Dataset : Abondances and genotypic characteristics of gram-negative bacteria in the environment - Ain River floodplain - 2019-2020

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Charles Henriot ; Didier Hocquet ; Gudrun Bornette (2021): Abondances and genotypic characteristics of gram-negative bacteria in the environment - Ain River floodplain - 2019-2020. Laboratoire Chrono-environnement (UMR 6249). doi:10.25666/DATAOSU-2021-10-22

General metadata

Identifier : local : FR-18008901306731-2021-10-22 external : doi:10.25666/DATAOSU-2021-10-22
Description :
34 sites (16 wetland sites, 15 river sites, and 3 groundwaters) distributed along the Ain River with different physicochemical characteristics were sampled. The abundances of some gram-negative bacteria (Escherichia coli, extended-spectrum beta-lactamase (ESBL)-producing E. coli, Klebsiella pneumoniae, ESBL-producing K. pneumoniae, and Pseudomonas aeruginosa) were determined. Strains of E. coli and ESBL-producing E. coli were genotypically characterized (phylogroups, plasmid incompatibility groups, resistance gene (blaESBL)).
Disciplines :
cell biology (fundamental biology), microbiology (fundamental biology), water resources (sciences of the universe)
Keywords :

Dates :
Data acquisition : from Mar 2019 to Feb 2020
Data provision : 26 Oct 2021
Metadata record :
Creation : 22 Oct 2021
Update : 26 Oct 2021

Update periodicity : no update
Language : English (eng)
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)
Audience : University: licence, University: master, Research


Spatial coverage :

Time coverage :

Taxonomic coverage :

  • Bactéries étudiées
    Escherichia coli (Escherichia coli), Klebsiella pneumoniae (Klebsiella pneumoniae), Pseudomonas aeruginosa Catalogue of Life (Pseudomonas aeruginosa)

Administrative metadata

Data creatorsAffiliation
Charles HenriotChrono-environnement (FRA)
Didier HocquetChrono-environnement (FRA)
Gudrun BornetteChrono-environnement (FRA)
Daniel MartakChrono-environnement (FRA)data collector
Alexandre MeunierChrono-environnement (FRA)data collector
Salomé GenetChrono-environnement (FRA)data collector
Emilia ChiapponiChrono-environnement (FRA)data collector
Vanessa StephaniChrono-environnement (FRA)data collector
Publisher : Laboratoire Chrono-environnement (UMR 6249)
Label : Plateforme UBFC
Science contact : Didier Hocquet website e-mail
Projects and funders :
Access : available

Technical metadata

Formats : application/, application/vnd.oasis.opendocument.spreadsheet, text/csv
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; Bréchet 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 ESBL-producing E. coli, and ESBL-producing K. pneumoniae, 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 and K. pneumoniae 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,, last consultation: 10 November 2018).
Datatype : Dataset
Terms of use