Exfoliative toxin A (ETA)-coding temperate bacteriophages are the main contributors to the toxic phenotype of impetigo strains of Staphylococcus aureus. Two eta gene-positive phages were isolated from S. aureus strains which were implicated in massive outbreaks of neonatal vesiculate infections in several Czech maternity hospitals. Phages designated phiB166 and phiB236 were characterized in detail to elucidate their genome diversity.

Both the phages were able to incorporate their genomes into the chromosome of a prophageless S. aureus strain which afterwards converted into an exfoliative toxin A producer. Complete phage genome sequences were determined and annotated. Besides identification of all coding ORFs, promoters and intrinsic terminators were predicted. With respect to the functional genomic architecture, the genomes were divided into five regions. The comparative analysis revealed major variances between the phages. They differed in the genome size, number of open reading frames (ORFs) and genome architecture. Many non-homologous and unique sequences located in the genomes were identified. High mutual sequence similarity was detected only in the terminal region. In addition, proteomic analysis, based on the SDS-PAGE, showed major differences between capsid compounds.

Conclusive sequence analyses revealed that phiB166 and phiB236 are not closely related to each other or to other previously reported eta or non eta phages. Sequences gained by possible recombination were identified in genomes of both phages. Thus, these phages represent the recent new lineages of as yet undescribed ETA-converting bacteriophages. Their genomic mosaicism reveals them as a fluid gene pool to confer new properties to co-replicating phages and also as mediators of the S. aureus pathogenicity.