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

Part II: Logistics of GenomeTrakr

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Read on to page two below.

Food Safety is Key Initiative as FDA Develops Lab Testing Standards

When President Barack Obama in 2011 signed the Food Safety Modernization Act, the most sweeping reform of American food safety laws in more than 70 years, the Food and Drug Administration’s job got a lot tougher.

As the FDA’s Palmer Orlandi explained at Pittcon [on March 9], they might need your help to get that job done. Orlandi, who spoke as part of the two-day Food Safety Tech Food Labs Conference at Pittcon, is the agency’s  acting chief science officer in the office of food and veterinary medicine. The FDA traditionally has been very good at reacting to safety issues in our food supply as they arise and finding the source of the problem, Orlandi said. But, now the agency is charged with more of a preventive role, which means identifying the biggest risks before they become a threat to the public. That’s a big job, and the FDA can’t do it alone. “We’re looking for burden-sharing,” Orlandi said.

Partnerships with other federal agencies such as the Department of Agriculture and the Department of Homeland Security are part of the solution. They’re also working with state-level laboratories and even the private sector, he said. As an example, he cites the Food Emergency Response Network, which includes food-testing laboratories at the local, state, and federal levels. Initially formed to deal with bioterrorism threats, Orlandi said it has become a useful food safety network as well. FERN-affiliated labs recently tested 1,600 samples of avocados for salmonella and listeria, he said.

Much of the burden of this new preventive approach will fall on food producers. Orlandi said FDA is willing to work with private labs to develop standards. This can be tricky, however, because the agency doesn’t want to create the impression that it is somehow favoring one private sector entity over another. Meanwhile, private companies have their own trade secrets to protect. “Where is the middle ground where we can cooperate?” Orlandi asked rhetorically.

FDA has developed validation standards that field labs can use, he said. But, he concedes, the agency hasn’t done a good job compiling and publishing those standards into an accessible document or reaching out to stakeholders to make sure they’re up to speed. “That’s another thing on our to-do list,” he said.

Funding for these efforts is scarce. Joe Konschnik, a market research manager for Restek Chromatography Products who attended Orlandi’s presentation, helps to supply scientists working in College Park, MD to develop new procedures to analyze pesticides. Traditionally, once the research is published, the researchers’ jobs are over. Konschnik says now they’re trying to send the information out to other labs in the U.S. and overseas. That way, everyone can work from the same page to validate the work and create consistent standards.

One of the problems is that, for example, aerating seeds to run multilevel validation studies can cost $35,000, he said. But the FDA only has about $75,000 to fund such studies, which obviously would run out very quickly. “There’s no money to fund the back-end stuff,” Konschnik said. He said he works with the American Council of Independent Laboratories, which is willing to do the testing for free. But it still costs money for the FDA to make samples, send them to the labs, gather the data, and validate the data.

In short, the partnerships FDA is building remain a work in progress. But it has a new tool: the America Competes Act, which gives federal agencies the authority to award prizes for solving significant problems. The FDA has issued a “food safety challenge,” Orlandi said, looking for ways to reduce turnaround times on food safety tests, checking for salmonella, for example, from a few weeks to a day or two. The agency has a $500,000 prize pool, with $400,000 potentially going to the winner.

This article originally appeared in CEN media group’s Pittcon Today on Tuesday, March 10 and has been republished with permission. 

Sangita Viswanathan, Former Editor-in-Chief, FoodSafetyTech

The Value of Effective LIMS

By Sangita Viswanathan
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Sangita Viswanathan, Former Editor-in-Chief, FoodSafetyTech

With the announcement of proposed rules under the Food Safety Modernization Act (or FSMA), the burden of food safety testing and record keeping placed on smaller and medium size food companies and use of contract testing labs is growing tremendously. So how do these labs manage growing requests for testing, and increasing volumes of data and demand for records? 

Here is where Laboratory Information Management Systems or LIMS play an important role, in helping labs manage the testing requests, handle all the data and records, be better prepared for audits, and comply with changing regulations, says Anthony Uzzo, President & Co-Founder of Core Informatics.

Uzzo has extensive experience in software engineering, informatics, laboratory automation, project management and science. He co-founded Core Informatics in 2006, along with Jim Gregory (Executive VP of Customer Solutions). A biomedical engineer, Uzzo started his career as a pharmaceutical lab scientist, and in that role, realized that most LIMS solutions were rigid in their scope. 

“This exposed me to different labs having different data management requirements, and gave me a profound appreciation of the impact of data management and having effective LIMS in labs. When starting Core Informatics, my goal was to provide labs with the opportunity to tailor their data management system to their needs without having to change their workflow, systems, personnel etc.,” he describes. 

We present below some excerpts from an interview with Food Safety Tech (FST).

FST: Why are LIMS so important for food and beverage companies in the current environment?

Uzzo:The food and beverage industry faces increasing regulatory scrutiny, pressures to control costs, and the challenge of maintaining quality throughout a global supply chain. A LIMS solution needs to be a solution to aid companies in the delivery and discovery of products, while complying with industry and government regulations.

The LIMS need to identify hazards, determine and monitor critical control points, and establish corrective actions and verification procedures to ensure that standards are met and the system is functioning properly. Our HACCP compliant system helps companies in the F&B industry to monitor products and make sure they do not become contaminated with chemicals or food pathogens. 

FST: How can food companies and labs choose the ideal LIMS solution?

Uzzo: According to me, the top criteria for choosing a LIMS solution would be flexibility; being web-based (able to use the LIMS with smart devices for data entry and access and no antiquated client server technology); and total cost of ownership.

There are now all sorts of novel testing methodologies being applied for food safety, and as a result, the data management requirements are constantly changing. Solutions would need to facilitate administrators to use the LIMS without writing a new code, and easily and quickly enable multi-site collaboration. For instance, there are new rapid detection technologies, such as PCR technologies for Salmonella detection, now in the market. An ideal LIMS should be able to rapidly process these results and use that data analysis, come up with efficient reports and enable lab scientists to do their job in a cost-effective manner. 

Cloud-based solutions offer great advantages in providing the ability to auto-scale, handle any amount of data, send out samples to other labs, support multi-site collaboration etc. Core Informatics, for instance, is fully embracing the power of the cloud. 

An ideal LIMS solution should address chain of custody from registration to report. The final report needs to be mentioned and be able to track who had handled that sample and every derivative of it, how it has been handled, under which condition it has been stored and for how long, and if appropriate procedures have been followed for storage and handling. Downstream, if there’s any problem, we need to be able to go back upstream and identify the correct source material.

LIMS solutions need to be prepared as new laws come into play in the next few years. Industry trends are accelerating the use of contract food testing labs. How effectively companies are able to process their data management requirements such as automatically receiving and recording test requests, preparing for their audits and complying with their food safety management programs, will all become critical.