Comparative phage genomics of family <I>Siphoviridae</I> in <I>Staphylococcus aureus</I>
| Authors | |
|---|---|
| Year of publication | 2004 |
| Type | Article in Proceedings |
| Conference | 11th International Symposium on Staphylococci & Staphylococcal Infections. Plenary Summaries & Poster Abstracts |
| MU Faculty or unit | |
| Citation | |
| Web | http://www.isssi.org/ |
| Field | Genetics and molecular biology |
| Keywords | staphylococcus; bacteriophage |
| Description | The family Siphoviridae includes temperate bacteriophages that play an important role in biology of this species, usually changing its phenotype as a result of lysogenic conversion associated with some virulence factors. Understanding of bacteriophage carriage is important not only from an overall genomics standpoint concerning evolution and virulence of the bacterial strains but also in determination of a high genomic variability in S. aureus. In this work eighteen complete S. aureus temperate phage and prophage genomes of Siphoviridae were compared and classified into phage types. Thirteen complete phage sequences were obtained from GenBank database. The sequence of prophage resident in strain COL and those of MRSA strain 252 and MSSA strain 476 designated phi252A, phi252B, phi476A and phi476B were extracted from preliminary sequence data obtained from TIGR website (http://www.tigr.org/tdb/mdb/ mdbinprogress.html) and from the Sanger Institute (ftp://ftp.sanger.ac.uk/pub/pathogens/sa/), respectively. Bioinformatics tools for local and global sequence alignment, dot-plot matrix analysis and comparison of ORF maps were used for classification of phages. Comparison of phage DNA sequences present in S. aureus genomes revealed high diversity and mosaicism resulting from recombination and horizontal transfer of DNA. Based on sequence similarity the phages were classified as 3A-like phages, 11-like phages and 77-like phages. These phage groups represent tentative staphylococcal phage species of the Siphoviridae family. Conserved genomic sequences distinctive of the proposed phage species 3A, 11, 77, representative of phage serogroups A, B, F, were identified, characterized and verified in additional phage strains. They coding for tail structural proteins or tail fibers. Global DNA sequence alignment of finished S. aureus bacteriophage genomes indicated only four universally conserved DNA regions present in all staphylococcal phages and prophages classified into species 3A, 11 or 77. The search of sequences over 50 bp with 65% identity revealed: (i) a noncoding 57 bp sequence with 95% identity between the integrase (int) and excisionase (xis) genes, containing a putative regulatory site with two highly conserved inverted repeats; (ii) a 178 bp sequence of ÖPVL ORF38-homolog with 89% identity, but in some phages with noncoding function; (iii) a 125 bp conserved sequence inside rinB gene with 87% identity; and (iv) a noncoding 60 bp region with 82% identity upstream the site in which genes encoding staphylococcal enterotoxin A (sea) or P (sep) integrate. PCR primers designed for the above genes and DNA sequences were used for development of a multiplex PCR assay which enabled us not only to classify phages, but also to detect prophages in S. aureus genomes. Comparative analysis of phage genome sequences provided the basis for their taxonomic classification. In addition, prophage profiling performed by selective hybridization or multiplex PCR can be a new approach to S. aureus typing. |
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