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Pathogenomic Characterisation of a Novel, Layer-Associated Avian

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Pathogenomic Characterisation of a Novel, Layer-Associated Avian Pathogenomic characterisation of a novel, layer‐associated Avian Pathogenic Escherichia coli Thesis submitted in accordance with the requirements of the University of Liverpool for the degree of Doctor in Philosophy by Charlotte Rose Collingwood July 2016 Author’s Declaration I declare that the work in this dissertation was carried out in accordance with the University’s Regulations and Code of Practice for Research. Except where indicated, the work is my own. Work done in collaboration, or with the assistance of others, is indicated as such. Any views expressed in the dissertation are those of the author. Signed: Date: i Acknowledgements Firstly I would like to thank my supervisor, Paul Wigley, for his help, support, guidance and most importantly encouragement during my studies. Your expertise, good humour, and kindness have been unparalleled. I’ve also learnt more about certain (obscure?) musical genres than I could have imagined. I’d also like to thank Craig Winstanley, in particular in enabling me to get the 3770 genome sequenced. Without your timely input, this particular chapter would be considerably briefer. I would also like to thank many people in the labs at Leahurst and in the Ronald Ross building for their help and friendship during my studies. Whether experiments went wrong or right; there was always someone there to commiserate or congratulate. There are too many to name individually, but special thanks go to Georgina Crayford, Elli Wright and Camilla Brena, you have helped more than you could know. On a practical note, I would like to thank Roy Chaudhuri for his expertise in genomics and phylogenetics, Mark Stevens for the kind gift of the χ7122 isolate, and Tim Wallis at Ridgeway Biologicals for sharing the SPS‐associated isolates used in this project. I’d like to thank my friends and family – Mum, Dad, my brother Richard, Grandma and Grandad. You never doubted that I could do this – even when I did. Jen Smith – thank you for your commiserations and support, and I’d like to take back our time machine agreement. Jo Moran, thank you for your friendship and advice. Finally, I would like to thank my husband Tom. You are my inspiration. Thank you for your help, support, and for being behind me every single step of the way. Without your love and emotional support, this thesis would most likely remain unwritten. I hope I’ve made you proud. ii Contributors I would like to thank the following people for their assistance with this project. 3770 genome assembly and phylogenetic tree creation was performed by Dr Roy Chaudhuri, previously of the Centre for Genomic Research at the University of Liverpool, now Lecturer in Bioinformatics at the University of Sheffield. Necropsies were performed with assistance from Dr Maria Camilla Brena, previously a Research Assistant in Infection Biology, University of Liverpool. iii Table of Contents Author’s Declaration .................................................................................................. i Acknowledgements ................................................................................................... ii Contributors ............................................................................................................... iii List of Figures .......................................................................................................... viii List of Tables ............................................................................................................ viii List of Abbreviations ................................................................................................ ix Abstract ......................................................................................................................... x 1.0 ‐ Introduction ....................................................................................................... 1 1.1 – Escherichia coli: the organism ............................................................................. 2 1.2 – Escherichia coli: the pathogen ............................................................................. 3 1.2.1 – Extra‐Intestinal Pathogenic Escherichia coli ...................................................... 5 1.2.1.1 – ExPEC as a public health concern ................................................................................... 5 1.2.2 – Avian pathogenic Escherichia coli ........................................................................... 7 1.2.2.1 – APEC disease manifestation .............................................................................................. 8 1.2.2.2 – APEC epidemiology ............................................................................................................ 10 1.2.3 – Urinary tract pathogenic Escherichia coli ..........................................................11 1.3 – Virulence factors of Escherichia coli ................................................................ 13 1.3.1 – Adhesins and lipopolysaccharide .........................................................................13 1.3.1.1 – Flagella ..................................................................................................................................... 14 1.3.1.2 – Type 1 Fimbriae .................................................................................................................. 14 1.3.1.3 – P Fimbriae .............................................................................................................................. 15 1.3.1.4 – Curli Fimbriae ....................................................................................................................... 16 1.3.1.5 – S Fimbriae .............................................................................................................................. 16 1.3.1.6 – ExPEC Adhesin 1 ................................................................................................................. 17 1.3.1.7 – Afimbrial Adhesins ............................................................................................................. 17 1.3.1.8 – Temperature Sensitive Haemagglutinin ................................................................... 18 1.3.1.9 – Lipopolysaccharide ............................................................................................................ 19 1.3.2 – Metal Transport Systems .........................................................................................19 1.3.2.1 ‐ sitABCD locus ......................................................................................................................... 20 1.3.2.2 – Enterobactin .......................................................................................................................... 20 1.3.2.3 ‐ Aerobactin ............................................................................................................................... 21 1.3.2.4 ‐ Salmochelin ............................................................................................................................ 22 1.3.3 – Capsules & Self‐Defence Mechanisms .................................................................23 1.3.3.1 – Colicin ...................................................................................................................................... 23 1.3.3.2. ‐ Increased Serum Survival ............................................................................................... 24 1.3.4 – Secreted Factors and Toxins ...................................................................................25 1.3.4.1 – Vacuolating Autotransporter Toxin ............................................................................ 27 1.3.4.2 – Haemolysins .......................................................................................................................... 27 1.3.4.3 – ibeA; invasion ........................................................................................................................ 28 1.3.4.4 – Cryptic Type 3 Secretion System.......................................................................29 1.4 – Genetics of Escherichia coli ................................................................................. 30 1.4.1 – Next‐Generation Sequencing, a seismic shift for genomics .......................31 1.4.2 – Phylogenetics ................................................................................................................32 1.4.3 – MLST types .....................................................................................................................33 1.4.4 – Virulence Plasmids and Pathogenicity Islands ...............................................34 1.4.5 – Pathogenicity and Virulotyping .............................................................................35 1.5 ‐ Aims ............................................................................................................................. 38 2 – General Materials and Methods .................................................................. 39 2.1 – Bacterial Strains, storage and growth conditions ...................................... 39 iv 2.2 – DNA Extractions ...................................................................................................... 40 2.2.1 – Simple DNA Extraction for PCR .............................................................................40 2.2.2 – Extraction of High Quality DNA for Genome Sequencing ...........................40 2.2.3 – Quality check of extracted
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