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© Michel-Robert Popoff
Clostridium difficile en microscopie à contraste de phase. On distingue des bactéries sporulées, non sporulées et d'autres en cours de lyse (destruction). Bactérie de l'environnement (sol, eau, foin, sable), elle est à l'origine d'infections nosocomiales survenant après un traitement antibiotique : Clostridium difficile prédomine alors que les autres bactéries de la flore intestinale ont été détruites. L'infection peut provoquer deux types de pathologies graves : les colites pseudo-membraneuses dont l'origine est quasiment due à 100 % à C. difficile et la diarrhée post-antibiothérapie due à C. difficile dans 30 % des cas de ces diarrhées.
Publication : BioRxiv

PhageTerm: a Fast and User-friendly Software to Determine Bacteriophage Termini and Packaging Mode using randomly fragmented NGS data

Scientific Fields
Diseases
Organisms
Applications
Technique

Published in BioRxiv - 15 Feb 2017

Garneau JR, Depardieu F, Fortier LC, Bikard D, Monot M.

Garneau JR, Depardieu F, Fortier LC, Bikard D, Monot M. 2017. PhageTerm: a Fast and User-friendly Software to Determine Bacteriophage Termini and Packaging Mode using randomly fragmented NGS data. bioRxiv doi: 10.1101/108100

Bacteriophages are the most abundant viruses on earth and display an impressive genetic as well as morphologic diversity. Among those, the most common order of phages is the Caudovirales, whose viral particles packages linear double stranded DNA (dsDNA). In this study we investigated how the information gathered by high throughput sequencing technologies can be used to determine the DNA termini and packaging mechanisms of dsDNA phages. The wet-lab procedures traditionally used for this purpose rely on the identification and cloning of restriction fragment which can be delicate and cumbersome. Here, we developed a theoretical and statistical framework to analyze DNA termini and phage packaging mechanisms using next-generation sequencing data. Our methods, implemented in the PhageTerm software, work with sequencing reads in fastq format and the corresponding assembled phage genome. PhageTerm was validated on a set of phages with well-established packaging mechanisms representative of the termini diversity: 5′cos (lambda), 3′cos (HK97), pac (P1), headful without a pac site (T4), DTR (T7) and host fragment (Mu). In addition, we determined the termini of 9 Clostridium difficile phages and 6 phages whose sequences where retrieved from the sequence read archive (SRA). A direct graphical interface is available as a Galaxy wrapper version at https://galaxy.pasteur.fr and a standalone version is accessible at https://sourceforge.net/projects/phageterm/.

http://biorxiv.org/content/early/2017/02/16/108100