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Uneven genotypic diversity of Escherichia coli in fecal sources limits the performance of a library-dependent method of microbial source tracking on the southwestern French Atlantic coast

dc.rights.licenseopenen_US
hal.structure.identifierEnvironnements et Paléoenvironnements OCéaniques [EPOC]
dc.contributor.authorGARABETIAN, Frederic
dc.contributor.authorVITTE, Isabelle
hal.structure.identifierEnvironnements et Paléoenvironnements OCéaniques [EPOC]
dc.contributor.authorSABOURIN, Antoine
hal.structure.identifierEnvironnements et Paléoenvironnements OCéaniques [EPOC]
dc.contributor.authorMOUSSARD, Helene
dc.contributor.authorJOUANILLOU, Adeline
hal.structure.identifierEnvironnements et Paléoenvironnements OCéaniques [EPOC]
dc.contributor.authorMORNET, Line
dc.contributor.authorLESNE, Mélanie
hal.structure.identifierCentre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques [CARRTEL]
dc.contributor.authorLYAUTEY, Emilie
dc.date.accessioned2024-04-03T08:24:41Z
dc.date.available2024-04-03T08:24:41Z
dc.date.issued2020-12
dc.identifier.issn0008-4166en_US
dc.identifier.urihttps://oskar-bordeaux.fr/handle/20.500.12278/189142
dc.description.abstractEnTo develop a library-dependent method of tracking fecal sources of contamination of beaches on the Atlantic coast of southwestern France, a library of 6368 Escherichia coli isolates was constructed from samples of feces, from 40 known human or animal sources collected in the vicinity of Arcachon Bay in 2010, and in French Basque Country, Landes, and Beam, between 2017 and 2018. Different schemes of source identification were tested: use of the complete or filtered reference library; characterization of the isolates by genotypic or proteomic profiling based on ERIC-PCR or MALDI-TOF mass spectrometry, respectively; isolate by isolate assignment using either classifiers based on the Pearson similarity or SVM (support vector machine). With the exception of one source identification scheme, which was discarded since it used self-assignment, all tested schemes resulted in low rates of correct classification (15%). The heterogeneous coverage of E. coli genotypic diversity between sources and the uneven distribution of E. coli genotypes in the library likely explain the difficulties encountered in identifying the sources of fecal contamination. Shannon diversity index of sources ranged from 0 for several wildlife species sampled once to 3.03 for sewage treatment plant effluents sampled on various occasions, showing discrepancies between sources. The uneven genotypic composition of the library was attested by the value of the Pielou index (0.54), the high proportion of nondiscriminatory genotypes (>91% of the isolates), and the very low proportion of discriminatory genotypes (<3%). Since efforts made to constitute such a library are not affordable for routine analyses, the results question the relevance of developing such a method for identifying sources of fecal contamination on such a coastline.
dc.language.isoENen_US
dc.rights.urihttp://creativecommons.org/licenses/by/
dc.subject.enrecreational waters
dc.subject.enbathing water quality
dc.subject.enfecal indicators
dc.subject.enE. coli
dc.title.enUneven genotypic diversity of Escherichia coli in fecal sources limits the performance of a library-dependent method of microbial source tracking on the southwestern French Atlantic coast
dc.typeArticle de revueen_US
dc.identifier.doi10.1139/cjm-2020-0244en_US
dc.subject.halSciences de l'environnementen_US
bordeaux.journalCanadian Journal of Microbiologyen_US
bordeaux.page698-712en_US
bordeaux.volume66en_US
bordeaux.hal.laboratoriesEPOC : Environnements et Paléoenvironnements Océaniques et Continentaux - UMR 5805en_US
bordeaux.issue12en_US
bordeaux.institutionUniversité de Bordeauxen_US
bordeaux.institutionCNRSen_US
bordeaux.teamECOBIOCen_US
bordeaux.peerReviewedouien_US
bordeaux.inpressnonen_US
bordeaux.import.sourcehal
hal.identifierhal-03031235
hal.version1
hal.popularnonen_US
hal.audienceInternationaleen_US
hal.exportfalse
workflow.import.sourcehal
dc.rights.ccPas de Licence CCen_US
bordeaux.COinSctx_ver=Z39.88-2004&amp;rft_val_fmt=info:ofi/fmt:kev:mtx:journal&amp;rft.jtitle=Canadian%20Journal%20of%20Microbiology&amp;rft.date=2020-12&amp;rft.volume=66&amp;rft.issue=12&amp;rft.spage=698-712&amp;rft.epage=698-712&amp;rft.eissn=0008-4166&amp;rft.issn=0008-4166&amp;rft.au=GARABETIAN,%20Frederic&amp;VITTE,%20Isabelle&amp;SABOURIN,%20Antoine&amp;MOUSSARD,%20Helene&amp;JOUANILLOU,%20Adeline&amp;rft.genre=article


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