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Microbiology and Biotechnology Letters

Genome Report(Note)

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Genome Report  |  Genome Report

Microbiol. Biotechnol. Lett. 2023; 51(4): 545-547

https://doi.org/10.48022/mbl.2311.11010

Received: November 16, 2023; Accepted: December 5, 2023

Complete Genome of Methicillin-Resistant Staphylococcus epidermidis Z0118SE0272 Isolated from a Residential Environment

Haeseong Lee, Jae-Young Oh, Kui Jae Lee*, and Jong-Chan Chae*

Division of Biotechnology, Jeonbuk National University, Iksan 54596, Republic of Korea

Correspondence to :
Kui Jae Lee,              leekj@jbnu.ac.kr
Jong-Chan Chae,       chae@jbnu.ac.kr

Abstract

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Staphylococcus epidermidis is a normal flora of human skin and is occasionally associated with pathogenic infections. We report the complete genome sequence of methicillin-resistant Staphylococcus epidermidis strain Z0118SE0272 isolated from the residential environment sharing by a companion dog and dwellers. Resistance to cefoxitin was observed in the strain, whereas it was susceptible to erythromycin, clindamycin, quinupristin-dalfopristin, trimethoprim-sulfamethoxazole, mupirocin, vancomycin, teicoplanin, linezolid, and tigecycline. The strain Z0118SE0272 identified as sequence type 130 possessed the mecA gene responsible for methicillin resistance, which composed the new type of staphylococcal cassette chromosome mec elements lacking mecRI.

Keywords: Staphylococcus epidermidis, methicillin-resistant, complete genome

Body

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The genus Staphylococcus is a gram-positive bacterium that colonizes in skin surface of humans and animals [1, 2]. Among the Staphylococcus spp., Staphylococcus epidermidis is known as a coagulase-negative bacterium and a major pathogen of nosocomial infection forming biofilm. This species can infect patients through their wound or medical devices, which may increase the patient's mortality rate [3, 4]. Currently, as the antibiotic resistance rate of S. epidermidis increases, problems are arising in treating bacteremia by antibiotic therapy in hospitals. Among them, methicillin-resistant S. epidermidis (MRSE) has attracted the major concern [5]. Methicillin-resistance is mediated by the mecA gene which comprises staphylococcal chromosome cassette mec (SCCmec) with mecA, ccr, orfX, and insertion sequences. And several different types have been identified in methicillin-resistant Staphylococcus aureus owing to the various genetic diversity [6]. However, the SCCmec structure of MRSE has not been classified. In this study, strain Z0118SE0272 was isolated from the surface of a sofa in a residential house where a veterinarian raised a companion dog and the complete genome was determined.

The swapped sample was inoculated into Chromagar Orientation (CHROMagar™) and incubated for 24 h at 30℃. The candidates of Staphylococcus species were separated through chromogenic selection. After purifying the colonies, identification of S. epidermidis was conducted by PCR and sequencing of the mutS gene [7]. An antibiotic susceptibility test was performed using the disk diffusion method against cefoxitin, erythromycin, clindamycin, quinupristin-dalfopristin, trimethoprimsulfamethoxazole, mupirocin, vancomycin, teicoplanin, linezolid, and tigecycline. As the results, the strain Z0118SE0272 showed resistance only to cefoxitin and susceptibility to all of other antibiotics.

For genome sequencing, total genomic DNA was extracted with a QIAamp DNA Mini Kit (Qiagen, Germany). The quantity and quality of the DNA were measured using a Qubit 4 fluorometer (Invitrogen, Singapore). The extracted DNA was sequenced using PacBio RSII (Pacific Biosciences, USA) and HiSeq X Ten (Illumina, USA) systems at the Macrogen (Republic of Korea). After sequencing, 271,066 and 11,673,674 reads were obtained from PacBio and HiSeq sequencers, respectively. The generated reads were hybrid assembled using Unicycler (v0.4.9) [8] with the default setting. Based on generated contigs, one chromosome (2,509,266 bp) and three plasmids (30,151 bp, 16,926 bp, and 2,563 bp) were determined (Table 1). Annotation was performed with NCBI prokaryotic genome annotation pipeline (PGAP) and found that strain Z0118SE0272 consisted of 2,369 coding sequences, 19 (7 of 5S, 6 of 16S, 6 of 23S) rRNA genes, and 61 tRNA genes (Table 1). The antimicrobial resistance genes were identified using the comprehensive antibiotic resistance database (CARD) [9]. The chromosome (accession no. CP069219) included resistance genes for quinolone (norA, norC, and sdrM), trimethoprim (dfrC), and beta-lactam antibiotics (mecA). The 30,151 bp of plasmid (accession no. CP06220) contained resistance genes for beta-lactams (blaZ), aminoglycosides (ant(4')-Ib), and chlorhexidine gluconate (qacB).

Table 1 . Genome features of Staphylococcus epidermidis Z0118SE0272.

ContigLength (bp)No of CDSNo of tRNANo of rRNAG+C ratio (%)
Contig 1 (Chromosome)2,509,2662,313611932.0
Contig 2 (plasmid)30,151340029.0
Contig 3 (plasmid)16,926200028.0
Contig 4 (plasmid)2,56320029.0
Total2,558,9062,369601932.16

CDS, coding sequences

A SCCmec structure was found using the SCCmec finder [10]. The ccrA2 and ccrB2 were located downstream of mecA and the ccrC1 also existed adjacent to upstream as shown in Fig. 1. However, the structure lacked mecRI encoding the signal transducer and the repressor proteins which usually were detected in previously known SCCmec types [6].

Figure 1.Genetic structure of staphylococcal cassette chromosome mec (SCCmec) in Staphylococcus epidermidis Z0118SE0272. mecA, penicillin-binding protein; ccr, recombinase; orfX, unknown open reading frame; IS, insertion sequence.

Nucleotide Sequence Accession Number

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The genome sequence of Staphylococcus epidermidis Z0118SE0272 has been deposited in GenBank/EMBL/DDBJ under accession CP069219-CP069222. The strain was deposited in KCTC under deposition number 43153.

Acknowledgments

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This work was supported by grants of Korea Disease Control and Prevention Agency (2022-ER2103-00), Ministry of Food and Drug Safety (23194MFDS012), and Jeonbuk National University.

Conflict of Interest

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The authors have no financial conflicts of interest to declare.

References

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