Pathogen2Read Automates Bacterial DNA Sequencing to Speed Up Disease Tracking

Overcoming the Bottleneck in Genomic Epidemiology

Next-generation sequencing has become a vital tool for public health, allowing scientists to rapidly decode the entire genomes of potential pathogens. However, the process is notoriously labor-intensive. Traditional methods often require eight to 10 hours of hands-on work followed by up to 16 hours of waiting time, creating a significant delay in real-time outbreak responses. Mistakes during this manual process—which includes isolating microbes, breaking open cell membranes (lysis), and purifying DNA—can force researchers to restart the entire workflow.

As Brown University reported, the Pathogen2Read system was designed to bypass these traditional constraints. By using a desktop liquid-handling machine paired with custom software and a specially prepared enzyme cocktail, the system manages lysis, DNA extraction, and library preparation without human intervention. Once an operator loads the samples, the system completes the task in a six-hour automated run.

The Role of the Custom Enzyme Cocktail

The efficiency of the new workflow relies heavily on its ability to handle different bacterial structures. Bacteria are broadly categorized into gram-negative and gram-positive forms. The latter possess a membrane structure that is notoriously difficult to break open, often leading to incomplete DNA extraction in standard protocols. According to researchers, the enzyme cocktail used in Pathogen2Read provides a nearly 2.5-fold improvement in capturing gram-positive DNA compared to standard methods.

“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

This precision is essential for public health surveillance, where identifying small mutations can be the difference between detecting a drug-resistant pathogen and missing it entirely. By reducing the waiting time for gram-positive bacteria extraction from 16 hours to just 30 minutes, the team has effectively streamlined a process that previously hampered rapid surveillance efforts.

Translational Research and Future Surveillance

The development of Pathogen2Read was not an isolated academic project; it was conducted in collaboration with the U.S. Food and Drug Administration (FDA) and received funding from the biotech firm Revvity. This partnership was intended to ensure that the method addresses the actual needs of public health laboratories, particularly smaller facilities that lack the high-throughput automation found in major research centers.

“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

By lowering the barrier to entry for local laboratories, the researchers hope to integrate more facilities into national outbreak-monitoring networks. This could lead to a more robust and responsive national system for tracking foodborne illnesses and other emerging threats. The team emphasizes that the project was developed with real-world impact in mind, bridging the gap between theoretical laboratory innovations and practical application in clinical and public health settings.