Recently I saw the Director of Public Health Genomics for the CDC tweet about a resource that was new to me, ePathGen, Pathogen Genomics for Epidemiology. This is an area that I’m glad to see getting attention. My undergrad degree was in microbiology, and certainly the most memorable class I had in college was about pathogenic bacteria and viruses and their consequences throughout history and to the present. One thing that was stressed to us, though, was that we could only study the things we could culture. Some things were really challenging to grow or couldn’t be grown at all with current methods. I was struck by this again in a seminar I heard where a physician described the assessment of the the organisms in a brain abscess sample, they were able to culture 22 organisms. With PCR, the same sample showed 72. Eek.
But our new abilities to look at unculturable organisms by sequencing them rapidly, and then to more quickly and appropriately target infections, is also even getting NYT press coverage at this point: In a First, Test of DNA Finds Root of Illness. And that’s just one kid’s illness–this can also be used to more quickly put the brakes on community-wide issues too. So here’s the tweet that caught my eye:
— Dr. Muin Khoury (@DrKhouryCDC) June 3, 2014
And I went to see what e-PathGen was about. What they provide are a couple of video tutorials–but I can’t embed them here, they are part of a learning module that also has additional details and two case studies to work through. The tutorials offer some guidance for folks who might be new to genomics and the sequencing technology from a public health perspective. Then the two case studies show how this type of information might be used on a specific outbreak of illness.
So here’s a look at their landing page, and you can click to go over there and watch their videos:
Or go to the site with this link: http://public-health-genomics.phe.org.uk/
And usually we like to highlight specific database resources or other bioinformatics tools in our tips. And in the first case study I came across a database collection that was new to me–the BIGSdb system, Bacterial Isolate Genome Sequence Database. This is a framework that offers researchers and clinicians a place to store details of specific isolates of patient or environmental samples. It doesn’t require whole genome data–but it is flexible enough to support that as well as we will increasingly see more of that kind of data coming along.
This framework has now been used by a number of different groups to create databases with their organisms of interest. Check out this list of organisms that you can find individual samples from: http://pubmlst.org/databases/. I hope to take a look at this in a future tip–I’ve already gone longer than I like to in our weekly introduction to a new resource. So check back with us for more on this later.
ePathGen videos and case studies: http://public-health-genomics.phe.org.uk/
Bacterial Isolate Genome Sequence Database (BIGSdb): http://pubmlst.org/software/database/bigsdb/
Jefferies J. & McCulloch J. (2014). ePathGen – a new e-learning package in pathogen genomics., Euro surveillance : bulletin Européen sur les maladies transmissibles = European communicable disease bulletin, PMID: 24906379
Jolley K.A. & Maiden M.C.J. (2010). BIGSdb: Scalable analysis of bacterial genome variation at the population level., BMC bioinformatics, DOI: 10.1186/1471-2105-11-595