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      Complete genome sequence of Peptoclostridium difficile strain Z31

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          Abstract

          Background

          Peptoclostridium ( Clostridium) difficile is a spore-forming bacterium responsible for nosocomial infections in humans. It is recognized as an important agent of diarrhea and colitis in several animal species and a possible zoonotic agent. Despite the known importance of P. difficile infection in humans and animals, no vaccine or other effective measure to control the disease is commercially available. A possible alternative treatment for P. difficile infection is the use of a nontoxigenic strain of P. difficile as a competitive exclusion agent. However, a thorough knowledge of this strain is necessary for this purpose. We selected P. difficile Z31, a nontoxigenic strain (PCR ribotype 009), for investigation because it prevents P. difficile infection in a hamster model.

          Results

          The genome sequence of P. difficile Z31 is a circular chromosome of 4298,263 bp, with a 29.21 % GC content, encoding 4128 proteins, and containing 78 pseudogenes. This strain belongs to ST 3, clade 1, and has five phage regions in its genome. Genes responsible for resistance to tetracycline and erythromycin were detected and more importantly, Z31 also contains genes that promote spore production and stability, cell attachment, intestinal adherence, and biofilm formation.

          Conclusion

          In this study, we present the first complete genome sequence of nontoxigenic P. difficile strain Z31. When the Z31 genome was compared with those of other isolates available in GenBank, including a draft genome of a nontoxigenic strain, several unique regions were evident. Z31 contains no toxin genes, but encodes several non-toxin virulence factors, which may favor host colonization.

          Electronic supplementary material

          The online version of this article (doi:10.1186/s13099-016-0095-3) contains supplementary material, which is available to authorized users.

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          Most cited references 52

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          SignalP 4.0: discriminating signal peptides from transmembrane regions.

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            Prokka: rapid prokaryotic genome annotation.

             T Seemann (2014)
            The multiplex capability and high yield of current day DNA-sequencing instruments has made bacterial whole genome sequencing a routine affair. The subsequent de novo assembly of reads into contigs has been well addressed. The final step of annotating all relevant genomic features on those contigs can be achieved slowly using existing web- and email-based systems, but these are not applicable for sensitive data or integrating into computational pipelines. Here we introduce Prokka, a command line software tool to fully annotate a draft bacterial genome in about 10 min on a typical desktop computer. It produces standards-compliant output files for further analysis or viewing in genome browsers. Prokka is implemented in Perl and is freely available under an open source GPLv2 license from http://vicbioinformatics.com/. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
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              PHAST: A Fast Phage Search Tool

              PHAge Search Tool (PHAST) is a web server designed to rapidly and accurately identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids. It accepts either raw DNA sequence data or partially annotated GenBank formatted data and rapidly performs a number of database comparisons as well as phage ‘cornerstone’ feature identification steps to locate, annotate and display prophage sequences and prophage features. Relative to other prophage identification tools, PHAST is up to 40 times faster and up to 15% more sensitive. It is also able to process and annotate both raw DNA sequence data and Genbank files, provide richly annotated tables on prophage features and prophage ‘quality’ and distinguish between intact and incomplete prophage. PHAST also generates downloadable, high quality, interactive graphics that display all identified prophage components in both circular and linear genomic views. PHAST is available at (http://phast.wishartlab.com).
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                Author and article information

                Contributors
                felipe@flpsw.com.br
                carlos.dirgel@hotmail.com
                rodrigo.otaviosilva@gmail.com
                fernandadorella@gmail.com
                alexficar@gmail.com
                gabriel.magno@gmail.com
                carlosleal@vet.ufmg.br
                flobato@vet.ufmg.br
                +55 31 3409 2126 , figueiredoh@yahoo.com
                Journal
                Gut Pathog
                Gut Pathog
                Gut Pathogens
                BioMed Central (London )
                1757-4749
                1 April 2016
                1 April 2016
                2016
                : 8
                Affiliations
                [1 ]National Reference Laboratory for Aquatic Animal Diseases (AQUACEN), Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, Belo Horizonte, Brazil
                [2 ]Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Brazil
                [3 ]Department of Preventive Veterinary Medicine, School of Veterinary, Federal University of Minas Gerais, Av. Antônio Carlos 6627, Pampulha, 30161-970 Belo Horizonte, MG Brazil
                Article
                95
                10.1186/s13099-016-0095-3
                5562067
                © Pereira et al. 2016

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                Categories
                Genome Report
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                © The Author(s) 2016

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