Determining the origin of the E. coli strain attacking Europe – Part 2

The search for the source of the E coli contagion in Germany has heated up in the past 24 hours. Focus was initially on a restaurant in Lubeck but has now shifted to a farm which supplied sprouts to this restaurant and others associated with illness. We should know within the next day or two what evidence German officials have that this farm is the source of the contamination. However, even if it is, it does not address the broader questions of how this novel strain of E coli came to exist.

As discussed in my previous blog, determining whether the current outbreak comes from a natural or man made source is difficult because E coli exchange genetic material in nature but are also easy to modify in a laboratory. If this outbreak was due to a well-characterised pathogen that had caused similar outbreaks in the past, there would be no reason to suspect anything but a natural source. However, early evidence suggests that this is an unusual bacteria, both in terms of its genetics, but also in the large number of people infected and in the severe symptoms it causes. Indeed, recent stories suggest that hospitals in Northern Germany are under severe pressure. This event is likely to go down as the worst E coli outbreak in recorded history. Thus, perhaps it is not surprising that the very novelty of the bacteria and the severe symptoms have raised suspicions:

From The Windsor Star, June 4, 2011:

A senior German doctor last night called for an investigation into the possibility that the bacteria had been spread deliberately.

Klaus-Dieter Zastrow, chief doctor for hygiene at Berlin’s Vivantes hospital, said: “It’s quite possible that there’s a crazy person out there who thinks ‘I’ll kill a few people or give 10,000 people diarrhoea’. It’s a negligent mistake not to investigate in that direction.”

Interestingly, there was a report that German authorities had launched a criminal investigation (The Daily Mail, June 4, 2011 ). The basis for this investigation has not been revealed.

However, it is important to note that given the unusual nature of this pathogen, it is unlikely that a solitary criminal is responsible for this outbreak. Further, given the rarity of at least some of the genetic material, stateless terrorists are probably not responsible for the production of this pathogen. The fact that there has been no claim of responsibility also undermines this hypothesis.

If this bacteria was made in the laboratory, it was likely produced by a well-funded group with extensive resources and skills. This could only be supported by a State. If such resources were available, is it possible to determine that this new E coli strain was not natural? It depends.

As I mentioned in my previous blog, genetic material from E coli can be manipulated using restriction enzymes. In common lab strains, there are specific and readily identifiable sequences called restriction sites which facilitate splicing different bits of genetic material together. The presence of such sequences at the junctions of unusual combinations of genetic material in this new strain would be a dead give away that this bacteria was a biological weapon. Currently, raw sequence is available from at least one isolate. However, to identify incriminating restriction sites, a high-quality, finished assembly of these sequences is necessary. Although a number of groups are working hard on this, only rough, incomplete drafts have been made public thus far. We should have more information on this next week.

If suspicious restriction sites are not found, can we conclude that this bacteria must be natural? Unfortunately, no. Molecular biology has advanced greatly in the last decade and there are now many ways to manipulate bacteria in a laboratory without leaving tell-tale signs. Indeed, if this new strain of E coli was made in a sophisticated laboratory, leaving restriction sites in would be tantamount to announcing that it was a bioweapon.

There are a number of ways the current investigation will end. I won’t pretend to know which is the most likely. However, one possibility is that we will be left in an ambiguous situation. The genetic analysis may point to an extremely odd configuration of genes, but no smoking DNA may be found. Detective work may find that agricultural products were contaminated, but may not find out where the bacteria that contaminated them came from. If this is the outcome, should we regard any consideration of the possibility of  a laboratory origin as “inappropriate”, “paranoid”, or “irresponsible”?

No, in my opinion. We should not.

From: Yi, et al 2010

Among the pathogenic E. coli strains, EHEC O157:H7 has been recognized as one of the most notorious pathogens featuring the properties of an extremely common and virulent serotype, and is responsible for a series of severe gastrointestinal illnesses with life-threatening consequences in North America, Europe, China, and Japan[7], [8], [9], [10]. Considering its high pathogenicity, EHEC O157:H7 has been listed as a potential bio-weapon in many countries[11].

Indeed, enterohaemorrhagic E coli has an official BioWeapon designation: WB3.

Yesterday, it was reported that the Centre for the Protection of National Infrastructure in the UK has issued a warning to manufacturers and retailers to be on the alert for attempts to poison food by politically motivated groups (The Telegraph, June 4, 2011).

It is true that Nature has killed many people. It is also true that humans have killed many of their own species. When someone dies in an unusual way, there is usually an investigation to determine whether or not foul play was involved. People in Germany are dying of an unusual pathogen which was explicitly listed as a possible Bioweapon. Maybe they are dying of natural causes. But assuming this, without an investigation which considers the other possibility, would be reckless, in my opinion.

Reference

Yi et al. (2010) Crystal structure of EHEC intimin: insights into the complementarity between EPEC and EHEC. PLoS One. 5: 15285.

Advertisements

7 thoughts on “Determining the origin of the E. coli strain attacking Europe – Part 2

  1. someone suggested that the bacterium evolved in biogas “reactors” where
    farmers in Germany put corn and liquid manure, waste from cows,
    to produce energy. These become more and more widespread in Germany
    in recent years.

  2. This is a speculation, of course. To prove it, they would need to find the same bacteria in the reactors. They also have to show that the bacteria was under selection to retain a large number of antibiotic resistance factors.

  3. I have heard that this bug has resistance to at least 6-7 different antibiotics. If true, would this happen by natural selection? How long would this take naturally and or created by lab?

    Thanks
    Kim

  4. Kim, it’s more than 7, I think. Normally, bacteria resistant to so many antibiotics are found in hospitals where people are being treated with many different antibiotics. In that environment, antibiotic resistance is under selection. There are lots of ways for bacteria to acquire resistance to antibiotics, but unless this resistance confers an advantage to the bacteria harboring it, you would not expect the resistance to be maintained. Another issue is how many plasmids this bacteria has. Antibiotic resistance is oftentimes due to these extrachromosomal bits of DNA. However, there is a fitness cost to the bacteria to harbor plasmids. I would like to know how many plasmids this bacteria has and how the antibiotic resistance genes are distributed amongst its genetic elements. I’m not an expert on this, but I’m not sure how it can be advantageous to a bacteria to harbor multiple plasmids which confer resistance to antibiotics in the absence of selection, ie, an environment like a hospital where only the bacteria resistant to antibiotics can survive.

    Adding plasmids to a bacteria is trivial. You could engineer whatever you want and get the plasmids into the bacteria in a week.

    1. when you “engineer” a new bacterium, wouldn’t you take parts from existing, known
      bacteria and recombine them ? So the parts would be identical to known ones.
      Finding and growing new unknown parts could be difficult with rare strains
      like this one. And how would you know that it survives and spreads well ?
      And why would you want to hide that it’s engineered ?

  5. gsgs, there are lots of ways a bacterium could be engineered. One way would be to recombine parts from existing bacteria. Some of the parts of new E coli *are* identical to older strains. However, creating entirely new elements would be quite easy. It is true that you would need to test it to be sure it spreads, but E coli biology is probably among the best understood of any organism on Earth. So, making intelligent guesses would certainly be possible.

    I agree that if the purpose of the E coli is to instill terror, you would not want to hide the fact that it is engineered. The assemblies of this novel strain are improving, but are still not of suffcient quality to say whether or not there are obvious signs of tampering. We’ll have to wait and see a bit longer on this. The other possibility is that it is being used for economic reasons. Certainly, this outbreak is having a very strong economic effect.

    If this is a bioweapon, there is a possibility that the outbreak in Germany is a test. If so, there may be a larger attack, perhaps in the US. This is why I think it is important not to reject the possibility of an attack out of hand. We need to do due diligence on this possibility or risk being responsible for not warning the public of the possibility of future attacks.

    1. Some More Thoughts About the German E. coli Outbreak
      Posted on: June 6, 2011 9:38 AM

      http://scienceblogs.com/mikethemadbiologist/2011/06/some_more_thoughts_about_the_g.php?utm_source=sbhomepage&utm_medium=link&utm_content=channellink

      From the link:

      5) This is a highly drug resistant strain. Its resistance profile:

      Ampicillin R
      Amoxicillin/Clavulanic acid R
      Piperacillin/Sulbactam R
      Piperacillin/Tazobactam R*
      Cefuroxime R
      Cefuroxime-Axetil R
      Cefoxitine R
      Cefotaxime R
      Cetfazidime R
      Cefpodoxim R
      Imipenem S
      Meropenem S
      Amikacin S
      Gentamicin S
      Kanamycin S
      Tobramycin S
      Streptomycin R
      Nalixidic Acid R
      Ciprofloxacin S
      Norfloxacin S
      Tetracycline R
      Nitrofurantoin S
      Trimethoprim/Sulfamethoxazole R
      Chloramphenicol S
      Fosfomycin S

      It also has a CTX-M-15 beta-lactamase, which confers resistance to most penicillin derivatives, except for the carbapenems. In English, any antibiotic that starts with “Cef-“, “Ceph-“, or ends with “-cillin” won’t work. What’s disconcerting about this is, if the recent reports are correct and the outbreak was initiated by contaminated bean sprouts, agricultural isolates now have many different drug resistance genes.

      Multidrug resistance is no longer confined to hospitals and other medical settings. Note however, most accepted treatments for Shiga-toxin producing infections do not involve antibiotics, as they are thought to stress the bacterium, leading to increased toxin production and more severe disease; resistance is not a problem for therapy in this particular case, despite claims to the contrary.

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s