Consulta: creatorFacets:"Gourmelon, Michele"
Registros recuperados: 49
Data/hora: 01/06/2024 10:36:07

Four European Salmonella Typhimurium datasets collected to develop WGS-based source attribution methods
Provedor de dados: 5
Autores: 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

Biodragages - Protocole de suivi de l'efficacité et de l'impact potentiel
Provedor de dados: 5
Autores: 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

Etude de la contamination microbiologique du milieu littoral : identification des sources de contamination fécale et évaluation de la persistance des bactéries entériques dans l'environnement
Provedor de dados: 5
Autores: 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

Application of a microbial source tracking based on bacterial and chemical markers in headwater and coastal catchments
Provedor de dados: 5
Autores: 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

Origin of fecal contamination in waters from contrasted areas: Stanols as Microbial Source Tracking markers
Provedor de dados: 5
Autores: 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

Human-Driven Microbiological Contamination of Benthic and Hyporheic Sediments of an Intermittent Peri-Urban River Assessed from MST and 16S rRNA Genetic Structure Analyses
Provedor de dados: 5
Autores: 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

Etude de la lumière visible comme facteur limitant de la survie de Escherichia Coli en milieu Marin
Provedor de dados: 5
Autores: 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

Validation of host-specific Bacteriodales 16S rRNA genes as markers to determine the origin of faecal pollution in Atlantic Rim countries of the European Union
Provedor de dados: 5
Autores: 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

Comparative assessment of human and farm animal faecal microbiota using real-time quantitative PCR
Provedor de dados: 5
Autores: 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

Responses of enteric bacteria to environmental stresses in seawater
Provedor de dados: 5
Autores: 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

Recherche des Escherichia coli vérotoxiques (VTEC) dont E. coli O157 : H7 dans l'environnement marin (coquillages)
Provedor de dados: 5
Autores: 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

Complete Genome Sequence of   Campylobacter armoricus   CA639, Which Carries Two Plasmids, Compiled Using Oxford Nanopore and Illumina Sequencing Technologies
Provedor de dados: 5
Autores: 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

Qualité microbiologique des coquillages destinés à la consommation humaine : contamination des coquillages par des bactéries pathogènes pour l’homme. Sous-région marine Golfe de Gascogne. Evaluation initiale DCSMM.
Provedor de dados: 5
Autores: Hervio-heath, Dominique; Gourmelon, Michele; Catherine, Martial.
Tipo: Text
Palavras-chave: Golfe de Gascogne; Coquillages; Contamination microbiologique; Bactéries; Pathogènes; Suivi.
Ano: 2012
URL: https://archimer.ifremer.fr/doc/00329/44061/43632.pdf

Mise en place d'éléments permettant le fonctionnement d'organismes stressés dans un écosystème pertubé - 2ème partie : rôle et expression du gène rpoS chez Escherichia Coli en situation de stress
Provedor de dados: 5
Autores: 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

Development of microbial and chemical MST tools to identify the origin of the faecal pollution in bathing and shellfish harvesting waters in France
Provedor de dados: 5
Autores: 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

Identification de l'origine de la contamination observée en baie de La Baule : Première partie de l'étude
Provedor de dados: 5
Autores: Caprais, Marie-paule; Gourmelon, Michele; Le Mennec, Cecile; Joubrel, Rozenn.
Afin d'améliorer la qualité sanitaire des coquillages du secteur La Baule - Le Pouliguen, la Communauté d'Agglomération CAP Atlantique a mis en place un programme d'étude pour identifier les sources de pollution sur ce secteur et initier des actions permettant de limiter les apports d'origine fécale aux coquillages. Dans le cadre de cette présente étude, de juin 2006 à décembre 2007, deux méthodes d'identification de l'origine de la contamination fécale en cours de développement au laboratoire de microbiologie d'Ifremer de Brest, ont été appliquées sur des lots de coquillages (n=87 ; 6 sites) et des échantillons d'eaux (n=40 ; 7 localisations). La première méthode consistait à rechercher par PCR conventionnelle les gènes codant les ARN ribosomiques (ARNr)...
Tipo: Text
Palavras-chave: Bacteroidales; Bactériophages F +ARN spécifiques; Marqueurs de contamination fécale; E. coli; Génotypage; PCR conventionnelle; Coquillage; Littoral.
Ano: 2008
URL: https://archimer.ifremer.fr/doc/00622/73452/72691.pdf

Potential of F-specific RNA bacteriophages to discriminate sources of faecal pollution in French shellfish
Provedor de dados: 5
Autores: 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

Effect of oxygen and temperature on the dynamic of the dominant bacterial populations of pig manure and on the persistence of pig-associated genetic markers, assessed in river water microcosms
Provedor de dados: 5
Autores: Marti, R.; Mieszkin, Sophie; Solecki, O.; Pourcher, A. -m.; Hervio-heath, Dominique; Gourmelon, Michele.
Aims: The aim is to evaluate the dynamic of Bacteroides-Prevotella and Bacillus-Streptococcus-Lactobacillus populations originating from pig manure and the persistence of pig-associated markers belonging to these groups according to temperature and oxygen. Methods and Results: River water was inoculated with pig manure and incubated under microaerophilic and aerobic conditions, at 4 and 20 degrees C over 43 days. The diversity of bacterial populations was analysed by capillary electrophoresis-single-strand conformation polymorphism. The persistence of the pig-associated markers was measured by real-time PCR and compared with the survival of Escherichia coli and enterococci. Decay was characterized by the estimation of the time needed to produce a 1-log...
Tipo: Text
Palavras-chave: Lactobacillus amylovorus; Microbial source tracking; Oxygen; Persistence; Pig-associated Bacteroidales markers; Quantitative real-time PCR; River water; Temperature.
Ano: 2011
URL: http://archimer.ifremer.fr/doc/00053/16470/14534.pdf

Prevalence and Characterization of Shiga Toxin-Producing and Enteropathogenic Escherichia coli in Shellfish-Harvesting Areas and Their Watersheds
Provedor de dados: 5
Autores: Baliere, Charlotte; Rince, Alain; Blanco, Jorge; Dahbi, Ghizlane; Harei, Josee; Vogeleer, Philippe; Giard, Jean-christophe; Mariani-kurkdfian-, Patricia; Gourmelon, Michele.
Tipo: Text
Palavras-chave: STEC; EPEC; Shellfish; Water; MLST; PFGE; Biofilms.
Ano: 2015
URL: http://archimer.ifremer.fr/doc/00298/40904/39949.pdf

Campylobacter armoricus sp. nov., a novel member of the Campylobacter lari group isolated from surface water and stools from humans with enteric infection
Provedor de dados: 5
Autores: 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

Performance of viruses and bacteriophages for fecal source determination in a multi-laboratory, comparative study
Provedor de dados: 5
Autores: Harwood, Valerie J.; Boehm, Alexandria B.; Sassoubre, Lauren M.; Vijayavel, Kannappan; Stewart, Jill R.; Fong, Theng-theng; Caprais, Marie-paule; Converse, Reagan R.; Diston, David; Ebdon, James; Fuhrman, Jed A.; Gourmelon, Michele; Gentry-shields, Jennifer; Griffith, John F.; Kashian, Donna R.; Noble, Rachel T.; Taylor, Huw; Wicki, Melanie.
An inter-laboratory study of the accuracy of microbial source tracking (MST) methods was conducted using challenge fecal and sewage samples that were spiked into artificial freshwater and provided as unknowns (blind test samples) to the laboratories. The results of the Source Identification Protocol Project (SIPP) are presented in a series of papers that cover 41 MST methods. This contribution details the results of the virus and bacteriophage methods targeting human fecal or sewage contamination. Human viruses used as source identifiers included adenoviruses (HAdV), enteroviruses (EV), norovirus Groups I and II (NoVI and NoVII), and polyomaviruses (HPyVs). Bacteriophages were also employed, including somatic coliphages and F-specific RNA bacteriophages...
Tipo: Text
Palavras-chave: Virus; Bacteriophage; Water quality; Fecal pollution; Validation.
Ano: 2013
URL: http://archimer.ifremer.fr/doc/00171/28197/27786.pdf

Dragages et environnement marin Etat des connaissances
Provedor de dados: 5
Autores: 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

Revue bibliographique : risques de contamination des coquillages par les contaminations d’origine aviaire
Provedor de dados: 5
Autores: Gourmelon, Michele; Serghine, Joelle; Boukerb, Mohamed; Garry, Pascal.
Tipo: Text
Ano: 2020
URL: https://archimer.ifremer.fr/doc/00623/73462/81203.pdf

Evaluation of two library-independent microbial source tracking methods to identify sources of fecal contamination in french estuaries
Provedor de dados: 5
Autores: 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 (&gt;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

Discrimination between human, pig and ruminant fecal contaminations in a river catchment by real-time PCR using host-specific markers
Provedor de dados: 5
Autores: 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

Change in the structure of Escherichia coli population and the pattern of virulence genes along a rural aquatic continuum
Provedor de dados: 5
Autores: 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

AB_SA: Accessory genes-Based Source Attribution – tracing the source of Salmonella enterica Typhimurium environmental strains
Provedor de dados: 5
Autores: 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

Recent innovation in microbial source tracking using bacterial real-time PCR markers in shellfish
Provedor de dados: 5
Autores: 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

Dénombrement des coliformes thermotolérants ou des Escherichia coli dans des sédiments côtiers vaseux
Provedor de dados: 5
Autores: 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

Contamination des coquillages par des bactéries pathogènes pour l’homme. Sous-région marine Méditerranée occidentale. Evaluation initiale DCSMM.
Provedor de dados: 5
Autores: Hervio-heath, Dominique; Gourmelon, Michele; Catherine, Martial.
Tipo: Text
Palavras-chave: Méditerranée; Coquillages; Contamination; Suivi; Bactéries pathogènes.
Ano: 2012
URL: https://archimer.ifremer.fr/doc/00331/44244/43813.pdf

Etude de la qualité du milieu marin littoral en Martinique (Baie de Fort de France)
Provedor de dados: 5
Autores: 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

Des micro-organismes et des composés chimiques pour identifier les sources de contamination fécale : étude de leur persistance en microcosmes et de leur présence dans les eaux à l'échelle d'un bassin versant
Provedor de dados: 5
Autores: 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

Fecal contamination in coastal areas: An engineering approach
Provedor de dados: 5
Autores: Pommepuy, Monique; Hervio Heath, Dominique; Caprais, Marie-paule; Gourmelon, Michele; Le Saux, Jean-claude; Le Guyader, Soizick.
Introduction : "The occurrence of pathogenic microorganisms in seawater or in shellfish could exist anytime sewage from human or animal origin would be discharged to the coast" (Metcalf, 1982). According to the diseases occurring in the human population or in animals, pathogens might be present in recreational waters or in shellfish. Thus, the presence of human enteric viruses (norovirus, astrovirus, rotavirus, hepatitisAvirus (HAV)) and pathogenic bacteria (Salmonella, Listeria monocytogenes, Shiga-toxin-producing Escherichia coli (STEC), Vibrio cholerae, Vibrio parahaemolyticus, etc.) has been reported in coastal areas for a long time (Colwell, 1978; Metcalf, 1978; Melnick et al., 1979; Grimes, 1991; Bosch et al., 2001;Kong et al., 2002). These...
Tipo: Text
Palavras-chave: Estimating model; Infection dose; Microorganisms; STEC; Bacteria; Virus; Fecal contamination; Pathogenic agent; Marine sediment; Estuarine water; Coastal area; Marine water.
Ano: 2006
URL: http://archimer.ifremer.fr/doc/2006/publication-1207.pdf

Relevance of Bacteroidales and F-Specific RNA Bacteriophages for Efficient Fecal Contamination Tracking at the Level of a Catchment in France
Provedor de dados: 5
Autores: Mauffret, Aourell; Caprais, Marie-paule; Gourmelon, Michele.
The relevance of three host-associated Bacteroidales markers (HF183, Rum2Bac, and Pig2Bac) and four F-specific RNA bacteriophage genogroups (FRNAPH I to IV) as microbial source tracking markers was assessed at the level of a catchment (Daoulas, France). They were monitored together with fecal indicators (Escherichia coli and enterococci) and chemophysical parameters (rainfall, temperature, salinity, pH, and turbidity) by monthly sampling over 2 years (n = 240 water samples) and one specific sampling following an accidental pig manure spillage (n = 5 samples). During the 2-year regular monitoring, levels of E. coil, enterococci, total F-specific RNA bacteriophages, and the general Bacteroidales marker AllBac were strongly correlated with one another and...
Tipo: Text
Ano: 2012
URL: http://archimer.ifremer.fr/doc/00089/20009/17680.pdf

Molecular Profiling of Shiga Toxin-Producing Escherichia coli and Enteropathogenic E. coli Strains Isolated from French Coastal Environments
Provedor de dados: 5
Autores: Baliere, Charlotte; Rince, A.; Delannoy, S.; Fach, P.; Gourmelon, Michele.
Shiga toxin-producing Escherichia coli (STEC) and enteropathogenic E. coli (EPEC) strains may be responsible for food-borne infections in humans. Twenty-eight STEC and 75 EPEC strains previously isolated from French shellfish-harvesting areas and their watersheds and belonging to 68 distinguishable serotypes were characterized in this study. High-throughput real-time PCR was used to search for the presence of 75 E. coli virulence-associated gene targets, and genes encoding Shiga toxin (stx) and intimin (eae) were subtyped using PCR tests and DNA sequencing, respectively. The results showed a high level of diversity between strains, with 17 unique virulence gene profiles for STEC and 56 for EPEC. Seven STEC and 15 EPEC strains were found to display a large...
Tipo: Text
Ano: 2016
URL: http://archimer.ifremer.fr/doc/00344/45514/45076.pdf

Occurrence of Bacterial Pathogens and Human Noroviruses in Shellfish-Harvesting Areas and Their Catchments in France
Provedor de dados: 5
Autores: 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

Recherche des Escherichia coli producteurs de Shiga-toxines (STEC) dans l’environnement marin (coquillages)
Provedor de dados: 5
Autores: Gourmelon, Michele.
L’originalité de cette étude était de rechercher si ces bactéries pouvaient être présentes dans l’environnement marin (tout particulièrement dans les coquillages) en développant ou adaptant des méthodes de détection. La présence de ces bactéries pourrait peut-être expliquer certaines TIACs liées à la consommation de coquillages dont l’agent responsable n’a pas été identifié.
Tipo: Text
Ano: 2006
URL: http://archimer.ifremer.fr/doc/00066/17752/15274.pdf

Phylogenetic analysis of Bacteroidales 16S rRNA gene sequences from human and animal effluents and assessment of ruminant faecal pollution by real-time PCR
Provedor de dados: 5
Autores: Mieszkin, Sophie; Yala, Jean Fabrice; Joubrel, Rozenn; Gourmelon, Michele.
Aims: The aims of this study were to evaluate the host-specific distribution of Bacteroidales 16S rRNA gene sequences from human- and animal-related effluents and faeces, and to define a ruminant-specific marker. Methods and Results: Bacteroidales 16S rRNA gene clone libraries were constructed from samples of effluent (sewage, bovine manure and pig slurry) and faeces (human, bovine, pig and wild bird), using PCR primers targeting order Bacteroidales. The phylogenetic analysis revealed six main distinct human-, bovine-, pig- and wild bird-specific clusters. From the bovine-specific cluster II, we designed a ruminant-specific marker, Rum-2-Bac, and this showed 97% sensitivity (n = 30) and 100% specificity (n = 40) when tested by TaqMan (R) real-time PCR....
Tipo: Text
Palavras-chave: 16S rRNA gene; Bacteroidales; Faecal contamination; Microbial Source Tracking; Sewage and manure.
Ano: 2010
URL: http://archimer.ifremer.fr/doc/00000/11156/8235.pdf

Prevalence and characterization of Salmonella spp. in three shellfish-harvesting areas in France
Provedor de dados: 5
Autores: 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
Ano: 2016
URL: http://archimer.ifremer.fr/doc/00341/45199/44609.pdf

Qualité microbiologique des coquillages destinés à la consommation humaine : contamination des coquillages par des bactéries pathogènes pour l’homme. Sous-région marine Mers celtiques. Evaluation initiale DCSMM.
Provedor de dados: 5
Autores: Hervio-heath, Dominique; Gourmelon, Michele; Catherine, Martial.
Tipo: Text
Palavras-chave: Mers celtiques; Coquillages; Contamination microbiologique; Bactéries pathogènes.
Ano: 2012
URL: https://archimer.ifremer.fr/doc/00329/43977/43549.pdf

First isolation of Shiga toxin 1d producing Escherichia coli variant strains in shellfish from coastal areas in France
Provedor de dados: 5
Autores: Gourmelon, Michele; Montet, M; Lozach, Solen; Le Mennec, Cecile; Pommepuy, Monique; Beutin, L; Vernozy Rozand, C.
Aims: This study was carried out to evaluate the presence of Shiga toxin-producing Escherichia coli (STEC) and E. coli O157:H7 in shellfish from French coastal environments.   Methods and Results: Shellfish were collected in six growing areas or natural beds (B category) and nonfarming areas (D category) from July 2002 to August 2004. PCR detection of stx genes was performed on homogenized whole shellfish and digestive gland tissues enrichments. STEC strains were detected by colony DNA hybridization using a stx-specific gene probe and E. coli O157 strains were additionally searched by immunomagnetic separation with O157-specific magnetic beads. Stx genes were detected in 40 of 144 (27.8%) sample enrichments from mussels, oysters or cockles, 32 of 130...
Tipo: Text
Palavras-chave: Shiga like toxin producing E. coli; Shellfish farming areas; Shellfish; Escherichia coli O157; Coastal environment.
Ano: 2006
URL: http://archimer.ifremer.fr/doc/2006/publication-1096.pdf

Passive Samplers, a Powerful Tool to Detect Viruses and Bacteria in Marine Coastal Areas
Provedor de dados: 5
Autores: 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 &amp;#956; Var; Vibrio spp; Microbial source tracking; Sea; Passive sampler; Oyster (Crassostrea gigas).
Ano: 2021
URL: https://archimer.ifremer.fr/doc/00682/79375/81893.pdf

Successful detection of pathogenic Shiga-toxin-producing Escherichia coli in shellfish, environmental waters and sediment using the ISO/TS-13136 method
Provedor de dados: 5
Autores: Baliere, Charlotte; Rince, Alain; Thevenot, Delphine; Gourmelon, Michele.
The presence of highly pathogenic Shiga-toxin-producing Escherichia coli (STEC) in shellfish, upstream waters and sediment from coastal shellfish sites was evaluated using the ISO/TS-13136 method. Shellfish (oysters, mussels and cockles), water and sediment samples were collected monthly over a period of 1 year. The method used real-time PCR detection of stx1, stx2 and eae genes and genetic markers corresponding to the five major serogroups (O157, O26, O103, O111 and O145) on enrichment broths and the identification of STEC when these genes and markers were detected. stx genes were detected in the broth of 33% of shellfish batches (n = 126), 91% of water samples (n = 117) and 28% of sediment (n = 39). One stx1+, eae+ O26:H11 strain was isolated from a...
Tipo: Text
Palavras-chave: Eae; Sediment; Shellfish; Shiga-toxin-producing Escherichia coli; Stx; Water.
Ano: 2015
URL: https://archimer.ifremer.fr/doc/00250/36124/34975.pdf

Rapport d’activités 2018 – Laboratoire Santé Environnement et Microbiologie.
Provedor de dados: 5
Autores: 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

Qualité microbiologique des coquillages destinés à la consommation humaine : contamination des coquillages par des bactéries pathogènes pour l’homme. Sous-région marine Manche - Mer du Nord. Evaluation initiale DCSMM.
Provedor de dados: 5
Autores: Hervio-heath, Dominique; Gourmelon, Michele; Catherine, Martial.
Tipo: Text
Palavras-chave: Manche; Mer du Nord; Coquillages; Contamination microbiologique; Bactéries pathogènes; Suivi.
Ano: 2012
URL: https://archimer.ifremer.fr/doc/00328/43874/43448.pdf

Estimation of Pig Fecal Contamination in a River Catchment by Real-Time PCR Using Two Pig-Specific Bacteroidales 16S rRNA Genetic Markers
Provedor de dados: 5
Autores: 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

Persistence of microbial and chemical pig manure markers as compared to faecal indicator bacteria survival in freshwater and seawater microcosms
Provedor de dados: 5
Autores: Solecki, O.; Jeanneau, L.; Jarde, E.; Gourmelon, Michele; Marin, Charlotte; Pourcher, A. M.
Natural seawater and freshwater microcosms inoculated with pig manure were set up to determine the persistence of pig faecal microbial and chemical markers in these two types of surface water. The concentrations of Lactobacillus amylovorus, the Bacteroidales Pig-2-Bac 165 rRNA genetic marker, five stanols and the evolution of two ratios of stanols, R(1) (coprostanol to the sum of coprostanol and 24-ethylcoprostanol) and R(2) (sitostanol to coprostanol) were analyzed during two months along with the concentration of Faecal Indicator Bacteria (FIB). Pig manure was inoculated to unfiltered water microcosms incubated aerobically at 18 degrees C in the dark. The faecal contamination load represented by the concentrations of culturable Escherichia coli and/or...
Tipo: Text
Palavras-chave: Faecal source tracking; Decay rates; Faecal stanols; Biphasic kinetic; Lactobacillus amylovorus; Bacteroidales marker.
Ano: 2011
URL: http://archimer.ifremer.fr/doc/00043/15417/12975.pdf

Identification of the origin of faecal contamination in estuarine oysters using Bacteroidales and F-specific RNA bacteriophage markers
Provedor de dados: 5
Autores: Mieszkin, Sophie; Caprais, Marie-paule; Le Mennec, Cecile; Le Goff, Manon; Edge, T. A.; Gourmelon, Michele.
Aims: The aim of this study was to identify the origin of faecal pollution impacting the Elorn estuary (Brittany, France) by applying microbial source tracking (MST) markers in both oysters and estuarine waters. Methods and Results: The MST markers used were as follows: (i) human-, ruminant- and pig-associated Bacteroidales markers by real-time PCR and (ii) human genogroup II and animal genogroup I of F-specific RNA bacteriophages (FRNAPH) by culture/genotyping and by direct real-time reverse-transcriptase PCR. The higher occurrence of the human genogroup II of F-specific RNA bacteriophages using a culture/genotyping method, and human-associated Bacteroidales marker by real-time PCR, allowed the identification of human faecal contamination as the...
Tipo: Text
Palavras-chave: Escherichia coli; Estuarine and river waters; F-specific RNA bacteriophages; Host-associated Bacteroidales markers; Microbial source tracking; Shellfish.
Ano: 2013
URL: http://archimer.ifremer.fr/doc/00153/26426/25250.pdf

Application of library-independent microbial source tracking methods for identifying the sources of faecal contamination in coastal areas
Provedor de dados: 5
Autores: 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