Genome Sequence and Analysis of aPropionibacterium acnesBacteriophage

Abstract

Cutaneous propionibacteria are important commensals of human skin and are implicated in a wide range of opportunistic infections. Propionibacterium acnes is also associated with inflammatory acne vulgaris. Bacteriophage PA6 is the first phage of P. acnes to be sequenced and demonstrates a high degree of similarity to many mycobacteriophages both morphologically and genetically. PA6 possesses an icosahedreal head and long noncontractile tail characteristic of the Siphoviridae. The overall genome organization of PA6 resembled that of the temperate mycobacteriophages, although the genome was much smaller, 29,739 bp (48 predicted genes), compared to, for example, 50,550 bp (86 predicted genes) for the Bxb1 genome. PA6 infected only P. acnes and produced clear plaques with turbid centers, but it lacked any obvious genes for lysogeny. The host range of PA6 was restricted to P. acnes, but the phage was able to infect and lyse all P. acnes isolates tested. Sequencing of the PA6 genome makes an important contribution to the study of phage evolution and propionibacterial genetics.

The diversity and host interactions of Propionibacterium acnes bacteriophages on human skin

“…On average 45 open reading frames were predicted in each genome. Consistent with previous reports (Farrar et al, 2007;Lood and Collin, 2011;Marinelli et al, 2012), these open reading frames were arranged compactly within the left and right arm regions of the genome (Figure 1, Supplementary Figure S2). Our analysis of the 48 new phage genomes supports the annotation of the gp22/gp23 locus as a single open reading frame (495 to 522 bp) on the minus strand (Supplementary Figure S2).…”

“…Our rate of phage detection (24% of investigated samples) is similar to those previously reported, ranging from 26 to 30% (Marples et al, 1973;Puhvel and Amirian, 1979). The phages that we isolated have the morphology of siphoviruses as previously described (Farrar et al, 2007). A representative electron micrograph is shown in Supplementary Figure S1.…”

“…The ratio between P. acnes phages and P. acnes was~1:20 in pilosebaceous units, based on a pooled healthy skin sample that we analyzed previously (Fitz-Gibbon et al, 2013), but can vary in a large range among individuals and over time. P. acnes phages do not encode integrases in their genomes (Farrar et al, 2007;Lood and Collin, 2011), suggesting their inability to stably integrate into the host chromosome. They can kill the host bacteria through cell lysis or can enter a pseudolysogenic state in the host strain (Lood and Collin, 2011), in which the phage DNA persists in infected cells without lysing the host or integrating into its genome.…”

“…However, in the past decades, the study of P. acnes phages had been limited to the development of phage typing systems to distinguish different serotypes of P. acnes (Jong et al, 1975;Webster and Cummins, 1978). Recent sequencing of 14 P. acnes phages (Farrar et al, 2007;Lood and Collin, 2011;Marinelli et al, 2012) suggested that they have limited genetic diversity with over 85% nucleotide identity in the genome. All sequenced genomes are similar in size and structure with 45-47 genes encoded in two oppositely transcribed regions named the left arm and right arm (Farrar et al, 2007;Lood and Collin, 2011;Marinelli et al, 2012).…”

“…It has been known for over 50 years that P. acnes phages exist on the human skin (Brzin, 1964). They have the morphology of siphoviruses, consisting of a~50 nm icosahedral head and ã 150 nm flexible tail (Farrar et al, 2007). Zierdt et al, (1968) isolated phage 174 from spontaneous plaques of a P. acnes isolate.…”