Arbitrarily primed PCR to type Vibrio spp. pathogenic for shrimp.

International audienceA molecular typing study on Vibrio strains implicated in shrimp disease outbreaks in New Caledonia and Japan was conducted by using AP-PCR (arbitrarily primed PCR). It allowed rapid identification of isolates at the genospecies level and studies of infraspecific population structures of epidemiological interest. Clusters identified within the species Vibrio penaeicida were related to their area of origin, allowing discrimination between Japanese and New Caledonian isolates, as well as between those from two different bays in New Caledonia separated by only 50 km. Other subclusters of New Caledonian V. penaeicida isolates could be identified, but it was not possible to link those differences to accurate epidemiological features. This contribution of AP-PCR to the study of vibriosis in penaeid shrimps demonstrates its high discriminating power and the relevance of the epidemiological information provided. This approach would contribute to better knowledge of the ecology of Vibrio spp. and their implication in shrimp disease in aquaculture

Drivers for emerging issues in animal and plant health.

The history of agriculture includes many animal and plant disease events that have had major consequences for the sector, as well as for humans. At the same time, human activities beyond agriculture have often driven the emergence of diseases. The more that humans expand the footprint of the global population, encroach into natural habitats, alter these habitats to extract resources and intensify food production, as well as move animals, people and commodities along with the pathogens they carry, the greater the potential for pathogens and pests to spread and for infection to emerge or re-emerge. While essential to human well-being, producing food also plays a major role in disease dynamics. The risk of emergence of pests and pathogens has increased as a consequence of global changes in the way food is produced, moved and consumed. Climate change is likely to increase pressure on the availability of food and provide newly suitable conditions for invasive pests and pathogens. Human population displacements due to economic, political and humanitarian crises represent another set of potential drivers for emerging issues. The overlapping drivers of plant, animal and human disease emergence and environmental changes point towards the concept of 'One Health'. This paradigm underlines the urgent need to understand the influence of human behaviour and incorporate this understanding into our approach to emerging risks. For this, we face two major challenges. One is cultural; the second is methodological. We have to look at systems not under the narrow view of specific hazards but with a wider approach to system dynamics, and consider a broad spectrum of potential outcomes in terms of risk. In addition, we have to make sense of the vast amounts of data that are available in the modern age. This paper aims to help in preparing for the cultural and methodological shifts needed in our approach to emerging risks

Impact of oil on bacterial community structure in bioturbated sediments

Oil spills threaten coastlines where biological processes supply essential ecosystem services. Therefore, it is crucial to understand how oil influences the microbial communities in sediments that play key roles in ecosystem functioning. Ecosystems such as sediments are characterized by intensive bioturbation due to burrowing macrofauna that may modify the microbial metabolisms. It is thus essential to consider the bioturbation when determining the impact of oil on microbial communities. In this study, an experimental laboratory device maintaining pristine collected mudflat sediments in microcosms closer to true environmental conditions - with tidal cycles and natural seawater - was used to simulate an oil spill under bioturbation conditions. Different conditions were applied to the microcosms including an addition of: standardized oil (Blend Arabian Light crude oil, 25.6 mg.g21 wet sediment), the common burrowing organism Hediste (Nereis) diversicolor and both the oil and H. diversicolor. The addition of H. diversicolor and its associated bioturbation did not affect the removal of petroleum hydrocarbons. After 270 days, 60% of hydrocarbons had been removed in all microcosms irrespective of the H. diversicolor addition. However, 16S-rRNA gene and 16S-cDNA T-RFLP and RT-PCR-amplicon libraries analysis showed an effect of the condition on the bacterial community structure, composition, and dynamics, supported by PerMANOVA analysis. The 16S-cDNA libraries from microcosms where H. diversicolor was added (oiled and un-oiled) showed a marked dominance of sequences related to Gammaproteobacteria. However, in the oiled-library sequences associated to Deltaproteobacteria and Bacteroidetes were also highly represented. The 16S-cDNA libraries from oiled-microcosms (with and without H. diversicolor addition) revealed two distinct microbial communities characterized by different phylotypes associated to known hydrocarbonoclastic bacteria and dominated by Gammaproteobacteria and Deltaproteobacteria. In the oiled-microcosms, the addition of H. diversicolor reduced the phylotype-richness, sequences associated to Actinobacteria, Firmicutes and Plantomycetes were not detected. These observations highlight the influence of the bioturbation on the bacterial community structure without affecting the biodegradation capacities

Madagascar’s extraordinary biodiversity: Threats and opportunities

Madagascar's unique biota is heavily affected by human activity and is under intense threat. Here, we review the current state of knowledge on the conservation status of Madagascar's terrestrial and freshwater biodiversity by presenting data and analyses on documented and predicted species-level conservation statuses, the most prevalent and relevant threats, ex situ collections and programs, and the coverage and comprehensiveness of protected areas. The existing terrestrial protected area network in Madagascar covers 10.4% of its land area and includes at least part of the range of the majority of described native species of vertebrates with known distributions (97.1% of freshwater fishes, amphibians, reptiles, birds, and mammals combined) and plants (67.7%). The overall figures are higher for threatened species (97.7% of threatened vertebrates and 79.6% of threatened plants occurring within at least one protected area). International Union for Conservation of Nature (IUCN) Red List assessments and Bayesian neural network analyses for plants identify overexploitation of biological resources and unsustainable agriculture as themost prominent threats to biodiversity. We highlight five opportunities for action at multiple levels to ensure that conservation and ecological restoration objectives, programs, and activities take account of complex underlying and interacting factors and produce tangible benefits for the biodiversity and people of Madagascar

Madagascar’s extraordinary biodiversity: Evolution, distribution, and use

Madagascar's biota is hyperdiverse and includes exceptional levels of endemicity. We review the current state of knowledge on Madagascar's past and current terrestrial and freshwater biodiversity by compiling and presenting comprehensive data on species diversity, endemism, and rates of species description and human uses, in addition to presenting an updated and simplified map of vegetation types. We report a substantial increase of records and species new to science in recent years; however, the diversity and evolution of many groups remain practically unknown (e.g., fungi and most invertebrates). Digitization efforts are increasing the resolution of species richness patterns and we highlight the crucial role of field- and collections-based research for advancing biodiversity knowledge and identifying gaps in our understanding, particularly as species richness corresponds closely to collection effort. Phylogenetic diversity patterns mirror that of species richness and endemism in most of the analyzed groups. We highlight humid forests as centers of diversity and endemism because of their role as refugia and centers of recent and rapid radiations. However, the distinct endemism of other areas, such as the grassland-woodland mosaic of the Central Highlands and the spiny forest of the southwest, is also biologically important despite lower species richness. The documented uses of Malagasy biodiversity are manifold, with much potential for the uncovering of new useful traits for food, medicine, and climate mitigation. The data presented here showcase Madagascar as a unique living laboratory for our understanding of evolution and the complex interactions between people and nature. The gathering and analysis of biodiversity data must continue and accelerate if we are to fully understand and safeguard this unique subset of Earth's biodiversity

Euclid Near Infrared Spectrometer and Photometer instrument concept and first test results obtained for different breadboards models at the end of phase C

The Euclid mission objective is to understand why the expansion of the Universe is accelerating through by mapping the geometry of the dark Universe by investigating the distance-redshift relationship and tracing the evolution of cosmic structures. The Euclid project is part of ESA's Cosmic Vision program with its launch planned for 2020 (ref [1]). The NISP (Near Infrared Spectrometer and Photometer) is one of the two Euclid instruments and is operating in the near-IR spectral region (900- 2000nm) as a photometer and spectrometer. The instrument is composed of: - a cold (135K) optomechanical subsystem consisting of a Silicon carbide structure, an optical assembly (corrector and camera lens), a filter wheel mechanism, a grism wheel mechanism, a calibration unit and a thermal control system - a detection subsystem based on a mosaic of 16 HAWAII2RG cooled to 95K with their front-end readout electronic cooled to 140K, integrated on a mechanical focal plane structure made with molybdenum and aluminum. The detection subsystem is mounted on the optomechanical subsystem structure - a warm electronic subsystem (280K) composed of a data processing / detector control unit and of an instrument control unit that interfaces with the spacecraft via a 1553 bus for command and control and via Spacewire links for science data This presentation describes the architecture of the instrument at the end of the phase C (Detailed Design Review), the expected performance, the technological key challenges and preliminary test results obtained for different NISP subsystem breadboards and for the NISP Structural and Thermal model (STM)

Development and Validation of a Risk Score for Chronic Kidney Disease in HIV Infection Using Prospective Cohort Data from the D:A:D Study

Ristola M. on työryhmien DAD Study Grp ; Royal Free Hosp Clin Cohort ; INSIGHT Study Grp ; SMART Study Grp ; ESPRIT Study Grp jäsen.Background Chronic kidney disease (CKD) is a major health issue for HIV-positive individuals, associated with increased morbidity and mortality. Development and implementation of a risk score model for CKD would allow comparison of the risks and benefits of adding potentially nephrotoxic antiretrovirals to a treatment regimen and would identify those at greatest risk of CKD. The aims of this study were to develop a simple, externally validated, and widely applicable long-term risk score model for CKD in HIV-positive individuals that can guide decision making in clinical practice. Methods and Findings A total of 17,954 HIV-positive individuals from the Data Collection on Adverse Events of Anti-HIV Drugs (D:A:D) study with >= 3 estimated glomerular filtration rate (eGFR) values after 1 January 2004 were included. Baseline was defined as the first eGFR > 60 ml/min/1.73 m2 after 1 January 2004; individuals with exposure to tenofovir, atazanavir, atazanavir/ritonavir, lopinavir/ritonavir, other boosted protease inhibitors before baseline were excluded. CKD was defined as confirmed (>3 mo apart) eGFR In the D:A:D study, 641 individuals developed CKD during 103,185 person-years of follow-up (PYFU; incidence 6.2/1,000 PYFU, 95% CI 5.7-6.7; median follow-up 6.1 y, range 0.3-9.1 y). Older age, intravenous drug use, hepatitis C coinfection, lower baseline eGFR, female gender, lower CD4 count nadir, hypertension, diabetes, and cardiovascular disease (CVD) predicted CKD. The adjusted incidence rate ratios of these nine categorical variables were scaled and summed to create the risk score. The median risk score at baseline was -2 (interquartile range -4 to 2). There was a 1: 393 chance of developing CKD in the next 5 y in the low risk group (risk score = 5, 505 events), respectively. Number needed to harm (NNTH) at 5 y when starting unboosted atazanavir or lopinavir/ritonavir among those with a low risk score was 1,702 (95% CI 1,166-3,367); NNTH was 202 (95% CI 159-278) and 21 (95% CI 19-23), respectively, for those with a medium and high risk score. NNTH was 739 (95% CI 506-1462), 88 (95% CI 69-121), and 9 (95% CI 8-10) for those with a low, medium, and high risk score, respectively, starting tenofovir, atazanavir/ritonavir, or another boosted protease inhibitor. The Royal Free Hospital Clinic Cohort included 2,548 individuals, of whom 94 individuals developed CKD (3.7%) during 18,376 PYFU (median follow-up 7.4 y, range 0.3-12.7 y). Of 2,013 individuals included from the SMART/ESPRIT control arms, 32 individuals developed CKD (1.6%) during 8,452 PYFU (median follow-up 4.1 y, range 0.6-8.1 y). External validation showed that the risk score predicted well in these cohorts. Limitations of this study included limited data on race and no information on proteinuria. Conclusions Both traditional and HIV-related risk factors were predictive of CKD. These factors were used to develop a risk score for CKD in HIV infection, externally validated, that has direct clinical relevance for patients and clinicians to weigh the benefits of certain antiretrovirals against the risk of CKD and to identify those at greatest risk of CKD.Peer reviewe

Experimental transmission of Marteilia refringens with special consideration of its life cycle

10 pages, 2 figures, 6 tables.Ever since its first description the paramyxean parasite Marteilia refringens has been recognised as one of the most significant pathogens of bivalve molluscs. The existence of a complex life cycle has been postulated by many authors. However, the transmission route of M. refringens and its life cycle remain unresolved. Experimental observations are presented here that may help lead to a satisfactory hypothesis of the M. refringens life cycle. Trials were performed to test the infectivity of purified early and late stages of M. refringens by different routes of inoculation. Horizontal transmission was also tested by cohabitation with carriers in experimental tanks. Field cohabitation and exposure to natural sources of the parasite helped examine the role of the environment in the transmission of M. refringens. Lastly, naturally infected oysters were monitored in experimental tanks, in order to study infection progression in the oysters through serial samples. These experiments provide no evidence to support direct horizontal transmission of M. refringens, but rather suggest that intermediate or alternative hosts, or free-living stages, are essential in the life cycle of the parasite.This study was carried out with financial assistance from the European Commission (E.C. Aquaculture Study 94C/85/13). M.Z. acknowledges the French and Algerian governments for his fellowship (95/6948 BFA).Peer reviewe

Dynamics of the parasite Marteilia refringens (Paramyxea) in Mytilus galloprovincialis and zooplankton populations in Alfacs Bay (Catalonia, Spain)

10 pages, 4 figuresSince the first description of Marteilia refringens (Paramyxea) in flat oysters Ostrea edulis in 1968 in the Aber Wrach, Brittany (France), the life-cycle of this parasite has remained unknown. However, recent studies, conducted in the ‘ claire ’ system, have proposed the planktonic copepod Acartia grani as a potential intermediate host for the parasite. Nevertheless, experimental transmission of the parasite through the copepod has failed. Recent studies in this field have reported the presence of the parasite in zooplankton from the bays of the Delta de l’Ebre, a more complex and natural estuarine environment than that of the claire. As a result, 2 new Marteilia host species were proposed: the copepods Oithona sp. (Cyclopoida) and an indeterminate Harpaticoida. Consequently, the objective of the present work was to study the dynamics of Marteilia in the zooplankton community from one of the bays, Alfacs Bay, as well as the dynamics of the parasite in cultivated mussels during 1 complete year. Six different zooplankton taxa appeared to be parasitized by M. refringens, including copepods (3 Calanoida, Acartia discaudata, A. clausi and A. italica ; 1 Cyclopoida, Oithona sp.; and 1 Harpacticoida, Euterpina acutifrons), and larval stages of decapod crustaceans (zoea larvae of Brachyura, probably Portumnus sp.). These taxa are thus proposed as new subjects for study, since they could be intermediate hosts in the infection process of mussels by MarteiliaThis work was carried out with funding from an INIA predoctoral grant from the Spanish Government and a Marie Curie training site UE grant to N.C., and INIA project RTA04-023 co-ordinated by Dr M. Ramón. Also an IFAPA post-doctoral grant (Junta de Andalucia) to I.L. and MCYT grants CTM2004-02575/MAR and REN2002-04151-C02-01/MAR to M.A.Peer reviewe

Rapport sur la pathologie des pénéides en Nouvelle-Calédonie. Eat et perspectives du programme d'assistance à la filière crevette de Nouvelle-Calédonie par la recherche en pathologie

La pénéiculture calédonienne connait, depuis 1993, de sévères difficultés de développement et son expansion, spectaculaire au cours des six dernières années, est aujourd'hui considérablement ralentie. Le «syndrome 93», terme consacré par l' usage, affecte les élevages dans leur phase dite de grossissement, et se traduit par des taux de survie inférieurs aux seuils de rentabilité des fermes. Les pertes infligées à la filière mettent celle-ci en péril.C'est pourquoi un programme d'assistance par la recherche en pathologie des pénéides a été élaboré afin de répondre à ces difficultés. Le but de cette démarche est d'établir un plan de lutte basé sur la détection précoce de situations critiques, caractérisées par la présence d'un agent pathogène (diagnostic) et concomitantes à la mise en jeu de facteurs de risques (conditions favorisantes). Ce programme mis en place et géré par le GIE/RA est financé conjointement par le Territoire de NouvelleCalédonie, la Province Sud et la Province Nord. Il développe un grand nombre de collaborations entre diverses équipes scientifiques, tant sur le Territoire qu'en Métropole. Après six mois d'exercice, la première phase de la démarche diagnostique arrive à son terme : l' identification de différents agents pathogènes impliqués dans Je syndrome 93, dont il importe aujourd'hui de préciser le rôle étiologique. Des enquêtes zootechniques, en cours d'analyse, devraient permettre de formuler des hypothèses quant aux facteurs de risque de ce phénomène. Cet ensemble, on le voit, tend vers une gestion rationnelle du système d'élevage en présence de pathogènes potentiels. Le présent rapport voudrait rassembler les connaissances acquises depuis plusieurs mois sur la pathologie des pénéides en Nouvelle-Calédonie. Parce que rassembler est une traduction étymologique de comprendre, il nous a semblé que ce travail pouvait être utile. Il s'agit donc dans ce qui suit de trouver les éléments d'une réflexion plutôt que les conclusions d' une étude ... qui en est encore à ses premiers pas