Search Results (1,556)

In the last decade, avocado production has increased in Italy due to the fruit’s high nutritional quality and economic value. During 2024, stem lesions, wood discoloration and dieback, often starting at the grafting point, were observed in young plants in a nursery in Sicily (Italy). Colletotrichum-like colonies were frequently isolated from symptomatic tissues. Multi-locus phylogenetic analysis (gapdh, chs-1, act, tub2, cal, gs and ApMat) was conducted on 11 representative isolates, identifying 6 as C. perseae and 5 as C. gloeosporioides sensu stricto (s.s.). Two representative isolates were selected for pathogenicity tests performed on 2-year-old avocado plants cultivated in a greenhouse. After two months, necrotic lesions, wood discoloration and reddish-brown streaking at the inoculation point were induced in both species. Additional inoculations of avocado fruit confirmed the ability of both species to cause fruit rot. All inoculated fungi were successfully re-isolated and identified, fulfilling Koch’s postulates. This is the first report of stem lesions and dieback caused by Colletotrichum species and the first occurrence of C. perseae in avocado plants in Europe. The results highlight the importance of early monitoring in nurseries during the propagation process and contribute to a better understanding of fungal diseases in avocado crops in Italy. Full article

Between 2022 and 2024, a severe branch dieback disease was observed affecting over 6% of sweet cherry trees of the ‘Tieton’ cultivar in commercial greenhouses in southern Liaoning Province, China. Symptoms primarily occurred at the top of young branches. At the early stage of disease onset, the lesions appeared as dark brown, irregularly shaped areas with a moist surface; as the disease progressed, these lesions turned dry and rotten, leading to tree decline symptoms in sweet cherry trees. Disease diagnosis was carried out in sweet cherry greenhouses across Liaoning Province, where 24 diseased samples were collected and 14 fungal isolates were obtained therefrom. Based on morphological traits, cultural characteristics, and multi-locus phylogenetic analyses of the internal transcribed spacer (ITS) region, beta-tubulin (TUB2) gene, and translation elongation factor 1-α (TEF1) gene, these isolates were identified as Botryosphaeria dothidea. Two representative isolates, namely zdcy-1 and zdcy-2, were selected for pathogenicity assays. Both mycelial plug and spore suspension inoculation methods confirmed the pathogenicity of the pathogen. The biological characteristic assays revealed that the optimal temperature range for the pathogen’s mycelial growth on PDA medium was 25–28 °C, and the optimal pH range was 6.0–8.0. This study improves the understanding of branch dieback disease in sweet cherry orchards in China, enriches the knowledge regarding the geographical distribution, host range, and infection sites of the pathogen, and provides novel insights for the management of sweet cherry diseases. Full article

Klebsiella oxytoca has emerged as an important opportunistic pathogen in nosocomial infections, particularly during the COVID-19 pandemic, due to its capacity to acquire and disseminate resistance and virulence genes through horizontal gene transfer (HGT). This study presents a genome-based comparative analysis of K. oxytoca within the genus Klebsiella, aimed at exploring the evolutionary plausibility of outer membrane vesicle (OMV) associated processes in bacterial adaptation. Using publicly available reference genomes, we analyzed pangenome structure, phylogenetic relationships, and the distribution of mobile genetic elements, resistance determinants, virulence factors, and genes related to OMV biogenesis. Our results reveal a conserved set of envelope associated and stress responsive genes involved in vesiculogenic pathways, together with an extensive mobilome and resistome characteristic of the genus. Although these genomic features are consistent with conditions that may favor OMV production, they do not constitute direct evidence of functional OMV mediated horizontal gene transfer. Instead, our findings support a hypothesis generating evolutionary framework in which OMVs may act as a complementary mechanism to established gene transfer routes, including conjugation, integrative mobile elements, and bacteriophages. Overall, this study provides a genomic framework for future experimental and metagenomic investigations into the role of OMV-associated processes in antimicrobial resistance dissemination and should be interpreted as a recently identified evolutionary strategy inferred from genomic data, rather than a novel or experimentally validated mechanism. Full article

‘Candidatus Phytoplasma solani’ of the 16SrXII group is an emerging vector-borne pathogen in European crop production. The cixiid planthopper Hyalesthes obsoletus transmits 16SrXII-A stolbur phytoplasmas that are associated with diseases in grapevine, potato, and various weeds. While 16SrXII-P genomes transmitted by Pentastiridius leporinus are available, no genome of an H. obsoletus-transmissible 16SrXII-A phytoplasma has been reported from Germany. Here, we present insights into the phylogenetic position and pathogen–host interactions through the functional reconstruction of the complete 832,614 bp genome of the H. obsoletus transmissible ‘Ca. P. solani’ 16SrXII-A strain POT from a potato field. Phylogenetic analyses highlight the heterogeneity within the stolbur group using whole-genome alignment and a BUSCO-based core gene analysis approach. The POT chromosome shares highest average nucleotide identity with Italian bindweed-associated genomes and displays strong synteny with the c5 strain. Consistent with the typical phytoplasma architecture, the POT genome combines mobile-element-driven instability with a conserved core metabolism. Virulence factors include transposon-linked effectors but lack pathogenicity island organisation. POT further differs from other 16SrXII-group phytoplasmas through unique collagen-like proteins that could contribute to virulence. These findings provide a robust genomic framework that improves diagnostics, enables strain-level resolution and supports the assessment of breeding materials under stolbur phytoplasma pressure, thereby refining our understanding of stolbur phytoplasma diversity and highlighting the evolutionary divergence within the 16SrXII subgroup. Full article

Betanodavirus infection poses a significant threat to marine fish species in the Mediterranean, affecting both aquaculture and wild populations. Despite increasing evidence of viral circulation in farmed and wild fish, data on natural outbreaks in wild groupers remain limited. This study investigated mortality episodes in wild dusky groupers (Epinephelus marginatus) within two marine protected areas (MPAs): Portofino MPA (Liguria, Italy) and Larvotto MPA (Principality of Monaco) during 2018–2019. Pathological examinations and virological diagnostics confirmed that the causative agents were betanodavirus strains belonging to the RGNNV genotype. Phylogenetic analyses revealed high genetic similarity among viral strains detected at geographically distant sites and across host species, suggesting potential regional connectivity mediated by mobile vectors or environmental transport. Seawater temperature analysis indicated that extreme and prolonged high-water temperatures were prodromal and coincided with observed outbreaks, supporting a role for thermal stress in triggering outbreak onsets. These findings highlight the susceptibility of wild dusky grouper populations to betanodavirus and underscore the interplay between host behavior, environmental conditions, and pathogen dynamics. The study emphasizes the importance of integrated health surveillance strategies within and around MPAs to monitor fish health and environmental parameters, thereby conserving wild fish populations and biodiversity. Full article

Agrobacterium tumefaciens, a destructive pathogen causing crown gall disease, results in substantial agricultural losses. Traditional chemical and existing biocontrol methods are limited by environmental pollution, pesticide resistance, and low efficacy, while bacteriophages emerge as a promising alternative due to their high host specificity, environmental compatibility, and low resistance risk. In this study, we isolated and characterized a lytic phage (PAT-A) targeting A. tumefaciens, evaluating its biological traits, genomic features, and biocontrol potential. The host strain A. tumefaciens CL-1 was isolated from cherry crown gall tissue and identified by 16S rDNA sequencing. Phage PAT-A was recovered from orchard soil via the double-layer agar method, showing a tadpole-shaped morphology (60 nm head diameter, 30 nm tail length) under transmission electron microscopy (TEM). Nucleic acid analysis confirmed a double-stranded DNA genome, susceptible to DNase I but resistant to RNase A and Mung Bean Nuclease. PAT-A exhibited an optimal MOI of 0.01, tolerated wide pH and temperature ranges, but was sensitive to UV (titer declined after 15 min of irradiation) and chloroform (8% survival at a 5% concentration). Whole-genome sequencing revealed a 44,828 bp genome with a compact structure, and phylogenetic/collinearity analyses placed it in the Atuphduvirus genus (Autographiviridae). Biocontrol experiments on tobacco plants demonstrated that PAT-A significantly reduced crown gall incidence. Specifically, simultaneous inoculation of PAT-A and A. tumefaciens CL-1 resulted in the lowest tumor incidence (12.0%), while pre-inoculation of PAT-A 2 days before pathogen exposure achieved an incidence rate of 33.3%. In conclusion, PAT-A is a novel strictly lytic phage with favorable biological properties and potent biocontrol efficacy against A. tumefaciens, enriching phage resources for crown gall management and supporting phage-based agricultural biocontrol strategies. Full article

Protoparvoviruses are highly contagious pathogens that cause severe, often fatal diseases in both domestic and wild carnivores. Golden jackal (Canis aureus) populations have experienced expansion in recent years, increasingly occupying urban and peri-urban areas. Despite this, they remain largely overlooked in scientific research. This study aimed to detect and characterise Protoparvovirus carnivoran1 circulating in a golden jackal population in Croatia and to assess their role in the epidemiology of parvovirus infections in companion animals. Small intestines from 55 jackals hunted in 2024 and 2025 were tested for Protoparvovirus carnivoran1 using real-time PCR. Positive samples were found across all sampling sites, with an overall positivity rate of 40%. Based on characteristic amino acid residues within the VP2 protein, the viruses detected in jackals were classified as feline panleukopenia virus (FPV). Phylogenetic analysis of the VP2 protein demonstrated considerable genetic diversity among strains circulating in Croatia. Additionally, a distinct group was identified, shared exclusively by Croatian domestic cats and golden jackals. Amino acid analysis revealed the novel A91T mutation, found only in jackals, and the E411Q mutation, unique to Croatian FPV strains. Structural modelling of the VP2 protein indicates that the observed mutations are located on the protein surface, within the antibody-binding site. These findings highlight the potential role of wild carnivores in parvovirus epidemiology and underscore the importance of including them in future surveillance and research efforts. Full article

Shiga toxin-producing Escherichia coli (STEC) is a zoonotic pathogen of public health concern, requiring a One Health approach to clarify its transmission and distribution. However, its prevalence and genomic characteristics in livestock and companion animals remain underexplored in low-income countries. We investigated prevalence and genomic features of STEC in animals in western Ghana, representing the first genomic report of STEC in Ghana. Fecal samples (97) were collected from goats (n = 33), sheep (n = 33), dogs (n = 30), and a cat (n = 1), with STEC detected in 12.1% of goats and sheep samples. Whole-genome sequencing identified serotypes O38:H26, O43:H2, and O157:H7. stx1c and stx2b genes were detected in O38:H26 and O43:H2, whereas stx2c and key virulence genes (chuA, eae, esp, nle, tir, and toxB) were exclusively found in O157:H7. Phylogenetic analysis revealed that O38:H26 isolates form a cluster closely related to clinical strains from the UK. O43:H2 isolates exhibited diverse stx profiles, linking animal, environmental, and clinical strains from North America and the UK. O157:H7 isolates were genetically similar to European clinical and food-derived strains, suggesting that goats and sheep are important STEC reservoirs in Ghana, offering data for public health risk assessment and effective One Health-based control strategies. Full article

Background: Endolichenic fungi represent an emerging source of bioactive secondary metabolites; however, the genomic basis of their chemical diversity remains largely poorly characterized. Specifically, the metabolic capabilities of Cladosporium limoniforme have not been explored at the genomic level. Objectives: This study aimed to characterize the biosynthetic potential of C. limoniforme by presenting its first whole-genome sequence and conducting a comparative analysis of its biosynthetic gene clusters (BGCs), with a specific focus on the evolutionary conservation of the DHN-melanin pathway. Methods: Genome mining was performed using antiSMASH and fungiSMASH tools. Comparative genomics involved heatmap-based distribution analysis across the Cladosporium genus, synteny profiling using Clinker to assess gene order conservation, and Maximum Likelihood phylogenetic analysis of the polyketide synthase (T1PKS) domain. Results: We identified 26 putative BGCs, revealing a largely untapped metabolic repertoire. Comparative analysis demonstrated a high degree of conservation for the metachelin C (siderophore) and 1,3,6,8-tetrahydroxynaphthalene (T4HN) clusters across the genus. Notably, synteny and phylogenetic analyses showed that while C. limoniforme retains a conserved, ancestral T1PKS core essential for stress survival, it exhibits a significant reduction in accessory genes compared to plant-pathogenic congeners. Conclusions: These findings support a “metabolic streamlining” hypothesis driven by the endolichenic lifestyle, where the fungus retains essential protective machinery while shedding costly accessory genes unnecessary in the buffered lichen niche. This study establishes C. limoniforme as a valuable genomic resource for future biotechnological research. Full article

Astroviruses are non-enveloped, positive-sense single-stranded RNA viruses known to infect various mammals and birds, including humans, often causing gastrointestinal disorders. In recent years, astroviruses have also been linked to neurological and respiratory diseases across several species, including ruminants, mink, deer, and other mammals. Notably, astrovirus infections in goats have been documented in countries such as Switzerland and China, where novel genotypes have been identified in fecal samples. However, their role in the context of disease remains unclear, and reports focusing solely on goat astrovirus in the United States have not been published. A necropsy case of a Boer goat kid with a history of diarrhea was submitted for investigation following death in January 2025. Fresh tissues were received and used for histopathology and enteric pathogen testing, including parasitic, bacterial, and viral workups. Metagenomic-based next-generation sequencing (mNGS) was also applied for this case. Histological examination revealed severe necrotizing enterocolitis. The small intestine exhibited epithelial ulcerations, villus atrophy, hyperplastic and dilated crypts with necrotic debris, few intraenterocytic coccidian parasites, and increased inflammatory cells in the lamina propria. The large intestine showed similar findings with pleomorphic crypt enterocytes. Standard enteric pathogen tests were negative except for aerobic culture that identified Escherichia.coli and Enterococcus hirae. mNGS and bioinformatic analysis identified a novel astrovirus in the intestinal content that showed the highest nucleotide identity (86%) to the sheep strain Mamastrovirus 13 sheep/HA3 from China based on BLAST analysis. Phylogenetic analysis indicated that the newly identified caprine astrovirus IL90175 clustered with astrovirus strains from small ruminants in Asia and Europe. This research reports the discovery, histopathologic features, and genetic characteristics of a gastrointestinal disease-causing astrovirus in a goat kid, which had not been previously described in the United States. Full article

European plum (Prunus domestica) orchards in the Kashi region, Xinjiang, China, suffer from fruit brown spot disease. The disease typically appears as red spots on the fruit surface that expand into brown necrotic lesions; affected fruit flesh can shrink, and fruits can harden and drop. We isolate and identify pathogens associated with this disease in this plum from five Kashi counties. Of 210 fungal isolates obtained through standard tissue isolation, Alternaria accounted for 84.8%, with the remainder comprising species of Aspergillus (9.5%), Diplodia (3.3%), and Neoscytalidium (2.4%). Using PCR amplification and sequencing of five loci, pathogens were identified using multi-gene phylogenetic analyses, combined with observations of colony and spore morphology. Multi-locus sequences of Alternaria isolates were highly homologous to those of the Alternaria alternata type strain, and we refer them to an A. alternata species complex. Pathogenicity tests confirm that Alternaria isolates reproduce brown spot symptoms on European plum fruits. By demonstrating that Alternaria is the primary pathogen causing brown spot disease in European plum in Xinjiang, we clarify both the fungal species composition and taxonomic placement of the dominant pathogen associated with this disease. Full article

The forest fly (Hippobosca equina) is an obligate haematophagous dipteran insect (order Diptera) that primarily infests horses and may contribute to the circulation of vector-borne pathogens. This study aimed to investigate the presence of Anaplasma phagocytophilum, Borrelia burgdorferi s.l., Babesia caballi, and Theileria equi, important vector-borne pathogens of equids, in forest flies collected from horses in endemic areas of Spain. A total of 170 forest flies were collected from 39 equids across four geographical regions in Spain (Segovia, Madrid, Toledo, and Menorca) and blood samples were collected from 27 of these horses. All flies were morphologically and molecularly identified as H. equina, and DNA extracted from flies and equine blood was screened using multiplex real-time and nested PCR, followed by sequencing and phylogenetic analysis. Neither flies nor horses tested positive for A. phagocytophilum, whereas one fly was positive for B. burgdorferi s.l. (0.6%). In contrast, T. equi and B. caballi DNA were detected in 11.2% and 1.2% of flies, respectively, and all positive flies were collected from horses positive for equine piroplasmosis (T. equi/B. caballi infection), with identical 18S rRNA sequences between hosts and flies. Nested PCR showed a higher detection rate than real-time PCR for the detection of these piroplasms in flies and blood samples. These findings provide the first molecular evidence of EP pathogens in H. equina and support further investigation into the epidemiological importance of forest flies in equine pathogen surveillance. Full article

Avian influenza viruses are predominantly associated with waterfowl and shorebirds, and are rarely detected in other avian hosts in nature. In 2021, an H1N1 virus was isolated from a Fieldfare Turdus pilaris in Zaporizhzhia Oblast, Ukraine. A phylogenetic analysis revealed that all eight gene segments belonged to the Eurasian low-pathogenic avian influenza lineages. The highest nucleotide identity of the HA gene was observed with viruses detected in Georgia, Sweden, and Ukraine (99.11%), while the NA gene showed the greatest identity to viruses from Western Europe (99.14–99.57%). Genetic analysis of the HA cleavage site showed a sequence (PSIQSR↓GLF) that contained a single basic amino acid. No deletions were detected in the stalk region of NA gene, and no specific mutations in PB2 protein were found. However, several amino acid substitutions were identified in the HA gene (D204E, S207T, and D239G) that may affect the binding affinity to specific antibodies. The occurrence of this virus in a wild, seemingly healthy thrush indicate that additional surveillance in poorly studied ecological groups such as Passeriformes is warranted. Full article

The historic Rockborn strain of the canine distemper virus was widely used as a vaccine, but its use was discontinued due to safety concerns. Yet, Rockborn-like canine distemper virus strains are still used in some vaccine formulations. Genetic analysis of this strain was previously limited to the H gene, leaving its full evolutionary and pathogenic potential unclear. This study aimed to determine the complete genome sequence of the Rockborn strain to reconstruct its origin, understand its evolution, and provide a reference for improving diagnostics and future research on virulence markers. An amplicon-based sequencing protocol using MinION nanopore technology was employed to determine the complete genome of the Rockborn-46th laboratory strain. The genome was assembled, annotated, and analyzed in comparison with 223 genomes. The complete genome of the Rockborn strain was 15,690 nucleotides in length. Phylogenetic analysis revealed that Rockborn forms a unique lineage with field isolates from a masked civet in China and a dog in the United States. Crucially, a significant recombination event was identified, showing that the Rockborn strain acted as a parental strain, contributing its F and H genes to create mosaic viruses. The full-genome characterization of the Rockborn strain confirms that Rockborn-like viruses persist and actively contribute to the evolution of canine distemper virus through recombination. This finding highlights the inadequacy of single-gene analysis for diagnostics and surveillance, and underscores the necessity of whole-genome sequencing to accurately track the virus epidemiology and evolution. Full article

Investigating the prevalence and molecular genetic characteristics of Anaplasma ovis, Theileria spp., Anaplasma phagocytophilum, and hemotropic Mycoplasma infections in sheep populations across different regions of Gansu Province is of significant importance for the prevention and control of these pathogens. A total of 1523 sheep blood samples were collected from 19 counties (districts) in Gansu Province. Pathogen screening was conducted using PCR-based molecular detection techniques, followed by sequencing and phylogenetic analysis of specific genes (e.g., Msp4, 18S rRNA) from selected positive samples. Blood-borne pathogens infections in Gansu Province were widespread but unevenly distributed geographically. Theileria spp. and Anaplasma ovis were the dominant pathogens, with overall infection rates of approximately 16.7% and 9.6%, respectively. The highest Anaplasma ovis infection rate (82.5%) was observed in the Gannan region, where co-infections were common (24/97). An exceptionally high Theileria spp. infection rate (87.5%) was detected in the Zagana area. No pathogens were detected in Wuwei, Jingyuan, Huining, Jingtai, Qinghuan, or Maqu. Phylogenetic analysis revealed that the Msp4 gene sequences of Anaplasma ovis isolates from Gansu shared 99.48% homology with strains from Europe, Asia, and Africa. Anaplasma phagocytophilum isolates also showed high homology (99.53–99.84%) with multiple global strains. Seasonal data indicated significantly higher Theileria spp. infection rates in spring (23–34%) compared to other seasons (approximately 12%). Gansu Province is an endemic area for multiple blood-borne pathogens, with distinct regional clustering and seasonality in prevalence. The high conservation of pathogen gene sequences suggests genetic stability. This study provides essential epidemiological baseline data and a scientific foundation for targeted prevention and control of blood-borne pathogen diseases in sheep in Gansu Province. Full article