serological antibodies to microbial antigens in populations with changing incidence offers great hope of identifying potentially important aetiological factors in IBD.
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ItemPost-operative Crohn's disease recurrence: clinical and microbiological studies( 2012)Crohn’s disease is a chronic inflammatory bowel disease that causes major morbidity. The cause is unknown but thought to relate to an exaggerated immune response to gut microbiota in genetically susceptible individuals. There is currently no known cure. The majority of patients with Crohn’s disease undergo surgery during their life, and 70 percent of these require a second operation due to disease recurrence. Surgery involves removing the diseased segment and joining the unaffected bowel. Even if all macroscopically involved bowel is removed disease usually recurs at, and proximal to, the anastomosis. Recurrent Crohn’s disease can be identified endoscopically before symptoms develop. However, it is unknown whether intervention based on endoscopic findings of recurrence influences the disease course. Immunosuppressive and antitumour necrosis factor therapy have emerged as effective treatments in the treatment of Crohn’s disease but their optimal usage for the prevention of post-operative recurrence of Crohn’s disease remains to be determined. This thesis encompasses the design and conduct of a clinical study which aimed to determine whether prospective endoscopic monitoring of post-operative patients, with treatment intensification for mucosal recurrence, is superior to the current standard of care based on treatment of symptoms. This thesis also includes a laboratory study, allied to the clinical study, in which the microbiota has been characterised and followed over time, from a starting point of absent mucosal disease at a site of known recurrence. This latter study aimed to establish whether specific changes in gut mucosal microbiota at the anastomosis are associated with disease recurrence. We initially demonstrated in a retrospective cohort study that the rates of endoscopic, clinical, and surgical recurrence are high after surgery and that that approaches to the management of postoperative recurrence have been variable in the past. Although there was no clinical benefit from colonoscopy or step-up therapy in this cohort we concluded that that this lack of benefit related to inconsistent timing of post-operative colonoscopy and a lack of standardised drug intervention in response to the endoscopic findings. We then devised a prospective randomized controlled trial to compare endoscopic monitoring of post-operative patients with treatment step-up for endoscopic recurrence, with standard care. In an analysis of the six month endoscopic outcome of patients with a high risk of recurrence we found that adalimumab was significantly superior to thiopurines in preventing endoscopic recurrence. In the laboratory we simultaneously characterised the mucosa associated microbiota in a sub-group of patients enrolled in the clinical study at the time of surgical resection and at the anastomosis six months post-operatively. We found that patients who developed recurrence or remained in remission could be differentiated on the basis of specific microbiota profiles, both at the time of surgery and six months later. In summary, postoperative recurrence remains an important issue despite the availability of immunosuppressive and anti-TNF drug therapy, when managing Crohn’s disease. This thesis comprises clinical studies focussing on the prevention of disease recurrence, and laboratory studies aimed at determining which bacteria may be implicated in recurrent disease.