This article was originally published Oct. 7.
Last week, PathoGenetix said that the US Department of Agriculture's Agricultural Research Service will evaluate its Genome Sequence Scanning technology for use in identifying strains of shigatoxin-producing Escherichia coli and Salmonella enterica.
The Woburn, Mass.-based company has been developing technology, which it has dubbed "sequence shorthand," for microbial identification. John Czajka, PathoGenetix's vice president of business development, told In Sequence that the company expects to commercially launch its platform, Resolution, in the third quarter of 2014 with assays to identify and serotype Salmonella and pathogenic E. coli strains.
Originally, the company had planned to launch its system in late 2012, but Czajka said that over the last two years, the firm decided to refocus on the food safety testing market as opposed to the clinical market, which delayed the original launch (IS 11/15/2011).
"What we learned over the last couple of years is that our technology is both able to give a strain type identification for confirmation as well as determine or predict the molecular serotype of Salmonella and pathogenic E. coli," he said. This "dual functionality" is a "good fit within the needs of the food safety market for rapid methods for serotyping and strain typing."
By contrast, the clinical diagnostics market "requires significant [US Food and Drug Administration] clearances and clinical trials," he said. "The food safety market will still require some validation, but is not nearly as expensive or costly as going into clinical diagnostics."
Additionally, Czajka said that the firm has begun an evaluation program of its system, whereby potential customers can come to the firm's Technology Center for two days of exclusive hands-on experience running real samples. The firm has several prototypes of its system operating in-house.
Czajka said PathoGenetix has representatives from eight companies scheduled to visit over the next six weeks.
Upon launch, the system will cost between $115,000 and $200,000, with each test running between $70 and $90. Along with the platform, the two initial assays will be for Salmonella and pathogenic E. coli identification.
The collaboration with USDA will last one to two years, during which time the USDA-ARS will send pathogenic E. coli and Salmonella strains to PathoGenetix. Czajka said he expects to receive around 1,000 E. coli samples, about 10 percent of which will be non-pathogenic.
PathoGenetix will "evaluate the strains with GSS technology and confirm the potential of identifying virulent versus non-virulent," he said. There are six major Shiga-toxigenic E. coli, or STEC, strains that are not readily identified by traditional molecular testing methods. One goal of the project will be to test whether PathoGenetix's platform can more readily identify these strains.
The Resolution system consists of a Genome Processor for sample-prep and a Genome Scanner that is composed of a microfluidic chip, optics, and lasers.
The user first loads the mixed sample into the Genome Processor, which lyses the cells, creates restriction digest fragments of DNA between 100 kilobases and 300 kilobases long. Then, those DNA fragments are tagged with fluorescent probes. The sample-prep process takes around four hours, after which the DNA is loaded into the microfluidic chip in the Genome Scanner.
The Genome Scanner stretches out the single DNA molecules and a detector scans the molecule at a rate of 10 million bases per second. The detector identifies the strains based on the spatial pattern of the probes. Finally, the bioinformatics compares the DNA to samples within the company's database, comprising both public and private collections.
Czajka said the company has built up its database through collaborations with the USDA, the FDA, and the Centers for Disease Control and has also tapped existing public databases of microbial genomes.
Currently, he said there are between 400 and 500 Salmonella strains and 300 E. coli strains and counting in the database.
Turnaround time from start to finish is around five hours, with the majority in the sample-prep stage. However, Czajka said the entire process is automated, requiring 20 minutes of hands-on time. Additionally, eight samples can be batched together, he said.
Compared to the current gold standard of molecular serotyping, pulsed-field gel electrophoresis, Czajka said PathoGenetix's technology is faster, more accurate, and less labor-intensive. Pulsed-field gel electrophoresis can take up to a week to yield an answer, he said, and the manual nature of the technique lends itself to errors and subjective interpretation.
Aside from Salmonella and E. coli strain identification and serotyping, Czajka said the firm will also launch assays for other food-borne pathogens like Campylobacter and Listeria monocytogenes.
Additionally, he said the company is looking to develop assays for microbes relevant in probiotics, nutraceuticals, and fermentation processes.
In terms of competition, Czajka said he thinks that the company's focus on food safety will set it apart from other companies with similar technology, such as OpGen and BioNano Genomics. BioNano Genomics is focusing its genome mapping technology on sequence finishing and structural variation analysis, while OpGen is focused on finishing and assembling genomes within a research context, as well as on hospital-acquired infections in a clinical setting.
Czajka said that as sequencing technology continues to advance and costs go down, PathoGenetix will compete with whole-genome sequencing, however, he did not anticipate that whole-genome sequencing for food safety applications would become widespread for at least another five to 10 years.
Additionally, he said that FDA researchers collaborating with PathoGenetix have found the technology to be useful as a "triage" to rapidly identify and serotype strains and then choose only the most interesting ones for whole-genome sequencing. "Rather than put everything through whole-genome sequencing, which is relatively labor intensive, our system is quite complementary to next-generation sequencing and they can work quite well together."