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High Throughput Analysis of Integron Gene Cassettes in Wastewater Environments
journal contribution
posted on 2016-09-30, 00:00 authored by 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 CytrynIntegrons
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.
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Keywords
novel high-throughput amplicon sequencing pipelinesoil microbiome172 995bla GES genesβ- lactamase databasesEuropean effluentsgene cassette compositioneffluent-associated β- lactamase genesDNA repairanthropogenic impacttoxin-antitoxin systemsQuantitative PCR assessmentIntegron Gene CassettesWastewater Environments Integrons38 100bla OXAHigh Throughput Analysisintegron amplicon sequencing pipelinethousandbla GESintegron gene cassette-associatedcell membrane functionβ- lactamasesβ- lactam resistanceeffluent-saturated soilscarbapenemase bla OXAorder-of-magnitude reductionsintegron-associated genesARDBwastewater treatment facilities
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