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| Registros recuperados: 15 | |
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| Guillier, Laurent; Gourmelon, Michele; Lozach, Solen; Cadel-six, Sabrina; Vignaud, Marie-léone; Munck, Nanna; Hald, Tine; Palma, Federica. |
| The partitioning of pathogenic strains isolated in environmental or human cases to their sources is challenging. The pathogens usually colonize multiple animal hosts, including livestock, which contaminate the food-production chain and the environment (e.g. soil and water), posing an additional public-health burden and major challenges in the identification of the source. Genomic data opens up new opportunities for the development of statistical models aiming to indicate the likely source of pathogen contamination. Here, we propose a computationally fast and efficient multinomial logistic regression source-attribution classifier to predict the animal source of bacterial isolates based on ‘source-enriched’ loci extracted from the accessory-genome profiles... |
| Tipo: Text |
Palavras-chave: Environmental contamination; Multinomial logistic regression; Pangenome-wide enrichment analysis; Source attribution; Salmonella Typhimurium.. |
| Ano: 2020 |
URL: https://archimer.ifremer.fr/doc/00624/73632/73072.pdf |
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| Jarde, Emilie; Jeanneau, Laurent; Harrault, Loic; Quenot, Emmanuelle; Solecki, Olivia; Petitjean, Patrice; Lozach, Solen; Cheve, Julien; Gourmelon, Michele. |
| This study identified sources of fecal contamination in three different French headwater and coastal catchments (the Justiçou, Pen an Traon, and La Fresnaye) using a combination of microbial source tracking tools. The tools included bacterial markers (three host-associated Bacteroidales) and chemical markers (six fecal stanols), which were monitored monthly over one or two years in addition to fecal indicator bacteria. 168 of the 240 freshwater and marine water samples had Escherichia coli (E. coli) or enterococci concentrations higher than “excellent” European water quality threshold. In the three catchments, the results suggested that the fecal contamination appeared to be primarily from an animal origin and particularly from a bovine origin in 52%... |
| Tipo: Text |
Palavras-chave: Fecal contamination; Host-associated Bacteroidales markers; Fecal stanols; Rainfall; MST toolbox; Mitigation actions. |
| Ano: 2018 |
URL: http://archimer.ifremer.fr/doc/00395/50597/51548.pdf |
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| Lee, R.j.; Rangdale, R.e.; Croci, L.; Hervio Heath, Dominique; Lozach, Solen. |
| A number of bacterial illnesses may arise from the consumption of seafood that has either been contaminated at source or which becomes contaminated during the processing and retail chain. Such illnesses may arise from infection with the bacteria themselves or by the ingestion of toxins formed in the foodstuff prior to consumption. This division is actually too simplistic: for example, the toxins of Clostridium botulinum and Staphylococcus aureus are preformed in food during bacterial growth, the toxin of Clostridium perfringens is usually only formed when the bacteria sporulate in the intestinal tract while the toxin of Vibrio cholerae O1 (and O139) is produced when the bacteria multiply in the intestinal tract. |
| Tipo: Text |
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| Ano: 2008 |
URL: http://archimer.ifremer.fr/doc/00066/17730/15252.pdf |
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| Deter, Julie; Lozach, Solen; Derrien, Annick; Veron, Antoine; Chollet, Jaufrey; Hervio-heath, Dominique. |
| The present study focused on the isolation of culturable bacteria from mussels and sea water to identify Vibrionaceae potentially pathogenic for humans. Three sites located on the French Atlantic coast were monitored monthly (twice each month during summer) for 1 year. Environmental parameters were surveyed (water temperature, salinity, turbidity, chlorophyll a) and bacteria were detected by culture and identified by API 20E(R) systems (BioMerieux) and PCR. A total of seven species were detected (Grimontia hollisae, Photobacterium damselae, Vibrio alginolyticus, V. cholerae, V. fluvialis, V. vulnificus and V. parahaemolyticus) and species diversity was higher at the end of summer. Surprisingly, V. cholerae non-O1/non-O139 was detected in spring. No site... |
| Tipo: Text |
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| Ano: 2010 |
URL: http://archimer.ifremer.fr/doc/00008/11928/8636.pdf |
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| Deter, Julie; Lozach, Solen; Veron, Antoine; Chollet, Jaufrey; Derrien, Annick; Hervio Heath, Dominique. |
| Vibrio parahaemolyticus is one of the principal bacterial causes for seafood-borne gastroenteritis in the world. In the present study, three sites located on the French Atlantic coast were monitored monthly for environmental parameters over 1 year. The presence of total and pathogenic V. parahaemolyticus in sediment, water and mussel samples was detected following enrichment by culture and real-time PCR (toxR gene, tdh, trh1 and trh2 virulence genes). Using generalized linear models, we showed that the presence of V. parahaemolyticus in water could be explained by a combination of mean temperature over the 7 days before the day of sampling (P < 0.001) and turbidity (P = 0.058). In mussels, an effect of chlorophyll a (P = 0.005) was detected when an... |
| Tipo: Text |
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| Ano: 2010 |
URL: http://archimer.ifremer.fr/doc/00003/11420/8363.pdf |
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| Gourmelon, Michele; Caprais, Marie-paule; Segura, Raphael; Le Mennec, Cecile; Lozach, Solen; Piriou, Jean-yves; Rince, A. |
| In order to identify the origin of the fecal contamination observed in French estuaries, two library-independent microbial source tracking (MST) methods were selected: (i) Bacteroidales host-specific 16S rRNA gene markers and (ii) F-specific RNA bacteriophage genotyping. The specificity of the Bacteroidales markers was evaluated on human and animal (bovine, pig, sheep, and bird) feces. Two human-specific markers (HF183 and HF134), one ruminant-specific marker (CF193'), and one pig-specific marker (PF163) showed a high level of specificity (>90%). However, the data suggest that the proposed ruminant-specific CF128 marker would be better described as an animal marker, as it was observed in all bovine and sheep feces and 96% of pig feces. F RNA... |
| Tipo: Text |
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| Ano: 2007 |
URL: http://archimer.ifremer.fr/doc/2007/publication-3535.pdf |
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| Verrez-bagnis, Veronique; Soree, Marion; Passerini, Delphine; Kolypczuk, Laetitia; Marchand, Laetitia; Bonnetot, Sandrine; Fecamp, Florian; Lozach, Solen; Hervio Heath, Dominique; Delbarre Ladrat, Christine. |
| Vibrio spp. are ubiquitous marine bacteria that are ecologically and metabolically diverse members of planktonic and animal associated microbial communities. They encompass the ancient and well-studied human pathogen, Vibrio cholerae, and two other human pathogens, V. vulnificus and V. parahaemolyticus, as well as some less thoroughly characterized animal pathogens. Virulence is based on a wide diversity of mechanisms involved in motility and host colonization, in ability to persist and develop, and in damage generation. Polysaccharides may play major roles in virulence and are major components of extracellular polymeric matrix synthesized upon biofilm growth. They may also exhibit biological features, especially those similar to animal-derived... |
| Tipo: Text |
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| Ano: 2019 |
URL: https://archimer.ifremer.fr/doc/00514/62605/66965.pdf |
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| Rince, Alain; Baliere, Charlotte; Hervio-heath, Dominique; Cozien, Joelle; Lozach, Solen; Parnaudeau, Sylvain; Le Guyader, Francoise S.; Le Hello, Simon; Giard, Jean-christophe; Sauvageot, Nicolas; Benachour, Abdellah; Strubbia, Sofia; Gourmelon, Michele. |
| 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.... |
| Tipo: Text |
Palavras-chave: Campylobacter; Salmonella; Vibrio; HuNoVs; Fecal bacterial indicators; Shellfish; Water. |
| Ano: 2018 |
URL: https://archimer.ifremer.fr/doc/00461/57243/59243.pdf |
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| Vincent Hubert, Francoise; Wacrenier, Candice; Morga, Benjamin; Lozach, Solen; Quenot, Emmanuelle; Mege, Mickael; Lecadet, Cyrielle; Gourmelon, Michele; Hervio-heath, Dominique; Le Guyader, Soizick. |
| The detection of viruses and bacteria which can pose a threat either to shellfish health or shellfish consumers remains difficult. The current detection methods rely on point sampling of water, a method that gives a snapshot of the microorganisms present at the time of sampling. In order to obtain better representativeness of the presence of these microorganisms over time, we have developed passive sampling using the adsorption capacities of polymer membranes. Our objectives here were to assess the feasibility of this methodology for field detection. Different types of membrane were deployed in coastal waters over 2 years and the microorganisms tested using qPCR were: human norovirus (NoV) genogroups (G)I and II, sapovirus, Vibrio spp. and the species... |
| Tipo: Text |
Palavras-chave: Norovirus; Ostreid herpes virus 1 μ Var; Vibrio spp; Microbial source tracking; Sea; Passive sampler; Oyster (Crassostrea gigas). |
| Ano: 2021 |
URL: https://archimer.ifremer.fr/doc/00682/79375/81893.pdf |
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| Gourmelon, Michele; Lozach, Solen; Garry, Pascal; Balliere, Clémence; Sauvageot, Nicolas; Le Hello, Simon; Rince, Alain. |
| Shellfish farming is an important economic activity in the Brittany and Normandy regions. However, a part of the production sites corresponds to relatively sensitive areas where the presence of faecal microorganisms is a major concern for shellfish and constitutes a possible health risk. Indeed, shellfish bioaccumulates in their tissues pathogenic contaminants present in water and can cause food-borne diseases such as salmonellosis. During a two-year study, we evaluated the presence of faecal indicators, measured the prevalence of Salmonella spp., isolated and characterized Salmonella spp. from three French shellfish-harvesting areas (shellfish and sediment) and their watersheds (from river water samples). |
| Tipo: Text |
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| Ano: 2016 |
URL: http://archimer.ifremer.fr/doc/00341/45199/44609.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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| Coutard, Francois; Lozach, Solen; Pommepuy, Monique; Hervio Heath, Dominique. |
| A real-time reverse transcription-PCR method was developed to determine whether the recovery of culturability of viable but nonculturable (VBNC) Vibrio parahaemolyticus induced the expression of virulence genes coding for the thermostable direct hemolysin and for type III secretion system 2 (TTSS2). The culturability of clinical strain Vp5 of V. parahaemolyticus in artificial seawater at 4°C was monitored, and the VBNC state was obtained. One day after entry into the VBNC state, temperature upshifts to 20 and 37°C allowed the recovery of culturability. Standard curves for the relative quantification of expression of the housekeeping genes rpoS, pvsA, fur, and pvuA; the tdh2 gene; and the TTSS2 genes (VPA1354, VPA1346, and VPA1342) were established. The... |
| Tipo: Text |
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| Ano: 2007 |
URL: http://archimer.ifremer.fr/doc/2007/publication-2787.pdf |
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| Mauffret, Aourell; Mieszkin, Sophie; Morizur, Mael; Alfiansah, Yustian Rovi; Lozach, Solen; Gourmelon, Michele. |
| We assessed the capacity of real-time PCR markers to identify the origin of contamination in shellfish. Oyster, cockles or clams were either contaminated with fecal materials and host-associated markers designed from Bacteroidales or Catellicoccus marimammalium 16S RNA genes were extracted from their intravalvular liquid, digestive tissues or shellfish flesh. Extraction of bacterial DNA from the oyster intravalvular liquid with FastDNA spin kit for soil enabled the selected markers to be quantified in 100% of artificially contaminated samples, and the source of contamination to be identified in 13 out of 38 naturally contaminated batches from European Class B and Class C areas. However, this protocol did not enable the origin of the contamination to be... |
| Tipo: Text |
Palavras-chave: Microbial source tracking; Shellfish; Bacteroidales; Real-time PCR; Intravalvular liquid; Digestive tissues. |
| Ano: 2013 |
URL: http://archimer.ifremer.fr/doc/00137/24776/25188.pdf |
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| Registros recuperados: 15 | |
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