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  1. New Era of Smarter Food Safety TechTalk Podcast

TechTalk Podcast Episode 2: Whole Genome Sequencing in the New Era of Smarter Food Safety

New Era TechTalk Episode 2: Whole Genome Sequencing in the New Era of Smarter Food Safety Panel
From left to right: Afreen Malik (Western Growers), Shari Shea (Association of Public Health Laboratories), William Wolfgang (New York State Department of Health)

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The second installment of FDA’s new podcast series on technology and food safety focuses on whole genome sequencing (WGS).

This quarterly podcast explores the potential for novel technological approaches and solutions in each of the core elements in the New Era of Smarter Food Safety Blueprint.

The second Core Element, called Smarter Tools and Approaches for Prevention and Outbreak Response, includes goals to achieve a more rapid response to outbreaks of foodborne illness. These goals include facilitating opportunities to speed whole genome sequencing of pathogens by public and private laboratories, and working with international, federal, state, and academic partners to increase the number of labs that can submit sequences of parasites, pathogens and viruses isolated from food samples via FDA’s GenomeTrakr.

In this second podcast, Mark Moorman, Ph.D., director of FDA’s Office of Food Safety, and Eric Brown, Ph.D., director of the Division of Microbiology in the Office of Regulatory Science at FDA’s Center for Food Safety and Applied Nutrition, lead a discussion with top experts in food safety and public health on subjects that include the potential of WGS to transform food safety, how the capacity for its use can be increased across all sectors of the food safety stakeholder community, and how more opportunities for its use can be made available to all laboratory communities.

The experts:

  • Association of Public Health Laboratories: Shari Shea, Director of Food Safety
  • Western Growers: Afreen Malik, Science Programs Director
  • New York State Department of Health: William Wolfgang, Division of Infectious Diseases

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TechTalk Podcast: Episode 2 – Transcript

Frank Yiannas

Welcome, everyone, to the second episode of TechTalk, which is going to focus on the role of whole genome sequencing today and its role in the New Era of Smarter Food Safety. Thank you for joining us. I'm really excited about today’s session.  My name is Frank Yiannas, FDA Deputy Commissioner for the Office of Food Policy and Response.  In this podcast series, we are focusing on technology and how it can be used by FDA, along with others in government, academia, and industry, to help what I call “bend the curve” of foodborne illness in this country once and for all. And we’re doing that. And we're going to do that.

Our first podcast looked at Tech-enabled Traceability, the first of four core elements in FDA's New Era of Smarter Food Safety blueprint, which we issued one short year ago. In today's podcast we’re going to focus on the second core element called Smarter Tools and Approaches for Prevention and Outbreak Response. This core element covers a lot of ground if you’ve read our blueprint.

So today we’re going to focus on the increased use of whole genome sequencing in both the public and private sectors and what they might mean to food safety. Let me begin with what is one of my favorite questions that I like to ask audiences all over the world when I present at conferences. That question is this:  Name the No. 1 thing you think has advanced food safety in the 21st century -- the No. 1 thing that has advanced food safety in the 21st century.  When I ask that question literally at international audiences all over the world, I get some interesting answers. Some say it’s HACCP -- Hazard Analysis of Critical Control Points, invented by NASA and Pillsbury, which we all know has been critical to helping companies better manage food safety risks. At times I hear people say more modern regulations such as the Food Safety Modernization Act or FSMA. I've also heard answers from microbiologists such as rapid microbiological testing of foods that has taken food safety from the petri dish and allowed us to obtain results in almost real-time or more realistic time frames.

And while I think all these answers are good and, clearly, I believe they probably all play a role in advancing food safety, my favorite answer is these three short letters: “WGS.” Before that it was “PFGE,” or Pulsed-field gel electrophoresis – the predecessor to WGS. Now why do I feel that way? Well, it’s this idea that we can increasingly detect what might have previously appeared to be sporadic or unrelated illnesses across the country. Because of these genetic sequencing techniques, now we know that these seemingly unrelated illnesses are increasingly having something in common. Oftentimes in our investigations, we find out that it’s a common food.  In other words, I like to say that whole genome sequencing has increasingly allowed us to make the invisible visible -- and that’s a good thing.  It has allowed us to detect outbreaks that might have previously gone undetected. It has allowed us to discover outbreaks linked to novel foods. I think without question it has allowed us to identify outbreaks earlier in their epidemic curve and prevent additional illnesses.

I'm pretty excited about today's topic. I’m going to turn this over to our experts. FDA has been at the forefront of encouraging the use of WGS in government labs at the state, federal and international level.  That work as I understand it has dated back to 2008, years before I actually joined the FDA. Fortunately, today you’re going to hear from someone who has been here from the beginning:  Eric Brown, Director of the Division of Microbiology in CFSAN’s Office of Regulatory Science.  He has passionately pioneered this important work since Day One. Joining him you will hear from Mark Moorman, another expert who directs our Office of Food Safety in FDA’s Center for Food Safety and Applied Nutrition and who also leads CORE Element 2 of the blueprint. Together they will lead what I believe is going to be a fascinating and useful discussion. They will also engage top experts from outside the FDA on the potential of WGS to transform both food safety detection and food safety prevention (detection and prevention of contaminants).  At the end of the discussion, I look forward to returning and sharing some of my key takeaways, which I’m sure will be quite a few. Before I do, I would love to begin by asking both Mark and Eric, to explain, in a few short sentences, what they see is the vital role that WSG plays in the foods arena. Mark?

Mark Moorman

Thanks, Frank. Before I start let me say to everyone who is new to this topic of WGS: We are talking about whole genome sequencing.  This is just that.  It’s the whole genetic sequence of bacteria. Just like everybody listening, if we sequenced everybody’s genetic material, we would all be proven different. And we now have the ability to do that same thing with bacteria. This is a new tool in the microbiologists’ toolbox. It gives us just profound ways to understand relationships of pathogenetic microorganisms related to foods and outbreaks. Really, the beauty of this, and the power of this -- because we’re talking about genetic sequences in the form of data – is we have the ability to capture and share that information globally at the click of the mouse. 

So, in answer to your question Frank, this gives a couple of groups powerful tools: First the public health community, it gives them a tool to attribute patient illness to foods.  Just as important it gives another group, the entire discipline of food microbiology -- we’re talking academia, industry, testing labs -- an amazingly powerful tool to determine the ecology or the movement of these microorganisms and how these strains of public health significance, or spoilage relevance, find their way in and around foods.

Frank Yiannas

Thanks, Mark, I cannot agree more. Eric, what do you have to say?

Eric Brown

Absolutely Frank, building on what Mark said, the thing about whole genome sequencing is it actually collects all of the DNA codes inside of bacteria. Because of that fact, it has the power to differentiate virtually all strains of foodborne pathogens no matter what the species. The best part, it discriminates between really closely related organisms. It can quickly point to the specific geographic locale of the pathogen, and it also points to a pathogen’s likely point of origin.  And the result of this, we can now identify the source of an outbreak sooner and avoid additional illnesses and possibly even deaths. Also, in the spirit of the New Era Initiative I just want to add that whole genome sequencing has really given us insight into root cause analysis where there is recurrent contamination on a farm, or a food facility. It is like Mark said, whole genome sequencing is a really special tool. We’re really excited to talk about it today. Thank you.

Frank Yiannas

Thanks, Eric. You see this will be a very interesting session. I will let you guys take it away from here. See you on the other side.

Mark Moorman

Thanks, Frank, we're really excited and fortunate today to be joined by some experts who will help us unpack all this. Bill Wolfgang is with the New York State Department of Health Division of Infectious Diseases. We also have Shari Shea, who’s the Director of Food Safety with the Association of Public Health Laboratories, or APHL.  And Afreen Malik, who’s the Science Program Director with the Western Growers, which represents farmers in Arizona, California, Colorado, and New Mexico. 

Bill, Sherry, Afreen, thank you for joining us.  Before we get into the WGS of the future let’s begin with a brief overview of WGS of today, and really how we got here.  Let’s start with Bill. The State of New York was an early adopter of WGS.  I would be interested in knowing what was your “wow moment,” where New York said there is something special here and realized the technology would be a game changer in food safety.  Can you talk about that?

Bill Wolfgang

Sure, Mark. Before I do, let me thank Mark and Eric for the opportunity to participate in this podcast. This is simply an extension of a long collaboration we have had with FDA in our work to improve food safety. The collaboration started in 2012. It’s a collaboration I value very much for a lot of reasons. It’s really been a terrific ride and I appreciate your support over all these years.

So, what was our “wow moment?” Too often in science there’s not really a “wow moment,” it’s really gradual.   But in this case I can actually point to a “wow moment” when I read two papers in 2011, one by Marc Allard's group out of CFSAN and the second by Martin Wiedmann’s group from the Food Safety Lab at Cornell. What they showed in these papers was that for the outbreak of Salmonella montevideo associated with black and red pepper and dried meat products, that WGS provided a far higher resolution than the current gold standard at the time, which was what we were using in our labs of course, PFGE. This increased resolution allowed them greater information to be passed on to epidemiologists to address issues of traceback and source attribution.

Coincidentally, at that time, we had also just purchased our first high frequency sequencer capable of sequencing a bacterial genome in the time frame and at a cost that was suitable for surveillance. This hadn’t existed before 2011. With these two pieces of information and our new tools we set about to sequence a Salmonella outbreak associated with cannoli consumption in a long-term care facility. This was an outbreak of Salmonella enteritidis, the most common serotype, and the PFGE type was also extraordinarily common. The epidemiologist had a slam dunk here. Someone was very nice, they brought cannoli in for their aging parents into the facility. And a number of residents became ill. But the PFGE was of no use whatsoever. It was so general and so common. Half of the isolates at the time identified by PFGE were the same.  So, it could not provide additional information.

When we used WGS to look at this outbreak, we saw that indeed, the patients were all closely related at the long-term care facility but remarkably, there were people outside the care facility in the surrounding community -- about twice as many people -- who also had the same clone of Salmonella enteritidis. Therefore, WGS would have allowed us to expand the outbreak investigation had it been available at that time. As Frank mentioned earlier, this was a clear case of making the invisible, not visible.

With this data under our arms, Dr. Kimberly Musser and I traveled to CFSAN where we were invited to present our findings to the GenomeTrakr folks there. We did not know this at the time, but Marc (Allard) and Eric got us aside after the presentation and asked us to join the GenomeTrakr collaboration.  “We’ll get you a sequencer, support you with reagents, and also provide, importantly, training.”   Of course, we said yes, and we have not looked back since. It has been a wonderful collaboration. We are very grateful for the opportunity to work with FDA on this project.

Mark Moorman 

Fantastic, Bill, thank you. Let’s change gears for a minute and talk about how laboratories think about this. There is the FDA's GenomeTrakr, which is a distributed network of laboratories that use whole genome sequences to identify the foodborne outbreaks.  Shari, you and the APHL have played an enormous role in expanding the GenomeTrakr network in the states since it was launched in 2012.  Can you talk about why this is a such a priority for APHL, and what you see as the outcome?

Shari Shea

Thanks Mark for the opportunity to be part of this discussion. A pleasure to be with this group today. APHL has been a strong proponent of the GenomeTrakr from the very beginning.  WGS was bringing revolutionary changes to microbiology, including public health microbiology. And the state laboratories were going to miss the boat without rapid deployment of resources, personnel, training, and equipment -- some of the things Bill just mentioned -- not to mention huge issues around data. Adequate ways to handle big data were almost nonexistent in 2012 in a public health setting. Remarkably, from 2010 to 2015, the United States went from zero states owning a sequencer to 37 laboratories with instruments, thanks to federal investment and state partners. Shortly thereafter, every state, even many local laboratories, were sequencing foodborne pathogens.

Honestly, we can look even beyond food safety. That early buildup of sequencing capability meant our country was more prepared to sequence SARS-CoV-2 in response to the ongoing pandemic -- a pretty clear example of having the right priorities at the right time. Yes, GenomeTrakr, along with CDC's PulseNet network have been course-changing for our APHL members. One could say the inclusion of state laboratories in the GenomeTrakr network since the very beginning was key to the success of the network. From that starting point, FDA's eagerness to collaborate with APHL, the state laboratories, so many other partners in private and academic settings ensured in my mind, the maximum impact of all of our work together.  We of course hope that APHL’s work in support of network provides a better GenomeTrakr experience for the states and the team at FDA.  This is all a great example of what mutual reliance looks like.

I also went to mention quickly the role of NCBI (National Center for Biotechnology Information) where the publicly available database is held.  Our members very must appreciate the NCBI pathogen detection browser as a fundamental tool for public health surveillance.   Really, as we see things by leveraging GenomeTrakr collaboration with the food industry and people like Afreen, FDA can provide data on safe growing and manufacturing processes that can inform risk attribution. Most importantly, we decrease the burden of foodborne illness that is really the outcome all of us working in public health are looking for.

Mark Moorman

Excellent, thank you, Shari.  We’ve heard from the public health lens of this, and the laboratory lens, I want to move to an application side of this.  Afreen, you think a lot about applications with your work within produce and food processing. I’d like to get a sense from you as to how widely is this technology understood in industry, and for those that have adopted it, how are they using it?

Afreen Malik

Good morning, Mark, and everyone else, it is a pleasure to be here with everyone. I appreciate the opportunity to participate in this discussion. To answer your question, Mark, I will begin with stating that whole genome sequencing is of great interest to the produce industry. We are all talking about it and trying to understand what it means and what it can tell us.  This becomes particularly important during outbreak investigations when a link is made between a clinical isolate and a suspected fruit vehicle and the subsequent root cause investigation that occurs.

Despite this interest, whole genome sequencing is not widely used in the produce industry. There are many reasons for this, right? So first, whole genome sequencing, in many cases, is not the best suited tool for a lot of the testing we are currently conducting. There are other simpler and more familiar subtyping tools that are sufficient for our needs. But when whole genome sequencing is used, it is more often applied within facilities, not open field agriculture, for things like root cause analysis or to study microbiomes in a particular environment, or to study spoilage of bacteria for shelf-life analysis, for example.

There are many reasons for this somewhat low adoption of whole genome sequencing in the produce industry. The most obvious reasons have to do with cost and the amount of time it takes for whole genome sequencing compared to other more familiar methods available to the produce industry. With fresh perishable products the shelf-life is often no greater than 14 days.  The time of sampling to results is too long for whole genome sequencing. Waiting one week, for example, is not practical in the produce industry. There are other, more significant hurdles as well, to the use of whole genome sequencing. So, although I think it is generally recognized that whole genome sequencing is a powerful tool, it requires a level of understanding and expertise that is generally lacking in the industry at present.

We are slowly overcoming this hurdle through external partnerships to help us understand the terminology, methodologies, and the interpretation of whole sequencing data and dispel some of the misconceptions surrounding whole genome sequencing. Even with outsourcing, you still need some level of expertise in-house.

To add to this, there are regulatory and legal issues an operation must consider before using the tool that may potentially link their operation to a past outbreak. Using whole genome sequencing could potentially expose an operation to some risk, such as a recall, or even a lawsuit. There are a lot of challenges to broad adoption of whole genome sequencing in the produce industry.

I think these challenges will take time to overcome. I think the FDA certainly has a role to play in making the adoption of these technologies easier in the produce industry. One way to do this, I think, besides addressing the uncertainties around the regulatory burden would be to maybe change the context around whole genome sequencing. What I mean by this is maybe we can provide some examples to show how whole genome sequencing might be used to exonerate product in a foodborne outbreak. This positive context may increase confidence in the use of whole genome sequencing. The FDA could also help by adding some more transparency to the NCBI database. Currently, there is very limited meta-data associated with isolates and it lends itself very well to speculation. With more transparency I believe the database could be more useful.

Mark Moorman 

Excellent. Afreen, thank you very much, I appreciate this.  Eric, over to you.

Eric Brown 

Thank you, Mark, thanks everyone for the first round. Very nice. I would like to start with the second round of questions and really turn our attention now to a subject near and dear to the New Era initiative and that is root cause analysis. How can WGS help state and industry laboratories identify causes and sources of contamination?  Again, we would like to start off with Bill. Bill, the State of New York was not only an early adopter of WGS, it also was one of the first state partners to join the GenomeTrakr network, which you pointed out a moment ago.  My question is, how does this technology really advance root cause analysis for your public health mission and outbreak response work?

Bill Wolfgang

Thanks, Eric. As I mentioned previously, we could reveal relationships that were not present before using whole genome sequencing. Now, I want to move to an example of how we can use whole genome sequencing to distinguish between persistent contamination at a facility by a single clone (a single recurring pathogen stain that is genetically identical) from its repeated introduction. In this example, from June 2014 to April 2019, over a five-year period, Wadsworth received nine clinical and 10 environmental samples of Listeria monocytogenes linked to a food preparation and delivery establishment. Over that time, the PFGE pattern remained the same for all those samples. Because of the low resolution of PFGE, it wasn’t possible to say that the same type of PFGE wasn't just being reintroduced repeatedly from an outside source.

Your efforts at remediation would be very different whether it was persisting in the facility or whether it was being reintroduced. Once WGS technology was brought to bear on the problem, we could unequivocally demonstrate that the same clone of Listeria was repeatedly contaminating the food produced by the service over that five-year period, ruling out -- or at least indicating a very low likelihood -- that a pathogen was being reintroduced during this long timeframe.

Lessons we learned and others of course learned from similar studies is that long-term surveillance by WGS can identify outbreaks resulting in persistent contamination by the same clone over many years. As always, WGS data must be considered in the context of epidemiological data. In this case, it was a single food facility, with a single genetic clone of Listeria indicates long-term persistence at the facility and not sporadic re-introductions. I would also add that after extensive remediation, we have seen no further outbreaks associated with this facility.

Eric Brown 

Fantastic, thank you. Shari, let's build on the great information that Bill just gave.  Let’s talk a little bit more about root cause analysis and pathogen source-tracking, which is a sweet spot for this technology. From your position you can see the entire enterprise across the states.  How do you see whole genome  sequencing being utilized by our state partners in the regular workflow? Maybe even show an example where we have seen it expedite identification of the source of a foodborne outbreak from one of your state or federal stakeholders. Thank you.

Shari Shea 

Great question, Eric, thanks. There are many use cases for whole genome sequencing in the public health setting. We can look at environmental exposures from pathogens such as Cryptosporidium or Legionella.        We can perhaps follow transmission pathways, perhaps hospital-acquired infections and prevent their spread. We can even predict how pathogens might become resistant, stopping emerging pathogens like resistant tuberculosis or Salmonella infantis before they wreak havoc on human health. Whole genome sequencing has transformed the investigation of infectious disease broadly just as it has improved the safety of our food supply. Of course, there are costs involved with all of this. The sequencing, transformation, affects the entire laboratory in our enterprise, not just one department. Also, we must take into consideration sustainability, workforce development, financial input.  So much thought and planning goes into this at a state laboratory.

As for an example, many states have effectively used sequencing to expedite large outbreak investigations, like the ones that might be in the news, as well as local investigations. It can help with small restaurants in a group of practices. One investigation involving the state of Rhode Island was pretty interesting. I think it was an early 2019 outbreak of E. coli O26 that grew to 21 cases in nine states.  Early case interviews during the investigation were pointing to contaminated all-purpose flour. In an unopened bag of that implicated flour, the Rhode Island public health laboratory found a genetic match to patient isolates, that connection later supported by product distribution records. Whole genome sequencing was crucial during this investigation as the PFGE patterns historically correspond to ground beef. In this case the health professions could easily delineate the outbreak-related isolates using the whole genome sequencing technology, bringing that outbreak to an end with minimal illnesses – and also limiting the economic impact on the producer, the important thing you brought up, Eric, at the beginning of the talk.  I think examples like these demonstrate that investment in whole genome sequencing technology at the state level, along with IT infrastructure and bioinformatic support behind it, are having far-reaching effects on food safety.

Eric Brown

Thank you, Shari.  My last question is for Afreen.  For sure, one of our New Era efforts is to increase the adoption of root cause analysis by industry. You touched on this a bit in your last answer. Let's drill down a little bit more on the importance of whole genome sequencing in RCA or root cause analysis.  I have a two-part question for you:  To what extent do produce growers and producers really see whole genome sequencing as a valuable tool in root cause analysis? Second, do large and small growers think of it and use it in similar ways or different ways? Do you see a difference there in the size of industries that are using it?

Afreen Malik

That's a great question. As I mentioned previously, the industry already sees the value of whole genome sequencing as a tool for root cause analysis and pathogen-forward striking. For example, one of the ways that whole genome sequencing is currently being used is in environmental monitoring programs within produce facilities to determine if recurring positives for a pathogen in an area is a transient contamination or resident strain. Other uses have to do with risk assessments on a farm. For example, if your farm is adjacent to a risk factor, such as a composting facility or concentrated animal feeding operation, how does this risk factor affect the microbiome within your farm as compared to a farm that doesn't have these adjacent risk factors?  Whole genome sequencing can be useful in these types of scenarios.  And it is currently being used by the produce industry in this way.

To answer the second part of your question, I think there is certainly a difference in how this tool is currently being used and applied by larger versus smaller operations. The use of whole genome sequencing requires specific resources.  We touched on this previously -- specific resources, both in terms of understanding how the testing works and how to interpret the results. These resources are generally more available in larger operations. Therefore, whole genome sequencing is more likely to be adopted by larger operations first.  I think, it is important to note, there are mechanisms to exchange such information between operations of different sizes through the supply chain that can facilitate the adoption of whole genome sequencing by smaller operations, over time.

In addition to the size of operations, there’s another layer in terms of variation and use of whole genome sequencing by the produce industry. As mentioned earlier, whole genome sequencing is being used in processing and packing facilities more than in the farm environment. This makes sense. When you think about the variables in a facility versus those in the open field environment. We have much more control in a closed facility environment than we do in the open farm environment. That's where the application of whole genome sequencing is being applied the most -- in the facility. But irrespective of the size and type of the operation, I think everyone understands that whole genome sequencing is a game changer and that it is something we really need to pay attention to in the produce industry.

Eric Brown

Thank you, Afreen. Mark, back to you. 

Mark Moorman

Excellent. Thank you, Eric. We have heard a lot about this today, about the current use of whole genome sequencing.  I want to pivot now to what the future looks like. We heard about how the New York State Department of Health has integrated WGS into its food safety surveillance response program.  Bill, I’m wondering how is it transforming the Department of Health's work for other public health areas involving outbreak surveillance and traceback? Can you talk to that?

Bill Wolfgang

Absolutely, Mark. As we have seen so clearly in the last year and a half, for public health laboratories the future can be uncertain. While we cannot predict the future of public health developments, we can prepare for them by having on hand cutting edge technologies. This is just exactly what happened at Wadsworth when COVID hit. We were already sequencing large numbers of isolates for various surveillance activities. It was not difficult to pivot and start to sequence COVID.  I believe we started sequencing in late March, after the shutdown in the middle of March. We have now sequenced, over 13,000 COVID genomes as a result of our activities there.

Apart from COVID, we're also working to extend our technologies and expertise to other foodborne pathogens such as Clostridium perfringens and Bacillus cereus and we are thinking of moving into Yersinia enterocolitica. We have also started to look at the population structure for Listeria monocytogenes in New York State. The process of building a comprehensive genomic database of all Listeria genomes. There will be approximately 2,500 of them collected since 2000 to now received by us and three other collaborating New York State institutions. We hope such data will aid our epidemiologists, and this is a work in progress, by answering some questions:  Are outbreaks local or are pathogens frequently imported?  Do we see new sources? Or exposure hazards? Are genetic types regionally localized? How many clusters do we see? How many clusters have we missed through our current surveillance system? By learning from the past and finding the answers to these sorts of questions, we hope to aid our epidemiologists in future investigations. Finally, application of WGS technology to foodborne diseases was first in our lab, absolutely. But it certainly will not be the last.  We have now extended that approach to surveillance in Legionella, TB, and other hospital acquired infections particularly those related to antimicrobial resistance, and viruses in addition to COVID.

In fact, I think it is a little immodest to say but in many of these areas we are acting as national leaders in these investigations. For Wadsworth, and other federal and state laboratories, I do not think there is any turning back.  There is no indication that we will slow down our sequencing. If anything, it will keep ramping up. We have just bought additional robotics to increase our throughput, as well as additional machines. Starting from a single FDA-supported MISEQ WGS instrument we have over the past nine years acquired through other funding sources 10 additional high frequency sequencers, and commensurate increases in in staff. For us, anyway, WGS, is our future.  We are certainly trying to pursue it vigorously.

Mark Moorman

Excellent, Bill. Thank you.  Shari, you heard Bill say there is no turning back. APHL has been essential to the expansion of the GenomeTrakr network. In building on what Bill said, what new directions are our next steps? What would you like APHL to see from the GenomeTrakr network?  If it could be expanded, what new scientific or application-based areas do you think would be most important to the states?

Shari Shea

Sure, Mark. First, let me say, I agree with everything Bill just said. He raises great questions, and his successes are examples of why we at APHL are so happy that the FDA leadership includes GenomeTrakr in the New Era for Smarter Food Safety blueprint.  We also appreciate the funding opportunity available through FDA’s new laboratory flexible funding model and the new GenomeTrakr laboratories joining the network through that mechanism.  That said, we do see areas for growth. I mentioned big data already.  The public health data infrastructure is struggling to handle the data produced by modern technologies like whole genome sequencing.  We are often using inefficient systems that hinder the flow of information.  We hope FDA can invest heavily to improve infrastructure from hardware and data flow to the bioinformatics workforce. Additionally, the bioinformatics pipeline should be as pushbutton as possible with tools to help states use markers like virulence factors and antimicrobial resistance genes that impact regulatory action and outbreak investigations in real time.

We like to see partnerships between state laboratories and academic institutions, like the ones that participate in the GenomeTrakr.  Such linkages can lead to sharing of bioinformatics capacity, perhaps specimen collection, and expertise in complex data analysis. More broadly, clinical microbiology is undergoing a different major revolution.  Diagnostic tests that use nucleic acid-based methods called culture independent diagnostic tests are making it possible for physicians to quickly obtain information about what is making their patient sick, which is great. We all want that, of course. But this shift impacts networks and systems that are based on genomic comparison of isolates.  Development of meta-genomic approaches – those that allow us to characterize pathogens directly through specimens -- will speed up the foodborne illness surveillance process. And the same could be said about food samples. Approaches such as amplicon sequencing and shotgun genomics, and others, are being explored, all with the potential to significantly increase speed and effectiveness of investigation.

One final thought comes to mind here, to acknowledge that addressing systemic improvements in the food safety system is an ambitious undertaking. APHL is really excited to see FDA advancing the conversation. We look forward to working together to make the food supply safer through strong science, data analysis, and smart regulation.

Mark Moorman

Thank you, Shari.  Let's move over to Afreen to talk about the application of this and your crystal ball moment. What do you think are the important questions in the world of produce in the processing space, that we will be answering in the next three or five years, using WGS technology?  You mentioned before, about the cost, the challenges associated with this industry. I’ll flip this to say, if you had a magic wand, and plenty of resources, dollars, people to do it, what would you like to see done with the WGS technology within the industry?

Afreen Malik

(laughter) Yeah, if I had a magic wand, I would take away all those hurdles, right? Whole genome sequencing can definitely help with us answer key questions related to the presence of hazard-associated risks in fresh food produce growing, harvesting, packaging environment, questions from a One Health perspective. How does the health of the environment impact the crops that we cultivate in that environment? How do animals and animal agriculture adjacent to or near plant crop production areas impact the safety of these fresh produce crops? How do pathogens move within the production environment? How long do they persist? What contributes to their environmental persistence? What other vehicles of transmission that we haven't considered?

I think whole genome sequencing can help us answer these and other important questions. There is ongoing research in this area to fill the knowledge gap. I'm also hopeful that we can address some of the uncertainties around the legal and regulatory implications in the near future. This is a significant barrier to widespread adoption of whole genome sequencing in the produce industry.  I often read about how whole genome sequencing helped implicate an operation in a foodborne outbreak. I wonder if there are examples, we could share with the industries that highlight the opposite -- when whole genome sequencing helped to clear a company of any wrongdoing.  This might help boost confidence in this powerful tool.

Lastly, I would aim to educate the industry on what whole genome sequencing can and cannot cover and dispel some of the misconceptions around whole genome sequencing.  I believe this would encourage the adoption of this tool, and root cause analysis and risk assessment, to prevent foodborne illness and protect public health. This is our goal here at Western Growers.

Mark Moorman 

Afreen, thank you, thank you very much. Eric, over to you.

Eric Brown

Thank you, Mark. I really want to think our guests so much today. I really appreciated all of the insightful answers and comments from our three experts. As promised when we started today, I will now circle back to Frank Yiannas and ask about his thoughts on today's discussion.  Frank, what are your key takeaways?

Frank Yiannas

Thanks Eric.  That is a tough task. There is so much great information. There is so much to unpack. As I listened very intently, I summarized three high-level takeaways that I would like to share with the audience. For me, number one, it was that WGS is a game changer for prevention.  WGS is a game changer for prevention and I’m underlining prevention because on the surface, many think WGS is intended for public health labs as a detection tool, not necessarily prevention.  But I think we’ve heard very clearly today that prevention and detection are not necessarily linear but a circular relationship. Better detection has clearly led to better prevention. We are just scratching the service.  That is what is so exciting. We might couple WGS with big data to look at trends over time.  These are questions we don't know about how pathogens move. It is a game changer for prevention.

The other thing I was struck by was just wait until we couple WGS with other technologies.  For example, WGS is allowing us to increasingly find the needles in that haystack. But we still struggle with the haystack at times at production facilities for the foods.  When we couple WGS with new and emerging technology such as real-time traceability – how that will really accelerate our ability to prevent further illnesses.  That is my first takeaway. 

The second one is I’m struck by this analogy. I've always believed this. You really made this a little bit clearer to me, today. Number two is that food safety is a race. WGS is illustrating this. Between our ability to detect foodborne illnesses and link cases together and our ability to prevent them. While we have all looked at the incidence of a foodborne disease over the past couple decades, by and large, we’ve said it’s flat and we’re not making progress.  Some of that is clearly because we are getting better at detecting foodborne illnesses, that is a good thing. But we cannot use that as a crutch. And if you heard today's conversation, you walk away saying we have to accelerate prevention. Just like the public health infrastructure has leveraged new approaches and new technologies such as WGS, we can do the same to accelerate prevention and win the race. And bend the curve on foodborne illnesses.

I was struck by when I was in the private sector -- many of you know I was in the private sector until not too long ago -- I was convinced that if I think I’m going to do food safety today the way I did it last year, I’m probably falling behind. Food safety is a race; we have to accelerate prevention.

My last takeaway is that WGS is a useful tool for both the private and public sector. I’m emphasizing the private because it is often talked about in the context of the public sector. You have heard how it is been used clearly to detect outbreaks and illnesses.  You also heard it could be and has been a useful tool for industry. In special applications, we heard that certainly for root cause analysis, for expiration of niches in the food processing plant, for expiration of closing knowledge gaps of how pathogens migrate outside. I would encourage the private sector to really step up, learn more about WGS.  Make sure that it is one of the tools that they add to their toolbox.

With that, I want to thank our co-hosts, who did a fabulous job, and our guests, a really impressive group of experts. I want to thank each and every one of you for tuning in. Please visit our TechTalk podcast page on FDA.gov on the next installment. And subscribe to this series. With that, until next time. Thanks, for listening.

     

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