Tag Archives: FDA

FDA

FDA Releases Five FSMA Guidance Documents

By Food Safety Tech Staff
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FDA

Today the FDA issued five guidance documents related to FSMA with the goal of assisting food importers and producers meet provisions in the regulation.

The first two documents are related to the Foreign Supplier Verification Program (FSVP) regulation. The FDA issued the draft guidance, Foreign Supplier Verification Programs for Importers of Food for Humans and Animals, along with a small entity compliance guide. The third draft guidance is related to whether a measure provides the same level of public health protection as the corresponding requirement in 21 CFR part 112 or the PC requirements in part 117 or 507 . “This draft guidance aims to provide a framework for determining the adequacy of a process, procedure, or other action intended to provide the same level of protection as those required under the FSMA regulations for produce and for human or animal food,” according to FDA.

The FDA also released a final chapter in the draft guidance related to FSMA requirements for hazard analysis and risk-based PCs for human food. The chapter is intended to assist food facilities in complying with the supply chain program requirements.

The fifth guidance is an announcement of the FDA’s policy to exercise enforcement discretion related to the FSVP rule regarding certain grain importers that bring the product into the United States as raw agricultural commodities. “This enforcement discretion is meant to better align the FSVP rule with the exemption for non-produce RACs under the PC rules,” stated FDA.

FDA

FDA Issues Guidance on FSMA Enforcement Discretions

By Food Safety Tech Staff
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FDA

FDA will be exercising enforcement discretion for specific provisions in four FSMA rules, which means that the agency doesn’t expect to enforce the provisions as they apply to certain entities or activities. The agency made the announcement yesterday.

“In general, the FDA is exercising enforcement discretion to allow time to consider changes or other approaches to address concerns regarding the application of these provisions to certain activities or entities. FDA had previously extended the compliance dates for many of the provisions covered by this enforcement discretion guidance but is now exercising enforcement discretion.”

According to an FDA release, the enforcement discretion applies to provisions in: Current Good Manufacturing Practice, Hazard Analysis, and Risk-Based Preventive Controls for Human Food rule (PC Human Food), Current Good Manufacturing Practice, Hazard Analysis, and Risk-Based Preventive Controls for Food for Animals rule (PC Animal Food), Foreign Supplier Verification Programs rule (FSVP), and Standards for the Growing, Harvesting, Packing, and Holding of Produce for Human Consumption rule (Produce Safety). The applications is as follows:

  • Facilities that would be farms except for certain factors and activities
  • Written assurances provisions in the four rules related to the control of identified hazards or microorganisms that could be a risk to public health
  • Animal food PC requirements for certain manufacturing/processing activities performed on human food by-products used as animal food
  • FSVP requirements for importers of food contact substances
Scott Gottlieb, M.D., FDA

FDA’s Gottlieb Says Some Food Recall Practices Raise Significant Concerns

By Food Safety Tech Staff
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Scott Gottlieb, M.D., FDA

Following the Office of Inspector General’s (OIG) final issuance of its report on FDA food recall practices, FDA Commissioner Scott Gottlieb, M.D., is voicing concern. The OIG report looked at FDA food recall practices from October 1, 2012 to May 4, 2015. Its findings are obvious in the report’s title: The Food And Drug Administration’s Food-Recall Process Did Not Always Ensure the Safety of the Nation’s Food Supply.

“Specifically, we found that FDA could not always ensure that firms initiated recalls promptly and that FDA did not always (1) evaluate health hazards in a timely manner, (2) issue audit check assignments at the appropriate level, (3) complete audit checks in accordance with its procedures, (4) collect timely and complete status reports from firms that have issued recalls, (5) track key recall data in the RES [Recall Enterprise System], and (6) maintain accurate recall data in the RES,” according to the OIG report.

Food Safety Tech first reported on the draft findings in June 2016 when the OIG said the FDA recall initiation process was not efficient or effective. Although Gottlieb noted that the agency took action after the draft was released, “we still have more work to do,” he said in an FDA statement.

One of the action steps for 2018 is that FDA will issue guidance on recall communications in the first half of the year. The agency is also looking at situations in which it can assist consumers in getting information about the stores and food service locations that may have sold or distributed recalled food, as well as the company that supplied the product.

“Much work remains to be done if we’re going to provide the highest assurance of safety.” – Scott Gottlieb, FDA

Gottlieb stated that the agency will be revealing more early this year about policy steps it will be taking to improve food safety oversight and how the recall process is implemented. FDA is also examining how it can expedite the timeliness and scope of information provided to consumers about food recalls.

Alert

FDA Inspections: Top Five Violations for FY2017

By Food Safety Tech Staff
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Alert

FDA’s Office of Regulatory Affairs has released the most frequently cited inspectional observations for fiscal year 2017. Among the items on the spreadsheet are food safety hazards, failure to clean, sanitation records, corrective action plan, and lack of sanitation.

“These observations, are listed on an FDA Form 483 when, in an investigator’s judgment, the observed conditions or practices indicate that an FDA-regulated product may be in violation of FDA’s requirements.” – FDA

The following are the top five (most frequent) observations.

  • 5. Contamination: Cleaning and sanitizing operations for utensils and equipment not conducted in a manner that protects against contamination of food, food contact surfaces and food packaging materials.
  • 4. Failure to implement HACCP plan procedures.
  • 3. Facility not constructed in a way that enables floors, walls and ceilings to be adequately cleaned; buildings, fixtures and other physical facilities not kept in sanitary condition.
  • 2. Sanitation monitoring: Sanitation conditions and practices not monitored with enough frequency to be in conformance with CGMP.
  • 1. Pests: Lack of effective pest exclusion from processing areas and contamination of foods, and failure to provide adequate screen against pests.
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.

FDA

FDA Issues Draft Guidance on Inspection Refusal for Foreign Food Facilities

By Food Safety Tech Staff
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FDA

Today FDA released a draft guidance to provide information about what actions by a foreign food establishment or government are considered a refusal of inspection. “FSMA gives the U.S. Food and Drug Administration the authority to refuse imported food admission into the United States if the agency is not permitted to inspect the foreign establishment that produced the food,” FDA stated in a release.

The 12-page draft guidance, Refusal of Inspection by a Foreign Food Establishment or Foreign Government, outlines how the agency goes about scheduling inspections of foreign establishments (despite the fact that FDA is not required to pre-announce inspections), the inspection activities themselves, and very detailed examples of what it considers an inspection refusal from a facility (from a lack of communication with FDA that delays the agency’s request to schedule an inspection, to preventing an FDA investigator from entering a facility, when a facility sends staff home and tells FDA that it is not producing product).

The draft also details what it considers to be refusal of inspection by a foreign government. Some of the actions include preventing FDA investigators from entering the country or asks them to leave the country before an inspection is scheduled; and limiting access to areas of the facility that manufacturing, processing and packaging occurs; and limiting investigators from collecting samples for analysis.

If either a foreign food establishment or a foreign government refuses an inspection, they will stay on the agency’s Red List of Import Alert 99-32 until FDA is able to schedule and conduct an inspection.

Stephen Ostroff, FDA

FDA’s Ostroff Says Foodborne Illness Still Resistant to Change

By Maria Fontanazza
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Stephen Ostroff, FDA

“Everything changes; nothing remains without change.” It’s the Buddha quote that Stephen Ostroff, M.D., FDA deputy commissioner for food and veterinary medicine, used to kick off his plenary presentation at this year’s Food Safety Consortium. Yet “there is one thing that is stubbornly resistant to change,” he commented, and that’s foodborne illness. The incidence of culture-confirmed human infections hasn’t improved, and it can be seen in the number of cases reported through CDC’s FoodNet system. Why?

Stephen Ostroff, FDA
FDA’s Stephen Ostroff, M.D. answers audience questions during a town hall meeting at the 2017 Food Safety Consortium.

Ostroff has a few theories. First, there are much better diagnostics and surveillance systems in place versus 10 or 20 years ago. “Those improvements in finding the cases may be masking improvements that have occurred,” he said. Second, looking at the data from the big picture perspective may mask positive sub-trends. “We are actually doing better,” Ostroff said. “Within the data, there is some good news and some bad news.”

Ostroff also proposed that emerging food safety risks are having an impact on the rates of foodborne illness, including new trends that are altering the food landscape. The global food supply is more diverse than ever. In addition, the change in consumer preferences and eating patterns may lead to gravitation towards higher risk foods that are improperly handled. Other areas of risk include new methods of food delivery (i.e., e-commerce—Ostroff added that within a few years, up to 20% of our food will be delivered to our homes.). The final risk he touched on was new food types, such as synthetic foods (i.e., synthetic meat). “Nobody is quite familiar with the potential hazards associated with those foods,” he said.

FSMA Update

Over the past year, a new administration has come into place, along with a new FDA commissioner. In addition, compliance dates for six out of the seven foundational rules are now in effect (the compliance date for the Intentional Adulteration rule is July 2019). Although the new administration is focused on reducing the regulatory burden, it doesn’t appear to be impacting FSMA requirements. “To date we have no requests to change or delay FSMA requirements,” said Ostroff. “And that’s very good news.”

Third-party certification program. In June FDA launched a website through which organizations could apply to be recognized as an accredited body. Ostroff said the response and interest related to the program has been “overwhelming”, with hundred of entities visiting the agency’s website to learn more.

Voluntary Qualified Importer Program (VQIP). The agency anticipates that the application window will open January 2018 (however, Ostroff hinted that it may be delayed a bit). October 2018 is the projected start of the first benefit period.

FSMA Fixes. “There have been quirky issues that ended up in the FSMA regulations either because of the way FSMA was written by Congress or because of the way the regulations ended up,” said Ostroff, who added that the most problematic “quirk” is the intersection of whether an entity must comply with the Preventive Controls rule or the Produce Safety rule, and it all comes down to the farm definition. As a result, the agency extended compliance dates for a number of situations, one of which involves the agricultural water provision (January 2022 for large farms, January 2023 for small farms, and January 2024 for very small farms). Related to this provision, FDA is looking to reducing the regulatory burden but will keep standards in the lab analytic methods, frequency of testing and determination of water quality.

Training. The FDA has been partnering with many entities around the world to implement FSMA training both for industry and regulators. More than 50,000 people have been trained for the Preventive Controls for Human Food rule and more than 5000 have been trained for the animal food rule.

Inspection. At last year’s Food Safety Consortium, there was a lot of chatter about agency enforcement and inspection. Although Ostroff didn’t touch on enforcement, he provided a few figures on inspection activity for fiscal year 2017:

  • Preventive Controls for Human Food
    • Modernized CGMPs: 720
  • Preventive controls: 165 (46 outside of the United States)
  • Preventive Controls for Animal Food
    • CGMPs: 220
  • Foreign Supplier Verification Program: 285
  • Produce safety rule: 8 (sprouts)
Patricia Wester, PA Wester Consulting

Q&A On FSMA Audits: A Conversation With AFSAP CEO Patricia Wester

By Food Safety Tech Staff
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Patricia Wester, PA Wester Consulting

As a trade association for auditors and the auditing industry, AFSAP has researched the various references to audits found in all of the FSMA rules, and monitored the steps taken across the auditing community to meet these requirements. In this Q&A, we sit down with Patricia Wester, chief executive officer of AFSAP, to talk FSMA audits, criteria for supplier audits, preventive controls and FDA guidance. She will be running the Pre-Conference AFSAP Food Safety Auditing Fundamentals Course at this year’s Food Safety Consortium.

Background on the AFSAP and FSC Alliance

In July 2016, GFSI announced they would re-open the Guidance document revision process so that FSMA’s requirements could be considered for inclusion. When the final GFSI Guidance document was released, it included most of FSMA’s requirements. At this point, the Schemes still had to accommodate these changes, which were then provided to the CB’s. Depending on the Scheme, a CB also had to consider including content to address any FSMA related gaps. In the end, these audits could take more than a year to reach the market, and depending on the individual site’s renewal period, it could be many more months before a supplier was actually audited.

Patricia Wester moderated the Plenary Panel “What’s Next for Audits”
and running the
Pre-Conference AFSAP Food Safety Auditing Fundamentals Course at the
2017 Food Safety Consortium November 29 – December 1, 2017 in Schaumburg, IL.

Recognizing the need to inform the market, the inaugural Plenary Panel on Auditing, moderated by AFSAP’s Patricia Wester was presented at the 2016 Food Safety Consortium meeting. Dr. Ostroff opened the discussion to share FDA’s perspective on the use of audits for FSMA. His remarks were followed by representatives from GFSI, Schemes and CB’s as each described their role and recent activities to meet the new regulatory requirements, and provide insight into the timelines involved.

Dr. Ostroff has agreed to join us again for the 2017 meeting, and will participate in the Plenary Panel “What’s Next for Audits” as Industry, Retailers and the auditing community prepares for the accredited certification audits necessary for VQIP.

FoodSafetyTech: How are audits used in FSMA?

Patricia Wester: In the Third Party Audit rule, FDA outlines an accredited certification program for imported food that applies in 2 specific situations. The first applies to any imports FDA designates as “a high risk food” and the second is the use of certification audits for importers in The Voluntary Qualified Importer Program, (VQIP). Under VQIP, participating importers are required to source their products from suppliers that are certified under the FDA program.

In addition to the certification audits for VQIP and high-risk foods, audits are one of the options for supplier verification activities under the human and animal food preventive controls rules. When the hazard analysis identifies a raw material has a serious hazard, (SAHCODHA hazard), that ONLY the supplier controls, a supply chain preventive control is required, and the supplier verification activity must be an onsite audit. FDA allows some flexibility here, the audit can be a second or third party audit as long as it meets the requirements listed in 117.435, and is performed by a qualified auditor as defined in 117.3. These requirements are applicable to audits used to verify foreign suppliers (FSVP) as well as domestic suppliers.

FST: Don’t GFSI Scheme audits meet the criteria for Supplier Audits?

Wester: FDA allows the use of any audit that meets FDA’s criteria for audit content. This includes second party audits executed by employees of the receiving facility and third party audits, including GFSI audits, as long as they meet the requirements for audit criteria and are performed by a qualified auditor.

FDA acknowledges that the GFSI Auditor Competence provisions are consistent with the Agency’s findings, but that recognition does not extend to the audit criteria/content of GFSI audits.

In fact, any audit program in use prior to the publication of FSMA’s rules would probably need to be updated for these new requirements. GFSI, the Schemes, the CB’s, and others involved in the delivery of audits have likely all updated their audits to eliminate the major gaps, however, there are still some key FDA requirements that remain unmet.

FST: So, even though audit programs have been updated for FSMA’s new requirements, they are still missing some of FDA’s requirements? Why didn’t they just add everything?

Wester: In most cases, it appears to be due to a misinterpretation of the audit criteria that underpins all FDA’s audits. FDA’s audits focus on assessing a suppliers compliance with “applicable food safety regulations, the HACCP and/or Food Safety Plan and the plan’s implementation”. The Preventive Controls for Human Food Rule states the audit requirements in Subpart G:

§117.435 states:

If the raw material or other ingredient at the supplier is subject to one or more FDA food safety regulations, an onsite audit must consider such regulations and include a review of the supplier’s written plan (e.g., Hazard Analysis and Critical Control Point (HACCP) plan or other food safety plan), if any, and its implementation, for the hazard being controlled.

We (FDA) have revised phrasing to state “and its implementation” to emphasize that implementation of the plan is distinct from the plan itself (e.g., § 117.126(c). (The PCHF Final rule preamble)

Similar phrasing such as “any applicable FDA regulations” is used elsewhere when FDA discusses audit criteria, such as FSVP and VQIP and the Third Party Certification Audit rules. Further, the PCHF rule, §117.190 provides a comprehensive list of “Implementation Records” that can be used as a guide to understanding what meets this element of the FDA’s requirement.

The auditing community and Industry have assumed the regulatory reference was limited to the FSMA regulations, such as Preventive Controls for Human or Animal Food or the Produce Safety final rules), and has focused on those regulations to update their audit programs. Other FSMA regulations, such as Intentional Adulteration and Sanitary Transport, could easily be considered part of the requirement, so there are a few audit options that include those rules.

FST: What about products that are exempt from the Preventive Controls Rules?

Wester: Audits for products that are exempt from the PCHF (human Food) rule, such as Juice and Seafood HACCP, are probably available under a general HACCP format, but they may not include the level of detail required under FSMA, and would have to specifically requested when arranging a supplier audit.

Audits for other PCHF exempt products, such as bottled water or low acid canned foods, would be audited using a general food safety audit, with the specific product treated as a product category under that audit. Once again, these audits lack the product specific regulatory content and implementation details required by FSMA.

The question becomes, which FDA regulations (beyond FSMA) apply to an audit used for regulatory compliance and how much detail in the audit is necessary?

In other words, what is the full scope of regulations needed for the audit, and what are the audit criteria? Is it just FSMA or does it go further?

FST: Where does one look for this information? Does FDA offer any guidance about the scope of the audit?

Wester: The CFR, or Code of Federal Regulations is the starting place for regulations. Finding the regulatory information would not be difficult, Title 21, CH 1 Parts 1-1499 include FDA’s food regulations. In addition each part can have multiple subparts etc.

Given the sheer quantity of regulations, and that some are product specific while some are not, developing different audits for all of the possible regulatory combinations would be a daunting task and enormously costly. Remember, every auditing company will have to go through this process.

There are FDA references to scope and criteria in several responses to comments:

Audit Criteria means the set of policies, procedures or requirements used as a reference against which audit evidence is compared. During regulatory and consultative audits, accredited third-party certification bodies will examine compliance with applicable food safety requirements of the FD&C Act and FDA regulations within the scope of the audit. In consultative audits, the third-party certification bodies also may be conducting an examination to determine conformance with applicable industry standards and practices.

The applicable requirements that accredited third-party certification bodies and their audit agents will use relate to the food safety standards under the FD&C Act, such as the adulterated food provisions in section 402 of the FD&C Act and the provisions on the misbranding of food allergens in section 403(w) of the FD&C Act. The applicable requirements of the FD&C Act and FDA regulations would depend on the type of eligible entity being audited. Other examples include labeling requirements and the CFR citations listed under scopes.

Certainly, more detail than this is needed, and AFSAP is working to engage all parties, including FDA, in collaborative discussions to resolve these questions and concerns. The auditing community will need to address these issues in the near future, and industry should be vigilant to understand the requirements and make sure any audits used for FSMA are compliant.

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.

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