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United States Department of Agriculture

Agricultural Research Service

Research Project: INTEGRATED APPROACHES FOR IMPROVING AQUATIC ANIMAL HEALTH IN COOL AND COLD WATER AQUACULTURE

Location: Cool and Cold Water Aquaculture Research

Title: Whole genome sequencing: the future for molecular epidemiological studies on aquatic pathogens

Authors
item Verner-Jeffreys, David -
item Baker-Austin, C -
item Amaro, C -
item Colquoun, D -
item Febrer, M -
item Feil, E -
item Gulig, P -
item Mccarthy, U -
item Rhodes, L -
item Wiens, Gregory

Submitted to: European Association of Fish Pathologists
Publication Type: Abstract Only
Publication Acceptance Date: May 15, 2011
Publication Date: September 14, 2011
Citation: Verner-Jeffreys, D., Baker-Austin, C., Amaro, C., Colquoun, D., Febrer, M., Feil, E.J., Gulig, P.A., Mccarthy, U., Rhodes, L., Wiens, G.D. 2011. Whole genome sequencing: the future for molecular epidemiological studies on aquatic pathogens [abstract]. European Association of Fish Pathologists. p. 105.

Technical Abstract: The advent of next generation sequencing (NGS) has transformed our ability to analyze the genomic content of isolated strains and communities of microorganisms. An important application of the new technology is for molecular epidemiology, as single sequencing reactions can generate nearly complete genome sequences of bacterial or viral isolates. As a proof of principle, we are sequencing more than 90 isolates from two important aquatic bacterial species, Renibacterium salmoninarum and Vibrio vulnificus. Renibacterium salmoninarum is the causative agent of bacterial kidney disease. Previous efforts to type this organism have been challenging as this organism is highly clonal and little is known about the molecular variation between isolates. In contrast, Vibrio vulnificus, responsible for disease in both humans and in fish (particularly eels) shows relatively high intraspecific genomic diversity. For this approach, approximately 2.5 million 120 bp paired end reads (600 Mbp) are being obtained by the Genome Analysis Centre in Norwich, UK for each of the 90+ isolates, using the Illumina Genome Analyzer GAII flow cell. Unique-index tagged libraries are made for each individual sample, thus making it is possible to simultaneously sequence up to twelve separate libraries in each of the eight GAII flow cell lanes. The index tags allow for downstream processing of the data to assign reads to individual samples for further analysis. Reads from each isolate will be mapped by the sequencing centre onto reference genomes (Rs accession number NC_010168, Vv accession numbers NC005139/NC005139), and candidate SNPs will be identified. Core and non-core genomic regions will be determined for both species. These data will reveal the detailed genetic variation within isolates of R salmoninarum and V. vulnificus, allowing the reconstruction of evolutionary relationships and patterns of recent epidemiological spread. The rationale and preliminary results of the project will be presented as well as cost-benefit analyses compared to other commonly used molecular typing methods (i.e. pulsed-field gel electrophoresis, multilocus sequencing typing, and random amplified polymorphic DNA typing schemes).

Last Modified: 7/24/2014