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Complete genome of methicillin resistant Staphylococcus epidermidis Z0117SE0042 isolated from human nasal mucosa
Korean J. Microbiol 2018;54(4):468-470
Published online December 31, 2018
© 2018 The Microbiological Society of Korea.

Kishor Sureshbhai Patil1, Jae-Young Oh2, Jae-Ik Han3, Wonkeun Song4, Hee-Myung Park2, and Jong-Chan Chae1,*

1Division of Biotechnology, Chonbuk National University, Iksan 54596, Republic of Korea,
2Department of Veterinary Internal Medicine, Konkuk University, Seoul 05029, Republic of Korea,
3Laboratory of Wildlife Diseases, College of Veterinary Medicine, Chonbuk National University, Iksan 54596, Republic of Korea,
4Department of Laboratory Medicine, College of Medicine, Hallym University, Chuncheon 24252, Republic of Korea
Correspondence to: E-mail: chae@jbnu.ac.kr; Tel.: +82-63-850-0840; Fax: +82-63-850-0834
Received December 7, 2018; Accepted December 9, 2018.
Abstract

Methicillin resistant Staphylococcus epidermidis Z0117SE0042 was isolated from nasal mucosa of veterinarian. The complete genome of strain Z0117SE0042 contains a 2.5 Mb chromosome and two circular plasmids of about 24 kb and 23 kb. Analysis of the genome determined in this study may contribute to evaluate the presence and prevalence of antibiotic resistant genes in normal flora of human.

Keywords : Staphylococcus epidermidis, genome, nasal mucosa
Body
!#italic#!#Staphylococcus epidermidis is a commensal bacterium that colonizes human skin and mucous membranes (Conlan et al., 2012). Due to its proximity to the insertion sites of catheters or other medical devices, S. epidermidis frequently colonizes these devices and forms biofilms that are inherently resistant to the host defense system and antibiotics (Galac et al., 2017). Staphylococcal species are frequently resistant to antibiotics, particularly belonging to penicillinase-resistant penicillin family (e.g. methicillin, oxacillin, and nafcillin), constraining treatment options especially in clinical environment (Diep et al., 2006). The mecA gene generally located on staphylococcal cassette chromosome mec (SCCmec) plays a key role in inactivation of β-lactam in Staphylococci. Currently, SCCmec is divided into 13 types (I–XIII) by mec gene complex and ccr gene complex (Baig et al., 2018).

S. epidermidis Z0117SE0042 (CDC121, the other strain name) was isolated from nasal mucosa of veterinarian. The enrichment was performed on CHROMagar MRSA (CHROMagar) at 30°C for 2 days. The strain was identified based on cpn60 gene sequences. The strain was deposited in Nakdonggang National Institute of Biological Resources (Sangju, Korea) under FBCC502765D of deposit number.

Genomic DNA of strain Z0117SE0042 was used to construct 20 kb SMRTbell™ template libraries. The whole genome sequencing was conducted with PacBio RSII and Illumina Hiseq sequencing platforms by Macrogen. The determined filtered subreads with about 263-fold coverage were assembled using hierarchical genome assembly process (HGAP, v3.0) including assembly polishing with Quiver (Chin et al., 2013). As a result of de novo assembly, three circularized contigs of 2,524,648 bp, 23,943 and 23,348 bp were generated. Automatic annotation for the genome was conducted with Prokka (v1.11, Victorian Bioinformatics Consortium) and found a total of 2,358 coding sequences (CDSs), 60 tRNA genes, and 19 rRNA genes (Table 1).

Genome features of Staphylococcus epidermidis Z0117SE0042

 ContigLength (bp)CDStRNArRNAG + C ratio
Contig 1 (Chromosome)2,524,6482,306601932.2
Contig 2 (plasmid)23,943240027.2
Contig 3 (plasmid)23,348280029.0

Total2,571,9392,358601932.1

Genome sequence of strain Z0117SE0042 contained staphylococcal chromosomal cassette mec (SCCmec) similar to type V consisting of class C2 mec and type 5 ccr gene complexes. As shown in Fig. 1, its structure contained two kinds of ccr genes (duplicated ccrC1 and ccrA4) which corresponded to excision and integration of SCCmec. The class C2 mec gene complex was composed of insertion sequence IS431 located on upstream of mecA and mecR1 genes but the other IS431 usually located on downstream of mecA was absent. The hsdR gene and two other ORFs (hsdS and hsdM) were also detected in the mec gene complex which encoded for restriction-modification system. Unexpectedly, ccrA4 was not only found with duplicated ccrC1, but duplicated hsdR, hsdS, and hsdM genes were also detected (Fig. 1). The SCCmec structure is unknown up to date. This might be caused by different bacterial origin since available SCCmec structure was generally reported from S. aureus.

Fig. 1.

SCCmec gene organization in Z0117SE0042 strain.


In addition, chromosome contained several genes for β-lactam antibiotics resistance such as pbp2a, pbpH, pbpB, blaZ, blaR1, and blaI. And tetA, msrA, msrB, isaB, and tcaA genes conferring resistance to tetracycline, macrolides, lincosamides (clindamycin), and glycopeptide (teicoplanin) were located in the chromosome.

Nucleotide sequence accession number

The genome sequence of Staphylococcus epidermidis Z0117SE0042 has been deposited in NCBI GenBank under accession nos. CP034115-CP034117.

적 요

메티실린 내성 Staphylococcus epidermidis Z0117SE0042을 수의사의 코점막으로부터 분리하였다. 완전 해독된 Z0117SE0042 균주의 게놈은 약 2.5 Mb의 염색체와 24 kb, 23 kb 크기의 2개 플라스미드로 구성되어 있었다. 본 연구에서 해독된 유전체 정보는 인간의 정상미생물상에 존재하는 항생제 내성유전자의 분포를 추적하는데 유용한 기반이 될 것으로 기대된다.

Acknowledgements

This study was supported by a grant of the Korea Healthcare Technology R&D Project, Ministry of Health and Welfare, Republic of Korea (2017N-ER5405-00).

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December 2018, 54 (4)