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).
Today FDA released a draft guidance to provide information about what actions by a foreign food establishment or government are considered a refusal of inspection.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The 12-page draft guidance, Refusal of Inspection by a Foreign Food Establishment or Foreign Government, outlines how the agency goes about scheduling inspections of foreign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.
“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?
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)
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.
By Douglas Marshall, Ph.D., Gregory Siragusa, Ph.D. No Comments
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.
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.
FDA Commissioner Scott Gottlieb, M.D., announced the next steps in their approach to implement the Produce Safety Rule that was established by FSMA. During the September 12th speech at the National Association of State Departments of Agriculture, Dr. Gottlieb outlined new measures the FDA will be taking, including compliance dates for agricultural water standards, recognized water-testing methods, and inspections related to non-water requirements of the produce rule.
According to the press release, Dr. Gottlieb also announced steps the FDA will take to “address concerns related to the complexity and feasibility of implementing standards for agricultural water.” One proposed rule concerning agricultural water compliance dates, if finalized, would extend compliance dates by up to four years for produce other than sprouts.
The press release states the reasoning behind this change is allowing the FDA to revisit those standards, ensuring they are implementable for farmers across the country. Sprouts are an exception here because of their high risk for contamination and will remain subject to original compliance dates.
The announcement also covered key changes to produce farm inspections, water testing methods and training opportunities for producers and regulators. For more information, see the press release here and the full text of Dr. Gottlieb’s speech here.
Learn more about FSMA implementation strategy at the 2017 Food Safety Consortium | November 28–December 1FDA has released a Small Entity Compliance Guide (SECG) to help small and very small businesses comply with the Produce Safety Rule. The SECG provides assistance for farmers in determining whether they are eligible for a qualified exemption and can help them understand the modified requirements as a result.
The compliance dates under the Produce Safety rule are as follows:
Small businesses: January 28, 2019
Very small businesses: January 27, 2020
Sprout operations: January 26, 2018 (small businesses) and January 28, 2019 (very small businesses)
There are also extended compliance dates for certain agricultural water requirements
Learn more about FSMA compliance at the 2017 Food Safety Consortium | November 28– December 1 | The 60-page draft guidance addresses the use of heat treatments as a process control, providing information on understanding potential hazards, design and validation of the heat treatment, establishing and implementing monitoring procedures (and how often), verification, and record keeping.
FDA states that it intends to publish at least 14 chapters of the guidance. In just two weeks, the compliance date for the preventive controls for human food rule falls for small businesses (fewer than 500 full-time employees).
By Gregory Siragusa, Douglas Marshall, Ph.D. No Comments
This month we are happy to welcome our guest co-authors and interviewees Eric Brown, Ph.D. and Marc Allard, Ph.D. of CFSAN as we explore the FDA’s GenomeTrakr program in a two-part Food Genomics column. Many of our readers have heard of GenomeTrakr, but are likely to have several questions regarding its core purpose and how it will impact food producers and processors in the United States and globally. In Part I we explore some technical aspects of the topic followed by Part II dealing with practical questions.
Part I: The basics of GenomeTrakr
Greg Siragusa/Doug Marshall: Thank you Dr. Allard and Dr. Brown for joining us in our monthly series, Food Genomics, to inform our readers about GenomeTrakr. Will you begin by telling us about yourselves and your team?
Eric Brown/Marc Allard: Hello, I am Eric, the director of the Division of Microbiology at the U.S. Food and Drug Administration at the Center for Food Safety and Applied Nutrition. Our team is made up of two branches, one that specializes in developing and validating methods for getting foodborne pathogens out of many different food matrices and the other branch conducts numerous tests to subtype and characterized foodborne pathogens. The GenomeTrakr program is in the subtyping branch as Whole Genome Sequencing (WGS) is the ultimate genomic subtyping tool for characterizing a foodborne pathogen at the DNA level.
Hello, my name is Marc, I am a senior biomedical research services officer and a senior advisor in Eric’s division. We are part of the group that conceived, evaluated and deployed the GenomeTrakr database and network.
Siragusa/Marshall: Drs. Allard and Brown, imagine yourself with a group of food safety professionals ranging from vice president for food safety to director, manager and technologists. Would you please give us the ‘elevator speech’ on GenomeTrakr?
Brown/Allard: GenomeTrakr is the first of its kind distributed network for rapidly characterizing bacterial foodborne pathogens using whole genome sequences (WGS). This genomic data can help FDA with many applications, including trace-back to determine the root cause of an outbreak as well providing one work-flow for rapidly characterizing all of the pathogens for which the agency has responsibility. These same methods are also very helpful for antimicrobial resistance monitoring and characterization.
Siragusa/Marshall: From the FDA website, GenomeTrakr is described as “a distributed network of labs to utilize whole genome sequencing for pathogen identification.” We of course have very time-proven methods of microbial identification and subtyping, so why do we need GenomeTrakr for identification and subtyping of microorganisms?
Brown/Allard: If all you want to know is species identification then you are correct, there are existing methods to do this. For some applications you need full characterization through subtyping (i.e., Below the level of species to the actual strain) with WGS. WGS of pathogens provides all of the genetic information about an organism as well as any mobile elements such as phages and plasmids that may be associated with these foodborne pathogens. The GenomeTrakr network and database compiles a large amount of new genetic or DNA sequence data to more fully characterize foodborne pathogens.
GenomeTrakr and WGS are a means to track bacteria based on knowing the sequence of all DNA that comprises that specific bacterium’s genome. It can be called the “ultimate identifier” in that it will show relationships at a very deep level of accuracy.
Siragusa/Marshall: Is it an accurate statement that GenomeTrakr can be considered the new iteration of PulseNet and Pulse field gel electrophoresis (PFGE)? Will PulseNet and PFGE disappear, or will PulseNet and GenomeTrkr merge into a single entity?
Brown/Allard: PulseNet is a network of public health labs run by the CDC, with USDA and FDA as active participants. The network is alive and well and will continue subtyping pathogens for public health. The current and historical subtyping tool used by PulseNet for more than 20 years is PFGE. It is expected that CDC, USDA and FDA’s PFGE data collection will be replaced by WGS data and methods. That transformation has already begun. GenomeTrakr is a network of public health labs run by the FDA to support FDA public health and regulatory activities using WGS methods. Starting in 2012, this network is relatively new and is focused currently on using WGS for trace back to support outbreak investigations and FDA regulatory actions. CDC PulseNet has used WGS data on Listeria and collects draft genomes (i.e., unfinished versions of a final genome are used for quicker assembly) of other foodborne pathogens as well, and USDA’s FSIS has used WGS for the pathogens found on the foods that they regulate. All of the data from GenomeTrakr and Pulsenet are shared at the NCBI Pathogen Detection website (see Figure 1).
Figure 1
Siragusa/Marshall: Does an organism have to be classified to the species level before submitting to GenomeTrakr?
Brown/Allard: Yes, species-level identification is part of the minimal metadata (all of the descriptors related to a sample such as geographic origin, lot number, sources, ingredients etc.) required to deposit data in the GenomeTrakr database. This allows initial QA/QC metrics to determine if the new genome is labeled properly.
Siragusa/Marshall: After an isolate is identified to the species level, would you describe to the reader what the basic process is going from an isolated and speciated bacterial colony on an agar plate to a usable whole genome sequence deposited in the GenomeTrakr database?
Brown/Allard: The FDA has a branch of scientists who specialize in ways to isolate foodborne pathogens from food. The detailed methods used ultimately end up in the Bacteriological Analytical Manual (BAM) of approved and validated methods. Once a pathogen is in pure culture then DNA is extracted from the bacterial cells. The DNA is then put into a DNA sequencing library, which modifies the DNA to properly attach and run sequencing reactions depending on the specific sequencing vendor used. The sequence data is downloaded from the sequencing equipment and then uploaded to the National Center for Biotechnology Information (NCBI) Pathogen Detection website. The database is publicly open to allow anyone with foodborne pathogens to upload their data and compare their sequences to what is available in the database.
Siragusa/Marshall: Suppose a specific sequence type of a foodborne bacterial pathogen is found and identified from a processing plant but that the plant has never had a positive assay result for that pathogen in any of its history of product production and ultimate consumption. If an outbreak occurred somewhere in the world and that same specific sequence type were identified as the causative agent, would a company be in anyway liable? Could one even make an association between the two isolates with the same sequence type isolated at great distances from open another?
Brown/Allard: The genetic evidence from WGS supports the hypothesis that the two isolates shared a recent common ancestor. If, for example, the isolate from the processing plant and the outbreak sample where genetically identical across the entire genome, the prediction is that the two samples are connected in some way that is currently not understood. The genetic matches guide the FDA and help point investigations to study the possible connections. This might include additional inspection of the processing plant as well as linking this to the typical epidemiological exposure data. Sometimes due to the indirect nature of how pathogens circulate through the farm to fork continuum and the complex methods of trade, no connection is made. More commonly, these investigative leads from genetic matches help the FDA establish direct links between the two bacterial isolates through a shared ingredient, shared processing, distribution or packaging process. The genetic information and cluster helps the FDA discover new ways that the pathogens are moving from farm to fork. We are unaware of any example where identical genomes somehow independently arose and were unrelated. This is counter to molecular evolutionary theory anyway. Genetic identity equals genetic relatedness and the closer two isolates are genetically to each other, the more recent that they shared a common ancestor. With regard to liability, this is a topic beyond the scope of our group, but genomic data does not by itself prove a direct linkage and that is why additional investigations must follow any close matches.
Siragusa/Marshall: We know that SNPs (Single Nucleotide Polymorphisms or single base pair differences in the same location in a genome) are commonly used to distinguish clonality of bacteria with highly similar genomes. Are there criteria used by GenomeTrakr bioinformaticists that are set to help define what is similar, different or the same?
Brown/Allard: As the database grows with more examples of diverse serotypes or kinds of foodborne pathogens, the FDA WGS group is observing common patterns that can be used as guidance to define what is same or different. For example, closely related for Salmonella and E. coli are usually in the five or fewer SNPs, and closely related for Listeria is 20 or fewer SNPs using the current FDA validated bioinformatics pipeline. These values are not set in stone but should be considered more like guidance for what FDA and GenomeTrakr have observed already from earlier case studies that have already been collected and examined. Often, a greater number (e.g., 21-50) of SNP differences have been observed between strains isolated in some outbreaks. Any close match might support or direct an outbreak investigation if there is evidence that suggests that a particular outbreak looks most closely like an early case from a specific geographic location. WGS data helps investigators focus their efforts toward and international verses domestic exposure or possible country of origin. Even more divergent WGS linkages, when SNPs are greater than 50-100, often connect to different foods or different geographic locations that would lead investigators away from the source of an outbreak as the data provides both inclusivity as well as exclusivity.
When two strains have more than 50–100 SNPs, different food or geographic sources of those strains can be incorrectly linked resulting in investigators pursuing an incorrect source.
Siragusa/Marshall: Can SNPs be identified from different agar-plate clones of the same strain (i.e., Different colonies on the same plate)?
Brown/Allard: Since understanding the natural genetic variation present in foodborne pathogens is the basis to understanding relatedness, the FDA conducted validation experiments on growing then sequencing colonies from the same plate, colonies from frozen inocula, thawing and plating, as well as running the same DNAs on different instruments and with different sequencing technicians. The FDA’s work with Salmonella enterica Montevideo sequencing as well as ongoing proficiency testing among laboratories shows that the same isolate most often has no differences, although some samples have 1-2 SNP differences. Genetic differences observed in isolates collected by FDA inspectors all related to a common outbreak generally have more genetic differences, and this appears to be dependent on the nature of the facility and the length of time that the foodborne pathogen has been resident in the facility and the selective pressure to which the pathogen was exposed to in a range from 0–5 SNPs different.
Siragusa/Marshall: Regarding the use of WGS to track strains in a particular processing plant, is it possible that within that closed microenvironment that strains will evolve sufficiently so that it becomes unique to that source?
Brown/Allard: Yes, we have discovered multiple examples of strains that have evolved in a unique way that they appear to be specific to that source. Hospitals use the same practice to understand hospital-acquired infections and the routes of transmission within a hospitals intensive care unit or surgery. Food industry laboratories as well as FDA investigators could use WGS data in a similar way to determine the root cause of the contamination by combining WGS data with inspection and surveillance. The FDA Office of Compliance uses WGS as one piece of evidence to ask the question: Have we seen this pathogen before?
Siragusa/Marshall: The number of sequences in the GenomeTrakr database is approaching 120,000 (~4,000 per month are added). Are the sequences in the GenomeTrakr database all generated by GenomeTrakr Network labs?
Brown/Allard: The sequences labeled as GenomeTrakr isolates at the NCBI biosample and bioproject databases are the WGS efforts supported by the U.S. FDA and USDA FSIS. GenomeTrakr is a label identifying the FDA, USDA FSIS and collaborative partner’s efforts to sequence food and environmental isolates. Additional laboratories, independent and beyond formal membership in the GT network, upload WGS data to the NCBI pathogen detection website of which GenomeTrakr is one part. CDC shares WGS data on primarily clinical PulseNet isolates and USDA FSIS shares WGS foodborne pathogens for foods that they regulate. Numerous international public health laboratories also upload WGS data to NCBI. The NCBI pathogen detection website includes all publicly released WGS data for the species that they are analyzing, and this might include additional research or public health data. The point of contact for who submitted the data is listed in the biosample data sheet, an example of which can be seen here.
Siragusa/Marshall: Once sequences are deposited into the GenomeTrakr database, are they also part of GenBank?
Brown/Allard: The majority of the GenomeTrakr database is part of the NCBI SRA (sequence read archive) database, which is a less finished version of the data in GenBank. GenBank data is assembled and annotated, which takes more time and analysis to complete. Once automated software is optimized and validated, NCBI likely will place all of the GenomeTrakr data into GenBank. Currently, only the published WGS data from GenomeTrakr is available in GenBank. All of the GenomeTrakr data is available in SRA both at GenomeTrakr bioprojects and in the NCBI pathogen detection website.
Readers, look for the Part II of this column where we continue our exploration with Drs. Brown and Allard and ask some general questions about the logistics surrounding GenomeTrakr. As always, please contact either Greg Siragusa or Doug Marshall with comments, questions or ideas for future Food Genomics columns.
About the Interviewees
Marc W. Allard, Ph.D.
Marc Allard, Ph.D. is a senior biomedical research services officer specializing in both phylogenetic analysis as well as the biochemical laboratory methods that generate the genetic information in the GenomeTrakr database, which is part of the NCBI Pathogen Detection website. Allard joined the Division of Microbiology in FDA’s Office of Regulatory Science in 2008 where he uses Whole Genome Sequencing of foodborne pathogens to identify and characterize outbreaks of bacterial strains, particularly Salmonella, E. coli, and Listeria. He obtained a B.A. from the University of Vermont, an M.S. from Texas A&M University and his Ph.D. in biology in from Harvard University. Allard was the Louis Weintraub Associate Professor of Biology at George Washington University for 14 years from 1994 to 2008. He is a Fellow of the American Academy of Microbiology.
Eric W. Brown, Ph.D.
Eric W. Brown, Ph.D. currently serves as director of the Division of Microbiology in the Office of Regulatory Science. He oversees a group of 50 researchers and support scientists engaged in a multi-parameter research program to develop and apply microbiological and molecular genetic strategies for detecting, identifying, and differentiating bacterial foodborne pathogens such as Salmonella and shiga-toxin producing E. coli. Brown received his Ph.D. in microbial genetics from The Genetics Program in the Department of Biological Sciences at The George Washington University. He has conducted research in microbial evolution and microbial ecology as a research fellow in the National Cancer Institute, the U.S. Department of Agriculture, and as a tenure-track Professor of Microbiology at Loyola University of Chicago. Brown came to the Food and Drug Administration in 1999 and has since carried out numerous experiments relating to the detection, identification, and discrimination of foodborne pathogens.
In an effort to determine the prevalence of Salmonella, Listeria and E. coli O157:H7 in sprouts, FDA conducted a large sampling study of sprouts, the results of which were released last week.
The agency collected 825 samples from 37 states, Puerto Rico and the District of Columbia and found 14 positive samples at eight of the 94 growers (10 samples came from four growers). Samples were collected from three production process points: Seeds, finished product and spent irrigation water, and tested for contamination. FDA found the following contamination:
Salmonella on 2.35% of seed samples, 0.21% in finished sprouts and 0.53% in spent irrigation water
Listeria monocytogenes on 1.28% of finished sprouts
No positive E. coli O157:H7 results in finished sprout or spent irrigation. Due to limitations of the test method, FDA didn’t test seed samples.
“Sprouts are especially vulnerable to pathogens given the warm, moist and nutrient-rich conditions needed to grow them. From 1996 to July 2016, there were 46 reported outbreaks of foodborne illness in the United States linked to sprouts. These outbreaks accounted for 2,474 illnesses, 187 hospitalizations, and three deaths.” – CFSAN
In the event that contaminated sprout samples were uncovered, FDA worked with the firms that own or released the affect sprouts to conduct voluntary recalls or destroy them. FDA inspections also followed.
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