Ribotyping Salmonella to speed detection

Posted on June 12, 2015 by Douglas Powell

I had this advisor 30 years ago who thought ribosomes were the center of the universe.

I had an ex-wife who thought veterinarians were the center of the universe.

I know less and question more.

According to the U.S. Department of Agriculture, a fast-reproducing genus of bacterium, Salmonella, can—depending on the group, or serotype—be a virulent pathogen that sickens farm animals and humans.

Now, Agricultural Research Service veterinary medical officer Jean Guard has developed an improved, cost-effective diagnostic tool and dataset for identifying various strains of Salmonella. The tool, called “Intergenic Sequence Ribotyping,” or ISR, is helping improve poultry production and human health internationally, because it helps control Salmonella’s presence in the field and in consumer poultry products.

At present, there are other sequence, or DNA-based, methods for serotyping Salmonella. The traditional method, Kauffmann-White (KW), is expensive, is not based on DNA, and is not as accurate as ISR. “KW identifies a particular serotype in only 80 percent of cases,” says Guard. “We can get unknowns on the other 20 percent of the samples.”

ISR is being used to serotype strains within a particularly virulent group called Salmonella enterica, which is the type associated with foodborne illness. ISR tested well when compared with KW for the ability to identify strains among 139 samples of S. enterica that had been submitted from a variety of farms.

“Decreasing the cost of serotyping S. enterica while maintaining reliability may encourage routine testing and early detection of Salmonella by producers who have an in-house laboratory with trained personnel,” says Guard. “Smaller farmers without an in-house lab can work with a diagnostic consultant who has access to both the ISR tool and dataset.”

Guard makes the ISR technology available to any specialized laboratories, producers, or other qualified users who sign a proprietary Material Transfer Agreement (MTA). MTA holders both contribute to and have access to the proprietary ISR-based dataset, which is curated by Guard. “Each text file represents one serotype, or group, that has common elements,” says Guard. “These files include individual sequences of DNA letters—each a little different from another—this is how we expand the dataset.”

A producer’s lab technician can test a sample for Salmonella by culturing and if positive, submit that sample to a specialized lab—also an MTA holder—that uses the ISR tool for sequencing. “The lab then simply sends the sequence results back to the producer by entering the sequence into a private online account,” says Guard. Producers and diagnostic consultants who hold an MTA can access their private accounts to download their sequences. They then compare their sequences to those in the ISR-based dataset for a perfect match.

Guard says the ISR technology provides an early-warning system for farmers. For example, while one producer had no Salmonella problem detected on the farm, the ISR technology located a problem truck where clean birds were being infected after having been loaded for transport. “ISR led to identifying a single trucker who needed to disinfect the truck,” says Guard.

Right now, ISR is being used by university laboratories, colleagues in South America, and a large U.S. provider of breeding-stock animals. A pharmaceutical company also is using the ISR tool in vaccine development.

What’s the frequency Kenneth: USDA finalizes rule to require labeling of mechanically tenderized beef

Posted on May 13, 2015 by Douglas Powell

After initially saying a rule would be delayed until 2018, the U.S. Department of Agriculture today announced new labeling requirements for raw or partially cooked beef products that have been mechanically tenderized.

, restaurants, and other food service facilities will now have more information about the products they are buying, as well as useful cooking instructions so they know how to safely prepare them.

“Labeling mechanically tenderized beef products and including cooking instructions on the package are important steps in helping consumers to safely prepare these products,” said Deputy Under Secretary Al Almanza. “This common sense change will lead to safer meals and fewer foodborne illnesses.”

Maybe.

And if it’s common sense, why did it take until today?

These new requirements will become effective in May 2016, or one year from the date of the rule’s publication in the Federal Register. Because of the public health significance of this change, FSIS is accelerating the effective date instead of waiting until the next Uniform Compliance Date for Food Labeling Regulations, which is January 1, 2018.

Product tenderness is a key selling point for beef products. To increase tenderness, some cuts of beef are tenderized mechanically by piercing them with needles or small blades in order to break up tissue. This process, however, can introduce pathogens from the surface of the cut to the interior, making proper cooking very important.

The potential presence of pathogens in the interior of these products means they should be cooked differently than intact cuts. FSIS is finalizing these new labeling requirements because mechanically tenderized products look no different than intact product, but it is important for consumers to know that they need to handle them differently.

Under this rule, these products must bear labels that state that they have been mechanically, blade or needle tenderized. The labels must also include validated cooking instructions so that consumers know how to safely prepare them. The instructions will have to specify the minimum internal temperatures and any hold or “dwell” times for the products to ensure that they are fully cooked.

Since 2000, the Centers for Disease Control and Prevention has received reports of six outbreaks attributable to needle or blade tenderized beef products prepared in restaurants and consumers’ homes. Failure to thoroughly cook a mechanically tenderized raw or partially cooked beef product was a significant contributing factor in each of these outbreaks. FSIS predicts that the changes brought about by this rule could prevent hundreds of illnesses every year.

Maybe.

About 11 percent, or 2.6 billion pounds, of beef products sold in the U.S. have been mechanically tenderized, according to USDA data.

Editorial: USDA must tighten up its oversight at chicken processing plants

Posted on May 6, 2015 by Douglas Powell

According to this editorial, if you ever doubted the capacity of the federal government to function in a timely manner in protecting those to whom it is sworn to protect, consider that hundreds of people in Oregon and Washington got sick from eating chicken over the last decade despite detailed reports by state health officials to federal officials that they could.

Consider, too, that product recalls of the sort that could prevent salmonella-exposure illnesses are few and far between, in part owing to the inability of the U.S. Department of Agriculture to order them.

An exhaustive report by Lynne Terry of The Oregonian/OregonLive shows state health officials linked salmonella outbreaks in 2004, 2009 and 2012 to the chicken producer Foster Farms, with a Kelso, Washington, processing plant fed by chicken farmers from across the Pacific Northwest. Among other things, Terry unmasks caution on the part of factory inspectors and outright fear among agency brass. She attributes to union officials who represent inspectors nationally the assertion that on-site inspectors at chicken plants are “pressured to go easy on food processors, citing one notable case in which the USDA transferred an inspector after Foster Farms complained he wrote too many citations.” Separately, she writes: “USDA officials are so worried about being sued by companies that they’ve set a high bar for evidence, even rejecting samples of tainted chicken that state health agencies believed would help clinch their case….”

Most galling is USDA’s toothlessness. In a 2012 salmonella outbreak that surged in Oregon and Washington, chicken from Foster Farms’ Kelso plant, as well as another in Fresno, California, was persuasively implicated after sample collection and testing by a Washington inspector. Terry reported: “A supervisor in the USDA’s district office in Denver questioned whether the salmonella test results were ‘necessarily the silver bullet’ in an investigation. In a separate email a few minutes later, the supervisor had a different message: ‘Reason I asked is that apparently Foster Farms brought the heavy hitter law firm in. I don’t know the name but I understand they are not taking this lightly.'”

Nobody’s taking it lightly. Foster Farms insists it leads the industry in cleanliness. But state-level public health officials, quick to respond to calls indicating foodborne illness, report their findings to federal authorities who allow weeks and months to pass and consumers to fall ill.

Good reg, lousy enforcement: Why USDA inspection means little

Posted on April 28, 2015 by Douglas Powell

Consumer Federation of America (CFA) today released an in-depth analysis of the U.S. Department of Agriculture’s (USDA) primary meat and poultry food safety regulatory program. The report found that while the program has resulted in benefits to public health, further progress has been hindered by gaps in the program and by a legal challenge which has constrained robust action.

The program, known as the Pathogen Reduction/Hazard Analysis and Critical Control Points (PR/HACCP) regulation, was implemented following the 1993 outbreak of E. coli O157:H7 illnesses and deaths linked to undercooked hamburgers sold at Jack in the Box restaurants in the northwestern United States. The PR/HACCP regulation, which went into effect in 1998, requires meat and poultry plants to develop food safety systems in which plants take steps to identify and prevent contamination of meat and poultry products.

CFA’s report, titled “The Promise and Problems of HACCP: A Review of USDA’s Approach to Meat and Poultry Safety” traces the history of USDA’s implementation of the PR/HACCP regulation and identifies gaps which have hindered the ability of the regulation to fully protect consumers.

Specifically, the report cites two examples of ongoing problems which have not been adequately addressed in the 17 years since the regulation first took effect:

Too often plants have failed to develop effective food safety plans while USDA has failed to adequately identify problems with those plans.

Plants are repeatedly cited for reoccurring food safety violations with little consequence.

These gaps have continued to occur and have often been identified in the wake of large, nationwide foodborne illness outbreaks, yet the problems have not been adequately addressed. CFA recommends that USDA develop better approaches to reviewing plant food safety plans, including requiring that plants be required to prevent specific pathogens; and that USDA establish clear procedures to address reoccurring violations and when to take increased enforcement action.

The report also identifies how a court case brought against USDA by meat processor Supreme Beef in 1999 has hindered how USDA enforces its food safety regulations. In particular, the court case (Supreme Beef v USDA) limited the ability of USDA to enforce its regulations, effectively barring the government from shutting down a plant which fails to meet safety standards for Salmonella. Consumer groups have argued since that Congress should provide USDA with explicit authority to set and enforce food safety performance standards.

“USDA needs to provide better assurance that plants are reducing contamination of meat and poultry products and that the agency is effectively enforcing its regulations,” said Chris Waldrop, Director of the Food Policy Institute at Consumer Federation of America. “Enforceable standards would allow the agency to take decisive action when a problem is first identified rather than after an outbreak has already occurred.”

Summary

In a new report, the Consumer Federation of America traces the history of USDA’s approach to meat and poultry safety regulations. The analysis of this food safety program, known as Pathogen Reduction/Hazard Analysis and Critical Control Points (PR/HACCP), identifies gaps which have hindered the ability of the regulation to fully protect consumers.

Findings

The analysis cites two examples of ongoing problems which have not been adequately addressed in the 17 years since the regulation first took effect:

Too often plants have failed to develop effective food safety plans while USDA has failed to adequately identify problems with those plans.

Plants are repeatedly cited for reoccurring food safety violations with little consequence.

Conclusion and recommendations for FSIS

Develop a better way to evaluate plants’ HACCP plans.

Require plants to identify pathogens most commonly associated with particular meat and poultry products as hazards likely to occur and address them in their HACCP plans

Establish clear procedures and repercussions for reoccurring violations

Frequently and routinely update performance standards that are based on improving public health outcomes

Seek authority from Congress to set and enforce performance standards for pathogen reduction

Improve FSIS sampling programs to target riskiest facilities and products

USDA strategies to reduce E. coli levels at beef slaughterhouses

Posted on March 12, 2015 by Douglas Powell

Reduction of E. coli O157 illnesses since the mid-1990’s has been one of the Food Safety and Inspection Service’s greatest public health successes, with illnesses having dropped by over 50% since 1998. While overall illnesses are down significantly, the most recently available outbreak data shows a slight increase in illnesses from this dangerous pathogen. FSIS’ Strategic Performance Working Group (SPWG) has released a six-point strategy to turn the trend back in the right direction.

The SPWG determined that a reduction in O157 could be achieved in two ways. First, the Agency needs to improve how FSIS inspection personnel verify plant performance of sanitary dressing procedures through better training, more correlations, and developing a standard to assess industry’s performance of sanitary dressing. Drawing on the experience of its members, the SPWG also stated that the training would be most effective if it included photographs and real-world scenarios to effectively illustrate the issues discussed in the documents.

Second, the SPWG recommended improving the information available to industry on how sanitary dressing should be performed. The SPWG said the Agency could do so by publishing a guide containing suggestions for best practices.

More detailed information about the SPWG’s findings and recommendations mentioned here can be found on the FSIS website at Strategic Performance Working Group: Shiga Toxin-Producing E. coli Findings.

But will fewer people get sick? USDA seeks alignment of GAPs audit with food safety law

Posted on March 12, 2015 by Douglas Powell

The Good Agricultural Practices audit offered by the U.S. Department of Agriculture for fruit and vegetable growers will be updated to reflect the requirements of the regulations from the Food Safety Modernization Act.

The new joint GAPs review project includes staff from the USDA Agricultural Marketing Service, the Food and Drug Administration and state partners, according to Leanne Skelton, USDA liaison to the Food and Drug Administration on food safety issues.

“We’re just getting started, and the first meeting will be in a couple of weeks,” Skelton told the U.S. Department of Agriculture’s Fruit and Vegetable Industry Advisory Committee March 10.

She estimated the process may take one year to 18 months to complete.

Nothing about choosing wisely: USDA sings Katy Perry to promote food safety

Posted on January 24, 2015 by Douglas Powell

As millions of Americans prepare to eat takeout on Super Bowl Sunday, the Agriculture Department is turning to the game’s half-time entertainment to help promote food safety.

In a blog titled “Hot N Cold”: A Katy Perry Guide for Food Safe Take-Out” the USDA embedded lyrics from some of the pop star’s hits to help get its message out to the 48 million people eating takeout and delivered food during the Super Bowl Feb. 1.

“When you hear your guests’ stomachs ‘ROAR,’ it’s time to order take out,” the USDA’s Food Safety and Inspection Service said, referring to “Roar,” one of Perry’s hit singles. “Avoid having your guests calling the doctor for food poisoning by following these quick tips for food-safe takeout.”

The USDA used one of Perry’s early hits, “Hot N Cold,” to remind consumers how to handle cold and hot foods to avoid food poisoning.

Perry is to perform during half time of the Super Bowl game between the Seattle Seahawks and New England Patriots (if they’re still there after ballgate).

Going public: Standards aim to cut down on Salmonella and campy in poultry pieces

Posted on January 21, 2015 by Douglas Powell

The U.S. government is pushing the poultry industry to make their chicken and turkey a little safer with new standards aimed at reducing the number of cases of foodborne illness by 50,000 a year.

The proposed standards announced Wednesday by the Agriculture Department apply to the most popular poultry products — chicken breasts, legs and wings, and ground chicken and turkey. They are voluntary but designed to pressure companies to lower rates of salmonella and campylobacter, another pathogen that can cause symptoms similar to salmonella, in their products.

Among the measures companies could take to reduce the rates of those pathogens: better screening of flocks and better sanitation.

The proposal would ask poultry producers to reduce the rates of salmonella in raw chicken parts from around 24 percent now to less than 16 percent, and campylobacter rates in raw chicken parts from 22 percent to 8 percent. Rates also would be reduced in ground chicken and turkey, and sampling would be done over a longer period of time to ensure accuracy.

The Agriculture Department says the standards could eventually reduce salmonella and campylobacter illnesses linked to raw poultry by about a quarter, or 50,000 illnesses a year.

“We are taking specific aim at making the poultry items that Americans most often purchase safer to eat,” said Agriculture Secretary Tom Vilsack.

Ashley Peterson of the National Chicken Council said the industry has already made improvements. She said poultry companies have been exploring options to reduce contamination, including

The standards come after a lengthy outbreak of salmonella illnesses linked to California chicken company Foster Farms, which sickened more than 600 people between March 2013 and July 2014. In 2013, USDA said inspectors at Foster Farms facilities had documented “fecal material on carcasses” along with poor sanitation.

Foster Farms took measures to improve its sanitation and screening, and the Centers for Disease Control and Prevention now says the company’s products have less than 5 percent salmonella.

Vilsack said the Foster Farms outbreaks led the department to realize it needed to be more focused on reducing salmonella in chicken parts. The department already had standards in place for whole carcasses, but not individual parts like breasts and wings. The new proposal would cover the parts, which the USDA says is about 80 percent of chicken available for purchase.

USDA also would make public which companies are meeting the standards or going beyond them, and which companies have more work to do, giving companies more incentive to comply.

The secretary said companies should realize that complying is good business. “It’s in the long-term best interest of the market to have safer food,” Vilsack said.

“These new standards, as well as improved testing patterns, will have a major impact on public health,” said USDA Deputy Under Secretary for Food Safety Al Almanza. “The proposed changes are another way we’re working to meet the ever-changing food safety landscape and better protect Americans from foodborne illness.”

“Getting more germs out of the chicken and turkey we eat is an important step in protecting people from foodborne illness,” said Robert V. Tauxe, MD, deputy director of the Division of Foodborne, Waterborne and Environmental Diseases at the Centers for Disease Control and Prevention. “I look forward to seeing fewer Americans get sick as a result of these proposed changes.”

A pathogen reduction performance standard is the measure that FSIS uses to assess the food safety performance of facilities that prepare meat and poultry products. By making the standards for ground poultry tougher to meet, ground poultry products nationwide will have less contamination and therefore result in fewer foodborne illnesses. FSIS implemented performance standards for whole chickens in 1996 but has since learned that Salmonella levels increase as chicken is further processed into parts. Poultry parts like breasts, wings and others represent 80 percent of the chicken available for Americans to purchase. By creating a standard for chicken parts, and by performing regulatory testing at a point closer to the final product, FSIS can greatly reduce consumer exposure to Salmonella and Campylobacter.

The federal register notice is available on FSIS’ website at http://www.fsis.usda.gov/wps/portal/fsis/topics/regulations/federal-register/federal-register-notices.

Consumer Federation of America today applauded the Food Safety and Inspection Service (FSIS) for issuing the first ever performance standards for Salmonella and Campylobacter for raw poultry parts and updated standards for ground poultry.

“Pathogen rates on poultry parts and ground poultry are way too high,” said Chris Waldrop, Director of the Food Policy Institute at Consumer Federation of America. “These standards are essential to protect consumers and help drive down rates of contamination in these products.”

FSIS’ performance standards related to poultry have historically focused only on poultry carcasses. While reducing contamination on the carcass is critical, this approach has failed to address contamination levels once the bird is cut up into parts or processed into ground poultry. FSIS’ own testing revealed high prevalence levels of contamination on raw chicken parts – 24.02% for Salmonella and 21.70% for Campylobacter. FSIS’ previous standards for ground poultry only addressed Salmonella (and not Campylobacter) and were set at nearly 50% so that a plant could fail almost half of FSIS’ sampling set and still meet the standard.

FSIS’ previous approach also did not account for the way consumers’ poultry purchases have changed over the years. Consumers today are more likely to purchase poultry parts such as breasts, wings and thighs, or ground poultry, than they are to purchase whole birds.

Why wait for government? Mechanically tenderized meat labels delayed in US until at least 2018

Posted on January 5, 2015 by Douglas Powell

The best food providers don’t wait for – or hide behind — government.

That’s why Costco already labels meat that is mechanically or needle tenderized.

Other retailers should do the same.

For those waiting for government, a labeling rule which would require packages to provide cooking instructions for the mechanically tenderized meat, had to be finalized by Dec. 31 in order for it to take effect before 2018 under separate requirements of the U.S. Department of Agriculture’s Food Safety and Inspection Service.

Philip Brasher writes in Agri-Pulse that FSIS first proposed the labeling for mechanically tenderized meat in June 2013 out of concern that consumers aren’t cooking the meat properly to eliminate pathogens. The meat is tenderized with knives and needles that can drive bacteria inside the product.

However, the meat industry strongly opposes the labeling requirement and USDA officials did not send the final rule to the White House Office of Management and Budget for review until Nov. 21. The regulation remains pending at OMB. Under FSIS labeling regulations, the labeling rule could have taken effect as soon as 2016 only if it had been cleared by OMB and approved by USDA by Dec. 31.

The meat industry has argued that the meat doesn’t pose a significant risk and that the special cooking instructions aren’t warranted. In comments filed with FSIS in October 2013, the American Meat Institute said that antimicrobial measures instituted by processors assure that the meat is safe.

The Costco label says the meat should be cooked to an internal temperature of 160 degrees Fahrenheit. Corbo said the final FSIS rule is likely to offer consumers an option to the 160-degree minimum: Cook the meat to 145 degrees and let it stand for least three minutes. The meat will continue to cook internally for the three minutes even though it is no longer on the heat source.

USDA fires back on inspection protocols

Posted on December 24, 2014 by Douglas Powell

Philip Derfler, deputy administrator of the U.S. Department of Agriculture’s Food Safety and Inspection Service writes in this letter to The New York Times that in “Making a Pig’s Ear of Food Safety” (Op-Ed, Dec. 13), Ted Genoways unfairly portrays a pilot food safety inspection program that is being run by the Department of Agriculture’s Food Safety and Inspection Service, or F.S.I.S. In the pilot, federal inspectors are actually able to perform more food safety checks per shift than in more traditional inspection programs.

Further, although Mr. Genoways cites problems that occurred during implementation of a new agency data collection system, no meat entered the market uninspected because of these problems. While the new system helps the agency analyze data, daily inspection does not rely on the system’s operation.

Mr. Genoways’s dire predictions about F.S.I.S.’s direction are without basis. The Government Accountability Office found in a recent report that F.S.I.S. is a “science-based, data-driven” organization.

Consumers can be assured that any changes to F.S.I.S.’s food safety system will be based on the best approaches to ensure food safety, as determined by relevant data and applicable science.

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