Retrospective survey of Dickeya fangzhongdai using a novel validated real-time PCR assay

Dickeya fangzhongdai, an aggressive plant pathogen, causes symptoms on a variety of crops and ornamental plants including bleeding canker of Asian pear trees. Historical findings stress the need for a specific detection tool for D. fangzhongdai to prevent overlooking the pathogen or assigning it to general Dickeya spp. Therefore, a qualitative real-time PCR for specific detection of D. fangzhongdai has been developed and validated. The developed assay shows selectivity of 100%, diagnostic sensitivity of 76% and limit of detection with 95% confidence interval in plant matrices ranging from 311 to 2,275 cells/mL of plant extracts. The assay was successfully used in a retrospective survey of selected host plants of relevance to Europe and environmental niches relevant to D. fangzhongdai. Samples of potato tubers and plants, plants from the Malinae subtribe (apple, pear, quince, and Asian pear tree) and fresh surface water from Slovenia were analyzed. D. fangzhongdai was not detected in any plant samples, however, 12% of surface water samples were found to be positive

Newly Isolated Bacteriophages from the Podoviridae, Siphoviridae, and Myoviridae Families Have Variable Effects on Putative Novel Dickeya spp.

Soft rot pathogenic bacteria from the genus Dickeya cause severe economic losses in orchid nurseries worldwide, and there is no effective control currently available. In the last decade, the genus Dickeya has undergone multiple changes as multiple new taxa have been described, and just recently a new putative Dickeya species was reported. This study reports the isolation of three bacteriophages active against putative novel Dickeya spp. isolates from commercially produced infected orchids that show variable host-range profiles. Bacteriophages were isolated through enrichment from Dickeya-infected orchid tissue. Convective interaction media monolith chromatography was used to isolate bacteriophages from wastewaters, demonstrating its suitability for the isolation of infective bacteriophages from natural sources. Based on bacteriophage morphology, all isolated bacteriophages were classified as being in the order Caudovirales, belonging to three different families, Podoviridae, Myoviridae, and Siphoviridae. The presence of three different groups of bacteriophages was confirmed by analyzing the bacteriophage specificity of bacterial hosts, restriction fragment length polymorphism and plaque morphology. Bacteriophage BF25/12, the first reported Podoviridae bacteriophage effective against Dickeya spp., was selected for further characterization. Its genome sequence determined by next-generation sequencing showed limited similarity to other characterized Podoviridae bacteriophages. Interactions among the bacteriophages and Dickeya spp. were examined using transmission electron microscopy, which revealed degradation of electron-dense granules in response to bacteriophage infection in some Dickeya strains. The temperature stability of the chosen Podoviridae bacteriophage monitored over 1 year showed a substantial decrease in the survival of bacteriophages stored at -20°C over longer periods. It showed susceptibility to low pH and UV radiation but was stable in neutral and alkaline pH. Furthermore, the stability of the tested bacteriophage was also connected to the incubation medium and bacteriophage concentration at certain pH values. Finally, the emergence of bacteriophage-resistant bacterial colonies is highly connected to the concentration of bacteriophages in the bacterial environment. This is the first report on bacteriophages against Dickeya from the Podoviridae family to expand on potential bacteriophages to include in bacteriophage cocktails as biocontrol agents. Some of these bacteriophage isolates also showed activity against Dickeya solani, an aggressive strain that causes the soft rot of potatoes, which indicates their broad potential as biocontrol agents

Violence by third parties against staff in the centres for social work

V teoretičnem delu diplomske naloge sem opisala zasnove nasilja tretjih oseb na delovnem mestu in socialno delo v neprostovoljnih transakcijah. Osredotočila sem se predvsem na nasilje tretjih oseb nad zaposlenimi na področjih in v socialnovarstvenih programih na Centru za socialno delo Gorenjska, zanimale so me morebitne razlike v pojavnosti in značilnostih. Moja raziskava je pretežno kvalitativna z izjemo kvantitativnega dela, v katerem so vsi sodelujoči odgovorili na vprašalnik. Opravila sem razgovore z dvema fokusnima skupinama s skupaj 8 zaposlenimi na Centru za socialno delo Gorenjska. Ena fokusna skupina je zajemala 4 zaposlene na področjih, druga pa 4 zaposlene v socialnovarstvenih programih omenjenega centra. Ugotovila sem, da so zaposleni pogosto podvrženi nasilju s strani tretjih oseb, najpogosteje psihičnemu nasilju. Raziskava je potrdila obstoj razlik v pogostosti in v obsežnosti oblik nasilja tretjih oseb do zaposlenih na področjih in v socialnovarstvenih programih centra za socialno delo. Zaposleni potrebujejo več izkustveno utemeljenih izobraževanj, kjer bi dobili konkretno znanje o preventivnih in kurativnih ukrepih za spoprijemanje z nasiljem tretjih oseb. Prav tako potrebujejo večjo mero odgovornosti centra za socialno delo v primeru nasilja tretjih oseb nad zaposlenimi.In the theoretical part of the thesis, I described the concepts of third party violence in the workplace and social work in involuntary transactions. I focused mainly on third party violence against employees in the fields and in social welfare programs in the Center for Social Work Gorenjska, I was interested in possible differences in frequency and characteristics. My research is mainly qualitative, except for the quantitative part, where all participants answered the questionnaire. I conducted 2 focus groups with a total of 8 employees in the Center for Social Work Gorenjska. One focus group included 4 employees in the fields and the other 4 employees in the social welfare programs of the said center. I found out that the employees are often exposed to violence by third parties, most often psychological violence. The research confirmed the existence of differences in the frequency and extent of forms of third party violence against staff in the areas and social welfare programs of the social work center. Staff need more experiential training where they would gain concrete knowledge on preventive and curative measures in dealing with third party violence. They also need a greater level of accountability from the Center for Social Work in the event of third-party violence against staff.ave found that employees are often subjected to violence by third parties, most commonly psychological violence. The research confirmed the existence of differences in the frequency and extent of forms of third-party violence against employees in the areas and social welfare programs of the Center for Social Work. Employees need more experientially based training, where they would gain concrete knowledge of preventive and curative measures to deal with third-party violence. They also need a greater degree of responsibility of the social work center in the event of third-party violence against employees

The Importance of a Quality Relationship in the Process of Support and Help

V teoretičnem delu magistrske naloge sem opisala zasnove verbalnega in neverbalnega komuniciranja, prakse socialnega dela, ki temelji na odnosih, in koncepta kakovostnega odnosa na centrih za socialno delo. Osredotočila sem se predvsem na grajenje kakovostnega odnosa na Centru za socialno delo Gorenjska. Moja raziskava je pretežno kvalitativna akcijska z izjemo kvantitativnega dela, v katerem so vsi sodelujoči odgovorili na vprašalnik z ocenjevalnimi lestvicami. Opravila sem tri sodelovalne pogovore s skupaj šestimi zaposlenimi na Centru za socialno delo Gorenjska. Potrdila sem že velikokrat navedeno razumevanje, da kakovosten odnos pripomore k preprečevanju in reševanju nasilja. Med ostalimi raziskovalnimi ugotovitvami izstopajo naslednje: na proučevano problematiko vpliva določeno področje delatako kot strokovne delavke definirajo kakovostni odnos, tako ga tudi gradijosodelovanje centra za socialno delo z institucijami, kot so zdravstvo, sodstvo in policija, strokovnim delavkam otežuje izgradnjo kakovostnega odnosa. Rezultati moje raziskave kažejo, da strokovne delavke na področju pravic potrebujejo več izobraževanj, usmerjenih na grajenje kakovostnega odnosa na njihovem področju. Prav tako vse strokovne delavke potrebujejo usposabljanja za namene učenja strategij, s katerimi lahko ublažijo nasilne odnose, prepoznajo svojo vlogo pri konstruiranju sovražnosti v odnosu, uspešneje ravnajo z odporom in sodelujejo s sogovorniki na spoštljive in vzajemne načine. Glavno sporočilo raziskave je, da morajo Ministrstvo za pravosodje, Ministrstvo za zdravje in Ministrstvo za delo, družino, socialne zadeve in enake možnosti proučiti nove možnosti sodelovanja med centri za socialno delo, sodstvom, policijo in zdravstvom.In the theoretical part of my master\u27s thesis, I described the concepts of verbal and nonverbal communication, relationship-based social work practise, and relationship quality in social work centres. I have focused mainly on building a quality relationship in the Gorenjska Centre for Social Work. My research is mostly action-oriented, except for the quantitative part, where all participants answered a questionnaire. I conducted three cooperative conversations with a total of 6 employees of the Centre for Social Work Gorenjska. I found that a quality relationship contributes to the prevention and resolution of violence, as does a specific work area. I also realised that professional employees not only define a good relationship, but also build it. In my research, I found that working with institutions that cooperate with the social work centre, such as health care, the judiciary, and the police, plays a difficult role for professionals in building a quality relationship. The social workers in the field of rights need more training to build a quality relationship in their field. Similarly, all women professionals need training to learn strategies to defuse violent relationships, recognise their role in co-constructing hostility, and learn how to manage resistance and work with their interlocutors in respectful and reciprocal ways. Most importantly, the Ministry of Justice, the Ministry of Health, the Ministry and the Ministry of Labour, Family, Social Affairs and Equal Opportunities are exploring new ways to collaborate and work between social work centres, the justice system, the police and the health system

Genomic characterisation of the new Dickeya fangzhongdai species regrouping plant pathogens and environmental isolates

Abstract Background The Dickeya genus is part of the Pectobacteriaceae family that is included in the newly described enterobacterales order. It comprises a group of aggressive soft rot pathogens with wide geographic distribution and host range. Among them, the new Dickeya fangzhongdai species groups causative agents of maceration-associated diseases that impact a wide variety of crops and ornamentals. It affects mainly monocot plants, but D. fangzhongdai strains have also been isolated from pear trees and water sources. Here, we analysed which genetic novelty exists in this new species, what are the D. fangzhongdai-specific traits and what is the intra-specific diversity. Results The genomes of eight D. fangzhongdai strains isolated from diverse environments were compared to 31 genomes of strains belonging to other Dickeya species. The D. fangzhongdai core genome regroups approximately 3500 common genes, including most genes that encode virulence factors and regulators characterised in the D. dadantii 3937 model strain. Only 38 genes are present in D. fangzhongdai and absent in all other Dickeyas. One of them encodes a pectate lyase of the PL10 family of polysaccharide lyases that is found only in a few bacteria from the plant environment, soil or human gut. Other D. fangzhongdai-specific genes with a known or predicted function are involved in regulation or metabolism. The intra-species diversity analysis revealed that seven of the studied D. fangzhongdai strains were grouped into two distinct clades. Each clade possesses a pool of 100–150 genes that are shared by the clade members, but absent from the other D. fangzhongdai strains and several of these genes are clustered into genomic regions. At the strain level, diversity resides mainly in the arsenal of T5SS- and T6SS-related toxin-antitoxin systems and in secondary metabolite biogenesis pathways. Conclusion This study identified the genome-specific traits of the new D. fangzhongdai species and highlighted the intra-species diversity of this species. This diversity encompasses secondary metabolites biosynthetic pathways and toxins or the repertoire of genes of extrachromosomal origin. We however didn’t find any relationship between gene content and phenotypic differences or sharing of environmental habitats

Data_Sheet_1_Retrospective survey of Dickeya fangzhongdai using a novel validated real-time PCR assay.docx

Dickeya fangzhongdai, an aggressive plant pathogen, causes symptoms on a variety of crops and ornamental plants including bleeding canker of Asian pear trees. Historical findings stress the need for a specific detection tool for D. fangzhongdai to prevent overlooking the pathogen or assigning it to general Dickeya spp. Therefore, a qualitative real-time PCR for specific detection of D. fangzhongdai has been developed and validated. The developed assay shows selectivity of 100%, diagnostic sensitivity of 76% and limit of detection with 95% confidence interval in plant matrices ranging from 311 to 2,275 cells/mL of plant extracts. The assay was successfully used in a retrospective survey of selected host plants of relevance to Europe and environmental niches relevant to D. fangzhongdai. Samples of potato tubers and plants, plants from the Malinae subtribe (apple, pear, quince, and Asian pear tree) and fresh surface water from Slovenia were analyzed. D. fangzhongdai was not detected in any plant samples, however, 12% of surface water samples were found to be positive.</p

Draft Genome Sequences of Dickeya

The genus Dickeya contains bacteria causing soft rot of economically important crops and ornamental plants. Here, we report the draft genome sequences of two Dickeya sp. isolates from rotted leaves of Phalaenopsis orchids

Taxonomy and epidemiology of Pectobacterium and Dickeya spp. in Europe, North America and South Africa

&lt;p&gt;The blackleg-soft rot-aerial stem rot disease complex causes serious losses to the potato industry. It is caused by species of the genera &lt;i&gt;Pectobacterium&lt;/i&gt; and &lt;i&gt;Dickeya&lt;/i&gt;, collectively known as the soft rot Pectobacteriaceae. These soft rot Pectobacteriaceae also cause damage in a wide range of other host plants. &lt;i&gt;Pectobacterium brasiliense&lt;/i&gt; has been the most prevalent in potato and pathogenic species in Europe and South Africa for the past decade, although the species composition is in constant flux due to the introduction of new species and taxonomic reclassification of current ones.&lt;/p&gt;&lt;p&gt;Updated information on the current species composition is required, as well as knowledge of possible differences in symptom expression between species. Such information would aid certification and diagnostic services in testing for the correct species and making accurate diagnoses.&lt;/p&gt;&lt;p&gt;Findings indicate that &lt;i&gt;Pectobacterium brasiliense&lt;/i&gt; remains the most prevalent and widely distributed species in potato production areas. Other species that were identified included e.g. &lt;i&gt;Pectobacterium carotovorum&lt;/i&gt;, &lt;i&gt;Pectobacterium parmentieri&lt;/i&gt;, &lt;i&gt;Dickeya chrysanthemi&lt;/i&gt; and &lt;i&gt;Pectobacterium versatile&lt;/i&gt;. &lt;i&gt;Pectobacterium brasiliense&lt;/i&gt; was also the most pathogenic species on potato. When looking at other host plants a wide variety of &lt;i&gt;Pectobacterium&lt;/i&gt; and &lt;i&gt;Dickeya&nbsp;&lt;/i&gt;species with large genetic variation occurs.&lt;/p&gt;&lt;p&gt;MALDI-TOF MS can only be used to identify &lt;i&gt;Pectobacterium&lt;/i&gt; and &lt;i&gt;Dickeya&nbsp;&lt;/i&gt;isolates at the genus level but preliminary results after improving the reference library look promising.&lt;/p&gt;&lt;p&gt;Given that there is also a large group of nonvirulent &lt;i&gt;P. brasiliense&lt;/i&gt; isolates, a specific PCR which can differentiate between virulent and nonvirulent isolates of this species is being developed.&lt;/p&gt