Health care-associated infections (HAI) pose a constant challenge for hospitals and health systems, resulting in increased morbidity and mortality and billions in costs each year. According to the Centers for Disease Control and Prevention, about 1 in 31 patients has at least one HAI at any given time. In 2016, the U.S. Department of Health and Human Services set a 2020 goal of reducing HAIs by 50% below a 2015 baseline. To that end, Biotia Inc. plans to launch an artificial intelligence (AI)-enabled test to detect harmful bugs and antimicrobial resistance (AMR) early in the new year.

The New York-based startup recently closed a $2.4 million seed round aimed at supporting the commercial rollout of its patient diagnostic test.

The technology employs next-generation DNA sequencing and Biotia’s AI-based software, Chelsea, to identify, in one test, known and emerging bacteria, fungi, parasites and viruses from a clinically curated and annotated database of more than 16,000 microbial species. It also provides a drug-resistance profile to aid in treating HAIs and virulence markers to help determine if the infection is caused by a pathogenic strain of a species, such as C. difficile, that may be more worrisome to treat.

“We can process any sample type as research use only, but with the clinical test that we’re launching, we’re focusing on urine and stool initially,” said Niamh O’Hara, Biotia’s co-founder and CEO. “The applications are recurrent urinary tract infections, drug-resistant UTIs, sexually transmitted infections and infectious diarrhea – so C. difficile and E. coli and other pathogens like that.”

24-hour turnaround

Turnaround time is about a day, and each test generates a microbiology report that lists microbial species, highlighted pathogens and clinical annotations, as well as the AMR and virulence markers.

Currently, hospitals use culturing, which is technology from the 1800s, to diagnose infectious diseases. “It’s pretty wild,” O’Hara told BioWorld MedTech. “Turnaround time is so essential for diagnosis, but then you’re just waiting for these bugs to grow.” She noted that while there is other software that provides a list of species found in a sample, Biotia is seeking to add value via its clinical insights.

Launched in 2016 from the Jacobs Institute at Cornell Tech, Biotia is the brainchild of O’Hara, an evolutionary geneticist, and the company’s other two co-founders, geneticist Christopher Mason, a professor at Weill Cornell Medicine, and Rachid Ounit, an expert in metagenomics, bioinformatics and AI who serves as chief technology officer. It was Mason’s work using sequencing to profile the microbes in the New York City subway system that provided the kernel for the broader goal of tackling harmful microbes in hospitals and in patient diagnosis.

To build its databases, Biotia worked with seven hospitals in New York and New Jersey, as well as a hospital in Bangkok, identifying organisms in the hospital environment. In doing so, the company strove to overcome shortcomings in existing software that can result in a tradeoff between sensitivity and specificity.

“There’s a hesitancy from doctors and infection control to over-identify pathogens, because they don’t want to overtreat … because too much antibiotic usage leads to drug resistance,” O’Hara explained. “One of the things we’ve worked on is making sure that our sensitivity is maintained and is high, but that our false positive rate is low. For example, we can look at specific unique markers in the genome, look at coverage across the genome [and] incorporate all these different metrics to decrease our false positive rate.”

Large clinical study

The company is currently screening thousands of urine samples in a large clinical study at the Bangkok hospital that have been cultured and sequenced. O’Hara said preliminary results show that “basically nothing grows” in about a third of the samples when they are cultured. In 80% of those same samples, Biotia’s test is able to identify microbial species. A lot of the species are E. coli and Klebsiella, pathogens that underlie UTIs, she noted. “We’re matching those results up with the clinical records, and it looks like they’re regularly missing even these pretty routine species in the culture.” The study also is demonstrating strong agreement – about 90% – between Biotia’s technology and culturing.

Biotia already has a product in the market for testing hospital environments. Users swab surface areas and medical equipment and receive and either ship those to Biotia’s partner lab for processing, or Biotia will set them up to process the samples in-house. The results include not only insights on microbes that are living in the facility, but also possible interventions.

Readying for launch

With the looming launch of its patient diagnostic, Biotia is busy submitting paperwork for CAP and CLIA certification, building a sales team and getting the word out about its product. “This is such new technology, that there’s a lot of education involved when we go to hospitals,” O’Hara said. “We’re really building out sales folks who have expertise in this area and doing direct sales.”

The company also recently expanded its scientific and clinical advisory board, bringing on industry veterans Barry Zeman, Don Goldmann and Steven Salzberg. Zeman previously served as CEO of three New York-based teaching hospitals and was on the board of the largest hospital purchasing group in the Greater New York area. Goldmann teaches pediatrics and immunology and infectious diseases at Harvard, and Salzberg is a professor of biomedical engineering, computer science and biostatistics at Johns Hopkins.

O’Hara said the company is interested in doing another raise, but hasn’t determined the timeframe yet. “We’re just happy, at this point, to be focused on validation and sales,” she added.

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