Genomic Characterization of 2 Cutibacterium acnes Isolates from a Surgical Site Infection Reveals Large Genomic Inversion

Main Article Content

D. Garrett Brown
Taylor A. Wahlig
Angela Ma
Laura K. Certain
Peter N. Chalmers
Mark A. Fisher
Daniel T. Leung


Background: Cutibacterium acnes is a common commensal of human skin but may also present as an opportunistic pathogen in prosthetic joint and wound infections. Unfortunately, few complete genomes of C. acnes are publicly available, and even fewer are of isolates associated with infection. Here we report the isolation, characterization, and complete genomes of 2 C. acnes isolates from a surgical site infection of an elbow.

Methods: We used standard microbiological methods for phenotypic characterization and performed whole genome sequencing on 2 C. acnes isolates using a combination of short-read and long-read sequencing. 

Results: Antibiotic susceptibility testing showed beta-lactamase negative and low minimal inhibitory concentrations to all antibiotics tested, with the exception of metronidazole. We assembled complete genomes of the 2 isolates, which are approximately 2.5 megabases in length. The isolates belong to the single-locus sequence type (SLST) H1 and the multi-locus sequence type (MLST) IB. Both isolates have similar composition of known virulence genes, and we found no evidence of plasmids but did find phage-associated genes. Notably, the 2 genomes are 99.97% identical but contain a large genomic inversion encompassing approximately half of the genome.

Conclusions: This is the first characterization of this large-scale genomic inversion in nearly identical isolates from the same wound. This report adds to the limited numbers of publicly available infection-associated complete genomes of C. acnes.


Download data is not yet available.

Article Details



1. McLaughlin J, Watterson S, Layton AM, Bjourson AJ, Barnard E, McDowell A. Propionibacterium acnes and Acne Vulgaris: New Insights from the Integration of Population Genetic, Multi-Omic, Biochemical and Host-Microbe Studies. Microorganisms. 2019;7(5). doi: 10.3390/microorganisms7050128. PubMed PMID: 31086023; PMCID: PMC6560440.

2. McDowell A, Barnard E, Nagy I, Gao A, Tomida S, Li H, Eady A, Cove J, Nord CE, Patrick S. An expanded multilocus sequence typing scheme for propionibacterium acnes: investigation of ‘pathogenic’, ‘commensal’ and antibiotic resistant strains. PLoS One. 2012;7(7):e41480. doi: 10.1371/journal.pone.0041480. PubMed PMID: 22859988; PMCID: PMC3408437.

3. Lee J, Greenwood Quaintance KE, Schuetz AN, Shukla DR, Cofield RH, Sperling JW, Patel R, Sanchez-Sotelo J. Correlation between hemolytic profile and phylotype of Cutibacterium acnes (formerly Propionibacterium acnes) and orthopedic implant infection. Shoulder Elbow. 2020;12(6):390-8. doi: 10.1177/1758573219865884. PubMed PMID: 33281943; PMCID: PMC7689609.

4. Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34(17):i884-i90. doi: 10.1093/bioinformatics/bty560. PubMed PMID: 30423086; PMCID: PMC6129281.

5. Shen W, Le S, Li Y, Hu F. SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation. PLoS One. 2016;11(10):e0163962. doi: 10.1371/journal.pone.0163962. PubMed PMID: 27706213; PMCID: PMC5051824.

6. Shakya M, Ahmed SA, Davenport KW, Flynn MC, Lo CC, Chain PSG. Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life. Sci Rep. 2020;10(1):1723. doi: 10.1038/s41598-020-58356-1. PubMed PMID: 32015354; PMCID: PMC6997174.

7. Huerta-Cepas J, Serra F, Bork P. ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data. Mol Biol Evol. 2016;33(6):1635-8. doi: 10.1093/molbev/msw046. PubMed PMID: 26921390; PMCID: PMC4868116.

8. Jolley KA, Bray JE, Maiden MCJ. Open-access bacterial population genomics: BIGSdb software, the website and their applications. Wellcome Open Res. 2018;3:124. doi: 10.12688/wellcomeopenres.14826.1. PubMed PMID: 30345391; PMCID: PMC6192448.

9. Scholz CF, Jensen A, Lomholt HB, Bruggemann H, Kilian M. A novel high-resolution single locus sequence typing scheme for mixed populations of Propionibacterium acnes in vivo. PLoS One. 2014;9(8):e104199. doi: 10.1371/journal.pone.0104199. PubMed PMID: 25111794; PMCID: PMC4128656.

10. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357-9. doi: 10.1038/nmeth.1923. PubMed PMID: 22388286; PMCID: PMC3322381.

11. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Genome Project Data Processing S. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. PubMed PMID: 19505943; PMCID: PMC2723002.

12. Kasimatis G, Fitz-Gibbon S, Tomida S, Wong M, Li H. Analysis of complete genomes of Propionibacterium acnes reveals a novel plasmid and increased pseudogenes in an acne associated strain. Biomed Res Int. 2013;2013:918320. doi: 10.1155/2013/918320. PubMed PMID: 23762865; PMCID: PMC3666418.

13. Khassebaf J, Hellmark B, Davidsson S, Unemo M, Nilsdotter-Augustinsson A, Soderquist B. Antibiotic susceptibility of Propionibacterium acnes isolated from orthopaedic implant-associated infections. Anaerobe. 2015;32:57-62. doi: 10.1016/j.anaerobe.2014.12.006. PubMed PMID: 25541476.

14. Huang F, Xiao L, Gao M, Vallely EJ, Dybvig K, Atkinson TP, Waites KB, Chong Z. B-assembler: a circular bacterial genome assembler. BMC Genomics. 2022;23(Suppl 4):361. doi: 10.1186/s12864-022-08577-7. PubMed PMID: 35546658; PMCID: PMC9092672.

15. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013;29(8):1072-5. doi: 10.1093/bioinformatics/btt086. PubMed PMID: 23422339; PMCID: PMC3624806.

16. Guo J, Bolduc B, Zayed AA, Varsani A, Dominguez-Huerta G, Delmont TO, Pratama AA, Gazitua MC, Vik D, Sullivan MB, Roux S. VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses. Microbiome. 2021;9(1):37. doi: 10.1186/s40168-020-00990-y. PubMed PMID: 33522966; PMCID: PMC7852108.

17. Brzuszkiewicz E, Weiner J, Wollherr A, Thurmer A, Hupeden J, Lomholt HB, Kilian M, Gottschalk G, Daniel R, Mollenkopf HJ, Meyer TF, Bruggemann H. Comparative genomics and transcriptomics of Propionibacterium acnes. PLoS One. 2011;6(6):e21581. doi: 10.1371/journal.pone.0021581. PubMed PMID: 21738717; PMCID: PMC3124536.

18. Arndt D, Grant JR, Marcu A, Sajed T, Pon A, Liang Y, Wishart DS. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res. 2016;44(W1):W16-21. doi: 10.1093/nar/gkw387. PubMed PMID: 27141966; PMCID: PMC4987931.

19. Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS. PHAST: a fast phage search tool. Nucleic Acids Res. 2011;39(Web Server issue):W347-52. doi: 10.1093/nar/gkr485. PubMed PMID: 21672955; PMCID: PMC3125810.

20. Salar-Vidal L, Achermann Y, Aguilera-Correa JJ, Poehlein A, Esteban J, Bruggemann H, On Behalf Of The Escmid Study Group For Implant-Associated Infections E. Genomic Analysis of Cutibacterium acnes Strains Isolated from Prosthetic Joint Infections. Microorganisms. 2021;9(7). doi: 10.3390/microorganisms9071500. PubMed PMID: 34361935; PMCID: PMC8307888.

21. Bruggemann H, Henne A, Hoster F, Liesegang H, Wiezer A, Strittmatter A, Hujer S, Durre P, Gottschalk G. The complete genome sequence of Propionibacterium acnes, a commensal of human skin. Science. 2004;305(5684):671-3. doi: 10.1126/science.1100330. PubMed PMID: 15286373.

22. Cobian N, Garlet A, Hidalgo-Cantabrana C, Barrangou R. Comparative Genomic Analyses and CRISPR-Cas Characterization of Cutibacterium acnes Provide Insights Into Genetic Diversity and Typing Applications. Front Microbiol. 2021;12:758749. doi: 10.3389/fmicb.2021.758749. PubMed PMID: 34803983; PMCID: PMC8595920.

23. Sorensen M, Mak TN, Hurwitz R, Ogilvie LA, Mollenkopf HJ, Meyer TF, Bruggemann H. Mutagenesis of Propionibacterium acnes and analysis of two CAMP factor knock-out mutants. J Microbiol Methods. 2010;83(2):211-6. doi: 10.1016/j.mimet.2010.09.008. PubMed PMID: 20850482.

24. Nodzo SRH, D. W.; John K Crane, J. K.; Duquin, T. R. Hemolysis as a clinical marker for propionibacterium acnes orthopedic infection. The American Journal of Orthopedics. 2014;43(5):E93-E7. PubMed PMID: 24839635.

25. Savic DJ, Nguyen SV, McCullor K, McShan WM. Biological Impact of a Large-Scale Genomic Inversion That Grossly Disrupts the Relative Positions of the Origin and Terminus Loci of the Streptococcus pyogenes Chromosome. J Bacteriol. 2019;201(17). doi: 10.1128/JB.00090-19. PubMed PMID: 31235514; PMCID: PMC6689312.

26. Guerillot R, Kostoulias X, Donovan L, Li L, Carter GP, Hachani A, Vandelannoote K, Giulieri S, Monk IR, Kunimoto M, Starrs L, Burgio G, Seemann T, Peleg AY, Stinear TP, Howden BP. Unstable chromosome rearrangements in Staphylococcus aureus cause phenotype switching associated with persistent infections. Proc Natl Acad Sci U S A. 2019;116(40):20135-40. doi: 10.1073/pnas.1904861116. PubMed PMID: 31527262; PMCID: PMC6778178.

Most read articles by the same author(s)