2291. A Real-Time Sequencing Approach for Simultaneous Metagenomic and Transcriptomic-Based Diagnosis of Infectious Diseases
Session: Poster Abstract Session: Molecular & Sequence Based Diagnostics
Saturday, October 6, 2018
Room: S Poster Hall
  • BJBIDweek2018.pdf (2.3 MB)
  • Background: Recent studies have demonstrated the utility of metagenomic next-generation sequencing (mNGS) and RNA gene expression sequencing (RNA-Seq) for identifying causes of infections. Although these approaches have been largely tested to date using established sequencing platforms such as the Illumina HiSeq, the use of nanopore sequencing on the MinION sequencer (Oxford Nanopore Technologies) is attractive given rapid library preparation and real-time analysis of sequencing data resulting in accelerated sample-to-answer turnaround times.

    Methods: We have developed a rapid molecular concatemerization library approach to increase the throughput of the nanopore sequencer analysis for metagenomic and RNA-Seq approaches. We have also developed a pipeline (SURPIrt, “Sequence-based ultra-rapid pathogen identification, real-time") that allows for real-time, simultaneous metagenomic and transcriptomic analyses on the same sample.

    Results: With the use of molecular concatemerization library approach, we show that metagenomic and transcriptomic data generated on the MinION are comparable to those on the Illumina platform, yet can be collected and analyzed in significantly less time (6 hours versus 2-3 days).

    Conclusion: Here we demonstrate simultaneous metagenomic and RNA-Seq analyses on a nanopore-based sequencing platform with real-time analysis of results. We foresee that this approach could be leveraged into a rapid screening test for diagnosis of infectious diseases in both hospital and field settings.

    Benjamin Briggs, M.D., Ph.D.1,2,3, Scot Federman, B.A.2,3, Xian Ding Deng, Ph.D.2,3, Wei Gu, M.D., Ph.D.2,3, Guixia Yu, B.S.2,3, Claudia Sanchez San Martin, Ph.D.2,3, Steve Miller, M.D., Ph.D.2,3 and Charles Y. Chiu, M.D., Ph.D.2,3,4, (1)Department of Pediatrics, Division of Infectious Disease, University of California, San Francisco, San Francisco, CA, (2)Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, (3)UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, (4)Department of Internal Medicine, Division of Infectious Disease, University of California, San Francisco, San Francisco, CA


    B. Briggs, None

    S. Federman, None

    X. D. Deng, None

    W. Gu, None

    G. Yu, None

    C. Sanchez San Martin, None

    S. Miller, None

    C. Y. Chiu, None

    Findings in the abstracts are embargoed until 12:01 a.m. PDT, Wednesday Oct. 3rd with the exception of research findings presented at the IDWeek press conferences.