High Throughput Analysis of Integron Gene Cassettes in Wastewater Environments

Joao Gatica, Vijay Tripathi, Stefan Green, Celia M. Manaia, Thomas Berendonk, Damiano Cacace, Christophe Merlin, Norbert Kreuzinger, Thomas Schwartz, Despo Fatta-Kassinos, Luigi Rizzo, Carsten U. Schwermer, Hemda Garelick, Edouard Jurkevitch, Eddie Cytryn*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

63 Scopus citations


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 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.

Original languageAmerican English
Pages (from-to)11825-11836
Number of pages12
JournalEnvironmental Science and Technology
Issue number21
StatePublished - 1 Nov 2016

Bibliographical note

Publisher Copyright:
© 2016 American Chemical Society.


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