High‐throughput sequencing (HTS) is a powerful tool that enables the simultaneous detection and potential identification of any organisms present in a sample. The growing interest in the application of HTS technologies for routine diagnostics in plant health laboratories is triggering the development of guidelines on how to prepare laboratories for performing HTS testing. This paper describes general and technical recommendations to guide laboratories through the complex process of preparing a laboratory for HTS tests within existing quality assurance systems. From nucleic acid extractions to data analysis and interpretation, all of the steps are covered to ensure reliable and reproducible results. These guidelines are relevant for the detection and identification of any plant pest (e.g. arthropods, bacteria, fungi, nematodes, invasive plants or weeds, protozoa, viroids, viruses), and from any type of matrix (e.g. pure microbial culture, plant tissue, soil, water), regardless of the HTS technology (e.g. amplicon sequencing, shotgun sequencing) and of the application (e.g. surveillance programme, phytosanitary certification, quarantine, import control). These guidelines are written in general terms to facilitate the adoption of HTS technologies in plant pest routine diagnostics and enable broader application in all plant health fields, including research. A glossary of relevant terms is provided among the Supplementary Material. Le séquençage haut débit (HTS) est un outil puissant qui permet, simultanément, la détection et l'identification potentielle de tout organisme présent dans un échantillon. L'application des technologies HTS suscite un intérêt croissant dans les laboratoires phytosanitaires pour les activités de diagnostic de routine et cet intérêt a conduit à l'élaboration de directives sur la manière de préparer les laboratoires à effectuer des tests HTS. Cet article décrit les recommandations générales et techniques, élaborées afin de guider les laboratoires dans le processus complexe de se préparer aux tests HTS, dans le cadre des systèmes d'assurance qualité existants. De l'extraction des acides nucléiques à l'analyse et interprétation des données, toutes les étapes sont décrites afin de garantir des résultats fiables et reproductibles. Ces directives sont applicables pour la détection et l'identification de tout organisme nuisible aux végétaux (p. ex. arthropodes, bactéries, champignons, nématodes, plantes ou adventices envahissantes, protozoaires, viroïdes, virus), et à partir de tout type de matrice (culture microbienne pure, tissu végétal, sol, eau), quelle que soit la technologie HTS (p. ex. séquençage d’amplicons, séquençage shotgun) et l'application (p. ex. programme de surveillance, certification phytosanitaire, quarantaine, contrôle des importations). Ces directives sont rédigées avec des termes génériques afin de faciliter l'adoption des technologies HTS dans les activités de diagnostic phytosanitaire de routine et de permettre une application plus large dans tous les domaines de la santé des végétaux, y compris le domaine de la recherche. Un glossaire des termes utiles est fourni dans les documents complémentaires. Высокопроизводительное секвенирование (HTS) ‐ это мощный инструмент, позволяющий одновременно обнаруживать и потенциально идентифицировать любые организмы, присутствующие в образце. Растущий интерес к применению технологий HTS для рутинной диагностики в лабораториях, занимающихся здоровьем растений, требует разработку рекомендаций по подготовке лабораторий к проведению HTS‐тестирования. В данном документе описаны общие и технические рекомендации, которые помогут лабораториям пройти сложный процесс подготовки лаборатории к проведению HTS‐тестов в рамках существующих систем обеспечения качества. Рассматриваются все этапы для обеспечения надежных и воспроизводимых результатов, начиная с выделения нуклеиновых кислот и заканчивая анализом и интерпретацией данных. Настоящее руководство актуально для обнаружения и идентификации любого вредного организма растений (например, членистоногих, бактерий, грибов, нематод, инвазивных растений или сорняков, простейших, вироидов, вирусов) и из любого типа матрицы (например, чистая культура микроорганизмов, ткани растений, почва, вода), независимо от технологии ВПC (например, ампликонное секвенирование, дробовое секвенирование) и области применения (например, программа надзора, фитосанитарная сертификация, карантин, контроль импорта). Настоящее руководство составлено в общих терминах, чтобы облегчить внедрение технологий HTS в рутинную диагностику вредителей растений и обеспечить её более широкое применение во всех областях защиты растений, включая научные исследования. В дополнительных материалах приводится глоссарий соответствующих терминов.
In 2001, New Zealand substantially modified its approach to implementation of the Quota Management System to make deemed values a central administrative tool. Catches in excess of a fisher’s annual catch entitlements (ACE) incur payments, called deemed values. Deemed values are an example of a price cap tool within a cap-and-trade regulatory system. The purpose of this paper is to develop four economic explanations for why deemed values may improve administration of individual transferable quota systems. First, deemed values can reduce transactions costs for catch balancing for both industry and government. Second, deemed values can provide liquidity in thin markets and improve the functioning of markets for ACE. Third, deemed values can reduce the incentives for discarding. These three administrative advantages are achieved because deemed values provide simpler administrative processes and because deemed values provide the industry greater flexibility in catch balancing. But the flexibility to land against deemed values carries the risk that deemed values could intentionally be set so low that intentional over-quota catches are incentivized. Fourth, differential deemed values can create an increasing marginal cost of overfishing incentive structure for harvesters.
Inter-pathologist variation is widely recognized across human and veterinary pathology and is often compounded by missing animal or clinical information on pathology submission forms. Variation in pathologist threshold levels of resident inflammatory cells in the tissue of interest can further decrease inter-pathologist agreement. This study applied a predictive modeling tool to bladder histology slides that were assessed by four pathologists: first without animal and clinical information, then with this information, and finally using the predictive tool. All three assessments were performed twice, using digital whole-slide images (WSI) and then glass slides. Results showed marked variation in pathologists’ interpretation of bladder slides, with kappa agreement values of 7–37% without any animal or clinical information, 23–37% with animal signalment and history, and 31–42% when our predictive tool was applied, for digital WSI and glass slides. The concurrence of test pathologists to the reference diagnosis was 60% overall. This study provides a starting point for the use of predictive modeling in standardizing pathologist agreement in veterinary pathology. It also highlights the importance of high-quality whole-slide imaging to limit the effect of digitization on inter-pathologist agreement and the benefit of continued standardization of tissue assessment in veterinary pathology.
Livestock abortion is an important cause of productivity losses worldwide and many infectious causes of abortion are zoonotic pathogens that impact on human health. Little is known about the relative importance of infectious causes of livestock abortion in Africa, including in subsistence farming communities that are critically dependent on livestock for food, income, and wellbeing. We conducted a prospective cohort study of livestock abortion, supported by cross-sectional serosurveillance, to determine aetiologies of livestock abortions in livestock in Tanzania. This approach generated several important findings including detection of a Rift Valley fever virus outbreak in cattle; high prevalence of C. burnetii infection in livestock; and the first report of Neospora caninum, Toxoplasma gondii, and pestiviruses associated with livestock abortion in Tanzania. Our approach provides a model for abortion surveillance in resource-limited settings. Our findings add substantially to current knowledge in sub-Saharan Africa, providing important evidence from which to prioritise disease interventions.
We conducted a retrospective study to examine the long-term trends for the global honey bee population and its two main products: honey and beeswax. Our analysis was based on the data collected by the Food and Agriculture Organization of the United Nations from 1961 to 2017. During this period, there were increases in the number of managed honey bee colonies (90.7%), honey production (236.2%) and beeswax production (115.8%). The amount of honey produced per colony increased by 50%, signifying improvements in the efficiency for producing honey. Concurrently, the human population grew by 135.3%. Whilst the absolute number of managed colonies increased globally, the number per capita declined by 19.9% from 13.6 colonies per 1000 population in 1961 to 10.9 colonies per 1000 population in 2017. Beeswax had a similar trend as the global production per capita reduced by 8.5% from 8.2 kg to 7.5 kg per 1000 population. In contrast, the global honey production per capita increased by 42.9% at the global level. The global human population growth outpaced that of managed honey bee colonies. Continuation of this trend raises the possibility of having a shortfall of pollinators to meet the increasing consumer demand for pollinated crops. To mitigate these challenges locally-driven solutions will be key as influencing factors differed geographically.
New Zealand’s temperate climate and bountiful flora are well suited to managed honey bees, and its geographic isolation and strict biosecurity laws have made sure that some pests and diseases affecting bees elsewhere are not present. Nevertheless, given the importance of pollination and high-value export honey to the economy, New Zealand began systematically measuring winter colony losses in 2015. The New Zealand Colony Loss Survey is modelled on the COLOSS survey but has been adapted to the New Zealand apicultural context. Some 49% of New Zealand beekeepers completed the winter 2021 survey. Between 2015 and 2021, overall colony loss rates increased monotonically from 8.37% [95% CI: 7.66%, 9.15%] to 13.59% [95% CI: 13.21%, 13.99%]. Whereas beekeepers most commonly attributed losses to queen problems between 2015 and 2020, attributions to varroa have escalated year-on-year to become the largest attributed cause of colony loss. Losses to varroa are perhaps amplified by the 23.4% of respondents who did not monitor mite loads and the 4.4% of beekeepers who did not treat varroa during the 2020/21 season. Indeed, most beekeepers consider their treatment to be effective and note that treating at the wrong time and reinvasion were major drivers of losses to varroa.
Shiga toxin-producing Escherichia coli (STEC) infection can cause mild to severe illness, such as nonbloody or bloody diarrhea, and the fatal hemolytic uremic syndrome (HUS). The molecular mechanism underlying the variable pathogenicity of STEC infection is not fully defined so far. Here, we performed a comparative genomics study on a large collection of clinical STEC strains collected from STEC-infected pediatric patients with and without HUS in Finland over a 16-year period, aiming to identify the bacterial genetic factors that can predict the risk to cause HUS and poor renal outcome. Of 240 STEC strains included in this study, 52 (21.7%) were from pediatric patients with HUS. Serotype O157:H7 was the main cause of HUS, and Shiga toxin gene subtype stx2a was significantly associated with HUS. Comparative genomics and pangenome-wide association studies identified a number of virulence and accessory genes overrepresented in HUS-associated STEC compared to non-HUS STEC strains, including genes encoding cytolethal distending toxins, type III secretion system effectors, adherence factors, etc. No virulence or accessory gene was significantly associated with risk factors for poor renal outcome among HUS patients assessed in this study, including need for and duration of dialysis, presence and duration of anuria, and leukocyte counts. Whole-genome phylogeny and multiple-correspondence analysis of pangenomes could not separate HUS STEC from non-HUS STEC strains, suggesting that STEC strains with diverse genetic backgrounds may independently acquire genetic elements that determine their varied pathogenicity. Our findings indicate that nonbacterial factors, i.e., characteristics of the host immunity, might affect STEC virulence and clinical outcomes. IMPORTANCE Shiga toxin-producing Escherichia coli (STEC) is a serious public health burden worldwide which causes outbreaks of gastrointestinal diseases and the fatal hemolytic uremic syndrome (HUS) characterized by the triad of mechanical hemolytic anemia, thrombocytopenia, and acute renal failure. Understanding the mechanism underlying the disease severity and patient outcome is of high importance. Using comparative genomics on a large collection of clinical STEC strains from STEC-infected patients with and without HUS, our study provides a reference of STEC genetic factors/variants that can be used as predictors of the development of HUS, which will aid risk assessment at the early stage of STEC infection. Additionally, our findings suggest that nonbacterial factors may play a primary role in the renal outcome in STEC-infected patients with HUS; further studies are needed to validate this.
We analyzed the large-scale drivers of biological invasions using freshwater fish in a Mediterranean country as a test case, and considering the contribution of single species to the overall invasion pattern. Using Boosted Regression Tree (BRT) models, variation partitioning and Redundancy Analysis (RDA), we found that human factors (especially eutrophication) and climate (especially temperature) were significant drivers of overall invasion. Geography was also relevant in BRT and RDA analysis, both at the overall invasion and the single species level. Only variation partitioning suggested that land use was the second most significant driver group, with considerable overlap between different invasion drivers and only land use and human factors standing out for single effects. There was general accordance both between different analyses, and between invasion outcomes at the overall and the species level, as most invasive species share similar ecological traits and prefer lowland river stretches. Human-mediated eutrophication was the most relevant invasion driver, but the role of geography and climate was at least equally important in explaining freshwater fish invasions. Overall, human factors were less prominent than natural factors in driving the spread and prevalence of invasion, and the species spearheading it.
Aim: Understanding the variation in community composition and species abundances (i.e., β-diversity) is at the heart of community ecology. A common approach to examine β-diversity is to evaluate directional variation in community composition by measuring the decay in the similarity among pairs of communities along spatial or environmental distance. We provide the first global synthesis of taxonomic and functional distance decay along spatial and environmental distance by analysing 148 datasets comprising different types of organisms and environments. Location: Global. Time period: 1990 to present. Major taxa studied: From diatoms to mammals. Method: We measured the strength of the decay using ranked Mantel tests (Mantel r) and the rate of distance decay as the slope of an exponential fit using generalized linear models. We used null models to test whether functional similarity decays faster or slower than expected given the taxonomic decay along the spatial and environmental distance. We also unveiled the factors driving the rate of decay across the datasets, including latitude, spatial extent, realm and organismal features. Results: Taxonomic distance decay was stronger than functional distance decay along both spatial and environmental distance. Functional distance decay was random given the taxonomic distance decay. The rate of taxonomic and functional spatial distance decay was fastest in the datasets from mid-latitudes. Overall, datasets covering larger spatial extents showed a lower rate of decay along spatial distance but a higher rate of decay along environmental distance. Marine ecosystems had the slowest rate of decay along environmental distances. Main conclusions: In general, taxonomic distance decay is a useful tool for biogeographical research because it reflects dispersal-related factors in addition to species responses to climatic and environmental variables. Moreover, functional distance decay might be a cost-effective option for investigating community changes in heterogeneous environments.
Inland recreational fisheries provide numerous socio-economic benefits to fishers, families and communities. Recreationally harvested fish are also frequently consumed and may provide affordable and sustainable but undervalued contributions to human nutrition. Quantifying the degree to which recreationally harvested fish contribute to food security and subsistence is impeded by lack of data on harvest and consumption and by the difficulty in differentiating among recreational and subsistence fisheries. Recreational harvest records tend to be limited to wealthy, food-secure countries and well-monitored fisheries with clear regulations or permitting systems. These records often neglect components of recreational harvest among food-insecure fishers who are potentially more likely to have consumption as a motivation. Here, we highlight the ‘fuzzy boundary’ that can exist between inland recreational and subsistence fisheries and argue that unreported consumption is likely to be a hidden contributor to food security in some populations. We draw on local case studies from around the world to highlight specific instances where recreationally harvested fish species contribute food and subsistence benefits to participating communities. We use these examples to highlight the diversity of ways that inland recreational fisheries contribute to human nutrition, knowledge gaps in understanding recreational fishing for food, and consequences of not accounting for them as food fisheries in policy and management. The aim of this paper is to draw the attention of resource managers and policy makers, create greater social awareness of the importance of recreational fisheries and bring to light this hidden contribution of inland fisheries to nutrition and subsistence.
The establishment of marine non-indigenous species (NIS) in new locations can degrade environmental, socio-cultural, and economic values. Vessels arriving from international waters are the main pathway for the entry of marine NIS, via exposure due to ballast water discharge (hereafter, ballast discharge) and biofouling. We developed a systematic statistical likelihood-based methodology to investigate port-level marine NIS propagule pressure from ballast discharge and biofouling exposure using a combination of techniques, namely k -Nearest-Neighbour and random forest algorithms. Vessel characteristics and travel patterns were assessed as candidate predictors. For the ballast discharge analysis, the predictors used for model building were vessel type, dead weight tonnage, and the port of first arrival; the predictors used for the biofouling analysis were days since last antifouling paint, mean vessel speed, dead weight tonnage, and hull niche area. Propagule pressure for both pathways was calculated at a voyage, port and annual level, which were used to establish the relative entry score for each port. The model was applied to a case study for New Zealand. Biosecurity New Zealand has commissioned targeted marine surveillance at selected ports since 2002 to enable early detection of newly arrived marine NIS (Marine High-Risk Site Surveillance, MHRSS). The reported methodology was used to compare contemporary entry likelihoods between New Zealand ports. The results suggested that Tauranga now receives the highest volume of discharged ballast water and has the second most biofouling exposure compared to all other New Zealand ports. Auckland was predicted to receive the highest biofouling mass and was ranked tenth for ballast discharge exposure. Lyttelton, Napier, and New Plymouth also had a high relative ranking for these two pathways. The outputs from this study will inform the refinement of the MHRSS programme, facilitating continued early detection and cost-effective management to support New Zealand’s wider marine biosecurity system. More generally, this paper develops an approach for using statistical models to estimate relative likelihoods of entry of marine NIS.
Crop uptake of ²²⁶Ra over a range of key New Zealand agricultural and horticultural growing areas was analysed to establish the dietary implications of an increase in soil ²²⁶Ra activity concentrations. Thirty crop samples, covering both feed and food commodities, were quantified for ²²⁶Ra activity concentrations, and concentration ratio (CRs) from the soil activity were calculated. The calculated CRs correlated with international default values for estimating crop uptake. Variation in CRs established that there was no increase in the crop activity concentration, relative to soil ²²⁶Ra from pasture foliage at a fertiliser impacted site, with a gradient of soil ²²⁶Ra activity concentrations. Based on the calculated CRs, the upper bound of the theoretical range of dietary exposures to ²²⁶Ra was 78.1 μSv/yr for teenage boys. Future forecasting of the increased dietary dose of ²²⁶Ra that might occur at the current soil loading rate, based on current fertiliser activity concentrations, confirmed that long-term loading of soil with ²²⁶Ra is unlikely to present a dietary risk. The forecast model calculated that the increase in dietary ionising radiation burden is unlikely to reach thresholds requiring regulatory intervention for two millennia.
Fish disease surveillance methods can be complicated and time consuming, which limits their value for timely intervention strategies on aquaculture farms. Novel molecular-based assays using droplet digital Polymerase Chain Reaction (ddPCR) can produce immediate results and enable high sample throughput with the ability to multiplex several targets using different fluorescent dyes. A ddPCR tetraplex assay was developed for priority salmon diseases for farmers in New Zealand including New Zealand Rickettsia-like organism 1 (NZ-RLO1), NZ-RLO2, Tenacibaculum maritimum, and Yersinia ruckeri. The limit of detection in singleplex and tetraplex assays was reached for most targets at 10 −9 ng/μl with, respectively, NZ-RLO1 = 0.931 and 0.14 copies/μl, NZ-RLO2 = 0.162 and 0.21 copies/μl, T. maritimum = 0.345 and 0.93 copies/μl, while the limit of detection for Y. ruckeri was 10 −8 with 1.0 copies/μl and 0.7 copies/μl. While specificity of primers was demonstrated in previous studies, we detected cross-reactivity of T. maritimum with some strains of Tenacibaculum dicentrarchi and Y. ruckeri with Serratia liquefaciens, respectively. The tetraplex assay was applied as part of a commercial fish disease surveillance program in New Zealand for 1 year to demonstrate the applicability of tetraplex tools for the salmonid aquaculture industry.
Predatory fish have occasionally been observed preying on birds, sometimes repeatedly, but few studies were able to unravel the overall significance of avian prey in fish diet and the predation impacts on bird populations. We used a control/impact study setup, using a Nature Reserve in northern Italy and a nearby control area, to determine: 1) the contribution of waterbirds to wels catfish diet in the Reserve, 2) the population density of wels catfish in the Reserve and control area and 3) the potential impacts of waterbird depredation by wels catfish on waterbird population trends. Our stable isotope Bayesian mixing model indicated that birds contributed 12.2% (5-27.9%, 50% confidence interval) of the diet of large wels catfish (> 98 cm in total length). Large individuals constituted the majority of the population in the shoreline areas of the reserve in 2013-2019, where the population was stable despite control efforts. Numbers were below detectable levels in the control area. Large wels catfish consumed an average of 224, 148 and 187 kg of birds during the 2019 chick growing period, as estimated through three different bioenergetic models. Compared to the control area, mallard reproductive success was diminished in the Reserve, likely due to higher rates of fish predation, although effects were variable in different years. Overall, our data suggest that high densities of invasive wels catfish might impact waterbird reproductive success through predation on bird chicks, but further studies would be needed to reduce uncertainties related to the intrinsic variability of field ecology data. Our study constitutes a preliminary attempt to assess the potential of introduced wels catfish to affect the conservation value of waterbird protection areas, and should be repeated at broader spatial and temporal scales.
Diffusive gradients in thin films (DGTs) have been established as useful tools for the determination of nitrate, phosphate, trace metals, and organic concentrations. General use of DGTs, however, is limited by the subsequent requirement for laboratory analysis. To increase the uptake of DGT as a tool for routine monitoring by nonspecialists, not researchers alone, methods for in-field analysis are required. Incorporation of color reagents into the binding layer, or as the binding layer, could enable the easy and accurate determination of analyteconcentrations in-field. Here, we sought to develop a chitosan-stabilized silver nanoparticle (AuNP) suspensionliquid-binding layer which developed color on exposure to nitrite, combined with an Fe(0)-impregnated poly-2-acrylamido-2-methyl-1-propanesulfonic acid/acrylamide copolymer hydrogel [Fe(0)-p(AMPS/AMA)] for the reduction of nitrate. The AuNP-chitosan suspension was housed in a 3D designed and printed DGT base, with a volume of 2 mL, for use with the standard DGT solution probe caps. A dialysis membrane with a molecular weight cut off of <15 kDa was used, as part of the material diffusion layer, to ensure that the AuNP-chitosan did not diffuse through to the bulk solution. This synthesized AuNP-chitosan provided quantitative nitrite concentrations (0 to1000 mg L−1) and masses (145 μg) in laboratory-based color development studies. An Fe(III)-impregnated poly-2-acrylamido-2-methyl-1-propanesulfonic acid/acrylamide copolymer hydrogel [Fe(III)-p(AMPS/AMA)] was developed (10% AMPS, and 90% AMA), which was treated with NaBH4 to form an Fe(0)-p(AMPS/AMA) hydrogel. The Fe(0)-p(AMPS/AMA) hydrogel quantitatively reduced nitrate to nitrite. The total nitrite mass produced was ∼110 μg, from nitrate. The diffusional characteristics of nitrite and nitrate through the Fe(III)-p(AMPS/AMA) and dialysis membrane were 1.40 × 10−5and 1.40 × 10−5 and 5.05 × 10−6 and 5.15 × 10−6 cm2 s−1 at 25 °C respectively. The Fe(0)-hydrogel and AuNP-chitosan suspension operated successfully in laboratory tests individually; however, the combined AuNP-chitosan suspension and Fe(0)-hydrogel DGT did not provide quantitative nitrate concentrations. Further research is required to improve the reaction rate of the AuNP-chitosan nitrite-binding layer, to meet the requirement of rapid binding to operate as a DGT.
Nutrition content and health claims are widely used globally on both food labels and in food advertising. This study explored how New Zealand consumers understand, perceive, and use nutrition content and health claims on food labels. A qualitative approach was used with semi-structured in-depth online interviews and in-person focus groups including 49 participants, aged ≥25 years responsible for household food shopping. Transcripts were analysed using reflexive thematic analysis using inductive coding, with development of five themes—(1) aware of claims but did not use, (2) mistrust and scepticism, (3) confusion and misinterpretation, (4) using claims to guide food choice, and (5) not all claims are equal. For theme 1, price and habit were found to be the most influential in driving food choice. Underlying theme 2 was the perception by most of nutrition and health claims as marketing. Scepticism was exacerbated when nutrient claims were displayed on inherently unhealthy products. However participants with specific dietary requirements did find claims helpful. Restricting nutrient claims to foods meeting a healthy nutrient profile aligned to the existing Health Star Rating system, education about regulation and supporting claims with more contextual information may increase trust, the perceived value of claims and therefore their utility.
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