TY - JOUR
T1 - High Throughput Analysis of Integron Gene Cassettes in Wastewater Environments
AU - Gatica, Joao
AU - Tripathi, Vijay
AU - Green, Stefan
AU - Manaia, Celia M.
AU - Berendonk, Thomas
AU - Cacace, Damiano
AU - Merlin, Christophe
AU - Kreuzinger, Norbert
AU - Schwartz, Thomas
AU - Fatta-Kassinos, Despo
AU - Rizzo, Luigi
AU - Schwermer, Carsten U.
AU - Garelick, Hemda
AU - Jurkevitch, Edouard
AU - Cytryn, Eddie
N1 - Publisher Copyright:
© 2016 American Chemical Society.
PY - 2016/11/1
Y1 - 2016/11/1
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=84993927168&partnerID=8YFLogxK
U2 - 10.1021/acs.est.6b03188
DO - 10.1021/acs.est.6b03188
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C2 - 27689892
AN - SCOPUS:84993927168
SN - 0013-936X
VL - 50
SP - 11825
EP - 11836
JO - Environmental Science and Technology
JF - Environmental Science and Technology
IS - 21
ER -