Dataset : Abondances of gram-negative bacteria in the environment - floodplains of the Ain, Doubs, and Loue Rivers - 2015-2016

Access to data

Rights

Collection	Bacilles à Gram négatif dans l'environnement Données de thèse Données de thèse de Charles Henriot

Quotation

Daniel Martak ; Didier Hocquet ; Charles Henriot ; Gudrun Bornette (2021): Abondances of gram-negative bacteria in the environment - floodplains of the Ain, Doubs, and Loue Rivers - 2015-2016. Laboratoire Chrono-environnement (UMR 6249). doi:10.25666/DATAOSU-2021-10-22-03

General metadata

Identifier : local : FR-18008901306731-2021-10-22-03 external : doi:10.25666/DATAOSU-2021-10-22-03

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 :

bacteriology, rivers, wetland

Dates :

Data acquisition : from Apr 2015 to Mar 2016

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

Coverages

Spatial coverage :

Longepierre: latitude 46° 55' 57" N, longitude 5° 13' 34" E
Meraton: latitude 46° 56' 10" N, longitude 5° 19' 18" E
Bras des Inglas: latitude 46° 56' 5" N, longitude 5° 22' 15" E
Charrette: latitude 46° 54' 36" N, longitude 5° 12' 35" E
Grimonts: latitude 46° 58' 13" N, longitude 5° 23' 7" E
Chemin des Creux: latitude 47° 0' 39" N, longitude 5° 38' 55" E
Chemillière: latitude 47° 0' 15" N, longitude 5° 40' 50" E
Le Baraquier: latitude 47° 0' 41" N, longitude 5° 30' 3" E
Le Clos: latitude 47° 0' 21" N, longitude 5° 33' 40" E
Sous-Bresse: latitude 45° 49' 21" N, longitude 5° 14' 32" E
Vilette Centre: latitude 45° 59' 10" N, longitude 5° 16' 57" E
Doubs - rivière: latitude 46° 55' 21" N, longitude 5° 21' 5" E
VER: latitude 47° 0' 42" N, longitude 5° 33' 39" E
Loue - rivière: latitude 47° 0' 54" N, longitude 5° 29' 41" E
VILM: latitude 45° 59' 15" N, longitude 5° 16' 57" E
Albarine: latitude 45° 58' 1" N, longitude 5° 15' 51" E
Luizard: latitude 45° 51' 27" N, longitude 5° 14' 2" E
Luizard Est: latitude 45° 51' 37" N, longitude 5° 14' 10" E
Ain - rivière: latitude 45° 57' 50" N, longitude 5° 15' 20" E

Time coverage :

Between 2015-04 and 2016-03

Taxonomic coverage :

Bactéries étudiées

Species
Escherichia coli (Escherichia coli), Klebsiella pneumoniae (Klebsiella pneumoniae), Pseudomonas aeruginosa (Pseudomonas aeruginosa)

Administrative metadata

Data creators	Affiliation
Daniel Martak	Chrono-environnement (FRA)
Didier Hocquet	Chrono-environnement (FRA)
Charles Henriot	Chrono-environnement (FRA)
Gudrun Bornette	Chrono-environnement (FRA)

Contributor	Affiliation	Role
Quentin Cuenot	Chrono-environnement (FRA)	data collector

Publisher : Laboratoire Chrono-environnement (UMR 6249)

Label : Plateforme UBFC

Science contact : Didier Hocquet

Projects and funders :

Thèse de doctorat en microbiologie environnementale - Charles Henriot
- allocation de thèse du Ministère de l'Enseignement Supérieur, de la Recherche et de l'Innovation (Ministry)
Fonctionnement des zones humides et risque sanitaire dans le contexte du changement global
- Structuring Initiative Continental and Coastal Ecosphere program (EC2CO) - INSU (CNRS)

Access : available

Technical metadata

Formats : application/vnd.ms-excel, 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; 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).

Datatype : Dataset

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)