Abondances of gram-negative bacteria in the environment - floodplains of the Ain, Doubs, and Loue Rivers - 2015-2016 (2021)

Data creators : Daniel Martak [1] [2], Didier Hocquet [1] [2], Charles Henriot [1] [2], Gudrun Bornette [1] [2]
Data collector : Quentin Cuenot [1] [2]
[1] : Laboratoire Chrono-environnement (UMR 6249) (Université de Franche-Comté)
[2] : Observatoire des Sciences de l'Univers - Terre, Homme, Environnement, Temps, Astronomie (UAR 3245) (Université de Franche-Comté)
Description :
19 sites (16 wetlands and 3 rivers) with different physicochemical characteristics and distributed along three rivers (Ain, Doubs, and Loue) were sampled. The abundances of some gram-negative bacteria (Escherichia coli, extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa) were determined.
Disciplines :
microbiology (fundamental biology), water resources (sciences of the universe)
Keywords :

General metadata

Data acquisition date : from Apr 2015 to Mar 2016
Data acquisition methods :
  • Observational data :
    Samples of water (250 ml) were collected in sterile conditions and stored at 4◦C before analysis, which occurred within 8 h of collection. The total concentrations of E. coli, K. pneumoniae and
    P. aeruginosa were measured as previously described (Slekovec et al. 2012; Brechet ´ et al. 2014). Aliquots of water (100 ml) were filtered through 0.45-μm membranes, which were then placed onto a Drigalski agar plate to measure the total E. coli and K. pneumoniae concentrations (Oxoid), a Cetrimide agar plate to measure the P. aeruginosa concentration (Bio-Rad) and a chromID ESBL agar plate to measure the concentration of E. coli producing extended-spectrum beta-lactamases (ESBL), which are resistant to β-lactam antibiotics. When we suspected high bacterial concentrations, we plated 500 μl an additional of sample on the selective media. The plates were incubated for 24 h at 37◦C. Colonies were counted and classified according to their phenotype. Each type of colony was identified using a MALDITOF MS spectrometer (Microflex, Bruker Daltonics, Bremen, Germany) according to the manufacturer’s recommendations. For each morphotype of E. coli growing on chromID ESBL, the production of ESBL was detected using a synergy test following the recommendations of the Antibiogram Committee of the French Society for Microbiology (CA-SFM, http://www.sfm-microbiologie.org/, last consultation: 10 November 2018).
Update periodicity : no update
Language : English (eng)
Formats : application/vnd.ms-excel, application/vnd.oasis.opendocument.spreadsheet, text/csv
Audience : University: licence, University: master, Research


Spatial coverage :

19 entries

Time coverage :

Taxonomic coverage :

  • Bactéries étudiées
    Escherichia coli TAXREF (Escherichia coli), Klebsiella pneumoniae TAXREF (Klebsiella pneumoniae), Pseudomonas aeruginosa COL (Pseudomonas aeruginosa)
Publications :
  • Occurrence and ecological determinants of the contamination of floodplain wetlands with Klebsiella pneumoniae and pathogenic or antibiotic-resistant Escherichia coli (doi:10.1093/femsec/fiz097)
  • Déterminismes environnementaux de la diffusion et de la survie des bacilles à Gram négatif commensaux et pathogènes dans les hydrosystèmes (hal:tel-03643429)
Label : Plateforme UBFC
Projects and funders :
Additional information :
Data acquired during Charles Henriot's PhD work, supervised by Pr. Didier Hocquet (University Professor - Hospital practitioner at the Chrono-environment laboratory) and Dr. Gudrun Bornette (Researcher in ecology at the Chrono-environment laboratory)
Record created 22 Oct 2021 by Charles Henriot.
Last modification : 7 Apr 2023.
Local identifier: FR-18008901306731-2021-10-22-03.


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Terms of use
Université de Bourgogne, Université de Franche-Comté, UTBM, AgroSup Dijon, ENSMM, BSB, Arts des Metiers