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

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. In this work, the authors developed a multiplexed, minimally invasive, CRISPR-Cas13-based approach to detect Mycobacterium tuberculosis cell-free DNA in the plasma of active pulmonary tuberculosis patients.

Automated summary

This study presents a new method called WATSON that can detect microbial cell-free DNA (cfDNA) for diagnosing infection. WATSON utilizes pooled amplification and CRISPR/Cas13-based detection to improve the detection of cfDNA compared to traditional methods. This approach shows potential for point-of-care diagnostic tests for infectious diseases.