Comparison of real-time PCR and droplet digital PCR for the detection of Xylella fastidiosa in plants

Enora Dupas; Bruno Legendre; Valérie Olivier; Françoise Poliakoff; Charles Manceau; Amandine Cunty

In our study, the two methods showed the same limit of detection for O. europaea, P. myrtifolia 371 and R. officinalis. Real-time PCR allowed better detection of 0.5 log for L. angustifolia, and 372 ddPCR allowed better detection of 0.5 log for Q. ilex and bacterial suspension. 373 ddPCR was also compared with real-time PCR on 22 naturally infected samples. Using real-374 time PCR, two samples P13 and Q04 had a Ct value higher than 38, and were thus considered 375 negative, i.e. not infected by Xf. As these two samples were frozen at -20°C for one year, it is 376 possible that the DNA was altered, explaining the higher Ct values obtained in this study. The 377 other 20 samples, considered positive, had a Ct value lower than 38. Using ddPCR, Xf was 378 detected in 21 samples, as more than two positive droplets were obtained. ddPCR did not reveal