Brown University Develops Pathogen2Read to Speed Bacterial Sample Prep

The process of genomic surveillance—essential for tracking foodborne illnesses and identifying drug-resistant bacteria—has long been hampered by a labor-intensive bottleneck. Traditional methods require eight to 10 hours of manual labor and 16 hours of waiting time, leaving little room for error. The new Pathogen2Read system automates the entire sequence, including cell lysis, DNA extraction, and library preparation, using a desktop liquid-handling machine and custom software.

Efficiency Gains and Technical Innovation

The core of this efficiency gain lies in an enzyme cocktail designed to break open bacterial cell membranes. This step is particularly critical for gram-positive bacteria, which have rigid structures that are notoriously difficult to penetrate. According to Brown University, the new method provides a nearly 2.5-fold improvement in capturing gram-positive DNA compared to standard techniques, while simultaneously slashing the required waiting time from 16 hours down to 30 minutes.

“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

Once an operator loads raw samples and reagents onto a plate, the system executes a six-hour automated run. This transition from manual to automated processing is intended to minimize the potential for human error, which in traditional protocols could force researchers to restart the entire workflow.

Collaboration with the FDA and Revvity

The development of Pathogen2Read was not a purely academic endeavor; it involved direct input from the U.S. Food and Drug Administration. This partnership ensured that the tool addressed the operational constraints faced by public health labs. As noted by Archyworldys, the project also received funding from the biotech firm Revvity, with the specific goal of bringing high-throughput capabilities to smaller facilities that currently lack such infrastructure.

“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 Brown University

By streamlining these steps, the researchers aim to integrate more local laboratories into national surveillance efforts. This could lead to faster, more granular data collection during disease outbreaks, as the method allows for the rapid sequencing of pathogen genomes that might otherwise be delayed by the complexities of manual preparation.

Next-Generation Sequencing in Modern Epidemiology

Next-generation sequencing has become a foundational element of public health, allowing for the identification of pathogens and the discovery of new mutations in a matter of hours or days. However, the transition from academic discovery to translational, real-world utility remains a challenge for many new genomic tools. The team behind Pathogen2Read believes their work bridges this gap by prioritizing accessibility for smaller labs.

The research describing the Pathogen2Read method was published in BMC Genomics (DOI: 10.1186/s12864-026-13075-1). While the initial results are promising for outbreak monitoring, the ultimate test for the system will be its adoption across diverse public health settings as labs look to modernize their response capabilities in the coming years.