Xylella fastidiosa is a plant pathogenic bacterium emerging in Europe. In France its emergence has been demonstrated through interceptions of contaminated coffee plants and, in 2015, by a survey of natural settings. The first French focus of contamination was detected in 2015 in Corsica; since then, almost 300 foci have been found and nearly 30 plant species have been declared contaminated, with Polygala myrtifolia remaining the principal host, suffering from severe leaf scorch. This study reports on the diversity of X. fastidiosa identified in France in 2015. Multilocus sequence analysis/typing revealed the presence of mainly X. fastidiosa subsp. multiplex sequence types (STs) ST6 and ST7. A focus of X. fastidiosa subsp. pauca ST53 was identified in mainland France; one sample contaminated by X. fastidiosa subsp. sandyi ST76, one novel recombinant, and coinfections of different isolates in individual samples were also identified, but could not be confirmed by successive samplings, indicating limited or transient contamination. Koch's postulates were fulfilled for two isolates of X. fastidiosa subsp. multiplex on P. myrtifolia, one being ST6 and the other ST7. Comparative genomics of the genome sequences of three French isolates (one ST6 and two ST7) with available sequences revealed that, unlike the American Dixon strain, the French ST6 and ST7 strains are devoid of a plasmid encoding a complete type IV secretion system. Other differences regarding phage sequences were highlighted. Altogether, the results suggest that the emergence of X. fastidiosa in France is linked to several introduction events of diverse strains from different subspecies.

Xylella fastidiosa is a xylem-limited phytopathogenic bacterium endemic to the Americas that has recently emerged in Asia and Europe. Although this bacterium is classified as a quarantine organism in the European Union, importation of plant material from contaminated areas and latent infection in asymptomatic plants have engendered its inevitable introduction. In 2012, four coffee plants (Coffea arabica and Coffea canephora) with leaf scorch symptoms growing in a confined greenhouse were detected and intercepted in France. After identification of the causal agent, this outbreak was eradicated. Three X. fastidiosa strains were isolated from these plants, confirming a preliminary identification based on immunology. The strains were characterized by multiplex PCR and by multilocus sequence analysis/typing (MLSA-MLST) based on seven housekeeping genes. One strain, CFBP 8073, isolated from C. canephora imported from Mexico, was assigned to X. fastidiosa subsp. fastidiosa/X. fastidiosa subsp. sandyi. This strain harbors a novel sequence type (ST) with novel alleles at two loci. The two other strains, CFBP 8072 and CFBP 8074, isolated from Coffea arabica imported from Ecuador, were allocated to X. fastidiosa subsp. pauca. These two strains shared a novel ST with novel alleles at two loci. These MLST profiles showed evidence of recombination events. We provide genome sequences for CFBP 8072 and CFBP 8073 strains. Comparative genomic analyses of these two genome sequences with publicly available X. fastidiosa genomes, including the Italian strain CoDiRO, confirmed these phylogenetic positions and provided candidate alleles for coffee plant adaptation. This study demonstrates the global diversity of X. fastidiosa and highlights the diversity of strains isolated from coffee plants.

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Xylella fastidiosa is a xylem-limited bacterium native to America and classified as a priority pest for EU regulation. Since 2013, X. fastidiosa has been identified in European countries with a Mediterranean climate, such as Italy, France, Spain and Portugal, with different subspecies and sequence types (ST) detected. Since 2015 X. fastidiosa subsp. multiplex ST6 and/or ST7 has been detected in Corsica and the Provence-Alpes-Côte d’Azur in almost 70 plant species, whereas X. fastidiosa subsp. pauca ST53 has been found in only two host plants. In this study, we report two new variants, recently detected in two separated areas of the PACA region, genetically related to the subspecies multiplex and assigned to (i) ST88 detected on Polygala myrtifolia, Hebe sp., Osteospermum ecklonis, Lavandula x intermedia, Coronilla glauca and Euryops chrysanthemoides and (ii) ST89: detected on Myoporum sp. and Viburnum tinus. Both variant strains were isolated in vitro. Moreover, we report here the identification of X. fastidiosa subsp. multiplex ST6 in a new region of the South of France, Occitanie (Aude), in plants from natural and urban settings and from a nursery.

In Europe, the meadow spittlebug Philaenus spumarius is the main known vector of the quarantine bacterium Xylella fastidiosa. So far detection and identification of X. fastidiosa has more often been performed from plant matrices than insects, mainly using a real‐time PCR and multilocus sequence typing (MLST) approach. Detection of X. fastidiosa in its insect vectors would enhance knowledge of the epidemiologic situation in France, specifically in the already infected Corsica and Provence‐Alpes‐Côte d’Azur (PACA) regions. The aim of this study was to validate a methodological approach to detect X. fastidiosa in P. spumarius, analysed individually or in groups of 10, using real‐time PCR and MLST, and to apply the approach to more than 4,000 individuals collected between 2015 and 2019 from infected areas. The corresponding results expanded our knowledge of the epidemiology of X. fastidiosa in France: (a) X. fastidiosa subsp. multiplex including the sequence types ST6 and ST7 were identified in the insect vector; (b) the rate of positive insects per infected area was as high as 33.3% in Corsica or 50% in the PACA region; (c) positive adults were found during winter; and (d) the bacterial load in P. spumarius (droplet digital PCR) usually ranged from 103 to 104 cells per insect, but could be as high as 105 or 106 cells per insect for some individuals (13%). The subspecies and sequence types detected in P. spumarius corresponded to the situation officially reported for plants in the same areas.