title: Identification of the origin of faecal contamination in estuarine oysters using Bacteroidales and F-specific RNA bacteriophage markers.
abstract: OBJECTIVE
  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.
  
  
  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 predominant source of contamination in oysters (total of 18 oyster batches tested) and waters (total of 24 water samples tested). The importance of using the intravalvular liquids instead of digestive tissues, when applying host-associated Bacteroidales markers in oysters, was also revealed.
  
  
  CONCLUSIONS
  This study has shown that the application of a MST toolbox of diverse bacterial and viral methods can provide multiple lines of evidence to identify the predominant source of faecal contamination in shellfish from an estuarine environment.
  
  
  CONCLUSIONS
  Application of this MST toolbox is a useful approach to understand the origin of faecal contamination in shellfish harvesting areas in an estuarine setting.
authors.affiliation: Laboratoire Santé Environnement et Microbiologie, Unité SG2M, Département RBE, IFREMER, Plouzané, France.
authors.forename: S
authors.initials: S
authors.lastname: Mieszkin
authors.forename: M P
authors.initials: MP
authors.lastname: Caprais
authors.forename: C
authors.initials: C
authors.lastname: Le Mennec
authors.forename: M
authors.initials: M
authors.lastname: Le Goff
authors.forename: T A
authors.initials: TA
authors.lastname: Edge
authors.forename: M
authors.initials: M
authors.lastname: Gourmelon
mesh_terms: D000818:Animals; D041963:Bacteroidetes / Q000235:genetics / Q000302:isolation & purification*; D004926:Escherichia coli / Q000302:isolation & purification; D063366:Estuaries; D005243:Feces / Q000382:microbiology* / Q000821:virology; D005602:France; D005819:Genetic Markers; D005838:Genotype; D010125:Ostreidae / Q000382:microbiology* / Q000821:virology; D012317:RNA Phages / Q000235:genetics / Q000302:isolation & purification*; D060888:Real-Time Polymerase Chain Reaction; D045483:Rivers / Q000382:microbiology; D012623:Seawater / Q000382:microbiology*; D012758:Shellfish / Q000382:microbiology / Q000821:virology; D014873:Water Pollutants / Q000032:analysis*
chemical_list: D005819:Genetic Markers; D014873:Water Pollutants
keywords: Escherichia coli; Estuarine and river waters; F-specific RNA bacteriophages; host-associated Bacteroidales markers; microbial source tracking; shellfish