Beyond the Chromosome: The Prevalence of Unique Extra-Chromosomal Bacteriophages with Integrated Virulence Genes in Pathogenic Staphylococcus aureus
Figure 3
Strategy for genome sequencing of φBU01 from VISA strain NRS19 and completion of a genetic map resulting in a single circular contig.
(A) Initial 454 sequencing of an unknown ExPФ in VISA strain NRS19 was assembled relative to S. aureus bacteriophage ФNM3 (NC_008617.1) template sequence. Alignment was generated using an algorithm with default settings in MacVector Version 12.6 [30], [31]. The preliminary alignments of 454 sequencing contigs (orange arrows, Table S3 in File S1, File S2) were used as a reference to generate PCR amplifications (black bars) to be used for primer walking and to determine unknown sequences. Numbers inside orange arrows designate specific contig numbers. Primers used to generate the ExPФ sequences (numbers within black bars designate PCR product) through primer walking (Sanger) are listed in Table S2 in File S1. (B) Physical map of VISA ΦBU01. Genes in orange indicate toxins encoded on the prophage, blue indicates genes associated with DNA replication and processing, and green indicates structural, miscellaneous, and hypothetical (blank arrows) genes. A list of the genes and descriptions are in Table S6 in File S1.