CosmosID brings metagenomics platform to Qiagen partnership

By Joseph James Whitworth

- Last updated on GMT

Picture: CosmosID
Picture: CosmosID

Related tags Food safety Bacteria Microbiology

CosmosID has partnered with Qiagen to launch its metagenomics analysis platform in the firm’s CLC Genomics Workbench.

The genomic big data company, which is focused on outbreak investigations using next-generation DNA sequencing, identifies bacteria, DNA viruses, fungi, parasites and virulence genes from a post-sequencing metagenomic sample.

CosmosID will enable Qiagen’s customers to use shotgun metagenomics and microbiome analysis for fields such as food safety. 

By adding the platform to the tool for analyzing, comparing, and visualizing next-generation sequencing data, researchers will be able to profile microbial communities from whole genome shotgun data, and determine relative abundance, said the firms. 

Making data access simple

CosmosID’s platform identifies to strain level by placement on a phylogenetic tree and allows comparative analyses of datasets using heat maps and principal component analysis.

“Researchers running metagenomic, microbial and other applications often need to rely on complicated data analysis tools from different sources,”​ said Laura Furmanski, SVP of Qiagen Bioinformatics business area.

“The addition of CosmosID expands the range of metagenomics applications that Qiagen customers can access in our single, user-friendly NGS data interpretation platform.”

CosmosID’s metagenomic microbial identification platform uses patented methods and curated databases (GenBook) of more than 65,000 microbial genomes, including bacteria, viruses, fungi, parasites, and antibiotic resistance and pathogenicity markers.

The company has analyzed over 20,000 biological samples from animals, plants, water and soil.

CosmosID said it can help to monitor food safety and quality assurance, characterize microbial communities, production and supply chain monitoring, ID known, novel and non-culturable agents and investigate foodborne disease outbreaks.

CosmosID speaks to FQN

Dr Nur Hasan, VP, R&D at CosmosID, said there are different methods to track pathogens and food safety is a very diverse market.

“The number of peer reviewed articles on the microbiome, NGS and metagenomics is increasing – with over 3,000 in 2014. Up until now there has not been a single method used as a universal diagnostic system,” ​he told FoodQualityNews.

“We can look at any food to detect any pathogen you get to know everything that is there.

“Predictive microbiology is what is in the environment, is there anything alarming, and identify pathogens like the cause of an outbreak in a facility. Food safety will benefit from our technology, people using bioinformatics can run it and get a complete answer in an outbreak investigation.”

Manoj Dadlani, CEO, told us it was a software company focussed on output.

“Whether the system is from Illumina, Thermo Fisher Scientific, or others, we can take sequence files, do the data analysis and characterize the microorganism in short and long reads,” ​he said.

“We have spent a lot of time creating cut offs and filters so you can have a shortlist of organisms in a sample. Other software gives you a laundry list of organisms, we filter out the noise and make confident calls and market relevant records are created.”

Dadlani, also associate partner at Applied Value Group (AVG) which recently invested in the firm, said it provides the metagenomics as part of the Qiagen partnership and moves such as that were important to approach customers in the food safety space.

“It is early days but the shift to adopting NGS is starting, we see it from industry and agencies such as the CDC in outbreak investigation,” ​he said.

“The next wave is how to analyse all the data, which can be confusing and overwhelming, this is where we fit in. We break down data to the end user. It is a bioinformatics platform and any lab can use the software.”

Dadlani added the Food and Drug Administration (FDA) awarded the firm a five year contract to work on identification of common and novel foodborne pathogens at the end of last year.

Dr Rita Colwell, founder, CSO and chairman said the system provides fast results.

“You take it out of sequence machine and have information within minutes to make an identification on species and strain. It is also flexible in operation, you don’t need a PhD in computer science to run documentation, the output is as complex or simple as you wish.”

The CosmosID system has a statistical probability value for identifications made for every sample.

Other features include functional analysis and virtual panels that allow clients to tabulate microorganisms and specific genes linked to foodborne outbreaks.

CosmosID’s platform analyzes data produced from commercially available sequencers, including Illumina, Thermo Fisher, Pacific Biosciences, and Oxford Nanopore systems.

Funding boost

CosmosID also recently raised $6M in Series B funding.

The company will expand engineering capabilities, R&D to improve linkage of the DNA genetic code to actual biological traits (genotype to phenotype), such as antibiotic resistance, and develop products directed at monitoring, predicting, and preventing disease outbreaks.

The funding round was led by AVG - a private investment firm.

CosmosID began generating revenue in 2015, with customers in the pharmaceutical, probiotics, microbiome research, and food safety markets.

The company is evaluating the clinical utility of its pathogen detection system in partnership with 15 research hospitals in the US and Europe. They added these EU partnerships will help the push in the region for the food safety market.

CosmosID offers its genomic analysis software platform in the cloud, on an appliance/server to handle study design, DNA sequencing, and microbiome analysis.

The algorithms, interface and database can be run on a laptop, without an internet connection. 

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