This article has been updated to correct the previously reported time needed for RipSeq to analyze sequences.
With $1.5 million in new funding, Norwegian bioinformatics firm iSentio plans to expand the customer base for its web-based bacterial identification software and add additional support for existing subscribers in the US and Europe.
The bulk of the new funds came from Sarsia Seed, a Norwegian seed capital fund that invests in early-phase technology companies within the energy, clean technology, and life science sectors.
“This financing will allow us to strengthen our market presence and address new markets," Bjarte Karlsen, CEO and co-founder of iSentio, said this week in a statement. "It will also ensure that we have a strong support organization to care for our customer base."
The company, which was founded in 2005, markets RipSeq, a web-based suite of DNA analysis tools designed to identify bacteria in patient samples. The software is built upon base-calling and database-searching algorithms developed by Karlsen and iSentio's other co-founders, Øyvind Kommedal and Øystein Sæbø.
Included in the suite are two tools: RipSeq Mixed, which lets users identify different types of bacteria in mixed samples; and RipSeq Loci, which lets users identify multiple gene targets in bacteria.
The key feature of RipSeq Mixed is its ability to analyze mixed DNA chromatograms, which means it can identify bacteria following direct 16S rRNA gene sequencing of polybacterial human clinical samples. Rather than culturing the sample to isolate the bacteria prior to analysis — a process that can take anywhere from two days to a week — clinicians can directly sequence patient samples and upload the data to RipSeq, which then sifts through the mixed chromatogram to pull out the bacterial sequences of interest.
The software is able to return the results of the analysis in 30 seconds, Karlsen told BioInform. "You save a lot of time to identification because you skip the culturing step, which is the most time-consuming part."
Furthermore, Karlsen said, RipSeq Mixed is the only tool that can identify multiple strains of bacteria in mixed clinical samples.
Meanwhile, RipSeq Loci allows for two different gene targets to be sequenced in a single tube, and "identifies both gene targets from the resulting mix." Currently the tool is used only for Mycobacteria identification.
While there are other bioinformatics companies that focus on microbial analysis, such as Switzerland's SmartGene and US-based Integrated Genomics, and there is also a wealth of open source software available to analyze bacterial sequences, Karlsen said that most of these tools can only identify "pure" or single sequences and fall short when it comes to separating sequences from many different bacteria, which is typical in most clinical samples.
The company is currently focused on "clinically relevant" bacteria and its tools can identify different strains of bacteria as well as different gene targets in bacteria. However, "we see a lot of different organisms that this [software] can be used on," such as fungi and viruses, Karlsen said, as well as "a lot of different market segments like veterinary, food, and pharma."
For now, the company's primary customers are infectious disease departments in hospitals and microbiology laboratories, Karlsen said. RipSeq Mixed is currently in use in several research labs and clinics in Europe and the US, including Karolinska Hospital in Sweden, the UK's Health Protection Agency, the University Hospital of Heidelberg in Germany, and the Mayo Clinic. RipSeq Dual Loci is being used at ARUP Laboratories.
To access the system and upload their sequences, researchers are required to obtain a username and password from the company. iSentio also offers a two-week free trial during which prospective customers are trained to use the system and allowed to analyze as many sequences as they choose.
ISentio uses a pay-per-sample pricing model, but specific prices depend on the number of samples that customers upload.
RipSeq accepts sequence data files from all Sanger-based instruments from Life Technologies, such as the 3730, AB 3500, and AB 310 sequencers. The company plans to adapt it to work with data from additional capillary electrophoresis sequencers, such as the Beckman sequencing platform from Beckman Coulter Genomics.
Karlsen observed that more researchers are turning to direct sequencing as a viable approach for identifying pathogens and that the market for the kinds of services iSentio offers is "sizable."
Direct sequencing, Karlsen noted, not only requires less time than culture-based approaches, but is more effective for patient samples that contain contaminants such as antibiotics. Because bacteria from samples that contain antibiotics can't be cultivated, physicians have no option but to "treat blind" and try different antibiotics until "they hit the correct one," Karlsen said.
Furthermore, methods such as multiplex kits are only effective "when you ... know what [bacteria] you are looking for," which limits their usefulness.
Although it has applications in the clinical setting, RipSeq is marketed as a research tool and getting the US Food and Drug Administration's approval to market it for clinical use in the US won't be easy, Karlsen said. He said that RipSeq hasn’t been CE marked for clinical use in Europe either, but that the company is "looking into" it.
He explained that because the software identifies multiple bacteria in multiple sample types, the FDA would require approval for each sample type as well as for each bacteria type.
"We could possibly get ... FDA clearance ... on one specific sample type, [for example] — sepsis or some abscess of some kind — but still we would have to include a sequencer" as part of the approval process — a prospect that the bioinformatics firm doesn't want to consider.
He did note, however, that some groups in the US that have adopted the tool have validated it in their labs and begun using it to analyze clinical samples.
Currently, iSentio has four employees. It plans to use its new funding to hire two sales people to manage the backlog of requests for RipSeq Mixed services as well as to identify and reach out to new customers, Karlsen said
In addition, he said that iSentio plans to open a US West Coast office next February where one of the new employees will be based.
"We have a lot of interest from different universities in the US for research purposes so we think there is quite a sizable market there," he said.
The US-based employee will handle requests from all the company's North American customers.
Karlsen isn't worried about competition from open source software because microbiologists and infectious disease researchers won't use software that hasn’t been validated and without any publications linked to it, a process that takes years.
"We have not seen any other software ... out there so far that does this," he said adding that even if a open source group tries to "force their way past our patents" with its software, "they will still have quite a few years of validation and publication to go through before they can compete with us. "
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