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

Publication: Canadian Journal of Microbiology30 July 2020https://doi.org/10.1139/cjm-2020-0244

Abstract

To 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 Béarn, 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 (<35%) and significant rates of incorrect 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.

Résumé

Pour développer et standardiser une méthode d’identification des sources de contamination fécale dite collection dépendante destinée à la surveillance de l’ensemble des plages du littoral atlantique du sud-ouest de la France, une collection de référence de 6368 isolats d’Escherichia coli a été constituée à partir d’échantillons de fèces, issus de 40 sources humaines ou animales connues, prélevés dans le voisinage immédiat du Bassin d’Arcachon, en 2010, et dans le Pays basque français, les Landes et le Béarn, entre 2017 et 2018. Différents scénarios d’identification des sources ont été testés : utilisation de la collection de référence complète ou filtrée; caractérisation des isolats par leur profil génotypique réalisé par ERIC-PCR, ou protéomique réalisé par MALDI-TOF MS; assignation par différents classificateurs basés sur la similarité de Pearson ou par une technique d’apprentissage machine (machine learning), le SVM (Séparateur à Vaste Marge). À l’exception d’un scénario, écarté puisqu’il s’avère recourir à l’autoassignation, tous les scénarios testés aboutissent à de faibles taux de classifications correctes (<35 %) et d’importants taux de classifications incorrectes (>15 %). L’hétérogénéité de la diversité génotypique des E. coli entre sources et la non-équitabilité de la collection recueillie expliqueraient les difficultés rencontrées pour identifier les sources de contamination. La valeur de l’indice de Shannon variable entre 0, pour différentes sources aviaires échantillonnées une seule fois, et 3,03 pour les effluents de stations d’épuration régulièrement échantillonnés, témoigne de fortes différences entre sources. La valeur de l’indice de Pielou (0,54), la très forte proportion de génotypes non discriminants (>91 % de la collection d’isolats) et la très faible proportion de génotypes discriminants (<3 %) montrent que la composition génotypique de la collection est non équitable alors que les efforts consentis pour constituer une telle collection sont difficilement envisageables pour des suivis de routine. Ces résultats questionnent la pertinence de développer une telle méthode pour l’identification des sources de contamination fécale à l’échelle d’une aussi grande façade littorale.
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Canadian Journal of Microbiology cover image
Canadian Journal of Microbiology
Volume 66Number 12December 2020
Pages: 698 - 712

History

Received: 22 May 2020
Revision received: 24 July 2020
Accepted: 27 July 2020
Published online: 30 July 2020

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Key Words

  1. recreational waters
  2. bathing water quality
  3. fecal indicators
  4. E. coli

Mots-clés

  1. eaux de loisirs
  2. qualité des eaux de baignade
  3. indicateurs fécaux
  4. E. coli

Authors

Affiliations

Frédéric Garabetian frederic.garabetian@u-bordeaux.fr
Université de Bordeaux, CNRS, EPOC, EPHE, UMR 5805, F-33600 Pessac, France.
Isabelle Vitte
Laboratoires des Pyrénées et des Landes, F-64150 Lagor, France.
Antoine Sabourin
Université de Bordeaux, CNRS, EPOC, EPHE, UMR 5805, F-33600 Pessac, France.
Laboratoires des Pyrénées et des Landes, F-64150 Lagor, France.
Hélène Moussard
Université de Bordeaux, CNRS, EPOC, EPHE, UMR 5805, F-33600 Pessac, France.
Adeline Jouanillou
Laboratoires des Pyrénées et des Landes, F-64150 Lagor, France.
Line Mornet
Université de Bordeaux, CNRS, EPOC, EPHE, UMR 5805, F-33600 Pessac, France.
Mélanie Lesne
Laboratoires des Pyrénées et des Landes, F-64150 Lagor, France.
Emilie Lyautey
Université Savoie Mont Blanc, INRAE, CARRTEL, 74200 Thonon-les-Bains, France.

Notes

Copyright remains with authors F. Garabetian, A. Sabourin, H. Moussard, L. Mornet, E. Lyautey, and with Laboratoires des Pyrénées et des Landes. Permission for reuse (free in most cases) can be obtained from copyright.com.

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