Head of Genome Analysis, Animal and Plant Health Agency, UK
Bovine tuberculosis is endemic in some parts of England and Wales and as part of the effort to control this disease, the Animal and Plant Health Agency has implemented routine whole genome sequencing of Mycobacterium bovis isolated from cattle. As there are approximately 5000 isolates from across GB each year we have developed an efficient yet comprehensive sample-to-result process. Data processing is fully automated via Nextfow using AWS, and includes a process to assign each sample to a WGS cluster based on matching pre-defined SNPs. This aids field staff in determining the likely source of infection, and aids in understanding the wider epidemiological picture. Furthermore, an approach for linking genetic relatedness and geographical neighborhood has been developed to aid visualization of the data in a readily usable format. These outputs are used in near-real time to manage disease outbreaks.
Dr Richard J Ellis has been at Animal and Plant Health Agency (and its predecessors) for over 10 years and since 2016 has been Head of Genome Analysis. He also oversees molecular biology and bioinformatics at the Agency. Prior to this he held post-doctoral positions at Cardiff University and Imperial College London. He has over 25 years’ experience in molecular microbiology, particularly studying the structure of complex communities and bacterial population genetics. His work now focuses on the application of next generation sequencing technologies for understanding the evolution and spread of pathogens (both bacterial and viral), for investigating diseases of unknown aetiology, and the development of new diagnostic procedures and surveillance programmes.
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