High Throughput Analysis of Integron Gene Cassettes in Wastewater Environments
Manaia, C. M.
Berendonk, Thomas U.
Schwermer, Carsten U.
SourceEnvironmental science & technology
Google Scholar check
MetadataShow full item record
Integrons 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 &beta-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 &beta-lactam resistance. Among the reads characterized as &beta-lactamases, the carbapenemase bla^sub OXA^ was dominant in most of the effluents, except for Cyprus and Israel where blaGES was also abundant. Quantitative PCR assessment of bla^sub OXA^ and bla^sub GES^ 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 &beta-lactamase genes in effluent-saturated soils, suggesting marginal persistence in the soil microbiome.