Below are notes from the WGS-Aqua Weymouth Workshop including an overview of the workshop, key outcomes and broad knowledge gaps.
Notes from WGS-aqua.net workshop 27/28 May 2015, Cefas, Weymouth.
The workshop was organised as an integral part of WP1 for the wgs-aqua.net project funded by the BBSRC/NERC sustainable aquaculture call. The project will initially focus on three exemplar pathogens; Vibrio anguillarum (Va), Flavobacterium psychrophilum (Fp) and Koi Herpes Virus (KHV). More details of the project are here (http://wgs-aqua.net/) including a full list of workshop participants (http://wgs-aqua.net/2015/06/). The aim of the workshop was to bring together experts from aquaculture with those from other fields (predominantly public health) for knowledge exchange and resource sharing, with an ultimate view to maximally exploit whole genome sequencing of aquaculture pathogens for disease management. Speaker abbreviations are given at the end of this document.
After a welcome and introduction to the project (EF), talks on the first day were focused on aquaculture, and included overviews of the work being carried out at Cefas (D-JV) and Stirling (SA). An overview of KHV was provided by DS, and RvE talked about recent metagenomics approaches to identifying pathogens associated with specific diseases. KB and TN gave an overview of their work on Fp in Stirling, whilst KU talked about her work on IPNV. Specifc case studies of bacterial genomics in aquaculture were provided by ED (Fp) and OB (R. Salmoninarum). DC provided an overview of the sitution regarding aquaculture disease in Norway. Industrial partners from Ridgeway (TW) and Elanco (SPC)were also represented.
The topics were broadened out on the second day to include and brief introduction to WGS and examples of its use for molecular epidemiology of MRSA (MH), bioinformatics and database design (DA, SS), genome-wide association studies (SS, JC, RZ), statistical tools (eg for population subdivision and recombination (JC)), inferring transmission from trees (CC), and ecological modelling (NT, RZ). An overview of the work being carried out in the Institute of Biodiversity, Animal Health and Comparative Medicine (University of Glasgow) was provided by BM. RE provided an overview of the work being carried out at the APHA, and CB-A talked about recent work on Vibrio vulnificus, with a focus on the key role of sea surface temperature and salinity on the incidence of infection. The workshop concluded with an open discussion chaired by EF, SA and DV-J which included feedback on future priorities.
There was a general consensus that the workshop had been a valuable exercise in knowledge exchange between disparate research communities. The potential power of whole genome sequence data for a multitude of applications for aquaculture disease managament, including molecular epidemiology and vaccine design, was well recognised. A number of research links were made, and it was strongly felt that future meetings of the network would be valuable for maintaining the momentum for making further areas of overlap and for exploring further funding opportunities. A number of promising possibilities were put forward to facilitate this. It was also felt that a training workshop covering the utilisation of some of the tools and bioinformatics concepts described would greatly facilitate the integration of these methods into the aquaculture community.
Regarding those participants coming from outside of aquaculture, there was a clear recognition of the rising importance aquaculture for global food security, and of the problems associated with intensification of fish and shellfish farming. The applicability and transferability of many of the approaches developed for public health purposes was also highly apparent. Moreover, there was tangible excitement at many of the basic bioscience questions being raised, and by many of the resources available within the aquaculture community which would be applicable to, and even aid in the development of, current research and modelling approaches (for example, large strain collections with excellent metadata, and the potential of combining genomics data to records relating to fish movements). More long-term possibilities under discussion included the use of the Minion nanopore for rapid sequencing in the field, potentially for diagnostic purposes.
Central to the project is the establishment of standardised and optimised database infrastructure for the data archiving, dissemination and sharing, and post-genomic analysis of genome data using community-oriented tools. Two database systems were described by Co-Is on the project (wgsa.net (DA) and BIGSdb (SS)), and the importance of spatial analysis was well recognised. It was noted that additional computational power and analytical tools are available via the CLIMB project (http://www.climb.ac.uk/), of which SS is a key partner. Challenges associated with the scalability of existing analytical tools for large genome databases were also discussed. Useful discussions were held on standardising metadata and ensuring mutual compatibilities between wgsa.net and BIGSdb. The importance and challenges associated with transitioning from existing technologies (eg MLST) and ensuring backwards compatability were addressed. The project website (www.wgs-aqua.net) will act as a central portal to these tools, with additional documentation and links and to other resources tailored for the aquaculture community.
Other broad themes of the talks included the development of genome-wide association studies (GWAS) approaches for identifying phenotype-genotype links. Such approaches are set to become a key component of post-genomic analysis, and have broad applicability for many key questions, eg identifying vaccine targets and understanding and predicting host specificity, environmental adaptations and virulence traits. The importance of being able to efficiently explore the pan-genome was repeatedly highlighted in this context. The utility – and challenges – of using metagenomics approaches for identifying the causative agents of emerging diseases was also recognised. In addition to the three focal pathogens of the project, the importance of many other species – including Francisella noatunensis, Streptococcus agalactiae, Yersinia ruckeri, Aeromonas salmonicida – was also discussed.
Broad knowledge gaps include:
Identifying key transmission routes and the source of outbreaks.
For example, the high frequency of KHV in fisheries appears to reflect a combination of local spread between farms, co-stocking, and import. More generally, the trade in eggs appears to play a key, yet unquantified role in the spread of a number of pathogens. The illegal movement of carp, and the release of companion fish into water bodies. Fisheries were also noted as examples of anthropogenic activities of potential importantance for disease transmission. The possible impact of the use of wild-caught cleaner fish (wrasse and lumpfish) for reduction sea lice on salmon for pathogen spread was also noted.
Exploiting genomic datasets optimally for the identification of novel vaccine targets (most notably for F. psychrophilum).
Host-pathogen interactions and the indentification of novel virulence factors and host defence mechanisms.
The rate and significance of co-infection and the impact of interactions between pathogens in disease etiology. High rates of co-infection may also have relevance for genomic evolution, for example by increasing the likelihood of recombination and horizontal gene transfer.
The role of the microbiome in disease resistance or susceptibility, and associated challenges with analysing and archiving metagenome data.
The ecology and environmental adaptations of bacterial aquaculture pathogens – for example, their environmental tenacity, identifying reservoir hosts and ecological and/or captive conditions leading to increased virulence.
The potential importance of farm design (eg recirculating aquaculture systems now being set up for trout and salmon in the freshwater phase) in pathogen maintenance and spread.
Potential of WGS to control antibiotic resistance-evolution of resistance in real time, identification of resistance mechanisms and novel drug design.
Speakers: EF: Ed Feil; Bath. DV-J: David Verner-Jeffries; Cefas. DS: David Stone; Cefas. RvE: Ronny van Earle; Cefas. SA: Sandra Adams; Stirling. KB: Kerry Bartie; Stirling. TN: Thao Ngo; Stirling. KU Kristina Ulrich; Stirling. ED: Eric Duchaud; INRA (Paris). OB: Ola Brynildsrud NMBU (Oslo). DC: Duncan Colquhoun; NVI (Oslo). TW: Tim Wallis; Ridgeway. SPC: Sara Picon Camacho; Novartis. MH: Matthew Holden; St. Andrews. DA: David Aanensen; Sanger Institute/Imperial College. SS: Sam Sheppard; Swansea. JC: Jukka Corander (Helsinki). CC: Caroline Colijn; Imperial College. BM: Barbara Mable; Glasgow. RZ: Ruth Zadocks, Glasgow. NT: Nick Taylor; Cefas. RE: Richard Ellis; APHA, CB-A: Craig Baker-Austin; Cefas.