Isolation and molecular characterization of a Xylella fastidiosa subsp. multiplex strain from almond (Prunus dulcis) in Apulia, Southern Italy

Xylella fastidiosa is a xylem-limited phytopathogenic bacterium under regulation in the European Union as a priority pest. Given the potential risk posed by this pathogen to cultivated and ornamental plants, mandatory annual surveys and laboratory testing are required in Member States to early detect outbreaks. In the course of surveys carried out during early spring 2024 in the Apulia region (Southern Italy), X. fastidiosa subsp. multiplex was identified using quantitative real-time Polymerase Chain Reaction (qPCR), in a non-symptomatic sample from an almond tree (Prunus dulcis) in an orchard located in Santeramo in Colle, in Bari province. Multilocus sequence typing (MLST) was used to identify the subspecies and sequence type (ST) of the bacterium using the genomic DNAs extracted from the infected sample. Comparative sequence analysis of the seven MLST allele genes indicated that the obtained nucleotide sequences completely matched allele sequences of X. fastidiosa in PubMLST database corresponding to the allelic profile (Sequence Type) ST26 related to subsp. multiplex. Bacterial colonies consistent in morphology with X. fastidiosa were isolated from asymptomatic host samples and identity was confirmed by real-time PCR analysis. This is the first report of detection of X. fastidiosa subsp. multiplex ST26 in the EU.