MICROFLUIDIC SAMPLE PREPARATION FOR GENOMIC SEQUENCING OF CLINICAL ISOLATES

Infections from drug-resistant bacteria cause over 2 million illnesses in the U.S. per year. In the case of MRSA (methicillin resistant staphylococcus aureus), a common hospital-acquired pathogen, patients have recurrent infections that lead to complications and potentially death. Our medical community does not understand how or why these recurrent infections occur, and we do not know the diversity of the bacteria causing these infections. In order to develop this understanding, we need to sequence the bacterial genomes of many samples. Currently, we face a “sample preparation cost bottleneck” – preparing samples for whole genome sequencing (WGS) costs $200-500 per sample, while sequencing only costs $10 per sample. In this work, we developed a microfluidic device to miniaturize and parallelize the sample preparation, which leads to a cost reduction of nearly 100-fold. We successfully prepared DNA libraries for sequencing starting from as low as 1,000 cells, and we show that the sequencing libraries are of equal quality as those from the standard protocol. In this project, we apply this device to preparing DNA libraries from 3,000 MRSA clinical isolates, as part of a large clinical trial to understand the genetic basis for MRSA infection and carriage. Such technology can be used to improve our understanding of transmission of pathogens and antibiotic resistance elements, in addition to our understanding of pathogen population dynamics, host risk factors, and host-pathogen interactions. With new access to genomic information from bacteria, we can move toward finding ways to overcome the problem of drug-resistant bacterial infections, such as MRSA.