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Complete genome sequence of Cutibacterium acnes KCOM 1315 isolated from a human jaw osteomyelitis lesion
Korean J. Microbiol 2019;55(1):64-66
Published online March 31, 2019
© 2019 The Microbiological Society of Korea.

Soon-Nang Park1,†, Jeong-Hwan Park2,†, Yun Kyong Lim1, Ja Young Shin3, Hanseong Roh3, and Joong-Ki Kook1,*

1Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju 61452, Republic of Korea
2School of Dentistry, Chosun University, Gwangju 61452, Republic of Korea
3Macrogen Inc., Seoul 08511, Republic of Korea
Correspondence to: E-mail: jkkook@chosun.ac.kr;
Tel.: +82-62-230-6877; Fax: +82-62-224-3706
Received November 21, 2018; Revised December 19, 2018; Accepted December 20, 2018.
Abstract

Cutibacterium acnes is a member of normal flora of human skin, conjunctiva, intestinal tract, the external auditory canal as well as oral cavity. It has been identified as an opportunistic pathogen related to acne vulagris, endocarditis infections, sarcoidosis, brain abscess, periodontitis, and osteomyelitis of the humerus. C. acnes KCOM 1315 (= ChDC KB81) was isolated from a human jaw osteomyelitis lesion. Here, we present the complete genome sequence of C. acnes KCOM 1315.

Keywords : Cutibacterium acnes, human, jaw osteomyelitis
Body

Cutibacterium acnes is Gram-positive, anaerobic, aerotolerant, diphtheroid, and rod-shaped bacterium. C. acnes is a member of normal flora of human skin, conjunctiva, intestinal tract, the external auditory canal as well as oral cavity (McDowell et al., 2013; Scholz and Kilian, 2016; Aubin et al., 2017). It has been reported that C. acnes was identified as an opportunistic pathogen related to acne vulgaris (Leyden, 2001), endodontic infections (Niazi et al., 2016), endocarditis (Günthard et al., 1994), sarcoidosis (Zhou et al., 2013), periodontitis (Narita et al., 2016), brain abscess (Zaffiri et al., 2013), and osteomyelitis of the humerus (Sainani et al., 2015). C. acnes KCOM 1315 (= ChDC KB81) was isolated from a human jaw osteomyelitis lesion. In this report, we present the complete genome sequence of C. acnes KCOM 1315.

The C. acnes KCOM 1315 was grown on tryptic soy agar (TSA; BD Difco Laboratories) supplemented with 5% sheep blood in an anaerobic chamber (Model Bactron I) maintained using a gas mixture of 10% H2, 5% CO2, and 85% N2. The bacterial genomic DNA was prepared as previously described (Cho et al., 2015).

The genomic DNA of C. acnes KCOM 1315 was sequenced using PacBio RSII SMRT sequencing platform using a 20 kb SMRTbell template library and Illumina HiSeq 2500 by Macrogen Inc. Approximately 1,509 Mb (589 ×) with 181,833 filtered subreads (mean subreads length 8,302 bp) were generated and assembled into a single contig by HGAP (version: 3.0, default setting) in PacBio’s SMRT portal (http://www.pacb.com/products-and-services/analytical-software/smrt-analysis). The initial assembly was polished by Pilon (version: 1.21) with 13,154,086 paired-end reads (518 ×, trimmed by trimmomatic 0.36) from Illumina Hiseq 2500 (https://github.com/broadinstitute/pilon/wiki) (Walker et al., 2014). The pilon fixed 33 INDELs and most of errors were A/T insertions or G/C deletions. Genome annotation was conducted by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (https://www.ncbi.nlm.nih.gov/genome/annotation_prok/) (Tatusova et al., 2016).

The complete genome of C. acnes KCOM 1315 was 2,560,301 bp in length and had a G+C content of 60.0%. A total of 2,368 protein-coding sequences (CDSs), 9 rRNAs, and 47 tRNAs were annotated (Table 1 and Fig. 1).

Genome features of Cutibacterium acnes KCOM 1315

Attribute Value
Genome size (bp) 2,087,706
GC content (%) 27.2
No. of contigs 1
Total genes 2,027
Protein-coding genes 1,885
tRNA 47
Complete rRNA (5S, 16S, 23S) 15 (5, 5, 5)
ncRNA 3
Pseudogene 77

Fig. 1.

Circular map of genome of Cutibacterium acnes KCOM 1315. Marked characteristics are shown from outside to the center; CDS on forward strand, CDS on reverse strand, tRNA, rRNA, GC content, and GC skew.



The genome sequence contained antibiotic-resistance-related genes; macrolide export ATP-binding/permease protein MacB, multiple antibiotic resistance protein MarR/MdtG, metallo- beta-lactamase type 2, multidrug resistance protein Stp, putative multidrug resistance ABC transporter ATP-binding/permease protein YheI, putative multidrug-efflux transporter, and multidrug efflux protein YfmO. It contained several protease genes; ATP- dependent zinc metalloprotease FtsH, tricorn protease, zinc metalloprotease Rip1, Lon protease, extracellular basic protease, rhomboid protease AarA, putative zinc protease, periplasmic serine endoprotease DegP, serine protease, and protease Hflk. The genome encoded for involving the biofilm formation, putative glycosyltransferase EpsJ and biofilm regulatory protein A. The genome contained the oxidative stress-response genes such as superoxide dismutase (Mn/Fe), thioredoxin-2, catalase, thioredoxin reductase, and thiol-disulfide oxidoreductase ResA. The genome also contained the two-component systems (MtrB/ MtrA and VraR/LiaS). Hemolysin C, diphtheria toxin repressor, hemolysin C, antitoxin YqcF, and putative antitoxin VapB12, putative sialic acid transporter and outer membrane porin F were founded in the genome sequence.

The C. acnes KCOM 1315 strain was deposited into the Korean Collection for Oral Microbiology.

Nucleotide sequence accession number

This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession CP031442. The version described in this paper is version CP031442.1.

적 요

Cutibacterium acnes는 사람의 피부, 결막, 장관, 외이도 및 구강의 정상 세균 총의 하나이다. 이 세균 종은 여드름, 심내막염 감염, 유육종증, 뇌 농양, 치주염 및 골수염과 관련된 기회감염성병원균으로 확인되었다. C. acnes KCOM 1315 (= ChDC KB81)는 사람 악골골수염 병소로부터 분리되었다. 여기에서 C. acnes KCOM 1315 균주 완전 유전체 염기서열을 해독하여 보고한다.

Acknowledgements

This research was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (No. 2018R1A2B5002239).

References
  1. Aubin GG, Lavigne JP, Foucher Y, Dellière S, Lepelletier D, Gouin F, and Corvec S. 2017. Tropism and virulence of Cutibacterium (formerly Propionibacterium) acnes involved in implant-associated infection. Anaerobe. 47, 73-78.
    Pubmed CrossRef
  2. Cho E, Park SN, Lim YK, Shin Y, Paek J, Hwang CH, Chang YH, and Kook JK. 2015. Fusobacterium hwasookii sp. nov., isolated from a human periodontitis lesion. Curr. Microbiol. 70, 169-175.
    Pubmed CrossRef
  3. Günthard H, Hany A, Turina M, and Wüst J. 1994. Propionibacterium acnes as a cause of aggressive aortic valve endocarditis and importance of tissue grinding: case report and review. J. Clin. Microbiol. 32, 3043-3045.
    Pubmed KoreaMed
  4. Leyden JJ. 2001. The evolving role of Propionibacterium acnes in acne. Semin. Cutan. Med. Surg. 20, 139-143.
    Pubmed CrossRef
  5. McDowell A, Patrick S, Eishi Y, Lambert P, and Eady A. 2013. Propionibacterium acnes in human health and disease. Biomed. Res. Int 2013, 493564.
    Pubmed KoreaMed CrossRef
  6. Narita M, Shibahara T, Takano N, Fujii R, Okuda K, and Ishihara K. 2016. Antimicrobial susceptibility of microorganisms isolated from periapical periodontitis lesions. Bull. Tokyo Dent. Coll. 57, 133-142.
    Pubmed CrossRef
  7. Niazi SA, Al Kharusi HS, Patel S, Bruce K, Beighton D, Foschi F, and Mannocci F. 2016. Isolation of Propionibacterium acnes among the microbiota of primary endodontic infections with and without intraoral communication. Clin. Oral Investig. 20, 2149-2160.
    Pubmed KoreaMed CrossRef
  8. Sainani NA, Rafeek H, Locati J, Penn R, and Washburn R. 2015. Osteomyelitis of the humerus caused by Propionibacterium acnes. J. La. State Med. Soc. 167, 153-154.
    Pubmed
  9. Scholz CF, and Kilian M. 2016. The natural history of cutaneous propionibacteria, and reclassification of selected species within the genus Propionibacterium to the proposed novel genera Acidipropionibacterium gen. nov Cutibacterium gen. nov. and Pseudopropionibacterium gen. nov. Int. J. Syst. Evol. Microbiol. 66, 4422-4432.
    Pubmed CrossRef
  10. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, and Ostell J. 2016. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 44, 6614-6624.
    Pubmed KoreaMed CrossRef
  11. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, and Young SK, et al. 2014. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One. 9, e112963.
    Pubmed KoreaMed CrossRef
  12. Zaffiri L, Abdulmassih R, Boyaji S, Bagh I, Campbell AR, and Loehrke ME. 2013. Brain abscess induced by Propionibacterium acnes in a patient with severe chronic sinusitis. New Microbiol. 36, 325-329.
    Pubmed
  13. Zhou Y, Hu Y, and Li H. 2013. Role of Propionibacterium acnes in sarcoidosis: a meta-analysis. Sarcoidosis Vasc. Diffuse Lung Dis. 30, 262-267.
    Pubmed


March 2019, 55 (1)