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

Year: 2019

Type: article

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.

Source: Nucleic Acids Research

DOI: 10.1093/nar/gkz418

Institutions: University of California, San Francisco, Chan Zuckerberg Biohub San Francisco, Chan Zuckerberg Initiative (United States), Wellcome Sanger Institute, University of Namibia, Children's Hospital Colorado, University of Colorado Anschutz, Stanford Medicine, Stanford University

Language: English

Topic: CRISPR and Genetic Engineering

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

SDG: Good health and well-being

Open Access status: gold

Estimated APC paid: $3,992

Funders: Wellcome Trust, Chan Zuckerberg Initiative, National Institutes of Health, National Heart, Lung, and Blood Institute, National Institute of General Medical Sciences, Claude D. Pepper Older Americans Independence Center, University of California San Francisco

Awards: ARDS Endotypes: Expanded Analysis of Clinical and Biological Phenotypes and Evolution Over Time, Resource centre for genomic epidemiology of malaria., The Microbiome, Virome and Host Responses Preceding Ventilator-Associated Pneumon, Precision Medicine in the Acute Respiratory Distress Syndrome, G7595298251, Cigarette Smoke Exposure and Acute Lung Injury After Severe Blunt Trauma, Wellcome Trust Sanger Institute - generic account for deposition of all core- funded research papers, Profiling the Lung Transcriptome for Precision Diagnosis of Respiratory Infections using Host/Pathogen Metagenomic Sequencing, Clinical Pharmacology, Drug Action and Pharmacogenetics

OpenAlex ID: W2952835014