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Povzetek: The increasing prevalence of Ralstonia pseudosolanacearum phylotype I (phy I) in agricultural regions across Europe highlights the need for heightened awareness and preventive measures. Recent detections in multiple European countries span a range of agricultural systems, host plants, and natural aquatic environments. These findings have been linked either to infected plant material at import (interceptions) or to plants cultivated in specific European regions, often after importation of infected plant material. To investigate the genetic diversity of these emerging populations, we analysed whole-genome sequence (WGS) data from a collection of 62 R. pseudosolanacearum phy I isolates, including those recently obtained in various European countries, using average nucleotide analysis (ANI) and core genome multilocus sequence typing (cgMLST). ANI analysis revealed two distinct major clades: the "rose clade", comprising isolates from rose, potato, surface water, and bittersweet, most closely matching with sequevar 33, and the "major ginger clade", including isolates from members of the Zingiberaceae family, with the best match to sequevar 30. Additionally, several minor clades of Zingiberaceae isolates and a "tomato clade” (most closely related to sequevar 18) were identified. Pathogenicity assays with high inoculation titers were performed on tomato to assess the biological relevance of the observed genetic diversity. Our findings suggest multiple independent introduction events of virulent R. pseudosolanacearum phy I populations into Europe between 2015 and 2024. Given the genetic variability of the introduced bacterial isolates, the pathogen’s ability to systemically infect a broad range of host plants which can differ per isolate, and its persistence in diverse agricultural and environmental niches, the implementation of stringent import control measures for plant material entering the European Union is strongly recommended.
Ključne besede: Ralstonia pseudosolanacearum, surface water, Zingiberaceae, Solanaceae, Rosaceae
Objavljeno v DiRROS: 02.03.2026; Ogledov: 250; Prenosov: 158
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Ključne besede: diagnostika, virusi, bakterije, fitoplazme, viroidi, varstvo rastlin
Objavljeno v DiRROS: 12.02.2026; Ogledov: 579; Prenosov: 0

Povzetek: Pseudomonas syringae (Psy) is a widely distributed bacterial species complex primarily recognized as a foliar pathogen but also inhabits diverse environments, including water habitats, where strains closely related to agricultural pathogens have been identified. The connection between Psy-caused epidemics and its potential presence in nearby irrigation systems remains underexplored. This study comprehensively examined the Psy complex in the Danube-Tisa-Danube Hydrosystem (DTD) in Serbia, assessing its abundance, phylogenetic diversity, and pathogenic potential. To reduce the reliance on the time-consuming steps of isolation and identification, we developed novel high-specific primers and probes for precise detection of strains belonging to phylogroup 2 within Psy complex. Our results demonstrated that dPCR, coupled with highly specific and sensitive primers, outperformed both traditional plating and qPCR in detecting the Psy complex and phylogroup 2 in irrigation waters, making Psy diagnostics more effective. Phylogenetic analysis indicated high strain diversity within the DTD, identifying phylogroups 1, 2, 7, 12, and 13 and haplotypes linked to strains previously encountered in epidemics on sugar beet in Serbia. Notably, 66.67% of the isolates from the DTD were capable of inducing disease. Phylogroup 2 isolates displayed a broad host range, suggesting that the dissemination of Psy from DTD through irrigation, poses a substantial threat to crop health and agricultural productivity.
Ključne besede: phytopathogen detection, irrigation, qPCR, dPCR
Objavljeno v DiRROS: 05.09.2025; Ogledov: 601; Prenosov: 311
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Povzetek: Comparative genomics of several strains of Erwinia amylovora, a plant pathogenic bacterium causal agent of fire blight disease, revealed that its diversity is primarily attributable to the flexible genome comprised of plasmids. We recently identified and sequenced in full a novel 65.8 kb plasmid, called pEI70. Annotation revealed a lack of known virulence-related genes, but found evidence for a unique integrative conjugative element related to that of other plant and human pathogens. Comparative analyses using BLASTN showed that pEI70 is almost entirely included in plasmid pEB102 from E. billingiae, an epiphytic Erwinia of pome fruits, with sequence identities superior to 98%. A duplex PCR assay was developed to survey the prevalence of plasmid pEI70 and also that of pEA29, which had previously been described in several E. amylovora strains. Plasmid pEI70 was found widely dispersed across Europe with frequencies of 5–92%, but it was absent in E. amylovora analyzed populations from outside of Europe. Restriction analysis and hybridization demonstrated that this plasmid was identical in at least 13 strains. Curing E. amylovora strains of pEI70 reduced their aggressiveness on pear, and introducing pEI70 into low-aggressiveness strains lacking this plasmid increased symptoms development in this host. Discovery of this novel plasmid offers new insights into the biogeography, evolution and virulence determinants in E. amylovora.
Ključne besede: plant diseases, bacteria, plamid
Objavljeno v DiRROS: 04.03.2025; Ogledov: 913; Prenosov: 569
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Povzetek: Rapid and accurate identification of bacterial pathogens is crucial for effective treatment and infection control, particularly in hospital settings. Conventional methods like culture techniques and MALDI-TOF mass spectrometry are often time-consuming and less sensitive. This study addresses the need for faster and more precise diagnostic methods by developing novel digital PCR (dPCR) assays for the rapid quantification of biomarkers from three Gram-negative bacteria: Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa. Utilizing publicly available genomes and the rapid identification of PCR primers for unique core sequences or RUCS algorithm, we designed highly specific dPCR assays. These assays were validated using synthetic DNA, bacterial genomic DNA, and DNA extracted from clinical samples. The developed dPCR methods demonstrated wide linearity, a low limit of detection (approx. 30 copies per reaction), and robust analytical performance with measurement uncertainty below 25 %. The assays showed high repeatability and intermediate precision, with no cross-reactivity observed. Comparison with MALDI-TOF mass spectrometry revealed substantial concordance, highlighting the methods’ suitability for clinical diagnostics. This study underscores the potential of dPCR for rapid and precise quantification of Gram-negative bacterial biomarkers. The developed methods offer significant improvements over existing techniques, providing faster, more accurate, and SI-traceable measurements. These advancements could enhance clinical diagnostics and infection control practices.
Ključne besede: digital PCR (dPCR), Gram-negative bacteria, pathogen detection, respiratory infections, biomarkers, RUCS algorithm
Objavljeno v DiRROS: 05.11.2024; Ogledov: 1151; Prenosov: 887
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