APRAFGAP: A Platform to Read About Foodborne-pathogen Genomics Analysis Platforms

TL;DR

  • There are at least 3 big genomics of foodborne pathogens/outbreak detection/analysis platforms/projects. If you know of any others/feel I have grossly misrepresented your project, get in touch.
  • I hope that there is some co-ordination between these, possibly via the GMI initiative, to make the most of the funding devoted to this area.
  • It’s a great time to work in the genomics of foodborne pathogens!

We all agree that the unrivalled portability of genomic data will provide an unprecedented opportunity to prospectively detect international outbreaks and help with source traceback. One field which seems to be leading the way in trying to turn this vision into a reality is the surveillance of foodborne pathogens. In fact, I’m currently aware of three/four/loads of projects in this area, in no particular order…

Enterobase/MRC CLIMB

Led by the mighty Mark Achtman, Enterobase will be a ‘powerful, user-friendly online resource for analyzing and visualizing genomic variation within Escherichia coli and Salmonella enterica‘. The backend will be hosted on the MRC CLIMB infrastructure (full disclosure – I’m involved with the beta-testing for Enterobase). They aim to ‘enable bacteriologists to identify, analyse, quantify and visualize genomic variation principally within Escherichia coli and Salmonella enterica, two key AgriFood pathogens and model organisms’.

Genome Trackr/NCBI

The Genome Trackr project is an FDA project, with NCBI providing technical and analytical support. It is a network of more than 20 labs, mainly in the USA but also in Argentina and elsewhere. Each of these labs has a MiSeq, which feeds into core bioinformatics (via Illumina’s Basespace platform I believe) teams at FDA/NCBI. Their main focus is outbreak detection and surveillance and they are the first team to be making data available (> 12000 so far) in real time (or close to real time, 1 week delay I think).

Compare/DTU

Then there is the EU Compare project, funded with a very large grant (€20 million), spread across a large number of collaborators, with the aim of providing a ‘COllaborative Management Platform for detection and Analyses of (Re-) emerging and foodborne outbreaks in Europe’. There is a bit more info in this talk that the leader of the Compare consortium, Frank Aarstrup, gave at ECCMID 2015.

Global Microbial Identifier

The GMI initiative, is apparently ‘The genomic epidemiological database for global identification of microorganisms or global identifier of microorganisms is a platform for storing whole genome sequencing(WGS) data of microorganisms, for the identification of relevant genes and for the comparison of genomes to detect outbreaks and emerging pathogens’. According to their development plan, they should be nearly done developing ‘a robust IT-backbone for the database, and development of novel genome analysis algorithms and software’ (emphasis mine). I think this is closely tied in with the Genome Trackr and Compare projects, or at least there are people on the GMI steering committee from both FDA and DTU.

The GMI is also a network that ‘aims to promote development and deployment of novel applications, data sharing and analysis systems across the diversity of pathogens, domains and sectors’.

Honourable mentions

Finally, I would like to mention the BIGsdb platform from Martin Maiden and Keith Jolley. They probably have the most experience at implementing databases that are used for bacterial population genomics, although I’m not aware of foodborne specific work they are doing on the scale on the above (multiple post-docs etc). Also WGSA from David Aanensen et al is the slickest front end I have seen to a genomics analysis platform.

Finally finally, we at PHE are contributing by trying to be open collaborators, and making all our data publically available.

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