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Education and the NGS future- ASM wrap-up

Amy Cullinan
| Jun 22, 2012

see you next yearAs the ASM meeting wrapped up on Tuesday, I think the majority of us were so invigorated that we couldn’t wait to get back home. At the same time, I think many of us wanted to start over from Sunday and attend all the great talks we missed while we were attending other great talks. Despite the fact that we all now know how many bacteria are commonly found in salad (100 million per gram) and where it comes from (manure), the seeds of many novel microbiology research ideas were planted in our minds.

Speaking of of learning, one of Tuesday’s most popular talks came from a new collaborative filtering session. In an experiment run by ASM Communications Committee, any presenter was able to submit a topic of interest to the greater microbiology community. Other microbiologists, ASM members or other interested individuals then voted on the topics, based on its impact, validity and/or relevance to the community. One of the voted-in talks was Mark Martin from the University of Puget Sound speaking on microbiology curriculum. He provided a revealing look into why basic concepts of microbial literacy are not effectively taught in entry level biology classes. Getting students interested in microbiology takes a whole PR plan, and is complemented with art and other media projects. As he memorably put it, “Microbes are the 99.999% (referring generally to the biomass on Earth), so they need top billing in biology curriculum!” Check out this article in Microbe magazine for more small (as in micro) perspectives on changing paradigms in microbiology.

In a highly anticipated and mostly standing room only session titled “On top of outbreaks: New rapid next-generation sequencing deployed for public health and clinical microbiology”, Peter Gerner-Smidt from the CDC echoed a sentiment that I’d heard often during this meeting. For small organisms, whole genome sequencing was rapidly becoming the ultimate diagnostic and subtyping tool, and that pathogens and outbreaks might better be examined based on virulence profiles rather than genus/species/genotype. Discussing insights gleaned from German EHEC O104:H4 and Dutch Klebsiella outbreak, Dag Harmsen from the University of Muenster spoke about how the rapid adoption of bench top sequencing machines make genomic epidemiology technically feasible for even small labs, and the vast scientific and public health advantages of crowdsourcing data to get on top of outbreak events. Speaking to early warning outbreak detection on a global scale, Dag made comparisons to PulseNet, a national network of public health and food regulatory agency laboratories performing standardized molecular subtyping of foodborne disease-causing bacteria by the once gold standard method of pulsed-field gel electrophoresis. Next-generation sequencing must evolve its own standards of quality scoring, reference sequences, and data outputs in a kind of “molecular Esperanto” that would let labs and researchers running various platforms talk about data in the same language. Michael Metzker of Human Genome Sequencing Center at Baylor showed off an impressive list of next-generation sequencing machines (they seem to have one of every available sequencing instrument) as he talked about NGS technologies in the past, present, and future. Citing its utility in understanding of human biology, pharmacogenomics, diagnostics, organismal and environmental microbiomes and forensics, he stated that the use of next-gen sequencing “is only limited by your imagination”. We couldn’t agree more.

Overall, ASM 2012 was a big success in and of itself, and a great experience for us at Illumina to learn more about how we can provide genomic tools to this diverse and rapidly expanding field. We are already looking forward to next year’s meeting in Denver.