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The complete genome sequence of Clostridium difficile phage C2 and comparisons to CD119 and inducible prophages of CD630

Shan Goh^1,

Keang Peng Song^1,

¹ National University of Singapore, Yong Loo Lin School of Medicine, Department of Microbiology, 5 Science Drive 2, #05-03, 117597, Singapore
² Microbiology and Immunology, School of Biomedical, Biomolecular and Chemical Sciences, The University of Western Australia, Queen Elizabeth II Medical Centre, Nedlands, WA 6009, Australia
³ Division of Microbiology and Infectious Diseases, The Western Australian Centre for Pathology and Medical Research, Nedlands, WA 6009, Australia

Correspondence
Barbara J. Chang
bchang{at}cyllene.uwa.edu.au

The complete genomic sequence of a previously characterized temperate phage of Clostridium difficile, C2, is reported. The genome is 56 538 bp and organized into 84 putative ORFs in six functional modules. The head and tail structural proteins showed similarities to that of C. difficile phage CD119 and Streptococcus pneumoniae phage EJ-1, respectively. Homologues of structural and replication proteins were found in prophages 1 and 2 of the sequenced C. difficile CD630 genome. A putative holin appears unique to the C. difficile phages and was functional when expressed in Escherichia coli. Nucleotide sequence comparisons of C2 to CD119 and the CD630 prophage sequences showed relatedness between C2 and the prophages, but less so to CD119. C2 integrated into a gene encoding a putative transcriptional regulator of the gntR family. C2, CD119 and CD630 prophage 1 genomes had a Cdu1-attP-integrase arrangement, suggesting that the pathogenicity locus (PaLoc) of C. difficile, flanked by cdu1, has phage origins. The attP sequences of C2, CD119 and CD630 prophages were dissimilar. C2-related sequences were found in 84 % of 37 clinical C. difficile isolates and typed reference strains.

The GenBank accession number for the sequence reported in this paper is DQ466086.

A supplementary table and figure are available with the online version of this paper.

Present address: Department of Cell and Molecular Biology, Programme for Genomics and Bioinformatics, Karolinska Institutet, Berzelius väg 35, SE-171 77 Stockholm, Sweden.

Present address: School of Arts and Sciences, Monash University Malaysia, No. 2 Jalan Kolej, Bandar Sunway, Petaling Jaya 46150, Selangor Darul Ehsan, Malaysia.

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