A one-pot, one-step CRISPR platform (CRISPR-one) for nucleic acid detection: Application for the detection of Mycoplasma pneumoniae

Abstract

The conventional CRISPR-mediated detection technologies typically involve two separate steps: target pre-amplification and CRISPR-mediated signal detection. This multi-step procedure is not only cumbersome but also prone to cross-contamination. Here, we propose a new CRISPR-mediated nucleic acid detection methodology, termed CRISPR-one (CRISPR-mediated testing in one-tube, one-pot). At a constant temperature, CRISPR-one carries out both multiple cross displacement amplification (MCDA) for target pre-amplification and CRISPR/AapCas12b-based cleavage for signal detection in a single reaction pot. The novel CRISPR-one technique is employed for detecting Mycoplasma pneumoniae (M. pneumoniae), a causative agent for community-acquired pneumonia in children. M. pneumoniae CRISPR-one targets the CARDS (community-acquired respiratory distress syndrome toxin) gene and performs at 60 ºC for 50 min with only basic instrumentation required. The results can be easily visualized through a real-time fluorescence instrument, with the entire process taking less than an hour. The lowest detection limit of M. pneumoniae CRISPR-one was 50 fg (∼55 copies) of genomic DNA per reaction, and no cross-reactivity with non-M. pneumoniae templates was observed. In clinical applications, the CRISPR-one assay demonstrated a high level of agreement with both the microfluidic chip method (Kappa value: 0.95) and real-time PCR (Kappa value: 0.93) when analyzing 135 oropharynx swab samples. There is no statistical difference in detection efficiency between our assay and other methods. Together, the CRISPR-one developed here offers a rapid, convenient, highly sensitive, and specific approach for pathogen detection (e.g., M. pneumoniae), serving as an invaluable tool for clinical diagnosis and epidemiologic surveillance, particularly in resource-limited laboratories.