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<p>The overall aims of this study are:</p>
<ul>
<li>to fully characterise UK campylobacter strains associated with human campylobacteriosis by whole genome sequencing using Next Generation Sequencing (NGS) technologies</li>
<li>to identify markers to assist with source attribution by integration of the data from IID study strains with published data obtained from non-human sources and genome data being derived from current funded projects at Liverpool</li>
</ul>
<p>We will isolate genomic DNA from all of the campylobacter isolates from the IID1 and IID2 studies. All isolate genomes will then be subjected to sequencing of paired-end libraries using the Illumina MiSeq platform. After this initial run, the genomes of a sub-set of isolates (approximately 25) will be improved using a long-read sequencing technique (PacBio by Pacific Biosciences). Using this combination approach we will construct a comprehensive genome sequence data-set from the IID isolates, and these data will be submitted to a publically accessible database. We will also extract and analyse MLST data from the IID isolates, in order to place the collection in the context of previous studies. Both MLST and genomic data will also be used to make comparisons between the IID1 and IID2 collections.</p>
<p>The major outcomes of the study will be:</p>
<ul>
<li>a comprehensive genome sequence data-set from the IID isolates, submitted to a publically accessible database</li>
<li>analysis of MLST data from the IID isolates to place the collection in the context of previous studies based on MLST</li>
<li>genome-wide phylogenetic analysis of the IID strains compared to others available in the wider database (and our parallel studies involving isolates from the environment, wildlife and farm animals)</li>
</ul>
<p>In addition, we will considerably enhance the community's knowledge on what constitutes the core genome of campylobacter, especially in relation to isolates associated with human infections, with the potential to link variations between strains (either in accessory genome content, or in SNP variations within the core genome) with other factors such as putative source or, potentially, clinical severity, as well as other important phenotypes, such as survival characteristics in the environment or during food processing.</p>
<p>Background: Campylobacter is the most common cause of acute bacterial gastroenteritis worldwide. In the UK alone it causes an estimated 500,000 infections each year. There have been two large studies of Infectious Intestinal Disease in the UK community (IID1 in the mid 1990s and IID2 in 2008-2009). Campylobacter was identified as the most common bacterial pathogen among patients presenting to primary care. Although there was little variation in the burden of illness between the two studies, the molecular epidemiology of the campylobacter isolates from these studies has not been investigated. Multi-locus sequence typing (MLST) and whole genome sequencing (WGS) comparative analyses can be used to understand not only the epidemiology and any variations between the two survey periods, but also the potential sources for transmission of the pathogen to humans, by comparison with isolates from the environment, wildlife and farm animals. </p>