Development of novel therapies for gut dysbioses

University of Technology Sydney. Faculty of Science.This thesis reports results of 30 years of systematic clinical investigations carried out by the author in the general area of “infection-driven inflammation”. The Centre for Digestive Diseases (CDD) endoscopy clinic was founded by the author in 1984 closely coinciding with Drs Barry Marshall and Robin Warren reporting gastric spiral bacteria with pathogenic role in ulcer disease. CDD was able to source gastric biopsies with Helicobacter pylori(HP) from numerous patients with ulcer disease creating the environment necessary for HP research. Hence, Section 1 of the Thesis describes systematic studies which asked questions such as ‘which is the best therapy’, ‘what is the role of acid suppression’ and the ‘role of cigarettes’? This culminated in the development of ‘triple therapy’, the first clinically effective HP cure commercialised later as Helidac. Success in HP research soon led to the treatment of the candidate infective cause of Crohn’s disease called Mycobacterium avium subspecies paratuberculosis (MAP). This comprised of three antibiotics which were active intracellularly - another ‘triple therapy’ akin to HP treatment. However, curing HP could be achieved in 7 days and ulcer healing in 6 weeks whereas MAP – one of the slowest growing bacterial pathogens – required treatment for many months to heal the bowel. So in Section 2 of the Thesis the effect of Anti-MAP therapy on healing Crohn’s disease was studied. Funding from the Broad Foundation supported culture and PCR of MAP while an Israeli company, RedHill Biopharma has funded current pivotal trials with a view to an FDA approval. Section 3 of the Thesis describes research in Faecal Microbiota Transplantation (FMT). FMT was first used at CDD in 1988 in a patient with indeterminate colitis - the first patient world-wide treated for colitis and cured. Generally Clostridium difficile infection (CDI) is treated with FMT at CDD with a cure rate exceeding 95%. Subsequently over 6,000 FMT treatments were carried out and new indications for FMT were discovered, both within and outside of the GI tract. These included ulcerative colitis, irritable bowel syndrome, constipation, MS, arthritis, acne, and others, reported in enclosed publications. CDD work in FMT contributed to the global growth of microbiome research and culminated in the creation of the lyophilised encapsulated FMT. Each of the three Sections has addressed “infection-driven inflammation” in different body regions. It is hoped that reported findings in this Thesis will lead to new therapies that will result in significant clinical improvements

Fecal Microbiota Transplantation: Indications, Methods, Evidence, and Future Directions

Fecal microbiota transplantation (FMT) has attracted great interest in recent years, largely due to the global Clostridium difficile infection (CDI) epidemic and major advances in metagenomic sequencing of the gastrointestinal (GI) microbiota, with growing understanding of its structure and function. FMT is now recommended as the most effective therapy for relapsing CDI and, with further refinement, may even be used in “first-time” CDI. There is interest also in other conditions related to GI dysbiosis—for example, inflammatory bowel disease, irritable bowel syndrome, obesity, and diabetes mellitus—although quality evidence is at present lacking. A few trials are now underway in FMT for ulcerative colitis. Many unanswered questions remain, including FMT methodology—for example, optimal route of administration, what makes a “good donor,” safety issues, and long-term effects of FMT

Fame and future of faecal transplantations - developing next-generation therapies with synthetic microbiomes

Peer reviewe

Facing the Spectator

We investigated the familiar phenomenon of the uncanny feeling that represented people in frontal pose invariably appear to ‘‘face you’’ from wherever you stand. We deploy two different methods. The stimuli include the conventional one—a flat portrait rocking back and forth about a vertical axis—augmented with two novel variations. In one alternative, the portrait frame rotates whereas the actual portrait stays motionless and fronto-parallel; in the other, we replace the (flat!) portrait with a volumetric object. These variations yield exactly the same optical stimulation in frontal view, but become grossly different in very oblique views. We also let participants sample their momentary awareness through ‘‘gauge object’’ settings in static displays. From our results, we conclude that the psychogenesis of visual awareness maintains a number—at least two, but most likely more—of distinct spatial frameworks simultaneously involving ‘‘cue–scission.’’ Cues may be effective in one of these spatial frameworks but ineffective or functionally different in other ones

Metagenomic Hi-C of a Healthy Human Fecal Microbiome Transplant Donor.

We report the availability of a high-quality metagenomic Hi-C data set generated from a fecal sample taken from a healthy fecal microbiome transplant donor subject. We report on basic features of the data to evaluate their quality

Gastroenterologist perceptions of faecal microbiota transplantation

© 2015 Baishideng Publishing Group Inc. All rights reserved. AIM: To explore gastroenterologist perceptions towards and experience with faecal microbiota transplantation (FMT). METHODS: A questionnaire survey consisting of 17 questions was created to assess gastroenterologists' attitude towards and experience with FMT. This was anonymously distributed in hard copy format amongst attendees at gastroenterology meetings in Australia between October 2013 and April 2014. Basic descriptive statistical analyses were performed. RESULTS: Fifty-two clinicians participated. Twenty one percent had previously referred patients for FMT, 8% more than once. Ninety percent would refer patients with Clostridium difficile infection (CDI) for FMT if easily available, 37% for ulcerative colitis, 13% for Crohn's disease and 6% for irritable bowel syndrome. Six percent would not refer any indication, including recurrent CDI. Eighty-six percent would enroll patients in FMT clinical trials. Thirty-seven percent considered the optimal mode of FMT administration transcolonoscopic, 17% nasoduodenal, 13% enema and 8% oral capsule. The greatest concerns regarding FMT were: 42% lack of evidence, 12% infection risk, 10% non infectious adverse effects/lack of safety data, 10% aesthetic, 10% lack of efficacy, 4% disease exacerbation, and 2% inappropriate use; 6% had no concerns. Seventy seven percent believed there is a lack of accessibility while 52% had an interest in learning how to provide FMT. Only 6% offered FMT at their institution. CONCLUSION: Despite general enthusiasm, most gastroenterologists have limited experience with, or access to, FMT. The greatest concerns were lack of supportive evidence and safety issues. However a significant proportion would refer indications other than CDI for FMT despite insufficient evidence. These data provide guidance on where education and training are required

A series of three cases of severe Clostridium difficile infection in Australia associated with a binary toxin producing clade 2 ribotype 251 strain

Three patients with severe Clostridium difficile infection (CDI) caused by an unusual strain of C. difficile, PCR ribotype (RT) 251, were identified in New South Wales, Australia. All cases presented with severe diarrhoea, two had multiple recurrences and one died following a colectomy. C. difficile RT251 strains were isolated by toxigenic culture. Genetic characterisation was performed using techniques including toxin gene profiling, PCR ribotyping, whole genome sequencing (WGS), in-silico multi-locus-sequence-typing (MLST) and core-genome single nucleotide variant (SNV) analyses. Antimicrobial susceptibility was determined using an agar incorporation method. In vitro toxin production was confirmed by Vero cell cytotoxicity assay and pathogenicity was assessed in a murine model of CDI. All RT251 isolates contained toxin A (tcdA), toxin B (tcdB) and binary toxin (cdtA and cdtB) genes. Core-genome analyses revealed the RT251 strains were clonal, with 0–5 SNVs between isolates. WGS and MLST clustered RT251 in the same evolutionary clade (clade 2) as RT027. Despite comparatively lower levels of in vitro toxin production, in the murine model RT251 infection resembled RT027 infection. Mice showed marked weight loss, severe disease within 48 h post-infection and death. All isolates were susceptible to metronidazole and vancomycin. Our observations suggest C. difficile RT251 causes severe disease and emphasise the importance of ongoing surveillance for new and emerging strains of C. difficile with enhanced virulence

Review article: faecal transplantation therapy for gastrointestinal disease

This is an accepted manuscript of an article published by Wiley in Alimentary Pharmacology and Therapeutics on 20/06/2011, available online: https://doi.org/10.1111/j.1365-2036.2011.04737.x The accepted version of the publication may differ from the final published version.Summary Background Evidence is emerging regarding the relationship between a dysbiosis of the human gut microbiota and a number of gastrointestinal diseases as well as diseases beyond the gut. Probiotics have been investigated in many gastrointestinal disease states, with variable and often modest outcomes. Faecal transplantation is an alternative approach to manipulate the gut microbiota. Aim To review the use of faecal transplantation therapy for the management of gastrointestinal disorders. Methods Available articles on faecal transplantation in the management of gastrointestinal disorders were identified using a Pubmed search and bibliographies of review articles on the subject were collated. Results A total of 239 patients who had undergone faecal transplantation were reported. Seventeen of 22 studies of faecal transplantation were in fulminant or refractory Clostridium difficile. Studies of faecal transplantation are heterogeneous regarding the patients, donors, screening, methods of administration and definition of response. Faecal transplantation for C. difficile has been demonstrated to be effective in 145/166 (87%) patients. Small numbers of patients are reported to have undergone successful faecal transplantation for irritable bowel syndrome and inflammatory bowel disease. Conclusions Faecal transplantation has been reported with good outcomes for fulminant and refractory C. difficile. No adverse effects of faecal transplantation have been reported. However, there are no level 1 data of faecal transplantation and reports to date may suffer from reporting bias of positive outcomes and under-reporting of adverse effects. This therapy holds great promise, where a dysbiosis of the gut microbiota is responsible for disease and further studies are necessary to explore this potential.Published versio

Social interaction, noise and antibiotic-mediated switches in the intestinal microbiota

The intestinal microbiota plays important roles in digestion and resistance against entero-pathogens. As with other ecosystems, its species composition is resilient against small disturbances but strong perturbations such as antibiotics can affect the consortium dramatically. Antibiotic cessation does not necessarily restore pre-treatment conditions and disturbed microbiota are often susceptible to pathogen invasion. Here we propose a mathematical model to explain how antibiotic-mediated switches in the microbiota composition can result from simple social interactions between antibiotic-tolerant and antibiotic-sensitive bacterial groups. We build a two-species (e.g. two functional-groups) model and identify regions of domination by antibiotic-sensitive or antibiotic-tolerant bacteria, as well as a region of multistability where domination by either group is possible. Using a new framework that we derived from statistical physics, we calculate the duration of each microbiota composition state. This is shown to depend on the balance between random fluctuations in the bacterial densities and the strength of microbial interactions. The singular value decomposition of recent metagenomic data confirms our assumption of grouping microbes as antibiotic-tolerant or antibiotic-sensitive in response to a single antibiotic. Our methodology can be extended to multiple bacterial groups and thus it provides an ecological formalism to help interpret the present surge in microbiome data.Comment: 20 pages, 5 figures accepted for publication in Plos Comp Bio. Supplementary video and information availabl

Reappraisal of non-invasive management strategies for uninvestigated dyspepsia: a cost-minimization analysis

Background : The benefits of the Helicobacter pylori test-and-treat strategy are attributable largely to the cure of peptic ulcer disease while limiting the use of endoscopy. Aim : To reappraise the test-and-treat strategy and empirical proton pump inhibitor therapy for the management of uninvestigated dyspepsia in the light of the decreasing prevalence of H. pylori infection, peptic ulcer disease and peptic ulcer disease attributable to H. pylori . Methods : Using a decision analytical model, we estimated the cost per patient with uninvestigated dyspepsia managed with the test-and-treat strategy ($25/test; H.pylori treatment,$200) or proton pump inhibitor ($90/month). Endoscopy ($550) guided therapy for persistent or recurrent symptoms. Results : In the base case (25% H. pylori prevalence, 20% likelihood of peptic ulcer disease, 75% of ulcers due to H.pylori ), the cost per patient is $545 with the test-and-treat strategy and$529 with proton pump inhibitor, and both strategies yield similar clinical outcomes at 1 year. H. pylori prevalence, the likelihood of peptic ulcer disease and the proportion of ulcers due to H.pylori are important determinants of the least costly strategy. At an H. pylori prevalence below 20%, proton pump inhibitor is consistently less costly than the test-and-treat strategy. Conclusions : As the H. pylori prevalence, the likelihood of peptic ulcer disease and the proportion of ulcers due to H. pylori decrease, empirical proton pump inhibitor becomes less costly than the test-and-treat strategy for the management of uninvestigated dyspepsia. Given the modest cost differential between the strategies, the test-and-treat strategy may be favoured if patients without peptic ulcer disease derive long-term benefit from H.pylori eradication.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/75747/1/j.1365-2036.2002.01306.x.pd