title: High-throughput automated microfluidic sample preparation for accurate microbial genomics.
abstract: 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 arbitrary numbers of reaction and clean-up or capture steps. By reducing the sample quantity requirements, we enabled low-input (∼10,000 cells) whole-genome shotgun (WGS) sequencing of Mycobacterium tuberculosis and soil micro-colonies with superior results. We also leveraged the enhanced throughput to sequence ∼400 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.
authors.affiliation: The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.|Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
authors.forename: Soohong
authors.initials: S
authors.lastname: Kim
authors.affiliation: The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.|Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK.
authors.forename: Joachim
authors.initials: J
authors.lastname: De Jonghe
authors.affiliation: The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.|Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
authors.forename: Anthony B
authors.initials: AB
authors.lastname: Kulesa
authors.affiliation: The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.|Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
authors.forename: David
authors.initials: D
authors.lastname: Feldman
authors.affiliation: The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.|Department of Computer Science, Aalto University School of Science, Espoo 02150, Finland.
authors.forename: Tommi
authors.identifier: 0000-0003-0949-1291
authors.initials: T
authors.lastname: Vatanen
authors.affiliation: The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.|Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.
authors.forename: Roby P
authors.initials: RP
authors.lastname: Bhattacharyya
authors.affiliation: Department of Biology, Northeastern University, Boston, Massachusetts 02115, USA.
authors.forename: Brittany
authors.identifier: 0000-0002-8593-0762
authors.initials: B
authors.lastname: Berdy
authors.affiliation: The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
authors.forename: James
authors.initials: J
authors.lastname: Gomez
authors.affiliation: The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
authors.forename: Jill
authors.initials: J
authors.lastname: Nolan
authors.affiliation: Department of Biology, Northeastern University, Boston, Massachusetts 02115, USA.
authors.forename: Slava
authors.initials: S
authors.lastname: Epstein
authors.affiliation: The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.|Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
authors.forename: Paul C
authors.initials: PC
authors.lastname: Blainey
mesh_terms: D001424:Bacterial Infections / Q000175:diagnosis / Q000382:microbiology; D004352:Drug Resistance, Microbial / Q000235:genetics; D004784:Environmental Monitoring / Q000295:instrumentation / Q000379:methods; D015723:Gene Library; D016680:Genome, Bacterial / Q000235:genetics*; D023281:Genomics / Q000295:instrumentation / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D057166:High-Throughput Screening Assays / Q000295:instrumentation / Q000379:methods*; D006801:Humans; D056656:Lab-On-A-Chip Devices; D044085:Microfluidics / Q000295:instrumentation / Q000379:methods*; D009169:Mycobacterium tuberculosis / Q000235:genetics / Q000302:isolation & purification; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D011550:Pseudomonas aeruginosa / Q000235:genetics / Q000302:isolation & purification; D012988:Soil Microbiology; D000073336:Whole Genome Sequencing / Q000295:instrumentation / Q000379:methods*