High Throughput Analysis of Integron Gene Cassettes in Wastewater Environments.
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 blaOXAwas dominant in most of the effluents, except for Cyprus and Israel where blaGESwas also abundant. Quantitative PCR assessment of blaOXAand blaGESgenes 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.
The Institute of Soil, Water and Environmental Sciences, The Volcani Center, Agricultural Research Organization, Bet-Dagan, Israel.|The Department of Soil and Water Sciences, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem , Rehovot, Israel.
Joao
J
Gatica
The Department of Soil and Water Sciences, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem , Rehovot, Israel.
Vijay
V
Tripathi
DNA Services Facility, Research Resources Center, University of Illinois at Chicago , Chicago, Illinois 60612, United States.
Stefan
S
Green
Escola Superior de Biotecnologia, Universidade Católica Portuguesa , Lisboa, Portugal.
Celia M
CM
Manaia
Faculty of Environmental Sciences, Technische Universität Dresden , Dresden, Germany.
Thomas
T
Berendonk
Faculty of Environmental Sciences, Technische Universität Dresden , Dresden, Germany.
Damiano
D
Cacace
CNRS, Laboratoire de Chimie Physique et Microbiologie pour l'Environnement (LCPME), UMR 7564, Institut Jean Barriol , 15 Avenue du Charmois, 54500 Vandoeuvre-lès-Nancy, France.|Université de Lorraine, LCPME , UMR 7564, 15 Avenue du Charmois, 54500 Vandoeuvre-lès-Nancy, France.
Christophe
C
Merlin
Institute for Water Quality, Resources and Waste Managment, Technische Universität Wien , Wien, Austria.
Norbert
N
Kreuzinger
Karlsruhe Institute of Technology , Eggenstein-Leopoldshafen, Germany.
Thomas
T
Schwartz
Department of Civil and Environmental Engineering and Nireas, International Water Research Center, University of Cyprus , P.O. Box 20537, 1678 Nicosia, Cyprus.
Despo
D
Fatta-Kassinos
Department of Civil Engineering, University of Salerno , Salerno, Italy.
Luigi
L
Rizzo
Norwegian Institute for Water Research, Oslo, Norway.
Carsten U
CU
Schwermer
School of Science and Technology, Middlesex University , London, U.K.
Hemda
H
Garelick
The Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem , Rehovot, Israel.
Edouard
E
Jurkevitch
The Institute of Soil, Water and Environmental Sciences, The Volcani Center, Agricultural Research Organization, Bet-Dagan, Israel.
Eddie
E
Cytryn
D000900:Anti-Bacterial Agents / Q000494:pharmacology; D032023:Integrons / Q000235:genetics*; D008826:Microbial Sensitivity Tests; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA; D062065:Wastewater; D018440:beta-Lactam Resistance / Q000235:genetics; D001618:beta-Lactamases / Q000378:metabolism
D000900:Anti-Bacterial Agents; D062065:Wastewater; D001618:beta-Lactamases