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      The role of biofilms as environmental reservoirs of antibiotic resistance

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          Abstract

          Antibiotic resistance has become a significant and growing threat to public and environmental health. To face this problem both at local and global scales, a better understanding of the sources and mechanisms that contribute to the emergence and spread of antibiotic resistance is required. Recent studies demonstrate that aquatic ecosystems are reservoirs of resistant bacteria and antibiotic resistance genes as well as potential conduits for their transmission to human pathogens. Despite the wealth of information about antibiotic pollution and its effect on the aquatic microbial resistome, the contribution of environmental biofilms to the acquisition and spread of antibiotic resistance has not been fully explored in aquatic systems. Biofilms are structured multicellular communities embedded in a self-produced extracellular matrix that acts as a barrier to antibiotic diffusion. High population densities and proximity of cells in biofilms also increases the chances for genetic exchange among bacterial species converting biofilms in hot spots of antibiotic resistance. This review focuses on the potential effect of antibiotic pollution on biofilm microbial communities, with special emphasis on ecological and evolutionary processes underlying acquired resistance to these compounds.

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          Most cited references88

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          Search and clustering orders of magnitude faster than BLAST.

          Biological sequence data is accumulating rapidly, motivating the development of improved high-throughput methods for sequence classification. UBLAST and USEARCH are new algorithms enabling sensitive local and global search of large sequence databases at exceptionally high speeds. They are often orders of magnitude faster than BLAST in practical applications, though sensitivity to distant protein relationships is lower. UCLUST is a new clustering method that exploits USEARCH to assign sequences to clusters. UCLUST offers several advantages over the widely used program CD-HIT, including higher speed, lower memory use, improved sensitivity, clustering at lower identities and classification of much larger datasets. Binaries are available at no charge for non-commercial use at http://www.drive5.com/usearch.
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            Fast and sensitive protein alignment using DIAMOND.

            The alignment of sequencing reads against a protein reference database is a major computational bottleneck in metagenomics and data-intensive evolutionary projects. Although recent tools offer improved performance over the gold standard BLASTX, they exhibit only a modest speedup or low sensitivity. We introduce DIAMOND, an open-source algorithm based on double indexing that is 20,000 times faster than BLASTX on short reads and has a similar degree of sensitivity.
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              The comprehensive antibiotic resistance database.

              The field of antibiotic drug discovery and the monitoring of new antibiotic resistance elements have yet to fully exploit the power of the genome revolution. Despite the fact that the first genomes sequenced of free living organisms were those of bacteria, there have been few specialized bioinformatic tools developed to mine the growing amount of genomic data associated with pathogens. In particular, there are few tools to study the genetics and genomics of antibiotic resistance and how it impacts bacterial populations, ecology, and the clinic. We have initiated development of such tools in the form of the Comprehensive Antibiotic Research Database (CARD; http://arpcard.mcmaster.ca). The CARD integrates disparate molecular and sequence data, provides a unique organizing principle in the form of the Antibiotic Resistance Ontology (ARO), and can quickly identify putative antibiotic resistance genes in new unannotated genome sequences. This unique platform provides an informatic tool that bridges antibiotic resistance concerns in health care, agriculture, and the environment.
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                Author and article information

                Contributors
                Journal
                Front Microbiol
                Front Microbiol
                Front. Microbiol.
                Frontiers in Microbiology
                Frontiers Media S.A.
                1664-302X
                31 October 2015
                2015
                : 6
                : 1216
                Affiliations
                [1] 1Catalan Institute for Water Research Girona, Spain
                [2] 2Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona Girona, Spain
                Author notes

                Edited by: Maurizio Labbate, University of Technology Sydney, Australia

                Reviewed by: Michael R. Twiss, Clarkson University, USA; Hans-Peter Grossart, IGB-Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Germany

                *Correspondence: José L. Balcázar, jlbalcazar@ 123456icra.cat

                This article was submitted to Aquatic Microbiology, a section of the journal Frontiers in Microbiology

                Article
                10.3389/fmicb.2015.01216
                4628128
                26583011
                5f48d8bf-385e-4f39-a406-335bfc3e0c5b
                Copyright © 2015 Balcázar, Subirats and Borrego.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 09 June 2015
                : 19 October 2015
                Page count
                Figures: 1, Tables: 1, Equations: 0, References: 85, Pages: 9, Words: 0
                Funding
                Funded by: Seventh Framework Programme 10.13039/501100004963
                Award ID: 603629-ENV-2013-6.2.1-GLOBAQUA
                Categories
                Microbiology
                Review

                Microbiology & Virology
                aquatic ecosystems,biofilms,mobile genetic elements,antibiotic resistance genes,aquatic resistome

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