FLASH: A next-generation CRISPR diagnostic for multiplexed detection of antimicrobial resistance sequences
Lara Pesce Ares,
Katherine A Travisano,
Davis R Mumbengegwi,
Jennifer L Smith,
Peter M Mourani,
Carolyn S Calfee,
Norma F. Neff,
Eric D. Chow,
Peter S. Kim,
Posted 27 Sep 2018
bioRxiv DOI: 10.1101/426338 (published DOI: 10.1093/nar/gkz418)
Posted 27 Sep 2018
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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