A Novel Dual Probe-based Method for Mutation Detection using Isothermal Amplification

Abstract

Cost efficient and rapid detection tools to detect mutations especially those linked to drug-resistance are important to address concerns of the rising multi-drug resistance infections. Here we integrated dual probes, namely a calibrator probe and an indicator probe, into isothermal amplification detection system. These two probes are designed to bind distinct regions on the same amplicon to determine the presence or absence of mutation. The calibrator probe signal is used as an internal signal calibrator for indicator probe which detects the presence or absence of the mutation. As an illustrative example, we evaluated the applicability of this dual probe method for detecting mutations associated with rifampicin (RIF) drug resistance at codons 516, 526 and 531 of the rpoB gene in Mycobacterium tuberculosis. In this assessment, we examined 127 artificial samples comprising wild type and mutant target sequences with single or multiple mutations. Our results demonstrated 100% accuracy of both wild type and mutant samples for mutations at codons 526 and 531. As regards to mutations at codon 516, the wild type was identified with 100% accuracy, while the mutant type was identified with 95% accuracy. Moreover, when we extended our evaluation using the Zeptometrix MTB Verification panel, our dual probe method correctly differentiated between the wild type and mutant, and identified the RIF-mutant strain which harbors mutations at codon 531 of the rpoB gene. Our isothermal mutation detection system, relying on dual probes exhibits a versatile approach. With the capability to identify mutations without prior knowledge of their specific mutation direction, our dual-probe method shows significant promise for applications in drug resistance nucleic acid testing, particularly in resource-limited settings.