This article was originally published on August 2 by The Midwest Center for Investigative Reporting as part of a series titled “Cracks in the System.”

Salmonella-tainted ground beef could be the biggest challenge facing the industry, said a leading beef researcher.

Scientists have realized they may have misidentified the source of Salmonella in beef cattle. They now realize it may be in the lymphatic system of cattle, making it harder to prevent than E. coli.

As recently as March 2013, Salmonella Typhimurium in ground beef was linked to more than 20 human illnesses in six states.

In September 2012, nearly 50 people in nine states became ill from eating ground beef tainted with Salmonella Enteritidis, according to the U.S. Centers for Disease Control and Prevention.

“It was always our working assumption that E. coli interventions should be controlling Salmonella,” said James Marsden, professor of animal science at Kansas State University. “E. coli is transferred from the beef hide to the carcass and works its way through the system. We thought this is what Salmonella did as well.”

Marsden has been writing about the topic for the industry blog, “MeatingPlace.”

“Incidences of E. coli have dropped sharply over the past 10 years, but Salmonella isn’t dropping, which is perplexing,” Marsden added. “And some strains of Salmonella that have been observed in beef are drug-resistant strains, so they pose a public health problem.”

Researchers at Texas Tech University now believe that, unlike E. coli, Salmonella is in the lymphatic system of cattle.

“In 2010, the industry was in a position to start asking questions,” said Guy Loneragan, professor of animal science and lead researcher at Texas Tech University. “We started looking at the lymph nodes, which are internal and exempt from current-prevention techniques.”

USDA standards for Salmonella in ground beef

The rate of Salmonella-positive tests for ground beef increased each year from 2009 to 2011, according to a 2011 report from the Food Safety and Inspection Service (FSIS), the food-safety branch of the U.S. Department of Agriculture.

The agency has been testing for Salmonella in meat since 1996 when it implemented a plan to test for pathogens and hazards.

The scope and rate of sampling ground-meat products is different than those used for intact products such as whole chickens and turkeys. Any processing plant that produces at least 1,000 pounds of ground beef per day is subject to Salmonella testing.

Processing plants are then prioritized for sampling based on the number of days since its last testing, results of that testing and the product. The groups are then prioritized based on the number of human-health pathogens identified in the sample from prior testing. CDC determines the top 20 human pathogens.

As of May 2013, processors were required to submit 325 grams of ground meat for testing. This is the same amount required for E. coli testing. The amount had previously been lower.

Marsden, the Kansas State expert, said that USDA recalls beef with any level of E. coli because it considers E. coli an adulterant. When the agency finds Salmonella, it doesn’t issue a recall because Salmonella is not classified as an adulterant.

“If USDA decides it is an adulterant, that changes everything,” he said. “That would put this on the front burner and will cause problems for the industry.”

Marsden said there have been citizen requests to USDA to declare Salmonella an adulterant, but the agency has yet to do so.

A new paradigm in Salmonella-beef research

An exploratory study in 2010 found that, during certain times of the year, there was more Salmonella in the lymph nodes of cows. Specifically, the summer and fall and certain Southern regions had higher rates of Salmonella in the lymph nodes. Loneragan, from Texas Tech, believes this could be the avenue by which ground beef is contaminated with Salmonella.

“This is important because lymph nodes are infinitely linked to beef, to ground chuck which is muscle, fat, lymph nodes and veins,” said Loneragan.

Loneragan’s team is looking at what can be done pre-harvest to reduce Salmonella. He said what can be done in a beef packing plant is limited.

“There are many lymph nodes, and it is not practical or achievable to remove them,” said Loneragan. “We have downstream measures and we have upstream measures. Downstream measures would include irradiation or pasteurization. We are focusing upstream, on the live animal.”

Marsden agrees with this view. “It is impossible to remove all the lymph nodes – it isn’t an option,” he said.

Salmonella vaccinations and a diet that includes probiotics or direct-fed microbials are being used to reduce the prevalence of Salmonella in cattle.

Loneragan said that while research is preliminary, the findings are encouraging and warrant further consideration.

Pharmaceutical companies which manufacture animal probiotics are also looking into this topic. One company recently funded a study at Southern Illinois University in Carbondale.

The study was conducted by Amanda Conder, graduate student, and supervised by Rebecca Atkinson, a professor in animal science. Conder was not allowed to share which company funded the research due to a confidentiality agreement.

Conder’s study looked at levels of probiotics fed to cattle in a feedlot environment and the impact on the weight gain of the animal and levels of E. coli, Salmonella and Clostridium perfringens, another pathogen. Specifically, she was trying to determine the cost-effectiveness of using a probiotic for pathogen reduction.

“There are benefits to feeding cattle for 30 days prior to slaughter with direct-fed microbial (probiotic) supplementation at the low- and medium-dose level,” she concluded..

Flies could play a major role in the transmission of Salmonella in beef cattle. Salmonella may live in flies and other insects associated with cattle, swine and poultry operations, Loneragan said.

There are more flies in warmer weather and in warmer locations. This could be the link to a higher rate of Salmonella found in summer and fall seasons and in Southern locations and will continue to be researched.

“Right now, we have a textbook understanding of this, but that is overly simplistic and it is not sufficient to explain the observed ecology,” said Loneragan. “We need to provide a better understanding of Salmonella in livestock populations and this will help us develop more effective controls.”

Beef cattle producers would need to assume responsibility for Salmonella prevention, if Loneragan’s research pans out.

“Producers have to understand that [Salmonella] is already in the animal when it arrives at the feed lot,” said Loneragan. “This cannot be addressed in the slaughter facility; it has to be upstream. The owners may be shipping cattle that have Salmonella in them.”

Atkinson, the animal science professor at Southern Illinois University, said producers could also alter their current transportation methods to reduce stress in cattle. Stress can trigger lymph system activity.

As for vaccines, the costs to a producer have not yet been determined. Probiotic costs could be about $2 per animal for the duration of time it is in a feed lot.

Options for reducing Salmonella

Reduction of Salmonella, not elimination, is the goal, Marsden said, adding that he believes it would be very difficult to get to zero cases of Salmonella or E. coli.

Due to the drug-resistant nature of Salmonella in ground beef, there are few post-slaughter prevention options.

“You would need some form of pasteurization to eliminate it, or irradiation, but I am not a big advocate for it. Consumers are against it. Irradiation has been a dead issue for a few years, but there was discussion about doing it again in a more acceptable manner. It is a possible solution,” Marsden said.

Another possible post-harvest solution would be to treat the ground beef with ammonium hydroxide. This practice of treating ground beef received mostly negative national media attention in 2012.

Ammonium hydroxide is used by Beef Products, Inc., a South Dakota ground-beef processor, in making lean finely textured beef, sometimes referred to as “pink slime.”

“I have done research with BPI for 10 years, and while their main concern was E. coli, we did look at Salmonella as well,” said James Dickson, professor of microbiology and animal science at Iowa State University. “Ammonium hydroxide does control E. coli and Salmonella in ground beef. It doesn’t eliminate it, but it does substantially reduce it.”

Ground beef trimmings were treated with Salmonella, E. coli and other pathogens during Dickson’s research. The ammonium hydroxide-treated beef displayed lower levels of pathogens. Further, when the treated beef was mixed with untreated beef, the new mix also displayed lower levels of pathogens.

Dickson’s research was funded by Beef Products Inc., but he says that didn’t influence the findings.

“Some people have said I have a conflict of interest when reporting what I found since BPI paid for my research,” Dickson said. “I didn’t feel any pressure to say or find anything. In fact, BPI was adamant that I publish the findings no matter what I found. That is unusual in this industry. Most companies want you to sign a confidentiality agreement agreeing not to publish anything.”

Ongoing research and public education

“If meat is prepared properly, Salmonella is neutralized,” Marsden noted. “It can be in steaks and roast, not just in ground beef. But if it is all cooked right, it can be managed.

“We need to continue the pre-harvest research to reduce this in cattle. USDA is looking at this from a public health point of view. If we start to see outbreaks associated with drug-resistant Salmonella, USDA will act,” he added.

“People do eat beef less than well-done. They have done a good job educating the public about Salmonella in chicken and pork, but not in beef,” he said.

Loneragan’s lymph-node research was initially funded as part of a Salmonella working group by the National Cattleman’s Beef Association beef check-off program. The check-off program is a producer-funded marketing and research program.

He later received a grant from the USDA Agricultural Research Service, with additional check-off funding for the 2010 study.

The most recent study was funded by a USDA National Institute of Food and Agriculture grant, more beef check-off money and private industry support.

Research on Salmonella in beef is much more recent than E. coli. E. coli was declared an adulterant by USDA in 1993, giving the industry time to study and understand the E. coli transmission and to work on solutions.

“You have to think about where we are at the moment with E. coli, and it is 20 years after a major outbreak,” Loneragan aid. “We are two-and-a-half years into this, and we have already come a long way, but it has been a short time. We have more to learn. We have only just begun to look at the ecology of Salmonella. We need to think about a three-year process to explore this.”

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