|
|
|
| Registros recuperados: 49 | |
|
|
| Munck, Nanna; Leekitcharoenphon, Pimlapas; Litrup, Eva; Kaas, Rolf; Meinen, Anika; Guillier, Laurent; Tang, Yue; Malorny, Burkhard; Palma, Federica; Borowiak, Maria; Gourmelon, Michele; Simon, Sandra; Banerji, Sangeeta; Petrovska, Liljana; Dallman, Timothy J.; Hald, Tine. |
| Zoonotic Salmonella causes millions of human salmonellosis infections worldwide each year. Information about the source of the bacteria guides risk managers on control and preventive strategies. Source attribution is the effort to quantify the number of sporadic human cases of a specific illness to specific sources and animal reservoirs. Source attribution methods for Salmonella have so far been based on traditional wet-lab typing methods. With the change to whole genome sequencing there is a need to develop new methods for source attribution based on sequencing data. Four European datasets collected in Denmark (DK), Germany (DE), the United Kingdom (UK) and France (FR) are presented in this descriptor. The datasets contain sequenced samples of Salmonella... |
| Tipo: Text |
|
| Ano: 2020 |
URL: https://archimer.ifremer.fr/doc/00612/72437/71383.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 |
| |
|
|
| 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 |
| |
|
|
| 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 |
| |
|
|
| Derrien, M.; Jarde, E.; Gruau, G.; Pourcher, A. M.; Gourmelon, Michele; Jadas-hecart, Alain; Wickmann, A. C. Pierson. |
| Improving the microbiological quality of coastal and river waters relies on the development of reliable markers that are capable of determining sources of fecal pollution. Recently, a principal component analysis (PCA) method based on six stanol compounds (i.e. 5 beta-cholestan-3 beta-ol (coprostanol), 5 beta-cholestan-3 alpha-ol (epicoprostanol), 24-methyl-5 alpha-cholestan-3 beta-ol (campestanol), 24-ethyl-5 alpha-cholestan-3 beta-ol (sitostanol), 24-ethyl-5 beta-cholestan-3 beta-ol (24-ethylcoprostanol) and 24-ethyl-5 beta-cholestan-3 alpha-ol (24-ethylepicoprostanol)) was shown to be suitable for distinguishing between porcine and bovine feces. In this study, we tested if this PCA method, using the above six stanols, could be used as a tool in... |
| Tipo: Text |
Palavras-chave: Stanols; Microbial Source Tracking; Principal component analysis; Microbial markers. |
| Ano: 2012 |
URL: http://archimer.ifremer.fr/doc/00090/20133/17829.pdf |
| |
|
|
| Marti, Romain; Ribun, Sebastien; Aubin, Jean-baptiste; Colinon, Celine; Petit, Stephanie; Marjolet, Laurence; Gourmelon, Michele; Schmitt, Laurent; Breil, Pascal; Cottet, Marylise; Cournoyer, Benoit. |
| Rivers are often challenged by fecal contaminations. The barrier effect of sediments against fecal bacteria was investigated through the use of a microbial source tracking (MST) toolbox, and by Next Generation Sequencing (NGS) of V5-V6 16S rRNA gene (rrs) sequences. Non-metric multi-dimensional scaling analysis of V5-V6 16S rRNA gene sequences differentiated bacteriomes according to their compartment of origin i.e., surface water against benthic and hyporheic sediments. Classification of these reads showed the most prevalent operating taxonomic units (OTU) to be allocated to Flavobacterium and Aquabacterium. Relative numbers of Gaiella, Haliangium, and Thermoleophilum OTU matched the observed differentiation of bacteriomes according to river compartments.... |
| Tipo: Text |
Palavras-chave: Peri-urban river; Benthic and hyporheic sediments; Microbial community; High throughput sequencing (HTS); Fecal contamination. |
| Ano: 2017 |
URL: http://archimer.ifremer.fr/doc/00378/48886/49316.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 |
| |
|
|
| Gawler, A; Beecher, J; Brandao, J; Carroll, N; Falcao, L; Gourmelon, Michele; Masterson, B; Nunes, B; Porter, J; Rince, A; Rodrigues, R; Thorp, M; Walters, J; Meijer, W. |
| The recent implementation of the Revised Bathing Water Directive in the European Union has highlighted the need for development of effective methods to differentiate between sources of faecal contamination. It had previously been shown that amplification of 16S rRNA genes of host-specific Bacteriodales species using the HF183F and CF128F primers could be used as markers for human and bovine faecal contamination in the United States. This paper determined the sensitivity and specificity of these markers in four Atlantic Rim countries (France, Ireland, Portugal and the United Kingdom) to evaluate their usefulness in determining the origin of faecal contamination. It was shown that the HF183F marker displayed high sensitivity (80-100%) and specificity... |
| Tipo: Text |
Palavras-chave: Sensitivity; Specificity; PCR; Microbial source tracking; Bacteriodales. |
| Ano: 2007 |
URL: http://archimer.ifremer.fr/doc/2007/publication-4957.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 |
| |
|
|
| Troussellier, Marc; Bonnefont, Jean-luc; Courties, Claude; Derrien, Annick; Dupray, Elizabeth; Gauthier, Michel; Gourmelon, Michele; Joux, Fabien; Lebaron, Philippe; Martin, Yvan; Pommepuy, Monique. |
| The effects of different environmental factors (nutrient deprivation, hyperosmotic shock, exposure to light) on enteric bacteria which have been transferred into the marine environment, have been studied experimentally (microcosms) by considering demographic, physiological and genetic responses in Escherichia coli or Salmonella typhimurium populations. Short-term experiments (less than or equal to 48 h) showed that nutrient deprivation induced limited changes in measured bacteriological variables, but when combined with hyperosmotic shock, it results in an energy charge decrease and inactivation of membrane transport. Light exposure mainly affects the colony-forming capacity of bacterial populations. Combining different stress factors confirmed the rapid... |
| Tipo: Text |
Palavras-chave: Genetics; Cellular states; Physiology; Seawater; Enteric bacteria; Génétique; Etats cellulaires; Physiologie; Eau de mer; Entérobactéries. |
| Ano: 1998 |
URL: http://archimer.ifremer.fr/doc/1998/publication-845.pdf |
| |
|
|
| Gourmelon, Michele; Montet, Mp; Loaec, Solen; Le Mennec, Cecile; Pommepuy, Monique; Vernoy-rozand, C. |
| La qualité sanitaire du milieu marin côtier est influencée par la présence de rejets urbains ou de rejets diffus d'origine agricole. Ces effluents sont riches en bactéries ou virus d'origine fécale, dont certains ont été mis en cause dans des pathologies humaines (Beeching, 1997 ; Feldhusen, 2000 ; Lipp et Rose, 1997 ; Yam et al., 1999). Parmi les microorganismes pouvant présenter un danger pour l'homme, certains, pathogènes émergents ces dernières années, n'ont été que récemment recherchés dans l'environnement : on peut citer les Cryptosporidium et les Giardia pour les parasites, les norovirus pour les virus et les Escherichia coli vérotoxiques (VTEC) pour les bactéries. Ces derniers ne sont connus que depuis 1982, date à laquelle E. coli 0157 : H7 a été... |
| Tipo: Text |
|
| Ano: 2003 |
URL: http://archimer.ifremer.fr/doc/00106/21697/19276.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 |
| |
|
| |
|
|
| Wieliczko, Etienne; Gourmelon, Michele; Dupray, Elisabeth; Derrien, A.; Caprais, Marie-paule; Pommepuy, Monique. |
| D'un point de vue purement écologique, le milieu marin est particulièrement agressif pour les bactéries d'origine entérique. Jusqu'à la fin des années soixante dix, il était généralement admis que ces bactéries pathogènes étaient détruites en quelques heures dans l'eau de mer, ou selon l'espèce en quelques jours. On parlait alors du "pouvoir auto-épurateur" de l'eau de mer. Depuis des travaux plus récents ont démontré la persistance de microorganismes dans les zones littorales. En fait, la survie en mer des bactéries d'origine fécale dans le milieu marin dépend de deux grands facteurs : la qualité de l'eau ou du sédiment permettant aux bactéries de mettre en oeuvre plus ou moins facilement des mécanismes de "résistance", et leur historique avant leur rejet... |
| Tipo: Text |
|
| Ano: 1997 |
URL: http://archimer.ifremer.fr/doc/00105/21630/19210.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 |
| |
|
| |
|
|
| Caprais, Marie-paule; Le Mennec, Cecile; Pommepuy, Monique; Le Saux, Jean-claude; Gourmelon, Michele. |
| In Europe, shellfish harvesting areas are classified according European Directive EC N°854/2004, using classic faecal indicator levels (Escherichia coli). A better indicator is needed, however, because shellfish may contain other human pathogens. Other indicator organisms have therefore been evaluated and, among these, coliphages meet most of the requirements to serve as indicators and models for enteroviruses. In order to evaluate the capacity of coliphages as indicators, a total of 764 shellfish were sampled in 2004 from 70 shellfish harvesting areas monitored by the Ifremer microbiological surveillance network (REMI, http://www.ifremer.fr/envlit/), and tested for F-specific RNA bacteriophages (FRNAPH). Two species of bivalve mollusc were collected... |
| Tipo: Text |
Palavras-chave: F-specific RNA bacteriophage; Shellfish; Faecal pollution; Discrimination. |
| Ano: 2009 |
URL: http://archimer.ifremer.fr/doc/00066/17749/15271.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 |
| |
| Registros recuperados: 49 | |
|
|
|
