Occurrence of Bacterial Pathogens and Human Noroviruses in Shellfish-Harvesting Areas and Their Catchments in France

During a 2-year study, the presence of human pathogenic bacteria and noroviruses was investigated in shellfish, seawater and/or surface sediments collected from three French coastal shellfish-harvesting areas as well as in freshwaters from the corresponding upstream catchments. Bacteria isolated from these samples were further analyzed. Escherichia coli isolates classified into the phylogenetic groups B2, or D and enterococci from Enterococcus faecalis and E. faecium species were tested for the presence of virulence genes and for antimicrobial susceptibility. Salmonella members were serotyped and the most abundant serovars (Typhimurium and its monophasic variants and Mbandaka) were genetically characterized by high discriminative subtyping methods. Campylobacter and Vibrio were identified at the species level, and haemolysin-producing Vibrio parahaemolyticus were searched by tdh- and trh- gene detection. Main results showed a low prevalence of Salmonella in shellfish samples where only members of S. Mbandaka were found. Campylobacter were more frequently isolated than Salmonella and a different distribution of Campylobacter species was observed in shellfish compared to rivers, strongly suggesting possible additional inputs of bacteria. Statistical associations between enteric bacteria, human noroviruses (HuNoVs) and concentration of fecal indicator bacteria revealed that the presence of Salmonella was correlated with that of Campylobacter jejuni and/or C. coli as well as to E. coli concentration. A positive correlation was also found between the presence of C. lari and the detection of HuNoVs. This study highlights the importance of simultaneous detection and characterization of enteric and marine pathogenic bacteria and human noroviruses not only in shellfish but also in catchment waters for a hazard assessment associated with microbial contamination of shellfish

Predicting where a radiation will occur: Acoustic and molecular surveys reveal overlooked diversity in Indian Ocean Island crickets (Mogoplistinae: Ornebius)

Recent theory suggests that the geographic location of island radiations (local accumulation of species diversity due to cladogenesis) can be predicted based on island area and isolation. Crickets are a suitable group for testing these predictions, as they show both the ability to reach some of the most isolated islands in the world, and to speciate at small spatial scales. Despite substantial song variation between closely related species in many island cricket lineages worldwide, to date this characteristic has not received attention in the western Indian Ocean islands; existing species descriptions are based on morphology alone. Here we use a combination of acoustics and DNA sequencing to survey these islands for Ornebius crickets. We uncover a small but previously unknown radiation in the Mascarenes, constituting a three-fold increase in the Ornebius species diversity of this archipelago (from two to six species). A further new species is detected in the Comoros. Although double archipelago colonisation is the best explanation for species diversity in the Seychelles, in situ cladogenesis is the best explanation for the six species in the Mascarenes and two species of the Comoros. Whether the radiation of Mascarene Ornebius results from intra- or purely inter- island speciation cannot be determined on the basis of the phylogenetic data alone. However, the existence of genetic, song and ecological divergence at the intra-island scale is suggestive of an intra-island speciation scenario in which ecological and mating traits diverge hand-in-hand. Our results suggest that the geographic location of Ornebius radiations is partially but not fully explained by island area and isolation. A notable anomaly is Madagascar, where our surveys are consistent with existing accounts in finding no Ornebius species present. Possible explanations are discussed, invoking ecological differences between species and differences in environmental history between islands. (Résumé d'auteur

Environmental Detection of Genogroup I, II, and IV Noroviruses by Using a Generic Real-Time Reverse Transcription-PCR Assay

Norovirus is the most common agent implicated in food-borne outbreaks and is frequently detected in environmental samples. These viruses are highly diverse, and three genogroups (genogroup I [GI], GII, and GIV) infect humans. Being noncultivable viruses, real-time reverse transcription-PCR (RT-PCR) is the only sensitive method available for their detection in food or environmental samples. Selection of consensus sequences for the design of sensitive assays has been challenging due to sequence diversity and has led to the development of specific real-time RT-PCR assays for each genogroup. Thus, sample screening can require several replicates for amplification of each genogroup (without considering positive and negative controls or standard curves). This study reports the development of a generic assay that detects all three human norovirus genogroups on a qualitative basis using a one-step real-time RT-PCR assay. The generic assay achieved good specificity and sensitivity for all three genogroups, detected separately or in combination. At variance with multiplex assays, the choice of the same fluorescent dye for all three probes specific to each genogroup allows the levels of fluorescence to be added and may increase assay sensitivity when multiple strains from different genogroups are present. When it was applied to sewage sample extracts, this generic assay successfully detected norovirus in all samples found to be positive by the genogroup-specific RT-PCRs. The generic assay also identified all norovirus-positive samples among 157 archived nucleic acid shellfish extracts, including samples contaminated by all three genogroups

Les Acrididae des îles Eparses (Orthoptera, Caelifera)

Acrididae from the Scattered Islands (Orthoptera, Caelifera). The Scattered Islands are an administrative entity grouping French low altitude islets in South Western Indian Ocean. Until now, seven Acrididae were known from at least one of these islands. Fieldworks organized by the Muséum d’Histoire naturelle de la Réunion, the Insectarium de la Réunion and the CIRAD-Réunion, allowed updating this checklist. Four additional species were recorded from at least one of these islands : Diabolocatantops axillaris saucius (Burmeister, 1838), Acrida madecassa (Brancsik, 1893), Acrotylus patruelis (Herrich-Schäffer, 1838) and Oedaleus virgula (Snellen van Vollenhoven, 1870).Les îles Eparses constituent une unité administrative regroupant des îlots français de basse altitude du sud-ouest de l’océan Indien. A ce jour, sept espèces d’Acrididae étaient signalées sur au moins une de ces îles. Une série de missions menées par le Muséum d’Histoire naturelle de la Réunion, l’Insectarium de la Réunion et le CIRAD-Réunion, permettent de compléter l’inventaire des Acrididae de ces îles. Quatre espèces additionnelles sont signalées sur au moins une de ces îles : Diabolocatantops axillaris saucius (Burmeister, 1838), Acrida madecassa (Brancsik, 1893), Acrotylus patruelis (Herrich-Schäffer, 1838) et Oedaleus virgula (Snellen van Vollenhoven, 1870).Parnaudeau Raphaël, Rochat Jacques, Franck Antoine, Gasnier Sophie, Cazanove Grégory, Hugel Sylvain. Les Acrididae des îles Eparses (Orthoptera, Caelifera). In: Bulletin de la Société entomologique de France, volume 118 (1),2013. pp. 111-117

Designing a DSS to reduce nitrogen losses in cropping systems

International audienc

Environmental detection of Genogroup I, II, and IV Noroviruses by using a generic Real-Time Reverse Transcription-PCR Assay

Norovirus is the most common agent implicated in food-borne outbreaks and is frequently detected in environmental samples. These viruses are highly diverse, and three genogroups (genogroup I [GI], GII, and GIV) infect humans. Being noncultivable viruses, real-time reverse transcription-PCR (RT-PCR) is the only sensitive method available for their detection in food or environmental samples. Selection of consensus sequences for the design of sensitive assays has been challenging due to sequence diversity and has led to the development of specific real-time RT-PCR assays for each genogroup. Thus, sample screening can require several replicates for amplification of each genogroup (without considering positive and negative controls or standard curves). This study reports the development of a generic assay that detects all three human norovirus genogroups on a qualitative basis using a one-step real-time RT-PCR assay. The generic assay achieved good specificity and sensitivity for all three genogroups, detected separately or in combination. At variance with multiplex assays, the choice of the same fluorescent dye for all three probes specific to each genogroup allows the levels of fluorescence to be added and may increase assay sensitivity when multiple strains from different genogroups are present. When it was applied to sewage sample extracts, this generic assay successfully detected norovirus in all samples found to be positive by the genogroup-specific RT-PCRs. The generic assay also identified all norovirus-positive samples among 157 archived nucleic acid shellfish extracts, including samples contaminated by all three genogroups

Virus entériques humains et coquillages

Human enteric viruses discharged in raw sewage are hightly resistant and may be detected in surface waters, coastal areas and shellfish. Whereas noroviruses, responsible for relatively benign acute gastroentritis, are the most common agents implicated in shellfish borne outbreaks, other human viruses which cause severe human diseases, such as hepatitis A virus, may also be transmitted. Environmental studies have demonstrated that virus concentrations detected in shellfish are higher than in surrounding waters. This concentration may explain the high prevalence of noroviruses detected in various shellfish species collected in different countries. If many questions remain regarding viral contamination of shellfish, the most important seems to be the prevention of coastal areas contamination by human sewages.Les virus entériques humains rejetés dans les eaux usées sont très résistants dans le milieu extérieur et peuvent être retrouvés dans les eaux de surface, les eaux littorales ou les coquillages. Si les pathologies induites sont souvent relativement bénignes (type gastroentérites aigües), le nombre de foyers épidémiques liés à la consommation de coquillages et la transmission possible du virus de l'hépatite A ou d'autres virus induisant des pathologies graves, justifie pleinement le développement de cette thématique. Des études environnementales montrent une quantité de virus détectés dans les coquillages supérieure à celles détectées dans les eaux. Cette concentration peut expliquer la prévalence parfois importante des norovirus dans les coquillages. Si de nombreuses questions persistent concernant la contamination des coquillages par les virus humains il semble important avant tout de prévenir la contamination des zones littorales par des rejets humains

Digital PCR for Quantifying Norovirus in Oysters Implicated in Outbreaks, France

Using samples from oysters clearly implicated in human disease, we quantified norovirus levels by using digital PCR. Concentrations varied from 43 to 1,170 RNA copies/oyster. The analysis of frozen samples from the production area showed the presence of norovirus 2 weeks before consumption

Detection and Quantification of Noroviruses in Shellfish▿

Noroviruses (NoVs) are the most common viral agents of acute gastroenteritis in humans, and high concentrations of NoVs are discharged into the environment. As these viruses are very resistant to inactivation, the sanitary consequences are contamination of food, including molluscan shellfish. There are four major problems with NoV detection in shellfish samples: low levels of virus contamination, the difficulty of efficient virus extraction, the presence of interfering substances that inhibit molecular detection, and NoV genetic variability. The aims of this study were to adapt a kit for use with a method previously shown to be efficient for detection of NoV in shellfish and to use a one step real-time reverse transcription-PCR method with addition of an external viral control. Comparisons of the two methods using bioaccumulated oysters showed that the methods reproducibly detected similar levels of virus in oyster samples. Validation studies using naturally contaminated samples also showed that there was a good correlation between the results of the two methods, and the variability was more attributable to the level of sample contamination. Magnetic silica very efficiently eliminated inhibitors, and use of extraction and amplification controls increased quality assurance. These controls increased the confidence in estimates of NoV concentrations in shellfish samples and strongly supported the conclusion that the results of the method described here reflected the levels of virus contamination in oysters. This approach is important for food safety and is under evaluationfor European regulation