Comparison of Biosensing Methods Based on Different Isothermal Amplification Strategies: A Case Study with Erwinia amylovora

• Published in: Biosensors (Basel) 2022-12, Vol.12 (12), p.1174
• Main Authors: Ivanov, Aleksandr V, Safenkova, Irina V, Drenova, Natalia V, Zherdev, Anatoly V, Dzantiev, Boris B
• Format: Article
• Language: English
• Subjects: Bacteria; Biosensors; Biotin; Blight; CRISPR; CRISPR/Cas; DNA polymerase; DNA Primers - genetics; Enzymes; Epidemics; Erwinia amylovora; Erwinia amylovora - genetics; Flowers & plants; Fluorescein; Gene amplification; highly sensitive detection; Laboratories; LAMP; lateral flow test; Microorganisms; Nucleic Acid Amplification Techniques - methods; Nucleic Acids; Pathogens; Quarantine; Recombinase; RNA polymerase; RPA; Sensitivity and Specificity; Thermal cycling
• ISSN: 2079-6374; 2079-6374
• DOI: 10.3390/bios12121174

Isothermal amplifications allow for the highly sensitive detection of nucleic acids, bypassing the use of instrumental thermal cycling. This work aimed to carry out an experimental comparison of the four most promising techniques: recombinase polymerase amplification (RPA) and loop-mediated isothermal amplification (LAMP) coupled with lateral flow test or coupled with additional amplification based on CRISPR/Cas12a resulting from the fluorescence of the Cas12a-cleaved probe. To compare the four amplification techniques, we chose the bacterial phytopathogen (causative agent of fire blight), which has a quarantine significance in many countries and possesses a serious threat to agriculture. Three genes were chosen as the targets and primers were selected for each one (two for RPA and six for LAMP). They were functionalized by labels (biotin, fluorescein) at the 5' ends for amplicons recognition by LFT. As a result, we developed LAMP-LFT, LAMP-CRISPR/Cas, RPA-LFT, and RPA-CRISPR/Cas for detection. The detection limit was 10 CFU/mL for LAMP-LFT, 10 CFU/mL for LAMP-CRISPR/Cas, and 10 CFU/mL for RPA-LFT and RPA-CRISPR/Cas. The results of four developed test systems were verified by qPCR on a panel of real samples. The developed assays based on RPA, LAMP, CRISPR/Cas12a, and LFT are rapid (30-55 min), user-friendly, and highly sensitive for detection. All proposed detection methods can be applied to fire blight diagnosis and effective management of this disease.