Comparative bacterial genomics

2839 19 20324 7 39143 document 20324 Loman12PhD.pdf application/pdf 83dbdeece60c36f8c6f630130624b4f2 MD5 3782206 2012-06-14 16:32:01 http://etheses.bham.ac.uk//id/eprint/2839/1/Loman12PhD.pdf 2839 1 1 application/pdf application/pdf en public

Loman12PhD.pdf

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http://eprints.org/relation/isVersionOf http://etheses.bham.ac.uk/id/document/20324 http://eprints.org/relation/isVolatileVersionOf http://etheses.bham.ac.uk/id/document/20324 http://eprints.org/relation/isIndexCodesVersionOf http://etheses.bham.ac.uk/id/document/20324 archive 4031 disk0/00/00/28/39 2012-06-14 16:45:46 2019-01-23 09:54:56 2012-06-14 16:45:46 thesis show 0 Loman Nicholas James Penn Charles Pallen Mark J. ftp://ubira.bham.ac.uk/eTheses/2839_Loman/ University of Birmingham Comparative bacterial genomics unpub QH426 QR180 RA 10col_life The thesis incorporates four published articles, which are available at http://eprints.bham.ac.uk/1163/ http://eprints.bham.ac.uk/1164/ http://eprints.bham.ac.uk/1165/ http://eprints.bham.ac.uk/1166/ Author chose open access, but the publication in chapter 5 can't be made openly accessible until 31 Oct 2012. OK to supply the whole thesis on request or to EThOS. For the most part, diagnostic clinical microbiology still relies on 19th century ideas and techniques, particularly microscopy and laboratory culture. In this thesis I investigate the utility of a new approach, whole-genome sequencing (WGS), to tackle current issues in infectious disease. I present four studies. The first demonstrates the utility of WGS in a hospital outbreak of Acinetobacter baumannii. The second study uses WGS to examine the evolution of drug resistance following antibiotic treatment. I then explore the use of WGS prospectively during an international outbreak of food-borne Escherichia coli infection, which caused over 50 deaths. The final study compares the performance of benchtop sequencers applied to the genome of this outbreak strain and touches on the issue of whether WGS is ready for routine use by clinical and public health laboratories. In conclusion, through this programme of work, I provide ample evidence that whole-genome sequencing of bacterial pathogens has great potential in clinical and public health microbiology. However, a number of technical and logistical challenges have yet to be addressed before such approaches can become routine. 2012-07 2012-05 graduation eng author unchecked This unpublished thesis/dissertation is copyright of the author and/or third parties. The intellectual property rights of the author or third parties in respect of this work are as defined by The Copyright Designs and Patents Act 1988 or as modified by any successor legislation. Any use made of information contained in this thesis/dissertation must be in accordance with that legislation and must be properly acknowledged. Further distribution or reproduction in any format is prohibited without the permission of the copyright holder. ubira@lists.bham.ac.uk public 166 University of Birmingham School of Biosciences d_ph TRUE na 2012-07 graduation