Tag Archives: pathogens

Eggs

Rose Acres Recalls Eggs, FDA Investigating Salmonella Link

By Food Safety Tech Staff
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Eggs

Rose Acre Farms has voluntarily recalled eggs from its farm in Hyde County, North Carolina following an investigation by FDA, CDC and other agencies involving Salmonella illnesses. FDA testing determined that eggs produced from this farm are connected to 22 cases of Salmonella Braenderup infections; the CDC is confirming illness information with state health departments.

The exact amount of eggs recalled totals 206,749,248.

The eggs are sold under several brand names, including Coburn Farms, Country Daybreak, Food Lion, Glenview, Great Value, Nelms, and Sunshine Farms, as well as restaurants.

FDA is advising restaurants and retailers that they should not sell or use any recalled shell eggs. In addition, they should take measures to avoid cross-contamination of the food processing environment and equipment by washing and sanitizing display cases and refrigerators regularly, washing and sanitizing cutting boards, surfaces and utensils, and washing hands with hot water and soap after any cleaning or sanitation process. Consumers are advised not to eat the recalled eggs.

A full list of the recalled eggs are available on FDA’s website.

Stephen Ostroff, 2016 Food Safety Consortium

Blockchain Transformational, Says Ostroff. FDA Updates on Pathogens, FSMA, WGS and More

By Maria Fontanazza
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Stephen Ostroff, 2016 Food Safety Consortium

Stephen Ostroff, M.D. deputy commissioner for foods and veterinary medicine, sounds excited about the promise of blockchain. He also continues to enthusiastically wave the flag for whole genome sequencing (WGS) in solving foodborne illness cases. At the recent GMA Science Forum, Ostroff shared his usual update on incidents involving pathogens, agency progress in inspections and FSMA, and what the future holds.

The 2018 Food Safety Supply Chain conference features a Blockchain panel discussion | June 12–13 | Learn morePathogens

“There’s been essentially zero change in incidents of pathogens, and in some [cases there have been] increases—despite the fact that we’ve been doing quite a bit to improve the profile of food safety in the United States,” said Ostroff. This isn’t the first time that Ostroff pointed to the fact that foodborne illness is resistant to change, but he still emphasized the disappointment that industry is “way off” from the Healthy People 2020 target rate for pathogens established by the government. “None of these are close to where we thought we would be,” he said, referring to the government’s established target rates for Campylobacter, E.coli O157, Listeria, Salmonella, Vibrio and Yersinia.

Ostroff has previously pointed to improved diagnostics and surveillance systems as being partially responsible for a lack of improvement in the number of foodborne illness cases (due to higher detection rates), but during this particular presentation he brought attention to culture independent diagnostic tests (CIDTs)—which he said are having a “major impact on data collected in FoodNet.” CIDT is relatively new and is more rapid than the culture method, but it doesn’t allow for subtyping or antimicrobial resistance testing.

According to Ostroff, CIDTs have major implications for folks who work in food safety. The overall incidence of infection with foodborne pathogens is not decreasing, and the use of CIDTs makes assessment of trends difficult. CIDTs appear to be finding infections previously undiagnosed or unrecognized. In addition, they could affect the agency’s ability to monitor FSMA impact measures.

Inspections

The agency continues to look at inspection data from both the perspective of the number of inspections and their outcomes. During FY 2017, there were 1253 domestic and 146 foreign inspections. For FY 2018, there have already been 1610 domestic inspections to date.

Enforcement Discretion

In January, FDA issued new enforcement discretion for certain provisions in four FSMA rules. This included resolving issues related to the “farm” definition, requirements for food contact substances under FSVP, and certain written assurances in place for the Preventive Controls (human and animal) rule until FDA comes up with a practical solution to issues raised by stakeholders, Ostroff said.

Oversight of Food Imports

FDA continues to take a risk-based approach to FSVP and overseas inspections. Part of these efforts includes the agency’s systems recognition program where it looks at other mature food safety systems around the world to recognize countries that have programs similar to the United States. Thus far FDA has recognized Australia, Canada and New Zealand food safety systems; It is currently in the process of evaluating European Union members.

Intentional Adulteration Rule

The International Adulteration rule continues to be a hot topic of discussion, especially as it relates to associated costs. FDA is actively working on putting out a draft guidance that will discuss how to conduct vulnerability assessments, along with its interpretation of the rule, according to Ostroff. Part one of the draft should be out “in the very near future”, he said. He added that the agency is trying to be flexible with the rule and although food defense is an important component of food safety, companies should never do anything in the context of food defense that could pose a food safety risk.

Whole Genome Sequencing

WGS provides more precise identification at a genetic level and helps expedite recognition and response time for nearly all current foodborne illness and outbreak investigations. “It’s the new normal—it’s here and it’s here big time,” said Ostroff, adding that the GenomeTrakr network has more than 167,000 isolates sequences in the database and is becoming more and more powerful. “It’s amazing what this tool can do,” he said, citing two recent cases involving strains of Salmonella in papayas and kratom.

Blockchain

“I think blockchain can be really transformational in the world of food safety,” said Ostroff, calling it “traceability on steroids without question”. He thinks the technology could also be useful in addressing food fraud and economically motivated adulteration, and provide more consumer transparency. Right now the FDA is looking very closely at blockchain in context of traceability and FSMA.

Campylobacter Enrichment Broth

3M Launches New Molecular Method to Detect Campylobacter

Campylobacter Enrichment Broth

3M Food Safety has launched the 3M Molecular Detection Assay 2 – Campylobacter with 3M Campylobacter Enrichment Broth. Poultry producers now have a complete solution for simultaneous monitoring of poultry for both Salmonella and Campylobacter. It can perform up to 96 tests of multiple types in a 60-minute run.

The Enrichment Broth requires just five steps and eliminates the need for microaerophilic incubation, supplements, blood, organic solvents or autoclaving the broth, only requiring the addition of sterile water.

For more information, visit 3M’s product website.

Martin Easter, Hygiena
In the Food Lab

The New Normal: Pinpointing Unusual Sources of Food Contamination

By Martin Easter, Ph.D.
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Martin Easter, Hygiena

Shiga toxin-producing E. coli in dry flour, and then romaine lettuce. E. coli O104 in fenugreek sprout seeds. Recent announcements of foodborne illness outbreaks have begun involving unusual combinations of bacteria and foods. These out-of-the-ordinary outbreaks and recalls are a small but growing part of the 600 million documented food poisonings that occur worldwide every year according to the World Health Organization. Preventing outbreaks from these new combinations of pathogen and food demand a range of accurate tests that can quickly identify these bacteria. Over the past several years, outbreaks from unusual sources included:

  • E. coli O121 (STEC) in flour: Last summer, at least 29 cases of a E. coli O121 infection were announced in six Canadian provinces. The source arose from uncooked flour, a rare source of such infections because typically flour is baked into final products. Eight people were hospitalized, and public health officials have now included raw, uncooked flour as well as raw batter and dough as a source of this type of infection.
  • E. coli O104:H4 in fenugreek sprouts: One of Europe’s biggest recent outbreaks (affecting more than 4,000 people in Germany in 2011, and killing more than 50 worldwide) was originally thought to be caused by a hemorrhagic (EHEC) E. coli strain that from cucumbers, but was but was later found to be from an enteroaggregative E. coli (EAEC) strain in imported fenugreek seeds—the strain had acquired the genes to produce Shiga toxins.
  • Mycoplasma in New Zealand dairy cows: While not unusual in cattle, the incident reported in August marks the pathogen’s first appearance in cows in New Zealand, a country known for strict standards on agricultural hygiene. The microorganism is not harmful to people, but can drastically impact livestock herds.
  • Listeria monocytogenes in food sources: Listeria monocytogenes causes fewer but more serious incidence of food poisoning due to a higher death rate compared to Salmonella and Campylobacter. Whereas Listeria has been historically associated with dairy and ready to eat cooked meat products, recent outbreaks have been associated with fruit, and the FDA, CDC and USDA are conducting a joint investigation of outbreaks in frozen as well as in fresh produce.
  • Listeria in cantaloupe: In 2011, one of the worst foodborne illnesses recorded in the United States killed 20 and sickened 147, from Listeria monocytogenes that was found in contaminated cantaloupes from a farm in Colorado. The outbreak bloomed when normal background levels of the bacteria grew to deadly concentrations in multiple locations, from transport trucks to a produce washer that was instead designed for potatoes.

The outbreaks underscore the fundamental need to have a robust food safety program. Bacteria can colonize many different locations and the opportunity is created by a change in processing methods and/or consumer use or misuse of products. So robust risk assessment and preventative QA procedures need to be frequently reviewed and supported by appropriate surveillance methods.

Food safety and public health agencies like the European Food Safety Authority (EFSA) or the CDC have employed a wide range of detection and identification tests, ranging from pulse field gel electrophoresis (PFGE), traditional cell culture, enzyme immunoassay, and the polymerase chain reaction (PCR). In the case of Germany’s fenugreek-based E. coli outbreak, the CDC and EFSA used all these techniques to verify the source of the contamination.

These tests have certain advantages and disadvantages. Cell culture can be very accurate, but it depends on good technique and usually takes a long time to present results. PFGE provides an accurate DNA fingerprint of a target bacteria, but cannot identify all strains of certain microorganisms. Enzyme immunoassays are precise, but can produce false-positive results in certain circumstances and require microbiological laboratory expertise. PCR is very quick and accurate, but doesn’t preserve an isolate for physicians to test further for pathogenic properties.

Identification of the pathogens behind foodborne contamination is crucial for determining treatment of victims of the outbreak, and helps public health officials decide what tools are necessary to pinpoint the outbreak’s cause and prevent a recurrence. Rapid methods such as the polymerase chain reaction (PCR), which can quickly and accurately amplify DNA from a pathogen and make specific detection easier, are powerful tools in our efforts to maintain a safe food supply.

Recently, scientists and a third-party laboratory showed that real-time PCR assays for STEC and E. coli O157:H7 could detect E. coli O121, O26 and O157:H7 in 25-g samples of flour at levels satisfying AOAC method validation requirements. The results of the study demonstrated that real-time PCR could accurately detect stx, eae and the appropriate E. coli serotype (O121, O26 or O157:H7) with no statistical difference from the FDA’s Bacteriological Analytical Manual (BAM) cell culture method.

Agencies like the World Health Organization and CDC have repeatedly stated that historical records of food poisoning represent a very small percentage of true incidents occurring every year worldwide. Many of today’s most common food pathogens, like Listeria monocytogenes, E. coli O157:H7 or Campylobacter jejuni, were unknown 30 years ago. It’s not clear yet if unusual sources of contamination arise from increasing vigilance and food safety testing, or from an increasingly interdependent, globally complex food supply. No matter the reason, food producers, processors, manufacturers, distributors and retailers need to keep their guard up, using the optimum combination of tools to protect the public and fend off food pathogens.

Tim Birmingham, Almond Board of California
In the Food Lab

10 Years, 0 Salmonella Outbreaks

By Tim Birmingham
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Tim Birmingham, Almond Board of California

Almond Board of California (ABC) tackled food safety head-on in the wake of emerging Salmonella concerns in the early 2000s. Conventional wisdom of the time suggested that low-moisture foods like almonds presented a minimal threat, but rather than simply accepting this, ABC engaged in research to better understand the risks. The resulting best practices and groundbreaking mandatory pasteurization program developed by ABC remain the gold standard for other sectors—and drive continued food safety and quality efforts for California Almonds.

In 2017, ABC marked the 10-year anniversary of its mandatory almond pasteurization program – and, most importantly, 10 years free of Salmonella recalls and outbreaks attributed to California Almonds. The almond industry is proud of its unified efforts over the last decade, as well as the food safety record we’ve been able to achieve. However, the work to protect and improve food safety and quality continues. Looking back at our initiatives and successes reminds us of how important this work is and drives our exploration of what’s next.

Understanding and Addressing the Risk

Outbreaks of Salmonella in 2001 and 2004 raised questions and concerns about food safety and quality across industries. For California Almonds, one of the biggest challenges was determining the true level of risk. The easy answer seemed to be that risk should be low, that, based on accepted conventions of the time, pathogens should not be able to grow in almonds and other low-moisture foods. However, ABC investigated further and quickly realized that the pathogen could present a problem. The organization decided to take action and tackle Salmonella and other potential threats.

In collaboration with food safety experts and research partners, ABC began research in 2001 to better understand the prevalence and concentration of contamination in almonds, conducted in tandem with efforts to develop strategies for contamination control. ABC was able to gather enough survey data over the course of several years to show that Salmonella was indeed present in about 1% of the almonds tested at very low concentrations. This data was fed into ABC’s risk assessment work, which enabled identification of appropriate performance criteria for ensuring consumer safety (>4-log reduction).

At the same time, ABC also worked to identify effective processing technologies and the best means of validating them. A technical expert review panel was assembled to help ABC develop a plan, assess research needs, establish standards and create guidelines for the industry. Extensive work went into determining how to validate equipment, including the determination of an appropriate surrogate (non-pathogenic microorganisms) that could be used in lieu of Salmonella in the plant. Concurrently, researchers worked to determine the specific time and temperature combinations needed for a >4-log (and 5-log) reduction for a range of pasteurization processes, including oil roasting, blanching and dry roasting, some steam processes and PPO processing. ABC and partners invested significant time and effort into this research, which culminated in the development of the groundbreaking mandatory pasteurization program for Salmonella reduction, and validation guidelines.

Process Implementation and Ongoing Education

Voluntary compliance with the pasteurization program began in 2004, well in advance of September 2007, when it became mandatory. By that time, pasteurization was established as the industry norm and laying the groundwork for ongoing food quality and safety efforts. Today, ABC has more than 1 billion pounds of validated pasteurization capacity for processes that maintain the raw characteristics of almonds, including steam, moist heat and propylene oxide (PPO). It also has close to 1 billion pounds of validated capacity for processes such as dry roasting, oil roasting and blanching. All reduce the level of potential contamination in almonds without diminishing the product’s quality, nutritional value or sensory qualities (taste and crunch).

ABC also developed a comprehensive round of updates to recommended food safety practices, creating a powerful program with tools that help growers and processors achieve their desired results. These tools include Good Agricultural Practices, Good Manufacturing Practices, HACCP guidelines and Pathogen Environmental Monitoring resources.

In total, ABC has made a $5 million investment in food quality and safety research and validated more than 200 treatment processes, to date. It remains committed to this mission, maintaining close connections with the scientific and regulatory communities to stay current on food safety in the broader context as well as issues specific to California Almonds. All relevant insights and information are disseminated to growers and processors in the form of clear, practical resources, including print publications and digital communications, and workshops and one-on-one field trainings.

What’s Next: Research, Tech and Regulatory Practices

The mandatory pasteurization program is now well established, but it isn’t static – ABC continues to stay on top of the latest methods, regulations and needs impacting California Almonds. Industry investment continues to increase, particularly in processes that maintain the raw characteristics of the product. And, while much information regarding processes and technologies are company-specific and confidential, equipment manufacturers continue evolving and growing their offerings, with a particular focus on maximizing almond quality and throughput.

On the regulatory side, FSMA continues to roll out for growers and processors. ABC helps growers and other stakeholders understand which rules apply, what actions to take to ensure compliance and when specific requirements come into effect for different operations, with FSMA-related resources, Preventative Controls and Produce Safety trainings and timely information available online. Many processors and non-farm huller/shellers started 2018 already meeting FSMA Preventive Control requirements, but the number of impacted orchards and huller/shellers expanded in January as the Produce Safety rule came into effect. At this point, the almond industry and the larger community of food and beverage industries have had time to assess the impact on their stakeholders and take action to ensure FSMA compliance.

FSMA reflects the evolving role of FDA in ensuring food safety. Traditionally, FDA has taken a reactive approach to food safety. The agency now has the authority to investigate farms and facilities regularly to ensure food safety regulations are followed. For the first time, growers and huller/shellers falling under the farm definition may be audited by FDA or FDA-designated agencies. While some growers may choose the exemption option, ABC encourages almond growers to understand the rule’s requirements and develop food safety plans appropriate to their farms. It will be new and uncertain territory for some, but with the FDA’s proactive approach, staying ahead of the curve on food safety and quality will be beneficial.

Currently, almonds are the only tree nut with a mandatory pasteurization program and defined performance criteria accepted by FDA. They have paved the way for validation of other tree nuts, and those industries should also consider implementing appropriate preventive controls for Salmonella. ABC’s work can be considered a road map for other nuts and low-moisture foods, but what works for almonds will not always work for other foods. Research specific to each type of nut needs to be conducted to uncover pathogen prevalence and concentration, as well as pathogen/surrogate resistance to various processes. We will continue to be proactive, as well, evaluating current practices and engaging in research to improve how we understand and control microbial contamination in almonds.

Even with a track record to take pride in, the responsibility and work of food quality and safety never end. We will continue to update and evolve programs, not only as a function of compliance, but to protect the almond customers who support us every day.

FDA

FDA Collaborates with AMA on Foodborne Illness Education

By Food Safety Tech Staff
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FDA

FDA and the American Medical Association (AMA) have joined forces to release continuing medical education videos for doctors about foodborne illness. FDA and AMA felt that the globalization of the food supply as well as the growth of foodborne pathogens necessitated more medical education and patient counseling on foodborne illness.

“These changes create a need for physicians to guide patients in protecting themselves from foodborne illness, especially those who are among the most vulnerable to serious consequences and who are most likely to be in a physician’s care: the very young whose immune systems are not yet fully developed; individuals whose immune systems are weakened by pregnancy, age, chronic conditions like diabetes, cancer and HIV/AIDS; and persons with organ transplants taking immuno-suppressive medications,” according to an FDA release.

The two videos, “What Physicians Need to Know About Foodborne Illness: Suspect, Identify, Treat, and Report” and “Preventing Foodborne Illness: Talking to Patients About Food Safety” are available on FDA’s Food Safety and Nutrition Resources for Healthcare Professionals webpage.

Pathogenic Contamination Among Top Food Safety Hazards for Cannabis

By Steven Burton
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“As more people gain access to and ingest cannabis products, it’s only a matter of time before food safety becomes a primary concern for producers and regulators,” says Steven Burton, CEO and founder of Icicle Technologies, Inc. Without federal regulation, there are so many questions about the food safety hazards associated with the use of cannabis in food products. In an article published in Food Safety Tech’s sister publication, Cannabis Industry Journal, Burton discusses the Top Four Safety Hazards for the Cannabis Industry, which includes pathogenic contamination from pests and improper handling.

USDA Logo

Thousands of Pounds of Meatballs Recalled Over Listeria Worry

By Food Safety Tech Staff
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USDA Logo

Rich Products Corp. recalled 3.420 pounds of ready-to-eat beef meatball products over concerns that they may be adulterated with Listeria monocytogenes. The recalled products, which were produced on December 17, 2017, include 36-lb cases that contain six bags of “Member’s Mark Casa Di Bertacchi Italian Style Beef Meatballs with a “best by” date of December 17, 2018. The meatballs were shipped to distributors in the South, including Alabama, Florida, Mississippi, North Carolina, Texas and Virginia. The issue was discovered on January 24 when FSIS was notified by Rich Products that it shipped adulterated products into commerce. More information about the meatball recall is available on USDA’s website.

Listeria

Four Pathogens Cause Nearly 2 Million Foodborne Illness Cases a Year

By Food Safety Tech Staff
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Listeria

The CDC estimates that Salmonella, E. coli O157, Listeria monocytogenes and Campylobacter cause 1.9 million cases of foodborne illness in the United States. A report just released from the Interagency Food Safety Analytics Collaboration (IFSAC) analyzed data from more than 1000 foodborne disease outbreaks involving these pathogens from1998 through 2013.

The report found the following:

  • Salmonella illnesses came from a wide variety of foods (more than 75% came from the seven food categories of seeded vegetables, eggs, chicken, other produce, pork, beef and fruit.
  • More than 75% of E.coli O157 illnesses were linked to vegetable row crops, like leaf greens, and beef.
  • More than 75% of Listeria monocytogenes illnesses came from fruits and dairy products.
  • More than 80% of non-dairy Campylobacter illnesses were linked to chicken, other seafood (i.e., shellfish), seeded vegetables, vegetable row crops, and other meat and poultry (i.e., lamb or duck).

A copy of the report, “Foodborne illness source attribution estimates for 2013 for Salmonella, Escherichia coli O157, Listeria monocytogenes, and Campylobacter using multi-year outbreak surveillance data, United States”, is available on the CDC’s website.

Dr. Douglass Marshall, Chief Scientific Officer – Eurofins Microbiology Laboratories
Food Genomics

Part II: Logistics of GenomeTrakr

By Douglas Marshall, Ph.D., Gregory Siragusa, Ph.D.
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Dr. Douglass Marshall, Chief Scientific Officer – Eurofins Microbiology Laboratories

Last month in Food Genomics we asked FDA scientists Drs. Marc Allard and Eric Brown to help the readers of Food Safety Tech understand the process used by GenomeTrakr. In part two we cover some logistical and more general questions.

Greg Siragusa/Douglas Marshall: Why should a food producer or processor submit its own pathogen isolates to GenomeTrakr? Are there any legal liabilities incurred by doing so?

Eric Brown/Marc Allard: The database is available publicly for any outside laboratory to be able to rapidly compare their new WGS data to all of the data in the database. The data is all publicly available so food industry members should carefully consider the strengths and weaknesses of sharing data. The main reason for sharing data is that if any matches arise then this would be immediately known for an investigation and corrective action. With knowledge, companies can better understand their risk and exposure to occasional contamination events.

Siragusa/Marshall: Are there private third-party providers who will perform the same method of sequence analysis for private companies that GenomeTrakr uses in the FDA?

Brown/Allard: Yes, as all of the FDA methods of data collection and analysis are fully transparent and publicly available, any expert third-party provider could easily set up and reproduce the GenomeTrakr methods. Third-party support may be an excellent mechanism for food industry partners that wish to examine the pathogens they have found connected to their products but do not wish to maintain an active WGS laboratory. An internet and reference search will uncover these private third-party providers, as this is a growing market with a diversity of services provided. The FDA works closely with the Institute for Food Safety and Health (IFSH) to share information that may be valuable to their industry partners.

Siragusa/Marshall: Will the FDA perform analysis of isolates for private parties and the sequence not made publicly available?

Brown/Allard: No. While we will sequence relevant strains from many different sources, as a matter of protocol we will submit all of these data to the GenomeTrakr database. That is, currently, the FDA sequences and uploads all available genomic strain data. All data are made publicly available through the GenomeTrakr and NCBI pathogen detection website. The metadata describing each isolate only includes species, date, state location and a general food description which could include the type of food (e.g., an egg) and/or the type of sample (e.g., environmental swab, surface water, sediment, etc.) as well as production date, pH, fat content and water activity. No trade or industry brand names are made publicly available, and the location is ambiguous down to the state level to allow for anonymity of specific farm names or processing centers. An example of metadata in the GenomeTrakr database might include Salmonella, from Washington State in spinach from 2015.

Siragusa/Marshall: Is the CDC tied into GenomeTrakr and if so, how?

Brown/Allard: CDC labels their clinical WGS data as PulseNet with the data uploaded to the NCBI Pathogen Detection website. USDA FSIS also uploads the isolates that they have collected and sequenced from foods that they regulate. All of this WGS data is housed in a centralized repository at NCBI Pathogen Detection website where NCBI conducts rapid analysis for QA/QC. The NCBI posts a daily tree for all species that recently have been uploaded. This way all of the data collected by these federal laboratories and their state and international partners are made publicly available for direct comparison. Numerous other international and academic laboratories also provide data to the NCBI centralized database. When isolates cluster together and appear to be closely related, the FDA works with CDC and USDA FSIS through the normal channels. The great benefit of combining food, environmental and clinical isolate genomes in a common database cannot be overstated.

Siragusa/Marshall: In the event of an outbreak, is it possible to obtain WGS’s from using a shotgun metagenome (a microbial and organismic profile obtain by sequencing all of the DNA in a sample, not just bacterial analysis of an enrichment thereby precluding isolation? (Refer to glossary; see Table 1)

Brown/Allard: Yes, preliminary research has documented the potential to obtain WGS data from cultural enrichments, saving the time it takes for full pure culture isolation, which potentially could provide time savings of two to five days depending on the pathogen. Having well characterized draft genomes such as those in the GenomeTrakr database will support rapid characterization from metagenomes after cultural enrichment. A future goal for the FDA is to transform and expand GenomeTrakr into metaGenomeTrakr to support either pure culture or enriched shotgun metagenomic samples.

Siragusa/Marshall: Is there any way that associated metadata tied to a strain (and hence its sequence) can be unmasked through legal action?

Brown/Allard: FDA protects confidential metadata collected during inspection just as it has always done with PFGE data. WGS data is protected at the same level as other types of subtyping information.

Siragusa/Marshall: Is the GenomeTrakr database associated with the GMI (Global Microbial Identifier)?

Brown/Allard: The GMI is a consortium of like-minded public health scientists who wish to collaborate to create a harmonized global system of DNA genome databases that is publicly available to promote a one-health approach. The GenomeTrakr is one of the databases that make up this larger effort that includes some data from members of the GMI.

Siragusa/Marshall: This column is meant to keep food safety professionals abreast of the latest knowledge, technology and uses of genomics for food safety and quality. Tell us your vision of how or which changes in technology (sequencing chemistry, bioinformatics, etc.) will be coming down the pike and how it might impact GenomeTrakr?

Brown/Allard: New technology has been constantly improving in WGS and in sequencing for the last 20 years, and there is no sign of this slowing down. Improvements continue to accrue in chemistry, equipment and software analysis. Likely future improvements will include more turnkey solutions for WGS from sample to report. This includes both DNA extraction and library preparation for sequencing, as well as data analysis pipelines (the system of analyzing the actual sequence data) that provide rapid, accurate and simple language results. Smaller mobile WGS devices are starting to show feasibility that would bring the lab to the samples and decrease the time to an answer (See: https://nanoporetech.com/products/minion) Metagenomics approaches appear to be maturing so that technology improvements are moving this out of a research phase and into direct applications. Currently MISeq (a commonly used workhorse nucleic acid sequencer made by the Illumina Co.) outputs are on the order of 300 base pair read lengths of nucleotides (i.e. A’s, T’s. C’s G’s), long read sequencing technologies, upwards of 1,500 base pairs may make analysis much easier so that more assembled and completed finished genomes are available in the databases. Cloud-based solutions of data analysis pipelines may provide simple solutions, giving wider access to rapid, validated data analysis and results. FDA researchers are working on all of these aspects of improvements in WGS technology as well as expanding the network to more global partners.

Siragusa/Marshall: Sequences deposited into GenBank (as part of GenomeTrakr) are accessible to anyone anywhere. Does this essentially usher in a whole new chapter in food microbiology especially at the pre-harvest level?

Brown/Allard: Yes, having well characterized reference genomes provided by GenomeTrakr partners will support microbial ecology and metagenomics studies. Metagenomics or microbiomes describing which species are present and what they may be doing in the ecology is providing new knowledge in all aspects of the farm to fork continuum. As the costs for these services decrease, we are seeing an increase in use to answer questions that have been impossible or extremely difficult in the past.

Siragusa/Marshall: GenomeTrakr is not a project per se; rather it is a program. How is it funded and will it continue on stable fiscal footing for the foreseeable future?

Brown/Allard: GenomeTrakr started as a research project in the Office of Regulatory Science in CFSAN, but much of this data collection is no longer research. Today, and for some time in the future, WGS at the FDA is collected as fully validated regulatory data to support outbreak and compliance investigations. As such, the FDA is in transition of moving WGS into a phase for more stable regulatory support. Research and development for future applications and technology exploration will always be a part of the FDA portfolio, although typically at lower funding levels than the regulatory offices. Public health funding is generally protected as everyone wants safe food.

Siragusa/Marshall: Are there any restrictions of isolate source? For instance, can isolates from poultry flocks or even wild birds be deposited?

Brown/Allard: The GenomeTrakr and NCBI pathogen detection databases are open to the public and thus there are no restrictions as long as the minimal metadata and QA and QC metrics are met. Current GenomeTrakr WGS foodborne pathogen data includes samples from both poultry and wild birds, as well as turtles, snakes and frogs. Members interested in what is in the database can go to the NCBI Pathogen Detection website and filter on simple words like avian, bird, gull, chicken, wheat, avocado, etc. An example is as follows for a snake.

Siragusa/Marshall: If a company deposits an isolate, will it have access to the GenomeTrakr derived sequence exclusively or at least initially for some period before that information becomes public?

Brown/Allard: No, currently the FDA does not hold WGS data. All data collected by the FDA is uploaded and released publicly at the GenomeTrakr bioprojects and at NCBI pathogen detection website with no delays. If companies wish to hold data then they need to look to third-party solutions for their needs. The reason that GenomeTrakr has been so successful is due to the real-time nature of the released information and that it is globally available.

Read on to page two below.