High-throughput automated microfluidic sample preparation for accurate microbial genomics

Soohong Kim, Joachim De Jonghe, Anthony B. Kulesa, David Feldman, Tommi Vatanen, Roby P. Bhattacharyya, Brittany Berdy, James Gomez, Jill Nolan, Slava Epstein, Paul C. Blainey
2017 Nature Communications  
Low-cost shotgun DNA sequencing is transforming the microbial sciences. Sequencing instruments are so effective that sample preparation is now the key limiting factor. Here, we introduce a microfluidic sample preparation platform that integrates the key steps in cells to sequence library sample preparation for up to 96 samples and reduces DNA input requirements 100-fold while maintaining or improving data quality. The general-purpose microarchitecture we demonstrate supports workflows with
more » ... rary numbers of reaction and clean-up or capture steps. By reducing the sample quantity requirements, we enabled low-input (B10,000 cells) whole-genome shotgun (WGS) sequencing of Mycobacterium tuberculosis and soil micro-colonies with superior results. We also leveraged the enhanced throughput to sequence B400 clinical Pseudomonas aeruginosa libraries and demonstrate excellent single-nucleotide polymorphism detection performance that explained phenotypically observed antibiotic resistance. Fully-integrated lab-on-chip sample preparation overcomes technical barriers to enable broader deployment of genomics across many basic research and translational applications.
doi:10.1038/ncomms13919 pmid:28128213 pmcid:PMC5290157 fatcat:4psfqq6h6nccpmjzg73plfcnty