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CosmosID Launches NGS Lab to Expand on Metagenomics Offerings; Plans Move Into Clinical Realm


SAN FRANCISCO (GenomeWeb) – CosmosID is moving beyond its core of developing bioinformatics tools for microbial analysis to offering full metagenomic and microbiome next-generation sequencing services with an eye toward eventually getting into clinical testing and diagnostics.

The company, which was founded in 2008, launched its NGS service laboratory last month at the American Society for Microbiology's Microbe meeting. Its sequencing service is geared toward clinical microbiologists, public health and food safety laboratories, as well as biotechnology and pharmaceutical companies.

The cost starts at $99 per sample for shotgun metagenomic sequencing that includes around 3 million reads. Turnaround time is as low as two days. Both cost and turnaround time increase depending on the number of samples, how deeply it will be sequenced, and the customer's specific question. For instance, CosmosID can also provide de novo assembly of a metagenome, 16S sequencing, and strain subtyping.

ComsosID's NGS laboratory is equipped with sequencing instruments from all the major platform providers: Illumina, Thermo Fisher, Pacific Biosciences, and Oxford Nanopore.

The sequencing services are currently for research use only, but as it looks to move into the clinical space, the company is working on developing its laboratory and its processes to be in compliance with regulatory requirements — its lab has CLIA certification — and it plans to work with clinical experts to validate its databases.

"It's definitely something we're working towards," CEO Manoj Dadlani said. Aside from regulatory compliance certifications for its lab, Dadlani said the firm is developing a HIPPA-compliant software platform that will be able to handle patient information. He said that he anticipates the company's first clinical entry will likely be within the food safety or environmental testing market before getting into the diagnostic space.

Historically, CosmosID has been known primarily for its bioinformatics services, and the company still offers these services. It has built up a database that includes more than 150,000 genomes of bacteria, archaea, viruses, bacteriophages, parasites, and fungi, which includes information on antimicrobial resistance, virulence genes, and other biomarkers. The bioinformatics tools also include machine learning-based filters that can yield strain-level resolution of metagenomic data.

It aims to harness its database and bioinformatics expertise to move into the clinical market, and two years ago, it raised $6 million in a Series B financing round to support those efforts.

The firm already has a collaboration with the Orange County Water District in California to test metagenomic sequencing as a way to assess water quality. Last year, it secured a $100,000 National Science Foundation grant to continue its work and CosmosID and its collaborators at the water district published a study in the Journal of the American Water Works Association describing microbial signatures from treated waste-water biofilms at a waste water purification plant that treats up to 100 million gallons per day of secondary waste water. The treatment is a three-step process that includes microfiltration, reverse osmosis, and UV irradiation. The researchers analyzed the biofilms of the microfiltration and reverse osmosis membranes, with the goal being to understand the microbial makeup at the various stages of water treatment.

Rita Colwell, CosmosID founder and chairman of the board and a senior author of the study, said that traditionally, drinking water analysis has focused primarily on screening for certain viruses and coliforms — bacteria in fecal matter that is a major cause of water contamination. Metagenomic sequencing, however, "allows characterization of everything that's there." That enables researchers, as shown in the study, to determine how the various treatment steps eliminate different microorganisms.

Colwell said that researchers are now also working to characterize the microbiomes of drinking water and bottled water to establish a standard for the water industry.

In an era of climate change and water shortage, water recycling will be important, and metagenomic sequencing can play an important role in determining the efficacy of treatment, Colwell said.

Colwell said that she foresees a future where metagenomic sequencing is a common tool for water treatment facilities. For instance, she said, Washington, DC recently issued a "boil water alert" due to a failure in the piping system. But, "the question is, 'what is the concern?'" In the future, she said, metagenomic sequencing could be used to determine whether the piping failure actually caused contamination and also to determine when the contamination was no longer a concern.

Aside from environmental and food safety testing, CosmosID is also looking to partner with pharmaceutical companies, initially for research and development and in the context of clinical trials, but eventually to develop companion diagnostics. That work will be primarily focused on microbiome sequencing and looking to identify markers in the microbiome that are indicative of disease or a specific illness. Dadlani said that microbiome sequencing could be used not only to identify the specific cause of an illness, but also to "match therapeutics to that condition. We're trying to understand what's the baseline and what are the variables that indicate a disease condition," he said.

As it moves into the clinical space, CosmosID will face competition from a number of other companies and academic laboratories developing NGS-based infectious disease tests. For instance, IDbyDNA last year announced a partnership with ARUP Laboratories to develop and commercialize NGS-based infectious disease tests based on metagenomic sequencing. Startup Karius has developed an infectious disease test that sequences cell-free pathogen DNA in patients' blood and is focusing on the sepsis and transplantation markets. Fry Laboratories, meantime, uses 16S sequencing in its NGS-based laboratory-developed bacterial and eukaryotic assays and is in discussions with Qiagen to develop its assays on the GeneReader platform.

The University of California, San Francisco also offers a clinical metagenomic test for meningitis and encephalitis.

In addition, Dadlani said, on the clinical side, there is still competition from the older technologies like culture and PCR. CosmosID's main clinical focus may be slightly different from some of its competitors, though. One direction the company plans to go in is to "use machine learning to try and understand patterns from microbiome data," Dadlani said, for conditions like inflammatory bowel disease or Crohn's disease.