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(BBC)   Faster DNA sequencing controls MRSA outbreak at socialist hospital. "We think this is the first case where whole genome sequencing has actually led to a clinical intervention and brought the outbreak to a close"   (bbc.co.uk) divider line 51
    More: Cool, MRSA, genome sequencing, Wellcome Trust Sanger Institute, DNA sequencing, The Lancet Infectious Diseases, genetic code  
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1996 clicks; posted to Geek » on 14 Nov 2012 at 7:20 AM (1 year ago)   |  Favorite    |   share:  Share on Twitter share via Email Share on Facebook   more»



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2012-11-14 12:31:27 AM  
Science!
 
2012-11-14 06:07:46 AM  
How many times has prayer been solely responsible for something similar?
 
2012-11-14 06:34:44 AM  

Bontesla: How many times has prayer been solely responsible for something similar?


Really? Do I have to be that guy?

www.designsbybethann.com
 
2012-11-14 07:28:16 AM  
A little ammonia and peroxide will fix that kind of thing right up.
 
2012-11-14 07:29:14 AM  
How can Bain Capitol make money from this?
 
2012-11-14 07:29:18 AM  

AverageAmericanGuy: A little ammonia and peroxide will fix that kind of thing right up.


Not together. Ammonia for surfaces. Peroxide for wounds.

Yeesh. Not getting a timeout for suggesting dangerous things again.
 
2012-11-14 07:47:47 AM  
Is this Geek or Politics?
 
2012-11-14 07:51:56 AM  
Foolish libtards.

MRSA is a judgement from the Almighty. You think your socialism and science can thwart God's will?

All the epidemiologists, entomologists, and herpetologists in the world cannot stop God from afflicting sinners with plagues, locusts, and swarms of venomous serpents.

He will intelligently design another virus or strain of drug-resistant bacteria to smite the wicked. Just you wait and see.
 
2012-11-14 07:56:26 AM  
They compared the entire genetic code of MRSA bugs from each baby to build a family tree. It showed they were all closely related and part of the same outbreak.

I've been told that The Theory of Evolution is of no use in medicine.
 
2012-11-14 08:01:07 AM  

The Muthaship: Is this Geek or Politics?


Its not even a climate change article...
 
2012-11-14 08:06:39 AM  
Not buying it. Rupert Murdoch says only his homeland of Australia can do socialized medicine correctly. And he never says anything just to ensure the status quo across foreign nations.
 
2012-11-14 08:10:28 AM  
But this can't be possible... they have national health care.. and thats bad.. nothing good could happen there...
 
2012-11-14 08:12:30 AM  
It's nice to see the good guys win once in a while.
 
2012-11-14 08:13:43 AM  

BronyMedic: Bontesla: How many times has prayer been solely responsible for something similar?

Really? Do I have to be that guy?

[www.designsbybethann.com image 360x360]


I think he was comparing prayer to an insidious infection that sweeps through a closed population killing all that stand it its way.

Which sounds about right.
 
2012-11-14 08:16:24 AM  
I think I almost wet myself with how exciting this is. I'm not ashamed to admit it.
 
Xai
2012-11-14 08:21:15 AM  
Hey, don't talk about prayer that way! Prayer always works in diligently sending all people afflicted with any ailment directly to Heaven.
 
2012-11-14 08:28:16 AM  
Medicine takes an amazing step so what do we discuss?

i224.photobucket.com
 
2012-11-14 08:39:23 AM  

GilRuiz1: Medicine takes an amazing step so what do we discuss?

[i224.photobucket.com image 500x391]


been trying to think of a more complicated way of saying this, now I can stop.
 
2012-11-14 08:41:48 AM  

AverageAmericanGuy: A little ammonia and peroxide will fix that kind of thing right up.


Unless you're one of the unlucky ones who happens to be a MRSA carrier. For the past 3 years everytime I get even a tiny scratch or cut, the MRSA bacteria that is always on my body will get into the cut and cause a nasty infection. I shower 2-3 times daily, change my clothes twice a day and wash myself with a surgical scrub every morning. I'm on a two year course of the strongest antibiotics available because its my only shot at beating this thing. MRSA is the devil :(
 
2012-11-14 08:49:42 AM  
Its pretty amazing how far sequencing has come in less than 10 years. "Second-Generation" sequencing only became widely available in 2008. In four years it has improved by orders of magnitude and third-generation technologies are now available. We are rapidly approaching $1000 for a whole human genome to be resequenced (its about 5k-10k right now) and exomes (just the gene coding regions) is about 1-2k at the moment. And for bacterial outbreaks like this or the E.coli outbreak last year, and viral outbreaks, we now really can leverage sequencing to intervene in real time. Clinical use of human genomics has already started as well. At least one children's hospital is doing it for every infant who has to be admitted in to NICU to try and identify any genetic conditions.
 
2012-11-14 08:52:31 AM  

reklamfox: AverageAmericanGuy: A little ammonia and peroxide will fix that kind of thing right up.

Unless you're one of the unlucky ones who happens to be a MRSA carrier. For the past 3 years everytime I get even a tiny scratch or cut, the MRSA bacteria that is always on my body will get into the cut and cause a nasty infection. I shower 2-3 times daily, change my clothes twice a day and wash myself with a surgical scrub every morning. I'm on a two year course of the strongest antibiotics available because its my only shot at beating this thing. MRSA is the devil :(


Damn... Sucks dude :( I seriously mean that, too
 
2012-11-14 08:54:59 AM  
images.wikia.com
/getting a kick
 
2012-11-14 08:58:54 AM  
It would scare the hooey out of me if I were in any sort of supervisory position in a hospital that had 12 babies infected with MRSA. Great, innovative work demonstrated though. I do hope it spreads and benefits many others.
 
2012-11-14 09:07:59 AM  

reklamfox: AverageAmericanGuy: A little ammonia and peroxide will fix that kind of thing right up.

Unless you're one of the unlucky ones who happens to be a MRSA carrier. For the past 3 years everytime I get even a tiny scratch or cut, the MRSA bacteria that is always on my body will get into the cut and cause a nasty infection. I shower 2-3 times daily, change my clothes twice a day and wash myself with a surgical scrub every morning. I'm on a two year course of the strongest antibiotics available because its my only shot at beating this thing. MRSA is the devil :(


Hope you are cleaning your nose as well, and anyone else in the house is getting similar treatment.
 
2012-11-14 09:17:22 AM  

Lunaville: It would scare the hooey out of me if I were in any sort of supervisory position in a hospital that had 12 babies infected with MRSA. Great, innovative work demonstrated though. I do hope it spreads and benefits many others.


Maybe not the best choice of words there...
 
2012-11-14 09:26:05 AM  
Damn. The Future is Here.
 
2012-11-14 09:27:45 AM  
I'm pretty sure I saw an episode of House that covered this exact topic.

And with that, I now have a perfect excuse to post a picture of Lisa Edelstein.

images.starpulse.com

/just finished the first season of The West Wing yesterday, and she was as fine as ever on that show
//what was the topic here again?
 
2012-11-14 09:31:37 AM  
Imma carrier. I'm considered a health worker. Usually once a year I get an itchy rash under my knee, then it goes away in a few weeks.

Good: If you go to the hospital for anything, you get your own room! And the workers practice quarantine protection stuff (for their protection, and so they don't spread it, even though they're probably already carriers as well) for a day or two. Kinda neat to watch.

Bad: the whole MRSA thing. A young guy on our VFD became badly sick from MRSA and was discharged from the military. Seems some are more sensitive than others.

/funfact- wifey still doesn't have it
 
2012-11-14 09:31:59 AM  

Xai: Hey, don't talk about prayer that way! Prayer always works in diligently sending all people afflicted with any ailment directly to Heaven.


I'm not sure how prayer go into the GEEK tab, but if we must discuss it ... I have a child who has/had an illness we have tracked since infancy. This child has a specialist, quarterly blood work, has had to undergo a biopsy. At times, depending on how the things with the illness were going, the blood work has been monthly or even weekly. This child had been placed on an experimental medication to control the illness, but it was a flop.

Our specialist knows that though I am merely an English major and not science savvy (please don't even ask about math); I have an interest in science. I like reading about science. I love reading on any topic that might benefit my children. The specialist encouraged me, helped me subscribe to a magazine meant for medical professionals, pointed me to websites, and so on.

My child got worse and the specialist was looking at controlling the illness only. So, I happened upon a medication approved for adults only that has a 10% cure rate. I read about it, went in, and requested the med for my child. The doctor said "No, because you're looking for a cure. That's not going to happen and you're going to get mad at me."

Well, that didn't dissuade me. We continued to talk. Finally, the doctor said "No one even really understands why the ten percent that are cured are cured. It's not approved. We're going to have to fight the insurance company. But you've sold me on trying it, but only if you will pray for and ask your meeting for worship (that probably was not the term he used) to pray for xxx." I agreed and he stated he would also put in a prayer request at his faith home. I did not know this mans' beliefs and would not have suggested prayer to him for fear of offending him. I just would have quietly done it without involving him. I went further and wrote each of my four siblings in four different cities and had them ask the people at their faith homes to pray for my child.

A woman at our meeting for worship who is a bit older than my mother, who lost a child to childhood cancer, and is very fond of my children; swung into action the best way she knew how. She emailed me diet tips for building the immune system with kid friendly recipes almost every week. She dug through alternative treatment literature and sent me articles on acupuncture among other things. And she carried a prayer request to the two other faith groups she attends: a Buddhist Temple and a local, liberal (her description) Mosque. Per this woman, someone at the Mosque passed that request onto all the other Mosques in the city.

So, people who attend at least one synagogue, five Christian groups, one Buddhist temple, and handful of Mosques prayed for my child. Here's the important part for those of you who think all Christians are anti-science: in addition to the prayers, I gave my child injections of medication. (You can't imagine how scary that task is until you have to do it.)

As far as we can tell at this time, my child has been blessed with the cure that her specialist, at one point, thought was impossible. S/he is due for lab work around Christmas. If it's all good, s/he'll have another follow-up a year from now. I think s/he'll have to be tracked most of his/her life. Still, we could not have hoped for a better outcome.

I do not believe G-d is judging either the children or the parents when an illness takes a child away as happened with my friend and her son. I do not believe G-d causes or inflicts illness on us. Nor do I believe G-d to be all-powerful with the capacity to override any and every bad thing that might ever happen to any of us. I suppose that's heresy to a certain extent.

I do believe that G-d is love. I believe that calling upon that love creates some subtle force or energy in our world. I believe that science glorifies G-d and that, if science threatens your notion of G-d, maybe your faith wasn't so great to begin with. I think both prayer and science are valuable and useful.

This statement came out longer than I had intended.
 
2012-11-14 09:35:08 AM  

BigLuca: reklamfox: AverageAmericanGuy: A little ammonia and peroxide will fix that kind of thing right up.

Unless you're one of the unlucky ones who happens to be a MRSA carrier. For the past 3 years everytime I get even a tiny scratch or cut, the MRSA bacteria that is always on my body will get into the cut and cause a nasty infection. I shower 2-3 times daily, change my clothes twice a day and wash myself with a surgical scrub every morning. I'm on a two year course of the strongest antibiotics available because its my only shot at beating this thing. MRSA is the devil :(

Hope you are cleaning your nose as well, and anyone else in the house is getting similar treatment.


Yeah me and my man use the nose ointment every month for 5 days at a time. Luckily he has been able to avoid any infection, but I just want this shiat to go away! Every doctor I have seen has told me that this type of chronic infection is EXTREMELY rare but sadly not much can be done to treat it other than constant antibiotics. I don't know what will happen when the MRSA becomes tolerant to the doxycycline :/
 
2012-11-14 09:44:17 AM  
They need to try this out at NIH where they've lost a few people already
 
2012-11-14 09:48:56 AM  
"We think this is the first case where whole genome sequencing has actually led to a clinical intervention and brought the outbreak to a close."

No.

NIH uses genome sequencing to help quell bacterial outbreak in Clinical Center
 
2012-11-14 09:59:20 AM  

rogue49: They need to try this out at NIH where they've lost a few people already


Actually, this is exactly what they did and pioneered at NIH, the study is in Science Translational Medicine. There were deaths because that was a more deadly bacteria that infected very sick, immuno-compromised patients. This method is essentially the same.
 
2012-11-14 10:24:37 AM  
Yea but what about faster pussy cat?

/obscure maybe?
 
2012-11-14 10:27:22 AM  

reklamfox: BigLuca: reklamfox: AverageAmericanGuy: A little ammonia and peroxide will fix that kind of thing right up.

Unless you're one of the unlucky ones who happens to be a MRSA carrier. For the past 3 years everytime I get even a tiny scratch or cut, the MRSA bacteria that is always on my body will get into the cut and cause a nasty infection. I shower 2-3 times daily, change my clothes twice a day and wash myself with a surgical scrub every morning. I'm on a two year course of the strongest antibiotics available because its my only shot at beating this thing. MRSA is the devil :(

Hope you are cleaning your nose as well, and anyone else in the house is getting similar treatment.

Yeah me and my man use the nose ointment every month for 5 days at a time. Luckily he has been able to avoid any infection, but I just want this shiat to go away! Every doctor I have seen has told me that this type of chronic infection is EXTREMELY rare but sadly not much can be done to treat it other than constant antibiotics. I don't know what will happen when the MRSA becomes tolerant to the doxycycline :/


Ouch, doxycycline is some powerful shiat. Stuff killed my gut bacteria which resulted in giving me cdiff. Worst month of my life.
 
2012-11-14 10:29:13 AM  

machoprogrammer: Lunaville: It would scare the hooey out of me if I were in any sort of supervisory position in a hospital that had 12 babies infected with MRSA. Great, innovative work demonstrated though. I do hope it spreads and benefits many others.

Maybe not the best choice of words there...


It's a terrible choice of words now that I look at it again.
 
2012-11-14 11:54:17 AM  

entropic_existence: Its pretty amazing how far sequencing has come in less than 10 years. "Second-Generation" sequencing only became widely available in 2008. In four years it has improved by orders of magnitude and third-generation technologies are now available. We are rapidly approaching $1000 for a whole human genome to be resequenced (its about 5k-10k right now) and exomes (just the gene coding regions) is about 1-2k at the moment. And for bacterial outbreaks like this or the E.coli outbreak last year, and viral outbreaks, we now really can leverage sequencing to intervene in real time. Clinical use of human genomics has already started as well. At least one children's hospital is doing it for every infant who has to be admitted in to NICU to try and identify any genetic conditions.


Imagine it from my perspective. I wrote my first grant application in the 1980s on DNA sequencing. At that time I was sequencing DNA in efforts regarding Philadelphia Chromosome. People were just starting to suggest complete human genome sequencing as a real possibility. My boss did a back-of-the-envelope calculation and figured 30 years. It turned out more like 20. But still...

Now I read articles whose abstracts begin like this: "We sequenced the entire genome of 15 individuals, 5 each from three populations..."

GATTACA coming, and I love it. Routine whole genome sequencing of all newborns. I love it. The sequencing, not the newborns.

By the way, it isn't in the popular press yet, or the scientific literature, but the Y-DNA root of humanity is getting an overhaul soon. A new "Y-Adam" is coming. A whole new Y haplogroup. You heard it from me first. I expect publication in a month or two. Press release imminent.
 
2012-11-14 12:11:18 PM  

BigLuca: BronyMedic: Bontesla: How many times has prayer been solely responsible for something similar?

Really? Do I have to be that guy?

[www.designsbybethann.com image 360x360]

I think he was comparing prayer to an insidious infection that sweeps through a closed population killing all that stand it its way.

Which sounds about right.


She.
and he nailed it. I was comparing the use of science to the use of prayer to fight deadly illnesses.
 
2012-11-14 12:15:07 PM  

SevenizGud: entropic_existence: Its pretty amazing how far sequencing has come in less than 10 years. "Second-Generation" sequencing only became widely available in 2008. In four years it has improved by orders of magnitude and third-generation technologies are now available. We are rapidly approaching $1000 for a whole human genome to be resequenced (its about 5k-10k right now) and exomes (just the gene coding regions) is about 1-2k at the moment. And for bacterial outbreaks like this or the E.coli outbreak last year, and viral outbreaks, we now really can leverage sequencing to intervene in real time. Clinical use of human genomics has already started as well. At least one children's hospital is doing it for every infant who has to be admitted in to NICU to try and identify any genetic conditions.

Imagine it from my perspective. I wrote my first grant application in the 1980s on DNA sequencing. At that time I was sequencing DNA in efforts regarding Philadelphia Chromosome. People were just starting to suggest complete human genome sequencing as a real possibility. My boss did a back-of-the-envelope calculation and figured 30 years. It turned out more like 20. But still...

Now I read articles whose abstracts begin like this: "We sequenced the entire genome of 15 individuals, 5 each from three populations..."

GATTACA coming, and I love it. Routine whole genome sequencing of all newborns. I love it. The sequencing, not the newborns.

By the way, it isn't in the popular press yet, or the scientific literature, but the Y-DNA root of humanity is getting an overhaul soon. A new "Y-Adam" is coming. A whole new Y haplogroup. You heard it from me first. I expect publication in a month or two. Press release imminent.


:D I think I love you.
 
2012-11-14 12:53:37 PM  

Lunaville: This statement came out longer than I had intended.


I can't for the life of me suggest anything you should have omitted. Thank you for the post.
 
2012-11-14 01:02:26 PM  

SevenizGud: Imagine it from my perspective. I wrote my first grant application in the 1980s on DNA sequencing. At that time I was sequencing DNA in efforts regarding Philadelphia Chromosome. People were just starting to suggest complete human genome sequencing as a real possibility. My boss did a back-of-the-envelope calculation and figured 30 years. It turned out more like 20. But still...

Now I read articles whose abstracts begin like this: "We sequenced the entire genome of 15 individuals, 5 each from three populations..."

GATTACA coming, and I love it. Routine whole genome sequencing of all newborns. I love it. The sequencing, not the newborns.

By the way, it isn't in the popular press yet, or the scientific literature, but the Y-DNA root of humanity is getting an overhaul soon. A new "Y-Adam" is coming. A whole new Y haplogroup. You heard it from me first. I expect publication in a month or two. Press release imminent.


Yeah I've heard the talk, I follow the human pop-gen stuff as I did my PhD work in molecular phylogenetics and now work on human disease genomics. We are just gearing up to try and do a project involving exome sequencing on 400 samples...
 
2012-11-14 01:21:15 PM  

entropic_existence: SevenizGud: Imagine it from my perspective. I wrote my first grant application in the 1980s on DNA sequencing. At that time I was sequencing DNA in efforts regarding Philadelphia Chromosome. People were just starting to suggest complete human genome sequencing as a real possibility. My boss did a back-of-the-envelope calculation and figured 30 years. It turned out more like 20. But still...

Now I read articles whose abstracts begin like this: "We sequenced the entire genome of 15 individuals, 5 each from three populations..."

GATTACA coming, and I love it. Routine whole genome sequencing of all newborns. I love it. The sequencing, not the newborns.

By the way, it isn't in the popular press yet, or the scientific literature, but the Y-DNA root of humanity is getting an overhaul soon. A new "Y-Adam" is coming. A whole new Y haplogroup. You heard it from me first. I expect publication in a month or two. Press release imminent.

Yeah I've heard the talk, I follow the human pop-gen stuff as I did my PhD work in molecular phylogenetics and now work on human disease genomics. We are just gearing up to try and do a project involving exome sequencing on 400 samples...


Sometimes I regret going into crops with talk like this.. But then I remember that I'm bringing better beer to fark parties. And all is well again.
 
2012-11-14 01:22:05 PM  
Lunaville:G-d ...

Why? Why with the dash? Are there Christians who still think their god's name is "God"?
 
2012-11-14 01:39:10 PM  

Kinek: Sometimes I regret going into crops with talk like this.. But then I remember that I'm bringing better beer to fark parties. And all is well again.


Luckily I work for a pretty well funded group, so I'm making more than the average post-doc salary. Still nowhere near what someone with a PhD and 10 years of education should be making mind.
 
2012-11-14 02:52:53 PM  

sp86: Lunaville:G-d ...

Why? Why with the dash? Are there Christians who still think their god's name is "God"?


Why Do Some Jews Spell "God" G-d?

TLDR: to show respect for the term, the thing it stands for, and/or other believers. Or, you know, out of habit. Sort of the same way that I don't say "for Christ's sake", even though I'm pretty sure that He isn't really watching over my shoulder as I type.
 
2012-11-14 03:01:44 PM  

jfarkinB: sp86: Lunaville:G-d ...

Why? Why with the dash? Are there Christians who still think their god's name is "God"?

Why Do Some Jews Spell "God" G-d?

TLDR: to show respect for the term, the thing it stands for, and/or other believers. Or, you know, out of habit. Sort of the same way that I don't say "for Christ's sake", even though I'm pretty sure that He isn't really watching over my shoulder as I type.


So the name of God has memetically infected shorthands used to stand-in for it? Clearly we need t- r-----y t--s be---re -- spr---- -nd -u- l-n--a--e be--m-- unr---gn---ble. S------- --LL SCP!
 
2012-11-14 04:24:48 PM  

jfarkinB: Why Do Some Jews Spell "God" G-d?


They haven't bought the "o" yet in Wheel of Fortune?
 
2012-11-14 04:26:35 PM  

entropic_existence: Kinek: Sometimes I regret going into crops with talk like this.. But then I remember that I'm bringing better beer to fark parties. And all is well again.

Luckily I work for a pretty well funded group, so I'm making more than the average post-doc salary. Still nowhere near what someone with a PhD and 10 years of education should be making mind.


Ah. Now you remind me why I got -out- of human and molecular genetics before I started on that path.
 
2012-11-15 05:58:32 AM  

GranoblasticMan: jfarkinB: Why Do Some Jews Spell "God" G-d?

They haven't bought the "o" yet in Wheel of Fortune?


I just assume anyone who does this is Tatsuma's alt.
 
2012-11-15 01:41:14 PM  

Kinek: Ah. Now you remind me why I got -out- of human and molecular genetics before I started on that path.


Except with how big sequencing is getting we are starting to move towards routine clinical application of whole-genome sequencing. So there's a hell of a lot of money starting to be made in human genomics now.
 
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