Whole genome sequencing in animal health: applications, challenges, and future directions

WGS is revolutionizing animal health diagnostics, offering unprecedented opportunities for pathogen detection and biomarker identification, while offering increased depth of data, in comparison to more targeted approaches such as amplicon sequencing. However current diagnostic approaches stay valuable as they are often still more cost-effective and easier to interpret. WGS can, however, offer the ability to carry out species identification and combine this with additional insights such as presence of antimicrobial resistance (AMR) mutations or genes, vaccine escape variants, recombination or reassortment, and virulence and pathogenicity factors. Moreover, the technology enables more systematic approaches, capable of screening the whole pathogenome or host genome instead of the traditional diagnostic approaches where a selection of pathogens or diagnostic markers needs to be made beforehand with a high chance of missing the (interplay of) causative agent(s) that has led to the disease. While already transforming epidemiological surveillance, practical diagnostic implementation remains challenging in some contexts due to genome complexity, sample processing requirements and accessibility of the technology. We make some recommendations on how research can overcome the remaining challenges to unlock the full potential of WGS technologies in the diagnosis of animal diseases.