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| Registros recuperados: 23 | |
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| Desdouits, Marion; Wacrenier, Candice; Ollivier, Joanna; Schaeffer, Julien; Le Guyader, Soizick. |
| Human noroviruses (NoV) cause epidemics of acute gastroenteritis (AGE) worldwide and can be transmitted through consumption of contaminated foods. Fresh products such as shellfish can be contaminated by human sewage during production, which results in the presence of multiple virus strains, at very low concentrations. Here, we tested a targeted metagenomics approach by deep-sequencing PCR amplicons of the capsid (VP1) and polymerase (RdRp) viral genes, on a set of artificial samples and on shellfish samples associated to AGE outbreaks, to evaluate its advantages and limitations in the identification of strains from the NoV genogroup (G) II. Using artificial samples, the method allowed the sequencing of most strains, but not all, and displayed variability... |
| Tipo: Text |
Palavras-chave: Norovirus; Foodborne virus; Metagenomics; Amplicon deep sequencing; Viral diversity. |
| Ano: 2020 |
URL: https://archimer.ifremer.fr/doc/00646/75831/76818.pdf |
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| Luz Vilarino, M.; Le Guyader, Soizick; Polo, David; Schaeffer, Julien; Krol, Joanna; Romalde, Jesus L.. |
| Standard and real-time reverse transcription-PCR (rRT-PCR) procedures were used to monitor cultured and wild bivalve molluscs from the Ria de Vigo (NW Spain) for the main human enteric RNA viruses, specifically, norovirus (NoV), hepatitis A virus (HAV), astrovirus (AsV), rotavirus (RT), enterovirus (EV), and Aichi virus (AiV). The results showed the presence of at least one enteric virus in 63.4% of the 41 samples analyzed. NoV GII was the most prevalent virus, detected in 53.7% of the samples, while NoV GI, AsV, EV, and RV were found at lower percentages (7.3, 12.2, 12.2, and 4.9%, respectively). In general, samples obtained in the wild were more frequently contaminated than those from Cultured (70.6 vs. 58.3%) molluscs and were more readily contaminated... |
| Tipo: Text |
Palavras-chave: Seafood industry; Viral quantification; Viral prevalence; Norovirus; Hepatitis A virus; Enteric viruses; Molluscs. |
| Ano: 2009 |
URL: http://archimer.ifremer.fr/doc/2009/publication-6957.pdf |
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| Grodzki, Marco; Schaeffer, Julien; Piquet, Jean-come; Le Saux, Jean-claude; Cheve, Julien; Ollivier, Joanna; Le Pendu, Jacques; Le Guyader, Soizick. |
| Hepatitis E virus (HEV), an enteric pathogen of both humans and animals, is excreted by infected individuals and is therefore present in wastewaters and coastal waters. As bivalve molluscan shellfish are known to concentrate viral particles during the process of filter feeding, they may accumulate this virus. The bioaccumulation efficiencies of oysters (Crassostrea gigas), flat oysters (Ostrea edulis), mussels (Mytilus edulis), and clams (Ruditapes philippinarum) were compared at different time points during the year. Tissue distribution analysis showed that most of the viruses were concentrated in the digestive tissues of the four species. Mussels and clams were found to be more sensitive to sporadic contamination events, as demonstrated by rapid... |
| Tipo: Text |
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| Ano: 2014 |
URL: http://archimer.ifremer.fr/doc/00204/31501/29905.pdf |
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| Sima, Laura C.; Schaeffer, Julien; Le Saux, Jean-claude; Parnaudeau, Sylvain; Elimelech, Menachem; Le Guyader, Soizick. |
| To evaluate membrane bioreactor wastewater treatment virus removal, a study was conducted in southwest France. Samples collected from plant influent, an aeration basin, membrane effluent, solid sludge, and effluent biweekly from October 2009 to June 2010 were analyzed for calicivirus (norovirus and sapovirus) by real-time reverse transcription-PCR (RT-PCR) using extraction controls to perform quantification. Adenovirus and Escherichia coli also were analyzed to compare removal efficiencies. In the influent, sapovirus was always present, while the norovirus concentration varied temporally, with the highest concentration being detected from February to May. All three human norovirus genogroups (GI, GII, and GIV) were detected in effluent, but GIV was never... |
| Tipo: Text |
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| Ano: 2011 |
URL: http://archimer.ifremer.fr/doc/00043/15378/12810.pdf |
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| Strubbia, Sofia; Phan, My V. T.; Schaeffer, Julien; Koopmans, Marion; Cotten, Matthew; Le Guyader, Soizick. |
| This study aimed to optimize a method to identify human enteric viruses in sewage and stool samples using random primed next-generation sequencing. We tested three methods, two employed virus enrichment based on the binding properties of the viral capsid using pig-mucin capture or by selecting viral RNA prior to library preparation through a capture using the SureSelect target enrichment. The third method was based on a non-specific biophysical precipitation with polyethylene glycol. Full genomes of a number of common human enteric viruses including norovirus, rotavirus, husavirus, enterovirus and astrovirus were obtained. In stool samples full norovirus genome were detected as well as partial enterovirus genome. A variety of norovirus sequences was... |
| Tipo: Text |
Palavras-chave: Human enteric viruses; Norovirus; Sewage; Metagenomic; Virome. |
| Ano: 2019 |
URL: https://archimer.ifremer.fr/doc/00512/62332/66592.pdf |
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| Boukerb, Amine Mohamed; Schaeffer, Julien; Serghine, Joelle; Carrier, Gregory; Le Guyader, Soizick; Gourmelon, Michele. |
| As determined by a hybrid approach combining Oxford Nanopore MinION and Illumina MiniSeq sequence data, Campylobacter armoricus strain CA639 harbored a circular chromosome of 1,688,169 bp with a G+C content of 28.47% and two plasmids named pCA639-1 and pCA639-2, with lengths of 51,123 and 28,139 bp, and G+C contents of 26.5% and 28.45%, respectively. |
| Tipo: Text |
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| Ano: 2020 |
URL: https://archimer.ifremer.fr/doc/00600/71164/69495.pdf |
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| Treguier, Cathy; Schaeffer, Julien; Le Saux, Jean-claude; Cochennec-laureau, Nathalie; Le Guyader, Soizick. |
| Les norovirus (NoV) sont responsables des épidémies hivernales de gastroentérites aiguës dans la population. Ils sont excrétés dans les fèces humains, puis se retrouvent, après épuration insuffisante, dans le milieu marin naturel où ils peuvent contaminer des coquillages, qui à leur tour risquent de déclencher des gastroentérites chez les consommateurs. Cette étude vise à améliorer les connaissances sur la contamination des coquillages en élevage en rivière d’Auray par les NoV, en lien avec les bactéries témoins de contamination fécale Escherichia coli (E. coli). L’objectif est de suivre les flux de NoV et d’E. coli apportés par différents rejets (dont une station d’épuration) impactant la zone conchylicole et leur influence sur la qualité des coquillages... |
| Tipo: Text |
Palavras-chave: Norovirus; Coquillages; Contamination; Station d’épuration; Flux; Rivière d’Auray; Escherichia coli.. |
| Ano: 2015 |
URL: http://archimer.ifremer.fr/doc/00267/37778/35829.pdf |
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| Le Guyader, Soizick; Parnaudeau, Sylvain; Schaeffer, Julien; Bosch, Albert; Loisy, Fabienne; Pommepuy, Monique; Atmar, Robert L.. |
| 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... |
| Tipo: Text |
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| Ano: 2009 |
URL: http://archimer.ifremer.fr/doc/2009/publication-6137.pdf |
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| Schaeffer, Julien; Treguier, Cathy; Piquet, Jean-come; Gachelin, Sonia; Cochennec-laureau, Nathalie; Le Saux, Jean-claude; Garry, Pascal; Le Guyader, Soizick. |
| As human population increases worldwide, water quality will become increasingly problematic, and food consumed raw may be of higher risk. This is already evident for oysters grown in coastal areas - despite regulations based on bacterial indicators, oysters are still implicated in food-borne outbreaks worldwide. The pathogens most frequently detected are human noroviruses, which are shed at high concentrations in human excreta and are very resistant to environmental conditions. Sewage treatment plants usually apply a variety of steps such as activated sludge treatment, chlorine or UV disinfection to eliminate contaminants, these processes have variable efficacy. This study demonstrates the impact of replacing an old lagoon-based sewage treatment plant with... |
| Tipo: Text |
Palavras-chave: Norovirus; Shellfish safety; Sewage treatment; Coastal water quality. |
| Ano: 2018 |
URL: https://archimer.ifremer.fr/doc/00450/56140/57707.pdf |
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| Polo, David; Schaeffer, Julien; Teunis, Peter; Buchet, Vincent; Le Guyader, Soizick. |
| Oysters, being filter feeders, can accumulate some human pathogens such as norovirus, a highly infectious calicivirus, most common cause of acute gastroenteritis worldwide. Accumulated virus decays over a period of days to weeks, possibly rendering contaminated oysters safe again. Sensitive molecular methods have been set up for shellfish analysis but without answering the question of infectious virus detection. Using the Tulane virus (TV), a norovirus surrogate that recognizes the same ligand as human norovirus in oyster tissues, the genome and infectious virus decay rates were estimated using inverse linear regression in a Bayesian framework for genome copies. Infectivity decreased faster than genome copies but infectious viruses were detected for... |
| Tipo: Text |
Palavras-chave: Infectious virus; Genome detection; Oysters; Persistence; Shellfish outbreaks. |
| Ano: 2018 |
URL: https://archimer.ifremer.fr/doc/00436/54736/56182.pdf |
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| Sala, Claudia; Mordhorst, Hanne; Grützke, Joesphine; Brinkmann, Annika; Petersen, Thomas N; Poulsen, Casper; Cotter, Paul D; Crispie, Fiona; Ellis, Richard J; Castellani, Gastone; Amid, Clara; Hakhverdyan, Mikhayil; Le Guyader, Soizick; Manfreda, Gerardo; Mossong, Joël; Nitsche, Andreas; Ragimbeau, Catherine; Schaeffer, Julien; Schlundt, Joergen; Tay, Moon Y. F.; Aarestrup, Frank M.; Hendriksen, Rene S.; Pamp, Sünje Johanna; De Cesare, Alessandra. |
| An inter-laboratory proficiency test was organized to assess the ability of participants to perform shotgun metagenomic sequencing of cold smoked salmon, experimentally spiked with a mock community composed of six bacteria, one parasite, one yeast, one DNA, and two RNA viruses. Each participant applied its in-house wet-lab workflow(s) to obtain the metagenomic dataset(s), which were then collected and analyzed using MG-RAST. A total of 27 datasets were analyzed. Sample pre-processing, DNA extraction protocol, library preparation kit, and sequencing platform, influenced the abundance of specific microorganisms of the mock community. Our results highlight that despite differences in wet-lab protocols, the reads corresponding to the mock community members... |
| Tipo: Text |
Palavras-chave: Shotgun metagenomics; Smoked salmon; Proficiency test; Experimentally spiked samples; Wet-lab protocols. |
| Ano: 2020 |
URL: https://archimer.ifremer.fr/doc/00664/77615/79636.pdf |
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| Strubbia, Sofia; Schaeffer, Julien; Oude Munnink, Bas B.; Besnard, Alban; Phan, My V. T.; Nieuwenhuijse, David F.; De Graaf, Miranda; Schapendonk, Claudia M. E.; Wacrenier, Candice; Cotten, Matthew; Koopmans, Marion P. G.; Le Guyader, Soizick. |
| Metagenomic sequencing is a promising method to determine the virus diversity in environmental samples such as sewage or shellfish. However, to identify the short RNA genomes of human enteric viruses among the large diversity of nucleic acids present in such complex matrices, method optimization is still needed. This work presents methodological developments focused on norovirus, a small ssRNA non-enveloped virus known as the major cause of human gastroenteritis worldwide and frequently present in human excreta and sewage. Different elution protocols were applied and Illumina MiSeq technology were used to study norovirus diversity. A double approach, agnostic deep sequencing and a capture-based approach (VirCapSeq-VERT) was used to identify norovirus in... |
| Tipo: Text |
Palavras-chave: Norovirus; Sewage; Oysters; Metagenomic sequencing; Metavirome. |
| Ano: 2019 |
URL: https://archimer.ifremer.fr/doc/00586/69765/67656.pdf |
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| Benabbes, Laila; Ollivier, Joanna; Schaeffer, Julien; Parnaudeau, Sylvain; Rhaissi, Houria; Nourlil, Jalal; Le Guyader, Soizick. |
| The aim of this study was to evaluate the presence of human enteric viruses in shellfish collected along the Mediterranean Sea and Atlantic Coast of Morocco. A total of 77 samples were collected from areas potentially contaminated by human sewage. Noroviruses were detected in 30 % of samples, with an equal representation of GI and GII strains, but were much more frequently found in cockles or clams than in oysters. The method used, including extraction efficiency controls, allowed the quantification of virus concentration. As in previous reports, results showed levels of contamination between 100 and 1,000 copies/g of digestive tissues. Sapoviruses were detected in 13 % of samples mainly in oyster and clam samples. Hepatitis A virus was detected in two... |
| Tipo: Text |
Palavras-chave: Shellfish; Norovirus; Hepatitis A virus; Environmental conditions; Quantification; Morocco. |
| Ano: 2013 |
URL: http://archimer.ifremer.fr/doc/00130/24102/22489.pdf |
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| Le Saux, Jean-claude; Lora, M.; Schaeffer, Julien; Poiraud, G.; Le Guyader, Soizick. |
| L’objet de cette étude est d’évaluer, par les méthodes de détection virale en cours de validation au niveau européen, le niveau de présence des norovirus dans les huîtres à l’expédition et sur les lieux de vente dans un département test, celui de la Vendée. En effet, aujourd’hui peu d’informations existent au niveau international et national sur la prévalence des norovirus dans les coquillages mis dans les circuits de consommation, alors que tous les ans des coquillages, répondant aux critères de mise en marché, sont incriminés ou suspectés dans des foyers de toxi-infections alimentaires collectives liés à la consommation de coquillages, majoritairement contaminés par des virus et plus particulièrement par les norovirus. Cette étude sur la période de... |
| Tipo: Text |
Palavras-chave: Microbiologie; Coquillages; Norovirus; Huître creuse; Détection; Santé publique; Département Vendée. |
| Ano: 2013 |
URL: http://archimer.ifremer.fr/doc/00185/29650/28019.pdf |
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| Desdouits, Marion; Garry, Pascal; Gourmelon, Michele; Hervio Heath, Dominique; Hubert, Francoise; Kaelin, Gaelle; Kergaravat, Cedric; Le Mennec, Cecile; Le Guyader, Soizick; Loiseau, Veronique; Lozach, Solen; Maillot, Jessica; Ollivier, Joanna; Parnaudeau, Sylvain; Piquet, Jean-come; Quenot, Emmanuelle; Rocq, Sophie; Schaeffer, Julien; Serghine, Joelle; Vallade, Emilie; Veron, Antoine; Wacrenier, Candice. |
| Ce rapport présente une synthèse des actions, et travaux réalisés par le laboratoire Santé Environnement et Microbiologie pendant l’année 2018. Les divers projets de recherche sont résumés et les derniers développements ou résultats sont brièvement évoqués. Les actions en tant que Laboratoire National de Référence pour la Microbiologie des Coquillages et les activités pour la coordination du réseau REMI sont également présentées. |
| Tipo: Text |
Palavras-chave: Microbiologie sanitaire; Bactéries entériques; Vibrions; Virus entériques humains; Norovirus; Coquillage; Activité de référence; REMI.. |
| Ano: 2019 |
URL: https://archimer.ifremer.fr/doc/00491/60218/63584.pdf |
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| Registros recuperados: 23 | |
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