Version II: Don’t eat poop, and if you do, cook it

The link in the previous story was wrong, but now corrected thanks to an eagle-eyed readerer.’s another version about the latest don’t eat poop paper.

Consumers don’t buy leafy greens and other healthy supermarket produce anticipating the food might make their families sick. Or at least, they didn’t used to.

But high profile recalls of fruits and veggies seem to be a new normal in the American food landscape. The recalls follow outbreaks of foodborne illnesses caused by microbes like E. coli. These outbreaks can send unsuspecting veggiephiles rushing to the nearest toilet or, worse yet, the hospital. Some outbreaks can even result in deaths.

The average American is still unlikely to wind up at the emergency room after eating tainted produce. Still, outbreaks have major consequences for supermarkets and growers. After outbreaks, they must regain public trust or face possible financial ruin.

Of concern is how nearby farming practices can taint produce with bacteria. This can happen when farmers apply animal manure to fields near fresh produce. Tiny particles, including bacteria, may go airborne and drift to nearby fields. But scientists weren’t sure just how likely microbes can travel from manure application sites to downwind produce.

That is, until now. New field research out of Clarkson University in upstate New York is providing an answer. Shane Rogers, an associate professor of civil and environmental engineering, led a research team that looked into the issue. They measured how far common bacteria, including Salmonella and E. coli, are likely to travel downwind from manure application sites. They hoped to better understand how fresh produce might be contaminated by nearby animal agriculture practices.

“Our goal was to provide a logical framework to study this pathway,” Rogers said. This helped them make science-based recommendations for setback distances that protect human health.

The team used field data to understand how these bacteria travel from manure application sites to produce. The research lasted three years. They took samples at several distances from manure application sites and measured the presence of illness-causing bacteria.

The researchers used computer models to expand their understanding. “It is not possible to obtain measurements for every possible set of circumstances that may exist,” Rogers said. “The models allow us to predict produce contamination over a larger range of probable conditions than our raw measurements would provide.” These include the type of manure, the terrain of the farm, and weather conditions at the time the manure is applied.

The team also evaluated the risk of illness. This gave the team a better understanding of how likely someone is to get sick from produce when a certain amount of bacteria is present.

Combining all that data, the team found that produce fields should be set back from areas of manure application by at least 160 meters. That distance should help lower the risk of foodborne illness to acceptable levels (1 in 10,000).

Rogers emphasized that the advice is for a minimum setback. “(160 meters is) the minimum distance that produce growers should maintain between manure application activities and produce growing areas,” Rogers said. Additional distance and delay between manure application and harvest would provide further protection.

The study appears in Journal of Environmental Quality. This project was supported by National Research Initiative Competitive Grant and the Agricultural Food and Research Initiative (AFRI) from the National Institute of Food and Agriculture (NIFA) Air Quality Program.

American Society of Agronomy

Michael A. Jahne, Shane W. Rogers, Thomas M. Holsen, Stefan J. Grimberg, Ivan P. Ramler, Seungo Kim

Journal of Environment Quality, 45 (2): Page 666 DOI:10.2134/jeq2015.04.0187

Dookie on show: Museum devoted to poo opens in the UK

The Isle of Wight Zoo is opening a museum on Friday devoted to poo.

poo@thezooA spokeswoman said, “It’s stinky, unpleasant and sometimes dangerous stuff — but it’s all around us and inside us too — and perhaps surprisingly our planet would be a much poorer place without it.”

The National Poo Museum “is set to be the place to immerse oneself in the wonder of excrement while finding out lots of extraordinary nuggets of information about all things poo-y, kids will love it,” the spokeswoman said.

The museum features relics such as freeze-dried poo, poop hanging from the ceiling and poop from various different species like meerkats, foxes, cows, owls and even human babies, says Mashable. There is also a 38 million-year-old fecal specimen.

How many people barf from poop on produce? FDA wants a risk assessment

Here’s one from the archives, and now that we’ve surpassed 70,000 direct subscribers in 70 countries, it’s worth a mention.

powell.kids_.ge_.sweet_.corn_.cider_.001-1024x775Oh, and FDA announced Friday it’s going to take another look at pathogens in produce from manure.

In the fall of 1998, I accompanied one of my then four daughters on a kindergarten trip to the farm. After petting the animals and touring the crops – I questioned the fresh manure on the strawberries that were about to be picked – we were assured that all the food produced was natural. We then returned for unpasteurized apple cider. The host served the cider in a coffee urn, heated, so my concern about it being unpasteurized was abated. I asked: “Did you serve the cider heated because you heard about other outbreaks and were concerned about liability?” She responded, “No. The stuff starts to smell when it’s a few weeks old and heating removes the smell.”

The U.S. Food and Drug Administration (FDA or we) is requesting scientific data, information, and comments that would assist the Agency in its plan to develop a risk assessment for produce grown in fields or other growing areas amended with untreated biological soil amendments of animal origin (including raw manure).

The risk assessment will evaluate and, if feasible, quantify the risk of human illness associated with consumption of produce grown in fields or other growing areas amended with untreated biological soil amendments of animal origin that are potentially contaminated with enteric pathogens, such as Escherichia coli O157:H7 or Salmonella. The risk assessment also will evaluate the impact of certain interventions, such as use of a time interval between application of the soil amendment and crop harvest, on the predicted risk. The risk assessment is intended to inform policy decisions with regard to produce safety.

organic-manure1Dates: Submit either electronic or written comments and scientific data and information by May 3, 2016.

The instructions for how to submit comments are available in the Federal Register notice as is additional supplementary information:

Biological soil amendments of animal origin (BSAAO) can be a source of contamination of produce with pathogens that can cause human illness. Human pathogens in BSAAO, once introduced to the growing environment, may be inactivated at a rate that is dependent upon a number of environmental, regional, and other agricultural and ecological factors. The rate of pathogen population decline over time is also influenced by the types of BSAAO and application methods. Furthermore, the types of produce and whether or not BSAAO may come into contact with a harvestable portion of the crop influences the likelihood of pathogen transfer from the amended soil to produce (Ref. 1).

Some produce farms use untreated BSAAO for various reasons, including that they are inexpensive, readily available, and rich nutrient sources for growing crops. Whether it is feasible for a farm to use untreated BSAAO as a principal nutrient source depends on numerous factors, including whether there is a required time interval between application and harvest and the length of such an interval (which may affect the nutrients retained or available from BSAAO), and crop nutrient demand (i.e., the nutrients needed to support crop growth). Typical examples of untreated BSAAO are raw cattle manure, poultry litter, swine slurry, and horse manure. FDA acknowledges that required application intervals for certain uses of untreated BSAAO could influence the number of crop cycles a farm is able to undertake each year and/or the choices farms make regarding which type of amendment to apply (e.g., raw manure, composted manure, or other nutrient sources).

In January 2013, based in part upon authority provided by the FDA Food Safety Modernization Act, we published a proposed Produce Safety Rule entitled “Standards for the Growing, Harvesting, Packing, and Holding of Produce for Human Consumption” (78 FR 3504, January 16, 2013). Among other provisions related to BSAAO, the proposed rule included at § 112.56(a)(1)(i) (21 CFR 112.56(a)(1)(i)) a 9-month minimum application interval for untreated BSAAO applied in a manner that does not contact covered produce during application and minimizes the potential for contact with covered produce after application (78 FR 3504 at 3637). In response to public comments, we withdrew this proposed 9-month minimum application interval in a supplemental proposed rulemaking that we published on September 29, 2014 (79 FR 58434 at 58457 through 58461). In the supplemental proposed rule, we acknowledged the limited body of currently available scientific evidence relating to the proposed 9-month interval and the need for additional research in this area, and described our planned risk assessment and research agenda (79 FR 58434 at 58460 through 58461). Accordingly, we deferred our decision on an appropriate minimum application interval. November 27, 2015, we published a final Produce Safety Rule entitled “Standards for the Growing, Harvesting, Packing, and Holding of Produce for Human Consumption,” (80 FR 74354). The final rule is now codified at 21 CFR part 112. In the preamble to the final rule, we restated our decision with respect to the appropriate minimum BSAAO application interval (80 FR 74354 at 74463). We reserved one of the provisions in the final rule’s Subpart F (Biological Soil Amendments of Animal Origin and Human Waste) because we continue to believe that a quantitative application interval standard is necessary and anticipate locating such a future standard in that provision. As finalized, the Produce Safety Rule establishes that there is no minimum application interval required when untreated BSAAO are applied in a manner that does not contact covered produce during or after application (§ 112.56(a)(1)(ii)), and the minimum application interval is [reserved] when applied in a manner that does not contact produce during application and minimizes the potential for contact with produce after application (§ 112.56(a)(1)(i))

FDA, in consultation with the U.S. Department of Agriculture, is conducting a risk assessment to evaluate the risk of human illness associated with the consumption of produce grown in growing areas amended with untreated BSAAO that are potentially contaminated with enteric pathogens such as E. coli O157:H7 or Salmonella. The risk assessment will evaluate the impact of different agricultural and ecological conditions and certain interventions, such as use of a time interval or intervals between application of untreated BSAAO and crop harvest, on the predicted risk. The risk assessment will take into account available data and information on relevant steps in the produce food safety continuum including: The initial prevalence and levels of pathogens in untreated BSAAO; the methods used to apply untreated BSAAO to soils; pathogen survival (and growth) in untreated BSAAO and soils amended with untreated BSAAO; pathogen transfer to produce grown in amended soils; pathogen survival and growth on produce; and pathogen survival, growth, and cross-contamination during storage and other steps in the supply chain (e.g., washing). The risk assessment will include characterization of the variability and uncertainty of pathogen survival and growth under different agricultural and ecological conditions (e.g., soil types, application methods, or geographic locations/climatic factors) and time intervals between application of untreated BSAAO and crop harvest. The risk assessment is intended to inform policy decisions with regard to produce safety.

FDA is requesting comments and scientific data and other information relevant to this risk assessment. We are particularly interested in scientific data and information concerning, but not limited to, the following factors that may affect the risk of human illness associated with the consumption of produce grown in fields or other growing areas amended with untreated BSAAO (including raw manure):

  1. Data on the prevalence and levels of pathogens.
  2. The frequency of detecting the presence of pathogens in untreated BSAAO and soil amended with BSAAO, such as Salmonella in poultry litter, and E. coli O157:H7 and other pathogenic Shiga-toxin producing E. coli in cattle manure. Samples may be obtained at different stages of untreated BSAAO storage prior to application, or after application. If available, for each data point, we also invite information regarding the following:

The type of untreated BSAAO (e.g., animal origin and content);

how the untreated BSAAO, including raw manure, was sampled and handled prior to analysis;

the size of the analytical unit (i.e., detection limit) and test method;

the number of positives, the total number of samples, and the time period in which the testing was conducted; and sampling protocol (e.g., simple random, stratified random, targeted).

  1. The pathogen concentration, i.e., the number of pathogen cells per amount (unit volume or weight), in contaminated untreated BSAAO or soil amended with untreated BSAAO, especially cattle manure and poultry litter. If available, for each data point, we ask that the data be provided in unaggregated form and that Most Probable Number (MPN) patterns as well as raw data (e.g., number of positive and negative tubes per serial dilution) be provided.
  2. Data and information on survival of pathogens (e.g., Salmonella, E. coli O157:H7), and pathogen transfer to produce.
  3. Kinetic data that describe the survival (or inactivation) or growth of pathogens in untreated BSAAO, especially cattle manure and poultry litter;
  4. Kinetic data that describe the survival (or inactivation) or growth of pathogens in soil amended with untreated BSAAO, especially cattle manure and poultry litter, as influenced by soil type, untreated BSAAO type, application method, geographic locations/climatic factors (e.g., temperature, days of sunlight, intensity of solar irradiation, moisture, rainfall) and other factors;
  5. The mechanisms for pathogen transfer from soils to specific types or categories of produce, such as leafy greens, or to produce generally, and associated transfer coefficients, including irrigation and rain water splash, direct contact between produce and soil, machinery or people or animals contaminated by soil and directly contacting produce during growth and harvest of produce;
  6. Pathogen transfer rates (i.e., transfer coefficients) from amended soils to specific types or categories of produce, such as leafy greens, or to produce generally, as influenced by soil type, untreated BSAAO type, application method, climate factors, commodity type or any other pertinent factors not listed here;
  7. The survival of pathogens on produce in the field or other growing area before harvest; and
  8. The variability in the survival of different Salmonella serotypes, different subtypes of E. coli O157:H7, or other pathogens of public health significance in amended soils under field, greenhouse, or laboratory conditions.
  9. On-farm practices with regard to the use of untreated BSAAO, including, but not limited to, the following aspects.
  10. The extent to which untreated BSAAO are used in different regions in the United States, as well outside the United States in regions that export produce to the United States;
  11. The types of untreated BSAAO and the soil type, and associated physical and chemical parameters (including but not exclusive to nutrient content, moisture and pH); and the crops typically grown in each BSAAO-amended soil type;
  12. Characterization of the proportion of produce farms that have one or more soil types per geographical location;
  13. The amount of untreated BSAAO applied per unit surface (e.g., per acre) or the ratio of untreated BSAAO/soil, including typical ratio and variability by commodity type, including, for example, row crops such as leafy greens;
  14. The time of year, number of applications, and amount of untreated BSAAO that are applied;
  15. The method of application (e.g., surface, incorporated), and whether or not the amended soil is covered (e.g., with plastic mulch);
  16. Produce commodity type and cropping cycles;
  17. Climate conditions and irrigation practices after soil is amended, before and after planting; and
  18. The crop density (e.g., the number of rows per bed, and the distance between adjacent rows in a bed), distance between two crop beds (furrow width), and the influence of such factors on pathogen transfer.
  19. Harvesting, handling, and storage conditions that may affect pathogen detection and levels, survival, growth, or inactivation between harvest and retail sale along the farm-to-fork continuum.
  20. cow.poop2The harvesting practices and the average conditions as well as the range of climactic conditions prior to harvesting (e.g., time and temperature, rain events) under which produce is handled in the field and in packing operations;
  21. The survival, growth, or inactivation of pathogens on produce (including, for example, specific commodities or categories such as leafy greens, or produce generally) during transportation and storage;
  22. Typical storage conditions (e.g., time, temperature) for produce (including, for example, specific commodities or categories, such as leafy greens, or produce generally), from harvest until consumer purchase and whether and how those storage conditions affect pathogen levels; and
  23. The types and concentration of antimicrobial chemicals or other treatments, if any, applied to the water used for wash or transport of produce during farm or other distribution operations prior to retail, and the efficacy of these treatments in reducing pathogen levels, as well as the likelihood of cross-contamination during wash or transport.
  24. Storage conditions such as times and temperatures that may affect pathogen growth and/or survival during transportation and storage of produce in the consumer’s home, and consumer handling practices with respect to produce after purchase, including data and information on consumer washing practices.

We are also interested in other comments concerning, but not limited to, the types of untreated BSAAO, produce commodities, relevant agricultural and ecological conditions, and appropriate mitigation strategies that the Agency should consider in the risk assessment.


Food and Drug Administration, 2015. “Final Qualitative Assessment of Risk to Public Health from On-Farm Contamination of Produce.” Available at: Accessed January 20, 2016.

Everyone’s got a camera — #2 in a supermarket cooler edition

Footage has surfaced of a woman walking through the aisles of a supermarket before doing a poo in a fridge.

The unnamed woman can be seen taking a leisurely stroll through the shop as she looks at products, before checking to see whether anyone is looking so she can do the deed.

She proceeds to lift her dress up, squat over a fully stocked chilling cabinet and calmly take care of her business, The Sun reports.

Perhaps even more worrying is the fact that another woman can be seen pushing a buggy just metres away while she looks at products on the opposite shelves.

Upon realisation of what the woman is up to, she brusquely walks away.

Though it is not clear precisely where and when the gross act occurred, some viewers believe the footage may have come from Russia.

Does that mean fewer sick people? Foodservice embraces big data

Tim York, CEO of Salinas, Calif.-based Markon Cooperative writes in The Packer that we have all been hearing for some time about “big data” and the value — and risk — it may pose. 

lsjpgI prefer to call it data.

York says New York-based restaurant Fig & Olive has used software to track more than 500,000 guests and $17.5 million in checks. 

But data, big or small, didn’t prevent Fig & Olive from sickening at least 150 people with Salmonella last year.

That’s not mentioned in the column.

Squatty potty: Too easy to be true

Thanks to an alert reader, I have the rebuttal to the Squatty Potty and its magical unicorn turds, via Because we all care about poop.

1223_squatty_potty_630x354The Squatty Potty is an invention by Robert Edwards; its express purpose to to improve the quality and ease of your bowel movements while on the toilet. It has a catchy name and is sold everywhere from Target to The squatty potty is a stool that is designed to fit around the front of a standard toilet bowl, providing lift to your legs and resulting in a squatting-type position rather than sitting position while moving your bowels.

Among the Squatty Potty’s claims are these:

The modern day toilet is convenient, but has one major fault; it requires us to sit. While sitting to do our business may be considered “civilized”, studies show the natural squat position improves our ability to eliminate.


The puborectalis muscle creates a natural kink to help maintain continence. Squatty Potty relaxes this muscle for fast, easy elimination.

The marketing declares that sitting on the toilet is not as beneficial or effective as squatting. Since this is an obvious naturalistic fallacy, we have the refreshing twist of a new device intended to make one more “natural.” This is common in marketing, where one often sees the equation of “natural=good,” with total disregard for reality. The Squatty Potty is a simple yet interesting device with a catchy name. The marketing is what draws my skeptical eye. They make very specific claims about the research and anatomical benefit—testable claims. Let’s take a close look at the research and find out if the claims are full of it.

The first thing any good skeptic should do when faced with a marketing claim is evaluate the plausibility of the claim. Low plausibility means that claims require more rigorous proof. The Squatty Potty actually scores pretty high on the plausibility scale. The position that the device places you in is a very plausible mechanism for easier stooling.

Raising your legs can be a mechanism to improve your bowel movements. This is irrelevant to the claimed colon-kinking anatomical issue. When you bear down on the toilet, you are performing what’s called a Valsalva maneuver. You are forcing expiration against either a closed glottis, or contracting strongly your thoracic and abdominal muscles increasing intra-abdominal pressure. Similar changes can also occur when a person lifts a heavy weight while holding their breath. Sitting in any squat-type position while bearing down is likely to increase that intra-abdominal pressure, resulting in a more effortless bowel movement. Although this is not the claim in the marketing, the Squatty Potty has a very plausible mechanism to improve the ease of bowel movements.

What about the other claims? Namely that it produces an anatomically improved position and produces a “cleaner colon.” These things are easy to claim and hard to prove. The Squatty Potty is not the first product to claim this benefit. It is a smaller and cheaper version of other squat-position devices, such as the Lilipad and the Nature’s Platform. There are others. Basically they all make the same claims. The Squatty potty claims that it has developed a sweet spot (pun intended) of not too much sitting, not to much squatting.

The website lists several research papers supporting their position:

The first is a Japanese study, “The Influence of Body Position on Defecation in Humans.” It is a small-scale, six-person, uncontrolled study. Sure, I buy it as research, but it is a index study. It limits include tiny non-heterogenous (one male, five female) cohort, with no controls and without blinding. Interestingly, full squat is considered the best, which is not the Squatty Potty position. It doesn’t support the claim that Squatty Potty’s squat is better than a full squat.

The next study has my favorite title of the the group: “Impact of Ethnic Habits on Defecographic Measurements.” (As an aside, I think I need to add “defecographic measurements,” which means “poop X-ray study,” to my medical lexicon… but I digress.) This was a small study that used barium enemas and radiography to evaluate the anorectic opening in defecation.Imaging revealed that the rectal opening was measurable larger in a squatting position. But this study has two major issues. If you use a population that squats to move their bowels and then place them on a first-world toilet bowl, as was done here, you are disrupting their accustomed maneuver. You would need a control group of Europeans to do the same tests to realistically support superior evacuation. Plus moving your bowels is an activity that has deep social and cultural taboos associated with it. Making major changes may cause the participants to rush or change their normal structure. Imaging revealed that the rectal opening was measurable larger in a squatting position. Any of these factors can have a major impact upon on bowel evacuation.

The third research paper posted was “Comparison of Straining During Defecation in Three Positions.” It’s a larger study than the first, but it’s still very small. Researchers used a subjective questionnaire to have subjects rate straining. The findings were similar to the other studies: full squat results in the lowest straining.

Overall the research is flawed and not very compelling. It does have the upside of replications of results. Interestingly, the results do not support the website’s assertion that the Squatty Potty is superior to squatting fully. So I’m not really sure why the website lists this research as scientific evidence for their modified toilet stool.

Based on my reading of the research offered I would say the squatting is the most beneficial for anatomical opening. That is about all the research says. How suboptimal sitting and partial squatting is remains unclear. The study related to straining is too qualitative and small to make that distinction.

Overall, the direct claims  The Squatty Potty specifically makes—such as “elevating your feet during elimination is healthier” and “primary (simple) constipation is a consequence of habitual bowel elimination on common toilet seats”—are unsupported by the research they provide.

This is where the Squatty claims are full of it, in my estimation. They cite figures such as these:

“4-10 million Americans have chronic constipation (defined as having a bowel movement less than three times per week), and as many as 63 million people are suffering at any time from occasional constipation.”

The real research is left out of the website’s facts page. Self-reported constipation in the United States and the United Kingdom is more prevalent in women, nonwhites, and those over age 60. And surveys of physician visits for constipation have also confirmed this, finding more visits by women, nonwhites, those with lower incomes, and patients with less than 12 years of education. After adjusting for these factors, it is more common in individuals with little daily physical activity, low income, and poor education.

The prevalence of chronic constipation rises with age, most dramatically in patients 65 years of age or older. In this older age group, approximately 26 percent of men and 34 percent of women complain of constipation. Constipation appears to correlate with decreased caloric intake in the elderly but not with either fluid or fiber intake.

The glaring omission by Squatty Potty here is the fact that constipation correlates with many issues. Yet none of them are position-related. So although the research they offer can suggest that squatting makes bowel movements easier it doesn’t automatically follow that sitting contributes to constipation.

Constipation is a complicated medical issue. There are a myriad of medical conditions, medications, and diseases that cause constipation. Constipation has too many variables to lock it down to a single vague, unproven supposition that your anatomy is interfering with your stooling. Your lower intestines are not a standpipe and fecal consistency is another variable. There is just no credible evidence that sitting is a problem. It may be dangerous to assume that sitting is a problem. Treating simple constipation with a stool may work but it could also be dangerous: you may miss a serious health issue early because you assume that your position is giving you constipation. That is not the only downside for using a toilet stool.

The Squatty Potty marketing gives the false impression that better bowel movements equates with better health. They are not alone; many alternative treatments tend to give the impression that our bowels are trying to kill us. Brian Dunning went over this in Skeptoid episode #83, “The Detoxification Myth.” There is no real evidence that better bowel movements equate with better health. There is no evidence that squatting produces a larger or more complete bowel movement. Even though the position may make an easier bowel movement, that doesn’t equate to bigger or healthier. Anyone who has had to undergo a colonoscopy will tell you that cleaning out your colon is fatiguing and undesirable. Medically speaking, bowel cleansing claims can be dangerous or nonsensical. Your colon is not the center of healthy living, and consequently cleansing is of marginal health benefit.

Overall I would say this about the Squatty Potty: on the positive side it almost certainly enhances your ability to bear down when you go. There is some replicated evidence that squatting does foster ease of going. As for the negatives, there is no evidence that it prevents or treats uncomplicated constipation. There’s no real evidence that anatomic position is a risk factor for constipation, and no real evidence that it is significantly different than other types of toilet squat devices. It leads you to believe that sitting is an impairment to normal bowel movements. That implied problem is not supported by the research and is unlikely, based on uneven distribution of constipation problems.

So why buy a Squatty Potty? I can’t say I think it’s worth it. Truthfully, it looks a little ridiculous, not that that means anything during a bowel movement. It really has no effect on other factors that impact constipation—diet, exercise, age and medical issues. I am uncertain that changing your position is enough of a benefit to help anyone suffering from chronic constipation. I can say that it is not dangerous and it may make it easier for you to bear down or reduce straining if you are constipated. It is just not reasonable to say that it has any significant effect on your overall bowel habits.

On the upside, Squatty Potty is relatively inexpensive, seems safe, and as long as you have a realistic view of the benefit I can see someone using it.

A pooping unicorn on proper posture

After a 6-2 victory last night – thanks to Amy and Sorenne for supporting my hockey fantasies – I returned home to find a teammate had posted about a pooping unicorn which had missed the radar.

It’s deeply weird and somewhat disturbing, but everyone poops.

Pooping will never be the same. This Unicorn shows the effects of improper toilet posture and how it can affect your health. The Squatty Potty toilet stool has been featured on Shark Tank and Dr OZ show and has thousands of happy customers.

There’s a lot of dangerous E. coli in cow poop

Shiga toxin–producing Escherichia coli (STEC) serogroups O26, O45, O103, O111, O121, and O145, called non-O157 STEC, are important foodborne pathogens., a major reservoir, harbor the organisms in the hindgut and shed them in the feces. Although limited data exist on fecal shedding, concentrations of non-O157 STEC in feces have not been reported. The objectives of our study were (i) to develop and validate two multiplex quantitative PCR (mqPCR) assays, targeting O-antigen genes of O26, O103, and O111 (mqPCR-1) and O45, O121, and O145 (mqPCR-2); (ii) to utilize the two assays, together with a previously developed four-plex qPCR assay (mqPCR-3) targeting the O157 antigen and three virulence genes (stx 1, stx 2, and eae), to quantify seven serogroups and three virulence genes in cattle feces; and (iii) to compare the three mqPCR assays to a 10-plex conventional PCR (cPCR) targeting seven serogroups and three virulence genes and culture methods to detect seven E. coli serogroups in cattle feces.

The two mqPCR assays (1 and 2) were shown to be specific to the target genes, and the detection limits were 4 and 2 log CFU/g of pure culture–spiked fecal samples, before and after enrichment, respectively. A total of 576 fecal samples collected from a feedlot were enriched in E. coli broth and were subjected to quantification (before enrichment) and detection (after enrichment).

cow.poop2Of the 576 fecal samples subjected, before enrichment, to three mqPCR assays for quantification, 175 (30.4%) were quantifiable (≥4 log CFU/g) for at least one of the seven serogroups, with O157 being the most common serogroup. The three mqPCR assays detected higher proportions of postenriched fecal samples (P > 0.01) as positive for one or more serogroups compared with cPCR and culture methods.

This is the first study to assess the applicability of qPCR assays to detect and quantify six non-O157 serogroups in cattle feces and to generate data on fecal concentration of the six serogroups.

Multiplex Quantitative PCR Assays for the Detection and Quantification of the Six Major Non-O157 Escherichia coli Serogroups in Cattle Feces

Journal of Food Protection, January 2016, No. 1, pp. 4-178, pp. 66-74(9)


B. Shridhar, L. W. Noll, X. Shi, B. An, N. Cernicchiaro, D. G. Renter, T. G. Nagaraja, J. Bai

It’s hard to poop on vacation

More than 100 million people in the U.S. are expected to travel at some point between this Christmas and New Year’s Day—and each and every one of them will take roughly 100 trillion intestinal microbes along for the ride.

poop.travelsAmong the various other things influenced by these gut bacteria—like eating habits, for example—they also help control how much, or how little, a person poops. For many travelers, “how little” is the operative phrase: By one estimate, as many as 40 percent of people experience constipation while they’re away from home, due partially to their gut bacteria’s reaction to the change of setting.

“Any time you leave your general habitat, it’s throwing your gut microflora off balance,” says Brooke Alpert, a New York-based registered dietician. Sometimes, that begins before you reach your new destination: In some people, the very act of traveling from point A to point B can cause constipation. Movement stimulates the gut, so sitting on a plane or in a car for long periods of time can cause the intestines to clog; ignoring the urge to go while in the air or on the road can also make it more difficult once you finally sit down on the toilet.

Time differences can also pose a problem. Many people have a normal bowel-movement routine, pooping at regular intervals throughout the day. But when jetlag or a new time zone shifts that schedule ahead or backwards by a few hours, it can mess up that routine, causing constipation.

Even the stress of traveling can make it difficult for people to poop while they’re away. Researchers have nicknamed the gut “the second brain” for the millions of neurons that line the intestines. These cells play a role in digestion, but less understood is the interplay between a person’s gut and her mental state. Researchers do know, however, that things like anxiety can affect the way this “second brain” functions. (Think of butterflies in the stomach, or a stomach tied up in knots.)