Tracing the Origin of <i>Xylella fastidiosa</i> Subspecies <i>pauca</i> ST53 Strains in France

<i>Xylella fastidiosa</i> is a plant-pathogenic bacterium native to the Americas. It has a wide host range and causes significant diseases in economically important crops, including grapevines, citrus, and olive trees. Since 2013, this bacterium has been detected in Europe and other countries of the Mediterranean basin, leading to the identification of several subspecies (<i>multiplex, fastidiosa</i> and <i>pauca</i>) and sequence types (STs) in various plant species in Italy, France, the Balearic Islands and mainland Spain, Portugal, Israel and Lebanon. This study focuses on genomic analyses of the subspecies <i>pauca</i> ST53 strains detected in France. ST53 was identified (i) on intercepted coffee plants in the Pays-de-la-Loire region in 2014 and 2015, and (ii) on two infected host plants collected in Menton in the Provence-Alpes-Côte d'Azur region in 2015 and 2019. As an efficient and promising alternative to cell culture, the targeted enrichment method developed specifically to capture <i>X. fastidiosa</i> gDNA was applied to obtain the whole genome. Phylogenetic and genomic comparisons were carried out to compare the ST53 genomic sequences of the samples from France with a range of <i>X. fastidiosa</i> subspecies <i>pauca</i> genomic sequences from public databases, including ST53 from Italy and Costa Rica. The results obtained from these different approaches revealed close genetic relatedness between the strains. A tip-dating analysis and transmission tree were performed, supporting the hypothesis that some ST53 strains from France may be related to the same introduction event than the Italian strains.