FLASH: a next-generation CRISPR diagnostic for multiplexed detection of antimicrobial resistance sequences. Issue 14 (22nd May 2019)

• Record Type: Journal Article
• Authors: Quan, Jenai; Langelier, Charles; Kuchta, Alison; Batson, Joshua; Teyssier, Noam; Lyden, Amy; Caldera, Saharai; McGeever, Aaron; Dimitrov, Boris; King, Ryan; Wilheim, Jordan; Murphy, Maxwell; Ares, Lara Pesce; Travisano, Katherine A; Sit, Rene; Amato, Roberto; Mumbengegwi, Davis R; Smith, Jennifer L; Bennett, Adam; Gosling, Roly; Mourani, Peter M; Calfee, Carolyn S; Neff, Norma F; Chow, Eric D; Kim, Peter S; Greenhouse, Bryan; DeRisi, Joseph L; Crawford, Emily D
• Is Part Of: Nucleic acids research. Volume 47:Issue 14(2019)
• Page Start: e83
• Page End: e83
• Publication Date: 2019-05-22
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gkz418
• Languages: English
• ISSNs: 0305-1048

Abstract

Abstract: The growing prevalence of deadly microbes with resistance to previously life-saving drug therapies is a dire threat to human health. Detection of low abundance pathogen sequences remains a challenge for metagenomic Next Generation Sequencing (NGS). We introduce FLASH (Finding Low Abundance Sequences by Hybridization), a next-generation CRISPR/Cas9 diagnostic method that takes advantage of the efficiency, specificity and flexibility of Cas9 to enrich for a programmed set of sequences. FLASH-NGS achieves up to 5 orders of magnitude of enrichment and sub-attomolar gene detection with minimal background. We provide an open-source software tool (FLASHit) for guide RNA design. Here we applied it to detection of antimicrobial resistance genes in respiratory fluid and dried blood spots, but FLASH-NGS is applicable to all areas that rely on multiplex PCR.