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Digital PCR reveals different effects of plant matrices on the recovery of Xylella fastidiosa DNA

Tanja Dreo: National Institute of Biology

<div><em>Xylella fastidiosa</em> infects many different host plants and some present a challenge for its reliable detection and quantification in both, diagnostics and research. To elucidate the inhibition arising from different host plants and the efficiency of molecular detection methods, altogether 129 samples of 29 genera were spiked with a low concentration of <em>X. fastidiosa</em> cells. The recovery of <em>X. fastidiosa</em> was determined with digital PCR after automated magnetic beads DNA extraction, and the results compared with the results of real-time PCR. Overall, real-time PCR was less sensitive and less resistant to inhibition than dPCR, in particular in <em>Rosmarinus</em>, <em>Lavandula</em>, <em>Origanum</em> and <em>Prunus</em> samples that necessitate analysis of diluted DNA. For samples of olives (<em>Olea europaea</em>), critical samples extensively tested for <em>X. fastidiosa</em> in Europe, high inhibitory effect was not alleviated with analysis of dilutions and dPCR revealed low recovery of <em>X. fastidiosa</em> DNA in addition to inhibitors. In olives and other samples with high inhibition and/or low DNA recovery, dPCR provided a more reliable and accurate detection and quantification method than real-time PCR at lower number of technical repeats.</div>