Abstract
Propionibacterium acnes is an anaerobic Gram-positive bacterium that has been linked to a wide range of opportunistic human infections and conditions, most notably acne vulgaris (I. Kurokawa et al., Exp. Dermatol. 18:821–832, 2009). We now present the whole-genome sequences of three P. acnes strains from the type IA2 cluster which were recovered from ophthalmic infections (A. McDowell et al., Microbiology 157:1990–2003, 2011).
GENOME ANNOUNCEMENT
Propionibacterium acnes is a member of the resident microbiota on the human skin and has been linked to various infections and conditions, most notably acne vulgaris. To date, complete and draft genome sequences available for P. acnes (1, 2, 5, 6) have identified numerous virulence factors, thus highlighting the pathogenic potential of the organism. This is further supported by in vitro studies demonstrating that distinct P. acnes strains trigger the secretion of various effector molecules from numerous cell types (4, 7, 8, 13, 14).
Recently, multilocus sequence typing (MLST) identified a distinct cluster of sequence types (STs) (ST9, ST22, and ST27) within the type I clade that were provisionally classified as type IB2 pending further analysis (10). Placement in the type IB division was based on a number of observations, including the consistent presence of key core housekeeping and virulence gene sequences previously used to define type IB strains (11, 12), clustering with known type IB strains upon eBURST analysis (ST9; ST22), and infection profile, in particular an apparent lack of association with acne (10). These STs did, however, express dermatan-sulfate adhesins, a common feature of type IA strains but not of type IB, II, or III strains (10). On this basis, whole-genome sequencing was performed to ascertain the exact nature of this group and its relationship to other P. acnes organisms.
Genome sequencing of strains P.acn33 (ST9), P.acn17 (ST22), and P.acn31 (ST27) (10) was performed by SOLiD (Life Technologies) sequencing technology. We generated 43,880,983, 33,313,255, and 47,628,010 reads, respectively, which yielded >400-fold coverage. Assembly was performed using Genomics Workbench 4.8 and the Omixon Gapped SOLiD Alignment 1.3.2 plugin (3) provided by CLC Bio and Omixon, respectively. Gap closing was accomplished using PCR followed by Sanger sequencing on a 3500 genetic analyzer instrument (Life Technologies). Automatic annotation 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.
The lengths of the single circular chromosomes of the three strains are as follows: 2,489,626 bp containing 2,236 putative coding sequences (CDSs) for P.acn33; 2,522,885 bp containing 2,266 putative CDSs for P.acn17, and 2,498,766 bp containing 2,247 putative CDSs for P.acn31. Each strain has 45 tRNAs and 6 rRNA loci with a GC content of 60%.
Based on whole-genome comparisons, isolates P.acn33, P.acn17, and P.acn31 belong to the type IA division. However, due to consistent phylogenetic and genomic differences in comparisons with other type IA strains, we propose this significantly distinct cluster as type IA2, with all other type IA strains as IA1. Currently, the type IA2 grouping comprises six STs (ST2, ST22, ST23, ST24, ST36, and ST57) based on an expanded eight-locus MLST scheme. While not normally isolated from acne patients, type IA2 strains appear to be associated with ophthalmic infections, along with type IA1 and some type IB strains (10).
Nucleotide sequence accession numbers.
The complete nucleotide sequences of strains P.acn33, P.acn17, and P.acn31 have been deposited in DDBJ/EMBL/GenBank under accession numbers CP003195, CP003196, and CP003197, respectively.
ACKNOWLEDGMENTS
This work was supported by Hungarian National Office for Research and Technology Teller Program OMFB-00441/2007, French-Hungarian Associated European Laboratory (LEA) SkinChroma OMFB-00272/2009, and TÁMOP-4.2.1.B-10/2/KONV-2010-0002. A.M. was funded by the R & D office of Health and Personal Social Services Northern Ireland, and E.B. was funded by The Prostate Cancer Charity, United Kingdom.
We thank Marianna Nagymihály and Judit Cseklye for their valuable work in sequencing.
REFERENCES
- 1. Brüggemann H, et al. 2004. The complete genome sequence of Propionibacterium acnes, a commensal of human skin. Science 305:671–673 [DOI] [PubMed] [Google Scholar]
- 2. Brzuszkiewicz E, et al. 2011. Comparative genomics and transcriptomics of Propionibacterium acnes. PLoS One 6:e21581. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3. Csuros M, Juhos S, Berces A. 2010. Fast mapping and precise alignment of AB SOLiD color reads to reference DNA, p 176–188 In Proceedings of the 10th International Conference on Algorithms in Bioinformatics. Springer-Verlag, Berlin, Germany [Google Scholar]
- 4. Graham GM, Farrar MD, Cruse-Sawyer JE, Holland KT, Ingham E. 2004. Proinflammatory cytokine production by human keratinocytes stimulated with Propionibacterium acnes and P. acnes GroEL. Br. J. Dermatol. 150:421–428 [DOI] [PubMed] [Google Scholar]
- 5. Horváth B, et al. 2012. Genome sequence of Propionibacterium acnes type II strain ATCC 11828. J. Bacteriol. 194:202–203 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6. Hunyadkürti J, et al. 2011. Complete genome sequence of Propionibacterium acnes type IB strain 6609. J. Bacteriol. 193:4561–4562 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7. Jugeau S, et al. 2005. Induction of toll-like receptors by Propionibacterium acnes. Br. J. Dermatol. 153:1105–1113 [DOI] [PubMed] [Google Scholar]
- 8. Kim J, et al. 2002. Activation of toll-like receptor 2 in acne triggers inflammatory cytokine responses. J. Immunol. 169:1535–1541 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9. Kurokawa I, et al. 2009. New developments in our understanding of acne pathogenesis and treatment. Exp. Dermatol. 18:821–832 [DOI] [PubMed] [Google Scholar]
- 10. McDowell A, et al. 2011. A novel multilocus sequence typing scheme for the opportunistic pathogen Propionibacterium acnes and characterization of type I cell surface-associated antigens. Microbiology 157:1990–2003 [DOI] [PubMed] [Google Scholar]
- 11. McDowell A, Perry AL, Lambert PA, Patrick S. 2008. A new phylogenetic group of Propionibacterium acnes. J. Med. Microbiol. 57:218–224 [DOI] [PubMed] [Google Scholar]
- 12. McDowell A, et al. 2005. Propionibacterium acnes types I and II represent phylogenetically distinct groups. J. Clin. Microbiol. 43:326–334 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13. Nagy I, et al. 2006. Propionibacterium acnes and lipopolysaccharide induce the expression of antimicrobial peptides and proinflammatory cytokines/chemokines in human sebocytes. Microbes Infect. 8:2195–2205 [DOI] [PubMed] [Google Scholar]
- 14. Nagy I, et al. 2005. Distinct strains of Propionibacterium acnes induce selective human beta-defensin-2 and interleukin-8 expression in human keratinocytes through toll-like receptors. J. Invest. Dermatol. 124:931–938 [DOI] [PubMed] [Google Scholar]