FLASH-TB: an Application of Next-Generation CRISPR to Detect Drug Resistant Tuberculosis from Direct Sputum

• Published in: Journal of clinical microbiology Vol. 61; no. 4; p. e0163422
• Main Authors: Tram, Trinh Thi Bich, Ha, Vu Thi Ngoc, Trieu, Le Pham Tien, Ashton, Philip M., Crawford, Emily D., Thu, Do Dang Anh, Quang, Nguyen Le, Thwaites, Guy E., Walker, Timothy M., Anscombe, Catherine, Thuong, Nguyen Thuy Thuong
• Format: Journal Article
• Language: English
• Published: United States American Society for Microbiology 20.04.2023
• Subjects: Antitubercular Agents - pharmacology; Antitubercular Agents - therapeutic use; Clinical Microbiology; Editor's Pick; Humans; Microbial Sensitivity Tests; Mycobacteriology and Aerobic Actinomycetes; Mycobacterium tuberculosis - genetics; Sputum - microbiology; Tuberculosis - drug therapy; Tuberculosis, Multidrug-Resistant - microbiology; RNA guide; CRISPR; drug resistance; Mycobacterium tuberculosis; FLASH; sequencing
• ISSN: 0095-1137; 1098-660X; 1098-660X
• DOI: 10.1128/jcm.01634-22

Offering patients with tuberculosis (TB) an optimal and timely treatment regimen depends on the rapid detection of Mycobacterium tuberculosis (Mtb) drug resistance from clinical samples. Finding Low Abundance Sequences by Hybridization (FLASH) is a technique that harnesses the efficiency, specificity, and flexibility of the Cas9 enzyme to enrich targeted sequences. Offering patients with tuberculosis (TB) an optimal and timely treatment regimen depends on the rapid detection of Mycobacterium tuberculosis (Mtb) drug resistance from clinical samples. Finding Low Abundance Sequences by Hybridization (FLASH) is a technique that harnesses the efficiency, specificity, and flexibility of the Cas9 enzyme to enrich targeted sequences. Here, we used FLASH to amplify 52 candidate genes probably associated with resistance to first- and second-line drugs in the Mtb reference strain (H37Rv), then detect drug resistance mutations in cultured Mtb isolates, and in sputum samples. 92% of H37Rv reads mapped to Mtb targets, with 97.8% of target regions covered at a depth ≥ 10X. Among cultured isolates, FLASH-TB detected the same 17 drug resistance mutations as whole genome sequencing (WGS) did, but with much greater depth. Among the 16 sputum samples, FLASH-TB increased recovery of Mtb DNA compared with WGS (from 1.4% [IQR 0.5-7.5] to 33% [IQR 4.6-66.3]) and average depth reads of targets (from 6.3 [IQR 3.8-10.5] to 1991 [IQR 254.4-3623.7]). FLASH-TB identified Mtb complex in all 16 samples based on IS 1081 and IS 6110 copies. Drug resistance predictions for 15/16 (93.7%) clinical samples were highly concordant with phenotypic DST for isoniazid, rifampicin, amikacin, and kanamycin [15/15 (100%)], ethambutol [12/15 (80%)] and moxifloxacin [14/15 (93.3%)]. These results highlighted the potential of FLASH-TB for detecting Mtb drug resistance from sputum samples.