NEW YORK (GenomeWeb) – Dutch firm IS-Diagnostics has developed a microbiota-based diagnostic tool for inflammatory bowel disease. The company's platform for microbiome analysis was CE marked earlier this year, along with a basic molecular kit for bacterial detection, and it anticipates obtaining CE mark on the IBD diagnostic within the year; it is expected to be the first PCR-based microbiome diagnostic for IBD on the market.
"The basic kit that we now have CE-IVD marking for is used to detect bacteria in any clinical sample," CEO Dries Budding explained in an interview. The core technology underlying that kit was described in a 2016 Journal of Clinical Microbiology study, as previously reported.
Now, the firm has adapted the method specifically for detection of IBD, publishing a study last month in JCM describing validation of the technique.
Chronic inflammation of the bowel is typically caused by either ulcerative colitis or Crohn's disease. But diagnosing IBD is tricky. In Europe, for example, patients usually present first to a general practitioner and are then referred to a gastroenterologist, where the standard is to perform a colonoscopy. However, Budding noted that only 1 in 10 patients come away from this invasive and expensive procedure with an IBD diagnosis, and for the rest nothing conclusive is found. "It is a very ineffective diagnostic means," he said.
Yet, the microbiome is altered in IBD, with studies describing it as more dynamic than in healthy people, with trends toward reduced biodiversity. Because treatments for IBD alter the microbiome, a few studies have also examined treatment-naive disease in pediatric populations. In these patients it has been shown that increased abundance of certain bacteria, coupled with decreased abundance of others, is strongly correlated with disease status.
Measuring bacterial species and abundance is the basis of the IS-Diagnostics IBD test. "With the IS-Pro technique, you'd be able to send in a fecal sample to know whether you should go for more testing, reducing useless colonoscopies," Budding said. In addition, the test could potentially be used alone as a diagnostic for IBD, he said.
Unlike most other microbiome analysis methods currently being used, which typically rely on sequencing, IS-Diagnostics uses a PCR-based method for determining the different species that make up a microbiota.
Specifically, the firm's technology detects the 16S to 23S ribosomal RNA intergenic spacer (IS) region of bacteria. "By amplifying this, we get a fragment from each bacterial species in a sample, and the interesting feature of this fragment is that its length can be used to determine species," Budding said.
The method, also called rRNA intergenic spacer analysis, or RISA, is enhanced by IS-Diagnostics' use of fluorescent tags for different phyla, such that fragment length and color are used to pinpoint which species are in a sample as well as the amount of each. The technique, which the firm also calls culture-free microbiology, takes about five hours to run, and can accommodate any PCR system and capillary electrophoresis instrument.
For the IBD diagnostic, it was particularly vital that the firm tackle issues of noise that are common to microbiome analyses. A previous meta-analysis concluded, for example, that research into the sometimes-subtle effects of IBD on the human microbiota require carefully selected control populations and standardized protocols.
For the recent JCM study, "We've put a lot of effort into standardizing [the IBD kit] because the measurement of the gut microbiome is extremely difficult to standardize between laboratories and hospitals, and any alteration in experimental technique will give you a different answer," Budding said.
To solve this problem, the firm completely standardized the workflow, from the process of taking a sample through to each step in the lab.
Then, to deal with remaining noise, IS-Diagnostics did analyses using software to develop an algorithm that was essentially a type of machine learning trained on noisy data sets.
"We measured all sources of noise that can occur, and modeled the effects on the algorithm by turning up the noise to max on all different parameters and seeing where different algorithms broke down," Budding said.
In the study, the firm then measured the real noise caused by variability between analysis platforms and between hospitals, to see if those noise levels were in line with levels where algorithms would break down, converging on "one algorithm that never broke down at the levels of noise measured in real settings."
By combining the standardized lab procedure with the specialized algorithm, "We can now do reliable diagnostics based on just the microbiome," Budding said.
For the initial characterization and validation, the company used pediatric samples from patients up to 18 years old who had not been treated before. In principle, the microbiome is in an adult-like state from the age of four years old onward, but the firm is also finalizing a study on adult IBD patients, as well, that will be used for the CE marking.
A research-use only version of the IBD kit is now ready to be tested in hospitals, and will be used to get additional clinical experience, and the firm is planning to initially reach out to a limited number of hospitals and large gastroenterology centers. It is also in discussions with patient and advocacy groups, such as the Dutch Society of Crohn's and Colitis, to see which patient groups would most like to see the test implemented and whether there is interest in implementing it at the general practitioner level. "That may be very interesting, because then they may be able to skip going to the hospital altogether," Budding said.
Since obtaining the CE mark on the general kit, the firm has also started getting initial customer feedback and performing final optimizations in anticipation of marketing on a larger scale. In addition, it is talking to parties in the US to discuss partnering and obtaining regulatory approval here, but Budding could not provide more detail on these discussions because of the early stage.
The firm is expecting to be the first entrant into the microbiota-based IBD diagnostic space.
"There are a lot of publications on IBD and the microbiome using next-generation sequencing, but that's very far from clinical implementation for a number of reasons." Budding said. Namely, NGS is not yet standardized between labs and workflows, and the batch numbers need to be high for NGS to become affordable. IS-Pro, on the other hand, can be run on any batch size, down to a single sample in a day, and still be cost effective, Budding said. "We're first to enter the market, and for now, we don't have huge competition."
The price of the test currently in the Netherlands is about €200 ($213), which is on the lower end of cost for a diagnostic test. And, "it beats a colonoscopy," Budding said.