ena-STUDY-CENTRE FOR GENOMIC RESEARCH (CGR)-29-08-2014-14:14:33:090-48
Application of whole genome sequencing to fully characterise Campylobacter isolates from the IID1 and IID2 studies
Isolates collected during the IID1 and IID2 studies will be subjected to a well-established pipeline leading to whole genome sequencing (WGS) using the Illumina MiSeq platform.  All isolates will be analysed using sequencing of paired-end libraries.  After this initial run, the genomes of a sub-set of isolates (approximately 25) will be improved using a PacBio approach.  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.  In addition, genome-wide phylogenetic analysis will be used to compare the IID strain collection to others available in the wider database, and from our parallel studies of Campylobacter isolates from a wide variety of animal and environmental sources.   These analyses 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.
Isolates collected during the IID1 and IID2 studies will be subjected to a well-established pipeline leading to whole genome sequencing (WGS) using the Illumina MiSeq platform.  All isolates will be analysed using sequencing of paired-end libraries.  After this initial run, the genomes of a sub-set of isolates (approximately 25) will be improved using a PacBio approach.  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.  In addition, genome-wide phylogenetic analysis will be used to compare the IID strain collection to others available in the wider database, and from our parallel studies of Campylobacter isolates from a wide variety of animal and environmental sources.   These analyses 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.