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Why This E. Coli Outbreak Has Me Scared

The views expressed are those of the author and are not necessarily those of Scientific American.

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rows of cropsThe E. coli outbreak that started in Germany is getting bigger and a lot scarier. Ten countries have reported a total of 1,614 severe cases to the European branch of the World Health Organization as of early June 2. Thousands more have no doubt fallen ill with less severe symptoms. On June 1, the U.S. Centers for Disease Control reported two cases (both travelers) in the U.S. of infection with the strain, called EHEC 0104:H4, and is asking state health departments to be on the lookout for more.*

It is still the early days in the outbreak but as a science journalist, I have three main questions for which I would really like to find a few answers.

1. Where did this rare EHEC 0104:H4 strain come from? I’m not talking about which country it came from but rather how did it develop? Given how quickly and how widespread the outbreak started, I’m particularly interested to learn if any particular industrial agriculture techniques—like liquid manure spreaders—were involved?**

2. Why are adults (and particularly women) being more severely affected than children or the elderly? Perhaps this is just a fluke—for instance, women probably eat more greens than men. Or is there some underlying biological reason—such as an overly robust inflammatory response to the infection called a cytokine storm, as has happened in other toxic E. coli outbreaks?

3. What is the likelihood that this new EHEC 0104:H4 might pick up even more genes that confer resistance to antibiotics? Part of the reason this strain is deadly is because it has picked up the genes to make two different deadly toxins (one that causes bloody diarrhea and the other that attacks the kidneys). And the Robert Koch Institute in Germany has determined that EHEC 00104:H4 strain is also resistant to 14 different antibiotics. Fortunately, it is still susceptible to two of the carbapenem antibiotics (imipenem and meropenem).

I shudder to think what would happen if EHEC 0104:H4 picked up the genes that confer resistance to carbapenems, which are drugs of last resort for gram-negative bacteria such as E. coli. As Maryn McKenna reported in "The Enemy Within" (preview) back in April, carbapenem resistance genes are now proliferating around the world and have already spread to a few strains of E. coli. Given how frequently severe E. coli outbreaks have occurred in recent years, it seems like only a matter of time before we have an E. coli outbreak that is both extremely deadly and completely immune to antibiotics.

Image: Courtesy of Agriculture and Agri-Food Canada

*Correction (6/2/11): The name of the current strain was corrected throughout the post.

**Clarification (6/2/11): A sentence was deleted after publication because it attributed the origin of a 2006 E. coli outbreak in California to chicken manure. According to the FDA, however, that outbreak’s origin remains inconclusive.

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  1. 1. AdrianaH 1:26 pm 06/2/2011

    Great article. I was thinking hard about your point 1, the origin, and the liquid manure issue. I was very surprised that not a single article I read, not even the New York Times article, even mentioned manure. Nobody even raised the issue that these nasty strains are likely to result from the atrocious practices of factory farms.

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  2. 2. tbellsmf 1:29 pm 06/2/2011

    To your statement that a "A single bad batch of chicken manure was the ultimate culprit in the California E. coli spinach outbreak of 2006."

    From the FDA’s press release: "FDA Finalizes Report on 2006 Spinach Outbreak"

    "Potential environmental risk factors for E.coli O157:H7 contamination at or near the field included the presence of wild pigs, the proximity of irrigation wells used to grow produce for ready-to-eat packaging, and surface waterways exposed to feces from cattle and wildlife.

    Because the contamination occurred before the start of the investigation, and because of the many ways that E.coli O157:H7 can be transferred — including animals, humans, and water — the precise means by which the bacteria spread to the spinach remain unknown."

    A press report regarding the release of the report, indicated that heat treated pelleted chicken manure was used as a fertilizer, but was never found with the target bacteria.

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  3. 3. Christine Gorman 2:03 pm 06/2/2011

    You are correct. Public health officials were never able to exactly pinpoint the cause of the contamination in the 2006 E coli outbreak. I read the California department of public health report too hastily. It went into great detail about the chicken manure but drew no definitive conclusions. A later 2007 report isolated the E coli strain from feral pigs but said it was unclear if the pigs contaminated the spinach fields or the agricultural practices on the fields let to the pigs being contaminated.


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  4. 4. parkerhere 2:13 pm 06/2/2011

    The E. coli strain is O104 not 0101. Also, in agreement with tbellsmf, the chicken manure was not shown to be a source of O157. Moreover, chickens are not known carriers of O157. The presence of O157 positive cows, feral pigs and water adjacent to the spinach fields suggests that one or all of these were the source. Molecular fingerprints of these E. coli O157 matched the molecular fingerprints of the spinach outbreak strains.

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  5. 5. Soccerdad 3:12 pm 06/2/2011

    Plenty of family farms spread liquid manure. There is nothing inherently wrong with so-called "factory farms. Just a different ownership structure and perhaps a different scale. I’d bet that generally their farming practices are safer than family farms.

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  6. 6. Darwin 3:44 pm 06/2/2011

    I know, probably you’ll take my head, but…….what if it’s not liquid manure? What if it’s a new sophisticated terrorism? I mean, no one knows the origin and usually if there is an outbreak somewhere they pretty quickly found the source. Latest news is, there are 500 critically ill patients remains just in Germany alone, about half of them showing signs of epilepsy and neuron demage.

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  7. 7. Christine Gorman 4:03 pm 06/2/2011

    Scale is exactly the issue. That’s how unusual combinations of bacterial genes get produced–the greater the mixing of different bacterial strains, the greater the chances of strains with genes to make two different toxins and be resistant to 14 different antibiotics, including extended release beta-lactams (which is apparently unusual in E. coli).

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  8. 8. mikethemadbiol 4:54 pm 06/2/2011

    One nitpicky thing: I think you mean extended spectrum beta-lactams, not release?

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  9. 9. Christine Gorman 5:05 pm 06/2/2011

    Yes indeed. Extended spectrum beta-lactams or ESBLs. Thanks.

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  10. 10. AdrianaH 5:16 pm 06/2/2011

    Factory farming means raising livestock in confinement at high stocking density. Scale is the issue. The concentration of large numbers of animals in a crowded space provides more opportunities for bacterial strains to exchange genes and become more harmful. Factory farming is inhumane and also dangerous.

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  11. 11. AdrianaH 5:33 pm 06/2/2011

    In all fairness, I just read a Nature news article that says this extremely strange strain may have come directly from the soil without passing through animals. Very good article. Here is the link:

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  12. 12. SpoonmanWoS 5:39 pm 06/2/2011

    I’m afraid the evidence doesn’t bear your statements out. Factory farms are much more likely to cut important corners because it directly affects their bottom lines. The family farmers are less likely so simply because "that ain’t the way my daddy taught me" (at least that’s been the experience I’ve had from the farmers in the small towns I frequent say).

    Factory farms are more likely to crowd animals together and shortcut proper care by giving them all antibiotics when not necessary just to be "preventative". The problem, of course, is that helps produce resistant strains. Not a problem for the execs, of course, they don’t live anywhere near where the farms are so it won’t affect them or their families.

    Large agrobusinesses are, to a degree, more financially efficient than their smaller brethren. Safer is never a concern, though, if it interferes with profits. After all, businesses only have a responsibility to their shareholders, right? Not the communities around that are affected by their negligence, not the employees who work for them, not even to the world at large…just to their pockets.

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  13. 13. Torbjörn Larsson, OM 6:14 pm 06/2/2011

    I thought EHEC in general was pretty resistant to antibiotics. So I don’t see how it raises the level of concern.

    "What is the likelihood that this new EHEC 0104:H4 might pick up even more genes that confer resistance to antibiotics?"

    The same as always, high; especially because of these outbreaks prompting both use and overuse of them.

    "it has picked up the genes to make two different deadly toxins (one that causes bloody diarrhea and the other that attacks the kidneys)"

    This is confusing and likely wrong.

    <a href="">WHO says</a>:

    "EHEC produces toxins, known as Shigatoxins or verotoxins, which damage blood cells and the kidneys. EHEC bacteria that produce these toxins are known as STEC or VTEC. The name Shigatoxins refers to their similarity to the toxins produced by <i>Shigella dysenteriae</i>."

    It is the same toxin having two names and two effects (perhaps bloody stools, kidney problems). Wikipedia says on vero(cyto)toxin:

    "Verocytotoxin is a Shiga-like toxin produced by the E. coli strain O157, and Shigella type 1.

    The toxin has two parts. The A part damages gut epithelium through inhibiting its protein synthesis, facilitating entry to the blood stream. The 5 B parts are adapted to inserting the A part into epithelial cells."

    This toxin has two parts. Nowhere do I see that there are two toxins.

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  14. 14. Atoma 6:30 pm 06/2/2011

    I dont think manure is the problem.
    The reason, cucumbers are grown seperated from cows and they grow differently, they let them grow up and dont put manure over them thats allready in the soil when the plant was young, they let them grow up for easy harvesting. So manure.. not likely.

    It could be contaminated water (maybe), for irrigation.

    Or and this is even more likely, some transport wasnt clean. That would explain a single food type, with a specific city range spreading into another country.

    More precise cucumbers might have been cleaned with contaminated water before transport.

    Or maybe the cooling system leaked, maybe a supermarket cleaned them or a truck driver, or maybe a farmer.

    It would be worse (but possible) if surface water in GErmany has becomme polluted and this made it to the food chain.

    To solve: chlorinate drinking and surface water..
    The rest of europe should be thinking of chlorinating drinking water too, now that the risks are high.

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  15. 15. Cloud-Cuckoo 8:30 pm 06/2/2011

    Surprised nobody – here especially – has reminded younger readers that the very first genetic engineering experiments were done with E.coli and phages. All kinds of nasty genes from more dangerous bacteria and I think (hazy memory) viruses, and also ones for antibiotic resistance, were dumped into E.coli – which was used just because it was conveniently right there routinely in the lab fridge.

    I wondered at the time (early 70s) whether it was a good idea to use a common, tough human gut bacterium for such experiments. And the possibility of disaster if one of these early engineered forms escaped and spread.

    Now, what do we have here but a ‘new’ form of E.coli which produces nasty toxins and has umpteen kinds of antibiotic resistance. OK, I know that E coli can transfer genes without any help from us, but those particular ones? And where did they come from in the first place?

    I also note that authorities are saying that this form is new ‘in an outbreak situation’ – seemingly meaning that someone has met it before somewhere…in a lab perhaps??

    Any of you reading this feeling just a little bit guilty right now?

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  16. 16. KittyAntonikWakfer 9:03 pm 06/2/2011

    How much of an influence would be the (increasing?) practice of antibiotics on the animals whose manure was then in the effluent used for crop irrigation? This coupled with high concentration of animals with greater opportunities for bacterial strain gene exchanges would seem a likely possibility. Any info on these?

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  17. 17. jtdwyer 11:54 pm 06/2/2011

    My thought exactly.

    I’m compelled to continuously point out that the fundamental factor producing many contributing conditions is overpopulation. The number of humans on Earth has quadrupled since 1900, which was then the largest human population ever assembled. At that time the industrial revolution and since the mechanization of agriculture have resulted in the migration of rural populace to larger and larger cities, mostly located near the oceanic coastlines. We are running an uncontrolled experiment on the planet and cannot imagine the potential consequences.

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  18. 18. m 3:25 am 06/3/2011

    The reason you are ill at ease is that the disease was manufactured.

    By whom you ask…

    2 possibilities.

    1. As revenge for stuxnet.
    2. A complicated evolutionary fluke.

    To be honest its likely to be the latter, but worryingly it could be the former.

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  19. 19. Soccerdad 10:04 am 06/3/2011

    Apparently you aren’t too familiar with family farms. They also have a "bottom line" which can be improved by "cutting corners". I’ve seen plenty of family farms with very crowded livestock. I believe your bias is a bias against corporations in general.

    Family farms are less at risk to be identified as a source in an outbreak such as this. This is because the outbreak would likely be of smaller scale and less traceable. Family farms are much less likely to be inspected. Therefore, I argue that the so-called "factory farms" are more likely to be careful in following all the food safety guidelines and regulations.

    Besides, this is in Europe, the land of heavy farming subsidies and small family farms. I’ll bet that the source, if found, will be totally unrelated to corporate farming or liquid manure.

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  20. 20. Torbjörn Larsson, OM 1:50 pm 06/3/2011

    "Nowhere do I see that there are two toxins."

    Later I found the german description of the strain: it has indeed only 1 toxin (Shigatoxin 2, IIRC). Also, a href="">several thinks it is close to an old strain from 10 years ago (or at least older strains)</a>, which AFAIU only had 1 toxin as well.

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  21. 21. jgrosay 3:10 pm 06/3/2011

    Is there somebody having experience or an opinion with good background on the use of Sulfametoxazol-Trimetroprim instead of Beta-lactams or Quinolones or other antibiotics for the severe E coli related diseases ?
    Microbicides do release toxines from dying bacteria, while bacteriostatics do slow all rod’s metabolic processes, including toxin production, they kill bugs more slowly, and perhaps this can be good in such situations.

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  22. 22. Soccerdad 8:10 am 06/6/2011

    Well, it appears this outbreak is linked neither to antibiotics or "factory farms". Rather it appears to be an organic farm and some kind of sprouts. As they say – think horses, not zebras.

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  23. 23. dhrosier 5:27 pm 06/6/2011

    Too narrow a focus on too many important issues.

    Factory farming – in addition to crowded spaces you have to consider that many use antibiotics in feed for prophylactic objectives.

    Cross link to the article in the same email newsleter issue regarding "New MRSA Strain Found in Dairy Cattle and Humans" and consider the role of prophylactic use of antibiotics there. There have been a great many essays and such about this issue. Penicillin was still a very new drug in WWII. Military doctors would give GIs going on liberty penicillin tablets (sic) to prevent VD. Guess what! Drug resistant strains evolved very quickly as a direct result.

    NEVER discussed in any of the factory farm discussion is "Why are they necessary?"

    They are necessary because such projects are critical to feeding the population of our planet, the overpopulation is stressing all systems. Of course, someone may find a way of processing sawdust to be suitable for human consumption, but there goes another rain forest.

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  24. 24. whtwouldudoif 7:51 pm 06/6/2011

    Good point Darwin, that was my first thought too. Even if it’s not this time, it seems to me we should be mindful of the chance of something of that nature happening anytime. It’s better to be prepared than sorry.

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  25. 25. Hel-n-highwater 6:38 pm 06/7/2011

    No one better take your head off, my partner is with FEMA and he thinks it is a non specific attack that is so far fetched that the Alex Jones and Tea Twizzlers in cahoots with the ACLU will forstall any investigation of who is working on those farms because of the ‘states rats’ issues the southern boys fought for in the Civil War, odd that the left and the right extremists can’t close the barn door before the horse gets out. But then they think Palin has a right to blather for one silly reason or another.

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  26. 26. Hel-n-highwater 6:47 pm 06/7/2011

    Jgrosay, I’m not a microbiologist but it was part of my studies, just read about methyglyoxal, it is in dark honey and the kind for New Zealand especially. It is supposed to be effective against MRSA, etc. infections that are resistent so maybe we should go back to open range cattle raising and feed the feedstock honey rather than prophalactic antibiotics. The Danish have started it with their pig farms. As for the extensive need for meat for the population – get the Republicons off the anti Planned Parenthood gig and use China’s one child policy. The other side of the freedom coin is the responsibility issue and this is post Roe v Wade. Only ‘creationists’ and followers of the German in the Vatican are into letting the population explode as a sacrifice to their God.

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  27. 27. Daniel35 9:56 pm 06/7/2011

    1. AdrianaH: " … these nasty strains are likely to result from the atrocious practices of factory farms."

    Let’s keep in mind that animals and plant etc. have been thriving off of each others’ "wastes" probably almost since the beginning of life on Earth. I like to think that being raised "close to the dirt" on subsistence farms, where animal manure was the original fertilizer, gave me a stronger immune system, or at least proved I had one. Maybe this is payback for those who only dirtied their hands in the stock market, though they also are beginning to feel some internal disruptions.

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  28. 28. spencerjonesy 3:40 am 06/10/2011

    There are seven separate clinical studies demonstrating that colloidal silver and other silver-based antimicrobials are highly effective against E. coli, including drug-resistant strains.

    Too bad the European Union banned colloidal silver sales back in January 2010.

    You can read about those seven clinical studies here:

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