Browsing by Author "Berendonk, Thomas"
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- High throughput analysis of integron gene cassettes in wastewater environmentsPublication . Gatica, Joao; Tripathi, Vijay; Green, Stefan; Manaia, Célia M.; Berendonk, Thomas; Cacace, Damiano; Merlin, Christophe; Kreuzinger, Norbert; Schwartz, Thomas; Fatta-Kassinos, Despo; Rizzo, Luigi; Schwermer, Carsten U.; Garelick, Hemda; Jurkevitch, Edouard; Cytryn, EddieIntegrons are extensively targeted as a proxy for anthropogenic impact in the environment. We developed a novel high-throughput amplicon sequencing pipeline that enables characterization of thousands of integron gene cassette-associated reads, and applied it to acquire a comprehensive overview of gene cassette composition in effluents from wastewater treatment facilities across Europe. Between 38 100 and 172 995 reads per-sample were generated and functionally characterized by screening against nr, SEED, ARDB and β-lactamase databases. Over 75% of the reads were characterized as hypothetical, but thousands were associated with toxin-antitoxin systems, DNA repair, cell membrane function, detoxification and aminoglycoside and β-lactam resistance. Among the reads characterized as β-lactamases, the carbapenemase blaOXA was dominant in most of the effluents, except for Cyprus and Israel where blaGES was also abundant. Quantitative PCR assessment of blaOXA and blaGES genes in the European effluents revealed similar trends to those displayed in the integron amplicon sequencing pipeline described above, corroborating the robustness of this method and suggesting that these integron-associated genes may be excellent targets for source tracking of effluents in downstream environments. Further application of the above analyses revealed several order-of-magnitude reductions in effluent-associated β-lactamase genes in effluent-saturated soils, suggesting marginal persistence in the soil microbiome.
- Making wavesPublication . Alygizakis, Nikiforos; Ng, Kelsey; Čirka, Ľuboš; Berendonk, Thomas; Cerqueira, Francisco; Cytryn, Eddie; Deviller, Geneviève; Fortunato, Gianuario; Iakovides, Iakovos C.; Kampouris, Ioannis; Michael-Kordatou, Irene; Lai, Foon Yin; Lundy, Lian; Manaia, Celia M.; Marano, Roberto B. M.; Paulus, Gabriela K.; Piña, Benjamin; Radu, Elena; Rizzo, Luigi; Ślipko, Katarzyna; Kreuzinger, Norbert; Thomaidis, Nikolaos S.; Ugolini, Valentina; Vaz-Moreira, Ivone; Slobodnik, Jaroslav; Fatta-Kassinos, DespoWith the global concerns on antibiotic resistance (AR) as a public health issue, it is pivotal to have data exchange platforms for studies on antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in the environment. For this purpose, the NORMAN Association is hosting the NORMAN ARB&ARG database, which was developed within the European project ANSWER. The present article provides an overview on the database functionalities, the extraction and the contribution of data to the database. In this study, AR data from three studies from China and Nepal were extracted and imported into the NORMAN ARB&ARG in addition to the existing AR data from 11 studies (mainly European studies) on the database. This feasibility study demonstrates how the scientific community can share their data on AR to generate an international evidence base to inform AR mitigation strategies. The open and FAIR data are of high potential relevance for regulatory applications, including the development of emission limit values / environmental quality standards in relation to AR. The growth in sharing of data and analytical methods will foster collaboration on risk management of AR worldwide, and facilitate the harmonization in the effort for identification and surveillance of critical hotspots of AR. The NORMAN ARB&ARG database is publicly available at: https://www.norman-network.com/nds/bacteria/.