Abstract

Nanopore Sequencing for Real-Time Pathogen Identification

Kamlesh Patel, Senior Member, Sandia National Laboratories

Effective global health response to emerging infectious disease requires a rapidly deployable, universal diagnostic capability. We will present our ongoing work to develop a fieldable device for universal bacterial pathogen characterization based on nanopore DNA sequencing. The relative small-size, portability, long-read lengths, and real-time informatics makes this commercially available technology a game-changer for bacterial pathogen identification. We will present our latest results in integrating a microfluidic front-end for rapid sample preparation and a unique bioinformatics strategy for sequencing the entire 16S-to-23S ribosomal DNA locus for identification. While DNA sequencing technology is advancing at an unprecedented rate, sample preparation technology still relies primarily on manual bench-top processes, which are slow, labor-intensive, inefficient and often inconsistent. Automation of sample preparation using microfluidic techniques is well-suited to address these limitations. However, fabricating a single monolithic microfluidic device that replicates all the relevant bench top processes can be prohibitively complicated and does not allow the flexibility to execute diverse protocols for processing different samples and sample volumes. We have designed, fabricated, and characterized a digital microfluidic (DMF) platform to function as a central hub for interfacing multiple lab-on-a-chip sample processing modules towards automating the preparation of clinically-derived DNA samples.