Clostridium Difficile Infection; Establishment, Prevention and the Role of the Microbiota
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Clostridium difficile infection; establishment, prevention and the role of the microbiota William Thomas Ferreira Thesis submitted to Royal Holloway, University of London in fulfilment of the requirements for the degree of Doctor of Philosophy School of Biological Sciences Royal Holloway, University of London 09 September 2019 1 Declaration of Authorship I declare that this work was carried out in accordance with the Regulations of the University of London. I declare that this submission is my own work, and to the best of my knowledge does not represent the works of others, published or unpublished, except where duly acknowledged in the text. No part of this thesis has been submitted for a higher degree at another university or institution. Signed: Date: 09/09/2019 William Thomas Ferreira Royal Holloway, University of London 2 Acknowledgements Firstly, I would like to thank my supervisor Prof. Simon Cutting who has provided me with continuous support, encouragement and inspiration. Also thank you to Hong, who has been a friend to me throughout my PhD and has made the joint projects we have worked on together so enjoyable. Many thanks also to Mikhail, you’ve provided me with many tools so useful in science, and I feel that my horizons have expanded by working with you. A big thank you to every member of the Cutting lab over the last 4 to 5 years, I would love to name all of you, but the list would be longer than my thesis… Of course, I couldn’t have done any of this without the loving support from my family, especially my Dad and my two amazing sisters. Thanks to all of my friends away from the lab for the never-ending support, you know who you are! Last but foremost I would like to thank my wife Suzie for her constant love and support, for the early mornings and late nights and for being the only thing keeping me sane the past few months. Thank you for being my editor, my audience, my collaborator and my muse. But most importantly, thanks for being my best friend. 3 Abstract Clostridium difficile is a leading cause of nosocomial, antibiotic-associated, diarrhoea in industrialised countries. C. difficile spores are dormant and resistant structures responsible for the colonisation and persistence of C. difficile infection (CDI) within patients as well as the transmission between them. This thesis examines firstly, the role of a C. difficile spore coat protein, CotE, in the establishment of CDI, and secondly, the role of allochthonous Bacillus within the GI tract in suppressing CDI. CotE is a protein displayed on the C. difficile spore surface which carries two functional elements, an N-terminal peroxiredoxin and a C-terminal chitinase domain. Using isogenic mutants, it was demonstrated in vitro and ex vivo that CotE enables binding of spores to mucus by direct interaction with mucin and contributes to its degradation. In animal models of CDI, it was shown that when CotE was absent, both colonisation and virulence were markedly reduced. It is demonstrated here that the attachment of spores to the intestine is essential in the development of CDI. The developments of infection within the host GI tract requires germination of the spore, followed by outgrowth of the vegetative cell; a process which requires a multitude of factors to favour C. difficile proliferation. In a series of experiments, it was shown that environmentally acquired Bacillus help to suppress CDI by the production of lipopeptides in vivo with activity against C. difficile and that the use of antibiotics abrogates this phenomenon. Using hamster and mouse models, it was demonstrated that the administration of these Bacillus provides complete colonisation resistance against CDI in clindamycin treated animals. Reversed-phase high-performance liquid chromatography, dynamic light scattering and MALDI-TOF analysis identified the active molecules to be a micellar complex of lipopeptides comprised of chlorotetaine, iturins, fengycins and surfactins. Through this work, it is demonstrated that the attachment of spores to the intestine is essential in the development of CDI and suggests a direct role for the spore in the establishment and promotion of disease. 4 Table of Contents Declaration of Authorship .................................................................................... 2 Acknowledgements ................................................................................................ 3 Abstract .................................................................................................................. 4 Table of Contents .................................................................................................. 5 List of Figures ...................................................................................................... 10 List of Tables ....................................................................................................... 13 Abbreviations ...................................................................................................... 14 1. Introduction ..................................................................................................... 17 1.1 Identification of C. difficile as a pathogen .................................................. 17 1.2 C. difficile infection ..................................................................................... 20 1.2.1 The disease ........................................................................................... 20 1.2.2 Presentation of the disease ................................................................... 23 1.2.3 Establishment of infection ................................................................... 24 1.2.4 Virulence factors .................................................................................. 28 1.2.4.1.Toxins……………………………….....……………………...….28 1.2.4.2 S-layer proteins…………………………………………………..33 1.2.5 Rise of community acquired infections ............................................... 34 1.3 The spore ..................................................................................................... 35 1.3.1 Spore structure and function ................................................................ 35 1.3.2 Sporulation pathway............................................................................. 40 1.3.3 Germination pathway ........................................................................... 42 1.4 Control and prevention of CDI ................................................................... 45 1.4.1 Diagnosis .............................................................................................. 45 1.4.2 Prevention ............................................................................................ 46 1.4.2.1 Hospital management and hygiene……………………………....46 5 1.4.2.2 Probiotics………………………………………………………...47 1.4.2.3 Developing a vaccine…………………………………………….49 1.4.3 Treatment ............................................................................................. 51 1.4.3.1.Antibiotics………………………………………………………..51 1.4.3.2 Faecal microbiota transplantation (FMT)………………………..51 1.5 The gut microbiome .................................................................................... 53 1.5.1 Role of the microbiota .......................................................................... 53 1.5.2 Effect of antibiotics .............................................................................. 58 1.5.3 Control of CDI ..................................................................................... 59 2. Materials and Methods ................................................................................... 62 2.1 General methods.......................................................................................... 62 2.2 Bacterial strains ........................................................................................... 62 2.3 Sporulation of C. difficile ............................................................................ 63 2.4 Spore purification ........................................................................................ 65 2.5 Spore coat extractions ................................................................................. 65 2.6 Antibody production ................................................................................... 65 2.7 Western blotting of spore coat proteins ...................................................... 65 2.8 Southern blotting ......................................................................................... 66 2.9 Germination assays ..................................................................................... 66 2.10 Spore adhesion to hydrocarbon (SATH) assay ......................................... 67 2.11 Cell culture ................................................................................................ 68 2.12 Cytotoxicity assays ................................................................................... 68 2.13 Induction of cytokines ............................................................................... 69 2.14 Spore adhesion assays ............................................................................... 70 2.15 Spore binding to pig mucus explants ........................................................ 70 2.16 Spore binding to ligands............................................................................ 71 6 2.17 Mucin degradation using amido black staining ........................................ 71 2.18 Mucin degradation using amido black staining