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Life Tech Alliance is Latest FDA Move to Incorporate Sequencing Data into Food Pathogen Detection

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A five-year deal between the US Food and Drug Administration and Life Technologies marks the latest sequencing-related move in the federal agency's ongoing efforts to characterize, detect, and track foodborne pathogens.

The agreement focuses on using genome sequence data as a source of information for finding markers that can be incorporated into rapid molecular tests to detect and distinguish between various strains and serotypes of Escherichia coli and Salmonella.

As part of the collaboration, researchers based at Life Tech and the FDA will work together to develop and validate real-time PCR-based detection tests for the bacterial foodborne pathogens using existing sequence data provided by the FDA, along with new genome sequences to be generated at the FDA or in Life Tech's food safety lab, as needed.

"We're trying to use genomic data to build, in collaboration with Life Tech, rapid molecular technologies such as real-time PCR assays and things of that nature," Eric Brown, director of the FDA's division of microbiology, told In Sequence.

With the advent of newer molecular diagnostic tests for potential food contaminants such as E. coli and Salmonella, he noted, it should be possible for the FDA to more quickly detect and deal with outbreaks when they occur and to do the sort of high-throughput food surveillance testing needed to prevent tainted food from reaching the market.

In addition to contributing bioinformatics know-how and in-house sequencing capabilities, Life Tech has committed to coming up with an Ion Torrent PGM sequencing pipeline as part of the collaboration, which will center on identifying foodborne pathogen features that inform the project's broader pathogen detection goals.

"This is a unique project because it is one that's really connecting all the dots: sequencing, bioinformatics, and the ability to develop molecular assays that will accurately detect those bugs," said Nir Nimrodi, Life Tech's vice president and general manager for food safety and animal health.

The new Life Tech-FDA projects come on the heels of an agreement between the FDA and Illumina, announced last year, that had the agency installing MiSeq instruments in state and regional microbiology labs across the US (IS 10/9/2012). That five-year instrument, reagent, and technical support contract includes a two-year pilot project aimed at assessing sequencing-based schemes for tracking food-borne pathogens.

Whereas FDA researchers are relying on Illumina MiSeq instruments for that food contaminant traceback and outbreak response project, the latest deal with Life Tech is intended to spur the development of rapid molecular tests based on genomic data.

"This collaboration with Life Tech is focused on a different aspect of food safety," Brown said.

"The Illumina project … is primarily focused on linking sources of contamination to foodborne events when they arise — so using whole-genome sequencing as a molecular epidemiological tool or as a molecular forensics tool," he explained. "[The new collaboration] is using that rich data primarily to work with Life Tech to build rapid molecular tools."

The agreement follows a long history of informal collaborations between the FDA and Life Tech. The sequencing firm has established itself as a player in the food safety sphere, not only through sequencing efforts such as the characterization of an E. coli strain behind a 2011 outbreak in Europe, but also because of its bioinformatics capabilities, FDA representatives noted.

By working more closely with the federal agency, meanwhile, Life Tech investigators hope to take advantage of the strains and sequences that the FDA has at its disposal — from the earliest stages of diagnostic test design to validation and test modification steps that may involve sequencing wider sets of microbial isolates.

"The benefit for us, obviously, is that we will have access to important samples that may contain invaluable information about new strains that haven't been known before," Life Tech's Nimrodi said. "By having those samples, we can develop new tests faster than others."

"It will also give us an opportunity to gain feedback from a world-leading organization on the platforms that we wish to develop," he added.

Along with the hundreds of draft genomes already published, the FDA has generated more than 1,000 draft sequences representing a broad swath of the genetic diversity found in foodborne pathogens — data that's expected to be crucial for designing tests that can accurately detect and distinguish between such bugs, noted Marc Allard, a microbiologist and research area coordinator for genomics at the FDA.

"We've got a huge effort that's been going for some time to essentially build large reference databases," he said.

The data is being made publicly available, meaning it may serve as fodder for diagnostic tests developed by any company or research team, Allard said, noting that "we are hopeful that many companies will have interest in developing these types of rapid test kits."

By entering into a more formal working relationship with Life Tech researchers, though, the FDA hopes to speed up the introduction of validated molecular tests for the forms of E. coli and Salmonella that tend to show up in various foods.

Once preliminary molecular tests — particularly real-time PCR-based assays — are developed through the collaboration, the researchers intend to tap FDA's storehouse of pathogen strains to validate and assess their power for discriminating between foodborne pathogen strains.

In instances where the beta version of such tests can't distinguish between the full suite of strains that may turn up in food products, the group expects to sequence additional isolates as a means of uncovering alternative molecular targets and refining the tests.

"This is an iterative process where you build a test set based on the data you have, then you test it against the broader [bacterial] diversity," Allard noted.

"A lot of kits, for example, fail when you're doing Salmonella-specific assays because of some of the weird sub-species," he explained. "But they're still Salmonella and they're still regulated, so we need kits that can identify those as well."

Researchers at the FDA may use Life Tech's Ion Torrent PGM instrument to crank out whole-genome sequences for specific foodborne pathogen strains as needed during the diagnostic test development process. The agency already has access to several PGMs through its own labs and specific state public health labs with which it collaborates.

Genome sequence data generated for the project will be submitted to the National Institutes of Health's GenBank database. As with existing sequence data for relevant E. coli and Salmonella strains, the FDA intends to pass some of the genome data back to Life Tech collaborators who will again use the firm's bioinformatics tools in molecular test development efforts.

In addition, Life Tech has its own dedicated food safety lab, which may sequence specific isolates relevant to the collaboration's goals. The firm has "a great facility" and "great capabilities," FDA's Brown said, "and they will help fill in the blanks on those isolates that need to be done specifically for rapid diagnostics methods development."

"The idea here is to be more proactive," Nimrodi said. "And rather than wait for disaster to happen, to continuously increase the database of different strains of Salmonella and E. coli."

As an extension of such efforts, the group is keen to come up with a sequencing pipeline centered on the Ion Torrent platform that can quickly characterize foodborne pathogen features, FDA research biologist Narjol Gonzalez-Escalona told In Sequence, from sequence type to the presence or absence of specific virulence features or drug resistance profiles in the microbe in question.

For his part, Gonzalez-Escalona is working with Life Tech to develop rapid, sensitive diagnostic tools focused on Salmonella in eggs, with the goal of more quickly developing and testing Salmonella kits that can be used in normal food screening and surveillance or in the event of a foodborne pathogen outbreak.

More generally, Nimrodi noted that Life Tech sees the collaboration as an opportunity to have the FDA evaluate its latest food safety products as they hit the market.

"We are going to give the FDA access to evaluate new technologies and new platforms that we're developing," he said. "It could be new genomic panels that will run on PGM or it could be a new food safety fully integrated system that would speed up the process of the actual detection, once you know what you're looking for."

It's too early to predict just how many organisms will be sequenced as part of the five-year agreement, Nimrodi said, though both Life Tech and the agency have a fairly good understanding of the PGM's current microbial sequencing capacity. These days, for instance, he noted that a couple of technicians working in the sequencing firm's food safety lab can get through around a dozen strains per week.

Nimrodi declined to provide details about the specific terms of the agreement or the types of reagents, equipment, and technical support that Life Tech will provide to the FDA during the collaboration.

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