Comparative genome and phenotypic analysis of three Clostridioides difficile strains isolated from a single patient provide insight into multiple infection of C. difficile.

There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

Abstract

Clostridioides difficile infections (CDI) have emerged over the past decade causing symptoms that range from mild, antibiotic-associated diarrhea (AAD) to life-threatening toxic megacolon. In this study, we describe a multiple and isochronal (mixed) CDI caused by the isolates DSM 27638, DSM 27639 and DSM 27640 that already initially showed different morphotypes on solid media.

Related collections

Most cited references 37

Record: found
Abstract: found
Article: found

Is Open Access

Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database

Tim Carver, Matthew Berriman, Adrian Tivey … (2008)

Motivation: Artemis and Artemis Comparison Tool (ACT) have become mainstream tools for viewing and annotating sequence data, particularly for microbial genomes. Since its first release, Artemis has been continuously developed and supported with additional functionality for editing and analysing sequences based on feedback from an active user community of laboratory biologists and professional annotators. Nevertheless, its utility has been somewhat restricted by its limitation to reading and writing from flat files. Therefore, a new version of Artemis has been developed, which reads from and writes to a relational database schema, and allows users to annotate more complex, often large and fragmented, genome sequences. Results: Artemis and ACT have now been extended to read and write directly to the Generic Model Organism Database (GMOD, http://www.gmod.org) Chado relational database schema. In addition, a Gene Builder tool has been developed to provide structured forms and tables to edit coordinates of gene models and edit functional annotation, based on standard ontologies, controlled vocabularies and free text. Availability: Artemis and ACT are freely available (under a GPL licence) for download (for MacOSX, UNIX and Windows) at the Wellcome Trust Sanger Institute web sites: http://www.sanger.ac.uk/Software/Artemis/ http://www.sanger.ac.uk/Software/ACT/ Contact: artemis@sanger.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.

0 comments Cited 334 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: found

Is Open Access

IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis

Bhavjinder Dhillon, Matthew R. Laird, Julie A. Shay … (2015)

IslandViewer (http://pathogenomics.sfu.ca/islandviewer) is a widely used web-based resource for the prediction and analysis of genomic islands (GIs) in bacterial and archaeal genomes. GIs are clusters of genes of probable horizontal origin, and are of high interest since they disproportionately encode genes involved in medically and environmentally important adaptations, including antimicrobial resistance and virulence. We now report a major new release of IslandViewer, since the last release in 2013. IslandViewer 3 incorporates a completely new genome visualization tool, IslandPlot, enabling for the first time interactive genome analysis and gene search capabilities using synchronized circular, horizontal and vertical genome views. In addition, more curated virulence factors and antimicrobial resistance genes have been incorporated, and homologs of these genes identified in closely related genomes using strict filters. Pathogen-associated genes have been re-calculated for all pre-computed complete genomes. For user-uploaded genomes to be analysed, IslandViewer 3 can also now handle incomplete genomes, with an improved queuing system on compute nodes to handle user demand. Overall, IslandViewer 3 represents a significant new version of this GI analysis software, with features that may make it more broadly useful for general microbial genome analysis and visualization.

0 comments Cited 167 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: not found

Evolutionary dynamics of Clostridium difficile over short and long time scales.

Miao He, Mohammed Sebaihia, Trevor D. Lawley … (2010)

Clostridium difficile has rapidly emerged as the leading cause of antibiotic-associated diarrheal disease, with the transcontinental spread of various PCR ribotypes, including 001, 017, 027 and 078. However, the genetic basis for the emergence of C. difficile as a human pathogen is unclear. Whole genome sequencing was used to analyze genetic variation and virulence of a diverse collection of thirty C. difficile isolates, to determine both macro and microevolution of the species. Horizontal gene transfer and large-scale recombination of core genes has shaped the C. difficile genome over both short and long time scales. Phylogenetic analysis demonstrates C. difficile is a genetically diverse species, which has evolved within the last 1.1-85 million years. By contrast, the disease-causing isolates have arisen from multiple lineages, suggesting that virulence evolved independently in the highly epidemic lineages.

0 comments Cited 159 times – based on 0 reviews      Review now

Bookmark

All references

Author and article information

Journal

Journal ID (iso-abbrev): BMC Genomics

Title: BMC genomics

Publisher: Springer Science and Business Media LLC

ISSN (Electronic): 1471-2164

ISSN (Print): 1471-2164

Publication date (Electronic): January 02 2018

Volume: 19

Issue: 1

Affiliations

[1 ] Institute for Medical Microbiology, University Medical Center Göttingen, Göttingen, Germany.

[2 ] Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany.

[3 ] Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.

[4 ] German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany.

[5 ] Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany. hlieseg@gwdg.de.

Article

Publisher Item ID: 10.1186/s12864-017-4368-0

DOI: 10.1186/s12864-017-4368-0

PMC ID: 5749029

PubMed ID: 29291715

SO-VID: 4f180cf8-6e71-4f4d-acf0-805611811a65

History

Keywords: Genetic switch,Clostridium difficile,Clostridioides difficile,Multiple infection,Horizontal gene transfer,Genomic adaptation

Data availability:

Keywords: Genetic switch, Clostridium difficile, Clostridioides difficile, Multiple infection, Horizontal gene transfer, Genomic adaptation

Comparative genome and phenotypic analysis of three Clostridioides difficile strains isolated from a single patient provide insight into multiple infection of C. difficile.

Read this article at

Abstract

Related collections

Decoding Infection and Transmission

Most cited references 37

Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database

IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis

Evolutionary dynamics of Clostridium difficile over short and long time scales.

Author and article information

Journal

Affiliations

Article

History

Comments

Comment on this article

Similar content 23

Cited by 194

Most referenced authors 778