Automated workflow speeds bacterial sample preparation for genetic sequencing

Biomedical engineers at Brown University have introduced a new automated workflow designed to transform bacterial sample preparation for genetic sequencing. The method, titled Pathogen2Read, addresses a major bottleneck in outbreak monitoring by moving beyond labor-intensive manual culture isolation.

Traditionally, preparing bacterial samples for genomic analysis requires eight to ten hours of hands-on labor, followed by significant waiting periods. Errors during this manual process can lead to the need for a complete restart. The new workflow uses a proprietary enzyme cocktail combined with custom software and a desktop liquid-handling machine. This system automates cell lysis, DNA extraction, and library preparation.

According to the researchers, this setup reduces hands-on prep time to under 45 minutes. Once the operator loads the raw samples and reagents onto a plate, the machine completes the process in six hours. This efficiency is particularly vital for detecting small mutations linked to drug resistance where sample quality is paramount.

The inclusion of a specialized enzyme cocktail provides a 2.5-fold improvement in capturing DNA from gram-positive bacteria compared to standard methods. By shortening the process and improving reliability, the team aims to bring smaller local public health laboratories into the national outbreak-monitoring fold. This research, funded by Revvity and conducted with FDA collaboration, appears in BMC Genomics.