
New program can identify drug resistance from bacterial genomes - phelimb
http://www.ox.ac.uk/news/2015-12-21-new-laptop-program-can-identify-drug-resistance-bacterial-genomes-0
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pak
This is a wonderful contribution from a group that has been working in this
field for a long time, and is further evidence that cheap and prevalent DNA
sequencing will likely make its greatest near term impact in how we manage
infectious diseases, not inheritable human diseases.

Why? Three quick reasons: (1) Sequencing bacteria is really cheap since their
genomes are 1000x smaller than a human's. Viruses are even smaller. (2)
Bacterial genetics is _much_ simpler than human genetics, and we have
reliable, well-developed tools for testing hypotheses _in vivo_ (i.e. you can
grow many generations of transformed bacteria in a Petri dish while
exquisitely controlling their environment, but human genetic manipulation is
out of bounds for almost all scientists for ethical reasons.) (3) Results from
sequencing pathogens are generally more actionable--you can detect
transmission or drug resistance which can inform changes in patient care, as
opposed to say, finding a putative increased relative risk of diabetes or
heart failure, which doesn't translate easily into a plan of care.

I wrote a open access article about this here:
[http://cid.oxfordjournals.org/content/61/11/1695.long](http://cid.oxfordjournals.org/content/61/11/1695.long)

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WhitneyLand
tdlr - "Scientists have developed an easy-to-use computer program that can
quickly analyse bacterial DNA from a patient's infection and predict which
antibiotics will work, and which will fail due to drug resistance."

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noname123
Quick question, what sequencer are they using? Nanpore MinION (since the
article refers to "laptop" sequencing) or Illumina?

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pak
The paper uses Illumina reads. The "laptop" in the article is referring only
to the platform for analysis, not sequencing.

