Environmental DNA/RNA for pathogen and parasite detection,surveillance, and ecology

Detection of pathogens, parasites, and other symbionts in environmental samples via eDNA/eRNA (collectively eNA) is an increasingly important source of information about their occurrence and activity. There is great potential for using such detections as a proxy for infection of host organisms in connected habitats, for pathogen monitoring and surveillance, and for early warning systems for disease. However, many factors require consideration, and appropriate methods developed and verified, in order that eNA detections can be reliably interpreted and adopted for surveillance and assessment of disease risk, and potentially inclusion in international standards, such as the World Organisation for Animal Health guidelines. Disease manifestation results from host–symbiont–environment interactions between hosts, demanding a multifactorial approach to interpretation of eNA signals.     

Pre-pregnancy risk assessment and counselling of the cardiac patient

Pregnant women with heart disease often have an increased risk of maternal cardiovascular and offspring complications. The magnitude of these risks varies depending on the type and severity of the underlying disease. Therefore risk assessment should be performed before pregnancy. This can be accomplished by taking into account predictors and risk scores that have been developed in large populations of pregnant women with heart disease, as well as by consulting disease-specific pregnancy literature. A system that integrates all available knowledge about the risk of pregnancy is the adapted World Health Organisation risk classification. The safety of pregnancy for women with heart disease can be enhanced by adequate risk assessment and counselling.     

A risk assessment approach for fresh fruits

Aims:  To describe the approach used in conducting a fit‐for‐purpose risk assessment of microbiological human pathogens associated with fresh fruit and the risk management recommendations made. Methods and Results:  A qualitative risk assessment for microbiological hazards in fresh fruit was carried out based on the Codex Alimentarius (Codex) framework, modified to consider multiple hazards and all fresh (whole) fruits. The assessment determines 14 significant bacterial, viral, protozoal and nematodal hazards associated with fresh produce, assesses the probable level of exposure from fresh fruit, concludes on the risk from each hazard, and considers and recommends risk management actions. A review of potential risk management options allowed the comparison of effectiveness with the potential exposure to each hazard. Conclusions:  Washing to a recommended protocol is an appropriate risk management action for the vast majority of consumption events, particularly when good agricultural and hygienic practices are followed and with the addition of refrigerated storage for low acid fruit. Additional safeguards are recommended for aggregate fruits with respect to the risk from protozoa. Significance and Impact of the Study:  The potentially complex process of assessing the risks of multiple hazards in multiple but similar commodities can be simplified in a qualitative assessment approach that employs the Codex methodology.     

A Comparison of Disease Risk Analysis Tools for Conservation Translocations

Conservation translocations are increasingly used to manage threatened species and restore ecosystems. Translocations increase the risk of disease outbreaks in the translocated and recipient populations. Qualitative disease risk analyses have been used as a means of assessing the magnitude of any effect of disease and the probability of the disease occurring associated with a translocation. Currently multiple alternative qualitative disease risk analysis packages are available to practitioners. Here we compare the ease of use, expertise required, transparency, and results from, three different qualitative disease risk analyses using a translocation of the endangered New Zealand passerine, the hihi (Notiomystis cincta), as a model. We show that the three methods use fundamentally different approaches to define hazards. Different methods are used to produce estimations of the risk from disease, and the estimations are different for the same hazards. Transparency of the process varies between methods from no referencing, or explanations of evidence to justify decisions, through to full documentation of resources, decisions and assumptions made. Evidence to support decisions on estimation of risk from disease is important, to enable knowledge acquired in the future, for example, from translocation outcome, to be used to improve the risk estimation for future translocations. Information documenting each disease risk analysis differs along with variation in emphasis of the questions asked within each package. The expertise required to commence a disease risk analysis varies and an action flow chart tailored for the non-wildlife health specialist are included in one method but completion of the disease risk analysis requires wildlife health specialists with epidemiological and pathological knowledge in all three methods. We show that disease risk analysis package choice may play a greater role in the overall risk estimation of the effect of disease on animal populations involved in a translocation than might previously have been realised.

     

Using Qualitative Disease Risk Analysis for Herpetofauna Conservation Translocations Transgressing Ecological and Geographical Barriers

Through the exploration of disease risk analysis methods employed for four different UK herpetofauna translocations, we illustrate how disease hazards can be identified, and how the risk of disease can be analysed. Where ecological or geographical barriers between source and destination sites exist, parasite populations are likely to differ in identity or strain between the two sites, elevating the risk from disease and increasing the number and category of hazards requiring analysis. Simplification of the translocation pathway through the avoidance of these barriers reduces the risk from disease. The disease risk analysis tool is intended to aid conservation practitioners in decision making relating to disease hazards prior to implementation of a translocation.

     

Which Effect Measure Should Be Used for Impact Assessment in a New Population Context?

One characteristic feature in impact assessment based on epidemiologic studies is the transfer of an exposure-response association into a new population context. The consequences of basing this estimation procedure either on relative effect measures (e.g., relative risks) or on measures on the difference scale (e.g., excess rate) were exemplary illustrated with two air pollution studies which quantified the association between lung cancer and PM₁₀ in cohorts with varying lung cancer incidence due to different smoking habits. This example showed that the type of measure chosen may markedly influence the result of an impact assessment, if the frequency of the disease of interest varies across different populations due to other risk factors than the one considered. Thus, it was concluded that whenever studies from different population contexts are pooled, careful considerations about the appropriate type of measure are required. In environmental health risk assessment with usually small risks and unspecific (i.e., multicausal) health endpoints, an excess rate-based approach may provide a more reliable and stable estimate than a relative risk based approach in many circumstances. Methodological details of an excess rate-based approach are presented in the paper.     

Costs and benefits of freedom from shrimp diseases in the European Union

The growth in penaeid shrimp aquaculture has been mirrored by the emergence of a number of serious diseases, some of which (e.g. white spot syndrome virus - WSSV) spread rapidly across the globe through movement of infected stock. The World Organisation for Animal Health (OIE) lists six penaeid shrimp pathogens of which three are notifiable in the EU: WSSV (listed as non-exotic to the EU), Taura syndrome virus (TSV) and yellow head disease (YHD) (both listed as exotic). EU Member States (MS) must determine a status for non-exotic diseases (e.g. disease free, unknown, infected). In developing a policy for WSSV, import risk analysis (IRA) can be used to systematically assess the risks of introduction and justify risk mitigation to maintain freedom. OIE guidelines recommend that countries assess the risk of disease introduction via commodities, not listed by the OIE as safe, and apply sanitary measures if necessary. The sanitary measures necessary to maintain freedom from WSSV may not be compatible with current EU animal health legislation. The recent revision by OIE of products listed as safe for international trade strengthens the case for the risks of TSV and YHD introduction into the EU to be assessed. Freedom from WSSV is an important criterion for the development of shrimp aquaculture in the EU. However, in developing disease control policy, governments need to balance the potentially competing interests of all stakeholders, including consumers. Thus economic modelling of the impact of possible sanitary measures on consumer prices of imported products is needed to support decision making. The creation of disease free compartments and post-import risk mitigation for commodities may create the conditions conducive to the development of shrimp aquaculture whilst minimising the costs of maintaining disease freedom.     

Assessment of occupational hazards and associated risks in fuzzy environment: A case study of a university chemical laboratory

University laboratories involve various occupational hazards during the research and course activities, which might affect health and safety of both researchers and students, including chemical, physical, electrical, mechanical, as well as ergonomic and psychosocial risk factors. There are many aspects open to improvements in Occupational Health and Safety management of laboratories, and it is required to deal with risks, reduce them in an acceptable level, and implement control measures. In this study, a risk assessment approach is proposed for the university laboratory operations. The proposed approach incorporates 5S methodology, failure modes and effects analysis (FMEA), interval type-two fuzzy sets (IT2FSs), analytic hierarchy process (AHP), and the VlseKriterijumska Optimizacija I Kompromisno Resenje (VIKOR). AHP is injected into IT2FSs in the phase of evaluation and weighting of severity (S), occurrence (O), and detectability (D) parameters of FMEA. By applying IT2FVIKOR, it is aimed at prioritizing the emerged hazards in the chemical laboratory of the observed university. The proposed approach reveals the important hazards and suggests control measures for managing them. The study methodologically contributes to risk assessment in the knowledge, while a case study in a chemical laboratory of a newly established university offers an insight into education industry in safety improvement.     

Transboundary movement of shrimp viruses in crustaceans and their products: a special risk?

Shrimp and shrimp products form the most valuable internationally traded fisheries commodity, and the volumes are huge, estimated to be about 3.6 million tonnes. However, despite the existence under the General Agreement on Tariffs and Trade, of the Sanitary and Phytosanitary Measures (SPS Agreement) and the activities of the World Organisation for Animal Health (OIE), viral shrimp epizootics have spread and continue to spread, affecting world production. Though most attention has focussed on the movement of live shrimp product, the spread of new and emerging diseases through other crustaceans and their nonviable products is of increasing concern. The risks associated with the unrestricted movement of nonviable product will be outlined and measures that can be taken to mitigate the risk are discussed. Ultimately, for crustacean diseases, the paradigm under which the OIE has operated for the past 80 years needs to change.     

Disease hazard identification and assessment associated with wildlife population declines

Disease is increasingly being recognised as a risk factor in declining wildlife populations around the globe. However, there are limited protocols to assess disease risks in declining wildlife. Using epidemiological principles, we define a step‐by‐step framework to complete this complex and critical task. As an example, we assessed the potential role of diseases in relation to the decline of the woylie or brush‐tailed bettong (Bettongia penicillata ogilbyi) in Western Australia. Between 1999 and 2006, woylie populations declined by 90%. The wildlife disease risk assessment began with a list of all known or suspected diseases to which the woylie, a species of macropod, is susceptible. This list was assessed against the spatial, temporal and demographic characteristics of the decline. Diseases causing widespread and high mortalities or debilitation leading to predation received high scores. Based on this assessment, priority diseases or pathogens for investigation identified were haemoparasites, gastrointestinal helminths, Neospora caninum, Toxoplasmosis (Toxoplasma gondii), Encephalomyocarditis virus, Macropod Orbiviruses (Wallal virus and Warrego virus), Macropod Herpesviruses (Macropodid herpesvirus 1 and 2) and Salmonella spp.     

Biosecurity for Translocations: Cirl Bunting (Emberiza cirlus), Fisher’s Estuarine Moth (Gortyna borelii lunata), Short-Haired Bumblebee (Bombus subterraneus) and Pool Frog (Pelophylax lessonae) Translocations as Case Studies

Exposure to parasites in conservation translocations increases the risks to recipient and translocated populations from disease, and therefore there has been interest in implementing biosecurity methods. Using four case examples we described how biosecurity was applied in practical translocation scenarios prior to and during a translocation and also post-release. We implemented biosecurity, including quarantine barriers, at specific points in the translocation pathway where hazards, identified by the disease risk analysis, had the potential to induce disease. Evidence that biosecurity protected translocated and recipient populations, included an absence of mortality associated with high-risk non-native parasites, a reduction in mortality associated with endemic parasites, the absence of high-risk pathogenic parasites, or associated diseases, at the destination; and the apparent absence of diseases in closely related species at the destination site. The biosecurity protocols did not alter the level or duration of translocated species confinement and therefore probably did not act as a stressor. There is a monetary cost involved in biosecurity but the epidemiological evidence suggests that conservation translocation managers should carefully consider its use. Breakdowns in quarantine have occurred in human hospitals despite considerable investment and training for health professionals, and we therefore judge that there is a need for training in the objectives and maintenance of quarantine barriers in conservation translocations. Biosecurity protocols for conservation translocations should be continually updated in response to findings from disease risk analysis and post-release disease surveillance and we recommend further studies to evaluate their effectiveness.

     

Summary of 1993 World Health Organisation-International Society of Hypertension guidelines for the management of mild hypertension. Subcommittee of WHO/ISH Mild Hypertension Liaison committee.

As part of the ongoing process of issuing guidelines for managing hypertension the World Health Organisation and International Society of Hypertension present a summary of the latest guidelines for the management of mild hypertension. In both young and elderly people this condition is a risk factor for cardiovascular disease and should be treated. Information is presented on methods of diagnostic evaluation and assessment of risk. Methods of treatment, including changes in lifestyle, are covered.     

Using fuzzy logic to determine the vulnerability of marine species to climate change

Marine species are being impacted by climate change and ocean acidification, although their level of vulnerability varies due to differences in species' sensitivity, adaptive capacity and exposure to climate hazards. Due to limited data on the biological and ecological attributes of many marine species, as well as inherent uncertainties in the assessment process, climate change vulnerability assessments in the marine environment frequently focus on a limited number of taxa or geographic ranges. As climate change is already impacting marine biodiversity and fisheries, there is an urgent need to expand vulnerability assessment to cover a large number of species and areas. Here, we develop a modelling approach to synthesize data on species‐specific estimates of exposure, and ecological and biological traits to undertake an assessment of vulnerability (sensitivity and adaptive capacity) and risk of impacts (combining exposure to hazards and vulnerability) of climate change (including ocean acidification) for global marine fishes and invertebrates. We use a fuzzy logic approach to accommodate the variability in data availability and uncertainties associated with inferring vulnerability levels from climate projections and species' traits. Applying the approach to estimate the relative vulnerability and risk of impacts of climate change in 1074 exploited marine species globally, we estimated their index of vulnerability and risk of impacts to be on average 52 ± 19 SD and 66 ± 11 SD, scaling from 1 to 100, with 100 being the most vulnerable and highest risk, respectively, under the ‘business‐as‐usual' greenhouse gas emission scenario (Representative Concentration Pathway 8.5). We identified 157 species to be highly vulnerable while 294 species are identified as being at high risk of impacts. Species that are most vulnerable tend to be large‐bodied endemic species. This study suggests that the fuzzy logic framework can help estimate climate vulnerabilities and risks of exploited marine species using publicly and readily available information.     

BMI and waist circumference as indicators of health among Samoan women

Objective: High rates of obesity and chronic disease make establishment of effective indicators of risk for chronic disease important. The objective was to examine adequacy of anthropometric cut‐off points as indicators of risk for chronic disease among Samoan women in Hawaii. Research Methods and Procedures: A cross‐sectional survey of 55 Samoan women 18 to 28 years of age that included blood lipids, cholesterol, and glucose (including after a 2‐hour oral glucose test); anthropometry (weight, height, waist circumference); and DXA of body composition. Results: Using the Centers for Disease Control and Prevention (CDC)/World Health Organization (WHO) cut‐off points for BMI, 22% of women were overweight and 58% were obese. Cholesterol, lipid, and glucose values were all linearly related to DXA body fat, BMI, and waist circumference. BMI and waist circumference at WHO/NIH cut‐off points predicted levels of blood lipids and glucose that indicate elevated risk for disease. Discussion: WHO/NIH cut‐off points for BMI and waist circumference reflect risk indicators of chronic disease among young Samoan women in Hawaii.     

Time-dependent covariates in the proportional subdistribution hazards model for competing risks

Separate Cox analyses of all cause-specific hazards are the standard technique of choice to study the effect of a covariate in competing risks, but a synopsis of these results in terms of cumulative event probabilities is challenging. This difficulty has led to the development of the proportional subdistribution hazards model. If the covariate is known at baseline, the model allows for a summarizing assessment in terms of the cumulative incidence function. black Mathematically, the model also allows for including random time-dependent covariates, but practical implementation has remained unclear due to a certain risk set peculiarity. We use the intimate relationship of discrete covariates and multistate models to naturally treat time-dependent covariates within the subdistribution hazards framework. The methodology then straightforwardly translates to real-valued time-dependent covariates. As with classical survival analysis, including time-dependent covariates does not result in a model for probability functions anymore. Nevertheless, the proposed methodology provides a useful synthesis of separate cause-specific hazards analyses. We illustrate this with hospital infection data, where time-dependent covariates and competing risks are essential to the subject research question.     

Incidence,prevalence, mortality,disability-adjusted life years and risk factors of cancer in Australia and comparison with OECD countries, 1990–2015: findings from the Global Burden of Disease Study 2015

BackgroundComparative evidence on the burden, trend, and risk factors of cancer is limited. Using data from the Global Burden of Disease (GBD) study, we aimed to assess cancer burden – incidence, prevalence, mortality, disability-adjusted life years (DALYs) – and attributable risk factors for Australia between 1990 and 2015, and to compare them with those of 34 members of the Organisation for Economic Co-operation and Development (OECD).MethodsThe general GBD cancer estimation methods were used with data input from vital registration systems and cancer registries. A comparative risk assessment approach was used to estimate the population-attributable fractions due to risk factors.ResultsIn 2015 there were 198,880 (95% uncertainty interval [UI]: 183,908–217,365) estimated incident cancer cases and 47,562 (95% UI: 46,061–49,004) cancer deaths in Australia. Twenty-nine percent (95% UI: 28.2–29.8) of total deaths and 17.0% (95% UI: 15.0–19.1) of DALYs were caused by cancer in Australia in 2015. Cancers of the trachea, bronchus and lung, colon and rectum, and prostate were the most common causes of cancer deaths. Thirty-six percent (95% UI: 33.1–37.9) of all cancer deaths were attributable to behavioral risks. The age-standardized cancer incidence rate (ASIR) increased between 1990 and 2015, while the age-standardized cancer death rate (ASDR) decreased over the same period. In 2015, compared to 34 other OECD countries Australia ranked first (highest) and 24^th based on ASIR and ASDR, respectively.ConclusionThe incidence of cancer has increased over 25 years, and behavioral risks are responsible for a large proportion of cancer deaths. Scaling up of prevention (using strategies targeting cancer risk factors), early detection, and treatment of cancer is required to effectively address this growing health challenge.     

Amphibian chytridiomycosis

Amphibian chytridiomycosis is a fungal disease caused by the chytrid fungus Batrachochytrium dendrobatidis. It is arguably the most significant recorded infectious disease of any vertebrate class. The disease is reducing amphibian biodiversity across most continents and regions of the world, affecting the resilience of surviving populations and driving multiple species to extinction. It is now recognised by the World Organisation for Animal Health (OIE) as an internationally notifiable disease. Collaborative research in areas including the development of diagnostic assays, distribution and impact of the disease, and management (treatment and policy) has assisted in leading a paradigm shift in accepting infectious disease as a major factor influencing wildlife population stability and biodiversity.     

Reviews of publications

Book reviewed in this article: Reproduction of Marine Invertebrates. Vol. VI. Echinoderms and Lophophorates, edited by A. C. Giese, J. S. Pearse and V. B. Pearse. Pacific Grove, California, U.S.A. The Butterflies of Kenya and their Natural History, by T. B. Larsen. The Land and Freshwater Molluscs of Suffolk, by I. J. Killeen. Ipswich, U.K. Flycatcher. Memoirs of an Amateur Entomologist by K. A. Spencer. Ecosystems of the World 24. Intertidal and Littoral Ecosystems, edited by A. C. Mathieson and P. H. Nienhuis. Revision of the Northeast Atlantic and Mediterranean Stylasteridae (Cnidaria: Hydrozoa), by Helmut Zibrowius and Stephen D. Cairns. Paris: Mémoires du Musée Nationale d'Histoire Naturellee, 1992. Animals and Disease. An Introduction to the History of Comparative Medicine, by L. Wilkinson. The Inevitable Bond. Examining Scientist-Animal Interactions, edited by H. Davis and D. Balfour. Martin Lister's English Spiders (1678), edited by J. Parker and B. Harley (translated by M. Davies and B. Harley)). The Ecology of Fishes on Coral Reefs, edited by P. F. Sale. San Diego, USA: The Lepidoptera: Form, Function and Diversity, by M. J. Scoble. Bats. A Community Perspective, by J. S. Findley. The Insects of Australia. A textbook for students and research workers, Commonwealth Scientific and Industrial Research Organisation. Second Edition. Botanical monkeys, by E. J. H. Corner. The Biology of Millipedes, by S. P. Hopkin and H. J. Read. Mammals in the Palaearctic Desert: Status and Trends in the Sahara-Gobian Region, edited by J. A. McNeely and V. M. Neronov. Coelenterate Biology: Recent Research on Cnidaria and Ctenophora, edited by R. B. Williams, P. F. S. Cornelius, R. G. Hughes and E. A. Robson. Dordrecht, The Netherlands: Kluwer Academic Publishers, 1991. Animal Behaviour, 4th ed., by A. Manning and M. S. Dawkins. Weevils, Naturalists' Handbook 16, by M. G. Morris. Insects on Cabbage and Oilseed Rape. Naturalists' Handbooks 18, by W. D. J. Kirk.     

Comparison of Human and Animal Surveillance Data for H5N1 Influenza A in Egypt 2006–2011

Background

The majority of emerging infectious diseases are zoonotic (transmissible between animals and humans) in origin, and therefore integrated surveillance of disease events in humans and animals has been recommended to support effective global response to disease emergence. While in the past decade there has been extensive global surveillance for highly pathogenic avian influenza (HPAI) infection in both animals and humans, there have been few attempts to compare these data streams and evaluate the utility of such integration.

Methodology

We compared reports of bird outbreaks of HPAI H5N1 in Egypt for 2006–2011 compiled by the World Organisation for Animal Health (OIE) and the UN Food and Agriculture Organization (FAO) EMPRESi reporting system with confirmed human H5N1 cases reported to the World Health Organization (WHO) for Egypt during the same time period.

Principal Findings

Both human cases and bird outbreaks showed a cyclic pattern for the country as a whole, and there was a statistically significant temporal correlation between the data streams. At the governorate level, the first outbreak in birds in a season usually but not always preceded the first human case, and the time lag between events varied widely, suggesting regional differences in zoonotic risk and/or surveillance effectiveness. In a multivariate risk model, lower temperature, lower urbanization, higher poultry density, and the recent occurrence of a bird outbreak were associated with increased risk of a human case of HPAI in the same governorate, although the positive predictive value of a bird outbreak was low.

Conclusions

Integrating data streams of surveillance for human and animal cases of zoonotic disease holds promise for better prediction of disease risk and identification of environmental and regional factors that can affect risk. Such efforts can also point out gaps in human and animal surveillance systems and generate hypotheses regarding disease transmission.     

基于故障树方法的非计划再次手术风险评估

目的 探索一种适合于在过程复杂、环境多变、风险多样的手术治疗系统中,对术前准备、术中操作、术后医疗护理及管理等贯穿围手术期全过程进行风险评估的方法。方法 通过危险事件的风险影响因子识别、定性分析与定量分析、基本事件综合风险等级评价,绘制具有实践操作意义的风险矩阵图,全面识别手术治疗系统风险、科学分析危险事件与风险影响因子,有效评价风险等级与可容忍度。结果 构建包括7个中间事件、29个基本事件、9个逻辑或门和1个逻辑与门的非计划再次手术故障树模型,故障树由8个一阶割集和104个二阶割集组成。当所有最小割集均存在时,被调查医院非计划再次手术的发生概率为0.950 10,同时确定25个基本事件在该医院的综合风险重要性等级,并根据绘制的风险图谱进一步确定风险应对的优先顺序。结论 基于故障树的手术治疗系统风险评估方法,可以全面识别手术治疗系统风险,科学分析风险影响因子,有效评价风险等级。