The EFSA quantitative approach to pest risk assessment – methodological aspects and case studies

A new method for pest risk assessment and the identification and evaluation of risk‐reducing options is currently under development by the European Food Safety Authority (EFSA) Plant Health Panel. The draft method has been tested on pests of concern to the European Union (EU). The method is adaptable and can focus either on all the steps and sub‐steps of the assessment process or on specific parts if necessary. It is based on assessing changes in pest population abundance as the major driver of the impact on cultivated plants and on the environment. Like other pest risk assessment systems the method asks questions about the likelihood and magnitude of factors that contribute to risk. Responses can be based on data or expert judgment. Crucially, the approach is quantitative, and it captures uncertainty through the provision by risk assessors of quantile estimates of the probability distributions for the assessed variables and parameters. The assessment is based on comparisons between different scenarios, and the method integrates risk‐reducing options where they apply to a scenario, for example current regulation against a scenario where risk‐reducing options are not applied. A strategy has been developed to communicate the results of the risk assessment in a clear, comparable and transparent way, with the aim of providing the requestor of the risk assessment with a useful answer to the question(s) posed to the EFSA Plant Health Panel. The method has been applied to four case studies, two fungi, Ceratocystis platani and Cryphonectria parasitica, the nematode Ditylenchus destructor and the Grapevine flavescence dorée phytoplasma. Selected results from these case studies illustrate the types of output that the method can deliver.     

The use of nuclear imaging for a mixed C cell microfollicular carcinoma of the thyroid gland in a mature horse

A 15‐year‐old Boerperd stallion presented for thyroid enlargement associated with inappetance. Ultrasonographic examination of the thyroid gland revealed an enlarged left lobe, which, on cytological examination, contained numerous anaplastic cells. A mixed C cell microfollicular thyroid carcinoma was diagnosed following histopathological examination of the excisional biopsy specimen. In order to determine metastasis, pulmonary radiographs revealed a poorly‐marginated soft tissue opacity caudo‐dorsal to the cardiac silhouette. Thyroid and pulmonary scintigraphy was performed comparing ^99mTc‐sestamibi with ^99mTc‐pertechnetate and no metastasis was detectable. Following hemithyroidectomy, the stallion made a full recovery without the need for neoadjuvant chemotherapy. Six months later, repeated thyroid and pulmonary scintigraphy using ^99mTc‐sestamibi was normal.     

Metastatic immune infiltrates correlate with those of the primary tumour in canine osteosarcoma

Our lack of understanding of the immune microenvironment in canine osteosarcoma (cOSA) has limited the identification of potential immunotherapeutic targets. In particular, our ability to utilize readily available tissue from a dog's primary tumour to predict the type and extent of immune response in their pulmonary metastatic lesions is unknown. We, therefore, collected 21 matched pairs of primary tumours and pulmonary metastatic lesions from dogs with OSA and performed immunohistochemistry to quantify T‐lymphocyte (CD3), FOXP3+ cell, B‐lymphocyte (Pax‐5), and CD204+ macrophage infiltration. We found that T‐lymphocytes and FOXP3+ infiltrates in primary tumours positively correlated with that of metastatic lesions (ρ = 0.512, P = 0.038 and ρ = 0.698, P = 0.007, respectively), while a strong trend existed for CD204+ infiltrates (ρ = 0.404, P = 0.087). We also observed T‐ and B‐lymphocytes, and CD204+ macrophages to be significantly higher in a dog's pulmonary metastasis compared to their primary tumour (P = 0.018, P = 0.018, P = 0.016, respectively), while FOXP3+ cells were only significantly higher in metastases when all primary tumour and metastasis lesions were compared without pairing (P = 0.036). Together, these findings suggest that the metastatic immune microenvironment may be influenced by that of the primary cOSA, and that primary tumour immune biomarkers could potentially be applied to predict immunotherapeutic responses in gross metastatic disease. We, therefore, provide a rationale for the treatment of cOSA pulmonary metastases with immunotherapeutics that enhance the anti‐tumour activity of these immune cells, particularly in dogs with moderate to high immune cell infiltration in their primary tumours.     

DNA barcoding of fish eggs collected off northwestern Cuba and across the Florida Straits demonstrates egg transport by mesoscale eddies

Identifying spawning sites for broadcast spawning fish species is a key element of delineating critical habitat for managing and regulating marine fisheries. Genetic barcoding has enabled accurate taxonomic identification of individual fish eggs, overcoming limitations of morphological classification techniques. In this study, planktonic fish eggs were collected at 23 stations along the northwestern coast of Cuba and across the Florida Straits to United States waters. A total of 564 fish eggs were successfully identified to 89 taxa within 30 families, with the majority of taxa resolved to species. We provide new spawning information for Luvarus imperialis (Louvar), Bothus lunatus (Plate Fish), Eumegistus illustris (Brilliant Pomfret), and many economically important species. Data from most sites supported previously established patterns of eggs from neritic fish species being found on continental shelves and oceanic species spawning over deeper waters. However, some sites deviated from this pattern, with eggs from reef‐associated fish species detected in the deep waters of the Florida Straits and pelagic species detected in the shallow, continental shelf waters off the coast of northwestern Cuba. Further investigation using satellite imagery revealed the presence of a mesoscale cyclonic eddy that likely entrained neritic fish eggs and transported them into the Florida Straits. The technique of combining DNA‐based fish egg identification with remotely‐sensed hydrodynamics provides an important new tool for assessing the interplay of regional oceanography with fish spawning strategies.     

Multilocus sequence typing detects new Piscirickettsia salmonis hybrid genogroup in Chilean fish farms: Evidence for genetic diversity and population structure

Piscirickettsia salmonisis the causative bacterial pathogen of piscirickettsiosis, a salmonid disease that causes notable mortalities in the worldwide aquaculture industry. Published research describes the phenotypic traits, virulence factors, pathogenicity and antibiotic‐resistance potential for various P. salmonisstrains. However, evolutionary and genetic information is scarce for P. salmonis. The present study used multilocus sequence typing (MLST) to gain insight into the population structure and evolution of P. salmonis. Forty‐two Chilean P. salmonisisolates, as well as the type strain LF‐89^T, were recovered from diseased Salmo salar, Oncorhynchus kisutchand Oncorhynchus mykissfrom two Chilean Regions. MLST assessed the loci sequences of dnaK, efp, fumC, glyA, murG, rpoD and trpB. Bioinformatics analyses established the genetic diversity among P. salmonis isolates (H = 0.5810). A total of 23 sequence types (ST) were identified, 53.48% of which were represented by ST1, ST5 and ST2. Population structure analysis through polymorphism patterns showed few polymorphic sites (218 nucleotides from 4,010 bp), while dN/dS ratio analysis indicated purifying selection for dnaK, epf, fumC, murG, and rpoD but neutral selection for the trpB loci. The standardized index of association indicated strong linkage disequilibrium, suggesting clonal population structure. However, recombination events were detected in a group of seven isolates. Findings included genogroups homologous to the LF‐89^T and EM‐90 strains, as well as a seven‐isolate hybrid genogroup recovered from both assessed regions (three O. mykiss and four S. salar isolates). The presented MLST scheme has comparative potential, with promising applications in studying distinct P. salmonis isolates (e.g., from different hosts, farms, geographical areas) and in understanding the epidemiology of this pathogen.