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      The mosaic architecture of Aeromonas salmonicida subsp. salmonicida pAsa4 plasmid and its consequences on antibiotic resistance

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          Abstract

          Aeromonas salmonicida subsp. salmonicida, the causative agent of furunculosis in salmonids, is an issue especially because many isolates of this bacterium display antibiotic resistances, which limit treatments against the disease. Recent results suggested the possible existence of alternative forms of pAsa4, a large plasmid found in A. salmonicida subsp. salmonicida and bearing multiple antibiotic resistance genes. The present study reveals the existence of two newly detected pAsa4 variants, pAsa4b and pAsa4c. We present the extensive characterization of the genomic architecture, the mobile genetic elements and the antimicrobial resistance genes of these plasmids in addition to the reference pAsa4 from the strain A449. The analysis showed differences between the three architectures with consequences on the content of resistance genes. The genomic plasticity of the three pAsa4 variants could be partially explained by the action of mobile genetic elements like insertion sequences. Eight additional isolates from Canada and Europe that bore similar antibiotic resistance patterns as pAsa4-bearing strains were genotyped and specific pAsa4 variants could be attributed to phenotypic profiles. pAsa4 and pAsa4c were found in Europe, while pAsa4b was found in Canada. In accordance with their content in conjugative transfer genes, only pAsa4b and pAsa4c can be transferred by conjugation in Escherichia coli. The plasticity of pAsa4 variants related to the acquisition of antibiotic resistance indicates that these plasmids may pose a threat in terms of the dissemination of antimicrobial-resistant A. salmonicida subsp. salmonicida bacteria.

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          Most cited references39

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          ISfinder: the reference centre for bacterial insertion sequences

          ISfinder () is a dedicated database for bacterial insertion sequences (ISs). It has superseded the Stanford reference center. One of its functions is to assign IS names and to provide a focal point for a coherent nomenclature. It is also the repository for ISs. Each new IS is indexed together with information such as its DNA sequence and open reading frames or potential coding sequences, the sequence of the ends of the element and target sites, its origin and distribution together with a bibliography where available. Another objective is to continuously monitor ISs to provide updated comprehensive groupings or families and to provide some insight into their phylogenies. The site also contains extensive background information on ISs and transposons in general. Online tools are gradually being added. At present an online Blast facility against the entire bank is available. But additional features will include alignment capability, PsiBLAST and HMM profiles. ISfinder also includes a section on bacterial genomes and is involved in annotating the IS content of these genomes. Finally, this database is currently recommended by several microbiology journals for registration of new IS elements before their publication.
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            Improved tools for biological sequence comparison.

            We have developed three computer programs for comparisons of protein and DNA sequences. They can be used to search sequence data bases, evaluate similarity scores, and identify periodic structures based on local sequence similarity. The FASTA program is a more sensitive derivative of the FASTP program, which can be used to search protein or DNA sequence data bases and can compare a protein sequence to a DNA sequence data base by translating the DNA data base as it is searched. FASTA includes an additional step in the calculation of the initial pairwise similarity score that allows multiple regions of similarity to be joined to increase the score of related sequences. The RDF2 program can be used to evaluate the significance of similarity scores using a shuffling method that preserves local sequence composition. The LFASTA program can display all the regions of local similarity between two sequences with scores greater than a threshold, using the same scoring parameters and a similar alignment algorithm; these local similarities can be displayed as a "graphic matrix" plot or as individual alignments. In addition, these programs have been generalized to allow comparison of DNA or protein sequences based on a variety of alternative scoring matrices.
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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
                PeerJ
                PeerJ
                PeerJ
                PeerJ
                PeerJ
                PeerJ Inc. (San Francisco, USA )
                2167-8359
                27 October 2016
                2016
                : 4
                : e2595
                Affiliations
                [1 ]Institut de biologie intégrative et des systèmes , Québec, Canada
                [2 ]Institut universitaire de cardiologie et de pneumologie de Québec , Québec, Canada
                [3 ]Département de biochimie, de microbiologie et de bio-informatique, Université Laval , Québec, Canada
                [4 ]Groupe de recherche en écologie buccale (GREB), Université Laval , Québec, Canada
                Article
                2595
                10.7717/peerj.2595
                5088629
                27812409
                58ab817b-83d6-49ab-a690-b933e5b3e1ad
                © 2016 Tanaka et al.

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.

                History
                : 21 May 2016
                : 21 September 2016
                Funding
                Funded by: Fonds de la recherche québécois sur la nature et les technologies (FRQNT) scholarships (B1 to KHT and B2 to ATV)
                Funded by: Natural Sciences and Engineering Research Council of Canada (NSERC) scholarships (Alexander Graham Bell Canada Graduate Scholarships to KHT and ATV) and grant (Discovery grant RGPIN-2014-04595) to SJC
                Funded by: Ressources Aquatiques Québec (RAQ) (CREATE scholarship to MVT and a grant to MF)
                Funded by: The Innovamer Program of the Ministère de l’Agriculture, des Pêcheries et de l’Alimentation du Québec
                This work was supported by the Fonds de la recherche québécois sur la nature et les technologies (FRQNT) (B1 scholarship to KHT and B2 scholarship to ATV), the Natural Sciences and Engineering Research Council of Canada (NSERC) (Alexander Graham Bell Canada Graduate Scholarships to KHT and ATV and Discovery grant RGPIN-2014-04595 to SJC), Ressources Aquatiques Québec (RAQ) (CREATE scholarship to MVT and a grant to MF), and the Innovamer Program of the Ministère de l’Agriculture, des Pêcheries et de l’Alimentation du Québec. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Aquaculture, Fisheries and Fish Science
                Genomics
                Marine Biology
                Microbiology

                aeromonas salmonicida subsp. salmonicida,plasmid,pasa4,insertion sequence,integron,comparative genomics,chloramphenicol,sulfonamide,tetracycline,antibiotic resistance

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