Update of the Xylella spp. host plant database
2018; Wiley; Volume: 16; Issue: 9 Linguagem: Inglês
10.2903/j.efsa.2018.5408
ISSN1831-4732
AutoresEwelina Czwienczek, Alice Delbianco, Tomasz Kałuski, Svetla Kozelska, Marco Pautasso, Giuseppe Stancanelli, Tramontini Sara, Andrea Baù, Olaf Mosbach‐Schulz, Irene Muñoz Guajardo, Mario Monguidi, Rodrigo P. P. Almeida, Marie‐Agnès Jacques, João Roberto Spotti Lopes, Leonard Nunney, Claude Bragard, Thierry Candresse,
Tópico(s)Plant Pathogens and Fungal Diseases
ResumoEFSA JournalVolume 16, Issue 9 e05408 Scientific ReportOpen Access Update of the Xylella spp. host plant database European Food Safety Authority (EFSA), European Food Safety Authority (EFSA)Search for more papers by this author European Food Safety Authority (EFSA), European Food Safety Authority (EFSA)Search for more papers by this author First published: 10 September 2018 https://doi.org/10.2903/j.efsa.2018.5408Citations: 23 Correspondence: alpha@efsa.europa.eu Requestor: European Commission Question number: EFSA-Q-2017-00215 Acknowledgements: EFSA wishes to thank EFSA staff members ALPHA UNIT: Ewelina Czwienczek, Alice Delbianco, Tomasz Kaluski, Svetla Kozelska, Marco Pautasso, Giuseppe Stancanelli, Sara Tramontini, AMU UNIT: Andrea Baù, Olaf Mosbach-Schulz, Irene Muñoz Guajardo, DATA UNIT: Mario Monguidi and the external contractor Minh Ngoc Quan for the preparatory work on this report, and to the experts of the WG: Rodrigo Almeida, Marie-Agnès Jacques, Joao Lopes and Leonard Nunney, Claude Bragard and Thierry Candresse for reviewing and providing suggestions for the draft. Approved: 30 July 2018 AboutSectionsPDF ToolsExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat Abstract Following a request from the European Commission, EFSA periodically updates the database on the host plants of Xylella spp. While previous editions of the database (2015 and 2016) dealt with the species Xylella fastidiosa only, this database version addresses the whole genus Xylella, including therefore both species X. fastidiosa and Xylella taiwanensis. The database now includes information on host plants of Xylella spp. retrieved from scientific literature up to November 2017 and from EUROPHYT notifications up to May 2018. An extensive literature search was performed to screen the scientific and technical literature published between the previous database update conducted in December 2015 and December 2017. The literature screening was supported by the DistillerSR software platform. The applied protocol for the extensive literature review and extensive information search, together with examples of data extraction, are described in detail in this report. This report also includes published information on resistance or tolerance of plant varieties to Xylella spp. The current database includes 563 plant species reported to be infected by X. fastidiosa, of which for 312 plant species the infection has been determined with at least two different detection methods. These species cover hundreds of host plant genera in 82 botanical families (61 botanical families when considering only records with at least two different detection methods). The update of this database of host plants of Xylella spp. reported world-wide provides a key tool for risk management, risk assessment and research on this polyphagous bacterial plant pathogen. 1 Introduction Xylella spp. is a well-studied plant pathogenic bacterium (Janse and Obradovic, 2010; Purcell, 2013; Almeida and Nunney, 2015). Xylella fastidiosa is listed as one of the top 10 plant pathogenic bacteria in Molecular Plant Pathology based on a survey among the international community (Mansfield et al., 2012). It is known to cause many different diseases like Pierce's disease of grapes in California, citrus variegated chlorosis in Brazil, bacterial leaf scorch in shaded trees in North America, oleander leaf scorch in California, olive diseases in Europe. Xylella spp. are polyphagous pathogens. They can cause severe diseases, but might also remain asymptomatic, without causing any serious damage. To understand a host range and host–bacteria relationship, it is necessary to review existing studies and ongoing research with new techniques of identification of the pathogen (Baldi and La Porta, 2017). The first list of host plant species of X. fastidiosa published by the European Food Safety Authority (EFSA) was compiled in 2013 on the basis of the online list provided by the University of Berkeley in California (EFSA, 2013) and it was focused mostly on the strains/subspecies related to Pierce's disease – disease of grapevine. In January 2015, EFSA published a Scientific Opinion of the EFSA PLH Panel on the risk to plant health posed by X. fastidiosa in the EU territory (EFSA PLH Panel, 2015), which included a table (Appendix B in EFSA PLH Panel, 2015) listing known host plants of X. fastidiosa together with the relevant references for each of them. This table provided information on host plant species, their botanical family, the country and location of the records, the detection methods used and also the subspecies (recorded from the publication and putatively assigned on the basis of the strain, host plant and location). In 2015, EFSA published an electronic version of the database of the host plants of X. fastidiosa, together with a categorisation of plants for planting on the risk of introduction of X. fastidiosa (EFSA, 2015). EFSA updated its X. fastidiosa host plant database at the end of 2015 (EFSA, 2016). Some preliminary results from the current EFSA Xylella spp. host plant database were presented at the European Conference on Xylella fastidiosa1 held in Palma de Mallorca in November 2017 (Figure 1). Figure 1Open in figure viewerPowerPoint Temporal pattern of the total number of reported Xylella spp. host plants (2013–2018) The increase in the total number of hosts of Xylella spp. reported in the database from 2013 to 2018 is particularly related to the new plant species reported being infected by X. fastidiosa in Europe since 2013. However, it also reflects the most extensive coverage of scientific literature in all languages and the inclusion of reports on the other species Xylella taiwanensis. 1.1 Background The extensive literature search (ELS) protocol was used in the context of the EFSA mandate M-2013-0321 on urgent technical assistance on the regulated harmful organism Xylella spp. periodical updates of a database of host plants of Xylella spp. (EFSA-Q-2017-00215). This update integrates the list of X. fastidiosa host plants, published on 20 November 2016. 1.2 Terms of Reference as provided by the requestor EFSA was asked to deliver by the end of March 2017 a preliminary report on the hosts of the Apulian strain of Xylella fastidiosa subsp. pauca, which was delivered within the deadline (EFSA, 2017). EFSA is asked to further specify and update the host plants database of Xylella fastidiosa currently available, taking into account the different Xylella fastidiosa subspecies and strains (with particular reference to the European isolates), with inclusion of information on non-susceptible host plants and varieties and negative results of diagnostic tests when available. EFSA is asked to maintain and update this database periodically and to make new releases available on the EFSA website, together with a report. Such report should specify the list of plants confirmed to be infected by at least two detection methods in field conditions or via vector transmission under experimental conditions and be published at least annually. 1.3 Interpretation of the Terms of Reference This scientific report provides a description of the methodology of the review undertaken, approach made to list the hosts and results obtained from this review (sample size, time span cover of the literature extracted, exclusion criteria for publications, etc.), as well as a detailed view on the different host plants listed (diagnostic tests used – including negative tests, isolates, subspecies and sequence types, susceptibility/resistance information retrieved from the publications on different hosts). This edition of the database covers both species Xylella fastidiosa and Xylella taiwanensis. 2 Data and methodologies The process was divided into the following steps: An extensive literature search to identify the relevant references. A selection of the identified studies based on titles, abstracts and full text. Data extraction of the relevant information from the selected references for the creation of an updated global database of Xylella host plants. Data analysis and reporting (EFSA data warehouse). 2.1 Extensive literature search During the search process, two main aspects were considered: the sources of information (literature databases) to be consulted (Table 1) and the development of the search strategy (Table 2). The review question (i.e. 'which plant species can host Xylella/Xylella-associated diseases?') was broken down into key stages using the P/O conceptual model listed in the EFSA systematic review guidance (EFSA, 2010): Population of interest (P) The population of interest is that of plant species, world-wide. Outcome (condition of interest) (O) The outcome (condition of interest) is that of Xylella infection. 2.1.1 Information sources The established search strategy was run in all the databases listed in Table 1 via the Web of Science platform (Clarivate Analytics). No language, date or document type restrictions were applied to retrieve as many relevant publications as possible. Table 1. Sources of information Database Time coverage Platform Web of Science Core Collection 1975–present Web of Science CABI: CAB Abstracts 1973–present Web of Science BIOSIS Citation Index 1926–present Web of Science Chinese Science Citation Database 1989–present Web of Science Current Contents Connect 1998–present Web of Science Data Citation Index 1900–present Web of Science FSTA 1969–present Web of Science KCI-Korean Journal Database 1980–present Web of Science Russian Science Citation Index 2005–present Web of Science MEDLINE 1950–present Web of Science SciELO Citation Index 1997–present Web of Science Zoological Record 1864–present Web of Science 2.1.2 Search terms The search strategy was designed combining the different terms describing both the pathogen and the diseases caused in the different host plants. The established search string is detailed in Table 2. The search was run in all the selected information sources (Table 1) on 16 May 2017 and 3,544 potentially relevant references were retrieved. Table 2. Search string applied Search string Platform: Web of Science Results TS=(xylella OR xyllela OR xylela OR (pierce* NEAR/2 disease) OR (((Plum OR plums) AND "leaf scald*")) OR ((Phony NEAR/2 (peach* OR disease*))) OR ((citrus AND variegat* AND chlorosis)) OR crespera OR "almond leaf scorch*" OR "bacterial leaf scorch*" OR "coffee leaf scorch*" OR "mulberry leaf scorch*" OR "oleander leaf scorch*" OR "sycamore leaf scorch*" OR "Periwinkle wilt" OR "Ragweed stunt" OR ((Olive NEAR "quick decline syndrome")) OR "Xylem inhabiting bacteri*" OR "Xylem limited bacteri*" OR FXIB OR FXJB OR "rickettsialike bacteri*" OR "rickettsia like bacteri*") 3,544 The search string was run again on 24 November 2017 and 51 additional references were obtained. The collected records were downloaded and imported into the EndNote X8 bibliographic management software (Clarivate Analytics). Duplicate entries were removed using EndNote and the remaining records were uploaded on DistillerSR online2 together with the full texts in portable document format (pdf). Additional redundant references were excluded by the Duplicate Detection function of DistillerSR. Nineteen references (e.g. from grey literature, information obtained via official requests to the different research groups, national authorities, references cross-check in publications, conference proceedings) were included at a later stage of the process. Moreover, additional information was retrieved consulting the EUROPHYT outbreak notification database on 8 May 2018. Some data were also provided through personal communications by experts. 2.2 Study selection The collected references were screened for relevance in two steps in the DistillerSR Web-Based Systematic Review Software (Evidence Partners): Title/abstract screening of all the references. Full-text screening of those references that passed the previous step. Specific inclusion/exclusion criteria (described in Tables 3 and 4, respectively) were applied at each step and two reviewers worked in parallel screening all the references. Whenever a discrepant outcome was identified by the software, the reviewers had to solve the conflict and reach a common agreement on that reference. The first step required the reviewers to reply to two questions (Table 3) considering only the title and abstract (if available) of the reference. The aim of this step was to include only the publications presenting original research data (i.e. primary research studies) on Xylella or Xylella-associated disease. So, in both questions, a positive answer was needed to select the reference. A negative reply to one of the two questions was enough to exclude the reference. Whenever the information provided in the title and abstract was insufficiently clear, the reference was accepted and passed to the following step for further consideration. Table 3. Inclusion criteria for the title/abstract screening Question text Type of answer Answer text Exclusion criteria Is Xylella/a Xylella-associated disease/a Xylella synonym the topic of the study? Only one of the possible alternative answers can be selected Yes Included No Excluded Is it a primary research study? Only one of the possible alternative answers can be selected Yes Included No Excluded All publications that passed the title/abstract screening were subjected to the full-text screening (second step), except for 10 publications for which the full text was not retrieved (despite best efforts to carry this out). This step required the reviewers to reply to four questions (Table 4): the first three questions were descriptive (neutral), whereas the fourth question had an inclusion/exclusion role. The descriptive questions were added to collect information about the type of reference. On the fourth question, only publications describing Xylella studied in association with a host plant (i.e. in vivo) were selected for the data extraction phase. Table 4. Inclusion criteria for the full-text screening Question text Type of answer Answer text Exclusion criteria Is an English abstract present? Only one of the possible alternative answers can be selected Yes Neutral No Neutral Which is the type of the publication? Only one of the possible alternative answers can be selected Peer-reviewed article Neutral Article Neutral Book Neutral Conference proceedings Neutral Abstract Neutral Technical publication/Report Neutral Other Neutral Is the Xylella host plant the main scope of the study? Only one of the possible alternative answers can be selected Yes Neutral No Neutral Is Xylella/a Xylella-associated disease/a Xylella synonym studied in association to a host plant? Only one of the possible alternative answers can be selected Yes Included No Excluded 2.3 Data extraction The last step of the procedure was the extraction of informative data from the selected references. The data extraction covered the information listed in Table 5. For each reference, one or more forms were filled to extract all relevant data reported in the publication. Each form represents a unique combination of data. Two reviewers worked in sequence: the first reviewer performed the data extraction whereas the second reviewer conducted the quality control of the extracted data. There was no language limit in the search and also publications written in different languages than English, such Chinese, French, German, Italian, Portuguese, Slovenian, Spanish and Russian, were retrieved. Those publications were sent for an official translation and some of these were included in the data extraction step. Table 5. Data extraction structure Extracted data Description General information In this section, the general information about the study is reported RecordID Unique number allocated to each row RefID Unique number allocated to each reference within the DistillerSR software Reference Full reference Publication year Year of the publication Starting year Starting year of the study, as reported in the publication Ending year Ending year of the study, as reported in the publication Botanical identification The botanical identification of the plant, both as reported in the publication and according to the updated taxonomy of the EPPO Global Database, is reported in this section Plant EPPO code EPPO code of the plant species, from the EPPO global databasea Plant family Plant family, from the EPPO global databasea Plant genus Plant genus, from the EPPO global databasea Plant species Plant species, from the EPPO global databasea Reported plant species Name of the plant species as reported in the publication Common name Common name of the plant species, as reported in the publication Cultivar Cultivar or plant variety, as reported in the publication Infection information Detailed information about the infection and location of the plant is reported in this section Infection method (Level 1) The infection of the plant can be natural, artificial or not specified Infection method (Level 2) Subcategories of natural infection: during survey activity, during research activity. 'Research activity' is used when plants are planted under natural inoculum pressure and infection development was monitored without interfering. Subcategories of artificial infection: mechanical inoculation (detailed at level 3a), vector transmission (detailed at level 3b) Mechanical inoculation (Level 3a) Subcategories of mechanical inoculation: budding, grafting, needle, root uptake, stem absorption, syringe Infection vector species (Level 3b) Insect species used in the artificial vector transmission Location type The place where the plant was placed or found: natural habitat, greenhouse, screenhouse, interception, not specified Geographical information In this section, the geographical location of the plant is reported, as detailed as possible. In case of intercepted plant, the reported location is the geographical origin of the plant and not the country and location where it was intercepted Country code From the EFSA catalogue Country From the EFSA catalogue Location From the EFSA catalogue, with additional detailed information as reported in the publication Coordinates explanation The reported coordinates (latitude and longitude) can represent the centroid of the area (region or country), or the exact location XY coordinates of the point of sample, or the near location XY coordinates based on village, town or identifiable geographical features (national park, lake, river etc.), or XY of study site coordinates indicates the centroid of the area sampled Latitude Latitude as reported in the publication or derived from Google maps (use WGS84, decimal format) Longitude Longitude as reported in the publication or derived from Google maps (use WGS84, decimal format) Pest description Information about the pest is reported in this section, together with genetic data Pest EPPO code EPPO code of the pest, from the EPPO global databasea Pest species Name of Xylella spp. as reported in the publication (from 1930 up to now): Alfalfa dwarf virus, Morus suffodiens virus, Phony peach bacterium, Pierce's disease bacterium, Pierce's disease virus, Rickettsia-like bacteria, Rod-shaped bacteria, Xylella fastidiosa, Xylella taiwanensis, Xylem-inhabiting bacteria Pest subspecies Xylella fastidiosa subspecies reported in the publication: fastidiosa, morus, multiplex, pauca, sandyi, tashke Reported pest Name of Xylella spp. as reported in the publication (from 1930 up to now). Disease Name of the disease caused by Xylella spp., as reported in the publication: Alfalfa dwarf, Almond leaf scorch, Bacterial leaf scorch, Blueberry bacterial leaf scorch, Citrus variegated chlorosis, Coffee leaf scorch, Crespera, Elm leaf scorch, Leaf scorch disease, Mulberry leaf scorch, Oleander leaf scorch, Olive quick decline syndrome, Pear leaf scorch, Pecan bacterial leaf scorch, Periwinkle wilt, Phony peach disease, Pierce disease, Plum leaf scald, Potato purple top disease, Ragweed stunt, Sweetgum dieback, Sycamore leaf scorch Strain Name of the strain of Xylella spp., as reported in the publication MLST (multilocus sequence type) Sequence type (ST) of Xylella fastidiosa, as reported in the publication. If the ST is inferred from another publication, a note is added in the genotyping comment Genotyping comment Additional information retrieved in the publication about the Xylella spp. strain or sequence type Methods of identification In this section, the identification methods applied to detect a Xylella spp. infection are listed. Eight detection methods were considered and for each of them the outcome of the analysis (positive or negative), together with the number of infected plants and the total number of analysed plants, were reported. Moreover, additional information could be added in the comment column beside each detection method Symptoms Observation of symptoms in the plant, as reported in the publication Symptoms expression in test plants Observation of symptom development in test plants after an attempt to transmit the pathogen through vectors Culture Isolation of cultivable bacteria from tissue samples on solid culture media Microscopy Observation of Xylella bacteria through microscopic analysis techniques ELISA Enzyme-linked immunosorbent assay Other immunological techniques Immunological techniques other than ELISA PCR-based methods Polymerase chain-reaction-based methods (PCR, nested PCR, qPCR, etc.) Sequencing Sequencing technique (Sanger, next generation sequencing, etc.) and sequence analysis (MLST, phylogenetic tree, etc.) Host status Information about the tolerance and resistance response of the plant Tolerance/Resistance reported Tolerant/Resistant status of the plant, as reported in the publication Tolerance/Resistance category Categories describing the response of the tolerant/resistant plant: lack of infection or negative reading, Lack of systemic movement, Lack or reduction of symptoms, Lack or reduction of symptoms – Lower bacterial population, Lack or reduction of symptoms – Lower bacterial population – Lower disease incidence, Lack or reduction of symptoms – Lower disease incidence, Lower bacterial population, Lower bacterial population – Lower disease incidence, Lower disease incidence, Infection not persistent, Reported as tolerant/resistant (no details) Tolerance/Resistance comment Comment reporting detailed information about the tolerant/resistant response of the plant, as reported in the publication General comment General comment on the study Comment Additional relevant information a EPPO (2018) EPPO Global Database (available online). https://gd.eppo.int 2.4 Data warehouse The Xylella spp. host plant database has been considered a good candidate for the prototyping of a pest in the plant data repository within the EFSA Scientific Data Warehouse (S-DWH). A harmonised data model has been established, also taking into account the feedback of a previous pilot focusing on the creation of a database about pests in apple. The aim was to establish a harmonised data flow for the collection and the collation of an extensive literature review generated data in the plant health domain. 2.4.1 Data management Data have been collected through DistillerSR and then submitted to the EFSA Data Collection Framework (DCF). DCF is the upfront system in the EFSA pipeline of data collection tools and allows a first step of harmonisation against the EFSA controlled reference terminology (as known as EFSA catalogues). Data have been then included in the S-DWH by means of a standardised Extract Transform Load (ETL) procedure and they have been further analysed and managed to generate needed statistics. Raw data and related metadata are published in Zenodo in the EFSA Knowledge Junction community (https://doi.org/10.5281/zenodo.1339344). Data will be available soon as interactive reports at the following link (expected to be active by end September 2018): https://www.efsa.europa.eu/en/microstrategy/xylella 2.4.2 Data reporting Data reporting was designed to distinguish the Xylella spp. host plant species, based on the number and type of detection methods applied for each finding. Different combinations of detection methods were considered: Plant species positive with at least two detection methods (among: symptoms observation on the test plant in experimental vector transmission, enzyme-linked immunosorbent assay (ELISA), other immunological techniques, polymerase chain reaction (PCR)-based methods, sequencing and culture) or positive with one method (between: sequencing, culture). The same as point A, but also including microscopy: plant species positive with at least two detection methods (among: microscopy, symptoms observation on the test plant in experimental vector transmission, ELISA, other immunological techniques, PCR-based methods, sequencing and culture) or positive with one method (between: sequencing, culture). Plant species positive with at least one detection method (among: symptoms observation on the test plant in experimental vector transmission, ELISA, other immunological techniques, PCR-based methods, sequencing and culture). Plant species positive with at least one detection method including microscopy (microscopy, symptoms observation on the test plant in experimental vector transmission, ELISA, other immunological techniques, PCR-based methods, sequencing and culture). All positives plant species reported, regardless of the detection methods (positive records but without the detection method specified, symptom observations, microscopy, symptoms observation on the test plant in experimental vector transmission, ELISA, other immunological techniques, PCR-based methods, sequencing, culturing). 3 Results 3.1 Results of the literature review 3.1.1 Collected literature and screening for relevance The literature search was conducted twice, in May and in November 2017, and 3,595 references were obtained. Nineteen additional references were retrieved by other sources. All the collected references were uploaded in DistillerSR and 3,098 references were selected after the removal of duplicates. These references were then screened (Figure 2). In the first step, the title and abstract screening, 1,565 references were excluded because they either did not focus on Xylella or Xylella-associated diseases and/or because they were not primary research studies. The accepted 1,533 references went through to the second step, the full-text screening. Ten references were not evaluated as the full text was not retrieved and 670 references were excluded at this step. The 853 references in which Xylella or Xylella-associated diseases were studied in association with a host plant (i.e. in vivo) were selected for the data extraction phase. To catch the latest available information on the topic, the EUROPHYT outbreak database was consulted on 8 May 2018 and additional information was provided by scientific experts and national authorities. The full list of the selected references used for data extraction step is reported in Appendix E. In total, 8,391 data extraction forms were filled in with informative data and subsequently analysed to retrieve the list of Xylella host plants. Figure 2Open in figure viewerPowerPoint Flow diagram of the screening process in the DistillerSR tool 3.1.2 Trend of publications The oldest publications retrieved through the literature search and included in the data extraction step were published in the USA in 1930 on the phony disease of peach (Hutchins, 1930). The publication of Saponari et al. (2017) that describes the isolation and pathogenicity of X. fastidiosa-associated with the olive quick decline syndrome in southern Italy was published in December 2017 and it is the most recent publication retrieved through the literature search. Figure 3Open in figure viewerPowerPoint Number of publications published per year from 1930 to 2017 and used for data extraction The temporal trend of published publications about Xylella spp. and related diseases is shown in Figure 3. The number of publications used to extract data for this database stayed more or less constant between 1930 and the 1960s, increased to 10–20 per year between the 1970s and the 1990s, increased again in the period 2000–2010, with the highest number of publications in 2007 (47 publications). 3.1.3 Unconfirmed records A subset of unconfirmed studies (or of dubious relevance) or single records, included in the data extraction, was excluded from the data analysis. The records excluded from the data analysis are as follows: Berisha et al. (1996, 1998) were considered unconfirmed/dubious. The EPPO Global Database states: 'Absent, invalid record. EPPO Reporting Service (98/006): in an abstract (Berisha et al., 1996), it was claimed that X. fastidiosa had been isolated from diseased grapevine grown in Kosovo. The authors of the abstract have not, when requested, provided any details to substantiate this claim, which can only be
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