E.coli’s use in GMOs: can you get E.coli poisoning?

posted in: Science | 30
E. coli bacteria viewed with electron microscopy. Image by Zeiss Microscopy via Flickr.
E. coli bacteria viewed with electron microscopy. Image by Zeiss Microscopy via Flickr.

For my first post on Biofortified, I’d like to share an account of an exchange that started on Twitter. It all began when I stumbled upon a doozy of a story, about how you can get E. coli poisoning from GMOs. The author outlines that E.coli is used during the course of genetic engineering to replicate DNA since it is highly prolific. But, the author highlights, E.coli is also able to transfer DNA laterally to and from other species. Then the author says: “It is possible that a mutated form of e-coli resulting from the cloning process used in creating GMOs could get into the gut of a person or animal that eats a transgenic plant.” The author then states that DuPont has partnered with the USDA in “identifying hard-to-identify strains of E.coli“. The theory comes full circle with the statement: “with this convenient partnership, even if harmful strains of e-coli relating to GMOs are discovered, it is likely that the public will never hear it from the USDA or DuPont.”

I feel like the author of this post missed out on an opportunity to write for the X-Files.

I then spent two days with the individuals posting these articles trying to discover how this could happen, but it never when beyond “the YUK factor” of using E.coli in generating our food. I even offered a 1 hour tutorial to share information on E.coli‘s use in genetic engineering, which got turned down. However, I did notice was that there were a couple of comments that probably made great memes for someone which got retweeted a whole bunch of times. They were mostly about how our babies are being exposed to E.coli and how our GMO corn is contaminated with E.coli. YUK.

Since my tutorial was turned down, I will write the facts about E.coli‘s use in genetic engineering here. I used E.coli, whose scientific name is Escherichia coli, quite a bit during grad school, but worked with it for the first time in one of my first or second year general biology classes in undergrad, where we made glow-in-the-dark bacteria. So here are some basic and irrefutable facts about E.coli.

  1. E.coli is used in the lab specifically because the strain used IS NOT HARMFUL. The non-virulent nature of the bacteria isn’t due to a mutation that might spontaneously arise to make it virulent again. There are entire genes that are different between virulent and non-virulent strains of E.coli. In fact, this paper looked at 61 different strains of E.coli and found that only 80% of their genomes are in common. That’s much less than the >95% that we share in common with chimps and closer to the amount we share with mice.
  2. E.coli and many other non-virulent bacteria live in our gut. This paper, which was examining the relative amount of bacteria in the gut of children recovering from cholera, found that E.coli accounts for approximately 40% of bacteria during recovery. These bacteria provide us with nutrients including vitamins K and B.
  3. E.coli is used in the lab because it grows like crazy. When it replicates it also copies its DNA.
  4. If you add the DNA that you’re interested in studying to E.coli‘s DNA, then that will also replicate.
  5. Why would you do this? Well, many procedures in the lab require a lot of DNA (by “a lot”, I actually mean microgram or nanogram quantities. But for a molecular biologist, that’s a lot). So how else can you get that much DNA that you’re interested in? The issue of amplifying and copying DNA is not unique to the process of making GMOs. So the technique of adding/removing DNA from E.coli, also known as cloning, is very common.
  6. Here’s an extremely simplistic overview of E.coli cloning (illustrated below): to add/remove DNA, you add an enzyme that cuts your gene of interest (known as “restriction enzyme”). Then you purify the piece that was cut. The way that your gene was cut will be in a specific pattern, similar to that of a puzzle piece. Then, you cut the bacterial DNA with the same enzyme so that the two puzzle pieces will fit together. The pieces get “glued” together with yet another enzyme known as a “ligase”. The glued piece of DNA goes into the bacteria, which then replicates. A few hours later… voila!! You have lots of bacteria that have lots of your DNA of interest.
  7. But then, and here’s the part that the authors of the lovely article above fail to mention, you have to get your DNA out of the E.coli. To get the DNA out of the bacteria, by definition, involves killing the bacteria. You pop the bacteria open, you clean up the goop, and you have bacterial DNA. THEN, you have to cut the DNA again so that you can get that piece of DNA that you were trying to amplify all along. So you leave the E.coli DNA behind, which again, was inconveniently left out in the article above. If you add DNA for entire genes to bacteria, sometimes they can actually produce that protein. This is the life-saving technology used to generate insulinmany synthetic vitamins, and drugs. In the case of insulin, the strain of bacteria used is E.coli. And despite my searches on the web, I’ve been unable to find a case of someone getting E.coli poisoning from insulin. Try telling a diabetic that there’s a YUK factor when it comes to their insulin.
The cloning process.
The cloning process.

I wrote this post during the week which celebrated International Women’s Day and I’m going to end with a very personal comment here:

This is to my fellow women. To all the brave moms out there doing their best, just like me. You do the ground breaking women in science an immense disservice by willingly choosing to remain ignorant on a topic and then perpetuating erroneous information. We women in science do what we do only because there was a Rosalind Franklin and a Nettie Stevens who paved the way for us. And you’re dropping shards of glass on that path. I kid you not. When you’re up-in-arms about babies being exposed to E.coli through GMOs, you spread misinformation, perhaps even prey on the susceptibilities of other moms, and you perpetuate decade-old stereotypes about gender. The specific one I refer to is depicted in this oft-used clip from the Simpsons, where Mrs. Lovejoy appears in town-hall meetings where progressive topics are addressed screaming “Think of the children!” and pulling her hair out. The stereotype is that we are emotionally driven creatures who sacrifice logic and common-sense when it comes to the safety of our children.

Aren’t we supposed to be helping each other out? Aren’t we supposed to be part of a brighter generation of women who can be moms AND be smart? So why is it that some women willingly turn down knowledge and choose to spew gibberish about how “GMOs are changing our evolution”? I find it extremely odd that you would be willing to trust a “scientific” article written by a correctional officer, but when a scientist tries to correct you, you dismiss the information. To paraphrase a recent interview I saw with Neil deGrasse Tyson, I can’t blame you if you are unaware of scientific facts and truths. That is probably just a factor of the education system that exists today. However (and this part is my own opinion, not Dr. Tyson’s), I can blame you if someone tries to correct you and educate you on these scientific truths and you choose to ignore them.

So let me make this abundantly clear: there is NOTHING, let me repeat that: NOTHING, written in that article about the risks and dangers of E.coli‘s use in genetic engineering that is accurate. If you want to argue against GMOs, please use arguments that are evidence based and do not propagate scientific illiteracy. Think of the children!

Follow Layla Katiraee:

Layla Parker-Katiraee holds a PhD in Molecular Genetics from the University of Toronto and a Bachelors degree in biochemistry from the University of Western Ontario. She is currently a Staff Scientist in DNA Sequencing Product Development. All views and opinions expressed are her own.

  • André

    I just came across this :


    « Look again: 88% of the corn grown in the U.S. is genetically engineered, reports the Environmental Working Group. “Almost all field corn is genetically modified to contain a bacteria, called bacillus thuringensis, that’s also an insecticide,” Lunder says. »

    Sonya Lunder, MPH, is senior scientist at the Environmental Working Group.


    • Pdiff

      Ditto. Unbelievable pretty much sums up the EWG.

    • Daryl

      Our experience with reporters has been that sometimes when they interview for an article, that the reporters can completely mangle a story. You have to check what the reporter has written prior to publication to assure that the article is factually correct. In fairness to Ms Lunder, it is possible that she knows the facts, but that the reporter and magazine have interpreted her in a way that it is not factually correct. Or, maybe she doesn’t know the facts.

      • Daryl, while I’d agree that reporter’s interpretations don’t always align with the intentions of those they had interviewed, S. Lunder is not being misquoted here. She is in fact directly quoted as saying bacteria has been put in the plant, which is entirely wrong. She is supposedly, a Senior Scientist at EWG specializing in food toxins, making this statement even more incredulous. I will say that the reporter/author did misrepresent the corn topic as the quote appears in a paragraph relating to popcorn, for which there are no current (or to my knowledge none anticipated) GMO varieties.

        • Daryl

          Well, this is the first time I have heard of S. Lunder. And unbelievable seemed an appropriate term for a quote like this from a senior scientist.

          • My appologies, I did not mean to come off so harsh. I just find EWG’s positioning themselves as knowledgable “experts” very trying at times.

  • Ann

    Thanks for trying to set the record straight. It is SO frustrating that women are so committed to spreading this kind of misinformation. I asked a left-leaning book club group what they thought of GMOs prior to the recent WA labeling vote. They unanimously shrieked in horror. I thnk they think they are being good environmentalists with this attitude, but there’s also the progressive anti-corporate spirit in there, too.

    This particular group was mildly split regarding vaccines. Some were completely opposed, but others thought they could discriminate between safe vaccines and dangerous ones. One or two older women were OK with vaccines.

    When I was teaching in K-5 schools, I was dismayed at the limited math and science literacy of the staff, mostly women. I like that that you ask moms to trust women scientists more than people with irrelevant backgrounds on these issues. Thanks, again.

  • Well said. The “Mommy” card is one played too often by both sides of the political spectrum. Glad to see you call it out and provide a good tutorial to boot! That author seems to have a massive paranoia thing going on from the “About” page you linked to. Yikes!

  • Kieselguhr Kid

    Now, the guys worried about E. coli used in the process of making a genetic modification, somehow going on and hurting the consumer, sound completely wacky, and the blogger is entirely right to point that out.

    That said, I’m not liking this post and I think it’s ill-considered. I think it acts as though scientists are unconcerned with something, when in fact we _are_ concerned with it and take considerable pains to manage risk, and I think the latter message is the much better one to be putting out to the public (besides being the factually correct one). Everywhere I’ve worked with genetic manipulations in bacteria for over 20 years, we’ve gone to some pains to demonstrate that we sterilize everything we get rid of, because of the formal possibility that we may disseminate genetic material from the lab in ways we don’t wish (right now I work in BSL2-3 environments and you can imagine it’s more strict still, even when we’re just manipulating _coli_. But that’s been true in other settings as well.) So, yeah, scientists don’t think it’s likely genetically engineered coli are going to do a lot of damage — but scientists ALSO think it’s a formal possibility and we work hard to control that risk. The author wrongly dismisses it.

    The history is a bit off too. We didn’t pick E. coli (out of Lwoff’s feces, among other things) because somehow we knew a lot about medical microbiology and decided it was safe. Elio Schaecter of all people once pointed out at a seminar that we really had no idea when we started what a significant pathogen coli could be, and indeed often is, and in fact the whole discussion of helpful gut bacteria versus pathogens is misleading or ill-informed; most infection after all is opportunistic. Moreover the numbers are a bit unfair: _Shigella_, for example, is really probably properly understood as coli, only since we lacked genetic sequencing and alignment tools when a lot of this stuff was speciated, we used somewhat arbitrary phenotypic discriminants. Moreover there’s a bad history of our getting “not harmful” wrong in the lab — about two years ago a researcher died from exposure to a _Yersinia_ that had been described in the literature as “safe as water.” I don’t think my normal, widely used lab strain coli are “safe as water,” or at least I behave like they aren’t, and I will sure as heck fire anybody who, say, mouth pipets them. I hope the author would do the same.

    The point isn’t that folks worried about the use of coli in making transgenics aren’t wrong. But they aren’t wrong because there is no risk or that it’s scientifically illiterate to imagine one. They’re wrong because we as scientists are aware of the risks involved, think they are slight, and have decades of proven experience controlling them.

    • Ewan R

      I dunno, even if you handled E.coli like a reckless moron during the entire process of plant transformation it is pretty much inconceivable that any would make it to the end product.

      You use the E.coli at the very start of the process to amplify up your gene of interest.
      You lyse the E.coli and extract the sequence and slap it into another plasmid with which you transform agrobacterium – (this will generally include a selection step such that you’re growing a clone of the agrobacterium that you know has your GOI in it)
      You then expose plant tissue to the agrobacterium and let it do it’s funky thing.
      Then there is another step of selection (for transformed cells) – grow up from callus to create the first generation transgenic plant.

      Following the creation of the first transgenic plant there’ll be multiple generations of grow out to achieve a homozygous individual from which you can grow out a population.

      Following this initial creation of a population homozygous for your GOI you’ll then go about the process of introgressing the GOI into other lines.

      It strikes me, that even if one were flinging E.coli at random around the lab in the first step that it’d be nigh on impossible for E.coli to transmit through mini/midi/maxi prep, Agro transformation, agro growout (including clone selection which really should avoid contamination given the nature of the procedure), agro selection, transformation, a generation or two of production of a homozygous population and then 3+ crosses per introgression.

      Not of course that one flings E.coli around the lab in the first place… as you state above precautions are taken along the way to ensure correct handling and disposal of bacteria.

      • Sanjay

        Absolutely. But your response reinforces the point — it’s not that the organism is risk-free, it’s that the process and handling minimize the risk. The post really flubs that. It doesn’t help that the subcloning diagram omits the (typical) resistance marker, which is one more reason you go to some pains to demonstrate that you’re not careless with bacteria containing cloned genes. You’re right, I’m right, the blogger is wrong and not really helping.

        • My post was not intended to be flippant about using E.coli in the lab. Sure, you take basic precautions: you use bleach to kill things off, you autoclave your equipment., and you use gloves. Yes, I wouldn’t drink water out of a flask that I grew E. coli in. The post was also meant to provide a high level overview of the cloning process, so yes, I omitted antibiotic selection.

          I appreciate the information you’ve provided on the background history of E.coli.

          As a follow-up question, how do you feel about demonstrating cloning in high-schools? Do you think it should not be done because high school students lack the training to work with E.coli or their facilities lack the appropriate Biosafety Level classification?

          • Sanjay

            I’ve seen molbio done in high school settings; I think it’s an obviously bad idea as stated. Public high schools are going to have — should be open to — immunocompromised and otherwise vulnerable students, and again, there’s a need to demonstrate sensitivity to the fact that what we’re doing is formally potentially dangerous. One bad event, even if it’s prompted by a doofus student mouth pipetting a bunch of stuff or whatever, will do a lot of damage to public understanding. Probably the way to do it is to take students from their high school _to_ a lab equipped with PPE/spill clean-up materials/aerosol handling procedures and so on. I think there is a useful message that this stuff is relatively straightforward, but there’s also a useful message that we do it with ample precautions at all times. I’m aware of facilities that handle BSAT and still have high school volunteers (obviously not working in BSL3 environments) and I have myself had a high school volunteer handle minimal quantities of staphylococcal enterotoxin under supervision in a BSL2, so you can do this stuff. But they’re not supposed to be just learning airy-fairy “science is cool” stuff; they need to be getting, hard, the “scientists are responsible and trustworthy” message in tandem.

            • tobun olatunji

              well said sir. But at times student are to be encouraged by those science is cool stuff you made mentioned about. Really, science is cool and those who teach the students should at times take things easy with them and teach them the importance of the use of PPE. And also the consequences involve in not using it

          • Rickinreallife

            I appreciate Sanjay’s point above. A favorite tactic of the ge technology-skeptics, or any constituency that has a fear of any new technology or process, is to catch the proponents in a lie. Most people are lay persons and don’t have the training or experience to assess the accuracy of the science or the claims of safety or no risk made by scientists or developers. They thus resort to proxy indicators. Anti’s know this, and exploit this by looking for any discrepancy, and if they find even a smidgent of actual risk or can contrive theoretical avenues of risk, then magnify that as science not disclosing that risk, either ignoring or covering it up, or proceeding carelessly without considering that risk. If scientists didn’t disclose a risk that even a layperson could conjure up, how can we trust their assurances of safety.

            If I understand your blog correctly, my understanding is that you were responding to a suggestion in the original article that somehow, the use of e-coli bacteria in genetic manipulation might transfer the characteristics of the e-coli to the target organism. In other words, they were saying “how do we know that the entire ge corn hasn’t acquired the trait of being schigella toxin producing. I don’t think science has thought of that risk or have failed to prove that it is not a risk.” I gather that anyone with the credentials and competence in relevant scientific fields recognizes that that is an absurd and silly worry. I think most people contributing to this site understand that utilizing e-coli as an aid to replication is not the same thing as inserting shigella-toxin producing genetic information into crop DNA. For starters, as you point out, only a minority of e-coli is dangerous, both animals and human naturally have beneficial e-coli present in their guts, and the bacteria utilized are not shigella toxin producing. But most importantly, we are not inserting e-coli dna into the plant.

            I agree with Loren E below. If we are worried about an escape of non toxic e-coli from the lab despite the sanitation and isolation protocols, then the relatively uncontrolled application of likely sources of bad e-coli in manure as a fertilizer should absolutely horrify us. Not only is ingesting dangerous e-coli a very real risk with manure fertilized crops, it regularly happens and people have died as a result.

            • Sanjay

              That’s not quite it, Rick (and, even though they’re nuts, usually if I want to know what they’re saying I go see what they’re saying — it’s not hard) — yes, they’re worried rather foolishly about horizontal gene tranfer into the plant, but (as the blogger points out) they’re also worried about the bug itself. And that’s NOT an “absurd and silly worry,” it’s one we protect against. The analogy to manure used in fertilizer isn’t a good one; lab strains of coli (1) typically contain introduced drug resistance factors, making them more dangerous and also more of a gene transfer threat, (2) are not uncommonly quite different from “wild-type” strains (for example, many lab wild-types are nonmotile), and (3) are coming from an environment, typically, where people may have worked with many other organisms or genetic constructs in coli vectors, so could formally be carrying particularly problematic genetic constructs that the bugs trying to compete in Bessie’s gut don’t — again, that’s why we handle coli in the BSL3 lab just like we handle Burkholderia or Brucella or Francisella, autoclaving or incinerating everything that the coli may have touched.

              I’m not saying the worriers aren’t silly; it’s a very improbable thing. But as it happens the scientific community shares the worry. The blogger plays some of the same silly game “Antis” do too — e.g. with her point (2) — “a related bug lives in ur gut therefore this one is harmless,” isn’t much different from the naturalistic fallacy of anti-GMO types (especally since, again, those bugs in our gut can and do kill you in opportunistic infections). There are fine defenses of genetic modifications but this one isn’t.

              • Rickinreallife

                I appreciate that explanation. Good points.

              • qetzal

                There’s no reason to handle the average lab strain of E. coli in a BSL3 environment!

                (1) The standard lab strains of E. coli are attenuated, meaning they have limited or no ability to colonize human (or other mammalian) guts. (People have tested this by drinking high density cultures of lab E. coli, and doing strain-specific fecal testing.)

                (2) The antibiotic resistance genes typically used in E. coli are not the types that make the bugs significantly more dangerous.

                (3) Even pathogenic Shiga-toxin-producing E. coli are only recommended for handling in BSL2. (See http://www.cdc.gov/biosafety/publications/bmbl5/BMBL5_sect_VIII_a.pdf.)

                To my knowledge, BSL3 would only be appropriate if one were working with E. coli that contained certain high-risk viruses, toxins, toxin-producing genes, etc.

                I can understand how non-scientists might worry about E. coli. There’s no particular reason they should know the differences between lab strains and the pathogenic ones they hear about in the news. But Rickinreallife is right. Environmental sources of E. coli (like manure) are MUCH more of a risk than the typical lab strain.

                • Sanjay

                  “Attenuated” isn’t quite the right term, but that’s certainly so — in most cases our lab wild-types are highly avirulent after GOd knows how many gnerations of culture in lab media. I just point out that they don’t compare really to wild strains in (say) manure. Your second point I don’t grasp; no, these are genes that confer resistance, typically to antibiotics we actually use: for something like pUC, at concentrations much higher than clinical, and no, I _wouldn’t_ want them transferring around — and indeed, those lab antibiotic reistance genes aren’;t things we synthesized but things which came from resistant bugs. As to your third, yes of course, we work with coli in the BSL3 lab only becuase it’s convenient when we’re using the genetic products with other organisms in that lab; my point isn’t that coli is BSL3 but that you assume that cultured organisms in a lab may easily become contaminated with other organisms from that lab, so you handle the bug in the manner appropriate to the lab setting not to the bug — coli from any lab setting are more dangerous, or should be treated as more dangerous, than just the known genotype.

                  But you echo the comments I object to with “I can understand how non-scientists might worry about E. coli.”. No. Realistically, _scientists_ worry about it and we go to great pains to show that we do. If you disagree by all means inform your lab that you are no longer bleaching your plain old K-12 derived strains before pouring them down the sink, or that you’re allowing students to mouth pipette, and see where that gets you.

                  • Ewan R

                    Aren’t you then, perhaps inflating the risk or the risk that scientists will associate because you work in an inherently risky environment?

                    The lab in which I worked with E.coli took precautions for sure (proper disposal of E.coli waste and whatnot, and clearly anyone caught doing anything as mental as mouth pipetting would be out on their ear (if only for the risk to self from chemical agents being used)) but E.coli and agrobacterium are literally the only two bacterial species utilized in the lab, and we know our constructs well enough to know that nothing risky is being moved about.

                    The risks within the lab are miniscule, likely meaningless, but are taken seriously (safety being king, to a ludicrous extent – this is an environment in which we were disallowed razor blades without 2 tiers of managerial approval (nobody ever went to the trouble)) – the risks down the line – similar, although so miniscule that to even bring them up is completely worthy of ridicule – and I say this as someone who accepts, at least in part, the logic of disbarring highly qualified careful scientists access to something I drag across my face every couple months at home.

                    • Sanjay

                      I totally agree. It would be really dumb to put up a post touting the dangers of lab coli for just the reasons you say — it’s not something that needs to be trumpeted. It’s just that it’s even worse to put up a post that acts like we think those dangers don’t exist or are minimal. It’s not something I’d want students in my lab to see, for example. We always talk, in public, the talk where “safety is king.”

                    • Hi Sanjay,
                      1) This article was meant to be a lay introduction to the concept of cloning and to highlight that it’s not possible to get E. coli poisoning from eating a GMO. It is not meant to be a guide for working with E. coli. In fact, if you’re a scientist who has worked with E. coli, then you already know more than enough on the topic. Note that I have not introduced the concept of picomol ends or even used the word “plasmid”. Now, if you can think of a way that someone can get E. coli poisoning when eating a GMO, please let me know and I’ll modify the piece.
                      2) Scientists deal with a separate set of risks and responsibilities at their work. That includes using best practices when working with bacteria. It includes not pouring chemicals down the drain. It includes disposing of sharps appropriately and the list goes on and on. But again, this piece isn’t entitled “The risks scientists take when working with E. coli”.
                      3) I wrote this piece because when I was going back and forth on twitter, I couldn’t find a simple explanation of how E.coli was used in the process of making a GMO. I couldn’t find a diagram simple enough that highlighted the key steps in cloning. Your opinion is that the diagram and the piece in general are an affront to science because they fail to point out that there are antibiotic resistance genes in there and that there are risks when working with E. coli. That’s a fair criticism. So by all means, write a piece that has all the information that you feel is key, doesn’t have scientific lingo, is accessible to the general public, and will help cancelling out all the noise that is out there on this topic.
                      4) Most of us who take the time to write to educate the general public and to communicate better science do it in our spare time. I started my blog for my friends and family, and to help share my learning as I started reading about GMOs. To semi-quote Tim McGraw, I’m “in my early 30’s, with a lot of life before me”, and there’s one hell of a lot of information out there that I don’t know and I sincerely appreciate it when people take the time to correct me. But if you want to work with a communicator/blogger to help them get it right, phrases such as “You’re right, I’m right, the blogger is wrong and not really helping”, aren’t the way to do it. So tell me what you think should be fixed, and I’ll work getting it right.

                    • qetzal

                      ” It’s just that it’s even worse to put up a post that acts like we think those dangers don’t exist or are minimal.”

                      Once again, we don’t just “think” those dangers are minimal. We have tons of data showing that those dangers are minimal, for multiple reasons. \

                      The OP accurately outlined some of the reasons why there is essentially no risk that E. coli from the lab could get into a GMO, intact, and make someone sick. Just because she didn’t mention your hot-button issue of containment (as yet another reason there is no such risk) doesn’t make this a bad post!

  • Eric Bjerregaard

    Thanks to all. I enjoy the logic. and sometimes archive this stuff to get folks around here to read and think…not feel. But Bill..if it saves even one child? Ann, Is it even possible for a left leaning group to be progressive. Or is the term progressive being Orwelled a bit?

  • Loren E

    I find it curious that the people most prone to buy into this nonsense are same people who think composted cattle manure as fertilizer is totally awesome and bristle anytime someone questions whether or not it is safe.

  • qetzal

    If you need to work with coli in a BSL3 lab alongside other experiments that actually require BSL3, then sure, you handle the coli according to the same procedures. But that’s because of the risks associated with those other agents, not because of risks associated with coli. And frankly, if your coli cultures are getting contaminated with other agents in your BSL3 lab, then someone’s not following proper procedure, and they are the risk.

    Otherwise, working with lab strains of coli does not require anything more than BSL1 (and actually not even that is officially required – see below).

    And yes, attenuated is an appropriate term to describe lab strains of E. coli (such as K12 and its derivatives). It’s exactly the same usage as an attenuated virus.

    What’s your opinion of the _scientists_ at EPA who wrote these guidelines: http://epa.gov/biotech_rule/pubs/fra/fra004.htm. Or the _scientists_ at NIH who decided that E. coli K12 is normally exempt from rDNA guidelines: http://osp.od.nih.gov/sites/default/files/NIH_Guidelines.html#_Toc351276313. Do you reject their assessments?

    Sure, as part of good lab practice, we still inactivate cultures, we don’t mouth pipette, etc. and that adds even more safety on top. But it’s still a fact that typical lab strains of coli (even those containing rDNA plasmids carrying amp or kan resistance) pose essentially NO RISK.

    And that’s really all the OP said in this regard. She didn’t say that it’s therefore OK to pour live coli culture into the sandbox at the elementary school. Your complaints and tone trolling have no legitimate basis.

    • Sanjay

      You’re obfuscating deliberately. The _scientists_ who said you can dispose of K12 — explicitly say in that link that it’s K12 _without cloned genes_. And the original post was about cloned genes.

      No, attenuated _isn’t_ the right term. We speak of attenuated virii because we know the pathogenicity and virulence of the parent strain. Not so with most lab wild-types. “Avirulent” is a better term.

      This isn’t “tone trolling.” It’s getting the science right to protect us all. Again — by all means tell your lab you think it’s fine to dispose of E. coli containing cloned genes as you wish. Let us know how that works out for you. Safety matters. Quite a bit, actually — as I mentioned, the pigment-negative _Yersinia_ had been described in the literature — literally — as “safe as water.” And a couple years ago it killed someone. Treating anything in the BSL3 lab as BSL3 _is_ proper procedure; in all likelihood, because researchers in those labs are necessarily better and cleaner with technique than most, there’s been no issue. But we _assume there has been_. And THAT is good scientfic practice. You talk up the risk, and acknowledge it. You don’t dismiss it.

      In general that’s a problem with defenders of GMOs. Often anti-GMO folks raise what are, formally, correct and possible scientific risks. The correct response isn’t to snort that the risk is fiction; it’s to point out that scientists care about this stuff, we _over_worry about it, and we go crazy taking precautions and testing our claims carefully and thoroughly. Pointing that out isn’t “trolling,” it’s getting the science, and the posture of the science, right.

  • qetzal

    I’m doing no such thing. Rather, it seems you’re not bothering to read closely.

    I’m perfectly aware that the OP was about cloned genes. That’s why I linked to the relevant NIH Guidelines on rDNA. If you had read them, you’d have seen that the default status for conducting rDNA work in E. coli K12 is exemption from NIH regs.

    Obviously, that exemption doesn’t apply if the genes being manipulated pose significant risks themselves. However, I doubt most GMO crop-related work involves risky genes, since those wouldn’t be suitable for use in crops anyway.

    As for terminology, coli can be avirulent without being attenuated. The coli in your gut right now are a perfect example. They’re avirulent because they lack specific virulence factors (such as shiga toxin genes). But they’re not attenuated.

    E. coli K12 is both avirulent and attenuated. In addition to lacking virulence factors, it has also lost the ability to colonize and thrive in its normal environment: the mammalian gut. It’s not just that it can’t cause disease outside a lab. It doesn’t survive outside a lab. That’s the meaning of attenuated here.

    Yes, we go crazy assessing risks, just as you say. And I’m absolutely in favor of that. But we’ve done that for routine cloning in coli K12, and the overwhelming evidence is that the risk is inconsequential. And yes, we STILL use physical containment, just in case. But that doesn’t make the OP wrong to state, factually and correctly, that lab coli IS NOT HARMFUL.

    And yes, you are tone trolling. You’re reading into the OP a suggestion that scientists are cavalier about how they handle coli and that the risks are being unjustifiably dismissed. There are no such suggestions in the post.

    The risks weren’t dismissed. They were studied and found to be insignificant. And the regs were written accordingly, and it’s entirely apprpriate to say so. Just as you shouldn’t dismiss known or possible risks, neither should you grossly exaggerate risks that are well demonstrated to be minimal.

  • I think this post and the ensuing discussion bring out an interesting topic for consideration.
    Scientists, in general, know what the safety procedures are. While there isn’t anything inherently risky about E. coli K12, or about transgenic E. coli (at least not for the sole reason of being transgenic – though it is possible that one could use a specific gene that does increase risk), scientists still use proper procedure of wearing gloves, washing glassware, etc. But the use of proper procedure is so common, so normal, that we do it without thought. And I think this is the first reason why Layla left out any discussion of that in this post (please correct me if I’m wrong, Layla).
    The second reason why she left it out (I think) is that she knew it wasn’t germane to this discussion. Regardless of the risk or lack thereof of the E. coli, it doesn’t matter because there’s no possibility of E. coli being on the final product, as she described in the article.

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