title: Identification of antimicrobial resistant bacteria in rivers: insights into the cultivation bias.
abstract: In the present study, the antimicrobial resistant (AR) bacteria were quantified and identified in different river samples using in parallel a culture-based approach and a culture-independent one. The objective was to evaluate the importance of the cultivation bias when studying antimicrobial resistance among environmental bacteria. Three different river samples covering a gradient of anthropic influence were tested and three different antimicrobial compounds were used as selective agents: amoxicillin, tetracycline and sulfamethoxazole. From a quantitative point of view, our results highlight the importance of the culture media used, as for the same sample and the same selective agent significant differences were observed in the counts of culturable AR bacteria depending on the culture media used. The identification of AR bacteria through culture or culture-independent methods put on evidence AR bacterial communities that differ dramatically: γ-proteobacteria and more specifically Aeromonadaceae dominated among the isolates while β-proteobacteria (Comamonadaceae), dominated among the sequences obtained without culture. Altogether these results highlight the necessity to develop a methodological consensus preferably without culture, to approach this important topic in the coming years.
authors.affiliation: Ecologie des Systèmes Aquatiques, Université Libre de Bruxelles, Campus de la Plaine, CP 221, Boulevard du Triomphe, 1050 Brussels, Belgium. tgarciaa@ulb.ac.be
authors.forename: Tamara
authors.initials: T
authors.lastname: Garcia-Armisen
authors.forename: Adriana
authors.initials: A
authors.lastname: Anzil
authors.forename: Pierre
authors.initials: P
authors.lastname: Cornelis
authors.forename: Marc
authors.initials: M
authors.lastname: Chevreuil
authors.forename: Pierre
authors.initials: P
authors.lastname: Servais
mesh_terms: D044044:Aeromonadaceae / Q000302:isolation & purification; D000900:Anti-Bacterial Agents / Q000032:analysis; D001431:Bacteriological Techniques / Q000379:methods*; D020562:Betaproteobacteria / Q000235:genetics; D003470:Culture Media; D058645:Denaturing Gradient Gel Electrophoresis / Q000379:methods; D024881:Drug Resistance, Bacterial; D005602:France; D020563:Gammaproteobacteria / Q000235:genetics; D008826:Microbial Sensitivity Tests; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012336:RNA, Ribosomal, 16S; D045483:Rivers / Q000382:microbiology*; D012722:Sewage; D014871:Water Microbiology; D014876:Water Pollution
chemical_list: D000900:Anti-Bacterial Agents; D003470:Culture Media; D012336:RNA, Ribosomal, 16S; D012722:Sewage
keywords: Antimicrobial resistance; Antimicrobials; Bacterial community composition; Sewage polluted river