Factors Affecting the Detection of Clostridium Difficile in Faecal Samples
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1 Factors affecting the detection of Clostridium difficile in faecal samples Kerrie Ann Davies Submitted in accordance with the requirements for the degree of Doctor of Philosophy The University of Leeds School of Medicine April 2019 2 The candidate confirms that the work submitted is her own, except where work which has formed part of jointly authored publications has been included. The contribution of the candidate and the other authors to this work has been explicitly indicated below. The candidate confirms that appropriate credit has been given within the thesis where reference has been made to the work of others. Section 6.2.1 of Chapter 4 contains work from a jointly authored publication; Davies K, Planche T and Wilcox M. The predictive value of quantitative nucleic acid amplification detection of Clostridium difficile toxin gene for faecal sample toxin status and patient outcome. PLoS One 13(12): e0205941 2018. The concept of the work was devised by Kerrie Davies, the analysis and initial draft of the manuscript was completed by Kerrie Davies with review by Dr Tim Planche and Prof Mark Wilcox. This copy has been supplied on the understanding that it is copyright material and that no quotation from the thesis may be published without proper acknowledgement. The right of Kerrie Davies to be identified as Author of this work has been asserted by Kerrie Davies in accordance with the Copyright, designs and Patents Act 1988. 3 Acknowledgements There are so many people who I need to thank for their part in helping me to achieve this thesis. The Department of Health study, for which I was scientific coordinator, was conducted prior to this PhD, but I have reused the data for further analysis within the thesis. I would therefore like to thank all of the sites that took part in the multi-centre study; Leeds Teaching Hospitals NHS trust, St Georges’ University Hospitals NHS Foundation Trust, UCL Hospitals NHS Foundation Trust and Oxford University Hospitals NHS Foundation Trust, with special thanks to Dr Tim Planche for all of his support and guidance. I would also like to thank the Department of Health, who funded both this initial study and the PlaciD study. The PlaciD study research was carried out by a team which has included Claire Berry (Clinical Scientist), Claire Brown (Research Nurse) and Faye Pinker (Research Nurse). My own contributions, fully and explicitly indicated in the thesis, for the PlaciD study were to devise the study, be study chief investigator, write the study protocol, apply for ethical approval, devise data collection sheets and databases, perform the majority of the laboratory testing of the samples and analyse the data. The other members of the team and their contributions have been as follows; The Research Nurses recruited all of the participants, collected their samples and their data; Claire Berry performed laboratory testing of the samples during my maternity leave (four months). Thanks go to all of the team. I would also like to thank all of the participants in the PlaciD study, who generously gave their time, and poo, to help make the study a success! The gut models require a huge team effort to keep them running, therefore the research using this system has been carried out by a team which has included; Dr Tony Buckley (PI), Dr Caroline Chilton (PI), Dr Ines Moura (research assistant), Dr Hannah Harris (research assistant), Duncan Ewin (technician), Sharie Shearman (technician), Emma Clarke (technician), Kate Owens (technician), Bill Spittal (senior technician) and Flor Sporta (Summer student). My own contributions, fully and explicitly indicated in the thesis, have been to devise the experiments using gut model samples to monitor proliferation of C. difficile within the gut models using commercial assays, to test the samples, except where tested by Flor Sporta, as detailed within the thesis, and analyse the data. The other members of the team and their contributions have been as follows; individual gut model experiments devised and overseen by the PI in each case; all the technical aspects of keeping the gut models running was completed by the technical team (technicians and 4 research assistants), including taking the daily samples; Flor Sporta tested some of the gut model samples using the DS2 assays, as explicitly indicated in the thesis. I would like to thank each and every one of them for their assistance. All PCR ribotyping was carried out by the C. difficile Ribotyping Network of England and Northern Ireland (CDRN), as explicitly stated within the thesis. I would like to thank Dr Warren Fawley and his team at CDRN for their contribution and support. The Healthcare Associated Infections Research Group is a special place to work and I feel very privileged to be part of such a great team. Every single person deserves my thanks, but I’d especially like to thank Dr Jane Freeman, for being my ever steady friend who always steers me right; Dr Baljit Saundh, my dear friend who helps me to ‘relax the chaos’; Georgina Davis, my great friend and dedicated cheering squad, who never lets me quit; and of course Prof Mark Wilcox, my PhD Supervisor and mentor, who has given me the opportunity to fly. A great debt of thanks also goes to Dr John Heritage; not only is he the reason I came to Leeds to study Microbiology as an undergraduate, but he was also my PhD co-supervisor, even after he had retired. I appreciate all of the wisdom and advice he has imparted over the many years I have known him. Huge thanks go to my family; for standing by me, for keeping me encouraged and inspired. To my children Alf and Sid, for being patient when I couldn’t play, and for making me laugh whenever they could; to my mum and dad for being so supportive and proud; to my extended Leeds family for supporting us all and providing ‘donations’ when needed. Special thanks obviously go to Graeme, my amazing husband; without him this thesis, my career and my self-belief would be naught. This PhD thesis is dedicated to my dad; for inspiring me to be the scientist that he never got the chance to be. 5 Abstract Clostridium difficile infection (CDI) laboratory diagnostic assays have variable performance, but reasons behind this variability are not well defined. In contrast to previous findings, the PCR ribotype of the organism only appears to be a factor in reduced sensitivity for toxin enzyme immunoassays (EIAs), not glutamate dehydrogenase (GDH) EIAs. Growth curve data demonstrated that GDH is produced during the exponential phase of growth, and the sensitivity of the GDH assay in vivo may be related to the amount of protein produced by the organism, as very high levels of GDH were detected during growth of C. difficile in an in vitro gut model. Indeed the levels of GDH, measured in both gut model and patient samples, correlated with organism bioload. In addition, the median faecal levels of GDH in recurrent CDI cases were significantly higher than in patients with a single infection episode. Interestingly, when patients had sequential faecal samples tested, 27% with an initial GDH- positive/toxin-negative result had a subsequent toxin positive sample, after a median of eight days. Further studies, with supplementary assays for gut inflammation, are required, to determine if these are ‘missed’ infections or insignificant sub-clinical levels of toxin. A laboratory test that could predict risk of recurrence would be an important tool to inform choice of appropriate C. difficile treatment and prevention options. Indeed GDH detection may offer such an opportunity; a cohort of patients has been identified who were consistently GDH positive, even after resolution of symptoms, who subsequently developed recurrent CDI following additional antimicrobial therapy. The cycle threshold (CT) value of PCR assays for the detection of toxin gene may also provide additional information, as low CT (<25) was significantly associated with toxin positivity, presence of PCR ribotype 027 and mortality. Low CT was also associated with recurrence but was not a significant finding. 6 Contents Acknowledgements .............................................................................................................. 3 Abstract ................................................................................................................................ 5 List of Tables ...................................................................................................................... 11 List of Figures ..................................................................................................................... 14 Abbreviations used in this thesis ....................................................................................... 19 1.0 Introduction ................................................................................................................. 21 1.1 Historical context ..................................................................................................... 21 1.2 Virulence factors ...................................................................................................... 22 1.2.1 Toxins ................................................................................................................ 22 1.2.2 Spores ................................................................................................................ 24 1.2.3 Other Virulence Factors .................................................................................... 25 1.3 Clinical manifestations ............................................................................................