Staphylococcus aureus, a pathogenic bacterium, is an opportunistic Gram-positive organism and one of the bacteria responsible for food poisoning (Grundmann et al., 2006). It is commonly found as a commensal microorganism on the skin and in the nostrils of approximately one-third of the global population (Krismer et al., 2017). This bacterium is notorious for its ability to cause a wide spectrum of infections, ranging from minor skin abscesses to life-threatening conditions such as septicemia and toxic shock syndrome (Lowy et al., 1998; Tong et al., 2015). Moreover, S. aureus has emerged as a significant global health threat, largely due to the rise of multidrug-resistant strains that complicate treatment efforts (Sonola et al., 2021).

The Staphylococcus aureus strain 24EBSta0529 was isolated from stream water near in Geoje, Gyeongsangnam-do of South Korea. Genomic DNA extraction for 24EBSta0529 was conducted using a Bacterial Genomic DNA Extraction Kit Ver. 3.0 (TaKaRa, MiniBEST), and genome sequencing was performed by the Nanopore sequencing platform (Oxford). The qualified genomic DNA was used to perform the Nanopore library using the Ligation Sequencing gDNA kit (SQK-LSK110). The library was sequenced using a MinION MK1C sequencer using Flongle R9.4.1 flow cell and a total of 33,532 sequence reads were assembled into 1 contig. The raw sequencing reads were de novo assembled using Flye (version 2.8.2), producing an assembly with 54X coverage. The assembled data was polished using Medaka (version 1.7.2) to correct errors in the long-read sequencing data. To further verify the genome structure, Circlator (version 1.5.5) was used to determine whether the genome is circular or linear. Genome annotation was performed using the NCBI prokaryotic genome annotation pipeline (Tatusova et al., 2016) (Fig. 1 and Table 1).

Table 1

Genome features of Staphylococcus aureus 24EBSta0529

Feature	Chromosome (24EBSta0529)
Size (bp)	2,767,774
G + C contents (%)	45.0%
Total number of
CDSs	2,654
rRNA genes (5S, 16S, 23S)	19 (7, 6, 6)
tRNA genes	59
Pseudo gene	69
GenBank Accession No.	CP166872

Fig. 1. Circular Genome Map of Staphylococcus aureus 24EBSta0529 Chromosomal DNA. The graphical maps above display the alignment of genes and other genomic data. The tracks are shown as concentric rings, arranged from the outermost to the innermost: Forward CDS, Reverse CDS, GC Skew, GC content, AMR genes, VF genes, transporters, and drug targets. Genes with specialized functions are color-coded, with virulence-related genes in red, and other functional genes, such as those involved in antimicrobial resistance, transporters, and drug targets, in yellow, blue, and black.

The genome of Staphylococcus aureus strain 24EBSta0529 consists of a single chromosomal DNA. The chromosome consists 2,767,774 bp with a GC content of 45.0%. Gene prediction analysis revealed 2,585 CDSs, 59 tRNAs, and 19 rRNAs in the chromosome. Additionally, an in silico antibiotic resistance analysis using the Comprehensive Antibiotic Resistance Database (Alcock et al., 2023) identified several clinically significant resistance factors. These include the mecA gene, responsible for resistance to methicillin and beta-lactam antibiotics (Foster, 2017), as well as gyrA and gyrB (Ito et al., 1994), which contribute to fluoroquinolone resistance, and norA (Monteiro et al., 2020), which is linked to quinolone resistance. Furthermore, the rifampin resistance-related genes rpoB and rpoC (Panchal et al., 2020), and the daptomycin resistance-related gene mprF (Jiang et al., 2022) were also identified.

Pathogenicity gene analysis using the Virulence Factor Database (Liu et al., 2019) revealed the spa gene (Gao and Stewart, 2004), encoding Protein A, which interferes with opsonization and phagocytosis, and the hla gene (Tavares et al., 2014), which is involved in severe infections like pneumonia and skin infections.

Staphylococcus aureus is a pathogenic bacterium that can cause various infections, and its antibiotic resistance presents significant challenges. Multidrug-resistant S. aureus, like the strain isolated in this study, has already become a global issue, including in countries such as Mexico (Martínez-Vázquez et al., 2021). Studies on antibiotic resistance gene mutations are crucial for understanding and combating this problem (Foster, 2017; Guo et al., 2020). Genomic study on S. aureus helps to uncover antibiotic resistance and virulence factors, and the genomic data will be a crucial resource for tracking the causes of foodborne illnesses as well as improving public health efforts.

Nucleotide sequence accession number(s)

Nucleotide sequence accession numbers. The complete genome sequence of Staphylococcus aureus 24EBSta0529 has been deposited at the NCBI GenBank database under the accession numbers CP166872 and the strain has been deposited in the Korean Culture Collection of Aquatic Microorganisms (KoCAM) under the strain number 24EBSta0529.

황색포도상구균은 사람의 피부와 비강 등에 존재하는 기회성 그람 양성균으로, 피부 및 호흡기 감염, 식중독 등을 유발할 수 있는 병원성 세균이다. 본 연구에서는 2023년 경상남도 거제 하천수에서 분리된 황색포도상구균의 전장 유전체 분석을 수행하였다. 분석 결과, 해당 균주는 단일 염색체로 구성되어 있었으며, G + C 함량은 45%로 나타났다. 또한, 2,585개의 단백질 코딩 유전자, 59개의 tRNA 유전자, 19개의 rRNA 유전자를 보유한 것으로 확인되었으며, 유전체 분석 결과에서는 주요 항생제 내성 인자(mecA, norA) 및 병원성 인자(spa, hly)가 확인되었다.

This research was financially supported by the National Institute of Fisheries Science, Republic of Korea (R2024057).

The authors have no conflict of interest to report.