FLASH: a next-generation CRISPR diagnostic for multiplexed detection of antimicrobial resistance sequences.

Quan, J; Langelier, C; Kuchta, A; Batson, J; Teyssier, N; Lyden, A; Caldera, S; McGeever, A; Dimitrov, B; King, R; +18 more...Wilheim, J; Murphy, M; Ares, LP; Travisano, KA; Sit, R; Amato, R; Mumbengegwi, DR; Smith, JL; Bennett, A; Gosling, RORCID logo; Mourani, PM; Calfee, CS; Neff, NF; Chow, ED; Kim, PS; Greenhouse, B; DeRisi, JL; Crawford, ED and (2019) FLASH: a next-generation CRISPR diagnostic for multiplexed detection of antimicrobial resistance sequences. Nucleic acids research, 47 (14). e83-. ISSN 0305-1048 DOI: 10.1093/nar/gkz418
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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.


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