Bacterial Skin Isolates againstLimited Genetic Diversity and Broad Killing Activity Bacteriophages Display Propionibacterium acnes 2012

Investigation of the human microbiome has revealed diverse and complex microbial communities at distinct anatomic sites. The microbiome of the human sebaceous follicle provides a tractable model in which to study its dominant bacterial inhabitant, Propionibacterium acnes, which is thought to contribute to the pathogenesis of the human disease acne. To explore the diversity of the bacteriophages that infect P. acnes, 11 P. acnes phages were isolated from the sebaceous follicles of donors with healthy skin or acne and their genomes were sequenced. Comparative genomic analysis of the P. acnes phage population, which spans a 30-year temporal period and a broad geographic range, reveals striking similarity in terms of genome length, percent GC content, nucleotide identity (>85%), and gene content. This was unexpected, given the far-ranging diversity observed in virtually all other phage populations. Although the P. acnes phages display a broad host range against clinical isolates of P. acnes, two bacterial isolates were resistant to many of these phages. Moreover, the patterns of phage resistance correlate closely with the presence of clustered regularly interspaced short palindromic repeat elements in the bacteria that target a specific subset of phages, conferring a system of prokaryotic innate immunity. The limited diversity of the P. acnes bacteriophages, which may relate to the unique evolutionary constraints imposed by the lipid-rich anaerobic environment in which their bacterial hosts reside, points to the potential utility of phage-based antimicrobial therapy for acne. IMPORTANCE Propionibacterium acnes is a dominant member of the skin microflora and has also been implicated in the pathogenesis of acne; however, little is known about the bacteriophages that coexist with and infect this bacterium. Here we present the novel genome sequences of 11 P. acnes phages, thereby substantially increasing the amount of available genomic information for this phage population. Surprisingly, we find that, unlike other well-studied bacteriophages, P. acnes phages are highly homogeneous and show a striking lack of genetic diversity, which is perhaps related to their unique and restricted habitat. They also share a broad ability to kill clinical isolates of P. acnes; phage resistance is not prevalent, but when detected, it appears to be conferred by chromosomally encoded immunity elements within the host genome. We believe that these phages display numerous features that would make them ideal candidates for the development of a phage-based therapy for acne. Received 16 August 2012 Accepted 17 August 2012 Published 25 September 2012 Citation Marinelli LJ, et al. 2012. Propionibacterium acnes bacteriophages display limited genetic diversity and broad killing activity against bacterial skin isolates. mBio 3(5): e00279-12. doi:10.1128/mBio.00279-12. Editor Julian Davies, University of British Columbia Copyright © 2012 Marinelli et al. This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-Share Alike 3.0 Unported License, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited. Address correspondence to Graham F. Hatfull, gfh@pitt.edu. The investigation of the microbiome at specific anatomic sites is essential toward understanding the pathogenesis of disease and the development of targeted therapies. In such microbial communities, there is an interaction between bacterial populations and the bacteriophages that infect them. These viruses influence bacterial community structure and function by several mechanisms, including their ability to kill their bacterial hosts and/or mediate genetic exchange that can increase diversity and potentially disseminate virulence genes. Virtually all of the bacteriophage populations that have been studied display a wide range of genetic diversity (1), including those that infect Mycobacterium (2–5), Staphylococcus (6, 7) and Pseudomonas (8, 9) species. The Gram-positive skin commensal Propionibacterium acnes is the dominant inhabitant of the human pilosebaceous unit (10), an invagination within the human epidermis containing a hair follicle, hair shaft, erector pili muscle, and associated sebaceous glands, which produce sebum. Despite its ubiquitous presence on the skin, P. acnes is also thought to play a major role in the pathogenesis of acne vulgaris, in part by eliciting a host inflammatory response (11). There is a significant increase in P. acnes colonization at puberty, the time during which acne commonly develops, and teenagers with acne can have as many as 100-fold more P. acnes bacteria present on their skin than healthy, age-matched counterparts (12). The efficacy of antibiotics for acne treatment is related to the reduction of the number of P. acnes bacteria on the skin, as well as to direct anti-inflammatory properties (13), which RESEARCH ARTICLE September/October 2012 Volume 3 Issue 5 e00279-12 ® mbio.asm. org 1 m b.asm . rg on O cber 4, 2012 P ubished by m b.asm . rg D ow nladed fom