Update of the Xylella spp. host plant database

Update of the Xylella spp. host plant database - systematic literature search up to 30 June 2023

This scientific report provides an update of the Xylella spp. host plant database, aiming to provide information and scientific support to risk assessors, risk managers and researchers dealing with Xylella spp. Upon a mandate of the European Commission, EFSA created and regularly updates a database of host plant species of Xylella spp. The current mandate covers the period 2021-2026. This report is related to the ninth version of the database published in Zenodo in the EFSA Knowledge Junction community, covering literature published from 1 January 2023 up to 30 June 2023, and recent Europhyt outbreak notifications. Informative data have been extracted from 47 selected publications. Seven new host plants were identified and added to the database. These plant species were naturally infected by X. fastidiosa subsp. multiplex in France, Spain and the United States. No additional data were retrieved for X. taiwanensis, and no additional multilocus sequence tipes (STs) were identified worldwide. New information on the tolerant/resistant response of plant species to X. fastidiosa infection were added to the database. The Xylella spp. host plant species were listed in different categories based on the number and type of detection methods applied for each finding. The overall number of Xylella spp. host plants determined with at least two different detection methods or positive with one method (between sequencing and pure culture isolation (category A), reaches now 439 plant species, 200 genera and 69 families. Such numbers rise to 696 plant species, 307 genera and 88 families if considered regardless of the detection methods applied (category E).

Update of the Xylella spp. host plant database - systematic literature search up to 31 December 2022

This scientific report provides an update of the Xylella spp. host plant database, aiming to provide information and scientific support to risk assessors, risk managers and researchers dealing with Xylella spp. Upon a mandate of the European Commission, EFSA created and regularly updates a database of host plant species of Xylella spp. The current mandate covers the period 2021-2026. This report is related to the eighth version of the database published in Zenodo in the EFSA Knowledge Junction community, covering literature published from 1 July 2022 up to 31 December 2022, and recent Europhyt outbreak notifications. Informative data have been extracted from 21 selected publications. Twelve new host plants were identified and added to the database. Nine plant species were reported from Portugal and naturally infected by subsp. multiplex or unknown (i.e. not reported). Three plant species were successfully artificially infected by subsp. fastidiosa. No additional data were retrieved for X. taiwanensis, and no additional STs were identified worldwide. New information on the tolerant/resistant response of plant species to X. fastidiosa infection were added to the database. The overall number of Xylella spp. host plants determined with at least two different detection methods or positive with one method (between sequencing and pure culture isolation) reaches now 433 plant species, 197 genera and 68 families. Such numbers rise to 690 plant species, 306 genera and 88 families if considered regardless of the detection methods applied.

Assessing the Genetic Diversity of Daylily Germplasm Using SSR Markers: Implications for Daylily Breeding

This work aims to characterize the genetic diversity of species, early hybrids, and cultivars using microsatellite simple sequence repeat (SSR) markers, as well as analyze and identify the origin of Hemerocallis spp. early hybrids. For this research, samples were collected from different types of daylily species, early hybrids (known or hypothetically first-generation hybrids from Hemerocallis species), foreign, and Lithuanian varieties. An initial screening of SSR primers developed for Hemerocallis citrina was performed, and their suitability for testing other daylily species and hybrids was evaluated. The genetic diversity was assessed with the selected eight-primer set, and molecular SSR profiles were created. Primer SAU00097 is the most informative according to heterozygosity (0.95) and polymorphism information content (PIC) (0.17). The highest heterozygosity was observed in Lithuanian cultivars (0.713), the lowest in species (0.583). Genetic relationships between species show that only fulvous daylilies are separated into a different cluster. The highest variation among genotypes was observed in the species group (18%), while modern cultivars had the slightest variation among genotypes (1%). The putative origin of early hybrids was analyzed using a likelihood heatmap of all genotypes. Results show what species might be used in breeding for early hybrids. Several modern diploid and tetraploid daylily cultivars have triploid species as ancestors.

Update of the Xylella spp. host plant database - systematic literature search up to 30 June 2022

This scientific report provides an update of the Xylella spp. host plant database, aiming to provide information and scientific support to risk assessors, risk managers and researchers dealing with Xylella spp. Upon a mandate of the European Commission, EFSA created and regularly updates a database of host plant species of Xylella spp. The current mandate covers the period 2021-2026. This report is related to the seventh version of the database published in Zenodo in the EFSA Knowledge Junction community, covering literature published from 1 January 2022 up to 30 June 2022, and recent Europhyt outbreak notifications. Informative data have been extracted from 30 selected publications. Fifteen new host plants were identified and added to the database. Those plant species were reported from Brazil, France, Italy, Portugal and Spain, and infected by subsp. multiplex, pauca or unknown (i.e. not reported). No additional data were retrieved for X. taiwanensis. Two new STs (namely ST88 and ST89) belonging to subspecies multiplex were identified in host plants in natural conditions, and new information on the tolerant/resistant response of plant species to X. fastidiosa infection were added to the database. The overall number of Xylella spp. host plants determined with at least two different detection methods or positive with one method (between sequencing and pure culture isolation) reaches now 423 plant species, 194 genera and 68 families. Such numbers rise to 679 plant species, 304 genera and 88 families if considered regardless of the detection methods applied.

Xylella fastidiosa in Europe: From the Introduction to the Current Status

Xylella fastidiosa is xylem-limited bacterium capable of infecting a wide range of host plants, resulting in Pierce's disease in grapevine, citrus variegated chlorosis, olive quick decline syndrome, peach phony disease, plum leaf scald, alfalfa dwarf, margin necrosis and leaf scorch affecting oleander, coffee, almond, pecan, mulberry, red maple, oak, and other types of cultivated and ornamental plants and forest trees. In the European Union, X. fastidiosa is listed as a quarantine organism. Since its first outbreak in the Apulia region of southern Italy in 2013 where it caused devastating disease on Olea europaea (called olive leaf scorch and quick decline), X. fastidiosa continued to spread and successfully established in some European countries (Corsica and PACA in France, Balearic Islands, Madrid and Comunitat Valenciana in Spain, and Porto in Portugal). The most recent data for Europe indicates that X. fastidiosa is present on 174 hosts, 25 of which were newly identified in 2021 (with further five hosts discovered in other parts of the world in the same year). From the six reported subspecies of X. fastidiosa worldwide, four have been recorded in European countries (fastidiosa, multiplex, pauca, and sandyi). Currently confirmed X. fastidiosa vector species are Philaenus spumarius, Neophilaenus campestris, and Philaenus italosignus, whereby only P. spumarius (which has been identified as the key vector in Apulia, Italy) is also present in Americas. X. fastidiosa control is currently based on pathogen-free propagation plant material, eradication, territory demarcation, and vector control, as well as use of resistant plant cultivars and bactericidal treatments.

Update of the Xylella spp. host plant database - systematic literature search up to 31 December 2021

This Scientific report provides an update of the Xylella spp. host plant database, aiming to provide information and scientific support to risk assessors, risk managers and researchers dealing with Xylella spp. Upon a mandate of the European Commission, EFSA created and regularly updated a database of host plant species of Xylella spp. The current mandate covers the period 2021–2026. This report is related to the sixth version of the database published in Zenodo in the EFSA Knowledge Junction community, covering literature published from 1 July 2021 up to 31 December 2021, and recent Europhyt outbreak notifications. Informative data have been extracted from 29 selected publications. Eleven new host plants were identified and added to the database: six plant species naturally infected by subsp. multiplex of X. fastidiosa in the EU (France, Italy and Portugal) and five plant species artificially infected by different X. fastidiosa subspecies (multiplex, pauca, fastidiosa and sandyi). No additional data were retrieved for X. taiwanensis. New information on the tolerant/resistant response of plant species to X. fastidiosa infection were added, while no new STs have been identified worldwide compared to the previous update published in January 2022. The overall number of Xylella spp. host plants determined with at least two different detection methods or positive with one method (between: sequencing, pure culture isolation) reaches now 412 plant species, 190 genera and 68 families. Such numbers rise to 664 plant species, 299 genera and 88 families if considered regardless of the detection methods applied.

Investigating plant disease outbreaks with long-read metagenomics: sensitive detection and highly resolved phylogenetic reconstruction applied to Xylella fastidiosa

Early disease detection is a prerequisite for enacting effective interventions for disease control. Strains of the bacterial plant pathogen Xylella fastidiosa have recurrently spread to new crops in new countries causing devastating outbreaks. So far, investigation of outbreak strains and highly resolved phylogenetic reconstruction have required whole-genome sequencing of pure bacterial cultures, which are challenging to obtain due to the fastidious nature of X. fastidiosa. Here, we show that culture-independent metagenomic sequencing, using the Oxford Nanopore Technologies MinION long-read sequencer, can sensitively and specifically detect the causative agent of Pierce’s disease of grapevine, X. fastidiosa subspecies fastidiosa. Using a DNA sample from a grapevine in Virginia, USA, it was possible to obtain a metagenome-assembled genome (MAG) of sufficient quality for phylogenetic reconstruction with SNP resolution. The analysis placed the MAG in a clade with isolates from Georgia, USA, suggesting introduction of X. fastidiosa subspecies fastidiosa to Virginia from the south-eastern USA. This proof of concept study, thus, revealed that metagenomic sequencing can replace culture-dependent genome sequencing for reconstructing transmission routes of bacterial plant pathogens.

Phylogenetics of Historical Host Switches in a Bacterial Plant Pathogen

Xylella fastidiosa is an insect-transmitted bacterial plant pathogen found across the Americas and, more recently, worldwide. X. fastidiosa infects plants of at least 563 species belonging to 82 botanical families. While the species X. fastidiosa infects many plants, particular strains have increased plant specificity. Understanding the molecular underpinnings of plant host specificity in X. fastidiosa is vital for predicting host shifts and epidemics. While there may exist multiple genetic determinants of host range in X. fastidiosa, the drivers of the unique relationships between X. fastidiosa and its hosts should be elucidated. Our objective with this study was to predict the ancestral plant hosts of this pathogen using phylogenetic and genomic methods based on a large data set of pathogen whole-genome data from agricultural hosts. We used genomic data to construct maximum-likelihood (ML) phylogenetic trees of subsets of the core and pan-genomes. With those trees, we ran ML ancestral state reconstructions of plant host at two taxonomic scales (genus and multiorder clades). Both the core and pan-genomes were informative in terms of predicting ancestral host state, giving new insight into the history of the plant hosts of X. fastidiosa. Subsequently, gene gain and loss in the pan-genome were found to be significantly correlated with plant host through genes that had statistically significant associations with particular hosts. IMPORTANCE Xylella fastidiosa is a globally important bacterial plant pathogen with many hosts; however, the underpinnings of host specificity are not known. This paper contains important findings about the usage of phylogenetics to understand the history of host specificity in this bacterial species, as well as convergent evolution in the pan-genome. There are strong signals of historical host range that give us insights into the history of this pathogen and its various invasions. The data from this paper are relevant in making decisions for quarantine and eradication, as they show the historical trends of host switching, which can help us predict likely future host shifts. We also demonstrate that using multilocus sequence type (MLST) genes in this system, which is still a commonly used process for policymaking, does not reconstruct the same phylogenetic topology as whole-genome data.

Update of the Xylella spp. host plant database - systematic literature search up to 30 June 2021

Following a request from the European Commission, EFSA was asked to create and regularly update a database of host plant species of Xylella spp. The mandate now covers the period 2021-2026 and EFSA is requested to release an update of the database twice per year. The aim of the database is to provide information and scientific support to risk assessors, risk managers and researchers dealing with Xylella spp. This report is related to the fifth version of the database published in Zenodo in the EFSA Knowledge Junction community, covering literature published from 1 January 2021 up to 30 June 2021, and recent Europhyt outbreak notifications. Informative data have been extracted from 41 selected publications. Nineteen new host plants were identified and added to the database since the previous update published in June 2021. Those plant species were reported naturally infected by subsp. multiplex or unknown (i.e. not reported in the publication) of X. fastidiosa in the UE (France, Spain and Portugal). No additional data were retrieved for X. taiwanensis. New information on the tolerant/resistant response of plant species to X. fastidiosa infection were added, while no new STs have been identified worldwide compared to the previous update published in May 2021. The overall number of Xylella spp. host plants determined with at least two different detection methods or positive with one method (between: sequencing, pure culture isolation) now reaches 407 plant species, 185 genera and 68 families. Such numbers raise to 655 plant species, 293 genera and 88 families if considered regardless of the detection method applied.

The potential direct economic impact and private management costs of an invasive alien species: Xylella fastidiosa on Lebanese wine grapes

Since its outbreak in 2013 in Italy, the harmful bacterium Xylella fastidiosa has continued to spread throughout the Euro-Mediterranean basin and, more recently, in the Middle East region. Xylella fastidiosa subsp. fastidiosa is the causal agent of Pierce’s disease on grapevines. At present, this alien subspecies has not been reported in Lebanon but if this biological invader was to spread with no cost-effective and sustainable management, it would put Lebanese vineyards at a certain level of risk. In the absence of an Xylella fastidiosa subsp. fastidiosa outbreak, the gross revenue generated by Lebanese wine growers is estimated as close to US$22 million/year for an average period of 5 years (2015–2019). The potential quantitative economic impacts of an Xylella fastidiosa subsp. fastidiosa outbreak and particularly, the private control costs have not been assessed yet for this country as well as for others which Xylella fastidiosa may invade. Here, we have aimed to estimate the potential direct economic impact on growers’ livelihoods and provide the first estimate of the private management costs that a theoretical Xylella fastidiosa subsp. fastidiosa outbreak in Lebanon would involve. For this purpose, we used a Partial Budget approach at the farm gate. For the country as a whole, we estimated that a hypothetical full spread of Xylella fastidiosa subsp. fastidiosa on Lebanese wine grapes would lead to maximum potential gross revenue losses of almost US$ 11 million for an average recovery period of 4 years, to around US$ 82.44 million for an average grapevine life span period of 30 years in which infected plants are not replaced at all. The first yearly estimated additional management cost is US$853 per potentially infected hectare. For a recovery period of 4 years, the aggregate estimated additional cost would reach US$2374/ha, while the aggregate net change in profit would be US$-4046/ha. Furthermore, additional work will be needed to estimate the public costs of an Xylella fastidiosa subsp. fastidiosa outbreak in Lebanon. The observed costs in this study support the concerned policy makers and stakeholders to implement a set of reduction management options against Xylella fastidiosa subsp. fastidiosa at both national and wine growers’ levels. This re-emerging alien biota should not be neglected in this country. This understanding of the potential direct economic impact of Xylella fastidiosa subsp. fastidiosa and the private management costs can also benefit further larger-scale studies covering other potential infection areas and plant hosts.

Aphrophoridae Role in Xylella fastidiosa subsp. pauca ST53 Invasion in Southern Italy

The Philaenus spumarius L. (Hemiptera Aphrophoridae) is a xylem-sap feeder vector that acquires Xylella fastidiosa subsp. pauca ST53 during feeding on infected plants. The bacterium is the plant pathogen responsible for olive quick decline syndrome that has decimated olive trees in Southern Italy. Damage originates mainly from the insect vector attitude that multiplies the pathogen potentialities propagating Xf in time and space. The principal action to manage insect-borne pathogens and to contain the disease spread consists in vector and transmission control. The analysis of an innovative and sustainable integrated pest management quantitative strategy that targets the vector and the infection by combining chemical and physical control means demonstrates that it is possible to stop the Xylella invasion. This review updates the available topics addressing vectors' identification, bionomics, infection management, and induced disease by Xylella invasion to discuss major available tools to mitigate the damage consequent to the disease.

Complete Genome Sequence of Xylella taiwanensis and Comparative Analysis of Virulence Gene Content With Xylella fastidiosa

The bacterial genus Xylella contains plant pathogens that are major threats to agriculture in America and Europe. Although extensive research was conducted to characterize different subspecies of Xylella fastidiosa (Xf), comparative analysis at above-species levels was lacking due to the unavailability of appropriate data sets. Recently, a bacterium that causes pear leaf scorch (PLS) in Taiwan was described as the second Xylella species (i.e., Xylella taiwanensis; Xt). In this work, we report the complete genome sequence of Xt type strain PLS229^T. The genome-scale phylogeny provided strong support that Xf subspecies pauca (Xfp) is the basal lineage of this species and Xylella was derived from the paraphyletic genus Xanthomonas. Quantification of genomic divergence indicated that different Xf subspecies share ∼87–95% of their chromosomal segments, while the two Xylella species share only ∼66–70%. Analysis of overall gene content suggested that Xt is most similar to Xf subspecies sandyi (Xfs). Based on the existing knowledge of Xf virulence genes, the homolog distribution among 28 Xylella representatives was examined. Among the 11 functional categories, those involved in secretion and metabolism are the most conserved ones with no copy number variation. In contrast, several genes related to adhesins, hydrolytic enzymes, and toxin-antitoxin systems are highly variable in their copy numbers. Those virulence genes with high levels of conservation or variation may be promising candidates for future studies. In summary, the new genome sequence and analysis reported in this work contributed to the study of several important pathogens in the family Xanthomonadaceae.

Update of the Xylella spp. host plant database - systematic literature search up to 31 December 2020

Following a request from the European Commission, EFSA was asked to create and regularly update a database of host plant species of Xylella spp. Complying with an extension of the previous mandate, which now covers the period 2021-2026, the current version of Xylella spp. host plant database updates the previous release dated April 2020. Informative data have been extracted from 86 recent publications retrieved through an extensive literature search. This report is related to the fourth version of the database published in Zenodo in the EFSA Knowledge Junction community, covering articles selected from: a systematic literature review conducted up to 31 December 2020, Europhyt outbreak notifications up to 18 March 2021 and communications from research groups and national authorities. Forty-three new host plant species of X. fastidiosa, identified through the data extracted from the selected publications, have been added to the database. Those plant species were reported as naturally or artificially infected by subsp. fastidiosa, multiplex, pauca or unknown (i.e. not reported in the publication) subspecies of X. fastidiosa. New information on the tolerant/resistant response of plant species or varieties to X. fastidiosa infection is also reported. No additional data were retrieved for X. taiwanensis. This new version of the database includes no update on the number of Sequence Types (STs) identified so far, which remains unchanged. The overall number of Xylella spp. host plants determined with at least two different detection methods or positive with one method (between: sequencing, pure culture isolation) reaches now 385 plant species, 179 genera and 67 families. Such numbers rise to 638 plant species, 289 genera and 87 families if considered regardless of the detection method applied. The database will be issued twice per year, with the aim to provide information and scientific support to risk assessors, risk managers and researchers dealing with Xylella spp.

Allopatric Plant Pathogen Population Divergence following Disease Emergence

Within the landscape of globally distributed pathogens, populations differentiate via both adaptive and nonadaptive forces. Individual populations are likely to show unique trends of genetic diversity, host-pathogen interaction, and ecological adaptation. In plant pathogens, allopatric divergence may occur particularly rapidly within simplified agricultural monoculture landscapes. As such, the study of plant pathogen populations in monocultures can highlight the distinct evolutionary mechanisms that lead to local genetic differentiation. Xylella fastidiosa is a plant pathogen known to infect and damage multiple monocultures worldwide. One subspecies, Xylella fastidiosa subsp. fastidiosa, was first introduced to the United States ∼150 years ago, where it was found to infect and cause disease in grapevines (Pierce's disease of grapevines, or PD). Here, we studied PD-causing subsp. fastidiosa populations, with an emphasis on those found in the United States. Our study shows that following their establishment in the United States, PD-causing strains likely split into populations on the East and West Coasts. This diversification has occurred via both changes in gene content (gene gain/loss events) and variations in nucleotide sequence (mutation and recombination). In addition, we reinforce the notion that PD-causing populations within the United States acted as the source for subsequent subsp. fastidiosa outbreaks in Europe and Asia.IMPORTANCE Compared to natural environments, the reduced diversity of monoculture agricultural landscapes can lead bacterial plant pathogens to quickly adapt to local biological and ecological conditions. Because of this, accidental introductions of microbial pathogens into naive regions represents a significant economic and environmental threat. Xylella fastidiosa is a plant pathogen with an expanding host and geographic range due to multiple intra- and intercontinental introductions. X. fastidiosa subsp. fastidiosa infects and causes disease in grapevines (Pierce's disease of grapevines [PD]). This study focused on PD-causing X. fastidiosa populations, particularly those found in the United States but also invasions into Taiwan and Spain. The analysis shows that PD-causing X. fastidiosa has diversified via multiple cooccurring evolutionary forces acting at an intra- and interpopulation level. This analysis enables a better understanding of the mechanisms leading to the local adaptation of X. fastidiosa and how a plant pathogen diverges allopatrically after multiple and sequential introduction events.

A non-targeted metabolomics study on Xylella fastidiosa infected olive plants grown under controlled conditions

In the last decade, the bacterial pathogen Xylella fastidiosa has devastated olive trees throughout Apulia region (Southern Italy) in the form of the disease called "Olive Quick Decline Syndrome" (OQDS). This study describes changes in the metabolic profile due to the infection by X. fastidiosa subsp. pauca ST53 in artificially inoculated young olive plants of the susceptible variety Cellina di Nardò. The test plants, grown in a thermo-conditioned greenhouse, were also co-inoculated with some xylem-inhabiting fungi known to largely occur in OQDS-affected trees, in order to partially reproduce field conditions in terms of biotic stress. The investigations were performed by combining NMR spectroscopy and MS spectrometry with a non-targeted approach for the analysis of leaf extracts. Statistical analysis revealed that Xylella-infected plants were characterized by higher amounts of malic acid, formic acid, mannitol, and sucrose than in Xylella-non-infected ones, whereas it revealed slightly lower amounts of oleuropein. Attention was paid to mannitol which may play a central role in sustaining the survival of the olive tree against bacterial infection. This study contributes to describe a set of metabolites playing a possible role as markers in the infections by X. fastidiosa in olive.

Xylella fastidiosa invasion of new countries in Europe, the Middle East and North Africa: Ranking the potential exposure scenarios

After the recent high-impact European outbreaks of Xylella fastidiosa (Xf), a xylem-limited plant pathogenic bacterium native to the Americas, this research aims to rank the risks of potential entry, establishment and spread of Xf in new countries across Europe, the Middle East and North Africa. A novel risk-ranking technique is developed, based on combining entry risk drivers (imported plants, direct flights and ferry connections) with risk factors related to establishment and spread (presence of potential insect vectors, vulnerable economic crops, alternative hosts and climate suitability) of this pathogen. This reveals that western European countries have the highest risk for entry, but that the Mediterranean basin runs the highest risk for establishment and spread of Xf. Lebanon in particular has the highest level of risk for Xf dispersal within its suitable territory. Countries without current outbreaks combining high risks of Xf arrival and establishment are mainly in the Mediterranean basin: Turkey is at the highest level of risk, followed by Greece, Morocco and Tunisia, which are ranked at the high level. The ranking model also confirms the vulnerability, in terms of invasion by Xf, of southern European countries (Italy, Portugal and Spain) in which the pathogen has already been reported. High summer temperatures in these southern countries are likely to be the significant determinant for the overall invasion process, while northern European countries have a high level risk for the arrival of the pathogen, but relatively low summer temperatures may limit establishment and spread of major outbreaks. In general, our study provides a useful approach for mapping and comparing risks of invasive non-native species and emerging pathogens between countries, which could be useful for regional horizon scanning and phytosanitary and biosecurity management.

A new inclusive MLVA assay to investigate genetic variability of Xylella fastidiosa with a specific focus on the Apulian outbreak in Italy

The Olive Quick Decline Syndrome by Xylella fastidiosa subspecies pauca is among the most severe phytopathological emergencies nowadays. In few years, the outbreak devastated olive groves in Apulia (Italy), potentially endangering the entire Mediterranean basin. This research aimed to develop a multiple locus VNTR analysis assay, a molecular tool to differentiate between populations of the pathogen. It has already been successfully applied to different X. fastidiosa subspecies from various plant hosts. The previously published TR loci, together with a set of new design, have been tested in silico on the genome of the Apulian De Donno strain. The resulting selection of 37 TR loci was amplified on the genomic DNAs of the Apulian strains AND from representatives of X. fastidiosa subspecies, and directly on DNA extracted from infected plants. The assay clearly discerned among subspecies or even sequence types (ST), but also pointed out variants within the same ST so as to provide more detailed information on the dynamics and pathogen diffusion pathways. Its effective application even on total DNAs extracted from infected tissues of different host plants makes it particularly useful for large-scale screening of infection and for the strengthening of containment measures.

From Nucleotides to Satellite Imagery: Approaches to Identify and Manage the Invasive Pathogen Xylella fastidiosa and Its Insect Vectors in Europe

Biological invasions represent some of the most severe threats to local communities and ecosystems. Among invasive species, the vector-borne pathogen Xylella fastidiosa is responsible for a wide variety of plant diseases and has profound environmental, social and economic impacts. Once restricted to the Americas, it has recently invaded Europe, where multiple dramatic outbreaks have highlighted critical challenges for its management. Here, we review the most recent advances on the identification, distribution and management of X. fastidiosa and its insect vectors in Europe through genetic and spatial ecology methodologies. We underline the most important theoretical and technological gaps that remain to be bridged. Challenges and future research directions are discussed in the light of improving our understanding of this invasive species, its vectors and host–pathogen interactions. We highlight the need of including different, complimentary outlooks in integrated frameworks to substantially improve our knowledge on invasive processes and optimize resources allocation. We provide an overview of genetic, spatial ecology and integrated approaches that will aid successful and sustainable management of one of the most dangerous threats to European agriculture and ecosystems.

Impacts of local population history and ecology on the evolution of a globally dispersed pathogen

BACKGROUND

Pathogens with a global distribution face diverse biotic and abiotic conditions across populations. Moreover, the ecological and evolutionary history of each population is unique. Xylella fastidiosa is a xylem-dwelling bacterium infecting multiple plant hosts, often with detrimental effects. As a group, X. fastidiosa is divided into distinct subspecies with allopatric historical distributions and patterns of multiple introductions from numerous source populations. The capacity of X. fastidiosa to successfully colonize and cause disease in naïve plant hosts varies among subspecies, and potentially, among populations. Within Central America (i.e. Costa Rica) two X. fastidiosa subspecies coexist: the native subsp. fastidiosa and the introduced subsp. pauca. Using whole genome sequences, the patterns of gene gain/loss, genomic introgression, and genetic diversity were characterized within Costa Rica and contrasted to other X. fastidiosa populations.

RESULTS

Within Costa Rica, accessory and core genome analyses showed a highly malleable genome with numerous intra- and inter-subspecific gain/loss events. Likewise, variable levels of inter-subspecific introgression were found within and between both coexisting subspecies; nonetheless, the direction of donor/recipient subspecies to the recombinant segments varied. Some strains appeared to recombine more frequently than others; however, no group of genes or gene functions were overrepresented within recombinant segments. Finally, the patterns of genetic diversity of subsp. fastidiosa in Costa Rica were consistent with those of other native populations (i.e. subsp. pauca in Brazil).

CONCLUSIONS

Overall, this study shows the importance of characterizing local evolutionary and ecological history in the context of world-wide pathogen distribution.

Update of the Xylella spp. host plant database - systematic literature search up to 30 June 2019

Following a request from the European Commission, EFSA was asked to create and regularly update a database of host plant species of Xylella spp. In 2018, EFSA released a new Xylella spp. host plant database that was now updated with informative data extracted from 76 recent publications retrieved through an extensive literature search. This report is related to the third version of the database published in Zenodo in the EFSA Knowledge Junction community, covering articles selected from: a systematic literature review conducted up of 30 June 2019; Europhyt database up to 15 October 2019; and relevant articles identified by EFSA Horizon scanning and personal communications from experts. Some data on Xylella fastidiosa strains and geographical coordinates included in the already published database were updated or modified with the purpose of increasing the accuracy and consistency of the database itself. Thirty-seven new host plant species of X. fastidiosa, identified through the data extracted from the selected publications, have been added to the database. Those plant species were reported as naturally infected, artificially infected or infected under unspecified conditions by subsp. multiplex, pauca or unknown (i.e. not reported in the publication) subspecies of X. fastidiosa. No additional data were retrieved for Xylella taiwanensis. Six new Sequence Types (STs) have been identified in Brazil, Italy and the USA. Information on the tolerant/resistant response of plant species or varieties to X. fastidiosa infection are also reported in the database. The overall number of Xylella spp. host plants reaches now 343 plant species, 163 genera and 64 families determined with two different detection methods, till 595 plant species, 275 genera and 85 families regardless the detection method applied. The EFSA database on Xylella spp. host plants is updated regularly with the aim to provide information and scientific support to risk assessors, risk managers and researchers dealing with Xylella spp.

Ooctonus vulgatus (Hymenoptera, Mymaridae), a potential biocontrol agent to reduce populations of Philaenus spumarius (Hemiptera, Aphrophoridae) the main vector of Xylella fastidiosa in Europe

As a vector of Xylella fastidiosa (Wells, 1987) in Europe, the meadow spittlebug Philaenus spumarius (Linnaeus, 1758) (Hemiptera, Aphrophoridae) is a species of major concern. Therefore, tools and agents to control this ubiquitous insect that develops and feeds on hundreds of plant species are wanted. We conducted a field survey of P. spumarius eggs in Corsica and provide a first report of Ooctonus vulgatus Haliday, 1833 (Hymenoptera, Mymaridae) as a potential biocontrol agent of P. spumarius in Europe. To allow species identification, we summarized the main characters distinguishing O. vulgatus from other European species of Ooctonus and generated COI DNA barcodes. Parasitism rates were variable in the four localities included in the survey but could reach 69% (for an average number of eggs that hatched per locality of 109). Based on the geographic occurrences of O. vulgatus obtained from the literature, we calibrated an ecological niche model to assess its potential distribution in the Holarctic. Obviously, several questions need to be addressed to determine whether O. vulgatus could become an effective biocontrol agent of P. spumarius in Europe. So far, O. vulgatus has been reared only from P. spumarius eggs, but its exact host-range should be evaluated to ensure efficiency and avoid non-target effect. The top-down impact of the parasitoid on vector populations should also be assessed on large data sets. Finally, the feasibility of mass rearing should be tested. We hope this report serves as a starting point to initiate research on this parasitoid wasp to assess whether it could contribute to reduce the spread and impact of X. fastidiosa in Europe.

Novel Tetraplex Quantitative PCR Assays for Simultaneous Detection and Identification of Xylella fastidiosa Subspecies in Plant Tissues

Xylella fastidiosa (Xf) is an insect-borne bacterium confined to the xylem vessels of plants. This plant pathogen has a broad host range estimated to 560 plant species. Five subspecies of the pathogen with different but overlapping host ranges have been described, but only three subspecies are widely accepted, namely subspecies fastidiosa, multiplex, and pauca. Initially limited to the Americas, Xf has been detected in Europe since 2013. As management of X. fastidiosa outbreaks in Europe depends on the identification of the subspecies, accurate determination of the subspecies in infected plants as early as possible is of major interest. Thus, we developed various tetraplex and triplex quantitative PCR (qPCR) assays for X. fastidiosa detection and subspecies identification in planta in a single reaction. We designed primers and probes using SkIf, a bioinformatics tool based on k-mers, to detect specific signatures of the species and subspecies from a data set of 58 genome sequences representative of X. fastidiosa diversity. We tested the qPCR assays on 39 target and 30 non-target strains, as well as on 13 different plant species spiked with strains of the different subspecies of X. fastidiosa, and on samples from various environmental and inoculated host plants. Sensitivity of simplex assays was equal or slightly better than the reference protocol on purified DNA. Tetraplex qPCR assays had the same sensitivity than the reference protocol and allowed X. fastidiosa detection in all spiked matrices up to 103 cells.ml-1. Moreover, mix infections of two to three subspecies could be detected in the same sample with tetraplex assays. In environmental plant samples, the tetraplex qPCR assays allowed subspecies identification when the current method based on multilocus sequence typing failed. The qPCR assays described here are robust and modular tools that are efficient for differentiating X. fastidiosa subspecies directly in plant samples.

Update of the Scientific Opinion on the risks to plant health posed by Xylella fastidiosa in the EU territory

EFSA was asked to update the 2015 EFSA risk assessment on Xylella fastidiosa for the territory of the EU. In particular, EFSA was asked to focus on potential establishment, short- and long-range spread, the length of the asymptomatic period, the impact of X. fastidiosa and an update on risk reduction options. EFSA was asked to take into account the different subspecies and Sequence Types of X. fastidiosa. This was attempted throughout the scientific opinion but several issues with data availability meant that this could only be partially achieved. Models for risk of establishment showed most of the EU territory may be potentially suitable for X. fastidiosa although southern EU is most at risk. Differences in estimated areas of potential establishment were evident among X. fastidiosa subspecies, particularly X. fastidiosa subsp. multiplex which demonstrated areas of potential establishment further north in the EU. The model of establishment could be used to develop targeted surveys by Member States. The asymptomatic period of X. fastidiosa varied significantly for different host and pathogen subspecies combinations, for example from a median of approximately 1 month in ornamental plants and up to 10 months in olive, for pauca. This variable and long asymptomatic period is a considerable limitation to successful detection and control, particularly where surveillance is based on visual inspection. Modelling suggested that local eradication (e.g. within orchards) is possible, providing sampling intensity is sufficient for early detection and effective control measures are implemented swiftly (e.g. within 30 days). Modelling of long-range spread (e.g. regional scale) demonstrated the important role of long-range dispersal and the need to better understand this. Reducing buffer zone width in both containment and eradication scenarios increased the area infected. Intensive surveillance for early detection, and consequent plant removal, of new outbreaks is crucial for both successful eradication and containment at the regional scale, in addition to effective vector control. The assessment of impacts indicated that almond and Citrus spp. were at lower impact on yield compared to olive. Although the lowest impact was estimated for grapevine, and the highest for olive, this was based on several assumptions including that the assessment considered only Philaenus spumarius as a vector. If other xylem-feeding insects act as vectors the impact could be different. Since the Scientific Opinion published in 2015, there are still no risk reduction options that can remove the bacterium from the plant in open field conditions. Short- and long-range spread modelling showed that an early detection and rapid application of phytosanitary measures, consisting among others of plant removal and vector control, are essential to prevent further spread of the pathogen to new areas. Further data collection will allow a reduction in uncertainty and facilitate more tailored and effective control given the intraspecific diversity of X. fastidiosa and wide host range.