Dual detection of hypervirulent genes of Klebsiella pneumoniae using a single CRISPR-Cas12a system modulated using entropy-driven circuits

Abstract

A set of different CRISPR-based analyses have been extensively used to detect nucleic acids owing to their characteristics of being sensitive, specific, rapid and easy to operate. However, one of its major challenges is application to multiplex detection (https://pubmed.ncbi.nlm.nih.gov/31460243/) using a single CRISPR-Cas system because the detection relies on the indiscriminate trans-cleavage activity of the Cas protein. Here we developed a CRISPR-based dual gene assay system for hypervirulent Klebsiella pneumoniae (hvKp) by integrating two parallel entropy-driven circuits (EDCs) and the trans-cleavage activity of the Cas12a protein towards fluorescent substrate reporters. The EDC reaction released two different fluorescent reporters and the same trigger probe according to different targets. The trigger probe activated the trans-cleavage activity of Cas12a towards reporter probes to achieve the purpose of the dual detection of different genes with a single CRISPR-Cas12a system in one tube. Furthermore, the assay system was designed to detect different mRNA sequences (rmpA and peg-344) of hvKp, requiring no reverse transcription procedure and providing technical support for the identification of hvKp and classical Klebsiella pneumoniae (cKp). The detection limits for rmpA and peg-344 were as low as 0.10 fmol L⁻¹ and 0.17 fmol L⁻¹, respectively, within 25 minutes under isothermal conditions. It enabled rapid dual detection of hvKp in a single tube using only a CRISPR-Cas12a system, demonstrating great potential for point-of-care testing due to its high sensitivity, low cost, and robust ability to detect various mRNA biomarkers.