Last week the CDC announced the end of its investigation involving Shiga toxin-producing E. coli (STEC) in General Mills flour and flour products. However, many consumers may still have these products in their homes, and thus the agency is warning that it expects to see more illnesses. As of September 26, 2016, the CDC recorded 63 infections with strains of STEC O121 or STEC O26 in 24 states, 17 of which resulted in hospitalizations, and no deaths. The agency continues to urge consumers to refrain from eating (this includes a simple “taste”) raw dough or batter. It is also advising against giving playdough made with raw flour to children.
CDC worked with FDA and used PulseNet to identify illnesses that were part of the outbreak. This investigation led General Mills to initiate several recalls of its branded flours (May 31, 2016, July 1, 2016 and July 25, 2016), affecting more than 10 million pounds of product.
“In an epidemiologic investigation, investigators compared the responses of ill people in this outbreak to those of people of similar age and gender reported to state health departments with other gastrointestinal illnesses. Results from this investigation indicated an association between getting sick with STEC and someone in the household using Gold Medal brand flour.
Federal, state, and local regulatory officials performed traceback investigations using package information collected from ill people’s homes and records collected from restaurants where ill people were exposed to raw dough. These initial investigations indicated that the flour used by ill people or used in the restaurants was produced during the same week in November 2015 at the General Mills facility in Kansas City, Missouri, where Gold Medal brand flour is produced,” according to the CDC’s outbreak summary.
Americans consume 350 billion pounds of food each year, with one out of six people falling victim to foodborne illness, and 3000 dying. The significant amount of Listeria outbreaks hitting the industry (most recently, the staggering number occurring in produce) has left many food safety and quality assurance professionals searching for better methods of prevention and detection. Using big data, specifically metagenomics, to improve food safety and detect potentially deadly outbreaks is indeed where the future is headed.
DID YOU KNOW? The estimated U.S. cost of one case of Listeriosis is $1.4 million. Listeria is a prime concern due to the high percentage of fatalities that occur as a result of contracting Listeriosis. And what’s worse is the fact that many of the cases are preventable.
During Food Safety Tech’s Listeria Detection & Control Workshop this week, John Besser, Ph.D., deputy chief of CDC’s Enteric Diseases Laboratory Branch, outlined how the agency is leveraging metagenomics to find unrecognized problems in the food supply. Perhaps the most important element of disease surveillance is that it enables the detection of new issues, especially those whose presence was previously unknown.
Pathogen-specific surveillance allows the detection of more outbreaks, which will in turn make the food supply safer, because it will enable industry to understand the root causes of outbreaks and help them address problems much sooner. The CDC is focused on genome-based outbreak detection because of its ability to achieve faster detection—and with greater precision in identifying the source. The method has also helped the agency solve outbreaks with fewer cases occurring, and it concurrently helps rule out sources.
PulseNet, a nationwide database (comprised of 87 labs in the United States) that links cases most likely to share a cause for illness, has prompted food safety improvements across a variety of products, including sprouts, peanut products, leafy greens, flour, melons, eggs and poultry. Combine this capability with the Listeria initiative, which was launched in the mid-2000s, and the CDC has been able to find more (and smaller) outbreaks than ever before. In fact, there’s been a dramatic increase in the number of outbreak cases that have been solved (with the food source being identified). During the pre-whole genome sequencing (WGS) stage (September 2012–August 2013), only one outbreak was solved; in year one of the WGS project (September 2013–August 2014), four cases were solved; in year 2 of the WGS project (September 2014–August 2015), nine outbreaks were solved. In these respective time periods, the median number of cases per cluster dropped from six to four to three. In addition, the number of cases linked to a food source jumped from 6 to 16 to 93 during this respective time period.
Besser also discussed the role of metagenomics, or the study of total genetic material recovered directly from environmental samples. A couple of years ago, this was science fiction and wasn’t possible, he said. But as we look to the future, metagenomics will become a lot cheaper as computers become more powerful—and at break-neck speed. He referenced IBM Research, who earlier this year announced a project being conducted in conjunction with Mars, Inc. and Biorad for sequencing the food supply chain (calling it the “largest-ever metagenomics study”).
Metagenomics enables the profiling of communities of microbiomes anywhere in the food supply chain. And the method is fast—it can potentially shave weeks off the process of identifying clusters of interest. In addition, it can increase the value of interviews conducted with patients who have fallen ill (Think about it: Do you remember what you ate two weeks ago? What about a month ago?).
Currently there are several limiting factors surrounding metagenomics: Cost; sequencing read length and error rate; specific software (and pipelines); computing processing power and bandwidth; and the signal-to-noise factor. However, with the rapid rate in which technology has been improving in this space, the high likelihood of these issues being addressed and resolved in the not-so-distant future will present exciting opportunities in outbreak prevention and detection.
The advent of PulseNet in the late 1990s enabled more effective identification of outbreaks, even as many of them overlapped. The database brought to light the fact that many of the products sold in commerce nationwide contained ingredients that were at risk of contamination with dangerous pathogens. In many instances, these ingredients were in products from a single lot or batch and then sold by a single supplier to dozens of customers. From there, they were used in hundreds of products that would be distributed into thousands of retail locations.
Attend Food Safety Tech‘s Listeria Detection & Control Workshop | May 31–June 1 in St. Paul, MN | LEARN MOREFDA created the Reportable Food Registry (RFR) as a way to prevent the shipment of contaminated ingredients into the food supply. If received ingredients or products test positive for contaminants, the RFR requires that the company inform FDA. The agency uses the reports to take regulatory action against the original supplier and requires that all ingredients or products from all potentially affected lots be recalled from commerce. Because the RFR allows FDA to immediately begin tracking and containing ingredients testing positive for pathogens, its introduction in 2009 resulted in a significant spike in recalls.
Driven by the recalls triggered by PulseNet and the RFR, a national perception about an extremely unsafe U.S. food supply began to emerge. The public and media demanded that Congress take action, and so FSMA was born. The regulations require all FDA-regulated food companies to develop and implement written preventative control programs designed to control pathogens and other hazards in food. As a result, food companies will face heightened regulatory risk, scrutiny and exposure.
To further decrease the incidence of outbreaks and recalls, FDA is implementing regulatory enforcement initiatives that include sampling food products at retail for the presence of pathogens; conducting microbiological profiling of food processing facilities during routine inspections; and exploring criminal sanctions against companies that have been linked to positive samples in food products or production facilities associated with an outbreak or foodborne illness.
Microbiological Sampling in Retail
FDA is sampling products intended for human consumption as well as those for animal consumption. As testing continues at the retail level, the likelihood of more food products testing positive for the presence of pathogens is much higher. When positive product samples are found, FDA will take immediate action against the company that processed the product and require the company to recall all affected product. The agency will also demand access to the production facility at issue and conduct extensive environmental sampling, including from drains, floors, walls, production equipment, and finished products, in an effort to find the same strain as the sample testing positive at retail. If product or environmental samples test positive, FDA will perform genetic DNA testing on the isolates and compare the DNA fingerprints against those of the isolates collected from sick case patients in PulseNet over the past 15 years. If a match between the DNA fingerprint and an illness(es) in PulseNet is found, the agency will presume that these illnesses were caused by product originating from that particular facility. FDA will also demand access to all food production and microbiological testing records from previous months, or years, and critique those records.
Microbiological Sampling in Food Production Facilities
In accordance with FSMA, FDA will inspect all food production facilities (drains, floors, walls, food processing equipment, and finished products) that process high-risk ingredients or food products within the next three years (lower risk facilities will be inspected within the next five years). The agency is also performing extensive microbiological profiling of the food processing environment in all production facilities during routine inspections. If a positive sample is found, FDA may require the company to recall the affected product. It is expected that the level of sampling will intensity in the coming months and years as a result of FSMA mandates. And as the extensive microbiological sampling in food production facilities continues, FDA will perform genetic DNA testing on any positive samples collected, once again comparing the DNA fingerprints of samples against those of sick case patients over the last two decades. If a match is found, FDA will take the same course of action as in retail and presume all illnesses were caused by a food product originating from that specific facility. When that occurs, in addition to the potential recalls that may be required, the food companies at issue may become the target of a criminal investigation as well.
My next column will cite recent examples of FDA’s criminal offensive against food companies.
There was been a significant uptick in the amount of foodborne illness outbreaks and food product recalls (there were more than 500 food product recalls last year), many of which have been caused by dangerous pathogens. As FSMA plays a role in addressing this alarming trend, FDA is making several policy changes that will only continue to intensify. The agency is conducting microbiological profiling both inside food processing facilities during routine inspections and testing large amounts of food at the retail level. In addition, it has launched criminal investigations against food companies distributing products that have the potential to cause human illness. In many of these cases, company executives did not have direct knowledge that their products were causing, or had the potential to cause, illness. Many investigations involve Listeria monocytogenes (LM) found in food processing environments or in food products in commerce. Under FDA’s new approach, the failure to eliminate sporadic LM findings in the environment can subject companies to criminal liability. The immediate challenge to the food industry is to find a more effective solution to identify and reduce pervasive pathogens in the processing environment using pathogen-reduction technologies, while simultaneously employing written food safety protocols that can provide additional protection against criminal sanctions.
PulseNet Makes Foodborne Illness Link
Following the conclusion of the infamous the Jack-In-The Box outbreak that sickened 600 and killed four people more than two decades ago, the federal government recognized that similar outbreaks were probably occurring throughout the country, but there were no viable means of detection. As a result, the CDC created the PulseNet database, a mandatory foodborne illness reporting system to detect and track outbreaks in real time. From there, when a patient tested positive for a pathogen of concern (such as Listeria Monocytogenes, Salmonella or E. coli O157:H7), his or her doctor had to report that finding to the state health department. Each state requests copies of the isolates and tests them for the specific genetic DNA fingerprint of the pathogen of interest. These fingerprints are uploaded to PulseNet, and when indistinguishable genetic DNA fingerprints are uploaded from multiple victims, the CDC can recognize that an outbreak is emerging. The agency shares this information with FDA and other federal, state and local health departments as they work to determine a common source. Despite the fact that most illnesses uploaded to PulseNet remain unsolved, the database has helped CDC and FDA solve hundreds of outbreaks that have affected thousands of victims.
My subsequent columns will look at the emerging challenges faced by the food industry, including recent federal criminal investigations, some solutions designed to assess environmental contamination and reduce pathogens, and strategies that you can employ to reduce criminal liability.
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