The characteristics of lysogenized PVL phage We determined the nucleotide sequence of a PVL phage lysogenized in a PVL-positive CA-MRSA strain, JCSC7401, isolated in 2006. The strain belonged to ST80 and carried nontypeable SCCmec (NT-B). This phi7401PVL was 45,334 bp in length from the rightmost phage attachment site (attP-R) to the leftmost site (attP-L), in which 44 predicted ORFs larger than 99 bp were identified. The core sequences of 29 nucleotides were located at both ends of phi7401PVL. The G+C content of phi7401PVL was 33.2%, and was comparable to other staphylococcal phages. The overall organization of phi7401PVL was the same as that of previously-reported #buy RG-7388 randurls[1|1|,|CHEM1|]# PVL

phages, which consisted of five regions relating to 1) lysogeny, 2) DNA replication/transcriptional regulation, 3) structural modules (the packaging/head and tail), 4) the lysis module, and 5) lukS-PV Selleckchem OSI-906 and lukF-PV (Figure

1a). The phage was highly homologous to phiSa2mw, which belongs to group 2 of sfi21-like Siphoviridae (Figure 1a and 1b). The entire genome of the phage showed nucleotide identity of more than 95% to that of phiSa2mw. Forty-two of the 44 ORFs were highly homologous to those of phiSa2mw, with the nucleotide identities ranging from 91-100% (Additional file 1: Table S1). The int gene was truncated, although it was highly homologous to extant PVL phages. Two ORFs, TUP03 encoding Na/K ATPase and TUP16 encoding dUTPase, were less homologous to phiSa2mw. Figure 1 a. Structural comparisons of the PVL phages. Structures of phi7401PVL and phiSa2mw are illustrated based on the nucleotide sequences deposited in databases DDBJ/EMBL/GenBank under accession nos. BA000033 for phiSa2mw and AP012341 RVX-208 for phi7401PVL. Red arrowhead indicates the location of attP. Black bars indicate the locus of amplified DNA fragments using 5 sets of primers. Green bars indicate the locus of amplified

DNA fragment identifying the carriage of gene linkages in phi7401PVL. ORFs are colored as follows: orange, ORFs related to lysogeny; red, a ORF in DNA replication/recombination region with assigned functions; bright green, ORFs related to capsid formation; yellowish orange, ORFs related to head formation; yellowish green, ORFs related to tail formation; blue, ORFs related to cell lysis; black, lukS-PV and lukF-PV. The locations of the primers are indicated in lines flanked by arrow heads. Nucleotide sequences of the primers are listed in Additional file 2: Table S2. b. Comparisons of the two phage genomes with a dot plot analysis. The genome sequence of phi7401PVL was compared to those of phiPVL (group 1 cos-site Siphoviridae), phiSa2mw (group 2 cos-site Siphoviridae), and phiN315 (group 3 cos-site Siphoviridae) using a specialized BLAST at NIBI (http://​blast.​ncbi.​nlm.​nih.​gov/​Blast.​cgi). Ordinate indicates the genome phi7401PVL.