|
|
|
| Registros recuperados: 49 | |
|
|
| 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 |
| |
|
|
| 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 |
| |
|
|
| Gourmelon, Michele; Caprais, Marie-paule; Le Mennec, Cecile; Mieszkin, Sophie; Ponthoreau, C.; Gendronneau, M.. |
| Faecal contamination sources were identified in coastal areas around the Guerande-Atlantique peninsula using two microbial source tracking (MST) methods: (i) Bacteroidales host-specific 16S rRNA gene markers measured by real-time PCR and (ii) F-specific bacteriophage (FRNAPH) genotyping. Both methods were used on 63 water samples from 7 water courses. HF183 marker and bacteriophage genogroup II (FRNAPH II) were detected in all water samples and in the majority of water samples, respectively, from La Torre stream (W5), Piriac (W2), R2000 (W3) and Mazy (W7) rain water drains, and also detected, less frequently, in Le Nau drain (W4), suggesting contamination by human faecal sources at these sites. These human markers were weakly detected in Pouliguen channel... |
| Tipo: Text |
Palavras-chave: Bacteroidales; F-specific RNA bacteriophages; Faecal bacterial indicators; Microbial source tracking; Water. |
| Ano: 2010 |
URL: http://archimer.ifremer.fr/doc/00003/11384/10304.pdf |
| |
|
|
| Alzieu, Claude; Andral, Bruno; Bassoulet, Philippe; Gourmelon, Michele; Le Quillec, Régis; L'Yavanc, Jacky; Quiniou, Francoise. |
| Les traitements in situ des sédiments, ou biodragages, consistent à disperser à la surface ou à injecter dans le sédiment des produits pulvérulents sur lesquels sont fixées des bactéries capables de dégrader les matières organiques. Peu de données expérimentales sont disponibles quant à l'efficacité et à l'impact de cette pratique qui, bien qu'utilisée dans certains milieux d'eau douce, n'a pas fait l'objet de réelles applications en milieu marin. L'offre de service de quelques opérateurs et la demande des gestionnaires des ports, ne peuvent être prises en considération, faute d'une connaissance approfondie des avantages et inconvénients de telles techniques. Il nous est donc apparu nécessaire de définir et de proposer, aux Services en charge des... |
| Tipo: Text |
|
| Ano: 1999 |
URL: http://archimer.ifremer.fr/doc/00040/15121/12457.pdf |
| |
|
|
| Boukerb, Amine M.; Penny, Christian; Serghine, Joelle; Walczak, Cécile; Cauchie, Henry-michel; Miller, William G.; Losch, Serge; Ragimbeau, Catherine; Mossong, Joël; Mégraud, Francis; Lehours, Philippe; Bénéjat, Lucie; Gourmelon, Michele. |
| During a study on the prevalence and diversity of members of the genus Campylobacter in a shellfish-harvesting area and its catchment in Brittany, France, six urease-positive isolates of members of the genus Campylobacter were recovered from surface water samples, as well as three isolates from stools of humans displaying enteric infection in the same period. These strains were initially identified as members of the Campylobacter lari group by MALDI-TOF mass spectrometry and placed into a distinct group in the genus Campylobacter, following atpA gene sequence analysis based on whole-genome sequencing data. This taxonomic position was confirmed by phylogenetic analysis of the 16S rRNA, rpoB and hsp60 (groEL) loci, and an analysis of the core genome that... |
| Tipo: Text |
Palavras-chave: Campylobacter; Novel species; Surface water; Coastal catchment; Human gastroenteritis; C. lari group; Whole genorne sequence. |
| Ano: 2019 |
URL: https://archimer.ifremer.fr/doc/00591/70346/69558.pdf |
| |
|
|
| Petit, Fabienne; Clermont, Olivier; Delannoy, Sabine; Servais, Pierre; Gourmelon, Michele; Fach, Patrick; Oberle, Kenny; Fournier, Matthieu; Denamur, Erick; Berthe, Thierry. |
| The aim of this study was to investigate the diversity of the E. coli population, focusing on the occurrence of pathogenic E. coli, in surface water draining a rural catchment. Two sampling campaigns were carried out in similar hydrological conditions (wet period, low flow) along a river continuum, characterized by two opposite density gradients of animals (cattle and wild animals) and human populations. While the abundance of E. coli slightly increased along the river continuum, the abundance of both human and ruminant-associated Bacteroidales markers, as well as the number of E. coli multi-resistant to antibiotics, evidenced a fecal contamination originating from animals at upstream rural sites, and from humans at downstream urban sites. A strong spatial... |
| Tipo: Text |
Palavras-chave: Water; Sediment; Pathogenic E. coli; Virulence gene; Shiga toxin. |
| Ano: 2017 |
URL: http://archimer.ifremer.fr/doc/00378/48887/49328.pdf |
| |
|
|
| Furet, Jean-pierre; Firmesse, Olivier; Gourmelon, Michele; Bridonneau, Chantal; Tap, Julien; Mondot, Stanislas; Dore, Joel; Corthier, Gerard. |
| Pollution of the environment by human and animal faecal pollution affects the safety of shellfish, drinking water and recreational beaches. To pinpoint the origin of contaminations, it is essential to define the differences between human microbiota and that of farm animals. A strategy based on real-time quantitative PCR (qPCR) assays was therefore developed and applied to compare the composition of intestinal microbiota of these two groups. Primers were designed to quantify the 16S rRNA gene from dominant and subdominant bacterial groups. TaqMan((R)) probes were defined for the qPCR technique used for dominant microbiota. Human faecal microbiota was compared with that of farm animals using faecal samples collected from rabbits, goats, horses, pigs, sheep... |
| Tipo: Text |
Palavras-chave: Quantitative PCR; Faecal microbiota; Human; Farm animals. |
| Ano: 2009 |
URL: http://archimer.ifremer.fr/doc/00000/11071/11297.pdf |
| |
|
|
| 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 |
|
| Ano: 2020 |
URL: https://archimer.ifremer.fr/doc/00600/71164/69495.pdf |
| |
|
| |
|
|
| Gourmelon, Michele; Derrien, A.; Crenn, Isabelle; Loaec, Solen. |
| Des bactéries fécales telles que les Escherichia coli ou les coliformes thermotolérants ont été recherchées dans des sédiments côtiers vaseux (prélevés sur deux sites différents: Morlaix et St Pol de Léon; Finistère). Ces vases, sous influence de rejets polluants, de par leur richesse en matière organique et en particules de faible taille sont susceptibles d'héberger ces bactéries. Une partie de l'étude a consisté à comparer différentes techniques de relargage des bactéries des particules de sédiment décrites dans la littérature. |
| Tipo: Text |
|
| Ano: 2002 |
URL: http://archimer.ifremer.fr/doc/00081/19213/16808.pdf |
| |
|
|
| Pourcher, Anne-marie; Jarde, Emilie; Jeanneau, Laurent; Solecki, Olivia; Jadas-hecart, Alain; Caprais, Marie-paule; Durand, Gaëlle; Gourmelon, Michele. |
| La dégradation de la qualité des eaux par la pollution microbiologique représente un problème majeur de santé publique, notamment dans les eaux ou s'exercent des activité humaines. Afin de définir les actions prioritaires à mener, une meilleure connaissance de l'origine des pollution fécales est nécessaire. Cet article nous présente le développement d'une méthode innovante utilisant des marqueurs chimiques et microbiologiques permettant de différencier trois sources majeures de contamination des eaux de baignade en Bretagne: les déjections humaines, bovines et porcines. |
| Tipo: Text |
|
| Ano: 2012 |
URL: http://archimer.ifremer.fr/doc/00315/42604/41980.pdf |
| |
|
|
| Gourmelon, Michele; Caprais, Marie-paule; Mieszkin, Sophie; Marti, Romain; Wery, Nathalie; Jarde, E.; Derrien, Marc; Jadas-hecart, A.; Communal, P. Y.; Jaffrezic, A.; Pourcher, A. M.. |
| The microbiological quality of coastal or river waters can be affected by faecal pollution from human or animal sources. An efficient MST (Microbial Source Tracking) toolbox consisting of several host-specific markers would therefore be valuable for identifying the origin of the faecal pollution in the environment and thus for effective resource management and remediation. In this multidisciplinary study, after having tested some MST markers on faecal samples, we compared a selection of 17 parameters corresponding to chemical (steroid ratios, caffeine, and synthetic compounds), bacterial (host-specific Bacteroidales, Lactobacillus amylovorus and Bifidobacterium adolescentis) and viral (genotypes I-IV of F-specific bacteriophages, FRNAPH) markers on... |
| Tipo: Text |
Palavras-chave: Microbial source tracking; Faecal pollution; Bacteroidales; Bifidobacterium adolescentis; Lactobacillus; FRNA bacteriophages; Steroids; Caffeine. |
| Ano: 2010 |
URL: http://archimer.ifremer.fr/doc/00016/12710/9690.pdf |
| |
|
|
| Mieszkin, Sophie; Furet, Jean-pierre; Corthier, Gerard; Pommepuy, Monique; Le Saux, Jean-claude; Bougeard, Morgane; Hervio Heath, Dominique; Gourmelon, Michele. |
| The microbiological quality of coastal waters and shellfish harvesting areas in Brittany (France) can be affected by faecal pollutions from human activities and animal breeding (especially pigs and cattle). To discriminate among faecal pollution of human and animal origin, a library-independent microbial source tracking method was selected: Bacteroidales host-specific 16S rRNA gene markers by real-time Polymerase Chain Reaction (PCR). A human-specific Bacteroidales marker (Hum-1-Bac) was designed. Tested on faecal samples, the Hum-1-Bac marker showed 95 % sensitivity and 95 % specificity (n= 80). Average values (± STD) of the Hum-1-Bac marker were found to be 7.3 ± 1.4 16S rRNA gene copies per g wet faeces in human faeces samples (n=10) and 5.7 ± 1.3 log10... |
| Tipo: Text |
Palavras-chave: Microbial Source Tracking; Host-Specific Bacteroidales Marker; 16S rRNA Gene; Real-Time PCR; Faecal Contamination. |
| Ano: 2009 |
URL: http://archimer.ifremer.fr/doc/00021/13259/10306.pdf |
| |
|
|
| Alzieu, Claude; Abarnou, Alain; Bassoullet, Philippe; Boutier, Bernard; Chiffoleau, Jean-francois; Crenn, Isabelle; Derrien, Annick; Erard-le Denn, Evelyne; Gourmelon, Michele; Guiliaud, Jean-françois; Silva Jacinto, Ricardo; Le Cann, Pierre; Le Guyader, Françoise; Le Hir, Pierre; L'Yavanc, Jacky; Mauvais, Jean-louis; Menard, Dominique; Michel, Pierre; Monbet, Yves; Pommepuy, Monique; Quiniou, Francoise. |
| Port activities require continuous or occasional dredging of considerable quantities of sediments : approximately 50 million m3 along the French coastline. A large proportion of the dredgings is authorized for dumping at sea in geographically delimited areas and following an impact evaluation of their potential harmfulness to the marine environment. The environmental risks assessment linked to dredging operations relies on knowledge related to several scientific disciplines contributing to changes in the regulations. This work, intended both for managers and for environmental scientists and engineers, is designed to take stock of the current state-of-the-art in the field of sediment contamination and related ecotoxicological hazards, along with a review of... |
| Tipo: Text |
Palavras-chave: Regulations; Management; Impact; Contaminants; Dredging; Réglementation; Gestion; Impact; Contaminants; Dragages. |
| Ano: 1999 |
URL: http://archimer.ifremer.fr/doc/1999/rapport-1040.pdf |
| |
|
| |
|
|
| Mieszkin, Sophie; Furet, Jean-pierre; Corthier, Gerard; Gourmelon, Michele. |
| The microbiological quality of coastal or river water can be affected by fecal contamination from human or animal sources. To discriminate pig fecal pollution from other pollution, a library-independent microbial source tracking method targeting Bacteroidales host-specific 16S rRNA gene markers by real-time PCR was designed. Two pig-specific Bacteroidales markers (Pig-1-Bac and Pig-2-Bac) were designed using 16S rRNA gene Bacteroidales clone libraries from pig feces and slurry. For these two pig markers, 98 to 100% sensitivity and 100% specificity were obtained when tested by TaqMan real-time PCR. A decrease in the concentrations of Pig-1-Bac and Pig-2-Bac markers was observed throughout the slurry treatment chain. The two newly designed pig-specific... |
| Tipo: Text |
|
| Ano: 2009 |
URL: http://archimer.ifremer.fr/doc/2009/publication-6493.pdf |
| |
|
|
| Gourmelon, Michele. |
| La contamination de l’environnement par des bactéries ou des virus d’origine fécale par le biais des rejets résultant des activités urbaines ou agricoles constitue un risque important pour la santé humaine et une préoccupation pour la pérennité de certains usages en zone littorale. La bactérie Escherichia coli (E. coli) a été retenue comme indicateur de contamination fécale pour évaluer la qualité sanitaire des zones conchylicoles et des zones de baignade et pour établir leur classification. L’étude des bactéries entériques et des marqueurs de l’origine des contaminations fécales dans l'environnement littoral constitue l’essentiel de mes activités de recherche à l’Ifremer. C’est ce travail qui sera présenté lors de cette soutenance. J'’ai tout d’abord... |
| Tipo: Text |
Palavras-chave: Contamination microbiologique; Littoral; Bactéries entériques; Environnement; Contaminatin fécale. |
| Ano: 2014 |
URL: http://archimer.ifremer.fr/doc/00256/36764/35369.pdf |
| |
|
|
| Gourmelon, Michele. |
| L'étude de Escherichia coli en microcosmes d'eau de mer à 34 /1000 de salinité, exposé à la lumière visible montre que cette bactérie évolue rapidement (en quelques heures) vers un état viable non cultivable tandis qu'à l'obscurité, la capacité à cultiver se maintient plus longtemps. Deux facteurs principaux semblent déterminer la survie de Escherichia coli dans l'eau de mer lors de l'exposition à la lumière visible : l'état de la bactérie au moment du rejet et la qualité du milieu récepteur. L'état de la bactérie avant exposition à la lumière visible joue un rôle important dans sa survie : en effet, quand il est en début de phase stationnaire avant son séjour dans l'eau de mer, Escherichia coli résiste mieux au stress lumineux que lorsqu'il est en phase... |
| Tipo: Text |
|
| Ano: 1995 |
URL: http://archimer.ifremer.fr/doc/00105/21577/19157.pdf |
| |
|
|
| Breton, Marguerite; Caprais, Marie-paule; Derrien, A.; Douillet, P; Dubois, E; Dupray, E; Gourmelon, Michele; Guillerm, Denise; Kempf, Marc; Lazure, P.; Le Guyader, Soizick; Le Menn, Remi; Menard, Dominique; Pommepuy, Monique; Salomon, Jean-claude. |
| Les départements et territoires d'outre mer sont généralement l'objet d'enjeux économiques importants, et de conflits d'activités liés au développement touristique, aquacole, agricole et industriel. Les études font généralement état d'une lente dégradation de l'environnement marin avec diminution des coraux et de la faune associée, au profit d'une augmentation de la couverture algale. On constate parfois un envasement ou un ensablement des sites, la présence dans l'eau de polluants organiques, dont des pesticides, des métaux ainsi que des microorganismes d'origine fécale. En Martinique, ce dernier aspect, lié à l'assainissement des zones rurales, urbaines et touristiques est actuellement considéré comme une préoccupation majeure pour les prochaines années.... |
| Tipo: Text |
|
| Ano: 1994 |
URL: http://archimer.ifremer.fr/doc/00132/24303/22301.pdf |
| |
|
|
| 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 |
|
| Ano: 2007 |
URL: http://archimer.ifremer.fr/doc/2007/publication-3535.pdf |
| |
| Registros recuperados: 49 | |
|
|
|
