NEWS FLASH: The German EHEC Germ DNA code displays evidence that it has been genetically engineered!

For a more recent updated post on this topic go here.
Kat Holt, the super-geek pathological-genome breaker at U. Melbourne (who works upstairs from the Pundit, in a room full of expensive computers and a lovely view of sheep) is at it again. She’s found gene rearrangements in the German EAEC outbreak germ. She reports her work in her blog post ” Tn21 resistance transposon in the chromosome?
These gene rearrangement are clearly the result of genetic engineering. The traces of this genetic engineering are right there in the bacteria’s DNA that has just been decoded by the scientists.
Super-computer whiz Kat has found a set of mobile set genes that once lived in another germ of a different species called Salmonella Paratyphi A. They are now neatly and precisely engineered into the main E. coli EHEC chromosome, Kat has discovered.
This discovery is explained by red color-code in the diagram below. The name pAKU1 refers to a mini-chromosome on which they lived when they were found  in the dangerous  Paratyphi germ — which is quite unconnected with the German outbreak. It’s not even an E. coli.
But its genes are in the German E. coli (shown in nice super-female purple). Blue shows genes almost identical to the quite distant African-grandparent of the German germ

Legend to Figure. Kat Holt’s latest discovery about the German EHEC germ. Purple color on the diagram is the BGI Institute data for the German outbreak strain. Blue show DNA code of an African parental strain Ec 55989 from French scientists. Red indicates detection of Paratyphoid like trans-genes in the E. coli genome.

These trans-genes confer resistance to antibiotics streptomycin, trimethoprim, sulfamethoxazole, and the antibacterial metal mercury.

Interestingly, German germ DNA also has a device made of DNA called an integron mentioned by Kat.
Integrons capture genes.
They are used to do genetic engineering.

But integrons are completely natural genetic tools. The genetic engineering with integrons is done by the germ itself.
(See for instance, the supporting quote from Dr Guillaume Cambray and colleagues fascinating and authoritative 2010 review provided below.)
Integrons are natural tools used by bacteria to systematically capture new genes. They are associated with certain mobile sets of genes that disseminate traits such as antibiotic resistance to new host chromosome locations.
They do exactly what human genetic engineers do. They clone DNA.  In the current example the GMO was engineered by the German germ to produce a natural GMO which has new genes systematically inserted in its chromosome — they were cloned, as you can plainly see from the diagram.
That is what has made the German beast so dangerous – completely natural gene cloning.
There are even superintegrons that have been found. I am not  kidding. These are exceptionally nasty natural weapons of germs encouraged to by circumstances of natural selection to do genetic engineering all by themselves.
Both integrons and superintegrons are famous among microbiologists for their amazing ability to capture numerous and diverse new genes at the DNA location of the integron DNA. Many examples of integrons have been found where they have provided bacteria with immunity to a wide range of antibiotics. People who don’t know about them- as for example a writer at a website putting forward conspiracy theories to explain the emergence of this dangerous EHEC germ,  “it seems virtually impossible to imagine how this could happen all by itself in the natural world.”  Bacteria  do the “virtually impossible” with the help of integrons.
It seems a pity to disappoint the conspiracy theorists among the readership who are keen to blame heartless corporations for all this, but if they knew their modern genetics as well as they can fantasise about about evil plots by drug companies to increase sales, they would be expecting these superpunchlines.
In a later post, the Pundit will explain how integrons do their amazing cloning task, or provide links to where someone else has done a good clear job of explaining this fantastic genetic capability of supposedly simple germs.
In the meantime, the summaries of current science below will perhaps convince the uninitiated that the Pundit’s deadly serious about integrons doing genetic engineering. And perhaps readers should also ask themselves why the anti-GM activists never honestly discuss the extent of this perfectly natural genetic engineering, and why they seem exempt it from their risk calculations, as they have so tragically done in Germany in recent years. It’s not carefully regulated and thoroughly tested GM food that’s done harm, but dangerous natural germs that are well established as the main cause of food-borne illness.
Science of Integrons:

Guillaume Cambray, Anne-Marie Guerout, and Didier Mazel’s 2010 review of the natural biology of integrons has this to say in introducing the topic:

Although the first bacteria resistant toward mutiple antibiotics were isolated in the mid-1950s in Japan, it was not until the 1970s that it was determined that these phenotypes are frequently associated with transmissible plasmids [optional germ mini-chromosomes] and more specifically with transposable elements [mobile genes]  located in these plasmids . Integrons were characterized even later, in the late 1980s. It was at this time that they were found to be the genetic system responsible for the gathering of resistance determinants in these mobile elements  and termed integrons. It is now well established that these mobile integrons (termed as such because of their intimate association to transposons) constitute the major vectors of antibiotic multiresistance in Gram-negative [such as E. coli] and to a lesser extent in Gram-positive bacteria. Their importance in clinical and agricultural settings is reflected by the impressive amount of epidemiological studies monitoring their prevalence and evolution. The presence in the bacterial genomes [i.e. the main bacterial chromosome] of sedentary chromosomal integrons,which are not involved in resistance phenotype, was only established in the late 1990s with the discovery of the Vibrio cholerae superintegron. Similar loci were further identified in a significant fraction of environmental bacteria. The evolutionary history of such chromosomal integrons suggests that this adaptive genetic system has been maintained in the genome of Gram-negative bacteria [relatives of E. coli] for a long while to help facing a changing world and that these chromosomal elements are the source of the mobile integrons’ backbones and of their antibiotic resistance gene cassettes .

This quotation strongly supports the judgement expressed above that emergence of the German EAEC germ is entirely expected from the known natural genetic engineering abilities of E. coli and related gut bacteria.

From
Integrons
Institut Pasteur, Unité Plasticité du Génome Bactérien, Département Génomes et Génétique, F-75015 Paris, France; email: mazel@pasteur.fr
CNRS, URA2171, F-75015 Paris, France
ABSTRACT
Integrons are genetic elements able to acquire and rearrange open reading frames (ORFs) embedded in gene cassette units and convert them to functional genes by ensuring their correct expression. They were originally identified as a mechanism used by Gram-negative bacteria to collect antibiotic resistance genes and express multiple resistance phenotypes in synergy with transposons. More recently, their role has been broadened with the discovery of chromosomal integron (CI) structures in the genomes of hundreds of bacterial species. This review focuses on the resources carried in these elements, on their unique recombination mechanisms, and on the different mechanisms controlling the cassette dynamics. We discuss the role of the toxin/antitoxin (TA) cassettes for the stabilization of the large cassette arrays carried in the larger CIs, known as superintegrons. Finally, we explore the central role played by single-stranded DNA in the integron cassette dynamics in light of the recent discovery that the integron integrase expression is controlled by the SOS response.
Annual Review of Genetics Vol. 44: 141-166 (Volume publication date December 2010) DOI: 10.1146/annurev-genet-102209-163504

Review: Integrons: agents of bacterial evolution
Didier Mazel
Abstract
Integrons are assembly platforms — DNA elements that acquire open reading frames embedded in exogenous gene cassettes and convert them to functional genes by ensuring their correct expression. They were first identified by virtue of their important role in the spread of antibiotic-resistance genes. More recently, our understanding of their importance in bacterial genome evolution has broadened with the discovery of larger integron structures, termed superintegrons. These DNA elements contain hundreds of accessory genes and constitute a significant fraction of the genomes of many bacterial species. Here, the basic biology of integrons and superintegrons, their evolutionary history and the evidence for the existence of a novel recombination pathway is reviewed. Nature Reviews Microbiology 4, 608-620 (August 2006) | doi:10.1038/nrmicro1462

For additional analysis of the genome of the E. coli causing the German outbreak, see Comparisons of E. coli TY2482 against previously sequenced E. coli genomes by David Studholme and TY2482, LB226692 vs Genbank Ecoli by Konrad Paszkiewicz.

Written by David Tribe

David Tribe’s research career in academia and industry has covered molecular genetics, biochemistry, microbial evolution and biotechnology. He has over 60 publications and patents. Dr. Tribe's recent activities focus on agricultural policy and food risk management. He teaches graduate programs in food science and risk management as a Senior Lecturer in the Department of Agriculture and Food Systems, University of Melbourne.

13 comments

  1. Dr. Tribe,
    For a while there you had me totally frightened. It would not be well to discover the crackpots got it right, even by accident.

  2. Dear Dr. Tribe,
    I’m far from beeing on par with your knowlege and wisdom (not in any way educated in your science profession), but pls. allow me to question your assertion:
    “But integrons are completely natural genetic tools. The genetic engineering with integrons is done by the germ itself.
    Integrons are natural tools used by bacteria to systematically capture new genes.”
    Isn’t bringing bacterion “in touch with each other” nothing else than “artificial” engineering – if done on purpose.
    I’m still wondering how the African parental strain Ec 55989 should have found its way onto German sprouts …
    Best regards & keep up your good coverage on the outbreak!

  3. In the gut, plants, in the soil, on rocks in water streams, on biofilms, bacteria are in contact all the time. They have many adaptations such as hairs (pili, = fimbrae) to enable this. They have evolved naturally to carry out this weird transgenic sex. They don’t need human help to do this.
    Sure humans can help (unintentionally facilitate) them by using antibiotics, increasing bacterial numbers and promoting transmission with poor hygiene and other activities.
    A huge food chain, trade (e.g. from Spain) and long distance transport can obviously help them be transmitted.
    They can get Africa to Europe quite easily inside any person’s gut.
    The emotional self-interested EU focus on GM crop safety (motivated by selfish trade protectionism in my opinion) has drawn attention away from all these proven food safety issue.
    Sadly, GM technology offers many options to improving safety, but apparently, Europeans “don’t wan’t it”.
    Well, famously Freeman Dyson said,: there is a hidden cost to saying no.
    Less famously, Paul Offitt has said: Doing nothing is doing something. Many Germans it seems have not been heeding these messages. All they hear is the Precautionary Prinzip.
    They need to learn more about how it transfers harm to others.
    Whose fault is all this mess ? It’s not the professional scientists I can assure you.
    Radiation of food could solve the problem too.
    But it seems that Europeans “don’t want that” either.
    Go figure.
    I think its fear and irresponsible politicking trumping reason and openness to innovation. Perhaps you can explain why this occurs. It seems to me from recent history, and from 1930s history, that Europeans are easily led like sheep by simple emotional rhetoric. This is the real problem, IMHO.
    As they say in America, what goes around, comes around.

  4. It seems to me from recent history, and from 1930s history, that Europeans are easily led like sheep by simple emotional rhetoric.

    I think this can be generalized to essentially any population anywhere in the world, laying it at the doors of Europeans in a certain timeframe seems rather silly (given the religiosity of the bulk of the planet this seems a sound conclusion, although if one wants to avoid that angle look no further than furor over WMDs in Iraq)

    Sadly, GM technology offers many options to improving safety, but apparently, Europeans “don’t wan’t it”.

    I posit that there is no currently available, or even just round the corner, GM technology which Europe is opposed to which would have helped. This whole thing simply isn’t about GM at all.
    There is obviously a good case to be made that inherently risky produce should undergo irradiation (or all produce, I’m down with whatever on that front) or that folk should be pre-warned that some produce is inherently riskier than others (this information is readily available – I have a list of stuff I’m supposed to avoid from my doctor, bean sprouts are on there, as is any buffet food, undercooked meats, eggs less than done medium etc etc) but it simply doesn’t follow that because food issue A could be solved with technology B therefore GMO is good – folk are ignorant about most things, it is celebrated in most cultures these days (even amongst apparently educated people it isn’t uncommon that professing an ignorance of the sciences, or mathematics for instance is seen as a good thing rather than being the embarassment that it should be (consider how horrified your average audience would be if you were to profess that you simply didn’t read anything because by the time you got to the end of a page you couldn’t remember what the start said (readers of my posts will no doubt be familiar with this feeling…))) – simply because people are ignorant and this ignorance has caused issues doesn’t mean that all manner of things they think are wrong (in the case of GMO they are still wrong, but it’s a different case entirely)

  5. Dr. Tribe,
    I have a question. I am under the impression that genes persist and spread in environments in which those genes confer a benefit. So the question becomes, what is the benefit to the ‘German’ E.coli?
    The multiple antibiotic resistant genes are likely not connected to human infections, because antibiotic treatments worsen, rather ameliorate, the amount of circulating shigatoxins. So it’s not treated with antibiotics.
    It might be that the multiple resistance confers benefits in the presence of ‘hostile’ bacteria in, e.g., the human gut.
    Then there’s the related notion of ‘competitive exclusion’ — it gives the German E. coli the ability to ‘crowd out’ other versions of E. coli.
    But this is all speculation on my part. Do you have any thoughts?

    1. Discussion of antibiotics and connection with evolution of this strain involves so many angles I think it would be foolish to tackle it here, without a thorough review. I would be trying to find things we should be doing now the prevent harm, rather than seeking to explain past evolution. There is an extremely fertile scientific debate about microbial evolution.

  6. Dear Dr. Tribe,
    admittedly wildly speculative – but by extrapolating your above statement of higly probable “natural origin” (because of the proven existence of the Integrons) one could think about a 2-components bioweapon which brings together a foreign bacteria with the German local one – in an environment (gut) which not only is an ideal incubator for mass production of E.coli but also greatly enhances the probability of horizontal reproduction or natural genetic engineering respectively.
    This leads me to kindly ask you, if your network of scientists has any knowledge about infection rates per 100.000 humans from both strains in question.
    My understanding of your past comments (and warnings) is, that you expect a high probability of future events like the current one – which in turn could be calculated for the current outbreak somewhat once we could multiply the probability of either infections.
    My hope still is, that we only encountered a Black Swan …
    Kind regards

    1. In spite of the death toll, I am not terrifically worried about this version of E. coli. Whether naturally occurring, or the product of a bioweapons program, the infectivity factor isn’t very great. Once the problem is known, it’s too easy to circumvent the bacterium.
      If you want to worry, worry about drug-resistant tuberculosis. It’s out there, it’s adding new resistance capabilities, and, what’s worse, it already knows how to spread from human to human. Some epidemiologists say that an outbreak similar to the Spanish Flu pandemic is not out of the question.

    2. 2-components bioweapon which brings together a foreign bacteria with the German local one – in an environment (gut) which not only is an ideal incubator for mass production of E.coli but also greatly enhances the probability of horizontal reproduction or natural genetic engineering respectively

      Your question is pretty interesting.
      Your reference to a “black swan” is helpful for creating a conversation but not totally apt. New diseases of some type are predictable but their exact form is very difficult to predict.
      A journal called Emerging Infectious Diseases arose in response to the realisation that we are witnessing exactly a series of newly emerging diseases. My memory tells me Joshua Lederberg first coined the term about the time that AIDS emerged in 1983. It hasn’t yet run out of topics to analyse.[Note added here is a timely video about emerging diseases as a general topic in biology]
      But the diversity of possibilities for a new disease, so perhaps the form and timing of the next disease is a black swan. A gut-illness disease outbreak from sprouts is predicable but an outcome as terrible as in Germany involving a form of E. coli that hasn’t caused problems in the past is a “black-swan” to many people, but perhaps not to those really involved in studying microbe evolution. The first huge out-break of E. coli O157:H7 in radish-sprouts in Japan was a real black-swan but disease was relatively mild. The following E. coli O157:H7 major outbreak in the US from hamburgers (meat patties) was a surprise and brought the acronyms HUS and EHEC to prominence. All subsequent outbreaks in industrialised countries should be scrutinised for incompetance and negligence. By 2008 we knew that E. coli O157:H7 EHEC was increasing in virulence over time (evolving nastiness):
      Variation in virulence among clades of Escherichia coli O157:H7 [EHEC HUS] associated with disease outbreaks

      Patients with hemolytic uremic syndrome were significantly more likely to be infected with clade 8 strains, which have increased in frequency over the past 5 years. Genome sequencing of a spinach outbreak strain, a member of clade 8, also revealed substantial genomic differences. These findings suggest that an emergent subpopulation of the clade 8 lineage has acquired critical factors that contribute to more severe disease. The ability to detect and rapidly genotype O157 strains belonging to such lineages is important and will have a significant impact on both disease diagnosis and treatment guidelines.

      This is formal science-speak for “the EHEC germ is evolving to do more harm”.
      Regarding natural 2-component bio-weapons, there are more than two components to consider. There are multiple possible sources of the new genes in the outbreak strain, and it evolved in a multiple series of steps, most likely. The various components or their equivalents are quite common. Your gut and mine has billions of ones very similar to them. There is some information on their distribution. And every time we take antibiotics we trigger selection from gene transfer events occurring in the gut.
      With so many sprouts oubreaks and knowledge of the past history evolution of E. coli EHEC to increased nastiness in an EHEC E. coli, the German black-swan is, in retrospect not a surprise. But the frequency, location, context and timing of new disease is very difficult to predict beforehand. What we can do is study the biology and the history and take steps to minimise the chance future outbreaks, especially large ones. We won’t stop bacterial evolution, so we will continue to see new disease surprises. We can tame their nastiness by pre-emptive action.
      The focus on a possible deliberate creation of this germ is a distraction. Public health negligence and incompetence are widespread. That’s all that’s needed. The germs can do the rest

      1. Dear Dr. Tribe,
        Thx. a lot for taking valuable time to give an elaborate answer to (my) lay-man’s questions.
        Eventually I’ll reopen the discussion once results of investigations (currently underway here in Germany) establish new doubts on the currently assumed natural origin.
        As Eric Baumholder already put it into perspective:
        “As long as similar threats to health exist – don’t worry to much …”
        Best regards

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