Biomedical engineers at Brown University have developed Pathogen2Read, a fully automated workflow that slashes DNA sample preparation time from nearly a full day to under 45 minutes. Published in BMC Genomics, the method uses a custom enzyme cocktail to streamline genetic sequencing, aiming to help smaller public health laboratories accelerate outbreak detection.
Pathogen2Read: Automating the Genetic Sequencing Bottleneck
Genetic sequencing has become a vital tool for epidemiologists, allowing them to map the full genome of pathogens in hours or days. However, the process of preparing these samples—isolating microbes, breaking down cell walls, and purifying DNA—has historically been a manual, labor-intensive hurdle. According to reporting from Phys.org, current laboratory techniques often require eight to 10 hours of hands-on work, followed by up to 16 hours of waiting time.
The new Pathogen2Read workflow, developed by researchers at Brown University, replaces these manual steps with an automated system. By utilizing custom software and a specialized enzyme cocktail, a desktop liquid-handling machine can now handle lysis, extraction, and library preparation without human intervention. Once a technician loads the raw samples onto a plate, the system completes the process in a six-hour run.
Engineering a Solution for Gram-Positive Bacteria
A significant challenge in sample preparation is the structural difference between types of bacteria. Gram-positive bacteria possess a membrane structure that is notoriously difficult to “crack” open for DNA extraction, often leading to their omission in sequencing results if the preparation is incomplete.
“Because you’re looking for small mutations that may be involved in drug resistance, for example, it’s easy to miss them if you’re not capturing all the sequences. So the quality of the sample preparation is critically important.”
Anubhav Tripathi, professor of engineering and faculty affiliate of Brown’s Institute for Biology, Engineering and Medicine, via Brown University
Furthermore, this specific innovation reduced the waiting time for these samples from 16 hours to just 30 minutes.
The development of Pathogen2Read was not an isolated academic project. The team worked in direct collaboration with researchers at the U.S. Food and Drug Administration (FDA) to ensure the method could meet real-world diagnostic needs. This partnership was intended to bridge the gap between academic theory and practical, translational research.
“Next-generation sequencing has become a staple in outbreak detection and prevention. But sample preparation involves labor-intensive manual preparation and culture isolation, which can delay real-time outbreak responses. Our laboratory has developed what is, to our knowledge, the first fully automated scientific method that bypasses these limitations.”
Photo: brown.edu
Kathryn Whitehead, graduate student in Brown’s School of Engineering, via Brown University
By reducing the technical barriers to high-quality sequencing, the researchers hope to integrate smaller, local public health laboratories into the broader outbreak-monitoring networks operated by the FDA and the Centers for Disease Control. This expansion could theoretically provide a more robust, decentralized defense against foodborne illnesses and other emerging pathogen threats. Funding for the development of the method was provided by the biotech firm Revvity.
“The reason we’re so excited about this is it was developed with real-world impact in mind. Having that collaboration with the FDA, being able to get their responses and their input on what they need to see, has allowed us to develop a method that actually can be used and doesn’t have some of the limitations that you may sometimes see going from academic to translational research.”
Kathryn Whitehead, graduate student in Brown’s School of Engineering, via Mirage News
