next generation sequencing strikes again

A while back I noted a "proof-of-concept" study where researchers took a problematic strain of E. coli from an outbreak, pumped out the genomic sequence and analysis in a few days and were able to make great strides in understanding the nature of why this particular strain was a problem.

The same research group have now applied that to Klebsiella pneumoniae Oxa-48 - a bacterial strain responsible for hospital infections in the Netherlands. This really seems to support the importance of DNA technology advances and how genomic level information will be used in the future.

New tech sequences bacterial genome in 2 hrs

http://www.iontorrent.com/technology-how-does-it-work-more/

How it works (if you're into this kind of thing): 

many miniwells, each with strand of DNA (stands that you want to sequence) anchored. Wash specific nucleotide (ex. dATP) over the slide. If that specific nucleotide gets incorporated, sensors detect the release of H+ ions from the reaction which lets you know "yep, that was an A". Generates 100 bp length reads - of course it's 1.4 million of them. They sequenced bacterial genomes (5x-10x coverage) in 2 hours with just 6 hours of prep time for each sample. 

Interestingly enough, they also sequenced Gordon Moore's genome as a test. He's the guy who developed Moore's Law which describes how technology doubles. His genome coast $50K to do but they think that this technology will advance quickly to get close to that target $1000 genome that everyone talks about. Not sure how much the bacterial genomes cost each

Link to the Nature summary

whole genome sequencing of E.coli in outbreak

Article in Genome Technology this month: (click to see it)

stresses the power of the genomics age. Check out this timeline:
- received sample on May 30
- completed genome sequencings on June 1
- Genomes assembled and submitted to NCBI by June 2

Findings
- that E. coli was a new strain
- that E. coli had many antibiotic resistance genes

concept of "Genomic epidemiology"discussed

Another part of this article looks at MRSA and genomic sequencing of 63 isolates - identifying 6700 SNP (single nucleotide polymorphisms) that accounted for the variability seen and related to the microevolutionary changes being seen.

E. coli outbreak resources from NY Times

http://topics.nytimes.com/topics/reference/timestopics/subjects/e/e_coli_bacteria/index.html