Genome-wide tiled detection of circulating Mycobacterium tuberculosis cell-free DNA using Cas13

Sri Gowtham Thakku, Jackson Lirette, Kanagavel Murugesan, Julie Chen, Grant Theron, Niaz Banaei, Paul C. Blainey, James Gomez, Sharon Y. Wong and Deborah T. Hung ()
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Sri Gowtham Thakku: Broad Institute of MIT and Harvard
Jackson Lirette: Broad Institute of MIT and Harvard
Kanagavel Murugesan: Stanford University School of Medicine
Julie Chen: Broad Institute of MIT and Harvard
Grant Theron: Stellenbosch University
Niaz Banaei: Stanford University School of Medicine
Paul C. Blainey: Broad Institute of MIT and Harvard
James Gomez: Broad Institute of MIT and Harvard
Sharon Y. Wong: Broad Institute of MIT and Harvard
Deborah T. Hung: Broad Institute of MIT and Harvard

Nature Communications, 2023, vol. 14, issue 1, 1-13

Abstract: Abstract Detection of microbial cell-free DNA (cfDNA) circulating in the bloodstream has emerged as a promising new approach for diagnosing infection. Microbial diagnostics based on cfDNA require assays that can detect rare and highly fragmented pathogen nucleic acids. We now report WATSON (Whole-genome Assay using Tiled Surveillance Of Nucleic acids), a method to detect low amounts of pathogen cfDNA that couples pooled amplification of genomic targets tiled across the genome with pooled CRISPR/Cas13-based detection of these targets. We demonstrate that this strategy of tiling improves cfDNA detection compared to amplification and detection of a single targeted locus. WATSON can detect cfDNA from Mycobacterium tuberculosis in plasma of patients with active pulmonary tuberculosis, a disease that urgently needs accurate, minimally-invasive, field-deployable diagnostics. We thus demonstrate the potential for translating WATSON to a lateral flow platform. WATSON demonstrates the ability to capitalize on the strengths of targeting microbial cfDNA to address the need for point-of-care diagnostic tests for infectious diseases.

Date: 2023
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DOI: 10.1038/s41467-023-37183-8

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