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      Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution

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          Abstract

          Around all human activity, there are zones of pollution with pesticides, heavy metals, pharmaceuticals, personal care products and the microorganisms associated with human waste streams and agriculture. This diversity of pollutants, whose concentration varies spatially and temporally, is a major challenge for monitoring. Here, we suggest that the relative abundance of the clinical class 1 integron-integrase gene, intI1, is a good proxy for pollution because: (1) intI1 is linked to genes conferring resistance to antibiotics, disinfectants and heavy metals; (2) it is found in a wide variety of pathogenic and nonpathogenic bacteria; (3) its abundance can change rapidly because its host cells can have rapid generation times and it can move between bacteria by horizontal gene transfer; and (4) a single DNA sequence variant of intI1 is now found on a wide diversity of xenogenetic elements, these being complex mosaic DNA elements fixed through the agency of human selection. Here we review the literature examining the relationship between anthropogenic impacts and the abundance of intI1, and outline an approach by which intI1 could serve as a proxy for anthropogenic pollution.

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          Most cited references85

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          Sampling the antibiotic resistome.

          Microbial resistance to antibiotics currently spans all known classes of natural and synthetic compounds. It has not only hindered our treatment of infections but also dramatically reshaped drug discovery, yet its origins have not been systematically studied. Soil-dwelling bacteria produce and encounter a myriad of antibiotics, evolving corresponding sensing and evading strategies. They are a reservoir of resistance determinants that can be mobilized into the microbial community. Study of this reservoir could provide an early warning system for future clinically relevant antibiotic resistance mechanisms.
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            Antibiotic resistance genes as emerging contaminants: studies in northern Colorado.

            This study explores antibiotic resistance genes (ARGs) as emerging environmental contaminants. The purpose of this study was to investigate the occurrence of ARGs in various environmental compartments in northern Colorado, including Cache La Poudre (Poudre) River sediments, irrigation ditches, dairy lagoons, and the effluents of wastewater recycling and drinking water treatment plants. Additionally, ARG concentrations in the Poudre River sediments were analyzed at three time points at five sites with varying levels of urban/agricultural impact and compared with two previously published time points. It was expected that ARG concentrations would be significantly higher in environments directly impacted by urban/agricultural activity than in pristine and lesser-impacted environments. Polymerase chain reaction (PCR) detection assays were applied to detect the presence/absence of several tetracycline and sulfonamide ARGs. Quantitative real-time PCR was used to further quantify two tetracycline ARGs (tet(W) and tet(O)) and two sulfonamide ARGs (sul(I) and sul(II)). The following trend was observed with respect to ARG concentrations (normalized to eubacterial 16S rRNA genes): dairy lagoon water > irrigation ditch water > urban/agriculturally impacted river sediments (p < 0.0001), except for sul(II), which was absent in ditch water. It was noted that tet(W) and tet(O) were also present in treated drinking water and recycled wastewater, suggesting that these are potential pathways for the spread of ARGs to and from humans. On the basis of this study, there is a need for environmental scientists and engineers to help address the issue of the spread of ARGs in the environment.
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              Integrons: agents of bacterial evolution.

              Integrons are assembly platforms - DNA elements that acquire open reading frames embedded in exogenous gene cassettes and convert them to functional genes by ensuring their correct expression. They were first identified by virtue of their important role in the spread of antibiotic-resistance genes. More recently, our understanding of their importance in bacterial genome evolution has broadened with the discovery of larger integron structures, termed superintegrons. These DNA elements contain hundreds of accessory genes and constitute a significant fraction of the genomes of many bacterial species. Here, the basic biology of integrons and superintegrons, their evolutionary history and the evidence for the existence of a novel recombination pathway is reviewed.
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                Author and article information

                Journal
                ISME J
                ISME J
                The ISME Journal
                Nature Publishing Group
                1751-7362
                1751-7370
                June 2015
                12 December 2014
                1 June 2015
                : 9
                : 6
                : 1269-1279
                Affiliations
                [1 ]Department of Biological Sciences, Genes to Geoscience Research Centre, Macquarie University , Sydney, New South Wales, Australia
                [2 ]European Centre for Environment and Human Health, University of Exeter Medical School, Royal Cornwall Hospital , Truro, UK
                [3 ]Via Department of Civil and Environmental Engineering, Virginia Tech , Blacksburg, VA, USA
                [4 ]Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants , Braunschweig, Germany
                [5 ]Center for Microbial Ecology, Michigan State University , East Lansing, MI, USA
                [6 ]Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences , Xiamen, China
                Author notes
                [* ]Department of Biological Sciences, Macquarie University , Sydney, New South Wales 2109, Australia. E-mail: michael.gillings@ 123456mq.edu.au
                Article
                ismej2014226
                10.1038/ismej.2014.226
                4438328
                25500508
                cd74754b-a589-4ad7-ad79-20a20f85aaf0
                Copyright © 2015 International Society for Microbial Ecology

                This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-nd/3.0/

                History
                : 13 July 2014
                : 18 September 2014
                : 23 October 2014
                Categories
                Perspective

                Microbiology & Virology
                Microbiology & Virology

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