LAMP-assisted CRISPR-Cas12a platform for detection of Bacillus anthracis spores in environmental samples

Environmental persistence of Bacillus anthracis spores sustains anthrax transmission, necessitating rapid and field-deployable detection tools. This study aimed to develop and quantitatively evaluate a LAMP-assisted CRISPR-Cas12a assay for sensitive and specific detection of B. anthracis spores in soil and meat meal matrices. Two B. anthracis-specific target genes plasmid-encoded lef and chromosomal SNP locus (CR5)- were selected. Target-specific LAMP primers and CRISPR crRNAs were designed using Primer Explorer, CRISPOR, and RNAfold platforms. The LAMP-CRISPR/Cas12a assay was optimised for reaction conditions and evaluated for analytical sensitivity and specificity using UV-inactivated spores and closely related Bacillus spp. Environmental applicability was assessed via spiking experiments in sterile soil and meat meal using the GABRI recovery method. Field validation was performed on 100 samples from anthrax-endemic regions of India, with performance compared against the WOAH-recommended lef gene-based real-time PCR. LAMP-CRISPR-Cas12a assay achieved detection limits of 10 spores/ml (lef) and 10² spores/ml (CR5), with no cross-reactivity against related species. In spiked matrices, spore recovery ranged from 50 to 75%, and detection sensitivity remained consistent. Field evaluation demonstrated a sensitivity of 91.70% and specificity of 100%, with near-perfect agreement (κ = 0.95) relative to real-time PCR. The assay delivered results within ∼70 min, including amplification and detection. The LAMP-assisted CRISPR-Cas12a platform provides a rapid, sensitive, and cost-effective approach for environmental detection of B. anthracis spores. The minimal equipment requirements and high diagnostic accuracy support its applicability for field-level surveillance and biosafety monitoring in resource-limited settings.