A Thesis Submitted for the Degree of PhD at the University of Warwick Permanent WRAP URL: http://wrap.warwick.ac.uk/129030 Copyright and reuse: This thesis is made available online and is protected by original copyright. Please scroll down to view the document itself. Please refer to the repository record for this item for information to help you to cite it. Our policy information is available from the repository home page. For more information, please contact the WRAP Team at:
[email protected] warwick.ac.uk/lib-publications Exploring the molecular mechanisms of antimicrobial resistance in Brachyspira hyodysenteriae using whole genome sequencing Ewart Jonathan Sheldon, BSc, MSc University of Warwick This thesis is submitted for the degree of Doctor of Philosophy May 2018 Declaration This thesis is submitted to the University of Warwick in support of my application for the degree of Doctor of Philosophy. It has been composed by myself and has not been submitted in any previous application for any degree The work presented (including data generated and data analysis) was carried out by the author except in the cases outlined below: 1. In chapter 3 twenty isolates were purified by Jon Rodgers at APHA Bury St Edmunds (js01, js21, js34, js35, js39, js41, js47, js51, js63, js64, js65, js68, js70, js78, js79, js83, js86, js89) The sequencing department at the APHA performed all sequencing conducted at the APHA, this involved one MiSeq metagenomic sequencing run and all NextSeq sequencing A Perl script written by Nicholas Dugget was used to automate the identification of SNPs by Snippy A python script designed by Richard Brown was used in chapter 3, 4 and 5 to automate processes Novel MLST sequence types were assigned by Tom La i Acknowledgements I would like to thank Warwick Medical School and the VMD for funding the work presented in this thesis.