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7. Exploiting whole genome sequencing for public health microbiology
 

7. Exploiting whole genome sequencing for public health microbiology

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Presented by Jonathan Green from Health Protection Agency. This is the seventh presentation from Eagle second symposium, held on 29th March 2012. ...

Presented by Jonathan Green from Health Protection Agency. This is the seventh presentation from Eagle second symposium, held on 29th March 2012.


Abstract:
"Next Generation Sequencing (NGS) represents a revolution in DNA sequencing technologies, making routine rapid analysis of the complete DNA sequence of viral and bacterial genomes a reality. It is already the case that microbiological investigations of any significant outbreak of infectious disease include whole genome sequencing (WGS) of a putative causative agent. for example pandemic influenza strains, MRSA and Acinetobacter baumannii.

The potential impact of these technologies on Organisations such as the HPA is far-reaching. The bioinformatics challenges of NGS and other 'omic technologies, in terms of IT infrastructure for the storage and management of the large amounts of data generated, are well-known but not resolved. A key challenge is how to ensure it has the appropriate workforce capability for the analysis of these data in order to best use the extracted information for public health purposes. This requires meaningful integration of 'omics data with other laboratory information pipelines, clinical datasets and surveillance systems which is a significant challenge. Public health microbiology is increasingly 'data-rich' and laboratory scientists are being required to spend more of their time on data analysis using desktop bioinformatics tools or working with bioinformaticians to deliver these analyses, and this will increase as automation replaces much of the current manual approach to development of data. This is likely to create a significant shift in the skill-mix required to deliver reference microbiology, epidemiology and surveillance. The need to enhance microbiology and to integrate molecular typing into International as well as national surveillance context is recognised as paramount and needs to be a component of the current strategy.The presentation will aim to describe the relevance and likely impact of these technologies on public health microbiology, to describe the challenges and the work being undertaken to provide a platform for further development."

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  • Turning to the methods… from a paper by Foxman et al, 2005 Optimistically has complete genome sequencing down as a typing method The case for sequenced-based methods is now well accepted The second thing, looking at these methods and their exotic acronyms is that you can’t help but be reminded…..
  • Timeliness: The recent emergence of NGS and subsequent technologies which are clearly already impacting on how we view and go about microbial investigations for surveillance and other purposes. This is not a ‘fad’, this is happening and will stay with us Important to explore what the vision look like and start making so important decisions
  • Interpret that we need these within the Agency as well as through collaborations
  • Should we store data centrally? Alternative is an assortment of servers containing data which may or may not have appropriate resilience However, you could argue that resilient, distributed interoperable databases within as well as outside the Agency is adequate.