Whole genome sequencing: US FDA wants food companies to hand over their pathogens

Investigations into foodborne illness are being radically transformed by whole genome sequencing, which federal officials say is enabling them to identify the source of an outbreak far more quickly and prevent additional cases.

whole.genome.sequencingPreviously, samples from sick patients were sent to state and federal labs, where disease detectives ran tests to see if the infections were caused by the same bug. When enough matches emerged, typically a dozen or so, epidemiologists interviewed sick people, looking for a common food that was causing the outbreak.

But the testing wasn’t definitive, and linking one case to another took time. “While all of this was going on, more contaminated product was getting out into the public,” said Dr. Steven Musser, deputy director for scientific operations at the U.S. Food and Drug Administration’s Center for Food Safety and Applied Nutrition.

Now, the FDA is building a network of state and federal labs equipped to map out the exact DNA sequence of strains of Listeria, Salmonella and other foodborne pathogens found in sick patients. These sequences are then uploaded to a public database housed at the National Institutes of Health. The technology can not only differentiate a pathogen from multiple related species, but can also show slight mutations within the same strain.

At the same time, the FDA has begun sequencing pathogens found during routine plant inspections and adding those to the database. One benefit of that, they say, is being able to quickly connect patients within an outbreak. Another is the potential to identify the source of an outbreak after just a few patients fall ill, shortening the time it takes to get tainted food off store shelves.

To increase the odds of a match, the FDA wants manufacturers to contribute samples of pathogens found during their own plant inspections. Some contamination is common in food plants. When it is found in the manufacturing facility, but not in food products, companies generally are required only to clean it up without recalling products.

But eliminating pathogens is tough, and convincing companies to offer up potentially incriminating evidence has been a hard sell, according to interviews with public health officials, food manufacturers and experts on recalls.


US apple industry questions FDA’s response on caramel apple outbreak

Tom Karst of The Packer writes that in a presentation to the U.S. Apple Association’s Outlook and Marketing Conference Aug. 20, the Food and Drug Administration’s Roberta Wagner took questions from the audience about pending food safety rules and the fallout from the foodborne illness outbreak in late 2014 linked to Listeria monocytogenes in caramel apples.

caramel.appleOne audience member asked Wagner, associate director for Food Safety Modernization Act Operations at FDA, about the agency’s unclear messages about whether whole apples were involved. He asked her if whole fresh apples were implicated in the outbreak.

“I can tell you the statistic we are showing are only for caramel apples,” she said.

According to the Centers for Disease Control and Prevention, 35 people were sickened, 34 hospitalized and three died as a result of the outbreak linked to caramel apples.

“One of the research areas we need to (address) is why caramel apples and not apples?” she said.

Another conference attendee noted that foreign governments blocked imports of whole fresh apples.

“What is the FDA going to do so we hopefully curb that in the future?” he said.

Wagner said the FDA can’t control actions by other governments, but that the FDA will work with agriculture officials in other countries to defuse any concerns.

Listeria be out there: FDA reports on cantaloupe safety inspections

Coral Beach of The Packer reports that after inspecting 17 operations, federal officials say that fresh cantaloupe packinghouses are generally following good agriculture practices even though tests at nine of the companies showed listeria contamination.

cantaloupe.handThe inspections by the Food and Drug Administration were part of the agency’s follow-up efforts after a 2011 cantaloupe-related listeria monocytogenes outbreak that sickened more than 150 nationwide and killed more than 30.

“FDA’s 2013 cantaloupe packinghouse (investigation) was intended to further inform FDA of current cantaloupe packinghouse operating practices and conditions and provide data on the expected prevalence of listeria monocytogenes in and on cantaloupes and within packinghouses’ food and non-food contact surfaces during packing, handling and storage,” according to a July 27 report from consumer safety officer Michael Mahovic, who works with the agency’s division of produce safety.

For the review, FDA only inspected “firms that pack fresh cantaloupe in a packinghouse,” according to the report. “Processing facilities, growing fields, cantaloupe that are ‘field-packed’ and firms that do not handle cantaloupe were considered out of scope.”

Initially, FDA identified 50 firms in 18 states for review, but some of those companies were no longer in business and others turned out to be distributors, not packers. The remaining 17 firms that met the review criteria received notice 24 hours before inspectors arrived.

The agency collected environmental and product samples before and after packing and used a standardized questionnaire tailored for cantaloupe packinghouses to collect information and observations about each firm, according to the report.

All 17 firms had food safety plans and all reported they were aware of the 2011 listeria outbreak and that they “took some action to evaluate or bolster their own operations, from re-evaluating their own food safety plans, to completely refitting their buildings,” according to the report.

Eight firms did not have any positive listeria test results. One had pathogenic listeria present and the other eight tested positive for non-pathogenic listeria.

“Such findings do, however, suggest the potential for (pathogenic) listeria monocytogenes to be present,” according to the report.

Nerd alert: US FDA releases supplement to the 2013 Food Code

The U.S. Food and Drug Administration has issued the Supplement to the 2013 Food Code. The update addresses recommendations made by regulatory officials, industry, academia, and consumers at the 2014 Biennial Meeting of the Conference for Food Protection.

nerd.finance.barfblogThe Food Code and its Supplement provide government and industry with practical, science-based controls for reducing the risk of foodborne illness in retail and foodservice establishments of all types. The Food Code and the Supplement are joint projects of the FDA, Centers for Disease Control and Prevention, and the United States Department of Agriculture – Food Safety Inspection Service.

The Supplement modifies the 2013 Food Code to:

Expand the duties of the Person in Charge in a food establishment to include overseeing the routine monitoring of food temperatures during hot and cold holding.

Expand and clarify the type of information that should be included when a Hazard Analysis and Critical Control Point Plan is required by a regulatory authority.

Emphasize that cleaning and sanitizing agents should be provided and available for use during all hours of operation.

Clarify the difference between Typhoid Fever and nontyphoidal Salmonellosis with regard to the reporting of illness and the exclusion and restriction of ill food employees.

Suggest that regulatory authorities ensure that inspection staff has access to the necessary training and continuing education.

The Food Code is the model for retail food regulations in all 50 states, the District of Columbia and Puerto Rico. The FDA encourages its state, local, tribal, and territorial partners to adopt the latest version of the FDA Food Code, including the Supplement to the 2013 Food Code.

FDA’s National Retail Food Team assists regulatory officials, educators, and industry in their efforts to understand, adopt, and implement, the FDA Food Code. Inquiries may be sent to: retailfoodprotectionteam@fda.hhs.gov or directly to a Regional Retail Food Specialist.

The 2013 FDA Food Code and its Supplement is available on the FDA website at http://www.fda.gov/FoodCode. 



Didn’t pay attention to the safety: Blue Bell, FDA had Listeria warning signs at Alabama plant years ago

On the heels of reaching a deal with Alabama state health officials to boost testing and other safety measures, federal reports show Blue Bell Creameries was also warned of leaks and hygiene issues at its facilities in that state as far back as 2011.

blue.bell.creameriesOver the course of at least a half dozen visits by Alabama state health department inspectors dating back to 2010, reports show that the Blue Bell facility in Sylacauga, Ala., saw issues also seen at its plants in Broken Arrow, Okla., and Brenham, where the company is based. The reports were obtained by the American-Statesman as part of an open records request.

The U.S. Food and Drug Administration, however, did not follow up directly at that plant until this year when reports revealed listeria-related concerns for Blue Bell’s products.

Blue Bell Creameries responded Tuesday afternoon to the federal and state inspection reports, saying the company takes inspections seriously and is currently conducting a thorough review of their operations.

On Monday, Blue Bell struck a deal with Alabama state health officials like ones it had brokered two weeks ago in Texas and Oklahoma to step up testing and safety measures when production resumes. The agreement with the state of Alabama also says there will be a trial production period before products are shipped to consumers.

Company warned to get its HACCP together for eel

The U.S. Food and Drug Administration issued a warning letter to seafood processing company Saemus on May 18 over what it called “serious” Hazard Analysis and Critical Control Point (HACCP) violations.

eelThe determination is based on inspection of the processing facility in Virginia from Oct. 29 through Nov. 5 of last year, the letter said.

Among concerns was that the firm does not have a HACCP plan in place for its frozen vacuum packed, cooked, ready to eat eel.

Also, its ready-to-eat broiled eel kabayaki and hot and spicy eel productslacked the required HACCP plan to assure the fish are cooked sufficiently.

It also found a product — Natural Fresh Water Eel — was misbranded, since the label fails to declare all major food allergens present in the product.

FDA alleges California crab, halibut importer violated food safety rules

The U.S. Food and Drug Administration has issued a warning letter to a California seafood firm, alleging violations of food safety rules.

Mr-Krabs-SpongeBob-SquarePants-300x214In an April letter stemming from February inspections, the government said that T&L Trading’s live king crab and halibut had been prepared, packed or held under insanitary conditions that may have rendered them injurious to health.

A phone call to the company in Montebello, California, on Thursday morning went unanswered.

Among the alleged violations, the company wasn’t in compliance with Hazard Analysis and Critical Control Point regulations because it did not have product specifications designed to ensure fish and fishery products the company imports are not injurious to health or have not been processed under insanitary conditions, the FDA said.

The firm also did not monitor the safety of water that comes into contact with food or food-contact surfaces, the condition and cleanliness of food contact surfaces or the prevention of cross contamination with sufficient frequency to ensure compliance with good manufacturing practice requirements, the FDA said.

Increased inspections mean little: FDA unaware of Listeria in Blue Bell plant before outbreak

I’ve always told my daughters, whenever someone says, “trust me,” immediately do not trust them.

Do-Not-Trust-MeTrust is earned by actions, not words.

Amidst reports that Listeria-contaminated Blue Bell ice cream is selling well on Craiglist and other Internet markets, U.S. Food and Drug Administration types said they were never told of repeated findings of Listeria at a Blue Bell Creameries facility before an outbreak linked to the ice cream turned deadly.

Results of a Food and Drug Administration investigation released last week showed the company had found 17 positive samples of Listeria on surfaces and floors in its Oklahoma plant dating back to 2013. The FDA said Friday that it “was not aware of these findings” before doing its own inspection this year.

“Although Blue Bell’s testing did identify Listeria, the company did not further identify the strain to determine if it was pathogenic,” FDA spokeswoman Lauren Sucher said.

Which is why all test results should be public.


Going public (sort of?): FDA issues draft guidance on mandatory food recalls for comment

The U.S. Food and Drug Administration has published a notice in the Federal Register that a draft guidance for industry on mandatory food recalls is available for public comment.

communicationThe FDA has the authority to order a responsible party to recall a food if there is reasonable probability that the food (other than infant formula, for which FDA has separate recall authority) is adulterated or misbranded under certain provisions of the Federal Food, Drug, and Cosmetic Act, and that the use of or exposure to that food will cause serious adverse health consequences or death.

This authority for mandatory food recalls was provided by the FDA Food Safety Modernization Act to better protect public health by strengthening food safety measures and providing more effective enforcement tools. Before the enactment of FSMA in January 2011, the FDA had to rely on manufacturers to voluntarily recall food products.

In February 2015, the FDA reported to Congress that it has used this new authority twice. In both cases, the FDA issued letters to the responsible party warning that if the firm did not voluntarily cease distribution and conduct a recall, FDA may, by order, require the firm to cease distribution and give notice to other parties.

The draft guidance is in the form of questions and answers that focus on common questions that might arise about how FDA will use this mandatory recall authority. They include:

What foods are subject to FDA’s mandatory food recall authority?

What are the criteria for a mandatory recall? 

What is the process FDA must follow for a mandatory recall?

The draft guidance will be available for public comment for 60 days starting May 7, 2015. The FDA will consider all comments before completing a final version.

For More Information:

Money where your mouth is: A shortage of funds for US food safety

The N.Y. Times writes in an editorial that a farsighted food safety law enacted in 2011 has faced obstacles to meaningful enforcement ever since, including delays in issuing necessary rules and a shortage of money.

restaurant.inspectionNow, in what may become the latest shameful chapter, Congress seems unwilling to provide enough money to effectively carry out regulations that are about to be issued. The losers, of course, will continue to be consumers, who live with the hazards of an unsafe food supply.

The Food Safety Modernization Act was designed to prevent deadly outbreaks, not just react to them. It put the burden on food producers to make sure that their products are safe and to develop plans to prevent contamination. It also gave the F.D.A. new powers to set standards for harvesting fresh produce, recall tainted foods and monitor produce imported from abroad.

The Congressional Budget Office had estimated that the F.D.A. would need a total of $580 million from 2011-15 to carry out its reforms. That is a pittance for policing an enormous sector of the nation’s economy and barely noticeable in the vast federal budget. Yet Congress has appropriated less than half that amount — roughly $162 million — over the five-year period.

The president’s budget request for fiscal year 2016, which starts in October, asks for an appropriation of $109.5 million, an increase from $27.5 million in the current year. In addition, it calls for an increase of almost $192 million in user fees from the industry that it is virtually certain not to get. The F.D.A. in its last five budget requests proposed user fees that would cover the bulk of the costs, but Congress rejected those proposals after industry lobbying.

That’s all nice, but the industry that profits from selling food should be taking control and far exceeding government standards, as Costco and Walmart have done.