Physicist, Startup Founder, Blogger, Dad

Thursday, June 02, 2011

E. Coli super strain

I was told about the sequencing results from E. Coli in the German outbreak just a few hours ago before I left BGI. This new strain has some very strange and lethal features. I wasn't going to blog about it -- the scientist involved said the results were confidential -- but it's already in the Times. At one point the words "man made" were used, but of course a rare natural event might produce a bacterium that seems to be optimized for killing people.

NYTimes: ... In a statement on Thursday, a Chinese laboratory collaborating with German scientists said the contagion had been caused by a “new strain of bacteria that is highly infectious and toxic.” The strain carries “several antibiotic resistant genes,” according to the Beijing Genomics Institute in the southern city of Shenzen, “which makes antibiotic treatment extremely difficult.”

The statement referred to the strain as “entirely new” and “super-toxic” and said it was similar to a strain known as EAEC 55989 found in the Central African Republic and known to cause serious diarrhea. The Chinese laboratory had been working with scientists at the University Medical Center Hamburg-Eppendorf at the epicenter of the outbreak.

“The situation is still tense,” said Jörg Debatin, director of the Hamburg-Eppendorf facility. “At the beginning of the week we had been hoping to see a trend towards fewer infections, but that has not happened.”

Holger Rohde, a bacteriologist at the same medical center, said tests conducted with the Chinese scientists in Shenzen had shown that the new strain was a hybrid that caused the virulent complication of E.coli known as hemolytic uremic syndrome, or HUS, which attacks the kidneys and can be lethal.

“This is a genetic combination we have not seen before,” he said. About 80 per cent of the genetic composition derived from the E.Coli strain 0104. But the other 20 per cent came from another more toxic bacterium.

Louise Brown, a spokeswoman for Britain’s Health Protection Agency, said the strain of E.coli causing the outbreak “has a combination of characteristics that have not been identified in strains that have caused illness before.”


Argos Van Buren said...

You're not supposed to use antibiotics to treat e coli because people will quite often be close to kidney failure and any antibiotics will put additional stress on the kidneys. Also antibiotics were shown ineffective against the original. The antibiotic resistance point is moot.

silkop said...

What's embarrassing is that despite some registered 1500 cases over two weeks the authorities still seem to have no clue about the source of infections, as indicated by general statements about unwashed vegetables. Why is it so hard to compare 1500 patient interviews, with out wonderful statistics and 500k a pop technology, to find what common food they have eaten during the period? Instead of that we get news about how the scientists sequenced the microbe and reveled how very toxic it is and others who achieved a "breakthrough" by developing a faster diagnostic test. Guess what, we already knew that it was toxic before and it's already not so hard to diagnose what you have if you happen to live in northern Germany and have a bloody diarrhea.

silkop said...

BTW, I the German press seems to give but little credit to BGI. It mentions how German scientists from Hamburg successfully completed the sequencing "with assistance from Chinese colleagues" or that "Chinese scientists also took part in the sequencing effort". Always nice to see how the same information is presented depending on the source.

Ralf Muschall said...

@Argos: The antibiotics problem is different: If the beast is similar to older EHECs, the poison is made using the genes from a Lambda phage.  As the poison gene sits at a late place in the phage genome, it is expressed rarely (but still often enough to be nasty).  If the bacteria get sick from antibiotics, the phage panicks and starts lysis, expressing its whole genome as many times as possible, thus making also lots of STX2.

Ralf Muschall said...

@silkop: Since the incubation period is about 10 days, finding the source is harder than for other things.  Do you know exactly everything (including the small "irrelevant" little stuff that nobody thinks about) you ate in the interval from 15 to 5 days ago?  Would you be able to tell it (including date, time and place of shopping) when rolling on the floor screaming in pain (if regaining consciousness before death at all)?

Another problem is that one does not need unwashed vegetables.  Washing can reduce the germ count for Salmonella or Cholera from a million to a few thousand, thus leaving a population that might be too weak to overpower the human defense.  With EHEC, a single cell is enough and you can't be sure to have washed that one off (but washing is still useful since it reduces the probability of that single cell to be present).

A diagnostic test *is* useful: Even if 1500 patients have EHEC, there are many more with ordinary diarrhea (Noro, Roto, Salmonella etc.) who need to be treated differently.

Max B said...

" which has killed at least 18 people, sickened more than 1,600". Pretty damn sloppy "optimizations" for a "man made".

Max B said...

" which has killed at least 18 people, sickened more than 1,600". Pretty damn sloppy "optimizations" for a "man made".

steve hsu said...

The sequencing was done here.

steve hsu said...

Not bad if it's a HS kid playing with synthetic biology.


Sabine Hossenfelder said...

If you want to kill people with bacteria, you don't need to go through HUS. I suspect some of the multi-resistant things that have been going around would do. There is also the question of how you find out what the damned thing does. I mean, if some kids plays around they might know the resistances, but I doubt they'd know the actual effect.  Further, they've had the first reported infections May 2. That's a month ago. And it's been in very different parts of the country. This means there has to be a source of recurring infections. 

silkop said...

Thanks for your reply. As a matter of fact, I started recording what I eat about a week ago "just in case" to be able to provide such information, should I become sick. It doesn't take much effort, but as far as I know hasn't been suggested by anyone in authority (to avoid panic?).

But you don't have to know exactly what you have eaten to provide some information, though. Fragmentary information could also be useful if sufficient in quantity. For example, it would be useful to know whether and how many patients exist who claim to NOT have consumed any raw vegetables during the incubation period, those who claim to NOT have consumed specific kinds of vegetables, vegetarians vs. non-vegetarians, those who cook at home versus those who eat in public places and so on.

Ralf Muschall said...

German weekly "Der Spiegel" correctly wrote "Chinesen entschlüsseln Ehec-Erreger" (http://www.spiegel.de/wissenschaft/medizin/0,1518,766285,00.html) -- and a commenter in the forum was unhappy about this and claimed that the german effort was not appreciated enough ;-)

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