The Promise of Whole Genome Pathogen Sequencing for the Molecular Epidemiology of Emerging Aquaculture Pathogens

Abstract

Aquaculture is the fastest growing food-producing sector, and the sustainability of this industry is critical both for global food security and economic welfare. The management of infectious disease represents a key challenge. Here, we discuss the opportunities afforded by whole genome sequencing of bacterial and viral pathogens of aquaculture to mitigate disease emergence and spread. We outline, by way of comparison, how sequencing technology is transforming the molecular epidemiology of pathogens of public health importance, emphasizing the importance of community-oriented databases and analysis tools.

Keywords: aquaculture; bacteria; genomics; infectious disease; molecular epidemiology; pathogens; viruses; whole genome sequencing.

FIGURE 1

Example workflow of how whole genome sequencing of pathogens maybe used to address research areas of particular relevance to the aquaculture setting.

FIGURE 2

Screenshot of the WGSA.net whole genome MLST scheme of 68 Renibacterium salmoninarum isolates from the collection of Brynildsrud et al. (2014). The assemblies and metadata are hosted at WGSA.net (http://wgsa.net/rensm/brynildsrud). The left-hand window shows the phylogenetic tree of the isolates built from the core genome MLST scheme. The right-hand window shows the geographical distribution of isolates. The bottom window shows metadata and summary statistics for individual isolates from the collection.

FIGURE 3

Screenshot of the Microreact project for 68 R. salmoninarum isolates from the collection of Brynildsrud et al. (2014). The left-hand window shows the geographical distribution of isolates colored by the host species from which they were isolated. The right-hand window shows the consensus phylogenetic tree inferred using a Bayesian Markov Chain Monte Carlo approach, with a generalized time-reversible model (Brynildsrud et al., 2014). The bottom window shows toggle buttons for displaying alternative metadata labels, shapes and colors on the phylogenetic tree and world map.