Draft Genome Sequence of an Antibiotic-Resistant Propionibacterium acnes Strain, PRP-38, from the Novel Type IC Cluster

Abstract

Propionibacterium acnes, a non-spore-forming, anaerobic Gram-positive bacterium, is most notably recognized for its association with acne vulgaris (I. Kurokawa et al., Exp. Dermatol. 18:821–832, 2009). We now present the draft genome sequence of an antibiotic-resistant P. acnes strain, PRP-38, isolated from an acne patient in the United Kingdom and belonging to the novel type IC cluster.

GENOME ANNOUNCEMENT

The human skin bacterium Propionibacterium acnes has been implicated in a wide range of opportunistic infections, most notably acne vulgaris, as well as prosthetic joint infections, sarcoidosis, and prostate cancer (4, 9, 14, 17). The mainstay of acne treatment over the decades has been the administration of oral and topical antibiotics (tetracyclines, erythromycin, and clindamycin). As individual treatments can last from months to even years, it is no surprise that antibiotic-resistant strains of P. acnes have emerged (3, 12, 13, 15).

To date, complete genome sequences for seven antibiotic-sensitive P. acnes isolates have been finished (1, 2, 6, 7, 16). We now present the first draft genome sequence of an antibiotic-resistant P. acnes strain, PRP-38, isolated from a United Kingdom acne patient (MICs: tetracycline, 32 μg/ml; erythromycin, ≥256 μg/ml; clindamycin, 0.38 μg/ml). Antibiotic resistance within this strain is mediated by specific point mutations in the rRNA operon (12, 13). Resistance to tetracyclines results from a single 1058G→C transversion mutation within the 16S rRNA of the small ribosomal subunit, while resistance to erythromycin and clindamycin results from a single 2059A→G transition mutation within domain V of 23S rRNA (peptidyltransferase loop).

Genome sequencing of strain PRP-38 was performed by the SOLiD (Life Technologies) sequencing technology. We have generated 14,338,984 reads on SOLiD, which yielded >275-fold coverage. Assembly was performed using the Genomics Workbench 4.9 and the Omixon Gapped SOLiD Alignment 1.3.2 plug-in (5) provided by CLC Bio and Omixon, respectively. Gap closing was accomplished using PCR followed by Sanger sequencing. Automatic annotation of the genome was performed by the NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP) (http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html), which utilizes GeneMark, Glimmer, and tRNAscan-SE searches. We have assembled the genome of P. acnes strain PRP-38 into 12 contigs with 2,507,426 bp, 2,233 putative coding sequences, 45 tRNAs, and 9 rRNAs.

On the basis of our previously described multilocus sequence typing (MLST) scheme, PRP-38 is ST29 (10). Using an expanded eight-locus MLST scheme (A. McDowell, E. Barnard, I. Nagy, A. Gao, H. Li, S. Tomida, A. Eady, J. Cove, C. E. Nord, and S. Patrick, unpublished data), it is represented by ST70. It forms a highly distinct MLST cluster (99% bootstrap) within the large type I division along with isolates PV66 (ST85), PRP-39 (ST70), and HL097PA1 (ST70), all from acne patients in the United Kingdom and United States (all singletons). The distinct nature of this group is further supported by phylogenetic analysis of whole-genome housekeeping gene sequences (8). All isolates within this group display resistance to antiacne antibiotics resulting from 16S (1058G→C) and 23S rRNA (2058/2059A→G) point mutations, display a dual reaction with anti-type IA and -type II monoclonal antibodies (11), express dermatan sulfate-binding proteins (10), are hemolytic, and do not ferment sorbitol. Based on their phylogenetic and phenotypic characteristics and potentially important clinical relevance, we propose this group as type IC. Compared to type IA₁, IA₂, IB, and II genomes, this group contains a number of deleted regions, including hypothetical proteins and various metabolic enzymes.

Nucleotide sequence accession numbers.

This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. AIJP00000000. The version described in this paper is the first version, AIJP01000000.