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BMC Genomics. 2015 Jan 31;16:31. doi: 10.1186/s12864-015-1252-7.

Complete genome sequence of the Clostridium difficile laboratory strain 630Δerm reveals differences from strain 630, including translocation of the mobile element CTn5.

Author information

1
Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands. e.van_eijk@lumc.nl.
2
Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands. S.Y.Anvar@lumc.nl.
3
Leiden Genome Technology Center, Human and Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands. S.Y.Anvar@lumc.nl.
4
Wellcome Trust Sanger Institute, Cambridge, Hinxton, UK. hb4@sanger.ac.uk.
5
Sequence Analysis Support Core, Leiden University Medical Center, Leiden, the Netherlands. W.Y.Leung@lumc.nl.
6
Leiden Genome Technology Center, Human and Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands. J.Frank@lumc.nl.
7
Leiden Genome Technology Center, Human and Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands. A.M.Schmitz@lumc.nl.
8
Department of Microbial Diseases, UCL Eastman Dental Institute, London, UK. adam.roberts@ucl.ac.uk.
9
Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands. w.k.smits@lumc.nl.

Abstract

BACKGROUND:

Clostridium difficile strain 630Δerm is a spontaneous erythromycin sensitive derivative of the reference strain 630 obtained by serial passaging in antibiotic-free media. It is widely used as a defined and tractable C. difficile strain. Though largely similar to the ancestral strain, it demonstrates phenotypic differences that might be the result of underlying genetic changes. Here, we performed a de novo assembly based on single-molecule real-time sequencing and an analysis of major methylation patterns.

RESULTS:

In addition to single nucleotide polymorphisms and various indels, we found that the mobile element CTn5 is present in the gene encoding the methyltransferase rumA rather than adhesin CD1844 where it is located in the reference strain.

CONCLUSIONS:

Together, the genetic features identified in this study may help to explain at least part of the phenotypic differences. The annotated genome sequence of this lab strain, including the first analysis of major methylation patterns, will be a valuable resource for genetic research on C. difficile.

PMID:
25636331
PMCID:
PMC4320837
DOI:
10.1186/s12864-015-1252-7
[Indexed for MEDLINE]
Free PMC Article

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