DOI: 10.25666/dataosu-2021-10-22
title: Abondances and genotypic characteristics of gram-negative bacteria in the environment - Ain River floodplain - 2019-2020
title: Abondances et caractéristiques génotypiques des bacilles à Gram négatif dans l'environnement - plaine alluviale de l'Ain - 2019-2020

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)).
description: 34 sites (16 sites de zones humides, 15 sites de rivières et 3 eaux souterraines) répartis le long de l'Ain et présentant différentes caractéristiques physico-chimiques ont été échantillonnés. Les abondances de certains bacilles à Gram négatif (Escherichia coli, E. coli producteur de bêta-lactamase à spectre étendu (BLSE), Klebsiella pneumoniae, K. pneumoniae producteur de BLSE, et Pseudomonas aeruginosa) ont été déterminées. Les souches d'E. coli et d'E. coli productrices de BLSE ont été caractérisées génotypiquement (phylogroupes, groupes d'incompatibilité plasmidique, gène de résistance (blaBLSE)).
description: Audience: University: master, Research, University: licence
description: UpdatePeriodicity: no update
description: Project: Thèse de doctorat de Charles Henriot, Contrat doctoral Ministère de l'Enseignement Supérieur, de la Recherche et de l'Innovation (MESRI) (Ministry)
description: Project: Fonctionnement des zones humides et risque sanitaire dans le contexte du changement global, Structuring Initiative Continental and Coastal Ecosphere program (EC2CO) - INSU (CNRS)
description: Project: Fonctionnement des hydrosystèmes et risque pathogène, Osez l'interdisciplinarité ! - INEE (CNRS)
description: Label: Plateforme UBFC (Plateforme UBFC)
description: 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, http://www.sfm-microbiologie.org/, last consultation: 10 November 2018).