Good to publish negative results: A Salmonella vaccine in feedlot cattle doesn’t work

The efficacy of a Salmonella vaccine for reducing fecal shedding of Salmonella during the finishing period and lymph node (LN) carriage at harvest was investigated in commercial feedlot cattle.

Cattle-Heat-Load-ForecastingThe study was designed as a pen-level randomized complete block with two treatment groups, a Salmonella Newport siderophore receptor and porin proteins-based vaccine (VAC) and a nonvaccinated control (CON).

Cattle were randomly allocated into 24 pens within 12 blocks based on the time of allocation. Twenty to 25 fecal pats were collected from each of the study pen floors once a month from June to August 2013. During harvest, a minimum of 25 sub-iliac LN were collected from carcasses within each study pen. Fecal and pulverized LN samples were cultured for Salmonella quantification and detection. Mixed models were used to analyze the effect of vaccination on fecal shedding and LN carriage of Salmonella. Montevideo and Anatum were the predominant Salmonella serotypes among fecal samples and LNs; no Newport isolates were recovered.

Vaccination was not significantly associated (p = 0.57) with the prevalence of Salmonella in feces over time; the mean within-pen prevalence was 62.3% and 66.0% among VAC and CON, respectively. Sampling month was significantly associated (p < 0.01) with fecal prevalence; mean prevalence was 71.4% for June, 48.6% for July, and 70.8% for August. Across all pens, the cumulative prevalence of Salmonella in LN was 86.4%.

Vaccination resulted in no significant reduction in LN prevalence (p = 0.52); mean prevalence was 85.7% for VAC and 87.4% for CON groups. Although vaccinated cattle had numerically fewer Salmonella LN and fecal positives, there were no statistically significant vaccine effects.

Potential reasons for the lack of vaccine efficacy could include an overwhelming Salmonella exposure, a lack of cross-protection against non-Newport serotypes, and insufficient duration of immunity relative to harvest.

Efficacy of a Salmonella siderophore receptor protein vaccine on fecal shedding and lymph node carriage of Salmonella in commercial feedlot cattle

Foodborne Pathogens and Disease. June 2016, ahead of print. doi:10.1089/fpd.2016.2129

Cernicchiaro Natalia, Ives Samuel E., Edrington Thomas S., Nagaraja Tiruvoor G., and Renter David G.


We don’t need no stinkin’ buffer zones – except to protect produce

Tom Karst of The Packer reports that current food safety guidelines on the proximity of cattle feedlots and leafy greens crops may not be enough to prevent the airborne spread of the E. coli pathogen.

cow.poop2__1.story_“Current leafy green field distance guidelines of 120 meters (400 feet) may not be adequate to limit the transmission of E. coli O157:H7 to produce crops planted near concentrated animal feeding operations,” the authors of the study said.

The study’s nine authors include researchers from the U.S. Department of Agriculture’s U.S. Meat Animal Research Center, Clay Center, Neb., the University of California-Davis, and the USDA’s Beltsville Agricultural Research Center, Beltsville, Md.

Trevor Suslow, plant pathologist with the University of California-Davis and one of the authors of the study, said the research indicates that proximity to large concentrated animal operations calls for extra diligence in determining risk and in putting in place processes that monitor potential contamination.

FDA produce safety regulations do not specify setback distances between leafy greens fields and cattle feedlots, although the Leafy Greens Marketing Agreement in California, followed by many other organizations, put the number at 400 feet, he said.

“Many times 400 feet is more than enough separation based on position relative to prevailing winds and other times it can clearly result in contamination,” he said. “It is not a simple formula to say everything has to be a mile between feedlot operations. That could make production very difficult in most places,”  he said.

Suslow said another part of the study, not published yet, looks at the role of certain types of flies that can carry bacteria from feedlot operations to fields.

Effect of proximity to a cattle feedlot on Escherichia coli O157:H7 contamination of leafy greens and evaluation of the potential for airborne transmission

Appl. Environ. Microbiol. February 2015 vol. 81 no. 3 1101-1110

Elaine D. Berry, James E. Wells, James L. Bono, Bryan L. Woodbury, Norasak Kalchayanand, Keri N. Norman, Trevor V. Suslow, Gabriela López-Velasco and Patricia D. Millner


The impact of proximity to a beef cattle feedlot on Escherichia coli O157:H7 contamination of leafy greens was examined. In each of 2 years, leafy greens were planted in nine plots located 60, 120, and 180 m from a cattle feedlot (3 plots at each distance).

Leafy greens (270) and feedlot manure samples (100) were collected six different times from June to September in each year. Both E. coli O157:H7 and total E. coli bacteria were recovered from leafy greens at all plot distances. E. coli O157:H7 was recovered from 3.5% of leafy green samples per plot at 60 m, which was higher (P < 0.05) than the 1.8% of positive samples per plot at 180 m, indicating a decrease in contamination as distance from the feedlot was increased.

Although E. coli O157:H7 was not recovered from air samples at any distance, total E. coli was recovered from air samples at the feedlot edge and all plot distances, indicating that airborne transport of the pathogen can occur.

Results suggest that risk for airborne transport of E. coli O157:H7 from cattle production is increased when cattle pen surfaces are very dry and when this situation is combined with cattle management or cattle behaviors that generate airborne dust.

Current leafy green field distance guidelines of 120 m (400 feet) may not be adequate to limit the transmission of E. coli O157:H7 to produce crops planted near concentrated animal feeding operations. Additional research is needed to determine safe set-back distances between cattle feedlots and crop production that will reduce fresh produce contamination.

Summer or winter? Effects on shiga toxin E. coli in feedlot cattle

The U.S. Department of Agriculture Food Safety and Inspection Service has declared seven Shiga toxin–producing Escherichia coli (STEC) serogroups (O26, O45, O103, O111, O121, O145, and O157) as adulterants in raw, nonintact beef products.

e.coli.stecThe objective of this study was to determine the prevalence of these seven serogroups and the associated virulence genes (Shiga toxin [stx1, stx2], and intimin [eae]) in cattle feces during summer (June–August 2013) and winter (January–March 2014) months.

Twenty-four pen floor fecal samples were collected from each of 24 cattle pens, in both summer and winter months, at a commercial feedlot in the United States. Samples were subjected to culture-based detection methods that included enrichment, serogroup-specific immunomagnetic separation and plating on selective media, followed by a multiplex polymerase chain reaction for serogroup confirmation and virulence gene detection. A sample was considered STEC positive if a recovered isolate harbored an O gene, stx1, and/or stx2, and eae genes.

All O serogroups of interest were detected in summer months, and model-adjusted prevalence estimates are as follows: O26 (17.8%), O45 (14.6%), O103 (59.9%), O111 (0.2%), O121 (2.0%), O145 (2.7%), and O157 (41.6%); however, most non-O157 isolates did not harbor virulence genes.

The cumulative model-adjusted sample-level prevalence estimates of STEC O26, O103, O145, and O157 during summer (n=576) were 1.0, 1.6, 0.8, and 41.4%, respectively; STEC O45, O111, and O121 were not detected during summer months.

In winter, serogroups O26 (0.9%), O45 (1.5%), O103 (40.2%), and O121 (0.2%) were isolated; however, no virulence genes were detected in isolates from cattle feces collected during winter (n=576). Statistically significant seasonal differences in prevalence were identified for STEC O103 and O157 (p<0.05), but data on other STEC were sparse.

The results of this study indicate that although non-O157 serogroups were present, non-O157 STEC were rarely detected in feces from the feedlot cattle populations tested in summer and winter months.

Summer and winter prevalence of shiga toxin–producing Escherichia coli (STEC) O26, O45, O103, O111, O121, O145, and O157 in feces of feedlot cattle

Foodborne Pathogens and Disease, Volume: 12 Issue 8: August 10, 2015

Dewsbury Diana M.A., Renter David G., Shridhar Pragathi B., Noll Lance W., Shi Xiaorong, Nagaraja Tiruvoor G., and Cernicchiaro Natalia


CANADA: Differing populations of endemic bacteriophages in cattle shedding high and low numbers of Escherichia coli O157:H7 bacteria in feces

The objectives of this study were to identify endemic bacteriophages (phages) in the feedlot environment and determine relationships of these phages to Escherichia coli O157:H7 from cattle shedding high and low numbers of naturally occurring E. coli O157:H7.

750px-PhageExterior.svgAngus crossbred steers were purchased from a southern Alberta (Canada) feedlot where cattle excreting ≥104 CFU · g−1 of E. coli O157:H7 in feces at a single time point were identified as supershedders (SS; n = 6), and cattle excreting <104 CFU · g−1 of feces were identified as low shedders (LS; n = 5).

Fecal pats or fecal grabs were collected daily from individual cattle for 5 weeks. E. coli O157:H7 in feces was detected by immunomagnetic separation and enumerated by direct plating, and phages were isolated using short- and overnight-enrichment methods. The total prevalence of E. coli O157:H7 isolated from feces was 14.4% and did not differ between LS and SS (P = 0.972). The total prevalence of phages was higher in the LS group (20.9%) than in the SS group (8.3%; P = 0.01). Based on genome size estimated by pulsed-field gel electrophoresis and morphology determined by transmission electron microscopy, T4- and O1-like phages of Myoviridae and T1-like phage of Siphoviridae were isolated. Compared to T1- and O1-like phages, T4-like phages exhibited a broad host range and strong lytic capability when targeting E. coli O157:H7. Moreover, the T4-like phages were more frequently isolated from feces of LS than SS, suggesting that endemic phages may impact the shedding dynamics of E. coli O157:H7 in cattle.

Appl. Environ. Microbiol. July 2014 vol. 80 no. 13 3819-3825 doi: 10.1128/AEM.00708-14

J. Hallewella,b, Y. D. Niuc, K. Munnsb, T. A. McAllisterb, R. P. Johnsond, H.-W. Ackermanne, J. E. Thomasa and K. Stanfordc

USDA scientists scrutinize role of supershedder cattle in E. coli O157:H7 contamination

On average, about 2 percent of the cattle grazing in a pasture, or eating high-energy rations in a feedlot pen, may be “supershedders” who shed high levels of pathogenic organisms such as Escherichia coli O157:H7 in their manure, according to research led by U.S. Department of Agriculture (USDA) scientist Terrance M. Arthur. 

supershedder.e.coliSupershedding is of concern because it could increase the amount of E. coli O157:H7 that makes its way from pasture or feedlot pen into packinghouses where steaks, roasts, ground round or other beef products are prepared. Often referred to as O157, this bacterium is apparently harmless to cattle, but can cause vomiting, severe stomach cramps, diarrhea or other illness in humans.

Findings from studies by Arthur and his colleagues at the USDA Agricultural Research Service (ARS) Roman L. Hruska U.S. Meat Animal Research Center in Clay Center, Nebraska, may provide a scientifically sound basis for new and effective strategies to curb shedding of this bacterium. ARS is USDA’s chief intramural scientific research agency. 

Arthur and his co-workers have designed and conducted studies of 6,000 head of feedlot cattle and more than 13,000 manure, hide and carcass samples. The team was the first to show that, in supershedders, O157 colonization may occur not just in the lower digestive tract, but also throughout the supershedders’ entire digestive system. Packinghouse managers can take that information into account when evaluating their facility’s sanitation procedures. 

The researchers were also the first to determine that supershedding was not restricted to any particular O157 strain. Their work rules out the idea that tactics designed to reduce supershedding should target a specific strain or strains. 

Research by Arthur’s group has also indicated that, in order for a cattle-management strategy to be deemed successful for reducing transmission of O157, no more than 20 percent of the cattle targeted by the intervention would be shedding the microbe at any one time, and none would be shedding it at supershedder quantities.

Arthur and his coinvestigators, including ARS scientists Joseph M. Bosilevac, James L. Bono, Dayna M. Brichta-Harhay, Norasak Kalchayanand, John W. Schmidt, Steven D. Shackelford and Tommy L. Wheeler, all at Clay Center, have documented these and related findings in peer-reviewed scientific articles published in 2014, 2013, and 2009 in Applied and Environmental Microbiology.

ARS and the Beef Checkoff program funded the research.

Where does E. coli O157:H7 come from? Food Inc. and cookie dough versions

Is E. coli O157:H7 associated with things other than feedlot cattle?

I had a few people call me recently, saying, I saw that movie, Food, Inc., which says that E. coli O157:H7 is predominately in feedlot cattle because of the grain they are fed, and that’s how the bug came to exist. So how did it get into Nestle cookie dough?

It’s sort of a mantra of raw milk enthusiasts and wannabe food safety types that E. coli O157:H7 is a product of feedlot cattle, and that grass-fed creatures are benign entities for the dinner plate.

A blogger yesterday wrote, “… hamburger tainted by e-coli, a virus that breeds in a cow’s stomach when it is feed grain instead of grass (which, of course, most cows are nowadays in order to fatten them quickly and cheaply).”

It’s a bacterium, not a virus.

Nicholas Kristof, a columnist for the N.Y. Times, wrote yesterday, on Sunday, June 21/09, that, “There is some evidence that pathogens, including E. coli, become much more common in factory farming operations. Move feedlot cattle out to a pasture for five days, and they will lose 80 percent of the E. coli in their gut, the film says.”

That evidence is about as strong as the whisps of evidence compiled by Danny Sugarman that The Doors’ frontman Jim Morrisson is still alive and didn’t die from excess in a Paris bathtub in 1971. But, every teenager goes through their Doors phase (I can only find the clip below in Spanish, but Canada’s The Guess Who stands up much better with the hindsight of time; they know they are drunken buffoons, and not a drunken buffoon trying to be a poet).

Scientific uncertainty can easily be exploited by the certainty of filmmakers, who cherry pick facts and flourish on rhetoric. And I guess if it’s repeated ad nauseum for 11 years by writers from the N.Y. Times to your-favorite-bullshit blogger it becomes fact.

That line, “Move feedlot cattle out to a pasture for five days, and they will lose 80 percent of the E. coli in their gut,” comes from a 1998 paper published in the journal Science by Diez-Gonzalez of Cornell University, and colleagues.

I had one of my colleagues, Rena Orr, write a review of the controversy back in Nov. 2000.

Since September 1998, there has been conflicting information on the effect of diet on E. coli shedding from cattle. The conflict arises in part from the effect of diet on the ability of E. coli to develop acid resistance. … Diez-Gonzalez et. al demonstrated that feeding a high-grain diet to cattle results in an acidic environment in the colon. Because the animals incompletely digested the starch in grains, some starch was able to reach the colon where it fermented, producing fermentation acids. The researchers believe an acidic environment selects for or induces acid resistance among the Escherichia coli population. … Diez-Gonzalez et al. concluded that if cattle were given hay for a brief period (five days) immediately before slaughter, the risk of foodborne E. coli infection would be significantly reduced because the acidity in the colon is greatly reduced. "Our studies indicate that cattle could be given hay for a brief period immediately before slaughter to significantly reduce the risk of food-borne E. coli infection."

The Science article received mainstream media attention, and was covered by the Associated Press and The New York Times, as well as scientific releases and reports. In the Irish Times, it was cited as the basis for concluding that because Irish cattle are fed a grass-based diet rather than grain, Ireland has a low incidence of E. coli O157:H7. Hancock et al. contend that this conclusion is unsupported or contradicted by several lines of evidence. The E. coli that contaminate beef typically originate from the hide, the hooves, or the equipment used in slaughter and processing rather than directly from the colon, and likely replicate in environments unlike the colon. Therefore, the induced acid resistance of E. coli contaminating beef is likely to be unrelated to the pH of its ancestral colonic environment. The E. coli O157:H7 bacterium uses several mechanisms to survive acid environments, some of which are innate and are not influenced by environment . Although acid resistance is likely a factor in an infective dose, induced acid resistance has not been shown to be a factor in E. coli O157:H7 infectivity by experimental (dose-inoculation) or observational (epidemiological) data . Therefore, acid resistance induced by exposure to weak acid may not influence the virulence of this pathogen.

Published data on E. coli O157:H7 tends to contradict or does not support the effects of the dietary change proposed by Diez-Gonzalez et al. In a recent study on three different grain diets (85% cracked corn, 15% whole cottonseed and 70% barley, or 85% barley), the fecal pH of the animals fed the corn diet was significantly lower (P < 0.05) than the fecal pH of the animals fed the cottonseed and barley and barley diets, likely resulting in a less suitable environment for E. coli O157:H7 in the hindgut of the corn fed animals (2000, Buchko et al). In the Journal of Food Protection, researchers concluded that changing from grain to a high roughage diet did not produce a change in the E. coli concentration that was large enough to deliver a drastic improvement in beef carcass hygiene. Sheep experiencing an abrupt diet change have higher concentrations and increased shedding of fecal E. coli O157:H7 for longer periods than sheep fed a consistent high-grain diet. Another study compared the duration of shedding E. coli O157:H7 isolates by hay-fed and grain-fed steers experimentally inoculated with E. coli O157:H7 as well as the acid resistance of the bacteria. The hay-fed animals shed E. coli O157:H7 longer than the grain-fed animals, and irrespective of diet, these bacteria were equally acid resistant.

These results suggest that the proposed dietary change would actually increase contamination with E. coli O157:H7. Also, the 1,000-fold reductions in total fecal E. coli demonstrated by Diez-Gonzales et al. are far greater than those recorded in cattle experiencing similar ration changes . Finally, extensive surveys show that grain-fed feedlot cattle have no higher E. coli O157:H7 infection prevalence than similarly aged dairy cattle fed forage (hay) diets. Abrupt feed change immediately before slaughter could have unexpected deleterious effects. The proposed diet change has the potential to increase the risk of bovine salmonella infections, a potential source of food poisoning. The dietary change results in sharply reduced volatile fatty acid concentrations in the large intestine as well as changes in the bacteria, allowing for colonization of Salmonella.

See, that’s a really long explanation. It’s not as soothing as, change cattle diet, disease prevented. And that was written nine years ago.

Mike Osterholm, director of the Center for Infectious Disease Research and Policy and professor in the School of Public Health at the University of Minnesota wrote a cleaner critique in 2007 in the Minneapolis-St. Paul Star Tribune:

"Russo cited conclusions from a 1998 study from Cornell University that cattle fed a diet of grass, not grain, had very few E. coli, and that those bacteria that survived in the cattle feces would not survive in the human when eaten in undercooked meat, particularly hamburger. This statement is based on a study of only three cows rotated on different diets and for which the researchers did not even test for E. coli O157:H7. Unfortunately, the authors extrapolated these incredibly sparse results to the entire cattle industry. The Cornell study is uncorroborated in numerous published scientific papers from renowned research groups around the world. Finally, work conducted by the Minnesota Department of Health as part of a national study on foodborne disease recently showed that eating red meat from local farms was a significant risk factor for E. coli infection. …

And as my colleague David Renter wrote in Sept. 2006,

"Cattle raised on diets of ‘grass, hay and other fibrous forage’ do contain E. coli O157:H7 bacteria in their feces as do other animals including deer, sheep, goats, bison, opossum, raccoons, birds, and many others.

"Cattle diet can affect levels of  E. coli O157:H7, but this is a complex issue that has been and continues to be studied by many scientists.  To suggest switching cattle from grain to forage based on a small piece of the scientific evidence is inappropriate and irresponsible.  Several pieces of evidence suggest that such a change would not eliminate and may even increase E. coli O157:H7 in cattle.

"The current spinach outbreak may be traced back to cattle manure, but there are many other potential sources.  Simplistically attacking one facet of livestock production may be politically expedient, but instead provides a false sense of security and ignores the biological realities of E. coli O157:H7. In 1999, for example, 90 children were felled by E. coli O157:H7 at a fair in London, Ont. The source? A goat at a petting zoo, hardly an intensively farmed animal."

Last time I looked, E. coli O157:H7 and about 60 other shiga-producing E. coli that are known to cause illness in humans are present in about 10 per cent of all ruminants – cattle, sheep, goats, deer, elk -– and I can point to outbreaks associated with all of those species. Pigs, chickens, humans, birds and rodents have all been shown to be carriers of shiga-producing E. coli but the resevoir appears to be ruminants. The final report of the fall 2006 spinach outbreak identifies nearby grass-fed beef cattle as the likely source of the E. coli O157:H7 that sickened 200 and killed 4.

How the E. coli O157:H7 got into the cookie dough remains to be seen. Biology is complex and constantly changing – even at farmer’s markets, which was the big solution of Food, Inc. But it’s only a movie.

That Cornell paper can be found here:

Diez-Gonzalez, Francisco, Todd R. Callaway, Menas G. Kizoulis, James B. Russell. Grain Feeding and the Dissemination of Acid-Resistance Escherichia coli from Cattle. Science: Sept 11, 1998. Volume 281, Number 5383, pages 1666-1668.