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Complete genome of methicillin resistant Staphylococcus epidermidis Z0117SE0041 isolated from human nasal mucosa
Korean J. Microbiol 2018;54(4):474-476
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 10, 2018.
Abstract

Methicillin resistant Staphylococcus epidermidis Z0117SE0041 was isolated from nasal mucosa of human who raised companion dog. The complete genome of strain Z0117SE0041 consists of a 2.5 Mb chromosome and three circular plasmids with about 47, 36, and 11 kb in size, respectively. Since strain Z0117SE0041 raises concerns due to its potential to cause a disease and disseminate antibiotic resistance, further genome analysis is required in detail.

Keywords : Staphylococcus epidermidis, genome, human
Body
taphylococci are common bacterial colonizers of the skin and mucous membranes of humans and other mammals. Staphylococcus epidermidis in particular is the most frequently isolated species from human epithelia (Otto, 2009). If S. epidermidis, a commensal on the skin, ruptures the skin surface and enters the bloodstream, it is considered as pathogen. Staphylococcus aureus and coagulase-negative Staphylococci (CoNS) cause 30% of hospital-acquired infections (Conlan et al., 2012). S. epidermidis belongs to the group of CoNS, which is distinguished from coagulase-positive staphylococci such as highly pathogenic S. aureus by lacking coagulase. CoNS infections are associated with increasing use of catheters and medical devices inserted through the skin (Watanabe et al., 2016). The increasing antibiotic resistance of nosocomial isolates of S. epidermidis poses a great challenge for the management of hospital-acquired infections in general (Du et al., 2013).

S. epidermidis Z0117SE0041 (CDC120, the other strain name) was isolated from nasal mucosa of human who raised companion dog after enrichment on CHROMagar MRSA (CHROMagar) at 30°C for 2 days under aerobic condition. A purified isolate was identified as S. epidermidis by cpn60 gene sequencing and deposited in Nakdonggang National Institute of Biological Resources under FBCC502764D of deposit number.

Genomic DNA of strain Z0117SE0041 was extracted from cells which were grown aerobically at 30°C for 20 h in blood agar medium and used to construct 20 kb SMRTbell™ template libraries. The whole genome sequencing was performed at Macrogen, Inc. using PacBio RSII and Illumina platforms. The determined filtered subreads with about 281-fold coverage were assembled as described previously (Patil et al., 2017) generating four circularized contigs of 2,477,784, 46,728, 36,008, and 11,218 bp. This indicated that the assembled contigs were completed. Automatic annotation for the genome with Prokka (v1.11, Victorian Bioinformatics Consortium) determined a total of 2,352 coding sequences (CDSs), 60 tRNA genes, and 19 rRNA genes as described in Table 1.

Genome features of Staphylococcus epidermidis Z0117SE0041

 ContigLength (bp)CDStRNArRNAG + C ratio
Contig 1 (Chromosome)2,477,7842,249601932.3
Contig 2 (plasmid)46,728560029.8
Contig 3 (plasmid)36,008360028.3
Contig 4 (plasmid)11,218110029.6

Total2,571,7382,352601932.16

Sequence analysis found that the β-lactam antibiotics resistant genes (mecA, blaZ, blaR1, and blaI) were located in the chromosome of Z0117SE0041. The staphylococcal chromosomal cassette mec (SCCmec) was detected in the genome which consisted of similar class C2 mec and type 5 ccr gene complexes including methicillin resistance regulatory sensor transducer (mecR1), methicillin resistance determinant (mecA), and cassette chromosome recombinase (ccrC1) genes with insertion sequence IS431 (Fig. 1). The structure of mecA-mecR1-IS431 in mec gene complex of Z0117SE0041 strain was highly similar to class C2 mec gene complex of type V SCCmec but IS431 on downstream of mecA is missing in this mec gene complex (Fig. 1). Two other ORFs (hsdS and hsdM) on downstream of hsdR were detected which encoded for restriction-modification system.

Fig. 1.

SCCmec gene organization in Z0117SE0041 strain.


Also, Z0117SE0041 chromosome harbored other antibiotic resistant genes such as tetA, msrA, msrB, isaB, and tcaA responsible for resistance to tetracycline, macrolides, lincosamides (clindamycin), glycopeptide (teicoplanin).

Nucleotide sequence accession number

The genome sequence of Staphylococcus epidermidis Z0117SE0041 has been deposited in NCBI GenBank under accession nos. CP034111-CP034114.

적 요

메티실린 내성 Staphylococcus epidermidis Z0117SE0041을 반려견 주인의 코점막으로부터 분리하였다. 완전 해독된 Z0117SE0041 균주의 게놈은 약 2.5 Mb의 염색체와 47 kb, 36 kb, 11 kb 크기의 3개 플라스미드로 구성되어 있었다. Z0117SE0041 균주는 병을 유발하거나 항생제 내성을 전파할 수 있는 가능성이 있으므로 보다 깊이 있는 유전체 분석이 요구된다.

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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